Merge pull request #1386 from alliance-genome/test

7.5.0 release
alliance-genome · Dec 20, 2024 · 5ba28af · 5ba28af
2 parents 305a83d + 6bc1817
commit 5ba28af
Show file tree

Hide file tree

Showing 29 changed files with 73 additions and 67 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-08138c1f889f670ca',
+  targetInstanceId: 'i-0af918724cfc524c8',
   env: {
     region: process.env.CDK_DEFAULT_REGION,
     account: process.env.CDK_DEFAULT_ACCOUNT,
@@ -30,7 +30,7 @@ new AmplifyALBStack(app, 'test-alb-stack', {
 new AmplifyALBStack(app, 'prod-alb-stack', {
   stackName: 'prod-alb-stack',
   dnsName: 'prod',
-  targetInstanceId: 'i-08138c1f889f670ca',
+  targetInstanceId: 'i-0af918724cfc524c8',
   env: {
     region: process.env.CDK_DEFAULT_REGION,
     account: process.env.CDK_DEFAULT_ACCOUNT,

diff --git a/package.json b/package.json
@@ -19,6 +19,7 @@
     "@testing-library/jest-dom": "^5.16.1",
     "@testing-library/react": "^11.2.5",
     "@testing-library/user-event": "^13.5.0",
+    "abortcontroller-polyfill": "^1.7.8",
     "agr_genomefeaturecomponent": "^0.3.24",
     "aws-cdk": "^2.118.0",
     "aws-cdk-lib": "^2.118.0",
@@ -28,7 +29,7 @@
     "custom-event-polyfill": "^1.0.6",
     "d3-selection": "2.0.0",
     "document-register-element": "1.13.1",
-    "generic-sequence-panel": "^1.4.1",
+    "generic-sequence-panel": "^1.6.0",
     "html-react-parser": "^0.10.0",
     "immutable": "^3.8.1",
     "lodash.clone": "^4.5.0",
@@ -96,4 +97,4 @@
   "devDependencies": {
     "ajv": "^8.16.0"
   }
-}
+}
diff --git a/src/components/ConstructLink.js b/src/components/ConstructLink.js
@@ -4,7 +4,7 @@ import DataSourceLink from './dataSourceLink';
 
 const ConstructLink = ({construct}) => {
   return (
-    <DataSourceLink reference={construct.crossReferenceMap.primary}>
+    <DataSourceLink reference={construct.crossReferenceMap?.primary}>
       <span dangerouslySetInnerHTML={{__html: construct.name}} />
     </DataSourceLink>
   );

diff --git a/src/components/OrthologPicker.js b/src/components/OrthologPicker.js
@@ -99,14 +99,13 @@ const OrthologPicker =({
     }
     let selectedOrthologs = [];
     if (checkboxValue) {
-      selectedOrthologs = orthology.data.results
-        .sort(compareBySpeciesThenAlphabetical)
+      selectedOrthologs = orthology.data.results?.sort(compareBySpeciesThenAlphabetical)
         .filter(o => geneHasData(getOrthologId(o)));
       if (stringency) {
-        selectedOrthologs = selectedOrthologs.filter(byStringency(stringency.value));
+        selectedOrthologs = selectedOrthologs?.filter(byStringency(stringency.value));
       }
       if (selectedSpecies.length) {
-        selectedOrthologs = selectedOrthologs.filter(bySpecies(selectedSpecies));
+        selectedOrthologs = selectedOrthologs?.filter(bySpecies(selectedSpecies));
       }
     }
     onChange(selectedOrthologs);
@@ -194,15 +193,13 @@ const OrthologPicker =({
     if (!geneHasDataTest) {
       return true;
     }
-    return orthology.data.results
-      .filter(bySpecies([species]))
+    return orthology.data.results?.filter(bySpecies([species]))
       .map(getOrthologId)
       .some(geneHasData);
   };
 
