Merge 0dfd0f8 into 0fe36d1

.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 }}

.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
 

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
 

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

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