Study Information
+ {generateStudyInputFormTextField(setStudy, 'studyName', study?.name, 'Study Name', 'Enter the study name', [FormValidators.REQUIRED])}
-
{
- setStudyPropertyByKey(formData, onChange, input, new StudyType(input.value as string))
+ setStudyPropertyByKey(study, setStudy, input, new StudyTypeProperty(input.value as string))
}}
/>
id="studyDescription"
title="Study Description"
placeholder="Description"
- defaultValue={formData?.description}
+ defaultValue={study?.description}
validators={[FormValidators.REQUIRED]}
- onChange={onChange}
+ onChange={setStudy}
/>
isCreatable={true}
isMulti={true}
optionsAreString={true}
- selectOptions={[
- // The top properties were extracted from the prod database and deduplicated using the query:
- // SELECT property_value, COUNT(*) FROM dataset_property WHERE property_key = 2 GROUP BY property_value ORDER BY COUNT(*) DESC;
- 'CITE-seq',
- 'Hybrid Capture',
- 'RNA-Seq',
- 'scRNA-Seq',
- 'Spatial Transcriptomics',
- 'snRNA-Seq',
- 'Whole Genome (WGS)',
- 'Whole Exome (WES)',
- ]}
- defaultValue={formData?.dataTypes}
- onChange={onChange}
- />
- {generateFormTextField(formData, onChange, new PhenotypeIndication())}
- {generateFormTextField(formData, onChange, new Species())}
- (`${entry.name}` + (entry.abbreviation ? ` (${entry.abbreviation})` : '')))}
+ defaultValue={study?.dataTypes}
+ onChange={setStudy}
/>
+ {generateStudyPropertyFormTextField(study, setStudy, new PhenotypeIndication())}
+ {generateStudyPropertyFormTextField(study, setStudy, new Species())}
+ {generateStudyInputFormTextField(setStudy, 'piName', study?.piName, 'Principal Investigator Name', 'Enter the Principal Investigator\'s name', [FormValidators.REQUIRED])}
},
}}
placeholder="Add one or more emails"
- defaultValue={getStudyPropertyByKey(formData, 'dataCustodianEmail')}
+ defaultValue={getStudyPropertyValueByKey(study, 'dataCustodianEmail')}
onChange={(input: { key: string[], value: unknown, isValid: boolean }) => {
- setStudyPropertyByKey(formData, onChange, input, new DataCustodianEmail(input.value as string[]))
+ setStudyPropertyByKey(study, setStudy, input, new DataCustodianEmail(input.value as string[]))
}}
/>
- {generateFormDateField(formData, onChange, new AlternativeDataSharingPlanTargetDeliveryDate(), [FormValidators.DATE], { width: '45%' })}
- {generateFormDateField(formData, onChange, new AlternativeDataSharingPlanTargetPublicReleaseDate(), [FormValidators.DATE], { width: '45%' })}
+ {generateStudyPropertyFormDateField(study, setStudy, new AlternativeDataSharingPlanTargetDeliveryDate(), [FormValidators.DATE], { width: '45%' })}
+ {generateStudyPropertyFormDateField(study, setStudy, new AlternativeDataSharingPlanTargetPublicReleaseDate(), [FormValidators.DATE], { width: '45%' })}
{ name: true, text: 'Yes, I want my dataset info to be visible and available for requests' },
{ name: false, text: 'No, I do not want my dataset info to be visible and available for requests' },
]}
- defaultValue={formData?.publicVisibility}
- onChange={onChange}
+ defaultValue={study?.publicVisibility}
+ onChange={setStudy}
/>
)
diff --git a/src/pages/data_submission/v2/NihAdministrativeInformation.tsx b/src/pages/data_submission/v2/NihAdministrativeInformation.tsx