   const speciesHasOrthologsMeetingStringency = (species) => {
-    return orthology.data.results
-      .filter(bySpecies([species]))
+    return orthology.data.results?.filter(bySpecies([species]))
       .filter(o => stringency ? orthologyMeetsStringency(o, stringency.value) : true)
       .some(o => geneHasData(getOrthologId(o)));
   };
@@ -299,7 +296,7 @@ const OrthologPicker =({
                   .filter(species => focusTaxonId ? species.taxonId !== focusTaxonId : true)
                   .map(species => {
                     const checkId = id + makeId(species.taxonId);
-                    const hasOrthologs = orthology.data.results.findIndex(o => getOrthologSpeciesId(o) === species.taxonId) >= 0;
+                    const hasOrthologs = orthology.data.results?.findIndex(o => getOrthologSpeciesId(o) === species.taxonId) >= 0;
                     const hasOrthologsWithData = speciesHasOrthologsWithData(species);
                     const hasOrthologsMeetingStringency = speciesHasOrthologsMeetingStringency(species);
                     const disabled = !hasOrthologs || !hasOrthologsWithData || !hasOrthologsMeetingStringency;

diff --git a/src/components/dataTable/AnnotatedEntitiesPopupCuration.js b/src/components/dataTable/AnnotatedEntitiesPopupCuration.js
@@ -28,8 +28,8 @@ import StrainBackground from './StrainBackground';
 function renderLink(entity) {
   const identifier = getIdentifier(entity.diseaseAnnotationSubject);
   const url = getResourceUrl({
-    identifier, 
-    type: entity.diseaseAnnotationSubject.type, 
+    identifier,
+    type: entity.diseaseAnnotationSubject.type,
     subtype: entity.diseaseAnnotationSubject.subtype
   })
 
@@ -90,15 +90,25 @@ function AnnotatedEntitiesPopupCuration({ children, entities, mainRowCurie, pubM
               {
                 entities.map(entity => {
                   const provider = buildProviderWithUrl(entity);
+                  var diseaseGeneticModifiers = entity.diseaseGeneticModifierAlleles;
+                  if(entity.diseaseGeneticModifierGenes != null){
+                    diseaseGeneticModifiers = entity.diseaseGeneticModifierGenes;
+                  }
+                  if(entity.diseaseGeneticModifierAgms != null){
+                    diseaseGeneticModifiers = entity.diseaseGeneticModifierAgms;
+                  }
+                  var expCondition = entity.conditionRelations;
+                  if(entity.conditionModifiers != null){
+                    expCondition = entity.conditionModifiers;
+                  }
                   return (
                     <tr key={entity.id}>
                       {columnNameSet.has("Name") && <td>{renderLink(entity)}</td>}
                       {columnNameSet.has("Type") && <td><TypeCellCuration subject={entity.diseaseAnnotationSubject}/></td>}
-                      {columnNameSet.has("Association") && <td><AssociationCellCuration association={entity.relation?.name}/></td>}
+                      {columnNameSet.has("Association") && <td><AssociationCellCuration association={entity.fullRelationString}/></td>}
                       {columnNameSet.has("Additional Implicated Genes") && <td><AssertedGenes assertedGenes={entity.assertedGenes} mainRowCurie={mainRowCurie}/></td>}
-                      {(columnNameSet.has("Experimental Condition") && entity.conditionRelations) && <td><ExperimentalConditionCellCuration conditions={entity.conditionRelations}/></td>}
-                      {(columnNameSet.has("Experimental Condition") && entity.conditionModifiers) && <td><ExperimentalConditionCellCuration conditions={entity.conditionModifiers}/></td>}
-                      {columnNameSet.has("Genetic Modifiers") && <td><GeneticModifiersCellCuration relation={entity.diseaseGeneticModifierRelation} modifiers={entity.diseaseGeneticModifiers}/></td>}
+                      {columnNameSet.has("Experimental Condition") && <td><ExperimentalConditionCellCuration conditions={expCondition}/></td>}
+                      {columnNameSet.has("Genetic Modifiers") && <td><GeneticModifiersCellCuration relation={entity.diseaseGeneticModifierRelation} modifiers={diseaseGeneticModifiers}/></td>}
                       {columnNameSet.has("Strain Background") && <td><StrainBackground strainBackground={entity.sgdStrainBackground}/></td>}
                       {columnNameSet.has("Genetic Sex") && <td><GeneticSex geneticSex={entity.geneticSex}/></td>}
                       {columnNameSet.has("Notes") && <td><RelatedNotes className={style.relatedNotes} relatedNotes={entity.relatedNotes}/></td>}

diff --git a/src/components/disease/diseaseAnnotationTable.js b/src/components/disease/diseaseAnnotationTable.js
@@ -157,7 +157,7 @@ const DiseaseAnnotationTable = ({
     }
   ];
 
