Merge pull request #1790 from alliance-genome/SCRUM-4672

SCRUM-4672 LinkML v2.9.1 migration
alliance-genome · Jan 13, 2025 · 423bed7 · 423bed7
2 parents ce325d6 + 3332b64
commit 423bed7
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Showing 611 changed files with 2,659 additions and 2,840 deletions.
diff --git a/SEARCH.md b/SEARCH.md
@@ -61,7 +61,7 @@ This will be the size of the page that comes back.
             "order": 1
         },
         {
-            "field": "diseaseAnnotationSubject.modEntityId",
+            "field": "diseaseAnnotationSubject.primaryExternalId",
             "order": 1
         }
     ],
@@ -204,7 +204,7 @@ Search Payload:
             "order": 1
         },
         {
-            "field": "diseaseAnnotationSubject.modEntityId",
+            "field": "diseaseAnnotationSubject.primaryExternalId",
             "order": 1
         }
     ],
@@ -224,7 +224,7 @@ Return Payload
     "totalResults": 1163,
     "returnedRecords": 1,
     "debug": "true",
-    "esQuery": "{\"query\":{\"bool\":{\"must\":[{\"simple_query_string\":{\"boost\":31000.0,\"query\":\"false\",\"default_operator\":\"or\",\"fields\":[\"internal\"]}},{\"simple_query_string\":{\"boost\":21000.0,\"query\":\"false\",\"default_operator\":\"or\",\"fields\":[\"obsolete\"]}},{\"simple_query_string\":{\"boost\":11000.0,\"query\":\"wb\",\"default_operator\":\"and\",\"fields\":[\"uniqueId\"]}},{\"match_all\":{}}],\"minimum_should_match\":\"0\"}},\"sort\":[{\"diseaseAnnotationSubject.symbol_keyword\":{\"order\":\"asc\",\"unmapped_type\":\"keyword\"}},{\"diseaseAnnotationSubject.name_keyword\":{\"order\":\"asc\",\"unmapped_type\":\"keyword\"}},{\"diseaseAnnotationSubject.modEntityId_keyword\":{\"order\":\"asc\",\"unmapped_type\":\"keyword\"}}],\"docvalue_fields\":[\"_entity_type\"],\"_source\":false}"
+    "esQuery": "{\"query\":{\"bool\":{\"must\":[{\"simple_query_string\":{\"boost\":31000.0,\"query\":\"false\",\"default_operator\":\"or\",\"fields\":[\"internal\"]}},{\"simple_query_string\":{\"boost\":21000.0,\"query\":\"false\",\"default_operator\":\"or\",\"fields\":[\"obsolete\"]}},{\"simple_query_string\":{\"boost\":11000.0,\"query\":\"wb\",\"default_operator\":\"and\",\"fields\":[\"uniqueId\"]}},{\"match_all\":{}}],\"minimum_should_match\":\"0\"}},\"sort\":[{\"diseaseAnnotationSubject.symbol_keyword\":{\"order\":\"asc\",\"unmapped_type\":\"keyword\"}},{\"diseaseAnnotationSubject.name_keyword\":{\"order\":\"asc\",\"unmapped_type\":\"keyword\"}},{\"diseaseAnnotationSubject.primaryExternalId_keyword\":{\"order\":\"asc\",\"unmapped_type\":\"keyword\"}}],\"docvalue_fields\":[\"_entity_type\"],\"_source\":false}"
 }
 ```
 
@@ -286,7 +286,7 @@ Destringify the esQuery:
             }
         },
         {
-            "diseaseAnnotationSubject.modEntityId_keyword": {
+            "diseaseAnnotationSubject.primaryExternalId_keyword": {
                 "order": "asc",
                 "unmapped_type": "keyword"
             }

diff --git a/src/main/cliapp/src/components/Editors/GeneEditor.js b/src/main/cliapp/src/components/Editors/GeneEditor.js
@@ -9,7 +9,7 @@ const geneSearch = (event, setFiltered, setInputValue) => {
 	const searchService = new SearchService();
 	const autocompleteFields = [
 		'curie',
-		'modEntityId',
+		'primaryExternalId',
 		'crossReferences.referencedCurie',
 		'geneFullName.formatText',
 		'geneFullName.displayText',
@@ -37,7 +37,7 @@ export const GeneEditor = ({ props, errorMessages, onChange, dataKey, fieldName
