Organise API endpoint utilities

README.md

@@ -41,6 +41,7 @@ Datahub configuration is spread among different files located in <kbd>src/config
 
 - `icat.js` - configure access to metadata catalogue
 - `icatPlus.js` - configure access to ICAT+ server
+- `ids.js` - configure IDs server for downloading datasets
 - [`techniques.js`](#techniquesjs) - configure known techniques
 - [`ui.js`](#uijs) - general UI configuration
 

src/actions/datacollections.js

 import axios from 'axios';
-import { getDataCollections } from '../api/icat/icatPlus';
+import { getDataCollections } from '../api/icat-plus/catalogue';
 import { FETCH_DATACOLLECTIONS } from '../constants/actionTypes';
 
 export function fetchDataCollections(sessionId) {

src/actions/datasets.js

 import axios from 'axios';
-import {
-  getDatasetByDOI,
-  getDatasetsByInvestigationId,
-} from '../api/icat/icatPlus';
+import { getDatasetsByInvestigationId } from '../api/icat-plus/catalogue';
 import {
   FETCH_DATASETS_BY_DOI,
   FETCH_DATASETS_BY_INVESTIGATION,
 } from '../constants/actionTypes';
+import { getDatasetByDOI } from '../api/icat-plus/doi';
 
 export function fetchDatasetsByDOI(sessionId, doi) {
   return function (dispatch) {

src/actions/instrumentscientists.js

 import axios from 'axios';
-import { getInstrumentScientistsBySessionId } from '../api/icat/icatPlus';
+import { getInstrumentScientistsBySessionId } from '../api/icat-plus/catalogue';
 import { FETCH_INSTRUMENTSCIENTISTS } from '../constants/actionTypes';
 
 export function fetchInstrumentScientistsBySessionId(sessionId) {

src/actions/investigations.js

@@ -4,7 +4,7 @@ import {
   getInvestigationsByInstrumentScientist,
   getInvestigationsByUser,
   getReleasedInvestigations,
-} from '../api/icat/icatPlus';
+} from '../api/icat-plus/catalogue';
 import {
   FETCH_INSTRUMENT_SCIENTIST_INVESTIGATIONS,
   FETCH_INVESTIGATIONS,

src/api/icat-plus/catalogue.js

+import ICATPLUS from '../../config/icatPlus';
+
+export function getFilesByDatasetId(sessionId, datasetIds) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/dataset/id/${datasetIds}/datafile`;
+}
+
+export function getUsers(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/user`;
+}
+
+export function getUsersByInvestigationIds(sessionId, investigationIds) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation/id/${investigationIds}/investigationusers`;
+}
+
+export function getInvestigationById(sessionId, investigationId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation/id/${investigationId}/investigation`;
+}
+
+export function getEmbargoedInvestigations(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation/status/embargoed/investigation`;
+}
+
+export function getReleasedInvestigations(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation/status/released/investigation`;
+}
+
+export function getInvestigationsByUser(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation?useris=participant`;
+}
+
+export function getInvestigationsByInstrumentScientist(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation/useris/instrumentscientist/investigation`;
+}
+
+export function getDatasetsById(sessionId, datasetIds) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/dataset/id/${datasetIds}/dataset`;
+}
+
+export function getDatasetsByInvestigationId(sessionId, investigationId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation/id/${investigationId}/dataset`;
+}
+
+export function getDatasetStatus(sessionId, datasetIds) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/dataset/id/${datasetIds}/status`;
+}
+
+export function getDataCollections(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/datacollection`;
+}
+
+export function getInvestigationUsersByInvestigationId(
+  sessionId,
+  investigationId
+) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/investigation/id/${investigationId}/investigationusers`;
+}
+
+export function getInstrumentScientistsBySessionId(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/instrumentscientist`;
+}
+
+export function createInstrumentScientists(sessionId) {
+  return `${ICATPLUS.server}/catalogue/${sessionId}/instrumentscientist`;
+}

