Merge pull request #1475 from alliance-genome/release/v0.31.0

Release/v0.31.0
alliance-genome · Mar 25, 2024 · bc758e5 · bc758e5
2 parents ffe7813 + a067d7d
commit bc758e5
Show file tree

Hide file tree

Showing 982 changed files with 12,375 additions and 4,705 deletions.
diff --git a/.github/workflows/alpha-build-and-deploy.yml b/.github/workflows/alpha-build-and-deploy.yml
@@ -22,14 +22,14 @@ jobs:
     # This step will configure environment variables to be used by all steps
     # involving AWS interaction further down
     - name: AWS credentials configuration
-      uses: aws-actions/configure-aws-credentials@v2
+      uses: aws-actions/configure-aws-credentials@v4
       with:
         role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
         role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-build-image
         aws-region: us-east-1
     - name: Amazon ECR login
       id: login-ecr
-      uses: aws-actions/amazon-ecr-login@v1
+      uses: aws-actions/amazon-ecr-login@v2
     - name: Build, tag, and push image to Amazon ECR
       env:
         ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
@@ -46,7 +46,7 @@ jobs:
       - name: Check out repository code
         uses: actions/checkout@v3
       - name: Set up Maven Central Repository
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -109,7 +109,7 @@ jobs:
     - name: Generate deployment package
       run: zip -r ${{ env.tagname }}.zip docker-compose.yml .ebextensions/
     - name: AWS credentials configuration
-      uses: aws-actions/configure-aws-credentials@v2
+      uses: aws-actions/configure-aws-credentials@v4
       with:
         role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
         role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-eb-deploy

diff --git a/.github/workflows/github-actions-PR-validation.yml b/.github/workflows/github-actions-PR-validation.yml
@@ -32,7 +32,7 @@ jobs:
           git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
           git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
       - name: Set up JDK 17
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'temurin'

diff --git a/.github/workflows/github-release-build-and-deploy.yml b/.github/workflows/github-release-build-and-deploy.yml
@@ -11,14 +11,14 @@ jobs:
     - name: Check out repository code
       uses: actions/checkout@v3
     - name: AWS credentials configuration
-      uses: aws-actions/configure-aws-credentials@v2
+      uses: aws-actions/configure-aws-credentials@v4
       with:
         role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
         role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-build-image
         aws-region: us-east-1
     - name: Amazon ECR login
       id: login-ecr
-      uses: aws-actions/amazon-ecr-login@v1
+      uses: aws-actions/amazon-ecr-login@v2
     - name: Build, tag, and push image to Amazon ECR
       env:
         ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
@@ -36,7 +36,7 @@ jobs:
       - name: Check out repository code
         uses: actions/checkout@v3
       - name: Set up Maven Central Repository
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -69,7 +69,7 @@ jobs:
     - name: Generate deployment package
       run: zip -r ${{ github.event.release.tag_name }}.zip docker-compose.yml .ebextensions/
     - name: Store deployment package in cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ github.event.release.tag_name }}.zip
         key: ${{github.workflow}}.${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-eb-deployment-zip
@@ -81,12 +81,12 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
     - name: Fetch deployment package from cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ github.event.release.tag_name }}.zip
         key: ${{github.workflow}}.${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-eb-deployment-zip
     - name: AWS credentials configuration
-      uses: aws-actions/configure-aws-credentials@v2
+      uses: aws-actions/configure-aws-credentials@v4
       with:
         role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
         role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-eb-deploy-production
@@ -117,12 +117,12 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
     - name: Fetch deployment package from cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ github.event.release.tag_name }}.zip
         key: ${{github.workflow}}.${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-eb-deployment-zip
     - name: AWS credentials configuration
-      uses: aws-actions/configure-aws-credentials@v2
+      uses: aws-actions/configure-aws-credentials@v4
       with:
         role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}}
         role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-eb-deploy-beta

diff --git a/.github/workflows/release-PR-merge-actions.yml b/.github/workflows/release-PR-merge-actions.yml
@@ -15,7 +15,7 @@ jobs:
       latestrelease: ${{ steps.releaseflags.outputs.latestrelease }}
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Generate release tag name (as step output)
         id: tagname
         shell: bash
@@ -51,7 +51,7 @@ jobs:
       tagmessage: ''
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Generate and store release message
         shell: bash
         run: |
@@ -86,7 +86,7 @@ jobs:
       mergeback-basebranchname: "alpha"
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}