 				initialValue={getIdentifier(props?.rowData?.[fieldName])}
 				rowProps={props}
 				fieldName={fieldName}
-				subField="modEntityId"
+				subField="primaryExternalId"
 				valueDisplay={(item, setAutocompleteHoverItem, op, query) => (
 					<SubjectAutocompleteTemplate
 						item={item}

diff --git a/src/main/cliapp/src/components/Templates/__tests__/GenomicEntityListTemplate.test.js b/src/main/cliapp/src/components/Templates/__tests__/GenomicEntityListTemplate.test.js
@@ -150,7 +150,7 @@ describe('GenomicEntityListTemplate', () => {
 				geneFullName: {
 					displayText: 'Gene Full Name 2',
 				},
-				modEntityId: 'ID2',
+				primaryExternalId: 'ID2',
 			},
 			{
 				geneSymbol: {

diff --git a/src/main/cliapp/src/components/Templates/__tests__/GenomicEntityTemplate.test.js b/src/main/cliapp/src/components/Templates/__tests__/GenomicEntityTemplate.test.js
@@ -61,7 +61,7 @@ describe('GenomicEntityTemplate', () => {
 	it('should render genomicEntity name and id when genomicEntity has name', () => {
 		const genomicEntity = {
 			name: 'genomicEntity Name',
-			modEntityId: 'ID',
+			primaryExternalId: 'ID',
 		};
 
 		const result = render(<GenomicEntityTemplate genomicEntity={genomicEntity} />);
@@ -94,7 +94,7 @@ describe('GenomicEntityTemplate', () => {
 			geneSymbol: {
 				displayText: 'Gene <sup>Symbol</sup>',
 			},
-			modEntityId: 'ID',
+			primaryExternalId: 'ID',
 		};
 
 		const { container } = render(<GenomicEntityTemplate genomicEntity={genomicEntity} />);

diff --git a/src/main/cliapp/src/constants/FilterFields.js b/src/main/cliapp/src/constants/FilterFields.js
@@ -13,15 +13,15 @@ export const FIELD_SETS = Object.freeze({
 	},
 	agmAggregationFieldSet: {
 		filterName: 'alleleAggregationFilter',
-		fields: ['dataProvider.sourceOrganization.abbreviation'],
+		fields: ['dataProvider.abbreviation'],
 	},
 	agmSecondaryIdsFieldSet: {
 		filterName: 'agmSecondaryIdsFilter',
 		fields: ['agmSecondaryIds.secondaryId', 'agmSecondaryIds.evidence.curie'],
 	},
 	alleleAggregationFieldSet: {
 		filterName: 'alleleAggregationFilter',
-		fields: ['dataProvider.sourceOrganization.abbreviation'],
+		fields: ['dataProvider.abbreviation'],
 	},
 	alleleFunctionalImpactsFieldSet: {
 		filterName: 'alleleFunctionalImpactsFilter',
@@ -92,7 +92,7 @@ export const FIELD_SETS = Object.freeze({
 			'assertedAllele.alleleSymbol.displayText',
 			'assertedAllele.alleleSymbol.formatText',
 			'assertedAllele.curie',
-			'assertedAllele.modEntityId',
+			'assertedAllele.primaryExternalId',
 			'assertedAllele.modInternalId',
 		],
 	},
@@ -102,7 +102,7 @@ export const FIELD_SETS = Object.freeze({
 			'assertedGenes.geneSymbol.displayText',
 			'assertedGenes.geneSymbol.formatText',
 			'assertedGenes.curie',
-			'assertedGenes.modEntityId',
+			'assertedGenes.primaryExternalId',
 			'assertedGenes.modInternalId',
 		],
 	},
@@ -176,7 +176,7 @@ export const FIELD_SETS = Object.freeze({
 	},
 	constructAggregationFieldSet: {
 		filterName: 'constructAggregationFilter',
-		fields: ['dataProvider.sourceOrganization.abbreviation'],
+		fields: ['dataProvider.abbreviation'],
 	},
 	constructComponentsFieldSet: {
 		filterName: 'constructComponentsFilter',
@@ -188,7 +188,7 @@ export const FIELD_SETS = Object.freeze({
 			'constructGenomicEntityAssociations.constructGenomicEntityAssociationObject.symbol',
 			'constructGenomicEntityAssociations.constructGenomicEntityAssociationObject.name',