src/api/icat-plus/doi.js

+import ICATPLUS from '../../config/icatPlus';
+
+/**
+ * Get the URL used to mint a DOI
+ * @param {*} sessionId session identifier
+ * @return {string} URL used to mint a DOI
+ */
+export function getMintDOI(sessionId) {
+  return `${ICATPLUS.server}/doi/${sessionId}/mint`;
+}
+
+export function getDatasetByDOI(sessionId, doi) {
+  return `${ICATPLUS.server}/doi/${doi}/datasets?sessionId=${sessionId}`;
+}

src/api/icat-plus/elasticsearch.js

+import ICATPLUS from '../../config/icatPlus';
+
+export function getDataStatistics(sessionId) {
+  return `${ICATPLUS.server}/elasticsearch/${sessionId}/stats/data/metrics`;
+}
+
+export function getInstrumentStatistics(sessionId) {
+  return `${ICATPLUS.server}/elasticsearch/${sessionId}/stats/instrument/metrics`;
+}

src/api/icat-plus/logbook.js

+import ICATPLUS from '../../config/icatPlus';
+
+/**
+ * Get URL needed to retrieve events for a given investigation
+ * @param {String} sessionId the session identifier
+ * @param {String} investigationId the session identifier
+ * @return {String} the URL to get the requested events. Null if investigationId or sessionId is missing.
+ */
+export function getEventsByInvestigationId(sessionId, investigationId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/event/query`;
+}
+
+/**
+ * Get URL needed to retrieve the event count for a given investigation
+ * @param {string} sessionId the session identifier
+ * @param {String} investigationId the investigation identifier
+ * @return {String} the URL to get the requested event count
+ */
+export function getEventCountByInvestigationId(sessionId, investigationId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/event/count`;
+}
+
+/**
+ * Get URL used to create a new event for a given investigation on ICAT+
+ * @param {*} investigationId investigation indentifier
+ * @param {String} sessionId session identifier
+ * @return {String} URL to get the requested events
+ */
+export function createEvent(sessionId, investigationId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/event/create`;
+}
+
+/**
+ * Get URL used to update an event on a given investigation on ICAT+
+ * @param {String} sessionId the session identifier
+ * @param {String} investigationId the investigation indentifier
+ * @return {String} the URL to get the requested events
+ */
+export function updateEvent(sessionId, investigationId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/event/update`;
+}
+
+/**
+ * Get URL used to download a PDF file for a given investigation from the logbook
+ * @param {string} sessionId session identifier
+ * @param {*} investigationId investigation identifier
+ * @param {object} selectionFilter selection filter used to retrieve part of the logbook. This is URI encoded and passed as query string
+ */
+export function getPDF(sessionId, investigationId, selectionFilter) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/event/pdf?find=&sort=&skip=&limit=`
+    .replace('find=', () => {
+      return `find=${
+        selectionFilter && selectionFilter.find
+          ? JSON.stringify(selectionFilter.find)
+          : ''
+      }`;
+    })
+    .replace('&sort=', () => {
+      return `&sort=${
+        selectionFilter && selectionFilter.sort
+          ? JSON.stringify(selectionFilter.sort)
+          : ''
+      }`;
+    })
+    .replace('&skip=', () => {
+      return `&skip=${
+        selectionFilter && selectionFilter.skip !== undefined
+          ? JSON.stringify(selectionFilter.skip)
+          : ''
+      }`;
+    })
+    .replace('&limit=', () => {
+      return `&limit=${
+        selectionFilter && selectionFilter.limit !== undefined
+          ? JSON.stringify(selectionFilter.limit)
+          : ''
+      }`;
+    });
+}
+
+/** Get the tags associated to a given investigation
+ * @param {string} sessionId session identifier
+ * @param {*} investigationId investigation identifier
+ */
+export function getTagsByInvestigationId(sessionId, investigationId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/tag`;
+}
+
+/** Create a given tag associated to a given investigation */
+export function createTagsByInvestigationId(sessionId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/tag/create`;
+}
+
+/** Update a given tag associated to a given investigation */
+export function updateTagsByInvestigationId(sessionId, investigationId, tagId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/tag/id/${tagId}/tag/update`;
+}
+
+export function createEventFromBase64(sessionId, investigationId) {
+  return `${ICATPLUS.server}/logbook/${sessionId}/investigation/id/${investigationId}/event/createfrombase64`;
+}

