Merge pull request #1214 from alliance-genome/release/v0.23.0

Release/v0.23.0

README.md

@@ -461,7 +461,7 @@ the new version of the application can function in a consistent state upon and a
  ```
  3. Check the logs for errors after app-server restart, which could indicate a DB restore failure
  and troubleshoot accordingly if necessary to fix any errors.
-3. Connect to the Environment's search domain and delete all indexes. A link to the Cerebro view into each environment's search indexes is available in the curation interface under `Other Links` > `Elastic Search UI` (VPN connection required).
+3. Connect to the Environment's search domain and delete all indexes. A link to the Cerebro view into each environment's search indexes is available in the curation interface under `Developer Links` > `Search index UI (cerebro)` (VPN connection required).
  Alternatively, you can reach this UI manually by browsing to the [AGR Cerebro interface](http://cerebro.alliancegenome.org:9000) and entering the environment's domain endpoint manually. The domain endpoint URL can be found through the [Amazon OpenSearch console](https://us-east-1.console.aws.amazon.com/aos/home?region=us-east-1#opensearch/domains).
 4. Tag and create the release in git and gitHub, as described in the [Release creation](#release-creation) section.
 5. Check the logs for the environment that you're releasing to and ensure the application started successfully

RELEASE-NOTES.md

@@ -2,6 +2,17 @@
 
 https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview
 
+## v0.23.0
+ * New features
+ * "Vocabulary Label" field added to vocabularies and vocabulary term sets (SCRUM-3167)
+ * Created Allele Detail page (SCRUM-3009)
+ * Enabled display and editing of simple properties on Allele Detail page (SCRUM-3121)
+ * Display short citation in human-readable values of reference field (SCRUM-2784)
+
+ * Fixes and maintenance
+ * Fixed display of load status in summary row (SCRUM-3117)
+ * Fixed reporting of load failures due to invalid URL (SCRUM-2248) 
+
 ## v0.22.0
  * New features
  * Loaded orthology data (SCRUM-2710)

src/main/cliapp/src/components/Editors/inCollection/InCollectionFormEditor.js

@@ -0,0 +1,40 @@
+import React from 'react';
+import { AutocompleteFormEditor } from '../../Autocomplete/AutocompleteFormEditor';
+import { inCollectionSearch } from './utils';
+import { FormErrorMessageComponent } from '../../Error/FormErrorMessageComponent';
+import { InCollectionAdditionalFieldData } from '../../FieldData/InCollectionAdditionalFieldData';
+import { VocabTermAutocompleteTemplate } from '../../Autocomplete/VocabTermAutocompleteTemplate';
+
+export const InCollectionFormEditor = ({ 
+ inCollection, 
+ onInCollectionValueChange, 
+ widgetColumnSize, 
+ labelColumnSize, 
+ fieldDetailsColumnSize, 
+ errorMessages 
+ }) => {
+
+ return (
+ <div className="grid">
+ <div className={labelColumnSize}>
+ <label htmlFor="inCollection">In Collection</label>
+ </div>
+ <div className={widgetColumnSize}>
+ <AutocompleteFormEditor
+ name="inCollection-input"
+ search={inCollectionSearch}
+ initialValue={inCollection}
+ fieldName='inCollection'
+ subField='name'
+ onValueChangeHandler={onInCollectionValueChange}
+ valueDisplay={(item, setAutocompleteSelectedItem, op, query) =>
+ <VocabTermAutocompleteTemplate item={item} op={op} query={query} setAutocompleteSelectedItem={setAutocompleteSelectedItem}/>}
+ />
+ <FormErrorMessageComponent errorMessages={errorMessages} errorField={"inCollection"}/>
+ </div>
+ <div className={fieldDetailsColumnSize}>
+ <InCollectionAdditionalFieldData name={inCollection?.name}/>
+ </div>
+ </div>
+ )
+}

src/main/cliapp/src/components/Editors/inCollection/utils.js

