Merge 6fcb3fc into 0fe36d1

askomics · Jul 25, 2023 · f48855a · f48855a
2 parents 0fe36d1 + 6fcb3fc
commit f48855a
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Showing 7 changed files with 107 additions and 28 deletions.
diff --git a/.github/workflows/github-publish-celery-flaskomics.yml b/.github/workflows/github-publish-celery-flaskomics.yml
@@ -1,4 +1,4 @@
-name: Publish Flaskomics Docker image to github 
+name: Publish Flaskomics Docker image to github
 
 on:
   push:
@@ -14,13 +14,14 @@ env:
 
 jobs:
   build-and-push-image:
+    if: github.repository == 'askomics/flaskomics'
     runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write
 
     steps:
-      - 
+      -
         name: Checkout repository
         uses: actions/checkout@v3
 
@@ -60,7 +61,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           context: .
-          file: ./docker/DockerfileCelery 
+          file: ./docker/DockerfileCelery
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/github-publish-flaskomics.yml b/.github/workflows/github-publish-flaskomics.yml
@@ -1,4 +1,4 @@
-name: Publish Flaskomics Docker image to github 
+name: Publish Flaskomics Docker image to github
 
 on:
   push:
@@ -14,13 +14,14 @@ env:
 
 jobs:
   build-and-push-image:
+    if: github.repository == 'askomics/flaskomics'
     runs-on: ubuntu-latest
     permissions:
       contents: read
       packages: write
 
     steps:
-      - 
+      -
         name: Checkout repository
         uses: actions/checkout@v3
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,8 @@ This changelog was started for release 4.2.0.
 - Fixed Gff Faldo integration (was only integrating the last selected entity)
 - Fixed an issue when using filters and an 'UNION' node
 - Fixed an issue when launching a query with a 'linked' attribute toggled but unselected
+- Fixed missing includeIn and includeInReference in bed files
+- Fixed 'overlap_with' faldo query
 
 ### Changed
 

diff --git a/askomics/libaskomics/BedFile.py b/askomics/libaskomics/BedFile.py
@@ -306,4 +306,14 @@ def generate_rdf_content(self):
                 self.graph_chunk.add((begin, rdflib.RDF.type, faldo_strand))
                 self.graph_chunk.add((end, rdflib.RDF.type, faldo_strand))
 
+            # blocks
+            block_base = self.settings.getint("triplestore", "block_size")
+            block_start = int(self.convert_type(feature.start + 1)) // block_base
+            block_end = int(self.convert_type(feature.end)) // block_base
+
+            for slice_block in range(block_start, block_end + 1):
+                self.graph_chunk.add((entity, self.namespace_internal['includeIn'], rdflib.Literal(int(slice_block))))
+                block_reference = self.rdfize(self.format_uri("{}_{}".format(feature.chrom, slice_block)))
+                self.graph_chunk.add((entity, self.namespace_internal["includeInReference"], block_reference))
+
             yield
diff --git a/askomics/libaskomics/GffFile.py b/askomics/libaskomics/GffFile.py
@@ -412,15 +412,15 @@ def generate_rdf_content(self):
                     self.graph_chunk.add((begin, rdflib.RDF.type, faldo_strand))
                     self.graph_chunk.add((end, rdflib.RDF.type, faldo_strand))
 
-                    # blocks
-                    block_base = self.settings.getint("triplestore", "block_size")
-                    block_start = int(self.convert_type(feature.location.start)) // block_base
-                    block_end = int(self.convert_type(feature.location.end)) // block_base
-
-                    for slice_block in range(block_start, block_end + 1):
-                        self.graph_chunk.add((entity, self.namespace_internal['includeIn'], rdflib.Literal(int(slice_block))))
-                        block_reference = self.rdfize(self.format_uri("{}_{}".format(rec.id, slice_block)))
-                        self.graph_chunk.add((entity, self.namespace_internal["includeInReference"], block_reference))
+                # blocks
+                block_base = self.settings.getint("triplestore", "block_size")
+                block_start = int(self.convert_type(feature.location.start)) // block_base
+                block_end = int(self.convert_type(feature.location.end)) // block_base
+
+                for slice_block in range(block_start, block_end + 1):
+                    self.graph_chunk.add((entity, self.namespace_internal['includeIn'], rdflib.Literal(int(slice_block))))
+                    block_reference = self.rdfize(self.format_uri("{}_{}".format(rec.id, slice_block)))
+                    self.graph_chunk.add((entity, self.namespace_internal["includeInReference"], block_reference))
 
                 yield
 

diff --git a/askomics/libaskomics/SparqlQuery.py b/askomics/libaskomics/SparqlQuery.py
@@ -799,6 +799,10 @@ def get_block_type(self, blockid):
             "minusNode": "MINUS"
         }
 
+        # Union sub-block
+        if '_' in blockid:
+            return "DEFAULT"
+
         for node in self.json["nodes"]:
             if node["type"] in ("unionNode", "minusNode"):
                 if node["specialNodeId"] == blockid:
@@ -970,6 +974,25 @@ def store_block(self, triple, blockid, sblockid, pblock_ids):
             }, ]
         })
 
