@openneuro/app 4.1.1 → 4.2.2

package/src/scripts/datalad/mutations/add-metadata.jsx

@@ -1,164 +0,0 @@
-import React, { useState } from 'react'
-import PropTypes from 'prop-types'
-import { Link, useHistory, useLocation } from 'react-router-dom'
-import { useCookies } from 'react-cookie'
-import MetadataForm from './metadata-form.jsx'
-import SubmitMetadata from './submit-metadata.jsx'
-import LoggedIn from '../../authentication/logged-in.jsx'
-import {
-  hasEditPermissions,
-  getProfile,
-} from '../../refactor_2021/authentication/profile.js'
-import { getDatasetUrl } from '../../utils/dataset-url'
-
-export const compileMetadata = dataset => {
-  const getFromMetadata = key => dataset.metadata && dataset.metadata[key]
-  const getFromSummary = key =>
-    dataset.draft && dataset.draft.summary && dataset.draft.summary[key]
-  const getFromDescription = key =>
-    dataset.draft && dataset.draft.description && dataset.draft.description[key]
-  const getSeniorAuthor = () => {
-    const authors = dataset.draft.description.Authors
-    if (authors.length) {
-      return authors[authors.length - 1]
-    } else {
-      return 'authors not listed in description.json'
-    }
-  }
-  const getAgesFromSummary = () => {
-    const subjectMetadata = getFromSummary('subjectMetadata')
-    return subjectMetadata && subjectMetadata.map(({ age }) => age)
-  }
-  return {
-    // get from form
-    associatedPaperDOI: getFromMetadata('associatedPaperDOI') || '',
-    species: getFromMetadata('species') || '',
-    studyLongitudinal: getFromMetadata('studyLongitudinal') || '',
-    studyDomain: getFromMetadata('studyDomain') || '',
-    trialCount: getFromMetadata('trialCount') || undefined,
-    studyDesign: getFromMetadata('studyDesign') || '',
-    openneuroPaperDOI: getFromMetadata('openneuroPaperDOI') || '',
-    dxStatus: getFromMetadata('dxStatus') || '',
-    grantFunderName: getFromMetadata('grantFunderName') || '',
-    grantIdentifier: getFromMetadata('grantIdentifier') || '',
-    affirmedDefaced: getFromMetadata('affirmedDefaced') || false,
-    affirmedConsent: getFromMetadata('affirmedConsent') || false,
-
-    // get from openneuro
-    datasetId: dataset.id || '',
-    datasetUrl: getDatasetUrl(dataset) || '',
-    firstSnapshotCreatedAt:
-      (Array.isArray(dataset.snapshots) &&
-        dataset.snapshots.length &&
-        dataset.snapshots[0].created) ||
-      null,
-    latestSnapshotCreatedAt:
-      (Array.isArray(dataset.snapshots) &&
-        dataset.snapshots.length &&
-        dataset.snapshots[dataset.snapshots.length - 1].created) ||
-      null,
-    adminUsers: (dataset.permissions &&
-      Array.isArray(dataset.permissions.userPermissions) &&
-      dataset.permissions.userPermissions
-        .filter(permission => permission.level === 'admin')
-        .map(({ user }) => user && user.email)) || ['dataset has no admins'],
-
-    // get from validator or description.json
-    datasetName:
-      getFromDescription('Name') || 'dataset unnamed in description.json',
-    seniorAuthor: getSeniorAuthor(),
-    dataProcessed: getFromSummary('dataProcessed') || false,
-    ages: getAgesFromSummary() || [],
-    modalities: getFromSummary('modalities') || [],
-    tasksCompleted: getFromSummary('tasks') || [],
-  }
-}
-
-const validations = [
-  {
-    fields: ['affirmedConsent', 'affirmedDefaced'],
-    check: ([affirmedConsent, affirmedDefaced]) =>
-      affirmedConsent || affirmedDefaced,
-    errorMessage:
-      'Uploader must affirm that structural scans are defaced or that they have consent to publish scans without defacing.',
-  },
-]
-
-const runValidations = values =>
-  validations
-    .map(validation => {
-      const relevantValues = validation.fields.map(key => values[key])
-      // TODO - This doesn't seem necessary?
-      // @ts-expect-error
-      const isValid = validation.check(relevantValues)
-      if (!isValid) return validation.errorMessage
-    })
-    .filter(error => error)
-
-const hasChanged = (errorsA, errorsB) =>
-  JSON.stringify(errorsA) !== JSON.stringify(errorsB)
-
-const AddMetadata = ({ dataset }) => {
-  const history = useHistory()
-  const location = useLocation()
-  const [cookies] = useCookies()
-  const [values, setValues] = useState(compileMetadata(dataset))
-  const [validationErrors, setValidationErrors] = useState([])
-  const handleInputChange = (name, value) => {
-    const newValues = {
-      ...values,
-      [name]: value,
-    }
-    setValues(newValues)
-
-    const errors = runValidations(newValues)
-    if (hasChanged(errors, validationErrors)) setValidationErrors(errors)
-  }
-  // @ts-expect-error Weak type definition for state
-  const submitPath = location.state && location.state.submitPath
-  const user = getProfile(cookies)
-  const hasEdit =
-    (user && user.admin) ||
-    hasEditPermissions(dataset.permissions, user && user.sub)
-
-  return (
-    <>
-      <header className="col-xs-12">
-        <h1>Add Metadata</h1>
-        <hr />
-      </header>
-      <MetadataForm
-        values={values}
-        onChange={handleInputChange}
-        hideDisabled={false}
-        hasEdit={hasEdit}
-        validationErrors={validationErrors}
-      />
-      <div className="col-xs-12 dataset-form-controls">
-        <div className="col-xs-12 modal-actions">
-          <Link to={`/datasets/${dataset.id}`}>
-            <button className="btn-admin-blue">Return to Dataset</button>
-          </Link>
-          {hasEdit && (
-            <LoggedIn>
-              <SubmitMetadata
-                datasetId={dataset.id}
-                metadata={values}
-                done={() => submitPath && history.push(submitPath)}
-                disabled={Boolean(validationErrors.length)}
-              />
-            </LoggedIn>
-          )}
-        </div>
-      </div>
-    </>
-  )
-}
-
-AddMetadata.propTypes = {
-  dataset: PropTypes.object,
-  history: PropTypes.object,
-  location: PropTypes.object,
-}
-
-export default AddMetadata

