Jim's improved query for models/gp w/ grouping handled in API. For #2

geneontology · Jan 5, 2022 · 5fe0a4b · 5fe0a4b
1 parent 3f2e995
commit 5fe0a4b
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Showing 2 changed files with 17 additions and 13 deletions.
diff --git a/app.js b/app.js
@@ -116,7 +116,11 @@ app.get('/models/gp', function(req, res) {
     gocams = utils.splitTrim(gocams, ",", "<http://model.geneontology.org/", ">");
     utils.fetchAndSend(res, sparqlModels.ModelsGPs(gocams), false, keysArrayGPs);
   } else {
-    utils.fetchAndSend(res, sparqlModels.AllModelsGPs(), false, keysArrayGPs);
+    // Must combine the results per gocam
+    utils.fetchData(sparqlModels.AllModelsGPs(), keysArrayGPs, (error, data) => {
+      utils.addCORS(res);
+      res.send(utils.mergeResults(data, "gocam"));
+    });
   }
 });
 

diff --git a/queries/sparql-models.js b/queries/sparql-models.js
@@ -262,32 +262,32 @@ module.exports = {
     AllModelsGPs() {
         // Transform the array in string
         var encoded = encodeURIComponent(`
+        PREFIX prov: <http://www.w3.org/ns/prov#>
         PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
         PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> 
         PREFIX owl: <http://www.w3.org/2002/07/owl#>
         PREFIX metago: <http://model.geneontology.org/>
-
         PREFIX enabled_by: <http://purl.obolibrary.org/obo/RO_0002333>
         PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
-
-        SELECT ?gocam   (GROUP_CONCAT(distinct ?identifier;separator="` + separator + `") as ?gpids)
-			        	(GROUP_CONCAT(distinct ?name;separator="` + separator + `") as ?gpnames)
-
+        SELECT DISTINCT ?gocam ?gpids ?gpnames
         WHERE 
         {
             GRAPH ?gocam {
                 ?gocam metago:graphType metago:noctuaCam .
+            }
+            FILTER NOT EXISTS {
+                ?gocam prov:wasDerivedFrom ?asserted_cam .
+            }
+            GRAPH ?gocam {
                 ?s enabled_by: ?gpnode .    
-                ?gpnode rdf:type ?identifier .
-                FILTER(?identifier != owl:NamedIndividual) .
-                FILTER(!contains(str(?gocam), "_inferred"))
+                ?gpnode rdf:type ?gpids .
+                FILTER(?gpids != owl:NamedIndividual) .
             }
-            optional {
-                ?identifier rdfs:label ?name
+            OPTIONAL {
+                ?gpids rdfs:label ?label
             }
-            BIND(IF(bound(?name), ?name, ?identifier) as ?name)
+            BIND(COALESCE(?label, ?gpids) AS ?gpnames)
         }
-        GROUP BY ?gocam
         `);
         return "?query=" + encoded;
     },