@openneuro/app 4.15.2-demo.1 → 4.16.1-alpha.0

package/src/scripts/dataset/mutations/delete-file.jsx

@@ -1,7 +1,6 @@
 import React from 'react'
 import PropTypes from 'prop-types'
-import { gql } from '@apollo/client'
-import { Mutation } from '@apollo/client/react/components'
+import { gql, useMutation } from '@apollo/client'
 import { WarnButton } from '@openneuro/components/warn-button'
 
 const DELETE_FILE = gql`
@@ -10,25 +9,99 @@ const DELETE_FILE = gql`
   }
 `
 
-const DeleteFile = ({ datasetId, path, filename }) => (
-  <Mutation mutation={DELETE_FILE} awaitRefetchQueries={true}>
-    {deleteFiles => (
-      <span className="delete-file">
-        <WarnButton
-          message=""
-          iconOnly={true}
-          icon="fa-trash"
-          className="edit-file"
-          onConfirmedClick={() => {
-            deleteFiles({
-              variables: { datasetId, files: [{ path, filename }] },
-            })
-          }}
-        />
-      </span>
-    )}
-  </Mutation>
-)
+/**
+ * Given a file object, path/filename for deletion, and a list of currently loaded files, filter any that will be deleted and orphan directories
+ */
+export function fileCacheDeleteFilter(file, path, filename, cachedFileObjects) {
+  const fullPath = [path, filename].filter(Boolean).join(':')
+  if (file.filename === fullPath) {
+    return false
+  } else {
+    if (file.directory && fullPath.startsWith(file.filename)) {
+      // If a file other than the deletion target is removed
+      // And no other files match this directory prefix
+      for (const f of cachedFileObjects) {
+        if (f.directory || f.filename === fullPath) {
+          continue
+        } else {
+          if (f.filename.startsWith(path)) {
+            return true
+          }
+        }
+      }
+      return false
+    }
+    return true
+  }
+}
+
+const DeleteFile = ({ datasetId, path, filename }) => {
+  const [deleteFiles] = useMutation(DELETE_FILE, {
+    awaitRefetchQueries: true,
+    update(cache, { data: { deleteFiles } }) {
+      if (deleteFiles) {
+        cache.modify({
+          id: `Draft:${datasetId}`,
+          fields: {
+            files(cachedFiles) {
+              // Filter any removed files from the Draft.files cache
+              const cachedFileObjects = cachedFiles.map(f =>
+                cache.readFragment({
+                  id: cache.identify(f),
+                  fragment: gql`
+                    fragment DeletedFile on DatasetFile {
+                      id
+                      key
+                      filename
+                      directory
+                    }
+                  `,
+                }),
+              )
+              const remainingFiles = cachedFiles.filter(f => {
+                // Get the cache key for each file we have loaded
+                const file = cache.readFragment({
+                  id: cache.identify(f),
+                  fragment: gql`
+                    fragment DeletedFile on DatasetFile {
+                      id
+                      key
+                      filename
+                      directory
+                    }
+                  `,
+                })
+                return fileCacheDeleteFilter(
+                  file,
+                  path,
+                  filename,
+                  cachedFileObjects,
+                )
+              })
+              return remainingFiles
+            },
+          },
+        })
+      }
+    },
+  })
+
+  return (
+    <span className="delete-file">
+      <WarnButton
+        message=""
+        iconOnly={true}
+        icon="fa-trash"
+        className="edit-file"
+        onConfirmedClick={() => {
+          deleteFiles({
+            variables: { datasetId, files: [{ path, filename }] },
+          })
+        }}
+      />
+    </span>
+  )
+}
 
 DeleteFile.propTypes = {
   datasetId: PropTypes.string,

package/src/scripts/dataset/routes/delete-page.tsx

@@ -3,7 +3,9 @@ import { useCookies } from 'react-cookie'
 import DeleteDatasetForm from '../mutations/delete-dataset-form.jsx'
 import DeleteDataset from '../mutations/delete.jsx'
 import LoggedIn from '../../authentication/logged-in.jsx'
-import { hasEditPermissions, getProfile } from '../../authentication/profile.js'
+import { getProfile } from '../../authentication/profile.js'
+import AdminUser from '../../authentication/admin-user.jsx'
+import { RegularUser } from '../../authentication/regular-user'
 import { DatasetPageBorder } from './styles/dataset-page-border'
 import { HeaderRow3 } from './styles/header-row'
 