package/src/scripts/datalad/mutations/comment.jsx

@@ -1,164 +0,0 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import { gql } from '@apollo/client'
-import { Mutation } from '@apollo/client/react/components'
-import { convertToRaw } from 'draft-js'
-import withProfile from '../../authentication/withProfile.jsx'
-import { DATASET_COMMENTS } from '../dataset/comments-fragments.js'
-import { datasetCacheId } from './cache-id.js'
-
-const NEW_COMMENT = gql`
-  mutation addComment($datasetId: ID!, $parentId: ID, $comment: String!) {
-    addComment(datasetId: $datasetId, parentId: $parentId, comment: $comment)
-  }
-`
-
-const EDIT_COMMENT = gql`
-  mutation editComment($commentId: ID!, $comment: String!) {
-    editComment(commentId: $commentId, comment: $comment)
-  }
-`
-
-/**
- * Create a new comment cache entry for Apollo update
- * @param {string} id Comment ID
- * @param {string|null} parentId Parent comment ID if one exists
- * @param {Object} body DraftJS ContentState
- * @param {Object} profile GraphQL User type
- * @param {Object} profile.email User email is the only required property for comments
- * @returns {{id: string, parent: Object, text: string, createDate: string, user: Object, replies: Array, __typename: string }}
- */
-export const commentStateFactory = (id, parentId, body, profile) => ({
-  id,
-  parent: parentId ? { __typename: 'Comment', id: parentId } : null,
-  text: JSON.stringify(convertToRaw(body)),
-  createDate: new Date().toISOString(),
-  user: { __typename: 'User', ...profile },
-  replies: [],
-  __typename: 'Comment',
-})
-
-/**
- * Add a new comment to comment state based on arguments
- * @param {Object[]} comments
- * @param {Object} arguments
- * @param {string} arguments.parentId
- * @param {string} arguments.commentId
- * @param {Object} arguments.comment
- * @param {Object} arguments.profile
- * @returns {Object[]}
- */
-export const newCommentsReducer = (
-  comments,
-  { parentId = null, commentId, comment, profile },
-) => {
-  const newComment = commentStateFactory(commentId, parentId, comment, profile)
-  // Must copy with freezeResults enabled
-  const nextCommentsState = [...comments, newComment]
-  // If this is not a root level comment, add to replies
-  if (parentId) {
-    const parentIndex = nextCommentsState.findIndex(
-      comment => comment.id === parentId,
-    )
-    const parentReplies = nextCommentsState[parentIndex].replies
-    nextCommentsState[parentIndex] = {
-      ...comments[parentIndex],
-      replies: [...parentReplies, { __typename: 'Comment', id: commentId }],
-    }
-  }
-  return nextCommentsState
-}
-
-/**
- * Modify an exsiting comment and return new state based on arguments
- * @param {Object[]} comments
- * @param {Object} arguments
- * @param {string} arguments.commentId
- * @param {Object} arguments.comment
- * @returns {Object[]}
- */
-export const modifyCommentsReducer = (comments, { commentId, comment }) => {
-  // Must copy with freezeResults enabled
-  const nextCommentsState = [...comments]
-  const modifiedCommentIndex = nextCommentsState.findIndex(
-    c => c.id === commentId,
-  )
-  const modifiedComment = nextCommentsState[modifiedCommentIndex]
-  nextCommentsState[modifiedCommentIndex] = {
-    ...modifiedComment,
-    text: JSON.stringify(convertToRaw(comment)),
-  }
-  return nextCommentsState
-}
-
-const CommentMutation = ({
-  datasetId,
-  parentId,
-  commentId,
-  comment,
-  disabled,
-  profile,
-  done = () => {
-    /* default no op function */
-  },
-}) => {
-  return (
-    <Mutation
-      mutation={commentId ? EDIT_COMMENT : NEW_COMMENT}
-      update={(cache, { data: { addComment } }) => {
-        const { comments } = cache.readFragment({
-          id: datasetCacheId(datasetId),
-          fragment: DATASET_COMMENTS,
-        })
-        // Apply state reduction to cache for new comment changes
-        const nextCommentsState = addComment
-          ? newCommentsReducer(comments, {
-              parentId,
-              commentId: addComment,
-              comment,
-              profile,
-            })
-          : modifyCommentsReducer(comments, { commentId, comment })
-        cache.writeFragment({
-          id: datasetCacheId(datasetId),
-          fragment: DATASET_COMMENTS,
-          data: {
-            __typename: 'Dataset',
-            id: datasetId,
-            comments: nextCommentsState,
-          },
-        })
-      }}>
-      {newComment => (
-        <button
-          className="btn-modal-action"
-          disabled={disabled}
-          onClick={async () => {
-            await newComment({
-              variables: {
-                datasetId,
-                parentId,
-                commentId,
-                comment: JSON.stringify(convertToRaw(comment)),
-              },
-            })
-            done()
-          }}>
-          Submit Comment
-        </button>
-      )}
-    </Mutation>
-  )
-}
-
-CommentMutation.propTypes = {
-  datasetId: PropTypes.string,
-  parentId: PropTypes.string,
-  commentId: PropTypes.string,
-  comment: PropTypes.object,
-  disabled: PropTypes.bool,
-  profile: PropTypes.object,
-  done: PropTypes.func,
-}
-
-export default withProfile(CommentMutation)

