Release 1.3.0

README.md

@@ -1,8 +1,7 @@
 # SINGLE CELL PORTAL README
 
 [![codecov](https://codecov.io/gh/broadinstitute/single_cell_portal_core/branch/development/graph/badge.svg?token=HMWE5BO2a4)](https://codecov.io/gh/broadinstitute/single_cell_portal_core)
-[![Build Status](https://travis-ci.com/broadinstitute/single_cell_portal_core.svg?branch=development)](https://travis-ci.com/broadinstitute/single_cell_portal_core)
-
+[![Build Status](https://app.travis-ci.com/broadinstitute/single_cell_portal_core.svg?branch=development)](https://app.travis-ci.com/broadinstitute/single_cell_portal_core)
 ## SETUP
 
 This application is built and deployed using [Docker](https://www.docker.com), specifically native

app/controllers/api/v1/bulk_download_controller.rb

@@ -57,14 +57,14 @@ def auth_code
         half_hour = 1800 # seconds
 
         totat = current_api_user.create_totat(half_hour, api_v1_bulk_download_generate_curl_config_path)
-        valid_params = params.permit({ file_ids: [], tdr_files: {} }).to_h
+        valid_params = params.permit({ file_ids: [], azul_files: {} }).to_h
 
         # for now, we don't do any permissions validation on the param values -- we'll do that during the actual download, since
         # quota/files/permissions may change between the creation of the download and the actual download.
         auth_download = DownloadRequest.create!(
           auth_code: totat[:totat],
           file_ids: valid_params[:file_ids],
-          tdr_files: valid_params[:tdr_files],
+          azul_files: valid_params[:azul_files],
           user_id: current_api_user.id
         )
         auth_code_response = {
@@ -245,6 +245,13 @@ def drs_info
             key :description, 'Name of directory folder to download (for single-study bulk download only), can be "all"'
             key :required, false
           end
+          parameter do
+            key :name, :context
+            key :type, :string
+            key :in, :query
+            key :description, 'Context of the download, its scope: either "study" or "global"'
+            key :required, false
+          end
           response 200 do
             key :description, 'Curl configuration file with signed URLs for requested data'
             key :type, :string
@@ -274,15 +281,18 @@ def drs_info
       def generate_curl_config
         valid_accessions = []
         file_ids = []
-        tdr_files = {}
+        azul_files = {}
+
+        # determine if this a single-study bulk download (from download tab) or from home page search
+        search_context = params[:context] || 'unknown'
 
         # branch based on whether they provided a download_id, file_ids, or accessions
         if params[:download_id]
           download_req = DownloadRequest.find(params[:download_id])
           render json: { error: 'Invalid download_id provided' }, status: 400 and return if download_req.blank?
 
           file_ids = download_req.file_ids
-          tdr_files = download_req.tdr_files
+          azul_files = download_req.azul_files
         elsif params[:file_ids]
           begin
             file_ids = RequestUtils.validate_id_list(params[:file_ids])
@@ -344,7 +354,8 @@ def generate_curl_config
                                                                            user: current_api_user,
                                                                            study_bucket_map: bucket_map,
                                                                            output_pathname_map: pathname_map,
-                                                                           tdr_files: tdr_files)
+                                                                           azul_files: azul_files,
+                                                                           context: search_context)
         end_time = Time.zone.now
         runtime = TimeDifference.between(start_time, end_time).humanize
         logger.info "Curl configs generated for studies #{valid_accessions}, #{files_requested.size + directory_files.size} total files"

app/controllers/api/v1/search_controller.rb

@@ -173,7 +173,7 @@ def index
 
         # filter results by branding group, if specified
         if @selected_branding_group.present?
-          @viewable = @viewable.where(branding_group_id: @selected_branding_group.id)
+          @viewable = @viewable.where(:branding_group_ids.in => [@selected_branding_group.id])
         end
         # variable for determining how we will sort search results for relevance
         sort_type = :none