src/api/icat-plus/resource.js

+import ICATPLUS from '../../config/icatPlus';
+
+/**
+ * Get URL used to upload data such as a file to ICAT+.
+ * @param {*} investigationId the investigationId
+ */
+export function uploadFile(sessionId, investigationId) {
+  return `${ICATPLUS.server}/resource/${sessionId}/file/investigation/id/${investigationId}/upload`;
+}
+
+/**
+ * Get URL used to retrieve the file of an event which category is 'file'
+ * @param {string} sessionId session identifier
+ * @param {*} investigationId investigation identifier
+ * @param {string} eventId event identifier where the file is stored
+ * @return {String} URL to get the file
+ */
+export function getFileByEventId(sessionId, investigationId, eventId) {
+  return `${ICATPLUS.server}/resource/${sessionId}/file/id/${eventId}/investigation/id/${investigationId}/download`;
+}

src/api/ids.js

+import IDS from '../config/ids';
+
+export function getDownloadURLByDatasetId(sessionId, datasetIds) {
+  return `${IDS.server}/ids/getData?sessionId=${sessionId}&datasetIds=${datasetIds}`;
+}
+
+export function getDownloadURLByDatafileId(sessionId, datafileIds) {
+  return `${IDS.server}/ids/getData?sessionId=${sessionId}&datafileIds=${datafileIds}`;
+}

src/components/Dataset/DatasetDownloadButton.js

 import axios, { CancelToken } from 'axios';
 import React from 'react';
 import { Button, Glyphicon } from 'react-bootstrap';
-import {
-  getDatasetStatus,
-  getDownloadURLByDatasetId,
-} from '../../api/icat/icatPlus';
+import { getDatasetStatus } from '../../api/icat-plus/catalogue';
+import { getDownloadURLByDatasetId } from '../../api/ids';
 
 export default class DatasetDownloadButton extends React.Component {
   constructor(props) {

src/components/Dataset/GalleryDatasetThumbnail.js

 import PropTypes from 'prop-types';
 import React, { Component } from 'react';
 import ImageZoom from 'react-medium-image-zoom';
-import { getFileByEventId } from '../../api/icat/icatPlus';
+import { getFileByEventId } from '../../api/icat-plus/resource';
 
 export default class GalleryDatasetThumbnail extends Component {
   render() {

src/components/Dataset/PublicationSummary.js

 import React from 'react';
 import { Col, Grid, Image, Row } from 'react-bootstrap';
-import { getFileByEventId } from '../../api/icat/icatPlus';
+import { getFileByEventId } from '../../api/icat-plus/resource';
 
 class PublicationSummary extends React.Component {
   getImageFromGalleyByIndex(index) {

src/components/File/DatasetFileTree.js

 import axios from 'axios';
 import React from 'react';
 import { Glyphicon } from 'react-bootstrap';
-import {
-  getDownloadURLByDatafileId,
-  getFilesByDatasetId,
-} from '../../api/icat/icatPlus';
+import { getFilesByDatasetId } from '../../api/icat-plus/catalogue';
 import { stringifyBytesSize } from '../../helpers';
 import ResponsiveTable from '../Table/ResponsiveTable';
+import { getDownloadURLByDatafileId } from '../../api/ids';
 
 class DatasetFileTree extends React.Component {
   constructor(props) {

src/components/Investigation/ParticipantsPanel.js

 import React, { useEffect, useState } from 'react';
 import { Alert } from 'react-bootstrap';
-import { getInvestigationUsersByInvestigationId } from '../../api/icat/icatPlus';
+import { getInvestigationUsersByInvestigationId } from '../../api/icat-plus/catalogue';
 import { groupBy } from 'lodash-es';
 import axios from 'axios';
 import ResponsiveTable from '../Table/ResponsiveTable';

