Update ref string

src/components/dataTable/AnnotatedEntitiesPopupCuration.js

@@ -38,11 +38,13 @@ function renderLink(entity) {
       return <Link to={`/gene/${entity.subject.curie}`}>{inner}</Link>;
   } else {
       const inner = <span dangerouslySetInnerHTML={{__html: entity.subject.name}}/>;
-    return <ExternalLink href={url}>{inner}</ExternalLink>;
+      return <ExternalLink href={url}>{inner}</ExternalLink>;
   }
 }
 
-function AnnotatedEntitiesPopupCuration({ children, entities, parentPage, mainRowCurie }) {
+
+
+function AnnotatedEntitiesPopupCuration({ children, entities, parentPage, mainRowCurie, pubModIds }) {
 
   if (!entities || !entities.length) {
     return null;
@@ -99,7 +101,7 @@ function AnnotatedEntitiesPopupCuration({ children, entities, parentPage, mainRo
                       <td><AnnotationType  annotationType={entity.annotationType}/></td>
                       <td><EvidenceCodesCellCuration evidenceCodes={entity.evidenceCodes}/></td>
                       <td><ProviderCellCuration provider={provider} /></td>
-                      <td><SingleReferenceCellCuration singleReference={entity.singleReference}/></td>
+                      <td><SingleReferenceCellCuration singleReference={entity.singleReference} pubModIds={pubModIds}/></td>
                     </tr>
                 )
               })

src/components/dataTable/DiseaseQualifiersColumn.js

@@ -7,10 +7,10 @@ const DiseaseQualifiersColumn = ({qualifiers}) => {
   if (!qualifiers || !qualifiers.length) {
     return null;
   }
-
+  
   return (
     <CommaSeparatedList>
-      {qualifiers.map(qualifier => qualifier)}
+      {qualifiers.map(qualifier => qualifier.replaceAll("_", " "))}
     </CommaSeparatedList>
   );
 };

src/components/dataTable/referencesCellCuration.js

@@ -2,26 +2,26 @@ import React from 'react';
 
 import ExternalLink from '../ExternalLink';
 import { CollapsibleList } from '../collapsibleList';
-import { getMultipleReferencesCuriesAndUrls } from "./utils";
+import { getMultipleReferencesUrls } from "./utils";
 
 const removeDuplicates = (refs) => {
-  const newArray = refs.map((ref) => [ref.curie, ref]);
+  const newArray = refs.map((ref) => [ref.pubModId, ref]);
   const newMap = new Map(newArray);
   const iterator = newMap.values();
   const uniqueRefs = [...iterator];
 
   return uniqueRefs;
-}
+};
 
-const ReferencesCellCuration = (refs) => {
-  const refStringsAndUrls = getMultipleReferencesCuriesAndUrls(refs);
-	const uniqueRefs = removeDuplicates(refStringsAndUrls);
+const ReferencesCellCuration = ({ pubModIds }) => {
+  const refStringsAndUrls = getMultipleReferencesUrls(pubModIds);
+  const uniqueRefs = removeDuplicates(refStringsAndUrls);
 
-    return refs &&
+  return pubModIds &&
     <CollapsibleList>
       {
-        uniqueRefs.map(({ curie, url }) => {
-          return <ExternalLink href={url} key={curie} title={curie}>{curie}</ExternalLink>;
+        uniqueRefs.map(({ pubModId, url }) => {
+          return <ExternalLink href={url} key={pubModId} title={pubModId}>{pubModId}</ExternalLink>;
         })
       }
     </CollapsibleList>;

src/components/dataTable/singleReferenceCellCuration.js

@@ -1,14 +1,19 @@
 import React from 'react';
 
 import ExternalLink from '../ExternalLink';
-import { getSingleReferenceCurieAndUrl } from "./utils";
-
-const SingleReferenceCellCuration = ({singleReference}) => {
-  if (singleReference) {
-    const { curie, url } = getSingleReferenceCurieAndUrl(singleReference);
-    return <ExternalLink href={url} key={curie} title={curie}>{curie}</ExternalLink>;
-  }
-  return <></>;
+import { getSingleReferenceUrl } from "./utils";
+
+const SingleReferenceCellCuration = ({ singleReference, pubModIds }) => {
+  if (!singleReference) return <></>;
+  const pubModId = getSingleReferencePubModId(singleReference, pubModIds);
+  const { url } = getSingleReferenceUrl(pubModId);
+  return <ExternalLink href={url} key={pubModId} title={pubModId}>{pubModId}</ExternalLink>;
+};
+
+const getSingleReferencePubModId = (reference, pubModIds) => {
+  return reference.crossReferences
+    .filter(crossRef => pubModIds.includes(crossRef.referencedCurie))
+    .map(crossRef => crossRef.referencedCurie)[0];
 };
 