app/controllers/api/v1/studies_controller.rb

@@ -597,7 +597,7 @@ def check_study_view_permission
       # study params list
       def study_params
         params.require(:study).permit(:name, :description, :public, :embargo, :use_existing_workspace, :firecloud_workspace,
-                                      :firecloud_project, :branding_group_id, :cell_count, :gene_count, :view_order,
+                                      :firecloud_project, :cell_count, :gene_count, :view_order,  branding_group_ids: [],
                                       study_shares_attributes: [:id, :_destroy, :email, :permission],
                                       study_detail_attributes: [:id, :full_description],
                                       :default_options => [:cluster, :annotation, :color_profile, :expression_label, :deliver_emails,

app/controllers/branding_groups_controller.rb

@@ -2,9 +2,11 @@ class BrandingGroupsController < ApplicationController
   before_action :set_branding_group, only: [:show, :edit, :update, :destroy]
   before_action except: [:list_navigate] do
     authenticate_user!
-    authenticate_admin
   end
 
+  before_action :authenticate_curator, only: [:show, :edit, :update]
+  before_action :authenticate_admin, only: [:index, :create, :destroy]
+
   # GET /branding_groups
   # GET /branding_groups.json
   def index
@@ -13,11 +15,7 @@ def index
 
   # show a list for display and linking, editable only if the user has appropriate permissions
   def list_navigate
-    @editable_branding_groups = []
     @branding_groups = BrandingGroup.visible_groups_to_user(current_user)
-    if current_user.present?
-      @editable_branding_groups = current_user.available_branding_groups.to_a
-    end
   end
 
   # GET /branding_groups/1
@@ -37,7 +35,10 @@ def edit
   # POST /branding_groups
   # POST /branding_groups.json
   def create
-    @branding_group = BrandingGroup.new(branding_group_params)
+    clean_params = branding_group_params.to_h
+    clean_params[:users] = self.class.merge_curator_params(params[:curator_emails], nil, current_user)
+    clean_params.delete(:user_ids)
+    @branding_group = BrandingGroup.new(clean_params)
 
     respond_to do |format|
       if @branding_group.save
@@ -65,6 +66,12 @@ def update
         end
         # delete the param since it is not a real model param
         clean_params.delete("reset_#{image_name}")
+
+        # merge in curator params
+        clean_params[:users] = self.class.merge_curator_params(
+          params[:curator_emails], @branding_group, current_user
+        )
+        clean_params.delete(:user_ids)
       end
 
       if @branding_group.update(clean_params)
@@ -90,6 +97,18 @@ def destroy
     end
   end
 
+  # helper to merge in the list of curators into the :users parameter
+  # will prevent curator from removing themselves from the collection
+  def self.merge_curator_params(curator_list, collection, user)
+    curators = curator_list.split(',').map(&:strip)
+    users = curators.map { |email| User.find_by(email: email) }.compact
+    return users if collection.nil?
+
+    # ensure current user cannot accidentally remove themselves from the list if this is an update
+    users << user if collection.users.include?(user) && !users.include?(user)
+    users
+  end
+
   private
 
   # Use callbacks to share common setup or constraints between actions.
@@ -99,8 +118,15 @@ def set_branding_group
 
   # Never trust parameters from the scary internet, only allow the permit list through.
   def branding_group_params
-    params.require(:branding_group).permit(:name, :tag_line, :public, :background_color, :font_family, :font_color, :user_id,
+    params.require(:branding_group).permit(:name, :tag_line, :public, :background_color, :font_family, :font_color,
                                            :splash_image, :banner_image, :footer_image, :external_link_url, :external_link_description,
-                                           :reset_splash_image, :reset_footer_image, :reset_banner_image)
+                                           :reset_splash_image, :reset_footer_image, :reset_banner_image,
+                                           user_ids: [])
+  end
+
+  def authenticate_curator
+    unless @branding_group.can_edit?(current_user)
+      redirect_to collection_list_navigate_path, alert: 'You do not have permission to perform that action' and return
+    end
   end
 end

