Merge 21a4c70 into 0fe36d1

askomics · Jul 21, 2023 · 0aba686 · 0aba686
2 parents 0fe36d1 + 21a4c70
commit 0aba686
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Showing 6 changed files with 40 additions and 21 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
@@ -1036,8 +1036,9 @@ 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
@@ -1093,12 +1094,17 @@ 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 +1191,7 @@ 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 +1569,6 @@ 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 = """