new file mode 100644
index 0000000000..efc9a4e5f4
--- /dev/null
+++ b/src/pages/data_submission/v2/NihAdministrativeInformation.tsx
@@ -0,0 +1,153 @@
+import React, { useEffect, useState } from 'react'
+import {
+ CollaboratingSites,
+ ControlledAccessRequiredForGenomicSummaryResultsGSR,
+ ControlledAccessRequiredForGenomicSummaryResultsGSRRequiredExplanation,
+ MultiCenterStudy,
+ NihAnvilUse,
+ NihGenomicProgramAdministratorName,
+ NihGrantContractNumber,
+ NihICsSupportingStudy,
+ NihInstitutionCenterSubmission,
+ NihProgramOfficerName,
+ PiInstitution,
+ Study,
+} from 'src/pages/data_submission/v2/v2-models'
+import {
+ generateStudyPropertyFormTextField, getStudyPropertyValueByKey,
+ removeStudyPropertiesByKeys, setStudyPropertyByKey,
+} from 'src/pages/data_submission/v2/v2-common-functions'
+import { FormField, FormFieldTypes, FormValidators } from 'src/components/forms/forms'
+import {
+ SelectInterfacePickerSelection,
+ SelectOptionsInterfacePicker,
+} from 'src/components/forms/SelectOptionsInterfacePicker'
+import { InstitutionPicker } from 'src/components/forms/InstitutionPicker'
+import { NIHInstitutesAndCenters } from 'src/components/forms/NIHInstitutesAndCenters'
+import { cloneDeep } from 'lodash'
+
+export interface NihAdministrativeInformationProps {
+ study: Study
+ setStudy: React.Dispatch>
+}
+
+export const NihAdministrativeInformation = (props: NihAdministrativeInformationProps) => {
+ const { setStudy, study } = props
+ const [isRequired, setIsRequired] = useState(false)
+
+ useEffect(() => {
+ const nihAnvilUse = getStudyPropertyValueByKey(study, new NihAnvilUse().key) as string
+ setIsRequired(NihAnvilUse.requiresNIHAdministrativeInformation(nihAnvilUse))
+ }, [study])
+
+ return (
+ <>{isRequired && (
+
+
NIH Administrative Information
+
+ {generateStudyPropertyFormTextField(study, setStudy, new NihGrantContractNumber(), [FormValidators.REQUIRED])}
+ entry.key)
+ setStudyPropertyByKey(study, setStudy, { isValid: isValid }, new NihICsSupportingStudy(myMap))
+ }
+ else if (value) {
+ const myVal = value as SelectInterfacePickerSelection
+ const keys = [] as string[]
+ keys.push(myVal.key)
+ setStudyPropertyByKey(study, setStudy, { isValid: isValid }, new NihICsSupportingStudy(keys))
+ }
+ else {
+ setStudyPropertyByKey(study, setStudy, { isValid: isValid }, new NihICsSupportingStudy([]))
+ }
+ }}
+ optionList={NIHInstitutesAndCenters.VALUES}
+ fieldTitle={NihICsSupportingStudy.fieldTitle}
+ fieldPlaceholder={NihICsSupportingStudy.fieldPlaceholderText}
+ isMulti={true}
+ />
+ {generateStudyPropertyFormTextField(study, setStudy, new NihProgramOfficerName(), [FormValidators.REQUIRED])}
+
+ {generateStudyPropertyFormTextField(study, setStudy, new NihGenomicProgramAdministratorName())}
+ {
+ setStudyPropertyByKey(study, setStudy, { isValid: true }, new MultiCenterStudy(value))
+ if (!value) {
+ setStudy((val) => {
+ const newVal = cloneDeep(val)
+ removeStudyPropertiesByKeys(newVal, new Set([CollaboratingSites.key]))
+ return newVal
+ })
+ }
+ }}
+ />
+ {getStudyPropertyValueByKey(study, MultiCenterStudy.key) === true && (
+ null,
+ },
+ }}
+ placeholder="List site and hit enter here..."