app/controllers/studies_controller.rb

@@ -1089,7 +1089,8 @@ def set_study
   # study params list
   def study_params
     params.require(:study).permit(:name, :description, :public, :user_id, :embargo, :use_existing_workspace, :firecloud_workspace,
-                                  :firecloud_project, :branding_group_id, study_shares_attributes: [:id, :_destroy, :email, :permission],
+                                  :firecloud_project, branding_group_ids: [],
+                                  study_shares_attributes: [:id, :_destroy, :email, :permission],
                                   external_resources_attributes: [:id, :_destroy, :title, :description, :url, :publication_url],
                                   study_detail_attributes: [:id, :full_description])
   end

app/helpers/branding_groups_helper.rb

@@ -26,4 +26,10 @@ def web_safe_fonts
         ]
     ]
   end
+
+  def get_published_label(branding_group)
+    text =  branding_group.public ? 'published' : 'private'
+    class_name = branding_group.public ? 'success' : 'danger'
+    "<span class='label label-#{class_name}'>#{text}</span>".html_safe
+  end
 end

app/javascript/components/search/controls/download/DownloadButton.js

@@ -41,12 +41,12 @@ export default function DownloadButton({ searchResults={} }) {
   /** Note that we are reading the TDR file information from the search results object, which
    * means we are reliant on the TDR results being on the current page.  Once we begin paging/sorting
    * TDR results, this approach will have to be revisited */
-  const tdrFileInfo = searchResults.studies
-    ?.filter(result => result.study_source === 'TDR')
+  const azulFileInfo = searchResults.studies
+    ?.filter(result => result.study_source === 'HCA')
     ?.map(result => ({
       accession: result.accession,
       name: result.name,
-      study_source: 'TDR',
+      study_source: 'HCA',
       description: result.description,
       hca_project_id: result.hca_project_id,
       studyFiles: result.file_information
@@ -72,7 +72,7 @@ export default function DownloadButton({ searchResults={} }) {
         <DownloadSelectionModal
           show={showModal}
           setShow={setShowModal}
-          tdrFileInfo={tdrFileInfo}
+          azulFileInfo={azulFileInfo}
           studyAccessions={matchingAccessions}/> }
     </>
   )

app/javascript/components/search/controls/download/DownloadCommand.js

@@ -5,7 +5,7 @@ import { fetchAuthCode, stringifyQuery } from 'lib/scp-api'
 
 /** component for rendering a copyable bulk download command for an array of file ids.
     Queries the server to retrieve the appropriate auth code. */
-export default function DownloadCommand({ fileIds=[], tdrFiles }) {
+export default function DownloadCommand({ fileIds=[], azulFiles }) {
   const [isLoading, setIsLoading] = useState(true)
   const [authInfo, setAuthInfo] = useState({ authCode: null, timeInterval: 3000 })
   const [refreshNum, setRefreshNum] = useState(0)
@@ -20,7 +20,7 @@ export default function DownloadCommand({ fileIds=[], tdrFiles }) {
 
   useEffect(() => {
     setIsLoading(true)
-    fetchAuthCode(fileIds, tdrFiles).then(result => {
+    fetchAuthCode(fileIds, azulFiles).then(result => {
       setAuthInfo(result)
       setIsLoading(false)
     })
@@ -84,7 +84,8 @@ export default function DownloadCommand({ fileIds=[], tdrFiles }) {
 function getDownloadCommand(authCode, downloadId) {
   const queryParams = {
     auth_code: authCode,
-    download_id: downloadId
+    download_id: downloadId,
+    context: 'global' // this is a search-based bulk download request
   }
   const queryString = stringifyQuery(queryParams)
 

app/javascript/components/search/controls/download/DownloadSelectionModal.js

@@ -10,57 +10,51 @@ import { bytesToSize } from 'lib/stats'
 
 import { fetchDownloadInfo, fetchDrsInfo } from 'lib/scp-api'
 