package/src/scripts/datalad/mutations/delete-dataset-form.jsx

@@ -1,82 +0,0 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import TextInput from '../fragments/text-input'
-import SelectInput from '../fragments/select-input'
-import styled from '@emotion/styled'
-
-const Form = styled.form({
-  minWidth: '40rem',
-  margin: '10px 0',
-})
-
-const fields = hasEdit => {
-  const fields = [
-    {
-      key: 'reason',
-      label: 'Reason',
-      component: SelectInput,
-      additionalProps: {
-        options: [
-          { value: 'subject privacy' },
-          { value: 'duplicate dataset' },
-          { value: 'abuse of service', admin: true },
-        ],
-        showOptionOther: true,
-        required: false,
-      },
-    },
-    {
-      key: 'redirect',
-      label: 'Superseded by (URL)',
-      component: TextInput,
-      additionalProps: {
-        required: false,
-      },
-    },
-  ]
-  return hasEdit
-    ? fields
-    : fields.map(field => {
-        field.additionalProps.disabled = true
-        return field
-      })
-}
-
-const DeleteDatasetForm = ({ values, onChange, hasEdit }) => (
-  <Form id="metadata-form" className="col-sm-6">
-    {fields(hasEdit).map(
-      (
-        {
-          key,
-          label,
-          hoverText,
-          component: FieldComponent,
-          additionalProps,
-          transformValue,
-        },
-        i,
-      ) => (
-        // @ts-expect-error
-        <FieldComponent
-          name={key}
-          label={label}
-          hoverText={hoverText}
-          value={transformValue ? transformValue(values[key]) : values[key]}
-          onChange={onChange}
-          {...additionalProps}
-          key={i}
-        />
-      ),
-    )}
-  </Form>
-)
-
-DeleteDatasetForm.propTypes = {
-  keyLabelMap: PropTypes.object,
-  values: PropTypes.object,
-  onChange: PropTypes.func,
-  hideDisabled: PropTypes.bool,
-  hasEdit: PropTypes.bool,
-}
-
-export default DeleteDatasetForm

