Chore/update get clinical trial metadata function

dev.html

@@ -11,7 +11,7 @@
       - https://atlas.qa-mickey.planx-pla.net for Atlas iframe in VHDC qa-mickey
       - https://*.quicksight.aws.amazon.com for loading AWS Quicksight dashboards into COVID-19 Home page
     -->
-    <meta http-equiv="Content-Security-Policy" content="default-src 'self' https://#.bionimbus.org https://wayf.incommonfederation.org; child-src blob:; connect-src 'self' blob: localhost https://localhost:9443 wss://localhost:9443 https://*.s3.amazonaws.com https://*.mapbox.com https://opendata.datacommons.io https://static.planx-pla.net https://*.logs.datadoghq.com https://classic.clinicaltrials.gov https://*.google-analytics.com https://*.analytics.google.com; img-src 'self' https://opendata.datacommons.io https://static.planx-pla.net https://www.google-analytics.com data: https://*.s3.amazonaws.com https://www.google-analytics.com; script-src 'self' 'unsafe-eval' https://*.google-analytics.com https://www.googletagmanager.com localhost https://localhost:9443; worker-src 'self' blob:; style-src 'self' 'unsafe-inline' https://fonts.googleapis.com localhost https://localhost:9443; object-src 'none'; font-src 'self' data: https://fonts.googleapis.com https://fonts.gstatic.com; frame-src 'self' https://auspice.planx-pla.net https://auspice.pandemicresponsecommons.org https://atlas.qa-mickey.planx-pla.net https://*.quicksight.aws.amazon.com; ">
+    <meta http-equiv="Content-Security-Policy" content="default-src 'self' https://#.bionimbus.org https://wayf.incommonfederation.org; child-src blob:; connect-src 'self' blob: localhost https://localhost:9443 wss://localhost:9443 https://*.s3.amazonaws.com https://*.mapbox.com https://opendata.datacommons.io https://static.planx-pla.net https://*.logs.datadoghq.com https://clinicaltrials.gov https://*.google-analytics.com https://*.analytics.google.com; img-src 'self' https://opendata.datacommons.io https://static.planx-pla.net https://www.google-analytics.com data: https://*.s3.amazonaws.com https://www.google-analytics.com; script-src 'self' 'unsafe-eval' https://*.google-analytics.com https://www.googletagmanager.com localhost https://localhost:9443; worker-src 'self' blob:; style-src 'self' 'unsafe-inline' https://fonts.googleapis.com localhost https://localhost:9443; object-src 'none'; font-src 'self' data: https://fonts.googleapis.com https://fonts.gstatic.com; frame-src 'self' https://auspice.planx-pla.net https://auspice.pandemicresponsecommons.org https://atlas.qa-mickey.planx-pla.net https://*.quicksight.aws.amazon.com; ">
     <meta name="viewport" content="width=device-width" />
     <link href="https://fonts.googleapis.com/icon?family=Source+Sans+Pro" rel="stylesheet">
     <link href="https://fonts.googleapis.com/css2?family=Roboto:ital,wght@0,400;0,700;1,700&display=swap" rel="stylesheet">

src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadVariableMetadata/DownloadVariableMetadata.tsx

@@ -24,7 +24,7 @@ const DownloadVariableMetadata = async (
       content: (
         <React.Fragment>
           <p>
-              Study with name <strong>{resourceInfo.project_title}</strong>
+              Study with name <strong>{resourceInfo.study_metadata?.minimal_info?.study_name || 'N/A'}</strong>
               &nbsp;cannot download data dictionary with name <strong>{key}</strong>.
           </p>
           <p>Please try again later and contact support.</p>

src/Discovery/DiscoveryDetails/Components/HeaderButtons/HeaderButtons.tsx

@@ -116,7 +116,7 @@ const HeaderButtons = ({ props, setTabActiveKey }) => {
                       props.modalData[
                         studyRegistrationConfig.studyRegistrationAccessCheckField
                       ],
-                      props.modalData.project_title,
+                      props.modalData.study_metadata?.minimal_info?.study_name,
                       props.modalData.project_number,
                       props.modalData[
                         studyRegistrationConfig.studyRegistrationUIDField
@@ -128,7 +128,7 @@ const HeaderButtons = ({ props, setTabActiveKey }) => {
                     props.modalData[
                       studyRegistrationConfig.studyRegistrationAccessCheckField
                     ],
-                    props.modalData.project_title,
+                    props.modalData.study_metadata?.minimal_info?.study_name,
                     props.modalData.project_number,
                     props.modalData[
                       studyRegistrationConfig.studyRegistrationUIDField
@@ -154,7 +154,7 @@ const HeaderButtons = ({ props, setTabActiveKey }) => {
               props.modalData[
                 studyRegistrationConfig.studyRegistrationAccessCheckField
               ],
-              props.modalData.project_title,
+              props.modalData.study_metadata?.minimal_info?.study_name,
               props.modalData.project_number,
               props.modalData[
                 studyRegistrationConfig.studyRegistrationUIDField
@@ -180,7 +180,7 @@ const HeaderButtons = ({ props, setTabActiveKey }) => {
               props.modalData[
                 studyRegistrationConfig.studyRegistrationAccessCheckField
               ],
-              props.modalData.project_title,
+              props.modalData.study_metadata?.minimal_info?.study_name,
               props.modalData.project_number,
               props.modalData[
                 studyRegistrationConfig.studyRegistrationUIDField

