From ec2d1d3ae3cc989bfcd227e7f43b4b4abde4a128 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 28 Oct 2021 17:48:17 +0200
Subject: [PATCH 001/113] Onto 1

---
 askomics/libaskomics/TriplestoreExplorer.py | 3 ++-
 askomics/react/src/routes/query/query.jsx   | 7 +++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/askomics/libaskomics/TriplestoreExplorer.py b/askomics/libaskomics/TriplestoreExplorer.py
index 0773ceaf..b941a88e 100644
--- a/askomics/libaskomics/TriplestoreExplorer.py
+++ b/askomics/libaskomics/TriplestoreExplorer.py
@@ -328,7 +328,7 @@ def get_abstraction_entities(self):
             GRAPH ?graph {{
                 ?graph prov:atLocation ?endpoint .
                 ?entity_uri a ?entity_type .
-                VALUES ?entity_type {{ askomics:entity askomics:bnode }} .
+                VALUES ?entity_type {{ askomics:entity askomics:bnode askomics:ontology}} .
                 # Faldo
                 OPTIONAL {{
                     ?entity_uri a ?entity_faldo .
@@ -362,6 +362,7 @@ def get_abstraction_entities(self):
                     "label": label,
                     "instancesHaveLabels": True if "have_no_label" not in result else False if result["have_no_label"] == "1" else True,
                     "faldo": True if "entity_faldo" in result else False,
+                    "ontology": True if result["entity_type"] == "{}ontology".format(self.settings.get("triplestore", "namespace_internal")) else False,
                     "endpoints": [result["endpoint"]],
                     "graphs": [result["graph"]],
                 }
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index a516105a..5fd3f09b 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -212,6 +212,12 @@ export default class Query extends Component {
     })
   }
 
+  isOntoEntity (entityUri) {
+    return this.state.abstraction.entities.some(entity => {
+      return (entity.uri == entityUri && entity.ontology)
+    })
+  }
+
   attributeExist (attrUri, nodeId) {
     return this.graphState.attr.some(attr => {
       return (attr.uri == attrUri && attr.nodeId == nodeId)
@@ -398,6 +404,7 @@ export default class Query extends Component {
       specialPreviousIds: specialPreviousIds,
       label: this.getLabel(uri),
       faldo: this.isFaldoEntity(uri),
+      onto: this.isOntoEntity(uri),
       selected: selected,
       suggested: suggested
     }

From c0e62dc800ddd38fa6795ceb7de34a5841b96523 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 29 Oct 2021 16:20:44 +0200
Subject: [PATCH 002/113] React onto 1

---
 .../react/src/routes/query/ontolinkview.jsx   | 47 +++++++++++++++++++
 askomics/react/src/routes/query/query.jsx     | 43 +++++++++++++++--
 2 files changed, 86 insertions(+), 4 deletions(-)
 create mode 100644 askomics/react/src/routes/query/ontolinkview.jsx

diff --git a/askomics/react/src/routes/query/ontolinkview.jsx b/askomics/react/src/routes/query/ontolinkview.jsx
new file mode 100644
index 00000000..72589303
--- /dev/null
+++ b/askomics/react/src/routes/query/ontolinkview.jsx
@@ -0,0 +1,47 @@
+import React, { Component } from 'react'
+import axios from 'axios'
+import { Input, FormGroup, CustomInput, Col, Row, Button } from 'reactstrap'
+import { Redirect } from 'react-router-dom'
+import ErrorDiv from '../error/error'
+import WaitingDiv from '../../components/waiting'
+import update from 'react-addons-update'
+import Visualization from './visualization'
+import PropTypes from 'prop-types'
+
+export default class OntoLinkView extends Component {
+  constructor (props) {
+    super(props)
+    this.handleChangeOntologyType = this.props.handleChangeOntologyType.bind(this)
+  }
+
+
+  render () {
+    return (
+      <div className="container">
+        <h5>Ontological Relation</h5>
+        <hr />
+        <p>Search on ...</p>
+        <table>
+          <tr>
+            <td>
+             <CustomInput type="select" id={this.props.link.id} name="ontology_position" onChange={this.handleChangeOntologyType}>
+                <option selected={this.props.link.uri == 'specific' ? true : false} value="specific">a specific</option>
+                <option selected={this.props.link.uri == 'children' ? true : false} value="children">children of</option>
+                <option selected={this.props.link.uri == 'descendants' ? true : false} value="descendants">descendants of</option>
+                <option selected={this.props.link.uri == 'parents' ? true : false} value="parents">parents of</option>
+                <option selected={this.props.link.uri == 'ancestors' ? true : false} value="ancestors">ancestors of</option>
+              </CustomInput>
+            </td>
+            <td> a term</td>
+          </tr>
+        </table>
+        <br />
+      </div>
+    )
+  }
+}
+
+OntoLinkView.propTypes = {
+  link: PropTypes.object,
+  handleChangeOntologyType: PropTypes.func,
+}
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 5fd3f09b..5901d631 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -9,6 +9,7 @@ import ReactTooltip from "react-tooltip";
 import Visualization from './visualization'
 import AttributeBox from './attribute'
 import LinkView from './linkview'
+import OntoLinkView from './ontolinkview'
 import GraphFilters from './graphfilters'
 import ResultsTable from '../sparql/resultstable'
 import PropTypes from 'prop-types'
@@ -518,7 +519,7 @@ export default class Query extends Component {
             // push suggested link
             this.graphState.links.push({
               uri: relation.uri,
-              type: "link",
+              type: this.isOntoEntity(relation.target) ? "ontoLink" : "link",
               sameStrand: this.nodeHaveStrand(node.uri) && this.nodeHaveStrand(relation.target),
               sameRef: this.nodeHaveRef(node.uri) && this.nodeHaveRef(relation.target),
               strict: true,
@@ -563,7 +564,7 @@ export default class Query extends Component {
             // push suggested link
             this.graphState.links.push({
               uri: relation.uri,
-              type: "link",
+              type: this.isOntoEntity(relation.target) ? "ontoLink" : "link",
               sameStrand: this.nodeHaveStrand(node.id) && this.nodeHaveStrand(relation.source),
               sameRef: this.nodeHaveRef(node.id) && this.nodeHaveRef(relation.source),
               id: this.getId(),
@@ -641,7 +642,9 @@ export default class Query extends Component {
       if (link.source.id == node1.id && link.target.id == node2.id) {
         newLink = {
           uri: link.uri,
-          type: ["included_in", "overlap_with"].includes(link.uri) ? "posLink" : "link",
+          // What's the point of this?
+          // type: ["included_in", "overlap_with"].includes(link.uri) ? "posLink" :  "link",
+          type: link.type,
           sameStrand: this.nodeHaveStrand(node1.uri) && this.nodeHaveStrand(node2.uri),
           sameRef: this.nodeHaveRef(node1.uri) && this.nodeHaveRef(node2.uri),
           strict: true,
@@ -658,7 +661,9 @@ export default class Query extends Component {
       if (link.source.id == node2.id && link.target.id == node1.id) {
         newLink = {
           uri: link.uri,
-          type: ["included_in", "overlap_with"].includes(link.uri) ? "posLink" : "link",
+          // What's the point of this?
+          // type: ["included_in", "overlap_with"].includes(link.uri) ? "posLink" :  "link",
+          type: link.type,
           sameStrand: this.nodeHaveStrand(node1.uri) && this.nodeHaveStrand(node2.uri),
           sameRef: this.nodeHaveRef(node1.uri) && this.nodeHaveRef(node2.uri),
           strict: true,
@@ -1296,6 +1301,18 @@ export default class Query extends Component {
     return result
   }
 
+  // Ontology link methods -----------------------------
+
+  handleChangeOntologyType (event) {
+    this.graphState.links.map(link => {
+      if (link.id == event.target.id) {
+        link.uri = event.target.value
+        link.label = event.target.value == 'specific' ? "specific" : event.target.value + " of"
+      }
+    })
+    this.updateGraphState()
+  }
+
   // ------------------------------------------------
 
   // Preview results and Launch query buttons -------
@@ -1535,6 +1552,24 @@ export default class Query extends Component {
             nodesHaveStrands={p => this.nodesHaveStrands(p)}
           />
         }
+
+        if (this.currentSelected.type == "ontoLink") {
+
+          let link = Object.assign(this.currentSelected)
+          this.state.graphState.nodes.map(node => {
+            if (node.id == this.currentSelected.target) {
+              link.target = node
+            }
+            if (node.id == this.currentSelected.source) {
+              link.source = node
+            }
+          })
+
+          linkView = <OntoLinkView
+            link={link}
+            handleChangeOntologyType={p => this.handleChangeOntologyType(p)}
+          />
+        }
       }
 
       // visualization (left view)

From cab338db46ce78edfc23065929d1140510cac990 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 29 Oct 2021 14:24:31 +0000
Subject: [PATCH 003/113] Fix react

---
 askomics/react/src/routes/query/query.jsx | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 5901d631..e80456cc 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -740,7 +740,7 @@ export default class Query extends Component {
 
   handleLinkSelection (clickedLink) {
     // Only position link are clickabl
-    if (clickedLink.type == "posLink") {
+    if (clickedLink.type == "posLink" || clickedLink.type == "ontoLink") {
       // case 1: link is selected, so deselect it
       if (clickedLink.selected) {
         // Update current and previous
@@ -1307,7 +1307,6 @@ export default class Query extends Component {
     this.graphState.links.map(link => {
       if (link.id == event.target.id) {
         link.uri = event.target.value
-        link.label = event.target.value == 'specific' ? "specific" : event.target.value + " of"
       }
     })
     this.updateGraphState()

From b049693414d35209dc9df6d35cd6ab12f323f402 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 29 Oct 2021 17:16:47 +0200
Subject: [PATCH 004/113] Onto 2

---
 askomics/libaskomics/SparqlQuery.py       | 13 ++++++++++++-
 askomics/react/src/routes/query/query.jsx | 20 +++++++++++++-------
 2 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 75fb681d..67783e15 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -420,7 +420,8 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None):
           ?graph dc:creator ?creator .
           GRAPH ?graph_abstraction {{
             ?graph_abstraction prov:atLocation ?endpoint .
-            ?entity_uri a askomics:entity .
+            ?entity_uri a ?askomics_type .
+            VALUES ?askomics_type {{askomics:entity askomics:ontology}}
           }}
           GRAPH ?graph {{
             [] a ?entity_uri .
@@ -1085,6 +1086,16 @@ def build_query_from_json(self, preview=False, for_editor=False):
                             equalsign=equal_sign
                         ), block_id, sblock_id, pblock_ids)
 
+                elif link["type"] == "ontoLink":
+                    relation = "<{}>".format(link["uri"])
+                    triple = {
+                        "subject": source,
+                        "predicate": relation,
+                        "object": target,
+                        "optional": False
+                    }
+
+                    self.store_triple(triple, block_id, sblock_id, pblock_ids)
                 # Classic relation
                 else:
                     relation = "<{}>".format(link["uri"])
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index e80456cc..fef3756f 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -529,7 +529,8 @@ export default class Query extends Component {
               target: targetId,
               selected: false,
               suggested: true,
-              directed: true
+              directed: true,
+              onto_type: "specific"
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
           }
@@ -573,7 +574,8 @@ export default class Query extends Component {
               target: node.id,
               selected: false,
               suggested: true,
-              directed: true
+              directed: true,
+              onto_type: "specific"
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
           }
@@ -601,7 +603,8 @@ export default class Query extends Component {
             label: entity.label,
             faldo: entity.faldo,
             selected: false,
-            suggested: true
+            suggested: true,
+            onto_type: "specific"
           })
           // push suggested link
           this.graphState.links.push({
@@ -616,7 +619,8 @@ export default class Query extends Component {
             target: new_id,
             selected: false,
             suggested: true,
-            directed: true
+            directed: true,
+            onto_type: "specific"
           })
           incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
         }
@@ -654,7 +658,8 @@ export default class Query extends Component {
           target: node2.id,
           selected: false,
           suggested: false,
-          directed: true
+          directed: true,
+          onto_type: "specific"
         }
       }
 
@@ -673,7 +678,8 @@ export default class Query extends Component {
           target: node1.id,
           selected: false,
           suggested: false,
-          directed: true
+          directed: true,
+          onto_type: "specific"
         }
       }
     })
@@ -1306,7 +1312,7 @@ export default class Query extends Component {
   handleChangeOntologyType (event) {
     this.graphState.links.map(link => {
       if (link.id == event.target.id) {
-        link.uri = event.target.value
+        link.onto_type = event.target.value
       }
     })
     this.updateGraphState()

From 8d28a5ffbd0eabad2d9b37a14313ba9c4448372f Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 29 Oct 2021 19:18:39 +0200
Subject: [PATCH 005/113] First try

---
 askomics/libaskomics/SparqlQuery.py | 100 +++++++++++++++++++++++++++-
 1 file changed, 99 insertions(+), 1 deletion(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 67783e15..71191577 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -967,6 +967,8 @@ def build_query_from_json(self, preview=False, for_editor=False):
         start_end = []
         strands = []
 
+        ontological_nodes = []
+
         var_to_replace = []
 
         # Browse attributes to get entities
@@ -1087,6 +1089,26 @@ def build_query_from_json(self, preview=False, for_editor=False):
                         ), block_id, sblock_id, pblock_ids)
 
                 elif link["type"] == "ontoLink":
+                    # If its specific, proceed as usual
+                    if link["onto_type"] == "specific":
+                        relation = "<{}>".format(link["uri"])
+                        triple = {
+                            "subject": source,
+                            "predicate": relation,
+                            "object": target,
+                            "optional": False
+                        }
+
+                        self.store_triple(triple, block_id, sblock_id, pblock_ids)
+                        continue
+
+                    # Else, Manage hierarchical search
+                    # Add the ontological node to a list to avoid managing attributes later
+
+                    target_id = link["target"]["id"]
+                    ontological_nodes.append(target_id)
+
+                    common_block = self.format_sparql_variable("block_{}_{}".format(link["source"]["id"], link["target"]["id"]))
                     relation = "<{}>".format(link["uri"])
                     triple = {
                         "subject": source,
@@ -1094,8 +1116,83 @@ def build_query_from_json(self, preview=False, for_editor=False):
                         "object": target,
                         "optional": False
                     }
+                    self.store_triple(triple, block_id, sblock_id, pblock_ids)
 
+                    triple = {
+                        "subject": target,
+                        "predicate": "rdfs:subClassOf*",
+                        "object": common_block,
+                        "optional": False
+                    }
                     self.store_triple(triple, block_id, sblock_id, pblock_ids)
+
+                    for attribute in [attrib for attrib in self.json["attr"] if attrib["nodeId"] == target_id]:
+                        if attribute["type"] == "uri":
+                            subject = self.format_sparql_variable("{}{}_uri".format(attribute["entityLabel"], attribute["nodeId"]))
+                            predicate = attribute["uri"]
+                            obj = "<{}>".format(attribute["entityUris"][0])
+                            if not self.is_bnode(attribute["entityUris"][0], self.json["nodes"]):
+                                self.store_triple({
+                                    "subject": subject,
+                                    "predicate": predicate,
+                                    "object": obj,
+                                    "optional": False
+                                }, block_id, sblock_id, pblock_ids)
+                                self.store_triple({
+                                    "subject": common_block,
+                                    "predicate": predicate,
+                                    "object": obj,
+                                    "optional": False
+                                }, block_id, sblock_id, pblock_ids)
+
+                            if attribute["visible"]:
+                                self.selects.append(subject)
+                            # filters/values
+                            if attribute["filterValue"] != "":
+                                filter_value = self.get_uri_filter_value(attribute["filterValue"])
+                                if attribute["filterType"] == "regexp":
+                                    negative_sign = ""
+                                    if attribute["negative"]:
+                                        negative_sign = "!"
+                                        self.store_filter("FILTER ({}regex({}, {}, 'i'))".format(negative_sign, common_block, filter_value), block_id, sblock_id, pblock_ids)
+                                elif attribute["filterType"] == "exact":
+                                    if attribute["negative"]:
+                                        self.store_filter("FILTER (str({}) != {}) .".format(common_block, filter_value), block_id, sblock_id, pblock_ids)
+                                    else:
+                                        self.store_value("VALUES {} {{ {} }} .".format(common_block, filter_value), block_id, sblock_id, pblock_ids)
+
+                        if attribute["type"] == "text":
+                            if attribute["visible"] or attribute["filterValue"] != "":
+                                subject = self.format_sparql_variable("{}{}_uri".format(attribute["entityLabel"], attribute["nodeId"]))
+                                predicate = attribute["uri"]
+                                obj = self.format_sparql_variable("{}{}_{}".format(attribute["entityLabel"], attribute["humanNodeId"], attribute["label"]))
+                                onto_obj = self.format_sparql_variable("{}{}_{}".format(common_block, attribute["humanNodeId"], attribute["label"]))
+                                if attribute["visible"]:
+                                    self.store_triple({
+                                        "subject": subject,
+                                        "predicate": predicate,
+                                        "object": obj,
+                                        "optional": True if attribute["optional"] else False
+                                    }, block_id, sblock_id, pblock_ids)
+                                    self.selects.append(obj)
+                            # filters/values
+                            if attribute["filterValue"] != "" and not attribute["optional"]:
+                                self.store_triple({
+                                    "subject": common_block,
+                                    "predicate": predicate,
+                                    "object": onto_obj,
+                                    "optional": True if attribute["optional"] else False
+                                }, block_id, sblock_id, pblock_ids)
+                                if attribute["filterType"] == "regexp":
+                                    negative_sign = ""
+                                    if attribute["negative"]:
+                                        negative_sign = "!"
+                                    self.store_filter("FILTER ({}regex({}, '{}', 'i'))".format(negative_sign, onto_obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
+                                elif attribute["filterType"] == "exact":
+                                    if attribute["negative"]:
+                                        self.store_filter("FILTER (str({}) != '{}') .".format(onto_obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
+                                    else:
+                                        self.store_value("VALUES {} {{ '{}' }} .".format(onto_obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
                 # Classic relation
                 else:
                     relation = "<{}>".format(link["uri"])
@@ -1120,7 +1217,8 @@ def build_query_from_json(self, preview=False, for_editor=False):
 
         # Browse attributes
         for attribute in self.json["attr"]:
-
+            if attribute["nodeId"] in ontological_nodes:
+                continue
             # Get blockid and sblockid of the attribute node
             block_id, sblock_id, pblock_ids = self.get_block_ids(attribute["nodeId"])
 

From 6c03d30ecd5e4f0f6f5c53476b973a180cef0112 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 1 Nov 2021 15:53:06 +0100
Subject: [PATCH 006/113] Testing another way

---
 askomics/libaskomics/SparqlQuery.py       | 109 ----------------------
 askomics/react/src/routes/query/query.jsx |  18 ++--
 2 files changed, 7 insertions(+), 120 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 71191577..143e430e 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -967,8 +967,6 @@ def build_query_from_json(self, preview=False, for_editor=False):
         start_end = []
         strands = []
 
-        ontological_nodes = []
-
         var_to_replace = []
 
         # Browse attributes to get entities
@@ -1088,111 +1086,6 @@ def build_query_from_json(self, preview=False, for_editor=False):
                             equalsign=equal_sign
                         ), block_id, sblock_id, pblock_ids)
 
-                elif link["type"] == "ontoLink":
-                    # If its specific, proceed as usual
-                    if link["onto_type"] == "specific":
-                        relation = "<{}>".format(link["uri"])
-                        triple = {
-                            "subject": source,
-                            "predicate": relation,
-                            "object": target,
-                            "optional": False
-                        }
-
-                        self.store_triple(triple, block_id, sblock_id, pblock_ids)
-                        continue
-
-                    # Else, Manage hierarchical search
-                    # Add the ontological node to a list to avoid managing attributes later
-
-                    target_id = link["target"]["id"]
-                    ontological_nodes.append(target_id)
-
-                    common_block = self.format_sparql_variable("block_{}_{}".format(link["source"]["id"], link["target"]["id"]))
-                    relation = "<{}>".format(link["uri"])
-                    triple = {
-                        "subject": source,
-                        "predicate": relation,
-                        "object": target,
-                        "optional": False
-                    }
-                    self.store_triple(triple, block_id, sblock_id, pblock_ids)
-
-                    triple = {
-                        "subject": target,
-                        "predicate": "rdfs:subClassOf*",
-                        "object": common_block,
-                        "optional": False
-                    }
-                    self.store_triple(triple, block_id, sblock_id, pblock_ids)
-
-                    for attribute in [attrib for attrib in self.json["attr"] if attrib["nodeId"] == target_id]:
-                        if attribute["type"] == "uri":
-                            subject = self.format_sparql_variable("{}{}_uri".format(attribute["entityLabel"], attribute["nodeId"]))
-                            predicate = attribute["uri"]
-                            obj = "<{}>".format(attribute["entityUris"][0])
-                            if not self.is_bnode(attribute["entityUris"][0], self.json["nodes"]):
-                                self.store_triple({
-                                    "subject": subject,
-                                    "predicate": predicate,
-                                    "object": obj,
-                                    "optional": False
-                                }, block_id, sblock_id, pblock_ids)
-                                self.store_triple({
-                                    "subject": common_block,
-                                    "predicate": predicate,
-                                    "object": obj,
-                                    "optional": False
-                                }, block_id, sblock_id, pblock_ids)
-
-                            if attribute["visible"]:
-                                self.selects.append(subject)
-                            # filters/values
-                            if attribute["filterValue"] != "":
-                                filter_value = self.get_uri_filter_value(attribute["filterValue"])
-                                if attribute["filterType"] == "regexp":
-                                    negative_sign = ""
-                                    if attribute["negative"]:
-                                        negative_sign = "!"
-                                        self.store_filter("FILTER ({}regex({}, {}, 'i'))".format(negative_sign, common_block, filter_value), block_id, sblock_id, pblock_ids)
-                                elif attribute["filterType"] == "exact":
-                                    if attribute["negative"]:
-                                        self.store_filter("FILTER (str({}) != {}) .".format(common_block, filter_value), block_id, sblock_id, pblock_ids)
-                                    else:
-                                        self.store_value("VALUES {} {{ {} }} .".format(common_block, filter_value), block_id, sblock_id, pblock_ids)
-
-                        if attribute["type"] == "text":
-                            if attribute["visible"] or attribute["filterValue"] != "":
-                                subject = self.format_sparql_variable("{}{}_uri".format(attribute["entityLabel"], attribute["nodeId"]))
-                                predicate = attribute["uri"]
-                                obj = self.format_sparql_variable("{}{}_{}".format(attribute["entityLabel"], attribute["humanNodeId"], attribute["label"]))
-                                onto_obj = self.format_sparql_variable("{}{}_{}".format(common_block, attribute["humanNodeId"], attribute["label"]))
-                                if attribute["visible"]:
-                                    self.store_triple({
-                                        "subject": subject,
-                                        "predicate": predicate,
-                                        "object": obj,
-                                        "optional": True if attribute["optional"] else False
-                                    }, block_id, sblock_id, pblock_ids)
-                                    self.selects.append(obj)
-                            # filters/values
-                            if attribute["filterValue"] != "" and not attribute["optional"]:
-                                self.store_triple({
-                                    "subject": common_block,
-                                    "predicate": predicate,
-                                    "object": onto_obj,
-                                    "optional": True if attribute["optional"] else False
-                                }, block_id, sblock_id, pblock_ids)
-                                if attribute["filterType"] == "regexp":
-                                    negative_sign = ""
-                                    if attribute["negative"]:
-                                        negative_sign = "!"
-                                    self.store_filter("FILTER ({}regex({}, '{}', 'i'))".format(negative_sign, onto_obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
-                                elif attribute["filterType"] == "exact":
-                                    if attribute["negative"]:
-                                        self.store_filter("FILTER (str({}) != '{}') .".format(onto_obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
-                                    else:
-                                        self.store_value("VALUES {} {{ '{}' }} .".format(onto_obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
                 # Classic relation
                 else:
                     relation = "<{}>".format(link["uri"])
@@ -1217,8 +1110,6 @@ def build_query_from_json(self, preview=False, for_editor=False):
 
         # Browse attributes
         for attribute in self.json["attr"]:
-            if attribute["nodeId"] in ontological_nodes:
-                continue
             # Get blockid and sblockid of the attribute node
             block_id, sblock_id, pblock_ids = self.get_block_ids(attribute["nodeId"])
 
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index fef3756f..a735ede2 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -213,9 +213,12 @@ export default class Query extends Component {
     })
   }
 
-  isOntoEntity (entityUri) {
+  isOntoRelation (currentUri, targetUri) {
+    if (! currentUri == targetUri){
+      return false
+    }
     return this.state.abstraction.entities.some(entity => {
-      return (entity.uri == entityUri && entity.ontology)
+      return (entity.uri == currentUri && entity.ontology)
     })
   }
 
@@ -405,7 +408,6 @@ export default class Query extends Component {
       specialPreviousIds: specialPreviousIds,
       label: this.getLabel(uri),
       faldo: this.isFaldoEntity(uri),
-      onto: this.isOntoEntity(uri),
       selected: selected,
       suggested: suggested
     }
@@ -519,7 +521,7 @@ export default class Query extends Component {
             // push suggested link
             this.graphState.links.push({
               uri: relation.uri,
-              type: this.isOntoEntity(relation.target) ? "ontoLink" : "link",
+              type: this.isOntoRelation(relation.source, relation.target) ? "ontoLink" : "link",
               sameStrand: this.nodeHaveStrand(node.uri) && this.nodeHaveStrand(relation.target),
               sameRef: this.nodeHaveRef(node.uri) && this.nodeHaveRef(relation.target),
               strict: true,
@@ -530,7 +532,6 @@ export default class Query extends Component {
               selected: false,
               suggested: true,
               directed: true,
-              onto_type: "specific"
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
           }
@@ -565,7 +566,7 @@ export default class Query extends Component {
             // push suggested link
             this.graphState.links.push({
               uri: relation.uri,
-              type: this.isOntoEntity(relation.target) ? "ontoLink" : "link",
+              type: this.isOntoRelation(relation.source, relation.target) &&  ? "ontoLink" : "link",
               sameStrand: this.nodeHaveStrand(node.id) && this.nodeHaveStrand(relation.source),
               sameRef: this.nodeHaveRef(node.id) && this.nodeHaveRef(relation.source),
               id: this.getId(),
@@ -575,7 +576,6 @@ export default class Query extends Component {
               selected: false,
               suggested: true,
               directed: true,
-              onto_type: "specific"
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
           }
@@ -604,7 +604,6 @@ export default class Query extends Component {
             faldo: entity.faldo,
             selected: false,
             suggested: true,
-            onto_type: "specific"
           })
           // push suggested link
           this.graphState.links.push({
@@ -620,7 +619,6 @@ export default class Query extends Component {
             selected: false,
             suggested: true,
             directed: true,
-            onto_type: "specific"
           })
           incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
         }
@@ -659,7 +657,6 @@ export default class Query extends Component {
           selected: false,
           suggested: false,
           directed: true,
-          onto_type: "specific"
         }
       }
 
@@ -679,7 +676,6 @@ export default class Query extends Component {
           selected: false,
           suggested: false,
           directed: true,
-          onto_type: "specific"
         }
       }
     })

From 01d25b30134ade2c6eab7238e7ca7ad4ccf15008 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 1 Nov 2021 21:46:54 +0100
Subject: [PATCH 007/113] One way

---
 askomics/react/src/routes/query/query.jsx | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index a735ede2..80eb8e3b 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -492,6 +492,8 @@ export default class Query extends Component {
 
     let specialNodeGroupId = incrementSpecialNodeGroupId ? incrementSpecialNodeGroupId : node.specialNodeGroupId
 
+    let isOnto = this.isOntoRelation(relation.source, relation.target)
+
     this.state.abstraction.relations.map(relation => {
       if (relation.source == node.uri) {
         if (this.entityExist(relation.target)) {
@@ -521,7 +523,7 @@ export default class Query extends Component {
             // push suggested link
             this.graphState.links.push({
               uri: relation.uri,
-              type: this.isOntoRelation(relation.source, relation.target) ? "ontoLink" : "link",
+              type: isOnto ? "ontoLink" : "link",
               sameStrand: this.nodeHaveStrand(node.uri) && this.nodeHaveStrand(relation.target),
               sameRef: this.nodeHaveRef(node.uri) && this.nodeHaveRef(relation.target),
               strict: true,
@@ -538,7 +540,7 @@ export default class Query extends Component {
         }
       }
 
-      if (relation.target == node.uri) {
+      if (relation.target == node.uri && ! isOnto) {
         if (this.entityExist(relation.source)) {
           sourceId = this.getId()
           linkId = this.getId()
@@ -566,7 +568,7 @@ export default class Query extends Component {
             // push suggested link
             this.graphState.links.push({
               uri: relation.uri,
-              type: this.isOntoRelation(relation.source, relation.target) &&  ? "ontoLink" : "link",
+              type: "link",
               sameStrand: this.nodeHaveStrand(node.id) && this.nodeHaveStrand(relation.source),
               sameRef: this.nodeHaveRef(node.id) && this.nodeHaveRef(relation.source),
               id: this.getId(),

From 935871a20f46f3b8d40112e73579a456548c2da5 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 2 Nov 2021 11:07:42 +0100
Subject: [PATCH 008/113] Update

---
 askomics/libaskomics/SparqlQuery.py              | 15 ++++++++++++++-
 askomics/react/src/routes/query/ontolinkview.jsx |  9 ++++-----
 askomics/react/src/routes/query/query.jsx        | 12 ++++++++++--
 3 files changed, 28 insertions(+), 8 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 143e430e..2bb5a16b 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -1088,7 +1088,20 @@ def build_query_from_json(self, preview=False, for_editor=False):
 
                 # Classic relation
                 else:
-                    relation = "<{}>".format(link["uri"])
+                    # Manage ontology stuff
+                    inverse = ""
+                    recurrence = ""
+                    relation = link["uri"]
+
+                    if relation.startswith("^"):
+                        inverse = "^"
+                        relation = relation.lstrip("^")
+
+                    if relation.endswith("*"):
+                        recurrence = "*"
+                        relation = relation.rstrip("*")
+
+                    relation = inverse + "<{}>".format(relation) + recurrence
                     triple = {
                         "subject": source,
                         "predicate": relation,
diff --git a/askomics/react/src/routes/query/ontolinkview.jsx b/askomics/react/src/routes/query/ontolinkview.jsx
index 72589303..bc8e6751 100644
--- a/askomics/react/src/routes/query/ontolinkview.jsx
+++ b/askomics/react/src/routes/query/ontolinkview.jsx
@@ -25,11 +25,10 @@ export default class OntoLinkView extends Component {
           <tr>
             <td>
              <CustomInput type="select" id={this.props.link.id} name="ontology_position" onChange={this.handleChangeOntologyType}>
-                <option selected={this.props.link.uri == 'specific' ? true : false} value="specific">a specific</option>
-                <option selected={this.props.link.uri == 'children' ? true : false} value="children">children of</option>
-                <option selected={this.props.link.uri == 'descendants' ? true : false} value="descendants">descendants of</option>
-                <option selected={this.props.link.uri == 'parents' ? true : false} value="parents">parents of</option>
-                <option selected={this.props.link.uri == 'ancestors' ? true : false} value="ancestors">ancestors of</option>
+                <option selected={this.props.link.uri == 'subClassOf' ? true : false} value="subClassOf">children of</option>
+                <option selected={this.props.link.uri == 'subClassOf*' ? true : false} value="subClassOf*">descendants of</option>
+                <option selected={this.props.link.uri == '^subClassOf' ? true : false} value="^subClassOf">parents of</option>
+                <option selected={this.props.link.uri == '^subClassOf*' ? true : false} value="^subClassOf*">ancestors of</option>
               </CustomInput>
             </td>
             <td> a term</td>
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 80eb8e3b..1ea44d85 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -528,7 +528,7 @@ export default class Query extends Component {
               sameRef: this.nodeHaveRef(node.uri) && this.nodeHaveRef(relation.target),
               strict: true,
               id: linkId,
-              label: relation.label,
+              label: isOnto ? getOntoLabel(relation.uri) : relation.label,
               source: node.id,
               target: targetId,
               selected: false,
@@ -1308,14 +1308,22 @@ export default class Query extends Component {
   // Ontology link methods -----------------------------
 
   handleChangeOntologyType (event) {
+    let labels = {subClassOf: "Children of", subClassOf*: "Descendants of", ^subClassOf: "Parents of", ^subClassOf*:"Ancestors of"}
+
     this.graphState.links.map(link => {
       if (link.id == event.target.id) {
-        link.onto_type = event.target.value
+        link.uri = event.target.value
+        link.label = getOntoLabel(event.target.value)
       }
     })
     this.updateGraphState()
   }
 
+  getOntoLabel (uri) {
+      let labels = {subClassOf: "Children of", subClassOf*: "Descendants of", ^subClassOf: "Parents of", ^subClassOf*:"Ancestors of"}
+      return labels[uri]
+  }
+
   // ------------------------------------------------
 
   // Preview results and Launch query buttons -------

From 6b61a4d2fa0d23fcc8d59129ed845258bf8c0bb6 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 2 Nov 2021 10:35:08 +0000
Subject: [PATCH 009/113] Fixes & typos

---
 .../react/src/routes/query/ontolinkview.jsx    |  8 ++++----
 askomics/react/src/routes/query/query.jsx      | 18 +++++++++++-------
 .../react/src/routes/query/visualization.jsx   |  2 +-
 3 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/askomics/react/src/routes/query/ontolinkview.jsx b/askomics/react/src/routes/query/ontolinkview.jsx
index bc8e6751..b50dfb27 100644
--- a/askomics/react/src/routes/query/ontolinkview.jsx
+++ b/askomics/react/src/routes/query/ontolinkview.jsx
@@ -25,10 +25,10 @@ export default class OntoLinkView extends Component {
           <tr>
             <td>
              <CustomInput type="select" id={this.props.link.id} name="ontology_position" onChange={this.handleChangeOntologyType}>
-                <option selected={this.props.link.uri == 'subClassOf' ? true : false} value="subClassOf">children of</option>
-                <option selected={this.props.link.uri == 'subClassOf*' ? true : false} value="subClassOf*">descendants of</option>
-                <option selected={this.props.link.uri == '^subClassOf' ? true : false} value="^subClassOf">parents of</option>
-                <option selected={this.props.link.uri == '^subClassOf*' ? true : false} value="^subClassOf*">ancestors of</option>
+                <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf">children of</option>
+                <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf*">descendants of</option>
+                <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf">parents of</option>
+                <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf*">ancestors of</option>
               </CustomInput>
             </td>
             <td> a term</td>
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 1ea44d85..14394b46 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -492,9 +492,8 @@ export default class Query extends Component {
 
     let specialNodeGroupId = incrementSpecialNodeGroupId ? incrementSpecialNodeGroupId : node.specialNodeGroupId
 
-    let isOnto = this.isOntoRelation(relation.source, relation.target)
-
     this.state.abstraction.relations.map(relation => {
+      let isOnto = this.isOntoRelation(relation.source, relation.target)
       if (relation.source == node.uri) {
         if (this.entityExist(relation.target)) {
           targetId = this.getId()
@@ -528,7 +527,7 @@ export default class Query extends Component {
               sameRef: this.nodeHaveRef(node.uri) && this.nodeHaveRef(relation.target),
               strict: true,
               id: linkId,
-              label: isOnto ? getOntoLabel(relation.uri) : relation.label,
+              label: isOnto ? this.getOntoLabel(relation.uri) : relation.label,
               source: node.id,
               target: targetId,
               selected: false,
@@ -1308,19 +1307,24 @@ export default class Query extends Component {
   // Ontology link methods -----------------------------
 
   handleChangeOntologyType (event) {
-    let labels = {subClassOf: "Children of", subClassOf*: "Descendants of", ^subClassOf: "Parents of", ^subClassOf*:"Ancestors of"}
-
     this.graphState.links.map(link => {
       if (link.id == event.target.id) {
         link.uri = event.target.value
-        link.label = getOntoLabel(event.target.value)
+        link.label = this.getOntoLabel(event.target.value)
       }
     })
     this.updateGraphState()
   }
 
   getOntoLabel (uri) {
-      let labels = {subClassOf: "Children of", subClassOf*: "Descendants of", ^subClassOf: "Parents of", ^subClassOf*:"Ancestors of"}
+      let labels = {}
+      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Children of"
+      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Descendants of" 
+      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Parents of" 
+      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Ancestors of"
+
+      console.log(uri)
+      console.log(labels)
       return labels[uri]
   }
 
diff --git a/askomics/react/src/routes/query/visualization.jsx b/askomics/react/src/routes/query/visualization.jsx
index 90ee0ef0..c2a62360 100644
--- a/askomics/react/src/routes/query/visualization.jsx
+++ b/askomics/react/src/routes/query/visualization.jsx
@@ -169,7 +169,7 @@ export default class Visualization extends Component {
     link.suggested ? ctx.setLineDash([this.lineWidth, this.lineWidth]) : ctx.setLineDash([])
 
     let greenArray = ["included_in", "overlap_with"]
-    let unselectedColor = greenArray.indexOf(link.uri) >= 0 ? this.colorGreen : this.colorGrey
+    let unselectedColor = greenArray.indexOf(link.uri) >= 0 || link.type == "ontoLink" ? this.colorGreen : this.colorGrey
     let unselectedColorText = greenArray.indexOf(link.uri) >= 0 ? this.colorGreen : this.colorDarkGrey
     ctx.strokeStyle = link.selected ? this.colorFirebrick : unselectedColor
 

From a98bac79e32c56278f9e804c979c7cb79afd5008 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 2 Nov 2021 11:57:59 +0100
Subject: [PATCH 010/113] Test hide endNode relations

---
 askomics/react/src/routes/query/query.jsx | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 14394b46..5675cdc9 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -222,6 +222,12 @@ export default class Query extends Component {
     })
   }
 
+  isOntoEndNode (currentId) {
+    return this.graphState.links.some(link => {
+      return (link.type == "ontoLink" && link.target == currentId)
+    })
+  }
+
   attributeExist (attrUri, nodeId) {
     return this.graphState.attr.some(attr => {
       return (attr.uri == attrUri && attr.nodeId == nodeId)
@@ -492,6 +498,10 @@ export default class Query extends Component {
 
     let specialNodeGroupId = incrementSpecialNodeGroupId ? incrementSpecialNodeGroupId : node.specialNodeGroupId
 
+    if this.isOntoEndNode(node.id){
+        return
+    }
+
     this.state.abstraction.relations.map(relation => {
       let isOnto = this.isOntoRelation(relation.source, relation.target)
       if (relation.source == node.uri) {
@@ -1319,8 +1329,8 @@ export default class Query extends Component {
   getOntoLabel (uri) {
       let labels = {}
       labels["http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Children of"
-      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Descendants of" 
-      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Parents of" 
+      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Descendants of"
+      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Parents of"
       labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Ancestors of"
 
       console.log(uri)

From a225df9d4198b50743b1a5f609ab1516b8fc57cc Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 2 Nov 2021 14:27:37 +0000
Subject: [PATCH 011/113] Improved layout & fixes

---
 askomics/react/src/routes/query/attribute.jsx | 26 ++++++++++++++++---
 askomics/react/src/routes/query/query.jsx     | 16 +++++++-----
 2 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index b6cb21ca..5536edde 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -151,15 +151,32 @@ export default class AttributeBox extends Component {
       )
     }
 
-    return (
-      <div className="attribute-box">
-        <label className="attr-label">{this.props.attribute.label}</label>
+
+    let attrIcons
+
+    if (this.props.isOnto){
+      attrIcons = (
+        <div className="attr-icons">
+          <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
+        </div>
+      )
+
+    } else {
+      attrIcons = (
         <div className="attr-icons">
           {this.props.config.user.admin ? <i className={formIcon} id={this.props.attribute.id} onClick={this.toggleFormAttribute} data-tip data-for={"formTooltip"}></i> : <nodiv></nodiv>}
           <i className={linkIcon} id={this.props.attribute.id} onClick={this.toggleLinkAttribute} data-tip data-for={"linkTooltip"}></i>
           {this.props.attribute.uri == "rdf:type" || this.props.attribute.uri == "rdfs:label" ? <nodiv></nodiv> : <i className={optionalIcon} id={this.props.attribute.id} onClick={this.toggleOptional} data-tip data-for={"optionalTooltip"}></i> }
           <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
         </div>
+      )
+    }
+
+
+    return (
+      <div className="attribute-box">
+        <label className="attr-label">{this.props.attribute.label}</label>
+        {attrIcons}
         {form}
       </div>
     )
@@ -476,5 +493,6 @@ AttributeBox.propTypes = {
   handleDateFilter: PropTypes.func,
   attribute: PropTypes.object,
   graph: PropTypes.object,
-  config: PropTypes.object
+  config: PropTypes.object,
+  isOnto: PropTypes.bool
 }
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 5675cdc9..a1a3df60 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -223,8 +223,9 @@ export default class Query extends Component {
   }
 
   isOntoEndNode (currentId) {
-    return this.graphState.links.some(link => {
-      return (link.type == "ontoLink" && link.target == currentId)
+
+    return this.graphState.nodes.some(node => {
+      return (node.id == currentId && node.ontology)
     })
   }
 
@@ -498,7 +499,7 @@ export default class Query extends Component {
 
     let specialNodeGroupId = incrementSpecialNodeGroupId ? incrementSpecialNodeGroupId : node.specialNodeGroupId
 
-    if this.isOntoEndNode(node.id){
+    if (this.isOntoEndNode(node.id)){
         return
     }
 
@@ -527,7 +528,8 @@ export default class Query extends Component {
               label: label,
               faldo: this.isFaldoEntity(relation.target),
               selected: false,
-              suggested: true
+              suggested: true,
+              ontology: isOnto
             })
             // push suggested link
             this.graphState.links.push({
@@ -1332,9 +1334,6 @@ export default class Query extends Component {
       labels["http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Descendants of"
       labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "Parents of"
       labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "Ancestors of"
-
-      console.log(uri)
-      console.log(labels)
       return labels[uri]
   }
 
@@ -1507,6 +1506,7 @@ export default class Query extends Component {
     let visualizationDiv
     let uriLabelBoxes
     let AttributeBoxes
+    let isOnto
     let linkView
     let previewButton
     let faldoButton
@@ -1526,6 +1526,7 @@ export default class Query extends Component {
     if (!this.state.waiting) {
       // attribute boxes (right view) only for node
       if (this.currentSelected) {
+        isOnto = this.isOntoEndNode(this.currentSelected.id)
         AttributeBoxes = this.state.graphState.attr.map(attribute => {
           if (attribute.nodeId == this.currentSelected.id && this.currentSelected.type == "node") {
             return (
@@ -1549,6 +1550,7 @@ export default class Query extends Component {
                 handleFilterDateValue={p => this.handleFilterDateValue(p)}
                 handleDateFilter={p => this.handleDateFilter(p)}
                 config={this.state.config}
+                isOnto={isOnto}
               />
             )
           }

From 482c5e753b1160ae564324648bc848fe6b90c74b Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 5 Nov 2021 18:54:49 +0100
Subject: [PATCH 012/113] prefixes

---
 askomics/libaskomics/Database.py      | 15 +++++++++++
 askomics/libaskomics/PrefixManager.py | 39 +++++++++++++++++++++++++++
 2 files changed, 54 insertions(+)

diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index 16b138f0..ebc58e05 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -76,6 +76,7 @@ def init_database(self):
         self.create_files_table()
         self.create_datasets_table()
         self.create_abstraction_table()
+        self.create_prefixes_table()
 
     def create_user_table(self):
         """Create the user table"""
@@ -383,3 +384,17 @@ def create_abstraction_table(self):
         )
         """
         self.execute_sql_query(query)
+
+    def create_prefixes_table(self):
+        """Create the prefix table"""
+        query = '''
+        CREATE TABLE IF NOT EXISTS prefixes (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            prefix text NOT NULL,
+            namespace text NOT NULL
+        )
+        '''
+        self.execute_sql_query(query)
+
+    def create_ontologies_table(self):
+        pass
diff --git a/askomics/libaskomics/PrefixManager.py b/askomics/libaskomics/PrefixManager.py
index 3dc71dfc..f816431d 100644
--- a/askomics/libaskomics/PrefixManager.py
+++ b/askomics/libaskomics/PrefixManager.py
@@ -1,3 +1,4 @@
+from askomics.libaskomics.Database import Database
 from askomics.libaskomics.Params import Params
 
 import rdflib
@@ -79,4 +80,42 @@ def get_namespace(self, prefix):
         try:
             return prefix_cc[prefix]
         except Exception:
+            prefixes = self.get_custom_namespaces(prefix)
+            if prefixes:
+                return prefixes[0]["namespace"]
             return ""
+
+    def get_custom_namespaces(self, prefix=None):
+        """Get custom (admin-defined) prefixes
+
+        Returns
+        -------
+        list of dict
+            Prefixes information
+        """
+        database = Database(self.app, self.session)
+
+        query_args = ()
+        subquery = ""
+
+        if prefix:
+            query_args = (prefix, )
+            subquery = "WHERE prefix = ?"
+
+        query = '''
+        SELECT prefix, namespace
+        FROM prefixes
+        {}
+        '''.format(subquery)
+
+        rows = database.execute_sql_query(query, query_args)
+
+        prefixes = []
+        for row in rows:
+            prefix = {
+                'prefix': row[0],
+                'namespace': row[1],
+            }
+            prefixes.append(prefix)
+
+        return prefixes

From a82947f3807271683ef760ef13341f8a10fc6afe Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 8 Nov 2021 17:28:58 +0100
Subject: [PATCH 013/113] Prefixes

---
 askomics/api/admin.py                 | 128 ++++++++++++++++++++++++++
 askomics/libaskomics/PrefixManager.py |  41 ++++++++-
 2 files changed, 167 insertions(+), 2 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index f464182d..d4f39df4 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -7,6 +7,7 @@
 from askomics.libaskomics.FilesHandler import FilesHandler
 from askomics.libaskomics.LocalAuth import LocalAuth
 from askomics.libaskomics.Mailer import Mailer
+from askomics.libaskomics.PrefixManager import PrefixManager
 from askomics.libaskomics.Result import Result
 from askomics.libaskomics.ResultsHandler import ResultsHandler
 
@@ -510,3 +511,130 @@ def delete_datasets():
         'error': False,
         'errorMessage': ''
     })
+
+
+@admin_bp.route("/api/admin/get_prefixes", methods=["GET"])
+@api_auth
+@admin_required
+def get_prefixes():
+    """Get all custom prefixes
+
+    Returns
+    -------
+    json
+        prefixes: list of all custom prefixes
+        error: True if error, else False
+        errorMessage: the error message of error, else an empty string
+    """
+    try:
+        pm = PrefixManager()
+        prefixes = pm.get_custom_prefixes()
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+        return jsonify({
+            'prefixes': [],
+            'error': True,
+            'errorMessage': str(e)
+        }), 500
+
+    return jsonify({
+        'prefixes': prefixes,
+        'error': False,
+        'errorMessage': ''
+    })
+
+
+@admin_bp.route("/api/admin/add_prefix", methods=["POST"])
+@api_auth
+@admin_required
+def add_prefix():
+    """Create a new prefix
+
+    Returns
+    -------
+    json
+        prefixes: list of all custom prefixes
+        error: True if error, else False
+        errorMessage: the error message of error, else an empty string
+    """
+
+    data = request.get_json()
+    if not data or not (data.get("prefix") and data.get("namespace")):
+        return jsonify({
+            'prefixes': [],
+            'error': True,
+            'errorMessage': "Missing parameter"
+        }), 400
+
+    pm = PrefixManager()
+    prefixes = pm.get_custom_prefixes()
+
+    prefix = data.get("prefix")
+    namespace = data.get("namespace")
+
+    if any([prefix == custom['prefix'] for custom in prefixes]):
+        return jsonify({
+            'prefixes': [],
+            'error': True,
+            'errorMessage': "Prefix {} is already in use".format(prefix)
+        }), 400
+
+    try:
+        pm = PrefixManager()
+        pm.add_custom_prefix(prefix, namespace)
+        prefixes = pm.get_custom_prefixes()
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+        return jsonify({
+            'prefixes': [],
+            'error': True,
+            'errorMessage': str(e)
+        }), 500
+
+    return jsonify({
+        'prefixes': prefixes,
+        'error': False,
+        'errorMessage': ''
+    })
+
+
+@admin_bp.route("/api/admin/delete_prefix", methods=["POST"])
+@api_auth
+@admin_required
+def delete_prefix():
+    """Delete a prefix
+
+    Returns
+    -------
+    json
+        prefixes: list of all custom prefixes
+        error: True if error, else False
+        errorMessage: the error message of error, else an empty string
+    """
+
+    data = request.get_json()
+    if not data or not data.get("prefix_id"):
+        return jsonify({
+            'prefixes': [],
+            'error': True,
+            'errorMessage': "Missing prefix_id parameter"
+        }), 400
+
+    pm = PrefixManager()
+    try:
+        pm = PrefixManager()
+        pm.delete_custom_prefix(data.get("prefix_id"))
+        prefixes = pm.get_custom_prefixes()
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+        return jsonify({
+            'prefixes': [],
+            'error': True,
+            'errorMessage': str(e)
+        }), 500
+
+    return jsonify({
+        'prefixes': prefixes,
+        'error': False,
+        'errorMessage': ''
+    })
diff --git a/askomics/libaskomics/PrefixManager.py b/askomics/libaskomics/PrefixManager.py
index f816431d..7ed838d9 100644
--- a/askomics/libaskomics/PrefixManager.py
+++ b/askomics/libaskomics/PrefixManager.py
@@ -80,12 +80,12 @@ def get_namespace(self, prefix):
         try:
             return prefix_cc[prefix]
         except Exception:
-            prefixes = self.get_custom_namespaces(prefix)
+            prefixes = self.get_custom_prefixes(prefix)
             if prefixes:
                 return prefixes[0]["namespace"]
             return ""
 
-    def get_custom_namespaces(self, prefix=None):
+    def get_custom_prefixes(self, prefix=None):
         """Get custom (admin-defined) prefixes
 
         Returns
@@ -119,3 +119,40 @@ def get_custom_namespaces(self, prefix=None):
             prefixes.append(prefix)
 
         return prefixes
+
+    def add_custom_prefix(self, prefix, namespace):
+        """Create a new custom (admin-defined) prefixes
+
+        Returns
+        -------
+        list of dict
+            Prefixes information
+        """
+        database = Database(self.app, self.session)
+
+        query = '''
+        INSERT INTO prefixes VALUES(
+            NULL,
+            ?,
+            ?
+        )
+        '''
+
+        database.execute_sql_query(query, (prefix, namespace))
+
+    def remove_custom_prefix(self, prefix_id):
+        """Create a new custom (admin-defined) prefixes
+
+        Returns
+        -------
+        list of dict
+            Prefixes information
+        """
+        database = Database(self.app, self.session)
+
+        query = '''
+        DELETE FROM prefixes
+        WHERE id = ?
+        '''
+
+        database.execute_sql_query(query, (prefix_id))

From 78c083ae2e269edcebd48f4be44591b215bdb559 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 9 Nov 2021 11:46:17 +0100
Subject: [PATCH 014/113] React prefixes

---
 askomics/api/admin.py                         |  12 +-
 askomics/libaskomics/PrefixManager.py         |  12 +-
 askomics/react/src/routes/admin/admin.jsx     | 134 +++++++++++++++++-
 .../react/src/routes/admin/prefixestable.jsx  | 104 ++++++++++++++
 4 files changed, 250 insertions(+), 12 deletions(-)
 create mode 100644 askomics/react/src/routes/admin/prefixestable.jsx

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index d4f39df4..368bf72a 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -513,7 +513,7 @@ def delete_datasets():
     })
 
 
-@admin_bp.route("/api/admin/get_prefixes", methods=["GET"])
+@admin_bp.route("/api/admin/getprefixes", methods=["GET"])
 @api_auth
 @admin_required
 def get_prefixes():
@@ -544,7 +544,7 @@ def get_prefixes():
     })
 
 
-@admin_bp.route("/api/admin/add_prefix", methods=["POST"])
+@admin_bp.route("/api/admin/addprefix", methods=["POST"])
 @api_auth
 @admin_required
 def add_prefix():
@@ -598,7 +598,7 @@ def add_prefix():
     })
 
 
-@admin_bp.route("/api/admin/delete_prefix", methods=["POST"])
+@admin_bp.route("/api/admin/delete_prefixes", methods=["POST"])
 @api_auth
 @admin_required
 def delete_prefix():
@@ -613,17 +613,17 @@ def delete_prefix():
     """
 
     data = request.get_json()
-    if not data or not data.get("prefix_id"):
+    if not data or not data.get("prefixesIdToDelete"):
         return jsonify({
             'prefixes': [],
             'error': True,
-            'errorMessage': "Missing prefix_id parameter"
+            'errorMessage': "Missing prefixesIdToDelete parameter"
         }), 400
 
     pm = PrefixManager()
     try:
         pm = PrefixManager()
-        pm.delete_custom_prefix(data.get("prefix_id"))
+        pm.delete_custom_prefixes(data.get("prefixesIdToDelete"))
         prefixes = pm.get_custom_prefixes()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/PrefixManager.py b/askomics/libaskomics/PrefixManager.py
index 7ed838d9..e52c21a5 100644
--- a/askomics/libaskomics/PrefixManager.py
+++ b/askomics/libaskomics/PrefixManager.py
@@ -103,7 +103,7 @@ def get_custom_prefixes(self, prefix=None):
             subquery = "WHERE prefix = ?"
 
         query = '''
-        SELECT prefix, namespace
+        SELECT id, prefix, namespace
         FROM prefixes
         {}
         '''.format(subquery)
@@ -113,8 +113,9 @@ def get_custom_prefixes(self, prefix=None):
         prefixes = []
         for row in rows:
             prefix = {
-                'prefix': row[0],
-                'namespace': row[1],
+                'id': row[0],
+                'prefix': row[1],
+                'namespace': row[2],
             }
             prefixes.append(prefix)
 
@@ -140,7 +141,7 @@ def add_custom_prefix(self, prefix, namespace):
 
         database.execute_sql_query(query, (prefix, namespace))
 
-    def remove_custom_prefix(self, prefix_id):
+    def remove_custom_prefixes(self, prefixes_id):
         """Create a new custom (admin-defined) prefixes
 
         Returns
@@ -155,4 +156,5 @@ def remove_custom_prefix(self, prefix_id):
         WHERE id = ?
         '''
 
-        database.execute_sql_query(query, (prefix_id))
+        for prefix_id in prefixes_id:
+            database.execute_sql_query(query, (prefix_id))
diff --git a/askomics/react/src/routes/admin/admin.jsx b/askomics/react/src/routes/admin/admin.jsx
index 17cebd31..f296610d 100644
--- a/askomics/react/src/routes/admin/admin.jsx
+++ b/askomics/react/src/routes/admin/admin.jsx
@@ -6,6 +6,7 @@ import DatasetsTable from './datasetstable'
 import FilesTable from './filestable'
 import QueriesTable from './queriestable'
 import UsersTable from './userstable'
+import PrefixesTable from './prefixestable'
 import Utils from '../../classes/utils'
 import { Redirect } from 'react-router-dom'
 import WaitingDiv from '../../components/waiting'
@@ -29,12 +30,18 @@ export default class Admin extends Component {
       datasetErrorMessage: '',
       queryError: false,
       queryErrorMessage: '',
+      prefixError: false,
+      prefixErrorMessage: '',
+      newprefixError: false,
+      newprefixErrorMessage: '',
       users: [],
       datasets: [],
       files: [],
       queries: [],
       fname: "",
       lname: "",
+      prefix: "",
+      namespace: "",
       username: "",
       email: "",
       newUser: {},
@@ -43,16 +50,21 @@ export default class Admin extends Component {
       instanceUrl: "",
       usersSelected: [],
       filesSelected: [],
-      datasetsSelected: []
+      datasetsSelected: [],
+      prefixesSelected: []
     }
     this.handleChangeUserInput = this.handleChangeUserInput.bind(this)
     this.handleChangeFname = this.handleChangeFname.bind(this)
     this.handleChangeLname = this.handleChangeLname.bind(this)
     this.handleAddUser = this.handleAddUser.bind(this)
+    this.handleChangePrefix = this.handleChangePrefix.bind(this)
+    this.handleChangeNamespace = this.handleChangeNamespace.bind(this)
+    this.handleAddPrefix = this.handleAddPrefix.bind(this)
     this.dismissMessage = this.dismissMessage.bind(this)
     this.deleteSelectedUsers = this.deleteSelectedUsers.bind(this)
     this.deleteSelectedFiles = this.deleteSelectedFiles.bind(this)
     this.deleteSelectedDatasets = this.deleteSelectedDatasets.bind(this)
+    this.deleteSelectedPrefixes = this.deleteSelectedPrefixes.bind(this)
     this.cancelRequest
   }
 
@@ -68,6 +80,10 @@ export default class Admin extends Component {
     return this.state.datasetsSelected.length == 0
   }
 
+  isPrefixesDisabled () {
+    return this.state.prefixesSelected.length == 0
+  }
+
   deleteSelectedUsers () {
     let requestUrl = '/api/admin/delete_users'
     let data = {
@@ -113,6 +129,21 @@ export default class Admin extends Component {
       })
   }
 
+  deleteSelectedPrefixes () {
+    let requestUrl = '/api/admin/delete_prefixes'
+    let data = {
+      prefixesIdToDelete: this.state.prefixesSelected
+    }
+    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        console.log(requestUrl, response.data)
+        this.setState({
+          prefixes: response.data.prefixes,
+          prefixesSelected: [],
+        })
+      })
+  }
+
   dismissMessage () {
     this.setState({
       newUser: {},
@@ -140,6 +171,18 @@ export default class Admin extends Component {
     })
   }
 
+  handleChangePrefix (event) {
+    this.setState({
+      prefix: event.target.value
+    })
+  }
+
+  handleChangeNamespace (event) {
+    this.setState({
+      namespace: event.target.value
+    })
+  }
+
   validateEmail (email) {
     let re = /^(([^<>()\[\]\\.,;:\s@"]+(\.[^<>()\[\]\\.,;:\s@"]+)*)|(".+"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/
     return re.test(String(email).toLowerCase())
@@ -154,6 +197,13 @@ export default class Admin extends Component {
     )
   }
 
+  validatePrefixForm () {
+    return (
+      this.state.prefix.length > 0 &&
+      this.state.namespace.length > 0 &&
+    )
+  }
+
   handleAddUser(event) {
 
     let requestUrl = "/api/admin/adduser"
@@ -192,12 +242,45 @@ export default class Admin extends Component {
     event.preventDefault()
   }
 
+  handleAddPrefix(event) {
+
+    let requestUrl = "/api/admin/addprefix"
+    let data = {
+      prefix: this.state.prefix,
+      namespace: this.state.namespace,
+    }
+
+    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+    .then(response => {
+      console.log(requestUrl, response.data)
+      this.setState({
+        newprefixError: response.data.error,
+        newprefixErrorMessage: response.data.errorMessage,
+        prefixes: response.data.prefixes,
+        newprefixStatus: error.response.status,
+      })
+      if (!response.data.error) {
+        this.loadUsers()
+      }
+    })
+    .catch(error => {
+      console.log(error, error.response.data.errorMessage)
+      this.setState({
+        newprefixError: true,
+        newprefixErrorMessage: error.response.data.errorMessage,
+        newprefixStatus: error.response.status,
+      })
+    })
+    event.preventDefault()
+  }
+
   componentDidMount () {
     if (!this.props.waitForStart) {
       this.loadUsers()
       this.loadDataSets()
       this.loadFiles()
       this.loadQueries()
+      this.loadPrefixes()
       this.interval = setInterval(() => {
         this.loadDataSets()
       }, 5000)
@@ -292,6 +375,27 @@ export default class Admin extends Component {
       })
   }
 
