@openneuro/app 4.20.5 → 4.20.6-alpha.2

package/src/scripts/search/use-search-results.tsx

@@ -1,17 +1,18 @@
-import React, { useContext } from 'react'
-import { gql, useQuery } from '@apollo/client'
-import { SearchParamsCtx } from './search-params-ctx'
-import initialSearchParams from './initial-search-params'
+import React, { useContext } from "react"
+import { gql, useQuery } from "@apollo/client"
+import { SearchParamsCtx } from "./search-params-ctx"
+import initialSearchParams from "./initial-search-params"
 import {
   BoolQuery,
-  simpleQueryString,
+  joinWithOR,
   matchQuery,
-  rangeQuery,
+  multiMatchQuery,
   rangeListLengthQuery,
+  rangeQuery,
+  simpleQueryString,
   sqsJoinWithAND,
-  joinWithOR,
-} from './es-query-builders'
-import { species_list } from '@openneuro/components/content'
+} from "./es-query-builders"
+import { species_list } from "@openneuro/components/content"
 
 const searchQuery = gql`
   query advancedSearchDatasets(
@@ -122,7 +123,7 @@ const searchQuery = gql`
   }
 `
 
-const isActiveRange = range =>
+const isActiveRange = (range) =>
   JSON.stringify(range) !== JSON.stringify([null, null])
 
 export const useSearchResults = () => {
@@ -152,192 +153,217 @@ export const useSearchResults = () => {
   } = searchParams
 
