Merge pull request #1198 from alliance-genome/release/v0.23.0-rc1

Release/v0.23.0-rc1

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

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>;
+}