-const TDR_COLUMNS = ['project_manifest', 'analysis', 'sequence']
+const AZUL_COLUMNS = ['project_manifest', 'analysis', 'sequence']
 const SCP_COLUMNS = ['matrix', 'metadata', 'cluster']
 
 /**
   * a modal that, given a list of study accessions, allows a user to select/deselect
   * studies and file types for download.  This queries the bulk_download/summary API method
   * to retrieve the list of study details and available files
   */
-export default function DownloadSelectionModal({ studyAccessions, tdrFileInfo, show, setShow }) {
+export default function DownloadSelectionModal({ studyAccessions, azulFileInfo, show, setShow }) {
   const [isLoading, setIsLoading] = useState(true)
-  const [isLoadingTDR, setIsLoadingTDR] = useState(true)
+  const [isLoadingAzul, setIsLoadingAzul] = useState(true)
   const [downloadInfo, setDownloadInfo] = useState([])
   const [selectedBoxes, setSelectedBoxes] = useState()
-  const [downloadInfoTDR, setDownloadInfoTDR] = useState([])
-  const [selectedBoxesTDR, setSelectedBoxesTDR] = useState()
+  const [downloadInfoAzul, setDownloadInfoAzul] = useState([])
+  const [selectedBoxesAzul, setSelectedBoxesAzul] = useState()
   const [stepNum, setStepNum] = useState(1)
 
   const scpAccessions = studyAccessions.filter(accession => accession.startsWith('SCP'))
-  const tdrAccessions = studyAccessions.filter(accession => !accession.startsWith('SCP'))
-  const showTDRSelectionPane = tdrAccessions.length > 0
+  const azulAccessions = studyAccessions.filter(accession => !accession.startsWith('SCP'))
+  const showAzulSelectionPane = azulAccessions.length > 0
   const { fileCount, fileSize } = getSelectedFileStats(downloadInfo, selectedBoxes, isLoading)
-  const { fileCount: fileCountTDR, fileSize: fileSizeTDR } =
-    getSelectedFileStats(downloadInfoTDR, selectedBoxesTDR, isLoadingTDR)
-  const prettyBytes = bytesToSize(fileSize + fileSizeTDR)
+  const { fileCount: fileCountAzul, fileSize: fileSizeAzul } =
+    getSelectedFileStats(downloadInfoAzul, selectedBoxesAzul, isLoadingAzul)
+  const prettyBytes = bytesToSize(fileSize + fileSizeAzul)
   const selectedFileIds = getSelectedFileHandles(downloadInfo, selectedBoxes)
-  const selectedTdrFiles = getSelectedFileHandles(downloadInfoTDR, selectedBoxesTDR, true)
-
-  /** For TDR studies, we will know from the tdrFileInfo object how many files of each type there are
-   * But we need to query the drsInfo so that we can get the file sizes and download urls */
-  function initializeTDRTable() {
-    setSelectedBoxesTDR(newSelectedBoxesState(tdrFileInfo, TDR_COLUMNS))
-    setDownloadInfoTDR(tdrFileInfo)
-    setIsLoadingTDR(false)
-  }
+  const selectedAzulFiles = getSelectedFileHandles(downloadInfoAzul, selectedBoxesAzul, true)
 
