@@ -18,12 +18,12 @@ import {
1818} from '@ant-design/icons' ;
1919import { FontAwesomeIcon } from '@fortawesome/react-fontawesome' ;
2020import { Link , useLocation } from 'react-router-dom' ;
21-
2221import './StudyRegistration.css' ;
2322import { userHasMethodForServiceOnResource } from '../authMappingUtils' ;
2423import { useArboristUI , studyRegistrationConfig } from '../localconf' ;
2524import loadStudiesFromMDS from '../Discovery/MDSUtils' ;
2625import { registerStudyInMDS , preprocessStudyRegistrationMetadata , createCEDARInstance } from './utils' ;
26+ import Spinner from '../components/Spinner' ;
2727
2828const { Option } = Select ;
2929const { Text } = Typography ;
@@ -73,13 +73,13 @@ const handleClinicalTrialIDValidation = async (_, ctID: string): Promise<boolean
7373 if ( ! ctID ) {
7474 return Promise . resolve ( true ) ;
7575 }
76- const resp = await fetch ( `https://classic. clinicaltrials.gov/api/query/field_values?expr= ${ encodeURIComponent ( `SEARCH[Study](AREA[NCTId] ${ ctID } )` ) } &field =NCTId&fmt=json ` ) ;
76+ const resp = await fetch ( `https://clinicaltrials.gov/api/v2/studies/ ${ ctID } ?fields =NCTId` ) ;
7777 if ( ! resp || resp . status !== 200 ) {
7878 return Promise . reject ( 'Unable to verify ClinicalTrials.gov ID' ) ;
7979 }
8080 try {
8181 const respJson = await resp . json ( ) ;
82- if ( respJson . FieldValuesResponse ?. FieldValues ?. length === 1 && respJson . FieldValuesResponse . FieldValues [ 0 ] . FieldValue === ctID ) {
82+ if ( respJson . protocolSection ?. identificationModule ?. nctId === ctID ) {
8383 return Promise . resolve ( true ) ;
8484 }
8585 return Promise . reject ( 'Invalid ClinicalTrials.gov ID' ) ;
@@ -90,55 +90,18 @@ const handleClinicalTrialIDValidation = async (_, ctID: string): Promise<boolean
9090
9191const getClinicalTrialMetadata = async ( ctID : string ) : Promise < object > => {
9292 const errMsg = 'Unable to fetch study metadata from ClinicalTrials.gov' ;
93-
94- // get metadata from the clinicaltrials.gov API
95- const promiseList : Promise < any > [ ] = [ ] ;
96- const limit = 20 ; // the API has a limit of 20 fields
97- let offset = 0 ;
9893 const clinicalTrialFieldsToFetch = studyRegistrationConfig . clinicalTrialFields || [ ] ;
99- while ( offset < clinicalTrialFieldsToFetch . length ) {
100- const fieldsToFetch = clinicalTrialFieldsToFetch . slice ( offset , offset + limit ) ;
101- offset += limit ;
102- promiseList . push (
103- fetch ( `https://classic.clinicaltrials.gov/api/query/study_fields?expr=${ encodeURIComponent ( `SEARCH[Study](AREA[NCTId] ${ ctID } ) } ${ fieldsToFetch . join ( ',' ) } )
104- . then (
105- ( resp ) => {
106- if ( ! resp || resp . status !== 200 ) {
107- return Promise . reject ( errMsg ) ;
108- }
109- return resp . json ( ) ;
110- } ,
111- ) ,
112- ) ;
94+ // get metadata from the clinicaltrials.gov API
95+ const resp = await fetch ( `https://clinicaltrials.gov/api/v2/studies/${ ctID } ${ clinicalTrialFieldsToFetch . join ( '|' ) } ) ;
96+ if ( ! resp || resp . status !== 200 ) {
97+ return Promise . reject ( 'Unable to verify ClinicalTrials.gov ID' ) ;
98+ }
99+ try {
100+ const respJson = await resp . json ( ) ;
101+ return respJson ;
102+ } catch {
103+ throw errMsg ;
113104 }
114- const responsesJson = await Promise . all ( promiseList ) ;
115-
116- // add the metadata returned by each call to a single `metadata` object
117- let metadata = { } ;
118- responsesJson . forEach ( ( respJson ) => {
119- // it should return data for a single study
120- if ( respJson . StudyFieldsResponse ?. StudyFields ?. length !== 1 ) {
121- // eslint-disable-next-line no-console
122- console . error ( `${ errMsg } , respJson ) ;
123- throw new Error ( errMsg ) ;
124- }
125- // `respData` looks like this:
126- // {Rank: value to discard, FieldWithData: [value], FieldWithoutData: []}
127- const respData = respJson . StudyFieldsResponse . StudyFields [ 0 ] ;
128- // `partialMetadata` looks like this: (remove Rank and fields without data)
129- // {FieldWithData: value}
130- delete respData . Rank ;
131- const partialMetadata = Object . keys ( respData ) . reduce ( ( res , key ) => {
132- if ( respData [ key ] . length > 0 ) {
133- res [ key ] = respData [ key ] [ 0 ] ;
134- }
135- return res ;
136- } , { } ) ;
137- // add the new key:value pairs to the ones we already have
138- metadata = { ...metadata , ...partialMetadata } ;
139- } ) ;
140-
141- return Promise . resolve ( metadata ) ;
142105} ;
143106
144107const isUUID = ( input : string ) => {
@@ -272,7 +235,9 @@ const StudyRegistration: React.FunctionComponent<StudyRegistrationProps> = (prop
272235 </ div >
273236 ) ;
274237 }
275-
238+ if ( ! studies ) {
239+ return < Spinner text = { 'Loading study registration form, please wait...' } /> ;
240+ }
276241 return (
277242 < div className = 'study-reg-container' >
278243 < div className = 'study-reg-form-container' >
@@ -292,7 +257,7 @@ const StudyRegistration: React.FunctionComponent<StudyRegistrationProps> = (prop
292257 key = { study [ studyRegistrationConfig . studyRegistrationUIDField ] }
293258 value = { study [ studyRegistrationConfig . studyRegistrationUIDField ] }
294259 >
295- { `${ study . project_number } ${ study . project_title } ${ study . appl_id } }
260+ { `${ study . project_number || 'N/A' } ${ study . study_metadata ?. minimal_info ?. study_name || 'N/A' } ${ study . study_metadata ?. metadata_location ?. nih_application_id || 'N/A' } }
296261 </ Option >
297262 ) ) }
298263 </ Select >
@@ -345,12 +310,14 @@ const StudyRegistration: React.FunctionComponent<StudyRegistrationProps> = (prop
345310 name = 'repository'
346311 label = 'Study Data Repository'
347312 hasFeedback
348- help = { (
349- < React . Fragment > If you have already selected a data repository, indicate it here; otherwise, leave empty.< br />
350- 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.
351- </ React . Fragment >
352- ) }
353- >
313+ help = { (
314+ < React . Fragment > If you have already selected a data repository, indicate it here;
315+ otherwise, leave empty.< br />
316+ If you have deposited your data and you have a unique Study ID for the data at
317+ the repository, enter it below; otherwise, leave blank.
318+ </ React . Fragment >
319+ ) }
320+ >
354321 < Select placeholder = 'Select a data repository' showSearch allowClear >
355322 < Option value = 'BioSystics-AP' > BioSystics-AP</ Option >
356323 < Option value = 'Database of Genotypes and Phenotypes (dbGaP)' > Database of Genotypes and Phenotypes (dbGaP)</ Option >
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