@@ -28,30 +30,38 @@ const DeletePage = ({ dataset }: DeletePageProps): React.ReactElement => {
   }
   const [cookies] = useCookies()
   const user = getProfile(cookies)
-  const hasEdit =
-    (user && user.admin) ||
-    hasEditPermissions(dataset.permissions, user && user.sub)
+  const hasEdit = user && user.admin
   const datasetId = dataset.id
   return (
     <DatasetPageBorder>
       <HeaderRow3>Delete Dataset</HeaderRow3>
-      <DeleteDatasetForm
-        values={values}
-        onChange={handleInputChange}
-        hideDisabled={false}
-        hasEdit={hasEdit}
-      />
-      <p>
-        <small className="warning-text">
-          * Warning: this action will permanently remove this dataset along with
-          associated snapshots.
-        </small>
-      </p>
-      <div className=" dataset-form-controls">
-        <LoggedIn>
-          <DeleteDataset datasetId={datasetId} metadata={values} />
-        </LoggedIn>
-      </div>
+      <AdminUser>
+        <DeleteDatasetForm
+          values={values}
+          onChange={handleInputChange}
+          hideDisabled={false}
+          hasEdit={hasEdit}
+        />
+        <p>
+          <small className="warning-text">
+            * Warning: this action will permanently remove this dataset along
+            with associated snapshots.
+          </small>
+        </p>
+        <div className="dataset-form-controls">
+          <LoggedIn>
+            <DeleteDataset datasetId={datasetId} metadata={values} />
+          </LoggedIn>
+        </div>
+      </AdminUser>
+      <RegularUser>
+        <p>
+          Please contact support to permanently remove a dataset and all
+          versions of it. Provide a reason for the removal request and if the
+          dataset is a duplicate or has been supplanted by another provide that
+          information for a redirect to be created.
+        </p>
+      </RegularUser>
     </DatasetPageBorder>
   )
 }

package/src/scripts/uploader/upload-issues.jsx

@@ -65,7 +65,7 @@ class UploadValidator extends React.Component {
     }
     const options = {
       config: {
-        error: ['NO_AUTHORS'],
+        error: ['NO_AUTHORS', 'EMPTY_DATASET_NAME'],
         ignoreSubjectConsistency: true,
         blacklistModalities: ['Microscopy'],
       },

package/src/scripts/users/username.tsx

@@ -4,7 +4,7 @@ import ORCIDiDLogo from '../../assets/ORCIDiD_iconvector.svg'
 /**
  * Display component for usernames showing ORCID linking if connected
  */
-export const Username = ({ user }) => {
+export const Username = ({ user }): JSX.Element => {
   if (user.orcid) {
     return (
       <>
@@ -15,6 +15,6 @@ export const Username = ({ user }) => {
       </>
     )
   } else {
-    return user.name
+    return user.name as JSX.Element
   }
 }

package/src/scripts/validation/validation-results.issues.jsx

@@ -11,7 +11,7 @@ class Issues extends React.Component {
   render() {
     const issueFiles = this.props.issues
     const issues = issueFiles.map((issue, index) => {
-      let totalFiles = issue.files.length || issue.files.size
+      let totalFiles = issue.files.length
       if (issue.additionalFileCount) {
         totalFiles += issue.additionalFileCount
       }
@@ -32,7 +32,7 @@ class Issues extends React.Component {
       )
 
       // issue sub-errors
-      const subErrors = Array.from(issue.files).map((error, index2) => {
+      const subErrors = issue.files.map((error, index2) => {
         return error ? (
           <Issue
             type={this.props.issueType}

package/src/scripts/validation/validation-results.jsx

@@ -78,7 +78,7 @@ class ValidationResults extends React.Component {
   _countFiles(issues) {
     let numFiles = 0
     for (const issue of issues) {
-      numFiles += Array.from(issue.files).length
+      numFiles += issue.files.length
       if (issue.additionalFileCount) {
         numFiles += issue.additionalFileCount
       }

package/src/scripts/workers/validate.worker.ts

@@ -1,25 +1,22 @@
 /* eslint-env worker */
-import { validate, fileListToTree } from '../utils/schema-validator.js'
+import validate from 'bids-validator'
 import { BIDSValidatorIssues } from './worker-interface'
 
