+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
class PipelineInstancesController < ApplicationController
skip_before_filter :find_object_by_uuid, only: :compare
before_filter :find_objects_by_uuid, only: :compare
+ skip_around_filter :require_thread_api_token, if: proc { |ctrl|
+ Rails.configuration.anonymous_user_token and
+ 'show' == ctrl.action_name
+ }
+
include PipelineInstancesHelper
include PipelineComponentsHelper
end
@object.state = 'New'
- # set owner_uuid to that of source, provided it is a project and wriable by current user
+ # set owner_uuid to that of source, provided it is a project and writable by current user
current_project = Group.find(source.owner_uuid) rescue nil
if (current_project && current_project.writable_by.andand.include?(current_user.uuid))
@object.owner_uuid = source.owner_uuid
if component[:script_parameters]
component[:script_parameters].each do |param, value_info|
if value_info.is_a? Hash
- if resource_class_for_uuid(value_info[:value]) == Link
+ value_info_partitioned = value_info[:value].partition('/') if value_info[:value].andand.class.eql?(String)
+ value_info_value = value_info_partitioned ? value_info_partitioned[0] : value_info[:value]
+ value_info_class = resource_class_for_uuid value_info_value
+ if value_info_class == Link
# Use the link target, not the link itself, as script
# parameter; but keep the link info around as well.
link = Link.find value_info[:value]
value_info[:link_uuid] = nil
value_info[:link_name] = nil
end
+ if value_info_class == Collection
+ # to ensure reproducibility, the script_parameter for a
+ # collection should be the portable_data_hash
+ # keep the collection name and uuid for human-readability
+ obj = Collection.find value_info_value
+ if value_info_partitioned
+ value_info[:value] = obj.portable_data_hash + value_info_partitioned[1] + value_info_partitioned[2]
+ value_info[:selection_name] = obj.name ? obj.name + value_info_partitioned[1] + value_info_partitioned[2] : obj.name
+ else
+ value_info[:value] = obj.portable_data_hash
+ value_info[:selection_name] = obj.name
+ end
+ value_info[:selection_uuid] = obj.uuid
+ end
end
end
end
def graph(pipelines)
return nil, nil if params['tab_pane'] != "Graph"
- count = {}
provenance = {}
pips = {}
n = 1
+ # When comparing more than one pipeline, "pips" stores bit fields that
+ # indicates which objects are part of which pipelines.
+
pipelines.each do |p|
collections = []
+ hashes = []
+ jobs = []
+
+ p[:components].each do |k, v|
+ provenance["component_#{p[:uuid]}_#{k}"] = v
- p.components.each do |k, v|
- j = v[:job] || next
+ collections << v[:output_uuid] if v[:output_uuid]
+ jobs << v[:job][:uuid] if v[:job]
+ end
- uuid = j[:uuid].intern
- provenance[uuid] = j
- pips[uuid] = 0 unless pips[uuid] != nil
- pips[uuid] |= n
+ jobs = jobs.compact.uniq
+ if jobs.any?
+ Job.where(uuid: jobs).each do |j|
+ job_uuid = j.uuid
- collections << j[:output]
- ProvenanceHelper::find_collections(j[:script_parameters]).each do |k|
- collections << k
+ provenance[job_uuid] = j
+ pips[job_uuid] = 0 unless pips[job_uuid] != nil
+ pips[job_uuid] |= n
+
+ hashes << j[:output] if j[:output]
+ ProvenanceHelper::find_collections(j) do |hash, uuid|
+ collections << uuid if uuid
+ hashes << hash if hash
+ end
+
+ if j[:script_version]
+ script_uuid = j[:script_version]
+ provenance[script_uuid] = {:uuid => script_uuid}
+ pips[script_uuid] = 0 unless pips[script_uuid] != nil
+ pips[script_uuid] |= n
+ end
end
+ end
- uuid = j[:script_version].intern
- provenance[uuid] = {:uuid => uuid}
- pips[uuid] = 0 unless pips[uuid] != nil
- pips[uuid] |= n
+ hashes = hashes.compact.uniq
+ if hashes.any?