 			'constructGenomicEntityAssociations.constructGenomicEntityAssociationObject.curie',
-			'constructGenomicEntityAssociations.constructGenomicEntityAssociationObject.modEntityId',
+			'constructGenomicEntityAssociations.constructGenomicEntityAssociationObject.primaryExternalId',
 			'constructGenomicEntityAssociations.constructGenomicEntityAssociationObject.modInternalId',
 			'constructGenomicEntityAssociations.relation.name',
 		],
@@ -223,11 +223,7 @@ export const FIELD_SETS = Object.freeze({
 	},
 	dataProviderFieldSet: {
 		filterName: 'dataProviderFilter',
-		fields: [
-			'dataProvider.sourceOrganization.abbreviation',
-			'dataProvider.sourceOrganization.fullName',
-			'dataProvider.sourceOrganization.shortName',
-		],
+		fields: ['dataProvider.abbreviation', 'dataProvider.fullName', 'dataProvider.shortName'],
 	},
 	dataCreatedFieldSet: {
 		filterName: 'dateCreatedFilter',
@@ -245,8 +241,8 @@ export const FIELD_SETS = Object.freeze({
 			'annotationType.name',
 			'diseaseGeneticModifierRelation.name',
 			'diseaseQualifiers.name',
-			'dataProvider.sourceOrganization.abbreviation',
-			'secondaryDataProvider.sourceOrganization.abbreviation',
+			'dataProvider.abbreviation',
+			'secondaryDataProvider.abbreviation',
 			'evidenceCodes.abbreviation',
 		],
 	},
@@ -264,7 +260,7 @@ export const FIELD_SETS = Object.freeze({
 	},
 	diseaseAnnotationSubjectFieldSet: {
 		filterName: 'diseaseAnnotationSubjectFilter',
-		fields: ['diseaseAnnotationSubject.symbol', 'diseaseAnnotationSubject.modEntityId'],
+		fields: ['diseaseAnnotationSubject.symbol', 'diseaseAnnotationSubject.primaryExternalId'],
 	},
 	diseaseQualifiersFieldSet: {
 		filterName: 'diseaseQualifiersFilter',
@@ -288,15 +284,15 @@ export const FIELD_SETS = Object.freeze({
 	},
 	geneAggregationFieldSet: {
 		filterName: 'geneAggregationFilter',
-		fields: ['dataProvider.sourceOrganization.abbreviation'],
+		fields: ['dataProvider.abbreviation'],
 	},
 	geneAssociationSubjectFieldSet: {
 		filterName: 'geneAssociationSubjectFilter',
 		fields: [
 			'geneAssociationSubject.geneSymbol.displayText',
 			'geneAssociationSubject.geneSymbol.formatText',
 			'geneAssociationSubject.curie',
-			'geneAssociationSubject.modEntityId',
+			'geneAssociationSubject.primaryExternalId',
 			'geneAssociationSubject.modInternalId',
 		],
 	},
@@ -306,7 +302,7 @@ export const FIELD_SETS = Object.freeze({
 			'geneGeneAssociationObject.geneSymbol.displayText',
 			'geneGeneAssociationObject.geneSymbol.formatText',
 			'geneGeneAssociationObject.curie',
-			'geneGeneAssociationObject.modEntityId',
+			'geneGeneAssociationObject.primaryExternalId',
 			'geneGeneAssociationObject.modInternalId',
 		],
 	},
@@ -335,7 +331,7 @@ export const FIELD_SETS = Object.freeze({
 		fields: [
 			'diseaseGeneticModifierAgms.name',
 			'diseaseGeneticModifierAgms.curie',
-			'diseaseGeneticModifierAgms.modEntityId',
+			'diseaseGeneticModifierAgms.primaryExternalId',
 			'diseaseGeneticModifierAgms.modInternalId',
 		],
 	},
@@ -345,7 +341,7 @@ export const FIELD_SETS = Object.freeze({
 			'diseaseGeneticModifierAlleles.alleleSymbol.displayText',
 			'diseaseGeneticModifierAlleles.alleleSymbol.formatText',
 			'diseaseGeneticModifierAlleles.curie',
-			'diseaseGeneticModifierAlleles.modEntityId',
+			'diseaseGeneticModifierAlleles.primaryExternalId',
 			'diseaseGeneticModifierAlleles.modInternalId',
 		],
 	},
@@ -355,7 +351,7 @@ export const FIELD_SETS = Object.freeze({
 			'diseaseGeneticModifierGenes.geneSymbol.displayText',