@@ -0,0 +1,19 @@
+import { buildAutocompleteFilter, autocompleteSearch } from "../../../utils/utils"; 
+import { SearchService } from "../../../service/SearchService";
+
+export const inCollectionSearch = (event, setFiltered, setQuery) => {
+ const searchService = new SearchService();
+ const autocompleteFields = ["name"];
+ const endpoint = "vocabularyterm";
+ const filterName = "taxonFilter";
+ const otherFilters = {
+ vocabularyFilter: {
+ "vocabulary.name": {
+ queryString: "Allele collection vocabulary"
+ }
+ }
+ }
+ setQuery(event.query);
+ const filter = buildAutocompleteFilter(event, autocompleteFields);
+ autocompleteSearch(searchService, endpoint, filterName, filter, setFiltered, otherFilters);
+}

src/main/cliapp/src/components/Editors/internal/InternalFormEditor.js

@@ -0,0 +1,38 @@
+import React from 'react';
+import { FormErrorMessageComponent } from '../../Error/FormErrorMessageComponent';
+import { Dropdown } from 'primereact/dropdown';
+import { InternalAdditionalFieldData } from '../../FieldData/InternalAdditionalFieldData';
+
+export const InternalFormEditor = ({ 
+ internal, 
+ onInternalValueChange, 
+ booleanTerms,
+ widgetColumnSize, 
+ labelColumnSize, 
+ fieldDetailsColumnSize, 
+ errorMessages 
+ }) => {
+
+ return (
+ <div className="grid">
+ <div className={labelColumnSize}>
+ <label htmlFor="internal">Internal</label>
+ </div>
+ <div className={widgetColumnSize}>
+ <Dropdown
+ name="internal"
+ value={internal}
+ options={booleanTerms}
+ optionLabel='text'
+ optionValue='name'
+ onChange={onInternalValueChange}
+ />
+ <FormErrorMessageComponent errorMessages={errorMessages} errorField={"internal"}/>
+ </div>
+ <div className={fieldDetailsColumnSize}>
+ <InternalAdditionalFieldData internal={internal?.toString()}/>
+ </div>
+ </div>
+
+ )
+}

src/main/cliapp/src/components/Editors/isExtinct/IsExtinctFormEditor.js

@@ -0,0 +1,37 @@
+import React from 'react';
+import { FormErrorMessageComponent } from '../../Error/FormErrorMessageComponent';
+import { IsExtinctAdditionalFieldData } from '../../FieldData/IsExtinctAdditionalFieldData';
+import { Dropdown } from 'primereact/dropdown';
+
+export const IsExtinctFormEditor = ({ 
+ isExtinct, 
+ onIsExtinctValueChange, 
+ booleanTerms,
+ widgetColumnSize, 
+ labelColumnSize, 
+ fieldDetailsColumnSize, 
+ errorMessages 
+ }) => {
+
+ return (
+ <div className="grid">
+ <div className={labelColumnSize}>
+ <label htmlFor="isExtinct">Is Extinct</label>
+ </div>
+ <div className={widgetColumnSize}>
+ <Dropdown
+ name="isExtinct"
+ value={isExtinct}
+ options={booleanTerms}
+ optionLabel='text'
+ optionValue='name'
+ onChange={onIsExtinctValueChange}
+ />
+ <FormErrorMessageComponent errorMessages={errorMessages} errorField={"isExtinct"}/>
+ </div>
+ <div className={fieldDetailsColumnSize}>
+ <IsExtinctAdditionalFieldData isExtinct={isExtinct?.toString()}/>
+ </div>
+ </div>
+ )
+}

src/main/cliapp/src/components/Editors/obsolete/ObsoleteFormEditor.js

@@ -0,0 +1,38 @@
+import React from 'react';
+import { FormErrorMessageComponent } from '../../Error/FormErrorMessageComponent';
+import { Dropdown } from 'primereact/dropdown';
+import { ObsoleteAdditionalFieldData } from '../../FieldData/ObsoleteAdditionalFieldData';
+
+export const ObsoleteFormEditor = ({ 
+ obsolete, 
+ onObsoleteValueChange, 
+ booleanTerms,
+ widgetColumnSize, 
+ labelColumnSize, 
+ fieldDetailsColumnSize, 
+ errorMessages 
+ }) => {
+
+ return (
+ <div className="grid">
+ <div className={labelColumnSize}>
+ <label htmlFor="obsolete">Obsolete</label>
+ </div>
+ <div className={widgetColumnSize}>
+ <Dropdown
+ name="obsolete"
+ value={obsolete}
