@openneuro/app 4.1.0 → 4.2.1

package/src/scripts/uploader/__tests__/file-upload.spec.js

@@ -1,116 +0,0 @@
-import { getRelativePath, encodeFilePath } from '../file-upload.js'
-
-describe('file upload helpers', () => {
-  describe('getRelativePath', () => {
-    it('works with a few directory levels', () => {
-      expect(
-        getRelativePath({ webkitRelativePath: 'test/paths/like/this' }),
-      ).toBe('paths/like/this')
-    })
-    it('works if the path is not actually relative', () => {
-      expect(
-        getRelativePath({ webkitRelativePath: 'dataset_description.json' }),
-      ).toBe('dataset_description.json')
-    })
-  })
-  describe('encodeFilePath', () => {
-    it('supports directory upload from a webkit-derived browser (stripRelativePath: true)', () => {
-      expect(
-        encodeFilePath(
-          {
-            name: 'sub-02_T1w.nii.gz',
-            lastModified: 1604713385516,
-            webkitRelativePath: 'dataset/sub-02/anat/sub-02_T1w.nii.gz',
-            size: 311112,
-            type: 'application/gzip',
-          },
-          { stripRelativePath: true },
-        ),
-      ).toEqual('sub-02:anat:sub-02_T1w.nii.gz')
-    })
-    it('supports directory upload from a webkit-derived browser (stripRelativePath: false)', () => {
-      expect(
-        encodeFilePath(
-          {
-            name: 'sub-02_T1w.nii.gz',
-            lastModified: 1604713385516,
-            webkitRelativePath: 'sub-02/anat/sub-02_T1w.nii.gz',
-            size: 311112,
-            type: 'application/gzip',
-          },
-          { stripRelativePath: false },
-        ),
-      ).toEqual('sub-02:anat:sub-02_T1w.nii.gz')
-    })
-    it('supports file upload from a webkit-derived browser (stripRelativePath: true)', () => {
-      expect(
-        encodeFilePath(
-          {
-            name: 'README',
-            lastModified: 1604713385516,
-            webkitRelativePath: '',
-            size: 809,
-            type: 'text/plain',
-          },
-          { stripRelativePath: true },
-        ),
-      ).toEqual('README')
-    })
-    it('supports file upload from a webkit-derived browser (stripRelativePath: false)', () => {
-      expect(
-        encodeFilePath(
-          {
-            name: 'README',
-            lastModified: 1604713385516,
-            webkitRelativePath: '',
-            size: 809,
-            type: 'text/plain',
-          },
-          { stripRelativePath: false },
-        ),
-      ).toEqual('README')
-    })
-    it('supports nested file upload from a webkit-derived browser (stripRelativePath: true)', () => {
-      expect(
-        encodeFilePath(
-          {
-            name: 'sub-02_T1w.nii.gz',
-            lastModified: 1604713385516,
-            webkitRelativePath: '/dataset/sub-02/anat/',
-            size: 2000,
-            type: 'text/plain',
-          },
-          { stripRelativePath: true },
-        ),
-      ).toEqual('sub-02:anat:sub-02_T1w.nii.gz')
-    })
-    it('supports nested file upload from a webkit-derived browser (stripRelativePath: false)', () => {
-      expect(
-        encodeFilePath(
-          {
-            name: 'sub-02_T1w.nii.gz',
-            lastModified: 1604713385516,
-            webkitRelativePath: '/sub-02/anat/',
-            size: 2000,
-            type: 'text/plain',
-          },
-          { stripRelativePath: false },
-        ),
-      ).toEqual('sub-02:anat:sub-02_T1w.nii.gz')
-    })
-    it('supports nested directory upload from a webkit-derived browser (stripRelativePath: false)', () => {
-      expect(
-        encodeFilePath(
-          {
-            name: 'sub-02_T1w.nii.gz',
-            lastModified: 1604713385516,
-            webkitRelativePath: '/sub-02/anat/sub-02_T1w.nii.gz',
-            size: 2000,
-            type: 'text/plain',
-          },
-          { stripRelativePath: false },
-        ),
-      ).toEqual('sub-02:anat:sub-02_T1w.nii.gz')
-    })
-  })
-})

