{app.description}
+ No Data Found+ |
+
| Value as String | +Value as Concept ID | +Concept Name | +Person Count | +
|---|---|---|---|
| + {valueSummaryObj.valueAsString} + | ++ {valueSummaryObj.valueAsConceptID} + | ++ {valueSummaryObj.name} + | ++ {valueSummaryObj.personCount.toLocaleString()} + | +
| Min Value | +Max Value | +Mean Value | +Standard Deviation | +
|---|---|---|---|
|
+ {rowObject.minValue.toLocaleString()}
+ |
+
+ {rowObject.maxValue.toLocaleString()}
+ |
+
+ {rowObject.meanValue.toLocaleString()}
+ |
+
+ {rowObject.standardDeviation.toLocaleString()}
+ |
+
+ The VADC website, privacy and security policies don't apply to the + site or app you're about to visit. +
+| {groupName} | ); + } else { + hareGroupNamesJSX.push({groupName} | ); + } + i += 1; + } + + return hareGroupNamesJSX; + }; + + const getBreakDownForGroup = (groupName, conceptBreakdownArray) => { + let matchingObject; + if (conceptBreakdownArray) { + matchingObject = conceptBreakdownArray.find( + (obj) => obj.concept_value_name === groupName, + ); + } + + return displayNumberOrX(matchingObject?.persons_in_cohort_with_value); + }; + + const displayGroupBreakDowns = (hareGroupNames, row) => { + const hareGroupCountsJSX = []; + + hareGroupNames.forEach((hareGroupName) => { + const count = getBreakDownForGroup(hareGroupName.concept_value_name, row?.concept_breakdown); + hareGroupCountsJSX.push({count} | ); + }); + + return hareGroupCountsJSX; + }; + + let hareGroupNames = defaultHareGroups; + + if (tableData.rows) { + hareGroupNames = getHareGroups(tableData.rows[0].concept_breakdown); + } + return (Size | -- Non-Hispanic Black - | -Non-Hispanic Asian | -Non-Hispanic White | -Hispanic | + {displayHareGroupHeaders(hareGroupNames)} @@ -51,29 +101,9 @@ const AttritionTable = ({ tableData, title }) => {{displayRowType(row?.type)} | {row?.name || ❌} |
- {row?.size || ❌} - |
- - {getBreakDownForGroup( - 'non-Hispanic Black', - row?.concept_breakdown, - )} - | -- {getBreakDownForGroup( - 'non-Hispanic Asian', - row?.concept_breakdown, - )} - | -- {getBreakDownForGroup( - 'non-Hispanic White', - row?.concept_breakdown, - )} - | -- {getBreakDownForGroup('Hispanic', row?.concept_breakdown)} + {displayNumberOrX(row?.size)} | + {displayGroupBreakDowns(hareGroupNames, row)} ))} @@ -84,6 +114,7 @@ const AttritionTable = ({ tableData, title }) => { ); }; + AttritionTable.propTypes = { tableData: PropTypes.object.isRequired, title: PropTypes.string.isRequired, diff --git a/src/Analysis/GWASResults/Views/Input/Input.css b/src/Analysis/GWASResults/Views/Input/Input.css index 21f4ca8df9..c066229047 100644 --- a/src/Analysis/GWASResults/Views/Input/Input.css +++ b/src/Analysis/GWASResults/Views/Input/Input.css @@ -29,6 +29,11 @@ margin: 2px 0; } +.job-details-cohort-name { + text-align: right; + width: 135px; +} + .job-details .GWASResults-flex-row div:first-child { font-weight: bold; } diff --git a/src/Analysis/GWASResults/Views/Input/JobDetails/JobDetails.jsx b/src/Analysis/GWASResults/Views/Input/JobDetails/JobDetails.jsx index 495318c639..69f75e9312 100644 --- a/src/Analysis/GWASResults/Views/Input/JobDetails/JobDetails.jsx +++ b/src/Analysis/GWASResults/Views/Input/JobDetails/JobDetails.jsx @@ -14,6 +14,7 @@ const JobDetails = ({ attritionTableData }) => { const { name, uid } = selectedRowData; const endpoint = `${gwasWorkflowPath}status/${name}?uid=${uid}`; const minimumRecommendedCohortSize = 1000; + const cohortNameValue = attritionTableData[0].rows[0].name; const fetchData = async () => { const res = await fetch(endpoint); @@ -189,7 +190,7 @@ const JobDetails = ({ attritionTableData }) => {
|---|
Please authorize these resources at the top of the - } - onClick={() => history.push('/identity', { from: `${location.pathname}` })} - > - profile page - -
-{output}
, - active: true, - }, - }); - } - }, - ).catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); - } else if (status === 'Completed') { - fetchWithCreds({ path: `${jobAPIPath}output?UID=${uid}` }).then( - (outputResponse) => { - const { output } = outputResponse.data; - if (outputResponse.status !== 200 || !output) { - setDownloadStatus(DOWNLOAD_FAIL_STATUS); - } else { - try { - const regexp = /^https?:\/\/(\S+)\.s3\.amazonaws\.com\/(\S+)/gm; - if (!new RegExp(regexp).test(output)) { - throw new Error('Invalid download URL'); - } - setDownloadStatus({ - inProgress: false, - message: { - title: 'Your download is ready', - content: ( -{ DOWNLOAD_SUCCEEDED_MESSAGE }