src/components/Logbook/Editor/EditorWrapper.js

@@ -17,7 +17,7 @@ import {
   LOCALSTORAGE_KEY_EDITED_EVENT_CONTENT_IN_HTML_FORMAT,
 } from '../../../constants/eventTypes';
 import UI from '../../../config/ui';
-import { getFileByEventId, uploadFile } from '../../../api/icat/icatPlus';
+import { getFileByEventId, uploadFile } from '../../../api/icat-plus/resource';
 
 const EDITOR_ID_FOR_CREATION = 'myEditorForCreation';
 const EDITOR_ID_FOR_EDITION = 'myEditorForEdition';

src/components/Logbook/Menu/EventListMenu.js

@@ -10,7 +10,7 @@ import {
   Well,
 } from 'react-bootstrap';
 import { ComboSearch } from 'react-combo-search';
-import { getPDF } from '../../../api/icat/icatPlus';
+import { getPDF } from '../../../api/icat-plus/logbook';
 import {
   DOC_VIEW,
   LIST_VIEW,

src/components/ManagerStats/DataVolumeManagerStats/DataVolumeStatisticsPanel.js

 import axios from 'axios';
 import moment from 'moment';
 import React from 'react';
-import { getDataStatistics } from '../../../api/icat/icatPlus';
+import { getDataStatistics } from '../../../api/icat-plus/elasticsearch';
 import Loader from '../../Loader';
 import ErrorUserMessage from '../../UserMessages/ErrorUserMessage';
 import FileCountPanel from './FileCountPanel';

src/components/ManagerStats/GeneralStats/GeneralStatsPanel.js

@@ -2,7 +2,7 @@ import axios from 'axios';
 import React, { Suspense, lazy } from 'react';
 import { Col, Grid, Row } from 'react-bootstrap';
 import createPlotlyComponent from 'react-plotly.js/factory';
-import { getInstrumentStatistics } from '../../../api/icat/icatPlus';
+import { getInstrumentStatistics } from '../../../api/icat-plus/elasticsearch';
 import ParameterTableWidget from '../../Instrument/ParameterTableWidget';
 import Loader from '../../Loader';
 import ErrorUserMessage from '../../UserMessages/ErrorUserMessage';

src/components/UserManagement/BeamlineManagerForm.js

@@ -2,7 +2,10 @@ import axios from 'axios';
 import React, { Component } from 'react';
 import { Button, Col, Glyphicon, Grid, InputGroup, Row } from 'react-bootstrap';
 import { Typeahead } from 'react-bootstrap-typeahead';
-import { createInstrumentScientists, getUsers } from '../../api/icat/icatPlus';
+import {
+  createInstrumentScientists,
+  getUsers,
+} from '../../api/icat-plus/catalogue';
 import {
   ErrorUserMessage,
   SuccessUserMessage,

src/components/UserManagement/InstrumentScientistTable.js

 import axios from 'axios';
 import React from 'react';
 import { Button } from 'react-bootstrap';
-import { createInstrumentScientists } from '../../api/icat/icatPlus';
+import { createInstrumentScientists } from '../../api/icat-plus/catalogue';
 import Loader from '../Loader';
 import ResponsiveTable from '../Table/ResponsiveTable';
 

src/components/doi/DOIForm.js

@@ -12,7 +12,7 @@ import {
   Panel,
   SplitButton,
 } from 'react-bootstrap';
-import { getMintDOI } from '../../api/icat/icatPlus';
+import { getMintDOI } from '../../api/icat-plus/doi';
 import BootstrapTable2 from 'react-bootstrap-table-next';
 
 class DOIForm extends React.Component {

src/config/ids.js

+const IDS = {
+  //server: "https://ovm-icat-test.esrf.fr:8181",
+  server: 'https://ids.esrf.fr',
+  connection: {
+    plugins: ['esrf'],
+  },
+};
+
+export default IDS;

src/containers/CameraPage.js

@@ -3,7 +3,7 @@ import React, { Component } from 'react';
 import Camera, { FACING_MODES } from 'react-html5-camera-photo';
 import { connect } from 'react-redux';
 import { setBreadCrumbs } from '../actions/breadcrumbs';
-import { createEventFromBase64 } from '../api/icat/icatPlus';
+import { createEventFromBase64 } from '../api/icat-plus/logbook';
 
