Subset#accessionIds renamed to accessionRefs

src/accessions/actions/public.ts

@@ -10,7 +10,7 @@ import AccessionMapInfo from 'model/AccessionMapInfo';
 
 import {RECEIVE_ACCESSIONS, RECEIVE_ACCESSION, RECEIVE_ACCESSION_OVERVIEW, APPEND_ACCESSIONS, RECEIVE_ACCESSION_MAPINFO} from 'accessions/constants';
 import AccessionService from 'service/genesys/AccessionService';
-import { AccessionIdentifier } from 'model/dataset.model';
+import { AccessionRef } from 'model/dataset.model';
 
 const receiveAccessions = (paged: FilteredPage<Accession>, error = null) => ({
   type: RECEIVE_ACCESSIONS,
@@ -37,7 +37,7 @@ const receiveAccession = (accession: AccessionDetails, error = null) => ({
   payload: { accession, error },
 });
 
-export const toUUIDPromise = (identifiers: AccessionIdentifier[]) => (dispatch, getState): Promise<Map<string, AccessionIdentifier>> => {
+export const toUUIDPromise = (identifiers: AccessionRef[]) => (dispatch, getState): Promise<Map<string, AccessionRef>> => {
   return AccessionService.toUUID(identifiers);
 };
 

src/model/Subset.ts

@@ -9,7 +9,7 @@ import Crop from 'model/Crop';
 
 class Subset {
   public accessionCount: number;
-  public accessionIds: string[];
+  public accessionRefs: string[];
   public active: boolean;
   public creators: Creator[];
   public createdBy: number;

src/model/dataset.model.ts

 import { EmptyModel } from 'model/common.model';
 
-export class AccessionIdentifier extends EmptyModel {
+export class AccessionRef extends EmptyModel {
   public doi: string;
   public instCode: string;
   public acceNumb: string;
@@ -12,6 +12,6 @@ export class AccessionIdentifier extends EmptyModel {
   }
 
   public getClassname(): string {
-    return 'org.genesys.catalog.model.dataset.AccessionIdentifier';
+    return 'org.genesys.catalog.model.dataset.AccessionRef';
   }
 }

src/model/filter.model.ts

-export interface IBasicModelFilter {
-  id?: number[];
-  _text?: string;
-}
-
-export interface IVersionedModelFilter extends IBasicModelFilter {
-  version?: number[];
-}
-
-export interface IDateFilter {
-  ge?: Date;
-  gt?: Date;
-  le?: Date;
-  lt?: Date;
-}
-
-export interface INumberFilter {
-  eq?: number;
-  gt?: number;
-  ge?: number;
-  lt?: number;
-  le?: number;
-}
-
-export interface IStringFilter {
-  eq?: string; // equals
-  contains?: string; // like
-  sw?: string; // starts with
-}
-
-
-export interface IAuditedVersionedModelFilter extends IVersionedModelFilter {
-  createdBy?: number[];
-  lastModifiedBy?: number[];
-  createdDate?: IDateFilter;
-  lastModifiedDate?: IDateFilter;
-}

src/requests/ui/admin/DisplayPage.tsx

@@ -72,7 +72,7 @@ class DisplayPage extends React.Component<IDisplayPageProps, any> {
                 { request.body.requestInfo && <PropertiesItem title="Purpose type">{ t(`request.purposeType.${request.body.requestInfo.purposeType}`) }</PropertiesItem> }
                 { request.body.requestInfo && <PropertiesItem title={ t(`request.preacceptSMTA`) }>{ request.body.requestInfo.preacceptSMTA ? 'Yes' : 'No' }</PropertiesItem> }
                 { request.body.requestInfo && <PropertiesItem title="Notes">{ request.body.requestInfo.notes }</PropertiesItem> }
-                <PropertiesItem title="Requested accession ids">{ request.body.accessionIds.reduce((id, acc) => `${acc}, ${id}`) }</PropertiesItem>
+                <PropertiesItem title="Requested accession ids">{ request.body.accessionRefs.reduce((id, acc) => `${acc}, ${id}`) }</PropertiesItem>
               </Properties>
             </MainSection>
             { request.body.pid && request.body.pid.type === 'in' &&

