Revert before blank node

askomics · Jul 11, 2022 · 54c760c · 54c760c
1 parent d154265
commit 54c760c
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Showing 8 changed files with 18 additions and 34 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,14 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 This changelog was started for release 4.2.0.
 
-## [4.4.1] - Unreleased
-
-### Changed
-
-- Using blank node for categories values
-- Changed documentation for blank nodes
-
-## [4.4.0] - 2022-07-01
+## Unreleased
 
 ### Fixed
 

diff --git a/askomics/libaskomics/BedFile.py b/askomics/libaskomics/BedFile.py
@@ -109,11 +109,10 @@ def set_rdf_abstraction_domain_knowledge(self):
             attribute_blanks[attribute["uri"]] = blank
             # Domain Knowledge
             if "values" in attribute.keys():
-                blank_category = attribute["range"]
                 for value in attribute["values"]:
                     self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(value)], rdflib.RDF.type, self.namespace_data[self.format_uri("{}CategoryValue".format(attribute["label"]))]))
                     self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(value)], rdflib.RDFS.label, rdflib.Literal(value)))
-                    self.graph_abstraction_dk.add((blank_category, self.namespace_internal[self.format_uri("category")], self.namespace_data[self.format_uri(value)]))
+                    self.graph_abstraction_dk.add((self.namespace_data[self.format_uri("{}Category".format(attribute["label"]))], self.namespace_internal[self.format_uri("category")], self.namespace_data[self.format_uri(value)]))
 
                     if attribute["label"] == rdflib.Literal("strand"):
                         self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(value)], rdflib.RDF.type, self.get_faldo_strand(value)))
@@ -176,14 +175,13 @@ def generate_rdf_content(self):
             self.graph_chunk.add((entity, relation, attribute))
 
             if "reference" not in attribute_list:
-                blank_category = BNode()
                 attribute_list.append("reference")
                 self.attribute_abstraction.append({
                     "uri": self.namespace_data[self.format_uri("reference")],
                     "label": rdflib.Literal("reference"),
                     "type": [self.namespace_internal[self.format_uri("AskomicsCategory")], rdflib.OWL.ObjectProperty],
                     "domain": entity_type,
-                    "range": blank_category,
+                    "range": self.namespace_data[self.format_uri("{}Category".format("reference"))],
                     "values": [feature.chrom]
                 })
             else:
@@ -259,14 +257,13 @@ def generate_rdf_content(self):
 
             if strand:
                 if ("strand", strand_type) not in attribute_list:
-                    blank_category = BNode()
                     attribute_list.append(("strand", strand_type))
                     self.attribute_abstraction.append({
                         "uri": self.namespace_data[self.format_uri("strand")],
                         "label": rdflib.Literal("strand"),
                         "type": [self.namespace_internal[self.format_uri("AskomicsCategory")], rdflib.OWL.ObjectProperty],
                         "domain": entity_type,
-                        "range": blank_category,
+                        "range": self.namespace_data[self.format_uri("{}Category".format("strand"))],
                         "values": [strand_type]
                     })
 

diff --git a/askomics/libaskomics/CsvFile.py b/askomics/libaskomics/CsvFile.py
@@ -362,8 +362,8 @@ def set_rdf_abstraction_domain_knowledge(self):
     def set_rdf_domain_knowledge(self):
         """Set the domain knowledge"""
         for index, attribute in enumerate(self.header):
-            if self.columns_type[index] in ('category', 'reference', 'strand') and self.header[index] in self.category_values and self.header[index] in self.category_blank:
-                s = self.category_blank[self.header[index]]
+            if self.columns_type[index] in ('category', 'reference', 'strand') and self.header[index] in self.category_values:
+                s = self.namespace_data["{}Category".format(self.format_uri(attribute, remove_space=True))]
                 p = self.namespace_internal["category"]
                 for value in self.category_values[self.header[index]]:
                     o = self.rdfize(value)
@@ -400,7 +400,6 @@ def set_rdf_abstraction(self):
         for ontology in OntologyManager(self.app, self.session).list_ontologies():
             available_ontologies[ontology['short_name']] = ontology['uri']
         attribute_blanks = {}
-        self.category_blank = {}
 