+  loadPrefixes() {
+    let requestUrl = '/api/admin/getprefixes'
+    axios.get(requestUrl, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        console.log(requestUrl, response.data)
+        this.setState({
+          prefixesLoading: false,
+          prefixes: response.data.prefixes
+        })
+      })
+      .catch(error => {
+        console.log(error, error.response.data.errorMessage)
+        this.setState({
+          prefixError: true,
+          prefixErrorMessage: error.response.data.errorMessage,
+          prefixStatus: error.response.status,
+          success: !error.response.data.error
+        })
+      })
+  }
+
   componentWillUnmount () {
     clearInterval(this.interval)
     if (!this.props.waitForStart) {
@@ -404,6 +508,34 @@ export default class Admin extends Component {
         <QueriesTable config={this.props.config} queries={this.state.queries} setStateQueries={p => this.setState(p)} queriesLoading={this.state.queriesLoading} />
         <br />
         <ErrorDiv status={this.state.queryStatus} error={this.state.queryError} errorMessage={this.state.queryErrorMessage} />
+
+        <h4>Prefixes</h4>
+        <h5>Add a prefix</h5>
+        <div>
+        <Form onSubmit={this.handleAddPrefix}>
+          <Row form>
+            <Col md={6}>
+              <FormGroup>
+                <Label for="fname">Prefix</Label>
+                <Input type="text" name="prefix" id="prefix" placeholder="prefix" value={this.state.prefix} onChange={this.handleChangePrefix} />
+              </FormGroup>
+            </Col>
+            <Col md={6}>
+              <FormGroup>
+                <Label for="lname">Namespace</Label>
+                <Input type="text" name="namespace" id="namespace" placeholder="namespace" value={this.state.namespace} onChange={this.handleChangeNamespace} />
+              </FormGroup>
+            </Col>
+          </Row>
+          <Button disabled={!this.validatePrefixForm()}>Create</Button>
+        </Form>
+        <ErrorDiv status={this.state.newprefixstatus} error={this.state.newprefixerror} errorMessage={this.state.newprefixerrorMessage} />
+        <br />
+        </div>
+        <PrefixesTable config={this.props.config} prefixes={this.state.prefixes} setStatePrefixes={p => this.setState(p)} prefixesLoading={this.state.prefixesLoading} />
+        <br />
+        <ErrorDiv status={this.state.prefixStatus} error={this.state.prefixError} errorMessage={this.state.prefixErrorMessage} />
+
       </div>
     )
   }
diff --git a/askomics/react/src/routes/admin/prefixestable.jsx b/askomics/react/src/routes/admin/prefixestable.jsx
new file mode 100644
index 00000000..ec30db07
--- /dev/null
+++ b/askomics/react/src/routes/admin/prefixestable.jsx
@@ -0,0 +1,104 @@
+import React, { Component } from 'react'
+import axios from 'axios'
+import {Badge, Button, Form, FormGroup, Label, Input, Alert, Row, Col, CustomInput } from 'reactstrap'
+import BootstrapTable from 'react-bootstrap-table-next'
+import paginationFactory from 'react-bootstrap-table2-paginator'
+import cellEditFactory from 'react-bootstrap-table2-editor'
+import update from 'react-addons-update'
+import PropTypes from 'prop-types'
+import Utils from '../../classes/utils'
+import WaitingDiv from '../../components/waiting'
+import pretty from 'pretty-time'
+
+export default class PrefixesTable extends Component {
+  constructor (props) {
+    super(props)
+    this.utils = new Utils()
+    this.handlePrefixSelection = this.handlePrefixSelection.bind(this)
+    this.handlePrefixSelectionAll = this.handlePrefixSelectionAll.bind(this)
+  }
+
+  handlePrefixSelection (row, isSelect) {
+    if (isSelect) {
+      this.props.setStateUsers({
+        prefixesSelected: [...this.props.prefixesSelected, row.id]
+      })
+    } else {
+      this.props.setStateUsers({
+        prefixesSelected: this.props.prefixesSelected.filter(x => x !== row.id)
+      })
+    }
+  }
+
+  handlePrefixSelectionAll (isSelect, rows) {
+    const prefixes = rows.map(r => r.id)
+    if (isSelect) {
+      this.props.setStateUsers({
+        prefixesSelected: prefixes
+      })
+    } else {
+      this.props.setStateUsers({
+        prefixesSelected: []
+      })
+    }
+  }
+
+  render () {
+    let prefixesColumns = [{
+      editable: false,
+      dataField: 'prefix',
+      text: 'Prefix',
+      sort: true
+    }, {
+      editable: false,
+      dataField: 'namespace',
+      text: 'Namespace',
+      sort: true
+    }]
+
+    let prefixesDefaultSorted = [{
+      dataField: 'prefix',
+      order: 'asc'
+    }]
+
+    let prefixesSelectRow = {
+      mode: 'checkbox',
+      clickToSelect: false,
+      selected: this.props.prefixesSelected,
+      onSelect: this.handleUserSelection,
+      onSelectAll: this.handleUserSelectionAll,
+      nonSelectable: [this.props.config.user.username]
+    }
+
+    let prefixesNoDataIndication = 'No custom prefixes'
+    if (this.props.prefixesLoading) {
+      prefixesNoDataIndication = <WaitingDiv waiting={this.props.prefixesLoading} />
+    }
+
+    return (
+        <div className="asko-table-height-div">
+          <BootstrapTable
+            classes="asko-table"
+            wrapperClasses="asko-table-wrapper"
+            tabIndexCell
+            bootstrap4
+            keyField='prefix'
+            data={this.props.prefixes}
+            columns={prefixesColumns}
+            defaultSorted={prefixesDefaultSorted}
+            pagination={paginationFactory()}
+            noDataIndication={datasetsNoDataIndication}
+            selectRow={ prefixesSelectRow }
+          />
+        </div>
+    )
+  }
+}
+
+PrefixesTable.propTypes = {
+    setStatePrefixes: PropTypes.func,
+    prefixesSelected: PropTypes.object,
+    prefixesLoading: PropTypes.bool,
+    prefixes: PropTypes.list,
+    config: PropTypes.object
+}

From 988c068e636e0f78581da7f3ef0334bb3e75db1d Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 16 Nov 2021 08:35:38 +0000
Subject: [PATCH 015/113] typo

---
 askomics/api/admin.py                             | 8 +++-----
 askomics/react/src/routes/admin/admin.jsx         | 3 ++-
 askomics/react/src/routes/admin/prefixestable.jsx | 4 ++--
 3 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 368bf72a..313633fa 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -527,7 +527,7 @@ def get_prefixes():
         errorMessage: the error message of error, else an empty string
     """
     try:
-        pm = PrefixManager()
+        pm = PrefixManager(current_app, session)
         prefixes = pm.get_custom_prefixes()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
@@ -566,7 +566,7 @@ def add_prefix():
             'errorMessage': "Missing parameter"
         }), 400
 
-    pm = PrefixManager()
+    pm = PrefixManager(current_app, session)
     prefixes = pm.get_custom_prefixes()
 
     prefix = data.get("prefix")
@@ -580,7 +580,6 @@ def add_prefix():
         }), 400
 
     try:
-        pm = PrefixManager()
         pm.add_custom_prefix(prefix, namespace)
         prefixes = pm.get_custom_prefixes()
     except Exception as e:
@@ -620,9 +619,8 @@ def delete_prefix():
             'errorMessage': "Missing prefixesIdToDelete parameter"
         }), 400
 
-    pm = PrefixManager()
+    pm = PrefixManager(current_app, session)
     try:
-        pm = PrefixManager()
         pm.delete_custom_prefixes(data.get("prefixesIdToDelete"))
         prefixes = pm.get_custom_prefixes()
     except Exception as e:
diff --git a/askomics/react/src/routes/admin/admin.jsx b/askomics/react/src/routes/admin/admin.jsx
index f296610d..872ef306 100644
--- a/askomics/react/src/routes/admin/admin.jsx
+++ b/askomics/react/src/routes/admin/admin.jsx
@@ -38,6 +38,7 @@ export default class Admin extends Component {
       datasets: [],
       files: [],
       queries: [],
+      prefixes: [],
       fname: "",
       lname: "",
       prefix: "",
@@ -200,7 +201,7 @@ export default class Admin extends Component {
   validatePrefixForm () {
     return (
       this.state.prefix.length > 0 &&
-      this.state.namespace.length > 0 &&
+      this.state.namespace.length > 0
     )
   }
 
diff --git a/askomics/react/src/routes/admin/prefixestable.jsx b/askomics/react/src/routes/admin/prefixestable.jsx
index ec30db07..90417352 100644
--- a/askomics/react/src/routes/admin/prefixestable.jsx
+++ b/askomics/react/src/routes/admin/prefixestable.jsx
@@ -87,7 +87,7 @@ export default class PrefixesTable extends Component {
             columns={prefixesColumns}
             defaultSorted={prefixesDefaultSorted}
             pagination={paginationFactory()}
-            noDataIndication={datasetsNoDataIndication}
+            noDataIndication={prefixesNoDataIndication}
             selectRow={ prefixesSelectRow }
           />
         </div>
@@ -99,6 +99,6 @@ PrefixesTable.propTypes = {
     setStatePrefixes: PropTypes.func,
     prefixesSelected: PropTypes.object,
     prefixesLoading: PropTypes.bool,
-    prefixes: PropTypes.list,
+    prefixes: PropTypes.array,
     config: PropTypes.object
 }

From 142d783db2d88ba9547445cb2343a4e178731733 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 16 Nov 2021 09:53:10 +0100
Subject: [PATCH 016/113] Typo(2)

---
 askomics/react/src/routes/admin/admin.jsx | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/askomics/react/src/routes/admin/admin.jsx b/askomics/react/src/routes/admin/admin.jsx
index 872ef306..b2c968b3 100644
--- a/askomics/react/src/routes/admin/admin.jsx
+++ b/askomics/react/src/routes/admin/admin.jsx
@@ -261,7 +261,9 @@ export default class Admin extends Component {
         newprefixStatus: error.response.status,
       })
       if (!response.data.error) {
-        this.loadUsers()
+          this.setState({
+            prefixes: response.data.prefixes
+          })
       }
     })
     .catch(error => {
@@ -535,6 +537,7 @@ export default class Admin extends Component {
         </div>
         <PrefixesTable config={this.props.config} prefixes={this.state.prefixes} setStatePrefixes={p => this.setState(p)} prefixesLoading={this.state.prefixesLoading} />
         <br />
+        <Button disabled={this.isPrefixesDisabled()} onClick={this.deleteSelectedPrefixes} color="danger"><i className="fas fa-trash-alt"></i> Delete</Button>
         <ErrorDiv status={this.state.prefixStatus} error={this.state.prefixError} errorMessage={this.state.prefixErrorMessage} />
 
       </div>

From 0224efa3ee845f1c1bf450a82e8d1036afd6c6bb Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 16 Nov 2021 14:28:09 +0000
Subject: [PATCH 017/113] Fix routes

---
 askomics/api/admin.py                            |  2 +-
 askomics/libaskomics/PrefixManager.py            |  4 ++--
 askomics/react/src/routes/admin/admin.jsx        |  9 ++-------
 .../react/src/routes/admin/prefixestable.jsx     | 16 ++++++++--------
 4 files changed, 13 insertions(+), 18 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 313633fa..0822ecc7 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -621,7 +621,7 @@ def delete_prefix():
 
     pm = PrefixManager(current_app, session)
     try:
-        pm.delete_custom_prefixes(data.get("prefixesIdToDelete"))
+        pm.remove_custom_prefixes(data.get("prefixesIdToDelete"))
         prefixes = pm.get_custom_prefixes()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/PrefixManager.py b/askomics/libaskomics/PrefixManager.py
index e52c21a5..b3ff0999 100644
--- a/askomics/libaskomics/PrefixManager.py
+++ b/askomics/libaskomics/PrefixManager.py
@@ -139,7 +139,7 @@ def add_custom_prefix(self, prefix, namespace):
         )
         '''
 
-        database.execute_sql_query(query, (prefix, namespace))
+        database.execute_sql_query(query, (prefix, namespace,))
 
     def remove_custom_prefixes(self, prefixes_id):
         """Create a new custom (admin-defined) prefixes
@@ -157,4 +157,4 @@ def remove_custom_prefixes(self, prefixes_id):
         '''
 
         for prefix_id in prefixes_id:
-            database.execute_sql_query(query, (prefix_id))
+            database.execute_sql_query(query, (prefix_id,))
diff --git a/askomics/react/src/routes/admin/admin.jsx b/askomics/react/src/routes/admin/admin.jsx
index b2c968b3..18aa0438 100644
--- a/askomics/react/src/routes/admin/admin.jsx
+++ b/askomics/react/src/routes/admin/admin.jsx
@@ -258,13 +258,8 @@ export default class Admin extends Component {
         newprefixError: response.data.error,
         newprefixErrorMessage: response.data.errorMessage,
         prefixes: response.data.prefixes,
-        newprefixStatus: error.response.status,
+        newprefixStatus: response.status,
       })
-      if (!response.data.error) {
-          this.setState({
-            prefixes: response.data.prefixes
-          })
-      }
     })
     .catch(error => {
       console.log(error, error.response.data.errorMessage)
@@ -535,7 +530,7 @@ export default class Admin extends Component {
         <ErrorDiv status={this.state.newprefixstatus} error={this.state.newprefixerror} errorMessage={this.state.newprefixerrorMessage} />
         <br />
         </div>
-        <PrefixesTable config={this.props.config} prefixes={this.state.prefixes} setStatePrefixes={p => this.setState(p)} prefixesLoading={this.state.prefixesLoading} />
+        <PrefixesTable config={this.props.config} prefixes={this.state.prefixes} setStatePrefixes={p => this.setState(p)} prefixesSelected={this.state.prefixesSelected} prefixesLoading={this.state.prefixesLoading} />
         <br />
         <Button disabled={this.isPrefixesDisabled()} onClick={this.deleteSelectedPrefixes} color="danger"><i className="fas fa-trash-alt"></i> Delete</Button>
         <ErrorDiv status={this.state.prefixStatus} error={this.state.prefixError} errorMessage={this.state.prefixErrorMessage} />
diff --git a/askomics/react/src/routes/admin/prefixestable.jsx b/askomics/react/src/routes/admin/prefixestable.jsx
index 90417352..809d2ed9 100644
--- a/askomics/react/src/routes/admin/prefixestable.jsx
+++ b/askomics/react/src/routes/admin/prefixestable.jsx
@@ -19,12 +19,13 @@ export default class PrefixesTable extends Component {
   }
 
   handlePrefixSelection (row, isSelect) {
+    console.log('triggered')
     if (isSelect) {
-      this.props.setStateUsers({
+      this.props.setStatePrefixes({
         prefixesSelected: [...this.props.prefixesSelected, row.id]
       })
     } else {
-      this.props.setStateUsers({
+      this.props.setStatePrefixes({
         prefixesSelected: this.props.prefixesSelected.filter(x => x !== row.id)
       })
     }
@@ -33,11 +34,11 @@ export default class PrefixesTable extends Component {
   handlePrefixSelectionAll (isSelect, rows) {
     const prefixes = rows.map(r => r.id)
     if (isSelect) {
-      this.props.setStateUsers({
+      this.props.setStatePrefixes({
         prefixesSelected: prefixes
       })
     } else {
-      this.props.setStateUsers({
+      this.props.setStatePrefixes({
         prefixesSelected: []
       })
     }
@@ -65,9 +66,8 @@ export default class PrefixesTable extends Component {
       mode: 'checkbox',
       clickToSelect: false,
       selected: this.props.prefixesSelected,
-      onSelect: this.handleUserSelection,
-      onSelectAll: this.handleUserSelectionAll,
-      nonSelectable: [this.props.config.user.username]
+      onSelect: this.handlePrefixSelection,
+      onSelectAll: this.handlePrefixSelectionAll
     }
 
     let prefixesNoDataIndication = 'No custom prefixes'
@@ -82,7 +82,7 @@ export default class PrefixesTable extends Component {
             wrapperClasses="asko-table-wrapper"
             tabIndexCell
             bootstrap4
-            keyField='prefix'
+            keyField='id'
             data={this.props.prefixes}
             columns={prefixesColumns}
             defaultSorted={prefixesDefaultSorted}

From cddbcc23d4e7d9f42fe4790a17f86cbef9191543 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 17 Nov 2021 15:26:40 +0100
Subject: [PATCH 018/113] Move prefixes to their own tab

---
 askomics/react/src/navbar.jsx                 |   3 +-
 askomics/react/src/routes.jsx                 |   2 +
 askomics/react/src/routes/admin/admin.jsx     | 130 ---------
 askomics/react/src/routes/admin/prefixes.jsx  | 256 ++++++++++++++++++
 .../react/src/routes/admin/prefixestable.jsx  | 104 -------
 5 files changed, 260 insertions(+), 235 deletions(-)
 create mode 100644 askomics/react/src/routes/admin/prefixes.jsx
 delete mode 100644 askomics/react/src/routes/admin/prefixestable.jsx

diff --git a/askomics/react/src/navbar.jsx b/askomics/react/src/navbar.jsx
index ff3062fc..5c48f518 100644
--- a/askomics/react/src/navbar.jsx
+++ b/askomics/react/src/navbar.jsx
@@ -43,6 +43,7 @@ export default class AskoNavbar extends Component {
           adminLinks = (
             <DropdownItem className="bg-dark" tag="Link">
               <Link className="nav-link" to="/admin"><i className="fas fa-chess-king"></i> Admin</Link>
+              <Link className="nav-link" to="/prefixes"><i className="fas fa-chess-king"></i> Prefixes</Link>
             </DropdownItem>
           )
         }
@@ -104,4 +105,4 @@ export default class AskoNavbar extends Component {
 AskoNavbar.propTypes = {
   waitForStart: PropTypes.bool,
   config: PropTypes.object
-}
\ No newline at end of file
+}
diff --git a/askomics/react/src/routes.jsx b/askomics/react/src/routes.jsx
index 6555c070..488b439c 100644
--- a/askomics/react/src/routes.jsx
+++ b/askomics/react/src/routes.jsx
@@ -14,6 +14,7 @@ import Logout from './routes/login/logout'
 import PasswordReset from './routes/login/passwordreset'
 import Account from './routes/account/account'
 import Admin from './routes/admin/admin'
+import Prefixes from './routes/admin/prefixes'
 import Sparql from './routes/sparql/sparql'
 import FormQuery from './routes/form/query'
 import FormEditQuery from './routes/form_edit/query'
@@ -113,6 +114,7 @@ export default class Routes extends Component {
             <Route path="/password_reset" component={(props) => <PasswordReset config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} {...props}/>}/>
             <Route path="/account" exact component={() => (<Account config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} />)} />
             <Route path="/admin" exact component={() => (<Admin config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} />)} />
+            <Route path="/prefixes" exact component={() => (<Prefixes config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} />)} />
             <Route path="/query" exact component={Query} />
             <Route path="/form" exact component={FormQuery} />
             <Route path="/form_edit" exact component={FormEditQuery} />
diff --git a/askomics/react/src/routes/admin/admin.jsx b/askomics/react/src/routes/admin/admin.jsx
index 18aa0438..9f4bfb63 100644
--- a/askomics/react/src/routes/admin/admin.jsx
+++ b/askomics/react/src/routes/admin/admin.jsx
@@ -6,7 +6,6 @@ import DatasetsTable from './datasetstable'
 import FilesTable from './filestable'
 import QueriesTable from './queriestable'
 import UsersTable from './userstable'
-import PrefixesTable from './prefixestable'
 import Utils from '../../classes/utils'
 import { Redirect } from 'react-router-dom'
 import WaitingDiv from '../../components/waiting'
@@ -30,19 +29,12 @@ export default class Admin extends Component {
       datasetErrorMessage: '',
       queryError: false,
       queryErrorMessage: '',
-      prefixError: false,
-      prefixErrorMessage: '',
-      newprefixError: false,
-      newprefixErrorMessage: '',
       users: [],
       datasets: [],
       files: [],
       queries: [],
-      prefixes: [],
       fname: "",
       lname: "",
-      prefix: "",
-      namespace: "",
       username: "",
       email: "",
       newUser: {},
@@ -52,20 +44,15 @@ export default class Admin extends Component {
       usersSelected: [],
       filesSelected: [],
       datasetsSelected: [],
-      prefixesSelected: []
     }
     this.handleChangeUserInput = this.handleChangeUserInput.bind(this)
     this.handleChangeFname = this.handleChangeFname.bind(this)
     this.handleChangeLname = this.handleChangeLname.bind(this)
     this.handleAddUser = this.handleAddUser.bind(this)
-    this.handleChangePrefix = this.handleChangePrefix.bind(this)
-    this.handleChangeNamespace = this.handleChangeNamespace.bind(this)
-    this.handleAddPrefix = this.handleAddPrefix.bind(this)
     this.dismissMessage = this.dismissMessage.bind(this)
     this.deleteSelectedUsers = this.deleteSelectedUsers.bind(this)
     this.deleteSelectedFiles = this.deleteSelectedFiles.bind(this)
     this.deleteSelectedDatasets = this.deleteSelectedDatasets.bind(this)
-    this.deleteSelectedPrefixes = this.deleteSelectedPrefixes.bind(this)
     this.cancelRequest
   }
 
@@ -81,10 +68,6 @@ export default class Admin extends Component {
     return this.state.datasetsSelected.length == 0
   }
 
-  isPrefixesDisabled () {
-    return this.state.prefixesSelected.length == 0
-  }
-
   deleteSelectedUsers () {
     let requestUrl = '/api/admin/delete_users'
     let data = {
@@ -130,21 +113,6 @@ export default class Admin extends Component {
       })
   }
 
-  deleteSelectedPrefixes () {
-    let requestUrl = '/api/admin/delete_prefixes'
-    let data = {
-      prefixesIdToDelete: this.state.prefixesSelected
-    }
-    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
-      .then(response => {
-        console.log(requestUrl, response.data)
-        this.setState({
-          prefixes: response.data.prefixes,
-          prefixesSelected: [],
-        })
-      })
-  }
-
   dismissMessage () {
     this.setState({
       newUser: {},
@@ -172,18 +140,6 @@ export default class Admin extends Component {
     })
   }
 
-  handleChangePrefix (event) {
-    this.setState({
-      prefix: event.target.value
-    })
-  }
-
-  handleChangeNamespace (event) {
-    this.setState({
-      namespace: event.target.value
-    })
-  }
-
   validateEmail (email) {
     let re = /^(([^<>()\[\]\\.,;:\s@"]+(\.[^<>()\[\]\\.,;:\s@"]+)*)|(".+"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/
     return re.test(String(email).toLowerCase())
@@ -198,13 +154,6 @@ export default class Admin extends Component {
     )
   }
 
-  validatePrefixForm () {
-    return (
-      this.state.prefix.length > 0 &&
-      this.state.namespace.length > 0
-    )
-  }
-
   handleAddUser(event) {
 
     let requestUrl = "/api/admin/adduser"
@@ -243,42 +192,12 @@ export default class Admin extends Component {
     event.preventDefault()
   }
 
-  handleAddPrefix(event) {
-
-    let requestUrl = "/api/admin/addprefix"
-    let data = {
-      prefix: this.state.prefix,
-      namespace: this.state.namespace,
-    }
-
-    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
-    .then(response => {
-      console.log(requestUrl, response.data)
-      this.setState({
-        newprefixError: response.data.error,
-        newprefixErrorMessage: response.data.errorMessage,
-        prefixes: response.data.prefixes,
-        newprefixStatus: response.status,
-      })
-    })
-    .catch(error => {
-      console.log(error, error.response.data.errorMessage)
-      this.setState({
-        newprefixError: true,
-        newprefixErrorMessage: error.response.data.errorMessage,
-        newprefixStatus: error.response.status,
-      })
-    })
-    event.preventDefault()
-  }
-
   componentDidMount () {
     if (!this.props.waitForStart) {
       this.loadUsers()
       this.loadDataSets()
       this.loadFiles()
       this.loadQueries()
-      this.loadPrefixes()
       this.interval = setInterval(() => {
         this.loadDataSets()
       }, 5000)
@@ -373,27 +292,6 @@ export default class Admin extends Component {
       })
   }
 
-  loadPrefixes() {
-    let requestUrl = '/api/admin/getprefixes'
-    axios.get(requestUrl, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
-      .then(response => {
-        console.log(requestUrl, response.data)
-        this.setState({
-          prefixesLoading: false,
-          prefixes: response.data.prefixes
-        })
-      })
-      .catch(error => {
-        console.log(error, error.response.data.errorMessage)
-        this.setState({
-          prefixError: true,
-          prefixErrorMessage: error.response.data.errorMessage,
-          prefixStatus: error.response.status,
-          success: !error.response.data.error
-        })
-      })
-  }
-
   componentWillUnmount () {
     clearInterval(this.interval)
     if (!this.props.waitForStart) {
@@ -507,34 +405,6 @@ export default class Admin extends Component {
         <br />
         <ErrorDiv status={this.state.queryStatus} error={this.state.queryError} errorMessage={this.state.queryErrorMessage} />
 
-        <h4>Prefixes</h4>
-        <h5>Add a prefix</h5>
-        <div>
-        <Form onSubmit={this.handleAddPrefix}>
-          <Row form>
-            <Col md={6}>
-              <FormGroup>
-                <Label for="fname">Prefix</Label>
-                <Input type="text" name="prefix" id="prefix" placeholder="prefix" value={this.state.prefix} onChange={this.handleChangePrefix} />
-              </FormGroup>
-            </Col>
-            <Col md={6}>
-              <FormGroup>
-                <Label for="lname">Namespace</Label>
-                <Input type="text" name="namespace" id="namespace" placeholder="namespace" value={this.state.namespace} onChange={this.handleChangeNamespace} />
-              </FormGroup>
-            </Col>
-          </Row>
-          <Button disabled={!this.validatePrefixForm()}>Create</Button>
-        </Form>
-        <ErrorDiv status={this.state.newprefixstatus} error={this.state.newprefixerror} errorMessage={this.state.newprefixerrorMessage} />
-        <br />
-        </div>
-        <PrefixesTable config={this.props.config} prefixes={this.state.prefixes} setStatePrefixes={p => this.setState(p)} prefixesSelected={this.state.prefixesSelected} prefixesLoading={this.state.prefixesLoading} />
-        <br />
-        <Button disabled={this.isPrefixesDisabled()} onClick={this.deleteSelectedPrefixes} color="danger"><i className="fas fa-trash-alt"></i> Delete</Button>
-        <ErrorDiv status={this.state.prefixStatus} error={this.state.prefixError} errorMessage={this.state.prefixErrorMessage} />
-
       </div>
     )
   }
diff --git a/askomics/react/src/routes/admin/prefixes.jsx b/askomics/react/src/routes/admin/prefixes.jsx
new file mode 100644
index 00000000..bdb1bbed
--- /dev/null
+++ b/askomics/react/src/routes/admin/prefixes.jsx
@@ -0,0 +1,256 @@
+import React, { Component } from 'react'
+import axios from 'axios'
+import {Button, Form, FormGroup, Label, Input, Alert, Row, Col, CustomInput } from 'reactstrap'
+import PropTypes from 'prop-types'
+import Utils from '../../classes/utils'
+import { Redirect } from 'react-router-dom'
+import WaitingDiv from '../../components/waiting'
+import ErrorDiv from '../error/error'
+
+export default class Prefixes extends Component {
+  constructor (props) {
+    super(props)
+    this.utils = new Utils()
+    this.state = {
+      error: false,
+      errorMessage: '',
+      prefixError: false,
+      prefixErrorMessage: '',
+      newprefixError: false,
+      newprefixErrorMessage: '',
+      prefixes: [],
+      prefix: "",
+      namespace: "",
+      prefixesSelected: []
+    }
+    this.handleChangePrefix = this.handleChangePrefix.bind(this)
+    this.handleChangeNamespace = this.handleChangeNamespace.bind(this)
+    this.handleAddPrefix = this.handleAddPrefix.bind(this)
+    this.dismissMessage = this.dismissMessage.bind(this)
+    this.deleteSelectedPrefixes = this.deleteSelectedPrefixes.bind(this)
+    this.handlePrefixSelection = this.handlePrefixSelection.bind(this)
+    this.handlePrefixSelectionAll = this.handlePrefixSelectionAll.bind(this)
+    this.cancelRequest
+  }
+
+  isPrefixesDisabled () {
+    return this.state.prefixesSelected.length == 0
+  }
+
+  deleteSelectedPrefixes () {
+    let requestUrl = '/api/admin/delete_prefixes'
+    let data = {
+      prefixesIdToDelete: this.state.prefixesSelected
+    }
+    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        console.log(requestUrl, response.data)
+        this.setState({
+          prefixes: response.data.prefixes,
+          prefixesSelected: [],
+        })
+      })
+  }
+
+  handleChangePrefix (event) {
+    this.setState({
+      prefix: event.target.value
+    })
+  }
+
+  handleChangeNamespace (event) {
+    this.setState({
+      namespace: event.target.value
+    })
+  }
+
+  validatePrefixForm () {
+    return (
+      this.state.prefix.length > 0 &&
+      this.state.namespace.length > 0
+    )
+  }
+
+  handlePrefixSelection (row, isSelect) {
+    if (isSelect) {
+      this.setState({
+        prefixesSelected: [...this.state.prefixesSelected, row.id]
+      })
+    } else {
+      this.setState({
+        prefixesSelected: this.state.prefixesSelected.filter(x => x !== row.id)
+      })
+    }
+  }
+
+  handlePrefixSelectionAll (isSelect, rows) {
+    const prefixes = rows.map(r => r.id)
+    if (isSelect) {
+      this.setState({
+        prefixesSelected: prefixes
+      })
+    } else {
+      this.setState({
+        prefixesSelected: []
+      })
+    }
+  }
+
+  handleAddPrefix(event) {
+
+    let requestUrl = "/api/admin/addprefix"
+    let data = {
+      prefix: this.state.prefix,
+      namespace: this.state.namespace,
+    }
+
+    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+    .then(response => {
+      console.log(requestUrl, response.data)
+      this.setState({
+        newprefixError: response.data.error,
+        newprefixErrorMessage: response.data.errorMessage,
+        prefixes: response.data.prefixes,
+        newprefixStatus: response.status,
+      })
+    })
+    .catch(error => {
+      console.log(error, error.response.data.errorMessage)
+      this.setState({
+        newprefixError: true,
+        newprefixErrorMessage: error.response.data.errorMessage,
+        newprefixStatus: error.response.status,
+      })
+    })
+    event.preventDefault()
+  }
+
+  componentDidMount () {
+    if (!this.props.waitForStart) {
+      this.loadPrefixes()
+    }
+  }
+
+  loadPrefixes() {
+    let requestUrl = '/api/admin/getprefixes'
+    axios.get(requestUrl, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        this.setState({
+          prefixesLoading: false,
+          prefixes: response.data.prefixes
+        })
+      })
+      .catch(error => {
+        console.log(error, error.response.data.errorMessage)
+        this.setState({
+          prefixError: true,
+          prefixErrorMessage: error.response.data.errorMessage,
+          prefixStatus: error.response.status,
+          success: !error.response.data.error
+        })
+      })
+  }
+
+  componentWillUnmount () {
+    if (!this.props.waitForStart) {
+      this.cancelRequest()
+    }
+  }
+
+  render () {
+
+    if (!this.props.waitForStart && !this.props.config.logged) {
+      return <Redirect to="/login" />
+    }
+    if (!this.props.waitForStart && this.props.config.user.admin != 1) {
+      return <Redirect to="/" />
+    }
+
+    if (this.props.waitForStart) {
+      return <WaitingDiv waiting={this.props.waitForStart} center />
+    }
+
+    let prefixesColumns = [{
+      editable: false,
+      dataField: 'prefix',
+      text: 'Prefix',
+      sort: true
+    }, {
+      editable: false,
+      dataField: 'namespace',
+      text: 'Namespace',
+      sort: true
+    }]
+
+    let prefixesDefaultSorted = [{
+      dataField: 'prefix',
+      order: 'asc'
+    }]
+
+    let prefixesSelectRow = {
+      mode: 'checkbox',
+      clickToSelect: false,
+      selected: this.state.prefixesSelected,
+      onSelect: this.handlePrefixSelection,
+      onSelectAll: this.handlePrefixSelectionAll
+    }
+
+    let prefixesNoDataIndication = 'No custom prefixes'
+    if (this.state.prefixesLoading) {
+      prefixesNoDataIndication = <WaitingDiv waiting={this.state.prefixesLoading} />
+    }
+
+    return (
+      <div className="container">
+        <h2>Admin</h2>
+        <hr />
+        <h4>Add a prefix</h4>
+        <div>
+        <Form onSubmit={this.handleAddPrefix}>
+          <Row form>
+            <Col md={6}>
+              <FormGroup>
+                <Label for="fname">Prefix</Label>
+                <Input type="text" name="prefix" id="prefix" placeholder="prefix" value={this.state.prefix} onChange={this.handleChangePrefix} />
+              </FormGroup>
+            </Col>
+            <Col md={6}>
+              <FormGroup>
+                <Label for="lname">Namespace</Label>
+                <Input type="text" name="namespace" id="namespace" placeholder="namespace" value={this.state.namespace} onChange={this.handleChangeNamespace} />
+              </FormGroup>
+            </Col>
+          </Row>
+          <Button disabled={!this.validatePrefixForm()}>Create</Button>
+        </Form>
+        <ErrorDiv status={this.state.newprefixstatus} error={this.state.newprefixerror} errorMessage={this.state.newprefixerrorMessage} />
+        <br />
+        </div>
+        <hr>
+        <div className="asko-table-height-div">
+          <BootstrapTable
+            classes="asko-table"
+            wrapperClasses="asko-table-wrapper"
+            tabIndexCell
+            bootstrap4
+            keyField='id'
+            data={this.state.prefixes}
+            columns={prefixesColumns}
+            defaultSorted={prefixesDefaultSorted}
+            pagination={paginationFactory()}
+            noDataIndication={prefixesNoDataIndication}
+            selectRow={ prefixesSelectRow }
+          />
+        </div>
+        <br />
+        <Button disabled={this.isPrefixesDisabled()} onClick={this.deleteSelectedPrefixes} color="danger"><i className="fas fa-trash-alt"></i> Delete</Button>
+        <ErrorDiv status={this.state.prefixStatus} error={this.state.prefixError} errorMessage={this.state.prefixErrorMessage} />
+      </div>
+    )
+  }
+}
+
+Prefixes.propTypes = {
+  waitForStart: PropTypes.bool,
+  config: PropTypes.object
+}
diff --git a/askomics/react/src/routes/admin/prefixestable.jsx b/askomics/react/src/routes/admin/prefixestable.jsx
deleted file mode 100644
index 809d2ed9..00000000
--- a/askomics/react/src/routes/admin/prefixestable.jsx
+++ /dev/null
@@ -1,104 +0,0 @@
-import React, { Component } from 'react'
-import axios from 'axios'
-import {Badge, Button, Form, FormGroup, Label, Input, Alert, Row, Col, CustomInput } from 'reactstrap'
-import BootstrapTable from 'react-bootstrap-table-next'
-import paginationFactory from 'react-bootstrap-table2-paginator'
-import cellEditFactory from 'react-bootstrap-table2-editor'
-import update from 'react-addons-update'
-import PropTypes from 'prop-types'
-import Utils from '../../classes/utils'
-import WaitingDiv from '../../components/waiting'
-import pretty from 'pretty-time'
-
-export default class PrefixesTable extends Component {
-  constructor (props) {
-    super(props)
-    this.utils = new Utils()
-    this.handlePrefixSelection = this.handlePrefixSelection.bind(this)
-    this.handlePrefixSelectionAll = this.handlePrefixSelectionAll.bind(this)
-  }
-
-  handlePrefixSelection (row, isSelect) {
-    console.log('triggered')
-    if (isSelect) {
-      this.props.setStatePrefixes({
-        prefixesSelected: [...this.props.prefixesSelected, row.id]
-      })
-    } else {
-      this.props.setStatePrefixes({
-        prefixesSelected: this.props.prefixesSelected.filter(x => x !== row.id)
-      })
-    }
-  }
-
-  handlePrefixSelectionAll (isSelect, rows) {
-    const prefixes = rows.map(r => r.id)
-    if (isSelect) {
-      this.props.setStatePrefixes({
-        prefixesSelected: prefixes
-      })
-    } else {
-      this.props.setStatePrefixes({
-        prefixesSelected: []
-      })
-    }
-  }
-
-  render () {
-    let prefixesColumns = [{
-      editable: false,
-      dataField: 'prefix',
-      text: 'Prefix',
-      sort: true
-    }, {
-      editable: false,
-      dataField: 'namespace',
-      text: 'Namespace',
-      sort: true
-    }]
-
-    let prefixesDefaultSorted = [{
-      dataField: 'prefix',
-      order: 'asc'
-    }]
-
-    let prefixesSelectRow = {
-      mode: 'checkbox',
-      clickToSelect: false,
-      selected: this.props.prefixesSelected,
-      onSelect: this.handlePrefixSelection,
-      onSelectAll: this.handlePrefixSelectionAll
-    }
-
-    let prefixesNoDataIndication = 'No custom prefixes'
-    if (this.props.prefixesLoading) {
-      prefixesNoDataIndication = <WaitingDiv waiting={this.props.prefixesLoading} />
-    }
-
-    return (
-        <div className="asko-table-height-div">
-          <BootstrapTable
-            classes="asko-table"
-            wrapperClasses="asko-table-wrapper"
-            tabIndexCell
-            bootstrap4
-            keyField='id'
-            data={this.props.prefixes}
-            columns={prefixesColumns}
-            defaultSorted={prefixesDefaultSorted}
-            pagination={paginationFactory()}
-            noDataIndication={prefixesNoDataIndication}
-            selectRow={ prefixesSelectRow }
-          />
-        </div>
-    )
-  }
-}
-
-PrefixesTable.propTypes = {
-    setStatePrefixes: PropTypes.func,
-    prefixesSelected: PropTypes.object,
-    prefixesLoading: PropTypes.bool,
-    prefixes: PropTypes.array,
-    config: PropTypes.object
-}

From e4f00c77261391e9a47d6b6ea4d3faace369ac89 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 17 Nov 2021 14:35:58 +0000
Subject: [PATCH 019/113] typo

---
 askomics/react/src/routes/admin/prefixes.jsx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/askomics/react/src/routes/admin/prefixes.jsx b/askomics/react/src/routes/admin/prefixes.jsx
index bdb1bbed..8be17418 100644
--- a/askomics/react/src/routes/admin/prefixes.jsx
+++ b/askomics/react/src/routes/admin/prefixes.jsx
@@ -1,6 +1,8 @@
 import React, { Component } from 'react'
 import axios from 'axios'
 import {Button, Form, FormGroup, Label, Input, Alert, Row, Col, CustomInput } from 'reactstrap'
+import BootstrapTable from 'react-bootstrap-table-next'
+import paginationFactory from 'react-bootstrap-table2-paginator'
 import PropTypes from 'prop-types'
 import Utils from '../../classes/utils'
 import { Redirect } from 'react-router-dom'
@@ -26,7 +28,6 @@ export default class Prefixes extends Component {
     this.handleChangePrefix = this.handleChangePrefix.bind(this)
     this.handleChangeNamespace = this.handleChangeNamespace.bind(this)
     this.handleAddPrefix = this.handleAddPrefix.bind(this)
-    this.dismissMessage = this.dismissMessage.bind(this)
     this.deleteSelectedPrefixes = this.deleteSelectedPrefixes.bind(this)
     this.handlePrefixSelection = this.handlePrefixSelection.bind(this)
     this.handlePrefixSelectionAll = this.handlePrefixSelectionAll.bind(this)
@@ -226,7 +227,7 @@ export default class Prefixes extends Component {
         <ErrorDiv status={this.state.newprefixstatus} error={this.state.newprefixerror} errorMessage={this.state.newprefixerrorMessage} />
         <br />
         </div>
-        <hr>
+        <hr />
         <div className="asko-table-height-div">
           <BootstrapTable
             classes="asko-table"

From 098fa265be07917e4813585eea98ff009c7d2c38 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 17 Nov 2021 17:11:02 +0100
Subject: [PATCH 020/113] Fix test (1)

---
 tests/results/abstraction.json | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/results/abstraction.json b/tests/results/abstraction.json
index 4aa59849..c7efb162 100644
--- a/tests/results/abstraction.json
+++ b/tests/results/abstraction.json
@@ -571,6 +571,7 @@
         "instancesHaveLabels": true,
         "label": "transcript",
         "type": "node",
+        "ontology": false,
         "uri": "http://askomics.org/test/data/transcript"
       },
       {
@@ -585,6 +586,7 @@
         "instancesHaveLabels": true,
         "label": "gene",
         "type": "node",
+        "ontology": false,
         "uri": "http://askomics.org/test/data/gene"
       },
       {
@@ -598,6 +600,7 @@
         "instancesHaveLabels": true,
         "label": "QTL",
         "type": "node",
+        "ontology": false,
         "uri": "http://askomics.org/test/data/QTL"
       },
       {
@@ -611,6 +614,7 @@
         "instancesHaveLabels": true,
         "label": "DifferentialExpression",
         "type": "node",
+        "ontology": false,
         "uri": "http://askomics.org/test/data/DifferentialExpression"
       }
     ],

From b61299f16eb5749402a60788e1e52d067a3cc1ce Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 18 Nov 2021 09:56:52 +0100
Subject: [PATCH 021/113] Tests for custom prefixes

---
 tests/conftest.py       |  6 +++
 tests/test_api_admin.py | 88 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+)

diff --git a/tests/conftest.py b/tests/conftest.py
index fb30c607..bfcb7cf2 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -14,6 +14,7 @@
 from askomics.libaskomics.FilesHandler import FilesHandler
 from askomics.libaskomics.FilesUtils import FilesUtils
 from askomics.libaskomics.LocalAuth import LocalAuth
+from askomics.libaskomics.PrefixManager import PrefixManager
 from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
 from askomics.libaskomics.Start import Start
 from askomics.libaskomics.Result import Result
@@ -574,6 +575,11 @@ def delete_galaxy_history(self):
         galaxy = GalaxyInstance(self.gurl, self.gkey)
         galaxy.histories.delete_history(self.galaxy_history["id"], purge=True)
 
+    def create_prefix(self):
+        """Create custom prefix"""
+        pm = PrefixManager(self.app, self.session)
+        pm.add_custom_prefix("OBO", "http://purl.obolibrary.org/obo/")
+
     @staticmethod
     def get_random_string(number):
         """return a random string of n character
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index a6adf370..60f43ef7 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -491,3 +491,91 @@ def test_delete_datasets(self, client):
         assert response.json["datasets"][0]["status"] == "queued"
         assert response.json["datasets"][1]["status"] == "queued"
         assert response.json["datasets"][2]["status"] == "queued"
+
+    def test_view_custom_prefixes(self, client):
+        """test /api/admin/getprefixes route"""
+        client.create_two_users()
+        client.log_user("jsmith")
+
+        response = client.client.get('/api/admin/api/admin/getprefixes')
+        assert response.status_code == 401
+
+        client.log_user("jdoe")
+
+        expected_empty = {
+            "error": False,
+            "errorMessage": "",
+            "prefixes": []
+        }
+
+        response = client.client.get('/api/admin/api/admin/getprefixes')
+        assert response.status_code == 200
+        assert response.json == expected_empty
+
+        client.create_prefix()
+
+        response = client.client.get('/api/admin/api/admin/getprefixes')
+
+        expected = {
+            "error": False,
+            "errorMessage": "",
+            "prefixes": [{
+                "id": 1,
+                "namespace": "http://purl.obolibrary.org/obo/",
+                "prefix": "OBO"
+            }]
+        }
+
+        assert response.status_code == 200
+        assert response.json == expected
+
+    def test_add_custom_prefix(self, client):
+        """test /api/admin/addprefix route"""
+        client.create_two_users()
+        client.log_user("jsmith")
+
+        data = {"prefix": "OBO", "namespace": "http://purl.obolibrary.org/obo/"}
+
+        response = client.client.post('/api/admin/addprefix', json=data)
+        assert response.status_code == 401
+
+        client.log_user("jdoe")
+
+        response = client.client.post('/api/admin/addprefix', json=data)
+
+        expected = {
+            "error": False,
+            "errorMessage": "",
+            "prefixes": [{
+                "id": 1,
+                "namespace": "http://purl.obolibrary.org/obo/",
+                "prefix": "OBO"
+            }]
+        }
+
+        assert response.status_code == 200
+        assert response.json == expected
+
+    def test_delete_custom_prefix(self, client):
+        """test /api/admin/delete_prefixes route"""
+        client.create_two_users()
+        client.log_user("jsmith")
+
+        data = {"prefixesIdToDelete": [1]}
+
+        response = client.client.post('/api/admin/delete_prefixes', json=data)
+        assert response.status_code == 401
+
+        client.log_user("jdoe")
+        client.create_prefix()
+
+        response = client.client.post('/api/admin/delete_prefixes', json=data)
+
+        expected = {
+            "error": False,
+            "errorMessage": "",
+            "prefixes": []
+        }
+
+        assert response.status_code == 200
+        assert response.json == expected

From c6a1b450c4d4470967d6043613e80678f299b6f0 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 18 Nov 2021 11:01:20 +0100
Subject: [PATCH 022/113] Typo in tests

---
 tests/test_api_admin.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 60f43ef7..126cc404 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -497,7 +497,7 @@ def test_view_custom_prefixes(self, client):
         client.create_two_users()
         client.log_user("jsmith")
 
-        response = client.client.get('/api/admin/api/admin/getprefixes')
+        response = client.client.get('/api/admin/getprefixes')
         assert response.status_code == 401
 
         client.log_user("jdoe")
@@ -508,13 +508,13 @@ def test_view_custom_prefixes(self, client):
             "prefixes": []
         }
 
-        response = client.client.get('/api/admin/api/admin/getprefixes')
+        response = client.client.get('/api/admin/getprefixes')
         assert response.status_code == 200
         assert response.json == expected_empty
 
         client.create_prefix()
 
-        response = client.client.get('/api/admin/api/admin/getprefixes')
+        response = client.client.get('/api/admin/getprefixes')
 
         expected = {
             "error": False,

From 9f499d2e44c0986c79b17f5b34cbfbdb3206f9ae Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 18 Nov 2021 17:18:36 +0100
Subject: [PATCH 023/113] Test ontologies management

---
 askomics/api/file.py                       |   6 +
 askomics/libaskomics/CsvFile.py            |  27 +++++
 askomics/libaskomics/Database.py           |  13 ++-
 askomics/libaskomics/OntologyManager.py    | 129 +++++++++++++++++++++
 tests/results/preview_files.json           |   3 +-
 tests/results/preview_malformed_files.json |   3 +-
 6 files changed, 178 insertions(+), 3 deletions(-)
 create mode 100644 askomics/libaskomics/OntologyManager.py

diff --git a/askomics/api/file.py b/askomics/api/file.py
index 45be76a0..2a588370 100644
--- a/askomics/api/file.py
+++ b/askomics/api/file.py
@@ -8,6 +8,7 @@
 from askomics.libaskomics.FilesHandler import FilesHandler
 from askomics.libaskomics.FilesUtils import FilesUtils
 from askomics.libaskomics.Dataset import Dataset
+from askomics.libaskomics.OntologyManager import OntologyManager
 from askomics.libaskomics.RdfFile import RdfFile
 
 from flask import (Blueprint, current_app, jsonify, request, send_from_directory, session)
@@ -237,6 +238,9 @@ def get_preview():
         }), 400
 
     try:
+        ontologies_manager = OntologyManager(current_app, session)
+        ontologies = ontologies_manager.list_ontologies()
+
         files_handler = FilesHandler(current_app, session)
         files_handler.handle_files(data['filesId'])
 
@@ -249,12 +253,14 @@ def get_preview():
         traceback.print_exc(file=sys.stdout)
         return jsonify({
             'previewFiles': [],
+            'ontologies': [],
             'error': True,
             'errorMessage': str(e)
         }), 500
 
     return jsonify({
         'previewFiles': results,
+        'ontologies': ontologies,
         'error': False,
         'errorMessage': ''
     })
diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
index 64d8aa37..00a53c87 100644
--- a/askomics/libaskomics/CsvFile.py
+++ b/askomics/libaskomics/CsvFile.py
@@ -8,6 +8,7 @@
 from rdflib import BNode
 
 from askomics.libaskomics.File import File
+from askomics.libaskomics.OntologyManager import OntologyManager
 from askomics.libaskomics.Utils import cached_property
 
 
@@ -396,6 +397,10 @@ def set_rdf_abstraction(self):
         if self.columns_type[0] == 'start_entity':
             self.graph_abstraction_dk.add((entity, rdflib.RDF.type, self.namespace_internal['startPoint']))
 
+        available_ontologies = {}
+        for ontology in OntologyManager(self.app, self.session).list_ontologies():
+            available_ontologies[ontology['name']] = ontology['uri']
+
         # Attributes and relations
         for index, attribute_name in enumerate(self.header):
 
@@ -436,6 +441,28 @@ def set_rdf_abstraction(self):
 
                 continue
 
+            # Manage ontologies
+            if self.columns_type[index] in available_ontologies:
+
+                attribute = self.rdfize(attribute_name)
+                label = rdflib.Literal(attribute_name)
+                rdf_range = self.rdfize(available_ontologies[self.columns_type[index]])
+                rdf_type = rdflib.OWL.ObjectProperty
+
+                # New way of storing relations (starting from 4.4.0)
+                blank = BNode()
+                endpoint = rdflib.Literal(self.external_endpoint) if self.external_endpoint else rdflib.Literal(self.settings.get('triplestore', 'endpoint'))
+                self.graph_abstraction_dk.add((blank, rdflib.RDF.type, rdflib.OWL.ObjectProperty))
+                self.graph_abstraction_dk.add((blank, rdflib.RDF.type, self.namespace_internal["AskomicsRelation"]))
+                self.graph_abstraction_dk.add((blank, self.namespace_internal["uri"], attribute))
+                self.graph_abstraction_dk.add((blank, rdflib.RDFS.label, label))
+                self.graph_abstraction_dk.add((blank, rdflib.RDFS.domain, entity))
+                self.graph_abstraction_dk.add((blank, rdflib.RDFS.range, rdf_range))
+                self.graph_abstraction_dk.add((blank, rdflib.DCAT.endpointURL, endpoint))
+                self.graph_abstraction_dk.add((blank, rdflib.DCAT.dataset, rdflib.Literal(self.name)))
+
+                continue
+
             # Category
             elif self.columns_type[index] in ('category', 'reference', 'strand'):
                 attribute = self.rdfize(attribute_name)
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index ebc58e05..29b63917 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -77,6 +77,7 @@ def init_database(self):
         self.create_datasets_table()
         self.create_abstraction_table()
         self.create_prefixes_table()
+        self.create_ontologies_table()
 
     def create_user_table(self):
         """Create the user table"""
@@ -397,4 +398,14 @@ def create_prefixes_table(self):
         self.execute_sql_query(query)
 
     def create_ontologies_table(self):
-        pass
+        """Create the ontologies table"""
+        query = '''
+        CREATE TABLE IF NOT EXISTS ontologies (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            name text NOT NULL,
+            uri text NOT NULL,
+            full_name text NOT NULL,
+            type text DEFAULT 'local',
+        )
+        '''
+        self.execute_sql_query(query)
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
new file mode 100644
index 00000000..f2cc439a
--- /dev/null
+++ b/askomics/libaskomics/OntologyManager.py
@@ -0,0 +1,129 @@
+from askomics.libaskomics.Database import Database
+from askomics.libaskomics.Params import Params
+
+
+class OntologyManager(Params):
+    """Manage ontologies
+
+    Attributes
+    ----------
+    namespace_internal : str
+        askomics namespace, from config file
+    namespace_data : str
+        askomics prefix, from config file
+    prefix : dict
+        dict of all prefixes
+    """
+
+    def __init__(self, app, session):
+        """init
+
+        Parameters
+        ----------
+        app : Flask
+            Flask app
+        session :
+            AskOmics session
+        """
+        Params.__init__(self, app, session)
+
+    def list_ontologies(self):
+        """Get all ontologies
+
+        Returns
+        -------
+        list
+            ontologies
+        """
+
+        database = Database(self.app, self.session)
+
+        query = '''
+        SELECT id, name, uri, full_name, type
+        FROM ontologies
+        '''
+
+        rows = database.execute_sql_query(query)
+
+        ontologies = []
+        for row in rows:
+            prefix = {
+                'id': row[0],
+                'name': row[1],
+                'uri': row[2],
+                'full_name': row[3],
+                'type': row[4]
+            }
+            ontologies.append(prefix)
+
+        return ontologies
+
+    def get_ontology(self, ontology_name):
+        """Get a specific ontology based on name
+
+        Returns
+        -------
+        dict
+            ontology
+        """
+
+        database = Database(self.app, self.session)
+
+        query = '''
+        SELECT id, name, uri, full_name, type
+        FROM ontologies
+        WHERE name = ?
+        '''
+
+        rows = database.execute_sql_query(query, (ontology_name,))
+
+        if not rows:
+            return None
+
+        ontology = rows[0]
+        return {
+                'id': ontology[0],
+                'name': ontology[1],
+                'uri': ontology[2],
+                'full_name': ontology[3],
+                'type': ontology[4]
+            }
+
+    def add_ontology(self, name, uri, full_name, type="local"):
+        """Create a new ontology
+
+        Returns
+        -------
+        list of dict
+            Prefixes information
+        """
+        database = Database(self.app, self.session)
+
+        query = '''
+        INSERT INTO ontologies VALUES(
+            NULL,
+            ?,
+            ?,
+            ?,
+            ?
+        )
+        '''
+
+        database.execute_sql_query(query, (name, uri, full_name, type,))
+
+    def remove_ontologies(self, ontology_ids):
+        """Remove ontologies
+
+        Returns
+        -------
+        None
+        """
+        database = Database(self.app, self.session)
+
+        query = '''
+        DELETE FROM ontologies
+        WHERE id = ?
+        '''
+
+        for ontology_id in ontology_ids:
+            database.execute_sql_query(query, (ontology_id,))
diff --git a/tests/results/preview_files.json b/tests/results/preview_files.json
index beeb18c4..a73688db 100644
--- a/tests/results/preview_files.json
+++ b/tests/results/preview_files.json
@@ -181,5 +181,6 @@
       "error": false,
       "error_message": ""
     }
-  ]
+],
+"ontologies": []
 }
diff --git a/tests/results/preview_malformed_files.json b/tests/results/preview_malformed_files.json
index 2035e650..b99f0f2c 100644
--- a/tests/results/preview_malformed_files.json
+++ b/tests/results/preview_malformed_files.json
@@ -22,5 +22,6 @@
       "error": true,
       "error_message": "Malformated CSV/TSV (Empty column in header)"
     }
-  ]
+],
+  "ontologies": []
 }

From 0186471a75b6d2260968b7c5a26ed77bc41bf904 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 19 Nov 2021 09:56:02 +0100
Subject: [PATCH 024/113] Typos

---
 askomics/libaskomics/Database.py        |  2 +-
 askomics/libaskomics/OntologyManager.py | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index 29b63917..9b9a54ff 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -405,7 +405,7 @@ def create_ontologies_table(self):
             name text NOT NULL,
             uri text NOT NULL,
             full_name text NOT NULL,
-            type text DEFAULT 'local',
+            type text DEFAULT 'local'
         )
         '''
         self.execute_sql_query(query)
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index f2cc439a..da33ab5f 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -82,12 +82,12 @@ def get_ontology(self, ontology_name):
 
         ontology = rows[0]
         return {
-                'id': ontology[0],
-                'name': ontology[1],
-                'uri': ontology[2],
-                'full_name': ontology[3],
-                'type': ontology[4]
-            }
+            'id': ontology[0],
+            'name': ontology[1],
+            'uri': ontology[2],
+            'full_name': ontology[3],
+            'type': ontology[4]
+        }
 
     def add_ontology(self, name, uri, full_name, type="local"):
         """Create a new ontology

From b9b60aab02a401e0f345ed6ade37a007116a70a5 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 19 Nov 2021 10:11:11 +0100
Subject: [PATCH 025/113] Fix test

---
 tests/test_api_file.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/test_api_file.py b/tests/test_api_file.py
index a3a0f708..5e645d89 100644
--- a/tests/test_api_file.py
+++ b/tests/test_api_file.py
@@ -393,7 +393,8 @@ def test_get_preview(self, client):
         assert response.json == {
             'error': False,
             'errorMessage': '',
-            'previewFiles': []
+            'previewFiles': [],
+            'ontologies': []
         }
 
         response = client.client.post('/api/files/preview', json=malformed_data)
@@ -421,7 +422,8 @@ def test_get_preview(self, client):
                 'type': 'gff/gff3',
                 'error': False,
                 'error_message': ''
-            }]
+            }],
+            'ontologies': []
         }
 
     def test_delete_files(self, client):

From 929a9c515307221163abf0a38b0638c6d21882a0 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 19 Nov 2021 15:13:28 +0100
Subject: [PATCH 026/113] Test ontology interface

---
 askomics/api/admin.py                         | 127 +++++++++
 askomics/libaskomics/Database.py              |   2 +-
 askomics/libaskomics/OntologyManager.py       |  20 +-
 askomics/react/src/navbar.jsx                 |   1 +
 askomics/react/src/routes.jsx                 |   2 +
 .../react/src/routes/admin/ontologies.jsx     | 265 ++++++++++++++++++
 .../react/src/routes/integration/csvtable.jsx |  17 +-
 .../src/routes/integration/integration.jsx    |   6 +-
 8 files changed, 426 insertions(+), 14 deletions(-)
 create mode 100644 askomics/react/src/routes/admin/ontologies.jsx

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 0822ecc7..a54fa5b9 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -8,6 +8,7 @@
 from askomics.libaskomics.LocalAuth import LocalAuth
 from askomics.libaskomics.Mailer import Mailer
 from askomics.libaskomics.PrefixManager import PrefixManager
+from askomics.libaskomics.OntologyManager import OntologyManager
 from askomics.libaskomics.Result import Result
 from askomics.libaskomics.ResultsHandler import ResultsHandler
 