src/requests/ui/admin/c/RequestCard.tsx

@@ -40,7 +40,7 @@ const RequestCard = ({request, classes, index, ...other}: { request: MaterialReq
                           <b> • </b>
                       </span>
                   }
-                  { request.body.accessionIds.length } accessions
+                  { request.body.accessionRefs.length } accessions
                 </div>
             </CardContent>
         </Card>

src/service/genesys/AccessionService.ts

@@ -8,7 +8,7 @@ import AccessionDetails from 'model/AccessionDetails';
 import AccessionFilter from 'model/AccessionFilter';
 import AccessionMapInfo from 'model/AccessionMapInfo';
 import FilteredPage, { IPageRequest } from 'model/FilteredPage';
-import {AccessionIdentifier} from 'model/dataset.model';
+import {AccessionRef} from 'model/dataset.model';
 
 const URL_GET_BY_DOI = `/api/v1/acn/{doi}`; // UrlTemplate doesn't like the / in DOI
 const URL_GET_BY_UUID = UrlTemplate.parse(`/api/v1/acn/{UUID}`);
@@ -99,7 +99,7 @@ class AccessionService {
     }).then(({ data }) => data as AccessionDetails);
   }
 
-  public static toUUID(identifiers: AccessionIdentifier[]) {
+  public static toUUID(identifiers: AccessionRef[]) {
     const apiUrl = URL_TO_UUID;
     const content = { data: identifiers };
 
@@ -107,7 +107,7 @@ class AccessionService {
       url: apiUrl,
       method: 'POST',
       ...content,
-    }).then(({ data }) => data as Map<string, AccessionIdentifier>);
+    }).then(({ data }) => data as Map<string, AccessionRef>);
   }
 
   /**

src/service/genesys/SubsetService.ts

@@ -39,13 +39,13 @@ class SubsetService {
    * @param authToken Authorization token
    * @param UUID UUID
    * @param version version
-   * @param accessionIds accessionIds
+   * @param accessionRefs accessionRefs
    */
-  public static addAccessions(UUID: string, version: number, accessionIds: string[]): Promise<Subset> {
+  public static addAccessions(UUID: string, version: number, accessionRefs: string[]): Promise<Subset> {
 
     const apiUrl = URL_ADD_ACCESSIONS.expand({UUID, version});
     // console.log(`Fetching from ${apiUrl}`);
-    const content = { data: accessionIds };
+    const content = { data: accessionRefs };
 
     return axiosBackend.request({
       url: apiUrl,

src/subsets/actions/editor.ts

@@ -10,7 +10,7 @@ import {ADD_CREATOR_TO_SUBSET, REMOVE_CREATOR_FROM_SUBSET, UPDATE_SUBSET_CREATOR
 import Creator from 'model/Creator';
 import Subset from 'model/Subset';
 import {PublishState} from 'model/common.model';
-import {AccessionIdentifier} from 'model/dataset.model';
+import {AccessionRef} from 'model/dataset.model';
 
 // Service
 import SubsetService from 'service/genesys/SubsetService';
@@ -19,10 +19,10 @@ import SubsetService from 'service/genesys/SubsetService';
 import steps from 'subsets/ui/dashboard/subset-stepper/steps';
 
 // Accession Identifiers step
-export const updateSubsetAccessionIdentifiers = (subset: Subset, accessionIdentifiers: AccessionIdentifier[]) => (dispatch) => {
-  dispatch(toUUIDPromise(accessionIdentifiers))
-    .then((accessionIdentifiers) => {
-      SubsetService.addAccessions(subset.uuid, subset.version, Object.keys(accessionIdentifiers))
+export const updateSubsetAccessionRefs = (subset: Subset, AccessionRefs: AccessionRef[]) => (dispatch) => {
+  dispatch(toUUIDPromise(AccessionRefs))
+    .then((AccessionRefs) => {
+      SubsetService.addAccessions(subset.uuid, subset.version, Object.keys(AccessionRefs))
         .then((subset) => {
           dispatch(receiveSubset(subset));
         });

src/subsets/ui/c/SubsetDisplay.tsx

@@ -39,21 +39,21 @@ class DetailInfo extends React.Component<IDetailInfoProps, any> {
     subsetAccessions: [],
   };
 
