Merge pull request #1276 from alliance-genome/release/v0.25.0

Release/v0.25.0

RELEASE-NOTES.md

@@ -2,6 +2,18 @@
 
 https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview
 
+## v0.25.0
+ * New features
+ * Display and editing of allele synonyms on allele detail page (SCRUM-3126)
+ * Keep the ontology browser term information panel in view while browsing the (SCRUM-3250)
+ * Display uniqueId error message in row edit mode of Disease Annotations table (SCRUM-3248)
+ * Display validation errors of hidden fields in row edit mode (SCRUM-3255)
+ * Enable access to curation API using admin tokens without Okta user (SCRUM-3078)
+ * Enable sorting of references by primary xref (SCRUM-2725)
+ * Fixes and maintenance
+ * Update curation system to align with LinkML v1.8.0 (SCRUM-3156)
+ * Fix short citation display, sorting, and filtering in Literature References table (SCRUM-3247)
+
 ## v0.24.0
  * New features
  * Load and display Allele 'allele_nomenclature_events' attribute (SCRUM-2340)

pom.xml

@@ -387,7 +387,12 @@
  <plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-javadoc-plugin</artifactId>
- <version>2.9.1</version>
+ <version>3.0.1</version>
+ <configuration>
+ <doclint>all,-html,-syntax,-accessibility,-missing</doclint>
+ <failOnError>false</failOnError>
+ <quiet>true</quiet>
+ </configuration>
  <executions>
  <execution>
  <id>attach-javadocs</id>

src/main/cliapp/src/components/Actions/DeletionAction.js

@@ -0,0 +1,8 @@
+import { Button } from "primereact/button";
+
+export const DeleteAction = ({ disabled, deletionHandler, index}) => {
+ return (
+ <Button icon="pi pi-trash" className="p-button-text" disabled={disabled}
+ onClick={(e) => deletionHandler(e, index)} />
+ );
+};

src/main/cliapp/src/components/Editors/ControlledVocabularyEditor.js

@@ -0,0 +1,31 @@
+import { DialogErrorMessageComponent } from "../Error/DialogErrorMessageComponent";
+import { useControlledVocabularyService } from "../../service/useControlledVocabularyService";
+import { ControlledVocabularyDropdown } from '../ControlledVocabularySelector';
+
+export const ControlledVocabularyEditor = ({
+ props,
+ onChangeHandler,
+ errorMessages,
+ rowIndex,
+ vocabType,
+ field,
+ showClear,
+ optionLabel="name"
+}) => {
+ const vocabTerms = useControlledVocabularyService(vocabType);
+
+ return (
+ <>
+ <ControlledVocabularyDropdown
+ field={field}
+ options={vocabTerms}
+ editorChange={onChangeHandler}
+ props={props}
+ showClear={showClear}
+ optionLabel={optionLabel}
+ dataKey='id'
+ />
+ <DialogErrorMessageComponent errorMessages={errorMessages[rowIndex]} errorField={field} />
+ </>
+ );
+};

src/main/cliapp/src/components/Editors/EvidenceEditor.js

@@ -0,0 +1,36 @@
+import { AutocompleteMultiEditor } from "../Autocomplete/AutocompleteMultiEditor";
+import { SearchService } from '../../service/SearchService';
+import { autocompleteSearch, buildAutocompleteFilter } from '../../utils/utils';
+import { LiteratureAutocompleteTemplate } from '../Autocomplete/LiteratureAutocompleteTemplate';
+import { DialogErrorMessageComponent } from "../Error/DialogErrorMessageComponent";
+
+const evidenceSearch = (event, setFiltered, setInputValue) => {
+ const searchService = new SearchService();
+ const autocompleteFields = ["curie", "cross_references.curie"];
+ const endpoint = "literature-reference";
+ const filterName = "evidenceFilter";
+ const filter = buildAutocompleteFilter(event, autocompleteFields);
+
+ setInputValue(event.query);
+ autocompleteSearch(searchService, endpoint, filterName, filter, setFiltered);
+}
+export const EvidenceEditor = ({ props, errorMessages, onChange }) => {
+ return (
+ <>
+ <AutocompleteMultiEditor
+ search={evidenceSearch}
+ initialValue={props?.rowData?.evidence}
+ rowProps={props}
+ fieldName='evidence'
+ subField='curie'
+ valueDisplay={(item, setAutocompleteHoverItem, op, query) =>
+ <LiteratureAutocompleteTemplate item={item} setAutocompleteHoverItem={setAutocompleteHoverItem} op={op} query={query}/>}
+ onValueChangeHandler={onChange}
+ />
+ <DialogErrorMessageComponent
+ errorMessages={errorMessages[props?.rowIndex]}
+ errorField={"evidence"}
+ />
+ </>
+ );
+};