+    def update_sub_block(self, block_dict, depths, type, value, current_depth):
+        depth = depths[current_depth]
+        if depth not in block_dict:
+            block_dict[depth] = {
+                "type": self.get_block_type(depth),
+                "triples": [],
+                "filters": [],
+                "values": [],
+                "sub_blocks": {}
+            }
+        # End of branch
+        if current_depth == len(depths) - 1:
+            block_dict[depth][type].append(value)
+        else:
+            self.update_sub_block(block_dict[depth]["sub_blocks"], depths, type, value, current_depth + 1)
+
+    def update_block_dict(self, depths, type, value):
+        self.update_sub_block(self.triples_blocks_dict, depths, type, value, 0)
+
     def replace_variables_in_triples(self, var_to_replace):
         """Replace variables in triples
 
@@ -1036,8 +1059,9 @@ def get_source_of_special_node(self, special_node_id):
         """
         for link in self.json["links"]:
             if link["type"] == "specialLink":
-                if link["source"]["id"] == special_node_id:
-                    return link["target"]["id"]
+                # Source is also a special node. Get source of source
+                if link["source"]['type'] in ['unionNode', 'minusNode']:
+                    return self.get_source_of_special_node(link["source"]['id'])
                 if link["target"]["id"] == special_node_id:
                     return link["source"]["id"]
         return None
@@ -1062,6 +1086,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
 
         self.triples = []
         self.triples_blocks = []
+        self.triples_blocks_dict = {}
 
         self.values = []
         self.filters = []
@@ -1093,12 +1118,17 @@ def build_query_from_json(self, preview=False, for_editor=False):
 
                 # if link is special, replace the special node variable with its real node
                 if link["type"] == "specialLink":
-                    special_node = link["source"] if link["source"]["type"] in ("unionNode", "minusNode") else link["target"]
-                    real_node = link["target"] if link["source"]["type"] in ("unionNode", "minusNode") else link["source"]
+                    special_node = link["target"]
+                    real_node = link["source"]
+                    real_node_id = real_node['id']
+
+                    # Both end are special nodes.
+                    if real_node['type'] in ['minusNode', 'unionNode']:
+                        real_node_id = self.get_source_of_special_node(real_node_id)
 
                     var_to_replace.append((
                         self.format_sparql_variable("{}{}_uri".format(special_node["label"], special_node["id"])),
-                        self.format_sparql_variable("{}{}_uri".format(real_node["label"], real_node["id"]))
+                        self.format_sparql_variable("{}{}_uri".format(real_node["label"], real_node_id))
                     ))
 
                     continue
@@ -1185,7 +1215,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
                         ), block_id, sblock_id, pblock_ids)
 
                     elif link["uri"] == "overlap_with":
-                        self.store_filter("FILTER (({start2} >{equalsign} {start1} && {start2} <{equalsign} {end1}) || ({end2} >{equalsign} {start1} && {end2} <{equalsign} {end1}))".format(
+                        self.store_filter("FILTER (({start2} >{equalsign} {start1} && {start2} <{equalsign} {end1}) || ({end2} >{equalsign} {start1} && {end2} <{equalsign} {end1}) || ({start1} >{equalsign} {start2} && {end1} <{equalsign} {end2}))".format(
                             start1=start_1,
                             start2=start_2,
                             end1=end_1,
@@ -1563,7 +1593,6 @@ def build_query_from_json(self, preview=False, for_editor=False):
         self.replace_variables_in_triples(var_to_replace)
 
         # Write the query
-
         # query is for editor (no froms, no federated)
         if for_editor:
             query = """

diff --git a/askomics/react/src/routes/query/query.jsx b/askomics/react/src/routes/query/query.jsx
@@ -432,20 +432,27 @@ export default class Query extends Component {
     this.graphState.attr = this.graphState.attr.concat(nodeAttributes)
   }
 
-  insertNode (uri, selected, suggested, special=null, forceSpecialId=null, specialNodeGroupId=null, specialPreviousIds=[null, null]) {
+  insertNode (uri, selected, suggested, special=null, forceSpecialId=null, specialNodeGroupId=null, specialPreviousIds=[null, null], newDepth=[]) {
     /*
     Insert a new node in the graphState
     */
     let nodeId = this.getId()
     let humanId = this.getHumanNodeId(uri)
     let specialNodeId = null
 
+    let depth = [...newDepth]
+
     if (special) {
       specialNodeId = this.getSpecialNodeId()
     }
 