-  private loadAccessions = (accessionIds) => {
+  private loadAccessions = (accessionRefs) => {
     const {listAccessions} = this.props;
 
     const filter = new AccessionFilter();
-    filter.uuid = accessionIds.map((id) => id.uuid);
+    filter.uuid = accessionRefs.map((id) => id.uuid);
 
-    listAccessions(filter, {page: 0, size: accessionIds.length, direction: 'ASC'})
+    listAccessions(filter, {page: 0, size: accessionRefs.length, direction: 'ASC'})
       .then((accessionPage) => this.setState({subsetAccessions: accessionPage.content}));
   }
 
   public componentWillMount() {
     const {subset} = this.props;
 
-    if (subset && subset.accessionIds && subset.accessionIds.length > 0) {
-      this.loadAccessions(subset.accessionIds);
+    if (subset && subset.accessionRefs && subset.accessionRefs.length > 0) {
+      this.loadAccessions(subset.accessionRefs);
     }
   }
 
@@ -61,8 +61,8 @@ class DetailInfo extends React.Component<IDetailInfoProps, any> {
     const {subset} = nextProps;
     const {subsetAccessions} = this.state;
 
-    if (subset && subset.accessionIds && subset.accessionIds.length > 0  && (!subsetAccessions || subsetAccessions.length === 0 || subsetAccessions.length !== subset.accessionIds.length)) {
-      this.loadAccessions(subset.accessionIds);
+    if (subset && subset.accessionRefs && subset.accessionRefs.length > 0  && (!subsetAccessions || subsetAccessions.length === 0 || subsetAccessions.length !== subset.accessionRefs.length)) {
+      this.loadAccessions(subset.accessionRefs);
     }
   }
 

src/subsets/ui/dashboard/subset-stepper/steps/accessions-list/ListOfAccessions.tsx

@@ -9,7 +9,7 @@ import {log} from 'utilities/debug';
 import {CSV, ICsvConfiguration} from 'utilities/CSV';
 
 // models
-import {AccessionIdentifier} from 'model/dataset.model';
+import {AccessionRef} from 'model/dataset.model';
 import Accession from 'model/Accession';
 import AccessionFilter from 'model/AccessionFilter';
 import {IPageRequest} from 'model/FilteredPage';
@@ -18,13 +18,13 @@ import Subset from 'model/Subset';
 
 // ui
 import CSVConfiguration, {CSVConfig} from 'ui/common/csv-configuration/CSVConfiguration';
-import AccessionIdentifiersTable from 'ui/catalog/accession/IdentifiersTable';
+import AccessionRefsTable from 'ui/catalog/accession/AccessionRefsTable';
 
 interface IListOfAccession extends React.ClassAttributes<any> {
   classes: any;
   listAccessions: (filter: string | AccessionFilter, page: IPageRequest) => Promise<Page<Accession>>;
   subset: Subset;
-  onAccessionsUpdated: (accessionIdentifiers: AccessionIdentifier[]) => void;
+  onAccessionsUpdated: (AccessionRefs: AccessionRef[]) => void;
 }
 
 const styleSheet = {
@@ -43,13 +43,13 @@ const styleSheet = {
 
 class ListOfAccession extends React.Component<IListOfAccession, any> {
 
-  private loadAccessions = (accessionIds) => {
+  private loadAccessions = (accessionRefs) => {
     const {listAccessions} = this.props;
 
     const filter = new AccessionFilter();
-    filter.uuid = accessionIds.map((id) => id.uuid);
+    filter.uuid = accessionRefs.map((id) => id.uuid);
 
-    listAccessions(filter, {page: 0, size: accessionIds.length, direction: 'ASC'})
+    listAccessions(filter, {page: 0, size: accessionRefs.length, direction: 'ASC'})
       .then((accessionPage) => this.setState({subsetAccessions: accessionPage.content}));
   }
 