+ options={booleanTerms}
+ optionLabel='text'
+ optionValue='name'
+ onChange={onObsoleteValueChange}
+ />
+ <FormErrorMessageComponent errorMessages={errorMessages} errorField={"obsolete"}/>
+ </div>
+ <div className={fieldDetailsColumnSize}>
+ <ObsoleteAdditionalFieldData obsolete={obsolete?.toString()}/>
+ </div>
+ </div>
+
+ )
+}

src/main/cliapp/src/components/Editors/references/ReferencesFormEditor.js

@@ -0,0 +1,39 @@
+import React from "react"
+import { AutocompleteFormMultiEditor } from '../../Autocomplete/AutocompleteFormMultiEditor';
+import { LiteratureAutocompleteTemplate } from "../../Autocomplete/LiteratureAutocompleteTemplate";
+import { FormErrorMessageComponent } from "../../Error/FormErrorMessageComponent";
+import { ReferencesAdditionalFieldData } from "../../FieldData/ReferencesAdditionalFieldData";
+import { referenceSearch } from "./utils";
+
+export const ReferencesFormEditor = ({ 
+ references, 
+ onReferencesValueChange, 
+ widgetColumnSize, 
+ labelColumnSize, 
+ fieldDetailsColumnSize, 
+ errorMessages 
+ }) => {
+
+ return (
+ <div className="grid">
+ <div className={labelColumnSize}>
+ <label htmlFor="referenes">References</label>
+ </div>
+ <div className={widgetColumnSize}>
+ <AutocompleteFormMultiEditor
+ search={referenceSearch}
+ initialValue={references}
+ fieldName='references'
+ valueDisplay={(item, setAutocompleteHoverItem, op, query) =>
+ <LiteratureAutocompleteTemplate item={item} setAutocompleteHoverItem={setAutocompleteHoverItem} op={op} query={query}/>}
+ onValueChangeHandler={onReferencesValueChange}
+ />
+ <FormErrorMessageComponent errorMessages={errorMessages} errorField={"references"}/>
+ </div>
+ <div className={fieldDetailsColumnSize}>
+ <ReferencesAdditionalFieldData references={references}/>
+ </div>
+ </div>
+
+ )
+}

src/main/cliapp/src/components/Editors/references/utils.js

@@ -0,0 +1,13 @@
+import { buildAutocompleteFilter, autocompleteSearch } from "../../../utils/utils"; 
+import { SearchService } from "../../../service/SearchService";
+
+export const referenceSearch = (event, setFiltered, setInputValue) => {
+ const searchService = new SearchService();
+ const autocompleteFields = ["curie", "cross_references.curie"];
+ const endpoint = "literature-reference";
+ const filterName = "curieFilter";
+ const filter = buildAutocompleteFilter(event, autocompleteFields);
+
+ setInputValue(event.query);
+ autocompleteSearch(searchService, endpoint, filterName, filter, setFiltered);
+ }

src/main/cliapp/src/components/Editors/taxon/TaxonFormEditor.js

@@ -0,0 +1,36 @@
+import React from 'react';
+import { AutocompleteFormEditor } from '../../Autocomplete/AutocompleteFormEditor';
+import { taxonSearch } from './utils';
+import { FormErrorMessageComponent } from '../../Error/FormErrorMessageComponent';
+import { TaxonAdditionalFieldData } from '../../FieldData/TaxonAdditionalFieldData';
+
+export const TaxonFormEditor = ({ 
+ taxon, 
+ onTaxonValueChange, 
+ widgetColumnSize, 
+ labelColumnSize, 
+ fieldDetailsColumnSize, 
+ errorMessages 
+ }) => {
+
+ return (
+ <div className="grid">
+ <div className={labelColumnSize}>
+ <label htmlFor="taxon">Taxon</label>
+ </div>
+ <div className={widgetColumnSize}>
+ <AutocompleteFormEditor
+ name="taxon-input"
+ search={taxonSearch}
+ initialValue={taxon}
+ fieldName='taxon'
+ onValueChangeHandler={onTaxonValueChange}
+ />
+ <FormErrorMessageComponent errorMessages={errorMessages} errorField={"taxon"}/>
+ </div>
+ <div className={fieldDetailsColumnSize}>
+ <TaxonAdditionalFieldData curie={taxon?.curie}/>
+ </div>
+ </div>
+ )
+}

src/main/cliapp/src/components/Editors/taxon/utils.js

@@ -0,0 +1,13 @@
