Merge pull request #1633 from alliance-genome/release/v0.35.0-rc1

As sprint review Jul 31st 2024

README.md

@@ -481,6 +481,7 @@ As the code goes through the different stages, it becomes more and more stable a
    *  Incrementing the `MAJOR` or `MINOR` release numbers as appropriate when
       the previous release candidate was (or will be) promoted to a full release
       and reset to rc1 for the next release.
+   *  When choosing an alpha release make sure to include the Pull Requests that may have fixed bugs shortly after the sprint review, if they needed to be included in beta release.
 4. Create a release/v`x`.`y`.`z`-rc`a` branch from the commit on the alpha branch
    that was chosen earlier to be promoted.
    ```bash

checkstyle.xml

@@ -27,7 +27,7 @@
 		<module name="LeftCurly" />
 		<module name="NeedBraces" />
 		<module name="RightCurly" />
-		<module name="HideUtilityClassConstructor" />
+<!--		<module name="HideUtilityClassConstructor" />-->
 		<module name="EmptyStatement" />
 		<module name="EqualsHashCode" />
 		<module name="InnerAssignment" />

pom.xml

@@ -120,7 +120,13 @@
 		<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>
 			<artifactId>owlapi-distribution</artifactId>
-			<version>5.1.19</version>
+			<version>5.5.0</version>
+		</dependency>
+
+		<dependency>
+			<groupId>io.github.liveontologies</groupId>
+			<artifactId>elk-owlapi</artifactId>
+			<version>0.6.0</version>
 		</dependency>
 
 		<dependency>

src/main/cliapp/src/components/GenericDataTable/GenericDataTable.js

@@ -16,6 +16,7 @@ import { EntityDetailsAction } from '../Actions/EntityDetailsAction';
 import { filterColumns, orderColumns, getIdentifier } from '../../utils/utils';
 import { useGenericDataTable } from './useGenericDataTable';
 
+import style from './styles.module.scss';
 export const GenericDataTable = (props) => {
 	const {
 		tableName,
@@ -160,8 +161,8 @@ export const GenericDataTable = (props) => {
 
 	const rowEditorFilterNameHeader = (options) => {
 		return (
-			<div className="p-column-header-content">
-				<span className="p-column-title">Filters</span>
+			<div>
+				<span className="p-column-title text-center">Filters</span>
 			</div>
 		);
 	};
@@ -325,13 +326,13 @@ export const GenericDataTable = (props) => {
 					<Column
 						field="rowEditor"
 						rowEditor
-						className={'p-text-center p-0 min-w-3rem max-w-3rem text-base'}
+						className={`text-center max-w-7 ${style.rowEditorColumn} p-0 text-base`}
 						filter
 						filterElement={rowEditorFilterNameHeader}
 						showFilterMenu={false}
 						bodyStyle={{ textAlign: 'center' }}
 						frozen
-						headerClassName="surface-0 w-3rem sticky"
+						headerClassName={`surface-0 max-w-7rem ${style.rowEditorColumn} sticky`}
 					/>
 				)}
 				{deletionEnabled && (
@@ -341,10 +342,10 @@ export const GenericDataTable = (props) => {
 						body={(props) => deleteAction(props, isInEditMode)}
 						filterElement={rowEditorFilterNameHeader}
 						showFilterMenu={false}
-						className={`p-text-center p-0 min-w-3rem max-w-3rem ${isEditable ? 'visible' : 'hidden'}`}
+						className={`text-center p-0 max-w-3rem ${isEditable ? 'visible' : 'hidden'}`}
 						bodyStyle={{ textAlign: 'center' }}
 						frozen
-						headerClassName="surface-0 w-3rem sticky"
+						headerClassName="surface-0 max-w-3rem sticky"
 					/>
 				)}
 				{duplicationEnabled && (
@@ -357,10 +358,10 @@ export const GenericDataTable = (props) => {
 							<DuplicationAction props={props} handleDuplication={handleDuplication} disabled={isInEditMode} />
 						)}
 						showFilterMenu={false}
-						className={`p-text-center p-0 min-w-3rem max-w-3rem ${isEditable ? 'visible' : 'hidden'}`}
+						className={`text-center p-0 max-w-3rem ${isEditable ? 'visible' : 'hidden'}`}
 						bodyStyle={{ textAlign: 'center' }}
 						frozen
-						headerClassName="surface-0 w-3rem sticky"
+						headerClassName="surface-0 max-w-3rem sticky"
 					/>
 				)}
 				{hasDetails && (
@@ -369,10 +370,10 @@ export const GenericDataTable = (props) => {
 						editor={(props) => <EntityDetailsAction identifier={getIdentifier(props.rowData)} disabled={true} />}
 						body={(props) => <EntityDetailsAction identifier={getIdentifier(props)} disabled={isInEditMode} />}
 						showFilterMenu={false}
-						className={`p-text-center p-0 min-w-3rem max-w-3rem ${isEditable ? 'visible' : 'hidden'}`}
+						className={`text-center p-0 max-w-3rem ${isEditable ? 'visible' : 'hidden'}`}
 						bodyStyle={{ textAlign: 'center' }}
 						frozen
-						headerClassName="surface-0 w-3rem sticky"
+						headerClassName="surface-0 max-w-3rem sticky"
 					/>
 				)}
 				{columnList}