- {output} -{output}
, - active: true, - }, - }); - } - } - }, - ).catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); - } else { - setTimeout(checkDownloadStatus, JOB_POLLING_INTERVAL, uid, downloadStatus, setDownloadStatus, selectedResources); - } - }, - ); -}; - -const handleDownloadZipClick = async ( - config: DiscoveryConfig, - selectedResources: any[], - downloadStatus: DownloadStatus, - setDownloadStatus: (arg0: DownloadStatus) => void, - history, - location, - healICPSRLoginNeeded, -) => { - if (config.features.exportToWorkspace.verifyExternalLogins) { - const { manifestFieldName } = config.features.exportToWorkspace; - const isLinked = await checkFederatedLoginStatus(setDownloadStatus, selectedResources, manifestFieldName, history, location); - if (!isLinked) { - return; - } - } - - if (healICPSRLoginNeeded) { - return; - } - - const studyIDs = selectedResources.map((study) => study[config.minimalFieldMapping.uid]); - fetchWithCreds({ - path: `${jobAPIPath}dispatch`, - method: 'POST', - body: JSON.stringify({ action: 'batch-export', input: { study_ids: studyIDs } }), - }).then( - (dispatchResponse) => { - const { uid } = dispatchResponse.data; - if (dispatchResponse.status === 403 || dispatchResponse.status === 302) { - setDownloadStatus({ - inProgress: false, - message: { - title: 'Download failed', - content:{ DOWNLOAD_UNAUTHORIZED_MESSAGE }
, - active: true, - }, - }); - } else if (dispatchResponse.status !== 200 || !uid) { - setDownloadStatus(DOWNLOAD_FAIL_STATUS); - } else { - setDownloadStatus({ - inProgress: true, - message: { - title: 'Your download is being prepared', - content:{ DOWNLOAD_STARTED_MESSAGE }
, - active: true, - }, - }); - setTimeout(checkDownloadStatus, JOB_POLLING_INTERVAL, uid, downloadStatus, setDownloadStatus, selectedResources); - } - }, - ).catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); -}; - -const handleDownloadManifestClick = (config: DiscoveryConfig, selectedResources: any[], healICPSRLoginNeeded: boolean) => { - const { manifestFieldName } = config.features.exportToWorkspace; - if (!manifestFieldName) { - throw new Error('Missing required configuration field `config.features.exportToWorkspace.manifestFieldName`'); - } - - if (healICPSRLoginNeeded) { - return; - } - // combine manifests from all selected studies - const manifest:any = []; - selectedResources.forEach((study) => { - if (study[manifestFieldName]) { - if ('commons_url' in study && !(hostname.includes(study.commons_url))) { // PlanX addition to allow hostname based DRS in manifest download clients - // like FUSE - manifest.push(...study[manifestFieldName].map((x) => ({ - ...x, - commons_url: ('commons_url' in x) - ? x.commons_url : study.commons_url, - }))); - } else { - manifest.push(...study[manifestFieldName]); - } - } - }); - const projectNumber = selectedResources.map((study) => study.project_number); - const studyName = selectedResources.map((study) => study.study_name); - const repositoryName = selectedResources.map((study) => study.commons); - datadogRum.addAction('manifestDownload', { - manifestDownloadProjectNumber: projectNumber, - manifestDownloadStudyName: studyName, - manifestDownloadRepositoryName: repositoryName, - }); - // download the manifest - const MANIFEST_FILENAME = 'manifest.json'; - const blob = new Blob([JSON.stringify(manifest, null, 2)], { type: 'text/json' }); - FileSaver.saveAs(blob, MANIFEST_FILENAME); -}; - -const handleExportToWorkspaceClick = async ( - config: DiscoveryConfig, - selectedResources: any[], - setExportingToWorkspace: (boolean) => void, - setDownloadStatus: (arg0: DownloadStatus) => void, - history: any, - location: any, - healICPSRLoginNeeded: boolean, -) => { - const { manifestFieldName } = config.features.exportToWorkspace; - if (!manifestFieldName) { - throw new Error('Missing required configuration field `config.features.exportToWorkspace.manifestFieldName`'); - } - - if (healICPSRLoginNeeded) { - return; - } - - if (config.features.exportToWorkspace.verifyExternalLogins) { - const isLinked = await checkFederatedLoginStatus( - setDownloadStatus, selectedResources, manifestFieldName, history, location, - ); - if (!isLinked) { - return; - } - } - - setExportingToWorkspace(true); - // combine manifests from all selected studies - const manifest:any = []; - selectedResources.forEach((study) => { - if (study[manifestFieldName]) { - if ('commons_url' in study && !