Merge branch 'stage' into update_cdk_jbrowse

alliance-genome · May 1, 2024 · f632691 · f632691
2 parents 690445a + 96047c4
commit f632691
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Showing 6 changed files with 29 additions and 23 deletions.
diff --git a/cdk/cdk-app.ts b/cdk/cdk-app.ts
@@ -20,7 +20,7 @@ new AmplifyALBStack(app, 'stage-alb-stack', {
 new AmplifyALBStack(app, 'test-alb-stack', {
   stackName: 'test-alb-stack',
   dnsName: 'test',
-  targetInstanceId: 'i-003fafec7d050fd97',
+  targetInstanceId: 'i-0ccfdcd8c43104be5',
   env: {
     region: process.env.CDK_DEFAULT_REGION,
     account: process.env.CDK_DEFAULT_ACCOUNT,

diff --git a/src/components/dataTable/AnnotatedEntitiesPopupCuration.js b/src/components/dataTable/AnnotatedEntitiesPopupCuration.js
@@ -92,11 +92,11 @@ function AnnotatedEntitiesPopupCuration({ children, entities, parentPage, mainRo
                       <td>{renderLink(entity)}</td>
                       <td><TypeCellCuration subject={entity.diseaseAnnotationSubject}/></td>
                       <td><AssociationCellCuration association={entity.relation?.name}/></td>
-                      { parentPage === 'gene' || 'disease' ?  <td><AssertedGenes assertedGenes={entity.assertedGenes} mainRowCurie={mainRowCurie}/></td> : <></>}
+                      { parentPage === 'gene' || parentPage === 'disease' ?  <td><AssertedGenes assertedGenes={entity.assertedGenes} mainRowCurie={mainRowCurie}/></td> : <></>}
                       <td><ExperimentalConditionCellCuration conditions={entity.conditionRelations}/></td>
                       <td><ExperimentalConditionCellCuration conditions={entity.conditionModifiers}/></td>
                       <td><GeneticModifiersCellCuration relation={entity.diseaseGeneticModifierRelation} modifiers={entity.diseaseGeneticModifiers}/></td>
-                      { parentPage === 'gene' || 'disease' ? <td><StrainBackground strainBackground={entity.sgdStrainBackground}/></td> : <></> }
+                      { parentPage === 'gene' || parentPage === 'disease' ? <td><StrainBackground strainBackground={entity.sgdStrainBackground}/></td> : <></> }
                       <td><GeneticSex geneticSex={entity.geneticSex}/></td>
                       <td><RelatedNotes className={style.relatedNotes} relatedNotes={entity.relatedNotes}/></td>
                       <td><AnnotationType  annotationType={entity.annotationType}/></td>

diff --git a/src/components/dataTable/GeneticModifiersCellCuration.js b/src/components/dataTable/GeneticModifiersCellCuration.js
@@ -3,28 +3,30 @@ import { CollapsibleList } from '../collapsibleList';
 import ExternalLink from '../ExternalLink';
 import { getResourceUrl } from './getResourceUrl';
 import { Link } from 'react-router-dom';
+import { getIdentifier } from './utils';
 
 
 function GeneticModifierLink(modifier) {
+    const identifier = getIdentifier(modifier);
     switch(modifier?.type) {
         case 'Gene':
             if (modifier.geneSymbol) {
                 return (
-                    <Link to={`/gene/${modifier.curie}`} target='_blank'>
+                    <Link to={`/gene/${identifier}`} target='_blank'>
                         <span dangerouslySetInnerHTML={{__html: modifier.geneSymbol.displayText}}/>
                     </Link>);
             }
             break;
         case 'Allele':
             if (modifier.alleleSymbol) {
                 return (
-                    <Link to={`/allele/${modifier.curie}`}  target='_blank'>
+                    <Link to={`/allele/${identifier}`}  target='_blank'>
                         <span dangerouslySetInnerHTML={{__html: modifier.alleleSymbol.displayText}}/>
                     </Link>);
             }
             break;
         case 'AffectedGenomicModel':
-            let url = getResourceUrl(modifier.curie, modifier.type, modifier.subtype);
+            let url = getResourceUrl(identifier, modifier.type, modifier.subtype);
             if (url && modifier.name) {                
                 return ( 
                     <ExternalLink href={url}>

diff --git a/src/components/dataTable/StrainBackground.js b/src/components/dataTable/StrainBackground.js
@@ -1,13 +1,16 @@
 import ExternalLink from '../ExternalLink';
+import { getIdentifier } from './utils';
 
 
 function StrainBackground({strainBackground}) {
-  if(strainBackground?.curie && strainBackground?.name) {
-    const strainName = <span dangerouslySetInnerHTML={{__html: strainBackground.name}}/>;
-    const strain = strainBackground.curie.slice('SGD:'.length);
-    return <ExternalLink href={`https://www.yeastgenome.org/strain/${strain}`}>{strainName}</ExternalLink>;
-  }
-  return <></>;
+  const indentifier = getIdentifier(strainBackground);
+
+  if(!indentifier || !strainBackground?.name) return null;
+
+  const strainName = <span dangerouslySetInnerHTML={{__html: strainBackground.name}}/>;
+  const strain = indentifier.slice('SGD:'.length);
+
+  return <ExternalLink href={`https://www.yeastgenome.org/strain/${strain}`}>{strainName}</ExternalLink>;
 }
 
 export default StrainBackground;
diff --git a/src/components/dataTable/basedOnGeneCellCuration.js b/src/components/dataTable/basedOnGeneCellCuration.js
@@ -1,21 +1,22 @@
 import { Link } from 'react-router-dom';
 import { shortSpeciesName } from '../../lib/utils';
 import { CollapsibleList } from '../../components/collapsibleList';
-import { removeDuplicates } from './utils';
+import { getIdentifier, removeDuplicates } from './utils';
 import GeneSymbolCuration from '../GeneSymbolCuration';
 
+const GeneLink = ({ gene }) => {
+  const identifier = getIdentifier(gene);
+  return (
+    <Link key={identifier} to={`/gene/${identifier}`}>
+      <GeneSymbolCuration gene={gene} /> ({shortSpeciesName(gene.taxon.curie)})
+    </Link>);
+};
 const BasedOnGeneCellCuration = (genes) => {
-  if (!genes) {
-    return null;
-  }
+  if (!genes) return null;
   const uniqueGenes = removeDuplicates(genes, (gene) => gene.geneSymbol.displayText);
   return (
     <CollapsibleList collapsedSize={uniqueGenes.length}>
-      {uniqueGenes.map(gene => (
-        <Link key={gene.curie} to={`/gene/${gene.curie}`}>
-          <GeneSymbolCuration gene={gene} /> ({shortSpeciesName(gene.taxon.curie)})
-        </Link>
-      ))}
+      {uniqueGenes.map(gene => <GeneLink gene={gene} /> )}
     </CollapsibleList>
   );
 };

diff --git a/src/containers/layout/ReleaseBanner.js b/src/containers/layout/ReleaseBanner.js
@@ -10,13 +10,13 @@ const ReleaseBanner = () => {
     isError,
   } = useRelease();
 
-  const { releaseVersion, releaseDate } = releaseInfo || {};
+  const { releaseVersion, snapShotDate } = releaseInfo || {};
 
   return isLoading ? <LoadingSpinner /> : 
     (
       <small className="text-secondary">
         Version: {isError ? 'Unknown' : releaseVersion}<br />
-        Date: { isError ? 'Unknown' : new Date(releaseDate).toDateString()}
+        Date: { isError ? 'Unknown' : new Date(snapShotDate).toDateString()}
       </small>
     );
 };