Merge pull request #760 from alliance-genome/release/v0.12.0-rc2

Release/v0.12.0-rc2
alliance-genome · Nov 3, 2022 · f9bf75e · f9bf75e
2 parents ceec965 + 70c9197
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diff --git a/.github/workflows/alpha-build-and-deploy.yml b/.github/workflows/alpha-build-and-deploy.yml
@@ -39,6 +39,32 @@ jobs:
         docker tag $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG $ECR_REGISTRY/$ECR_REPOSITORY:${GITHUB_REF#refs/heads/}
         docker push $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG
         docker push $ECR_REGISTRY/$ECR_REPOSITORY:${GITHUB_REF#refs/heads/}
+  build-deploy-maven-central-package:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - name: Set up Maven Central Repository
+        uses: actions/setup-java@v3
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+          server-id: ossrh
+          server-username: MAVEN_USERNAME
+          server-password: MAVEN_PASSWORD
+      - run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
+      - name: Set Proper version
+        run: mvn versions:set -ntp -DnewVersion=0.0.0-SNAPSHOT
+      - id: install-secret-key
+        name: Install gpg secret key
+        run: |
+          cat <(echo -e "${{ secrets.OSSRH_GPG_SECRET_KEY }}") | gpg --batch --import
+          gpg --list-secret-keys --keyid-format LONG
+      - name: Publish package
+        run: mvn --batch-mode deploy
+        env:
+          MAVEN_USERNAME: ${{ secrets.OSSRH_USERNAME }}
+          MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}
   deploy-to-alpha:
     if: github.event.pull_request.merged == true && !contains(github.event.pull_request.labels.*.name, 'no-deploy')
     needs: [build-and-push-docker-image]

diff --git a/README.md b/README.md
@@ -585,6 +585,16 @@ This is a grouping mechanism to group files together
 | WB    | Worm Base |
 | ZFIN  | Zebrafish Information Network |
 
+### Including corresponding LinkML version in the JSON file submission header
+
+The LinkML version for which the file is being submitted now needs to be added to the JSON file header, for example:
+
+```json
+{
+  "linkml_version" : "v1.3.2",
+  "disease_agm_ingest_set" : [ {
+```
+
 ## EB Deployment (beta)
 This section is WIP.
 

diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -1,29 +1,60 @@
 # AGR curation release notes
 
-## v0.9.0
+https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview
+
+## v0.11.0
+
+ * New Features
+    * Enable creation of disease annotation; 1st & 2nd iteration pop-up (SCRUM-1709, SCRUM-1903)
+    * Enabled simple deletion of disease annotations (SCRUM-1890)
+    * Condition Summaries & Unique IDs for Experimental Conditions (plan to retire Condition Statements)
+       * Generate consistent condition_summary entries for experimental conditions (SCRUM-2036)
+       * Generate consistent unique_id values for experimental conditions (SCRUM-2037)
+       * Clean up experimental conditions (redundant entries + usage of condition_summary in place of condition_statement) (SCRUM-2038)
+       * Add tooltip to condition autosuggest options to display unique_id values for each experimental condition displayed (SCRUM-2040)
+       * Replace experimental condition autosuggest display with condition_summary instead of condition_statement (SCRUM-2039)
+    * Add display of compatible LinkML schema versions (SCRUM-2091)
+ * Fixes
+    * Fix broken autocomplete for experimental conditions (SCRUM-2089)
+    * Fix sort order of data loads by reverse chronological order (SCRUM-2010)
+    * Fix missing ontologies from dashboard (SCRUM-2076)
+    * Fix blank screen bug in Data Loads widget (SCRUM-2042)
+    * Clean up and address stale file loads in Data Loads widget (SCRUM-2004)
+
+## v0.10.0
 
  * New features
+    * Enabled disease annotation deletion (through UI) (SCRUM-1890)
+    * Enabled disease annotation creation (through UI) (SCRUM-1709)
+ * Data and schema changes
+    * Synchronised curation application data model with LinkML schema v1.2.4 (SCRUM-1926)
+ * Bugfixes, minor enhancements & maintenance
+    * Enabled preventing disease-annotation save without reference/subject/object (SCRUM-1916)
+    * Added additional integration tests for required fields (SCRUM-1939)
+    * Minor indexing improvements (for the index everything endpoint)
+    * Minor deployment notification fixes
+    * Updated data validation to treat empty strings as empty values (SCRUM-1942)
+    * Updated bulk load to correctly new null values on update (SCRUM-1975)
+    * Fixed bulk load last loaded date (SCRUM-2000)
+    * Cleanup of inconsistent records in DB (SCRUM-2005)
+    * Fixed experimentalConditions UI filter (SCRUM-2003)
+    * Fixed file sorting in data loads widget (SCRUM-2010)
+    * Added additional note reference validation (SCRUM-2028)
 
