From 79e71757fc0f4ac1da5a779a1b46dbdd65cb1aac Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Wed, 21 Aug 2024 16:42:33 -0400
Subject: [PATCH 1/2] chore: reduce query ids by only using bound nodes

---
 src/results_assembly/pfocr.ts | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/results_assembly/pfocr.ts b/src/results_assembly/pfocr.ts
index fbe651c2..41f0dee7 100644
--- a/src/results_assembly/pfocr.ts
+++ b/src/results_assembly/pfocr.ts
@@ -188,13 +188,16 @@ export async function enrichTrapiResultsWithPfocrFigures(response: TrapiResponse
   const curiesByResult: Map<TrapiResult, Set<string>> = new Map();
 
   const curieCombos: Set<string> = results.reduce((combos: Set<string>, result: TrapiResult) => {
-    const nodes: Set<TrapiKGNode> = traverseResultForNodes(result, response);
+    const nodes: Set<TrapiKGNode> = new Set();
+    Object.values(result.node_bindings).forEach((bindings) =>
+      bindings.forEach((binding) => nodes.add(response.message.knowledge_graph.nodes[binding.id])),
+    );
     const combo: Set<string> = new Set();
     let matchedNodes = 0;
     [...nodes].forEach((node) => {
       let nodeMatched = false;
-      const equivalentCuries = node.attributes?.find((attribute) => attribute.attribute_type_id === 'biolink:xref')
-        .value as string[];
+      const equivalentCuries =
+        (node.attributes?.find((attribute) => attribute.attribute_type_id === 'biolink:xref')?.value as string[]) ?? [];
       equivalentCuries.forEach((curie) => {
         const prefix = curie.split(':')[0];
         const suffix = curie.replace(`${prefix}:`, '');
@@ -257,7 +260,14 @@ export async function enrichTrapiResultsWithPfocrFigures(response: TrapiResponse
     // No figures match this result
     if (!figuresByCuries[curieCombosByResult.get(trapiResult)]) continue;
 
-    const resultCuries = curiesByResult.get(trapiResult);
+    const resultNodes = traverseResultForNodes(trapiResult, response);
+    const resultCuries: Set<string> = [...resultNodes].reduce((curies, node) => {
+      const equivalentCuries =
+        (node.attributes?.find((attribute) => attribute.attribute_type_id === 'biolink:xref')?.value as string[]) ?? [];
+      equivalentCuries.forEach((curie) => curies.add(curie.split(':').slice(1).join('')));
+      return curies;
+    }, new Set<string>());
+
     const resultGenesInAllFigures = intersection(allGenesInAllFigures, resultCuries);
 
     (figuresByCuries[curieCombosByResult.get(trapiResult)] ?? []).forEach((figure) => {

From 5a527a5627535e0a8f06adb5637136f8988d13ef Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 22 Aug 2024 10:55:41 -0400
Subject: [PATCH 2/2] fix: only keep supported prefixes

---
 src/results_assembly/pfocr.ts | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/results_assembly/pfocr.ts b/src/results_assembly/pfocr.ts
index 41f0dee7..5fab0980 100644
--- a/src/results_assembly/pfocr.ts
+++ b/src/results_assembly/pfocr.ts
@@ -264,7 +264,11 @@ export async function enrichTrapiResultsWithPfocrFigures(response: TrapiResponse
     const resultCuries: Set<string> = [...resultNodes].reduce((curies, node) => {
       const equivalentCuries =
         (node.attributes?.find((attribute) => attribute.attribute_type_id === 'biolink:xref')?.value as string[]) ?? [];
-      equivalentCuries.forEach((curie) => curies.add(curie.split(':').slice(1).join('')));
+      equivalentCuries.forEach((curie) => {
+        const prefix = curie.split(':')[0];
+        const suffix = curie.replace(`${prefix}:`, '');
+        if (Object.keys(SUPPORTED_PREFIXES).includes(prefix)) curies.add(suffix);
+      });
       return curies;
     }, new Set<string>());