From 37f768005feafbd63d36cf8c30e72d4887ef6c58 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Mon, 5 Aug 2024 15:05:08 -0400
Subject: [PATCH 1/2] fix: more specific direct edge criteria

---
 src/inferred_mode/inferred_mode.ts | 47 ++++++++++++++++++++----------
 1 file changed, 32 insertions(+), 15 deletions(-)

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
index bc6f3dd7..0061edbb 100644
--- a/src/inferred_mode/inferred_mode.ts
+++ b/src/inferred_mode/inferred_mode.ts
@@ -309,8 +309,28 @@ export default class InferredQueryHandler {
       const resultID = `${resultCreativeSubjectID}-${resultCreativeObjectID}`;
 
       // Direct edge answers stand on their own, not as an inferred edge.
-      if (Object.keys(result.node_bindings).length == 2) {
-        const boundEdgeID = Object.values(result.analyses[0].edge_bindings)[0][0].id;
+      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
+        qEdge.predicates.some(
+          (predicate) =>
+            predicate === boundEdge.predicate ||
+            biolink.getDescendantPredicates(predicate).includes(boundEdge.predicate),
+        ),
+        // All query qualifiers (if any) are accounted for (more is fine)
+        qEdge.qualifier_constraints.every(({ 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,
+            ),
+          );
+        }),
+      ].every((test) => test);
+      if (specialHandling) {
         translatedResult.analyses[0].edge_bindings = { [qEdgeID]: [{ id: boundEdgeID, attributes: [] }] };
       } else {
         // Create an aux graph using the result and associate it with an inferred Edge
@@ -334,8 +354,8 @@ export default class InferredQueryHandler {
             ],
             attributes: [
               { attribute_type_id: 'biolink:support_graphs', value: [] },
-              { attribute_type_id: 'biolink:knowledge_level', value: "prediction" },
-              { attribute_type_id: 'biolink:agent_type', value: "computational_model" },
+              { attribute_type_id: 'biolink:knowledge_level', value: 'prediction' },
+              { attribute_type_id: 'biolink:agent_type', value: 'computational_model' },
             ],
           };
         }
@@ -357,7 +377,7 @@ export default class InferredQueryHandler {
             },
             [] as string[],
           ),
-          attributes: []
+          attributes: [],
         };
       }
 
@@ -390,9 +410,9 @@ export default class InferredQueryHandler {
         if (typeof combinedResponse.message.results[resultID].analyses[0].score !== 'undefined') {
           combinedResponse.message.results[resultID].analyses[0].score = resScore
             ? scaled_sigmoid(
-                inverse_scaled_sigmoid(combinedResponse.message.results[resultID].analyses[0].score) +
-                  inverse_scaled_sigmoid(resScore),
-              )
+              inverse_scaled_sigmoid(combinedResponse.message.results[resultID].analyses[0].score) +
+              inverse_scaled_sigmoid(resScore),
+            )
             : combinedResponse.message.results[resultID].analyses[0].score;
         } else {
           combinedResponse.message.results[resultID].analyses[0].score = resScore;
@@ -560,11 +580,9 @@ export default class InferredQueryHandler {
           const message = [
             `Addition of ${creativeLimitHit} results from Template ${i + 1}`,
             Object.keys(combinedResponse.message.results).length === this.CREATIVE_LIMIT ? ' meets ' : ' exceeds ',
-            `creative result maximum of ${this.CREATIVE_LIMIT} (reaching ${
-              Object.keys(combinedResponse.message.results).length
+            `creative result maximum of ${this.CREATIVE_LIMIT} (reaching ${Object.keys(combinedResponse.message.results).length
             } merged). `,
-            `Response will be truncated to top-scoring ${this.CREATIVE_LIMIT} results. Skipping remaining ${
-              subQueries.length - (i + 1)
+            `Response will be truncated to top-scoring ${this.CREATIVE_LIMIT} results. Skipping remaining ${subQueries.length - (i + 1)
             } `,
             subQueries.length - (i + 1) === 1 ? `template.` : `templates.`,
           ].join('');
@@ -589,9 +607,8 @@ export default class InferredQueryHandler {
       const total =
         Object.values(mergedResultsCount).reduce((sum, count) => sum + count, 0) +
         Object.keys(mergedResultsCount).length;
-      const message = `Merging Summary: (${total}) inferred-template results were merged into (${
-        Object.keys(mergedResultsCount).length
-      }) final results, reducing result count by (${total - Object.keys(mergedResultsCount).length})`;
+      const message = `Merging Summary: (${total}) inferred-template results were merged into (${Object.keys(mergedResultsCount).length
+        }) final results, reducing result count by (${total - Object.keys(mergedResultsCount).length})`;
       debug(message);
       combinedResponse.logs.push(new LogEntry('INFO', null, message).getLog());
     }

From f4e63f7e46aeede6f17ee1d6acf51d6ca2fa4eb8 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Mon, 5 Aug 2024 15:09:56 -0400
Subject: [PATCH 2/2] fix: satisfy 1+ qualifier set, not all necessarily

---
 src/inferred_mode/inferred_mode.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
index 0061edbb..1c973fc6 100644
--- a/src/inferred_mode/inferred_mode.ts
+++ b/src/inferred_mode/inferred_mode.ts
@@ -320,7 +320,7 @@ export default class InferredQueryHandler {
             biolink.getDescendantPredicates(predicate).includes(boundEdge.predicate),
         ),
         // All query qualifiers (if any) are accounted for (more is fine)
-        qEdge.qualifier_constraints.every(({ qualifier_set }) => {
+        qEdge.qualifier_constraints.some(({ qualifier_set }) => {
           return qualifier_set.every((queryQualifier) =>
             boundEdge.qualifiers.some(
               (qualifier) =>