package/src/scripts/datalad/mutations/description.jsx

@@ -1,129 +0,0 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import { gql } from '@apollo/client'
-import { Mutation } from '@apollo/client/react/components'
-import SaveButton from '../fragments/save-button.jsx'
-import { DRAFT_FRAGMENT } from '../dataset/dataset-query-fragments.js'
-import { datasetCacheId } from './cache-id.js'
-
-export const UPDATE_DESCRIPTION = gql`
-  mutation updateDescription(
-    $datasetId: ID!
-    $field: String!
-    $value: String!
-  ) {
-    updateDescription(datasetId: $datasetId, field: $field, value: $value) {
-      id
-      Name
-      BIDSVersion
-      License
-      Authors
-      Acknowledgements
-      HowToAcknowledge
-      Funding
-      ReferencesAndLinks
-      DatasetDOI
-      EthicsApprovals
-    }
-  }
-`
-
-export const UPDATE_DESCRIPTION_LIST = gql`
-  mutation updateDescriptionList(
-    $datasetId: ID!
-    $field: String!
-    $value: [String!]
-  ) {
-    updateDescriptionList(datasetId: $datasetId, field: $field, value: $value) {
-      id
-      Name
-      BIDSVersion
-      License
-      Authors
-      Acknowledgements
-      HowToAcknowledge
-      Funding
-      ReferencesAndLinks
-      DatasetDOI
-      EthicsApprovals
-    }
-  }
-`
-
-export const mergeFieldValue = (
-  datasetId,
-  draft,
-  updateDescription,
-  updateDescriptionList,
-) => ({
-  __typename: 'Dataset',
-  id: datasetId,
-  draft: {
-    ...draft,
-    description: {
-      ...updateDescription,
-      ...updateDescriptionList,
-    },
-  },
-})
-
-/**
- * Update dataset_description.json on the draft
- */
-const UpdateDescription = ({ datasetId, field, value, done }) => {
-  const mutation = Array.isArray(value)
-    ? UPDATE_DESCRIPTION_LIST
-    : UPDATE_DESCRIPTION
-  return (
-    <Mutation
-      mutation={mutation}
-      update={(
-        cache,
-        { data: { updateDescription, updateDescriptionList } },
-      ) => {
-        const { draft } = cache.readFragment({
-          id: datasetCacheId(datasetId),
-          fragment: DRAFT_FRAGMENT,
-        })
-        cache.writeFragment({
-          id: datasetCacheId(datasetId),
-          fragment: DRAFT_FRAGMENT,
-          data: mergeFieldValue(
-            datasetId,
-            draft,
-            updateDescription,
-            updateDescriptionList,
-          ),
-        })
-      }}>
-      {updateDescription => (
-        <SaveButton
-          action={async () => {
-            await updateDescription({ variables: { datasetId, field, value } })
-            done()
-          }}
-        />
-      )}
-    </Mutation>
-  )
-}
-
-UpdateDescription.propTypes = {
-  datasetId: PropTypes.string,
-  field: PropTypes.oneOf([
-    'Name',
-    'BIDSVersion',
-    'License',
-    'Authors',
-    'Acknowledgements',
-    'HowToAcknowledge',
-    'Funding',
-    'ReferencesAndLinks',
-    'DatasetDOI',
-    'EthicsApprovals',
-  ]),
-  value: PropTypes.oneOfType([PropTypes.string, PropTypes.array]),
-  done: PropTypes.func,
-}
-
-export default UpdateDescription

package/src/scripts/datalad/mutations/flag-annex-object.jsx

@@ -1,62 +0,0 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import { gql } from '@apollo/client'
-import { Mutation } from '@apollo/client/react/components'
-import WarnButton from '../../common/forms/warn-button.jsx'
-import { TooltipSpan } from '../fragments/copyable-tooltip.jsx'
-
-const FLAG_ANNEX_OBJECT = gql`
-  mutation flagAnnexObject(
-    $datasetId: ID!
-    $snapshot: String!
-    $filepath: String!
-    $annexKey: String!
-  ) {
-    flagAnnexObject(
-      datasetId: $datasetId
-      snapshot: $snapshot
-      filepath: $filepath
-      annexKey: $annexKey
-    )
-  }
-`
-
-const FlagAnnexObject = ({ datasetId, snapshot, filepath, annexKey }) => (
-  <Mutation mutation={FLAG_ANNEX_OBJECT} awaitRefetchQueries={true}>
-    {flagAnnexObject => (
-      // fa-exclamation-triangle might be better
-      <TooltipSpan
-        className="flag-annex-object"
-        data-tip="Use this to alert site admins if this file has been found to contain subject sensitive data.">
-        <WarnButton
-          message="Flag"
-          icon="fa-exclamation-triangle"
-          warn={true}
-          className="edit-file"
-          action={cb => {
-            flagAnnexObject({
-              variables: {
-                datasetId,
-                snapshot: snapshot || 'HEAD',
-                filepath,
-                annexKey,
-              },
-            }).then(() => {
-              cb()
-            })
-          }}
-        />
-      </TooltipSpan>
-    )}
-  </Mutation>
-)
-
-FlagAnnexObject.propTypes = {
-  datasetId: PropTypes.string,
-  snapshot: PropTypes.string,
-  annexKey: PropTypes.string,
-  path: PropTypes.string,
-  filename: PropTypes.string,
-}
-
-export default FlagAnnexObject