+++ /dev/null
-class ContainerRequestsController < ApplicationController
- skip_around_filter :require_thread_api_token, if: proc { |ctrl|
- Rails.configuration.anonymous_user_token and
- 'show' == ctrl.action_name
- }
-
- def generate_provenance(cr)
- return if params['tab_pane'] != "Provenance"
-
- nodes = {cr[:uuid] => cr}
- 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])
-
- 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
-
- output_cols = {} # Indexed by UUID
- input_cols = {} # 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]]).each do |c|
- output_cols[c[:uuid]] = c
- output_pdhs << c[:portable_data_hash]
- end
- # Then, get only input collections by PDH. There could be more than one collection
- # per PDH: the number of collections is used on the collection node label.
- Collection.filter(
- [['portable_data_hash', 'in', col_pdhs - output_pdhs]]).each do |c|
- if input_cols[c[:portable_data_hash]]
- input_cols[c[:portable_data_hash]] << c
- else
- input_cols[c[:portable_data_hash]] = [c]
- end
- end
-
- @svg = ProvenanceHelper::create_provenance_graph(
- nodes, "provenance_svg",
- {
- :request => request,
- :direction => :top_down,
- :output_collections => output_cols,
- :input_collections => input_cols,
- :cr_children_of => {
- cr[:uuid] => child_crs.select{|child| child[:uuid]},
- },
- })
- 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
- @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]}",
- "arv:collection" => input_obj[param_id]}
- end
- end
- end
- end
- params[:merge] = true
- begin
- super
- rescue => e
- flash[:error] = e.to_s
- show
- end
- end
-
- def copy
- src = @object
-
- @object = ContainerRequest.new
-
- # By default the copied CR won't be reusing containers, unless use_existing=true
- # param is passed.
- command = src.command
- if params[:use_existing]
- @object.use_existing = true
- # Pass the correct argument to arvados-cwl-runner command.
- if src.command[0] == 'arvados-cwl-runner'
- command = src.command - ['--disable-reuse']
- command.insert(1, '--enable-reuse')
- end
- else
- @object.use_existing = false
- # Pass the correct argument to arvados-cwl-runner command.
- if src.command[0] == 'arvados-cwl-runner'
- command = src.command - ['--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'
-
- # set owner_uuid to that of source, provided it is a project and writable by current user
- 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
-
- super
- end
-
- def index
- @limit = 20
- super
- end
-
-end
projects / arvados.git / blobdiff