(hostname.includes(study.commons_url))) { // PlanX addition to allow hostname based DRS in manifest download clients - // like FUSE - manifest.push(...study[manifestFieldName].map((x) => ({ - ...x, - commons_url: ('commons_url' in x) - ? x.commons_url : study.commons_url, - }))); - } else { - manifest.push(...study[manifestFieldName]); - } - } - }); - - const projectNumber = selectedResources.map((study) => study.project_number); - const studyName = selectedResources.map((study) => study.study_name); - const repositoryName = selectedResources.map((study) => study.commons); - datadogRum.addAction('exportToWorkspace', { - exportToWorkspaceProjectNumber: projectNumber, - exportToWorkspaceStudyName: studyName, - exportToWorkspaceRepositoryName: repositoryName, - }); - - // post selected resources to manifestservice - const res = await fetchWithCreds({ - path: `${manifestServiceApiPath}`, - body: JSON.stringify(manifest), - method: 'POST', - }); - if (res.status !== 200) { - throw new Error(`Encountered error while exporting to Workspace: ${JSON.stringify(res)}`); - } - setExportingToWorkspace(false); - // redirect to Workspaces page - history.push('/workspace'); -}; - -const DiscoveryActionBar = (props: Props) => { - const history = useHistory(); - const location = useLocation(); - const [downloadStatus, setDownloadStatus] = useState({ - inProgress: false, - message: { title: '', content:+ {' '} + There was a problem preparing your download. Please consider using the + Gen3 SDK for Python (w/ CLI) to download these files via a manifest. +
+ ), + active: true, + }, +}; + +export { + BATCH_EXPORT_JOB_PREFIX, GUID_PREFIX_PATTERN, JOB_POLLING_INTERVAL, DOWNLOAD_FAIL_STATUS, +}; diff --git a/src/Discovery/DiscoveryActionBar/DiscoveryActionBarInterfaces.ts b/src/Discovery/DiscoveryActionBar/DiscoveryActionBarInterfaces.ts new file mode 100644 index 0000000000..c89d0f5e86 --- /dev/null +++ b/src/Discovery/DiscoveryActionBar/DiscoveryActionBarInterfaces.ts @@ -0,0 +1,21 @@ +interface User { + username: string; + fence_idp?: string; // eslint-disable-line camelcase + } + interface JobStatus { + uid: string; + status: 'Running' | 'Completed' | 'Failed' | 'Unknown'; + name: string; + } + interface DownloadStatus { + inProgress: boolean; + message: { + content: JSX.Element; + active: boolean; + title: string; + }; + } + +export { + User, JobStatus, DownloadStatus, +}; diff --git a/src/Discovery/DiscoveryActionBar/components/DownloadManifestButton.tsx b/src/Discovery/DiscoveryActionBar/components/DownloadManifestButton.tsx new file mode 100644 index 0000000000..72b90df2c5 --- /dev/null +++ b/src/Discovery/DiscoveryActionBar/components/DownloadManifestButton.tsx @@ -0,0 +1,72 @@ +import React from 'react'; +import { FileTextOutlined } from '@ant-design/icons'; +import { Popover, Button } from 'antd'; +import handleDownloadManifestClick from '../utils/handleDownloadManifestClick'; +import { handleRedirectToLoginClickResumable } from '../../Utils/HandleRedirectToLoginClick'; + +const DownloadManifestButton = ({ + props, healIDPLoginNeeded, onlyInCommonMsg, history, location, +}) => (props.config.features.exportToWorkspace?.enableDownloadManifest ? ( +{output}
, + active: true, + }, + }); + } + }) + .catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); + } else if (status === 'Completed') { + fetchWithCreds({ path: `${jobAPIPath}output?UID=${uid}` }) + .then((outputResponse) => { + const { output } = outputResponse.data; + if (outputResponse.status !== 200 || !output) { + setDownloadStatus(DOWNLOAD_FAIL_STATUS); + } else { + try { + const regexp = /^https?:\/\/(\S+)\.s3\.amazonaws\.com\/(\S+)/gm; + if (!new RegExp(regexp).test(output)) { + throw new Error('Invalid download URL'); + } + setDownloadStatus({ + inProgress: false, + message: { + title: 'Your download is ready', + content: ( +Your download has been prepared. If your download doesn't start automatically, please click this link
