Added some query efficiency and flexibility to the incoming and outgo…

…ing view.
tetherless-world · Nov 18, 2024 · 6243690 · 6243690
1 parent c542c19
commit 6243690
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Showing 8 changed files with 92 additions and 24 deletions.
diff --git a/whyis/_version.py b/whyis/_version.py
@@ -1,4 +1,4 @@
-__version__='2.3.17'
+__version__='2.3.18'
 
 if __name__ == '__main__':
     print(__version__)
diff --git a/whyis/filters.py b/whyis/filters.py
@@ -225,22 +225,23 @@ def probquery(select):
 
 #    ?assertion a np:Assertion.
     ?np np:hasAssertion ?assertion.
-    optional {
-      ?np np:hasProvenance ?provenance
-      graph ?provenance {
-        ?assertion prov:wasDerivedFrom|dc:references ?article.
-        #?article a sio:PeerReviewedArticle.
-      }
+
+        #    optional {
+#     ?np np:hasProvenance ?provenance
+#      graph ?provenance {
+#        ?assertion prov:wasDerivedFrom|dc:references ?article.
+#        #?article a sio:PeerReviewedArticle.
+#      }
       optional {
-        ?article sio:hasAttribute|sio:SIO_000008 [ a whyis:ConfidenceScore; sio:hasValue|sio:SIO_000300 ?probability].
+        ?article sio:hasAttribute [ a whyis:ConfidenceScore; sio:hasValue ?probability].
       }
       minus { ?article a np:Nanopublication.}
     }
     optional {
       graph ?prob_assertion {
-        { ?assertion sio:hasAttribute|sio:SIO_000008 [ a sio:ProbabilityMeasure; sio:hasValue|sio:SIO_000300 ?probability]. }
+        { ?assertion sio:hasAttribute [ a sio:ProbabilityMeasure; sio:hasValue ?probability]. }
         UNION
-        { ?assertion sio:hasAttribute|sio:SIO_000008 [ a sio:SIO_000638; sio:hasValue|sio:SIO_000300 ?probability]. }
+        { ?assertion sio:SIO_000008 [ a sio:SIO_000638; sio:SIO_000300 ?probability]. }
       }
       ?prob_np np:hasAssertion ?prob_assertion.
     }
@@ -284,8 +285,10 @@ def merge(links):
                         i['probability'] = combine_pvalues([tfidf/(1+tfidf)],method='stouffer')[1]
                 else:
                     i['probability'] = i['probability'].value
-                result['from'].append(i['np'])
-                result['articles'].extend(i['articles'])
+                if 'np' in i:
+                    result['from'].append(i['np'])
+                if 'artciles' in i:
+                    result['articles'].extend(i['articles'])
             result['probability'] = max([i['probability'] for i in links])
             #print "end: "
             return result
@@ -308,7 +311,8 @@ def merge(links):
             result = dict(links[0])
             result['from'] = []
             result['articles'] = []
-            del result['np']
+            if 'np' in result:
+                del result['np']
             for i in links:
                 result['from'].extend(i['from'])
                 result['articles'].extend(i['articles'])
@@ -338,6 +342,11 @@ def probit(q, **values):
         results = query_filter(q, values=values)
         results = mergeLink(results)
         results = sorted(mergeLinkTypes(results), key=lambda x: x['probability'], reverse=True)
+        results = add_types_and_labels(results)
+        return results
+
+    @app.template_filter('add_types_and_labels')
+    def add_types_and_labels(results):
         for r in results:
             if 'link_type' in r:
                 labelize(r, 'link_type', 'link_label')

diff --git a/whyis/templates/incoming_class.json b/whyis/templates/incoming_class.json
@@ -6,10 +6,20 @@
     }
     bind(1 as ?probability)
     bind(?assertion as ?link)
-    minus { ?source owl:sameAs|rdfs:seeAlso|rdf:type|<http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
-    minus { ?source sio:hasPart|sio:SIO_000028|sio:hasAttribute|sio:SIO_000008 ?target }
+
+    filter(!isLiteral(?target))
+    minus { ?source owl:sameAs ?target.}
+    minus { ?source rdfs:seeAlso ?target.}
+    minus { ?source rdf:type ?target.}
+    minus { ?source <http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
+    minus { ?source foaf:depiction ?target.
+    minus { ?source sio:hasPart  ?target.}
+    minus { ?source sio:SIO_000028 ?target.}
+    minus { ?source sio:hasAttribute ?target.}
+    minus { ?source sio:SIO_000008 ?target. }
     minus { ?target a sio:Term.}
     minus { ?target a sio:SIO_000275.}
     filter (!sameTerm(?source, ?target) && isIRI(?target))
+
     FILTER (!regex(str(?source), "^bnode:"))
 ''' | probit(target=this.identifier) | tojson }}
diff --git a/whyis/templates/incoming_ontology.json b/whyis/templates/incoming_ontology.json
@@ -7,10 +7,20 @@
     bind(1 as ?probability)
     values ?link_type {owl:imports}
     bind(?assertion as ?link)
-    minus { ?source owl:sameAs|rdfs:seeAlso|rdf:type|<http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
-    minus { ?source sio:hasPart|sio:SIO_000028|sio:hasAttribute|sio:SIO_000008 ?target }
+
+    filter(!isLiteral(?target))
+    minus { ?source owl:sameAs ?target.}
+    minus { ?source rdfs:seeAlso ?target.}
+    minus { ?source rdf:type ?target.}
+    minus { ?source <http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
+    minus { ?source foaf:depiction ?target.
+    minus { ?source sio:hasPart  ?target.}
+    minus { ?source sio:SIO_000028 ?target.}
+    minus { ?source sio:hasAttribute ?target.}
+    minus { ?source sio:SIO_000008 ?target. }
     minus { ?target a sio:Term.}
     minus { ?target a sio:SIO_000275.}
     filter (!sameTerm(?source, ?target) && isIRI(?target))
+
     FILTER (!regex(str(?source), "^bnode:"))
 ''' | probit(target=this.identifier) | tojson }}
diff --git a/whyis/templates/incoming_resource.json b/whyis/templates/incoming_resource.json
@@ -4,9 +4,17 @@
       }
     }
     bind(?assertion as ?link)
-    minus { ?source owl:sameAs|rdfs:seeAlso|rdf:type|<http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
-    minus { ?source sio:hasPart|sio:SIO_000028|sio:hasAttribute|sio:SIO_000008 ?target }
-    minus { ?source a sio:Term }
+    filter(!isLiteral(?target))
+    minus { ?source owl:sameAs ?target.}
+    minus { ?source rdfs:seeAlso ?target.}
+    minus { ?source rdf:type ?target.}
+    minus { ?source <http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
+    minus { ?source foaf:depiction ?target.
+    minus { ?source sio:hasPart  ?target.}
+    minus { ?source sio:SIO_000028 ?target.}
+    minus { ?source sio:hasAttribute ?target.}
+    minus { ?source sio:SIO_000008 ?target. }
+    minus { ?target a sio:Term.}
     minus { ?target a sio:SIO_000275.}
     filter (!sameTerm(?source, ?target) && isIRI(?target))
 