 			'diseaseGeneticModifierGenes.geneSymbol.formatText',
 			'diseaseGeneticModifierGenes.curie',
-			'diseaseGeneticModifierGenes.modEntityId',
+			'diseaseGeneticModifierGenes.primaryExternalId',
 			'diseaseGeneticModifierGenes.modInternalId',
 		],
 	},
@@ -405,7 +401,7 @@ export const FIELD_SETS = Object.freeze({
 			'inferredAllele.alleleSymbol.displayText',
 			'inferredAllele.alleleSymbol.formatText',
 			'inferredAllele.curie',
-			'inferredAllele.modEntityId',
+			'inferredAllele.primaryExternalId',
 			'inferredAllele.modInternalId',
 		],
 	},
@@ -415,7 +411,7 @@ export const FIELD_SETS = Object.freeze({
 			'inferredGene.geneSymbol.displayText',
 			'inferredGene.geneSymbol.formatText',
 			'inferredGene.curie',
-			'inferredGene.modEntityId',
+			'inferredGene.primaryExternalId',
 			'inferredGene.modInternalId',
 		],
 	},
@@ -425,7 +421,7 @@ export const FIELD_SETS = Object.freeze({
 			'interactorAGeneticPerturbation.alleleSymbol.displayText',
 			'interactorAGeneticPerturbation.alleleSymbol.formatText',
 			'interactorAGeneticPerturbation.curie',
-			'interactorAGeneticPerturbation.modEntityId',
+			'interactorAGeneticPerturbation.primaryExternalId',
 			'interactorAGeneticPerturbation.modInternalId',
 		],
 	},
@@ -435,7 +431,7 @@ export const FIELD_SETS = Object.freeze({
 			'interactorBGeneticPerturbation.alleleSymbol.displayText',
 			'interactorBGeneticPerturbation.alleleSymbol.formatText',
 			'interactorBGeneticPerturbation.curie',
-			'interactorBGeneticPerturbation.modEntityId',
+			'interactorBGeneticPerturbation.primaryExternalId',
 			'interactorBGeneticPerturbation.modInternalId',
 		],
 	},
@@ -483,9 +479,9 @@ export const FIELD_SETS = Object.freeze({
 		filterName: 'memberTermsFilter',
 		fields: ['memberTerms.name'],
 	},
-	modentityidFieldSet: {
-		filterName: 'modentityidFilter',
-		fields: ['modEntityId'],
+	primaryexternalidFieldSet: {
+		filterName: 'primaryexternalidFilter',
+		fields: ['primaryExternalId'],
 	},
 	modinternalidFieldSet: {
 		filterName: 'modinternalidFilter',
@@ -532,7 +528,7 @@ export const FIELD_SETS = Object.freeze({
 	},
 	paAggregationFieldSet: {
 		filterName: 'paAggregationFilter',
-		fields: ['relation.name', 'dataProvider.sourceOrganization.abbreviation'],
+		fields: ['relation.name', 'dataProvider.abbreviation'],
 	},
 	paConditionRelationsSummaryFieldSet: {
 		filterName: 'paConditionRelationsFilter',
@@ -548,7 +544,7 @@ export const FIELD_SETS = Object.freeze({
 			'phenotypeAnnotationSubject.symbol',
 			'phenotypeAnnotationSubject.name',
 			'phenotypeAnnotationSubject.curie',
-			'phenotypeAnnotationSubject.modEntityId',
+			'phenotypeAnnotationSubject.primaryExternalId',
 			'phenotypeAnnotationSubject.modInternalId',
 		],
 	},
@@ -578,11 +574,7 @@ export const FIELD_SETS = Object.freeze({
 	},
 	secondaryDataProviderFieldSet: {
 		filterName: 'secondaryDataProviderFilter',
-		fields: [
-			'secondaryDataProvider.sourceOrganization.abbreviation',
-			'secondaryDataProvider.sourceOrganization.fullName',
-			'secondaryDataProvider.sourceOrganization.shortName',
-		],
+		fields: ['secondaryDataProvider.abbreviation', 'secondaryDataProvider.fullName', 'secondaryDataProvider.shortName'],
 	},
 	secondaryIdsFieldSet: {
 		filterName: 'secondaryIdsFilter',
@@ -593,7 +585,7 @@ export const FIELD_SETS = Object.freeze({
 		fields: [
 			'sgdStrainBackground.name',
 			'sgdStrainBackground.curie',
-			'sgdStrainBackground.modEntityId',