diff --git a/Makefile b/Makefile
@@ -46,7 +46,7 @@ uirunlomu:
 run: docker-run
 
 apirun:
-	mvn compile quarkus:dev
+	mvn compile quarkus:dev -Djvm.args="-XX:ReservedCodeCacheSize=1g"
 
 docker:
 	docker build --build-arg OVERWRITE_VERSION=${GIT_VERSION} -t ${REG}/agr_curation:${RELEASE} .

diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -3,6 +3,22 @@
 https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview
 
 
+## v0.31.0
+* New features
+  * Replaced Negated column/field with NOT in disease annotation table and new annotation form (SCRUM-3794)
+  * Enabled loading of AGM Phenotype Annotations from FMS (SCRUM-3712)
+  * Added restrictions to Allele Gene Associations to prevent duplicate associations or multiple is_allele_of associations (SCRUM-3625 & SCRUM-3626)
+  * Added GENO Ontology load (SCRUM-3694)
+  * Establised persistence of new annotation pop-up field visibility settings for disease annotations (SCRUM-3661)
+* Fixes and maintenance
+  * Aligned codebase with LinkML v2.2.0 (SCRUM-3515)
+  * Fixed WB Molecular bulk load error (SCRUM-3823)
+  * Added warning and provided openAPI definition download link on Swagger page (SCRUM-3779)
+  * Automated cleanup of exception messages from old submissions (SCRUM-3795)
+  * Removed unnecessary glyphs from ontology tree where no child terms (SCRUM-3249)
+  * Improved speed of closure queries to address failing ontology loads (SCRUM-3780)
+  * Improved speed of ID retrieval for data cleanup (SCRUM-3770)
+
 ## v0.30.0
 * New features
    * Enable "New Annotation" pop-up field-visibility custom settings for disease annotations (SCRUM-2680)

diff --git a/pom.xml b/pom.xml
@@ -154,10 +154,6 @@
 			<groupId>io.quarkus</groupId>
 			<artifactId>quarkus-resteasy-multipart</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>io.quarkus</groupId>
-			<artifactId>quarkus-hibernate-envers</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>io.quarkus</groupId>
 			<artifactId>quarkus-jdbc-postgresql</artifactId>

diff --git a/src/main/cliapp/src/components/Actions/EntityDetailsAction.js b/src/main/cliapp/src/components/Actions/EntityDetailsAction.js
@@ -1,17 +1,17 @@
 import { Link } from 'react-router-dom/cjs/react-router-dom.min';
 import { Tooltip } from 'primereact/tooltip';
 
-export const EntityDetailsAction = ({ curie, disabled }) =>{
+export const EntityDetailsAction = ({ identifier, disabled }) =>{
   const disabledClasses = disabled ? "pointer-events-none opacity-50" : "";
 
-  if (!curie) return null;
+  if (!identifier) return null;
 
   return (
     <>
-      <Link to={`allele/${curie}`} target="_blank" className={`${curie.replace(':', '')} ${disabledClasses}`}>
+      <Link to={`allele/${identifier}`} target="_blank" className={`${identifier.replace(':', '')} ${disabledClasses}`}>
         <i className="pi pi-info-circle"></i>
       </Link>
-      <Tooltip target={`.${curie.replace(':', '')}`} content= {"Open Details"} />
+      <Tooltip target={`.${identifier.replace(':', '')}`} content= {"Open Details"} />
     </>
   );
 };
diff --git a/src/main/cliapp/src/components/Autocomplete/AutocompleteEditor.js b/src/main/cliapp/src/components/Autocomplete/AutocompleteEditor.js
@@ -2,6 +2,7 @@ import React, { useRef, useState } from 'react';
 import { AutoComplete } from "primereact/autocomplete";
 import { onSelectionOver } from '../../utils/utils';
 import { EditorTooltip } from "./EditorTooltip";
+import { getIdentifier } from '../../utils/utils';
 