-    * Enabled deletion of relations in Condition Relation table (SCRUM-1605)
+## v0.9.0
 
+ * New features
+    * Enabled deletion of relations in Condition Relation table (SCRUM-1605)
     * Enabled creation of Experimental Conditions (SCRUM-1848, SCRUM-1849, SCRUM-1850)
-
     * Added ATP ontology (SCRUM-1840)
-
     * Automatic population of createdBy field when creating new entries (SCRUM-1868)
-
     * Repurposed Condition Relation Handles table for all Condition Relations, with or without handle (SCRUM-1867)
-
     * Enabled deletion of controlled vocabulary terms (SCRUM-1889)
-
     * Added parents, ancestors, and closure to ontologies
-
     * Enabled per-class reporting of LinkML schema version compatibility
 
  * Bugfixes, minor enhancements & maintenance
-
     * API updates to enable deletion of disease annotations (SCRUM-1711)
-
     * Improved filter functionality for Experiments and Experimental Conditions columns in Disease Annotation table (SCRUM-1816)
 
 ## v0.8.0
@@ -48,7 +79,7 @@
     * SCRUM-1765 Bring functionality of editing of 'related notes' in Disease Annotation table in line with that of 'condition relations' by @markquintontulloch in #559
  * Maintenance
     * SCRUM-1712 Synchronisation of References with Literature System by @markquintontulloch in #552, #557, #561, #564
-    # SCRUM-1732 Fixed validation of references in conditionRelations #560
+    * SCRUM-1732 Fixed validation of references in conditionRelations #560
     * SCRUM-1710 Fixed multiple tooltips bug by @markquintontulloch in #565
     * SCRUM-1722 Fixed multi-line cell warnings bug by @adamgibs in #562
     * Added indexing params to reindexing endpoints by @mluypaert in #555

diff --git a/pom.xml b/pom.xml
@@ -25,7 +25,7 @@
 		<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>2.10.0.Final</quarkus.platform.version>
+		<quarkus.platform.version>2.13.3.Final</quarkus.platform.version>
 		<surefire-plugin.version>3.0.0-M5</surefire-plugin.version>
 	</properties>
 
@@ -217,7 +217,6 @@
 		<dependency>
 			<groupId>io.rest-assured</groupId>
 			<artifactId>rest-assured</artifactId>
-			<scope>test</scope>
 		</dependency>
 
 		<dependency>
@@ -353,9 +352,7 @@
 			<artifactId>reflections</artifactId>
 			<version>0.10.2</version>
 		</dependency>
-
-
-	</dependencies>
+    </dependencies>
 
 	<build>
 		<finalName>${project.artifactId}</finalName>

diff --git a/src/main/cliapp/src/components/Autocomplete/AutocompleteRowEditor.js b/src/main/cliapp/src/components/Autocomplete/AutocompleteRowEditor.js
@@ -29,7 +29,7 @@ export const AutocompleteRowEditor = (
 	const [query, setQuery] = useState();
 	const [fieldValue, setFieldValue] = useState(() => {
 			if(!rowProps) return "";
-			if (isReference)
+			if (isReference && !isMultiple)
 				return getRefString(rowProps.rowData[fieldName]);
 			return isMultiple ?
 				rowProps.rowData[fieldName] :

