Merge 38bd328 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/Database.py

@@ -270,6 +270,7 @@ def create_results_table(self):
             template boolean,
             has_form_attr boolean,
             form boolean,
+            version text,
             FOREIGN KEY(user_id) REFERENCES users(user_id)
         )
         '''
@@ -355,6 +356,17 @@ def update_results_table(self):
         except Exception:
             pass
 
+        query = '''
+        ALTER TABLE results
+        ADD version text NULL
+        DEFAULT(NULL)
+        '''
+
+        try:
+            self.execute_sql_query(query)
+        except Exception:
+            pass
+
     def create_endpoints_table(self):
         """Create the endpoints table"""
         query = '''

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
 

askomics/libaskomics/Result.py

@@ -9,6 +9,8 @@
 from askomics.libaskomics.Params import Params
 from askomics.libaskomics.Utils import Utils
 
+from pkg_resources import get_distribution
+
 
 class Result(Params):
     """Result represent a query result file
@@ -381,6 +383,7 @@ def save_in_db(self, start=None):
             ?,
             ?,
             ?,
+            ?,
             ?
         )
         '''
@@ -396,7 +399,8 @@ def save_in_db(self, start=None):
             json.dumps({"graphs": self.graphs, "endpoints": self.endpoints}),
             False,
             self.session["user"]["admin"] and any([attrib.get("form") for attrib in self.graph_state["attr"]]) if (self.graph_state and self.graph_state.get("attr")) else False,
-            False
+            False,
+            get_distribution('askomics').version
         ), get_id=True)
 
         return self.id