+ defaultValue={getStudyPropertyValueByKey(study, CollaboratingSites.key)}
+ onChange={(_key: string, value: string[], isValid: boolean) => setStudyPropertyByKey(study, setStudy, { isValid: isValid }, new CollaboratingSites(value))}
+ />
+ )}
+
+ {
+ setStudyPropertyByKey(study, setStudy, { isValid: true }, new ControlledAccessRequiredForGenomicSummaryResultsGSR(value))
+ if (!value) {
+ setStudy((val) => {
+ const newVal = cloneDeep(val)
+ removeStudyPropertiesByKeys(newVal, new Set([ControlledAccessRequiredForGenomicSummaryResultsGSRRequiredExplanation.key]))
+ return newVal
+ })
+ }
+ }}
+ />
+ {getStudyPropertyValueByKey(study, ControlledAccessRequiredForGenomicSummaryResultsGSR.key) === true && generateStudyPropertyFormTextField(study, setStudy, new ControlledAccessRequiredForGenomicSummaryResultsGSRRequiredExplanation())}
+
+ )}
+
+ )
+}
diff --git a/src/pages/data_submission/v2/NihAnvilUseRelated.tsx b/src/pages/data_submission/v2/NihAnvilUseRelated.tsx
index c0bf89fbe7..cdd889a16d 100644
--- a/src/pages/data_submission/v2/NihAnvilUseRelated.tsx
+++ b/src/pages/data_submission/v2/NihAnvilUseRelated.tsx
@@ -2,26 +2,34 @@ import React from 'react'
import {
Study,
NihAnvilUse, DbGaPPhsID,
- DbGaPStudyRegistrationName, EmbargoReleaseDate, SequencingCenter,
+ DbGaPStudyRegistrationName, EmbargoReleaseDate, SequencingCenter, PiInstitution, NihGrantContractNumber,
+ NihICsSupportingStudy, NihProgramOfficerName, NihInstitutionCenterSubmission, NihGenomicProgramAdministratorName,
+ MultiCenterStudy, CollaboratingSites, ControlledAccessRequiredForGenomicSummaryResultsGSR,
+ ControlledAccessRequiredForGenomicSummaryResultsGSRRequiredExplanation, AlternativeDataSharingPlan,
+ AlternativeDataSharingPlanReasons, AlternativeDataSharingPlanExplanation, AlternativeDataSharingPlanDataSubmitted,
+ AlternativeDataSharingPlanDataReleased,
} from 'src/pages/data_submission/v2/v2-models'
import { FormField, FormFieldTypes, FormValidators } from 'src/components/forms/forms'
import {
- generateFormDateField,
- generateFormTextField,
- getStudyPropertyByKey,
- MasterChangeHandler,
+ generateStudyPropertyFormDateField,
+ generateStudyPropertyFormTextField,
+ getStudyPropertyValueByKey, removeStudyPropertiesByKeys,
setStudyPropertyByKey,
} from 'src/pages/data_submission/v2/v2-common-functions'
+import { cloneDeep, unset } from 'lodash'
+import { ALTERNATIVE_DATA_SHARING_PLAN_FILE, FileProperty } from 'src/pages/data_submission/v2/DataSubmissionFormV2'
export interface NihAnvilUseRelatedProps {
- formData: Study
- onChange: MasterChangeHandler
+ study: Study
+ setStudy: React.Dispatch>
+ setFiles: React.Dispatch>
}
export const NihAnvilUseRelated = (props: NihAnvilUseRelatedProps) => {
const {
- onChange,
- formData,
+ setStudy,
+ study,
+ setFiles,
} = props
return (
@@ -32,18 +40,51 @@ export const NihAnvilUseRelated = (props: NihAnvilUseRelatedProps) => {
title="Will you or did you submit data to the NIH?"