diff --git a/whyis/templates/outgoing_class.json b/whyis/templates/outgoing_class.json
@@ -6,8 +6,17 @@
     }
     bind(1 as ?probability)
     bind(?assertion as ?link)
-    minus { ?source owl:sameAs|rdfs:seeAlso|rdf:type|<http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
-    minus { ?source sio:hasPart|sio:SIO_000028|sio:hasAttribute|sio:SIO_000008 ?target }
+
+    filter(!isLiteral(?target))
+    minus { ?source owl:sameAs ?target.}
+    minus { ?source rdfs:seeAlso ?target.}
+    minus { ?source rdf:type ?target.}
+    minus { ?source <http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
+    minus { ?source foaf:depiction ?target.
+    minus { ?source sio:hasPart  ?target.}
+    minus { ?source sio:SIO_000028 ?target.}
+    minus { ?source sio:hasAttribute ?target.}
+    minus { ?source sio:SIO_000008 ?target. }
     minus { ?target a sio:Term.}
     minus { ?target a sio:SIO_000275.}
     filter (!sameTerm(?source, ?target) && isIRI(?target))

diff --git a/whyis/templates/outgoing_ontology.json b/whyis/templates/outgoing_ontology.json
@@ -19,10 +19,24 @@
     }
     bind(1 as ?probability)
     bind(?assertion as ?link)
+
+    filter(!isLiteral(?target))
+
     minus { ?source owl:sameAs|rdfs:seeAlso|rdf:type|<http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
     minus { ?source sio:hasPart|sio:SIO_000028|sio:hasAttribute|sio:SIO_000008 ?target }
     minus { ?target a sio:Term.}
     minus { ?target a sio:SIO_000275.}
+    minus { ?source owl:sameAs ?target.}
+    minus { ?source rdfs:seeAlso ?target.}
+    minus { ?source rdf:type ?target.}
+    minus { ?source <http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
+    minus { ?source foaf:depiction ?target.
+    minus { ?source sio:hasPart  ?target.}
+    minus { ?source sio:SIO_000028 ?target.}
+    minus { ?source sio:hasAttribute ?target.}
+    minus { ?source sio:SIO_000008 ?target. }
+    minus { ?target a sio:Term.}
+    minus { ?target a sio:SIO_000275.}
     filter (!sameTerm(?source, ?target) && isIRI(?target))
     FILTER (!regex(str(?source), "^bnode:"))
 ''' | probit(source=this.identifier) | tojson }}
diff --git a/whyis/templates/outgoing_resource.json b/whyis/templates/outgoing_resource.json
@@ -4,8 +4,16 @@
       }
     }
     bind(?assertion as ?link)
-    minus { ?source owl:sameAs|rdfs:seeAlso|rdf:type|<http://dbpedia.org/ontology/wikiPageExternalLink>|foaf:depiction ?target.}
-    minus { ?source sio:hasPart|sio:SIO_000028|sio:hasAttribute|sio:SIO_000008 ?target }
+    filter(!isLiteral(?target))
+    minus { ?source owl:sameAs ?target.}
+    minus { ?source rdfs:seeAlso ?target.}
+    minus { ?source rdf:type ?target.}
+    minus { ?source <http://dbpedia.org/ontology/wikiPageExternalLink> ?target.}
+    minus { ?source foaf:depiction ?target.
+    minus { ?source sio:hasPart  ?target.}
+    minus { ?source sio:SIO_000028 ?target.}
+    minus { ?source sio:hasAttribute ?target.}
+    minus { ?source sio:SIO_000008 ?target. }
     minus { ?target a sio:Term.}
     minus { ?target a sio:SIO_000275.}
     filter (!sameTerm(?source, ?target) && isIRI(?target))