+const asyncValidateBIDS = (files, options): Promise<BIDSValidatorIssues> =>
+  new Promise(resolve => {
+    validate.BIDS(files, options, (issues, summary) =>
+      resolve({ issues, summary }),
+    )
+  })
+
 export async function runValidator(
   files,
   options,
   cb,
 ): Promise<BIDSValidatorIssues> {
   let error, output: BIDSValidatorIssues
-  output = { issues: { errors: [], warnings: [] }, summary: {} }
   try {
-    const tree = await fileListToTree(files)
-    const result = await validate(tree, { json: true })
-    const issues = Array.from(result.issues, ([key, value]) => value)
-    console.log(issues)
-    output.issues.warnings = issues.filter(
-      issue => issue.severity === 'warning',
-    )
-    output.issues.errors = issues.filter(issue => issue.severity === 'error')
-    output.summary = result.summary
-    console.log(output)
+    output = await asyncValidateBIDS(files, options)
   } catch (err) {
     error = err
   }

package/src/scripts/workers/worker-interface.ts

@@ -1,8 +1,5 @@
 // Shared interface for BIDSValidatorIssues shared without cross import for validate and validate.worker
 export interface BIDSValidatorIssues {
-  issues: {
-    errors: Record<string, unknown>[]
-    warnings: Record<string, unknown>[]
-  }
+  issues: Record<string, unknown>[]
   summary: Record<string, unknown>
 }

package/vite.config.js

@@ -7,7 +7,6 @@ export default defineConfig({
   server: {
     port: 80,
     host: '0.0.0.0',
-    cors: true,
   },
   build: {
     sourcemap: true,

package/src/scripts/datalad/mutations/delete-dir.jsx

@@ -1,43 +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'
-
-export const DELETE_FILES = gql`
-  mutation deleteFiles($datasetId: ID!, $files: [DeleteFile]!) {
-    deleteFiles(datasetId: $datasetId, files: $files)
-  }
-`
-
-const DeleteDir = ({ datasetId, path }) => (
-  <Mutation mutation={DELETE_FILES} awaitRefetchQueries={true}>
-    {deleteFiles => (
-      <span className="delete-file">
-        <WarnButton
-          message="Delete"
-          icon="fa-trash"
-          warn={true}
-          className="edit-file"
-          action={cb => {
-            deleteFiles({
-              variables: {
-                datasetId,
-                files: [{ path }],
-              },
-            }).then(() => {
-              cb()
-            })
-          }}
-        />
-      </span>
-    )}
-  </Mutation>
-)
-
-DeleteDir.propTypes = {
-  datasetId: PropTypes.string,
-  path: PropTypes.string,
-}
-
-export default DeleteDir

package/src/scripts/datalad/mutations/delete-file.jsx

@@ -1,41 +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'
-
-const DELETE_FILE = gql`
-  mutation deleteFiles($datasetId: ID!, $files: [DeleteFile]) {
-    deleteFiles(datasetId: $datasetId, files: $files)
-  }
-`
-
-const DeleteFile = ({ datasetId, path, filename }) => (
-  <Mutation mutation={DELETE_FILE} awaitRefetchQueries={true}>
-    {deleteFiles => (
-      <span className="delete-file">
-        <WarnButton
-          message="Delete"
-          icon="fa-trash"
-          warn={true}
-          className="edit-file"
-          action={cb => {
-            deleteFiles({
-              variables: { datasetId, files: [{ path, filename }] },
-            }).then(() => {
-              cb()
-            })
-          }}
-        />
-      </span>
-    )}
-  </Mutation>
-)
-
-DeleteFile.propTypes = {
-  datasetId: PropTypes.string,
-  path: PropTypes.string,
-  filename: PropTypes.string,
-}
-
-export default DeleteFile

package/src/scripts/dataset/mutations/delete-dir.jsx

@@ -1,43 +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 '@openneuro/components/warn-button'
-
-export const DELETE_FILES = gql`
-  mutation deleteFiles($datasetId: ID!, $files: [DeleteFile]!) {
-    deleteFiles(datasetId: $datasetId, files: $files)
-  }
-`
-
-const DeleteDir = ({ datasetId, path, name }) => (
-  <Mutation mutation={DELETE_FILES} awaitRefetchQueries={true}>
-    {deleteFiles => (
-      <span className="delete-file">
-        <WarnButton
-          message=""
-          iconOnly={true}
-          icon="fa-trash"
-          className="edit-file"
-          tooltip={'Delete ' + name}
-          onConfirmedClick={() => {
-            deleteFiles({
-              variables: {
-                datasetId,
-                files: [{ path }],
-              },
-            })
-          }}
-        />
-      </span>
-    )}
-  </Mutation>
-)
-
-DeleteDir.propTypes = {
-  datasetId: PropTypes.string,
-  path: PropTypes.string,
-  name: PropTypes.string,
-}
-
-export default DeleteDir