type={FormFieldTypes.RADIOGROUP}
options={NihAnvilUse.NIH_ANVIL_USE_RADIOGROUP_OPTIONS}
- defaultValue={getStudyPropertyByKey(formData, 'nihAnvilUse')}
+ defaultValue={getStudyPropertyValueByKey(study, 'nihAnvilUse')}
validators={[FormValidators.REQUIRED]}
- onChange={(input: { key: string, value: unknown, isValid: boolean }) => {
- setStudyPropertyByKey(formData, onChange, input, new NihAnvilUse(input.value as string))
+ onChange={(input: { key: string, value: string | undefined, isValid: boolean }) => {
+ setStudyPropertyByKey(study, setStudy, input, new NihAnvilUse(input.value as string))
+ if (NihAnvilUse.requiresNIHAdministrativeInformation(input.value)) {
+ setStudy((val) => {
+ const newVal = cloneDeep(val)
+ removeStudyPropertiesByKeys(newVal, new Set([DbGaPPhsID.key,
+ DbGaPStudyRegistrationName.key,
+ EmbargoReleaseDate.key,
+ SequencingCenter.key,
+ PiInstitution.key,
+ NihGrantContractNumber.key,
+ NihICsSupportingStudy.key,
+ NihProgramOfficerName.key,
+ NihInstitutionCenterSubmission.key,
+ NihGenomicProgramAdministratorName.key,
+ MultiCenterStudy.key,
+ CollaboratingSites.key,
+ ControlledAccessRequiredForGenomicSummaryResultsGSR.key,
+ ControlledAccessRequiredForGenomicSummaryResultsGSRRequiredExplanation.key,
+ AlternativeDataSharingPlan.key,
+ AlternativeDataSharingPlanReasons.key,
+ AlternativeDataSharingPlanExplanation.key,
+ AlternativeDataSharingPlanDataSubmitted.key,
+ AlternativeDataSharingPlanDataReleased.key,
+ ]))
+ return newVal
+ })
+ setFiles((val) => {
+ const newVal = cloneDeep(val)
+ if (val?.key === ALTERNATIVE_DATA_SHARING_PLAN_FILE) {
+ unset(newVal, ALTERNATIVE_DATA_SHARING_PLAN_FILE)
+ }
+ return newVal
+ })
+ }
}}
/>
- {getStudyPropertyByKey(formData, 'nihAnvilUse') === NihAnvilUse.YES_NHGRI_YES_PHS_ID && (
+ {getStudyPropertyValueByKey(study, 'nihAnvilUse') === NihAnvilUse.YES_NHGRI_YES_PHS_ID && (
<>
- {generateFormTextField(formData, onChange, new DbGaPPhsID(), [FormValidators.REQUIRED])}
- {generateFormTextField(formData, onChange, new DbGaPStudyRegistrationName())}
- {generateFormDateField(formData, onChange, new EmbargoReleaseDate(), [FormValidators.DATE])}
- {generateFormTextField(formData, onChange, new SequencingCenter())}
+ {generateStudyPropertyFormTextField(study, setStudy, new DbGaPPhsID(), [FormValidators.REQUIRED])}
+ {generateStudyPropertyFormTextField(study, setStudy, new DbGaPStudyRegistrationName())}
+ {generateStudyPropertyFormDateField(study, setStudy, new EmbargoReleaseDate(), [FormValidators.DATE])}
+ {generateStudyPropertyFormTextField(study, setStudy, new SequencingCenter())}
)}
diff --git a/src/pages/data_submission/v2/NihDataManagement.tsx b/src/pages/data_submission/v2/NihDataManagement.tsx
new file mode 100644
index 0000000000..17aa008bb8
--- /dev/null
+++ b/src/pages/data_submission/v2/NihDataManagement.tsx
@@ -0,0 +1,185 @@
+import React from 'react'
+import {
+ AlternativeDataSharingPlan,
+ AlternativeDataSharingPlanDataReleased, AlternativeDataSharingPlanDataSubmitted,
+ AlternativeDataSharingPlanExplanation, AlternativeDataSharingPlanReasons,
+ NihAnvilUse,
+ Study,
+} from 'src/pages/data_submission/v2/v2-models'
+import {
+ generateStudyPropertyFormTextField,
+ generateStudyPropertyYesNoField,
+ getStudyPropertyValueByKey,