src/main/cliapp/src/components/GenericDataTable/styles.module.scss

@@ -0,0 +1,3 @@
+.rowEditorColumn{
+	min-width : 6rem !important;
+}

src/main/cliapp/src/constants/Classes.js

@@ -54,7 +54,7 @@ export const CLASSES = Object.freeze({
 	WBPhenotypeTerm: { name: 'WBPheno', link: '/#/ontology/wbpheno', type: 'ontology' },
 	PATOTerm: { name: 'PATO', link: '/#/ontology/pato', type: 'ontology' },
 	HPTerm: { name: 'HP', link: '/#/ontology/hp', type: 'ontology' },
-	DPOTerm: { name: 'DPO', link: '/#/ontology/dpo', type: 'ontology' },
+	FBCVTerm: { name: 'FBCV', link: '/#/ontology/fbcv', type: 'ontology' },
 	MMOTerm: { name: 'MMO', link: '/#/ontology/mmo', type: 'ontology' },
 	APOTerm: { name: 'APO', link: '/#/ontology/apo', type: 'ontology' },
 	MITerm: { name: 'MI', link: '/#/ontology/mi', type: 'ontology' },

src/main/cliapp/src/constants/FilterFields.js

@@ -344,6 +344,10 @@ export const FIELD_SETS = Object.freeze({
 		filterName: 'geneticSexFilter',
 		fields: ['geneticSex.name'],
 	},
+	geneTypeFieldSet: {
+		filterName: 'geneTypeFilter',
+		fields: ['geneType.curie', 'geneType.name'],
+	},
 	gmiAggregationFieldSet: {
 		filterName: 'gmiAggregationFilter',
 		fields: ['relation.name'],
@@ -788,6 +792,7 @@ export const FILTER_CONFIGS = Object.freeze({
 	geneSymbolFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.geneSymbolFieldSet] },
 	geneSynonymsFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.geneSynonymsFieldSet] },
 	geneSystematicNameFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.geneSystematicNameFieldSet] },
+	geneTypeFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.geneTypeFieldSet] },
 	geneticModifiersFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.geneticModifiersFieldSet] },
 	idExampleFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.idExampleFieldSet] },
 	idPatternFilterConfig: { filterComponentType: 'input', fieldSets: [FIELD_SETS.idPatternFieldSet] },

src/main/cliapp/src/constants/SortFields.js

@@ -73,6 +73,7 @@ export const SORT_FIELDS = Object.freeze([
 	'geneSymbol.displayText',
 	'geneSecondaryIds.secondaryId',
 	'geneSystematicName.displayText',
+	'geneType.name',
 	'inchi',
 	'inchiKey',
 	'iupac',

src/main/cliapp/src/containers/genesPage/GenesTable.js

@@ -16,6 +16,7 @@ import { TextDialogTemplate } from '../../components/Templates/dialog/TextDialog
 import { ListDialogTemplate } from '../../components/Templates/dialog/ListDialogTemplate';
 import { TaxonTemplate } from '../../components/Templates/TaxonTemplate';
 import { BooleanTemplate } from '../../components/Templates/BooleanTemplate';
+import { OntologyTermTemplate } from '../../components/Templates/OntologyTermTemplate';
 
 import { SearchService } from '../../service/SearchService';
 
