[DUOS-1966][risk=no] NIH Administrative Data Submission Section (#1822)

* old branch into develop

* first pass - working ish

* fix codacy

* fix reasons

* fix codacy / tests

* fix field

* remove comment

* fix header / file structure

* feedback / clarifiaction

cypress/component/Forms/forms.spec.js

@@ -612,7 +612,7 @@ describe('FormField - Tests', () => {
       });
 
       mount(<FormField {
-        ...{asdf: 'asdf', id: 'example'}
+        ...{asdf: 'asdf', id: 'example', onChange: () => {},}
       } />);
     });
 
@@ -624,7 +624,7 @@ describe('FormField - Tests', () => {
       });
 
       mount(<FormField {
-        ...{type: FormFieldTypes.TEXT,} // requires id
+        ...{type: FormFieldTypes.TEXT, onChange: () => {},} // requires id
       } />);
     });
 
@@ -647,6 +647,7 @@ describe('FormField - Tests', () => {
             }
           },
           id: 'example',
+          onChange: () => {},
         } // requires id
       } />);
     });

src/components/data_submission/NIHAdministrativeInformation.js

@@ -0,0 +1,135 @@
+import {div, h, h2} from 'react-hyperscript-helpers';
+import { FormFieldTypes, FormField, FormValidators } from '../forms/forms';
+import { nihInstitutions } from './nih_institutions';
+import { isEmpty } from 'lodash/fp';
+import { useState } from 'react';
+
+export const NIHAdministrativeInformation = (props) => {
+  const {
+    initialFormData,
+    onChange,
+    institutions,
+  } = props;
+
+  const [showMultiCenterStudy, setShowMultiCenterStudy] = useState(initialFormData?.multiCenterStudy === true || false);
+  const [showGSRNotRequiredExplanation, setShowGSRNotRequiredExplanation] = useState(initialFormData?.controlledAccessRequiredForGenomicSummaryResultsGSR === false || false);
+  const [gsrNotRequiredExplanation, setGSRNotRequiredExplanation] = useState('');
+
+  return div({
+    className: 'data-submitter-section',
+  }, [
+    h2('NIH Administrative Information'),
+    h(FormField, {
+      id: 'piName',
+      title: 'Principal Investigator Name',
+      validators: [FormValidators.REQUIRED],
+      onChange,
+      defaultValue: initialFormData?.piName,
+    }),
+    h(FormField, {
+      id: 'piInstitution',
+      title: 'Principal Investigator Institution',
+      isRendered: !isEmpty(institutions),
+      validators: [FormValidators.REQUIRED],
+      type: FormFieldTypes.SELECT,
+      selectOptions: institutions,
+      isCreatable: false,
+      selectConfig: {},
+      onChange,
+      defaultValue: initialFormData?.piInstitution,
+    }),
+    h(FormField, {
+      id: 'nihGrantContractNumber',
+      title: 'NIH Grant or Contract Number',
+      validators: [FormValidators.REQUIRED],
+      onChange,
+      defaultValue: initialFormData?.nihGrantContractNumber,
+    }),
+    h(FormField, {
+      id: 'nihICsSupportingStudy',
+      title: 'NIH ICs Supporting the Study',
+      placeholder: 'Institute/Center Name',
+      onChange,
+      type: FormFieldTypes.SELECT,
+      isMulti: true,
+      validators: [FormValidators.REQUIRED],