+    if (special == "minusNode"){
+      depth = [...newDepth, specialNodeId, specialNodeId + "_1"]
+    }
+
     if (forceSpecialId) {
       specialNodeId = forceSpecialId
+      depth = [...depth, forceSpecialId, forceSpecialId + "_" + specialNodeGroupId]
     }
 
     let node = {
@@ -459,6 +466,7 @@ export default class Query extends Component {
       specialNodeId: specialNodeId,
       specialNodeGroupId: specialNodeGroupId,
       specialPreviousIds: specialPreviousIds,
+      depth: depth,
       label: this.getLabel(uri),
       faldo: this.isFaldoEntity(uri),
       selected: selected,
@@ -544,6 +552,11 @@ export default class Query extends Component {
     let reLink = new RegExp(node.filterLink.toLowerCase(), 'g')
 
     let specialNodeGroupId = incrementSpecialNodeGroupId ? incrementSpecialNodeGroupId : node.specialNodeGroupId
+    let depth = [...node.depth]
+
+    if(incrementSpecialNodeGroupId){
+      depth = [...node.depth, node.specialNodeGroupId, node.specialNodeGroupId + "_" + incrementSpecialNodeGroupId]
+    }
 
     if (this.isOntoEndNode(node.id)){
         return
@@ -575,7 +588,8 @@ export default class Query extends Component {
               faldo: this.isFaldoEntity(relation.target),
               selected: false,
               suggested: true,
-              ontology: isOnto
+              ontology: isOnto,
+              depth: depth
             })
             // push suggested link
             this.graphState.links.push({
@@ -594,6 +608,9 @@ export default class Query extends Component {
               faldoFilters: this.defaultFaldoFilters
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
+            if (incrementSpecialNodeGroupId){
+              depth = [...node.depth, node.specialNodeGroupId, node.specialNodeGroupId + "_" + incrementSpecialNodeGroupId]
+            }
           }
         }
       }
@@ -621,7 +638,8 @@ export default class Query extends Component {
               label: label,
               faldo: this.isFaldoEntity(relation.source),
               selected: false,
-              suggested: true
+              suggested: true,
+              depth: depth
             })
             // push suggested link
             this.graphState.links.push({
@@ -639,6 +657,9 @@ export default class Query extends Component {
               faldoFilters: this.defaultFaldoFilters
             })
             incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
+            if (incrementSpecialNodeGroupId){
+              depth = [...node.depth, node.specialNodeGroupId, node.specialNodeGroupId + "_" + incrementSpecialNodeGroupId]
+            }
           }
         }
       }
@@ -665,6 +686,7 @@ export default class Query extends Component {
             faldo: entity.faldo,
             selected: false,
             suggested: true,
+            depth: depth
           })
           // push suggested link
           this.graphState.links.push({
@@ -683,6 +705,9 @@ export default class Query extends Component {
             faldoFilters: this.defaultFaldoFilters
           })
           incrementSpecialNodeGroupId ? specialNodeGroupId += 1 : specialNodeGroupId = specialNodeGroupId
+          if (incrementSpecialNodeGroupId){
+            depth = [...node.depth, node.specialNodeGroupId, node.specialNodeGroupId + "_" + incrementSpecialNodeGroupId]
+          }
         }
       })
     }
@@ -971,11 +996,18 @@ export default class Query extends Component {
     // Get previous special node ids
     let specialPreviousIds = [sourceNode.specialNodeId, sourceNode.specialNodeGroupId]
 
+    let depth
+    if (this.currentSelected.type == "unionNode"){
+      depth = [...sourceNode.depth, sourceNode.specialNodeId + "_" + this.getLargestSpecialNodeGroupId(sourceNode) + 1]
+    } else {
+      depth = [...sourceNode.depth]
+    }
+
     // insert a special node and select it
-    let specialNode = this.insertNode(sourceNode.uri, true, false, data.convertTo, null, null, specialPreviousIds)
+    let specialNode = this.insertNode(sourceNode.uri, true, false, data.convertTo, null, null, specialPreviousIds, depth)
 
     // insert target node with specialNodeGroupId = 1
-    let targetNode = this.insertNode(data.node.uri, false, false, null, specialNode.specialNodeId, 1, specialPreviousIds)
+    let targetNode = this.insertNode(data.node.uri, false, false, null, specialNode.specialNodeId, 1, specialPreviousIds, depth)
 
     // insert link between source and special node
     this.insertSpecialLink(sourceNode, specialNode, data.convertTo)
@@ -989,7 +1021,11 @@ export default class Query extends Component {
     this.graphState.links.push(relation)
 
     //insert suggestion with first specialNodeGroupId = 2 (will be incremented for each suggestion)
-    this.insertSuggestion(specialNode, 2)
+    if (this.currentSelected.type == "unionNode"){
+      this.insertSuggestion(specialNode, 2)
+    } else {
+      this.insertSuggestion(specialNode)
+    }
 
     // Manage selection
     this.manageCurrentPreviousSelected(specialNode)
@@ -1718,7 +1754,7 @@ export default class Query extends Component {
             if (this.currentSelected) {
               if (this.currentSelected.type != "link" && this.currentSelected.type != "posLink" && this.currentSelected.type != "ontoLink") {
                 if (this.currentSelected.type == "unionNode") {
-                  this.insertSuggestion(this.currentSelected, this.getLargestSpecialNodeGroupId(this.currentSelected) + 1, true)
+                  this.insertSuggestion(this.currentSelected, this.getLargestSpecialNodeGroupId(this.currentSelected) + 1)
                 } else {
                   this.insertSuggestion(this.currentSelected)
                 }