+			'sgdStrainBackground.primaryExternalId',
 			'sgdStrainBackground.modInternalId',
 		],
 	},
@@ -631,7 +623,7 @@ export const FIELD_SETS = Object.freeze({
 	},
 	speciesAggregationFieldSet: {
 		filterName: 'speciesAggregationFilter',
-		fields: ['dataProvider.sourceOrganization.abbreviation'],
+		fields: ['dataProvider.abbreviation'],
 	},
 	speciesAssemblyFieldSet: {
 		filterName: 'speciesAssemblyFilter',
@@ -667,7 +659,7 @@ export const FIELD_SETS = Object.freeze({
 	},
 	variantAggregationFieldSet: {
 		filterName: 'variantAggregationFilter',
-		fields: ['variantStatus.name', 'dataProvider.sourceOrganization.abbreviation'],
+		fields: ['variantStatus.name', 'dataProvider.abbreviation'],
 	},
 	variantStatusFieldSet: {
 		filterName: 'variantStatusFilter',
@@ -703,7 +695,7 @@ export const FIELD_SETS = Object.freeze({
 			'with.geneSymbol.displayText',
 			'with.geneSymbol.formatText',
 			'with.curie',
-			'with.modEntityId',
+			'with.primaryExternalId',
 			'with.modInternalId',
 		],
 	},
@@ -860,7 +852,7 @@ export const FILTER_CONFIGS = Object.freeze({
 		filterComponentType: 'input',
 		fieldSets: [FIELD_SETS.literatureCrossReferenceFieldSet],
 	},
-	modentityidFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.modentityidFieldSet] },
+	primaryexternalidFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.primaryexternalidFieldSet] },
 	modinternalidFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.modinternalidFieldSet] },
 	nameFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.nameFieldSet] },
 	namespaceFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.namespaceFieldSet] },

diff --git a/src/main/cliapp/src/constants/SortFields.js b/src/main/cliapp/src/constants/SortFields.js
@@ -1,6 +1,6 @@
 export const SORT_FIELDS = Object.freeze([
 	'uniqueId',
-	'modEntityId',
+	'primaryExternalId',
 	'modInternalId',
 	'diseaseAnnotationSubject.symbol',
 	'phenotypeAnnotationSubject.symbol',
@@ -26,8 +26,8 @@ export const SORT_FIELDS = Object.freeze([
 	'assertedGenes.geneSymbol.displayText',
 	'inferredAllele.alleleSymbol.displayText',
 	'assertedAllele.alleleSymbol.displayText',
-	'dataProvider.sourceOrganization.abbreviation',
-	'secondaryDataProvider.sourceOrganization.abbreviation',
+	'dataProvider.abbreviation',
+	'secondaryDataProvider.abbreviation',
 	'updatedBy.uniqueId',
 	'dateUpdated',
 	'createdBy.uniqueId',

diff --git a/src/main/cliapp/src/containers/affectedGenomicModelPage/AffectedGenomicModelTable.js b/src/main/cliapp/src/containers/affectedGenomicModelPage/AffectedGenomicModelTable.js
@@ -52,11 +52,11 @@ export const AffectedGenomicModelTable = () => {
 			filterConfig: FILTER_CONFIGS.curieFilterConfig,
 		},
 		{
-			field: 'modEntityId',
-			header: 'MOD Entity ID',
-			body: (rowData) => <IdTemplate id={rowData.modEntityId} />,
+			field: 'primaryExternalId',
+			header: 'Primary External ID',
+			body: (rowData) => <IdTemplate id={rowData.primaryExternalId} />,
 			sortable: true,
-			filterConfig: FILTER_CONFIGS.modentityidFilterConfig,
+			filterConfig: FILTER_CONFIGS.primaryexternalidFilterConfig,
 		},
 		{
 			field: 'modInternalId',
@@ -107,7 +107,7 @@ export const AffectedGenomicModelTable = () => {
 			filterConfig: FILTER_CONFIGS.taxonFilterConfig,
 		},
 		{
-			field: 'dataProvider.sourceOrganization.abbreviation',
+			field: 'dataProvider.abbreviation',
 			header: 'Data Provider',
 			sortable: true,
 			filterConfig: FILTER_CONFIGS.agmDataProviderFilterConfig,