@openneuro/app 4.20.4 → 4.20.6-alpha.2

package/src/scripts/uploader/upload-disclaimer-input.tsx

@@ -1,5 +1,5 @@
-import React from 'react'
-import styled from '@emotion/styled'
+import React from "react"
+import styled from "@emotion/styled"
 
 interface UploadDisclaimerInputProps {
   affirmedDefaced: boolean
@@ -21,67 +21,67 @@ const DisclaimerLabel = styled.label`
   padding-top: 10px;
 `
 
-export const UploadDisclaimerInput: React.FunctionComponent<UploadDisclaimerInputProps> =
-  ({ affirmedDefaced, affirmedConsent, onChange }) => {
-    return (
-      <>
-        <h4>
-          By uploading this dataset to OpenNeuro I agree to the following
-          conditions:
-        </h4>
-        <p>
-          I am the owner of this dataset and have any necessary ethics
-          permissions to share the data publicly. This dataset does not include
-          any identifiable personal health information as defined by the{' '}
-          <a href="https://www.hhs.gov/hipaa/for-professionals/privacy/laws-regulations/">
-            Health Insurance Portability and Accountability Act of 1996
-          </a>{' '}
-          (including names, zip codes, dates of birth, acquisition dates, etc).
-          I agree to destroy any key linking the personal identity of research
-          participants to the subject codes used in the dataset.
-        </p>
-        <p>
-          I agree that this dataset will become publicly available under a{' '}
-          <a href="https://wiki.creativecommons.org/wiki/CC0">
-            Creative Commons CC0
-          </a>{' '}
-          license after a grace period of 36 months counted from the date of the
-          first snapshot creation for this dataset. You will be able to apply
-          for up to two 6 month extensions to increase the grace period in case
-          the publication of a corresponding paper takes longer than expected.
-          See <a href="/faq">FAQ</a> for details.
-        </p>
-        <p>This dataset is not subject to GDPR protections.</p>
-        <p>
-          Generally, data should only be uploaded to a single data archive. In
-          the rare cases where it is necessary to upload the data to two
-          databases (such as the NIMH Data Archive), I agree to ensure that the
-          datasets are harmonized across archives.
-        </p>
-        <p>Please affirm one of the following:</p>
-        <DisclaimerLabel>
-          <input
-            type="checkbox"
-            onChange={(): void =>
-              onChange({ affirmedDefaced: !affirmedDefaced, affirmedConsent })
-            }
-            defaultChecked={affirmedDefaced}
-          />
-          &nbsp; All structural scans have been defaced, obscuring any tissue on
-          or near the face that could potentially be used to reconstruct the
-          facial structure.
-        </DisclaimerLabel>
-        <DisclaimerLabel>
-          <input
-            type="checkbox"
-            onChange={(): void =>
-              onChange({ affirmedDefaced, affirmedConsent: !affirmedConsent })
-            }
-            defaultChecked={affirmedConsent}
-          />
-          &nbsp; I have explicit participant consent and ethical authorization
-          to publish structural scans without defacing.
-        </DisclaimerLabel>
-      </>
-    )
-  }
+export const UploadDisclaimerInput: React.FunctionComponent<
+  UploadDisclaimerInputProps
+> = ({ affirmedDefaced, affirmedConsent, onChange }) => {
+  return (
+    <>
+      <h4>
+        By uploading this dataset to OpenNeuro I agree to the following
+        conditions:
+      </h4>
+      <p>
+        I am the owner of this dataset and have any necessary ethics permissions
+        to share the data publicly. This dataset does not include any
+        identifiable personal health information as defined by the{" "}
+        <a href="https://www.hhs.gov/hipaa/for-professionals/privacy/laws-regulations/">
+          Health Insurance Portability and Accountability Act of 1996
+        </a>{" "}
+        (including names, zip codes, dates of birth, acquisition dates, etc). I
+        agree to destroy any key linking the personal identity of research
+        participants to the subject codes used in the dataset.
+      </p>
+      <p>
+        I agree that this dataset will become publicly available under a{" "}
+        <a href="https://wiki.creativecommons.org/wiki/CC0">
+          Creative Commons CC0
+        </a>{" "}
+        license after a grace period of 36 months counted from the date of the
+        first snapshot creation for this dataset. You will be able to apply for
+        up to two 6 month extensions to increase the grace period in case the
+        publication of a corresponding paper takes longer than expected. See
+        {" "}
+        <a href="/faq">FAQ</a> for details.
+      </p>
+      <p>This dataset is not subject to GDPR protections.</p>
+      <p>
+        Generally, data should only be uploaded to a single data archive. In the
+        rare cases where it is necessary to upload the data to two databases
+        (such as the NIMH Data Archive), I agree to ensure that the datasets are
+        harmonized across archives.
+      </p>
+      <p>Please affirm one of the following:</p>
+      <DisclaimerLabel>
+        <input
+          type="checkbox"
+          onChange={(): void =>
+            onChange({ affirmedDefaced: !affirmedDefaced, affirmedConsent })}
+          defaultChecked={affirmedDefaced}
+        />
+        &nbsp; All structural scans have been defaced, obscuring any tissue on
+        or near the face that could potentially be used to reconstruct the
+        facial structure.
+      </DisclaimerLabel>
+      <DisclaimerLabel>
+        <input
+          type="checkbox"
+          onChange={(): void =>
+            onChange({ affirmedDefaced, affirmedConsent: !affirmedConsent })}
+          defaultChecked={affirmedConsent}
+        />
+        &nbsp; I have explicit participant consent and ethical authorization to
+        publish structural scans without defacing.
+      </DisclaimerLabel>
+    </>
+  )
+}