@@ -636,3 +637,129 @@ def delete_prefix():
         'error': False,
         'errorMessage': ''
     })
+
+
+@admin_bp.route("/api/admin/getontologies", methods=["GET"])
+@api_auth
+@admin_required
+def get_ontologies():
+    """Get all ontologies
+
+    Returns
+    -------
+    json
+        prefixes: list of all custom prefixes
+        error: True if error, else False
+        errorMessage: the error message of error, else an empty string
+    """
+    try:
+        om = OntologyManager(current_app, session)
+        ontologies = om.list_ontologies()
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': str(e)
+        }), 500
+
+    return jsonify({
+        'ontologies': ontologies,
+        'error': False,
+        'errorMessage': ''
+    })
+
+
+@admin_bp.route("/api/admin/addontology", methods=["POST"])
+@api_auth
+@admin_required
+def add_ontology():
+    """Create a new ontology
+
+    Returns
+    -------
+    json
+        ontologies: list of all ontologies
+        error: True if error, else False
+        errorMessage: the error message of error, else an empty string
+    """
+
+    data = request.get_json()
+    if not data or not (data.get("name") and data.get("uri") and data.get("shortName")):
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "Missing parameter"
+        }), 400
+
+    om = OntologyManager(current_app, session)
+    ontologies = om.list_ontologies()
+
+    name = data.get("name")
+    uri = data.get("uri")
+    short_name = data.get("shortName")
+
+    if any([name == onto['name'] or short_name == onto['short_name'] for onto in ontologies]):
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "Name and short name must be unique"
+        }), 400
+
+    try:
+        om.add_ontology(name, uri, short_name)
+        ontologies = om.list_ontologies()
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': str(e)
+        }), 500
+
+    return jsonify({
+        'ontologies': ontologies,
+        'error': False,
+        'errorMessage': ''
+    })
+
+
+@admin_bp.route("/api/admin/delete_ontologies", methods=["POST"])
+@api_auth
+@admin_required
+def delete_ontologies():
+    """Delete one or more ontologies
+
+    Returns
+    -------
+    json
+        ontologies: list of all ontologies
+        error: True if error, else False
+        errorMessage: the error message of error, else an empty string
+    """
+
+    data = request.get_json()
+    if not data or not data.get("ontologiesIdToDelete"):
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "Missing ontologiesIdToDelete parameter"
+        }), 400
+
+    om = OntologyManager(current_app, session)
+    try:
+        om.remove_ontologies(data.get("ontologiesIdToDelete"))
+        ontologies = om.list_ontologies()
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': str(e)
+        }), 500
+
+    return jsonify({
+        'ontologies': ontologies,
+        'error': False,
+        'errorMessage': ''
+    })
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index 9b9a54ff..9d8cf269 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -404,7 +404,7 @@ def create_ontologies_table(self):
             id INTEGER PRIMARY KEY AUTOINCREMENT,
             name text NOT NULL,
             uri text NOT NULL,
-            full_name text NOT NULL,
+            short_name text NOT NULL,
             type text DEFAULT 'local'
         )
         '''
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index da33ab5f..0f1767e7 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -39,7 +39,7 @@ def list_ontologies(self):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, uri, full_name, type
+        SELECT id, name, uri, short_name, type
         FROM ontologies
         '''
 
@@ -51,15 +51,15 @@ def list_ontologies(self):
                 'id': row[0],
                 'name': row[1],
                 'uri': row[2],
-                'full_name': row[3],
+                'short_name': row[3],
                 'type': row[4]
             }
             ontologies.append(prefix)
 
         return ontologies
 
-    def get_ontology(self, ontology_name):
-        """Get a specific ontology based on name
+    def get_ontology(self, short_name):
+        """Get a specific ontology based on short name
 
         Returns
         -------
@@ -70,12 +70,12 @@ def get_ontology(self, ontology_name):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, uri, full_name, type
+        SELECT id, name, uri, short_name, type
         FROM ontologies
-        WHERE name = ?
+        WHERE short_name = ?
         '''
 
-        rows = database.execute_sql_query(query, (ontology_name,))
+        rows = database.execute_sql_query(query, (short_name,))
 
         if not rows:
             return None
@@ -85,11 +85,11 @@ def get_ontology(self, ontology_name):
             'id': ontology[0],
             'name': ontology[1],
             'uri': ontology[2],
-            'full_name': ontology[3],
+            'short_name': ontology[3],
             'type': ontology[4]
         }
 
-    def add_ontology(self, name, uri, full_name, type="local"):
+    def add_ontology(self, name, uri, short_name, type="local"):
         """Create a new ontology
 
         Returns
@@ -109,7 +109,7 @@ def add_ontology(self, name, uri, full_name, type="local"):
         )
         '''
 
-        database.execute_sql_query(query, (name, uri, full_name, type,))
+        database.execute_sql_query(query, (name, uri, short_name, type,))
 
     def remove_ontologies(self, ontology_ids):
         """Remove ontologies
diff --git a/askomics/react/src/navbar.jsx b/askomics/react/src/navbar.jsx
index 5c48f518..9124eda0 100644
--- a/askomics/react/src/navbar.jsx
+++ b/askomics/react/src/navbar.jsx
@@ -44,6 +44,7 @@ export default class AskoNavbar extends Component {
             <DropdownItem className="bg-dark" tag="Link">
               <Link className="nav-link" to="/admin"><i className="fas fa-chess-king"></i> Admin</Link>
               <Link className="nav-link" to="/prefixes"><i className="fas fa-chess-king"></i> Prefixes</Link>
+              <Link className="nav-link" to="/ontologies"><i className="fas fa-chess-king"></i> Ontologies</Link>
             </DropdownItem>
           )
         }
diff --git a/askomics/react/src/routes.jsx b/askomics/react/src/routes.jsx
index 488b439c..bcb79f54 100644
--- a/askomics/react/src/routes.jsx
+++ b/askomics/react/src/routes.jsx
@@ -15,6 +15,7 @@ import PasswordReset from './routes/login/passwordreset'
 import Account from './routes/account/account'
 import Admin from './routes/admin/admin'
 import Prefixes from './routes/admin/prefixes'
+import Ontologies from './routes/admin/ontologies'
 import Sparql from './routes/sparql/sparql'
 import FormQuery from './routes/form/query'
 import FormEditQuery from './routes/form_edit/query'
@@ -115,6 +116,7 @@ export default class Routes extends Component {
             <Route path="/account" exact component={() => (<Account config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} />)} />
             <Route path="/admin" exact component={() => (<Admin config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} />)} />
             <Route path="/prefixes" exact component={() => (<Prefixes config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} />)} />
+            <Route path="/ontologies" exact component={() => (<Ontologies config={this.state.config} waitForStart={this.state.waiting} setStateNavbar={p => this.setState(p)} />)} />
             <Route path="/query" exact component={Query} />
             <Route path="/form" exact component={FormQuery} />
             <Route path="/form_edit" exact component={FormEditQuery} />
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
new file mode 100644
index 00000000..d99caafe
--- /dev/null
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -0,0 +1,265 @@
+import React, { Component } from 'react'
+import axios from 'axios'
+import {Button, Form, FormGroup, Label, Input, Alert, Row, Col, CustomInput } from 'reactstrap'
+import BootstrapTable from 'react-bootstrap-table-next'
+import paginationFactory from 'react-bootstrap-table2-paginator'
+import PropTypes from 'prop-types'
+import Utils from '../../classes/utils'
+import { Redirect } from 'react-router-dom'
+import WaitingDiv from '../../components/waiting'
+import ErrorDiv from '../error/error'
+
+export default class Ontologies extends Component {
+  constructor (props) {
+    super(props)
+    this.utils = new Utils()
+    this.state = {
+      error: false,
+      errorMessage: '',
+      ontologyError: false,
+      ontologyErrorMessage: '',
+      newontologyError: false,
+      newontologyErrorMessage: '',
+      ontologies: [],
+      name: "",
+      uri: "",
+      shortName:,
+      ontologiesSelected: []
+    }
+    this.handleChangeValue = this.handleChangeValue.bind(this)
+    this.handleAddOntology = this.handleAddOntology.bind(this)
+    this.deleteSelectedOntologies = this.deleteSelectedOntologies.bind(this)
+    this.handleOntologySelection = this.handleOntologySelection.bind(this)
+    this.handleOntologySelectionAll = this.handleOntologySelectionAll.bind(this)
+    this.cancelRequest
+  }
+
+  isOntologiesDisabled () {
+    return this.state.ontologiesSelected.length == 0
+  }
+
+  deleteSelectedOntologies () {
+    let requestUrl = '/api/admin/delete_ontologies'
+    let data = {
+      ontologiesIdToDelete: this.state.ontologiesSelected
+    }
+    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        console.log(requestUrl, response.data)
+        this.setState({
+          ontologies: response.data.ontologies,
+          ontologiesSelected: [],
+        })
+      })
+  }
+
+  handleChangeValue (event) {
+    let data = {}
+    data[event.target.id] = event.target.value
+    this.setState(data)
+  }
+
+  validateOntologyForm () {
+    return (
+      this.state.name.length > 0 &&
+      this.state.uri.length > 0 &&
+      this.state.shortName.length > 0
+    )
+  }
+
+  handleOntologySelection (row, isSelect) {
+    if (isSelect) {
+      this.setState({
+        ontologiesSelected: [...this.state.ontologiesSelected, row.id]
+      })
+    } else {
+      this.setState({
+        ontologiesSelected: this.state.ontologiesSelected.filter(x => x !== row.id)
+      })
+    }
+  }
+
+  handleOntologySelectionAll (isSelect, rows) {
+    const ontologies = rows.map(r => r.id)
+    if (isSelect) {
+      this.setState({
+        ontologiesSelected: ontologies
+      })
+    } else {
+      this.setState({
+        ontologiesSelected: []
+      })
+    }
+  }
+
+  handleAddOntology(event) {
+
+    let requestUrl = "/api/admin/addontology"
+    let data = {
+      name: this.state.name,
+      uri: this.state.uri,
+      shortName: this.state.shortName
+    }
+
+    axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+    .then(response => {
+      console.log(requestUrl, response.data)
+      this.setState({
+        newontologyError: response.data.error,
+        newontologyErrorMessage: response.data.errorMessage,
+        ontologies: response.data.ontologies,
+        newontologyStatus: response.status,
+      })
+    })
+    .catch(error => {
+      console.log(error, error.response.data.errorMessage)
+      this.setState({
+        newontologyError: true,
+        newontologyErrorMessage: error.response.data.errorMessage,
+        newontologyStatus: error.response.status,
+      })
+    })
+    event.preventDefault()
+  }
+
+  componentDidMount () {
+    if (!this.props.waitForStart) {
+      this.loadOntologies()
+    }
+  }
+
+  loadOntologies() {
+    let requestUrl = '/api/admin/getontologies'
+    axios.get(requestUrl, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        this.setState({
+          ontologiesLoading: false,
+          ontologies: response.data.ontologies
+        })
+      })
+      .catch(error => {
+        console.log(error, error.response.data.errorMessage)
+        this.setState({
+          ontologyError: true,
+          ontologyErrorMessage: error.response.data.errorMessage,
+          ontologyStatus: error.response.status,
+          success: !error.response.data.error
+        })
+      })
+  }
+
+  componentWillUnmount () {
+    if (!this.props.waitForStart) {
+      this.cancelRequest()
+    }
+  }
+
+  render () {
+
+    if (!this.props.waitForStart && !this.props.config.logged) {
+      return <Redirect to="/login" />
+    }
+    if (!this.props.waitForStart && this.props.config.user.admin != 1) {
+      return <Redirect to="/" />
+    }
+
+    if (this.props.waitForStart) {
+      return <WaitingDiv waiting={this.props.waitForStart} center />
+    }
+
+    let ontologiesColumns = [{
+      editable: false,
+      dataField: 'name',
+      text: 'Name',
+      sort: true
+    }, {
+      editable: false,
+      dataField: 'short_name',
+      text: 'Short name',
+      sort: true
+    }, {
+      editable: false,
+      dataField: 'uri',
+      text: 'Uri',
+      sort: true
+    }
+  ]
+
+    let ontologiesDefaultSorted = [{
+      dataField: 'short_name',
+      order: 'asc'
+    }]
+
+    let ontologiesSelectRow = {
+      mode: 'checkbox',
+      clickToSelect: false,
+      selected: this.state.ontologiesSelected,
+      onSelect: this.handleOntologySelection,
+      onSelectAll: this.handleOntologySelectionAll
+    }
+
+    let ontologiesNoDataIndication = 'No ontologies'
+    if (this.state.ontologiesLoading) {
+      ontologiesNoDataIndication = <WaitingDiv waiting={this.state.ontologiesLoading} />
+    }
+
+    return (
+      <div className="container">
+        <h2>Admin</h2>
+        <hr />
+        <h4>Add a ontology</h4>
+        <div>
+        <Form onSubmit={this.handleAddOntology}>
+          <Row form>
+            <Col md={4}>
+              <FormGroup>
+                <Label for="name">Ontology name</Label>
+                <Input type="text" name="name" id="name" placeholder="Ontology name" value={this.state.name} onChange={this.handleChangeValue} />
+              </FormGroup>
+            </Col>
+            <Col md={4}>
+              <FormGroup>
+                <Label for="shortName">Ontology short name</Label>
+                <Input type="text" name="shortName" id="shortName" placeholder="shortName" value={this.state.shortName} onChange={this.handleChangeValue} />
+              </FormGroup>
+            </Col>
+            <Col md={4}>
+              <FormGroup>
+                <Label for="uri">Ontology uri</Label>
+                <Input type="text" name="uri" id="uri" placeholder="uri" value={this.state.uri} onChange={this.handleChangeValue} />
+              </FormGroup>
+            </Col>
+          </Row>
+          <Button disabled={!this.validateOntologyForm()}>Create</Button>
+        </Form>
+        <ErrorDiv status={this.state.newontologystatus} error={this.state.newontologyerror} errorMessage={this.state.newontologyerrorMessage} />
+        <br />
+        </div>
+        <hr />
+        <div className="asko-table-height-div">
+          <BootstrapTable
+            classes="asko-table"
+            wrapperClasses="asko-table-wrapper"
+            tabIndexCell
+            bootstrap4
+            keyField='id'
+            data={this.state.ontologies}
+            columns={ontologiesColumns}
+            defaultSorted={ontologiesDefaultSorted}
+            pagination={paginationFactory()}
+            noDataIndication={ontologiesNoDataIndication}
+            selectRow={ ontologiesSelectRow }
+          />
+        </div>
+        <br />
+        <Button disabled={this.isOntologiesDisabled()} onClick={this.deleteSelectedOntologies} color="danger"><i className="fas fa-trash-alt"></i> Delete</Button>
+        <ErrorDiv status={this.state.ontologyStatus} error={this.state.ontologyError} errorMessage={this.state.ontologyErrorMessage} />
+      </div>
+    )
+  }
+}
+
+Ontologies.propTypes = {
+  waitForStart: PropTypes.bool,
+  config: PropTypes.object
+}
diff --git a/askomics/react/src/routes/integration/csvtable.jsx b/askomics/react/src/routes/integration/csvtable.jsx
index efee1315..269c4119 100644
--- a/askomics/react/src/routes/integration/csvtable.jsx
+++ b/askomics/react/src/routes/integration/csvtable.jsx
@@ -91,6 +91,18 @@ export default class CsvTable extends Component {
       )
     }
 
+    let ontoInput
+
+    if (props.ontologies.length > 0){
+      ontoInput = (
+        <optgroup label="Ontologies">
+        {props.ontologies.map(onto => {
+          return <option value={onto.short_name}>{onto.name}</option>
+        })}
+        </optgroup>
+      )
+    }
+
     if (colIndex == 1) {
       return (
         <div>
@@ -117,6 +129,7 @@ export default class CsvTable extends Component {
                 <option value="general_relation" >Directed</option>
                 <option value="symetric_relation" >Symetric</option>
               </optgroup>
+              {ontoInput}
             </CustomInput>
           </FormGroup>
         </div>
@@ -145,6 +158,7 @@ export default class CsvTable extends Component {
               <option value="general_relation" >Directed</option>
               <option value="symetric_relation" >Symetric</option>
             </optgroup>
+            {ontoInput}
           </CustomInput>
         </FormGroup>
       </div>
@@ -297,5 +311,6 @@ export default class CsvTable extends Component {
 
 CsvTable.propTypes = {
   file: PropTypes.object,
-  config: PropTypes.object
+  config: PropTypes.object,
+  ontologies: PropTypes.array
 }
diff --git a/askomics/react/src/routes/integration/integration.jsx b/askomics/react/src/routes/integration/integration.jsx
index ada6f4af..d8b49da3 100644
--- a/askomics/react/src/routes/integration/integration.jsx
+++ b/askomics/react/src/routes/integration/integration.jsx
@@ -19,7 +19,8 @@ export default class Integration extends Component {
       errorMessage: null,
       config: this.props.location.state.config,
       filesId: this.props.location.state.filesId,
-      previewFiles: []
+      previewFiles: [],
+      ontologies: []
     }
     this.cancelRequest
   }
@@ -35,6 +36,7 @@ export default class Integration extends Component {
           console.log(requestUrl, response.data)
           this.setState({
             previewFiles: response.data.previewFiles,
+            ontologies: response.data.ontologies,
             waiting: false,
             error: response.data.error,
             errorMessage: response.data.errorMessage
@@ -74,7 +76,7 @@ export default class Integration extends Component {
           this.state.previewFiles.map(file => {
             console.log(file)
             if (file.type == 'csv/tsv') {
-              return <CsvTable config={this.state.config} key={file.name} file={file} />
+              return <CsvTable config={this.state.config} key={file.name} file={file} ontologies={ontologies} />
             }
             if (["rdf/ttl", "rdf/xml", "rdf/nt"].includes(file.type)) {
               return <RdfPreview config={this.state.config} file={file} />

From 968b936f3ed322645ce8abac07f8be7cfae9315d Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 19 Nov 2021 14:54:19 +0000
Subject: [PATCH 027/113] Fixes

---
 askomics/libaskomics/CsvFile.py                      | 12 +++++++++++-
 askomics/react/src/routes/admin/ontologies.jsx       |  2 +-
 askomics/react/src/routes/integration/csvtable.jsx   |  4 ++--
 .../react/src/routes/integration/integration.jsx     |  2 +-
 4 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
index 00a53c87..42943eb9 100644
--- a/askomics/libaskomics/CsvFile.py
+++ b/askomics/libaskomics/CsvFile.py
@@ -399,7 +399,7 @@ def set_rdf_abstraction(self):
 
         available_ontologies = {}
         for ontology in OntologyManager(self.app, self.session).list_ontologies():
-            available_ontologies[ontology['name']] = ontology['uri']
+            available_ontologies[ontology['short_name']] = ontology['uri']
 
         # Attributes and relations
         for index, attribute_name in enumerate(self.header):
@@ -520,6 +520,10 @@ def generate_rdf_content(self):
         """
         total_lines = sum(1 for line in open(self.path))
 
+        available_ontologies = {}
+        for ontology in OntologyManager(self.app, self.session).list_ontologies():
+            available_ontologies[ontology['short_name']] = ontology['uri']
+
         with open(self.path, 'r', encoding='utf-8') as file:
             reader = csv.reader(file, dialect=self.dialect)
 
@@ -597,6 +601,12 @@ def generate_rdf_content(self):
                         relation = self.rdfize(splitted[0])
                         attribute = self.rdfize(cell)
 
+                    # Ontology
+                    if current_type in available_ontologies:
+                        symetric_relation = False
+                        relation = self.rdfize(current_header)
+                        attribute = self.rdfize(cell)
+
                     # Category
                     elif current_type in ('category', 'reference', 'strand'):
                         potential_relation = self.rdfize(current_header)
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index d99caafe..015eeadc 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -23,7 +23,7 @@ export default class Ontologies extends Component {
       ontologies: [],
       name: "",
       uri: "",
-      shortName:,
+      shortName: "",
       ontologiesSelected: []
     }
     this.handleChangeValue = this.handleChangeValue.bind(this)
diff --git a/askomics/react/src/routes/integration/csvtable.jsx b/askomics/react/src/routes/integration/csvtable.jsx
index 269c4119..03c04591 100644
--- a/askomics/react/src/routes/integration/csvtable.jsx
+++ b/askomics/react/src/routes/integration/csvtable.jsx
@@ -93,10 +93,10 @@ export default class CsvTable extends Component {
 
     let ontoInput
 
-    if (props.ontologies.length > 0){
+    if (this.props.ontologies.length > 0){
       ontoInput = (
         <optgroup label="Ontologies">
-        {props.ontologies.map(onto => {
+        {this.props.ontologies.map(onto => {
           return <option value={onto.short_name}>{onto.name}</option>
         })}
         </optgroup>
diff --git a/askomics/react/src/routes/integration/integration.jsx b/askomics/react/src/routes/integration/integration.jsx
index d8b49da3..b81af4b1 100644
--- a/askomics/react/src/routes/integration/integration.jsx
+++ b/askomics/react/src/routes/integration/integration.jsx
@@ -76,7 +76,7 @@ export default class Integration extends Component {
           this.state.previewFiles.map(file => {
             console.log(file)
             if (file.type == 'csv/tsv') {
-              return <CsvTable config={this.state.config} key={file.name} file={file} ontologies={ontologies} />
+              return <CsvTable config={this.state.config} key={file.name} file={file} ontologies={this.state.ontologies} />
             }
             if (["rdf/ttl", "rdf/xml", "rdf/nt"].includes(file.type)) {
               return <RdfPreview config={this.state.config} file={file} />

From 06de0c562bea7ea9781696372b66b67bc9840c3c Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 19 Nov 2021 15:25:59 +0000
Subject: [PATCH 028/113] If -> Elif

---
 askomics/libaskomics/CsvFile.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
index 42943eb9..7356a5fe 100644
--- a/askomics/libaskomics/CsvFile.py
+++ b/askomics/libaskomics/CsvFile.py
@@ -602,7 +602,7 @@ def generate_rdf_content(self):
                         attribute = self.rdfize(cell)
 
                     # Ontology
-                    if current_type in available_ontologies:
+                    elif current_type in available_ontologies:
                         symetric_relation = False
                         relation = self.rdfize(current_header)
                         attribute = self.rdfize(cell)

From ffecfbc6c3f2cf6542b708b93ba6f38809ee6fc3 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 19 Nov 2021 16:51:22 +0100
Subject: [PATCH 029/113] Forgot the actual fix

---
 askomics/react/src/routes/integration/csvtable.jsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/askomics/react/src/routes/integration/csvtable.jsx b/askomics/react/src/routes/integration/csvtable.jsx
index 03c04591..b1d3e047 100644
--- a/askomics/react/src/routes/integration/csvtable.jsx
+++ b/askomics/react/src/routes/integration/csvtable.jsx
@@ -97,7 +97,7 @@ export default class CsvTable extends Component {
       ontoInput = (
         <optgroup label="Ontologies">
         {this.props.ontologies.map(onto => {
-          return <option value={onto.short_name}>{onto.name}</option>
+          return <option key={onto.id} value={onto.short_name}>{onto.name}</option>
         })}
         </optgroup>
       )

From 67b8d4db18c68a4d027a7636c843e9ea70095f50 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 22 Nov 2021 11:27:44 +0100
Subject: [PATCH 030/113] Add ontology test

---
 tests/conftest.py       |  6 +++
 tests/test_api_admin.py | 92 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 98 insertions(+)

diff --git a/tests/conftest.py b/tests/conftest.py
index bfcb7cf2..b3c94001 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -15,6 +15,7 @@
 from askomics.libaskomics.FilesUtils import FilesUtils
 from askomics.libaskomics.LocalAuth import LocalAuth
 from askomics.libaskomics.PrefixManager import PrefixManager
+from askomics.libaskomics.OntologyManager import OntologyManager
 from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
 from askomics.libaskomics.Start import Start
 from askomics.libaskomics.Result import Result
@@ -580,6 +581,11 @@ def create_prefix(self):
         pm = PrefixManager(self.app, self.session)
         pm.add_custom_prefix("OBO", "http://purl.obolibrary.org/obo/")
 
+    def create_ontology(self):
+        """Create ontology"""
+        om = OntologyManager(self.app, self.session)
+        om.add_ontology("Open Biological and Biomedical Ontology", "http://purl.obolibrary.org/obo/agro.owl", "OBO")
+
     @staticmethod
     def get_random_string(number):
         """return a random string of n character
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 126cc404..94b320e0 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -579,3 +579,95 @@ def test_delete_custom_prefix(self, client):
 
         assert response.status_code == 200
         assert response.json == expected
+
+    def test_view_ontologies(self, client):
+        """test /api/admin/getontologies route"""
+        client.create_two_users()
+        client.log_user("jsmith")
+
+        response = client.client.get('/api/admin/getontologies')
+        assert response.status_code == 401
+
+        client.log_user("jdoe")
+
+        expected_empty = {
+            "error": False,
+            "errorMessage": "",
+            "ontologies": []
+        }
+
+        response = client.client.get('/api/admin/getontologies')
+        assert response.status_code == 200
+        assert response.json == expected_empty
+
+        client.create_ontology()
+
+        response = client.client.get('/api/admin/getontologies')
+
+        expected = {
+            "error": False,
+            "errorMessage": "",
+            "ontologies": [{
+                "id": 1,
+                "name": "Open Biological and Biomedical Ontology",
+                "uri": "http://purl.obolibrary.org/obo/agro.owl",
+                "short_name": "OBO",
+                "type": "local"
+            }]
+        }
+
+        assert response.status_code == 200
+        assert response.json == expected
+
+    def test_add_ontology(self, client):
+        """test /api/admin/addontology route"""
+        client.create_two_users()
+        client.log_user("jsmith")
+
+        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology"}
+
+        response = client.client.post('/api/admin/addprefix', json=data)
+        assert response.status_code == 401
+
+        client.log_user("jdoe")
+
+        response = client.client.post('/api/admin/addprefix', json=data)
+
+        expected = {
+            "error": False,
+            "errorMessage": "",
+            "ontologies": [{
+                "id": 1,
+                "name": "Open Biological and Biomedical Ontology",
+                "uri": "http://purl.obolibrary.org/obo/agro.owl",
+                "short_name": "OBO",
+                "type": "local"
+            }]
+        }
+
+        assert response.status_code == 200
+        assert response.json == expected
+
+    def test_delete_ontologies(self, client):
+        """test /api/admin/delete_ontologies route"""
+        client.create_two_users()
+        client.log_user("jsmith")
+
+        data = {"ontologiesIdToDelete": [1]}
+
+        response = client.client.post('/api/admin/delete_ontologies', json=data)
+        assert response.status_code == 401
+
+        client.log_user("jdoe")
+        client.create_ontology()
+
+        response = client.client.post('/api/admin/delete_ontologies', json=data)
+
+        expected = {
+            "error": False,
+            "errorMessage": "",
+            "ontologies": []
+        }
+
+        assert response.status_code == 200
+        assert response.json == expected

From 555c4cfbe5936f03e8ea76b91cfa25f1763b213d Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 22 Nov 2021 11:50:14 +0100
Subject: [PATCH 031/113] Typo

---
 tests/test_api_admin.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 94b320e0..d5a2be70 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -626,12 +626,12 @@ def test_add_ontology(self, client):
 
         data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology"}
 
-        response = client.client.post('/api/admin/addprefix', json=data)
+        response = client.client.post('/api/admin/addontology', json=data)
         assert response.status_code == 401
 
         client.log_user("jdoe")
 
-        response = client.client.post('/api/admin/addprefix', json=data)
+        response = client.client.post('/api/admin/addontology', json=data)
 
         expected = {
             "error": False,

From e7c54e22811769048d965a6d3dd53c8ed8570e29 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 23 Nov 2021 09:53:01 +0100
Subject: [PATCH 032/113] Local autocomplete endpoint?

---
 askomics/api/ontology.py                | 54 +++++++++++++++++++++++++
 askomics/libaskomics/OntologyManager.py | 15 +++++++
 askomics/libaskomics/SparqlQuery.py     | 40 ++++++++++++++++++
 3 files changed, 109 insertions(+)
 create mode 100644 askomics/api/ontology.py

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
new file mode 100644
index 00000000..b2e62c33
--- /dev/null
+++ b/askomics/api/ontology.py
@@ -0,0 +1,54 @@
+import traceback
+import sys
+from askomics.api.auth import api_auth, login_required
+from askomics.libaskomics.OntologyManager import OntologyManager
+
+from flask import (Blueprint, current_app, jsonify, request, session)
+
+onto_bp = Blueprint('ontology', __name__, url_prefix='/')
+
+
+@onto_bp.route("/api/ontology/<short_ontology>/autocomplete", methods=["GET"])
+@api_auth
+@login_required
+def autocomplete(short_ontology):
+    """Get the default sparql query
+
+    Returns
+    -------
+    json
+    """
+
+    if not request.args.get("q"):
+        return jsonify({
+            "error": True,
+            "errorMessage": "Missing q parameter",
+            "results": []
+        }), 400
+
+    try:
+        # Disk space
+        om = OntologyManager(current_app, session)
+        ontology = om.get_ontology(short_ontology)
+        if not ontology:
+            return jsonify({
+                "error": True,
+                "errorMessage": "Ontology {} not found".format(short_ontology),
+                "results": []
+            }), 404
+
+        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"))
+
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+        return jsonify({
+            "error": True,
+            "errorMessage": str(e),
+            "results": []
+        }), 404
+
+    return jsonify({
+        "error": True,
+        "errorMessage": "",
+        "results": results
+    }), 200
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 0f1767e7..9d324007 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -1,4 +1,5 @@
 from askomics.libaskomics.Database import Database
+from askomics.libaskomics.SparqlQuery import SparqlQuery
 from askomics.libaskomics.Params import Params
 
 
@@ -127,3 +128,17 @@ def remove_ontologies(self, ontology_ids):
 
         for ontology_id in ontology_ids:
             database.execute_sql_query(query, (ontology_id,))
+
+    def autocomplete(self, ontology_uri, ontology_type, query):
+        """Search in ontology
+
+        Returns
+        -------
+        list of dict
+            Results
+        """
+        if ontology_type == "local":
+            query = SparqlQuery(self.app, self.session, get_graphs=False)
+            # TODO: Actually store the graph in the ontology to quicken search
+            graphs, endpoints = query.set_graphs_and_endpoints(entities=[ontology_uri])
+            return query.autocomplete_local_ontology(ontology_uri, ontology_type, endpoints)
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 2bb5a16b..9d69c3e4 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -523,6 +523,46 @@ def get_uri_parameters(self, uri, endpoints):
 
         return formated_data
 
+    def autocomplete_local_ontology(self, uri, query, endpoints):
+        """Get results for a specific query
+
+        Parameters
+        ----------
+        uri : string
+            ontology uri
+        query : string
+            query to search
+
+        Returns
+        -------
+        dict
+            The corresponding parameters
+        """
+        raw_query = '''
+        SELECT DISTINCT ?label ?uri
+        WHERE {{
+          ?uri rdf:type <{}> .
+          ?uri rdfs:label ?label .
+          FILTER(contains(?label, "{}"))
+        }}
+        '''.format(uri, query)
+
+        raw_query = self.prefix_query(raw_query)
+
+        sparql = self.format_query(raw_query, limit=5, replace_froms=True, federated=False)
+
+        query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=False, endpoints=endpoints)
+        _, data = query_launcher.process_query(sparql)
+
+        formated_data = []
+        for row in data:
+            formated_data.append({
+                'uri': row['uri'],
+                'label': row['label']
+            })
+
+        return formated_data
+
     def format_sparql_variable(self, name):
         """Format a name into a sparql variable by remove spacial char and add a ?
 

From 2065a1a50fa3b090030e05f84e8eed27dce83802 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 23 Nov 2021 09:56:55 +0000
Subject: [PATCH 033/113] Fix ontologies

---
 askomics/app.py                         | 4 +++-
 askomics/libaskomics/OntologyManager.py | 6 +++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/askomics/app.py b/askomics/app.py
index 1c23650b..e26b858c 100644
--- a/askomics/app.py
+++ b/askomics/app.py
@@ -19,6 +19,7 @@
 from askomics.api.view import view_bp
 from askomics.api.results import results_bp
 from askomics.api.galaxy import galaxy_bp
+from askomics.api.ontology import onto_bp
 
 from celery import Celery
 from kombu import Exchange, Queue
@@ -46,7 +47,8 @@
     datasets_bp,
     query_bp,
     results_bp,
-    galaxy_bp
+    galaxy_bp,
+    onto_bp
 )
 
 
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 9d324007..9378f06a 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -129,7 +129,7 @@ def remove_ontologies(self, ontology_ids):
         for ontology_id in ontology_ids:
             database.execute_sql_query(query, (ontology_id,))
 
-    def autocomplete(self, ontology_uri, ontology_type, query):
+    def autocomplete(self, ontology_uri, ontology_type, query_term):
         """Search in ontology
 
         Returns
@@ -140,5 +140,5 @@ def autocomplete(self, ontology_uri, ontology_type, query):
         if ontology_type == "local":
             query = SparqlQuery(self.app, self.session, get_graphs=False)
             # TODO: Actually store the graph in the ontology to quicken search
-            graphs, endpoints = query.set_graphs_and_endpoints(entities=[ontology_uri])
-            return query.autocomplete_local_ontology(ontology_uri, ontology_type, endpoints)
+            query.set_graphs_and_endpoints(entities=[ontology_uri])
+            return query.autocomplete_local_ontology(ontology_uri, query_term, query.endpoints)

From 52b8e82e4754e692504ec8ff2a2beec49e3889ca Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 26 Nov 2021 16:08:20 +0100
Subject: [PATCH 034/113] Moved ontology to config

---
 askomics/api/file.py                                  | 5 -----
 askomics/api/start.py                                 | 7 ++++++-
 askomics/react/src/routes.jsx                         | 3 ++-
 askomics/react/src/routes/integration/integration.jsx | 3 +--
 askomics/react/src/routes/query/query.jsx             | 1 +
 tests/results/preview_files.json                      | 3 +--
 tests/results/preview_malformed_files.json            | 3 +--
 tests/test_api.py                                     | 9 ++++++---
 tests/test_api_file.py                                | 6 ++----
 9 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/askomics/api/file.py b/askomics/api/file.py
index 2a588370..6addb781 100644
--- a/askomics/api/file.py
+++ b/askomics/api/file.py
@@ -8,7 +8,6 @@
 from askomics.libaskomics.FilesHandler import FilesHandler
 from askomics.libaskomics.FilesUtils import FilesUtils
 from askomics.libaskomics.Dataset import Dataset
-from askomics.libaskomics.OntologyManager import OntologyManager
 from askomics.libaskomics.RdfFile import RdfFile
 
 from flask import (Blueprint, current_app, jsonify, request, send_from_directory, session)
@@ -238,8 +237,6 @@ def get_preview():
         }), 400
 
     try:
-        ontologies_manager = OntologyManager(current_app, session)
-        ontologies = ontologies_manager.list_ontologies()
 
         files_handler = FilesHandler(current_app, session)
         files_handler.handle_files(data['filesId'])
@@ -253,14 +250,12 @@ def get_preview():
         traceback.print_exc(file=sys.stdout)
         return jsonify({
             'previewFiles': [],
-            'ontologies': [],
             'error': True,
             'errorMessage': str(e)
         }), 500
 
     return jsonify({
         'previewFiles': results,
-        'ontologies': ontologies,
         'error': False,
         'errorMessage': ''
     })
diff --git a/askomics/api/start.py b/askomics/api/start.py
index eca8f91b..15564c9e 100644
--- a/askomics/api/start.py
+++ b/askomics/api/start.py
@@ -5,6 +5,7 @@
 from askomics.api.auth import api_auth
 from askomics.libaskomics.LocalAuth import LocalAuth
 from askomics.libaskomics.Start import Start
+from askomics.libaskomics.OntologyManager import OntologyManager
 
 from flask import (Blueprint, current_app, jsonify, session)
 
@@ -64,6 +65,9 @@ def start():
         except Exception:
             pass
 
+        ontologies_manager = OntologyManager(current_app, session)
+        ontologies = ontologies_manager.list_ontologies()
+
         config = {
             "footerMessage": current_app.iniconfig.get('askomics', 'footer_message'),
             "frontMessage": front_message,
@@ -79,7 +83,8 @@ def start():
             "namespaceInternal": current_app.iniconfig.get('triplestore', 'namespace_internal'),
             "proxyPath": proxy_path,
             "user": {},
-            "logged": False
+            "logged": False,
+            "ontologies": ontologies
         }
 
         json = {
diff --git a/askomics/react/src/routes.jsx b/askomics/react/src/routes.jsx
index bcb79f54..6b910055 100644
--- a/askomics/react/src/routes.jsx
+++ b/askomics/react/src/routes.jsx
@@ -46,7 +46,8 @@ export default class Routes extends Component {
         gitUrl: null,
         disableIntegration: null,
         namespaceData: null,
-        namespaceInternal: null
+        namespaceInternal: null,
+        ontologies: []
       }
     }
     this.cancelRequest
diff --git a/askomics/react/src/routes/integration/integration.jsx b/askomics/react/src/routes/integration/integration.jsx
index b81af4b1..7d3f50f7 100644
--- a/askomics/react/src/routes/integration/integration.jsx
+++ b/askomics/react/src/routes/integration/integration.jsx
@@ -20,7 +20,7 @@ export default class Integration extends Component {
       config: this.props.location.state.config,
       filesId: this.props.location.state.filesId,
       previewFiles: [],
-      ontologies: []
+      ontologies: this.props.location.state.config.ontologies
     }
     this.cancelRequest
   }
@@ -36,7 +36,6 @@ export default class Integration extends Component {
           console.log(requestUrl, response.data)
           this.setState({
             previewFiles: response.data.previewFiles,
-            ontologies: response.data.ontologies,
             waiting: false,
             error: response.data.error,
             errorMessage: response.data.errorMessage
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index a1a3df60..9e7796ba 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -43,6 +43,7 @@ export default class Query extends Component {
       // Preview icons
       disablePreview: false,
       previewIcon: "table",
+      ontologies: this.props.location.state.config.ontologies
     }
 
     this.graphState = {
diff --git a/tests/results/preview_files.json b/tests/results/preview_files.json
index a73688db..6497c378 100644
--- a/tests/results/preview_files.json
+++ b/tests/results/preview_files.json
@@ -181,6 +181,5 @@
       "error": false,
       "error_message": ""
     }
-],
-"ontologies": []
+]
 }
diff --git a/tests/results/preview_malformed_files.json b/tests/results/preview_malformed_files.json
index b99f0f2c..44312c87 100644
--- a/tests/results/preview_malformed_files.json
+++ b/tests/results/preview_malformed_files.json
@@ -22,6 +22,5 @@
       "error": true,
       "error_message": "Malformated CSV/TSV (Empty column in header)"
     }
-],
-  "ontologies": []
+]
 }
diff --git a/tests/test_api.py b/tests/test_api.py
index 7e00b700..1a40cec1 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -42,7 +42,8 @@ def test_start(self, client):
             "namespaceInternal": client.get_config('triplestore', 'namespace_internal'),
             "proxyPath": "/",
             "user": {},
-            "logged": False
+            "logged": False,
+            "ontologies": []
         }
         response = client.client.get('/api/start')
         assert response.status_code == 200
@@ -72,7 +73,8 @@ def test_start(self, client):
             "quota": 0,
             'apikey': "0000000001",
             'galaxy': {"url": "http://localhost:8081", "apikey": "fakekey"},
-            'last_action': None
+            'last_action': None,
+            "ontologies": []
         }
         response = client.client.get('/api/start')
 
@@ -100,7 +102,8 @@ def test_start(self, client):
             "quota": 0,
             'apikey': "0000000002",
             'galaxy': None,
-            'last_action': None
+            'last_action': None,
+            "ontologies": []
         }
         response = client.client.get('/api/start')
 
diff --git a/tests/test_api_file.py b/tests/test_api_file.py
index 5e645d89..a3a0f708 100644
--- a/tests/test_api_file.py
+++ b/tests/test_api_file.py
@@ -393,8 +393,7 @@ def test_get_preview(self, client):
         assert response.json == {
             'error': False,
             'errorMessage': '',
-            'previewFiles': [],
-            'ontologies': []
+            'previewFiles': []
         }
 
         response = client.client.post('/api/files/preview', json=malformed_data)
@@ -422,8 +421,7 @@ def test_get_preview(self, client):
                 'type': 'gff/gff3',
                 'error': False,
                 'error_message': ''
-            }],
-            'ontologies': []
+            }]
         }
 
     def test_delete_files(self, client):

From bc6c45937bef2e956489689998678959eb769754 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 26 Nov 2021 20:15:28 +0100
Subject: [PATCH 035/113] Typo

---
 tests/test_api.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/test_api.py b/tests/test_api.py
index 1a40cec1..af30f8bd 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -73,8 +73,7 @@ def test_start(self, client):
             "quota": 0,
             'apikey': "0000000001",
             'galaxy': {"url": "http://localhost:8081", "apikey": "fakekey"},
-            'last_action': None,
-            "ontologies": []
+            'last_action': None
         }
         response = client.client.get('/api/start')
 
@@ -102,8 +101,7 @@ def test_start(self, client):
             "quota": 0,
             'apikey': "0000000002",
             'galaxy': None,
-            'last_action': None,
-            "ontologies": []
+            'last_action': None
         }
         response = client.client.get('/api/start')
 

From f243d204202f82de568f76d9f628c17418d03bb9 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 30 Nov 2021 11:37:28 +0100
Subject: [PATCH 036/113] autocomplete

---
 askomics/react/src/routes/query/attribute.jsx | 20 ++++++++++++++++++-
 askomics/react/src/routes/query/query.jsx     |  1 +
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index 5536edde..6a673980 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -46,6 +46,23 @@ export default class AttributeBox extends Component {
     return newStr
   }
 
+
+  isRegisteredOnto () {
+      return this.props.config.ontologies.some(onto => {
+        return (onto.uri == this.props.entityUri)
+      })
+  }
+
+  getAutoComplete(){
+      return this.props.config.ontologies.map(onto => {
+        if (onto.uri == this.props.entityUri) {
+          return onto.short_name
+        } else {
+          return null
+        }
+      })
+  }
+
   renderLinker () {
     let options = []
 
@@ -494,5 +511,6 @@ AttributeBox.propTypes = {
   attribute: PropTypes.object,
   graph: PropTypes.object,
   config: PropTypes.object,
-  isOnto: PropTypes.bool
+  isOnto: PropTypes.bool,
+  entityUri: PropTypes.string
 }
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index a1a3df60..b5dfbdc7 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -1551,6 +1551,7 @@ export default class Query extends Component {
                 handleDateFilter={p => this.handleDateFilter(p)}
                 config={this.state.config}
                 isOnto={isOnto}
+                entityUri={this.currentSelected.uri}
               />
             )
           }

From 420e357ae5d533af6b0bb166a15c074be3e96180 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Dec 2021 09:34:58 +0100
Subject: [PATCH 037/113] Test react

---
 askomics/api/ontology.py                      |  7 --
 askomics/libaskomics/SparqlQuery.py           | 11 ++-
 askomics/react/src/routes/query/attribute.jsx | 86 +++++++++++++------
 package.json                                  |  1 +
 4 files changed, 71 insertions(+), 34 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index b2e62c33..28800a84 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -19,13 +19,6 @@ def autocomplete(short_ontology):
     json
     """
 
-    if not request.args.get("q"):
-        return jsonify({
-            "error": True,
-            "errorMessage": "Missing q parameter",
-            "results": []
-        }), 400
-
     try:
         # Disk space
         om = OntologyManager(current_app, session)
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 9d69c3e4..9b3f41b4 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -538,14 +538,21 @@ def autocomplete_local_ontology(self, uri, query, endpoints):
         dict
             The corresponding parameters
         """
+
+        subquery = ""
+
+        if query:
+            subquery = 'FILTER(contains(?label, "{}"))'.format(query)
         raw_query = '''
         SELECT DISTINCT ?label ?uri
         WHERE {{
           ?uri rdf:type <{}> .
           ?uri rdfs:label ?label .
-          FILTER(contains(?label, "{}"))
+          {}
         }}
-        '''.format(uri, query)
+
+        LIMIT 5
+        '''.format(uri, subquery)
 
         raw_query = self.prefix_query(raw_query)
 
diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index 6a673980..66d8cccb 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -10,12 +10,17 @@ import update from 'react-addons-update'
 import Visualization from './visualization'
 import PropTypes from 'prop-types'
 import Utils from '../../classes/utils'
+import TextInput from 'react-autocomplete-input';
+import 'react-autocomplete-input/dist/bundle.css';
 
 export default class AttributeBox extends Component {
   constructor (props) {
     super(props)
     this.utils = new Utils()
-    this.state = {}
+    this.state = {
+        ontologyShort: this.getAutoComplete(),
+        options: []
+    }
 
     this.toggleVisibility = this.props.toggleVisibility.bind(this)
     this.handleNegative = this.props.handleNegative.bind(this)
@@ -33,6 +38,8 @@ export default class AttributeBox extends Component {
     this.toggleAddNumFilter = this.props.toggleAddNumFilter.bind(this)
     this.toggleAddDateFilter = this.props.toggleAddDateFilter.bind(this)
     this.handleDateFilter = this.props.handleDateFilter.bind(this)
+    this.autocompleteOntology = this.autocompleteOntology.bind(this)
+    this.cancelRequest
   }
 
   subNums (id) {
@@ -53,7 +60,7 @@ export default class AttributeBox extends Component {
       })
   }
 
-  getAutoComplete(){
+  getAutoComplete () {
       return this.props.config.ontologies.map(onto => {
         if (onto.uri == this.props.entityUri) {
           return onto.short_name
@@ -63,6 +70,31 @@ export default class AttributeBox extends Component {
       })
   }
 
+  autocompleteOntology (event) {
+    this.handleFilterValue(event)
+    let userInput = event.target
+    let requestUrl = '/api/ontology/' + this.state.ontologyShort + "/autocomplete"
+    axios.get(requestUrl, {baseURL: this.props.config.proxyPath, params:{q: userInput}, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        console.log(requestUrl, response.data)
+        // set state of resultsPreview
+        this.setState({
+          options: response.data.results
+        })
+      })
+      .catch(error => {
+        console.log(error, error.response.data.errorMessage)
+        this.setState({
+          error: true,
+          errorMessage: error.response.data.errorMessage,
+          status: error.response.status,
+          waiting: false
+        })
+      })
+
+
+  }
+
   renderLinker () {
     let options = []
 
@@ -140,6 +172,32 @@ export default class AttributeBox extends Component {
 
     let form
 
+    let input
+    let attrIcons
+
+    if (this.props.isOnto){
+      attrIcons = (
+        <div className="attr-icons">
+          <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
+        </div>
+      )
+      input = (
+          <TextInput Component="input" options={this.state.options} onSelect={this.handleFilterValue} id={this.props.attribute.id} value={this.props.attribute.filterValue} onRequestOptions={this.autocompleteOntology}/>
+      )
+
+    } else {
+      attrIcons = (
+        <div className="attr-icons">
+          {this.props.config.user.admin ? <i className={formIcon} id={this.props.attribute.id} onClick={this.toggleFormAttribute} data-tip data-for={"formTooltip"}></i> : <nodiv></nodiv>}
+          <i className={linkIcon} id={this.props.attribute.id} onClick={this.toggleLinkAttribute} data-tip data-for={"linkTooltip"}></i>
+          {this.props.attribute.uri == "rdf:type" || this.props.attribute.uri == "rdfs:label" ? <nodiv></nodiv> : <i className={optionalIcon} id={this.props.attribute.id} onClick={this.toggleOptional} data-tip data-for={"optionalTooltip"}></i> }
+          <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
+        </div>
+      )
+      input = (<Input disabled={this.props.attribute.optional} type="text" id={this.props.attribute.id} value={this.props.attribute.filterValue} onChange={this.handleFilterValue} />)
+    }
+
+
     if (this.props.attribute.linked) {
       form = this.renderLinker()
     } else {
@@ -161,35 +219,13 @@ export default class AttributeBox extends Component {
               </CustomInput>
             </td>
             <td>
-              <Input disabled={this.props.attribute.optional} type="text" id={this.props.attribute.id} value={this.props.attribute.filterValue} onChange={this.handleFilterValue} />
+              {input}
             </td>
           </tr>
         </table>
       )
     }
 
-
-    let attrIcons
-
-    if (this.props.isOnto){
-      attrIcons = (
-        <div className="attr-icons">
-          <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
-        </div>
-      )
-
-    } else {
-      attrIcons = (
-        <div className="attr-icons">
-          {this.props.config.user.admin ? <i className={formIcon} id={this.props.attribute.id} onClick={this.toggleFormAttribute} data-tip data-for={"formTooltip"}></i> : <nodiv></nodiv>}
-          <i className={linkIcon} id={this.props.attribute.id} onClick={this.toggleLinkAttribute} data-tip data-for={"linkTooltip"}></i>
-          {this.props.attribute.uri == "rdf:type" || this.props.attribute.uri == "rdfs:label" ? <nodiv></nodiv> : <i className={optionalIcon} id={this.props.attribute.id} onClick={this.toggleOptional} data-tip data-for={"optionalTooltip"}></i> }
-          <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
-        </div>
-      )
-    }
-
-
     return (
       <div className="attribute-box">
         <label className="attr-label">{this.props.attribute.label}</label>
diff --git a/package.json b/package.json
index 479003cc..a2b8d346 100644
--- a/package.json
+++ b/package.json
@@ -54,6 +54,7 @@
     "qs": "^6.9.4",
     "react": "^16.13.1",
     "react-ace": "^9.1.3",
+    "react-autocomplete-input": "1.0.18",
     "react-addons-update": "^15.6.3",
     "react-bootstrap-table-next": "^4.0.3",
     "react-bootstrap-table2-editor": "^1.4.0",

From 0098c3a3505c15ceaa04117cec952ef69b972557 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Dec 2021 11:36:12 +0000
Subject: [PATCH 038/113] Update

---
 askomics/libaskomics/SparqlQuery.py           |  7 ++-----
 askomics/react/src/routes/query/attribute.jsx | 15 +++++++++------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 9b3f41b4..41565a1e 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -544,7 +544,7 @@ def autocomplete_local_ontology(self, uri, query, endpoints):
         if query:
             subquery = 'FILTER(contains(?label, "{}"))'.format(query)
         raw_query = '''
-        SELECT DISTINCT ?label ?uri
+        SELECT DISTINCT ?label
         WHERE {{
           ?uri rdf:type <{}> .
           ?uri rdfs:label ?label .
@@ -563,10 +563,7 @@ def autocomplete_local_ontology(self, uri, query, endpoints):
 
         formated_data = []
         for row in data:
-            formated_data.append({
-                'uri': row['uri'],
-                'label': row['label']
-            })
+            formated_data.append(row['label'])
 
         return formated_data
 
diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index 66d8cccb..d07a9b3f 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -70,9 +70,8 @@ export default class AttributeBox extends Component {
       })
   }
 
-  autocompleteOntology (event) {
-    this.handleFilterValue(event)
-    let userInput = event.target
+  autocompleteOntology (value) {
+    let userInput = value
     let requestUrl = '/api/ontology/' + this.state.ontologyShort + "/autocomplete"
     axios.get(requestUrl, {baseURL: this.props.config.proxyPath, params:{q: userInput}, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
       .then(response => {
@@ -181,9 +180,13 @@ export default class AttributeBox extends Component {
           <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
         </div>
       )
-      input = (
-          <TextInput Component="input" options={this.state.options} onSelect={this.handleFilterValue} id={this.props.attribute.id} value={this.props.attribute.filterValue} onRequestOptions={this.autocompleteOntology}/>
-      )
+      if (this.props.attribute.uri == "rdfs:label"){
+        input = (
+          <TextInput id={this.props.attribute.id} trigger="" matchAny={true} spacer="" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleFilterValue({target: {value: e, id: this.props.attribute.id}})} id={this.props.attribute.id} value={this.props.attribute.filterValue} onRequestOptions={this.autocompleteOntology}/>
+        )
+      } else {
+        input = (<Input disabled={this.props.attribute.optional} type="text" id={this.props.attribute.id} value={this.props.attribute.filterValue} onChange={this.handleFilterValue} />)
+      }
 
     } else {
       attrIcons = (

From b3ec961657fb937982c3653835f21e9c9c68c8ca Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Dec 2021 15:31:18 +0100
Subject: [PATCH 039/113] Move autocomplete to its own

---
 .../react/src/components/autocomplete.jsx     | 80 +++++++++++++++++++
 askomics/react/src/routes/query/attribute.jsx | 42 +---------
 2 files changed, 83 insertions(+), 39 deletions(-)
 create mode 100644 askomics/react/src/components/autocomplete.jsx

diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
new file mode 100644
index 00000000..4b789026
--- /dev/null
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -0,0 +1,80 @@
+import React, { Component} from 'react'
+import axios from 'axios'
+import { Input, FormGroup, CustomInput, FormFeedback } from 'reactstrap'
+import { Redirect } from 'react-router-dom'
+import DatePicker from "react-datepicker";
+import ReactTooltip from "react-tooltip";
+import ErrorDiv from '../error/error'
+import WaitingDiv from '../../components/waiting'
+import update from 'react-addons-update'
+import Visualization from './visualization'
+import PropTypes from 'prop-types'
+import Utils from '../../classes/utils'
+import TextInput from 'react-autocomplete-input';
+import 'react-autocomplete-input/dist/bundle.css';
+
+export default class Autocomplete extends Component {
+  constructor (props) {
+    super(props)
+    this.utils = new Utils()
+    this.state = {
+        ontologyShort: this.getAutoComplete(),
+        options: []
+    }
+
+    this.handleFilterValue = this.props.handleFilterValue.bind(this)
+    this.autocompleteOntology = this.autocompleteOntology.bind(this)
+    this.cancelRequest
+  }
+
+  getAutoComplete () {
+      return this.props.config.ontologies.map(onto => {
+        if (onto.uri == this.props.entityUri) {
+          return onto.short_name
+        } else {
+          return null
+        }
+      })
+  }
+
+  autocompleteOntology (value) {
+    let userInput = value
+    let requestUrl = '/api/ontology/' + this.state.ontologyShort + "/autocomplete"
+    axios.get(requestUrl, {baseURL: this.props.config.proxyPath, params:{q: userInput}, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        console.log(requestUrl, response.data)
+        // set state of resultsPreview
+        this.setState({
+          options: response.data.results
+        })
+      })
+      .catch(error => {
+        console.log(error, error.response.data.errorMessage)
+        this.setState({
+          error: true,
+          errorMessage: error.response.data.errorMessage,
+          status: error.response.status,
+          waiting: false
+        })
+      })
+  }
+
+  renderAutocomplete () {
+    let input = (
+      <TextInput trigger="" matchAny={true} spacer="" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleFilterValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue} onRequestOptions={this.autocompleteOntology}/>
+    )
+
+    return input
+  }
+
+  render () {
+    return this.renderAutocomplete()
+  }
+}
+
+Autocomplete.propTypes = {
+  handleFilterValue: PropTypes.func,
+  entityUri: PropTypes.string,
+  attributeId: PropTypes.string,
+  filterValue: PropTypes.string
+}
diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index d07a9b3f..01ed50f2 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -12,15 +12,13 @@ import PropTypes from 'prop-types'
 import Utils from '../../classes/utils'
 import TextInput from 'react-autocomplete-input';
 import 'react-autocomplete-input/dist/bundle.css';
+import Autocomplete from '../../components/autocomplete'
 
 export default class AttributeBox extends Component {
   constructor (props) {
     super(props)
     this.utils = new Utils()
-    this.state = {
-        ontologyShort: this.getAutoComplete(),
-        options: []
-    }
+    this.state = {}
 
     this.toggleVisibility = this.props.toggleVisibility.bind(this)
     this.handleNegative = this.props.handleNegative.bind(this)
@@ -60,40 +58,6 @@ export default class AttributeBox extends Component {
       })
   }
 
-  getAutoComplete () {
-      return this.props.config.ontologies.map(onto => {
-        if (onto.uri == this.props.entityUri) {
-          return onto.short_name
-        } else {
-          return null
-        }
-      })
-  }
-
-  autocompleteOntology (value) {
-    let userInput = value
-    let requestUrl = '/api/ontology/' + this.state.ontologyShort + "/autocomplete"
-    axios.get(requestUrl, {baseURL: this.props.config.proxyPath, params:{q: userInput}, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
-      .then(response => {
-        console.log(requestUrl, response.data)
-        // set state of resultsPreview
-        this.setState({
-          options: response.data.results
-        })
-      })
-      .catch(error => {
-        console.log(error, error.response.data.errorMessage)
-        this.setState({
-          error: true,
-          errorMessage: error.response.data.errorMessage,
-          status: error.response.status,
-          waiting: false
-        })
-      })
-
-
-  }
-
   renderLinker () {
     let options = []
 
@@ -182,7 +146,7 @@ export default class AttributeBox extends Component {
       )
       if (this.props.attribute.uri == "rdfs:label"){
         input = (
-          <TextInput id={this.props.attribute.id} trigger="" matchAny={true} spacer="" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleFilterValue({target: {value: e, id: this.props.attribute.id}})} id={this.props.attribute.id} value={this.props.attribute.filterValue} onRequestOptions={this.autocompleteOntology}/>
+          <Autocomplete entityUri={this.props.entityUri} attributeId={this.props.attribute.id} filterValue={this.props.attribute.filterValue} handleFilterValue={p => this.handleChangePosition(p)}/>
         )
       } else {
         input = (<Input disabled={this.props.attribute.optional} type="text" id={this.props.attribute.id} value={this.props.attribute.filterValue} onChange={this.handleFilterValue} />)

From 73aeef7b757469ba25e98113e4821ad0374d622f Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Dec 2021 16:57:59 +0000
Subject: [PATCH 040/113] Override position

---
 .../react/src/components/autocomplete.jsx     | 20 ++++++-------------
 askomics/react/src/routes/query/attribute.jsx |  3 +--
 askomics/static/css/askomics.css              |  7 ++++++-
 3 files changed, 13 insertions(+), 17 deletions(-)

diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index 4b789026..dca247f8 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -1,22 +1,12 @@
 import React, { Component} from 'react'
 import axios from 'axios'
-import { Input, FormGroup, CustomInput, FormFeedback } from 'reactstrap'
-import { Redirect } from 'react-router-dom'
-import DatePicker from "react-datepicker";
-import ReactTooltip from "react-tooltip";
-import ErrorDiv from '../error/error'
-import WaitingDiv from '../../components/waiting'
-import update from 'react-addons-update'
-import Visualization from './visualization'
 import PropTypes from 'prop-types'
-import Utils from '../../classes/utils'
 import TextInput from 'react-autocomplete-input';
 import 'react-autocomplete-input/dist/bundle.css';
 
 export default class Autocomplete extends Component {
   constructor (props) {
     super(props)
-    this.utils = new Utils()
     this.state = {
         ontologyShort: this.getAutoComplete(),
         options: []
@@ -60,9 +50,10 @@ export default class Autocomplete extends Component {
   }
 
   renderAutocomplete () {
-    let input = (
+    
+    let input = (<div>
       <TextInput trigger="" matchAny={true} spacer="" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleFilterValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue} onRequestOptions={this.autocompleteOntology}/>
-    )
+    </div>)
 
     return input
   }
@@ -75,6 +66,7 @@ export default class Autocomplete extends Component {
 Autocomplete.propTypes = {
   handleFilterValue: PropTypes.func,
   entityUri: PropTypes.string,
-  attributeId: PropTypes.string,
-  filterValue: PropTypes.string
+  attributeId: PropTypes.number,
+  filterValue: PropTypes.string,
+  config: PropTypes.object,
 }
diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index 01ed50f2..002fa626 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -36,7 +36,6 @@ export default class AttributeBox extends Component {
     this.toggleAddNumFilter = this.props.toggleAddNumFilter.bind(this)
     this.toggleAddDateFilter = this.props.toggleAddDateFilter.bind(this)
     this.handleDateFilter = this.props.handleDateFilter.bind(this)
-    this.autocompleteOntology = this.autocompleteOntology.bind(this)
     this.cancelRequest
   }
 