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

@@ -1,67 +0,0 @@
-import React from 'react'
-import { render, screen, fireEvent } from '@testing-library/react'
-import UploadDisclaimer from '../upload-disclaimer.jsx'
-import UploaderContext from '../uploader-context.js'
-
-describe('UploadDisclaimer component', () => {
-  it('renders as expected', () => {
-    expect(() =>
-      render(
-        <UploaderContext.Provider value={{ uploader: jest.fn() }}>
-          <UploadDisclaimer />
-        </UploaderContext.Provider>,
-      ),
-    ).not.toThrowError()
-  })
-  it('starts with the upload button disabled', () => {
-    render(
-      <UploaderContext.Provider value={{ uploader: jest.fn() }}>
-        <UploadDisclaimer />
-      </UploaderContext.Provider>,
-    )
-    expect(screen.getByText('I Agree')).toBeDisabled()
-  })
-  it('disable the upload button when both boxes are checked', () => {
-    const { getByLabelText } = render(
-      <UploaderContext.Provider value={{ uploader: jest.fn() }}>
-        <UploadDisclaimer />
-      </UploaderContext.Provider>,
-    )
-    fireEvent.click(
-      getByLabelText(
-        'All structural scans have been defaced, obscuring any tissue on or near the face that could potentially be used to reconstruct the facial structure.',
-      ),
-    )
-    fireEvent.click(
-      getByLabelText(
-        'I have explicit participant consent and ethical authorization to publish structural scans without defacing.',
-      ),
-    )
-    expect(screen.getByText('I Agree')).toBeDisabled()
-  })
-  it('enable the upload button when one box is checked', () => {
-    const { getByLabelText } = render(
-      <UploaderContext.Provider value={{ uploader: jest.fn() }}>
-        <UploadDisclaimer />
-      </UploaderContext.Provider>,
-    )
-    fireEvent.click(
-      getByLabelText(
-        'All structural scans have been defaced, obscuring any tissue on or near the face that could potentially be used to reconstruct the facial structure.',
-      ),
-    )
-    expect(screen.getByText('I Agree')).not.toBeDisabled()
-    // Disable the first and enable the second to test the alternate state
-    fireEvent.click(
-      getByLabelText(
-        'All structural scans have been defaced, obscuring any tissue on or near the face that could potentially be used to reconstruct the facial structure.',
-      ),
-    )
-    fireEvent.click(
-      getByLabelText(
-        'I have explicit participant consent and ethical authorization to publish structural scans without defacing.',
-      ),
-    )
-    expect(screen.getByText('I Agree')).not.toBeDisabled()
-  })
-})