-  const data = results.map(annotation => ({
+  const data = results?.map(annotation => ({
     species: annotation.subject.taxon,
     providers: buildProvidersWithUrl(annotation.primaryAnnotations),
     basedOn: buildWith(annotation),
@@ -168,7 +168,7 @@ const DiseaseAnnotationTable = ({
     <DataTable
       {...tableProps}
       columns={columns}
-      data={data}
+      data={data || []}
       downloadUrl={downloadUrl}
       keyField='id'
     />

diff --git a/src/components/expression/expressionAnnotationTable.js b/src/components/expression/expressionAnnotationTable.js
@@ -96,7 +96,7 @@ const ExpressionAnnotationTable = ({
   ];
 
 
-  const data = results.map(result => ({
+  const data = results?.map(result => ({
     key: hash(result),
     species: result.gene.species.name,
     gene: result.gene,
@@ -134,7 +134,7 @@ const ExpressionAnnotationTable = ({
     <DataTable
       {...tableProps}
       columns={columns}
-      data={data}
+      data={data || []}
       downloadUrl={downloadUrl}
       keyField='key'
       sortOptions={sortOptions}

diff --git a/src/components/interaction/GeneGeneticInteractionDetailTable.js b/src/components/interaction/GeneGeneticInteractionDetailTable.js
@@ -132,7 +132,7 @@ const GeneGeneticInteractionDetailTable = ({
         headerStyle: {
           width: '250px',
         },
-        formatter: (crossReferences = [], {sourceDatabase = {}, aggregationDatabase = {}} = {}) => (
+        formatter: (crossReferences = [], {sourceDatabase = {}, aggregationDatabase} = {}) => (
           <div>
             {
               crossReferences && crossReferences.map(({primaryKey, displayName, prefix, crossRefCompleteUrl} = {}) => (
@@ -142,7 +142,7 @@ const GeneGeneticInteractionDetailTable = ({
               ))
             }
             {
-              (!aggregationDatabase || sourceDatabase.label === aggregationDatabase.label) ?
+              (!aggregationDatabase || sourceDatabase?.label === aggregationDatabase?.label) ?
                 null :
                 <span>
                   <ExternalLink href={sourceDatabase.url}>{sourceDatabase.label}</ExternalLink>

diff --git a/src/components/interaction/genePhysicalInteractionDetailTable.js b/src/components/interaction/genePhysicalInteractionDetailTable.js
@@ -27,7 +27,7 @@ const GenePhysicalInteractionDetailTable = ({focusGeneDisplayName, focusGeneId})
     return `${DEFAULT_TABLE_KEY}-${fieldKey}-${rowIndex}`;
   };
 
-  const data = results.map((interaction = {}) => ({
+  const data = results?.map((interaction = {}) => ({
     id: interaction.primaryKey,
     moleculeType: interaction.interactorAType,
     interactorGeneSymbol: interaction.geneB,
@@ -193,7 +193,7 @@ const GenePhysicalInteractionDetailTable = ({focusGeneDisplayName, focusGeneId})
     <DataTable
       {...tableProps}
       columns={columns}
-      data={data}
+      data={data || []}
       downloadUrl={`/api/gene/${focusGeneId}/interactions/download?filter.joinType=molecular_interaction`}
       keyField='id'
       sortOptions={sortOptions}

diff --git a/src/components/orthology/orthologyTable.js b/src/components/orthology/orthologyTable.js
@@ -57,9 +57,8 @@ class OrthologyTable extends Component {
               compareByFixedOrder(TAXON_ORDER, o => getOrthologSpeciesId(o)),
               (orthDataA, orthDataB) => orthDataB.predictionMethodsMatched.length - orthDataA.predictionMethodsMatched.length
             ]).map((orthData, idx, orthList) => {
-              const scoreNumerator = orthData.predictionMethodsMatched.length;
-              const scoreDemominator = scoreNumerator +
-                orthData.predictionMethodsNotMatched.length;
+              const scoreNumerator = orthData.predictionMethodsMatched?.length;
+              const scoreDemominator = scoreNumerator + (orthData.predictionMethodsNotMatched?.length || 0);
               const orthId = getOrthologId(orthData);
 
               if (idx > 0 && getOrthologSpeciesName(orthList[idx - 1]) !== getOrthologSpeciesName(orthData)) {

diff --git a/src/components/paralogy/paralogyTable.js b/src/components/paralogy/paralogyTable.js
@@ -15,11 +15,11 @@ const ParalogyTable = ({geneId}) => {
   if (isLoading) {
     return <LoadingSpinner />;
   }
-  if (data?.results.length === 0) {
+  if (data?.results?.length === 0) {
     return <NoData>No paralogs for the gene.</NoData>
   }
 