+{output}
, + active: true, + }, + }); + } + } + }) + .catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); + } else { + setTimeout( + checkDownloadStatus, + JOB_POLLING_INTERVAL, + uid, + downloadStatus, + setDownloadStatus, + selectedResources, + ); + } + }, + ); +}; + +export default checkDownloadStatus; diff --git a/src/Discovery/DiscoveryActionBar/utils/checkFederatedStatus.tsx b/src/Discovery/DiscoveryActionBar/utils/checkFederatedStatus.tsx new file mode 100644 index 0000000000..810dccf060 --- /dev/null +++ b/src/Discovery/DiscoveryActionBar/utils/checkFederatedStatus.tsx @@ -0,0 +1,109 @@ +import React from 'react'; +import { Button, Table } from 'antd'; +import { LinkOutlined } from '@ant-design/icons'; +import { fetchWithCreds } from '../../../actions'; +import { externalLoginOptionsUrl } from '../../../localconf'; +import { DownloadStatus } from '../DiscoveryActionBarInterfaces'; +import { GUID_PREFIX_PATTERN } from '../DiscoveryActionBarConstants'; + +const checkFederatedLoginStatus = async ( + setDownloadStatus: (arg0: DownloadStatus) => void, + selectedResources: any[], + manifestFieldName: string, + history, + location, +) => fetchWithCreds({ + path: `${externalLoginOptionsUrl}`, + method: 'GET', +}) + .then(async ({ data, status }) => { + if (status !== 200) { + return false; + } + const { providers } = data; + const unauthenticatedProviders = providers.filter( + (provider) => !provider.refresh_token_expiration, + ); + + const guidsForHostnameResolution: any = []; + const guidPrefixes: any = []; + selectedResources.forEach((selectedResource) => { + (selectedResource[manifestFieldName] || []).forEach((fileMetadata) => { + if (fileMetadata.object_id) { + const guidDomainPrefix = ( + fileMetadata.object_id.match(GUID_PREFIX_PATTERN) || [] + ).shift(); + if (guidDomainPrefix) { + if (!guidPrefixes.includes(guidDomainPrefix)) { + guidPrefixes.push(guidDomainPrefix); + guidsForHostnameResolution.push(fileMetadata.object_id); + } + } else { + guidsForHostnameResolution.push(fileMetadata.object_id); + } + } + }); + }); + const guidResolutions = await Promise.all( + guidsForHostnameResolution.map((guid) => fetch(`https://dataguids.org/index/${guid}`) + .then((r) => r.json()) + .catch(() => {}), + ), + ); + const externalHosts = guidResolutions + .filter( + (resolvedGuid) => resolvedGuid && resolvedGuid.from_index_service, + ) + .map( + (resolvedGuid) => new URL(resolvedGuid.from_index_service.host).host, + ); + const providersToAuthenticate = unauthenticatedProviders.filter( + (unauthenticatedProvider) => externalHosts.includes( + new URL(unauthenticatedProvider.base_url).hostname, + ), + ); + if (providersToAuthenticate.length) { + setDownloadStatus({ + inProgress: false, + message: { + title: 'Authorization Required', + active: true, + content: ( ++ The data you have selected requires authorization with the + following data resources: +
++ Please authorize these resources at the top of the + } + onClick={() => history.push('/identity', { + from: `${location.pathname}`, + })} + > + profile page + +
+{DOWNLOAD_UNAUTHORIZED_MESSAGE}
, + active: true, + }, + }); + } else if (dispatchResponse.status !== 200 || !uid) { + setDownloadStatus(DOWNLOAD_FAIL_STATUS); + } else { + setDownloadStatus({ + inProgress: true, + message: { + title: 'Your download is being prepared', + content:{DOWNLOAD_STARTED_MESSAGE}
, + active: true, + }, + }); + setTimeout( + checkDownloadStatus, + JOB_POLLING_INTERVAL, + uid, + downloadStatus, + setDownloadStatus, + selectedResources, + ); + } + }) + .catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); +}; + +export default handleDownloadZipClick; diff --git a/src/Discovery/DiscoveryActionBar/utils/handleExportToWorkspaceClick/assembleAndExportMetadata.test.ts b/src/Discovery/DiscoveryActionBar/utils/handleExportToWorkspaceClick/assembleAndExportMetadata.test.ts new file mode 100644 index 0000000000..0d6fc5af87 --- /dev/null +++ b/src/Discovery/DiscoveryActionBar/utils/handleExportToWorkspaceClick/assembleAndExportMetadata.test.ts @@ -0,0 +1,158 @@ +import { + removeKeys, + assembleMetadata, + exportAssembledMetadata, + assembleAndExportMetadata, +} from './assembleAndExportMetadata'; +import { fetchWithCreds } from '../../../../actions'; + +jest.mock('../../../../actions', () => ({ + fetchWithCreds: jest.fn(), +})); + +describe('removeKeys', () => { + it('should remove specified keys from the object', () => { + const obj = { + a: 1, + b: { + c: 2, + d: 3, + }, + }; + const keysToRemove = ['b.c']; + removeKeys(obj, keysToRemove); + expect(obj).toEqual({ a: 1, b: { d: 3 } }); + }); + it('should return the same object if the specified keys do not exist', () => { + const obj = { + a: 1, + b: { + c: 2, + d: 3, + }, + }; + const keysToRemove = ['b.c.f']; + removeKeys(obj, keysToRemove); + expect(obj).toEqual(obj); + }); +}); + +describe('assembleMetadata', () => { + it('should return an array of objects with specified keys removed', () => { + const keysToRemove = ['b.c']; + const selectedResources = [ + { a: 1, b: { c: 2, d: 3 } }, + { x: 10, y: { z: 20 } }, + ]; + const result = assembleMetadata(keysToRemove, selectedResources); + expect(result).toEqual([ + { a: 1, b: { d: 3 } }, + { x: 10, y: { z: 20 } }, + ]); + }); + it('should return an array of objects with specified keys removed and remove their children', () => { + const keysToRemove = ['b.c']; + const selectedResources = [ + { + a: 1, + b: { + c: { d: { e: { f: 'test' } } }, + g: 3, + }, + }, + { x: 10, y: { z: 20 } }, + ]; + const result = assembleMetadata(keysToRemove, selectedResources); + expect(result).toEqual([ + { a: 1, b: { g: 3 } }, + { x: 10, y: { z: 20 } }, + ]); + }); + it('should return an array of objects with no specified keys removed when keysToRemove is empty', () => { + const keysToRemove = []; + const selectedResources = [ + { a: 1, b: { c: 2, d: 3 } }, + { x: 10, y: { z: 20 } }, + ]; + const result = assembleMetadata(keysToRemove, selectedResources); + expect(result).toEqual(selectedResources); + }); + it('should return an array of objects with specified keys removed when there are multiple nestings', () => { + const keysToRemove = ['b.c.d.e.f', 'x', 'y.z']; + const selectedResources = [ + { + a: 1, + b: { + c: { + d: { + e: { + f: 'test', + }, + }, + }, + }, + }, + { x: 10, y: { z: 20 } }, + ]; + const result = assembleMetadata(keysToRemove, selectedResources); + expect(result).toEqual([ + { + a: 1, + b: { + c: { + d: { + e: {}, + }, + }, + }, + }, + { + y: {}, + }, + ]); + }); +}); + +describe('exportAssembledMetadata', () => { + it('should call fetchWithCreds with the correct parameters', async () => { + const filteredData = [{ a: 1 }, { b: 2 }]; + const mockResponse = { status: 200 }; + fetchWithCreds.mockResolvedValue(mockResponse); + + await exportAssembledMetadata(filteredData); + + expect(fetchWithCreds).toHaveBeenCalledWith({ + path: expect.any(String), + body: JSON.stringify(filteredData), + method: 'POST', + }); + }); + + it('should throw an error if response status is not 200', async () => { + const filteredData = [{ a: 1 }, { b: 2 }]; + const mockResponse = { status: 500 }; + fetchWithCreds.mockResolvedValue(mockResponse); + await expect(exportAssembledMetadata(filteredData)).rejects.toThrow( + `Encountered error while exporting assembled metadata: ${JSON.stringify( + mockResponse, + )}`, + ); + }); +}); + +describe('assembleAndExportMetadata', () => { + it(`should call fetchWithCreds with the correct parameters after calling + assembleMetadata and exportAssembledMetadata`, async () => { + const unfilteredData = [{ a: 1 }, { b: 2 }]; + const filteredData = [{}, { b: 2 }]; + const selectedResources = ['a']; + const mockResponse = { status: 200 }; + fetchWithCreds.mockResolvedValue(mockResponse); + await assembleAndExportMetadata(selectedResources, unfilteredData); + expect(fetchWithCreds).toHaveBeenCalledWith({ + path: expect.any(String), + body: JSON.stringify(filteredData), + method: 'POST', + }); + }); +}); diff --git a/src/Discovery/DiscoveryActionBar/utils/handleExportToWorkspaceClick/assembleAndExportMetadata.ts b/src/Discovery/DiscoveryActionBar/utils/handleExportToWorkspaceClick/assembleAndExportMetadata.ts new file mode 100644 index 0000000000..36c9d70231 --- /dev/null +++ b/src/Discovery/DiscoveryActionBar/utils/handleExportToWorkspaceClick/assembleAndExportMetadata.ts @@ -0,0 +1,50 @@ +import { get, unset, cloneDeep } from 'lodash'; +import { manifestServiceApiPath } from '../../../../localconf'; +import { fetchWithCreds } from '../../../../actions'; + +const removeKeys = (obj: object, keysToRemove: Array{ARBORIST_READ_PRIV} access to {props.authzFieldName}.{ARBORIST_READ_PRIV} access to {props.authzFieldName}. + There was a problem preparing your download. Please consider using the + Gen3 SDK for Python (w/ CLI) to download these files via a manifest. +