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

@@ -1,57 +0,0 @@
-import { mkLevels, treeFromList } from '../upload-mutation.js'
-
-describe('Uploader mutations', () => {
-  describe('mkLevels', () => {
-    it('updates the parent argument by pushing file objects', () => {
-      const file = new Blob(['Trouble on Blobolonia'], { type: 'text/plain' })
-      const parent = { files: [], directories: [], name: '' }
-      mkLevels(file, parent, ['README'])
-      expect(parent.files).toEqual([file])
-      expect(parent.directories).toEqual([])
-    })
-    it('creates new directories for nested paths', () => {
-      const file = new Blob(['1234'], { type: 'text/plain' })
-      const parent = { files: [], directories: [], name: '' }
-      mkLevels(file, parent, ['derivatives', 'README'])
-      expect(parent.files).toEqual([])
-      expect(parent.directories).toHaveLength(1)
-      expect(parent.directories[0].files).toHaveLength(1)
-      expect(parent.directories[0].files[0]).toEqual(file)
-    })
-    it('updates existing directories with newly found files', () => {
-      const file = new Blob(['{}'], { type: 'application/json' })
-      const parent = {
-        files: [],
-        directories: [{ name: '/derivatives', files: [], directories: [] }],
-        name: '',
-      }
-      mkLevels(file, parent, ['derivatives', 'data.json'])
-      expect(parent.files).toEqual([])
-      expect(parent.directories).toHaveLength(1)
-      expect(parent.directories[0].files).toHaveLength(1)
-      expect(parent.directories[0].files[0]).toEqual(file)
-    })
-  })
-  describe('treeFromList', () => {
-    it('handles a tree from <input type="file" multiple />', () => {
-      const mockFileA = new Blob(['file one'], { type: 'text/plain' })
-      const mockFileB = new Blob(['file two'], { type: 'text/plain' })
-      mockFileA.webkitRelativePath = '/'
-      mockFileB.webkitRelativePath = '/'
-      const mockFileList = [mockFileA, mockFileB]
-      const fileTree = treeFromList(mockFileList)
-      expect(typeof fileTree).toBe('object')
-      expect(fileTree.directories).toEqual([])
-      expect(fileTree.files).toHaveLength(2)
-      expect(fileTree.name).toBe('')
-    })
-    it('should work for files without webkitRelativePath', () => {
-      const mockFile = new Blob(['a boy and his blob'], { type: 'text/plain' })
-      const mockFileList = [mockFile]
-      const fileTree = treeFromList(mockFileList)
-      expect(fileTree.directories).toEqual([])
-      expect(fileTree.files).toHaveLength(1)
-      expect(fileTree.name).toBe('')
-    })
-  })
-})

package/src/scripts/uploader/__tests__/uploader.spec.js

@@ -1,31 +0,0 @@
-import React from 'react'
-import { shallow } from 'enzyme'
-import { UploadClient } from '../uploader.jsx'
-import { JSDOM } from 'jsdom'
-const { window } = new JSDOM('', { runScripts: 'outside-only' })
-
-// Stub constructor for File-like objects with webkitRelativePath
-function TestFile(body, name, webkitRelativePath) {
-  const file = new window.Blob(body)
-  file.name = name
-  file.webkitRelativePath = webkitRelativePath ? webkitRelativePath : name
-  return file
-}
-
-describe('uploader', () => {
-  it('select files updates state', async done => {
-    const wrapper = shallow(<UploadClient />)
-    try {
-      await wrapper.instance().selectFiles({
-        files: [
-          new TestFile(['file body one'], 'file_one'),
-          new TestFile(['file body two'], 'file_two'),
-        ],
-      })
-      expect(wrapper.instance().state.files).toHaveLength(2)
-      done()
-    } catch (e) {
-      done.fail(e)
-    }
-  })
-})

package/src/scripts/uploader/add-path-to-files.js

@@ -1,19 +0,0 @@
-/**
- * Prefix all files with a path
- * This supports uploading within another directory
- * @param {any[]} fileList FileList for upload
- * @param {string} path Prefix path for all files
- * @returns {Array} Updated array of files with adapted paths
- */
-export const addPathToFiles = (fileList, path) => {
-  return path
-    ? Array.prototype.map.call(fileList, file => {
-        // Override webkitRelativePath with a new property
-        Object.defineProperty(file, 'webkitRelativePath', {
-          value: `/${path}/${file.webkitRelativePath}`,
-          writable: false,
-        })
-        return file
-      })
-    : fileList
-}

