Merge 6c05bfd into e440bb1

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)
 
@@ -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, 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)

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))

askomics/api/ontology.py

@@ -1,6 +1,7 @@
 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)
@@ -10,7 +11,6 @@
 
 @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 +19,13 @@ 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:
@@ -37,18 +42,18 @@ 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'], ontology['remote_graph'])
 
     except Exception as e:
         traceback.print_exc(file=sys.stdout)
         return jsonify({
             "error": True,
             "errorMessage": str(e),
             "results": []
-        }), 404
+        }), 500
 
     return jsonify({
-        "error": True,
+        "error": False,
         "errorMessage": "",
         "results": results
     }), 200

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 = {

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

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"""
@@ -59,7 +61,7 @@ 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 +78,9 @@ def set_info_from_db(self, admin=False):
         self.end = rows[0][6]
         self.ontology = rows[0][7]
         self.endpoint = rows[0][8]
+        self.remote_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 +92,8 @@ def save_in_db(self, endpoint, set_graph=False):
             self.name,
             self.public,
             0,
-            endpoint
+            endpoint,
+            remote_graph
         )
 
         if set_graph:
@@ -102,7 +106,8 @@ def save_in_db(self, endpoint, set_graph=False):
                 self.graph_name,
                 self.public,
                 0,
-                endpoint
+                endpoint,
+                remote_graph
             )
 
         query = '''
@@ -122,6 +127,7 @@ def save_in_db(self, endpoint, set_graph=False):
             NULL,
             NULL,
             0,
+            ?,
             ?
         )
         '''.format(subquery)

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, ontologies.remote_graph
         FROM ontologies
         INNER JOIN datasets ON datasets.id=ontologies.dataset_id
         '''
@@ -94,7 +94,9 @@ 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],
+                'remote_graph': row[10]
             }
             ontologies.append(prefix)
 
@@ -123,7 +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
+        SELECT id, name, uri, short_name, type, dataset_id, graph, label_uri, endpoint, remote_graph
         FROM ontologies
         {}
         '''.format(where_clause)
@@ -142,10 +144,12 @@ 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],
+            'remote_graph': ontology[9]
         }
 
-    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
@@ -167,11 +171,12 @@ 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
@@ -225,7 +230,7 @@ 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, remote_graph):
         """Search in ontology
 
         Returns
@@ -242,13 +247,18 @@ 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)
+            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"
+            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)
@@ -260,6 +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

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
 
@@ -299,11 +309,13 @@ 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())
+            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()
 
         query_lines = query.split('\n')
 
@@ -314,6 +326,7 @@ def format_query(self, query, limit=30, replace_froms=True, federated=False, ign
             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'):
@@ -378,7 +391,6 @@ 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):
@@ -567,7 +579,7 @@ 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
@@ -590,17 +602,17 @@ def autocomplete_local_ontology(self, uri, query, max_terms):
         raw_query = '''
         SELECT DISTINCT ?label
         WHERE {{
-          ?uri rdf:type <{}> .
-          ?uri rdfs:label ?label .
+          ?uri rdf:type owl:Class .
+          ?uri {} ?label .
           {}
         }}
-        '''.format(uri, subquery)
+        '''.format(label, subquery)
 
         raw_query = self.prefix_query(raw_query)
 
         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)