+ ), + active: true, + }, +}; + +export const JOB_POLLING_INTERVAL = 5000; diff --git a/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadDataFiles/CheckDownloadStatus.tsx b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadDataFiles/CheckDownloadStatus.tsx new file mode 100644 index 0000000000..ea363f6b95 --- /dev/null +++ b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadDataFiles/CheckDownloadStatus.tsx @@ -0,0 +1,91 @@ +import React from 'react'; +import { fetchWithCreds } from '../../../../../../../../../actions'; +import { jobAPIPath } from '../../../../../../../../../localconf'; +import DownloadStatus from '../../../Interfaces/DownloadStatus'; +import { + DOWNLOAD_FAIL_STATUS, + JOB_POLLING_INTERVAL, +} from '../Constants'; + +const CheckDownloadStatus = ( + uid: string, + downloadStatus: DownloadStatus, + setDownloadStatus: (arg0: DownloadStatus) => void, +) => { + fetchWithCreds({ path: `${jobAPIPath}status?UID=${uid}` }).then( + (statusResponse) => { + const { status } = statusResponse.data; + if (statusResponse.status !== 200 || !status) { + // usually empty status message means Sower can't find a job by its UID + setDownloadStatus(DOWNLOAD_FAIL_STATUS); + } else if (status === 'Failed') { + fetchWithCreds({ path: `${jobAPIPath}output?UID=${uid}` }) + .then((outputResponse) => { + const { output } = outputResponse.data; + if (outputResponse.status !== 200 || !output) { + setDownloadStatus(DOWNLOAD_FAIL_STATUS); + } else { + setDownloadStatus({ + inProgress: false, + message: { + title: 'Download failed', + content:{output}
, + active: true, + }, + }); + } + }) + .catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); + } else if (status === 'Completed') { + fetchWithCreds({ path: `${jobAPIPath}output?UID=${uid}` }) + .then((outputResponse) => { + const { output } = outputResponse.data; + if (outputResponse.status !== 200 || !output) { + setDownloadStatus(DOWNLOAD_FAIL_STATUS); + } else { + try { + const regexp = /^https?:\/\/(\S+)\.s3\.amazonaws\.com\/(\S+)/gm; + if (!new RegExp(regexp).test(output)) { + throw new Error('Invalid download URL'); + } + setDownloadStatus({ + inProgress: false, + message: { + title: 'Your download is ready', + content: ( +Your download has been prepared. If your download doesn't start automatically, please click this link
+{output}
, + active: true, + }, + }); + } + } + }) + .catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); + } else { + setTimeout( + CheckDownloadStatus, + JOB_POLLING_INTERVAL, + uid, + downloadStatus, + setDownloadStatus, + ); + } + }, + ); +}; + +export default CheckDownloadStatus; diff --git a/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadDataFiles/CheckFederatedLoginStatus.tsx b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadDataFiles/CheckFederatedLoginStatus.tsx new file mode 100644 index 0000000000..3fce3c8061 --- /dev/null +++ b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadDataFiles/CheckFederatedLoginStatus.tsx @@ -0,0 +1,117 @@ +import React from 'react'; +import { Button, Table } from 'antd'; +import { LinkOutlined } from '@ant-design/icons'; +import { RouteComponentProps } from 'react-router-dom'; +import { fetchWithCreds } from '../../../../../../../../../actions'; +import { externalLoginOptionsUrl } from '../../../../../../../../../localconf'; +import DownloadStatus from '../../../Interfaces/DownloadStatus'; + +/* eslint-disable camelcase */ +interface Iprovider { + base_url: string; + idp: string; + name: string; + refresh_token_expiration: any; +} + +const GUID_PREFIX_PATTERN = /^dg.[a-zA-Z0-9]+\//; +const CheckFederatedLoginStatus = async ( + setDownloadStatus: (arg0: DownloadStatus) => void, + fileManifest: any[], + history: RouteComponentProps['history'], + location: RouteComponentProps['location'], +) => fetchWithCreds({ + path: `${externalLoginOptionsUrl}`, + method: 'GET', +}) + .then(async ({ data, status }) => { + if (status !