+ removeStudyPropertiesByKeys, setStudyPropertyByKey,
+} from 'src/pages/data_submission/v2/v2-common-functions'
+import { FormField, FormFieldTypes, FormValidators } from 'src/components/forms/forms'
+import { cloneDeep, set, unset } from 'lodash'
+import { ALTERNATIVE_DATA_SHARING_PLAN_FILE, FileProperty } from 'src/pages/data_submission/v2/DataSubmissionFormV2'
+
+export interface NihDataManagementProps {
+ study: Study
+ setStudy: React.Dispatch>
+ files: FileProperty
+ setFiles: React.Dispatch>
+}
+export const NihDataManagement = (props: NihDataManagementProps) => {
+ const { setStudy, setFiles, files, study } = props
+
+ const onAlternativeDataSharingPlanReasonsChange = ({ key }: { key: string }) => {
+ let setReasons: string[] = getStudyPropertyValueByKey(study, AlternativeDataSharingPlanReasons.key) as string[] ?? []
+ if (Object.keys(AlternativeDataSharingPlanReasons.VALUES).includes(key)) {
+ const target = AlternativeDataSharingPlanReasons.VALUES[key as keyof typeof AlternativeDataSharingPlanReasons.VALUES]
+ const index = setReasons.indexOf(target)
+ let removed = false
+ if (index > -1) {
+ setReasons.splice(index, 1)
+ removed = true
+ }
+ else {
+ setReasons.push(target)
+ }
+ if ((target === AlternativeDataSharingPlanReasons.VALUES.isInformedConsentProcessesInadequate) && removed) {
+ if (setReasons.includes(AlternativeDataSharingPlanReasons.VALUES.legalRestrictions)) {
+ setReasons = [AlternativeDataSharingPlanReasons.VALUES.legalRestrictions]
+ }
+ else {
+ setReasons = []
+ }
+ }
+ setStudyPropertyByKey(study, setStudy, { isValid: true }, new AlternativeDataSharingPlanReasons(setReasons))
+ }
+ }
+
+ return (
+
+ {(
+ NihAnvilUse.requiresNIHAdministrativeInformation(getStudyPropertyValueByKey(study, NihAnvilUse.key) as string | undefined) && (
+ <>
+
NIH Data Management & Sharing Policy Details
+
{
+ setStudyPropertyByKey(study, setStudy, { isValid: true }, new AlternativeDataSharingPlan(value))
+ if (!value) {
+ setStudy((val) => {
+ const newVal = cloneDeep(val)
+ removeStudyPropertiesByKeys(newVal, new Set([AlternativeDataSharingPlanReasons.key,
+ AlternativeDataSharingPlanExplanation.key,
+ AlternativeDataSharingPlanDataSubmitted.key,
+ AlternativeDataSharingPlanDataReleased.key]))
+ unset(study, 'alternativeDataSharingPlanFile')
+ return newVal
+ })
+ }
+ }}
+ />
+ {(getStudyPropertyValueByKey(study, AlternativeDataSharingPlan.key) === true) && (
+
+
Please mark the reasons for which you are requesting an Alternative Data Sharing plan (check all that apply)*
+
+
+ {(getStudyPropertyValueByKey(study, AlternativeDataSharingPlanReasons.key) as string[] ?? []).includes(AlternativeDataSharingPlanReasons.VALUES.isInformedConsentProcessesInadequate) && (
+
+
+
+
+
+
+
+
+ )}
+ {generateStudyPropertyFormTextField(study, setStudy, new AlternativeDataSharingPlanExplanation(), [FormValidators.REQUIRED])}
+
{
+ setFiles((val: FileProperty) => {
+ const newFiles = cloneDeep(val)
+ set(newFiles, key, value)
+ return newFiles
+ })
+ }}
+ />
+ {
+ setStudyPropertyByKey(study, setStudy, input, new AlternativeDataSharingPlanDataSubmitted(input.value as string))
+ }}
+ />
+ {generateStudyPropertyYesNoField(study, setStudy, new AlternativeDataSharingPlanDataReleased())}
+ 
+