Merge pull request #1719 from alliance-genome/release/v0.35.0

As sprint review on Oct 30th 2024

Makefile

@@ -31,6 +31,9 @@ uirun:
 	make -B -C src/main/cliapp
 	make -B -C src/main/cliapp run
 
+pretty:
+	make -B -C src/main/cliapp pretty
+
 uirunalpha:
 	export API_URL=https://alpha-curation.alliancegenome.org; make -B -C src/main/cliapp run; unset API_URL
 

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

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)

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" />

docker/run_opensearch

@@ -1 +1 @@
-docker run -d --net curation -p 9200:9200 -p 9600:9600 -e "discovery.type=single-node" -e "DISABLE_SECURITY_PLUGIN=true" --name opensearch opensearchproject/opensearch:1.2.4
+docker run -d --net curation -p 9200:9200 -p 9600:9600 -e "discovery.type=single-node" -e "DISABLE_SECURITY_PLUGIN=true" --name opensearch opensearchproject/opensearch:2.16.0

pom.xml

@@ -23,7 +23,7 @@
 		<okta.version>3.0.1</okta.version>
 		<okta.authn.version>2.0.0</okta.authn.version>
 		<okta-jwt.version>0.5.1</okta-jwt.version>
-		<quarkus.platform.version>3.5.0</quarkus.platform.version>
+		<quarkus.platform.version>3.13.3</quarkus.platform.version>
 		<surefire-plugin.version>3.0.0-M7</surefire-plugin.version>
 		<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
 		<checkstyle.version>10.17.0</checkstyle.version>
@@ -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>
@@ -241,6 +247,11 @@
 			<artifactId>commons-collections4</artifactId>
 			<version>4.4</version>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-compress</artifactId>
+			<version>1.27.1</version>
+		</dependency>
 		<dependency>
 			<groupId>commons-collections</groupId>
 			<artifactId>commons-collections</artifactId>

src/main/cliapp/Makefile

@@ -6,6 +6,9 @@ all:
 run:
 	npm start
 
+pretty:
+	npx prettier --write .
+
 runalpha:
 	export API_URL=https://alpha-curation.alliancegenome.org; make run; unset API_URL
 

src/main/cliapp/package.json

@@ -31,6 +31,7 @@
         "immer": "^9.0.15",
         "jose": "^4.10.0",
         "moment": "^2.29.1",
+        "moment-timezone": "^0.5.45",
         "primeflex": "3.1.0",
         "primeicons": "^5.0.0",
         "primereact": "^10.0.9",
@@ -45,6 +46,7 @@
         "react-use-websocket": "^3.0.0",
         "react18-json-view": "^0.2.8",
         "sass": "^1.32.8",
+        "update-browserslist-db": "^1.1.0",
         "use-immer": "^0.7.0"
     },
     "scripts": {
@@ -56,7 +58,7 @@
     "eslintConfig": {
         "extends": [
             "react-app",
-            "prettier" 
+            "prettier"
         ]
     },
     "browserslist": [

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

@@ -3,6 +3,7 @@ import { DataTable } from 'primereact/datatable';
 import { Column } from 'primereact/column';
 import { SystemService } from '../service/SystemService';
 import { CLASSES } from '../constants/Classes';
+import { NumberTemplate } from './Templates/NumberTemplate';
 