-  const results = data.results.sort( (a,b) => {
+  const results = data.results?.sort( (a,b) => {
     if (Number(a.rank) < Number(b.rank)) {
       return -1;
     }
@@ -47,7 +47,7 @@ const ParalogyTable = ({geneId}) => {
                 </thead>
                 <tbody>                 
                 {              
-                  results.map( result => {
+                  results?.map( result => {
                     const rowKey = 'paralogyrowkey-' + result.homologGene.id.replace(/\s/g, '-');
                     return (<tr key={rowKey}>
                       <td>
@@ -79,4 +79,4 @@ ParalogyTable.propTypes = {
   geneId: PropTypes.string.isRequired,
 };
 
-export default ParalogyTable;
+export default ParalogyTable;
diff --git a/src/components/synonymList.js b/src/components/synonymList.js
@@ -4,13 +4,13 @@ import { CollapsibleList } from './collapsibleList';
 import { compareAlphabeticalCaseInsensitive } from '../lib/utils';
 
 const SynonymList = ({synonyms}) => {
-  return synonyms &&
+  return (synonyms &&
     <CollapsibleList>
       {synonyms
         .sort(compareAlphabeticalCaseInsensitive())
         .map(synonym => <span dangerouslySetInnerHTML={{__html: synonym}} key={synonym} />)
       }
-    </CollapsibleList>;
+    </CollapsibleList>) || <></>;
 };
 
 SynonymList.propTypes = {

diff --git a/src/containers/allelePage/AlleleMolecularConsequences.js b/src/containers/allelePage/AlleleMolecularConsequences.js
@@ -39,7 +39,7 @@ const AlleleMolecularConsequences = ({
     const { genomeLocations: geneLocations } = gene;
     const [geneLocation] = geneLocations || [];
 
-    return data.map((variant) => ({
+    return data?.map((variant) => ({
       ...variant,
       geneLocation,
       species: allele.species

diff --git a/src/containers/allelePage/AlleleSequenceView.js b/src/containers/allelePage/AlleleSequenceView.js
@@ -39,7 +39,7 @@ const AlleleSequenceView = ({ allele }) => {
 
   const genomeLocations = allele.gene.genomeLocations;
   const genomeLocation = genomeLocations && genomeLocations.length > 0 ? genomeLocations[0] : null;
-  if (!genomeLocation || variants.isLoading || variants.isError || variants.data.length === 0 ||visibleTranscripts.data.length === 0) {
+  if (!genomeLocation || variants.isLoading || variants.isError || !variants.data || variants.data.length === 0 || visibleTranscripts.data.length === 0) {
     return null;
   }
 

diff --git a/src/containers/allelePage/AlleleSummary.js b/src/containers/allelePage/AlleleSummary.js
@@ -35,7 +35,7 @@ const AlleleSummary = ({allele}) => {
         {allele.constructs && allele.constructs.length && (
           <CommaSeparatedList>
             {allele.constructs.map(construct => (
-              <DataSourceLink key={construct.id} reference={construct.crossReferenceMap.primary}>
+              <DataSourceLink key={construct.id} reference={construct.crossReferenceMap?.primary}>
                 <span dangerouslySetInnerHTML={{__html: construct.name}} />
               </DataSourceLink>
             ))}

diff --git a/src/containers/allelePage/AlleleToDiseaseTable.js b/src/containers/allelePage/AlleleToDiseaseTable.js
@@ -22,7 +22,7 @@ const AlleleToDiseaseTable = ({alleleId}) => {
     ...tableProps
   } = useDataTableQuery(`/api/allele/${alleleId}/diseases`);
 
-  const tableData = results.map(annotation => ({
+  const tableData = results?.map(annotation => ({
     providers: buildProvidersWithUrl(annotation.primaryAnnotations),
     ...annotation,
   }));

diff --git a/src/containers/allelePage/AlleleToPhenotypeTable.js b/src/containers/allelePage/AlleleToPhenotypeTable.js
@@ -47,7 +47,7 @@ const AlleleToPhenotypeTable = ({alleleId}) => {
     },
   ];
 
-  const data = results.map(record => ({
+  const data = results?.map(record => ({
     ...record,
     id: hash(record),
   }));

diff --git a/src/containers/allelePage/AlleleTransgenicConstructs.js b/src/containers/allelePage/AlleleTransgenicConstructs.js
@@ -32,21 +32,21 @@ const AlleleTransgenicConstructs = ({constructs}) => {
 