+import { buildAutocompleteFilter, autocompleteSearch } from "../../../utils/utils"; 
+import { SearchService } from "../../../service/SearchService";
+
+
+export const taxonSearch = (event, setFiltered, setQuery) => {
+ const searchService = new SearchService();
+ const autocompleteFields = ["curie", "name", "crossReferences.referencedCurie", "secondaryIdentifiers", "synonyms.name"];
+ const endpoint = "ncbitaxonterm";
+ const filterName = "taxonFilter";
+ setQuery(event.query);
+ const filter = buildAutocompleteFilter(event, autocompleteFields);
+ autocompleteSearch(searchService, endpoint, filterName, filter, setFiltered);
+}

src/main/cliapp/src/components/EntityDetailsAction.js

@@ -0,0 +1,17 @@
+import { Link } from 'react-router-dom/cjs/react-router-dom.min';
+import { Tooltip } from 'primereact/tooltip';
+
+export const EntityDetailsAction = ({ curie, disabled }) =>{
+ const disabledClasses = disabled ? "pointer-events-none opacity-50" : "";
+
+ if (!curie) return null;
+
+ return (
+ <>
+ <Link to={`allele/${curie}`} target="_blank" className={`${curie.replace(':', '')} ${disabledClasses}`}>
+ <i className="pi pi-info"></i>
+ </Link>
+ <Tooltip target={`.${curie.replace(':', '')}`} content= {"Open Details"} />
+ </>
+ );
+};

src/main/cliapp/src/components/EvidenceComponent.js

@@ -2,7 +2,7 @@ import React from 'react'
 import { EllipsisTableCell } from './EllipsisTableCell';
 import { ListTableCell } from './ListTableCell';
 import { AutocompleteMultiEditor } from './Autocomplete/AutocompleteMultiEditor';
-import { DialogErrorMessageComponent } from './DialogErrorMessageComponent';
+import { DialogErrorMessageComponent } from './Error/DialogErrorMessageComponent';
 import { SearchService } from '../service/SearchService';
 import { autocompleteSearch, buildAutocompleteFilter, multipleAutocompleteOnChange, getRefStrings } from '../utils/utils';
 import { LiteratureAutocompleteTemplate } from './Autocomplete/LiteratureAutocompleteTemplate';

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

@@ -0,0 +1,6 @@
+import React from 'react';
+
+export const InCollectionAdditionalFieldData = ({ name }) => {
+ if(!name) return null;
+ return <div className="p-info">{name}</div>;
+};

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

@@ -0,0 +1,6 @@
+import React from 'react';
+
+export const InternalAdditionalFieldData = ({ internal }) => {
+ if(!internal) return null;
+ return <div className="p-info">{internal}</div>;
+};

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

@@ -0,0 +1,6 @@
+import React from 'react';
+
+export const IsExtinctAdditionalFieldData = ({ isExtinct }) => {
+ if(!isExtinct) return null;
+ return <div className="p-info">{isExtinct}</div>;
+};

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

@@ -0,0 +1,6 @@
+import React from 'react';
+
+export const ObsoleteAdditionalFieldData = ({ obsolete }) => {
+ if(!obsolete) return null;
+ return <div className="p-info">{obsolete}</div>;
+};

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

@@ -0,0 +1,15 @@
+import React from 'react';
+import { SingleReferenceAdditionalFieldData } from "./SingleReferenceAdditionalFieldData";
+
+export const ReferencesAdditionalFieldData = ({ references }) => {
+
+ const referencesDivs = references?.map((reference) => {
+ return (
+ <div key={reference.curie}>
+ <SingleReferenceAdditionalFieldData key={reference.curie} fieldData={reference} />
+ </div>
+ )
+ })
+
+ return referencesDivs || null;
+};

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

@@ -0,0 +1,6 @@
+import React from "react";
+
+export const TaxonAdditionalFieldData = ({ curie }) => {
+ if(!curie) return null;
+ return <div className="p-info">{curie}</div>;
+}