 export const AutocompleteEditor = (
 	{
@@ -29,7 +30,7 @@ export const AutocompleteEditor = (
 		return (
 			<div>
 				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)}
-					dangerouslySetInnerHTML={{ __html: item.name + ' (' + item.curie + ') ' }} />
+					dangerouslySetInnerHTML={{ __html: item.name + ' (' + getIdentifier(item) + ') ' }} />
 			</div>
 		);
 	};

diff --git a/src/main/cliapp/src/components/Autocomplete/AutocompleteFormEditor.js b/src/main/cliapp/src/components/Autocomplete/AutocompleteFormEditor.js
@@ -2,6 +2,7 @@ import React, { useRef, useState } from 'react';
 import { AutoComplete } from "primereact/autocomplete";
 import { onSelectionOver } from '../../utils/utils';
 import { EditorTooltip } from "./EditorTooltip";
+import { getIdentifier } from '../../utils/utils';
 
 export const AutocompleteFormEditor = (
 	{
@@ -29,7 +30,7 @@ export const AutocompleteFormEditor = (
 		return (
 			<div>
 				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)}
-					dangerouslySetInnerHTML={{__html: item.name + ' (' + item.curie + ') '}}/>
+					dangerouslySetInnerHTML={{__html: item.name + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	};

diff --git a/src/main/cliapp/src/components/Autocomplete/AutocompleteFormMultiEditor.js b/src/main/cliapp/src/components/Autocomplete/AutocompleteFormMultiEditor.js
@@ -2,6 +2,7 @@ import React, { useRef, useState } from 'react';
 import { AutoComplete } from "primereact/autocomplete";
 import { onSelectionOver } from '../../utils/utils';
 import { EditorTooltip } from "./EditorTooltip";
+import { getIdentifier } from '../../utils/utils';
 
 export const AutocompleteFormMultiEditor = (
 	{
@@ -29,7 +30,7 @@ export const AutocompleteFormMultiEditor = (
 		return (
 			<div>
 				<div onMouseOver={(event) => onSelectionOver(event, item, inputValue, op, setAutocompleteHoverItem)}
-					dangerouslySetInnerHTML={{__html: item.name + ' (' + item.curie + ') '}}/>
+					dangerouslySetInnerHTML={{__html: item.name + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	};

diff --git a/src/main/cliapp/src/components/Autocomplete/AutocompleteMultiEditor.js b/src/main/cliapp/src/components/Autocomplete/AutocompleteMultiEditor.js
@@ -2,6 +2,7 @@ import React, { useRef, useState } from 'react';
 import { AutoComplete } from "primereact/autocomplete";
 import { onSelectionOver } from '../../utils/utils';
 import { EditorTooltip } from "./EditorTooltip";
+import { getIdentifier } from '../../utils/utils';
 
 export const AutocompleteMultiEditor = (
 	{
@@ -30,7 +31,7 @@ export const AutocompleteMultiEditor = (
 		return (
 			<div>
 				<div onMouseOver={(event) => onSelectionOver(event, item, inputValue, op, setAutocompleteHoverItem)}
-					dangerouslySetInnerHTML={{__html: item.name + ' (' + item.curie + ') '}}/>
+					dangerouslySetInnerHTML={{__html: item.name + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	};

diff --git a/src/main/cliapp/src/components/Autocomplete/EditorTooltip.js b/src/main/cliapp/src/components/Autocomplete/EditorTooltip.js
@@ -1,12 +1,16 @@
 import React from "react";
 import {Tooltip} from "primereact/tooltip";
+import { getIdentifier } from "../../utils/utils";
 
 export const EditorTooltip = ({op, autocompleteHoverItem}) => {
+	const identifier = getIdentifier(autocompleteHoverItem);
+	const identifierText = `Indentifier: ${identifier}`;
+
 	return (
 		<>
 			<Tooltip ref={op} style={{width: '450px', maxWidth: '450px'}} position={'right'} mouseTrack mouseTrackLeft={30}>
-				{autocompleteHoverItem.curie &&
-				<div>Curie: {autocompleteHoverItem.curie}
+				{identifier &&
+				<div>{identifierText}
 					<br/>
 				</div>
 				}