 export const EntityCountsComponent = () => {
 	const [tableData, setTableData] = useState({});
@@ -44,28 +45,80 @@ export const EntityCountsComponent = () => {
 		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;
+
+		if (rowData?.dbCount !== rowData.esCount) {
+			return 'bg-gray-500 text-white';
+		}
+	};
+
 	return (
 		<>
 			<div className="grid nested dashboard">
 				<div className="col-4">
-					<DataTable header="Entities" value={tableData.entity} sortField="name" sortOrder={1}>
+					<DataTable
+						header="Entities"
+						value={tableData.entity}
+						sortField="name"
+						sortOrder={1}
+						rowClassName={(rowData) => getRowClass(rowData)}
+					>
 						<Column field="name" header="Entity Name" body={nameHyperlinkTemplate} />
-						<Column field="dbCount" header="Database Entity Count" />
-						<Column field="esCount" header="Search index Entity Count" />
+						<Column
+							field="dbCount"
+							header="Database Entity Count"
+							body={(rowData) => <NumberTemplate number={rowData.dbCount} />}
+						/>
+						<Column
+							field="esCount"
+							header="Search index Entity Count"
+							body={(rowData) => <NumberTemplate number={rowData.esCount} />}
+						/>
 					</DataTable>
 				</div>
 				<div className="col-4">
-					<DataTable header="Ontologies" value={tableData.ontology} sortField="name" sortOrder={1}>
+					<DataTable
+						header="Ontologies"
+						value={tableData.ontology}
+						sortField="name"
+						sortOrder={1}
+						rowClassName={(rowData) => getRowClass(rowData)}
+					>
 						<Column field="name" header="Ontology Name" body={nameHyperlinkTemplate} />
-						<Column field="dbCount" header="Database Term Count" />
-						<Column field="esCount" header="Search index Term Count" />
+						<Column
+							field="dbCount"
+							header="Database Term Count"
+							body={(rowData) => <NumberTemplate number={rowData.dbCount} />}
+						/>
+						<Column
+							field="esCount"
+							header="Search index Term Count"
+							body={(rowData) => <NumberTemplate number={rowData.esCount} />}
+						/>
 					</DataTable>
 				</div>
 				<div className="col-4">
-					<DataTable header="System" value={tableData.system} sortField="name" sortOrder={1}>
+					<DataTable
+						header="System"
+						value={tableData.system}
+						sortField="name"
+						sortOrder={1}
+						rowClassName={(rowData) => getRowClass(rowData)}
+					>
 						<Column field="name" header="System Name" body={nameHyperlinkTemplate} />
-						<Column field="dbCount" header="Database Object Count" />
-						<Column field="esCount" header="Search index Object Count" />
+						<Column
+							field="dbCount"
+							header="Database Object Count"
+							body={(rowData) => <NumberTemplate number={rowData.dbCount} />}
+						/>
+						<Column
+							field="esCount"
+							header="Search index Object Count"
+							body={(rowData) => <NumberTemplate number={rowData.esCount} />}
+						/>
 					</DataTable>
 				</div>
 			</div>

src/main/cliapp/src/components/FieldData/GeneticModifierAgmsAdditionalFieldData.js

@@ -0,0 +1,14 @@
+import React from 'react';
+import { getIdentifier } from '../../utils/utils';
+
+export function GeneticModifierAgmsAdditionalFieldData({ fieldData }) {
+	let ret = [];
+	if (fieldData && fieldData.length > 0) {
+		for (let i = 0; i < fieldData.length; i++) {
+			if (getIdentifier(fieldData[i]) !== '') {
+				ret.push(<div key={i} className="p-info" dangerouslySetInnerHTML={{ __html: fieldData[i]['name'] }}></div>);
+			}
+		}
+	}
+	return ret;
+}

src/main/cliapp/src/components/FieldData/GeneticModifierAllelesAdditionalFieldData.js

@@ -0,0 +1,20 @@
+import React from 'react';
+import { getIdentifier } from '../../utils/utils';
+
+export function GeneticModifierAllelesAdditionalFieldData({ fieldData }) {
+	let ret = [];
+	if (fieldData && fieldData.length > 0) {
+		for (let i = 0; i < fieldData.length; i++) {
+			if (getIdentifier(fieldData[i]) !== '') {
+				ret.push(
+					<div
+						key={i}
+						className="p-info"
+						dangerouslySetInnerHTML={{ __html: fieldData[i]['alleleSymbol']['displayText'] }}
+					></div>
+				);
+			}
+		}
+	}
+	return ret;
+}

src/main/cliapp/src/components/FieldData/GeneticModifierGenesAdditionalFieldData.js

@@ -0,0 +1,20 @@
+import React from 'react';
+import { getIdentifier } from '../../utils/utils';
+
+export function GeneticModifierGenesAdditionalFieldData({ fieldData }) {
+	let ret = [];
+	if (fieldData && fieldData.length > 0) {
+		for (let i = 0; i < fieldData.length; i++) {
+			if (getIdentifier(fieldData[i]) !== '') {
+				ret.push(
+					<div
+						key={i}
+						className="p-info"
+						dangerouslySetInnerHTML={{ __html: fieldData[i]['geneSymbol']['displayText'] }}
+					></div>
+				);
+			}
+		}
+	}
+	return ret;
+}