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

@@ -1,6 +1,6 @@
-import React, { useState } from 'react'
-import UploaderContext from './uploader-context.js'
-import { UploadDisclaimerInput } from './upload-disclaimer-input'
+import React, { useState } from "react"
+import UploaderContext from "./uploader-context.js"
+import { UploadDisclaimerInput } from "./upload-disclaimer-input"
 
 /**
  * Defacing/consent input logic
@@ -16,7 +16,7 @@ const UploadDisclaimer = () => {
   const [affirmedConsent, setAffirmedConsent] = useState(false)
   return (
     <UploaderContext.Consumer>
-      {uploader => (
+      {(uploader) => (
         <div className="disclaimer fade-in">
           <UploadDisclaimerInput
             affirmedDefaced={affirmedDefaced}
@@ -37,7 +37,8 @@ const UploadDisclaimer = () => {
                 })
                 uploader.upload({ affirmedDefaced, affirmedConsent })
               }}
-              disabled={testAffirmed(affirmedDefaced, affirmedConsent)}>
+              disabled={testAffirmed(affirmedDefaced, affirmedConsent)}
+            >
               I Agree
             </button>
           </span>

package/src/scripts/uploader/upload-file-status.jsx

@@ -1,12 +1,12 @@
-import React from 'react'
-import PropTypes from 'prop-types'
+import React from "react"
+import PropTypes from "prop-types"
 
 const UploadFileStatus = ({ uploadingFiles, failedFiles }) => (
   <>
-    <p>{[...uploadingFiles].join(', ')}</p>
+    <p>{[...uploadingFiles].join(", ")}</p>
     <p>
       {failedFiles.size
-        ? `Too many failed attempts for '${[...failedFiles].join(', ')}'`
+        ? `Too many failed attempts for '${[...failedFiles].join(", ")}'`
         : null}
     </p>
   </>

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

@@ -1,11 +1,11 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import pluralize from 'pluralize'
-import { Loading } from '@openneuro/components/loading'
-import Results from '../validation/validation-results.jsx'
-import UploaderContext from './uploader-context.js'
-import validate from '../workers/validate'
-import schemaValidate from '../workers/schema'
+import React from "react"
+import PropTypes from "prop-types"
+import pluralize from "pluralize"
+import { Loading } from "@openneuro/components/loading"
+import Results from "../validation/validation-results.jsx"
+import UploaderContext from "./uploader-context.js"
+import validate from "../workers/validate"
+import schemaValidate from "../workers/schema"
 