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

@@ -1,88 +0,0 @@
-import { config } from '../config'
-import { uploads } from '@openneuro/client'
-
-/**
- * Trim the webkitRelativePath value to only include the dataset relative path
- * @param {File} file FileAPI object from a browser multiple file selector
- */
-export const getRelativePath = (
-  file,
-  options = { stripRelativePath: true },
-) => {
-  const path = file.webkitRelativePath
-  const pathTokens = path.split('/')
-  if (pathTokens.length === 1) {
-    return path
-  }
-  if (pathTokens[0] === '') {
-    pathTokens.shift()
-  }
-  if (pathTokens[pathTokens.length - 1] === '') {
-    pathTokens[pathTokens.length - 1] = file.name
-  }
-  if (options.stripRelativePath) {
-    return pathTokens.slice(1).join('/')
-  } else {
-    return pathTokens.join('/')
-  }
-}
-
-/**
- * Handle all variants of File objects and return the encoded upload file path
- *
- * Top level files have webkitRelativePath '' in some scenarios, use just the filename in that case
- *
- * @param {File} file
- * @param {object} options
- * @param {boolean} options.stripRelativePath
- **/
-export const encodeFilePath = (file, options = { stripRelativePath: false }) =>
-  file.webkitRelativePath
-    ? uploads.encodeFilePath(getRelativePath(file, options))
-    : file.name
-
-/**
- * This provides a similar interface to Apollo mutation for a background fetch with a promise that resolves once all promises have settled
- * @param {object} options
- * @param {string} options.uploadId Upload identifier for resume
- * @param {string} options.datasetId Accession number
- * @param {number} options.endpoint Offset for upload endpoint
- * @param {Array<object>} options.filesToUpload Array of file objects
- * @param {string} options.token Credentials
- * @param {import('./upload-progress-class').UploadProgress} options.uploadProgress Controller for reporting upload progress
- * @param {AbortController} options.abortController Fetch AbortController for halting uploads
- * @param {boolean} options.stripRelativePath True will remove the top-most directory name
- */
-export async function uploadFiles({
-  uploadId,
-  datasetId,
-  endpoint,
-  filesToUpload,
-  token,
-  uploadProgress,
-  abortController,
-  stripRelativePath = true,
-}) {
-  // Maps FileAPI objects to Request with the correct URL and body
-  let totalSize = 0
-  const requests = filesToUpload.map(f => {
-    totalSize += f.size
-    const encodedFilePath = encodeFilePath(f, {
-      stripRelativePath,
-    })
-    const fileUrl = `${config.url}/uploads/${endpoint}/${datasetId}/${uploadId}/${encodedFilePath}`
-    return new Request(fileUrl, {
-      method: 'POST',
-      body: f,
-      headers: {
-        Authorization: `Bearer ${token}`,
-      },
-      credentials: 'omit',
-      signal: abortController.signal,
-    })
-  })
-
-  // No background fetch
-  // Parallelism is handled by the client in this case
-  return uploads.uploadParallel(requests, totalSize, uploadProgress, fetch)
-}

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

@@ -1,18 +0,0 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-
-const UploadButton = ({ onClick }) => (
-  <span className="upload-btn-wrap">
-    <a className="nav-link nl-upload" onClick={onClick}>
-      <span className="link-name">
-        <i className="fa fa-upload" /> Upload Dataset
-      </span>
-    </a>
-  </span>
-)
-
-UploadButton.propTypes = {
-  onClick: PropTypes.func,
-}
-
-export default UploadButton

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

@@ -1,91 +0,0 @@
-import React, { useState } from 'react'
-import UploaderContext from './uploader-context.js'
-
-const UploadDisclaimer = () => {
-  const [affirmedDefaced, setAffirmedDefaced] = useState(false)
-  const [affirmedConsent, setAffirmedConsent] = useState(false)
-  return (
-    <UploaderContext.Consumer>
-      {uploader => (
-        <div className="disclaimer fade-in">
-          <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>
-            If the dataset is being uploaded to another database (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>
-          <label>
-            <input
-              type="checkbox"
-              onChange={() => setAffirmedDefaced(!affirmedDefaced)}
-              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.
-          </label>
-          <label>
-            <input
-              type="checkbox"
-              onChange={() => setAffirmedConsent(!affirmedConsent)}
-              defaultChecked={affirmedConsent}
-            />
-            &nbsp; I have explicit participant consent and ethical authorization
-            to publish structural scans without defacing.
-          </label>
-          <span className="message">
-            <button
-              className="fileupload-btn btn-blue"
-              onClick={() => {
-                uploader.captureMetadata({
-                  ...uploader.metadata,
-                  affirmedDefaced,
-                  affirmedConsent,
-                })
-                uploader.upload({ affirmedDefaced, affirmedConsent })
-              }}
-              disabled={
-                !(
-                  (affirmedDefaced && !affirmedConsent) ||
-                  (!affirmedDefaced && affirmedConsent)
-                )
-              }
-            >
-              I Agree
-            </button>
-          </span>
-        </div>
-      )}
-    </UploaderContext.Consumer>
-  )
-}
-
-export default UploadDisclaimer