== 200) { + return false; + } + const { providers } = data; + const unauthenticatedProviders = providers.filter( + (provider: Iprovider) => !provider.refresh_token_expiration, + ); + + const guidsForHostnameResolution: any = []; + const guidPrefixes: any = []; + + fileManifest.forEach((fileManifestItem) => { + if (fileManifestItem.object_id) { + const guidDomainPrefix = ( + fileManifestItem.object_id.match(GUID_PREFIX_PATTERN) || [] + ).shift(); + if (guidDomainPrefix) { + if (!guidPrefixes.includes(guidDomainPrefix)) { + guidPrefixes.push(guidDomainPrefix); + guidsForHostnameResolution.push(fileManifestItem.object_id); + } + } else { + guidsForHostnameResolution.push(fileManifestItem.object_id); + } + } + }); + + const guidResolutions = await Promise.all( + guidsForHostnameResolution.map((guid) => fetch(`https://dataguids.org/index/${guid}`) + .then((r) => r.json()) + .catch(() => {}), + ), + ); + const externalHosts = guidResolutions + .filter( + (resolvedGuid) => resolvedGuid && resolvedGuid.from_index_service, + ) + .map( + (resolvedGuid) => new URL(resolvedGuid.from_index_service.host).host, + ); + const providersToAuthenticate = unauthenticatedProviders.filter( + (unauthenticatedProvider) => externalHosts.includes( + new URL(unauthenticatedProvider.base_url).hostname, + ), + ); + if (providersToAuthenticate.length) { + setDownloadStatus({ + inProgress: '', + message: { + title: 'Authorization Required', + active: true, + content: ( ++ The data you have selected requires authorization with the + following data resources: +
++ Please authorize these resources at the top of the + } + onClick={() => history.push('/identity', { + from: `${location.pathname}`, + })} + > + profile page + +
++ Unable to authorize download. Please refresh the page and ensure + you are logged in. +
+ ), + active: true, + }, + }); + } else if (dispatchResponse.status !== 200 || !uid) { + setDownloadStatus(DOWNLOAD_FAIL_STATUS); + } else { + setDownloadStatus({ + inProgress: 'DownloadDataFiles', + message: { + title: 'Your download is being prepared', + content: ( ++ Please remain on this page until your download completes. When + your download is ready, it will begin automatically. You can + close this window. +
+ ), + active: true, + }, + }); + setTimeout( + CheckDownloadStatus, + JOB_POLLING_INTERVAL, + uid, + downloadStatus, + setDownloadStatus, + ); + } + }) + .catch(() => setDownloadStatus(DOWNLOAD_FAIL_STATUS)); +}; + +export default DownloadDataFiles; diff --git a/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadJsonFile.test.ts b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadJsonFile.test.ts new file mode 100644 index 0000000000..92598dc96a --- /dev/null +++ b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadJsonFile.test.ts @@ -0,0 +1,23 @@ +import FileSaver from 'file-saver'; +import DownloadJsonFile from './DownloadJsonFile'; + +jest.mock('file-saver', () => ({ + saveAs: jest.fn(), +})); + +describe('DownloadJsonFile', () => { + test('downloads JSON file with correct title', () => { + // Set up mock data + const fileName = 'testFile'; + const testData = { key: 'value' }; + + // Call the DownloadJsonFile function + DownloadJsonFile(fileName, testData); + + // Assert that saveAs is called with the correct arguments + expect(FileSaver.saveAs).toHaveBeenCalledWith( + expect.any(Blob), + 'testFile.json', + ); + }); +}); diff --git a/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadJsonFile.ts b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadJsonFile.ts new file mode 100644 index 0000000000..db1a7bba70 --- /dev/null +++ b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadJsonFile.ts @@ -0,0 +1,10 @@ +import FileSaver from 'file-saver'; + +const DownloadJsonFile = (fileName: string, data: object) => { + const blob = new Blob([JSON.stringify(data, null, 2)], { + type: 'text/json', + }); + FileSaver.saveAs(blob, `${fileName}.json`); +}; + +export default DownloadJsonFile; diff --git a/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadVariableMetadata/DownloadVariableMetadata.test.tsx b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadVariableMetadata/DownloadVariableMetadata.test.tsx new file mode 100644 index 0000000000..c3717b3891 --- /dev/null +++ b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadVariableMetadata/DownloadVariableMetadata.test.tsx @@ -0,0 +1,77 @@ +import JSZip from 'jszip'; +import { act } from 'react-dom/test-utils'; +import DownloadVariableMetadata from './DownloadVariableMetadata'; +import { fetchWithCreds } from '../../../../../../../../../actions'; +import { INITIAL_DOWNLOAD_STATUS } from '../Constants'; +import { DiscoveryResource } from '../../../../../../../../Discovery'; + +/* eslint global-require: 0 */ // --> OFF +jest.mock('../../../../../../../../../actions', () => ({ + fetchWithCreds: jest.fn(), +})); +jest.mock('file-saver', () => ({ + saveAs: jest.fn(), +})); +const mockResourceInfo = { + _hdp_uid: 'HDP00001', + project_title: 'Sample Project', +}; + +const mockVariableLevelMetadata = { + dataDictionaries: { 'anotherDataDictionary.json': 'string-associated-with-file-name' }, +}; + +const mockSetDownloadStatus = jest.fn(); +console.error = jest.fn(); + +afterEach(() => { + jest.clearAllMocks(); +}); + +describe('DownloadVariableMetadata', () => { + it('should download variable metadata when called with valid resource info', async () => { + const mockStatusResponse = { + status: 200, + data: { test: 'json-response' }, + }; + const mockGenerateAsync = jest.fn().mockResolvedValue('zipContent'); + jest + .spyOn(JSZip.prototype, 'generateAsync') + .mockImplementation(mockGenerateAsync); + (fetchWithCreds as jest.Mock).mockResolvedValue(mockStatusResponse); + await act(async () => { + await DownloadVariableMetadata( + mockVariableLevelMetadata, + mockResourceInfo as unknown as DiscoveryResource, + mockSetDownloadStatus, + ); + }); + expect(mockSetDownloadStatus).toHaveBeenCalled(); // Status should be set to in progress and then cleared + expect(mockSetDownloadStatus).toHaveBeenCalledWith({ + inProgress: 'DownloadVariableMetadata', + message: INITIAL_DOWNLOAD_STATUS.message, + }); + expect(mockSetDownloadStatus).toHaveBeenCalledWith({ + ...INITIAL_DOWNLOAD_STATUS, + inProgress: 'DownloadVariableMetadata', + }); + expect(require('file-saver').saveAs).toHaveBeenCalled(); // Zip file downloaded + }); + + it('should not download variable metadata when status response is not 200', async () => { + const mockStatusResponse = { + status: 500, + data: { test: 'json-response' }, + }; + (fetchWithCreds as jest.Mock).mockResolvedValue(mockStatusResponse); + await act(async () => { + await DownloadVariableMetadata( + mockVariableLevelMetadata, + mockResourceInfo as unknown as DiscoveryResource, + mockSetDownloadStatus, + ); + }); + expect(mockSetDownloadStatus).toHaveBeenCalled(); + expect(require('file-saver').saveAs).not.toHaveBeenCalled(); // Zip file downloaded + }); +}); diff --git a/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadVariableMetadata/DownloadVariableMetadata.tsx b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadVariableMetadata/DownloadVariableMetadata.tsx new file mode 100644 index 0000000000..b4bdea6936 --- /dev/null +++ b/src/Discovery/DiscoveryDetails/Components/FieldGrouping/TabField/DataDownloadList/ActionButtons/DownloadUtils/DownloadVariableMetadata/DownloadVariableMetadata.tsx @@ -0,0 +1,88 @@ +import React from 'react'; +import JSZip from 'jszip'; +import FileSaver from 'file-saver'; +import { fetchWithCreds } from '../../../../../../../../../actions'; +import { mdsURL } from '../../../../../../../../../localconf'; +import { INITIAL_DOWNLOAD_STATUS } from '../Constants'; +import DownloadStatus from '../../../Interfaces/DownloadStatus'; +import { DiscoveryResource } from '../../../../../../../../Discovery'; +import VariableLevelMetadata from '../../../Interfaces/VariableLevelMetadata'; +import SanitizeFileName from './SanitizeFileName'; + +enum fetchType { + CDE = 'cde', + DD = 'dd' +} + +const DownloadVariableMetadata = async ( + variableLevelMetadataRecords: VariableLevelMetadata, + resourceInfo: DiscoveryResource, + setDownloadStatus: Function, +) => { + const zip = new JSZip(); + + const createUniqueDownloadErrorMsg = (key: string) => ({ + inProgress: '', + message: { + title: 'Download failed', + active: true, + content: ( ++ Study with name {resourceInfo.study_metadata?.minimal_info?.study_name || 'N/A'} + cannot download data dictionary with name {key}. +
+Please try again later and contact support.
+