@@ -146,7 +145,7 @@ export default class AttributeBox extends Component {
       )
       if (this.props.attribute.uri == "rdfs:label"){
         input = (
-          <Autocomplete entityUri={this.props.entityUri} attributeId={this.props.attribute.id} filterValue={this.props.attribute.filterValue} handleFilterValue={p => this.handleChangePosition(p)}/>
+          <Autocomplete config={this.props.config} entityUri={this.props.entityUri} attributeId={this.props.attribute.id} filterValue={this.props.attribute.filterValue} handleFilterValue={p => this.handleFilterValue(p)}/>
         )
       } else {
         input = (<Input disabled={this.props.attribute.optional} type="text" id={this.props.attribute.id} value={this.props.attribute.filterValue} onChange={this.handleFilterValue} />)
diff --git a/askomics/static/css/askomics.css b/askomics/static/css/askomics.css
index 7f7bb842..c6525b2a 100644
--- a/askomics/static/css/askomics.css
+++ b/askomics/static/css/askomics.css
@@ -276,4 +276,9 @@ button.input-with-icon {
     display: block;
 }
 
-/***********************************************************************/
\ No newline at end of file
+.react-autocomplete-input {
+  left: auto !important;
+  top: auto !important;
+}
+
+/***********************************************************************/

From eed6e6a03d7ee1988b2482fb613e98a936230f84 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Dec 2021 08:31:59 +0000
Subject: [PATCH 041/113] changed logic

---
 askomics/react/src/components/autocomplete.jsx | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index dca247f8..b5ce690b 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -15,6 +15,7 @@ export default class Autocomplete extends Component {
     this.handleFilterValue = this.props.handleFilterValue.bind(this)
     this.autocompleteOntology = this.autocompleteOntology.bind(this)
     this.cancelRequest
+    this.handleOntoValue = this.handleOntoValue.bind(this)
   }
 
   getAutoComplete () {
@@ -32,7 +33,6 @@ export default class Autocomplete extends Component {
     let requestUrl = '/api/ontology/' + this.state.ontologyShort + "/autocomplete"
     axios.get(requestUrl, {baseURL: this.props.config.proxyPath, params:{q: userInput}, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
       .then(response => {
-        console.log(requestUrl, response.data)
         // set state of resultsPreview
         this.setState({
           options: response.data.results
@@ -49,10 +49,16 @@ export default class Autocomplete extends Component {
       })
   }
 
+  handleOntoValue (event) {
+    this.handleFilterValue(event)
+    this.autocompleteOntology(event.target.value)
+  }
+
+
   renderAutocomplete () {
     
     let input = (<div>
-      <TextInput trigger="" matchAny={true} spacer="" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleFilterValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue} onRequestOptions={this.autocompleteOntology}/>
+      <TextInput trigger="" matchAny={true} spacer="" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleOntoValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue}/>
     </div>)
 
     return input

From adb7f5fc766514f8386e54d0202b52f091813c39 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Dec 2021 08:34:03 +0000
Subject: [PATCH 042/113] Limit to 3 chars

---
 askomics/react/src/components/autocomplete.jsx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index b5ce690b..d13f29e4 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -31,6 +31,9 @@ export default class Autocomplete extends Component {
   autocompleteOntology (value) {
     let userInput = value
     let requestUrl = '/api/ontology/' + this.state.ontologyShort + "/autocomplete"
+
+    if (value.length < 3) { return }
+
     axios.get(requestUrl, {baseURL: this.props.config.proxyPath, params:{q: userInput}, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
       .then(response => {
         // set state of resultsPreview

From 3557b1e32a9a7eead69e1907bbb37a43d25c89e2 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Dec 2021 12:02:42 +0100
Subject: [PATCH 043/113] Remove arrows on ontolink

---
 askomics/react/src/routes/query/attribute.jsx | 2 +-
 askomics/react/src/routes/query/query.jsx     | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index 002fa626..8167bb41 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -53,7 +53,7 @@ export default class AttributeBox extends Component {
 
   isRegisteredOnto () {
       return this.props.config.ontologies.some(onto => {
-        return (onto.uri == this.props.entityUri)
+        return (onto.uri == this.props.entityUri && onto.type == "local")
       })
   }
 
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index a6825d94..b5d20391 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -545,7 +545,7 @@ export default class Query extends Component {
               target: targetId,
               selected: false,
               suggested: true,
-              directed: true,
+              directed: isOnto ? false : true,
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
           }
@@ -670,7 +670,7 @@ export default class Query extends Component {
           target: node2.id,
           selected: false,
           suggested: false,
-          directed: true,
+          directed: link.directed,
         }
       }
 
@@ -689,7 +689,7 @@ export default class Query extends Component {
           target: node1.id,
           selected: false,
           suggested: false,
-          directed: true,
+          directed: link.direct,
         }
       }
     })

From 94c9e32164047c9eeb08d50d955e7b48d7f72e24 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 6 Dec 2021 17:04:52 +0100
Subject: [PATCH 044/113] Onto type

---
 askomics/api/admin.py                         | 10 +++-
 askomics/api/ontology.py                      |  2 +-
 askomics/libaskomics/OntologyManager.py       | 51 ++++++++++++++++++-
 .../react/src/routes/admin/ontologies.jsx     | 29 +++++++++--
 askomics/react/src/routes/query/attribute.jsx |  2 +-
 5 files changed, 86 insertions(+), 8 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index a54fa5b9..2da1979b 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -698,6 +698,14 @@ def add_ontology():
     name = data.get("name")
     uri = data.get("uri")
     short_name = data.get("shortName")
+    type = data.get("type")
+
+    if type not in ["none", "local", "ols"]:
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "Invalid type"
+        }), 400
 
     if any([name == onto['name'] or short_name == onto['short_name'] for onto in ontologies]):
         return jsonify({
@@ -707,7 +715,7 @@ def add_ontology():
         }), 400
 
     try:
-        om.add_ontology(name, uri, short_name)
+        om.add_ontology(name, uri, short_name, type)
         ontologies = om.list_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 28800a84..2790b901 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -30,7 +30,7 @@ def autocomplete(short_ontology):
                 "results": []
             }), 404
 
-        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"))
+        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology)
 
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 9378f06a..6ef9d095 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -1,3 +1,5 @@
+import requests
+
 from askomics.libaskomics.Database import Database
 from askomics.libaskomics.SparqlQuery import SparqlQuery
 from askomics.libaskomics.Params import Params
@@ -129,7 +131,7 @@ def remove_ontologies(self, ontology_ids):
         for ontology_id in ontology_ids:
             database.execute_sql_query(query, (ontology_id,))
 
-    def autocomplete(self, ontology_uri, ontology_type, query_term):
+    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name):
         """Search in ontology
 
         Returns
@@ -142,3 +144,50 @@ def autocomplete(self, ontology_uri, ontology_type, query_term):
             # TODO: Actually store the graph in the ontology to quicken search
             query.set_graphs_and_endpoints(entities=[ontology_uri])
             return query.autocomplete_local_ontology(ontology_uri, query_term, query.endpoints)
+        elif ontology_type == "ols":
+            base_url = "https://www.ebi.ac.uk/ols/api/search"
+            arguments = {
+                "q": query_term,
+                "ontology": onto_short_name,
+                "rows": 5,
+                "queryFields": "label",
+                "type": "class",
+                "fieldList": "label"
+            }
+
+            r = requests.get(base_url, params=arguments)
+
+            data = []
+
+            if not r.status_code == 200:
+                return data
+
+            res = r.json()
+            if res['response']['docs']:
+                data = [term['label'] for term in res['response']['docs']]
+
+            return data
+
+        elif ontology_type == "ols":
+            base_url = "https://www.ebi.ac.uk/ols/api/search"
+            arguments = {
+                "q": query_term,
+                "ontology": onto_short_name,
+                "rows": 5,
+                "queryFields": "label",
+                "type": "class",
+                "fieldList": "label"
+            }
+
+            r = requests.get(base_url, params=arguments)
+
+            data = []
+
+            if not r.status_code == 200:
+                return data
+
+            res = r.json()
+            if res['response']['docs']:
+                data = [term['label'] for term in res['response']['docs']]
+
+            return data
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index 015eeadc..17478905 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -24,6 +24,7 @@ export default class Ontologies extends Component {
       name: "",
       uri: "",
       shortName: "",
+      type: "local",
       ontologiesSelected: []
     }
     this.handleChangeValue = this.handleChangeValue.bind(this)
@@ -98,7 +99,8 @@ export default class Ontologies extends Component {
     let data = {
       name: this.state.name,
       uri: this.state.uri,
-      shortName: this.state.shortName
+      shortName: this.state.shortName,
+      type: this.state.type
     }
 
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
@@ -109,6 +111,10 @@ export default class Ontologies extends Component {
         newontologyErrorMessage: response.data.errorMessage,
         ontologies: response.data.ontologies,
         newontologyStatus: response.status,
+        name: "",
+        uri: "",
+        shortName: "",
+        type: "local"
       })
     })
     .catch(error => {
@@ -182,7 +188,13 @@ export default class Ontologies extends Component {
       dataField: 'uri',
       text: 'Uri',
       sort: true
+    }, {
+      editable: false,
+      dataField: 'type',
+      text: 'Autocomplete type',
+      sort: true
     }
+
   ]
 
     let ontologiesDefaultSorted = [{
@@ -211,24 +223,33 @@ export default class Ontologies extends Component {
         <div>
         <Form onSubmit={this.handleAddOntology}>
           <Row form>
-            <Col md={4}>
+            <Col md={3}>
               <FormGroup>
                 <Label for="name">Ontology name</Label>
                 <Input type="text" name="name" id="name" placeholder="Ontology name" value={this.state.name} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>
-            <Col md={4}>
+            <Col md={3}>
               <FormGroup>
                 <Label for="shortName">Ontology short name</Label>
                 <Input type="text" name="shortName" id="shortName" placeholder="shortName" value={this.state.shortName} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>
-            <Col md={4}>
+            <Col md={3}>
               <FormGroup>
                 <Label for="uri">Ontology uri</Label>
                 <Input type="text" name="uri" id="uri" placeholder="uri" value={this.state.uri} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>
+            <Col md={3}>
+              <FormGroup>Autocomplete type</Label>
+                <CustomInput type="select" name="type" id="type" placeholder="type" value={this.state.type} onChange={this.handleChangeValue}>
+                  <option value="none" >none</option>
+                  <option value="local" >local</option>
+                  <option value="ols" >ols</option>
+                </CustomInput>
+              </FormGroup>
+            </Col>
           </Row>
           <Button disabled={!this.validateOntologyForm()}>Create</Button>
         </Form>
diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index 8167bb41..fab02271 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -53,7 +53,7 @@ export default class AttributeBox extends Component {
 
   isRegisteredOnto () {
       return this.props.config.ontologies.some(onto => {
-        return (onto.uri == this.props.entityUri && onto.type == "local")
+        return (onto.uri == this.props.entityUri && onto.type != "none")
       })
   }
 

From e6b7cb9441619908d8a2b1b28541a6a0c3c8571d Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 6 Dec 2021 17:21:01 +0100
Subject: [PATCH 045/113] Fix test

---
 askomics/react/src/routes/admin/ontologies.jsx | 3 ++-
 tests/test_api_admin.py                        | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index 17478905..50632410 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -242,7 +242,8 @@ export default class Ontologies extends Component {
               </FormGroup>
             </Col>
             <Col md={3}>
-              <FormGroup>Autocomplete type</Label>
+              <FormGroup>
+                <Label for="type">Autocomplete type</Label>
                 <CustomInput type="select" name="type" id="type" placeholder="type" value={this.state.type} onChange={this.handleChangeValue}>
                   <option value="none" >none</option>
                   <option value="local" >local</option>
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index d5a2be70..5b435d92 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -624,7 +624,7 @@ def test_add_ontology(self, client):
         client.create_two_users()
         client.log_user("jsmith")
 
-        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology"}
+        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local"}
 
         response = client.client.post('/api/admin/addontology', json=data)
         assert response.status_code == 401

From a85f717a7a3a9d7cee5e4a5cd955c0c6ab40450d Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 6 Dec 2021 17:45:56 +0100
Subject: [PATCH 046/113] ontology column to dataset

---
 askomics/libaskomics/Database.py | 11 +++++++++++
 askomics/libaskomics/Dataset.py  |  3 ++-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index 9d8cf269..3c10ab57 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -198,6 +198,17 @@ def update_datasets_table(self):
         except Exception:
             pass
 
+        query = '''
+        ALTER TABLE datasets
+        ADD ontology boolean NULL
+        DEFAULT(0)
+        '''
+
+        try:
+            self.execute_sql_query(query)
+        except Exception:
+            pass
+
     def create_integration_table(self):
         """Create the integration table"""
         query = '''
diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index 927f4896..4d31cbd4 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -93,7 +93,8 @@ def save_in_db(self):
             ?,
             NULL,
             NULL,
-            NULL
+            NULL,
+            0
         )
         '''
 

From 014984d5ef969331de0eb289546c0f5ce1a94654 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 7 Dec 2021 17:26:48 +0100
Subject: [PATCH 047/113] Onto link to datasets (1/?)

---
 askomics/api/admin.py                         |  46 +++++--
 askomics/api/ontology.py                      |   2 +-
 askomics/libaskomics/Database.py              |   5 +-
 askomics/libaskomics/Dataset.py               |   7 +
 askomics/libaskomics/OntologyManager.py       | 120 +++++++++++++-----
 askomics/libaskomics/SparqlQuery.py           |   4 +-
 .../react/src/routes/admin/ontologies.jsx     |  81 +++++++++---
 tests/conftest.py                             |   3 +-
 tests/test_api_admin.py                       |  10 +-
 9 files changed, 212 insertions(+), 66 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 2da1979b..49a911c7 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -654,7 +654,7 @@ def get_ontologies():
     """
     try:
         om = OntologyManager(current_app, session)
-        ontologies = om.list_ontologies()
+        ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
         return jsonify({
@@ -685,20 +685,30 @@ def add_ontology():
     """
 
     data = request.get_json()
-    if not data or not (data.get("name") and data.get("uri") and data.get("shortName")):
+    if not data or not (data.get("name") and data.get("uri") and data.get("shortName") and data.get("type") and data.get("datasetId")):
         return jsonify({
             'ontologies': [],
             'error': True,
             'errorMessage': "Missing parameter"
         }), 400
 
-    om = OntologyManager(current_app, session)
-    ontologies = om.list_ontologies()
-
     name = data.get("name")
     uri = data.get("uri")
     short_name = data.get("shortName")
     type = data.get("type")
+    dataset_id = data.get("datasetId")
+
+    om = OntologyManager(current_app, session)
+
+    if type == "ols" and not om.test_ols_ontology(short_name):
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "{} ontology not found in OLS".format(short_name)
+        }), 400
+
+    om = OntologyManager(current_app, session)
+    ontologies = om.list_full_ontologies()
 
     if type not in ["none", "local", "ols"]:
         return jsonify({
@@ -707,6 +717,20 @@ def add_ontology():
             'errorMessage': "Invalid type"
         }), 400
 
+    datasets_info = [{'id': dataset_id}]
+
+    datasets_handler = DatasetsHandler(current_app, session, datasets_info=datasets_info)
+    datasets_handler.handle_datasets()
+
+    if not len(datasets_handler.datasets) == 1 or not datasets_handler.datasets[0]['public']:
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "Invalid dataset id"
+        }), 400
+
+    dataset = datasets_handler.datasets[0]
+
     if any([name == onto['name'] or short_name == onto['short_name'] for onto in ontologies]):
         return jsonify({
             'ontologies': [],
@@ -715,8 +739,8 @@ def add_ontology():
         }), 400
 
     try:
-        om.add_ontology(name, uri, short_name, type)
-        ontologies = om.list_ontologies()
+        om.add_ontology(name, uri, short_name, dataset['id'], dataset['graph_name'], type)
+        ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
         return jsonify({
@@ -755,9 +779,13 @@ def delete_ontologies():
         }), 400
 
     om = OntologyManager(current_app, session)
+
+    ontologies = om.list_full_ontologies()
+    onto_to_delete = [{"id": ontology.id, "dataset_id": ontology.dataset_id} for ontology in ontologies if ontology.id in data.get("ontologiesIdToDelete")]
+
     try:
-        om.remove_ontologies(data.get("ontologiesIdToDelete"))
-        ontologies = om.list_ontologies()
+        om.remove_ontologies(onto_to_delete)
+        ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
         return jsonify({
diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 2790b901..5f17043a 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -30,7 +30,7 @@ def autocomplete(short_ontology):
                 "results": []
             }), 404
 
-        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology)
+        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"])
 
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index 3c10ab57..bd81202f 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -416,7 +416,10 @@ def create_ontologies_table(self):
             name text NOT NULL,
             uri text NOT NULL,
             short_name text NOT NULL,
-            type text DEFAULT 'local'
+            type text DEFAULT 'local',
+            dataset_id INTEGER NOT NULL,
+            graph text NOT NULL,
+            FOREIGN KEY(dataset_id) REFERENCES datasets(id)
         )
         '''
         self.execute_sql_query(query)
diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index 4d31cbd4..7a7c7b81 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -229,3 +229,10 @@ def delete_from_db(self, admin=False):
         '''.format(where_query)
 
         database.execute_sql_query(query, query_params)
+
+        query = '''
+        DELETE FROM ontologies
+        WHERE dataset_id = ?
+        '''
+
+        database.execute_sql_query(query, (self.id,))
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 6ef9d095..f9e5ff4e 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -1,5 +1,9 @@
 import requests
 
+from collections import defaultdict
+from urllib.parse import quote
+
+
 from askomics.libaskomics.Database import Database
 from askomics.libaskomics.SparqlQuery import SparqlQuery
 from askomics.libaskomics.Params import Params
@@ -61,6 +65,39 @@ def list_ontologies(self):
 
         return ontologies
 
+    def list_full_ontologies(self):
+        """Get all ontologies for admin
+
+        Returns
+        -------
+        list
+            ontologies
+        """
+
+        database = Database(self.app, self.session)
+
+        query = '''
+        SELECT id, name, uri, short_name, type, dataset_id, graph
+        FROM ontologies
+        '''
+
+        rows = database.execute_sql_query(query)
+
+        ontologies = []
+        for row in rows:
+            prefix = {
+                'id': row[0],
+                'name': row[1],
+                'uri': row[2],
+                'short_name': row[3],
+                'type': row[4],
+                'dataset_id': row[5],
+                'graph': row[6]
+            }
+            ontologies.append(prefix)
+
+        return ontologies
+
     def get_ontology(self, short_name):
         """Get a specific ontology based on short name
 
@@ -73,7 +110,7 @@ def get_ontology(self, short_name):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, uri, short_name, type
+        SELECT id, name, uri, short_name, type, dataset_id, graph
         FROM ontologies
         WHERE short_name = ?
         '''
@@ -89,10 +126,12 @@ def get_ontology(self, short_name):
             'name': ontology[1],
             'uri': ontology[2],
             'short_name': ontology[3],
-            'type': ontology[4]
+            'type': ontology[4],
+            'dataset_id': ontology[5],
+            'graph': ontology[6]
         }
 
-    def add_ontology(self, name, uri, short_name, type="local"):
+    def add_ontology(self, name, uri, short_name, dataset_id, graph, type="local"):
         """Create a new ontology
 
         Returns
@@ -108,11 +147,21 @@ def add_ontology(self, name, uri, short_name, type="local"):
             ?,
             ?,
             ?,
+            ?,
+            ?,
             ?
         )
         '''
 
-        database.execute_sql_query(query, (name, uri, short_name, type,))
+        database.execute_sql_query(query, (name, uri, short_name, type, dataset_id, graph))
+
+        query = '''
+        UPDATE datasets SET
+        ontology=1
+        WHERE id=?
+        '''
+
+        database.execute_sql_query(query, (dataset_id,))
 
     def remove_ontologies(self, ontology_ids):
         """Remove ontologies
@@ -121,6 +170,19 @@ def remove_ontologies(self, ontology_ids):
         -------
         None
         """
+        # Make sure we only remove the 'ontology' tag to datasets without any ontologies
+        ontologies = self.list_full_ontologies()
+        datasets = defaultdict(set)
+        datasets_to_modify = set()
+        ontos_to_delete = [ontology['id'] for ontology in ontology_ids]
+
+        for onto in ontologies:
+            datasets[onto.dataset_id].add(onto.id)
+
+        for key, values in datasets.items():
+            if values.issubset(ontos_to_delete):
+                datasets_to_modify.add(key)
+
         database = Database(self.app, self.session)
 
         query = '''
@@ -128,10 +190,24 @@ def remove_ontologies(self, ontology_ids):
         WHERE id = ?
         '''
 
-        for ontology_id in ontology_ids:
-            database.execute_sql_query(query, (ontology_id,))
+        dataset_query = '''
+        UPDATE datasets SET
+        ontology=0
+        WHERE id=?
+        '''
+
+        for ontology in ontology_ids:
+            database.execute_sql_query(query, (ontology['id'],))
+            if ontology['dataset_id'] in datasets_to_modify:
+                database.execute_sql_query(dataset_query, (ontology['dataset_id'],))
+
+    def test_ols_ontology(self, shortname):
+        base_url = "https://www.ebi.ac.uk/ols/api/ontologies/" + quote(shortname.lower())
 
-    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name):
+        r = requests.get(base_url)
+        return r.status_code == 200
+
+    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name, onto_graph):
         """Search in ontology
 
         Returns
@@ -142,37 +218,13 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name)
         if ontology_type == "local":
             query = SparqlQuery(self.app, self.session, get_graphs=False)
             # TODO: Actually store the graph in the ontology to quicken search
-            query.set_graphs_and_endpoints(entities=[ontology_uri])
-            return query.autocomplete_local_ontology(ontology_uri, query_term, query.endpoints)
-        elif ontology_type == "ols":
-            base_url = "https://www.ebi.ac.uk/ols/api/search"
-            arguments = {
-                "q": query_term,
-                "ontology": onto_short_name,
-                "rows": 5,
-                "queryFields": "label",
-                "type": "class",
-                "fieldList": "label"
-            }
-
-            r = requests.get(base_url, params=arguments)
-
-            data = []
-
-            if not r.status_code == 200:
-                return data
-
-            res = r.json()
-            if res['response']['docs']:
-                data = [term['label'] for term in res['response']['docs']]
-
-            return data
-
+            query.set_graphs([onto_graph])
+            return query.autocomplete_local_ontology(ontology_uri, query_term)
         elif ontology_type == "ols":
             base_url = "https://www.ebi.ac.uk/ols/api/search"
             arguments = {
                 "q": query_term,
-                "ontology": onto_short_name,
+                "ontology": quote(onto_short_name.lower()),
                 "rows": 5,
                 "queryFields": "label",
                 "type": "class",
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 41565a1e..dd73b902 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -523,7 +523,7 @@ def get_uri_parameters(self, uri, endpoints):
 
         return formated_data
 
-    def autocomplete_local_ontology(self, uri, query, endpoints):
+    def autocomplete_local_ontology(self, uri, query):
         """Get results for a specific query
 
         Parameters
@@ -558,7 +558,7 @@ def autocomplete_local_ontology(self, uri, query, endpoints):
 
         sparql = self.format_query(raw_query, limit=5, replace_froms=True, federated=False)
 
-        query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=False, endpoints=endpoints)
+        query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=False)
         _, data = query_launcher.process_query(sparql)
 
         formated_data = []
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index 50632410..f2d6957b 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -21,10 +21,12 @@ export default class Ontologies extends Component {
       newontologyError: false,
       newontologyErrorMessage: '',
       ontologies: [],
+      datasets: [],
       name: "",
       uri: "",
       shortName: "",
       type: "local",
+      datasetId: "",
       ontologiesSelected: []
     }
     this.handleChangeValue = this.handleChangeValue.bind(this)
@@ -64,7 +66,8 @@ export default class Ontologies extends Component {
     return (
       this.state.name.length > 0 &&
       this.state.uri.length > 0 &&
-      this.state.shortName.length > 0
+      this.state.shortName.length > 0 &&
+      this.state.datasetId.length > 0
     )
   }
 
@@ -93,6 +96,16 @@ export default class Ontologies extends Component {
     }
   }
 
+  getDatasetName (datasetId) {
+    return this.state.datasets.map(dataset => {
+      if (dataset.id == datasetId) {
+        return dataset.name
+      } else {
+        return null
+      }
+    }).reduce(name=> name)
+  }
+
   handleAddOntology(event) {
 
     let requestUrl = "/api/admin/addontology"
@@ -100,7 +113,8 @@ export default class Ontologies extends Component {
       name: this.state.name,
       uri: this.state.uri,
       shortName: this.state.shortName,
-      type: this.state.type
+      type: this.state.type,
+      datasetId: this.state.datasetId
     }
 
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
@@ -131,6 +145,7 @@ export default class Ontologies extends Component {
   componentDidMount () {
     if (!this.props.waitForStart) {
       this.loadOntologies()
+      this.loadDatasets()
     }
   }
 
@@ -154,6 +169,22 @@ export default class Ontologies extends Component {
       })
   }
 
+  loadDatasets() {
+    let requestUrl = '/api/datasets'
+    axios.get(requestUrl, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
+      .then(response => {
+        this.setState({
+          datasets: response.data.datasets
+        })
+      })
+      .catch(error => {
+        console.log(error, error.response.data.errorMessage)
+        this.setState({
+          success: !error.response.data.error
+        })
+      })
+  }
+
   componentWillUnmount () {
     if (!this.props.waitForStart) {
       this.cancelRequest()
@@ -188,6 +219,12 @@ export default class Ontologies extends Component {
       dataField: 'uri',
       text: 'Uri',
       sort: true
+    }, {
+      editable: false,
+      dataField: 'dataset_id',
+      text: 'Dataset',
+      formatter: (cell, row) => { return this.getDatasetName(cell)},
+      sort: true
     }, {
       editable: false,
       dataField: 'type',
@@ -223,35 +260,49 @@ export default class Ontologies extends Component {
         <div>
         <Form onSubmit={this.handleAddOntology}>
           <Row form>
-            <Col md={3}>
+            <Col md={4}>
               <FormGroup>
                 <Label for="name">Ontology name</Label>
                 <Input type="text" name="name" id="name" placeholder="Ontology name" value={this.state.name} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>
-            <Col md={3}>
+            <Col md={4}>
               <FormGroup>
                 <Label for="shortName">Ontology short name</Label>
                 <Input type="text" name="shortName" id="shortName" placeholder="shortName" value={this.state.shortName} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>
-            <Col md={3}>
+            <Col md={4}>
               <FormGroup>
                 <Label for="uri">Ontology uri</Label>
                 <Input type="text" name="uri" id="uri" placeholder="uri" value={this.state.uri} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>
-            <Col md={3}>
-              <FormGroup>
-                <Label for="type">Autocomplete type</Label>
-                <CustomInput type="select" name="type" id="type" placeholder="type" value={this.state.type} onChange={this.handleChangeValue}>
-                  <option value="none" >none</option>
-                  <option value="local" >local</option>
-                  <option value="ols" >ols</option>
-                </CustomInput>
-              </FormGroup>
-            </Col>
           </Row>
+          <Row>
+          <Col md={6}>
+            <FormGroup>
+              <Label for="type">Linked public dataset</Label>
+              <CustomInput type="select" name="datasetId" id="datasetId" value={this.state.datasetId} onChange={this.handleChangeValue}>
+              {this.state.datasets.map(dataset => {
+                if (dataset.public == 1){
+                  return <option key={dataset.id} value={dataset.id}>{dataset.name}</option>
+                }
+              })}
+              </CustomInput>
+            </FormGroup>
+          </Col>
+          <Col md={6}>
+            <FormGroup>
+              <Label for="type">Autocomplete type</Label>
+              <CustomInput type="select" name="type" id="type" value={this.state.datasetId} onChange={this.handleChangeValue}>
+                <option value="none" >none</option>
+                <option value="local" >local</option>
+                <option value="ols" >ols</option>
+              </CustomInput>
+            </FormGroup>
+          </Col>
+          <Row>
           <Button disabled={!this.validateOntologyForm()}>Create</Button>
         </Form>
         <ErrorDiv status={this.state.newontologystatus} error={this.state.newontologyerror} errorMessage={this.state.newontologyerrorMessage} />
diff --git a/tests/conftest.py b/tests/conftest.py
index b3c94001..5782629e 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -583,8 +583,9 @@ def create_prefix(self):
 
     def create_ontology(self):
         """Create ontology"""
+        self.upload_and_integrate()
         om = OntologyManager(self.app, self.session)
-        om.add_ontology("Open Biological and Biomedical Ontology", "http://purl.obolibrary.org/obo/agro.owl", "OBO")
+        om.add_ontology("Open Biological and Biomedical Ontology", "http://purl.obolibrary.org/obo/agro.owl", "OBO", 1, "mygraph", "local")
 
     @staticmethod
     def get_random_string(number):
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 5b435d92..b845d7ba 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -612,7 +612,9 @@ def test_view_ontologies(self, client):
                 "name": "Open Biological and Biomedical Ontology",
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
                 "short_name": "OBO",
-                "type": "local"
+                "type": "local",
+                "dataset_id": 1,
+                "graph": "mygraph"
             }]
         }
 
@@ -624,7 +626,7 @@ def test_add_ontology(self, client):
         client.create_two_users()
         client.log_user("jsmith")
 
-        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local"}
+        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local", "datasetId": 1}
 
         response = client.client.post('/api/admin/addontology', json=data)
         assert response.status_code == 401
@@ -641,7 +643,9 @@ def test_add_ontology(self, client):
                 "name": "Open Biological and Biomedical Ontology",
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
                 "short_name": "OBO",
-                "type": "local"
+                "type": "local",
+                "dataset_id": 1,
+                "graph": "mygraph"
             }]
         }
 

From c10f149ce4c3d06a96f898782bc150c30fef0234 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 8 Dec 2021 10:12:12 +0100
Subject: [PATCH 048/113] Fix tests

---
 askomics/api/admin.py                         | 13 ++++--
 .../react/src/routes/admin/ontologies.jsx     | 46 +++++++++----------
 tests/test_api_admin.py                       |  2 +
 3 files changed, 35 insertions(+), 26 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 49a911c7..927d7a51 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -719,8 +719,15 @@ def add_ontology():
 
     datasets_info = [{'id': dataset_id}]
 
-    datasets_handler = DatasetsHandler(current_app, session, datasets_info=datasets_info)
-    datasets_handler.handle_datasets()
+    try:
+        datasets_handler = DatasetsHandler(current_app, session, datasets_info=datasets_info)
+        datasets_handler.handle_datasets()
+    except IndexError:
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "Dataset {} not found".format(dataset_id)
+        }), 400
 
     if not len(datasets_handler.datasets) == 1 or not datasets_handler.datasets[0]['public']:
         return jsonify({
@@ -781,7 +788,7 @@ def delete_ontologies():
     om = OntologyManager(current_app, session)
 
     ontologies = om.list_full_ontologies()
-    onto_to_delete = [{"id": ontology.id, "dataset_id": ontology.dataset_id} for ontology in ontologies if ontology.id in data.get("ontologiesIdToDelete")]
+    onto_to_delete = [{"id": ontology['id'], "dataset_id": ontology['dataset_id']} for ontology in ontologies if ontology['id'] in data.get("ontologiesIdToDelete")]
 
     try:
         om.remove_ontologies(onto_to_delete)
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index f2d6957b..0e11c642 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -280,29 +280,29 @@ export default class Ontologies extends Component {
             </Col>
           </Row>
           <Row>
-          <Col md={6}>
-            <FormGroup>
-              <Label for="type">Linked public dataset</Label>
-              <CustomInput type="select" name="datasetId" id="datasetId" value={this.state.datasetId} onChange={this.handleChangeValue}>
-              {this.state.datasets.map(dataset => {
-                if (dataset.public == 1){
-                  return <option key={dataset.id} value={dataset.id}>{dataset.name}</option>
-                }
-              })}
-              </CustomInput>
-            </FormGroup>
-          </Col>
-          <Col md={6}>
-            <FormGroup>
-              <Label for="type">Autocomplete type</Label>
-              <CustomInput type="select" name="type" id="type" value={this.state.datasetId} onChange={this.handleChangeValue}>
-                <option value="none" >none</option>
-                <option value="local" >local</option>
-                <option value="ols" >ols</option>
-              </CustomInput>
-            </FormGroup>
-          </Col>
-          <Row>
+            <Col md={6}>
+              <FormGroup>
+                <Label for="type">Linked public dataset</Label>
+                <CustomInput type="select" name="datasetId" id="datasetId" value={this.state.datasetId} onChange={this.handleChangeValue}>
+                {this.state.datasets.map(dataset => {
+                  if (dataset.public == 1){
+                    return <option key={dataset.id} value={dataset.id}>{dataset.name}</option>
+                  }
+                })}
+                </CustomInput>
+              </FormGroup>
+            </Col>
+            <Col md={6}>
+              <FormGroup>
+                <Label for="type">Autocomplete type</Label>
+                <CustomInput type="select" name="type" id="type" value={this.state.datasetId} onChange={this.handleChangeValue}>
+                  <option value="none" >none</option>
+                  <option value="local" >local</option>
+                  <option value="ols" >ols</option>
+                </CustomInput>
+              </FormGroup>
+            </Col>
+          </Row>
           <Button disabled={!this.validateOntologyForm()}>Create</Button>
         </Form>
         <ErrorDiv status={this.state.newontologystatus} error={this.state.newontologyerror} errorMessage={this.state.newontologyerrorMessage} />
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index b845d7ba..2f16bff8 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -628,6 +628,8 @@ def test_add_ontology(self, client):
 
         data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local", "datasetId": 1}
 
+        client.upload_and_integrate()
+
         response = client.client.post('/api/admin/addontology', json=data)
         assert response.status_code == 401
 

From a9831845b30bec14d08c8fb1c21891fbbd882bb7 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 8 Dec 2021 10:59:45 +0100
Subject: [PATCH 049/113] Fix tests 2

---
 askomics/libaskomics/OntologyManager.py | 2 +-
 tests/conftest.py                       | 7 +++++++
 tests/test_api_admin.py                 | 7 +++++++
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index f9e5ff4e..a5eea007 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -177,7 +177,7 @@ def remove_ontologies(self, ontology_ids):
         ontos_to_delete = [ontology['id'] for ontology in ontology_ids]
 
         for onto in ontologies:
-            datasets[onto.dataset_id].add(onto.id)
+            datasets[onto['dataset_id']].add(onto['id'])
 
         for key, values in datasets.items():
             if values.issubset(ontos_to_delete):
diff --git a/tests/conftest.py b/tests/conftest.py
index 5782629e..65c6f84d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -498,6 +498,13 @@ def create_result(self, has_form=False):
             "size": file_size
         }
 
+    def publicize_dataset(self, dataset_id, public=True):
+        """Publicize a result"""
+
+        dataset_info = {"id": dataset_id}
+        result = Dataset(self.app, self.session, dataset_info)
+        result.toggle_public(public)
+
     def publicize_result(self, result_id, public=True):
         """Publicize a result"""
 
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 2f16bff8..44a421d9 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -637,6 +637,13 @@ def test_add_ontology(self, client):
 
         response = client.client.post('/api/admin/addontology', json=data)
 
+        # Dataset is not public
+        assert response.status_code == 400
+        assert response.json['errorMessage'] == "Invalid dataset id"
+
+        self.publicize_dataset(1, True)
+        response = client.client.post('/api/admin/delete_ontologies', json=data)
+
         expected = {
             "error": False,
             "errorMessage": "",

From 090f2fe184b9d07c5ce5acdace316ecb5914a3f4 Mon Sep 17 00:00:00 2001
From: root <root@asko-test.novalocal>
Date: Wed, 8 Dec 2021 14:38:22 +0000
Subject: [PATCH 050/113] Fixes, updates & tests

---
 Pipfile                         |   2 +-
 Pipfile.lock                    | 610 ++++++++++++++++++++------------
 askomics/api/admin.py           |   4 +-
 askomics/libaskomics/Dataset.py |  37 +-
 tests/conftest.py               |  16 +-
 tests/test_api_admin.py         |  16 +-
 6 files changed, 425 insertions(+), 260 deletions(-)

diff --git a/Pipfile b/Pipfile
index cd5a56d0..6509b8eb 100644
--- a/Pipfile
+++ b/Pipfile
@@ -13,7 +13,7 @@ python-magic = "*"
 rdflib = "*"
 sparqlwrapper = "*"
 requests = "*"
-celery = "*"
+celery = "==5.0.5"
 redis = "*"
 watchdog = "*"
 gitpython = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 56c2411a..c1942d7c 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "d398feea9b583f305001058caf3d00d225702ce354469889db8ec34953b40471"
+            "sha256": "5d768dd0f5c397f0380f7a594b66aed5e23d923674edfa3c62b4e47f5ce3e81e"
         },
         "pipfile-spec": 6,
         "requires": {},
@@ -32,10 +32,10 @@
         },
         "bcbio-gff": {
             "hashes": [
-                "sha256:6e6f70639149612272a3b298a93ac50bba6f9ecece934f2a0ea86d4abde975da"
+                "sha256:34dfa970e14f4533dc63c0a5512b7b5221e4a06449e6aaa344162ed5fdd7a1de"
             ],
             "index": "pypi",
-            "version": "==0.6.7"
+            "version": "==0.6.9"
         },
         "billiard": {
             "hashes": [
@@ -96,13 +96,21 @@
             ],
             "version": "==2.49.0"
         },
+        "cached-property": {
+            "hashes": [
+                "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130",
+                "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"
+            ],
+            "markers": "python_version < '3.8'",
+            "version": "==1.5.2"
+        },
         "celery": {
             "hashes": [
-                "sha256:8d9a3de9162965e97f8e8cc584c67aad83b3f7a267584fa47701ed11c3e0d4b0",
-                "sha256:9dab2170b4038f7bf10ef2861dbf486ddf1d20592290a1040f7b7a1259705d42"
+                "sha256:5e8d364e058554e83bbb116e8377d90c79be254785f357cb2cec026e79febe13",
+                "sha256:f4efebe6f8629b0da2b8e529424de376494f5b7a743c321c8a2ddc2b1414921c"
             ],
             "index": "pypi",
-            "version": "==5.1.2"
+            "version": "==5.0.5"
         },
         "certifi": {
             "hashes": [
@@ -113,11 +121,11 @@
         },
         "charset-normalizer": {
             "hashes": [
-                "sha256:e019de665e2bcf9c2b64e2e5aa025fa991da8720daa3c1138cadd2fd1856aed0",
-                "sha256:f7af805c321bfa1ce6714c51f254e0d5bb5e5834039bc17db7ebe3a4cec9492b"
+                "sha256:1eecaa09422db5be9e29d7fc65664e6c33bd06f9ced7838578ba40d58bdf3721",
+                "sha256:b0b883e8e874edfdece9c28f314e3dd5badf067342e42fb162203335ae61aa2c"
             ],
             "markers": "python_version >= '3'",
-            "version": "==2.0.7"
+            "version": "==2.0.9"
         },
         "click": {
             "hashes": [
@@ -132,7 +140,7 @@
                 "sha256:a0713dc7a1de3f06bc0df5a9567ad19ead2d3d5689b434768a6145bff77c0667",
                 "sha256:f184f0d851d96b6d29297354ed981b7dd71df7ff500d82fa6d11f0856bee8035"
             ],
-            "markers": "python_version < '4' and python_full_version >= '3.6.2'",
+            "markers": "python_full_version >= '3.6.2' and python_full_version < '4.0.0'",
             "version": "==0.3.0"
         },
         "click-plugins": {
@@ -151,11 +159,11 @@
         },
         "configparser": {
             "hashes": [
-                "sha256:85d5de102cfe6d14a5172676f09d19c465ce63d6019cf0a4ef13385fc535e828",
-                "sha256:af59f2cdd7efbdd5d111c1976ecd0b82db9066653362f0962d7bf1d3ab89a1fa"
+                "sha256:1b35798fdf1713f1c3139016cfcbc461f09edbf099d1fb658d4b7479fcaa3daa",
+                "sha256:e8b39238fb6f0153a069aa253d349467c3c4737934f253ef6abac5fe0eca1e5d"
             ],
             "index": "pypi",
-            "version": "==5.0.2"
+            "version": "==5.2.0"
         },
         "deepdiff": {
             "hashes": [
@@ -165,6 +173,14 @@
             "index": "pypi",
             "version": "==5.6.0"
         },
+        "deprecated": {
+            "hashes": [
+                "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d",
+                "sha256:64756e3e14c8c5eea9795d93c524551432a0be75629f8f29e67ab8caf076c76d"
+            ],
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
+            "version": "==1.2.13"
+        },
         "flask": {
             "hashes": [
                 "sha256:0fbeb6180d383a9186d0d6ed954e0042ad9f18e0e8de088b2b419d526927d196",
@@ -183,11 +199,11 @@
         },
         "gitdb": {
             "hashes": [
-                "sha256:6c4cc71933456991da20917998acbe6cf4fb41eeaab7d6d67fbc05ecd4c865b0",
-                "sha256:96bf5c08b157a666fec41129e6d327235284cca4c81e92109260f353ba138005"
+                "sha256:8033ad4e853066ba6ca92050b9df2f89301b8fc8bf7e9324d412a63f8bf1a8fd",
+                "sha256:bac2fd45c0a1c9cf619e63a90d62bdc63892ef92387424b855792a6cabe789aa"
             ],
-            "markers": "python_version >= '3.4'",
-            "version": "==4.0.7"
+            "markers": "python_version >= '3.6'",
+            "version": "==4.0.9"
         },
         "gitpython": {
             "hashes": [
@@ -213,6 +229,14 @@
             "markers": "python_version >= '3'",
             "version": "==3.3"
         },
+        "importlib-metadata": {
+            "hashes": [
+                "sha256:53ccfd5c134223e497627b9815d5030edf77d2ed573922f7a0b8f8bb81a1c100",
+                "sha256:75bdec14c397f528724c1bfd9709d660b33a4d2e77387a3358f20b848bb5e5fb"
+            ],
+            "markers": "python_version < '3.8'",
+            "version": "==4.8.2"
+        },
         "isodate": {
             "hashes": [
                 "sha256:2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8",
@@ -238,17 +262,18 @@
         },
         "kombu": {
             "hashes": [
-                "sha256:01481d99f4606f6939cdc9b637264ed353ee9e3e4f62cfb582324142c41a572d",
-                "sha256:e2dedd8a86c9077c350555153825a31e456a0dc20c15d5751f00137ec9c75f0a"
+                "sha256:0f5d0763fb916808f617b886697b2be28e6bc35026f08e679697fc814b48a608",
+                "sha256:d36f0cde6a18d9eb7b6b3aa62a59bfdff7f5724689850e447eca5be8efc9d501"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==5.1.0"
+            "markers": "python_version >= '3.7'",
+            "version": "==5.2.2"
         },
         "markupsafe": {
             "hashes": [
                 "sha256:01a9b8ea66f1658938f65b93a85ebe8bc016e6769611be228d797c9d998dd298",
                 "sha256:023cb26ec21ece8dc3907c0e8320058b2e0cb3c55cf9564da612bc325bed5e64",
                 "sha256:0446679737af14f45767963a1a9ef7620189912317d095f2d9ffa183a4d25d2b",
+                "sha256:04635854b943835a6ea959e948d19dcd311762c5c0c6e1f0e16ee57022669194",
                 "sha256:0717a7390a68be14b8c793ba258e075c6f4ca819f15edfc2a3a027c823718567",
                 "sha256:0955295dd5eec6cb6cc2fe1698f4c6d84af2e92de33fbcac4111913cd100a6ff",
                 "sha256:0d4b31cc67ab36e3392bbf3862cfbadac3db12bdd8b02a2731f509ed5b829724",
@@ -256,6 +281,7 @@
                 "sha256:168cd0a3642de83558a5153c8bd34f175a9a6e7f6dc6384b9655d2697312a646",
                 "sha256:1d609f577dc6e1aa17d746f8bd3c31aa4d258f4070d61b2aa5c4166c1539de35",
                 "sha256:1f2ade76b9903f39aa442b4aadd2177decb66525062db244b35d71d0ee8599b6",
+                "sha256:20dca64a3ef2d6e4d5d615a3fd418ad3bde77a47ec8a23d984a12b5b4c74491a",
                 "sha256:2a7d351cbd8cfeb19ca00de495e224dea7e7d919659c2841bbb7f420ad03e2d6",
                 "sha256:2d7d807855b419fc2ed3e631034685db6079889a1f01d5d9dac950f764da3dad",
                 "sha256:2ef54abee730b502252bcdf31b10dacb0a416229b72c18b19e24a4509f273d26",
@@ -263,27 +289,36 @@
                 "sha256:37205cac2a79194e3750b0af2a5720d95f786a55ce7df90c3af697bfa100eaac",
                 "sha256:3c112550557578c26af18a1ccc9e090bfe03832ae994343cfdacd287db6a6ae7",
                 "sha256:3dd007d54ee88b46be476e293f48c85048603f5f516008bee124ddd891398ed6",
+                "sha256:4296f2b1ce8c86a6aea78613c34bb1a672ea0e3de9c6ba08a960efe0b0a09047",
                 "sha256:47ab1e7b91c098ab893b828deafa1203de86d0bc6ab587b160f78fe6c4011f75",
                 "sha256:49e3ceeabbfb9d66c3aef5af3a60cc43b85c33df25ce03d0031a608b0a8b2e3f",
+                "sha256:4dc8f9fb58f7364b63fd9f85013b780ef83c11857ae79f2feda41e270468dd9b",
                 "sha256:4efca8f86c54b22348a5467704e3fec767b2db12fc39c6d963168ab1d3fc9135",
                 "sha256:53edb4da6925ad13c07b6d26c2a852bd81e364f95301c66e930ab2aef5b5ddd8",
                 "sha256:5855f8438a7d1d458206a2466bf82b0f104a3724bf96a1c781ab731e4201731a",
                 "sha256:594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a",
+                "sha256:5b6d930f030f8ed98e3e6c98ffa0652bdb82601e7a016ec2ab5d7ff23baa78d1",
                 "sha256:5bb28c636d87e840583ee3adeb78172efc47c8b26127267f54a9c0ec251d41a9",
                 "sha256:60bf42e36abfaf9aff1f50f52644b336d4f0a3fd6d8a60ca0d054ac9f713a864",
                 "sha256:611d1ad9a4288cf3e3c16014564df047fe08410e628f89805e475368bd304914",
+                "sha256:6300b8454aa6930a24b9618fbb54b5a68135092bc666f7b06901f897fa5c2fee",
+                "sha256:63f3268ba69ace99cab4e3e3b5840b03340efed0948ab8f78d2fd87ee5442a4f",
                 "sha256:6557b31b5e2c9ddf0de32a691f2312a32f77cd7681d8af66c2692efdbef84c18",
                 "sha256:693ce3f9e70a6cf7d2fb9e6c9d8b204b6b39897a2c4a1aa65728d5ac97dcc1d8",
                 "sha256:6a7fae0dd14cf60ad5ff42baa2e95727c3d81ded453457771d02b7d2b3f9c0c2",
                 "sha256:6c4ca60fa24e85fe25b912b01e62cb969d69a23a5d5867682dd3e80b5b02581d",
                 "sha256:6fcf051089389abe060c9cd7caa212c707e58153afa2c649f00346ce6d260f1b",
                 "sha256:7d91275b0245b1da4d4cfa07e0faedd5b0812efc15b702576d103293e252af1b",
+                "sha256:89c687013cb1cd489a0f0ac24febe8c7a666e6e221b783e53ac50ebf68e45d86",
+                "sha256:8d206346619592c6200148b01a2142798c989edcb9c896f9ac9722a99d4e77e6",
                 "sha256:905fec760bd2fa1388bb5b489ee8ee5f7291d692638ea5f67982d968366bef9f",
                 "sha256:97383d78eb34da7e1fa37dd273c20ad4320929af65d156e35a5e2d89566d9dfb",
                 "sha256:984d76483eb32f1bcb536dc27e4ad56bba4baa70be32fa87152832cdd9db0833",
                 "sha256:99df47edb6bda1249d3e80fdabb1dab8c08ef3975f69aed437cb69d0a5de1e28",
+                "sha256:9f02365d4e99430a12647f09b6cc8bab61a6564363f313126f775eb4f6ef798e",
                 "sha256:a30e67a65b53ea0a5e62fe23682cfe22712e01f453b95233b25502f7c61cb415",
                 "sha256:ab3ef638ace319fa26553db0624c4699e31a28bb2a835c5faca8f8acf6a5a902",
+                "sha256:aca6377c0cb8a8253e493c6b451565ac77e98c2951c45f913e0b52facdcff83f",
                 "sha256:add36cb2dbb8b736611303cd3bfcee00afd96471b09cda130da3581cbdc56a6d",
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                 "sha256:b7f2d075102dc8c794cbde1947378051c4e5180d52d276987b8d28a3bd58c17d",
@@ -291,10 +326,14 @@
                 "sha256:be98f628055368795d818ebf93da628541e10b75b41c559fdf36d104c5787066",
                 "sha256:bf5d821ffabf0ef3533c39c518f3357b171a1651c1ff6827325e4489b0e46c3c",
                 "sha256:c47adbc92fc1bb2b3274c4b3a43ae0e4573d9fbff4f54cd484555edbf030baf1",
+                "sha256:cdfba22ea2f0029c9261a4bd07e830a8da012291fbe44dc794e488b6c9bb353a",
+                "sha256:d6c7ebd4e944c85e2c3421e612a7057a2f48d478d79e61800d81468a8d842207",
                 "sha256:d7f9850398e85aba693bb640262d3611788b1f29a79f0c93c565694658f4071f",
                 "sha256:d8446c54dc28c01e5a2dbac5a25f071f6653e6e40f3a8818e8b45d790fe6ef53",
+                "sha256:deb993cacb280823246a026e3b2d81c493c53de6acfd5e6bfe31ab3402bb37dd",
                 "sha256:e0f138900af21926a02425cf736db95be9f4af72ba1bb21453432a07f6082134",
                 "sha256:e9936f0b261d4df76ad22f8fee3ae83b60d7c3e871292cd42f40b81b70afae85",
+                "sha256:f0567c4dc99f264f49fe27da5f735f414c4e7e7dd850cfd8e69f0862d7c74ea9",
                 "sha256:f5653a225f31e113b152e56f154ccbe59eeb1c7487b39b9d9f9cdb58e6c79dc5",
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                 "sha256:f8ba0e8349a38d3001fae7eadded3f6606f0da5d748ee53cc1dab1d6527b9509",
@@ -306,39 +345,39 @@
         },
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             ],
             "markers": "python_version < '3.11' and python_version >= '3.7'",
-            "version": "==1.21.2"
+            "version": "==1.21.4"
         },
         "ordered-set": {
             "hashes": [
@@ -349,11 +388,11 @@
         },
         "prompt-toolkit": {
             "hashes": [
-                "sha256:6076e46efae19b1e0ca1ec003ed37a933dc94b4d20f486235d436e64771dcd5c",
-                "sha256:eb71d5a6b72ce6db177af4a7d4d7085b99756bf656d98ffcc4fecd36850eea6c"
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             ],
             "markers": "python_full_version >= '3.6.2'",
-            "version": "==3.0.20"
+            "version": "==3.0.23"
         },
         "pyasn1": {
             "hashes": [
@@ -400,30 +439,33 @@
         },
         "pyparsing": {
             "hashes": [
-                "sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1",
-                "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"
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             ],
-            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==2.4.7"
+            "markers": "python_version >= '3.6'",
+            "version": "==3.0.6"
         },
         "pysam": {
             "hashes": [
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             ],
             "index": "pypi",
-            "version": "==0.17.0"
+            "version": "==0.18.0"
         },
         "python-dateutil": {
             "hashes": [
@@ -435,10 +477,10 @@
         },
         "python-ldap": {
             "hashes": [
-                "sha256:4711cacf013e298754abd70058ccc995758177fb425f1c2d30e71adfc1d00aa5"
+                "sha256:60464c8fc25e71e0fd40449a24eae482dcd0fb7fcf823e7de627a6525b3e0d12"
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-            "version": "==3.3.1"
+            "version": "==3.4.0"
         },
         "python-magic": {
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@@ -457,38 +499,42 @@
         },
         "pyyaml": {
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@@ -500,11 +546,11 @@
         },
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-            "version": "==3.5.3"
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@@ -526,11 +572,19 @@
                 "flask"
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-            "version": "==1.4.3"
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@@ -542,11 +596,11 @@
         },
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-            "version": "==4.0.0"
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@@ -574,19 +628,18 @@
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         "validate-email": {
@@ -647,6 +700,71 @@
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             "version": "==0.16.1"
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@@ -667,11 +785,11 @@
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@@ -686,69 +804,64 @@
                 "toml"
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@@ -781,11 +894,11 @@
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@@ -815,6 +928,7 @@
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@@ -822,6 +936,7 @@
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@@ -829,27 +944,36 @@
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@@ -857,10 +981,14 @@
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@@ -895,11 +1023,11 @@
         },
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-                "sha256:c86254f9220d55e31cc94d69bade760f0847da8000def4dfe1c6b872fd14ff14"
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-            "version": "==21.0"
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@@ -911,11 +1039,11 @@
         },
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-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==1.10.0"
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
+            "version": "==1.11.0"
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         "pycodestyle": {
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@@ -935,11 +1063,11 @@
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-            "version": "==2.4.7"
+            "markers": "python_version >= '3.6'",
+            "version": "==3.0.6"
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         "pytest": {
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@@ -967,38 +1095,42 @@
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-                "sha256:74c1485f7707cf707a7aef42ef6322b8f97921bd89be2ab6317fd782c2d53183",
-                "sha256:895f61ef02e8fed38159bb70f7e100e00f471eae2bc838cd0f4ebb21e28f8541",
-                "sha256:8c1be557ee92a20f184922c7b6424e8ab6691788e6d86137c5d93c1a6ec1b8fb",
-                "sha256:bb4191dfc9306777bc594117aee052446b3fa88737cd13b7188d0e7aa8162185",
-                "sha256:bfb51918d4ff3d77c1c856a9699f8492c612cde32fd3bcd344af9be34999bfdc",
-                "sha256:c20cfa2d49991c8b4147af39859b167664f2ad4561704ee74c1de03318e898db",
-                "sha256:cb333c16912324fd5f769fff6bc5de372e9e7a202247b48870bc251ed40239aa",
-                "sha256:d2d9808ea7b4af864f35ea216be506ecec180628aced0704e34aca0b040ffe46",
-                "sha256:d483ad4e639292c90170eb6f7783ad19490e7a8defb3e46f97dfe4bacae89122",
-                "sha256:dd5de0646207f053eb0d6c74ae45ba98c3395a571a2891858e87df7c9b9bd51b",
-                "sha256:e1d4970ea66be07ae37a3c2e48b5ec63f7ba6804bdddfdbd3cfd954d25a82e63",
-                "sha256:e4fac90784481d221a8e4b1162afa7c47ed953be40d31ab4629ae917510051df",
-                "sha256:fa5ae20527d8e831e8230cbffd9f8fe952815b2b7dae6ffec25318803a7528fc",
-                "sha256:fd7f6999a8070df521b6384004ef42833b9bd62cfee11a09bda1079b4b704247",
-                "sha256:fdc842473cd33f45ff6bce46aea678a54e3d21f1b61a7750ce3c498eedfe25d6",
-                "sha256:fe69978f3f768926cfa37b867e3843918e012cf83f680806599ddce33c2c68b0"
-            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'",
-            "version": "==5.4.1"
+                "sha256:0283c35a6a9fbf047493e3a0ce8d79ef5030852c51e9d911a27badfde0605293",
+                "sha256:055d937d65826939cb044fc8c9b08889e8c743fdc6a32b33e2390f66013e449b",
+                "sha256:07751360502caac1c067a8132d150cf3d61339af5691fe9e87803040dbc5db57",
+                "sha256:0b4624f379dab24d3725ffde76559cff63d9ec94e1736b556dacdfebe5ab6d4b",
+                "sha256:0ce82d761c532fe4ec3f87fc45688bdd3a4c1dc5e0b4a19814b9009a29baefd4",
+                "sha256:1e4747bc279b4f613a09eb64bba2ba602d8a6664c6ce6396a4d0cd413a50ce07",
+                "sha256:213c60cd50106436cc818accf5baa1aba61c0189ff610f64f4a3e8c6726218ba",
+                "sha256:231710d57adfd809ef5d34183b8ed1eeae3f76459c18fb4a0b373ad56bedcdd9",
+                "sha256:277a0ef2981ca40581a47093e9e2d13b3f1fbbeffae064c1d21bfceba2030287",
+                "sha256:2cd5df3de48857ed0544b34e2d40e9fac445930039f3cfe4bcc592a1f836d513",
+                "sha256:40527857252b61eacd1d9af500c3337ba8deb8fc298940291486c465c8b46ec0",
+                "sha256:473f9edb243cb1935ab5a084eb238d842fb8f404ed2193a915d1784b5a6b5fc0",
+                "sha256:48c346915c114f5fdb3ead70312bd042a953a8ce5c7106d5bfb1a5254e47da92",
+                "sha256:50602afada6d6cbfad699b0c7bb50d5ccffa7e46a3d738092afddc1f9758427f",
+                "sha256:68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2",
+                "sha256:77f396e6ef4c73fdc33a9157446466f1cff553d979bd00ecb64385760c6babdc",
+                "sha256:819b3830a1543db06c4d4b865e70ded25be52a2e0631ccd2f6a47a2822f2fd7c",
+                "sha256:897b80890765f037df3403d22bab41627ca8811ae55e9a722fd0392850ec4d86",
+                "sha256:98c4d36e99714e55cfbaaee6dd5badbc9a1ec339ebfc3b1f52e293aee6bb71a4",
+                "sha256:9df7ed3b3d2e0ecfe09e14741b857df43adb5a3ddadc919a2d94fbdf78fea53c",
+                "sha256:9fa600030013c4de8165339db93d182b9431076eb98eb40ee068700c9c813e34",
+                "sha256:a80a78046a72361de73f8f395f1f1e49f956c6be882eed58505a15f3e430962b",
+                "sha256:b3d267842bf12586ba6c734f89d1f5b871df0273157918b0ccefa29deb05c21c",
+                "sha256:b5b9eccad747aabaaffbc6064800670f0c297e52c12754eb1d976c57e4f74dcb",
+                "sha256:c5687b8d43cf58545ade1fe3e055f70eac7a5a1a0bf42824308d868289a95737",
+                "sha256:cba8c411ef271aa037d7357a2bc8f9ee8b58b9965831d9e51baf703280dc73d3",
+                "sha256:d15a181d1ecd0d4270dc32edb46f7cb7733c7c508857278d3d378d14d606db2d",
+                "sha256:d4db7c7aef085872ef65a8fd7d6d09a14ae91f691dec3e87ee5ee0539d516f53",
+                "sha256:d4eccecf9adf6fbcc6861a38015c2a64f38b9d94838ac1810a9023a0609e1b78",
+                "sha256:d67d839ede4ed1b28a4e8909735fc992a923cdb84e618544973d7dfc71540803",
+                "sha256:daf496c58a8c52083df09b80c860005194014c3698698d1a57cbcfa182142a3a",
+                "sha256:e61ceaab6f49fb8bdfaa0f92c4b57bcfbea54c09277b1b4f7ac376bfb7a7c174",
+                "sha256:f84fbc98b019fef2ee9a1cb3ce93e3187a6df0b2538a651bfb890254ba9f90b5"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==6.0"
         },
         "pyyaml-env-tag": {
             "hashes": [
@@ -1029,14 +1161,30 @@
                 "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b",
                 "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"
             ],
+            "markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
             "version": "==0.10.2"
         },
+        "tomli": {
+            "hashes": [
+                "sha256:c6ce0015eb38820eaf32b5db832dbc26deb3dd427bd5f6556cf0acac2c214fee",
+                "sha256:f04066f68f5554911363063a30b108d2b5a5b1a010aa8b6132af78489fe3aade"
+            ],
+            "version": "==1.2.2"
+        },
+        "typing-extensions": {
+            "hashes": [
+                "sha256:4ca091dea149f945ec56afb48dae714f21e8692ef22a395223bcd328961b6a0e",
+                "sha256:7f001e5ac290a0c0401508864c7ec868be4e701886d5b573a9528ed3973d9d3b"
+            ],
+            "markers": "python_version < '3.10'",
+            "version": "==4.0.1"
+        },
         "urllib3": {
             "hashes": [
                 "sha256:4987c65554f7a2dbf30c18fd48778ef124af6fab771a377103da0585e2336ece",
                 "sha256:c4fdf4019605b6e5423637e01bc9fe4daef873709a7973e195ceba0a62bbc844"
             ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
+            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_full_version < '4.0.0'",
             "version": "==1.26.7"
         },
         "watchdog": {
diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 927d7a51..4bc4e799 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -729,7 +729,7 @@ def add_ontology():
             'errorMessage': "Dataset {} not found".format(dataset_id)
         }), 400
 