         # Attributes and relations
         for index, attribute_name in enumerate(self.header):
@@ -469,9 +468,7 @@ def set_rdf_abstraction(self):
             elif self.columns_type[index] in ('category', 'reference', 'strand'):
                 attribute = self.rdfize(attribute_name)
                 label = rdflib.Literal(attribute_name)
-                category_blank = BNode()
-                self.category_blank[attribute_name] = category_blank
-                rdf_range = category_blank
+                rdf_range = self.namespace_data["{}Category".format(self.format_uri(attribute_name, remove_space=True))]
                 rdf_type = rdflib.OWL.ObjectProperty
                 self.graph_abstraction_dk.add((blank, rdflib.RDF.type, self.namespace_internal["AskomicsCategory"]))
 

diff --git a/askomics/libaskomics/GffFile.py b/askomics/libaskomics/GffFile.py
@@ -136,11 +136,10 @@ def set_rdf_abstraction_domain_knowledge(self):
             attribute_blanks[attribute["uri"]] = blank
             # Domain Knowledge
             if "values" in attribute.keys():
-                blank_category = attribute["range"]
                 for value in attribute["values"]:
                     self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(value)], rdflib.RDF.type, self.namespace_data[self.format_uri("{}CategoryValue".format(attribute["label"]))]))
                     self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(value)], rdflib.RDFS.label, rdflib.Literal(value)))
-                    self.graph_abstraction_dk.add((blank_category, self.namespace_internal[self.format_uri("category")], self.namespace_data[self.format_uri(value)]))
+                    self.graph_abstraction_dk.add((self.namespace_data[self.format_uri("{}Category".format(attribute["label"]))], self.namespace_internal[self.format_uri("category")], self.namespace_data[self.format_uri(value)]))
 
                     if attribute["label"] == rdflib.Literal("strand"):
                         self.graph_abstraction_dk.add((self.namespace_data[self.format_uri(value)], rdflib.RDF.type, self.get_faldo_strand(value)))
@@ -238,14 +237,13 @@ def generate_rdf_content(self):
                 # self.graph_chunk.add((entity, relation, attribute))
 
                 if (feature.type, "reference") not in attribute_list:
-                    blank_category = BNode()
                     attribute_list.append((feature.type, "reference"))
                     self.attribute_abstraction.append({
                         "uri": self.namespace_data[self.format_uri("reference")],
                         "label": rdflib.Literal("reference"),
                         "type": [self.namespace_internal[self.format_uri("AskomicsCategory")], rdflib.OWL.ObjectProperty],
                         "domain": entity_type,
-                        "range": blank_category,
+                        "range": self.namespace_data[self.format_uri("{}Category".format("reference"))],
                         "values": [rec.id]
                     })
                 else:
@@ -314,14 +312,13 @@ def generate_rdf_content(self):
                     strand_type = "."
 
                 if (feature.type, "strand", strand_type) not in attribute_list:
-                    blank_category = BNode()
                     attribute_list.append((feature.type, "strand", strand_type))
                     self.attribute_abstraction.append({
                         "uri": self.namespace_data[self.format_uri("strand")],
                         "label": rdflib.Literal("strand"),
                         "type": [self.namespace_internal[self.format_uri("AskomicsCategory")], rdflib.OWL.ObjectProperty],
                         "domain": entity_type,
-                        "range": blank_category,
+                        "range": self.namespace_data[self.format_uri("{}Category".format("strand"))],
                         "values": [strand_type]
                     })
 

diff --git a/docs/abstraction.md b/docs/abstraction.md
@@ -82,12 +82,12 @@ _:blank rdf:type owl:ObjectProperty .
 _:blank rdf:type askomics:AskomicsCategory .
 _:blank rdfs:label "category_attribute" .
 _:blank rdfs:domain :EntityName .
-_:blank rdfs:range _:blank2 .
+_:blank rdfs:range :category_attributeCategory .
 _:blank askomics:uri :category_attribute_uri
 
 
-_:blank2 askomics:category :value_1 .
-_:blank2 askomics:category :value_2 .
+:category_attributeCategory askomics:category :value_1 .
+:category_attributeCategory askomics:category :value_2 .
 
 :value_1 rdf:type :category_attributeCategoryValue .
 :value_1 rdfs:label "value_1" .
@@ -122,7 +122,7 @@ _:blank rdf:type askomics:AskomicsCategory .
 _:blank rdf:type owl:ObjectProperty .
 _:blank rdfs:label "reference_attribute" .
 _:blank rdfs:domain :EntityName .
-_:blank rdfs:range _:blank2.
+_:blank rdfs:range :reference_attributeCategory.
 _:blank askomics:uri :reference_attribute
 ```
 
@@ -136,7 +136,7 @@ _:blank rdf:type askomics:AskomicsCategory .
 _:blank rdf:type owl:ObjectProperty .
 _:blank rdfs:label "strand_attribute" .
 _:blank rdfs:domain :EntityName .
-_:blank rdfs:range _:blank2.
+_:blank rdfs:range :strand_attributeCategory.
 _:blank askomics:uri :strand_attribute
 ```
 

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -8,7 +8,7 @@
     "ontology"
   ],
   "name": "AskOmics",
-  "version": "4.4.1",
+  "version": "4.4.0",
   "description": "Visual SPARQL query builder",
   "author": "Xavier Garnier",
   "license": "AGPL-3.0",

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setup(
     name='askomics',
-    version='4.4.1',
+    version='4.4.0',
     description='''
         AskOmics is a visual SPARQL query interface supporting both intuitive
         data integration and querying while shielding the user from most of the