@@ -57,8 +57,8 @@ class ListOfAccession extends React.Component<IListOfAccession, any> {
     const {subset} = this.props;
     const {subsetAccessions} = this.state;
 
-    if (subset  && subset.accessionIds && subset.accessionIds.length > 0 && (!subsetAccessions || subsetAccessions.length === 0)) {
-      this.loadAccessions(subset.accessionIds);
+    if (subset  && subset.accessionRefs && subset.accessionRefs.length > 0 && (!subsetAccessions || subsetAccessions.length === 0)) {
+      this.loadAccessions(subset.accessionRefs);
     }
   }
 
@@ -66,8 +66,8 @@ class ListOfAccession extends React.Component<IListOfAccession, any> {
     const {subset} = nextProps;
     const {subsetAccessions} = this.state;
 
-    if (subset && subset.accessionIds && subset.accessionIds.length > 0  && (!subsetAccessions || subsetAccessions.length === 0 || subsetAccessions.length !== subset.accessionIds.length)) {
-      this.loadAccessions(subset.accessionIds);
+    if (subset && subset.accessionRefs && subset.accessionRefs.length > 0  && (!subsetAccessions || subsetAccessions.length === 0 || subsetAccessions.length !== subset.accessionRefs.length)) {
+      this.loadAccessions(subset.accessionRefs);
     }
   }
 
@@ -129,7 +129,7 @@ class ListOfAccession extends React.Component<IListOfAccession, any> {
 
         <h3>Accession list: { subsetAccessions ? subsetAccessions.length : 0 } rows</h3>
         { subsetAccessions &&
-          <AccessionIdentifiersTable accessionIdentifiers={ subsetAccessions.map((accession) => ({doi: accession.doi, instCode: accession.institute.code, acceNumb: accession.accessionNumber, genus: accession.taxonomy.genus})) }/>
+          <AccessionRefsTable AccessionRefs={ subsetAccessions.map((accession) => ({doi: accession.doi, instCode: accession.institute.code, acceNumb: accession.accessionNumber, genus: accession.taxonomy.genus})) }/>
         }
       </div>
     );
@@ -146,11 +146,11 @@ class ListOfAccession extends React.Component<IListOfAccession, any> {
 
     log('CSV config', config);
 
-    const newIdentifiers: AccessionIdentifier[] = [];
+    const newIdentifiers: AccessionRef[] = [];
 
     CSV.parse(csvText, config, {headers: [ 'instCode', 'acceNumb', 'genus', 'species', 'doi']})
       .subscribe((jsonObj) => {
-        const aid: AccessionIdentifier = new AccessionIdentifier(jsonObj);
+        const aid: AccessionRef = new AccessionRef(jsonObj);
         newIdentifiers.push(aid);
         log(aid);
       }).then(() => {

src/subsets/ui/dashboard/subset-stepper/steps/accessions-list/index.tsx

@@ -2,14 +2,14 @@ import * as React from 'react';
 import {bindActionCreators} from 'redux';
 import {connect} from 'react-redux';
 // actions
-import {updateSubsetAccessionIdentifiers} from 'subsets/actions/editor';
+import {updateSubsetAccessionRefs} from 'subsets/actions/editor';
 import {listAccessionsPromise} from 'accessions/actions/public'; // TODO maybe move to dashboard or import from service
 
 // models
 import Subset from 'model/Subset';
 import Page from 'model/Page';
 import Accession from 'model/Accession';
-import {AccessionIdentifier} from 'model/dataset.model';
+import {AccessionRef} from 'model/dataset.model';
 import AccessionFilter from 'model/AccessionFilter';
 import {IPageRequest} from 'model/FilteredPage';
 // ui
@@ -19,7 +19,7 @@ import Loading from 'ui/common/Loading';
 
 interface IAccessionsListStep extends React.ClassAttributes<any> {
   item: Subset;
-  updateSubsetAccessionIdentifiers: (subset: Subset, accessionIds: AccessionIdentifier[]) => Promise<Subset>;
+  updateSubsetAccessionRefs: (subset: Subset, accessionRefs: AccessionRef[]) => Promise<Subset>;
   listAccessions: (filter: string | AccessionFilter, page: IPageRequest) => Promise<Page<Accession>>;
 }
 