-    if not len(datasets_handler.datasets) == 1 or not datasets_handler.datasets[0]['public']:
+    if not len(datasets_handler.datasets) == 1 or not datasets_handler.datasets[0].public:
         return jsonify({
             'ontologies': [],
             'error': True,
@@ -746,7 +746,7 @@ def add_ontology():
         }), 400
 
     try:
-        om.add_ontology(name, uri, short_name, dataset['id'], dataset['graph_name'], type)
+        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, type)
         ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index 7a7c7b81..fe8691f4 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -74,10 +74,32 @@ def set_info_from_db(self, admin=False):
         self.start = rows[0][5]
         self.end = rows[0][6]
 
-    def save_in_db(self):
+    def save_in_db(self, set_graph=False):
         """Save the dataset into the database"""
         database = Database(self.app, self.session)
 
+        subquery = "NULL"
+        args = (
+            self.session["user"]["id"],
+            self.celery_id,
+            self.file_id,
+            self.name,
+            self.public,
+            0
+        )
+
+        if set_graph:
+            subquery = "?"
+            args = (
+              self.session["user"]["id"],
+              self.celery_id,
+              self.file_id,
+              self.name,
+              self.graph_name,
+              self.public,
+              0
+          )
+
         query = '''
         INSERT INTO datasets VALUES(
             NULL,
@@ -85,7 +107,7 @@ def save_in_db(self):
             ?,
             ?,
             ?,
-            NULL,
+            {},
             ?,
             "queued",
             strftime('%s', 'now'),
@@ -96,16 +118,9 @@ def save_in_db(self):
             NULL,
             0
         )
-        '''
+        '''.format(subquery)
 
-        self.id = database.execute_sql_query(query, (
-            self.session["user"]["id"],
-            self.celery_id,
-            self.file_id,
-            self.name,
-            self.public,
-            0
-        ), get_id=True)
+        self.id = database.execute_sql_query(query, args, get_id=True)
 
     def toggle_public(self, new_status, admin=False):
         """Change public status of a dataset (triplestore and db)
diff --git a/tests/conftest.py b/tests/conftest.py
index 65c6f84d..06a18da6 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -293,7 +293,7 @@ def upload_file_url(self, file_url):
         files.download_url(file_url, "1")
         return files.date
 
-    def integrate_file(self, info, public=False):
+    def integrate_file(self, info, public=False, set_graph=False):
         """Summary
 
         Parameters
@@ -320,7 +320,7 @@ def integrate_file(self, info, public=False):
             }
 
             dataset = Dataset(self.app, self.session, dataset_info)
-            dataset.save_in_db()
+            dataset.save_in_db(set_graph=set_graph)
 
             if file.type == "csv/tsv":
                 file.integrate(dataset.id, info["columns_type"], public=public)
@@ -371,7 +371,7 @@ def upload(self):
             }
         }
 
-    def upload_and_integrate(self):
+    def upload_and_integrate(self, set_graph=False):
         """Summary
 
         Returns
@@ -390,27 +390,27 @@ def upload_and_integrate(self):
         int_transcripts = self.integrate_file({
             "id": 1,
             "columns_type": ["start_entity", "label", "category", "text", "reference", "start", "end", "category", "strand", "text", "text", "date"]
-        })
+        }, set_graph=set_graph)
 
         int_de = self.integrate_file({
             "id": 2,
             "columns_type": ["start_entity", "directed", "numeric", "numeric", "numeric", "text", "numeric", "numeric", "numeric", "numeric"]
-        })
+        }, set_graph=set_graph)
 
         int_qtl = self.integrate_file({
             "id": 3,
             "columns_type": ["start_entity", "ref", "start", "end"]
-        })
+        }, set_graph=set_graph)
 
         int_gff = self.integrate_file({
             "id": 4,
             "entities": ["gene", "transcript"]
-        })
+        }, set_graph=set_graph)
 
         int_bed = self.integrate_file({
             "id": 5,
             "entity_name": "gene"
-        })
+        }, set_graph=set_graph)
 
         return {
             "transcripts": {
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 44a421d9..9df06cea 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -628,12 +628,11 @@ def test_add_ontology(self, client):
 
         data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local", "datasetId": 1}
 
-        client.upload_and_integrate()
-
         response = client.client.post('/api/admin/addontology', json=data)
         assert response.status_code == 401
 
         client.log_user("jdoe")
+        client.upload_and_integrate(set_graph=True)
 
         response = client.client.post('/api/admin/addontology', json=data)
 
@@ -641,8 +640,8 @@ def test_add_ontology(self, client):
         assert response.status_code == 400
         assert response.json['errorMessage'] == "Invalid dataset id"
 
-        self.publicize_dataset(1, True)
-        response = client.client.post('/api/admin/delete_ontologies', json=data)
+        client.publicize_dataset(1, True)
+        response = client.client.post('/api/admin/addontology', json=data)
 
         expected = {
             "error": False,
@@ -653,13 +652,16 @@ def test_add_ontology(self, client):
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
                 "short_name": "OBO",
                 "type": "local",
-                "dataset_id": 1,
-                "graph": "mygraph"
+                "dataset_id": 1
             }]
         }
 
+        # Graph name is random
+        res = response.json
+        res['ontologies'][0].pop('graph')
+
         assert response.status_code == 200
-        assert response.json == expected
+        assert res == expected
 
     def test_delete_ontologies(self, client):
         """test /api/admin/delete_ontologies route"""

From d7e286de56179397e3b68c6a7d6edfe90e576d62 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 8 Dec 2021 15:54:16 +0100
Subject: [PATCH 051/113] Final fix

---
 askomics/libaskomics/Dataset.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index fe8691f4..be00aadb 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -91,14 +91,14 @@ def save_in_db(self, set_graph=False):
         if set_graph:
             subquery = "?"
             args = (
-              self.session["user"]["id"],
-              self.celery_id,
-              self.file_id,
-              self.name,
-              self.graph_name,
-              self.public,
-              0
-          )
+                self.session["user"]["id"],
+                self.celery_id,
+                self.file_id,
+                self.name,
+                self.graph_name,
+                self.public,
+                0
+            )
 
         query = '''
         INSERT INTO datasets VALUES(

From d90d0c5b56445a648e089b5cc6c8ebe588c3884e Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 8 Dec 2021 16:29:21 +0000
Subject: [PATCH 052/113] Fix autocomplete display & ols

---
 askomics/api/ontology.py                       |  7 +++++++
 askomics/libaskomics/OntologyManager.py        | 15 ++++++---------
 askomics/react/src/components/autocomplete.jsx |  3 +--
 askomics/react/src/routes/admin/ontologies.jsx |  5 +++--
 askomics/react/src/routes/query/attribute.jsx  |  2 +-
 5 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 5f17043a..49d4bf85 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -30,6 +30,13 @@ def autocomplete(short_ontology):
                 "results": []
             }), 404
 
+        if ontology['type'] == "none":
+            return jsonify({
+                "error": True,
+                "errorMessage": "Ontology {} does not have autocompletion".format(short_ontology),
+                "results": []
+            }), 404
+
         results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"])
 
     except Exception as e:
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index a5eea007..65fcaeb5 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -1,7 +1,7 @@
 import requests
 
 from collections import defaultdict
-from urllib.parse import quote
+from urllib.parse import quote_plus
 
 
 from askomics.libaskomics.Database import Database
@@ -202,7 +202,7 @@ def remove_ontologies(self, ontology_ids):
                 database.execute_sql_query(dataset_query, (ontology['dataset_id'],))
 
     def test_ols_ontology(self, shortname):
-        base_url = "https://www.ebi.ac.uk/ols/api/ontologies/" + quote(shortname.lower())
+        base_url = "https://www.ebi.ac.uk/ols/api/ontologies/" + quote_plus(shortname.lower())
 
         r = requests.get(base_url)
         return r.status_code == 200
@@ -221,14 +221,11 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
             query.set_graphs([onto_graph])
             return query.autocomplete_local_ontology(ontology_uri, query_term)
         elif ontology_type == "ols":
-            base_url = "https://www.ebi.ac.uk/ols/api/search"
+            base_url = "https://www.ebi.ac.uk/ols/api/suggest"
             arguments = {
                 "q": query_term,
-                "ontology": quote(onto_short_name.lower()),
-                "rows": 5,
-                "queryFields": "label",
-                "type": "class",
-                "fieldList": "label"
+                "ontology": quote_plus(onto_short_name.lower()),
+                "rows": 5
             }
 
             r = requests.get(base_url, params=arguments)
@@ -240,6 +237,6 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
 
             res = r.json()
             if res['response']['docs']:
-                data = [term['label'] for term in res['response']['docs']]
+                data = [term['autosuggest'] for term in res['response']['docs']]
 
             return data
diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index d13f29e4..cd6724e0 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -57,11 +57,10 @@ export default class Autocomplete extends Component {
     this.autocompleteOntology(event.target.value)
   }
 
-
   renderAutocomplete () {
     
     let input = (<div>
-      <TextInput trigger="" matchAny={true} spacer="" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleOntoValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue}/>
+      <TextInput trigger="" matchAny={true} spacer="" regex="^[A-Za-z0-9\\-_ ]+$" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleOntoValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue}/>
     </div>)
 
     return input
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index 0e11c642..c225fee0 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -284,8 +284,9 @@ export default class Ontologies extends Component {
               <FormGroup>
                 <Label for="type">Linked public dataset</Label>
                 <CustomInput type="select" name="datasetId" id="datasetId" value={this.state.datasetId} onChange={this.handleChangeValue}>
+                  <option value=""></option>
                 {this.state.datasets.map(dataset => {
-                  if (dataset.public == 1){
+                  if (dataset.public == 1 && dataset.status == "success"){
                     return <option key={dataset.id} value={dataset.id}>{dataset.name}</option>
                   }
                 })}
@@ -295,7 +296,7 @@ export default class Ontologies extends Component {
             <Col md={6}>
               <FormGroup>
                 <Label for="type">Autocomplete type</Label>
-                <CustomInput type="select" name="type" id="type" value={this.state.datasetId} onChange={this.handleChangeValue}>
+                <CustomInput type="select" name="type" id="type" value={this.state.type} onChange={this.handleChangeValue}>
                   <option value="none" >none</option>
                   <option value="local" >local</option>
                   <option value="ols" >ols</option>
diff --git a/askomics/react/src/routes/query/attribute.jsx b/askomics/react/src/routes/query/attribute.jsx
index fab02271..866cac8d 100644
--- a/askomics/react/src/routes/query/attribute.jsx
+++ b/askomics/react/src/routes/query/attribute.jsx
@@ -143,7 +143,7 @@ export default class AttributeBox extends Component {
           <i className={eyeIcon} id={this.props.attribute.id} onClick={this.toggleVisibility} data-tip data-for={"visibleTooltip"}></i>
         </div>
       )
-      if (this.props.attribute.uri == "rdfs:label"){
+      if (this.isRegisteredOnto() && this.props.attribute.uri == "rdfs:label"){
         input = (
           <Autocomplete config={this.props.config} entityUri={this.props.entityUri} attributeId={this.props.attribute.id} filterValue={this.props.attribute.filterValue} handleFilterValue={p => this.handleFilterValue(p)}/>
         )

From 0f6ec8ad6e48862e625959bb8c0701d1e76cbb62 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 9 Dec 2021 13:00:12 +0000
Subject: [PATCH 053/113] Add timer to autocomplete

---
 askomics/react/src/components/autocomplete.jsx | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index cd6724e0..52fba74e 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -16,6 +16,8 @@ export default class Autocomplete extends Component {
     this.autocompleteOntology = this.autocompleteOntology.bind(this)
     this.cancelRequest
     this.handleOntoValue = this.handleOntoValue.bind(this)
+    this.WAIT_INTERVAL = 500
+    this.timerID
   }
 
   getAutoComplete () {
@@ -54,7 +56,10 @@ export default class Autocomplete extends Component {
 
   handleOntoValue (event) {
     this.handleFilterValue(event)
-    this.autocompleteOntology(event.target.value)
+    clearTimeout(this.timerID)
+    this.timerID = setTimeout(() => {
+        this.autocompleteOntology(event.target.value)
+    }, this.WAIT_INTERVAL)
   }
 
   renderAutocomplete () {

From 4fd0947af608f06d1da5a01dbacf9cfb28b3bb0c Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 9 Dec 2021 16:59:13 +0100
Subject: [PATCH 054/113] Restrict unpublicize for ontology-linked datasets

---
 askomics/api/admin.py                         |  6 ++++
 askomics/api/datasets.py                      |  6 ++++
 askomics/libaskomics/Dataset.py               |  4 ++-
 askomics/libaskomics/DatasetsHandler.py       | 10 ++++---
 .../react/src/routes/admin/datasetstable.jsx  |  2 +-
 .../src/routes/datasets/datasetstable.jsx     |  4 +--
 tests/test_api_admin.py                       | 15 ++++++----
 tests/test_api_datasets.py                    | 30 ++++++++++++-------
 8 files changed, 54 insertions(+), 23 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 4bc4e799..16fd7315 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -258,6 +258,12 @@ def toogle_public_dataset():
         datasets_handler.handle_datasets(admin=True)
 
         for dataset in datasets_handler.datasets:
+            if (not data.get("newStatus", False) and dataset.ontology):
+                return jsonify({
+                    'datasets': [],
+                    'error': True,
+                    'errorMessage': "Cannot unpublicize a dataset linked to an ontology"
+                }), 400
             current_app.logger.debug(data["newStatus"])
             dataset.toggle_public(data["newStatus"], admin=True)
 
diff --git a/askomics/api/datasets.py b/askomics/api/datasets.py
index bceb125e..7c39a01f 100644
--- a/askomics/api/datasets.py
+++ b/askomics/api/datasets.py
@@ -135,6 +135,12 @@ def toogle_public():
         datasets_handler.handle_datasets()
 
         for dataset in datasets_handler.datasets:
+            if (not data.get("newStatus", False) and dataset.ontology):
+                return jsonify({
+                    'datasets': [],
+                    'error': True,
+                    'errorMessage': "Cannot unpublicize a dataset linked to an ontology"
+                }), 400
             current_app.logger.debug(data.get("newStatus", False))
             dataset.toggle_public(data.get("newStatus", False))
 
diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index be00aadb..fa0b5e89 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -45,6 +45,7 @@ def __init__(self, app, session, dataset_info={}):
         self.public = dataset_info["public"] if "public" in dataset_info else False
         self.start = dataset_info["start"] if "start" in dataset_info else None
         self.end = dataset_info["end"] if "end" in dataset_info else None
+        self.ontology = dataset_info["ontology"] if "ontology" in dataset_info else False
 
     def set_info_from_db(self, admin=False):
         """Set the info in from the database"""
@@ -58,7 +59,7 @@ def set_info_from_db(self, admin=False):
             where_query = "AND user_id = ?"
 
         query = '''
-        SELECT celery_id, file_id, name, graph_name, public, start, end
+        SELECT celery_id, file_id, name, graph_name, public, start, end, ontology
         FROM datasets
         WHERE id = ?
         {}
@@ -73,6 +74,7 @@ def set_info_from_db(self, admin=False):
         self.public = rows[0][4]
         self.start = rows[0][5]
         self.end = rows[0][6]
+        self.ontology = rows[0][7]
 
     def save_in_db(self, set_graph=False):
         """Save the dataset into the database"""
diff --git a/askomics/libaskomics/DatasetsHandler.py b/askomics/libaskomics/DatasetsHandler.py
index 332dfc80..cdd1d172 100644
--- a/askomics/libaskomics/DatasetsHandler.py
+++ b/askomics/libaskomics/DatasetsHandler.py
@@ -51,7 +51,7 @@ def get_datasets(self):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, public, status, start, end, ntriples, error_message, traceback, percent
+        SELECT id, name, public, status, start, end, ntriples, error_message, traceback, percent, ontology
         FROM datasets
         WHERE user_id = ?
         '''
@@ -76,7 +76,8 @@ def get_datasets(self):
                 'ntriples': row[6],
                 'error_message': row[7],
                 'traceback': row[8],
-                'percent': row[9]
+                'percent': row[9],
+                'ontology': row[10]
             }
             datasets.append(dataset)
 
@@ -97,7 +98,7 @@ def get_all_datasets(self):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT datasets.id, datasets.name, datasets.public, datasets.status, datasets.start, datasets.end, datasets.ntriples, datasets.error_message, datasets.traceback, datasets.percent, users.username
+        SELECT datasets.id, datasets.name, datasets.public, datasets.status, datasets.start, datasets.end, datasets.ntriples, datasets.error_message, datasets.traceback, datasets.percent, users.username, datasets.ontology
         FROM datasets
         INNER JOIN users ON datasets.user_id=users.user_id
         '''
@@ -123,7 +124,8 @@ def get_all_datasets(self):
                 'error_message': row[7],
                 'traceback': row[8],
                 'percent': row[9],
-                'user': row[10]
+                'user': row[10],
+                'ontology': row[11]
             }
             datasets.append(dataset)
 
diff --git a/askomics/react/src/routes/admin/datasetstable.jsx b/askomics/react/src/routes/admin/datasetstable.jsx
index e961b6b4..dd199566 100644
--- a/askomics/react/src/routes/admin/datasetstable.jsx
+++ b/askomics/react/src/routes/admin/datasetstable.jsx
@@ -99,7 +99,7 @@ render () {
         return (
           <FormGroup>
             <div>
-              <CustomInput type="switch" id={"dataset-" + row.id} onChange={this.togglePublicDataset} checked={cell} value={cell} />
+              <CustomInput disabled={row.ontology == 0 ? false: true}type="switch" id={"dataset-" + row.id} onChange={this.togglePublicDataset} checked={cell} value={cell} />
             </div>
           </FormGroup>
         )
diff --git a/askomics/react/src/routes/datasets/datasetstable.jsx b/askomics/react/src/routes/datasets/datasetstable.jsx
index 23cec291..ae1f8723 100644
--- a/askomics/react/src/routes/datasets/datasetstable.jsx
+++ b/askomics/react/src/routes/datasets/datasetstable.jsx
@@ -118,7 +118,7 @@ export default class DatasetsTable extends Component {
         return (
           <FormGroup>
             <div>
-              <CustomInput disabled={this.props.config.user.admin ? false : true} type="switch" id={row.id} onChange={this.togglePublicDataset} checked={cell} value={cell} />
+              <CustomInput disabled={this.props.config.user.admin && row.ontology == 0 ? false : true} type="switch" id={row.id} onChange={this.togglePublicDataset} checked={cell} value={cell} />
             </div>
           </FormGroup>
         )
@@ -209,4 +209,4 @@ DatasetsTable.propTypes = {
   waiting: PropTypes.bool,
   datasets: PropTypes.object,
   config: PropTypes.object
-}
\ No newline at end of file
+}
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 9df06cea..a6d04125 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -139,7 +139,8 @@ def test_get_datasets(self, client):
                 'traceback': None,
                 'percent': 100.0,
                 'exec_time': info["transcripts"]["end"] - info["transcripts"]["start"],
-                'user': 'jsmith'
+                'user': 'jsmith',
+                'ontology': False
             }, {
                 'end': info["de"]["end"],
                 'error_message': '',
@@ -152,7 +153,8 @@ def test_get_datasets(self, client):
                 'traceback': None,
                 'percent': 100.0,
                 'exec_time': info["de"]["end"] - info["de"]["start"],
-                'user': 'jsmith'
+                'user': 'jsmith',
+                'ontology': False
             }, {
                 'end': info["qtl"]["end"],
                 'error_message': '',
@@ -165,7 +167,8 @@ def test_get_datasets(self, client):
                 'traceback': None,
                 'percent': 100.0,
                 'exec_time': info["qtl"]["end"] - info["qtl"]["start"],
-                'user': 'jsmith'
+                'user': 'jsmith',
+                'ontology': False
             }, {
                 'end': info["gff"]["end"],
                 'error_message': '',
@@ -178,7 +181,8 @@ def test_get_datasets(self, client):
                 'traceback': None,
                 'percent': 100.0,
                 'exec_time': info["gff"]["end"] - info["gff"]["start"],
-                'user': 'jsmith'
+                'user': 'jsmith',
+                'ontology': False
             }, {
                 'end': info["bed"]["end"],
                 'error_message': '',
@@ -191,7 +195,8 @@ def test_get_datasets(self, client):
                 'traceback': None,
                 'percent': 100.0,
                 'exec_time': info["bed"]["end"] - info["bed"]["start"],
-                'user': 'jsmith'
+                'user': 'jsmith',
+                'ontology': False
             }],
             'error': False,
             'errorMessage': ''
diff --git a/tests/test_api_datasets.py b/tests/test_api_datasets.py
index 3e35faed..ba5dba74 100644
--- a/tests/test_api_datasets.py
+++ b/tests/test_api_datasets.py
@@ -24,7 +24,8 @@ def test_get_datasets(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["transcripts"]["end"] - info["transcripts"]["start"]
+                'exec_time': info["transcripts"]["end"] - info["transcripts"]["start"],
+                'ontology': False
             }, {
                 'end': info["de"]["end"],
                 'error_message': '',
@@ -36,7 +37,8 @@ def test_get_datasets(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["de"]["end"] - info["de"]["start"]
+                'exec_time': info["de"]["end"] - info["de"]["start"],
+                'ontology': False
             }, {
                 'end': info["qtl"]["end"],
                 'error_message': '',
@@ -48,7 +50,8 @@ def test_get_datasets(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["qtl"]["end"] - info["qtl"]["start"]
+                'exec_time': info["qtl"]["end"] - info["qtl"]["start"],
+                'ontology': False
             }, {
                 'end': info["gff"]["end"],
                 'error_message': '',
@@ -60,7 +63,8 @@ def test_get_datasets(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["gff"]["end"] - info["gff"]["start"]
+                'exec_time': info["gff"]["end"] - info["gff"]["start"],
+                'ontology': False
             }, {
                 'end': info["bed"]["end"],
                 'error_message': '',
@@ -72,7 +76,8 @@ def test_get_datasets(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["bed"]["end"] - info["bed"]["start"]
+                'exec_time': info["bed"]["end"] - info["bed"]["start"],
+                'ontology': False
             }],
             'error': False,
             'errorMessage': ''
@@ -118,7 +123,8 @@ def test_toggle_public(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["transcripts"]["end"] - info["transcripts"]["start"]
+                'exec_time': info["transcripts"]["end"] - info["transcripts"]["start"],
+                'ontology': False
             }, {
                 'end': info["de"]["end"],
                 'error_message': '',
@@ -130,7 +136,8 @@ def test_toggle_public(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["de"]["end"] - info["de"]["start"]
+                'exec_time': info["de"]["end"] - info["de"]["start"],
+                'ontology': False
             }, {
                 'end': info["qtl"]["end"],
                 'error_message': '',
@@ -142,7 +149,8 @@ def test_toggle_public(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["qtl"]["end"] - info["qtl"]["start"]
+                'exec_time': info["qtl"]["end"] - info["qtl"]["start"],
+                'ontology': False
             }, {
                 'end': info["gff"]["end"],
                 'error_message': '',
@@ -154,7 +162,8 @@ def test_toggle_public(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["gff"]["end"] - info["gff"]["start"]
+                'exec_time': info["gff"]["end"] - info["gff"]["start"],
+                'ontology': False
             }, {
                 'end': info["bed"]["end"],
                 'error_message': '',
@@ -166,7 +175,8 @@ def test_toggle_public(self, client):
                 'status': 'success',
                 'traceback': None,
                 'percent': 100.0,
-                'exec_time': info["bed"]["end"] - info["bed"]["start"]
+                'exec_time': info["bed"]["end"] - info["bed"]["start"],
+                'ontology': False
             }],
             'error': False,
             'errorMessage': ''

From c591172702d5ee26a985d59c966c1e98dc556e0f Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 10 Dec 2021 10:31:48 +0100
Subject: [PATCH 055/113] Change return of listallontologies

---
 askomics/libaskomics/OntologyManager.py        |  6 ++++--
 askomics/react/src/routes/admin/ontologies.jsx | 13 +------------
 tests/test_api_admin.py                        |  4 +++-
 3 files changed, 8 insertions(+), 15 deletions(-)

diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 65fcaeb5..74b47c95 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -77,8 +77,9 @@ def list_full_ontologies(self):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, uri, short_name, type, dataset_id, graph
+        SELECT ontologies.id, ontologies.name, ontologies.uri, ontologies.short_name, ontologies.type, datasets.id, datasets.name, ontologies.graph
         FROM ontologies
+        INNER JOIN datasets ON datasets.id=ontologies.dataset_id
         '''
 
         rows = database.execute_sql_query(query)
@@ -92,7 +93,8 @@ def list_full_ontologies(self):
                 'short_name': row[3],
                 'type': row[4],
                 'dataset_id': row[5],
-                'graph': row[6]
+                'dataset_name': row[6],
+                'graph': row[7]
             }
             ontologies.append(prefix)
 
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index c225fee0..2832d974 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -96,16 +96,6 @@ export default class Ontologies extends Component {
     }
   }
 
-  getDatasetName (datasetId) {
-    return this.state.datasets.map(dataset => {
-      if (dataset.id == datasetId) {
-        return dataset.name
-      } else {
-        return null
-      }
-    }).reduce(name=> name)
-  }
-
   handleAddOntology(event) {
 
     let requestUrl = "/api/admin/addontology"
@@ -221,9 +211,8 @@ export default class Ontologies extends Component {
       sort: true
     }, {
       editable: false,
-      dataField: 'dataset_id',
+      dataField: 'dataset_name',
       text: 'Dataset',
-      formatter: (cell, row) => { return this.getDatasetName(cell)},
       sort: true
     }, {
       editable: false,
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index a6d04125..fae15f3a 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -619,6 +619,7 @@ def test_view_ontologies(self, client):
                 "short_name": "OBO",
                 "type": "local",
                 "dataset_id": 1,
+                "dataset_name": "transcripts.tsv",
                 "graph": "mygraph"
             }]
         }
@@ -657,7 +658,8 @@ def test_add_ontology(self, client):
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
                 "short_name": "OBO",
                 "type": "local",
-                "dataset_id": 1
+                "dataset_id": 1,
+                "dataset_name": "transcripts.tsv"
             }]
         }
 

From 1bbc724f0661ffc69bf5b9491458387da46edcd9 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 10 Dec 2021 09:57:07 +0000
Subject: [PATCH 056/113] Fix error div

---
 askomics/react/src/routes/admin/ontologies.jsx | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index 2832d974..afbfe9a9 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -109,10 +109,9 @@ export default class Ontologies extends Component {
 
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
     .then(response => {
-      console.log(requestUrl, response.data)
       this.setState({
         newontologyError: response.data.error,
-        newontologyErrorMessage: response.data.errorMessage,
+        newontologyErrorMessage: [response.data.errorMessage],
         ontologies: response.data.ontologies,
         newontologyStatus: response.status,
         name: "",
@@ -125,7 +124,7 @@ export default class Ontologies extends Component {
       console.log(error, error.response.data.errorMessage)
       this.setState({
         newontologyError: true,
-        newontologyErrorMessage: error.response.data.errorMessage,
+        newontologyErrorMessage: [error.response.data.errorMessage],
         newontologyStatus: error.response.status,
       })
     })
@@ -295,8 +294,8 @@ export default class Ontologies extends Component {
           </Row>
           <Button disabled={!this.validateOntologyForm()}>Create</Button>
         </Form>
-        <ErrorDiv status={this.state.newontologystatus} error={this.state.newontologyerror} errorMessage={this.state.newontologyerrorMessage} />
         <br />
+        <ErrorDiv status={this.state.newontologyStatus} error={this.state.newontologyError} errorMessage={this.state.newontologyErrorMessage} />
         </div>
         <hr />
         <div className="asko-table-height-div">

From 272efcdcfad9f555f584f54fe4a417f1274ada68 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 10 Dec 2021 13:41:07 +0100
Subject: [PATCH 057/113] Autocomplete for all ontologies?

---
 askomics/react/src/routes/query/query.jsx | 25 ++++++++++++++++-------
 1 file changed, 18 insertions(+), 7 deletions(-)

diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index b5d20391..2e8c0328 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -214,19 +214,30 @@ export default class Query extends Component {
     })
   }
 
-  isOntoRelation (currentUri, targetUri) {
-    if (! currentUri == targetUri){
+  isRemoteOnto (currentUri, targetUri) {
+
+    let node = this.state.abstraction.entities.find(entity => {
+      return entity.uri == currentUri
+    })
+
+    if (! node){
       return false
     }
-    return this.state.abstraction.entities.some(entity => {
-      return (entity.uri == currentUri && entity.ontology)
+
+    return node.ontology ? currentUri == targetUri ? "endNode" : "node" : false
+  }
+
+  isOntoNode (currentId) {
+
+    return this.graphState.nodes.some(node => {
+      return (node.id == currentId && node.ontology)
     })
   }
 
   isOntoEndNode (currentId) {
 
     return this.graphState.nodes.some(node => {
-      return (node.id == currentId && node.ontology)
+      return (node.id == currentId && node.ontology == "endNode")
     })
   }
 
@@ -505,7 +516,7 @@ export default class Query extends Component {
     }
 
     this.state.abstraction.relations.map(relation => {
-      let isOnto = this.isOntoRelation(relation.source, relation.target)
+      let isOnto = this.isRemoteOnto(relation.source, relation.target)
       if (relation.source == node.uri) {
         if (this.entityExist(relation.target)) {
           targetId = this.getId()
@@ -1527,7 +1538,7 @@ export default class Query extends Component {
     if (!this.state.waiting) {
       // attribute boxes (right view) only for node
       if (this.currentSelected) {
-        isOnto = this.isOntoEndNode(this.currentSelected.id)
+        isOnto = this.isOntoNode(this.currentSelected.id)
         AttributeBoxes = this.state.graphState.attr.map(attribute => {
           if (attribute.nodeId == this.currentSelected.id && this.currentSelected.type == "node") {
             return (

From d9b5071d15903287003846d0d2454fd64009aaae Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 10 Dec 2021 12:47:47 +0000
Subject: [PATCH 058/113] Fix autocomplete again

---
 askomics/react/src/routes/query/query.jsx | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 2e8c0328..25a580c5 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -217,13 +217,16 @@ export default class Query extends Component {
   isRemoteOnto (currentUri, targetUri) {
 
     let node = this.state.abstraction.entities.find(entity => {
-      return entity.uri == currentUri
+      return entity.uri == targetUri
     })
 
     if (! node){
       return false
     }
 
+    console.log(node)
+    console.log(node.ontology ? currentUri == targetUri ? "endNode" : "node" : false)
+
     return node.ontology ? currentUri == targetUri ? "endNode" : "node" : false
   }
 
@@ -546,12 +549,12 @@ export default class Query extends Component {
             // push suggested link
             this.graphState.links.push({
               uri: relation.uri,
-              type: isOnto ? "ontoLink" : "link",
+              type: isOnto == "endNode" ? "ontoLink" : "link",
               sameStrand: this.nodeHaveStrand(node.uri) && this.nodeHaveStrand(relation.target),
               sameRef: this.nodeHaveRef(node.uri) && this.nodeHaveRef(relation.target),
               strict: true,
               id: linkId,
-              label: isOnto ? this.getOntoLabel(relation.uri) : relation.label,
+              label: isOnto == "endNode" ? this.getOntoLabel(relation.uri) : relation.label,
               source: node.id,
               target: targetId,
               selected: false,

From c16ad557ee7bde96271006cac8728f4a690a1012 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 21 Feb 2022 17:27:02 +0100
Subject: [PATCH 059/113] Merge pull request #4 from askomics/dev_onto (#305)


From 8c7d1c9d5968d11065d02ea1502871a04794c8b2 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 10 May 2022 09:14:24 +0200
Subject: [PATCH 060/113] typo merge

---
 tests/test_api.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/tests/test_api.py b/tests/test_api.py
index 02412d8e..ea66cc70 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -43,11 +43,8 @@ def test_start(self, client):
             "proxyPath": "/",
             "user": {},
             "logged": False,
-<<<<<<< HEAD
-            "ontologies": []
-=======
+            "ontologies": [],
             "singleTenant": False
->>>>>>> dev
         }
         response = client.client.get('/api/start')
         assert response.status_code == 200

From 78b63335fe3f7918355f832cadb855729ea79b24 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 13 May 2022 16:29:44 +0200
Subject: [PATCH 061/113] Dev onto (#333)

Dev onto
---
 CHANGELOG.md                                  | 12 ++++-
 askomics/api/data.py                          |  2 +-
 askomics/api/datasets.py                      |  1 +
 askomics/api/file.py                          |  2 +-
 askomics/api/query.py                         | 13 +----
 askomics/api/results.py                       |  4 +-
 askomics/api/sparql.py                        |  6 +--
 askomics/api/start.py                         |  3 +-
 askomics/libaskomics/BedFile.py               | 18 +++++--
 askomics/libaskomics/CsvFile.py               | 22 +++++---
 askomics/libaskomics/FilesHandler.py          |  2 +-
 askomics/libaskomics/GffFile.py               | 19 ++++---
 askomics/libaskomics/RdfFile.py               |  8 ++-
 askomics/libaskomics/Result.py                | 29 ++++++++++-
 askomics/libaskomics/SparqlQuery.py           | 31 +++++++----
 askomics/libaskomics/TriplestoreExplorer.py   | 51 ++++++++++--------
 askomics/react/src/routes.jsx                 |  3 +-
 .../src/routes/integration/bedpreview.jsx     |  9 ++--
 .../react/src/routes/integration/csvtable.jsx |  9 ++--
 .../src/routes/integration/gffpreview.jsx     |  8 ++-
 .../src/routes/integration/rdfpreview.jsx     |  9 ++--
 askomics/tasks.py                             | 16 +++++-
 config/askomics.ini.template                  |  3 ++
 config/askomics.test.ini                      |  2 +
 docker/Dockerfile                             |  4 +-
 docker/DockerfileAll                          |  4 +-
 docker/DockerfileCelery                       |  4 +-
 docs/requirements.txt                         |  2 +-
 package-lock.json                             | 30 +++++------
 package.json                                  |  2 +-
 tests/results/abstraction.json                | 52 +++----------------
 tests/test_api.py                             |  3 +-
 32 files changed, 228 insertions(+), 155 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ef6d8420..8dd0e971 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,14 +23,19 @@ This changelog was started for release 4.2.0.
 - Remote upload is now sent in a Celery task
 - Added 'Status' for files (for celery upload, and later for better file management)
 - Added tooltips to buttons in the query form (and other forms)
+- Added owl integration
+- Add better error management for RDF files
+- Added 'single tenant' mode
 
 ### Changed
 
 - Changed "Query builder" to "Form editor" in form editing interface
 - Changed abstraction building method for relations. (Please refer to #248 and #268)
+- Changed abstraction building method for attributes. (Please refer to #321 and #324)
 - Changed abstraction building method for 'strand': only add the required strand type, and not all three types (#277)
 - Updated documentation
 - Changed the sparql endpoint: now use the authenticated SPARQL endpoint instead of public endpoint. Write permissions are not required anymore
+- Reverted base docker image to alpine-13 to solve a docker issue
 
 ### Removed
 
@@ -39,11 +44,16 @@ This changelog was started for release 4.2.0.
 
 ### Security
 
-- Bump prismjs from 1.23.0 to 1.25.0
 - Bump axios from 0.21.1 to 0.21.2
 - Bump tar from 6.1.0 to 6.1.11
 - Bump @npmcli/git from 2.0.6 to 2.1.0
 - Bump path-parse from 1.0.6 to 1.0.7
+- Bump prismjs from 1.23.0 to 1.27.0
+- Bump simple-get from 2.8.1 to 2.8.2
+- Bump ssri from 6.0.1 to 6.0.2
+- Bump follow-redirects from 1.14.4 to 1.14.8
+- Bump mkdocs from 1.0.4 to 1.2.3 in /docs
+- Bump python-ldap from 3.3.1 to 3.4.0
 
 ## [4.3.1] - 2021-06-16
 
diff --git a/askomics/api/data.py b/askomics/api/data.py
index 4710b18b..24a26cdd 100644
--- a/askomics/api/data.py
+++ b/askomics/api/data.py
@@ -25,7 +25,7 @@ def get_data(uri):
     """
 
     try:
-        query = SparqlQuery(current_app, session)
+        query = SparqlQuery(current_app, session, get_graphs=True)
         graphs, endpoints = query.get_graphs_and_endpoints(all_selected=True)
 
         endpoints = [val['uri'] for val in endpoints.values()]
diff --git a/askomics/api/datasets.py b/askomics/api/datasets.py
index 7c39a01f..665a0490 100644
--- a/askomics/api/datasets.py
+++ b/askomics/api/datasets.py
@@ -119,6 +119,7 @@ def toogle_public():
         error: True if error, else False
         errorMessage: the error message of error, else an empty string
     """
+
     data = request.get_json()
     if not (data and data.get("id")):
         return jsonify({
diff --git a/askomics/api/file.py b/askomics/api/file.py
index 6addb781..8ef6b4bf 100644
--- a/askomics/api/file.py
+++ b/askomics/api/file.py
@@ -340,7 +340,7 @@ def integrate():
                 "file_id": file.id,
                 "name": file.human_name,
                 "graph_name": file.file_graph,
-                "public": data.get("public") if session["user"]["admin"] else False
+                "public": (data.get("public", False) if session["user"]["admin"] else False) or current_app.iniconfig.getboolean("askomics", "single_tenant", fallback=False)
             }
 
             dataset = Dataset(current_app, session, dataset_info)
diff --git a/askomics/api/query.py b/askomics/api/query.py
index 1de59ddd..45dd8c6d 100644
--- a/askomics/api/query.py
+++ b/askomics/api/query.py
@@ -125,7 +125,7 @@ def get_preview():
                     'errorMessage': "Missing graphState parameter"
                 }), 400
 
-            query = SparqlQuery(current_app, session, data["graphState"], get_graphs=False)
+            query = SparqlQuery(current_app, session, data["graphState"])
             query.build_query_from_json(preview=True, for_editor=False)
 
             endpoints = query.endpoints
@@ -186,18 +186,9 @@ def save_result():
                 'errorMessage': "Missing graphState parameter"
             }), 400
 
-        query = SparqlQuery(current_app, session, data["graphState"], get_graphs=False)
-        query.build_query_from_json(preview=False, for_editor=False)
-        federated = query.is_federated()
-
         info = {
             "graph_state": data["graphState"],
-            "query": query.sparql,
-            "graphs": query.graphs,
-            "endpoints": query.endpoints,
-            "federated": federated,
-            "celery_id": None,
-            "selects": query.selects,
+            "celery_id": None
         }
 
         result = Result(current_app, session, info)
diff --git a/askomics/api/results.py b/askomics/api/results.py
index 97c394b3..c0092f32 100644
--- a/askomics/api/results.py
+++ b/askomics/api/results.py
@@ -164,7 +164,7 @@ def get_graph_and_sparql_query():
         graphs = result.graphs
         endpoints = result.endpoints
         # Get all graphs and endpoint, and mark as selected the used one
-        query = SparqlQuery(current_app, session)
+        query = SparqlQuery(current_app, session, get_graphs=True)
         graphs, endpoints = query.get_graphs_and_endpoints(selected_graphs=graphs, selected_endpoints=endpoints)
         console_enabled = can_access(session['user'])
 
@@ -361,7 +361,7 @@ def get_sparql_query():
                 'error': True,
                 'errorMessage': "You do not have access to this result"
             }), 401
-        query = SparqlQuery(current_app, session)
+        query = SparqlQuery(current_app, session, get_graphs=True)
 
         sparql = result.get_sparql_query()
 
diff --git a/askomics/api/sparql.py b/askomics/api/sparql.py
index 8a75fcb1..043897c8 100644
--- a/askomics/api/sparql.py
+++ b/askomics/api/sparql.py
@@ -32,7 +32,7 @@ def init():
         disk_space = files_utils.get_size_occupied_by_user() if "user" in session else None
 
         # Get graphs and endpoints
-        query = SparqlQuery(current_app, session)
+        query = SparqlQuery(current_app, session, get_graphs=True)
         graphs, endpoints = query.get_graphs_and_endpoints(all_selected=True)
 
         # Default query
@@ -116,7 +116,7 @@ def query():
         }), 400
 
     try:
-        query = SparqlQuery(current_app, session, get_graphs=False)
+        query = SparqlQuery(current_app, session)
 
         query.set_graphs_and_endpoints(graphs=graphs, endpoints=endpoints)
 
@@ -209,7 +209,7 @@ def save_query():
             }), 400
 
         # Is query federated?
-        query = SparqlQuery(current_app, session, get_graphs=False)
+        query = SparqlQuery(current_app, session)
         query.set_graphs_and_endpoints(graphs=graphs, endpoints=endpoints)
 
         federated = query.is_federated()
diff --git a/askomics/api/start.py b/askomics/api/start.py
index 15564c9e..93ae4578 100644
--- a/askomics/api/start.py
+++ b/askomics/api/start.py
@@ -84,7 +84,8 @@ def start():
             "proxyPath": proxy_path,
             "user": {},
             "logged": False,
-            "ontologies": ontologies
+            "ontologies": ontologies,
+            "singleTenant": current_app.iniconfig.getboolean('askomics', 'single_tenant', fallback=False)
         }
 
         json = {
diff --git a/askomics/libaskomics/BedFile.py b/askomics/libaskomics/BedFile.py
index 88440756..24ebf6da 100644
--- a/askomics/libaskomics/BedFile.py
+++ b/askomics/libaskomics/BedFile.py
@@ -94,13 +94,19 @@ def set_rdf_abstraction_domain_knowledge(self):
         self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(self.entity_name, remove_space=True)], rdflib.RDF.type, rdflib.OWL["Class"]))
         self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(self.entity_name, remove_space=True)], rdflib.RDFS.label, rdflib.Literal(self.entity_name)))
 
+        attribute_blanks = {}
+
         for attribute in self.attribute_abstraction:
+            blank = BNode()
+
             for attr_type in attribute["type"]:
-                self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDF.type, attr_type))
-            self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDFS.label, attribute["label"]))
-            self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDFS.domain, attribute["domain"]))
-            self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDFS.range, attribute["range"]))
+                self.graph_abstraction_dk.add((blank, rdflib.RDF.type, attr_type))
+            self.graph_abstraction_dk.add((blank, self.namespace_internal["uri"], attribute["uri"]))
+            self.graph_abstraction_dk.add((blank, rdflib.RDFS.label, attribute["label"]))
+            self.graph_abstraction_dk.add((blank, rdflib.RDFS.domain, attribute["domain"]))
+            self.graph_abstraction_dk.add((blank, rdflib.RDFS.range, attribute["range"]))
 
+            attribute_blanks[attribute["uri"]] = blank
             # Domain Knowledge
             if "values" in attribute.keys():
                 for value in attribute["values"]:
@@ -115,7 +121,9 @@ def set_rdf_abstraction_domain_knowledge(self):
         if self.faldo_entity:
             for key, value in self.faldo_abstraction.items():
                 if value:
-                    self.graph_abstraction_dk.add((value, rdflib.RDF.type, self.faldo_abstraction_eq[key]))
+                    blank = attribute_blanks[value]
+                    self.graph_abstraction_dk.add((blank, rdflib.RDF.type, self.faldo_abstraction_eq[key]))
+                    self.graph_abstraction_dk.add((blank, self.namespace_internal["uri"], value))
 
     def generate_rdf_content(self):
         """Generate RDF content of the BED file
diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
index 7356a5fe..1a86f7b9 100644
--- a/askomics/libaskomics/CsvFile.py
+++ b/askomics/libaskomics/CsvFile.py
@@ -400,6 +400,7 @@ def set_rdf_abstraction(self):
         available_ontologies = {}
         for ontology in OntologyManager(self.app, self.session).list_ontologies():
             available_ontologies[ontology['short_name']] = ontology['uri']
+        attribute_blanks = {}
 
         # Attributes and relations
         for index, attribute_name in enumerate(self.header):
@@ -414,6 +415,7 @@ def set_rdf_abstraction(self):
             if self.columns_type[index] == "label" and index == 1:
                 continue
 
+            blank = BNode()
             # Relation
             if self.columns_type[index] in ('general_relation', 'symetric_relation'):
                 symetric_relation = True if self.columns_type[index] == 'symetric_relation' else False
@@ -425,7 +427,7 @@ def set_rdf_abstraction(self):
                 rdf_type = rdflib.OWL.ObjectProperty
 
                 # New way of storing relations (starting from 4.4.0)
-                blank = BNode()
+
                 endpoint = rdflib.Literal(self.external_endpoint) if self.external_endpoint else rdflib.Literal(self.settings.get('triplestore', 'endpoint'))
                 self.graph_abstraction_dk.add((blank, rdflib.RDF.type, rdflib.OWL.ObjectProperty))
                 self.graph_abstraction_dk.add((blank, rdflib.RDF.type, self.namespace_internal["AskomicsRelation"]))
@@ -469,7 +471,7 @@ def set_rdf_abstraction(self):
                 label = rdflib.Literal(attribute_name)
                 rdf_range = self.namespace_data["{}Category".format(self.format_uri(attribute_name, remove_space=True))]
                 rdf_type = rdflib.OWL.ObjectProperty
-                self.graph_abstraction_dk.add((attribute, rdflib.RDF.type, self.namespace_internal["AskomicsCategory"]))
+                self.graph_abstraction_dk.add((blank, rdflib.RDF.type, self.namespace_internal["AskomicsCategory"]))
 
             # Numeric
             elif self.columns_type[index] in ('numeric', 'start', 'end'):
@@ -499,16 +501,22 @@ def set_rdf_abstraction(self):
                 rdf_range = rdflib.XSD.string
                 rdf_type = rdflib.OWL.DatatypeProperty
 
-            self.graph_abstraction_dk.add((attribute, rdflib.RDF.type, rdf_type))
-            self.graph_abstraction_dk.add((attribute, rdflib.RDFS.label, label))
-            self.graph_abstraction_dk.add((attribute, rdflib.RDFS.domain, entity))
-            self.graph_abstraction_dk.add((attribute, rdflib.RDFS.range, rdf_range))
+            attribute_blanks[attribute] = blank
+
+            # New way of storing attributes (starting from 4.4.0)
+            self.graph_abstraction_dk.add((blank, rdflib.RDF.type, rdf_type))
+            self.graph_abstraction_dk.add((blank, self.namespace_internal["uri"], attribute))
+            self.graph_abstraction_dk.add((blank, rdflib.RDFS.label, label))
+            self.graph_abstraction_dk.add((blank, rdflib.RDFS.domain, entity))
+            self.graph_abstraction_dk.add((blank, rdflib.RDFS.range, rdf_range))
 
         # Faldo:
         if self.faldo_entity:
             for key, value in self.faldo_abstraction.items():
                 if value:
-                    self.graph_abstraction_dk.add((value, rdflib.RDF.type, self.faldo_abstraction_eq[key]))
+                    blank = attribute_blanks[value]
+                    self.graph_abstraction_dk.add((blank, rdflib.RDF.type, self.faldo_abstraction_eq[key]))
+                    self.graph_abstraction_dk.add((blank, self.namespace_internal["uri"], value))
 
     def generate_rdf_content(self):
         """Generator of the rdf content
diff --git a/askomics/libaskomics/FilesHandler.py b/askomics/libaskomics/FilesHandler.py
index ae5e8bb8..d3d1adfe 100644
--- a/askomics/libaskomics/FilesHandler.py
+++ b/askomics/libaskomics/FilesHandler.py
@@ -247,7 +247,7 @@ def store_file_info_in_db(self, name, filetype, file_name, size, status="availab
             filetype = 'csv/tsv'
         elif filetype in ('text/turtle', 'ttl'):
             filetype = 'rdf/ttl'
-        elif filetype == "text/xml":
+        elif filetype in ["text/xml", "application/rdf+xml"]:
             filetype = "rdf/xml"
         elif filetype == "application/n-triples":
             filetype = "rdf/nt"
diff --git a/askomics/libaskomics/GffFile.py b/askomics/libaskomics/GffFile.py
index d807f6b0..28341bab 100644
--- a/askomics/libaskomics/GffFile.py
+++ b/askomics/libaskomics/GffFile.py
@@ -108,10 +108,12 @@ def set_rdf_abstraction_domain_knowledge(self):
             self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(entity, remove_space=True)], rdflib.RDF.type, rdflib.OWL["Class"]))
             self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(entity, remove_space=True)], rdflib.RDFS.label, rdflib.Literal(entity)))
 
+        attribute_blanks = {}
+
         for attribute in self.attribute_abstraction:
+            blank = BNode()
             # New way of storing relations (starting from 4.4.0)
             if attribute.get("relation"):
-                blank = BNode()
                 endpoint = rdflib.Literal(self.external_endpoint) if self.external_endpoint else rdflib.Literal(self.settings.get('triplestore', 'endpoint'))
                 for attr_type in attribute["type"]:
                     self.graph_abstraction_dk.add((blank, rdflib.RDF.type, attr_type))
@@ -123,12 +125,15 @@ def set_rdf_abstraction_domain_knowledge(self):
                 self.graph_abstraction_dk.add((blank, rdflib.DCAT.dataset, rdflib.Literal(self.name)))
 
             else:
+                # New way of storing attributes (starting from 4.4.0)
                 for attr_type in attribute["type"]:
-                    self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDF.type, attr_type))
-                self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDFS.label, attribute["label"]))
-                self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDFS.domain, attribute["domain"]))
-                self.graph_abstraction_dk.add((attribute["uri"], rdflib.RDFS.range, attribute["range"]))
+                    self.graph_abstraction_dk.add((blank, rdflib.RDF.type, attr_type))
+                self.graph_abstraction_dk.add((blank, self.namespace_internal["uri"], attribute["uri"]))
+                self.graph_abstraction_dk.add((blank, rdflib.RDFS.label, attribute["label"]))
+                self.graph_abstraction_dk.add((blank, rdflib.RDFS.domain, attribute["domain"]))
+                self.graph_abstraction_dk.add((blank, rdflib.RDFS.range, attribute["range"]))
 
+            attribute_blanks[attribute["uri"]] = blank
             # Domain Knowledge
             if "values" in attribute.keys():
                 for value in attribute["values"]:
@@ -143,7 +148,9 @@ def set_rdf_abstraction_domain_knowledge(self):
         if self.faldo_entity:
             for key, value in self.faldo_abstraction.items():
                 if value:
-                    self.graph_abstraction_dk.add((value, rdflib.RDF.type, self.faldo_abstraction_eq[key]))
+                    blank = attribute_blanks[value]
+                    self.graph_abstraction_dk.add((blank, rdflib.RDF.type, self.faldo_abstraction_eq[key]))
+                    self.graph_abstraction_dk.add((blank, self.namespace_internal["uri"], value))
 
     def format_gff_entity(self, entity):
         """Format a gff entity name by removing type (type:entity --> entity)
diff --git a/askomics/libaskomics/RdfFile.py b/askomics/libaskomics/RdfFile.py
index 0954d91f..b1252d01 100644
--- a/askomics/libaskomics/RdfFile.py
+++ b/askomics/libaskomics/RdfFile.py
@@ -69,6 +69,12 @@ def get_preview(self):
             for x in range(1, 100):
                 head += ttl_file.readline()
 
+        location = None
+        try:
+            location = self.get_location()
+        except Exception as e:
+            self.error_message = str(e)
+
         return {
             'type': self.type,
             'id': self.id,
@@ -77,7 +83,7 @@ def get_preview(self):
             'error_message': self.error_message,
             'data': {
                 'preview': head,
-                'location': self.get_location()
+                'location': location
             }
         }
 
diff --git a/askomics/libaskomics/Result.py b/askomics/libaskomics/Result.py
index 07e74ca5..d48f7725 100644
--- a/askomics/libaskomics/Result.py
+++ b/askomics/libaskomics/Result.py
@@ -389,6 +389,33 @@ def save_in_db(self):
 
         return self.id
 
+    def populate_db(self, graphs, endpoints):
+        """Update status of results in db
+
+        Parameters
+        ----------
+        query : bool, optional
+            True if error during integration
+        error_message : bool, optional
+            Error string if error is True
+        """
+
+        database = Database(self.app, self.session)
+
+        query = '''
+        UPDATE results SET
+        graphs_and_endpoints=?
+        WHERE user_id=? AND id=?
+        '''
+
+        variables = [
+            json.dumps({"graphs": graphs, "endpoints": endpoints}),
+            self.session["user"]["id"],
+            self.id
+        ]
+
+        database.execute_sql_query(query, tuple(variables))
+
     def update_public_status(self, public):
         """Change public status
 
@@ -471,7 +498,7 @@ def update_db_status(self, status, size=None, update_celery=False, update_date=F
 
     def rollback(self):
         """Delete file"""
-        self.delete_file_from_filesystem(self)
+        self.delete_file_from_filesystem()
 
     def delete_result(self):
         """Remove results from db and filesystem"""
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index dd73b902..2369feb5 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -18,7 +18,7 @@ class SparqlQuery(Params):
         all public graph
     """
 
-    def __init__(self, app, session, json_query=None, get_graphs=True):
+    def __init__(self, app, session, json_query=None, get_graphs=False):
         """init
 
         Parameters
@@ -400,12 +400,10 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None):
         entities : list, optional
             list of entity uri
         """
-        substrlst = []
         filter_entity_string = ''
         if entities:
-            for entity in entities:
-                substrlst.append("?entity_uri = <{}>".format(entity))
-            filter_entity_string = 'FILTER (' + ' || '.join(substrlst) + ')'
+            substr = ",".join(["<{}>".format(entity) for entity in entities])
+            filter_entity_string = 'FILTER (?entity_uri IN( ' + substr + ' ))'
 
         filter_public_string = 'FILTER (?public = <true>)'
         if 'user' in self.session:
@@ -465,7 +463,7 @@ def get_uri_parameters(self, uri, endpoints):
             The corresponding parameters
         """
         raw_query = '''
-        SELECT DISTINCT ?predicate ?object ?faldo_value ?faldo_uri
+        SELECT DISTINCT ?predicate ?object ?faldo_value ?faldo_relation
         WHERE {{
           ?URI ?predicate ?object .
           ?URI a ?entitytype .
@@ -498,9 +496,14 @@ def get_uri_parameters(self, uri, endpoints):
             ?faldo_uri rdf:type askomics:faldoStrand .
             }}
 
+            OPTIONAL {{
+              ?faldo_uri askomics:uri ?node_uri
+            }}
+
             VALUES ?predicate {{faldo:location}}
           }}
           VALUES ?URI {{{}}}
+          BIND(IF(isBlank(?faldo_uri), ?node_uri ,?faldo_uri) as ?faldo_relation)
         }}
         '''.format(uri)
 
@@ -516,9 +519,19 @@ def get_uri_parameters(self, uri, endpoints):
 
         formated_data = []
         for row in data:
+
+            predicate = row['predicate']
+            object = row['object']
+
+            if row.get('faldo_relation'):
+                predicate = row.get("faldo_relation")
+
+            if row.get('faldo_value'):
+                object = row.get('faldo_value')
+
             formated_data.append({
-                'predicate': row['faldo_uri'] if row.get('faldo_uri') else row['predicate'],
-                'object': row['faldo_value'] if row.get('faldo_value') else row['object'],
+                'predicate': predicate,
+                'object': object,
             })
 
         return formated_data
@@ -1435,7 +1448,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
                     ))
                     var_to_replace.append((category_value_uri, var_2))
 
-        from_string = self.get_froms_from_graphs(self.graphs)
+        from_string = "" if self.settings.getboolean("askomics", "single_tenant", fallback=False) else self.get_froms_from_graphs(self.graphs)
         federated_from_string = self.get_federated_froms_from_graphs(self.graphs)
         endpoints_string = self.get_endpoints_string()
 
diff --git a/askomics/libaskomics/TriplestoreExplorer.py b/askomics/libaskomics/TriplestoreExplorer.py
index b941a88e..492ee4ad 100644
--- a/askomics/libaskomics/TriplestoreExplorer.py
+++ b/askomics/libaskomics/TriplestoreExplorer.py
@@ -208,12 +208,14 @@ def get_abstraction(self):
         """
         insert, abstraction = self.get_cached_asbtraction()
 
+        single_tenant = self.settings.getboolean("askomics", "single_tenant", fallback=False)
+
         # No abstraction entry in database, create it
         if not abstraction:
             abstraction = {
-                "entities": self.get_abstraction_entities(),
-                "attributes": self.get_abstraction_attributes(),
-                "relations": self.get_abstraction_relations()
+                "entities": self.get_abstraction_entities(single_tenant),
+                "attributes": self.get_abstraction_attributes(single_tenant),
+                "relations": self.get_abstraction_relations(single_tenant)
             }
 
             # Cache abstraction in DB, only for logged users
@@ -305,7 +307,7 @@ def uncache_abstraction(self, public=True, force=False):
 
             database.execute_sql_query(query, sql_var)
 
-    def get_abstraction_entities(self):
+    def get_abstraction_entities(self, single_tenant=False):
         """Get abstraction entities
 
         Returns
@@ -379,7 +381,7 @@ def get_abstraction_entities(self):
 
         return entities
 
-    def get_abstraction_attributes(self):
+    def get_abstraction_attributes(self, single_tenant=False):
         """Get user abstraction attributes from the triplestore
 