+      defaultValue: initialFormData?.nihICsSupportingStudy,
+      selectOptions: nihInstitutions,
+    }),
+    h(FormField, {
+      id: 'nihProgramOfficerName',
+      title: 'NIH Program Officer Name',
+      validators: [FormValidators.REQUIRED],
+      onChange,
+      placeholder: 'Officer Name',
+      defaultValue: initialFormData?.nihProgramOfficerName,
+    }),
+    h(FormField, {
+      id: 'nihInstitutionCenterSubmission',
+      title: 'NIH Institute/Center for Submission',
+      placeholder: 'Institute/Center Name',
+      onChange,
+      type: FormFieldTypes.SELECT,
+      validators: [FormValidators.REQUIRED],
+      defaultValue: initialFormData?.nihInstitutionCenterSubmission,
+      selectOptions: nihInstitutions,
+    }),
+    h(FormField, {
+      id: 'nihGenomicProgramAdministratorName',
+      title: 'NIH Genomic Program Administrator Name',
+      validators: [FormValidators.REQUIRED],
+      defaultValue: initialFormData?.nihGenomicProgramAdministratorName,
+      onChange,
+    }),
+    h(FormField, {
+      id: 'multiCenterStudy',
+      title: 'Is this a multi-center study?',
+      type: FormFieldTypes.YESNORADIOGROUP,
+      validators: [FormValidators.REQUIRED],
+      defaultValue: initialFormData?.multiCenterStudy,
+      onChange: ({key, value}) => {
+        setShowMultiCenterStudy(value);
+        onChange({key, value});
+      }
+    }),
+    h(FormField, {
+      id: 'collaboratingSites',
+      isRendered: showMultiCenterStudy,
+      title: 'What are the collaborating sites?',
+      type: FormFieldTypes.MULTITEXT,
+      placeholder: 'List site(s) here...',
+      defaultValue: initialFormData?.collaboratingSites,
+      validators: [FormValidators.REQUIRED],
+      onChange,
+    }),
+    //NOTE: radio group not equipped to handle yes/no groupings
+    h(FormField, {
+      id: 'controlledAccessRequiredForGenomicSummaryResultsGSR',
+      title: 'Is controlled access required for genomic summary results (GSR)?',
+      defaultValue: initialFormData?.controlledAccessRequiredForGenomicSummaryResultsGSR,
+      type: FormFieldTypes.YESNORADIOGROUP,
+      validators: [FormValidators.REQUIRED],
+      onChange: ({key, value}) => {
+        setShowGSRNotRequiredExplanation(!value);
+        onChange({key, value});
+        onChange({
+          key: 'controlledAccessRequiredForGenomicSummaryResultsGSRNotRequiredExplanation',
+          value: (!value ? gsrNotRequiredExplanation : undefined),
+        });
+      }
+    }),
+    h(FormField, {
+      id: 'controlledAccessRequiredForGenomicSummaryResultsGSRNotRequiredExplanation',
+      title: 'If no, explain why controlled access is needed for GSR.',
+      isRendered: showGSRNotRequiredExplanation,
+      defaultValue: gsrNotRequiredExplanation,
+      validators: [FormValidators.REQUIRED],
+      onChange: ({key, value}) => {
+        setGSRNotRequiredExplanation(value);
+        onChange({key, value});
+      },
+    }),
+  ]);
+};
+
+export default NIHAdministrativeInformation;