 const UploadValidatorStatus = ({ issues, next, reset }) => {
   const errorCount = issues.errors.length
@@ -23,10 +23,10 @@ const UploadValidatorStatus = ({ issues, next, reset }) => {
   } else if (errorCount === 0 && warnCount > 0) {
     return (
       <div className="message warn fade-in">
-        We found {warnCount} {pluralize('warning', warnCount)} in your dataset.
-        You are not required to fix warnings, but doing so will make your
-        dataset more BIDS compliant. Continue or fix the issues and select
-        folder again.
+        We found {warnCount} {pluralize("warning", warnCount)}{" "}
+        in your dataset. You are not required to fix warnings, but doing so will
+        make your dataset more BIDS compliant. Continue or fix the issues and
+        select folder again.
         <button className="fileupload-btn btn-blue" onClick={next}>
           Continue
         </button>
@@ -35,19 +35,21 @@ const UploadValidatorStatus = ({ issues, next, reset }) => {
   } else {
     return (
       <div className="message error fade-in">
-        Your dataset is not a valid BIDS dataset. Fix the{' '}
+        Your dataset is not a valid BIDS dataset. Fix the{" "}
         <strong>
-          {errorCount} {pluralize('error', errorCount)}
-        </strong>{' '}
-        and{' '}
+          {errorCount} {pluralize("error", errorCount)}
+        </strong>{" "}
+        and{" "}
         <a
           href="#"
-          onClick={e => {
+          onClick={(e) => {
             e.preventDefault()
             reset()
-          }}>
+          }}
+        >
           select your folder again.
-        </a>{' '}
+        </a>
+        {" "}
       </div>
     )
   }
@@ -66,9 +68,9 @@ class UploadValidator extends React.Component {
     }
     const options = {
       config: {
-        error: ['NO_AUTHORS', 'EMPTY_DATASET_NAME'],
+        error: ["NO_AUTHORS", "EMPTY_DATASET_NAME"],
         ignoreSubjectConsistency: true,
-        blacklistModalities: ['Microscopy'],
+        blacklistModalities: ["Microscopy"],
       },
     }
     if (this.props.schemaValidator) {
@@ -77,13 +79,13 @@ class UploadValidator extends React.Component {
       // Test for dataset_description.json and use the schemaValidator for DatasetType == 'derivative'
       // Fall back if anything fails
       const dsDescription = Array.from(this.props.files).find(
-        f => f.name === 'dataset_description.json',
+        (f) => f.name === "dataset_description.json",
       )
       if (dsDescription) {
-        dsDescription.text().then(dsDescriptionData => {
+        dsDescription.text().then((dsDescriptionData) => {
           try {
             const descriptionFields = JSON.parse(dsDescriptionData)
-            if (descriptionFields.DatasetType === 'derivative') {
+            if (descriptionFields.DatasetType === "derivative") {
               schemaValidate(this.props.files, options).then(this.done)
             } else {
               validate(this.props.files, options).then(this.done)
@@ -121,11 +123,12 @@ class UploadValidator extends React.Component {
             warnings={this.state.issues.warnings}
           />
           <span className="bids-link">
-            Click to view details on{' '}
+            Click to view details on{" "}
             <a
               href="http://bids.neuroimaging.io"
               target="_blank"
-              rel="noopener noreferrer">
+              rel="noopener noreferrer"
+            >
               BIDS specification
             </a>
           </span>
@@ -145,12 +148,12 @@ UploadValidator.propTypes = {
 
 const UploadIssues = () => (
   <UploaderContext.Consumer>
-    {uploader => (
+    {(uploader) => (
       <UploadValidator
         schemaValidator={uploader.schemaValidator}
         files={uploader.selectedFiles}
-        next={() => uploader.setLocation('/upload/metadata')}
-        reset={() => uploader.setLocation('/upload')}
+        next={() => uploader.setLocation("/upload/metadata")}
+        reset={() => uploader.setLocation("/upload")}
       />
     )}
   </UploaderContext.Consumer>

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

@@ -1,7 +1,7 @@
-import React, { useState } from 'react'
-import MetadataForm from '../dataset/mutations/metadata-form.jsx'
-import UploaderContext from './uploader-context.js'
-import styled from '@emotion/styled'
+import React, { useState } from "react"
+import MetadataForm from "../dataset/mutations/metadata-form.jsx"
+import UploaderContext from "./uploader-context.js"
+import styled from "@emotion/styled"
 
 const Container = styled.div`
   &.message.fade-in {
@@ -11,16 +11,16 @@ const Container = styled.div`
 
 const UploadMetadata = () => {
   const [values, setValues] = useState({
-    associatedPaperDOI: '',
-    species: '',
-    studyLongitudinal: '',
-    studyDomain: '',
+    associatedPaperDOI: "",
+    species: "",
+    studyLongitudinal: "",
+    studyDomain: "",
     trialCount: undefined,
-    studyDesign: '',
-    openneuroPaperDOI: '',
-    dxStatus: '',
-    grantFunderName: '',
-    grantIdentifier: '',
+    studyDesign: "",
+    openneuroPaperDOI: "",
+    dxStatus: "",
+    grantFunderName: "",
+    grantIdentifier: "",
   })
   const handleInputChange = (name, value) => {
     const newValues = {
@@ -32,13 +32,13 @@ const UploadMetadata = () => {
 