src/main/cliapp/src/components/Editors/InternalEditor.js

@@ -0,0 +1,20 @@
+import { DialogErrorMessageComponent } from "../Error/DialogErrorMessageComponent";
+import { useControlledVocabularyService } from "../../service/useControlledVocabularyService";
+import { TrueFalseDropdown } from "../TrueFalseDropDownSelector";
+
+export const InternalEditor = ({ props, internalOnChangeHandler, errorMessages, rowIndex }) => {
+ const booleanTerms = useControlledVocabularyService("generic_boolean_terms");
+
+ return (
+ <>
+ <TrueFalseDropdown
+ props={props}
+ field="internal"
+ options={booleanTerms}
+ editorChange={internalOnChangeHandler}
+ showClear={false}
+ />
+ <DialogErrorMessageComponent errorMessages={errorMessages[rowIndex]} errorField={"internal"} />
+ </>
+ );
+};

src/main/cliapp/src/components/Editors/TableInputTextEditor.js

@@ -0,0 +1,24 @@
+import { InputText } from "primereact/inputtext";
+import { DialogErrorMessageComponent } from "../Error/DialogErrorMessageComponent";
+import { useState } from "react";
+
+export const TableInputTextEditor = ({ value, errorMessages, textOnChangeHandler, rowIndex, field }) => {
+ const [localValue, setLocalValue] = useState(value);
+
+ const onChange = (e) => {
+ setLocalValue(e.target.value);
+ textOnChangeHandler(rowIndex, e, field)
+ }
+
+ return (
+ <>
+ <InputText
+ id={field}
+ value={localValue}
+ onChange={onChange}
+ fieldName={field}
+ />
+ <DialogErrorMessageComponent errorMessages={errorMessages[rowIndex]} errorField={field} />
+ </>
+ );
+};

src/main/cliapp/src/components/FormTableWrapper.js

@@ -0,0 +1,21 @@
+export const FormTableWrapper = ({
+ labelColumnSize,
+ table,
+ tableName,
+ showTable,
+ button,
+}) => {
+ return (
+ <div className="grid">
+ <div className="col-12">
+ <div className="mb-3">
+ <label>{tableName}</label>
+ </div>
+ {showTable && table}
+ <div className={`${showTable ? "pt-3" : ""} p-field p-col col-4`}>
+ {button}
+ </div>
+ </div>
+ </div>
+ );
+};

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

@@ -10,8 +10,8 @@ import { Checkbox } from 'primereact/checkbox';
 
 import { FilterComponent } from '../Filters/FilterComponent'
 import { DataTableHeaderFooterTemplate } from "../DataTableHeaderFooterTemplate";
-import { DuplicationAction } from "../DuplicationAction";
-import { EntityDetailsAction } from "../EntityDetailsAction";
+import { DuplicationAction } from "../Actions/DuplicationAction";
+import { EntityDetailsAction } from "../Actions/EntityDetailsAction";
 
 
 import { filterColumns, orderColumns } from '../../utils/utils';
@@ -65,6 +65,7 @@ export const GenericDataTable = (props) => {
  exceptionMessage,
  } = useGenericDataTable(props);
 
+ const toast_topleft = useRef(null);
  const toast_topright = useRef(null);
  const [deleteDialog, setDeleteDialog] = useState(false);
  const [deprecateDialog, setDeprecateDialog] = useState(false);
@@ -251,6 +252,7 @@ export const GenericDataTable = (props) => {
 
  return (
  <div className="card">
+ <Toast ref={toast_topleft} position="top-left" />
  <Toast ref={toast_topright} position="top-right" />
  <DataTable dataKey={dataKey} value={entities} header={header} ref={dataTable}
  filterDisplay="row" scrollHeight="62vh" scrollable= {true} tableClassName='p-datatable-md'

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

@@ -231,6 +231,16 @@ export const useGenericDataTable = ({
  toast_topright.current.show([
  { life: 7000, severity: 'error', summary: 'Update error: ', detail: errorMessage, sticky: false }
  ]);
+ if (error.response.data.errorMessages && Object.keys(error.response.data.errorMessages).length > 0) {
+ let messages = [];
+ for (let errorField in error.response.data.errorMessages) {
+ messages.push(errorField + ": " + error.response.data.errorMessages[errorField]);
+ }
+ let messageSummary = messages.join(" / ");
+ toast_topleft.current.show([
+ { life: 7000, severity: 'error', summary: 'Errors found: ', detail: messageSummary, sticky: false }
+ ]);
+ }
  }
  else if(error.response.data !== undefined) {
  setExceptionMessage(error.response.data);

src/main/cliapp/src/components/GenericDataTree.js

@@ -113,7 +113,7 @@ export const GenericDataTree = (props) => {
  </div>
  <div className="col-6">
  <div className="card">
- <div><pre style={{whiteSpace: "pre-wrap"}}>{JSON.stringify(selectedTerm, null, 2) }</pre></div>
+ <div className="fixed"><pre style={{whiteSpace: "pre-wrap"}}>{JSON.stringify(selectedTerm, null, 2) }</pre></div>
  </div>
  </div>
  </div>

