+ skip_around_action :require_thread_api_token, if: proc { |ctrl|
+ !Rails.configuration.Users.AnonymousUserToken.empty? and
+ 'show' == ctrl.action_name
+ }
+
+ def generate_provenance(cr)
+ return if params['tab_pane'] != "Provenance"
+
+ nodes = {}
+ child_crs = []
+ col_uuids = []
+ col_pdhs = []
+ col_uuids << cr[:output_uuid] if cr[:output_uuid]
+ col_pdhs += ProvenanceHelper::cr_input_pdhs(cr)
+
+ # Search for child CRs
+ if cr[:container_uuid]
+ child_crs = ContainerRequest.where(requesting_container_uuid: cr[:container_uuid]).with_count("none")
+
+ child_crs.each do |child|
+ nodes[child[:uuid]] = child
+ col_uuids << child[:output_uuid] if child[:output_uuid]
+ col_pdhs += ProvenanceHelper::cr_input_pdhs(child)
+ end
+ end
+
+ if nodes.length == 0
+ nodes[cr[:uuid]] = cr
+ end
+
+ pdh_to_col = {} # Indexed by PDH
+ output_pdhs = []
+
+ # Batch requests to get all related collections
+ # First fetch output collections by UUID.
+ Collection.filter([['uuid', 'in', col_uuids.uniq]]).with_count("none").each do |c|
+ output_pdhs << c[:portable_data_hash]
+ pdh_to_col[c[:portable_data_hash]] = c
+ nodes[c[:uuid]] = c
+ end
+ # Next, get input collections by PDH.
+ Collection.filter(
+ [['portable_data_hash', 'in', col_pdhs - output_pdhs]]).with_count("none").each do |c|
+ nodes[c[:portable_data_hash]] = c
+ end
+
+ @svg = ProvenanceHelper::create_provenance_graph(
+ nodes, "provenance_svg",
+ {
+ :request => request,
+ :pdh_to_uuid => pdh_to_col,
+ }
+ )
+ end
+
+ def show_pane_list
+ panes = %w(Status Log Provenance Advanced)
+ if @object.andand.state == 'Uncommitted'
+ panes = %w(Inputs) + panes - %w(Log Provenance)
+ end
+ panes
+ end
+
+ def show
+ generate_provenance(@object)
+ super
+ end
+
+ def cancel
+ if @object.container_uuid
+ c = Container.select(['state']).where(uuid: @object.container_uuid).with_count("none").first
+ if c && c.state != 'Running'
+ # If the container hasn't started yet, setting priority=0
+ # leaves our request in "Committed" state and doesn't cancel
+ # the container (even if no other requests are giving it
+ # priority). To avoid showing this container request as "on
+ # hold" after hitting the Cancel button, set state=Final too.
+ @object.state = 'Final'
+ end
+ end
+ @object.update_attributes! priority: 0
+ if params[:return_to]
+ redirect_to params[:return_to]
+ else
+ redirect_to @object
+ end
+ end
+
+ def update
+ @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
+ input_obj = @updates[:mounts].andand[:"/var/lib/cwl/cwl.input.json"].andand[:content]
+ if input_obj
+ workflow = @object.mounts[:"/var/lib/cwl/workflow.json"][:content]
+ get_cwl_inputs(workflow).each do |input_schema|
+ if not input_obj.include? cwl_shortname(input_schema[:id])
+ next
+ end
+ required, primary_type, param_id = cwl_input_info(input_schema)
+ if input_obj[param_id] == ""
+ input_obj[param_id] = nil
+ elsif primary_type == "boolean"
+ input_obj[param_id] = input_obj[param_id] == "true"
+ elsif ["int", "long"].include? primary_type
+ input_obj[param_id] = input_obj[param_id].to_i
+ elsif ["float", "double"].include? primary_type
+ input_obj[param_id] = input_obj[param_id].to_f
+ elsif ["File", "Directory"].include? primary_type
+ re = CollectionsHelper.match_uuid_with_optional_filepath(input_obj[param_id])
+ if re
+ c = Collection.find(re[1])
+ input_obj[param_id] = {"class" => primary_type,
+ "location" => "keep:#{c.portable_data_hash}#{re[4]}",
+ "http://arvados.org/cwl#collectionUUID" => re[1]}
+ end
+ end
+ end
+ end
+ params[:merge] = true
+
+ if !@updates[:reuse_steps].nil?
+ if @updates[:reuse_steps] == "false"
+ @updates[:reuse_steps] = false
+ end
+ @updates[:command] ||= @object.command
+ @updates[:command] -= ["--disable-reuse", "--enable-reuse"]
+ if @updates[:reuse_steps]
+ @updates[:command].insert(1, "--enable-reuse")
+ else
+ @updates[:command].insert(1, "--disable-reuse")
+ end
+ @updates.delete(:reuse_steps)
+ end
+
+ begin
+ super
+ rescue => e
+ flash[:error] = e.to_s
+ show
+ end
+ end
+
+ def copy
+ src = @object
+
+ @object = ContainerRequest.new
+
+ # set owner_uuid to that of source, provided it is a project and writable by current user
+ if params[:work_unit].andand[:owner_uuid]
+ @object.owner_uuid = src.owner_uuid = params[:work_unit][:owner_uuid]
+ else
+ current_project = Group.find(src.owner_uuid) rescue nil
+ if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
+ @object.owner_uuid = src.owner_uuid
+ end
+ end
+
+ command = src.command
+ if command[0] == 'arvados-cwl-runner'
+ command.each_with_index do |arg, i|
+ if arg.start_with? "--project-uuid="
+ command[i] = "--project-uuid=#{@object.owner_uuid}"
+ end
+ end
+ command -= ["--disable-reuse", "--enable-reuse"]
+ command.insert(1, '--enable-reuse')
+ end
+
+ if params[:use_existing] == "false"
+ params[:use_existing] = false
+ elsif params[:use_existing] == "true"
+ params[:use_existing] = true
+ end
+
+ if params[:use_existing] || params[:use_existing].nil?
+ # If nil, reuse workflow steps but not the workflow runner.
+ @object.use_existing = !!params[:use_existing]
+
+ # Pass the correct argument to arvados-cwl-runner command.
+ if command[0] == 'arvados-cwl-runner'
+ command -= ["--disable-reuse", "--enable-reuse"]
+ command.insert(1, '--enable-reuse')
+ end
+ else
+ @object.use_existing = false
+ # Pass the correct argument to arvados-cwl-runner command.
+ if command[0] == 'arvados-cwl-runner'
+ command -= ["--disable-reuse", "--enable-reuse"]
+ command.insert(1, '--disable-reuse')
+ end
+ end
+
+ @object.command = command
+ @object.container_image = src.container_image
+ @object.cwd = src.cwd
+ @object.description = src.description
+ @object.environment = src.environment
+ @object.mounts = src.mounts
+ @object.name = src.name
+ @object.output_path = src.output_path
+ @object.priority = 1
+ @object.properties[:template_uuid] = src.properties[:template_uuid]
+ @object.runtime_constraints = src.runtime_constraints
+ @object.scheduling_parameters = src.scheduling_parameters
+ @object.state = 'Uncommitted'
+
+ super
+ end
+
+ def index
+ @limit = 20
+ super
+ end
+