   const boolQuery = new BoolQuery()
-  if (keywords.length)
+  if (keywords.length) {
     boolQuery.addClause(
-      'must',
+      "must",
       simpleQueryString(sqsJoinWithAND(keywords), [
-        'id^6',
-        'latestSnapshot.readme',
-        'latestSnapshot.description.Name^6',
-        'latestSnapshot.description.Authors^3',
+        "id^6",
+        "latestSnapshot.readme",
+        "latestSnapshot.description.Name^6",
+        "latestSnapshot.description.Authors^3",
       ]),
     )
+  }
   if (modality_selected) {
     const secondaryModalities = {
       Diffusion: {
-        secondary: 'MRI_Diffusion',
-        primary: 'MRI',
+        secondary: "MRI_Diffusion",
+        primary: "MRI",
       },
       Structural: {
-        secondary: 'MRI_Structural',
-        primary: 'MRI',
+        secondary: "MRI_Structural",
+        primary: "MRI",
       },
       Functional: {
-        secondary: 'MRI_Functional',
-        primary: 'MRI',
+        secondary: "MRI_Functional",
+        primary: "MRI",
       },
       Perfusion: {
-        secondary: 'MRI_Perfusion',
-        primary: 'MRI',
+        secondary: "MRI_Perfusion",
+        primary: "MRI",
       },
       Static: {
-        secondary: 'PET_Static',
-        primary: 'PET',
+        secondary: "PET_Static",
+        primary: "PET",
       },
       Dynamic: {
-        secondary: 'PET_Dynamic',
-        primary: 'PET',
+        secondary: "PET_Dynamic",
+        primary: "PET",
       },
     }
     if (Object.keys(secondaryModalities).includes(modality_selected)) {
       boolQuery.addClause(
-        'filter',
+        "filter",
         matchQuery(
-          'latestSnapshot.summary.secondaryModalities',
+          "latestSnapshot.summary.secondaryModalities",
           secondaryModalities[modality_selected].secondary,
         ),
       )
     } else {
       boolQuery.addClause(
-        'filter',
-        matchQuery('latestSnapshot.summary.modalities', modality_selected),
+        "filter",
+        matchQuery("latestSnapshot.summary.modalities", modality_selected),
       )
     }
   }
-  if (isActiveRange(ageRange))
+  if (isActiveRange(ageRange)) {
     boolQuery.addClause(
-      'filter',
-      rangeQuery('latestSnapshot.summary.subjectMetadata.age', ...ageRange),
+      "filter",
+      rangeQuery("latestSnapshot.summary.subjectMetadata.age", ...ageRange),
     )
-  if (isActiveRange(subjectCountRange))
+  }
+  if (isActiveRange(subjectCountRange)) {
     boolQuery.addClause(
-      'filter',
+      "filter",
       rangeListLengthQuery(
-        'latestSnapshot.summary.subjects',
+        "latestSnapshot.summary.subjects",
         subjectCountRange[0] || 0,
         subjectCountRange[1] || 1000000,
       ),
     )
-  if (diagnosis_selected)
+  }
+  if (diagnosis_selected) {
     boolQuery.addClause(
-      'filter',
-      matchQuery('metadata.dxStatus', diagnosis_selected),
+      "filter",
+      matchQuery("metadata.dxStatus", diagnosis_selected),
     )
-  if (tasks.length)
+  }
+  if (tasks.length) {
     boolQuery.addClause(
-      'must',
+      "must",
       simpleQueryString(sqsJoinWithAND(tasks), [
-        'latestSnapshot.summary.tasks',
+        "latestSnapshot.summary.tasks",
       ]),
     )
-  if (authors.length)
+  }
+  if (authors.length) {
     boolQuery.addClause(
-      'must',
+      "must",
       matchQuery(
-        'latestSnapshot.description.Authors',
+        "latestSnapshot.description.Authors",
         joinWithOR(authors),
-        '3',
+        "3",
       ),
     )
-  if (sex_selected !== 'All')
+  }
+  if (sex_selected !== "All") {
+    // Possible values for this field are specified here:
+    // https://bids-specification.readthedocs.io/en/stable/glossary.html#objects.columns.sex
+    let queryStrings = []
+    if (sex_selected == "Male") {
+      queryStrings = ["male", "m", "M", "MALE", "Male"]
+    } else if (sex_selected == "Female") {
+      queryStrings = ["female", "f", "F", "FEMALE", "Female"]
+    }
     boolQuery.addClause(
-      'filter',
-      matchQuery('latestSnapshot.summary.subjectMetadata.sex', sex_selected),
+      "filter",
+      multiMatchQuery(
+        "latestSnapshot.summary.subjectMetadata.sex",
+        queryStrings,
+      ),
     )
-  if (date_selected !== 'All Time') {
+  }
+  if (date_selected !== "All Time") {
     let d: number
-    if (date_selected === 'Last 30 days') {
+    if (date_selected === "Last 30 days") {
       d = 30
-    } else if (date_selected === 'Last 180 days') {
+    } else if (date_selected === "Last 180 days") {
       d = 180
     } else {
       d = 365
     }
-    boolQuery.addClause('filter', rangeQuery('created', `now-${d}d/d`, 'now/d'))
+    boolQuery.addClause("filter", rangeQuery("created", `now-${d}d/d`, "now/d"))
   }
   if (species_selected) {
-    if (species_selected === 'Other') {
+    if (species_selected === "Other") {
       // if species is 'Other', search for every species that isn't an available option
       const species = initialSearchParams.species_available
-        .filter(s => s !== 'Other')
-        .join(' ')
+        .filter((s) => s !== "Other")
+        .join(" ")
       boolQuery.addClause(
-        'must_not',
-        matchQuery('metadata.species', species, 'AUTO', 'OR'),
+        "must_not",
+        matchQuery("metadata.species", species, "AUTO", "OR"),
       )
-    } else if (species_selected === 'Human') {
+    } else if (species_selected === "Human") {
       // if species is 'Human', search for Human or null values (BIDS assumes human by default)
-      boolQuery.query.bool['should'] = [
-        matchQuery('metadata.species', 'Human', 'AUTO'),
-        { term: { _content: '' } },
+      boolQuery.query.bool["should"] = [
+        matchQuery("metadata.species", "Human", "AUTO"),
+        { term: { _content: "" } },
       ]
     } else {
       boolQuery.addClause(
-        'filter',
-        matchQuery('metadata.species', species_selected, 'AUTO'),
+        "filter",
+        matchQuery("metadata.species", species_selected, "AUTO"),
       )
     }
   }
-  if (section_selected)
+  if (section_selected) {
     boolQuery.addClause(
-      'filter',
-      matchQuery('metadata.studyLongitudinal', section_selected, 'AUTO'),
+      "filter",
+      matchQuery("metadata.studyLongitudinal", section_selected, "AUTO"),
     )
-  if (studyDomains.length)
+  }
+  if (studyDomains.length) {
     boolQuery.addClause(
-      'must',
-      matchQuery('metadata.studyDomain', joinWithOR(studyDomains)),
+      "must",
+      matchQuery("metadata.studyDomain", joinWithOR(studyDomains)),
     )
-  if (modality_selected === 'PET' || modality_selected === null) {
-    if (bodyParts.length)
+  }
+  if (modality_selected === "PET" || modality_selected === null) {
+    if (bodyParts.length) {
       boolQuery.addClause(
-        'must',
+        "must",
         simpleQueryString(sqsJoinWithAND(bodyParts), [
-          'latestSnapshot.summary.pet.BodyPart',
+          "latestSnapshot.summary.pet.BodyPart",
         ]),
       )
-    if (scannerManufacturers.length)
+    }
+    if (scannerManufacturers.length) {
       boolQuery.addClause(
-        'must',
+        "must",
         simpleQueryString(sqsJoinWithAND(scannerManufacturers), [
-          'latestSnapshot.summary.pet.ScannerManufacturer',
+          "latestSnapshot.summary.pet.ScannerManufacturer",
         ]),
       )
-    if (scannerManufacturersModelNames.length)
+    }
+    if (scannerManufacturersModelNames.length) {
       boolQuery.addClause(
-        'must',
+        "must",
         simpleQueryString(sqsJoinWithAND(scannerManufacturersModelNames), [
-          'latestSnapshot.summary.pet.ScannerManufacturersModelName',
+          "latestSnapshot.summary.pet.ScannerManufacturersModelName",
         ]),
       )
-    if (tracerNames.length)
+    }
+    if (tracerNames.length) {
       boolQuery.addClause(
-        'must',
+        "must",
         simpleQueryString(sqsJoinWithAND(tracerNames), [
-          'latestSnapshot.summary.pet.TracerName',
+          "latestSnapshot.summary.pet.TracerName",
         ]),
       )
-    if (tracerRadionuclides.length)
+    }
+    if (tracerRadionuclides.length) {
       boolQuery.addClause(
-        'must',
+        "must",
         simpleQueryString(sqsJoinWithAND(tracerRadionuclides), [
-          'latestSnapshot.summary.pet.TracerRadionuclide',
+          "latestSnapshot.summary.pet.TracerRadionuclide",
         ]),
       )
+    }
   }
 
