Merge pull request #97 from broadinstitute/development

10X Market Exchange Format support

Author: bistline

Gemfile

@@ -76,4 +76,5 @@ gem 'mongoid-encrypted-fields'
 gem 'gibberish'
 gem 'parallel'
 gem 'ruby_native_statistics'
-gem 'mongoid_rails_migrations'
+gem 'mongoid_rails_migrations'
+gem 'nmatrix'

Gemfile.lock

@@ -96,6 +96,7 @@ GEM
     arel (6.0.4)
     autoprefixer-rails (7.2.5)
       execjs
+    backports (3.11.1)
     bcrypt (3.1.11)
     bson (4.3.0)
     bson_ext (1.5.1)
@@ -238,6 +239,8 @@ GEM
     multipart-post (2.0.0)
     naturally (2.1.0)
     netrc (0.11.0)
+    nmatrix (0.2.4)
+      packable (~> 1.3, >= 1.3.5)
     nokogiri (1.8.1)
       mini_portile2 (~> 2.3.0)
     non-stupid-digest-assets (1.0.9)
@@ -262,6 +265,8 @@ GEM
     origin (2.3.1)
     orm_adapter (0.5.0)
     os (0.9.6)
+    packable (1.3.9)
+      backports
     paperclip (5.2.1)
       activemodel (>= 4.2.0)
       activesupport (>= 4.2.0)
@@ -404,6 +409,7 @@ DEPENDENCIES
   mongoid_rails_migrations
   naturally
   nested_form!
+  nmatrix
   non-stupid-digest-assets
   omniauth-google-oauth2
   parallel

app/assets/javascripts/application.js

@@ -910,4 +910,18 @@ function closeUserAnnotationsForm() {
 function validateEmail(email) {
     var re = /^(([^<>()\[\]\\.,;:\s@"]+(\.[^<>()\[\]\\.,;:\s@"]+)*)|(".+"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$/;
     return re.test(email);
+}
+
+// gather all MM Coordinate Matrix instances from a page
+function gatherCoordinateMatrices() {
+    var matrices = [];
+    $('.file-type').each(function(index, fileType) {
+        if ($(fileType).val() == 'MM Coordinate Matrix') {
+            var mForm = $(fileType).closest('.unsynced-study-file');
+            var mId = $(mForm).attr('id').split('-')[2];
+            var mName = $(mForm).find('.filename').val();
+            matrices.push([mName, mId]);
+        }
+    });
+    return matrices;
 }

app/controllers/site_controller.rb

@@ -956,7 +956,7 @@ def get_workspace_submissions
 
   # retrieve any optional parameters for a selected workflow
   def get_workflow_options
-    @options = WorkflowConfiguration.get_optional_parameters(params[:workflow_identifier])
+    @options = WorkflowConfiguration.get_additional_parameters(params[:workflow_identifier])
   end
 
   # create a workspace analysis submission for a given sample
@@ -1115,7 +1115,11 @@ def get_submission_metadata
   # export a submission analysis metadata file
   def export_submission_metadata
     @metadata = AnalysisMetadatum.find_by(study_id: @study.id, submission_id: params[:submission_id])
-    send_data JSON.pretty_generate(@metadata.payload), content_type: :json, filename: 'analysis.json'
+    respond_to do |format|
+      format.html {send_data JSON.pretty_generate(@metadata.payload), content_type: :json, filename: 'analysis.json'}
+      format.json {render json: @metadata.payload}
+    end
+
   end
 
   # delete all files from a submission
@@ -1135,7 +1139,7 @@ def delete_submission_files
       AnalysisMetadatum.where(submission_id: params[:submission_id]).delete
       logger.info "#{Time.now}: queueing submission #{params[:submission]} deletion in #{@study.firecloud_workspace}"
       submission_files = Study.firecloud_client.execute_gcloud_method(:get_workspace_files, @study.firecloud_project, @study.firecloud_workspace, prefix: params[:submission_id])
-      DeleteQueueJob.new(submission_files).delay.perform
+      DeleteQueueJob.new(submission_files).perform
     rescue => e
       logger.error "#{Time.now}: unable to remove submission #{params[:submission_id]} files from #{@study.firecloud_workspace} due to: #{e.message}"
       @alert = "Unable to delete the outputs for #{params[:submission_id]} due to the following error: #{e.message}"
@@ -1993,8 +1997,8 @@ def load_available_workflows
 
     # parellelize gets to speed up performance if there are a lot of workflows
     Parallel.map(allowed_workflows, in_threads: 100) do |workflow_opts|
-      namespace, name = workflow_opts.split('/')
-      all_workflows << Study.firecloud_client.get_methods(namespace: namespace, name: name)
+      namespace, name, snapshot = workflow_opts.split('/')
+      all_workflows << Study.firecloud_client.get_methods(namespace: namespace, name: name, snapshotId: snapshot)
     end
 