 

src/components/dataTable/utils.js

@@ -22,65 +22,13 @@ export const getIsViaOrthology = (annotation) => {
   return annotation.generatedRelationString.includes("orthology");
 };
 
-export function getRefStrings(referenceItems) {
-  if (!referenceItems)
-    return;
-
-  let refStrings = referenceItems.map((referenceItem) => getRefString(referenceItem));
-
-  return refStrings.sort();
-}
-
-export function getRefString(referenceItem) {
-  if (!referenceItem)
-    return;
-
-  if (!referenceItem.cross_references && !referenceItem.crossReferences){
-    return referenceItem.curie
-  }
-  let xrefCuries = referenceItem.crossReferences.map((crossReference) => crossReference.referencedCurie);
-  let primaryXrefCurie = '';
-
-  if (indexWithPrefix(xrefCuries, 'PMID:') > -1) {
-    [primaryXrefCurie] = xrefCuries.splice(indexWithPrefix(xrefCuries, 'PMID:'), 1);
-  } else if (indexWithPrefix(xrefCuries, 'FB:') > -1) {
-    [primaryXrefCurie] = xrefCuries.splice(indexWithPrefix(xrefCuries, 'FB:'), 1);
-  } else if (indexWithPrefix(xrefCuries, 'MGI:') > -1) {
-    [primaryXrefCurie] = xrefCuries.splice(indexWithPrefix(xrefCuries, 'MGI:'), 1);
-  } else if (indexWithPrefix(xrefCuries, 'RGD:') > -1) {
-    [primaryXrefCurie] = xrefCuries.splice(indexWithPrefix(xrefCuries, 'RGD:'), 1);
-  } else if (indexWithPrefix(xrefCuries, 'SGD:') > -1) {
-    [primaryXrefCurie] = xrefCuries.splice(indexWithPrefix(xrefCuries, 'SGD:'), 1);
-  } else if (indexWithPrefix(xrefCuries, 'WB:') > -1) {
-    [primaryXrefCurie] = xrefCuries.splice(indexWithPrefix(xrefCuries, 'WB:'), 1);
-  } else if (indexWithPrefix(xrefCuries, 'ZFIN:') > -1) {
-    [primaryXrefCurie] = xrefCuries.splice(indexWithPrefix(xrefCuries, 'ZFIN:'), 1);
-  } else {
-    [primaryXrefCurie] = xrefCuries.splice(0, 1);
-  }
-
-  return primaryXrefCurie;
-}
-
-
-function indexWithPrefix(array, prefix) {
-
-  for (let i = 0; i < array.length; i++) {
-    if (array[i].startsWith(prefix)) {
-      return i;
-    }
-  }
-  return -1;
-}
-
-export const getSingleReferenceCurieAndUrl = (reference) => {
-  const curie = getRefString(reference);
-  const url = getResourceUrl(curie);
-  return {curie, url};
+export const getSingleReferenceUrl = (pubModId) => {
+  const url = getResourceUrl(pubModId);
+  return {pubModId, url};
 }
 