@@ -191,6 +192,13 @@ export const GenesTable = () => {
 			filter: true,
 			filterConfig: FILTER_CONFIGS.geneSystematicNameFilterConfig,
 		},
+		{
+			field: 'geneType.name',
+			header: 'Gene Type',
+			body: (rowData) => <OntologyTermTemplate object={rowData.geneType} />,
+			sortable: true,
+			filterConfig: FILTER_CONFIGS.geneTypeFilterConfig,
+		},
 		{
 			field: 'taxon.name',
 			header: 'Taxon',

src/main/cliapp/src/containers/genesPage/__tests__/GenesTable.test.js

@@ -46,6 +46,7 @@ describe('<GenesPage />', () => {
 		const systematicNameTd = await result.findByText('C35C5.5');
 		const taxonTd = await result.findByText(/Caenorhabditis elegans/i);
 		const xrefsTd = await result.findByText(/WBGene00003771Xref \(gene\)/);
+		const geneTypeTd = await result.findByText(/protein_coding_gene/i);
 
 		await waitFor(() => {
 			expect(modEntityIdTd).toBeInTheDocument();
@@ -56,6 +57,7 @@ describe('<GenesPage />', () => {
 			expect(systematicNameTd).toBeInTheDocument();
 			expect(taxonTd).toBeInTheDocument();
 			expect(xrefsTd).toBeInTheDocument();
+			expect(geneTypeTd).toBeInTheDocument();
 		});
 	});
 });

src/main/cliapp/src/containers/genesPage/mockData/mockData.js

@@ -28,6 +28,13 @@ export const data = {
 				curie: 'NCBITaxon:6239',
 				name: 'Caenorhabditis elegans',
 			},
+			geneType: {
+				internal: false,
+				obsolete: false,
+				curie: 'SO:0001272',
+				name: 'tRNA_gene',
+				id: 25665,
+			},
 			dataProvider: {
 				internal: false,
 				obsolete: false,

src/main/cliapp/src/containers/layout/SiteLayout.js

@@ -282,6 +282,7 @@ export const SiteLayout = (props) => {
 								},
 							],
 						},
+						{ label: 'Flybase Controlled Vocabulary (FBcv)', icon: 'pi pi-fw pi-home', to: '/ontology/fbcv' },
 						{ label: 'Gene Ontology (GO)', icon: 'pi pi-fw pi-home', to: '/ontology/go' },
 						{ label: 'Genotype Ontology (GENO)', icon: 'pi pi-fw pi-home', to: '/ontology/geno' },
 						{ label: 'Measurement Method Ontology (MMO)', icon: 'pi pi-fw pi-home', to: '/ontology/mmo' },
@@ -304,7 +305,6 @@ export const SiteLayout = (props) => {
 									icon: 'pi pi-fw pi-home',
 									to: '/ontology/wbpheno',
 								},
-								{ label: 'Drosophila Phenotype Ontology (DPO)', icon: 'pi pi-fw pi-home', to: '/ontology/dpo' },
 								{ label: 'Human Phenotype Ontology (HP)', icon: 'pi pi-fw pi-home', to: '/ontology/hp' },
 								{ label: 'Mammalian Phenotype Ontology (MP)', icon: 'pi pi-fw pi-home', to: '/ontology/mp' },
 								{ label: 'Xenopus Phenotype Ontology (XPO)', icon: 'pi pi-fw pi-home', to: '/ontology/xpo' },

src/main/cliapp/src/routes.js

@@ -472,10 +472,10 @@ export default (
 			)}
 		/>
 		<SecureRoute
-			path="/ontology/dpo"
+			path="/ontology/fbcv"
 			render={() => (
 				<ErrorBoundary>
-					<GeneralOntologyComponent name="DPO" endpoint="dpoterm" />
+					<GeneralOntologyComponent showNamespace={true} name="FBcv" endpoint="fbcvterm" />
 				</ErrorBoundary>
 			)}
 		/>

src/main/cliapp/src/service/DataLoadService.js

@@ -80,6 +80,8 @@ export class DataLoadService extends BaseAuthService {
 	getBackendBulkLoadTypes(loadType) {
 		const bulkLoadTypes = {
 			BulkFMSLoad: [
+				'GFF',
+				'HTPDATASET',
 				'INTERACTION-GEN',
 				'INTERACTION-MOL',
 				'MOLECULE',
@@ -121,9 +123,9 @@ export class DataLoadService extends BaseAuthService {
 			'CMO',
 			'DAO',
 			'DO',
-			'DPO',
 			'ECO',
 			'EMAPA',
+			'FBCV',
 			'FBDV',
 			'GENO',
 			'GO',