src/StudyRegistration/StudyRegistration.tsx

@@ -18,12 +18,12 @@ import {
 } from '@ant-design/icons';
 import { FontAwesomeIcon } from '@fortawesome/react-fontawesome';
 import { Link, useLocation } from 'react-router-dom';
-
 import './StudyRegistration.css';
 import { userHasMethodForServiceOnResource } from '../authMappingUtils';
 import { useArboristUI, studyRegistrationConfig } from '../localconf';
 import loadStudiesFromMDS from '../Discovery/MDSUtils';
 import { registerStudyInMDS, preprocessStudyRegistrationMetadata, createCEDARInstance } from './utils';
+import Spinner from '../components/Spinner';
 
 const { Option } = Select;
 const { Text } = Typography;
@@ -73,13 +73,13 @@ const handleClinicalTrialIDValidation = async (_, ctID: string): Promise<boolean
   if (!ctID) {
     return Promise.resolve(true);
   }
-  const resp = await fetch(`https://classic.clinicaltrials.gov/api/query/field_values?expr=${encodeURIComponent(`SEARCH[Study](AREA[NCTId] ${ctID})`)}&field=NCTId&fmt=json`);
+  const resp = await fetch(`https://clinicaltrials.gov/api/v2/studies/${ctID}?fields=NCTId`);
   if (!resp || resp.status !== 200) {
     return Promise.reject('Unable to verify ClinicalTrials.gov ID');
   }
   try {
     const respJson = await resp.json();
-    if (respJson.FieldValuesResponse?.FieldValues?.length === 1 && respJson.FieldValuesResponse.FieldValues[0].FieldValue === ctID) {
+    if (respJson.protocolSection?.identificationModule?.nctId === ctID) {
       return Promise.resolve(true);
     }
     return Promise.reject('Invalid ClinicalTrials.gov ID');
@@ -90,55 +90,18 @@ const handleClinicalTrialIDValidation = async (_, ctID: string): Promise<boolean
 
 const getClinicalTrialMetadata = async (ctID: string): Promise<object> => {
   const errMsg = 'Unable to fetch study metadata from ClinicalTrials.gov';
-
-  // get metadata from the clinicaltrials.gov API
-  const promiseList: Promise<any>[] = [];
-  const limit = 20; // the API has a limit of 20 fields
-  let offset = 0;
   const clinicalTrialFieldsToFetch = studyRegistrationConfig.clinicalTrialFields || [];
-  while (offset < clinicalTrialFieldsToFetch.length) {
-    const fieldsToFetch = clinicalTrialFieldsToFetch.slice(offset, offset + limit);
-    offset += limit;
-    promiseList.push(
-      fetch(`https://classic.clinicaltrials.gov/api/query/study_fields?expr=${encodeURIComponent(`SEARCH[Study](AREA[NCTId] ${ctID})`)}&fields=${fieldsToFetch.join(',')}&fmt=json`)
-        .then(
-          (resp) => {
-            if (!resp || resp.status !== 200) {
-              return Promise.reject(errMsg);
-            }
-            return resp.json();
-          },
-        ),
-    );
+  // get metadata from the clinicaltrials.gov API
+  const resp = await fetch(`https://clinicaltrials.gov/api/v2/studies/${ctID}?fields=${clinicalTrialFieldsToFetch.join('|')}`);
+  if (!resp || resp.status !== 200) {
+    return Promise.reject('Unable to verify ClinicalTrials.gov ID');
+  }
+  try {
+    const respJson = await resp.json();
+    return respJson;
+  } catch {
+    throw errMsg;
   }
-  const responsesJson = await Promise.all(promiseList);
-
-  // add the metadata returned by each call to a single `metadata` object
-  let metadata = {};
-  responsesJson.forEach((respJson) => {
-    // it should return data for a single study
-    if (respJson.StudyFieldsResponse?.StudyFields?.length !== 1) {
-      // eslint-disable-next-line no-console
-      console.error(`${errMsg}; received response:`, respJson);
-      throw new Error(errMsg);
-    }
-    // `respData` looks like this:
-    // {Rank: value to discard, FieldWithData: [value], FieldWithoutData: []}
-    const respData = respJson.StudyFieldsResponse.StudyFields[0];
-    // `partialMetadata` looks like this: (remove Rank and fields without data)
-    // {FieldWithData: value}
-    delete respData.Rank;
-    const partialMetadata = Object.keys(respData).reduce((res, key) => {
-      if (respData[key].length > 0) {
-        res[key] = respData[key][0];
-      }
-      return res;
-    }, {});
-    // add the new key:value pairs to the ones we already have
-    metadata = { ...metadata, ...partialMetadata };
-  });
-
-  return Promise.resolve(metadata);
 };
 
