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HP-1179: Updates to Study Registration / VLMD Submission page to support nested fields (#1365)
* HP-1179: Updates to Study Registration / VLMD Submission page to support nested fields * HP-1179: fix typo in cedar id * HP-1179: update clinicaltrials.gov api to classic endpoint * HP-1179: update CSP * HP-1179: dont create metadata clinicaltrials_gov if it does not exist --------- Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>
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‎dev.html

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@@ -11,7 +11,7 @@
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- https://atlas-qa-mickey.planx-pla.net for Atlas iframe in VHDC qa-mickey
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- https://*.quicksight.aws.amazon.com for loading AWS Quicksight dashboards into COVID-19 Home page
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-->
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<meta http-equiv="Content-Security-Policy" content="default-src 'self' https://login.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; ">
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<meta http-equiv="Content-Security-Policy" content="default-src 'self' https://login.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; ">
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<meta name="viewport" content="width=device-width" />
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<link href="https://fonts.googleapis.com/icon?family=Source+Sans+Pro" rel="stylesheet">
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<link href="https://fonts.googleapis.com/css2?family=Roboto:ital,wght@0,400;0,700;1,700&display=swap" rel="stylesheet">

‎src/StudyRegistration/StudyRegistration.tsx

+3-5
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@@ -73,7 +73,7 @@ const handleClinicalTrialIDValidation = async (_, ctID: string): Promise<boolean
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if (!ctID) {
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return Promise.resolve(true);
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}
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const resp = await fetch(`https://clinicaltrials.gov/api/query/field_values?expr=${encodeURIComponent(`SEARCH[Study](AREA[NCTId] ${ctID})`)}&field=NCTId&fmt=json`);
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const resp = await fetch(`https://classic.clinicaltrials.gov/api/query/field_values?expr=${encodeURIComponent(`SEARCH[Study](AREA[NCTId] ${ctID})`)}&field=NCTId&fmt=json`);
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if (!resp || resp.status !== 200) {
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return Promise.reject('Unable to verify ClinicalTrials.gov ID');
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}
@@ -100,7 +100,7 @@ const getClinicalTrialMetadata = async (ctID: string): Promise<object> => {
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const fieldsToFetch = clinicalTrialFieldsToFetch.slice(offset, offset + limit);
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offset += limit;
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promiseList.push(
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fetch(`https://clinicaltrials.gov/api/query/study_fields?expr=${encodeURIComponent(`SEARCH[Study](AREA[NCTId] ${ctID})`)}&fields=${fieldsToFetch.join(',')}&fmt=json`)
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fetch(`https://classic.clinicaltrials.gov/api/query/study_fields?expr=${encodeURIComponent(`SEARCH[Study](AREA[NCTId] ${ctID})`)}&fields=${fieldsToFetch.join(',')}&fmt=json`)
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.then(
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(resp) => {
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if (!resp || resp.status !== 200) {
@@ -207,10 +207,8 @@ const StudyRegistration: React.FunctionComponent<StudyRegistrationProps> = (prop
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repository: formValues.repository || '',
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repository_study_ids: ((!formValues.repository_study_ids || formValues.repository_study_ids[0] === '') ? [] : formValues.repository_study_ids),
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clinical_trials_id: ctgovID || '',
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clinicaltrials_gov: ctgovID ? await getClinicalTrialMetadata(ctgovID) : undefined,
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};
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if (ctgovID) {
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valuesToUpdate['clinicaltrials.gov'] = await getClinicalTrialMetadata(ctgovID);
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}
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preprocessStudyRegistrationMetadata(props.user.username, studyID, valuesToUpdate)
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.then(
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(preprocessedMetadata) => createCEDARInstance(cedarUserUUID, preprocessedMetadata)

‎src/StudyRegistration/utils.tsx

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@@ -33,26 +33,47 @@ export const preprocessStudyRegistrationMetadata = async (username, metadataID,
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}
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metadataToUpdate[STUDY_DATA_FIELD][studyRegistrationValidationField] = true;
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metadataToUpdate[STUDY_DATA_FIELD][studyRegistrationTrackingField] = username;
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metadataToUpdate[STUDY_DATA_FIELD] = { ...metadataToUpdate[STUDY_DATA_FIELD], ...updatedValues };
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// add all repository_study_ids as separate objects
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if (updatedValues.repository_study_ids?.length > 0) {
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const tempStudyIDObj = updatedValues.repository_study_ids.map((studyId) => ({
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repository_name: updatedValues.repository,
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repository_study_ID: studyId,
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}));
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metadataToUpdate[STUDY_DATA_FIELD].study_metadata.metadata_location.data_repositories = tempStudyIDObj;
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}
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metadataToUpdate[STUDY_DATA_FIELD].study_metadata.metadata_location.clinical_trials_study_ID = updatedValues.clinical_trials_id;
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if (updatedValues.clinical_trials_id) {
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metadataToUpdate.clinicaltrials_gov = updatedValues.clinicaltrials_gov;
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}
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return metadataToUpdate;
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} catch (err) {
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throw new Error(`Request for query MDS failed: ${err}`);
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}
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};
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export const createCEDARInstance = async (cedarUserUUID, metadataToRegister = {}):Promise<any> => {
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export const createCEDARInstance = async (cedarUserUUID, metadataToRegister = { clinicaltrials_gov: {} }):Promise<any> => {
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const cedarCreationURL = `${cedarWrapperURL}/create`;
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let updatedMetadataToRegister = { ...metadataToRegister };
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updatedMetadataToRegister = await fetchWithCreds({
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path: cedarCreationURL,
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method: 'POST',
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customHeaders: { 'Content-Type': 'application/json' },
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body: JSON.stringify({ cedar_user_uuid: cedarUserUUID, metadata: metadataToRegister[STUDY_DATA_FIELD] }),
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body: JSON.stringify({
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cedar_user_uuid: cedarUserUUID,
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metadata: {
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appl_id: metadataToRegister[STUDY_DATA_FIELD].study_metadata.metadata_location.nih_application_id,
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project_title: metadataToRegister[STUDY_DATA_FIELD].study_metadata.minimal_info.study_name,
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study_description_summary: metadataToRegister[STUDY_DATA_FIELD].study_metadata.minimal_info.study_description,
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clinicaltrials_gov: metadataToRegister.clinicaltrials_gov,
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},
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}),
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}).then(({ status, data }) => {
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if (status !== 201) {
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throw new Error(`Request for create CEDAR instance failed with status ${status}`);
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}
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updatedMetadataToRegister[STUDY_DATA_FIELD].cedar_instance_id = data?.cedar_instance_id || '';
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updatedMetadataToRegister[STUDY_DATA_FIELD].study_metadata.metadata_location.cedar_study_level_metadata_template_instance_ID = data?.cedar_instance_id || '';
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return Promise.resolve(updatedMetadataToRegister);
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})
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.catch((err) => { throw new Error(`Request for create CEDAR instance failed: ${err}`); });

‎webpack.config.js

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@@ -36,7 +36,7 @@ if (configFile.featureFlags && configFile.featureFlags.discoveryUseAggMDS) {
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connectSrcURLs.push('https://dataguids.org');
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}
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if (configFile.featureFlags && configFile.featureFlags.studyRegistration) {
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connectSrcURLs.push('https://clinicaltrials.gov');
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connectSrcURLs.push('https://classic.clinicaltrials.gov');
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}
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if (process.env.DATADOG_APPLICATION_ID && process.env.DATADOG_CLIENT_TOKEN) {
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connectSrcURLs.push('https://*.logs.datadoghq.com');

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