     # flatten list as it will be nested arrays

app/controllers/studies_controller.rb

@@ -269,7 +269,7 @@ def get_submission_actions(submission, study)
 		if submission['status'] == 'Done' && submission['workflowStatuses'].keys.include?('Succeeded')
 			# actions << link_to("<i class='fa fa-files-o'></i> Download".html_safe, '#', class: 'btn btn-xs btn-block btn-primary get-submission-outputs', title: 'Download outputs from this run', data: {toggle: 'tooltip', url: get_submission_outputs_path(study_name: study.url_safe_name, submission_id: submission['submissionId']), id: submission['submissionId']})
 			actions << link_to("<i class='fa fa-fw fa-code'></i> View Run Info".html_safe, 'javascript:;', class: 'btn btn-xs btn-block btn-info view-submission-metadata', title: 'View HCA-formatted analysis metadata', data: {toggle: 'tooltip', id: submission['submissionId'], url: get_submission_metadata_path(study_name: @study.url_safe_name, submission_id: submission['submissionId'])})
-			actions << link_to("<i class='fa fa-fw fa-refresh'></i> Sync".html_safe, sync_submission_outputs_study_path(id: @study.id, submission_id: submission['submissionId']), class: 'btn btn-xs btn-block btn-warning sync-submission-outputs', title: 'Sync outputs from this run back to study', data: {toggle: 'tooltip', id: submission['submissionId']})
+			actions << link_to("<i class='fa fa-fw fa-refresh'></i> Sync".html_safe, sync_submission_outputs_study_path(id: @study.id, submission_id: submission['submissionId'], configuration_name: submission['methodConfigurationName']), class: 'btn btn-xs btn-block btn-warning sync-submission-outputs', title: 'Sync outputs from this run back to study', data: {toggle: 'tooltip', id: submission['submissionId']})
 		end
 		# submission has failed
 		if %w(Done Aborted).include?(submission['status']) && submission['workflowStatuses'].keys.include?('Failed')

app/helpers/application_helper.rb

@@ -29,7 +29,7 @@ def url_safe_name
   end
 
   def self.config_types
-    ['Daily User Download Quota', 'Workflow Name', 'Portal FireCloud User Group', API_NOTIFIER_NAME]
+    ['Daily User Download Quota', 'Workflow Name', 'Portal FireCloud User Group', 'Reference Data Workspace', API_NOTIFIER_NAME]
   end
 
   def self.value_types

app/models/admin_configuration.rb

@@ -46,6 +46,10 @@ def perform
             Gene.where(study_file_id: object.id, study_id: study.id).delete_all
             DataArray.where(study_file_id: object.id, study_id: study.id).delete_all
             study.set_gene_count
+          when 'MM Coordinate Matrix'
+            Gene.where(study_file_id: object.id, study_id: study.id).delete_all
+            DataArray.where(study_file_id: object.id, study_id: study.id).delete_all
+            study.set_gene_count
           when 'Metadata'
             CellMetadatum.where(study_file_id: object.id, study_id: study.id).delete_all
             DataArray.where(study_file_id: object.id, study_id: study.id).delete_all
@@ -74,7 +78,7 @@ def perform
         object.user_annotation_shares.delete_all
       when 'Google::Cloud::Storage::File::List'
         # called when a user wants to delete an entire directory of files from a FireCloud submission
-        # this list could be very large, hence the background process so we don't tie the UI up
+        # this is run in the foreground as Delayed::Job cannot deserialize the list anymore
         files = object
         files.each {|f| f.delete}
         while files.next?

app/models/delete_queue_job.rb

@@ -772,6 +772,56 @@ def get_workspace_submission_outputs(workspace_namespace, workspace_name, submis
 		process_firecloud_request(:get, path)
 	end
 
+	# get permissions for a method configuration namespace
+	#
+	# * *params*
+	#   - +config_namespace+ (String) => namespace of configuraiton
+	#
+	# * *return*
+	#   - +Array+ of users & permission levels
+	def get_config_namespace_permissions(config_namespace)
+		path = self.api_root + "/api/configurations/#{config_namespace}/permissions"
+		process_firecloud_request(:get, path)
+	end
+
+	# get permissions for a method configuration namespace
+	#
+	# * *params*
+	#   - +config_namespace+ (String) => namespace of configuraiton
+	#   - +permissions+ (Array) => Array of permission objects (Hash of user & role)
+	#
+	# * *return*
+	#   - +Array+ of users & permission levels
+	def update_config_namespace_permissions(config_namespace, permissions)
+		path = self.api_root + "/api/configurations/#{config_namespace}/permissions"
+		process_firecloud_request(:post, path, permissions.to_json)
+	end
+
+	# get permissions for a method namespace
+	#
+	# * *params*
+	#   - +config_namespace+ (String) => namespace of configuraiton
+	#
+	# * *return*
+	#   - +Array+ of users & permission levels
+	def get_method_namespace_permissions(config_namespace)
+		path = self.api_root + "/api/methods/#{config_namespace}/permissions"
+		process_firecloud_request(:get, path)
+	end
+
+	# get permissions for a method namespace
+	#
+	# * *params*
+	#   - +config_namespace+ (String) => namespace of configuraiton
+	#   - +permissions+ (Array) => Array of permission objects (Hash of user & role)
+	#
+	# * *return*
+	#   - +Array+ of users & permission levels
+	def update_method_namespace_permissions(config_namespace, permissions)
+		path = self.api_root + "/api/methods/#{config_namespace}/permissions"
+		process_firecloud_request(:post, path, permissions.to_json)
+	end
+
 	##
 	## WORKSPACE ENTITY METHODS
 	##