fix: preserve qualifier biolink prefix

biothings · Aug 9, 2024 · 6a8d1e5 · 6a8d1e5
1 parent 9fad32d
commit 6a8d1e5
Show file tree

Hide file tree

Showing 2 changed files with 28 additions and 19 deletions.
diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -313,25 +313,32 @@ export default class InferredQueryHandler {
       // Direct edge answers stand on their own, not as an inferred edge.
       const boundEdgeID = Object.values(result.analyses[0].edge_bindings)[0][0].id;
       const boundEdge = combinedResponse.message.knowledge_graph.edges[boundEdgeID];
-      const specialHandling = [
-        Object.keys(result.node_bindings).length === 2, // Direct edge
-        // Predicate matches or is descendant
+      const oneHop = Object.keys(result.node_bindings).length === 2; // Direct edge
+      // Predicate matches or is descendant
+      const predicateMatch =
         qEdge.predicates?.some(
           (predicate) =>
             predicate === boundEdge.predicate ||
             biolink.getDescendantPredicates(predicate).includes(boundEdge.predicate),
-        ) ?? false,
-        // All query qualifiers (if any) are accounted for (more is fine)
+        ) ?? false;
+      // All query qualifiers (if any) are accounted for (more is fine)
+      const qualifierMatch =
         qEdge.qualifier_constraints?.some(({ qualifier_set }) => {
-          return qualifier_set.every((queryQualifier) =>
-            boundEdge.qualifiers?.some(
-              (qualifier) =>
-                queryQualifier.qualifier_type_id === qualifier.qualifier_type_id &&
-                queryQualifier.qualifier_value === qualifier.qualifier_value,
-            ) ?? false,
-          );
-        }) ?? false,
-      ].every((test) => test);
+          return qualifier_set.every((queryQualifier) => {
+            return (
+              boundEdge.qualifiers?.some((qualifier) => {
+                const typeMatch = queryQualifier.qualifier_type_id === qualifier.qualifier_type_id;
+                const valueMatch =
+                  queryQualifier.qualifier_value === qualifier.qualifier_value ||
+                  biolink
+                    .getDescendantQualifiers(queryQualifier.qualifier_value as string)
+                    .includes(qualifier.qualifier_value as string);
+                return typeMatch && valueMatch;
+              }) ?? false
+            );
+          });
+        }) ?? false;
+      const specialHandling = oneHop && predicateMatch && qualifierMatch;
       if (specialHandling) {
         translatedResult.analyses[0].edge_bindings = { [qEdgeID]: [{ id: boundEdgeID, attributes: [] }] };
       } else {

diff --git a/src/inferred_mode/template_lookup.ts b/src/inferred_mode/template_lookup.ts
@@ -62,21 +62,23 @@ export async function getTemplates(lookups: TemplateLookup[]): Promise<MatchedTe
   const matchingTemplatePaths: PathMatch[] = templateGroups.reduce((matches: PathMatch[], group: TemplateGroup) => {
     let matchingQualifers: CompactQualifiers;
     const lookupMatch = lookups.some((lookup) => {
-      const match = (
+      const match =
         group.subject.includes(lookup.subject) &&
         group.object.includes(lookup.object) &&
         group.predicate.includes(lookup.predicate) &&
         Object.entries(lookup.qualifiers || {}).every(([qualifierType, qualifierValue]) => {
-          return (group.qualifiers || {})[qualifierType] && group.qualifiers[qualifierType] === qualifierValue;
-        })
-      );
+          return (
+            (group.qualifiers || {})[qualifierType.replace('biolink:', '')] &&
+            group.qualifiers[qualifierType.replace('biolink:', '')] === qualifierValue.replace('biolink:', '')
+          );
+        });
       if (match) matchingQualifers = lookup.qualifiers;
       return match;
     });
 
     if (lookupMatch) {
       group.templates.forEach((template) => {
-        if (!matches.find(t => t.path === templatePaths[template])) {
+        if (!matches.find((t) => t.path === templatePaths[template])) {
           matches.push({ path: templatePaths[template], qualifiers: matchingQualifers });
         }
       });