   /**
-    render bulk download table for SCP & TDR/HCA studies
+    render bulk download table for SCP & HCA studies
    */
   function renderFileTables(result=[]) {
     setSelectedBoxes(newSelectedBoxesState(result, SCP_COLUMNS))
     setDownloadInfo(result)
     setIsLoading(false)
-    if (showTDRSelectionPane) {
-      initializeTDRTable()
+    if (showAzulSelectionPane) {
+      setSelectedBoxesAzul(newSelectedBoxesState(azulFileInfo, AZUL_COLUMNS))
+      setDownloadInfoAzul(azulFileInfo)
+      setIsLoadingAzul(false)
     }
   }
 
   useEffect(() => {
     if (show) {
       setIsLoading(true)
-      setIsLoadingTDR(true)
+      setIsLoadingAzul(true)
       fetchDownloadInfo(scpAccessions).then(result => {
         renderFileTables(result)
       })
@@ -73,7 +67,7 @@ export default function DownloadSelectionModal({ studyAccessions, tdrFileInfo, s
     data-analytics-name="download-modal-next">
     NEXT
   </button>
-  if (fileCount + fileCountTDR === 0) {
+  if (fileCount + fileCountAzul === 0) {
     downloadButton = <button className="btn btn-primary" disabled="disabled">
       No files selected
     </button>
@@ -116,23 +110,23 @@ export default function DownloadSelectionModal({ studyAccessions, tdrFileInfo, s
               selectedBoxes={selectedBoxes}
               setSelectedBoxes={setSelectedBoxes}
               columnTypes={SCP_COLUMNS}/>
-            { showTDRSelectionPane &&
+            { showAzulSelectionPane &&
               <div>
                 <h4>Human Cell Atlas studies</h4>
                 <DownloadSelectionTable
-                  isLoading={isLoadingTDR}
-                  downloadInfo={downloadInfoTDR}
-                  selectedBoxes={selectedBoxesTDR}
-                  setSelectedBoxes={setSelectedBoxesTDR}
-                  columnTypes={TDR_COLUMNS}/>
+                  isLoading={isLoadingAzul}
+                  downloadInfo={downloadInfoAzul}
+                  selectedBoxes={selectedBoxesAzul}
+                  setSelectedBoxes={setSelectedBoxesAzul}
+                  columnTypes={AZUL_COLUMNS}/>
               </div>
             }
           </div>
         }
         { stepNum === 2 && <DownloadCommand
           closeParent={() => setShow(false)}
           fileIds={selectedFileIds}
-          tdrFiles={selectedTdrFiles}/> }
+          azulFiles={selectedAzulFiles}/> }
         { !isLoading &&
           <div className="download-size-message">
             <label htmlFor="download-size-amount">Total size</label>

app/javascript/components/search/controls/download/DownloadSelectionTable.js

@@ -259,7 +259,9 @@ export function getSelectedFileStats(downloadInfo, selectedBoxes, isLoading) {
   */
 export function getFileStats(study, fileTypes) {
   const files = study.studyFiles.filter(file => fileTypes.includes(file.file_type))
-  const fileCount = files.length
+  const fileCount = study.study_source === 'HCA' ? files.reduce((sum, studyFile) => {
+    return sum + studyFile.count
+  }, 0) : files.length
   const fileSize = files.reduce((sum, studyFile) => {
     return sum + (studyFile.upload_file_size ? studyFile.upload_file_size : 0)
   }, 0)
@@ -283,7 +285,16 @@ export function getSelectedFileHandles(downloadInfo, selectedBoxes, hashByStudy=
       if (selectedBoxes.studies[index][colType]) {
         const filesOfType = study.studyFiles.filter(file => COLUMNS[colType].types.includes(file.file_type))
         {/* eslint-disable-next-line max-len */}
-        const selectedHandles = filesOfType.map(file => hashByStudy ? { drs_id: file.drs_id, url: file.url, name: file.name, file_type: file.file_type } : file.id)
+        const selectedHandles = filesOfType.map(file => {
+          if (hashByStudy) {
+            return {
+              project_id: file.project_id, name: file.name, file_format: file.file_format,
+              file_type: file.file_type, count: file.count
+            }
+          } else {
+            return file.id
+          }
+        })
         if (hashByStudy) {
           fileHandles[study.accession].push(...selectedHandles)
         } else {