From 1eadee72283d3c74bd5d873c41d4b346f5a595f0 Mon Sep 17 00:00:00 2001
From: Colleen Xu <colleenhxu@gmail.com>
Date: Thu, 21 Mar 2024 23:26:20 -0700
Subject: [PATCH 1/2] feat: update templates for treats-refactor

---
 data/templates/Drug-treats-Disease/Chem-treats-DoP.json         | 2 +-
 .../Drug-treats-Disease/Chem-treats-PhenoOfDisease.json         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/data/templates/Drug-treats-Disease/Chem-treats-DoP.json b/data/templates/Drug-treats-Disease/Chem-treats-DoP.json
index 1bdf23ad..663d467b 100644
--- a/data/templates/Drug-treats-Disease/Chem-treats-DoP.json
+++ b/data/templates/Drug-treats-Disease/Chem-treats-DoP.json
@@ -13,7 +13,7 @@
                 "eA": {
                     "subject": "creativeQuerySubject",
                     "object": "creativeQueryObject",
-                    "predicates": ["biolink:treats"]
+                    "predicates": ["biolink:treats_or_applied_or_studied_to_treat"]
                 }
             }
         }
diff --git a/data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json b/data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json
index a8f23fc1..e54787f1 100644
--- a/data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json
+++ b/data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json
@@ -17,7 +17,7 @@
                 "eA": {
                     "subject": "creativeQuerySubject",
                     "object": "nA",
-                    "predicates": ["biolink:treats"]
+                    "predicates": ["biolink:treats_or_applied_or_studied_to_treat"]
                 },
                 "eB": {
                     "subject": "creativeQueryObject",

From e602f5a16d626a51694737a790ffa46c0bcc8fff Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Fri, 22 Mar 2024 13:28:45 -0400
Subject: [PATCH 2/2] fix: terminate on broken chain

---
 src/edge_manager.ts | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/src/edge_manager.ts b/src/edge_manager.ts
index 145e415c..d62db752 100644
--- a/src/edge_manager.ts
+++ b/src/edge_manager.ts
@@ -231,7 +231,7 @@ export default class QueryEdgeManager {
     return keep;
   }
 
-  collectRecords(): void {
+  collectRecords(): boolean {
     //go through edges and collect records organized by edge
     let recordsByQEdgeID: RecordsByQEdgeID = {};
     //all res merged
@@ -268,12 +268,10 @@ export default class QueryEdgeManager {
         new LogEntry(
           'WARNING',
           null,
-          `qEdges ${JSON.stringify(brokenEdges)} ` + `resulted in (0) records. No complete paths can be formed.`,
+          `qEdges ${brokenEdges} resulted in (0) records. No complete paths can be formed.`,
         ).getLog(),
       );
-      debug(
-        `(12) qEdges ${JSON.stringify(brokenEdges)} ` + `resulted in (0) records. No complete paths can be formed.`,
-      );
+      debug(`(12) qEdges ${brokenEdges} resulted in (0) records. No complete paths can be formed.`);
     }
     //Organized by edge: update query records
     this._organizedRecords = recordsByQEdgeID;
@@ -289,8 +287,12 @@ export default class QueryEdgeManager {
     //         console.log(err);
     //     }
     // });
-    debug(`(12) Collected (${this._records.length}) records!`);
-    this.logs.push(new LogEntry('DEBUG', null, `Edge manager collected (${this._records.length}) records!`).getLog());
+    if (!brokenChain) {
+      debug(`(12) Collected (${this._records.length}) records!`);
+      this.logs.push(new LogEntry('DEBUG', null, `Edge manager collected (${this._records.length}) records!`).getLog());
+    }
+
+    return !brokenChain;
   }
 
   updateEdgeRecords(currentQEdge: QEdge): void {
@@ -474,7 +476,13 @@ export default class QueryEdgeManager {
     }
     this._logSkippedQueries(unavailableAPIs);
     // collect and organize records
-    this.collectRecords();
+    if (!this.collectRecords()) {
+      debug(`(X) Terminating...No complete paths.`);
+      this.logs.push(
+        new LogEntry('WARNING', null, `No complete paths could be formed. Your query terminates.`).getLog(),
+      );
+      return;
+    }
     // dump records if set to do so
     if (process.env.DUMP_RECORDS) {
       await this.dumpRecords(this.getRecords());