 class CameraPage extends Component {
   /* TODO: This should be refactored */

src/containers/Logbook/LogbookContainer.js

@@ -8,7 +8,7 @@ import {
   getEventCountByInvestigationId,
   getEventsByInvestigationId,
   updateEvent as updateEventURL,
-} from '../../api/icat/icatPlus';
+} from '../../api/icat-plus/logbook';
 import Loader from '../../components/Loader';
 import EventList from '../../components/Logbook/List/EventList';
 import EventListMenu from '../../components/Logbook/Menu/EventListMenu';

src/containers/Logbook/Tags/TagsManagerContainer.js

@@ -8,7 +8,7 @@ import {
   createTagsByInvestigationId,
   getTagsByInvestigationId,
   updateTagsByInvestigationId,
-} from '../../../api/icat/icatPlus';
+} from '../../../api/icat-plus/logbook';
 import Loader from '../../../components/Loader';
 import NewOrEditTagPanel from '../../../components/Logbook/Tag/NewOrEditTagPanel';
 import TagListMenu from '../../../components/Logbook/Tag/TagListMenu';

src/containers/Logbook/Tags/TagsSelectorContainer.js

@@ -5,7 +5,7 @@ import { connect } from 'react-redux';
 import {
   createTagsByInvestigationId,
   getTagsByInvestigationId,
-} from '../../../api/icat/icatPlus';
+} from '../../../api/icat-plus/logbook';
 import TagSelector from '../../../components/Logbook/Tag/TagSelector';
 
 class TagsSelectorContainer extends Component {

src/containers/SearchPage.js

@@ -11,7 +11,7 @@ import React, { Component } from 'react';
 import { Col, Grid, Label, Row } from 'react-bootstrap';
 import { connect } from 'react-redux';
 import { setBreadCrumbs } from '../actions/breadcrumbs';
-import { getFileByEventId } from '../api/icat/icatPlus';
+import { getFileByEventId } from '../api/icat-plus/resource';
 import ICATPLUS from '../config/icatPlus';
 import TECHNIQUES from '../config/techniques';
 import { stringifyBytesSize } from '../helpers';

src/containers/Selection/MintSelectionPage.js

@@ -11,7 +11,7 @@ import { addDatasetById, removeDatasetById } from '../../actions/selection';
 import {
   getDatasetsById,
   getUsersByInvestigationIds,
-} from '../../api/icat/icatPlus';
+} from '../../api/icat-plus/catalogue';
 import DOIForm from '../../components/doi/DOIForm';
 import Loader from '../../components/Loader';
 import { PERSPECTIVE } from '../../constants';

src/containers/Selection/SelectionPage.js

@@ -13,7 +13,7 @@ import { bindActionCreators } from 'redux';
 import { setBreadCrumbs } from '../../actions/breadcrumbs';
 import { doSignIn, doLogOut } from '../../actions/login';
 import { addDatasetById, removeDatasetById } from '../../actions/selection';
-import { getDatasetsById } from '../../api/icat/icatPlus';
+import { getDatasetsById } from '../../api/icat-plus/catalogue';
 import DatasetTable from '../../components/Dataset/DatasetTable';
 import Loader from '../../components/Loader';
 import { PERSPECTIVE } from '../../constants';

src/tests/unitTests/icatPlusAPI.test.js

@@ -3,14 +3,13 @@ import {
   createTagsByInvestigationId,
   getEventCountByInvestigationId,
   getEventsByInvestigationId,
-  getFileByEventId,
   getPDF,
   getTagsByInvestigationId,
   updateEvent,
   updateTagsByInvestigationId,
-  uploadFile,
-} from '../../api/icat/icatPlus';
+} from '../../api/icat-plus/logbook';
 import ICATPLUS from '../../config/icatPlus';
+import { getFileByEventId, uploadFile } from '../../api/icat-plus/resource';
 
 describe('Tests URL generation used to hit ICAT+', () => {
   describe('Events', () => {