-export const getMultipleReferencesCuriesAndUrls = (references) => {
-  return references.map((reference) => getSingleReferenceCurieAndUrl(reference));
+export const getMultipleReferencesUrls = (pubModIds) => {
+  return pubModIds.sort().map((pubModId) => getSingleReferenceUrl(pubModId));
 }
 
 const buildProvider = (annotation) => {

src/components/disease/diseaseAnnotationTable.js

@@ -67,7 +67,12 @@ const DiseaseAnnotationTable = ({
         <React.Fragment>
           <div>{GeneCellCuration(row.subject)}</div>
           <small>
-            <AnnotatedEntitiesPopupCuration parentPage='gene' entities={row.primaryAnnotations} mainRowCurie={row.subject.curie}>
+            <AnnotatedEntitiesPopupCuration
+              parentPage='gene'
+              entities={row.primaryAnnotations}
+              mainRowCurie={row.subject.curie}
+              pubModIds={row.pubmedPubModIDs}
+            >
               Annotation details
             </AnnotatedEntitiesPopupCuration>
           </small>
@@ -142,12 +147,12 @@ const DiseaseAnnotationTable = ({
       formatter: BasedOnGeneCellCuration,
     },
     {
-      dataField: 'references',
+      dataField: 'pubmedPubModIDs',
       text: 'References',
       filterable: true,
       filterName: 'reference',
       headerStyle: {width: '150px'},
-      formatter: ReferencesCellCuration,
+      formatter: (pubModIds) => <ReferencesCellCuration pubModIds={pubModIds}/>,
     }
   ];
 

src/containers/allelePage/AlleleToDiseaseTable.js

@@ -53,7 +53,7 @@ const AlleleToDiseaseTable = ({alleleId}) => {
     {
       dataField: 'primaryAnnotations',
       text: 'Annotation details',
-      formatter: entities => <AnnotatedEntitiesPopupCuration parentPage='allele' entities={entities}/>,
+      formatter: (entities, row) => <AnnotatedEntitiesPopupCuration parentPage='allele' entities={entities} pubModIds={row.pubmedPubModIDs}/>,
       headerStyle: {width: '90px'},
     },
     {
@@ -71,9 +71,9 @@ const AlleleToDiseaseTable = ({alleleId}) => {
       filterName: 'dataProvider',
     },
     {
-      dataField: 'references',
+      dataField: 'pubmedPubModIDs',
       text: 'References',
-      formatter: references => ReferencesCellCuration(references),
+      formatter: (pubModIds) => <ReferencesCellCuration pubModIds={pubModIds}/>,
       headerStyle: {width: '150px'},
       filterable: true,
       filterName: 'reference',

src/containers/diseasePage/DiseaseToGeneTable.js

@@ -21,8 +21,6 @@ import DiseaseQualifiersColumn from '../../components/dataTable/DiseaseQualifier
 import AnnotatedEntitiesPopupCuration from '../../components/dataTable/AnnotatedEntitiesPopupCuration';
 import ReferenceCellViaOrthologyCuration from '../../components/dataTable/ReferencesCellViaOrthologyCuration';
 
-//TODO: once tickets SCRUM-3647, SCRUM-3648, and SCRUM-3649 are complete, refactor this and the diseaseAnnotationTable component
-//if needed
 const DiseaseToGeneTable = ({ id }) => {
   const {
     data: results,
@@ -43,7 +41,12 @@ const DiseaseToGeneTable = ({ id }) => {
             <div>{GeneCellCuration(row.subject)}</div>
             {!isViaOrthology && (
               <small>
-                <AnnotatedEntitiesPopupCuration parentPage='disease' entities={row.primaryAnnotations} mainRowCurie={row.subject.curie}>
+                <AnnotatedEntitiesPopupCuration
+                  parentPage='disease'
+                  entities={row.primaryAnnotations}
+                  mainRowCurie={row.subject.curie}
+                  pubModIds={row.pubmedPubModIDs}
+                >
                   Annotation details
                 </AnnotatedEntitiesPopupCuration>
               </small>
@@ -133,12 +136,12 @@ const DiseaseToGeneTable = ({ id }) => {
       filterName: 'dataProvider',
     },
     {
-      dataField: 'references',
+      dataField: 'pubmedPubModIDs',
       text: 'References',
       headerStyle: { width: '150px' },
-      formatter: (references, row) => {
+      formatter: (pubModIds, row) => {
         const isViaOrthology = getIsViaOrthology(row);
-        if(!isViaOrthology) return ReferencesCellCuration(references);
+        if(!isViaOrthology) return <ReferencesCellCuration pubModIds={pubModIds}/>
         return <ReferenceCellViaOrthologyCuration/>
       },
       filterable: true,