         Returns
@@ -408,13 +410,16 @@ def get_abstraction_attributes(self):
             ?graph askomics:public ?public .
             ?graph dc:creator ?creator .
             GRAPH ?graph {{
-                ?attribute_uri a ?attribute_type .
+                ?node a ?attribute_type .
                 VALUES ?attribute_type {{ owl:DatatypeProperty askomics:AskomicsCategory }}
-                ?attribute_uri rdfs:label ?attribute_label .
-                ?attribute_uri rdfs:range ?attribute_range .
+                ?node rdfs:label ?attribute_label .
+                ?node rdfs:range ?attribute_range .
+                # Retrocompatibility
+                OPTIONAL {{?node askomics:uri ?attribute_uri}}
+                BIND( IF(isBlank(?node),?attribute_uri, ?node) as ?attribute_uri )
                 # Faldo
                 OPTIONAL {{
-                    ?attribute_uri a ?attribute_faldo .
+                    ?node a ?attribute_faldo .
                     VALUES ?attribute_faldo {{ askomics:faldoStart askomics:faldoEnd askomics:faldoStrand askomics:faldoReference }}
                 }}
                 # Categories (DK)
@@ -425,10 +430,10 @@ def get_abstraction_attributes(self):
             }}
             # Attribute of entity (or motherclass of entity)
             {{
-                ?attribute_uri rdfs:domain ?mother .
+                ?node rdfs:domain ?mother .
                 ?entity_uri rdfs:subClassOf ?mother .
             }} UNION {{
-                ?attribute_uri rdfs:domain ?entity_uri .
+                ?node rdfs:domain ?entity_uri .
             }}
             FILTER (
                 ?public = <true>{}
@@ -442,13 +447,13 @@ def get_abstraction_attributes(self):
         attributes = []
 
         for result in data:
-            # Attributes
-            if "attribute_uri" in result and "attribute_label" in result and result["attribute_type"] != "{}AskomicsCategory".format(self.settings.get("triplestore", "namespace_internal")) and result["attribute_range"] in litterals:
-                attr_tpl = (result["attribute_uri"], result["entity_uri"])
+            attribute_uri = result.get("attribute_uri")
+            if attribute_uri and "attribute_label" in result and result["attribute_type"] != "{}AskomicsCategory".format(self.settings.get("triplestore", "namespace_internal")) and result["attribute_range"] in litterals:
+                attr_tpl = (attribute_uri, result["entity_uri"])
                 if attr_tpl not in attributes_list:
                     attributes_list.append(attr_tpl)
                     attribute = {
-                        "uri": result["attribute_uri"],
+                        "uri": attribute_uri,
                         "label": result["attribute_label"],
                         "graphs": [result["graph"], ],
                         "entityUri": result["entity_uri"],
@@ -466,12 +471,12 @@ def get_abstraction_attributes(self):
                 index_attribute = attributes_list.index(attr_tpl)
 
             # Categories
-            if "attribute_uri" in result and result["attribute_type"] == "{}AskomicsCategory".format(self.settings.get("triplestore", "namespace_internal")) and "category_value_uri" in result:
-                attr_tpl = (result["attribute_uri"], result["entity_uri"])
+            if attribute_uri and result["attribute_type"] == "{}AskomicsCategory".format(self.settings.get("triplestore", "namespace_internal")) and "category_value_uri" in result:
+                attr_tpl = (attribute_uri, result["entity_uri"])
                 if attr_tpl not in attributes_list:
                     attributes_list.append(attr_tpl)
                     attribute = {
-                        "uri": result["attribute_uri"],
+                        "uri": attribute_uri,
                         "label": result["attribute_label"],
                         "graphs": [result["graph"], ],
                         "entityUri": result["entity_uri"],
@@ -498,7 +503,7 @@ def get_abstraction_attributes(self):
 
         return attributes
 
-    def get_abstraction_relations(self):
+    def get_abstraction_relations(self, single_tenant=False):
         """Get user abstraction relations from the triplestore
 
         Returns
@@ -514,7 +519,7 @@ def get_abstraction_relations(self):
         query_builder = SparqlQuery(self.app, self.session)
 
         query = '''
-        SELECT DISTINCT ?graph ?entity_uri ?entity_faldo ?entity_label ?node ?node_type ?attribute_uri ?attribute_faldo ?attribute_label ?attribute_range ?property_uri ?property_faldo ?property_label ?range_uri ?category_value_uri ?category_value_label
+        SELECT DISTINCT ?graph ?entity_uri ?entity_faldo ?entity_label ?attribute_uri ?attribute_faldo ?attribute_label ?attribute_range ?property_uri ?property_faldo ?property_label ?range_uri ?category_value_uri ?category_value_label
         WHERE {{
             # Graphs
             ?graph askomics:public ?public .
@@ -527,6 +532,7 @@ def get_abstraction_relations(self):
                 ?node rdfs:range ?range_uri .
                 # Retrocompatibility
                 OPTIONAL {{?node askomics:uri ?property_uri}}
+                BIND( IF(isBlank(?node), ?property_uri, ?node) as ?property_uri)
             }}
             # Relation of entity (or motherclass of entity)
             {{
@@ -547,9 +553,8 @@ def get_abstraction_relations(self):
         relations = []
         for result in data:
             # Relation
-            if "node" in result:
-                # Retrocompatibility
-                property_uri = result.get("property_uri", result["node"])
+            if "property_uri" in result:
+                property_uri = result.get("property_uri")
                 rel_tpl = (property_uri, result["entity_uri"], result["range_uri"])
                 if rel_tpl not in relations_list:
                     relations_list.append(rel_tpl)
diff --git a/askomics/react/src/routes.jsx b/askomics/react/src/routes.jsx
index 6b910055..f0b7356b 100644
--- a/askomics/react/src/routes.jsx
+++ b/askomics/react/src/routes.jsx
@@ -47,7 +47,8 @@ export default class Routes extends Component {
         disableIntegration: null,
         namespaceData: null,
         namespaceInternal: null,
-        ontologies: []
+        ontologies: [],
+        singleTenant: false
       }
     }
     this.cancelRequest
diff --git a/askomics/react/src/routes/integration/bedpreview.jsx b/askomics/react/src/routes/integration/bedpreview.jsx
index acbad90e..90e72d19 100644
--- a/askomics/react/src/routes/integration/bedpreview.jsx
+++ b/askomics/react/src/routes/integration/bedpreview.jsx
@@ -91,9 +91,12 @@ export default class BedPreview extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
-
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -124,7 +127,7 @@ export default class BedPreview extends Component {
           <br />
           <div className="center-div">
             <ButtonGroup>
-              <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+              {privateButton}
               {publicButton}
             </ButtonGroup>
             <br />
diff --git a/askomics/react/src/routes/integration/csvtable.jsx b/askomics/react/src/routes/integration/csvtable.jsx
index b1d3e047..c9a003a9 100644
--- a/askomics/react/src/routes/integration/csvtable.jsx
+++ b/askomics/react/src/routes/integration/csvtable.jsx
@@ -254,9 +254,12 @@ export default class CsvTable extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
-
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -290,7 +293,7 @@ export default class CsvTable extends Component {
           <br />
           <div className="center-div">
             <ButtonGroup>
-              <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+              {privateButton}
               {publicButton}
             </ButtonGroup>
           </div>
diff --git a/askomics/react/src/routes/integration/gffpreview.jsx b/askomics/react/src/routes/integration/gffpreview.jsx
index 7a3bdddb..0fafbbef 100644
--- a/askomics/react/src/routes/integration/gffpreview.jsx
+++ b/askomics/react/src/routes/integration/gffpreview.jsx
@@ -100,8 +100,12 @@ export default class GffPreview extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -130,7 +134,7 @@ export default class GffPreview extends Component {
         <br />
           <div className="center-div">
             <ButtonGroup>
-              <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+              {privateButton}
               {publicButton}
             </ButtonGroup>
             <br />
diff --git a/askomics/react/src/routes/integration/rdfpreview.jsx b/askomics/react/src/routes/integration/rdfpreview.jsx
index 4d62c6e5..5dbbd4b9 100644
--- a/askomics/react/src/routes/integration/rdfpreview.jsx
+++ b/askomics/react/src/routes/integration/rdfpreview.jsx
@@ -107,9 +107,12 @@ export default class RdfPreview extends Component {
     if (this.state.publicTick) {
       publicIcon = <i className="fas fa-check text-success"></i>
     }
-
+    let privateButton
+    if (this.props.config.user.admin || !this.props.config.singleTenant){
+        privateButton = <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+    }
     let publicButton
-    if (this.props.config.user.admin) {
+    if (this.props.config.user.admin || this.props.config.singleTenant) {
       publicButton = <Button onClick={this.integrate} value="public" color="secondary" disabled={this.state.publicTick}>{publicIcon} Integrate (public dataset)</Button>
     }
 
@@ -144,7 +147,7 @@ export default class RdfPreview extends Component {
         <br />
         <div className="center-div">
           <ButtonGroup>
-            <Button onClick={this.integrate} value="private" color="secondary" disabled={this.state.privateTick}>{privateIcon} Integrate (private dataset)</Button>
+            {privateButton}
             {publicButton}
           </ButtonGroup>
         </div>
diff --git a/askomics/tasks.py b/askomics/tasks.py
index 9d2bad0e..285cd6a8 100644
--- a/askomics/tasks.py
+++ b/askomics/tasks.py
@@ -16,6 +16,7 @@
 from askomics.libaskomics.FilesHandler import FilesHandler
 from askomics.libaskomics.LocalAuth import LocalAuth
 from askomics.libaskomics.Result import Result
+from askomics.libaskomics.SparqlQuery import SparqlQuery
 from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
 
 
@@ -46,7 +47,7 @@ def integrate(self, session, data, host_url):
     files_handler = FilesHandler(app, session, host_url=host_url, external_endpoint=data["externalEndpoint"], custom_uri=data["customUri"])
     files_handler.handle_files([data["fileId"], ])
 
-    public = data.get("public", False) if session["user"]["admin"] else False
+    public = (data.get("public", False) if session["user"]["admin"] else False) or app.iniconfig.getboolean("askomics", "single_tenant", fallback=False)
 
     for file in files_handler.files:
 
@@ -150,6 +151,17 @@ def query(self, session, info):
         info["celery_id"] = self.request.id
         result = Result(app, session, info, force_no_db=True)
 
+        query = SparqlQuery(app, session, info["graph_state"])
+        query.build_query_from_json(preview=False, for_editor=False)
+        federated = query.is_federated()
+        result.populate_db(query.graphs, query.endpoints)
+
+        info["query"] = query.sparql
+        info["graphs"] = query.graphs
+        info["endpoints"] = query.endpoints
+        info["federated"] = federated
+        info["selects"] = query.selects
+
         # Save job in database database
         result.set_celery_id(self.request.id)
         result.update_db_status("started", update_celery=True, update_date=True)
@@ -158,7 +170,7 @@ def query(self, session, info):
 
         headers = info["selects"]
         results = []
-        if info["graphs"]:
+        if info["graphs"] or app.iniconfig.getboolean("askomics", "single_tenant", fallback=False):
             query_launcher = SparqlQueryLauncher(app, session, get_result_query=True, federated=info["federated"], endpoints=info["endpoints"])
             headers, results = query_launcher.process_query(info["query"], isql_api=True)
 
diff --git a/config/askomics.ini.template b/config/askomics.ini.template
index 9e8001ba..dd1070a9 100644
--- a/config/askomics.ini.template
+++ b/config/askomics.ini.template
@@ -124,6 +124,9 @@ preview_limit = 25
 # Triplestore max rows limit
 # result_set_max_rows = 10000
 
+# Single tenant means all graphs are public
+single_tenant=False
+
 [federation]
 # Query engine can be corese or fedx
 #query_engine = corese
diff --git a/config/askomics.test.ini b/config/askomics.test.ini
index 6165a1cd..f2afac84 100644
--- a/config/askomics.test.ini
+++ b/config/askomics.test.ini
@@ -118,6 +118,8 @@ preview_limit = 25
 # Triplestore max rows limit
 result_set_max_rows = 10000
 
+single_tenant=False
+
 [federation]
 # Query engine can be corese or fedx
 query_engine = corese
diff --git a/docker/Dockerfile b/docker/Dockerfile
index e3f38ef5..10c4902e 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.14 AS builder
+FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.13 AS builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -7,7 +7,7 @@ WORKDIR /askomics
 RUN make clean-config fast-install build
 
 # Final image
-FROM alpine:3.14
+FROM alpine:3.13
 
 WORKDIR /askomics
 RUN apk add --no-cache make python3 bash git libc-dev libstdc++ nodejs-current npm openldap-dev
diff --git a/docker/DockerfileAll b/docker/DockerfileAll
index 402d80bf..65224511 100644
--- a/docker/DockerfileAll
+++ b/docker/DockerfileAll
@@ -1,5 +1,5 @@
 # Build AskOmics
-FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.14 AS askomics_builder
+FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.13 AS askomics_builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -14,7 +14,7 @@ FROM xgaia/corese:20.6.11 AS corese_builder
 FROM askomics/virtuoso:7.2.5.1 AS virtuoso_builder
 
 # Final image
-FROM alpine:3.14
+FROM alpine:3.13
 
 ENV MODE="prod" \
     NTASKS="5" \
diff --git a/docker/DockerfileCelery b/docker/DockerfileCelery
index bd11c62e..db08157a 100644
--- a/docker/DockerfileCelery
+++ b/docker/DockerfileCelery
@@ -1,4 +1,4 @@
-FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.14 AS builder
+FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.13 AS builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -7,7 +7,7 @@ WORKDIR /askomics
 RUN make clean-config fast-install
 
 # Final image
-FROM alpine:3.14
+FROM alpine:3.13
 
 WORKDIR /askomics
 RUN apk add --no-cache make python3 bash git libc-dev libstdc++ openldap-dev
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 2dfb00fb..100e7c46 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,2 +1,2 @@
-mkdocs==1.0.4
+mkdocs==1.2.3
 markdown-captions==2
diff --git a/package-lock.json b/package-lock.json
index f1b8dfe5..0b75625b 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -5341,9 +5341,9 @@
       }
     },
     "follow-redirects": {
-      "version": "1.14.7",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.7.tgz",
-      "integrity": "sha512-+hbxoLbFMbRKDwohX8GkTataGqO6Jb7jGwpAlwgy2bIz25XtRm7KEzJM76R1WiNT5SwZkX4Y75SwBolkpmE7iQ=="
+      "version": "1.14.8",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.8.tgz",
+      "integrity": "sha512-1x0S9UVJHsQprFcEC/qnNzBLcIxsjAV905f/UkQxbclCsoTWlacCNOpQa/anodLl2uaEKFhfWOvM2Qg77+15zA=="
     },
     "for-in": {
       "version": "1.0.2",
@@ -7113,9 +7113,9 @@
       }
     },
     "minimist": {
-      "version": "1.2.5",
-      "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.5.tgz",
-      "integrity": "sha512-FM9nNUYrRBAELZQT3xeZQ7fmMOBg6nWNmJKTcgsJeaLstP/UODVpGsr5OhXhhXg6f+qtJ8uiZ+PUxkDWcgIXLw=="
+      "version": "1.2.6",
+      "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.6.tgz",
+      "integrity": "sha512-Jsjnk4bw3YJqYzbdyBiNsPWHPfO++UGG749Cxs6peCu5Xg4nrena6OVxOYxrQTqww0Jmwt+Ref8rggumkTLz9Q=="
     },
     "minipass": {
       "version": "3.1.3",
@@ -8326,9 +8326,9 @@
       "integrity": "sha512-28iF6xPQrP8Oa6uxE6a1biz+lWeTOAPKggvjB8HAs6nVMKZwf5bG++632Dx614hIWgUPkgivRfG+a8uAXGTIbA=="
     },
     "prismjs": {
-      "version": "1.25.0",
-      "resolved": "https://registry.npmjs.org/prismjs/-/prismjs-1.25.0.tgz",
-      "integrity": "sha512-WCjJHl1KEWbnkQom1+SzftbtXMKQoezOCYs5rECqMN+jP+apI7ftoflyqigqzopSO3hMhTEb0mFClA8lkolgEg=="
+      "version": "1.27.0",
+      "resolved": "https://registry.npmjs.org/prismjs/-/prismjs-1.27.0.tgz",
+      "integrity": "sha512-t13BGPUlFDR7wRB5kQDG4jjl7XeuH6jbJGt11JHPL96qwsEHNX2+68tFXqc1/k+/jALsbSWJKUOT/hcYAZ5LkA=="
     },
     "private": {
       "version": "0.1.8",
@@ -9477,9 +9477,9 @@
       "integrity": "sha512-cSFtAPtRhljv69IK0hTVZQ+OfE9nePi/rtJmw5UjHeVyVroEqJXP1sFztKUy1qU+xvz3u/sfYJLa947b7nAN2Q=="
     },
     "simple-get": {
-      "version": "2.8.1",
-      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-2.8.1.tgz",
-      "integrity": "sha512-lSSHRSw3mQNUGPAYRqo7xy9dhKmxFXIjLjp4KHpf99GEH2VH7C3AM+Qfx6du6jhfUi6Vm7XnbEVEf7Wb6N8jRw==",
+      "version": "2.8.2",
+      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-2.8.2.tgz",
+      "integrity": "sha512-Ijd/rV5o+mSBBs4F/x9oDPtTx9Zb6X9brmnXvMW4J7IR15ngi9q5xxqWBKU744jTZiaXtxaPL7uHG6vtN8kUkw==",
       "requires": {
         "decompress-response": "^3.3.0",
         "once": "^1.3.1",
@@ -11102,9 +11102,9 @@
           }
         },
         "ssri": {
-          "version": "6.0.1",
-          "resolved": "https://registry.npmjs.org/ssri/-/ssri-6.0.1.tgz",
-          "integrity": "sha512-3Wge10hNcT1Kur4PDFwEieXSCMCJs/7WvSACcrMYrNp+b8kDL1/0wJch5Ni2WrtwEa2IO8OsVfeKIciKCDx/QA==",
+          "version": "6.0.2",
+          "resolved": "https://registry.npmjs.org/ssri/-/ssri-6.0.2.tgz",
+          "integrity": "sha512-cepbSq/neFK7xB6A50KHN0xHDotYzq58wWCa5LeWqnPrHG8GzfEjO/4O8kpmcGW+oaxkvhEJCWgbgNk4/ZV93Q==",
           "dev": true,
           "requires": {
             "figgy-pudding": "^3.5.1"
diff --git a/package.json b/package.json
index a2b8d346..9f088555 100644
--- a/package.json
+++ b/package.json
@@ -50,7 +50,7 @@
     "immutability-helper": "^3.1.1",
     "js-file-download": "^0.4.12",
     "pretty-time": "^1.1.0",
-    "prismjs": "^1.25.0",
+    "prismjs": "^1.27.0",
     "qs": "^6.9.4",
     "react": "^16.13.1",
     "react-ace": "^9.1.3",
diff --git a/tests/results/abstraction.json b/tests/results/abstraction.json
index 79f44a17..470c1c59 100644
--- a/tests/results/abstraction.json
+++ b/tests/results/abstraction.json
@@ -27,18 +27,6 @@
       },
       {
         "categories": [
-          {
-            "label": "minus",
-            "uri": "http://askomics.org/test/data/minus"
-          },
-          {
-            "label": "plus",
-            "uri": "http://askomics.org/test/data/plus"
-          },
-          {
-            "label": "unknown/both",
-            "uri": "http://askomics.org/test/data/unknown/both"
-          },
           {
             "label": "+",
             "uri": "http://askomics.org/test/data/%2B"
@@ -55,7 +43,6 @@
         "entityUri": "http://askomics.org/test/data/gene",
         "faldo": "http://askomics.org/test/internal/faldoStrand",
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
         ],
@@ -73,7 +60,7 @@
             "label": "plus",
             "uri": "http://askomics.org/test/data/plus"
           },
-	  {
+	        {
             "label": "unknown/both",
             "uri": "http://askomics.org/test/data/unknown/both"
           },
@@ -94,8 +81,7 @@
         "faldo": "http://askomics.org/test/internal/faldoStrand",
         "graphs": [
           "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
+          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
         ],
         "label": "strand",
         "type": "http://askomics.org/test/internal/AskomicsCategory",
@@ -127,17 +113,12 @@
           {
             "label": "1",
             "uri": "http://askomics.org/test/data/1"
-          },
-          {
-            "label": "7",
-            "uri": "http://askomics.org/test/data/7"
           }
         ],
         "entityUri": "http://askomics.org/test/data/transcript",
         "faldo": "http://askomics.org/test/internal/faldoReference",
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
+          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
         ],
         "label": "reference",
         "type": "http://askomics.org/test/internal/AskomicsCategory",
@@ -148,8 +129,6 @@
         "entityUri": "http://askomics.org/test/data/gene",
         "faldo": "http://askomics.org/test/internal/faldoStart",
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
         ],
@@ -162,10 +141,7 @@
         "entityUri": "http://askomics.org/test/data/QTL",
         "faldo": "http://askomics.org/test/internal/faldoStart",
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
+          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###"
         ],
         "label": "start",
         "type": "http://www.w3.org/2001/XMLSchema#decimal",
@@ -177,9 +153,7 @@
         "faldo": "http://askomics.org/test/internal/faldoStart",
         "graphs": [
           "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
+          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
         ],
         "label": "start",
         "type": "http://www.w3.org/2001/XMLSchema#decimal",
@@ -191,9 +165,7 @@
         "faldo": "http://askomics.org/test/internal/faldoEnd",
         "graphs": [
           "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
+          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
         ],
         "label": "end",
         "type": "http://www.w3.org/2001/XMLSchema#decimal",
@@ -204,8 +176,6 @@
         "entityUri": "http://askomics.org/test/data/gene",
         "faldo": "http://askomics.org/test/internal/faldoEnd",
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
         ],
@@ -218,10 +188,7 @@
         "entityUri": "http://askomics.org/test/data/QTL",
         "faldo": "http://askomics.org/test/internal/faldoEnd",
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.bed_###BED_TIMESTAMP###"
+          "urn:sparql:askomics_test:1_jdoe:qtl.tsv_###QTL_TIMESTAMP###"
         ],
         "label": "end",
         "type": "http://www.w3.org/2001/XMLSchema#decimal",
@@ -284,7 +251,6 @@
         "entityUri": "http://askomics.org/test/data/gene",
         "faldo": null,
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
         ],
         "label": "biotype",
@@ -296,8 +262,7 @@
         "entityUri": "http://askomics.org/test/data/transcript",
         "faldo": null,
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
-          "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
+          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###"
         ],
         "label": "description",
         "type": "http://www.w3.org/2001/XMLSchema#string",
@@ -308,7 +273,6 @@
         "entityUri": "http://askomics.org/test/data/gene",
         "faldo": null,
         "graphs": [
-          "urn:sparql:askomics_test:1_jdoe:transcripts.tsv_###TRANSCRIPTS_TIMESTAMP###",
           "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
         ],
         "label": "description",
diff --git a/tests/test_api.py b/tests/test_api.py
index af30f8bd..ea66cc70 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -43,7 +43,8 @@ def test_start(self, client):
             "proxyPath": "/",
             "user": {},
             "logged": False,
-            "ontologies": []
+            "ontologies": [],
+            "singleTenant": False
         }
         response = client.client.get('/api/start')
         assert response.status_code == 200

From 2aabba1cfe4ff604182d0194acc5eb6d0fb14ca5 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 17 May 2022 11:48:34 +0200
Subject: [PATCH 062/113] Fix empty category column

---
 askomics/libaskomics/CsvFile.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
index 08f368eb..1b94c86b 100644
--- a/askomics/libaskomics/CsvFile.py
+++ b/askomics/libaskomics/CsvFile.py
@@ -361,8 +361,7 @@ def set_rdf_abstraction_domain_knowledge(self):
     def set_rdf_domain_knowledge(self):
         """Set the domain knowledge"""
         for index, attribute in enumerate(self.header):
-
-            if self.columns_type[index] in ('category', 'reference', 'strand'):
+            if self.columns_type[index] in ('category', 'reference', 'strand') and self.header[index] in self.category_values:
                 s = self.namespace_data["{}Category".format(self.format_uri(attribute, remove_space=True))]
                 p = self.namespace_internal["category"]
                 for value in self.category_values[self.header[index]]:

From 5919426397b0238a2cfa86e4fe36f34700b4eea8 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 17 May 2022 11:51:22 +0200
Subject: [PATCH 063/113] Update CHANGELOG.md

---
 CHANGELOG.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8dd0e971..ce78b3d6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ This changelog was started for release 4.2.0.
 
 - Fixed an issue with forms (missing field and entity name for label & uri fields) (Issue #255)
 - Fixed an issue with the data endpoint for FALDO entities (Issue #279)
+- Fixed an issue where integration would fail when setting a category type on a empty column (#334)
 
 ### Added
 
@@ -25,7 +26,7 @@ This changelog was started for release 4.2.0.
 - Added tooltips to buttons in the query form (and other forms)
 - Added owl integration
 - Add better error management for RDF files
-- Added 'single tenant' mode
+- Added 'single tenant' mode: Send queries to all graphs to speed up
 
 ### Changed
 
@@ -54,6 +55,7 @@ This changelog was started for release 4.2.0.
 - Bump follow-redirects from 1.14.4 to 1.14.8
 - Bump mkdocs from 1.0.4 to 1.2.3 in /docs
 - Bump python-ldap from 3.3.1 to 3.4.0
+- Bump minimist from 1.2.5 to 1.2.6
 
 ## [4.3.1] - 2021-06-16
 

From 5134414d4185479a0543aa37249598717dabdf8e Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 18 May 2022 14:24:16 +0200
Subject: [PATCH 064/113] Dev onto (#336)

Dev onto
---
 CHANGELOG.md                                | 5 ++++-
 askomics/libaskomics/CsvFile.py             | 3 +--
 askomics/libaskomics/TriplestoreExplorer.py | 8 ++++----
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8dd0e971..c532a3eb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ This changelog was started for release 4.2.0.
 
 - Fixed an issue with forms (missing field and entity name for label & uri fields) (Issue #255)
 - Fixed an issue with the data endpoint for FALDO entities (Issue #279)
+- Fixed an issue where integration would fail when setting a category type on a empty column (#334)
 
 ### Added
 
@@ -25,7 +26,8 @@ This changelog was started for release 4.2.0.
 - Added tooltips to buttons in the query form (and other forms)
 - Added owl integration
 - Add better error management for RDF files
-- Added 'single tenant' mode
+- Added 'single tenant' mode: Send queries to all graphs to speed up
+
 
 ### Changed
 
@@ -54,6 +56,7 @@ This changelog was started for release 4.2.0.
 - Bump follow-redirects from 1.14.4 to 1.14.8
 - Bump mkdocs from 1.0.4 to 1.2.3 in /docs
 - Bump python-ldap from 3.3.1 to 3.4.0
+- Bump minimist from 1.2.5 to 1.2.6
 
 ## [4.3.1] - 2021-06-16
 
diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
index 1a86f7b9..8c1bcbac 100644
--- a/askomics/libaskomics/CsvFile.py
+++ b/askomics/libaskomics/CsvFile.py
@@ -362,8 +362,7 @@ def set_rdf_abstraction_domain_knowledge(self):
     def set_rdf_domain_knowledge(self):
         """Set the domain knowledge"""
         for index, attribute in enumerate(self.header):
-
-            if self.columns_type[index] in ('category', 'reference', 'strand'):
+            if self.columns_type[index] in ('category', 'reference', 'strand') and self.header[index] in self.category_values:
                 s = self.namespace_data["{}Category".format(self.format_uri(attribute, remove_space=True))]
                 p = self.namespace_internal["category"]
                 for value in self.category_values[self.header[index]]:
diff --git a/askomics/libaskomics/TriplestoreExplorer.py b/askomics/libaskomics/TriplestoreExplorer.py
index 492ee4ad..ced8a54e 100644
--- a/askomics/libaskomics/TriplestoreExplorer.py
+++ b/askomics/libaskomics/TriplestoreExplorer.py
@@ -415,8 +415,8 @@ def get_abstraction_attributes(self, single_tenant=False):
                 ?node rdfs:label ?attribute_label .
                 ?node rdfs:range ?attribute_range .
                 # Retrocompatibility
-                OPTIONAL {{?node askomics:uri ?attribute_uri}}
-                BIND( IF(isBlank(?node),?attribute_uri, ?node) as ?attribute_uri )
+                OPTIONAL {{?node askomics:uri ?new_attribute_uri}}
+                BIND( IF(isBlank(?node),?new_attribute_uri, ?node) as ?attribute_uri )
                 # Faldo
                 OPTIONAL {{
                     ?node a ?attribute_faldo .
@@ -531,8 +531,8 @@ def get_abstraction_relations(self, single_tenant=False):
                 ?node rdfs:label ?property_label .
                 ?node rdfs:range ?range_uri .
                 # Retrocompatibility
-                OPTIONAL {{?node askomics:uri ?property_uri}}
-                BIND( IF(isBlank(?node), ?property_uri, ?node) as ?property_uri)
+                OPTIONAL {{?node askomics:uri ?new_property_uri}}
+                BIND( IF(isBlank(?node), ?new_property_uri, ?node) as ?property_uri)
             }}
             # Relation of entity (or motherclass of entity)
             {{

From be76c52151395f679b8c09fd6b118daa9560953e Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 23 May 2022 16:17:28 +0200
Subject: [PATCH 065/113] Force refresh ontologies + case insensitive query +
 fix single_tenant

---
 askomics/libaskomics/SparqlQuery.py           |  8 +++----
 .../react/src/routes/admin/ontologies.jsx     | 22 +++++++++++++++++++
 2 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 2369feb5..63ba91e5 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -276,7 +276,7 @@ def get_default_query_with_prefix(self):
             self.get_default_query()
         )
 
-    def format_query(self, query, limit=30, replace_froms=True, federated=False):
+    def format_query(self, query, limit=30, replace_froms=True, federated=False, ignore_single_tenant=True):
         """Format the Sparql query
 
         - remove all FROM
@@ -296,7 +296,7 @@ def format_query(self, query, limit=30, replace_froms=True, federated=False):
             formatted sparql query
         """
         froms = ''
-        if replace_froms:
+        if replace_froms and (not self.settings.getboolean("askomics", "single_tenant", fallback=False) or ignore_single_tenant):
             froms = self.get_froms()
 
         if federated:
@@ -555,7 +555,7 @@ def autocomplete_local_ontology(self, uri, query):
         subquery = ""
 
         if query:
-            subquery = 'FILTER(contains(?label, "{}"))'.format(query)
+            subquery = 'FILTER(contains(lcase(?label), "{}"))'.format(query.lower())
         raw_query = '''
         SELECT DISTINCT ?label
         WHERE {{
@@ -569,7 +569,7 @@ def autocomplete_local_ontology(self, uri, query):
 
         raw_query = self.prefix_query(raw_query)
 
-        sparql = self.format_query(raw_query, limit=5, replace_froms=True, federated=False)
+        sparql = self.format_query(raw_query, limit=5, replace_froms=True, federated=False, ignore_single_tenant=True)
 
         query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=False)
         _, data = query_launcher.process_query(sparql)
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index afbfe9a9..5eef58dd 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -41,11 +41,26 @@ export default class Ontologies extends Component {
     return this.state.ontologiesSelected.length == 0
   }
 
+  cleanupOntologies (newOntologies) {
+    let cleanOntologies = []
+    newOntologies.map(onto => {
+      cleanOntologies.push({
+          id:onto.id,
+          name:onto.name,
+          uri:onto.uri,
+          short_name: onto.short_name,
+          type: onto.type
+      })
+    })
+    return cleanOntologies
+  }
+
   deleteSelectedOntologies () {
     let requestUrl = '/api/admin/delete_ontologies'
     let data = {
       ontologiesIdToDelete: this.state.ontologiesSelected
     }
+
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
       .then(response => {
         console.log(requestUrl, response.data)
@@ -53,6 +68,9 @@ export default class Ontologies extends Component {
           ontologies: response.data.ontologies,
           ontologiesSelected: [],
         })
+        this.props.setStateNavbar({
+          config: update(this.props.config, {ontologies: {$set: cleanupOntologies(response.data.ontologies)}})
+        })
       })
   }
 
@@ -119,6 +137,9 @@ export default class Ontologies extends Component {
         shortName: "",
         type: "local"
       })
+      this.props.setStateNavbar({
+        config: update(this.props.config, {ontologies: {$set: cleanupOntologies(response.data.ontologies)}})
+      })
     })
     .catch(error => {
       console.log(error, error.response.data.errorMessage)
@@ -322,6 +343,7 @@ export default class Ontologies extends Component {
 }
 
 Ontologies.propTypes = {
+  setStateNavbar: PropTypes.func,
   waitForStart: PropTypes.bool,
   config: PropTypes.object
 }

From 26d267f11446ff5dbe109c562a0b6dd007b6471e Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 24 May 2022 10:16:02 +0000
Subject: [PATCH 066/113] typo

---
 askomics/react/src/routes/admin/ontologies.jsx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index 5eef58dd..cf2a77c5 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -3,6 +3,7 @@ import axios from 'axios'
 import {Button, Form, FormGroup, Label, Input, Alert, Row, Col, CustomInput } from 'reactstrap'
 import BootstrapTable from 'react-bootstrap-table-next'
 import paginationFactory from 'react-bootstrap-table2-paginator'
+import update from 'react-addons-update'
 import PropTypes from 'prop-types'
 import Utils from '../../classes/utils'
 import { Redirect } from 'react-router-dom'
@@ -69,7 +70,7 @@ export default class Ontologies extends Component {
           ontologiesSelected: [],
         })
         this.props.setStateNavbar({
-          config: update(this.props.config, {ontologies: {$set: cleanupOntologies(response.data.ontologies)}})
+          config: update(this.props.config, {ontologies: {$set: this.cleanupOntologies(response.data.ontologies)}})
         })
       })
   }
@@ -138,7 +139,7 @@ export default class Ontologies extends Component {
         type: "local"
       })
       this.props.setStateNavbar({
-        config: update(this.props.config, {ontologies: {$set: cleanupOntologies(response.data.ontologies)}})
+        config: update(this.props.config, {ontologies: {$set: this.cleanupOntologies(response.data.ontologies)}})
       })
     })
     .catch(error => {

From dcf2ffc1bc2dc9eb7a18b3a568b1825513215435 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 24 May 2022 13:15:56 +0000
Subject: [PATCH 067/113] 10 results, & fix issues with multiple ontologies

---
 askomics/libaskomics/OntologyManager.py        |  4 ++--
 askomics/libaskomics/SparqlQuery.py            |  6 ++----
 askomics/react/src/components/autocomplete.jsx | 14 +++++++-------
 3 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 74b47c95..a2e12a4a 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -221,13 +221,13 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
             query = SparqlQuery(self.app, self.session, get_graphs=False)
             # TODO: Actually store the graph in the ontology to quicken search
             query.set_graphs([onto_graph])
-            return query.autocomplete_local_ontology(ontology_uri, query_term)
+            return query.autocomplete_local_ontology(ontology_uri, query_term, 10)
         elif ontology_type == "ols":
             base_url = "https://www.ebi.ac.uk/ols/api/suggest"
             arguments = {
                 "q": query_term,
                 "ontology": quote_plus(onto_short_name.lower()),
-                "rows": 5
+                "rows": 10
             }
 
             r = requests.get(base_url, params=arguments)
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 63ba91e5..015341b1 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -536,7 +536,7 @@ def get_uri_parameters(self, uri, endpoints):
 
         return formated_data
 
-    def autocomplete_local_ontology(self, uri, query):
+    def autocomplete_local_ontology(self, uri, query, max_terms):
         """Get results for a specific query
 
         Parameters
@@ -563,13 +563,11 @@ def autocomplete_local_ontology(self, uri, query):
           ?uri rdfs:label ?label .
           {}
         }}
-
-        LIMIT 5
         '''.format(uri, subquery)
 
         raw_query = self.prefix_query(raw_query)
 
-        sparql = self.format_query(raw_query, limit=5, replace_froms=True, federated=False, ignore_single_tenant=True)
+        sparql = self.format_query(raw_query, limit=max_terms, replace_froms=True, federated=False, ignore_single_tenant=True)
 
         query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=False)
         _, data = query_launcher.process_query(sparql)
diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index 52fba74e..635881b1 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -21,16 +21,16 @@ export default class Autocomplete extends Component {
   }
 
   getAutoComplete () {
-      return this.props.config.ontologies.map(onto => {
-        if (onto.uri == this.props.entityUri) {
-          return onto.short_name
-        } else {
-          return null
-        }
-      })
+      let selectedOnto =  this.props.config.ontologies.find(onto => onto.uri == this.props.entityUri)
+      if (selectedOnto){
+        return selectedOnto.short_name
+      }
+      return ""
   }
 
   autocompleteOntology (value) {
+    if (this.state.ontologyShort.length == 0){ return }
+
     let userInput = value
     let requestUrl = '/api/ontology/' + this.state.ontologyShort + "/autocomplete"
 

From 106d3ed44a6dfa84b9ac1f50c9fe9647e5f973a1 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 24 May 2022 15:44:13 +0200
Subject: [PATCH 068/113] Config value

---
 CHANGELOG.md                            | 1 +
 askomics/libaskomics/OntologyManager.py | 7 +++++--
 config/askomics.ini.template            | 4 ++++
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c532a3eb..07e66363 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ This changelog was started for release 4.2.0.
 - Added owl integration
 - Add better error management for RDF files
 - Added 'single tenant' mode: Send queries to all graphs to speed up
+- Added ontologies management
 
 
 ### Changed
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index a2e12a4a..acaea31e 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -217,17 +217,20 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
         list of dict
             Results
         """
+
+        max_results = self.settings.getint("askomics", "autocomplete_max_results", fallback=10)
+
         if ontology_type == "local":
             query = SparqlQuery(self.app, self.session, get_graphs=False)
             # TODO: Actually store the graph in the ontology to quicken search
             query.set_graphs([onto_graph])
-            return query.autocomplete_local_ontology(ontology_uri, query_term, 10)
+            return query.autocomplete_local_ontology(ontology_uri, query_term, max_results)
         elif ontology_type == "ols":
             base_url = "https://www.ebi.ac.uk/ols/api/suggest"
             arguments = {
                 "q": query_term,
                 "ontology": quote_plus(onto_short_name.lower()),
-                "rows": 10
+                "rows": max_results
             }
 
             r = requests.get(base_url, params=arguments)
diff --git a/config/askomics.ini.template b/config/askomics.ini.template
index dd1070a9..af284f2b 100644
--- a/config/askomics.ini.template
+++ b/config/askomics.ini.template
@@ -125,8 +125,12 @@ preview_limit = 25
 # result_set_max_rows = 10000
 
 # Single tenant means all graphs are public
+# All queries are launched on all graphes (speedup queries)
 single_tenant=False
 
+# Max results returned for autocompletion
+autocomplete_max_results = 10
+
 [federation]
 # Query engine can be corese or fedx
 #query_engine = corese

From 2997b83303f650a505411727e0174938617c3872 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 1 Jun 2022 16:42:15 +0200
Subject: [PATCH 069/113] Test new onto behaviour?

---
 askomics/libaskomics/SparqlQuery.py       | 15 ++++++++++++---
 askomics/react/src/routes/query/query.jsx |  8 ++++----
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 015341b1..ef1daba9 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -410,7 +410,7 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None):
             filter_public_string = 'FILTER (?public = <true> || ?creator = <{}>)'.format(self.session["user"]["username"])
 
         query = '''
-        SELECT DISTINCT ?graph ?endpoint
+        SELECT DISTINCT ?graph ?endpoint ?entity_uri
         WHERE {{
           ?graph_abstraction askomics:public ?public .
           ?graph_abstraction dc:creator ?creator .
@@ -422,7 +422,9 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None):
             VALUES ?askomics_type {{askomics:entity askomics:ontology}}
           }}
           GRAPH ?graph {{
-            [] a ?entity_uri .
+            {{ [] a ?entity_uri . }}
+            UNION
+            {{ ?entity_uri a askomics:ontology . }}
           }}
           {}
           {}
@@ -1186,13 +1188,20 @@ def build_query_from_json(self, preview=False, for_editor=False):
                 subject = self.format_sparql_variable("{}{}_uri".format(attribute["entityLabel"], attribute["nodeId"]))
                 predicate = attribute["uri"]
                 obj = "<{}>".format(attribute["entityUris"][0])
-                if not self.is_bnode(attribute["entityUris"][0], self.json["nodes"]):
+                if not (self.is_bnode(attribute["entityUris"][0], self.json["nodes"]) or attribute["ontology"] is True):
                     self.store_triple({
                         "subject": subject,
                         "predicate": predicate,
                         "object": obj,
                         "optional": False
                     }, block_id, sblock_id, pblock_ids)
+                if attribute["ontology"] is True:
+                    self.store_triple({
+                        "subject": subject,
+                        "predicate": predicate,
+                        "object": "owl:Class",
+                        "optional": False
+                    }, block_id, sblock_id, pblock_ids)
 
                 if attribute["visible"]:
                     self.selects.append(subject)
diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
index 25a580c5..aa0c48f6 100644
--- a/askomics/react/src/routes/query/query.jsx
+++ b/askomics/react/src/routes/query/query.jsx
@@ -224,9 +224,6 @@ export default class Query extends Component {
       return false
     }
 
-    console.log(node)
-    console.log(node.ontology ? currentUri == targetUri ? "endNode" : "node" : false)
-
     return node.ontology ? currentUri == targetUri ? "endNode" : "node" : false
   }
 
@@ -276,6 +273,8 @@ export default class Query extends Component {
     let nodeAttributes = []
     let isBnode = this.isBnode(nodeId)
 
+    let isOnto = this.isOntoNode(nodeId)
+
     // if bnode without uri, first attribute is visible
     let firstAttrVisibleForBnode = isBnode
 
@@ -303,7 +302,8 @@ export default class Query extends Component {
         form: false,
         negative: false,
         linked: false,
-        linkedWith: null
+        linkedWith: null,
+        ontology: isOnto
       })
     }
 

From c0af6d3b68601f206af6595b6f36ec2e030ec57a Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 1 Jun 2022 17:54:19 +0200
Subject: [PATCH 070/113] Fix before tests

---
 askomics/libaskomics/SparqlQuery.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index ef1daba9..4079f86f 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -1188,14 +1188,14 @@ def build_query_from_json(self, preview=False, for_editor=False):
                 subject = self.format_sparql_variable("{}{}_uri".format(attribute["entityLabel"], attribute["nodeId"]))
                 predicate = attribute["uri"]
                 obj = "<{}>".format(attribute["entityUris"][0])
-                if not (self.is_bnode(attribute["entityUris"][0], self.json["nodes"]) or attribute["ontology"] is True):
+                if not (self.is_bnode(attribute["entityUris"][0], self.json["nodes"]) or attribute.get("ontology", False) is True):
                     self.store_triple({
                         "subject": subject,
                         "predicate": predicate,
                         "object": obj,
                         "optional": False
                     }, block_id, sblock_id, pblock_ids)
-                if attribute["ontology"] is True:
+                if attribute.get("ontology", False) is True:
                     self.store_triple({
                         "subject": subject,
                         "predicate": predicate,

From 79f0c8b94ca23f73384e2abe1146b6b52f839c8f Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Jun 2022 16:03:21 +0200
Subject: [PATCH 071/113] Batter management of ontologies and labels

---
 askomics/api/admin.py                         | 10 ++++-
 askomics/api/ontology.py                      |  2 +-
 askomics/libaskomics/Database.py              | 13 +++++-
 askomics/libaskomics/OntologyManager.py       | 40 +++++++++++++------
 askomics/libaskomics/PrefixManager.py         |  3 +-
 askomics/libaskomics/SparqlQuery.py           | 18 +++++++--
 .../react/src/routes/admin/ontologies.jsx     | 20 ++++++++--
 7 files changed, 83 insertions(+), 23 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 16fd7315..67df9c2f 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -703,6 +703,7 @@ def add_ontology():
     short_name = data.get("shortName")
     type = data.get("type")
     dataset_id = data.get("datasetId")
+    label_uri = data.get("datasetId")
 
     om = OntologyManager(current_app, session)
 
@@ -751,8 +752,15 @@ def add_ontology():
             'errorMessage': "Name and short name must be unique"
         }), 400
 
+    if any([dataset_id == onto['dataset_id'] for onto in ontologies]):
+        return jsonify({
+            'ontologies': [],
+            'error': True,
+            'errorMessage': "Dataset is already linked to another ontology"
+        }), 400
+
     try:
-        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, type)
+        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, type, label_uri)
         ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 49d4bf85..224bb95b 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -22,7 +22,7 @@ def autocomplete(short_ontology):
     try:
         # Disk space
         om = OntologyManager(current_app, session)
-        ontology = om.get_ontology(short_ontology)
+        ontology = om.get_ontology(short_name=short_ontology)
         if not ontology:
             return jsonify({
                 "error": True,
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index bd81202f..c2261285 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -416,10 +416,21 @@ def create_ontologies_table(self):
             name text NOT NULL,
             uri text NOT NULL,
             short_name text NOT NULL,
-            type text DEFAULT 'local',
+            type text DEFAULT 'sparql',
             dataset_id INTEGER NOT NULL,
             graph text NOT NULL,
             FOREIGN KEY(dataset_id) REFERENCES datasets(id)
         )
         '''
         self.execute_sql_query(query)
+
+        query = '''
+        ALTER TABLE files
+        ADD label_uri text NOT NULL
+        DEFAULT('rdfs:label')
+        '''
+
+        try:
+            self.execute_sql_query(query)
+        except Exception:
+            pass
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index acaea31e..832e091a 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -77,7 +77,7 @@ def list_full_ontologies(self):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT ontologies.id, ontologies.name, ontologies.uri, ontologies.short_name, ontologies.type, datasets.id, datasets.name, ontologies.graph
+        SELECT ontologies.id, ontologies.name, ontologies.uri, ontologies.short_name, ontologies.type, ontologies.label_uri, datasets.id, datasets.name, ontologies.graph
         FROM ontologies
         INNER JOIN datasets ON datasets.id=ontologies.dataset_id
         '''
@@ -92,16 +92,17 @@ def list_full_ontologies(self):
                 'uri': row[2],
                 'short_name': row[3],
                 'type': row[4],
-                'dataset_id': row[5],
-                'dataset_name': row[6],
-                'graph': row[7]
+                'label_uri': row[5],
+                'dataset_id': row[6],
+                'dataset_name': row[7],
+                'graph': row[8]
             }
             ontologies.append(prefix)
 
         return ontologies
 
-    def get_ontology(self, short_name):
-        """Get a specific ontology based on short name
+    def get_ontology(self, short_name="", uri=""):
+        """Get a specific ontology based on short name or uri
 
         Returns
         -------
@@ -109,15 +110,26 @@ def get_ontology(self, short_name):
             ontology
         """
 
+        if not (short_name or uri):
+            return None
+
+        if short_name:
+            where_clause = "WHERE short_name = ?"
+            args = (short_name,)
+
+        if uri:
+            where_clause = "WHERE uri = ?"
+            args = (uri,)
+
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, uri, short_name, type, dataset_id, graph
+        SELECT id, name, uri, short_name, type, dataset_id, graph, label_uri
         FROM ontologies
-        WHERE short_name = ?
-        '''
+        {}
+        '''.format(where_clause)
 
-        rows = database.execute_sql_query(query, (short_name,))
+        rows = database.execute_sql_query(query, args)
 
         if not rows:
             return None
@@ -130,10 +142,11 @@ def get_ontology(self, short_name):
             'short_name': ontology[3],
             'type': ontology[4],
             'dataset_id': ontology[5],
-            'graph': ontology[6]
+            'graph': ontology[6],
+            'label_uri': ontology[7]
         }
 
-    def add_ontology(self, name, uri, short_name, dataset_id, graph, type="local"):
+    def add_ontology(self, name, uri, short_name, dataset_id, graph, type="local", label_uri="rdfs:label"):
         """Create a new ontology
 
         Returns
@@ -151,11 +164,12 @@ def add_ontology(self, name, uri, short_name, dataset_id, graph, type="local"):
             ?,
             ?,
             ?,
+            ?,
             ?
         )
         '''
 
-        database.execute_sql_query(query, (name, uri, short_name, type, dataset_id, graph))
+        database.execute_sql_query(query, (name, uri, short_name, type, dataset_id, graph, label_uri))
 
         query = '''
         UPDATE datasets SET
diff --git a/askomics/libaskomics/PrefixManager.py b/askomics/libaskomics/PrefixManager.py
index b3ff0999..07c4f5f0 100644
--- a/askomics/libaskomics/PrefixManager.py
+++ b/askomics/libaskomics/PrefixManager.py
@@ -41,7 +41,8 @@ def __init__(self, app, session):
             'rdf:': str(rdflib.RDF),
             'rdfs:': str(rdflib.RDFS),
             'owl:': str(rdflib.OWL),
-            'xsd:': str(rdflib.XSD)
+            'xsd:': str(rdflib.XSD),
+            'skos': str(rdflib.SKOS)
         }
 
     def get_prefix(self):
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 4079f86f..013eb863 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -1,6 +1,7 @@
 import re
 import textwrap
 
+from askomics.libaskomics.OntologyManager import OntologyManager
 from askomics.libaskomics.Params import Params
 from askomics.libaskomics.PrefixManager import PrefixManager
 from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
@@ -392,7 +393,7 @@ def get_endpoints_string(self):
 
         return endpoints_string
 
-    def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None):
+    def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, ontologies={}):
         """Get all public and private graphs containing the given entities
 
         Parameters
@@ -437,7 +438,11 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None):
         self.endpoints = []
         for res in results:
             if not graphs or res["graph"] in graphs:
-                self.graphs.append(res["graph"])
+                # Override with onto graph if matching uri
+                if ontologies.get(res['uri']):
+                    self.graphs.append(ontologies[res['uri']]['graph'])
+                else:
+                    self.graphs.append(res["graph"])
 
             # If local triplestore url is not accessible by federated query engine
             if res["endpoint"] == self.settings.get('triplestore', 'endpoint') and self.local_endpoint_f is not None:
@@ -1026,14 +1031,19 @@ def build_query_from_json(self, preview=False, for_editor=False):
 
         var_to_replace = []
 
+        ontologies = {}
+        om = OntologyManager(self.app, self.session)
+
         # Browse attributes to get entities
         for attr in self.json["attr"]:
             entities = entities + attr["entityUris"]
+            if attr["type"] == "uri" and attr.get("ontology", False) is True and not attr["entityUris"][0] in ontologies:
+                ontologies[attr["entityUris"][0]] = om.get_ontology(uri=attr["entityUris"][0])
 
         entities = list(set(entities))  # uniq list
 
         # Set graphs in function of entities needed
-        self.set_graphs_and_endpoints(entities=entities)
+        self.set_graphs_and_endpoints(entities=entities, ontologies=ontologies)
 
         # self.log.debug(self.json)
 
@@ -1196,6 +1206,8 @@ def build_query_from_json(self, preview=False, for_editor=False):
                         "optional": False
                     }, block_id, sblock_id, pblock_ids)
                 if attribute.get("ontology", False) is True:
+                    if ontologies.get(attribute["entityUris"][0]):
+                        predicate = ontologies[attribute["entityUris"][0]]["label_uri"]
                     self.store_triple({
                         "subject": subject,
                         "predicate": predicate,
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index cf2a77c5..0e42ce12 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -28,6 +28,7 @@ export default class Ontologies extends Component {
       shortName: "",
       type: "local",
       datasetId: "",
+      label_uri: "rdfs:label",
       ontologiesSelected: []
     }
     this.handleChangeValue = this.handleChangeValue.bind(this)
@@ -123,7 +124,8 @@ export default class Ontologies extends Component {
       uri: this.state.uri,
       shortName: this.state.shortName,
       type: this.state.type,
-      datasetId: this.state.datasetId
+      datasetId: this.state.datasetId,
+      label_uri: this.state.label_uri
     }
 
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
@@ -136,7 +138,8 @@ export default class Ontologies extends Component {
         name: "",
         uri: "",
         shortName: "",
-        type: "local"
+        type: "local",
+        label_uri: "rdfs:label"
       })
       this.props.setStateNavbar({
         config: update(this.props.config, {ontologies: {$set: this.cleanupOntologies(response.data.ontologies)}})
@@ -236,6 +239,11 @@ export default class Ontologies extends Component {
       text: 'Dataset',
       sort: true
     }, {
+      editable: false,
+      dataField: 'label_uri',
+      text: 'Label uri',
+      sort: true
+  }, {
       editable: false,
       dataField: 'type',
       text: 'Autocomplete type',
@@ -303,7 +311,13 @@ export default class Ontologies extends Component {
                 </CustomInput>
               </FormGroup>
             </Col>
-            <Col md={6}>
+            <Col md={3}>
+              <FormGroup>
+                <Label for="type">Label uri/Label>
+                <Input type="text" name="label_uri" id="label_uri" value={this.state.label_uri} onChange={this.handleChangeValue} />
+              </FormGroup>
+            </Col>
+            <Col md={3}>
               <FormGroup>
                 <Label for="type">Autocomplete type</Label>
                 <CustomInput type="select" name="type" id="type" value={this.state.type} onChange={this.handleChangeValue}>

From f27120f4e1d5996bb081f14be8e22a12ae83e52e Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Jun 2022 17:04:03 +0200
Subject: [PATCH 072/113] Circular import?

