X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6d8a27a40903f0dc61876947cecc9401edd3a32c..28b6afc1e8ccf652c7a8fd43e22a8ac788febd85:/apps/workbench/app/controllers/pipeline_instances_controller.rb

diff --git a/apps/workbench/app/controllers/pipeline_instances_controller.rb b/apps/workbench/app/controllers/pipeline_instances_controller.rb
index a618d43517..81417ff165 100644
--- a/apps/workbench/app/controllers/pipeline_instances_controller.rb
+++ b/apps/workbench/app/controllers/pipeline_instances_controller.rb
@@ -1,6 +1,15 @@
+# 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_before_action :find_object_by_uuid, only: :compare
+  before_action :find_objects_by_uuid, only: :compare
+  skip_around_action :require_thread_api_token, if: proc { |ctrl|
+    !Rails.configuration.Users.AnonymousUserToken.empty? and
+    'show' == ctrl.action_name
+  }
+
   include PipelineInstancesHelper
   include PipelineComponentsHelper
 
@@ -48,7 +57,7 @@ class PipelineInstancesController < ApplicationController
     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
@@ -58,13 +67,16 @@ class PipelineInstancesController < ApplicationController
   end
 
   def update
-    @updates ||= params[@object.class.to_s.underscore.singularize.to_sym]
+    @updates ||= params.to_unsafe_hash[@object.class.to_s.underscore.singularize.to_sym]
     if (components = @updates[:components])
       components.each do |cname, component|
         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]
@@ -76,6 +88,20 @@ class PipelineInstancesController < ApplicationController
                 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
@@ -87,38 +113,67 @@ class PipelineInstancesController < ApplicationController
   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).with_count("none").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).with_count("none").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).with_count("none").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
@@ -128,12 +183,9 @@ class PipelineInstancesController < ApplicationController
   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)
@@ -142,8 +194,10 @@ class PipelineInstancesController < ApplicationController
         :request => request,
         :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
@@ -211,18 +265,7 @@ class PipelineInstancesController < ApplicationController
     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
@@ -245,9 +288,69 @@ class PipelineInstancesController < ApplicationController
     %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
@@ -259,8 +362,12 @@ class PipelineInstancesController < ApplicationController
     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