X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/8716b38d3cd20640c28b6fe048927309a0f916cd..5dd7bd8a05d52838b1cb8df7b341a843abae7a0a:/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 8ee06c3d01..fa724b82b4 100644
--- a/apps/workbench/app/controllers/pipeline_instances_controller.rb
+++ b/apps/workbench/app/controllers/pipeline_instances_controller.rb
@@ -16,12 +16,16 @@ class PipelineInstancesController < ApplicationController
       @object.components.each do |cname, component|
         # Go through the script parameters of each component
         # that are marked as user input and copy them over.
-        component[:script_parameters].each do |pname, val|
-          if val.is_a? Hash and val[:dataclass]
-            # this is user-inputtable, so check the value from the source pipeline
-            srcvalue = source.components[cname][:script_parameters][pname]
-            if not srcvalue.nil?
-              component[:script_parameters][pname] = srcvalue
+        # Skip any components that are not present in the
+        # source instance (there's nothing to copy)
+        if source.components.include? cname
+          component[:script_parameters].each do |pname, val|
+            if val.is_a? Hash and val[:dataclass]
+              # this is user-inputtable, so check the value from the source pipeline
+              srcvalue = source.components[cname][:script_parameters][pname]
+              if not srcvalue.nil?
+                component[:script_parameters][pname] = srcvalue
+              end
             end
           end
         end
@@ -33,7 +37,7 @@ class PipelineInstancesController < ApplicationController
     if params['script'] == 'use_same'
       # Go through each component and copy the script_version from each job.
       @object.components.each do |cname, component|
-        if source.components[cname][:job]
+        if source.components.include? cname and source.components[cname][:job]
           component[:script_version] = source.components[cname][:job][:script_version]
         end
       end
@@ -43,6 +47,13 @@ class PipelineInstancesController < ApplicationController
       component.delete :job
     end
     @object.state = 'New'
+
+    # set owner_uuid to that of source, provided it is a project and wriable 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
+    end
+
     super
   end
 
@@ -53,7 +64,8 @@ class PipelineInstancesController < ApplicationController
         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_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]
@@ -65,6 +77,15 @@ 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]
+                value_info[:value] = obj.portable_data_hash
+                value_info[:selection_uuid] = obj.uuid
+                value_info[:selection_name] = obj.name
+              end
             end
           end
         end
@@ -76,38 +97,67 @@ 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|
-        j = v[:job] || next
+      p[:components].each do |k, v|
+        provenance["component_#{p[:uuid]}_#{k}"] = v
+
+        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
@@ -131,8 +181,10 @@ 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