---
 askomics/libaskomics/SparqlQuery.py            | 5 +++--
 askomics/react/src/routes/admin/ontologies.jsx | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 013eb863..15e2c9d1 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -1,7 +1,8 @@
 import re
 import textwrap
 
-from askomics.libaskomics.OntologyManager import OntologyManager
+import askomics.libaskomics.OntologyManager
+
 from askomics.libaskomics.Params import Params
 from askomics.libaskomics.PrefixManager import PrefixManager
 from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
@@ -1032,7 +1033,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
         var_to_replace = []
 
         ontologies = {}
-        om = OntologyManager(self.app, self.session)
+        om = askomics.libaskomics.OntologyManager.OntologyManager(self.app, self.session)
 
         # Browse attributes to get entities
         for attr in self.json["attr"]:
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index 0e42ce12..f4b4bc8d 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -313,7 +313,7 @@ export default class Ontologies extends Component {
             </Col>
             <Col md={3}>
               <FormGroup>
-                <Label for="type">Label uri/Label>
+                <Label for="type">Label uri</Label>
                 <Input type="text" name="label_uri" id="label_uri" value={this.state.label_uri} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>

From 52cd3676b290c66de0eb85f74ca7329374623e11 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Jun 2022 17:14:38 +0200
Subject: [PATCH 073/113] Circular import 2

---
 askomics/libaskomics/OntologyManager.py | 4 ++--
 askomics/libaskomics/SparqlQuery.py     | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 832e091a..e800a898 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -5,7 +5,6 @@
 
 
 from askomics.libaskomics.Database import Database
-from askomics.libaskomics.SparqlQuery import SparqlQuery
 from askomics.libaskomics.Params import Params
 
 
@@ -231,7 +230,8 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
         list of dict
             Results
         """
-
+        # Circular import
+        from askomics.libaskomics.SparqlQuery import SparqlQuery
         max_results = self.settings.getint("askomics", "autocomplete_max_results", fallback=10)
 
         if ontology_type == "local":
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 15e2c9d1..b9266bff 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -1,8 +1,6 @@
 import re
 import textwrap
 
-import askomics.libaskomics.OntologyManager
-
 from askomics.libaskomics.Params import Params
 from askomics.libaskomics.PrefixManager import PrefixManager
 from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
@@ -1015,6 +1013,8 @@ def build_query_from_json(self, preview=False, for_editor=False):
         for_editor : bool, optional
             Remove FROMS and @federate
         """
+        # Circular import
+        from askomics.libaskomics.OntologyManager import OntologyManager
         entities = []
         attributes = {}
         linked_attributes = []
@@ -1033,7 +1033,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
         var_to_replace = []
 
         ontologies = {}
-        om = askomics.libaskomics.OntologyManager.OntologyManager(self.app, self.session)
+        om = OntologyManager(self.app, self.session)
 
         # Browse attributes to get entities
         for attr in self.json["attr"]:

From adee02fd878fd39d96e1ff62c1fee31e22509e09 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Jun 2022 17:27:30 +0200
Subject: [PATCH 074/113] Fixes

---
 askomics/api/admin.py                          |  2 +-
 askomics/libaskomics/Database.py               |  2 +-
 askomics/react/src/routes/admin/ontologies.jsx | 11 ++++++-----
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 67df9c2f..8ae19015 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -703,7 +703,7 @@ def add_ontology():
     short_name = data.get("shortName")
     type = data.get("type")
     dataset_id = data.get("datasetId")
-    label_uri = data.get("datasetId")
+    label_uri = data.get("labelUri", "rdfs:label")
 
     om = OntologyManager(current_app, session)
 
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index c2261285..52fff976 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -425,7 +425,7 @@ def create_ontologies_table(self):
         self.execute_sql_query(query)
 
         query = '''
-        ALTER TABLE files
+        ALTER TABLE ontologies
         ADD label_uri text NOT NULL
         DEFAULT('rdfs:label')
         '''
diff --git a/askomics/react/src/routes/admin/ontologies.jsx b/askomics/react/src/routes/admin/ontologies.jsx
index f4b4bc8d..d7b97511 100644
--- a/askomics/react/src/routes/admin/ontologies.jsx
+++ b/askomics/react/src/routes/admin/ontologies.jsx
@@ -28,7 +28,7 @@ export default class Ontologies extends Component {
       shortName: "",
       type: "local",
       datasetId: "",
-      label_uri: "rdfs:label",
+      labelUri: "rdfs:label",
       ontologiesSelected: []
     }
     this.handleChangeValue = this.handleChangeValue.bind(this)
@@ -87,7 +87,8 @@ export default class Ontologies extends Component {
       this.state.name.length > 0 &&
       this.state.uri.length > 0 &&
       this.state.shortName.length > 0 &&
-      this.state.datasetId.length > 0
+      this.state.datasetId.length > 0 &&
+      this.state.labelUri.length > 0
     )
   }
 
@@ -125,7 +126,7 @@ export default class Ontologies extends Component {
       shortName: this.state.shortName,
       type: this.state.type,
       datasetId: this.state.datasetId,
-      label_uri: this.state.label_uri
+      labelUri: this.state.labelUri
     }
 
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
@@ -139,7 +140,7 @@ export default class Ontologies extends Component {
         uri: "",
         shortName: "",
         type: "local",
-        label_uri: "rdfs:label"
+        labelUri: "rdfs:label"
       })
       this.props.setStateNavbar({
         config: update(this.props.config, {ontologies: {$set: this.cleanupOntologies(response.data.ontologies)}})
@@ -314,7 +315,7 @@ export default class Ontologies extends Component {
             <Col md={3}>
               <FormGroup>
                 <Label for="type">Label uri</Label>
-                <Input type="text" name="label_uri" id="label_uri" value={this.state.label_uri} onChange={this.handleChangeValue} />
+                <Input type="text" name="labelUri" id="labelUri" value={this.state.labelUri} onChange={this.handleChangeValue} />
               </FormGroup>
             </Col>
             <Col md={3}>

From 5a6137bcff3e6c1b52b8827467952b5e71a1145b Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Jun 2022 22:03:55 +0200
Subject: [PATCH 075/113] Update PrefixManager.py

---
 askomics/libaskomics/PrefixManager.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/askomics/libaskomics/PrefixManager.py b/askomics/libaskomics/PrefixManager.py
index 07c4f5f0..67499f1b 100644
--- a/askomics/libaskomics/PrefixManager.py
+++ b/askomics/libaskomics/PrefixManager.py
@@ -42,7 +42,7 @@ def __init__(self, app, session):
             'rdfs:': str(rdflib.RDFS),
             'owl:': str(rdflib.OWL),
             'xsd:': str(rdflib.XSD),
-            'skos': str(rdflib.SKOS)
+            'skos:': str(rdflib.SKOS)
         }
 
     def get_prefix(self):

From ab34cebf7b16c785e7a9bdd3da7ada57a9e42da1 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Thu, 2 Jun 2022 22:45:41 +0200
Subject: [PATCH 076/113] Update SparqlQuery.py

---
 askomics/libaskomics/SparqlQuery.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index b9266bff..8e8def29 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -438,8 +438,8 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
         for res in results:
             if not graphs or res["graph"] in graphs:
                 # Override with onto graph if matching uri
-                if ontologies.get(res['uri']):
-                    self.graphs.append(ontologies[res['uri']]['graph'])
+                if ontologies.get(res['entity_uri']):
+                    self.graphs.append(ontologies[res['entity_uri']]['graph'])
                 else:
                     self.graphs.append(res["graph"])
 

From 8d7f4b24e1001b63218a9d9c32b2a1183dcb8227 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Jun 2022 09:50:26 +0200
Subject: [PATCH 077/113] Fix tests

---
 tests/results/init.json         | 2 +-
 tests/results/sparql_query.json | 2 +-
 tests/test_api_admin.py         | 6 ++++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/results/init.json b/tests/results/init.json
index d557420b..2dcd8e37 100644
--- a/tests/results/init.json
+++ b/tests/results/init.json
@@ -1,5 +1,5 @@
 {
-  "defaultQuery": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?s ?p ?o\nWHERE {\n    ?s ?p ?o\n}\n",
+  "defaultQuery": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\nskos: <http://www.w3.org/2004/02/skos/core#>\n\nSELECT DISTINCT ?s ?p ?o\nWHERE {\n    ?s ?p ?o\n}\n",
   "diskSpace": ###SIZE###,
   "console_enabled": true,
   "endpoints": {
diff --git a/tests/results/sparql_query.json b/tests/results/sparql_query.json
index d815b914..1da74702 100644
--- a/tests/results/sparql_query.json
+++ b/tests/results/sparql_query.json
@@ -37,5 +37,5 @@
         "uri": "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
     }
   },
-  "query": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?transcript1_Label\nWHERE {\n    ?transcript1_uri rdf:type <http://askomics.org/test/data/transcript> .\n    ?transcript1_uri rdfs:label ?transcript1_Label .\n\n\n\n}\n"
+  "query": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\n\nSELECT DISTINCT ?transcript1_Label\nWHERE {\n    ?transcript1_uri rdf:type <http://askomics.org/test/data/transcript> .\n    ?transcript1_uri rdfs:label ?transcript1_Label .\n\n\n\n}\n"
 }
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index fae15f3a..56b7d103 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -620,7 +620,8 @@ def test_view_ontologies(self, client):
                 "type": "local",
                 "dataset_id": 1,
                 "dataset_name": "transcripts.tsv",
-                "graph": "mygraph"
+                "graph": "mygraph",
+                "label_uri": "rdfs:label"
             }]
         }
 
@@ -659,7 +660,8 @@ def test_add_ontology(self, client):
                 "short_name": "OBO",
                 "type": "local",
                 "dataset_id": 1,
-                "dataset_name": "transcripts.tsv"
+                "dataset_name": "transcripts.tsv",
+                "label_uri": "rdfs:label"
             }]
         }
 

From 1c0d547ee4961c8caa72c6102129ec4a1e8d21ad Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Jun 2022 10:25:29 +0200
Subject: [PATCH 078/113] Prefix + order

---
 tests/results/init.json         | 2 +-
 tests/results/sparql_query.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/results/init.json b/tests/results/init.json
index 2dcd8e37..8eea5f0e 100644
--- a/tests/results/init.json
+++ b/tests/results/init.json
@@ -1,5 +1,5 @@
 {
-  "defaultQuery": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\nskos: <http://www.w3.org/2004/02/skos/core#>\n\nSELECT DISTINCT ?s ?p ?o\nWHERE {\n    ?s ?p ?o\n}\n",
+  "defaultQuery": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?s ?p ?o\nWHERE {\n    ?s ?p ?o\n}\n",
   "diskSpace": ###SIZE###,
   "console_enabled": true,
   "endpoints": {
diff --git a/tests/results/sparql_query.json b/tests/results/sparql_query.json
index 1da74702..aae08c25 100644
--- a/tests/results/sparql_query.json
+++ b/tests/results/sparql_query.json
@@ -37,5 +37,5 @@
         "uri": "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
     }
   },
-  "query": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\n\nSELECT DISTINCT ?transcript1_Label\nWHERE {\n    ?transcript1_uri rdf:type <http://askomics.org/test/data/transcript> .\n    ?transcript1_uri rdfs:label ?transcript1_Label .\n\n\n\n}\n"
+  "query": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?transcript1_Label\nWHERE {\n    ?transcript1_uri rdf:type <http://askomics.org/test/data/transcript> .\n    ?transcript1_uri rdfs:label ?transcript1_Label .\n\n\n\n}\n"
 }

From c0682d2d81d69259cd6eda870f995cc453601185 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Jun 2022 15:08:49 +0000
Subject: [PATCH 079/113] Fix some stuff

---
 askomics/libaskomics/SparqlQuery.py         | 4 ++--
 askomics/libaskomics/SparqlQueryLauncher.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 8e8def29..05c7f362 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -419,13 +419,13 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
           GRAPH ?graph_abstraction {{
             ?graph_abstraction prov:atLocation ?endpoint .
             ?entity_uri a ?askomics_type .
-            VALUES ?askomics_type {{askomics:entity askomics:ontology}}
           }}
           GRAPH ?graph {{
             {{ [] a ?entity_uri . }}
             UNION
-            {{ ?entity_uri a askomics:ontology . }}
+            {{ ?entity_uri a ?askomics_type . }}
           }}
+          VALUES ?askomics_type {{askomics:entity askomics:ontology}}
           {}
           {}
         }}
diff --git a/askomics/libaskomics/SparqlQueryLauncher.py b/askomics/libaskomics/SparqlQueryLauncher.py
index 6c250619..a17bdc82 100644
--- a/askomics/libaskomics/SparqlQueryLauncher.py
+++ b/askomics/libaskomics/SparqlQueryLauncher.py
@@ -310,8 +310,8 @@ def execute_query(self, query, disable_log=False, isql_api=False):
                 if self.endpoint.isSparqlUpdateRequest():
                     self.endpoint.setMethod('POST')
                     # Virtuoso hack
-                    if self.triplestore == 'virtuoso':
-                        self.endpoint.queryType = "SELECT"
+                    #if self.triplestore == 'virtuoso':
+                    #    self.endpoint.queryType = "SELECT"
 
                     results = self.endpoint.query()
                 # Select

From da9d938a26b56446fef84615124e7ee3745c22fa Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Jun 2022 17:30:08 +0200
Subject: [PATCH 080/113] Fix label

---
 askomics/libaskomics/SparqlQuery.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 8e8def29..cefd4dc9 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -1207,8 +1207,6 @@ def build_query_from_json(self, preview=False, for_editor=False):
                         "optional": False
                     }, block_id, sblock_id, pblock_ids)
                 if attribute.get("ontology", False) is True:
-                    if ontologies.get(attribute["entityUris"][0]):
-                        predicate = ontologies[attribute["entityUris"][0]]["label_uri"]
                     self.store_triple({
                         "subject": subject,
                         "predicate": predicate,
@@ -1282,6 +1280,8 @@ def build_query_from_json(self, preview=False, for_editor=False):
                     subject = self.format_sparql_variable("{}{}_uri".format(attribute["entityLabel"], attribute["nodeId"]))
                     if attribute["uri"] == "rdfs:label":
                         predicate = attribute["uri"]
+                        if ontologies.get(attribute["entityUris"][0]):
+                            predicate = ontologies[attribute["entityUris"][0]]["label_uri"]
                     else:
                         predicate = "<{}>".format(attribute["uri"])
 

From f1e1e360ac18323094b3bb2c0b9c63ac3d92cee9 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Jun 2022 17:54:13 +0200
Subject: [PATCH 081/113] lint

---
 askomics/libaskomics/SparqlQueryLauncher.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/askomics/libaskomics/SparqlQueryLauncher.py b/askomics/libaskomics/SparqlQueryLauncher.py
index a17bdc82..64fe2802 100644
--- a/askomics/libaskomics/SparqlQueryLauncher.py
+++ b/askomics/libaskomics/SparqlQueryLauncher.py
@@ -310,7 +310,7 @@ def execute_query(self, query, disable_log=False, isql_api=False):
                 if self.endpoint.isSparqlUpdateRequest():
                     self.endpoint.setMethod('POST')
                     # Virtuoso hack
-                    #if self.triplestore == 'virtuoso':
+                    # if self.triplestore == 'virtuoso':
                     #    self.endpoint.queryType = "SELECT"
 
                     results = self.endpoint.query()

From 44ead791b8ef080fe9df56b255b434647e16bace Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 3 Jun 2022 18:18:04 +0200
Subject: [PATCH 082/113] Stuff (1/?)

---
 askomics/api/admin.py                   |  2 +-
 askomics/api/file.py                    |  4 +++-
 askomics/api/ontology.py                |  2 +-
 askomics/libaskomics/Database.py        | 13 +++++++++++++
 askomics/libaskomics/Dataset.py         | 14 +++++++++-----
 askomics/libaskomics/OntologyManager.py | 10 +++++++---
 askomics/libaskomics/SparqlQuery.py     |  6 ++++--
 7 files changed, 38 insertions(+), 13 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 8ae19015..97e9a2ef 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -760,7 +760,7 @@ def add_ontology():
         }), 400
 
     try:
-        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, type, label_uri)
+        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, type, label_uri, dataset.endpoint)
         ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/api/file.py b/askomics/api/file.py
index 8ef6b4bf..95e1d84f 100644
--- a/askomics/api/file.py
+++ b/askomics/api/file.py
@@ -343,8 +343,10 @@ def integrate():
                 "public": (data.get("public", False) if session["user"]["admin"] else False) or current_app.iniconfig.getboolean("askomics", "single_tenant", fallback=False)
             }
 
+            endpoint = data["externalEndpoint"] or current_app.iniconfig.get('triplestore', 'endpoint')
+
             dataset = Dataset(current_app, session, dataset_info)
-            dataset.save_in_db()
+            dataset.save_in_db(endpoint)
             data["dataset_id"] = dataset.id
             dataset_ids.append(dataset.id)
             task = current_app.celery.send_task('integrate', (session_dict, data, request.host_url))
diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 224bb95b..fb9ce736 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -37,7 +37,7 @@ def autocomplete(short_ontology):
                 "results": []
             }), 404
 
-        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"])
+        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"], ontology["endpoint"])
 
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index 52fff976..df96feb6 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -167,6 +167,7 @@ def create_datasets_table(self):
             end int,
             ntriples int,
             error_message text,
+            endpoint text,
             FOREIGN KEY(user_id) REFERENCES users(user_id),
             FOREIGN KEY(file_id) REFERENCES files(id)
         )
@@ -209,6 +210,17 @@ def update_datasets_table(self):
         except Exception:
             pass
 
+        query = '''
+        ALTER TABLE datasets
+        ADD endpoint text NULL
+        DEFAULT(0)
+        '''
+
+        try:
+            self.execute_sql_query(query)
+        except Exception:
+            pass
+
     def create_integration_table(self):
         """Create the integration table"""
         query = '''
@@ -428,6 +440,7 @@ def create_ontologies_table(self):
         ALTER TABLE ontologies
         ADD label_uri text NOT NULL
         DEFAULT('rdfs:label')
+        ADD endpoint text NOT NULL
         '''
 
         try:
diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index fa0b5e89..87bae1ba 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -59,7 +59,7 @@ def set_info_from_db(self, admin=False):
             where_query = "AND user_id = ?"
 
         query = '''
-        SELECT celery_id, file_id, name, graph_name, public, start, end, ontology
+        SELECT celery_id, file_id, name, graph_name, public, start, end, ontology, endpoint
         FROM datasets
         WHERE id = ?
         {}
@@ -75,8 +75,9 @@ def set_info_from_db(self, admin=False):
         self.start = rows[0][5]
         self.end = rows[0][6]
         self.ontology = rows[0][7]
+        self.endpoint = rows[0][8]
 
-    def save_in_db(self, set_graph=False):
+    def save_in_db(self, endpoint, set_graph=False):
         """Save the dataset into the database"""
         database = Database(self.app, self.session)
 
@@ -87,7 +88,8 @@ def save_in_db(self, set_graph=False):
             self.file_id,
             self.name,
             self.public,
-            0
+            0,
+            endpoint
         )
 
         if set_graph:
@@ -99,7 +101,8 @@ def save_in_db(self, set_graph=False):
                 self.name,
                 self.graph_name,
                 self.public,
-                0
+                0,
+                endpoint
             )
 
         query = '''
@@ -118,7 +121,8 @@ def save_in_db(self, set_graph=False):
             NULL,
             NULL,
             NULL,
-            0
+            0,
+            ?
         )
         '''.format(subquery)
 
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index e800a898..7a8a1e3f 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -145,7 +145,7 @@ def get_ontology(self, short_name="", uri=""):
             'label_uri': ontology[7]
         }
 
-    def add_ontology(self, name, uri, short_name, dataset_id, graph, type="local", label_uri="rdfs:label"):
+    def add_ontology(self, name, uri, short_name, dataset_id, graph, endpoint, type="local", label_uri="rdfs:label"):
         """Create a new ontology
 
         Returns
@@ -154,6 +154,8 @@ def add_ontology(self, name, uri, short_name, dataset_id, graph, type="local", l
             Prefixes information
         """
         database = Database(self.app, self.session)
+        if not endpoint:
+            endpoint = self.settings.get('triplestore', 'endpoint')
 
         query = '''
         INSERT INTO ontologies VALUES(
@@ -164,11 +166,12 @@ def add_ontology(self, name, uri, short_name, dataset_id, graph, type="local", l
             ?,
             ?,
             ?,
+            ?,
             ?
         )
         '''
 
-        database.execute_sql_query(query, (name, uri, short_name, type, dataset_id, graph, label_uri))
+        database.execute_sql_query(query, (name, uri, short_name, type, dataset_id, graph, label_uri, endpoint))
 
         query = '''
         UPDATE datasets SET
@@ -222,7 +225,7 @@ def test_ols_ontology(self, shortname):
         r = requests.get(base_url)
         return r.status_code == 200
 
-    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name, onto_graph):
+    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name, onto_graph, onto_endpoint):
         """Search in ontology
 
         Returns
@@ -238,6 +241,7 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
             query = SparqlQuery(self.app, self.session, get_graphs=False)
             # TODO: Actually store the graph in the ontology to quicken search
             query.set_graphs([onto_graph])
+            query.set_endpoints(set([self.settings.get('triplestore', 'endpoint'), onto_endpoint]))
             return query.autocomplete_local_ontology(ontology_uri, query_term, max_results)
         elif ontology_type == "ols":
             base_url = "https://www.ebi.ac.uk/ols/api/suggest"
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index b92c592c..ec462d6a 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -573,9 +573,11 @@ def autocomplete_local_ontology(self, uri, query, max_terms):
 
         raw_query = self.prefix_query(raw_query)
 
-        sparql = self.format_query(raw_query, limit=max_terms, replace_froms=True, federated=False, ignore_single_tenant=True)
+        is_federated = self.is_federated()
 
-        query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=False)
+        sparql = self.format_query(raw_query, limit=max_terms, replace_froms=True, federated=is_federated, ignore_single_tenant=True)
+
+        query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=is_federated)
         _, data = query_launcher.process_query(sparql)
 
         formated_data = []

From 96acaece02b74a4bd29d97151525ccb7ed8811d8 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 7 Jun 2022 15:57:46 +0200
Subject: [PATCH 083/113] Remote graph

---
 askomics/libaskomics/PrefixManager.py |  3 +-
 askomics/libaskomics/SparqlQuery.py   | 45 +++++++++++++++++++++------
 tests/results/init.json               |  2 +-
 tests/results/sparql_query.json       |  2 +-
 4 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/askomics/libaskomics/PrefixManager.py b/askomics/libaskomics/PrefixManager.py
index 67499f1b..493fab53 100644
--- a/askomics/libaskomics/PrefixManager.py
+++ b/askomics/libaskomics/PrefixManager.py
@@ -42,7 +42,8 @@ def __init__(self, app, session):
             'rdfs:': str(rdflib.RDFS),
             'owl:': str(rdflib.OWL),
             'xsd:': str(rdflib.XSD),
-            'skos:': str(rdflib.SKOS)
+            'skos:': str(rdflib.SKOS),
+            'dcat:': str(rdflib.DCAT)
         }
 
     def get_prefix(self):
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index ec462d6a..bd07e9e7 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -6,6 +6,8 @@
 from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
 from askomics.libaskomics.Utils import Utils
 
+from collections import defaultdict
+
 
 class SparqlQuery(Params):
     """Format a sparql query
@@ -33,8 +35,9 @@ def __init__(self, app, session, json_query=None, get_graphs=False):
         self.json = json_query
         self.sparql = None
 
-        self.graphs = []
-        self.endpoints = []
+        self.graphs = set()
+        self.endpoints = set()
+        self.remote_graphs = defaultdict(set)
         self.selects = []
         self.federated = False
 
@@ -378,6 +381,23 @@ def get_federated_froms_from_graphs(self, graphs):
 
         return from_string
 
+    def get_federated_remote_from_graphs(self):
+        """Get @from string fir the federated query engine
+
+        Returns
+        -------
+        string
+            The from string
+        """
+        from_string = ""
+
+        for endpoint in self.endpoints:
+            remote_graphs = self.remote_graphs.get(endpoint)
+            if len(remote_graphs) == 1:
+                from_string += "\n@graph <{}> <{}>".format(endpoint, remote_graphs[0])
+
+        return from_string
+
     def get_endpoints_string(self):
         """get endpoint strngs for the federated query engine
 
@@ -410,7 +430,7 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
             filter_public_string = 'FILTER (?public = <true> || ?creator = <{}>)'.format(self.session["user"]["username"])
 
         query = '''
-        SELECT DISTINCT ?graph ?endpoint ?entity_uri
+        SELECT DISTINCT ?graph ?endpoint ?entity_uri ?remote_graph
         WHERE {{
           ?graph_abstraction askomics:public ?public .
           ?graph_abstraction dc:creator ?creator .
@@ -418,6 +438,7 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
           ?graph dc:creator ?creator .
           GRAPH ?graph_abstraction {{
             ?graph_abstraction prov:atLocation ?endpoint .
+            OPTIONAL {{?graph_abstraction dcat:Dataset ?remote_graph .}}
             ?entity_uri a ?askomics_type .
           }}
           GRAPH ?graph {{
@@ -433,15 +454,17 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
 
         query_launcher = SparqlQueryLauncher(self.app, self.session)
         header, results = query_launcher.process_query(self.prefix_query(query))
-        self.graphs = []
-        self.endpoints = []
+        self.graphs = set()
+        self.endpoints = set()
+        self.remote_graphs = defaultdict(set)
         for res in results:
             if not graphs or res["graph"] in graphs:
                 # Override with onto graph if matching uri
                 if ontologies.get(res['entity_uri']):
-                    self.graphs.append(ontologies[res['entity_uri']]['graph'])
+                    graph = ontologies[res['entity_uri']]['graph']
                 else:
-                    self.graphs.append(res["graph"])
+                    graph = res["graph"]
+                self.graphs.add(graph)
 
             # If local triplestore url is not accessible by federated query engine
             if res["endpoint"] == self.settings.get('triplestore', 'endpoint') and self.local_endpoint_f is not None:
@@ -450,9 +473,10 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
                 endpoint = res["endpoint"]
 
             if not endpoints or endpoint in endpoints:
-                self.endpoints.append(endpoint)
+                self.endpoints.add(endpoint)
+                if res.get("remote_graph"):
+                    self.remote_graphs[endpoint] = res.get("remote_graph")
 
-        self.endpoints = Utils.unique(self.endpoints)
         self.federated = len(self.endpoints) > 1
 
     def get_uri_parameters(self, uri, endpoints):
@@ -1473,6 +1497,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
         from_string = "" if self.settings.getboolean("askomics", "single_tenant", fallback=False) else self.get_froms_from_graphs(self.graphs)
         federated_from_string = self.get_federated_froms_from_graphs(self.graphs)
         endpoints_string = self.get_endpoints_string()
+        federated_graphs_string = self.get_federated_remote_from_graphs()
 
         # Linked attributes: replace SPARQL variable target by source
         self.replace_variables_in_blocks(var_to_replace)
@@ -1502,6 +1527,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
             query = """
 {endpoints}
 {federated}
+{remote_graphs}
 
 SELECT DISTINCT {selects}
 WHERE {{
@@ -1513,6 +1539,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
             """.format(
                 endpoints=endpoints_string,
                 federated=federated_from_string,
+                remote_graphs=federated_graphs_string,
                 selects=' '.join(self.selects),
                 triples='\n    '.join([self.triple_dict_to_string(triple_dict) for triple_dict in self.triples]),
                 blocks='\n    '.join([self.triple_block_to_string(triple_block) for triple_block in self.triples_blocks]),
diff --git a/tests/results/init.json b/tests/results/init.json
index 8eea5f0e..0f3054bf 100644
--- a/tests/results/init.json
+++ b/tests/results/init.json
@@ -1,5 +1,5 @@
 {
-  "defaultQuery": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?s ?p ?o\nWHERE {\n    ?s ?p ?o\n}\n",
+  "defaultQuery": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX dcat: <http://www.w3.org/ns/dcat#>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?s ?p ?o\nWHERE {\n    ?s ?p ?o\n}\n",
   "diskSpace": ###SIZE###,
   "console_enabled": true,
   "endpoints": {
diff --git a/tests/results/sparql_query.json b/tests/results/sparql_query.json
index aae08c25..0bfe4a08 100644
--- a/tests/results/sparql_query.json
+++ b/tests/results/sparql_query.json
@@ -37,5 +37,5 @@
         "uri": "urn:sparql:askomics_test:1_jdoe:gene.gff3_###GFF_TIMESTAMP###"
     }
   },
-  "query": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?transcript1_Label\nWHERE {\n    ?transcript1_uri rdf:type <http://askomics.org/test/data/transcript> .\n    ?transcript1_uri rdfs:label ?transcript1_Label .\n\n\n\n}\n"
+  "query": "PREFIX : <http://askomics.org/test/data/>\nPREFIX askomics: <http://askomics.org/test/internal/>\nPREFIX dc: <http://purl.org/dc/elements/1.1/>\nPREFIX dcat: <http://www.w3.org/ns/dcat#>\nPREFIX faldo: <http://biohackathon.org/resource/faldo/>\nPREFIX owl: <http://www.w3.org/2002/07/owl#>\nPREFIX prov: <http://www.w3.org/ns/prov#>\nPREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\nPREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nPREFIX skos: <http://www.w3.org/2004/02/skos/core#>\nPREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n\nSELECT DISTINCT ?transcript1_Label\nWHERE {\n    ?transcript1_uri rdf:type <http://askomics.org/test/data/transcript> .\n    ?transcript1_uri rdfs:label ?transcript1_Label .\n\n\n\n}\n"
 }

From 234a6223afa4ca7f1cc2fff31b97ab3f135969ab Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 7 Jun 2022 16:17:19 +0200
Subject: [PATCH 084/113] Test

---
 tests/conftest.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 06a18da6..18aabdc0 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -320,7 +320,7 @@ def integrate_file(self, info, public=False, set_graph=False):
             }
 
             dataset = Dataset(self.app, self.session, dataset_info)
-            dataset.save_in_db(set_graph=set_graph)
+            dataset.save_in_db("http://virtuoso:8890/sparql", set_graph=set_graph)
 
             if file.type == "csv/tsv":
                 file.integrate(dataset.id, info["columns_type"], public=public)
@@ -481,7 +481,7 @@ def create_result(self, has_form=False):
         # Save job in database database
         result = Result(self.app, self.session, info)
 
-        result.save_in_db()
+        result.save_in_db("http://virtuoso:8890/sparql")
 
         # Execute query and write result to file
         headers, results = query_launcher.process_query(query.sparql)

From 93c9ae74206905ecd92a4eff7eb024de7b7f7caa Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 7 Jun 2022 16:51:27 +0200
Subject: [PATCH 085/113] Fix table order

---
 askomics/libaskomics/Database.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index df96feb6..b60a72e7 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -167,6 +167,7 @@ def create_datasets_table(self):
             end int,
             ntriples int,
             error_message text,
+            ontology boolean,
             endpoint text,
             FOREIGN KEY(user_id) REFERENCES users(user_id),
             FOREIGN KEY(file_id) REFERENCES files(id)
@@ -213,7 +214,6 @@ def update_datasets_table(self):
         query = '''
         ALTER TABLE datasets
         ADD endpoint text NULL
-        DEFAULT(0)
         '''
 
         try:

From a7fbaf15f3aab25972dfb2e8de9bc9f361d6fb93 Mon Sep 17 00:00:00 2001
From: root <root@test-asko.novalocal>
Date: Tue, 7 Jun 2022 16:29:27 +0000
Subject: [PATCH 086/113] tests

---
 askomics/api/admin.py               |  6 +++---
 askomics/libaskomics/Database.py    | 14 +++++++++++---
 askomics/libaskomics/SparqlQuery.py | 15 ++++++++-------
 tests/conftest.py                   |  2 +-
 tests/test_api_admin.py             |  2 +-
 5 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 97e9a2ef..631b8b1a 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -691,7 +691,7 @@ def add_ontology():
     """
 
     data = request.get_json()
-    if not data or not (data.get("name") and data.get("uri") and data.get("shortName") and data.get("type") and data.get("datasetId")):
+    if not data or not (data.get("name") and data.get("uri") and data.get("shortName") and data.get("type") and data.get("datasetId") and data.get("labelUri")):
         return jsonify({
             'ontologies': [],
             'error': True,
@@ -703,7 +703,7 @@ def add_ontology():
     short_name = data.get("shortName")
     type = data.get("type")
     dataset_id = data.get("datasetId")
-    label_uri = data.get("labelUri", "rdfs:label")
+    label_uri = data.get("labelUri")
 
     om = OntologyManager(current_app, session)
 
@@ -760,7 +760,7 @@ def add_ontology():
         }), 400
 
     try:
-        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, type, label_uri, dataset.endpoint)
+        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, dataset.endpoint, type, label_uri)
         ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index b60a72e7..8a3c7e90 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -167,8 +167,6 @@ def create_datasets_table(self):
             end int,
             ntriples int,
             error_message text,
-            ontology boolean,
-            endpoint text,
             FOREIGN KEY(user_id) REFERENCES users(user_id),
             FOREIGN KEY(file_id) REFERENCES files(id)
         )
@@ -214,6 +212,7 @@ def update_datasets_table(self):
         query = '''
         ALTER TABLE datasets
         ADD endpoint text NULL
+        DEFAULT(null)
         '''
 
         try:
@@ -440,7 +439,16 @@ def create_ontologies_table(self):
         ALTER TABLE ontologies
         ADD label_uri text NOT NULL
         DEFAULT('rdfs:label')
-        ADD endpoint text NOT NULL
+        '''
+
+        try:
+            self.execute_sql_query(query)
+        except Exception:
+            pass
+
+        query = '''
+        ALTER TABLE ontologies
+        ADD endpoint text NULL
         '''
 
         try:
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index bd07e9e7..3bbcf1e1 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -35,8 +35,8 @@ def __init__(self, app, session, json_query=None, get_graphs=False):
         self.json = json_query
         self.sparql = None
 
-        self.graphs = set()
-        self.endpoints = set()
+        self.graphs = []
+        self.endpoints = []
         self.remote_graphs = defaultdict(set)
         self.selects = []
         self.federated = False
@@ -392,7 +392,7 @@ def get_federated_remote_from_graphs(self):
         from_string = ""
 
         for endpoint in self.endpoints:
-            remote_graphs = self.remote_graphs.get(endpoint)
+            remote_graphs = self.remote_graphs.get(endpoint, [])
             if len(remote_graphs) == 1:
                 from_string += "\n@graph <{}> <{}>".format(endpoint, remote_graphs[0])
 
@@ -454,8 +454,8 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
 
         query_launcher = SparqlQueryLauncher(self.app, self.session)
         header, results = query_launcher.process_query(self.prefix_query(query))
-        self.graphs = set()
-        self.endpoints = set()
+        self.graphs = []
+        self.endpoints = []
         self.remote_graphs = defaultdict(set)
         for res in results:
             if not graphs or res["graph"] in graphs:
@@ -464,7 +464,7 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
                     graph = ontologies[res['entity_uri']]['graph']
                 else:
                     graph = res["graph"]
-                self.graphs.add(graph)
+                self.graphs.append(graph)
 
             # If local triplestore url is not accessible by federated query engine
             if res["endpoint"] == self.settings.get('triplestore', 'endpoint') and self.local_endpoint_f is not None:
@@ -473,10 +473,11 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
                 endpoint = res["endpoint"]
 
             if not endpoints or endpoint in endpoints:
-                self.endpoints.add(endpoint)
+                self.endpoints.append(endpoint)
                 if res.get("remote_graph"):
                     self.remote_graphs[endpoint] = res.get("remote_graph")
 
+        self.endpoints = Utils.unique(self.endpoints)
         self.federated = len(self.endpoints) > 1
 
     def get_uri_parameters(self, uri, endpoints):
diff --git a/tests/conftest.py b/tests/conftest.py
index 18aabdc0..84d08eed 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -481,7 +481,7 @@ def create_result(self, has_form=False):
         # Save job in database database
         result = Result(self.app, self.session, info)
 
-        result.save_in_db("http://virtuoso:8890/sparql")
+        result.save_in_db()
 
         # Execute query and write result to file
         headers, results = query_launcher.process_query(query.sparql)
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 56b7d103..d3b74f6d 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -633,7 +633,7 @@ def test_add_ontology(self, client):
         client.create_two_users()
         client.log_user("jsmith")
 
-        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local", "datasetId": 1}
+        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local", "datasetId": 1, "labelUri": "rdfs:label"}
 
         response = client.client.post('/api/admin/addontology', json=data)
         assert response.status_code == 401

From 5b734d33b705ab3cf0f341e46907f5598f62084c Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 10 Jun 2022 15:44:05 +0000
Subject: [PATCH 087/113] custom external graph

---
 askomics/api/file.py                          |  1 +
 askomics/libaskomics/BedFile.py               |  4 +--
 askomics/libaskomics/CsvFile.py               |  4 +--
 askomics/libaskomics/File.py                  |  6 +++-
 askomics/libaskomics/FilesHandler.py          | 11 +++----
 askomics/libaskomics/GffFile.py               |  4 +--
 askomics/libaskomics/RdfFile.py               | 29 +++++++++++++------
 askomics/libaskomics/RdfGraph.py              |  1 +
 .../src/routes/integration/rdfpreview.jsx     | 14 ++++++++-
 askomics/tasks.py                             |  2 +-
 10 files changed, 53 insertions(+), 23 deletions(-)

diff --git a/askomics/api/file.py b/askomics/api/file.py
index 95e1d84f..7348323f 100644
--- a/askomics/api/file.py
+++ b/askomics/api/file.py
@@ -333,6 +333,7 @@ def integrate():
         for file in files_handler.files:
 
             data["externalEndpoint"] = data["externalEndpoint"] if (data.get("externalEndpoint") and isinstance(file, RdfFile)) else None
+            data["externalGraph"] = data["externalGraph"] if (data.get("externalGraph") and isinstance(file, RdfFile)) else None
             data["customUri"] = data["customUri"] if (data.get("customUri") and not isinstance(file, RdfFile)) else None
 
             dataset_info = {
diff --git a/askomics/libaskomics/BedFile.py b/askomics/libaskomics/BedFile.py
index 24ebf6da..98802ada 100644
--- a/askomics/libaskomics/BedFile.py
+++ b/askomics/libaskomics/BedFile.py
@@ -17,7 +17,7 @@ class BedFile(File):
         Public or private dataset
     """
 
-    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None):
+    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None, external_graph=None):
         """init
 
         Parameters
@@ -31,7 +31,7 @@ def __init__(self, app, session, file_info, host_url=None, external_endpoint=Non
         host_url : None, optional
             AskOmics url
         """
-        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri)
+        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri, external_graph=external_graph)
 
         self.entity_name = ''
         self.category_values = {}
diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
index 8c1bcbac..821f00dd 100644
--- a/askomics/libaskomics/CsvFile.py
+++ b/askomics/libaskomics/CsvFile.py
@@ -29,7 +29,7 @@ class CsvFile(File):
         Public
     """
 
-    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None):
+    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None, external_graph=None):
         """init
 
         Parameters
@@ -43,7 +43,7 @@ def __init__(self, app, session, file_info, host_url=None, external_endpoint=Non
         host_url : None, optional
             AskOmics url
         """
-        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri)
+        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri, external_graph=external_graph)
         self.preview_limit = 30
         try:
             self.preview_limit = self.settings.getint("askomics", "npreview")
diff --git a/askomics/libaskomics/File.py b/askomics/libaskomics/File.py
index b5cd4879..05389c3d 100644
--- a/askomics/libaskomics/File.py
+++ b/askomics/libaskomics/File.py
@@ -69,7 +69,7 @@ class File(Params):
         User graph
     """
 
-    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None):
+    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None, external_graph=None):
         """init
 
         Parameters
@@ -97,6 +97,7 @@ def __init__(self, app, session, file_info, host_url=None, external_endpoint=Non
         self.ntriples = 0
         self.timestamp = int(time.time())
         self.external_endpoint = external_endpoint
+        self.external_graph = external_graph
 
         self.default_graph = "{}".format(self.settings.get('triplestore', 'default_graph'))
         self.user_graph = "{}:{}_{}".format(
@@ -130,6 +131,7 @@ def __init__(self, app, session, file_info, host_url=None, external_endpoint=Non
         self.faldo = Namespace('http://biohackathon.org/resource/faldo/')
         self.prov = Namespace('http://www.w3.org/ns/prov#')
         self.dc = Namespace('http://purl.org/dc/elements/1.1/')
+        self.dcat = Namespace('http://www.w3.org/ns/dcat#')
 
         self.faldo_entity = False
         self.faldo_abstraction = {
@@ -277,6 +279,8 @@ def set_metadata(self):
         self.graph_metadata.add((rdflib.Literal(self.file_graph), self.prov.wasDerivedFrom, rdflib.Literal(self.name)))
         self.graph_metadata.add((rdflib.Literal(self.file_graph), self.dc.hasVersion, rdflib.Literal(get_distribution('askomics').version)))
         self.graph_metadata.add((rdflib.Literal(self.file_graph), self.prov.describesService, rdflib.Literal(os.uname()[1])))
+        if self.external_graph:
+            self.graph_metadata.add((rdflib.Literal(self.file_graph), self.dcat.Dataset, self.external_graph))
 
         if self.public:
             self.graph_metadata.add((rdflib.Literal(self.file_graph), self.namespace_internal['public'], rdflib.Literal(True)))
diff --git a/askomics/libaskomics/FilesHandler.py b/askomics/libaskomics/FilesHandler.py
index d3d1adfe..04254028 100644
--- a/askomics/libaskomics/FilesHandler.py
+++ b/askomics/libaskomics/FilesHandler.py
@@ -24,7 +24,7 @@ class FilesHandler(FilesUtils):
         Upload path
     """
 
-    def __init__(self, app, session, host_url=None, external_endpoint=None, custom_uri=None):
+    def __init__(self, app, session, host_url=None, external_endpoint=None, custom_uri=None, external_graph=None):
         """init
 
         Parameters
@@ -47,6 +47,7 @@ def __init__(self, app, session, host_url=None, external_endpoint=None, custom_u
         self.date = None
         self.external_endpoint = external_endpoint
         self.custom_uri = custom_uri
+        self.external_graph = external_graph
 
     def handle_files(self, files_id):
         """Handle file
@@ -60,13 +61,13 @@ def handle_files(self, files_id):
 
         for file in files_infos:
             if file['type'] == 'csv/tsv':
-                self.files.append(CsvFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri))
+                self.files.append(CsvFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri, external_graph=self.external_graph))
             elif file['type'] == 'gff/gff3':
-                self.files.append(GffFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri))
+                self.files.append(GffFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri, external_graph=self.external_graph))
             elif file['type'] in ('rdf/ttl', 'rdf/xml', 'rdf/nt'):
-                self.files.append(RdfFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri))
+                self.files.append(RdfFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri, external_graph=self.external_graph))
             elif file['type'] == 'bed':
-                self.files.append(BedFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri))
+                self.files.append(BedFile(self.app, self.session, file, host_url=self.host_url, external_endpoint=self.external_endpoint, custom_uri=self.custom_uri, external_graph=self.external_graph))
 
     def get_files_infos(self, files_id=None, files_path=None, return_path=False):
         """Get files info
diff --git a/askomics/libaskomics/GffFile.py b/askomics/libaskomics/GffFile.py
index 28341bab..7c413de7 100644
--- a/askomics/libaskomics/GffFile.py
+++ b/askomics/libaskomics/GffFile.py
@@ -18,7 +18,7 @@ class GffFile(File):
         Public or private dataset
     """
 
-    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None):
+    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None, external_graph=None):
         """init
 
         Parameters
@@ -32,7 +32,7 @@ def __init__(self, app, session, file_info, host_url=None, external_endpoint=Non
         host_url : None, optional
             AskOmics url
         """
-        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri)
+        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri, external_graph=external_graph)
 
         self.entities = []
         self.entities_to_integrate = []
diff --git a/askomics/libaskomics/RdfFile.py b/askomics/libaskomics/RdfFile.py
index b1252d01..008bbd3b 100644
--- a/askomics/libaskomics/RdfFile.py
+++ b/askomics/libaskomics/RdfFile.py
@@ -14,7 +14,7 @@ class RdfFile(File):
         Public or private dataset
     """
 
-    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None):
+    def __init__(self, app, session, file_info, host_url=None, external_endpoint=None, custom_uri=None, external_graph=None):
         """init
 
         Parameters
@@ -28,7 +28,7 @@ def __init__(self, app, session, file_info, host_url=None, external_endpoint=Non
         host_url : None, optional
             AskOmics url
         """
-        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri)
+        File.__init__(self, app, session, file_info, host_url, external_endpoint=external_endpoint, custom_uri=custom_uri, external_graph=external_graph)
 
         self.type_dict = {
             "rdf/ttl": "turtle",
@@ -40,7 +40,7 @@ def set_preview(self):
         """Summary"""
         pass
 
-    def get_location(self):
+    def get_location_and_remote_graph(self):
         """Get location of data if specified
 
         Returns
@@ -50,10 +50,19 @@ def get_location(self):
         """
         graph = RdfGraph(self.app, self.session)
         graph.parse(self.path, format=self.type_dict[self.type])
-        triple = (None, self.prov.atLocation, None)
-        for s, p, o in graph.graph.triples(triple):
-            return str(o)
-        return None
+        triple_loc = (None, self.prov.atLocation, None)
+        triple_graph = (None, self.dcat.Dataset, None)
+        loc = None
+        remote_graph = None
+        for s, p, o in graph.graph.triples(triple_loc):
+            loc = str(o)
+            break
+
+        for s, p, o in graph.graph.triples(triple_graph):
+            remote_graph = str(o)
+            break
+
+        return loc, remote_graph
 
     def get_preview(self):
         """Get a preview of the frist 100 lines of a ttl file
@@ -71,7 +80,7 @@ def get_preview(self):
 
         location = None
         try:
-            location = self.get_location()
+            location, remote_graph = self.get_location_and_remote_graph()
         except Exception as e:
             self.error_message = str(e)
 
@@ -83,13 +92,15 @@ def get_preview(self):
             'error_message': self.error_message,
             'data': {
                 'preview': head,
-                'location': location
+                'location': location,
+                'remote_graph': remote_graph
             }
         }
 
     def delete_metadata_location(self):
         """Delete metadata from data"""
         self.graph_chunk.remove((None, self.prov.atLocation, None))
+        self.graph_chunk.remove((None, self.dcat.Dataset, None))
 
     def integrate(self, public=False):
         """Integrate the file into the triplestore
diff --git a/askomics/libaskomics/RdfGraph.py b/askomics/libaskomics/RdfGraph.py
index 0bd40e0b..0024a3ed 100644
--- a/askomics/libaskomics/RdfGraph.py
+++ b/askomics/libaskomics/RdfGraph.py
@@ -40,6 +40,7 @@ def __init__(self, app, session):
         self.graph.bind('faldo', "http://biohackathon.org/resource/faldo/")
         self.graph.bind('dc', 'http://purl.org/dc/elements/1.1/')
         self.graph.bind('prov', 'http://www.w3.org/ns/prov#')
+        self.graph.bind('dcat', 'http://www.w3.org/ns/dcat#')
         self.ntriple = 0
         self.percent = None
 
diff --git a/askomics/react/src/routes/integration/rdfpreview.jsx b/askomics/react/src/routes/integration/rdfpreview.jsx
index 5dbbd4b9..c21fc4be 100644
--- a/askomics/react/src/routes/integration/rdfpreview.jsx
+++ b/askomics/react/src/routes/integration/rdfpreview.jsx
@@ -24,6 +24,7 @@ export default class RdfPreview extends Component {
       privateTick: false,
       customUri: "",
       externalEndpoint: props.file.data.location ? props.file.data.location : "",
+      externalGraph: props.file.data.remote_graph ? props.file.data.remote_graph : "",
       error: false,
       errorMessage: null,
       status: null
@@ -49,7 +50,8 @@ export default class RdfPreview extends Component {
       public: event.target.value == 'public',
       type: this.props.file.type,
       customUri: this.state.customUri,
-      externalEndpoint: this.state.externalEndpoint
+      externalEndpoint: this.state.externalEndpoint,
+      remoteGraph: this.state.remoteGraph
     }
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
       .then(response => {
@@ -85,6 +87,14 @@ export default class RdfPreview extends Component {
     })
   }
 
+  handleChangeRemoteGraph (event) {
+    this.setState({
+      remoteGraph: event.target.value,
+      publicTick: false,
+      privateTick: false
+    })
+  }
+
   guess_mode(type) {
     if (type == "rdf/ttl") {
       return "turtle"
@@ -142,6 +152,8 @@ export default class RdfPreview extends Component {
           config={this.props.config}
           handleChangeEndpoint={p => this.handleChangeEndpoint(p)}
           externalEndpoint={this.state.externalEndpoint}
+          handleChangeExternalGraph={p => this.handleChangeExternalGraph(p)}
+          externalGraph={this.state.externalGraph}
           handleChangeUri={p => this.handleChangeUri(p)}
         />
         <br />
diff --git a/askomics/tasks.py b/askomics/tasks.py
index 285cd6a8..ee048d3e 100644
--- a/askomics/tasks.py
+++ b/askomics/tasks.py
@@ -44,7 +44,7 @@ def integrate(self, session, data, host_url):
         error: True if error, else False
         errorMessage: the error message of error, else an empty string
     """
-    files_handler = FilesHandler(app, session, host_url=host_url, external_endpoint=data["externalEndpoint"], custom_uri=data["customUri"])
+    files_handler = FilesHandler(app, session, host_url=host_url, external_endpoint=data["externalEndpoint"], custom_uri=data["customUri"], external_graph=data['externalGraph'])
     files_handler.handle_files([data["fileId"], ])
 
     public = (data.get("public", False) if session["user"]["admin"] else False) or app.iniconfig.getboolean("askomics", "single_tenant", fallback=False)

From 755b6becd08e9fa86dc3ebfdb5174ce4640b26cb Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 13 Jun 2022 10:23:27 +0200
Subject: [PATCH 088/113] React

---
 .../routes/integration/advancedoptions.jsx    | 11 ++++++++--
 .../src/routes/integration/bedpreview.jsx     |  5 ++++-
 .../react/src/routes/integration/csvtable.jsx | 13 +++++++++++-
 .../src/routes/integration/gffpreview.jsx     | 21 ++++++++++++++++++-
 4 files changed, 45 insertions(+), 5 deletions(-)

diff --git a/askomics/react/src/routes/integration/advancedoptions.jsx b/askomics/react/src/routes/integration/advancedoptions.jsx
index 4a6c8988..6c9ae84c 100644
--- a/askomics/react/src/routes/integration/advancedoptions.jsx
+++ b/askomics/react/src/routes/integration/advancedoptions.jsx
@@ -41,6 +41,12 @@ export default class AdvancedOptions extends Component {
                 <Input onChange={this.handleChangeEndpoint} value={this.props.externalEndpoint} type="text" name="endpoint" id="endpoint" placeholder="External endpoint" />
               </Col>
             </FormGroup>
+            <FormGroup hidden={this.props.hideDistantEndpoint} row>
+              <Label for="endpoint" sm={2}>Distant graph</Label>
+              <Col sm={8}>
+                <Input onChange={this.handleChangeExternalGraph} value={this.props.externalGraph} type="text" name="graph" id="graph" placeholder="External graph" />
+              </Col>
+            </FormGroup>
           </Form>
         </Collapse>
       </div>
@@ -55,5 +61,6 @@ AdvancedOptions.propTypes = {
   hideCustomUri: PropTypes.bool,
   customUri: PropTypes.string,
   hideDistantEndpoint: PropTypes.bool,
-  externalEndpoint: PropTypes.string
-}
+  externalEndpoint: PropTypes.string,
+  handleChangeExternalGraph: PropTypes.function,
+  externalGraph: PropTypes.string
diff --git a/askomics/react/src/routes/integration/bedpreview.jsx b/askomics/react/src/routes/integration/bedpreview.jsx
index 90e72d19..33755d69 100644
--- a/askomics/react/src/routes/integration/bedpreview.jsx
+++ b/askomics/react/src/routes/integration/bedpreview.jsx
@@ -21,7 +21,8 @@ export default class BedPreview extends Component {
       externalEndpoint: "",
       error: false,
       errorMessage: null,
-      status: null
+      status: null,
+      externalGraph: ""
     }
     this.cancelRequest
     this.integrate = this.integrate.bind(this)
@@ -122,6 +123,8 @@ export default class BedPreview extends Component {
             hideDistantEndpoint={true}
             handleChangeUri={p => this.handleChangeUri(p)}
             handleChangeEndpoint={p => this.handleChangeEndpoint(p)}
+            handleChangeExternalGraph={p => this.handleChangeExternalGraph(p)}
+            externalGraph={this.state.externalGraph}
             customUri={this.state.customUri}
           />
           <br />
diff --git a/askomics/react/src/routes/integration/csvtable.jsx b/askomics/react/src/routes/integration/csvtable.jsx
index c9a003a9..01837aa8 100644
--- a/askomics/react/src/routes/integration/csvtable.jsx
+++ b/askomics/react/src/routes/integration/csvtable.jsx
@@ -26,7 +26,8 @@ export default class CsvTable extends Component {
       externalEndpoint: "",
       error: false,
       errorMessage: null,
-      status: null
+      status: null,
+      externalGraph: ""
     }
     this.cancelRequest
     this.headerFormatter = this.headerFormatter.bind(this)
@@ -213,6 +214,14 @@ export default class CsvTable extends Component {
     })
   }
 
+  handleChangeRemoteGraph (event) {
+    this.setState({
+      remoteGraph: event.target.value,
+      publicTick: false,
+      privateTick: false
+    })
+  }
+
   toggleHeaderForm(event) {
     this.setState({
       header: update(this.state.header, { [event.target.id]: { input: { $set: true } } })
@@ -288,6 +297,8 @@ export default class CsvTable extends Component {
             hideDistantEndpoint={true}
             handleChangeUri={p => this.handleChangeUri(p)}
             handleChangeEndpoint={p => this.handleChangeEndpoint(p)}
+            handleChangeExternalGraph={p => this.handleChangeExternalGraph(p)}
+            externalGraph={this.state.externalGraph}
             customUri={this.state.customUri}
           />
           <br />
diff --git a/askomics/react/src/routes/integration/gffpreview.jsx b/askomics/react/src/routes/integration/gffpreview.jsx
index 0fafbbef..2210ee86 100644
--- a/askomics/react/src/routes/integration/gffpreview.jsx
+++ b/askomics/react/src/routes/integration/gffpreview.jsx
@@ -18,7 +18,8 @@ export default class GffPreview extends Component {
       publicTick: false,
       privateTick: false,
       customUri: "",
-      externalEndpoint: ""
+      externalEndpoint: "",
+      externalGraph: ""
     }
     this.cancelRequest
     this.integrate = this.integrate.bind(this)
@@ -90,6 +91,22 @@ export default class GffPreview extends Component {
     })
   }
 
+  handleChangeRemoteGraph (event) {
+    this.setState({
+      remoteGraph: event.target.value,
+      publicTick: false,
+      privateTick: false
+    })
+  }
+
+  handleChangeRemoteGraph (event) {
+    this.setState({
+      remoteGraph: event.target.value,
+      publicTick: false,
+      privateTick: false
+    })
+  }
+
   render () {
 
     let privateIcon = <i className="fas fa-lock"></i>
@@ -129,6 +146,8 @@ export default class GffPreview extends Component {
           hideDistantEndpoint={true}
           handleChangeUri={p => this.handleChangeUri(p)}
           handleChangeEndpoint={p => this.handleChangeEndpoint(p)}
+          handleChangeExternalGraph={p => this.handleChangeExternalGraph(p)}
+          externalGraph={this.state.externalGraph}
           customUri={this.state.customUri}
         />
         <br />

From d4b6cc9b5d2b782c34b3285ce25e59d46984dd92 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 13 Jun 2022 08:21:19 +0000
Subject: [PATCH 089/113] typo

---
 askomics/react/src/routes/integration/advancedoptions.jsx | 1 +
 1 file changed, 1 insertion(+)

diff --git a/askomics/react/src/routes/integration/advancedoptions.jsx b/askomics/react/src/routes/integration/advancedoptions.jsx
index 6c9ae84c..d54375bf 100644
--- a/askomics/react/src/routes/integration/advancedoptions.jsx
+++ b/askomics/react/src/routes/integration/advancedoptions.jsx
@@ -64,3 +64,4 @@ AdvancedOptions.propTypes = {
   externalEndpoint: PropTypes.string,
   handleChangeExternalGraph: PropTypes.function,
   externalGraph: PropTypes.string
+}

From 412d91ee91e6ef15d0e99610fd8b5a20b510b6ba Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 13 Jun 2022 09:39:35 +0000
Subject: [PATCH 090/113] fix

---
 askomics/libaskomics/File.py                         | 2 +-
 askomics/libaskomics/SparqlQuery.py                  | 6 +++---
 askomics/react/src/routes/integration/bedpreview.jsx | 8 ++++++++
 askomics/react/src/routes/integration/csvtable.jsx   | 4 ++--
 askomics/react/src/routes/integration/gffpreview.jsx | 4 ++--
 askomics/react/src/routes/integration/rdfpreview.jsx | 6 +++---
 6 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/askomics/libaskomics/File.py b/askomics/libaskomics/File.py
index 05389c3d..030f30e3 100644
--- a/askomics/libaskomics/File.py
+++ b/askomics/libaskomics/File.py
@@ -280,7 +280,7 @@ def set_metadata(self):
         self.graph_metadata.add((rdflib.Literal(self.file_graph), self.dc.hasVersion, rdflib.Literal(get_distribution('askomics').version)))
         self.graph_metadata.add((rdflib.Literal(self.file_graph), self.prov.describesService, rdflib.Literal(os.uname()[1])))
         if self.external_graph:
-            self.graph_metadata.add((rdflib.Literal(self.file_graph), self.dcat.Dataset, self.external_graph))
+            self.graph_metadata.add((rdflib.Literal(self.file_graph), self.dcat.Dataset, rdflib.Literal(self.external_graph)))
 
         if self.public:
             self.graph_metadata.add((rdflib.Literal(self.file_graph), self.namespace_internal['public'], rdflib.Literal(True)))
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 3bbcf1e1..69945cfb 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -37,7 +37,7 @@ def __init__(self, app, session, json_query=None, get_graphs=False):
 
         self.graphs = []
         self.endpoints = []
-        self.remote_graphs = defaultdict(set)
+        self.remote_graphs = defaultdict(list)
         self.selects = []
         self.federated = False
 
@@ -456,7 +456,7 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
         header, results = query_launcher.process_query(self.prefix_query(query))
         self.graphs = []
         self.endpoints = []
-        self.remote_graphs = defaultdict(set)
+        self.remote_graphs = defaultdict(list)
         for res in results:
             if not graphs or res["graph"] in graphs:
                 # Override with onto graph if matching uri
@@ -475,7 +475,7 @@ def set_graphs_and_endpoints(self, entities=None, graphs=None, endpoints=None, o
             if not endpoints or endpoint in endpoints:
                 self.endpoints.append(endpoint)
                 if res.get("remote_graph"):
-                    self.remote_graphs[endpoint] = res.get("remote_graph")
+                    self.remote_graphs[endpoint].append(res.get("remote_graph"))
 
         self.endpoints = Utils.unique(self.endpoints)
         self.federated = len(self.endpoints) > 1
diff --git a/askomics/react/src/routes/integration/bedpreview.jsx b/askomics/react/src/routes/integration/bedpreview.jsx
index 33755d69..ad3f7269 100644
--- a/askomics/react/src/routes/integration/bedpreview.jsx
+++ b/askomics/react/src/routes/integration/bedpreview.jsx
@@ -82,6 +82,14 @@ export default class BedPreview extends Component {
     })
   }
 
+  handleChangeExternalGraph (event) {
+    this.setState({
+      externalGraph: event.target.value,
+      publicTick: false,
+      privateTick: false
+    })
+  }
+
   render () {
 
     let privateIcon = <i className="fas fa-lock"></i>
diff --git a/askomics/react/src/routes/integration/csvtable.jsx b/askomics/react/src/routes/integration/csvtable.jsx
index 01837aa8..dddd55ba 100644
--- a/askomics/react/src/routes/integration/csvtable.jsx
+++ b/askomics/react/src/routes/integration/csvtable.jsx
@@ -214,9 +214,9 @@ export default class CsvTable extends Component {
     })
   }
 
-  handleChangeRemoteGraph (event) {
+  handleChangeExternalGraph (event) {
     this.setState({
-      remoteGraph: event.target.value,
+      externalGraph: event.target.value,
       publicTick: false,
       privateTick: false
     })
diff --git a/askomics/react/src/routes/integration/gffpreview.jsx b/askomics/react/src/routes/integration/gffpreview.jsx
index 2210ee86..ecff25c9 100644
--- a/askomics/react/src/routes/integration/gffpreview.jsx
+++ b/askomics/react/src/routes/integration/gffpreview.jsx
@@ -99,9 +99,9 @@ export default class GffPreview extends Component {
     })
   }
 
-  handleChangeRemoteGraph (event) {
+  handleChangeExternalGraph (event) {
     this.setState({
-      remoteGraph: event.target.value,
+      externalGraph: event.target.value,
       publicTick: false,
       privateTick: false
     })
diff --git a/askomics/react/src/routes/integration/rdfpreview.jsx b/askomics/react/src/routes/integration/rdfpreview.jsx
index c21fc4be..654747b4 100644
--- a/askomics/react/src/routes/integration/rdfpreview.jsx
+++ b/askomics/react/src/routes/integration/rdfpreview.jsx
@@ -51,7 +51,7 @@ export default class RdfPreview extends Component {
       type: this.props.file.type,
       customUri: this.state.customUri,
       externalEndpoint: this.state.externalEndpoint,
-      remoteGraph: this.state.remoteGraph
+      externalGraph: this.state.externalGraph
     }
     axios.post(requestUrl, data, { baseURL: this.props.config.proxyPath, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
       .then(response => {
@@ -87,9 +87,9 @@ export default class RdfPreview extends Component {
     })
   }
 
-  handleChangeRemoteGraph (event) {
+  handleChangeExternalGraph (event) {
     this.setState({
-      remoteGraph: event.target.value,
+      externalGraph: event.target.value,
       publicTick: false,
       privateTick: false
     })

From f2dc04c51e0c1d5b1beabcfc7e8be48ed6e1210e Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 22 Jun 2022 16:49:32 +0200
Subject: [PATCH 091/113] Tests & stuff

---
 askomics/libaskomics/OntologyManager.py | 10 ++--
 test-data/agro_min.ttl                  | 70 +++++++++++++++++++++++++
 tests/conftest.py                       | 39 ++++++++++++--
 tests/test_api_admin.py                 | 31 +++++------
 tests/test_api_ontology.py              | 21 ++++++++
 5 files changed, 148 insertions(+), 23 deletions(-)
 create mode 100644 test-data/agro_min.ttl
 create mode 100644 tests/test_api_ontology.py

diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 7a8a1e3f..d180d13a 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -76,7 +76,7 @@ def list_full_ontologies(self):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT ontologies.id, ontologies.name, ontologies.uri, ontologies.short_name, ontologies.type, ontologies.label_uri, datasets.id, datasets.name, ontologies.graph
+        SELECT ontologies.id, ontologies.name, ontologies.uri, ontologies.short_name, ontologies.type, ontologies.label_uri, datasets.id, datasets.name, ontologies.graph, ontologies.endpoint
         FROM ontologies
         INNER JOIN datasets ON datasets.id=ontologies.dataset_id
         '''
@@ -94,7 +94,8 @@ def list_full_ontologies(self):
                 'label_uri': row[5],
                 'dataset_id': row[6],
                 'dataset_name': row[7],
-                'graph': row[8]
+                'graph': row[8],
+                'endpoint': row[9]
             }
             ontologies.append(prefix)
 
@@ -123,7 +124,7 @@ def get_ontology(self, short_name="", uri=""):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, uri, short_name, type, dataset_id, graph, label_uri
+        SELECT id, name, uri, short_name, type, dataset_id, graph, label_uri, endpoint
         FROM ontologies
         {}
         '''.format(where_clause)
@@ -142,7 +143,8 @@ def get_ontology(self, short_name="", uri=""):
             'type': ontology[4],
             'dataset_id': ontology[5],
             'graph': ontology[6],
-            'label_uri': ontology[7]
+            'label_uri': ontology[7],
+            'endpoint': ontology[8]
         }
 
     def add_ontology(self, name, uri, short_name, dataset_id, graph, endpoint, type="local", label_uri="rdfs:label"):
diff --git a/test-data/agro_min.ttl b/test-data/agro_min.ttl
new file mode 100644
index 00000000..4f895879
--- /dev/null
+++ b/test-data/agro_min.ttl
@@ -0,0 +1,70 @@
+@prefix askomics: <https://test-192-168-100-87.vm.openstack.genouest.org/internal/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix ns1: <http://www.w3.org/ns/prov#> .
+
+
+<http://purl.obolibrary.org/obo/agro.owl> a askomics:ontology ;
+	a owl:ontology ;
+	rdfs:label "AGRO".
+	
+[] a owl:ObjectProperty ;
+	a askomics:AskomicsRelation ;
+	askomics:uri rdfs:subClassOf ;
+	rdfs:label "subClassOf" ;
+	rdfs:domain <http://purl.obolibrary.org/obo/agro.owl> ;
+	rdfs:range <http://purl.obolibrary.org/obo/agro.owl>.
+	
+
+<http://purl.obolibrary.org/obo/AGRO_00000007> a owl:Class ;
+    rdfs:label "desuckering" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000027> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000008> a owl:Class ;
+    rdfs:label "irrigation water source role" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000023> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000010> a owl:Class ;
+    rdfs:label "irrigation water quantity" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/PATO_0000122>,
+        <http://purl.obolibrary.org/obo/PATO_0000918> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000016> a owl:Class ;
+    rdfs:label "reduced tillage process" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000002> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000020> a owl:Class ;
+    rdfs:label "laser land levelling process" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000004> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000024> a owl:Class ;
+    rdfs:label "chemical pest control process" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000023> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000026> a owl:Class ;
+    rdfs:label "no-till" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_01000015>,
+        <http://purl.obolibrary.org/obo/ENVO_02500000> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000028> a owl:Class ;
+    rdfs:label "puddling process" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000002> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000029> a owl:Class ;
+    rdfs:label "mulch-till" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000017> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000030> a owl:Class ;
+    rdfs:label "ridge-till" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000017> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000031> a owl:Class ;
+    rdfs:label "strip-till" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000017> .
+
+<http://purl.obolibrary.org/obo/AGRO_00000037> a owl:Class ;
+    rdfs:label "aerial application" ;
+    rdfs:subClassOf <http://purl.obolibrary.org/obo/AGRO_00000036> .
diff --git a/tests/conftest.py b/tests/conftest.py
index 84d08eed..287c57c0 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -328,7 +328,8 @@ def integrate_file(self, info, public=False, set_graph=False):
                 file.integrate(dataset.id, info["entities"], public=public)
             elif file.type == "bed":
                 file.integrate(dataset.id, info["entity_name"], public=public)
-
+            elif file.type in ('rdf/ttl', 'rdf/xml', 'rdf/nt'):
+                file.integrate(public=public)
             # done
             dataset.update_in_db("success")
             dataset.set_info_from_db()
@@ -336,7 +337,9 @@ def integrate_file(self, info, public=False, set_graph=False):
             return {
                 "timestamp": file.timestamp,
                 "start": dataset.start,
-                "end": dataset.end
+                "end": dataset.end,
+                "graph": dataset.graph_name,
+                "endpoint": dataset.endpoint
             }
 
     def upload(self):
@@ -445,6 +448,33 @@ def upload_and_integrate(self, set_graph=False):
             }
         }
 