diff --git a/src/main/cliapp/src/components/ConditionRelationHandleFormSelector.js b/src/main/cliapp/src/components/ConditionRelationHandleFormSelector.js
@@ -0,0 +1,48 @@
+import React, { useState } from 'react';
+import { Dropdown } from "primereact/dropdown"
+import { SearchService } from '../service/SearchService';
+
+export function ConditionRelationHandleFormDropdown({ editorChange, referenceCurie, value, name, showClear, placeholderText, isEnabled, customRef }) {
+	const [selectedValue, setSelectedValue] = useState(value);
+	const searchService = new SearchService();
+	const [handles, setHandles] = useState(null);
+
+	const onShow = () => {
+			searchService.find(
+				"condition-relation",
+				15,
+				0,
+				{"singleReference.curie": referenceCurie}
+			).then((data) => {
+				if (data.results?.length > 0) {
+					setHandles(data.results);
+				} else {
+					setHandles(null);
+				}
+			})
+	}
+
+	const onChange = (e) => {
+		setSelectedValue(e.value);
+		editorChange(e);
+	}
+
+	return (
+		<>
+			<Dropdown
+				ref={customRef}
+				name={name}
+				value={selectedValue}
+				disabled={!isEnabled}
+				options={handles}
+				onShow={onShow}
+				onChange={(e) => onChange(e)}
+				optionLabel="handle"
+				showClear={showClear}
+				placeholder={placeholderText}
+				style={{ width: '100%' }}
+			/>
+		</>
+	)
+}
+
diff --git a/src/main/cliapp/src/components/ConditionRelationHandleSelector.js b/src/main/cliapp/src/components/ConditionRelationHandleSelector.js
@@ -7,8 +7,8 @@ export function ConditionRelationHandleDropdown({ field, options, editorChange,
 		const [selectedValue, setSelectedValue] = useState(props.rowData[field]);
 		const searchService = new SearchService();
 		const [handles, setHandles] = useState(null);
-			
-			
+
+
 		const onShow = () => {
 				setSelectedValue(props.rowData[field])
 				if (props.props.value[props.rowIndex]?.singleReference?.curie) {

diff --git a/src/main/cliapp/src/components/GenericDataTable/GenericDataTable.js b/src/main/cliapp/src/components/GenericDataTable/GenericDataTable.js
@@ -16,7 +16,7 @@ import { useGenericDataTable } from "./useGenericDataTable";
 
 export const GenericDataTable = (props) => {
 
-	const { tableName, isEnabled, aggregationFields, endpoint, columns, headerButtons, deletionEnabled } = props;
+	const { tableName, isEnabled, aggregationFields, endpoint, columns, headerButtons, deletionEnabled, dataKey = 'id' } = props;
 
 	const {
 		setSelectedColumnNames,
@@ -126,7 +126,7 @@ export const GenericDataTable = (props) => {
 	}
 
 	const showDeleteDialog = (props) => {
-		let _idToDelete = props.rowData ? props.rowData.id : props.id;
+		let _idToDelete = props.rowData ? props.rowData[dataKey] : props[dataKey];
 		setIdToDelete(_idToDelete);
 		setEntityToDelete(props);
 		setDeleteDialog(true);
@@ -158,24 +158,24 @@ export const GenericDataTable = (props) => {
 
 	const deleteDialogFooter = () => {
 		return (
-        	<React.Fragment>
-            	<Button label="Cancel" icon="pi pi-times" className="p-button-text" onClick={hideDeleteDialog} />
-            	<Button label="Confirm" icon="pi pi-check" className="p-button-text" onClick={() => deleteRow(idToDelete, entityToDelete)} />
-        	</React.Fragment>
-    	);
+					<React.Fragment>
+							<Button label="Cancel" icon="pi pi-times" className="p-button-text" onClick={hideDeleteDialog} />
+							<Button label="Confirm" icon="pi pi-check" className="p-button-text" onClick={() => deleteRow(idToDelete, entityToDelete)} />
+					</React.Fragment>
+			);
 	}
 
 	const errorDialogFooter = () => {
 		return (
-        	<React.Fragment>
-            	<Button label="OK" icon="pi pi-times" className="p-button-text" onClick={hideErrorDialog} />
-            </React.Fragment>
-    	);
+					<React.Fragment>
+							<Button label="OK" icon="pi pi-times" className="p-button-text" onClick={hideErrorDialog} />
+						</React.Fragment>
+			);
 	}
 	return (
 			<div className="card">
 				<Toast ref={toast_topright} position="top-right" />
-				<DataTable dataKey='id' value={entities} header={header} ref={dataTable}
+				<DataTable dataKey={dataKey} value={entities} header={header} ref={dataTable}
 					filterDisplay="row" scrollHeight="62vh" scrollable= {true} tableClassName='p-datatable-md'
 					editMode= "row" onRowEditInit= {onRowEditInit} onRowEditCancel= {onRowEditCancel}
 					onRowEditSave= {onRowEditSave} editingRows={editingRows} onRowEditChange={onRowEditChange}
@@ -199,21 +199,21 @@ export const GenericDataTable = (props) => {
 				</DataTable>
 
