Adapted metadata query to pathways

src/pathme/reactome/rdf_sparql.py

@@ -81,13 +81,13 @@
 
 #: SPARQL query to get all the possible metadate (optional statements) of an entity (Protein, Dna, Pathway...).
 GET_ENTITY_METADATA = """
-SELECT DISTINCT (STRAFTER(STR(?entity), '#') AS ?identifier) (STR(?entity) AS ?uri_reactome_id) ?uri_id ?name ?identifier ?cell_locat ?display_name ?complex_components ?comment (STRAFTER (STR(?uri_type), str(biopax3:)) AS ?entity_type) 
+SELECT DISTINCT (STRAFTER(STR(?entity), '#') AS ?identifier) (STR(?entity) AS ?uri_reactome_id) (STR(?entity) AS ?uri_id) (STR(?entity_reference) AS ?uri_id) ?name ?cell_locat ?display_name ?complex_components ?comment (STRAFTER (STR(?uri_type), str(biopax3:)) AS ?entity_type) 
 WHERE
     {        
         ?entity rdf:type ?uri_type .
-        ?entity biopax3:comment ?comment .
+        optional {?entity biopax3:comment ?comment .}
         
-        optional {?entity biopax3:entityReference ?uri_id .}
+        optional {?entity biopax3:entityReference ?entity_reference .}
         optional {?entity biopax3:name ?name .}
         optional {?entity biopax3:displayName ?display_name .}
         
@@ -117,7 +117,7 @@ def _get_all_entry_types(rdf_graph: rdflib.Graph) -> Set[str]:
     }
 
 
-def _get_pathway_metadata(pathway_uri: str, rdf_graph: rdflib.Graph) -> Dict[str, Union[str, Set[str]]]:
+def _get_pathway_metadata(pathway_uri: str, rdf_graph: rdflib.Graph) -> Dict[str, Dict[str, Dict[str, str]]]:
     """Get metadata for a pathway entry.
 
     :param pathway_uri: URI reference of the queried graph
@@ -130,7 +130,7 @@ def _get_pathway_metadata(pathway_uri: str, rdf_graph: rdflib.Graph) -> Dict[str
             initNs=PREFIXES,
             initBindings={'entity': pathway_uri}
         ),
-        attr_empty=['display_name', 'identifier', 'uri_reactome_id', 'comment'],
+        attr_empty=['display_name', 'identifier', 'uri_id', 'uri_reactome_id', 'comment'],
         id_dict=False
     )