   let sortBy
-  if (sortBy_selected.label === 'Relevance') {
+  if (sortBy_selected.label === "Relevance") {
     // If filters are set, sort by relevance (default sort),
     //   otherwise, sort from newest to oldest
-    sortBy = boolQuery.isEmpty() ? { created: 'desc' } : null
-  } else if (sortBy_selected.label === 'Newest') {
-    sortBy = { created: 'desc' }
-  } else if (sortBy_selected.label === 'Oldest') {
-    sortBy = { created: 'asc' }
-  } else if (sortBy_selected.label === 'Activity') {
+    sortBy = boolQuery.isEmpty() ? { created: "desc" } : null
+  } else if (sortBy_selected.label === "Newest") {
+    sortBy = { created: "desc" }
+  } else if (sortBy_selected.label === "Oldest") {
+    sortBy = { created: "asc" }
+  } else if (sortBy_selected.label === "Activity") {
     // TODO: figure out
-    sortBy = { 'analytics.downloads': 'desc' }
+    sortBy = { "analytics.downloads": "desc" }
   }
   return useQuery(searchQuery, {
     variables: {
@@ -347,10 +373,10 @@ export const useSearchResults = () => {
       datasetType: datasetType_selected,
       datasetStatus: datasetStatus_selected,
     },
-    errorPolicy: 'ignore',
+    errorPolicy: "ignore",
     // fetchPolicy is workaround for stuck loading bug (https://github.com/apollographql/react-apollo/issues/3270#issuecomment-579614837)
     // TODO: find better solution
-    fetchPolicy: 'cache-and-network',
-    nextFetchPolicy: 'cache-first',
+    fetchPolicy: "cache-and-network",
+    nextFetchPolicy: "cache-first",
   })
 }

package/src/scripts/styles/media.tsx

@@ -1,6 +1,6 @@
-import React from 'react'
-import { createMedia } from '@artsy/fresnel'
-import '@artsy/fresnel/dist/Media'
+import React from "react"
+import { createMedia } from "@artsy/fresnel"
+import "@artsy/fresnel/dist/Media"
 
 const AppMedia = createMedia({
   breakpoints: {

package/src/scripts/styles/support-modal.jsx

@@ -1,4 +1,4 @@
-import styled from '@emotion/styled'
+import styled from "@emotion/styled"
 