             <AttributeLabel>Expressed Components</AttributeLabel>
             <AttributeValue placeholder='None'>
-              {construct.expressedGenes.length && (
+              {construct.expressedGenes?.length && (
                 <CommaSeparatedGeneList genes={construct.expressedGenes} />
               )}
             </AttributeValue>
 
             <AttributeLabel>Knock-down Targets</AttributeLabel>
             <AttributeValue placeholder='None'>
-              {construct.targetGenes.length && (
+              {construct.targetGenes?.length && (
                 <CommaSeparatedGeneList genes={construct.targetGenes} />
               )}
             </AttributeValue>
 
             <AttributeLabel>Regulatory Regions</AttributeLabel>
             <AttributeValue placeholder='None'>
-              {construct.regulatedByGenes.length && (
+              {construct.regulatedByGenes?.length && (
                 <CommaSeparatedGeneList genes={construct.regulatedByGenes} />
               )}
             </AttributeValue>

diff --git a/src/containers/allelePage/AlleleVariantsSummary.js b/src/containers/allelePage/AlleleVariantsSummary.js
@@ -21,7 +21,7 @@ const AlleleVariantsSummary = ({allele, alleleId}) => {
   return (
     <>
       {
-        data.map(variant => {
+        data && data.map(variant => {
           const {
             displayName,
           } = variant || {};

diff --git a/src/containers/genePage/TransgenicAlleleTable.js b/src/containers/genePage/TransgenicAlleleTable.js
@@ -26,7 +26,7 @@ const TransgenicAlleleTable = ({geneId}) => {
     ...tableProps
   } = useDataTableQuery(`/api/gene/${geneId}/transgenic-alleles`);
 
-  const data = results.map(result => ({
+  const data = results?.map(result => ({
     ...result,
     constructExpressedGene: result.constructs.map(construct => ({
       id: construct.id,

diff --git a/src/containers/genePage/alleleTable.js b/src/containers/genePage/alleleTable.js
@@ -28,15 +28,15 @@ const AlleleTable = ({ isLoadingGene, gene, geneId}) => {
   } = tableProps;
 
   const data = useMemo(() => {
-    return resolvedData ? resolvedData.results.map(allele => ({
+    return resolvedData ? resolvedData.results?.map(allele => ({
       ...allele,
       symbol: allele.symbol,
       synonym: allele.synonyms,
       source: {
         dataProvider: gene.dataProvider,
         url: allele.crossReferenceMap.primary.url,
       },
-      disease: allele.diseases.sort(compareAlphabeticalCaseInsensitive(disease => disease.name))
+      disease: allele.diseases?.sort(compareAlphabeticalCaseInsensitive(disease => disease.name))
     })) : [];
   // eslint-disable-next-line react-hooks/exhaustive-deps
   }, [resolvedData]);
@@ -50,12 +50,12 @@ const AlleleTable = ({ isLoadingGene, gene, geneId}) => {
   const allelesFiltered = useAllVariants(geneId, tableProps.tableState);
 
   const variantsSequenceViewerProps = useMemo(() => {
-    const variantsFiltered = allelesFiltered.data ? allelesFiltered.data.results.flatMap(
+    const variantsFiltered = (allelesFiltered.data && allelesFiltered.data.results) ? allelesFiltered.data.results.flatMap(
       allele => (allele && allele.variants) || []
     ) : [];
     const variantLocations = variantsFiltered.map(variant => variant && variant.location);
     const { fmin, fmax } = findFminFmax([geneLocation, ...variantLocations]);
-    const alleleIdsFiltered = allelesFiltered.data ? allelesFiltered.data.results.map(allele => (allele.id)) : [];
+    const alleleIdsFiltered = (allelesFiltered.data && allelesFiltered.data.results) ? allelesFiltered.data.results.map(allele => (allele.id)) : [];
 
     /*
        Warning!
@@ -151,7 +151,7 @@ const AlleleTable = ({ isLoadingGene, gene, geneId}) => {
       formatter: (variants) => (
         <div>
           {
-            variants.map(({id, variantType: type = {}, location = {}, transcriptLevelConsequence}) => (
+            variants?.map(({id, variantType: type = {}, location = {}, transcriptLevelConsequence}) => (
               <div key={id} style={{display: 'flex'}}>
                 <div
                   style={{