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

@@ -1,20 +0,0 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-
-const UploadFileStatus = ({ uploadingFiles, failedFiles }) => (
-  <>
-    <p>{[...uploadingFiles].join(', ')}</p>
-    <p>
-      {failedFiles.size
-        ? `Too many failed attempts for '${[...failedFiles].join(', ')}'`
-        : null}
-    </p>
-  </>
-)
-
-UploadFileStatus.propTypes = {
-  uploadingFiles: PropTypes.instanceOf(Set),
-  failedFiles: PropTypes.instanceOf(Set),
-}
-
-export default UploadFileStatus

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

@@ -1,131 +0,0 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import pluralize from 'pluralize'
-import Spinner from '../common/partials/spinner.jsx'
-import Results from '../validation/validation-results.jsx'
-import UploaderContext from './uploader-context.js'
-import validate from '../workers/validate'
-
-const UploadValidatorStatus = ({ issues, next, reset }) => {
-  const errorCount = issues.errors.length
-  const warnCount = issues.warnings.length
-  const issuesCount = errorCount + warnCount
-  if (issuesCount === 0) {
-    return (
-      <div className="message fade-in">
-        This dataset has no issues.
-        <button className="fileupload-btn btn-blue" onClick={next}>
-          Continue
-        </button>
-      </div>
-    )
-  } 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.
-        <button className="fileupload-btn btn-blue" onClick={next}>
-          Continue
-        </button>
-      </div>
-    )
-  } else {
-    return (
-      <div className="message error fade-in">
-        Your dataset is not a valid BIDS dataset. Fix the{' '}
-        <strong>
-          {errorCount} {pluralize('error', errorCount)}
-        </strong>{' '}
-        and{' '}
-        <a
-          href="#"
-          onClick={e => {
-            e.preventDefault()
-            reset()
-          }}>
-          select your folder again.
-        </a>{' '}
-      </div>
-    )
-  }
-}
-
-class UploadValidator extends React.Component {
-  constructor(props) {
-    super(props)
-    this.state = {
-      validating: true,
-      issues: {
-        errors: [],
-        warnings: [],
-      },
-      summary: {},
-    }
-    const options = {
-      config: {
-        error: ['NO_AUTHORS'],
-        ignoreSubjectConsistency: true,
-      },
-    }
-    validate(this.props.files, options).then(this.done)
-  }
-
-  /**
-   * Called when validation finishes
-   */
-  done = ({ issues, summary }) => {
-    this.setState({ issues, summary, validating: false })
-  }
-
-  render() {
-    if (this.state.validating) {
-      return <Spinner text="validating" active={true} />
-    } else {
-      return (
-        <div>
-          <UploadValidatorStatus
-            issues={this.state.issues}
-            next={this.props.next}
-            reset={this.props.reset}
-          />
-          <Results
-            errors={this.state.issues.errors}
-            warnings={this.state.issues.warnings}
-          />
-          <span className="bids-link">
-            Click to view details on{' '}
-            <a
-              href="http://bids.neuroimaging.io"
-              target="_blank"
-              rel="noopener noreferrer">
-              BIDS specification
-            </a>
-          </span>
-        </div>
-      )
-    }
-  }
-}
-
-UploadValidator.propTypes = {
-  // Files can be an FileList object or an array of File objects
-  files: PropTypes.oneOfType([PropTypes.object, PropTypes.array]),
-  next: PropTypes.func,
-  reset: PropTypes.func,
-}
-
-const UploadIssues = () => (
-  <UploaderContext.Consumer>
-    {uploader => (
-      <UploadValidator
-        files={uploader.selectedFiles}
-        next={() => uploader.setLocation('/upload/metadata')}
-        reset={() => uploader.setLocation('/upload')}
-      />
-    )}
-  </UploaderContext.Consumer>
-)
-
-export default UploadIssues