src/main/cliapp/src/service/TableStateService.js

@@ -47,6 +47,9 @@ const modTableSettings = {
 					'dataProvider.sourceOrganization.fullName': { queryString: 'RGD', tokenOperator: 'AND' },
 					'dataProvider.sourceOrganization.shortName': { queryString: 'RGD', tokenOperator: 'AND' },
 				},
+				obsoleteFilter: {
+					obsolete: { queryString: 'false' },
+				},
 			},
 			tableKeyName: 'DiseaseAnnotations',
 			tableSettingsKeyName: 'DiseaseAnnotationsTableSettings',
@@ -93,6 +96,9 @@ const modTableSettings = {
 					'dataProvider.sourceOrganization.fullName': { queryString: 'SGD', tokenOperator: 'AND' },
 					'dataProvider.sourceOrganization.shortName': { queryString: 'SGD', tokenOperator: 'AND' },
 				},
+				obsoleteFilter: {
+					obsolete: { queryString: 'false' },
+				},
 			},
 			tableKeyName: 'DiseaseAnnotations',
 			tableSettingsKeyName: 'DiseaseAnnotationsTableSettings',
@@ -103,14 +109,6 @@ const modTableSettings = {
 			page: 0,
 			rows: 50,
 			first: 0,
-			filters: {
-				dataProviderFilter: {
-					'dataProvider.sourceOrganization.abbreviation': { queryString: 'WB', tokenOperator: 'AND' },
-					'dataProvider.sourceOrganization.fullName': { queryString: 'WB', tokenOperator: 'AND' },
-					'dataProvider.sourceOrganization.shortName': { queryString: 'WB', tokenOperator: 'AND' },
-				},
-			},
-			tableKeyName: 'DiseaseAnnotations',
 			multiSortMeta: [{ field: 'dateCreated', order: -1 }],
 			selectedColumnNames: [
 				'MOD Annotation ID',
@@ -148,6 +146,17 @@ const modTableSettings = {
 				'Genetic Modifiers',
 				'Asserted Genes',
 			],
+			filters: {
+				dataProviderFilter: {
+					'dataProvider.sourceOrganization.abbreviation': { queryString: 'WB', tokenOperator: 'AND' },
+					'dataProvider.sourceOrganization.fullName': { queryString: 'WB', tokenOperator: 'AND' },
+					'dataProvider.sourceOrganization.shortName': { queryString: 'WB', tokenOperator: 'AND' },
+				},
+				obsoleteFilter: {
+					obsolete: { queryString: 'false' },
+				},
+			},
+			tableKeyName: 'DiseaseAnnotations',
 			tableSettingsKeyName: 'DiseaseAnnotationsTableSettings',
 		},
 	},
@@ -187,14 +196,14 @@ const modTableSettings = {
 				'Genetic Modifiers',
 			],
 			filters: {
-				obsoleteFilter: {
-					obsolete: { queryString: 'false' },
-				},
 				dataProviderFilter: {
 					'dataProvider.sourceOrganization.abbreviation': { queryString: 'FB', tokenOperator: 'AND' },
 					'dataProvider.sourceOrganization.fullName': { queryString: 'FB', tokenOperator: 'AND' },
 					'dataProvider.sourceOrganization.shortName': { queryString: 'FB', tokenOperator: 'AND' },
 				},
+				obsoleteFilter: {
+					obsolete: { queryString: 'false' },
+				},
 			},
 			tableKeyName: 'DiseaseAnnotations',
 			tableSettingsKeyName: 'DiseaseAnnotationsTableSettings',
@@ -229,6 +238,9 @@ const modTableSettings = {
 					'dataProvider.sourceOrganization.fullName': { queryString: 'ZFIN', tokenOperator: 'AND' },
 					'dataProvider.sourceOrganization.shortName': { queryString: 'ZFIN', tokenOperator: 'AND' },
 				},
+				obsoleteFilter: {
+					obsolete: { queryString: 'false' },
+				},
 			},
 			tableKeyName: 'DiseaseAnnotations',
 			tableSettingsKeyName: 'DiseaseAnnotationsTableSettings',
@@ -269,6 +281,9 @@ const modTableSettings = {
 					'dataProvider.sourceOrganization.fullName': { queryString: 'ZFIN', tokenOperator: 'AND' },
 					'dataProvider.sourceOrganization.shortName': { queryString: 'ZFIN', tokenOperator: 'AND' },
 				},
+				obsoleteFilter: {
+					obsolete: { queryString: 'false' },
+				},
 			},
 			tableKeyName: 'DiseaseAnnotations',
 			tableSettingsKeyName: 'DiseaseAnnotationsTableSettings',
@@ -375,7 +390,11 @@ const modTableSettings = {
 				'Genetic Modifiers',
 				'Internal',
 			],
-			filters: {},
+			filters: {
+				obsoleteFilter: {
+					obsolete: { queryString: 'false' },
+				},
+			},
 			tableKeyName: 'DiseaseAnnotations',
 			tableSettingsKeyName: 'DiseaseAnnotationsTableSettings',
 		},

src/main/java/org/alliancegenome/curation_api/constants/EntityFieldConstants.java