 //styled components for custom support modal
 const Overlay = styled.div`
@@ -40,4 +40,4 @@ const ExitButton = styled.a`
   z-index: 100;
 `
 
-export { Overlay, ModalContainer, ExitButton }
+export { ExitButton, ModalContainer, Overlay }

package/src/scripts/sw.ts

@@ -6,36 +6,37 @@
 export default null
 declare const self: ServiceWorkerGlobalScope
 const globalAny: any = global // Workaround for serviceWorkerOption type missing
-const CACHE_NAME = 'openneuro'
+const CACHE_NAME = "openneuro"
 const CACHE_PATHS = globalAny.serviceWorkerOption.assets
 
-self.addEventListener('install', event => {
+self.addEventListener("install", (event) => {
   void self.skipWaiting()
   event.waitUntil(
-    caches.open(CACHE_NAME).then(cache => {
+    caches.open(CACHE_NAME).then((cache) => {
       return cache.addAll(CACHE_PATHS)
     }),
   )
 })
 
-self.addEventListener('activate', event => {
+self.addEventListener("activate", (event) => {
   event.waitUntil(self.clients.claim())
 })
 
-self.addEventListener('fetch', event => {
+self.addEventListener("fetch", (event) => {
   // Let the browser do its default thing
   // for non-GET requests.
-  if (event.request.method === 'GET') {
+  if (event.request.method === "GET") {
     // Skip serving from cache for cross origin 'only-if-cached' requests
     if (
-      event.request.cache === 'only-if-cached' &&
-      event.request.mode !== 'same-origin'
-    )
+      event.request.cache === "only-if-cached" &&
+      event.request.mode !== "same-origin"
+    ) {
       return
+    }
     // Respond from cache, then the network
     event.respondWith(
-      caches.open(CACHE_NAME).then(cache => {
-        return cache.match(event.request).then(response => {
+      caches.open(CACHE_NAME).then((cache) => {
+        return cache.match(event.request).then((response) => {
           return response || fetch(event.request)
         })
       }),

package/src/scripts/test-utils.js

@@ -1,12 +1,12 @@
-import cookies from './utils/cookies.js'
+import cookies from "./utils/cookies.js"
 
 /**
  * Sets a login cookie during a test run
  */
 export const testLogin = () => {
   cookies.set(
-    'accessToken',
-    'eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJzdWIiOiIxMjM0IiwiZW1haWwiOiJleGFtcGxlQGV4YW1wbGUuY29tIiwicHJvdmlkZXIiOiJqZXN0IiwibmFtZSI6IlRlc3RlciIsImFkbWluIjp0cnVlLCJqdGkiOiIwNjc2M2JjMi02ZTkwLTRjNTMtOWNkNi01ODE2MGM0ZGM1YzMiLCJpYXQiOjE1NTQyMzc0NDAsImV4cCI6MTU1NDI0MTA0MH0._zfwOPqNZUT8DAUB_rIcIbcaKu7nzDs0OZjqaXfhymM',
+    "accessToken",
+    "eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJzdWIiOiIxMjM0IiwiZW1haWwiOiJleGFtcGxlQGV4YW1wbGUuY29tIiwicHJvdmlkZXIiOiJqZXN0IiwibmFtZSI6IlRlc3RlciIsImFkbWluIjp0cnVlLCJqdGkiOiIwNjc2M2JjMi02ZTkwLTRjNTMtOWNkNi01ODE2MGM0ZGM1YzMiLCJpYXQiOjE1NTQyMzc0NDAsImV4cCI6MTU1NDI0MTA0MH0._zfwOPqNZUT8DAUB_rIcIbcaKu7nzDs0OZjqaXfhymM",
   )
 }
 
@@ -14,5 +14,5 @@ export const testLogin = () => {
  * Clear a login cookie during a test run
  */
 export const testLogout = () => {
-  cookies.set('accessToken', null)
+  cookies.set("accessToken", null)
 }

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

@@ -7,13 +7,13 @@
  */
 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
+    ? 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-select.tsx

@@ -1,7 +1,7 @@
 // dependencies -------------------------------------------------------
 
