Merge pull request #1705 from alliance-genome/release/v0.35.0-rc2

Release/v0.35.0 rc2

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
 

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>
@@ -247,6 +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;
+}

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

@@ -0,0 +1,40 @@
+import React from 'react';
+import { Paginator } from 'primereact/paginator';
+import { NumberTemplate } from '../Templates/NumberTemplate';
+
+export const DataTableFooter = ({ first, rows, totalRecords, onLazyLoad, isInEditMode }) => {
+	return (
+		!isInEditMode && (
+			<Paginator
+				data-testid="datatable-footer"
+				first={first}
+				rows={rows}
+				totalRecords={totalRecords}
+				rowsPerPageOptions={[10, 20, 50, 100, 250, 1000]}
+				onPageChange={onLazyLoad}
+				template={{
+					layout:
+						'CurrentPageReport FirstPageLink PrevPageLink PageLinks NextPageLink LastPageLink RowsPerPageDropdown',
+					CurrentPageReport: (options) => {
+						const totalRecordsDisplay = <NumberTemplate number={options.totalRecords} />;
+						const firstDisplay = <NumberTemplate number={options.first} />;
+						const lastDisplay = <NumberTemplate number={options.last} />;
+						return (
+							<>
+								Showing {firstDisplay} to {lastDisplay} of {totalRecordsDisplay}
+							</>
+						);
+					},
+					PageLinks: (options) => {
+						const pageDisplay = <NumberTemplate number={options.page + 1} />;
+						return (
+							<button type="button" className={options.className} onClick={options.onClick}>
+								{pageDisplay}
+							</button>
+						);
+					},
+				}}
+			/>
+		)
+	);
+};