   return (
     <UploaderContext.Consumer>
-      {uploader => (
+      {(uploader) => (
         <Container className="message fade-in">
           <MetadataForm
             values={values}
             onChange={handleInputChange}
             hideDisabled={true}
-            hiddenFields={['affirmedConsent', 'affirmedDefaced']}
+            hiddenFields={["affirmedConsent", "affirmedDefaced"]}
             hasEdit={true}
           />
           <br />
@@ -47,8 +47,9 @@ const UploadMetadata = () => {
             disabled={false}
             onClick={() => {
               uploader.captureMetadata(values)
-              uploader.setLocation('/upload/disclaimer')
-            }}>
+              uploader.setLocation("/upload/disclaimer")
+            }}
+          >
             Continue
           </button>
         </Container>

package/src/scripts/uploader/upload-mutation.js

@@ -1,18 +1,17 @@
-import { datasets, uploads } from '@openneuro/client'
-import { SUBMIT_METADATA } from '../dataset/mutations/submit-metadata.jsx'
+import { datasets, uploads } from "@openneuro/client"
+import { SUBMIT_METADATA } from "../dataset/mutations/submit-metadata.jsx"
 
 /**
  * Create a dataset and update the label
  * @param {object} client Apollo client
  */
 export const createDataset =
-  client =>
-  ({ affirmedDefaced, affirmedConsent }) => {
+  (client) => ({ affirmedDefaced, affirmedConsent }) => {
     return client
       .mutate({
         mutation: datasets.createDataset,
         variables: { affirmedDefaced, affirmedConsent },
-        errorPolicy: 'all',
+        errorPolicy: "all",
       })
       .then(({ data }) => data.createDataset.id)
   }
@@ -21,20 +20,18 @@ export const createDataset =
  * Create a dataset and update the label
  * @param {object} client Apollo client
  */
-export const prepareUpload =
-  client =>
-  ({ datasetId, uploadId }) => {
-    return client.mutate({
-      mutation: uploads.prepareUpload,
-      variables: { datasetId, uploadId },
-    })
-  }
+export const prepareUpload = (client) => ({ datasetId, uploadId }) => {
+  return client.mutate({
+    mutation: uploads.prepareUpload,
+    variables: { datasetId, uploadId },
+  })
+}
 
 /**
  * Complete upload
  * @param {object} client Apollo client
  */
-export const finishUpload = client => uploadId => {
+export const finishUpload = (client) => (uploadId) => {
   return client.mutate({
     mutation: uploads.finishUpload,
     variables: { uploadId },
@@ -57,7 +54,7 @@ export const mkLevels = (file, parent, tokens) => {
     // Nodes are directories
     const dirName = tokens.shift()
     const dirIndex = parent.directories.findIndex(
-      dir => dir.name === `${parent.name}/${dirName}`,
+      (dir) => dir.name === `${parent.name}/${dirName}`,
     )
     if (dirIndex !== -1) {
       // Directory exists
@@ -79,12 +76,12 @@ export const mkLevels = (file, parent, tokens) => {
  * Convert from an file input list to a FileTreeInput object
  * @param {object} fileList Browser FileList from file input
  */
-export const treeFromList = fileList => {
-  const tree = { name: '', files: [], directories: [] }
+export const treeFromList = (fileList) => {
+  const tree = { name: "", files: [], directories: [] }
 
   for (const file of fileList) {
     if (file.webkitRelativePath) {
-      const tokens = file.webkitRelativePath.split('/')
+      const tokens = file.webkitRelativePath.split("/")
       // Skip the top level, it is created above
       tokens.shift()
       mkLevels(file, tree, tokens)
@@ -97,7 +94,7 @@ export const treeFromList = fileList => {
   return tree
 }
 
-export const submitMetadata = client => (datasetId, metadata) => {
+export const submitMetadata = (client) => (datasetId, metadata) => {
   return client.mutate({
     mutation: SUBMIT_METADATA,
     variables: {
@@ -107,6 +104,6 @@ export const submitMetadata = client => (datasetId, metadata) => {
         ...metadata,
       },
     },
-    errorPolicy: 'all',
+    errorPolicy: "all",
   })
 }

package/src/scripts/uploader/upload-progress-button.jsx

@@ -1,12 +1,13 @@
-import React from 'react'
-import UploaderContext from './uploader-context.js'
+import React from "react"
+import UploaderContext from "./uploader-context.js"
 
 const UploadProgressButton = () => (
   <UploaderContext.Consumer>
-    {uploader => (
+    {(uploader) => (
       <a
         className="nav-link nl-upload nl-progress"
-        onClick={() => uploader.setLocation('/upload')}>
+        onClick={() => uploader.setLocation("/upload")}
+      >
         view details
       </a>
     )}