 const isUUID = (input: string) => {
@@ -272,7 +235,9 @@ const StudyRegistration: React.FunctionComponent<StudyRegistrationProps> = (prop
       </div>
     );
   }
-
+  if (!studies) {
+    return <Spinner text={'Loading study registration form, please wait...'} />;
+  }
   return (
     <div className='study-reg-container'>
       <div className='study-reg-form-container'>
@@ -292,7 +257,7 @@ const StudyRegistration: React.FunctionComponent<StudyRegistrationProps> = (prop
                   key={study[studyRegistrationConfig.studyRegistrationUIDField]}
                   value={study[studyRegistrationConfig.studyRegistrationUIDField]}
                 >
-                  {`${study.project_number} : ${study.project_title} : ${study.appl_id}`}
+                  {`${study.project_number || 'N/A'} : ${study.study_metadata?.minimal_info?.study_name || 'N/A'} : ${study.study_metadata?.metadata_location?.nih_application_id || 'N/A'}`}
                 </Option>
               ))}
             </Select>
@@ -345,12 +310,14 @@ const StudyRegistration: React.FunctionComponent<StudyRegistrationProps> = (prop
             name='repository'
             label='Study Data Repository'
             hasFeedback
-             help={(
-               <React.Fragment> If you have already selected a data repository, indicate it here; otherwise, leave empty.<br />
-                 If you have deposited your data and you have a unique Study ID for the data at the repository, enter it below; otherwise, leave blank.
-               </React.Fragment>
-             )}
-            >
+            help={(
+              <React.Fragment> If you have already selected a data repository, indicate it here;
+                 otherwise, leave empty.<br />
+                 If you have deposited your data and you have a unique Study ID for the data at
+                  the repository, enter it below; otherwise, leave blank.
+              </React.Fragment>
+            )}
+          >
             <Select placeholder='Select a data repository' showSearch allowClear>
               <Option value='BioSystics-AP'>BioSystics-AP</Option>
               <Option value='Database of Genotypes and Phenotypes (dbGaP)'>Database of Genotypes and Phenotypes (dbGaP)</Option>

src/StudyRegistration/utils.tsx

@@ -73,9 +73,15 @@ export const createCEDARInstance = async (cedarUserUUID, metadataToRegister = {
     body: JSON.stringify({
       cedar_user_uuid: cedarUserUUID,
       metadata: {
-        appl_id: metadataToRegister[STUDY_DATA_FIELD].study_metadata.metadata_location.nih_application_id,
-        project_title: metadataToRegister[STUDY_DATA_FIELD].study_metadata.minimal_info.study_name,
-        study_description_summary: metadataToRegister[STUDY_DATA_FIELD].study_metadata.minimal_info.study_description,
+        study_metadata: {
+          metadata_location: {
+            nih_application_id: metadataToRegister[STUDY_DATA_FIELD].study_metadata.metadata_location.nih_application_id,
+          },
+          minimal_info: {
+            study_name: metadataToRegister[STUDY_DATA_FIELD].study_metadata.minimal_info.study_name,
+            study_description: metadataToRegister[STUDY_DATA_FIELD].study_metadata.minimal_info.study_description,
+          },
+        },
         clinicaltrials_gov: metadataToRegister.clinicaltrials_gov,
       },
     }),

webpack.config.js

@@ -37,7 +37,7 @@ if (configFile.featureFlags && configFile.featureFlags.discoveryUseAggMDS) {
   connectSrcURLs.push('https://dataguids.org');
 }
 if (configFile.featureFlags && configFile.featureFlags.studyRegistration) {
-  connectSrcURLs.push('https://classic.clinicaltrials.gov');
+  connectSrcURLs.push('https://clinicaltrials.gov');
 }
 if (process.env.DATADOG_APPLICATION_ID && process.env.DATADOG_CLIENT_TOKEN) {
   connectSrcURLs.push('https://*.logs.datadoghq.com');