Merge pull request #1749 from alliance-genome/release/v0.36.0-rc1

SCRUM-4633: release/v0.36.0-rc1

RELEASE-NOTES.md

@@ -2,6 +2,41 @@
 
 https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview
 
+## v0.35.0
+* New features
+   * Load FBcv into the persistent store (SCRUM-2190)
+   * Implement Gene Type field/column for Genes data table (SCRUM-3983)
+   * Turn off auxiliary clean up for associated entities (e.g. clean up of disease annotations based on a gene load) - public site Indexer work	(SCRUM-4150)
+   * SQTR Gene Associations import into Persistent store (SCRUM-4185, SCRUM-4187, SCRUM-4188)
+   * HTPdataset loaded into persistent store (SCRUM-4192,SCRUM-4303, SCRUM-4341)
+   * Make obsolete disease annotations hidden by default for all MOD default settings	(SCRUM-4277)
+   * HTPdataset ZFIN Fms files having wrong naming of property	(SCRUM-4328)
+   * Clean up erroneous DOTerms (SCRUM-4337)
+   * Importing expression annotations into the persistent store - Load ExpressionPattern, TemporalContext, and AnatomicalSite (SCRUM-3952)
+   * Implement programmatic, regular purging of exception message history for all exceptions older than 2 weeks (SCRUM-4377)
+   * HTPdatasetSample import P1 - Creating entities and migration file (SCRUM-4426)
+   * Reenable downloading of all exception messages for a given data load (SCRUM-4452)
+   * P1: Expression Atlas Import: Load accession data files from Ensembl, etc... (SCRUM-4118)
+   * GFF Loading (Load assembly, transcripts, exons, and CDSs without positional information; Load positional information for Transcripts, Exons, and CDSs; Load associations between Genes, Transcripts, Exons, and CDSs) (SCRUM-4174, SCRUM-4175, SCRUM-4176)
+   * Associate Expression Annotations with Go Slim Terms	(SCRUM-4300)
+   * Implement caching of references for DQM loads	(SCRUM-4336)
+   * Accommodate BIOGRID-ORCS loader data type: to establish 3rd part link out to BIOGRID from gene page phenotypes section P1 - create DTO, load via migration, and loading infrastructure (SCRUM-4440)
+   * Investigate: Accommodate BIOGRID-ORCS loader data type: to establish 3rd part link out to BIOGRID from gene page phenotypes section (SCRUM-4471)
+   * Load VariantGenomicLocationAssociation from FMS submissions and generate HGVSg identifiers	(SCRUM-4499)
+   * Test effect of removing AuditedObject fields on disease annotation indexing speed	(SCRUM-4520)
+   * Java model changes for disease genetic modifier changes to split based on modifier type	(SCRUM-4523)
+   * Curation UI changes to Disease Annotations table to split out Genetic Modifiers into 3 separate fields for each of Gene, Allele and AGM modifier types	(SCRUM-4524)
+* Fixes and maintenance
+   * Edit cancelation button getting squeezed out of frame on alpha data tables (SCRUM-4236)
+   * Constructs data table on alpha-curation throwing 500 error and not loading	(SCRUM-4259)
+   * Fix SQTR Gene Association Integration Tests (SCRUM-4299)
+   * Curl timing out when uploading to persistent store (SCRUM-3683)
+   * Annotations and interactions not indexed on alpha-curation (despite attempts to reindex) (SCRUM-4254)
+   * Loads not showing in the Data Loads page "Data Processing Info Table" widget (SCRUM-4428)
+   * New "Running Time" showing negative time counting down	(SCRUM-4429)
+   * Molecule table columns expand automatically when sorting	(SCRUM-4531)
+
+
 ## v0.34.0
 * New features
   * Paralogy annotations loaded into persistent store (SCRUM-4086, SCRUM-4088, SCRUM-4089, SCRUM-4090)

src/main/cliapp/src/components/EntityCountsComponent.js

@@ -28,6 +28,8 @@ export const EntityCountsComponent = () => {
 					_tableData[type].push({
 						name: CLASSES[key].name,
 						link: CLASSES[key].link,
+						type: CLASSES[key].type,
+						isIndexed: CLASSES[key].isIndexed,
 						dbCount: res.entity[key]['dbCount'],
 						esCount: res.entity[key]['esCount'],
 					});
@@ -42,13 +44,15 @@ export const EntityCountsComponent = () => {
 	}, []);
 
 	const nameHyperlinkTemplate = (rowData) => {
+		if (!rowData.link) {
+			return rowData.name;
+		}
 		return <a href={rowData.link}>{rowData.name}</a>;
 	};
 
-	const ROW_HIGHLIGHT_IGNORE = ['Disease Annotations', 'Literature References', 'Bulk Loads / Failed Loads'];
-
 	const getRowClass = (rowData) => {
-		if (ROW_HIGHLIGHT_IGNORE.includes(rowData.name)) return;
+		console.log(rowData);
+		if (!rowData.isIndexed) return;
 
 		if (rowData?.dbCount !== rowData.esCount) {
 			return 'bg-gray-500 text-white';
@@ -58,7 +62,7 @@ export const EntityCountsComponent = () => {
 	return (
 		<>
 			<div className="grid nested dashboard">
-				<div className="col-4">
+				<div className="col-3">
 					<DataTable
 						header="Entities"
 						value={tableData.entity}
@@ -79,7 +83,7 @@ export const EntityCountsComponent = () => {
 						/>
 					</DataTable>
 				</div>
-				<div className="col-4">
+				<div className="col-3">
 					<DataTable
 						header="Ontologies"
 						value={tableData.ontology}
@@ -100,7 +104,23 @@ export const EntityCountsComponent = () => {
 						/>
 					</DataTable>
 				</div>
-				<div className="col-4">
+				<div className="col-3">
+					<DataTable
+						header="Associations"
+						value={tableData.association}
+						sortField="name"
+						sortOrder={1}
+						rowClassName={(rowData) => getRowClass(rowData)}
+					>
+						<Column field="name" header="Association Type" body={nameHyperlinkTemplate} />
+						<Column
+							field="dbCount"
+							header="Database Association Count"
+							body={(rowData) => <NumberTemplate number={rowData.dbCount} />}
+						/>
+					</DataTable>
+				</div>
+				<div className="col-3">
 					<DataTable
 						header="System"
 						value={tableData.system}

src/main/cliapp/src/components/Templates/dialog/ListDialogTemplate.js

@@ -9,7 +9,7 @@ export const ListDialogTemplate = ({ entities, handleOpen, getTextField, underli
 
 	const listTemplate = (item) => (
 		<div
-			className={`overflow-hidden text-overflow-ellipsis ${underline ? 'underline' : ''}`}
+			className={`overflow-hidden text-left text-overflow-ellipsis ${underline ? 'underline' : ''}`}
 			dangerouslySetInnerHTML={{ __html: item }}
 		/>
 	);