src/components/data_submission/NIHDataManagement.js

@@ -0,0 +1,221 @@
+import {div, h, h2, h3} from 'react-hyperscript-helpers';
+import { FormFieldTypes, FormField, FormValidators } from '../forms/forms';
+import { useState } from 'react';
+
+
+const alternativeDataSharingPlanReasonValues = {
+  legalRestrictions: 'Legal Restrictions',
+  isInformedConsentProcessesInadequate: 'Informed consent processes are inadequate to support data for sharing for the following reasons:',
+  consentFormsUnavailable: 'The consent forms are unavailable or non-existent for samples collected after January 25, 2015',
+  consentProcessDidNotAddressFutureUseOrBroadSharing: 'The consent process did not specifically address future use or broad data sharing for samples collected after January 25, 2015',
+  consentProcessInadequatelyAddressesRisk: 'The consent process inadequately addresses risks related to future use or broad data sharing for samples collected after January 25, 2015',
+  consentProcessPrecludesFutureUseOrBroadSharing: 'The consent process specifically precludes future use or broad data sharing (including a statement that use of data will be limited to the original researchers)',
+  otherInformedConsentLimitationsOrConcerns: 'Other informed consent limitations or concerns',
+  otherReasonForRequest: 'Other',
+};
+
+export const NIHDataManagement = (props) => {
+  const {
+    initialFormData,
+    onChange,
+  } = props;
+
+  const [showAlternativeDataSharingPlan, setShowAlternativeDataSharingPlan] = useState(initialFormData?.alternativeDataSharingPlan === true || false);
+
+  const [showInadequateConsentProcessesQuestions, setShowInadequateConsentProcessesQuestions] =
+    useState(
+      initialFormData
+        ?.alternativeDataSharingPlanReasons
+        ?.includes(
+          alternativeDataSharingPlanReasonValues
+            .isInformedConsentProcessesInadequate)
+        || false);
+
+  const [alternativeDataSharingPlanReasons, setAlternativeDataSharingPlanReasons] = useState(initialFormData?.alternativeDataSharingPlanReasons || []);
+
+  const onAlternativeDataSharingPlanReasonsChange = ({key, value}) => {
+    const reason = alternativeDataSharingPlanReasonValues[key];
+    const shouldBeIncluded = value;
+
+    if (shouldBeIncluded) {
+      if (!alternativeDataSharingPlanReasons.includes(reason)) {
+        const newDataSharingPlanReasons = alternativeDataSharingPlanReasons.concat(reason);
+        setAlternativeDataSharingPlanReasons(newDataSharingPlanReasons);
+        onChange({key: 'alternativeDataSharingPlanReasons', value: newDataSharingPlanReasons});
+      }
+    } else {
+      if (alternativeDataSharingPlanReasons.includes(reason)) {
+        const newDataSharingPlanReasons = alternativeDataSharingPlanReasons.filter((r) => r !== reason);
+        setAlternativeDataSharingPlanReasons(newDataSharingPlanReasons);
+        onChange({key: 'alternativeDataSharingPlanReasons', value: newDataSharingPlanReasons});
+      }
+    }
+  };
+
+  return div({
+    className: 'data-submitter-section',
+  }, [
+    h2('NIH Data Management & Sharing Policy Details'),
+    h(FormField, {
+      type: FormFieldTypes.YESNORADIOGROUP,
+      id: 'alternativeDataSharingPlan',
+      defaultValue: initialFormData?.alternativeDataSharingPlan,
+      title: 'Are you requesting an Alternative Data Sharing Plan for samples that cannot be shared through a public repository or database?',
+      onChange: ({key, value}) => {
+        setShowAlternativeDataSharingPlan(value);
+        onChange({key, value});
+      },
+    }),
+    div({
+      isRendered: showAlternativeDataSharingPlan,
+    }, [
+      h3(
+        'Please mark the reasons for which you are requesting an Alernative Data Sharing plan (check all that apply)'
+      ),
+      h(FormField, {
+        id: 'legalRestrictions',
+        defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.legalRestrictions),
+        type: FormFieldTypes.CHECKBOX,
+        onChange: onAlternativeDataSharingPlanReasonsChange,
+        toggleText: 'Legal Restrictions',
+      }),
+      h(FormField, {
+        id: 'isInformedConsentProcessesInadequate',
+        defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.isInformedConsentProcessesInadequate),
+        type: FormFieldTypes.CHECKBOX,
+        onChange: ({key, value}) => {
+          setShowInadequateConsentProcessesQuestions(value);
+          onAlternativeDataSharingPlanReasonsChange({key, value});
+        },
+        toggleText:
+          'Informed consent processes are inadequate to support data for sharing for the following reasons:',
+      }),
+      div({
+        isRendered: showInadequateConsentProcessesQuestions,
+        style: {
+          marginLeft: '2rem',
+        },
+      }, [
+        h(FormField, {
+          id: 'consentFormsUnavailable',
+          defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.consentFormsUnavailable),
+          type: FormFieldTypes.CHECKBOX,
+          onChange: onAlternativeDataSharingPlanReasonsChange,
+          toggleText:
+          'The consent forms are unavailable or non-existant for samples collected after January 25, 2015',