+ Collection.where(portable_data_hash: hashes).each do |c|
+ hash_uuid = c.portable_data_hash
+ provenance[hash_uuid] = c
+ pips[hash_uuid] = 0 unless pips[hash_uuid] != nil
+ pips[hash_uuid] |= n
+ end
end
- Collection.where(uuid: collections.compact).each do |c|
- uuid = c.uuid.intern
- provenance[uuid] = c
- pips[uuid] = 0 unless pips[uuid] != nil
- pips[uuid] |= n
+ collections = collections.compact.uniq
+ if collections.any?
+ Collection.where(uuid: collections).each do |c|
+ collection_uuid = c.uuid
+ provenance[collection_uuid] = c
+ pips[collection_uuid] = 0 unless pips[collection_uuid] != nil
+ pips[collection_uuid] |= n
+ end
end
n = n << 1
end
def show
- @pipelines = [@object]
-
- if params[:compare]
- PipelineInstance.where(uuid: params[:compare]).each do |p|
- @pipelines << p
- end
+ # the #show action can also be called by #compare, which does its own work to set up @pipelines
+ unless defined? @pipelines
+ @pipelines = [@object]
end
provenance, pips = graph(@pipelines)
if provenance
@prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
:request => request,
+ :direction => :top_down,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
- :script_version_nodes => true,
- :pips => pips }
+ :pips => pips,
+ :only_components => true,
+ :no_docker => true,
+ :no_log => true}
end
super
end
if params['tab_pane'] == "Graph"
- provenance, pips = graph(@objects)
-
@pipelines = @objects
-
- if provenance
- @prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
- :request => request,
- :all_script_parameters => true,
- :combine_jobs => :script_and_version,
- :script_version_nodes => true,
- :pips => pips }
- end
end
@object = @objects.first
%w(Compare Graph)
end
- def index
- @limit = 20
- super
+ helper_method :unreadable_inputs_present?
+ def unreadable_inputs_present?
+ unless @unreadable_inputs_present.nil?
+ return @unreadable_inputs_present
+ end
+
+ input_uuids = []
+ input_pdhs = []
+ @object.components.each do |k, component|
+ next if !component
+ component[:script_parameters].andand.each do |p, tv|
+ if (tv.is_a? Hash) and ((tv[:dataclass] == "Collection") || (tv[:dataclass] == "File"))
+ if tv[:value]
+ value = tv[:value]
+ elsif tv[:default]
+ value = tv[:default]
+ else
+ value = ''
+ end
+ if value.present?
+ split = value.split '/'
+ if CollectionsHelper.match(split[0])
+ input_pdhs << split[0]
+ else
+ input_uuids << split[0]
+ end
+ end
+ end
+ end
+ end
+
+ input_pdhs = input_pdhs.uniq
+ input_uuids = input_uuids.uniq
+
+ preload_collections_for_objects input_uuids if input_uuids.any?
+ preload_for_pdhs input_pdhs if input_pdhs.any?
+
+ @unreadable_inputs_present = false
+ input_uuids.each do |uuid|
+ if !collections_for_object(uuid).any?
+ @unreadable_inputs_present = true
+ break
+ end
+ end
+ if !@unreadable_inputs_present
+ input_pdhs.each do |pdh|
+ if !collection_for_pdh(pdh).any?
+ @unreadable_inputs_present = true
+ break
+ end
+ end
+ end
+
+ @unreadable_inputs_present
+ end
+
+ def cancel
+ @object.cancel
+ if params[:return_to]
+ redirect_to params[:return_to]
+ else
+ redirect_to @object
+ end
end
protected
end
end
+ def load_filters_and_paging_params
+ params[:limit] = 20
+ super
+ end
+
def find_objects_by_uuid
@objects = model_class.where(uuid: params[:uuids])
end
-
end
projects / arvados.git / blobdiff