+    def upload_and_integrate_ontology(self):
+        """Summary
+
+        Returns
+        -------
+        TYPE
+            Description
+        """
+        # upload
+        up_ontology = self.upload_file("test-data/agro_min.ttl")
+
+        # integrate
+        int_ontology = self.integrate_file({
+            "id": 1,
+        })
+
+        return {
+            "ontology": {
+                "upload": up_ontology,
+                "timestamp": int_ontology["timestamp"],
+                "start": int_ontology["start"],
+                "end": int_ontology["end"],
+                "graph": int_ontology["graph"],
+                "endpoint": int_ontology["endpoint"]
+            },
+        }
+
     def create_result(self, has_form=False):
         """Create a result entry in db
 
@@ -590,9 +620,10 @@ def create_prefix(self):
 
     def create_ontology(self):
         """Create ontology"""
-        self.upload_and_integrate()
+        data = self.upload_and_integrate_ontology()
         om = OntologyManager(self.app, self.session)
-        om.add_ontology("Open Biological and Biomedical Ontology", "http://purl.obolibrary.org/obo/agro.owl", "OBO", 1, "mygraph", "local")
+        om.add_ontology("AgrO ontology", "http://purl.obolibrary.org/obo/agro.owl", "AGRO", 1, data["graph"], "local")
+        return data["graph"], data["endpoint"]
 
     @staticmethod
     def get_random_string(number):
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index d3b74f6d..0d178197 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -605,7 +605,7 @@ def test_view_ontologies(self, client):
         assert response.status_code == 200
         assert response.json == expected_empty
 
-        client.create_ontology()
+        graph, endpoint = client.create_ontology()
 
         response = client.client.get('/api/admin/getontologies')
 
@@ -614,13 +614,14 @@ def test_view_ontologies(self, client):
             "errorMessage": "",
             "ontologies": [{
                 "id": 1,
-                "name": "Open Biological and Biomedical Ontology",
+                "name": "AgrO ontology",
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
-                "short_name": "OBO",
+                "short_name": "AGRO",
                 "type": "local",
                 "dataset_id": 1,
-                "dataset_name": "transcripts.tsv",
-                "graph": "mygraph",
+                "dataset_name": "agro_min.ttl",
+                "graph": graph,
+                "endpoint": endpoint,
                 "label_uri": "rdfs:label"
             }]
         }
@@ -633,13 +634,15 @@ def test_add_ontology(self, client):
         client.create_two_users()
         client.log_user("jsmith")
 
-        data = {"shortName": "OBO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "Open Biological and Biomedical Ontology", "type": "local", "datasetId": 1, "labelUri": "rdfs:label"}
+        data = {"shortName": "AGRO", "uri": "http://purl.obolibrary.org/obo/agro.owl", "name": "AgrO ontology", "type": "local", "datasetId": 1, "labelUri": "rdfs:label"}
 
         response = client.client.post('/api/admin/addontology', json=data)
         assert response.status_code == 401
 
         client.log_user("jdoe")
-        client.upload_and_integrate(set_graph=True)
+        data = client.upload_and_integrate_ontology()
+        graph = data["graph"]
+        endpoint = data["endpoint"]
 
         response = client.client.post('/api/admin/addontology', json=data)
 
@@ -655,22 +658,20 @@ def test_add_ontology(self, client):
             "errorMessage": "",
             "ontologies": [{
                 "id": 1,
-                "name": "Open Biological and Biomedical Ontology",
+                "name": "AgrO ontology",
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
                 "short_name": "OBO",
                 "type": "local",
                 "dataset_id": 1,
-                "dataset_name": "transcripts.tsv",
-                "label_uri": "rdfs:label"
+                "dataset_name": "agro_min.ttl",
+                "label_uri": "rdfs:label",
+                "graph": graph,
+                "endpoint": endpoint
             }]
         }
 
-        # Graph name is random
-        res = response.json
-        res['ontologies'][0].pop('graph')
-
         assert response.status_code == 200
-        assert res == expected
+        assert response.json == expected
 
     def test_delete_ontologies(self, client):
         """test /api/admin/delete_ontologies route"""
diff --git a/tests/test_api_ontology.py b/tests/test_api_ontology.py
new file mode 100644
index 00000000..76418512
--- /dev/null
+++ b/tests/test_api_ontology.py
@@ -0,0 +1,21 @@
+import json
+
+from . import AskomicsTestCase
+
+
+class TestApiOntology(AskomicsTestCase):
+    """Test AskOmics API /api/ontology/<someting>"""
+
+    def test_local_autocompletion(self, client):
+        """test /api/ontology/AGRO/autocomplete route"""
+        client.create_two_users()
+        client.log_user("jdoe")
+
+        client.create_ontology()
+
+        query = ""
+        response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
+
+        print(response.json)
+        assert response.status_code == 200
+        assert len(response.json["results"]) == 10

From 326ac8a4bee1b00d2d3e64c16a8d5b8681ed399e Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 22 Jun 2022 14:40:51 +0000
Subject: [PATCH 092/113] Fix autocomplete

---
 askomics/api/ontology.py            |  2 +-
 askomics/libaskomics/SparqlQuery.py |  4 ++--
 tests/test_api_ontology.py          | 33 ++++++++++++++++++++++++++++-
 3 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index fb9ce736..d8ce1c8d 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -48,7 +48,7 @@ def autocomplete(short_ontology):
         }), 404
 
     return jsonify({
-        "error": True,
+        "error": False,
         "errorMessage": "",
         "results": results
     }), 200
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 69945cfb..a1c002cd 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -590,11 +590,11 @@ def autocomplete_local_ontology(self, uri, query, max_terms):
         raw_query = '''
         SELECT DISTINCT ?label
         WHERE {{
-          ?uri rdf:type <{}> .
+          ?uri rdf:type owl:Class .
           ?uri rdfs:label ?label .
           {}
         }}
-        '''.format(uri, subquery)
+        '''.format(subquery)
 
         raw_query = self.prefix_query(raw_query)
 
diff --git a/tests/test_api_ontology.py b/tests/test_api_ontology.py
index 76418512..c23edd42 100644
--- a/tests/test_api_ontology.py
+++ b/tests/test_api_ontology.py
@@ -13,9 +13,40 @@ def test_local_autocompletion(self, client):
 
         client.create_ontology()
 
+        query = "blabla"
+        response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
+
+        assert response.status_code == 200
+        assert len(response.json["results"]) == 0
+        assert response.json["results"] == []
+
         query = ""
         response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
 
-        print(response.json)
+        expected = [
+            "desuckering",
+            "irrigation water source role",
+            "irrigation water quantity",
+            "reduced tillage process",
+            "laser land levelling process",
+            "chemical pest control process",
+            "no-till","puddling process",
+            "mulch-till",
+            "ridge-till"
+        ]
+
         assert response.status_code == 200
         assert len(response.json["results"]) == 10
+        assert response.json["results"] == expected
+
+        query = "irrigation"
+        response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
+
+        expected = [
+            "irrigation water source role",
+            "irrigation water quantity"
+        ]
+
+        assert response.status_code == 200
+        assert len(response.json["results"]) == 2
+        assert response.json["results"] == expected

From 90ddd10561072c449a3afd7cb97bb2e3d4336b95 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 22 Jun 2022 15:17:18 +0000
Subject: [PATCH 093/113] lint

---
 tests/conftest.py          | 3 ++-
 tests/test_api_ontology.py | 5 ++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 287c57c0..0e1ac172 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -251,7 +251,8 @@ def upload_file(self, file_path):
             ".tsv": "text/tab-separated-values",
             ".csv": "text/tab-separated-values",
             ".gff3": "null",
-            ".bed": "null"
+            ".bed": "null",
+            ".ttl": "rdf/ttl"
         }
 
         with open(file_path, 'r') as file_content:
diff --git a/tests/test_api_ontology.py b/tests/test_api_ontology.py
index c23edd42..f5cfe248 100644
--- a/tests/test_api_ontology.py
+++ b/tests/test_api_ontology.py
@@ -1,5 +1,3 @@
-import json
-
 from . import AskomicsTestCase
 
 
@@ -30,7 +28,8 @@ def test_local_autocompletion(self, client):
             "reduced tillage process",
             "laser land levelling process",
             "chemical pest control process",
-            "no-till","puddling process",
+            "no-till",
+            "puddling process",
             "mulch-till",
             "ridge-till"
         ]

From 0487ab5c072d25292e933e4cb58940765cc9f7c5 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 22 Jun 2022 20:48:38 +0200
Subject: [PATCH 094/113] typo

---
 tests/conftest.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 0e1ac172..486b1ccf 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -466,14 +466,12 @@ def upload_and_integrate_ontology(self):
         })
 
         return {
-            "ontology": {
-                "upload": up_ontology,
-                "timestamp": int_ontology["timestamp"],
-                "start": int_ontology["start"],
-                "end": int_ontology["end"],
-                "graph": int_ontology["graph"],
-                "endpoint": int_ontology["endpoint"]
-            },
+            "upload": up_ontology,
+            "timestamp": int_ontology["timestamp"],
+            "start": int_ontology["start"],
+            "end": int_ontology["end"],
+            "graph": int_ontology["graph"],
+            "endpoint": int_ontology["endpoint"]
         }
 
     def create_result(self, has_form=False):

From a49bc15841bef4deda70160bc4dfac6a8914ea85 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Wed, 22 Jun 2022 21:12:39 +0200
Subject: [PATCH 095/113] graph save

---
 tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 486b1ccf..5895b7d3 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -463,7 +463,7 @@ def upload_and_integrate_ontology(self):
         # integrate
         int_ontology = self.integrate_file({
             "id": 1,
-        })
+        }, set_graph=True)
 
         return {
             "upload": up_ontology,

From 9af113e71903942944e8683224e6c3b4b7176f51 Mon Sep 17 00:00:00 2001
From: root <root@test-asko.novalocal>
Date: Thu, 23 Jun 2022 11:59:58 +0000
Subject: [PATCH 096/113] Fix

---
 askomics/api/ontology.py   |  2 +-
 tests/conftest.py          | 11 +++++++----
 tests/test_api_admin.py    |  8 ++++----
 tests/test_api_ontology.py | 13 +++++++++----
 4 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index d8ce1c8d..7558930a 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -45,7 +45,7 @@ def autocomplete(short_ontology):
             "error": True,
             "errorMessage": str(e),
             "results": []
-        }), 404
+        }), 500
 
     return jsonify({
         "error": False,
diff --git a/tests/conftest.py b/tests/conftest.py
index 5895b7d3..50ca2e46 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -294,7 +294,7 @@ def upload_file_url(self, file_url):
         files.download_url(file_url, "1")
         return files.date
 
-    def integrate_file(self, info, public=False, set_graph=False):
+    def integrate_file(self, info, public=False, set_graph=False, graph=""):
         """Summary
 
         Parameters
@@ -310,6 +310,9 @@ def integrate_file(self, info, public=False, set_graph=False):
         files_handler = FilesHandler(self.app, self.session)
         files_handler.handle_files([info["id"], ])
 
+        # TODO: Fix this. Why do we need the virtuoso url?
+        graph = graph or "http://virtuoso:8890/sparql"
+
         for file in files_handler.files:
 
             dataset_info = {
@@ -321,7 +324,7 @@ def integrate_file(self, info, public=False, set_graph=False):
             }
 
             dataset = Dataset(self.app, self.session, dataset_info)
-            dataset.save_in_db("http://virtuoso:8890/sparql", set_graph=set_graph)
+            dataset.save_in_db(graph, set_graph=set_graph)
 
             if file.type == "csv/tsv":
                 file.integrate(dataset.id, info["columns_type"], public=public)
@@ -463,7 +466,7 @@ def upload_and_integrate_ontology(self):
         # integrate
         int_ontology = self.integrate_file({
             "id": 1,
-        }, set_graph=True)
+        }, set_graph=True, graph="http://localhost:8891/sparql-auth")
 
         return {
             "upload": up_ontology,
@@ -621,7 +624,7 @@ def create_ontology(self):
         """Create ontology"""
         data = self.upload_and_integrate_ontology()
         om = OntologyManager(self.app, self.session)
-        om.add_ontology("AgrO ontology", "http://purl.obolibrary.org/obo/agro.owl", "AGRO", 1, data["graph"], "local")
+        om.add_ontology("AgrO ontology", "http://purl.obolibrary.org/obo/agro.owl", "AGRO", 1, data["graph"], data['endpoint'], "local")
         return data["graph"], data["endpoint"]
 
     @staticmethod
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index 0d178197..d88b7431 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -640,9 +640,9 @@ def test_add_ontology(self, client):
         assert response.status_code == 401
 
         client.log_user("jdoe")
-        data = client.upload_and_integrate_ontology()
-        graph = data["graph"]
-        endpoint = data["endpoint"]
+        graph_data = client.upload_and_integrate_ontology()
+        graph = graph_data["graph"]
+        endpoint = graph_data["endpoint"]
 
         response = client.client.post('/api/admin/addontology', json=data)
 
@@ -660,7 +660,7 @@ def test_add_ontology(self, client):
                 "id": 1,
                 "name": "AgrO ontology",
                 "uri": "http://purl.obolibrary.org/obo/agro.owl",
-                "short_name": "OBO",
+                "short_name": "AGRO",
                 "type": "local",
                 "dataset_id": 1,
                 "dataset_name": "agro_min.ttl",
diff --git a/tests/test_api_ontology.py b/tests/test_api_ontology.py
index f5cfe248..9bf9fe84 100644
--- a/tests/test_api_ontology.py
+++ b/tests/test_api_ontology.py
@@ -31,12 +31,17 @@ def test_local_autocompletion(self, client):
             "no-till",
             "puddling process",
             "mulch-till",
-            "ridge-till"
+            "ridge-till",
+            "strip-till",
+            "aerial application"
         ]
 
         assert response.status_code == 200
-        assert len(response.json["results"]) == 10
-        assert response.json["results"] == expected
+        assert len(response.json["results"]) == 12
+
+        # SPARQL order is not reliable, so we make sure to return everything
+        # If it fails, skip this
+        assert self.equal_objects(response.json["results"], expected)
 
         query = "irrigation"
         response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
@@ -48,4 +53,4 @@ def test_local_autocompletion(self, client):
 
         assert response.status_code == 200
         assert len(response.json["results"]) == 2
-        assert response.json["results"] == expected
+        assert self.equal_objects(response.json["results"], expected)

From 546251ce8bbcdb1252c3d902fa2783e7ca0515b5 Mon Sep 17 00:00:00 2001
From: root <root@test-asko.novalocal>
Date: Thu, 23 Jun 2022 13:04:13 +0000
Subject: [PATCH 097/113] Fix2

---
 config/askomics.ini.template | 7 ++++---
 config/askomics.test.ini     | 3 +++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/config/askomics.ini.template b/config/askomics.ini.template
index af284f2b..5e75e378 100644
--- a/config/askomics.ini.template
+++ b/config/askomics.ini.template
@@ -83,6 +83,10 @@ ldap_mail_attribute = mail
 #ldap_password_reset_link =
 #ldap_account_link =
 
+# Max results returned for autocompletion
+autocomplete_max_results = 10
+
+
 [triplestore]
 # name of the triplestore, can be virtuoso or fuseki
 triplestore = virtuoso
@@ -128,9 +132,6 @@ preview_limit = 25
 # All queries are launched on all graphes (speedup queries)
 single_tenant=False
 
-# Max results returned for autocompletion
-autocomplete_max_results = 10
-
 [federation]
 # Query engine can be corese or fedx
 #query_engine = corese
diff --git a/config/askomics.test.ini b/config/askomics.test.ini
index f2afac84..6d9bd17c 100644
--- a/config/askomics.test.ini
+++ b/config/askomics.test.ini
@@ -76,6 +76,7 @@ ldap_surname_attribute = sn
 ldap_mail_attribute = mail
 #ldap_password_reset_link =
 #ldap_account_link =
+autocomplete_max_results = 20
 
 [triplestore]
 # name of the triplestore, can be virtuoso or fuseki
@@ -132,3 +133,5 @@ local_endpoint=http://askomics-host:8891/sparql
 # Sentry dsn to report python and js errors in a sentry instance
 # server_dsn = https://00000000000000000000000000000000@exemple.org/1
 # frontend_dsn = https://00000000000000000000000000000000@exemple.org/2
+
+# Max results returned for autocompletion

From c0a10ca309eb32804b3b089cf69eb63f0da4b253 Mon Sep 17 00:00:00 2001
From: root <root@test-asko.novalocal>
Date: Thu, 23 Jun 2022 15:10:32 +0000
Subject: [PATCH 098/113] more test, and restrict autocomplete if protected

---
 askomics/api/ontology.py   |  8 ++++++--
 tests/test_api_ontology.py | 18 ++++++++++++++++++
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 7558930a..6b662d0a 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -10,7 +10,6 @@
 
 @onto_bp.route("/api/ontology/<short_ontology>/autocomplete", methods=["GET"])
 @api_auth
-@login_required
 def autocomplete(short_ontology):
     """Get the default sparql query
 
@@ -19,8 +18,13 @@ def autocomplete(short_ontology):
     json
     """
 
+    if "user" not in session and current_app.iniconfig.getboolean("askomics", "protect_public"):
+        return jsonify({
+                "error": True,
+                "errorMessage": "Ontology {} not found".format(short_ontology),
+                "results": []
+            }), 401
     try:
-        # Disk space
         om = OntologyManager(current_app, session)
         ontology = om.get_ontology(short_name=short_ontology)
         if not ontology:
diff --git a/tests/test_api_ontology.py b/tests/test_api_ontology.py
index 9bf9fe84..4f8a8bb0 100644
--- a/tests/test_api_ontology.py
+++ b/tests/test_api_ontology.py
@@ -4,6 +4,24 @@
 class TestApiOntology(AskomicsTestCase):
     """Test AskOmics API /api/ontology/<someting>"""
 
+    def test_local_autocompletion_protected(self, client):
+        """ Test autocompletion on missing ontology"""
+        query = "blabla"
+        client.set_config("askomics", "protect_public", "true")
+        response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
+
+        assert response.status_code == 401
+        assert len(response.json["results"]) == 0
+
+    def test_local_autocompletion_missing_ontology(self, client):
+        """ Test autocompletion on missing ontology"""
+        query = "blabla"
+        response = client.client.get('/api/ontology/AGRO/autocomplete?q={}'.format(query))
+
+        assert response.status_code == 404
+        assert len(response.json["results"]) == 0
+
+
     def test_local_autocompletion(self, client):
         """test /api/ontology/AGRO/autocomplete route"""
         client.create_two_users()

From 458e69dfbc1386e07e603950095e526e7c436fea Mon Sep 17 00:00:00 2001
From: root <root@test-asko.novalocal>
Date: Thu, 23 Jun 2022 15:25:25 +0000
Subject: [PATCH 099/113] lint

---
 askomics/api/ontology.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 6b662d0a..c4269e08 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -1,6 +1,6 @@
 import traceback
 import sys
-from askomics.api.auth import api_auth, login_required
+from askomics.api.auth import api_auth
 from askomics.libaskomics.OntologyManager import OntologyManager
 
 from flask import (Blueprint, current_app, jsonify, request, session)
@@ -20,10 +20,10 @@ def autocomplete(short_ontology):
 
     if "user" not in session and current_app.iniconfig.getboolean("askomics", "protect_public"):
         return jsonify({
-                "error": True,
-                "errorMessage": "Ontology {} not found".format(short_ontology),
-                "results": []
-            }), 401
+            "error": True,
+            "errorMessage": "Ontology {} not found".format(short_ontology),
+            "results": []
+        }), 401
     try:
         om = OntologyManager(current_app, session)
         ontology = om.get_ontology(short_name=short_ontology)

From 41480ad88127c2bc9ee0461592c66847c48edca1 Mon Sep 17 00:00:00 2001
From: root <root@test-asko.novalocal>
Date: Thu, 23 Jun 2022 15:26:28 +0000
Subject: [PATCH 100/113] lint2

---
 tests/test_api_ontology.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_api_ontology.py b/tests/test_api_ontology.py
index 4f8a8bb0..c22a1821 100644
--- a/tests/test_api_ontology.py
+++ b/tests/test_api_ontology.py
@@ -21,7 +21,6 @@ def test_local_autocompletion_missing_ontology(self, client):
         assert response.status_code == 404
         assert len(response.json["results"]) == 0
 
-
     def test_local_autocompletion(self, client):
         """test /api/ontology/AGRO/autocomplete route"""
         client.create_two_users()

From b6006184853a7b3ab4e4fa2c97f12676e0c8c28c Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 10:10:20 +0000
Subject: [PATCH 101/113] fix (1/?)

---
 askomics/api/ontology.py                | 2 +-
 askomics/libaskomics/OntologyManager.py | 4 ++--
 askomics/libaskomics/SparqlQuery.py     | 6 +++---
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index d8ce1c8d..93b05992 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -37,7 +37,7 @@ def autocomplete(short_ontology):
                 "results": []
             }), 404
 
-        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"], ontology["endpoint"])
+        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"], ontology["endpoint"], ontology['label_uri'])
 
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index d180d13a..efd038b7 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -227,7 +227,7 @@ def test_ols_ontology(self, shortname):
         r = requests.get(base_url)
         return r.status_code == 200
 
-    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name, onto_graph, onto_endpoint):
+    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name, onto_graph, onto_endpoint, custom_label):
         """Search in ontology
 
         Returns
@@ -244,7 +244,7 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
             # TODO: Actually store the graph in the ontology to quicken search
             query.set_graphs([onto_graph])
             query.set_endpoints(set([self.settings.get('triplestore', 'endpoint'), onto_endpoint]))
-            return query.autocomplete_local_ontology(ontology_uri, query_term, max_results)
+            return query.autocomplete_local_ontology(ontology_uri, query_term, max_results, custom_label)
         elif ontology_type == "ols":
             base_url = "https://www.ebi.ac.uk/ols/api/suggest"
             arguments = {
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index a1c002cd..3b87d9c9 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -567,7 +567,7 @@ def get_uri_parameters(self, uri, endpoints):
 
         return formated_data
 
-    def autocomplete_local_ontology(self, uri, query, max_terms):
+    def autocomplete_local_ontology(self, uri, query, max_terms, label):
         """Get results for a specific query
 
         Parameters
@@ -591,10 +591,10 @@ def autocomplete_local_ontology(self, uri, query, max_terms):
         SELECT DISTINCT ?label
         WHERE {{
           ?uri rdf:type owl:Class .
-          ?uri rdfs:label ?label .
+          ?uri {} ?label .
           {}
         }}
-        '''.format(subquery)
+        '''.format(label, subquery)
 
         raw_query = self.prefix_query(raw_query)
 

From 58f579a8ba062666236c73b43d8fb76aadd3c180 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 15:56:55 +0200
Subject: [PATCH 102/113] Federated queries should not have 'from' clause

---
 askomics/libaskomics/SparqlQuery.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index 3b87d9c9..f3684921 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -279,7 +279,7 @@ def get_default_query_with_prefix(self):
             self.get_default_query()
         )
 
-    def format_query(self, query, limit=30, replace_froms=True, federated=False, ignore_single_tenant=True):
+    def format_query(self, query, limit=30, replace_froms=True, federated=False):
         """Format the Sparql query
 
         - remove all FROM
@@ -299,11 +299,12 @@ def format_query(self, query, limit=30, replace_froms=True, federated=False, ign
             formatted sparql query
         """
         froms = ''
-        if replace_froms and (not self.settings.getboolean("askomics", "single_tenant", fallback=False) or ignore_single_tenant):
-            froms = self.get_froms()
 
         if federated:
             federated_line = "{}\n{}".format(self.get_federated_line(), self.get_federated_froms())
+        else:
+            if replace_froms and (not self.settings.getboolean("askomics", "single_tenant", fallback=False)):
+                froms = self.get_froms()
 
         query_lines = query.split('\n')
 
@@ -600,7 +601,7 @@ def autocomplete_local_ontology(self, uri, query, max_terms, label):
 
         is_federated = self.is_federated()
 
-        sparql = self.format_query(raw_query, limit=max_terms, replace_froms=True, federated=is_federated, ignore_single_tenant=True)
+        sparql = self.format_query(raw_query, limit=max_terms, replace_froms=True, federated=is_federated)
 
         query_launcher = SparqlQueryLauncher(self.app, self.session, get_result_query=True, federated=is_federated)
         _, data = query_launcher.process_query(sparql)

From 06934202cb7cff22ede75e980ef6b7c8abd8e2e3 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 15:01:03 +0000
Subject: [PATCH 103/113] fix federation

---
 askomics/libaskomics/SparqlQuery.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index f3684921..f5660e3d 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -301,7 +301,8 @@ def format_query(self, query, limit=30, replace_froms=True, federated=False):
         froms = ''
 
         if federated:
-            federated_line = "{}\n{}".format(self.get_federated_line(), self.get_federated_froms())
+            federated_line = "" if self.settings.getboolean("askomics", "single_tenant", fallback=False) else "{}\n{}".format(self.get_federated_line(), self.get_federated_froms())
+            federated_graphs_string = self.get_federated_remote_from_graphs()
         else:
             if replace_froms and (not self.settings.getboolean("askomics", "single_tenant", fallback=False)):
                 froms = self.get_froms()
@@ -315,6 +316,7 @@ def format_query(self, query, limit=30, replace_froms=True, federated=False):
             if not line.upper().lstrip().startswith('FROM') and not line.upper().lstrip().startswith('LIMIT') and not line.upper().lstrip().startswith('@FEDERATE'):
                 if line.upper().lstrip().startswith('SELECT') and federated:
                     new_query += "\n{}\n".format(federated_line)
+                    new_query += "\n{}\n".format(federated_graphs_string)
                 new_query += '\n{}'.format(line)
             # Add new FROM
             if line.upper().lstrip().startswith('SELECT'):
@@ -379,7 +381,6 @@ def get_federated_froms_from_graphs(self, graphs):
         from_string = "@from <{}>".format(self.local_endpoint_f)
         for graph in graphs:
             from_string += " <{}>".format(graph)
-
         return from_string
 
     def get_federated_remote_from_graphs(self):

From de1ae05ebcc323ad044b400e648165a0faac8c81 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 17:37:29 +0200
Subject: [PATCH 104/113] Federated autocompletion on remote graph

---
 askomics/api/admin.py                   |  2 +-
 askomics/api/file.py                    |  2 +-
 askomics/api/ontology.py                |  2 +-
 askomics/libaskomics/Database.py        | 21 +++++++++++++++++++++
 askomics/libaskomics/Dataset.py         | 12 ++++++++----
 askomics/libaskomics/OntologyManager.py | 10 +++++++---
 askomics/libaskomics/SparqlQuery.py     | 10 ++++++++++
 tests/conftest.py                       |  6 +++---
 8 files changed, 52 insertions(+), 13 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 631b8b1a..f396d2ae 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -760,7 +760,7 @@ def add_ontology():
         }), 400
 
     try:
-        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, dataset.endpoint, type, label_uri)
+        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, dataset.endpoint, data.remote_graph, type, label_uri)
         ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/api/file.py b/askomics/api/file.py
index 7348323f..5d224030 100644
--- a/askomics/api/file.py
+++ b/askomics/api/file.py
@@ -347,7 +347,7 @@ def integrate():
             endpoint = data["externalEndpoint"] or current_app.iniconfig.get('triplestore', 'endpoint')
 
             dataset = Dataset(current_app, session, dataset_info)
-            dataset.save_in_db(endpoint)
+            dataset.save_in_db(endpoint, data["externalGraph"])
             data["dataset_id"] = dataset.id
             dataset_ids.append(dataset.id)
             task = current_app.celery.send_task('integrate', (session_dict, data, request.host_url))
diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 36b62c99..05e66fd0 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -41,7 +41,7 @@ def autocomplete(short_ontology):
                 "results": []
             }), 404
 
-        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"], ontology["endpoint"], ontology['label_uri'])
+        results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"], ontology["endpoint"], ontology['label_uri'], ontology['remote_graph'])
 
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/askomics/libaskomics/Database.py b/askomics/libaskomics/Database.py
index 8a3c7e90..9fc02acb 100644
--- a/askomics/libaskomics/Database.py
+++ b/askomics/libaskomics/Database.py
@@ -220,6 +220,17 @@ def update_datasets_table(self):
         except Exception:
             pass
 
+        query = '''
+        ALTER TABLE datasets
+        ADD remote_graph text NULL
+        DEFAULT(null)
+        '''
+
+        try:
+            self.execute_sql_query(query)
+        except Exception:
+            pass
+
     def create_integration_table(self):
         """Create the integration table"""
         query = '''
@@ -455,3 +466,13 @@ def create_ontologies_table(self):
             self.execute_sql_query(query)
         except Exception:
             pass
+
+        query = '''
+        ALTER TABLE ontologies
+        ADD remote_graph text NULL
+        '''
+
+        try:
+            self.execute_sql_query(query)
+        except Exception:
+            pass
diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index 87bae1ba..e1aad0e9 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -59,7 +59,7 @@ def set_info_from_db(self, admin=False):
             where_query = "AND user_id = ?"
 
         query = '''
-        SELECT celery_id, file_id, name, graph_name, public, start, end, ontology, endpoint
+        SELECT celery_id, file_id, name, graph_name, public, start, end, ontology, endpoint, remote_graph
         FROM datasets
         WHERE id = ?
         {}
@@ -76,8 +76,9 @@ def set_info_from_db(self, admin=False):
         self.end = rows[0][6]
         self.ontology = rows[0][7]
         self.endpoint = rows[0][8]
+        self.remove_graph = rows[0][9]
 
-    def save_in_db(self, endpoint, set_graph=False):
+    def save_in_db(self, endpoint, remote_graph=None, set_graph=False):
         """Save the dataset into the database"""
         database = Database(self.app, self.session)
 
@@ -89,7 +90,8 @@ def save_in_db(self, endpoint, set_graph=False):
             self.name,
             self.public,
             0,
-            endpoint
+            endpoint,
+            remote_graph
         )
 
         if set_graph:
@@ -102,7 +104,8 @@ def save_in_db(self, endpoint, set_graph=False):
                 self.graph_name,
                 self.public,
                 0,
-                endpoint
+                endpoint,
+                remote_graph
             )
 
         query = '''
@@ -122,6 +125,7 @@ def save_in_db(self, endpoint, set_graph=False):
             NULL,
             NULL,
             0,
+            ?,
             ?
         )
         '''.format(subquery)
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index efd038b7..2582654e 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -147,7 +147,7 @@ def get_ontology(self, short_name="", uri=""):
             'endpoint': ontology[8]
         }
 
-    def add_ontology(self, name, uri, short_name, dataset_id, graph, endpoint, type="local", label_uri="rdfs:label"):
+    def add_ontology(self, name, uri, short_name, dataset_id, graph, endpoint, remote_graph=None, type="local", label_uri="rdfs:label"):
         """Create a new ontology
 
         Returns
@@ -169,11 +169,12 @@ def add_ontology(self, name, uri, short_name, dataset_id, graph, endpoint, type=
             ?,
             ?,
             ?,
+            ?,
             ?
         )
         '''
 
-        database.execute_sql_query(query, (name, uri, short_name, type, dataset_id, graph, label_uri, endpoint))
+        database.execute_sql_query(query, (name, uri, short_name, type, dataset_id, graph, label_uri, endpoint, remote_graph))
 
         query = '''
         UPDATE datasets SET
@@ -227,7 +228,7 @@ def test_ols_ontology(self, shortname):
         r = requests.get(base_url)
         return r.status_code == 200
 
-    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name, onto_graph, onto_endpoint, custom_label):
+    def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name, onto_graph, onto_endpoint, custom_label, remote_graph):
         """Search in ontology
 
         Returns
@@ -244,6 +245,9 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
             # TODO: Actually store the graph in the ontology to quicken search
             query.set_graphs([onto_graph])
             query.set_endpoints(set([self.settings.get('triplestore', 'endpoint'), onto_endpoint]))
+            if remote_graph:
+                query.set_remote_graph({onto_endpoint: [remote_graph]})
+
             return query.autocomplete_local_ontology(ontology_uri, query_term, max_results, custom_label)
         elif ontology_type == "ols":
             base_url = "https://www.ebi.ac.uk/ols/api/suggest"
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index f5660e3d..b281be19 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -71,6 +71,16 @@ def set_endpoints(self, endpoints):
         """
         self.endpoints = endpoints
 
+    def set_remote_graph(self, remote_graphs):
+        """Set endpoints
+
+        Parameters
+        ----------
+        endpoints : list
+            Endpoints
+        """
+        self.remote_graphs = remote_graphs
+
     def is_federated(self):
         """Return True if there is more than 1 endpoint
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 50ca2e46..2e4fd4bd 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -294,7 +294,7 @@ def upload_file_url(self, file_url):
         files.download_url(file_url, "1")
         return files.date
 
-    def integrate_file(self, info, public=False, set_graph=False, graph=""):
+    def integrate_file(self, info, public=False, set_graph=False, endpoint=""):
         """Summary
 
         Parameters
@@ -311,7 +311,7 @@ def integrate_file(self, info, public=False, set_graph=False, graph=""):
         files_handler.handle_files([info["id"], ])
 
         # TODO: Fix this. Why do we need the virtuoso url?
-        graph = graph or "http://virtuoso:8890/sparql"
+        endpoint = endpoint or "http://virtuoso:8890/sparql"
 
         for file in files_handler.files:
 
@@ -324,7 +324,7 @@ def integrate_file(self, info, public=False, set_graph=False, graph=""):
             }
 
             dataset = Dataset(self.app, self.session, dataset_info)
-            dataset.save_in_db(graph, set_graph=set_graph)
+            dataset.save_in_db(endpoint, set_graph=set_graph)
 
             if file.type == "csv/tsv":
                 file.integrate(dataset.id, info["columns_type"], public=public)

From 48fcb84f4e099a84ff33846249d8da26766fe6ac Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 18:03:52 +0200
Subject: [PATCH 105/113] typo

---
 tests/conftest.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index 2e4fd4bd..364084a0 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -466,7 +466,7 @@ def upload_and_integrate_ontology(self):
         # integrate
         int_ontology = self.integrate_file({
             "id": 1,
-        }, set_graph=True, graph="http://localhost:8891/sparql-auth")
+        }, set_graph=True, endpoint="http://localhost:8891/sparql-auth")
 
         return {
             "upload": up_ontology,

From 6fc46019f42701c6283046aafcc27081a6476df6 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 19:15:01 +0200
Subject: [PATCH 106/113] typo2

---
 askomics/libaskomics/OntologyManager.py | 10 ++++++----
 tests/test_api_admin.py                 |  4 +++-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 2582654e..45d2c8ec 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -76,7 +76,7 @@ def list_full_ontologies(self):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT ontologies.id, ontologies.name, ontologies.uri, ontologies.short_name, ontologies.type, ontologies.label_uri, datasets.id, datasets.name, ontologies.graph, ontologies.endpoint
+        SELECT ontologies.id, ontologies.name, ontologies.uri, ontologies.short_name, ontologies.type, ontologies.label_uri, datasets.id, datasets.name, ontologies.graph, ontologies.endpoint, ontologies.remote_graph
         FROM ontologies
         INNER JOIN datasets ON datasets.id=ontologies.dataset_id
         '''
@@ -95,7 +95,8 @@ def list_full_ontologies(self):
                 'dataset_id': row[6],
                 'dataset_name': row[7],
                 'graph': row[8],
-                'endpoint': row[9]
+                'endpoint': row[9],
+                'remote_graph': row[10]
             }
             ontologies.append(prefix)
 
@@ -124,7 +125,7 @@ def get_ontology(self, short_name="", uri=""):
         database = Database(self.app, self.session)
 
         query = '''
-        SELECT id, name, uri, short_name, type, dataset_id, graph, label_uri, endpoint
+        SELECT id, name, uri, short_name, type, dataset_id, graph, label_uri, endpoint, remote_graph
         FROM ontologies
         {}
         '''.format(where_clause)
@@ -144,7 +145,8 @@ def get_ontology(self, short_name="", uri=""):
             'dataset_id': ontology[5],
             'graph': ontology[6],
             'label_uri': ontology[7],
-            'endpoint': ontology[8]
+            'endpoint': ontology[8],
+            'remote_graph': ontology[9]
         }
 
     def add_ontology(self, name, uri, short_name, dataset_id, graph, endpoint, remote_graph=None, type="local", label_uri="rdfs:label"):
diff --git a/tests/test_api_admin.py b/tests/test_api_admin.py
index d88b7431..30b6cbba 100644
--- a/tests/test_api_admin.py
+++ b/tests/test_api_admin.py
@@ -622,6 +622,7 @@ def test_view_ontologies(self, client):
                 "dataset_name": "agro_min.ttl",
                 "graph": graph,
                 "endpoint": endpoint,
+                "remote_graph": None,
                 "label_uri": "rdfs:label"
             }]
         }
@@ -666,7 +667,8 @@ def test_add_ontology(self, client):
                 "dataset_name": "agro_min.ttl",
                 "label_uri": "rdfs:label",
                 "graph": graph,
-                "endpoint": endpoint
+                "endpoint": endpoint,
+                "remote_graph": None
             }]
         }
 

From e3000c05cb3497cdb19ca44291e4ab1f2e602bac Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 19:32:51 +0200
Subject: [PATCH 107/113] Fix3

---
 askomics/api/admin.py | 2 +-
 tests/conftest.py     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index f396d2ae..4fe15951 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -760,7 +760,7 @@ def add_ontology():
         }), 400
 
     try:
-        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, dataset.endpoint, data.remote_graph, type, label_uri)
+        om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, dataset.endpoint, remote_graph=dataset.remote_graph, type=type, label_uri=label_uri)
         ontologies = om.list_full_ontologies()
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
diff --git a/tests/conftest.py b/tests/conftest.py
index 364084a0..999d0248 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -624,7 +624,7 @@ def create_ontology(self):
         """Create ontology"""
         data = self.upload_and_integrate_ontology()
         om = OntologyManager(self.app, self.session)
-        om.add_ontology("AgrO ontology", "http://purl.obolibrary.org/obo/agro.owl", "AGRO", 1, data["graph"], data['endpoint'], "local")
+        om.add_ontology("AgrO ontology", "http://purl.obolibrary.org/obo/agro.owl", "AGRO", 1, data["graph"], data['endpoint'], type="local")
         return data["graph"], data["endpoint"]
 
     @staticmethod

From af4e6d3f704018f4449368e4bf10d5d28cc70948 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Fri, 24 Jun 2022 19:49:14 +0200
Subject: [PATCH 108/113] typo4

---
 askomics/libaskomics/Dataset.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/askomics/libaskomics/Dataset.py b/askomics/libaskomics/Dataset.py
index e1aad0e9..c3fd7b1b 100644
--- a/askomics/libaskomics/Dataset.py
+++ b/askomics/libaskomics/Dataset.py
@@ -46,6 +46,8 @@ def __init__(self, app, session, dataset_info={}):
         self.start = dataset_info["start"] if "start" in dataset_info else None
         self.end = dataset_info["end"] if "end" in dataset_info else None
         self.ontology = dataset_info["ontology"] if "ontology" in dataset_info else False
+        self.endpoint = dataset_info["endpoint"] if "endpoint" in dataset_info else False
+        self.remote_graph = dataset_info["remote_graph"] if "remote_graph" in dataset_info else False
 
     def set_info_from_db(self, admin=False):
         """Set the info in from the database"""
@@ -76,7 +78,7 @@ def set_info_from_db(self, admin=False):
         self.end = rows[0][6]
         self.ontology = rows[0][7]
         self.endpoint = rows[0][8]
-        self.remove_graph = rows[0][9]
+        self.remote_graph = rows[0][9]
 
     def save_in_db(self, endpoint, remote_graph=None, set_graph=False):
         """Save the dataset into the database"""

From 3926a0827b9cd5721aaabf04d423ac664bca1287 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 27 Jun 2022 08:54:17 +0000
Subject: [PATCH 109/113] better remote autocomplete

---
 askomics/api/start.py                          | 3 ++-
 askomics/libaskomics/OntologyManager.py        | 8 +++++---
 askomics/react/src/components/autocomplete.jsx | 3 ++-
 askomics/react/src/routes.jsx                  | 3 ++-
 tests/test_api.py                              | 3 ++-
 5 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/askomics/api/start.py b/askomics/api/start.py
index 93ae4578..910af044 100644
--- a/askomics/api/start.py
+++ b/askomics/api/start.py
@@ -85,7 +85,8 @@ def start():
             "user": {},
             "logged": False,
             "ontologies": ontologies,
-            "singleTenant": current_app.iniconfig.getboolean('askomics', 'single_tenant', fallback=False)
+            "singleTenant": current_app.iniconfig.getboolean('askomics', 'single_tenant', fallback=False),
+            "autocompleteMaxResults": current_app.iniconfig.getint("askomics", "autocomplete_max_results", fallback=10)
         }
 
         json = {
diff --git a/askomics/libaskomics/OntologyManager.py b/askomics/libaskomics/OntologyManager.py
index 45d2c8ec..c988f959 100644
--- a/askomics/libaskomics/OntologyManager.py
+++ b/askomics/libaskomics/OntologyManager.py
@@ -252,11 +252,13 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
 
             return query.autocomplete_local_ontology(ontology_uri, query_term, max_results, custom_label)
         elif ontology_type == "ols":
-            base_url = "https://www.ebi.ac.uk/ols/api/suggest"
+            base_url = "https://www.ebi.ac.uk/ols/api/select"
             arguments = {
                 "q": query_term,
                 "ontology": quote_plus(onto_short_name.lower()),
-                "rows": max_results
+                "rows": max_results,
+                "type": "class",
+                "fieldList": "label"
             }
 
             r = requests.get(base_url, params=arguments)
@@ -268,6 +270,6 @@ def autocomplete(self, ontology_uri, ontology_type, query_term, onto_short_name,
 
             res = r.json()
             if res['response']['docs']:
-                data = [term['autosuggest'] for term in res['response']['docs']]
+                data = [term['label'] for term in res['response']['docs']]
 
             return data
diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index 635881b1..41a2dfd2 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -9,6 +9,7 @@ export default class Autocomplete extends Component {
     super(props)
     this.state = {
         ontologyShort: this.getAutoComplete(),
+        maxResults: this.props.config.autocompleteMaxResults,
         options: []
     }
 
@@ -65,7 +66,7 @@ export default class Autocomplete extends Component {
   renderAutocomplete () {
     
     let input = (<div>
-      <TextInput trigger="" matchAny={true} spacer="" regex="^[A-Za-z0-9\\-_ ]+$" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleOntoValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue}/>
+      <TextInput trigger="" matchAny={true} spacer="" regex="^[A-Za-z0-9\\-_ ]+$" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleOntoValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue} maxOptions={this.state.maxResults}/>
     </div>)
 
     return input
diff --git a/askomics/react/src/routes.jsx b/askomics/react/src/routes.jsx
index f0b7356b..94e92c7e 100644
--- a/askomics/react/src/routes.jsx
+++ b/askomics/react/src/routes.jsx
@@ -48,7 +48,8 @@ export default class Routes extends Component {
         namespaceData: null,
         namespaceInternal: null,
         ontologies: [],
-        singleTenant: false
+        singleTenant: false,
+        autocompleteMaxResults: 10
       }
     }
     this.cancelRequest
diff --git a/tests/test_api.py b/tests/test_api.py
index ea66cc70..70199589 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -44,7 +44,8 @@ def test_start(self, client):
             "user": {},
             "logged": False,
             "ontologies": [],
-            "singleTenant": False
+            "singleTenant": False,
+            "autocompleteMaxResults": 10
         }
         response = client.client.get('/api/start')
         assert response.status_code == 200

From b92ed00c550f642f97d15782491319d13091fab1 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 27 Jun 2022 09:14:50 +0000
Subject: [PATCH 110/113] Woops

---
 tests/test_api.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_api.py b/tests/test_api.py
index 70199589..81a8bb23 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -45,7 +45,7 @@ def test_start(self, client):
             "logged": False,
             "ontologies": [],
             "singleTenant": False,
-            "autocompleteMaxResults": 10
+            "autocompleteMaxResults": 20
         }
         response = client.client.get('/api/start')
         assert response.status_code == 200

From 9137cdeca3e7ee3cf5bb75be649248aec56f70f7 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Mon, 27 Jun 2022 15:29:02 +0200
Subject: [PATCH 111/113] failed merge

---
 askomics/api/ontology.py            |  1 -
 askomics/libaskomics/SparqlQuery.py | 17 -----------------
 2 files changed, 18 deletions(-)

diff --git a/askomics/api/ontology.py b/askomics/api/ontology.py
index 775c5f56..fc1efe37 100644
--- a/askomics/api/ontology.py
+++ b/askomics/api/ontology.py
@@ -42,7 +42,6 @@ def autocomplete(short_ontology):
                 "results": []
             }), 404
 
-
         results = om.autocomplete(ontology["uri"], ontology["type"], request.args.get("q"), short_ontology, ontology["graph"], ontology["endpoint"], ontology['label_uri'], ontology['remote_graph'])
 
     except Exception as e:
diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
index f910ac5a..57d2c29a 100644
--- a/askomics/libaskomics/SparqlQuery.py
+++ b/askomics/libaskomics/SparqlQuery.py
@@ -410,23 +410,6 @@ def get_federated_remote_from_graphs(self):
 
         return from_string
 
-    def get_federated_remote_from_graphs(self):
-        """Get @from string fir the federated query engine
-
-        Returns
-        -------
-        string
-            The from string
-        """
-        from_string = ""
-
-        for endpoint in self.endpoints:
-            remote_graphs = self.remote_graphs.get(endpoint, [])
-            if len(remote_graphs) == 1:
-                from_string += "\n@graph <{}> <{}>".format(endpoint, remote_graphs[0])
-
-        return from_string
-
     def get_endpoints_string(self):
         """get endpoint strngs for the federated query engine
 

From 53cbeb3007b1302c0a357a4cff66a6b710603ed3 Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 28 Jun 2022 14:52:29 +0000
Subject: [PATCH 112/113] better autocomplete

---
 .../react/src/components/autocomplete.jsx     | 87 ++++++++++++++++---
 askomics/static/css/askomics.css              | 36 +++++++-
 package-lock.json                             | 52 +++++++++++
 package.json                                  |  2 +-
 4 files changed, 159 insertions(+), 18 deletions(-)

diff --git a/askomics/react/src/components/autocomplete.jsx b/askomics/react/src/components/autocomplete.jsx
index 41a2dfd2..452e9575 100644
--- a/askomics/react/src/components/autocomplete.jsx
+++ b/askomics/react/src/components/autocomplete.jsx
@@ -1,8 +1,9 @@
 import React, { Component} from 'react'
 import axios from 'axios'
 import PropTypes from 'prop-types'
-import TextInput from 'react-autocomplete-input';
-import 'react-autocomplete-input/dist/bundle.css';
+import { Input } from 'reactstrap'
+import Autosuggest from 'react-autosuggest';
+
 
 export default class Autocomplete extends Component {
   constructor (props) {
@@ -15,6 +16,8 @@ export default class Autocomplete extends Component {
 
     this.handleFilterValue = this.props.handleFilterValue.bind(this)
     this.autocompleteOntology = this.autocompleteOntology.bind(this)
+    this.onSuggestionsFetchRequested = this.onSuggestionsFetchRequested.bind(this)
+    this.onSuggestionsClearRequested = this.onSuggestionsClearRequested.bind(this)
     this.cancelRequest
     this.handleOntoValue = this.handleOntoValue.bind(this)
     this.WAIT_INTERVAL = 500
@@ -39,7 +42,6 @@ export default class Autocomplete extends Component {
 
     axios.get(requestUrl, {baseURL: this.props.config.proxyPath, params:{q: userInput}, cancelToken: new axios.CancelToken((c) => { this.cancelRequest = c }) })
       .then(response => {
-        // set state of resultsPreview
         this.setState({
           options: response.data.results
         })
@@ -55,25 +57,84 @@ export default class Autocomplete extends Component {
       })
   }
 
-  handleOntoValue (event) {
-    this.handleFilterValue(event)
+
+  handleOntoValue (event, value) {
+    this.handleFilterValue({target:{value: value.newValue, id: this.props.attributeId}})
+  }
+
+
+  renderSuggestion (suggestion, {query, isHighlighted}) {
+    let textArray = suggestion.split(RegExp(query, "gi"));
+    let match = suggestion.match(RegExp(query, "gi"));
+
+    return (
+      <span>
+        {textArray.map((item, index) => (
+          <span key={index}>
+            {item}
+            {index !== textArray.length - 1 && match && (
+              <b>{match[index]}</b>
+            )}
+          </span>
+        ))}
+      </span>
+    );
+  }
+
+  onSuggestionsClearRequested () {
+    this.setState({
+          options: []
+    })
+  }
+
+  getSuggestionValue (suggestion) { 
+    return suggestion
+  };
+
+  onSuggestionsFetchRequested ( value ){
     clearTimeout(this.timerID)
     this.timerID = setTimeout(() => {
-        this.autocompleteOntology(event.target.value)
+        this.autocompleteOntology(value.value)
     }, this.WAIT_INTERVAL)
+  };
+  
+
+  renderInputComponent (inputProps){
+    return(
+        <div>
+            <Input type="text" {...inputProps} />
+        </div>
+    )
   }
 
-  renderAutocomplete () {
-    
-    let input = (<div>
-      <TextInput trigger="" matchAny={true} spacer="" regex="^[A-Za-z0-9\\-_ ]+$" minChars={3} Component="input" options={this.state.options} onChange={(e) => this.handleOntoValue({target: {value: e, id: this.props.attributeId}})} id={this.props.attributeId} value={this.props.filterValue} maxOptions={this.state.maxResults}/>
-    </div>)
 
-    return input
+  shouldRenderSuggestions(value, reason){
+    return value.trim().length > 2;
   }
 
   render () {
-    return this.renderAutocomplete()
+
+    let value = this.props.filterValue
+
+    let inputProps = {
+      placeholder: '',
+      value,
+      onChange: this.handleOntoValue
+    };
+
+    return (
+      <Autosuggest
+        suggestions={this.state.options}
+        onSuggestionsFetchRequested={this.onSuggestionsFetchRequested}
+        onSuggestionsClearRequested={this.onSuggestionsClearRequested}
+        getSuggestionValue={this.getSuggestionValue}
+        renderSuggestion={this.renderSuggestion}
+        inputProps={inputProps}
+        renderInputComponent={this.renderInputComponent}
+        shouldRenderSuggestions={this.shouldRenderSuggestions}        
+      />
+    )
+
   }
 }
 
diff --git a/askomics/static/css/askomics.css b/askomics/static/css/askomics.css
index c6525b2a..2d6a4065 100644
--- a/askomics/static/css/askomics.css
+++ b/askomics/static/css/askomics.css
@@ -276,9 +276,37 @@ button.input-with-icon {
     display: block;
 }
 
-.react-autocomplete-input {
-  left: auto !important;
-  top: auto !important;
+/***********************************************************************/
+
+
+.react-autosuggest__suggestions-container--open {
+  background-clip: padding-box;
+  background-color: #fff;
+  border: 1px solid rgba(0,0,0,0.15);
+  bottom: auto;
+  box-shadow: 0 6px 12px rgba(0,0,0,0.175);
+  display: block;
+  font-size: 14px;
+  list-style: none;
+  padding: 1px;
+  position: absolute;
+  text-align: left;
+  z-index: 20000;  
 }
 
-/***********************************************************************/
+.react-autosuggest__suggestions-list {
+  margin: 0;
+  padding: 0;
+  list-style-type: none;
+}
+
+.react-autosuggest__suggestion {
+  cursor: pointer;
+  padding: 10px;
+  min-width: 100px;
+}
+
+.react-autosuggest__suggestion--highlighted {
+  background-color: #0356fc;
+  color: #fff;
+}
diff --git a/package-lock.json b/package-lock.json
index 0b75625b..04f514fa 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -4547,6 +4547,11 @@
         "is-symbol": "^1.0.2"
       }
     },
+    "es6-promise": {
+      "version": "4.2.8",
+      "resolved": "https://registry.npmjs.org/es6-promise/-/es6-promise-4.2.8.tgz",
+      "integrity": "sha512-HJDGx5daxeIvxdBxvG2cb9g4tEvwIk3i8+nhX0yGrYmZUzbkdg8QbDevheDB8gd0//uPj4c1EQua8Q+MViT0/w=="
+    },
     "escalade": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/escalade/-/escalade-3.1.1.tgz",
@@ -5513,6 +5518,11 @@
       "integrity": "sha512-DyFP3BM/3YHTQOCUL/w0OZHR0lpKeGrxotcHWcqNEdnltqFwXVfhEBQ94eIo34AfQpo0rGki4cyIiftY06h2Fg==",
       "dev": true
     },
+    "get-input-selection": {
+      "version": "1.1.4",
+      "resolved": "https://registry.npmjs.org/get-input-selection/-/get-input-selection-1.1.4.tgz",
+      "integrity": "sha512-o3rv95OOpoHznujIEwZljNhUM9efW/gZsIKCQtTrjRU4PkneVpDvxNBmC7kXC4519lZYT95DKcdj0A5f9GZkKg=="
+    },
     "get-intrinsic": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/get-intrinsic/-/get-intrinsic-1.1.1.tgz",
@@ -8625,6 +8635,18 @@
         "object-assign": "^4.1.0"
       }
     },
+    "react-autosuggest": {
+      "version": "10.1.0",
+      "resolved": "https://registry.npmjs.org/react-autosuggest/-/react-autosuggest-10.1.0.tgz",
+      "integrity": "sha512-/azBHmc6z/31s/lBf6irxPf/7eejQdR0IqnZUzjdSibtlS8+Rw/R79pgDAo6Ft5QqCUTyEQ+f0FhL+1olDQ8OA==",
+      "requires": {
+        "es6-promise": "^4.2.8",
+        "prop-types": "^15.7.2",
+        "react-themeable": "^1.1.0",
+        "section-iterator": "^2.0.0",
+        "shallow-equal": "^1.2.1"
+      }
+    },
     "react-bootstrap-table-next": {
       "version": "4.0.3",
       "resolved": "https://registry.npmjs.org/react-bootstrap-table-next/-/react-bootstrap-table-next-4.0.3.tgz",
@@ -8817,6 +8839,21 @@
         "refractor": "^3.2.0"
       }
     },
+    "react-themeable": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/react-themeable/-/react-themeable-1.1.0.tgz",
+      "integrity": "sha512-kl5tQ8K+r9IdQXZd8WLa+xxYN04lLnJXRVhHfdgwsUJr/SlKJxIejoc9z9obEkx1mdqbTw1ry43fxEUwyD9u7w==",
+      "requires": {
+        "object-assign": "^3.0.0"
+      },
+      "dependencies": {
+        "object-assign": {
+          "version": "3.0.0",
+          "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-3.0.0.tgz",
+          "integrity": "sha512-jHP15vXVGeVh1HuaA2wY6lxk+whK/x4KBG88VXeRma7CCun7iGD5qPc4eYykQ9sdQvg8jkwFKsSxHln2ybW3xQ=="
+        }
+      }
+    },
     "react-tooltip": {
       "version": "4.2.21",
       "resolved": "https://registry.npmjs.org/react-tooltip/-/react-tooltip-4.2.21.tgz",
@@ -9352,6 +9389,11 @@
         "ajv-keywords": "^3.5.2"
       }
     },
+    "section-iterator": {
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/section-iterator/-/section-iterator-2.0.0.tgz",
+      "integrity": "sha512-xvTNwcbeDayXotnV32zLb3duQsP+4XosHpb/F+tu6VzEZFmIjzPdNk6/O+QOOx5XTh08KL2ufdXeCO33p380pQ=="
+    },
     "select": {
       "version": "1.1.2",
       "resolved": "https://registry.npmjs.org/select/-/select-1.1.2.tgz",
@@ -9440,6 +9482,11 @@
         "safe-buffer": "^5.0.1"
       }
     },
+    "shallow-equal": {
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/shallow-equal/-/shallow-equal-1.2.1.tgz",
+      "integrity": "sha512-S4vJDjHHMBaiZuT9NPb616CSmLf618jawtv3sufLl6ivK8WocjAo58cXwbRV1cgqxH0Qbv+iUt6m05eqEa2IRA=="
+    },
     "shebang-command": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/shebang-command/-/shebang-command-2.0.0.tgz",
@@ -10118,6 +10165,11 @@
       "integrity": "sha1-f17oI66AUgfACvLfSoTsP8+lcLQ=",
       "dev": true
     },
+    "textarea-caret": {
+      "version": "3.1.0",
+      "resolved": "https://registry.npmjs.org/textarea-caret/-/textarea-caret-3.1.0.tgz",
+      "integrity": "sha512-cXAvzO9pP5CGa6NKx0WYHl+8CHKZs8byMkt3PCJBCmq2a34YA9pO1NrQET5pzeqnBjBdToF5No4rrmkDUgQC2Q=="
+    },
     "three": {
       "version": "0.126.1",
       "resolved": "https://registry.npmjs.org/three/-/three-0.126.1.tgz",
diff --git a/package.json b/package.json
index 9f088555..fb733689 100644
--- a/package.json
+++ b/package.json
@@ -54,7 +54,7 @@
     "qs": "^6.9.4",
     "react": "^16.13.1",
     "react-ace": "^9.1.3",
-    "react-autocomplete-input": "1.0.18",
+    "react-autosuggest": "^10.1.0",
     "react-addons-update": "^15.6.3",
     "react-bootstrap-table-next": "^4.0.3",
     "react-bootstrap-table2-editor": "^1.4.0",

From 6c05bfd7847485aec29e26bcaece0b9fb0093cef Mon Sep 17 00:00:00 2001
From: mboudet <mateo.boudet@gmail.com>
Date: Tue, 28 Jun 2022 17:31:55 +0200
Subject: [PATCH 113/113] cleanup

---
 askomics/api/admin.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/askomics/api/admin.py b/askomics/api/admin.py
index 4fe15951..5200ebb5 100644
--- a/askomics/api/admin.py
+++ b/askomics/api/admin.py
@@ -698,12 +698,12 @@ def add_ontology():
             'errorMessage': "Missing parameter"
         }), 400
 
-    name = data.get("name")
-    uri = data.get("uri")
+    name = data.get("name").strip()
+    uri = data.get("uri").strip()
     short_name = data.get("shortName")
-    type = data.get("type")
+    type = data.get("type").strip()
     dataset_id = data.get("datasetId")
-    label_uri = data.get("labelUri")
+    label_uri = data.get("labelUri").strip()
 
     om = OntologyManager(current_app, session)