@@ -31,15 +31,15 @@ class AccessionsListStep extends  StepperTemplate<IAccessionsListStep> {
     return !item ? <Loading /> : (
       <ListOfAccessions
         listAccessions={ listAccessions }
-        onAccessionsUpdated={ this.updateAccessionIds }
+        onAccessionsUpdated={ this.updateaccessionRefs }
         subset={ item }
       />
     );
   }
 
-  protected updateAccessionIds = (accessionIdentifiers: AccessionIdentifier[]) => {
-    const {item: subset, updateSubsetAccessionIdentifiers} = this.props;
-    updateSubsetAccessionIdentifiers(subset, accessionIdentifiers);
+  protected updateaccessionRefs = (AccessionRefs: AccessionRef[]) => {
+    const {item: subset, updateSubsetAccessionRefs} = this.props;
+    updateSubsetAccessionRefs(subset, AccessionRefs);
   }
 
 }
@@ -48,7 +48,7 @@ const mapStateToProps = (state, ownProps) => ({
 });
 
 const mapDispatchToProps = (dispatch) => bindActionCreators({
-  updateSubsetAccessionIdentifiers,
+  updateSubsetAccessionRefs,
   listAccessions: listAccessionsPromise,
 }, dispatch);
 

src/ui/catalog/accession/IdentifiersTable.tsx → src/ui/catalog/accession/AccessionRefsTable.tsx

 import * as React from 'react';
 import { withStyles } from '@material-ui/core/styles';
 
-import { AccessionIdentifier } from 'model/dataset.model';
+import { AccessionRef } from 'model/dataset.model';
 import { Table as VTable, Column as VColumn, AutoSizer } from 'react-virtualized';
 import DOI from 'ui/common/DOI';
 // import Hidden from '@material-ui/core/Hidden';
@@ -31,24 +31,24 @@ const styles = (theme) => ({
     },
 });
 
-interface IAccessionIdentifiersTableProps extends React.ClassAttributes<any> {
+interface IAccessionRefsTableProps extends React.ClassAttributes<any> {
     classes: any;
-    accessionIdentifiers: AccessionIdentifier[];
+    AccessionRefs: AccessionRef[];
 }
 
-class AccessionIdentifiersTable extends React.Component<IAccessionIdentifiersTableProps, any> {
+class AccessionRefsTable extends React.Component<IAccessionRefsTableProps, any> {
 
     constructor(props, context) {
         super(props, context);
     }
 
     public render() {
-        const { accessionIdentifiers, classes } = this.props;
-        const rowGetter = ({ index }) => accessionIdentifiers[index];
+        const { AccessionRefs, classes } = this.props;
+        const rowGetter = ({ index }) => AccessionRefs[index];
         const renderDoi = ({ cellData }) => <DOI noPrefix value={ cellData } />;
         const rowClassName = ({ index }) => index === -1 ? '' : `${classes.tableCell} ${index % 2 === 0 ? classes.evenRow : classes.oddRow}`;
 
-        return accessionIdentifiers && accessionIdentifiers.sort((a, b) => a.acceNumb.localeCompare(b.acceNumb)) && (
+        return AccessionRefs && AccessionRefs.sort((a, b) => a.acceNumb.localeCompare(b.acceNumb)) && (
             <AutoSizer disableHeight>
               { ({ width }) => (
                 <VTable
@@ -57,7 +57,7 @@ class AccessionIdentifiersTable extends React.Component<IAccessionIdentifiersTab
                   height={ 500 }
                   headerHeight={ 25 }
                   rowHeight={ 30 }
-                  rowCount={ accessionIdentifiers.length }
+                  rowCount={ AccessionRefs.length }
                   rowGetter={ rowGetter }
                   rowClassName={ rowClassName }
                   headerClassName={ `back-green` }
@@ -74,4 +74,4 @@ class AccessionIdentifiersTable extends React.Component<IAccessionIdentifiersTab
     }
 }
 
-export default withStyles(styles)(AccessionIdentifiersTable);
+export default withStyles(styles)(AccessionRefsTable);