@@ -6,16 +6,41 @@ private EntityFieldConstants() {
 		// Hidden from view, as it is a utility class
 	}
 
+	public static final String ASSEMBLY = "genomeAssembly.modEntityId";
 	public static final String TAXON = "taxon.curie";
-	public static final String DATA_PROVIDER = "dataProvider.sourceOrganization.abbreviation";
-	public static final String SECONDARY_DATA_PROVIDER = "secondaryDataProvider.sourceOrganization.abbreviation";
+	public static final String SOURCE_ORGANIZATION = "sourceOrganization.abbreviation";
+	public static final String DATA_PROVIDER = "dataProvider." + SOURCE_ORGANIZATION;
+	public static final String SECONDARY_DATA_PROVIDER = "secondaryDataProvider." + SOURCE_ORGANIZATION;
+
 	public static final String DA_SUBJECT = "diseaseAnnotationSubject";
-	public static final String DA_SUBJECT_TAXON = DA_SUBJECT + "." + TAXON;
+	public static final String EA_SUBJECT = "expressionAnnotationSubject";
 	public static final String PA_SUBJECT = "phenotypeAnnotationSubject";
+	public static final String ALLELE_ASSOCIATION_SUBJECT = "alleleAssociationSubject";
+	public static final String CODING_SEQUENCE_ASSOCIATION_SUBJECT = "codingSequenceAssociationSubject";
+	public static final String CONSTRUCT_ASSOCIATION_SUBJECT = "constructAssociationSubject";
+	public static final String EXON_ASSOCIATION_SUBJECT = "exonAssociationSubject";
+	public static final String SQTR_ASSOCIATION_SUBJECT = "sequenceTargetingReagentAssociationSubject";
+	public static final String TRANSCRIPT_ASSOCIATION_SUBJECT = "transcriptAssociationSubject";
+
+	public static final String DA_SUBJECT_TAXON = DA_SUBJECT + "." + TAXON;
+	public static final String EA_SUBJECT_TAXON = EA_SUBJECT + "." + TAXON;
 	public static final String PA_SUBJECT_TAXON = PA_SUBJECT + "." + TAXON;
-	public static final String ALLELE_ASSOCIATION_SUBJECT_DATA_PROVIDER = "alleleAssociationSubject." + DATA_PROVIDER;
-	public static final String CONSTRUCT_ASSOCIATION_SUBJECT_DATA_PROVIDER = "constructAssociationSubject." + DATA_PROVIDER;
+
+	public static final String ALLELE_ASSOCIATION_SUBJECT_DATA_PROVIDER = ALLELE_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
+	public static final String CODING_SEQUENCE_ASSOCIATION_SUBJECT_DATA_PROVIDER = CODING_SEQUENCE_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
+	public static final String CONSTRUCT_ASSOCIATION_SUBJECT_DATA_PROVIDER = CONSTRUCT_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
+	public static final String EXON_ASSOCIATION_SUBJECT_DATA_PROVIDER = EXON_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
+	public static final String SQTR_ASSOCIATION_SUBJECT_DATA_PROVIDER = SQTR_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
+	public static final String TRANSCRIPT_ASSOCIATION_SUBJECT_DATA_PROVIDER = TRANSCRIPT_ASSOCIATION_SUBJECT + "." + DATA_PROVIDER;
+
+	public static final String GENOMIC_LOCATION_ASSOCIATION_OBJECT = "GenomicLocationAssociationObject";
+	public static final String CODING_SEQUENCE_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "codingSequence" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + ".name";
+	public static final String EXON_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "exon" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + ".name";
+	public static final String TRANSCRIPT_GENOMIC_LOCATION_ASSOCIATION_OBJECT = "transcript" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + ".name";
+	public static final String CODING_SEQUENCE_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY = "codingSequence" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + "." + ASSEMBLY;
+	public static final String EXON_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY = "exon" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + "." + ASSEMBLY;
+	public static final String TRANSCRIPT_GENOMIC_LOCATION_ASSOCIATION_OBJECT_ASSEMBLY = "transcript" + GENOMIC_LOCATION_ASSOCIATION_OBJECT + "." + ASSEMBLY;
+
 	public static final String SUBJECT_GENE_DATA_PROVIDER = "subjectGene." + DATA_PROVIDER;
 	public static final String SUBJECT_GENE_TAXON = "subjectGene." + TAXON;
-	public static final String EA_SUBJECT_TAXON = "expressionAnnotationSubject.taxon.curie";
 }