From 6929eee1ef945501a0dbae8f2dae260929532496 Mon Sep 17 00:00:00 2001
From: Adam Gibson <agibson@mcw.edu>
Date: Mon, 6 May 2024 12:42:38 -0500
Subject: [PATCH] SCRUM-4012 add reference name lookup for mod references

---
 src/components/dataTable/AnnotatedEntitiesPopupCuration.js | 6 +++++-
 src/components/dataTable/GeneticModifiersCellCuration.js   | 2 +-
 src/components/dataTable/getResourceUrl.js                 | 2 +-
 src/components/dataTable/utils.js                          | 7 ++++++-
 4 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/components/dataTable/AnnotatedEntitiesPopupCuration.js b/src/components/dataTable/AnnotatedEntitiesPopupCuration.js
index 3558ccf9c..dc14bf115 100644
--- a/src/components/dataTable/AnnotatedEntitiesPopupCuration.js
+++ b/src/components/dataTable/AnnotatedEntitiesPopupCuration.js
@@ -27,7 +27,11 @@ import StrainBackground from './StrainBackground';
 
 function renderLink(entity) {
   const curie = getIdentifier(entity.diseaseAnnotationSubject);
-  const url = getResourceUrl(curie, entity.diseaseAnnotationSubject.type, entity.diseaseAnnotationSubject.subtype)
+  const url = getResourceUrl({
+    curie, 
+    type: entity.diseaseAnnotationSubject.type, 
+    subtype: entity.diseaseAnnotationSubject.subtype
+  })
 
   if (entity.type === 'AlleleDiseaseAnnotation') {
     const innerText = entity.diseaseAnnotationSubject.alleleSymbol ? entity.diseaseAnnotationSubject.alleleSymbol.displayText : entity.diseaseAnnotationSubject.name;
diff --git a/src/components/dataTable/GeneticModifiersCellCuration.js b/src/components/dataTable/GeneticModifiersCellCuration.js
index 80923132b..af2e9ed60 100644
--- a/src/components/dataTable/GeneticModifiersCellCuration.js
+++ b/src/components/dataTable/GeneticModifiersCellCuration.js
@@ -26,7 +26,7 @@ function GeneticModifierLink(modifier) {
             }
             break;
         case 'AffectedGenomicModel':
-            let url = getResourceUrl(identifier, modifier.type, modifier.subtype);
+            let url = getResourceUrl({ curie: identifier, type: modifier.type, subtype: modifier.subtype});
             if (url && modifier.name) {                
                 return ( 
                     <ExternalLink href={url}>
diff --git a/src/components/dataTable/getResourceUrl.js b/src/components/dataTable/getResourceUrl.js
index b85adcb45..2b58a02b1 100644
--- a/src/components/dataTable/getResourceUrl.js
+++ b/src/components/dataTable/getResourceUrl.js
@@ -1,6 +1,6 @@
 import { resourceDescriptors } from "../../resourceDescriptors";
 
-export const getResourceUrl = (curie, type, subtype ) => {
+export const getResourceUrl = ({ curie, type, subtype }) => {
   const [prefix, id] = curie.split(':');
 
   let resource;
diff --git a/src/components/dataTable/utils.js b/src/components/dataTable/utils.js
index 23ddaab65..2f6f4738f 100644
--- a/src/components/dataTable/utils.js
+++ b/src/components/dataTable/utils.js
@@ -28,7 +28,12 @@ export const getIsViaOrthology = (annotation) => {
 };
 
 export const getSingleReferenceUrl = (pubModId) => {
-  const url = getResourceUrl(pubModId);
+  let url;
+  if(pubModId.includes("PMID")){
+    url = getResourceUrl({curie: pubModId});
+  } else {
+    url = getResourceUrl({curie: pubModId, type: "reference"});
+  }
   return {pubModId, url};
 }