-import React from 'react'
-import PropTypes from 'prop-types'
+import React from "react"
+import PropTypes from "prop-types"
 
 type UploadProps = {
   resume?: boolean
@@ -21,7 +21,7 @@ class Upload extends React.Component<UploadProps> {
       </span>
     )
     const icon = this.props.resume ? resumeIcon : null
-    const text = this.props.resume ? 'Resume' : 'Select folder'
+    const text = this.props.resume ? "Resume" : "Select folder"
 
     return (
       <div className="fileupload-btn">

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

@@ -1,5 +1,5 @@
-import { config } from '../config'
-import { uploads } from '@openneuro/client'
+import { config } from "../config"
+import { uploads } from "@openneuro/client"
 
 /**
  * Trim the webkitRelativePath value to only include the dataset relative path
@@ -10,20 +10,20 @@ export const getRelativePath = (
   options = { stripRelativePath: true },
 ) => {
   const path = file.webkitRelativePath
-  const pathTokens = path.split('/')
+  const pathTokens = path.split("/")
   if (pathTokens.length === 1) {
     return path
   }
-  if (pathTokens[0] === '') {
+  if (pathTokens[0] === "") {
     pathTokens.shift()
   }
-  if (pathTokens[pathTokens.length - 1] === '') {
+  if (pathTokens[pathTokens.length - 1] === "") {
     pathTokens[pathTokens.length - 1] = file.name
   }
   if (options.stripRelativePath) {
-    return pathTokens.slice(1).join('/')
+    return pathTokens.slice(1).join("/")
   } else {
-    return pathTokens.join('/')
+    return pathTokens.join("/")
   }
 }
 
@@ -35,7 +35,7 @@ export const getRelativePath = (
  * @param {File} file
  * @param {object} options
  * @param {boolean} options.stripRelativePath
- **/
+ */
 export const encodeFilePath = (file, options = { stripRelativePath: false }) =>
   file.webkitRelativePath
     ? uploads.encodeFilePath(getRelativePath(file, options))
@@ -65,19 +65,20 @@ export async function uploadFiles({
 }) {
   // Maps FileAPI objects to Request with the correct URL and body
   let totalSize = 0
-  const requests = filesToUpload.map(f => {
+  const requests = filesToUpload.map((f) => {
     totalSize += f.size
     const encodedFilePath = encodeFilePath(f, {
       stripRelativePath,
     })
-    const fileUrl = `${config.url}/uploads/${endpoint}/${datasetId}/${uploadId}/${encodedFilePath}`
+    const fileUrl =
+      `${config.url}/uploads/${endpoint}/${datasetId}/${uploadId}/${encodedFilePath}`
     return new Request(fileUrl, {
-      method: 'POST',
+      method: "POST",
       body: f,
       headers: {
         Authorization: `Bearer ${token}`,
       },
-      credentials: 'omit',
+      credentials: "omit",
       signal: abortController.signal,
     })
   })

package/src/scripts/uploader/input.jsx

@@ -1,7 +1,7 @@
 // dependencies -------------------------------------------------------
 
-import React, { Component } from 'react'
-import PropTypes from 'prop-types'
+import React, { Component } from "react"
+import PropTypes from "prop-types"
 
 // component setup ----------------------------------------------------
 
@@ -11,13 +11,13 @@ class Input extends React.Component {
   constructor(props) {
     super(props)
     this.state = {
-      value: props.initialValue ? props.initialValue : '',
+      value: props.initialValue ? props.initialValue : "",
     }
   }
 
   static getDerivedStateFromProps(nextProps) {
     // Will reset value when prop changes
-    if ('value' in nextProps) {
+    if ("value" in nextProps) {
       return { value: nextProps.value }
     } else {
       return null
@@ -33,8 +33,9 @@ class Input extends React.Component {
     return (
       <div
         className={`form-group float-label-input ${
-          this.props.containerClass || ''
-        }`}>
+          this.props.containerClass || ""
+        }`}
+      >
         {value && value.length > 0 ? <label>{placeholder}</label> : null}
         {this._input(type, name, placeholder, value)}
       </div>
@@ -44,7 +45,7 @@ class Input extends React.Component {
   // custom methods -----------------------------------------------------
 
   _input(type, name, placeholder, value) {
-    if (type === 'textarea') {
+    if (type === "textarea") {
       return (
         <textarea
           name={name}

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

@@ -1,6 +1,6 @@
-import React from 'react'
-import PropTypes from 'prop-types'
-import styled from '@emotion/styled'
+import React from "react"
+import PropTypes from "prop-types"
+import styled from "@emotion/styled"
 
 const UploadAnchor = styled.a`
   @media (max-width: 450px) {