diff --git a/src/main/cliapp/src/components/Autocomplete/SubjectAutocompleteTemplate.js b/src/main/cliapp/src/components/Autocomplete/SubjectAutocompleteTemplate.js
@@ -1,43 +1,42 @@
 import React from 'react';
-import { onSelectionOver } from '../../utils/utils';
+import { onSelectionOver, getIdentifier } from '../../utils/utils';
 
 export const SubjectAutocompleteTemplate = ({ item, setAutocompleteHoverItem, op, query }) => {
-
 	if (item.geneSymbol) {
 		return (
 			<div>
 				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)}
-					dangerouslySetInnerHTML={{__html: item.geneSymbol.displayText + ' (' + item.curie + ') '}}/>
+					dangerouslySetInnerHTML={{__html: item.geneSymbol.displayText + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	} else if (item.alleleSymbol) {
 		return (
 			<div>
-				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.alleleSymbol.displayText + ' (' + item.curie + ') '}}/>
+				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.alleleSymbol.displayText + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	} else if (item.geneFullName) {
 		return (
 			<div>
-				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.geneFullName.displayText + ' (' + item.curie + ') '}}/>
+				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.geneFullName.displayText + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	} else if (item.alleleFullName) {
 		return (
 			<div>
-				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.alleleFullName.displayText + ' (' + item.curie + ') '}}/>
+				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.alleleFullName.displayText + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	} else if (item.name) {
 		return (
 			<div>
-				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.name + ' (' + item.curie + ') '}}/>
+				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.name + ' (' + getIdentifier(item) + ') '}}/>
 			</div>
 		);
 	} else {
 		return (
 			<div>
-				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: item.curie}}/>
+				<div onMouseOver={(event) => onSelectionOver(event, item, query, op, setAutocompleteHoverItem)} dangerouslySetInnerHTML={{__html: getIdentifier(item)}}/>
 			</div>
 		);
 	};

diff --git a/...notationsPage/ConditionRelationsDialog.js → ...rc/components/ConditionRelationsDialog.js b/...notationsPage/ConditionRelationsDialog.js → ...rc/components/ConditionRelationsDialog.js
@@ -5,18 +5,18 @@ import { Column } from 'primereact/column';
 import { Button } from 'primereact/button';
 import { ColumnGroup } from 'primereact/columngroup';
 import { Row } from 'primereact/row';
-import { EllipsisTableCell } from '../../components/EllipsisTableCell';
-import { ListTableCell } from '../../components/ListTableCell';
+import { EllipsisTableCell } from './EllipsisTableCell';
+import { ListTableCell } from './ListTableCell';
 import { Toast } from 'primereact/toast';
-import { useControlledVocabularyService } from '../../service/useControlledVocabularyService';
-import { ValidationService } from '../../service/ValidationService';
-import { DialogErrorMessageComponent } from '../../components/Error/DialogErrorMessageComponent';
-import { TrueFalseDropdown } from '../../components/TrueFalseDropDownSelector';
-import { ControlledVocabularyDropdown } from '../../components/ControlledVocabularySelector';
-import { ExConAutocompleteTemplate } from '../../components/Autocomplete/ExConAutocompleteTemplate';
-import { SearchService } from '../../service/SearchService';
-import {autocompleteSearch, buildAutocompleteFilter, multipleAutocompleteOnChange} from "../../utils/utils";
-import {AutocompleteMultiEditor} from "../../components/Autocomplete/AutocompleteMultiEditor";
+import { useControlledVocabularyService } from '../service/useControlledVocabularyService';
+import { ValidationService } from '../service/ValidationService';
+import { DialogErrorMessageComponent } from './Error/DialogErrorMessageComponent';
+import { TrueFalseDropdown } from './TrueFalseDropDownSelector';
+import { ControlledVocabularyDropdown } from './ControlledVocabularySelector';
+import { ExConAutocompleteTemplate } from './Autocomplete/ExConAutocompleteTemplate';
+import { SearchService } from '../service/SearchService';
+import {autocompleteSearch, buildAutocompleteFilter, multipleAutocompleteOnChange} from "../utils/utils";
+import {AutocompleteMultiEditor} from "./Autocomplete/AutocompleteMultiEditor";
 
 export const ConditionRelationsDialog = ({
 		originalConditionRelationsData, setOriginalConditionRelationsData,