src/main/cliapp/src/constants/FilterFields.js

@@ -72,9 +72,9 @@ export const FIELD_SETS = Object.freeze({
  filterName: "citationFilter",
  fields: ["citation"],
  },
- shortCitationFieldSet: {
- filterName: "shortCitationFilter",
- fields: ["shortCitation"],
+ literatureShortCitationFieldSet: {
+ filterName: "literatureShortCitationFilter",
+ fields: ["short_citation"],
  },
  conditionAnatomyFieldSet: {
  filterName: "conditionAnatomyFilter",
@@ -430,7 +430,7 @@ export const FILTER_CONFIGS = Object.freeze({
  assertedAlleleFilterConfig: { filterComponentType: "input", fieldSets: [FIELD_SETS.assertedAlleleFieldSet] },
  assertedGenesFilterConfig: { filterComponentType: "input", fieldSets: [FIELD_SETS.assertedGenesFieldSet] },
  citationFilterConfig: { filterComponentType: "input", fieldSets: [FIELD_SETS.citationFieldSet]},
- shortCitationFilterConfig:  { filterComponentType: "input", fieldSets: [FIELD_SETS.shortCitationFieldSet]},
+ literatureShortCitationFilterConfig: { filterComponentType: "input", fieldSets: [FIELD_SETS.literatureShortCitationFieldSet]},
  conditionAnatomyFilterConfig: { filterComponentType: "input", fieldSets: [FIELD_SETS.conditionAnatomyFieldSet] },
  conditionChemicalFilterConfig: { filterComponentType: "input", fieldSets: [FIELD_SETS.conditionChemicalFieldSet] },
  conditionClassFilterConfig: { filterComponentType: "input", fieldSets: [FIELD_SETS.conditionClassFieldSet] },

src/main/cliapp/src/constants/SortFields.js

@@ -5,7 +5,7 @@ export const SORT_FIELDS = Object.freeze([
  "diseaseRelation.name",
  "negated",
  "object.name",
- "singleReference.curie",
+ "singleReference.primaryCrossReferenceCurie",
  "evidenceCodes.abbreviation",
  "with.geneSymbol.displayText",
  "relatedNotes.freeText",
@@ -44,7 +44,7 @@ export const SORT_FIELDS = Object.freeze([
  "alleleDatabaseStatus.databaseStatus.name",
  "alleleInheritanceModes.inheritanceMode.name",
  "alleleNomenclatureEvents.nomenclatureEvent.name",
- "references.curie",
+ "references.primaryCrossReferenceCurie",
  "inCollection.name",
  "isExtinct",
  "handle",
@@ -77,6 +77,7 @@ export const SORT_FIELDS = Object.freeze([
  "title",
  "abstract",
  "citation",
+ "short_citation",
  "prefix",
  "idPattern",
  "idExample",

src/main/cliapp/src/containers/allelesPage/AlleleDetailPage.js

@@ -16,6 +16,8 @@ import { CurieFormTemplate } from '../../components/Templates/CurieFormTemplate'
 import { DataProviderFormTemplate } from '../../components/Templates/DataProviderFormTemplate';
 import { DateFormTemplate } from '../../components/Templates/DateFormTemplate';
 import { UserFormTemplate } from '../../components/Templates/UserFormTemplate';
+import { SynonymsForm } from './SynonymsForm';
+import { validateTable } from '../../utils/utils';
 
 export default function AlleleDetailPage(){
  const { curie } = useParams();
@@ -46,15 +48,24 @@ const { isLoading } = useQuery([curie],
  return alleleService.saveAllele(allele);
  });
 
- const handleSubmit = (event) => {
+
+ const handleSubmit = async (event) => {
+ event.preventDefault();
  alleleDispatch({
  type: "SUBMIT" 
  })
- event.preventDefault();
+
+ const isSynonymsErrors = await validateTable(
+ "allelesynonymslotannotation", 
+ "synonymsErrorMessages", 
+ alleleState.allele.alleleSynonyms,
+ alleleDispatch,
+ );
+
  mutation.mutate(alleleState.allele, {
- onSuccess: (data) => {
+ onSuccess: () => {
+ if(isSynonymsErrors) return;
  toastSuccess.current.show({severity: 'success', summary: 'Successful', detail: 'Allele Saved'});
- console.log(alleleState.errorMessages);
  },
  onError: (error) => {
  let message;
@@ -175,6 +186,14 @@ const { isLoading } = useQuery([curie],
 
  <Divider />
 
+ <SynonymsForm
+ state={alleleState}
+ dispatch={alleleDispatch}
+ labelColumnSize={labelColumnSize}
+ />
+
+ <Divider />
+
  <TaxonFormEditor 
  taxon={alleleState.allele?.taxon} 
  onTaxonValueChange={onTaxonValueChange} 

src/main/cliapp/src/containers/allelesPage/AllelesTable.js

@@ -1161,7 +1161,7 @@ export const AllelesTable = () => {
  filterConfig: FILTER_CONFIGS.alleleDatabaseStatusFilterConfig,
  },
  {
- field: "references.curie",
+ field: "references.primaryCrossReferenceCurie",
  header: "References",
  body: referencesTemplate,
  sortable: isEnabled,