+        }),
+        h(FormField, {
+          id: 'consentProcessDidNotAddressFutureUseOrBroadSharing',
+          defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.consentProcessDidNotAddressFutureUseOrBroadSharing),
+          type: FormFieldTypes.CHECKBOX,
+          onChange: onAlternativeDataSharingPlanReasonsChange,
+          toggleText: 'The consent process did not specifically address future use or broad data sharing for samples collected after January 25, 2015',
+        }),
+        h(FormField, {
+          id: 'consentProcessInadequatelyAddressesRisk',
+          defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.consentProcessInadequatelyAddressesRisk),
+          type: FormFieldTypes.CHECKBOX,
+          onChange: onAlternativeDataSharingPlanReasonsChange,
+          toggleText: 'The consent processes inadequately addresses risks related to future use or broad data sharing for samples collected after January 25, 2015',
+        }),
+        h(FormField, {
+          id: 'consentProcessPrecludesFutureUseOrBroadSharing',
+          defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.consentProcessPrecludesFutureUseOrBroadSharing),
+          type: FormFieldTypes.CHECKBOX,
+          onChange: onAlternativeDataSharingPlanReasonsChange,
+          toggleText: 'The consent specifically precludes future use or broad sharing (including a statement that use of data will be limited to the original researchers)',
+        }),
+        h(FormField, {
+          id: 'otherInformedConsentLimitationsOrConcerns',
+          defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.otherInformedConsentLimitationsOrConcerns),
+          type: FormFieldTypes.CHECKBOX,
+          onChange: onAlternativeDataSharingPlanReasonsChange,
+          toggleText: 'Other informed consent limitations or concerns',
+        }),
+        h(FormField, {
+          id: 'otherReasonForRequest',
+          defaultValue: initialFormData?.alternativeDataSharingPlanReasons?.includes(alternativeDataSharingPlanReasonValues.otherReasonForRequest),
+          type: FormFieldTypes.CHECKBOX,
+          onChange: onAlternativeDataSharingPlanReasonsChange,
+          toggleText: 'Other'
+        }),
+      ]),
+      h(FormField, {
+        isRendered: true, // todo: otherReasonForRequest,
+        id: 'alternativeDataSharingPlanExplanation',
+        defaultValue: initialFormData?.alternativeDataSharingPlanExplanation,
+        onChange,
+        title: 'Explanation for request',
+        validators: [FormValidators.REQUIRED]
+      }),
+      h(FormField, {
+        type: FormFieldTypes.FILE,
+        title: 'Upload your alternative sharing plan.',
+        id: 'alternativeDataSharingPlanFile',
+        onChange,
+      }),
+
+      h(FormField, {
+        type: FormFieldTypes.RADIOGROUP,
+        title: 'Data will be submitted:',
+        id: 'alternativeDataSharingPlanDataSubmitted',
+        defaultValue: initialFormData?.alternativeDataSharingPlanDataSubmitted,
+        options: [
+          {
+            text: 'Within 3 months of the last data generated or last clinical visit',
+            name: 'Within 3 months of the last data generated or last clinical visit',
+            id: 'withinThreeMonths',
+          },
+          {
+            text: 'By batches over Study Timeline (e.g. based on clinical trial enrollment benchmarks)',
+            name: 'By batches over Study Timeline (e.g. based on clinical trial enrollment benchmarks)',
+            id: 'batches',
+          }
+        ],
+        onChange,
+      }),
+      h(FormField, {
+        type: FormFieldTypes.YESNORADIOGROUP,
+        id: 'alternativeDataSharingPlanDataReleased',
+        defaultValue: initialFormData?.alternativeDataSharingPlanDataReleased,
+        title: 'Data to be released will meet the timeframes specified in the NHGRI Guidance for Data Submission and Data Release',
+        onChange,
+      }),
+
+      div({
+        style: {
+          display: 'flex',
+          flexDirection: 'row',
+          justifyContent: 'space-between',
+        },
+      }, [
+
+        h(FormField, {
+          id: 'alternativeDataSharingPlanTargetDeliveryDate',
+          style: {
+            width: '45%',
+          },
+          defaultValue: initialFormData?.alternativeDataSharingPlanTargetDeliveryDate,
+          title: 'Target Delivery Date',
+          placeholder: 'Please enter date (YYYY-MM-DD)',
+          validators: [FormValidators.DATE],
+          onChange,
+        }),
+        h(FormField, {
+          id: 'alternativeDataSharingPlanTargetPublicReleaseDate',
+          style: {
+            width: '45%',
+          },
+          defaultValue: initialFormData?.alternativeDataSharingPlanTargetPublicReleaseDate,
+          title: 'Target Public Release Date',
+          placeholder: 'Please enter date (YYYY-MM-DD)',
+          validators: [FormValidators.DATE],
+          onChange,
+        }),
+      ]),
+    ]),
+
+  ]);
+};
+
+export default NIHDataManagement;

src/components/data_submission/ds_common.css

@@ -74,5 +74,5 @@
 }
 
 .data-submitter-section {
-  padding: 25px 0;
+  padding: 12.5px 0 30px 0;
 }