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

@@ -1,6 +1,6 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import { ProgressBar } from '@openneuro/components/progress-bar'
+import React from "react"
+import PropTypes from "prop-types"
+import { ProgressBar } from "@openneuro/components/progress-bar"
 
 const UploadProgress = ({ progress }) => {
   return (

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

@@ -1,10 +1,10 @@
-import React from 'react'
-import Input from './input.jsx'
-import UploaderContext from './uploader-context.js'
+import React from "react"
+import Input from "./input.jsx"
+import UploaderContext from "./uploader-context.js"
 
 const UploadRename = () => (
   <UploaderContext.Consumer>
-    {uploader => (
+    {(uploader) => (
       <div className="message fade-in">
         Rename your dataset (optional)
         <div className="dir-name has-input clearfix fade-in">
@@ -22,7 +22,8 @@ const UploadRename = () => (
         <button
           className="fileupload-btn btn-blue"
           disabled={false}
-          onClick={() => uploader.setLocation('/upload/issues')}>
+          onClick={() => uploader.setLocation("/upload/issues")}
+        >
           Continue
         </button>
       </div>

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

@@ -1,30 +1,32 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import FileSelect from './file-select'
-import UploaderContext from './uploader-context.js'
+import React from "react"
+import PropTypes from "prop-types"
+import FileSelect from "./file-select"
+import UploaderContext from "./uploader-context.js"
 
 const UploadResume = ({ datasetId }) => (
   <UploaderContext.Consumer>
-    {uploader =>
-      uploader.uploading ? (
-        <button
-          className="fileupload-btn btn-admin"
-          disabled={true}
-          title="Please wait for your current upload to finish before resuming">
-          <span>
-            <i className="fa fa-repeat" />
-            &nbsp;
-          </span>
-          Resume
-        </button>
-      ) : (
-        <FileSelect
-          onChange={uploader.resumeDataset(datasetId)}
-          resume
-          disabled={uploader.uploading}
-        />
-      )
-    }
+    {(uploader) =>
+      uploader.uploading
+        ? (
+          <button
+            className="fileupload-btn btn-admin"
+            disabled={true}
+            title="Please wait for your current upload to finish before resuming"
+          >
+            <span>
+              <i className="fa fa-repeat" />
+              &nbsp;
+            </span>
+            Resume
+          </button>
+        )
+        : (
+          <FileSelect
+            onChange={uploader.resumeDataset(datasetId)}
+            resume
+            disabled={uploader.uploading}
+          />
+        )}
   </UploaderContext.Consumer>
 )
 

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

@@ -1,24 +1,25 @@
-import React from 'react'
-import FileSelect from './file-select'
-import UploaderContext from './uploader-context.js'
-import AdminUser from '../authentication/admin-user'
+import React from "react"
+import FileSelect from "./file-select"
+import UploaderContext from "./uploader-context.js"
+import AdminUser from "../authentication/admin-user"
 
 const UploadSelect = () => (
   <div>
     <UploaderContext.Consumer>
-      {uploader => (
+      {(uploader) => (
         <div className="message fade-in">
           <p>
             To protect the privacy of the individuals who have been scanned, we
             require that all scan data be defaced before publishing a dataset.
           </p>
-          Select a{' '}
+          Select a{" "}
           <a
             href="http://bids.neuroimaging.io"
             target="_blank"
-            rel="noopener noreferrer">
+            rel="noopener noreferrer"
+          >
             BIDS dataset
-          </a>{' '}
+          </a>{" "}
           to upload
           <FileSelect onChange={uploader.selectFiles} />
           <AdminUser>
@@ -29,7 +30,7 @@ const UploadSelect = () => (
               defaultChecked={uploader.schemaValidator}
             />
             <label htmlFor="schema-validator-checkbox">
-              {' '}
+              {" "}
               Use schema based validator
             </label>
           </AdminUser>

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

@@ -1,11 +1,11 @@
-import React from 'react'
-import UploaderContext from './uploader-context.js'
-import UploadProgress from './upload-progress.jsx'
-import UploadFileStatus from './upload-file-status.jsx'
+import React from "react"
+import UploaderContext from "./uploader-context.js"
+import UploadProgress from "./upload-progress.jsx"
+import UploadFileStatus from "./upload-file-status.jsx"
 
 const UploadStatus = () => (
   <UploaderContext.Consumer>
-    {uploader => (
+    {(uploader) => (
       <div>
         <h4>
           {uploader.name} - Uploading {uploader.files.length} files.