 			 <Dialog visible={deleteDialog} style={{ width: '450px' }} header="Confirm Deletion" modal footer={deleteDialogFooter} onHide={hideDeleteDialog}>
-                <div className="confirmation-content">
-                    <i className="pi pi-exclamation-triangle mr-3" style={{ fontSize: '2rem'}} />
-                    {<span>Warning: You are about to delete this data object from the database. This cannot be undone. Please confirm deletion or cancel.</span>}
-                </div>
-            </Dialog>
+								<div className="confirmation-content">
+										<i className="pi pi-exclamation-triangle mr-3" style={{ fontSize: '2rem'}} />
+										{<span>Warning: You are about to delete this data object from the database. This cannot be undone. Please confirm deletion or cancel.</span>}
+								</div>
+						</Dialog>
 			<Dialog visible={errorDialog} style={{ width: '450px' }} header="Deletion Error" modal footer={errorDialogFooter} onHide={hideErrorDialog}>
-                <div className="error-message-dialog">
-                    <i className="pi pi-ban mr-3" style={{ fontSize: '2rem'}} />
-                    {<span>ERROR: The data object you are trying to delete is in use by other data objects. Remove data connections to all other data objects and try to delete again.</span>}
-                </div>
+								<div className="error-message-dialog">
+										<i className="pi pi-ban mr-3" style={{ fontSize: '2rem'}} />
+										{<span>ERROR: The data object you are trying to delete is in use by other data objects. Remove data connections to all other data objects and try to delete again.</span>}
+								</div>
 				<hr/>
 				<div className="error-message-detail">
 					{<span style={{fontSize: '0.85rem'}}>{deletionErrorMessage}</span>}
 				</div>
-            </Dialog>
+						</Dialog>
 			</div>
 	)
 }

diff --git a/src/main/cliapp/src/components/GenericDataTable/useGenericDataTable.js b/src/main/cliapp/src/components/GenericDataTable/useGenericDataTable.js
@@ -70,22 +70,6 @@ export const useGenericDataTable = ({
 
 	const { toast_topleft, toast_topright } = toasts;
 
-
-	useQuery([`${tableState.tableKeyName}Aggregations`, aggregationFields, tableState],
-		() => searchService.search(endpoint, 0, 0, null, {}, {}, aggregationFields), {
-		onSuccess: (data) => {
-		},
-		onError: (error) => {
-			toast_topleft.current.show([
-				{ life: 7000, severity: 'error', summary: 'Page error: ', detail: error.message, sticky: false }
-			]);
-		},
-		keepPreviousData: true,
-		refetchOnWindowFocus: false,
-		enabled: !!(tableState)
-	}
-	);
-
 	useQuery([tableState.tableKeyName, tableState],
 		() => searchService.search(endpoint, tableState.rows, tableState.page, tableState.multiSortMeta, tableState.filters, sortMapping, [], nonNullFieldsTable), {
 		onSuccess: (data) => {
@@ -107,7 +91,7 @@ export const useGenericDataTable = ({
 		if (
 			!tableState.filters
 			|| Object.keys(tableState.filters).length > 0
-			|| tableState.multiSortMeta.length > 0
+			|| (tableState.multiSortMeta && tableState.multiSortMeta.length > 0)
 			|| tableState.page > 0
 			|| !newEntity
 		) return;

diff --git a/src/main/cliapp/src/components/TrueFalseDropDownSelector.js b/src/main/cliapp/src/components/TrueFalseDropDownSelector.js
@@ -1,7 +1,7 @@
 import React, { useState } from 'react';
 import { Dropdown } from "primereact/dropdown"
 
-export function TrueFalseDropdown({ field, options, editorChange, props }) {
+export function TrueFalseDropdown({ field, options, showClear = false, editorChange, props }) {
 		const [selectedValue, setSelectedValue] = useState(props.rowData[field]);
 
 		const onShow = () => {
@@ -21,7 +21,8 @@ export function TrueFalseDropdown({ field, options, editorChange, props }) {
 								onShow={onShow}
 								onChange={(e) => onChange(e)}
 								optionLabel="text"
-								placeholder={JSON.stringify(props.rowData[field])}
+								showClear={showClear}
+								placeholder={selectedValue === null ? '' : JSON.stringify(selectedValue)}
 								style={{ width: '100%' }}
 						/>
 				</>