Merge branch '10674-wb-workflow-defaults' closes #10674

diff --git a/apps/workbench/app/controllers/work_units_controller.rb b/apps/workbench/app/controllers/work_units_controller.rb
index 3b611aa25b74e28663d9b7ecc2b0647670f066c8..550bdb7e953f7fe47a899cbe674a39ed457a9529 100644 (file)
--- a/apps/workbench/app/controllers/work_units_controller.rb
+++ b/apps/workbench/app/controllers/work_units_controller.rb
@@ -57,7 +57,7 @@ class WorkUnitsController < ApplicationController
       workflow = Workflow.find? template_uuid
       if workflow.definition
         begin
-          wf_json = YAML::load(workflow.definition)
+          wf_json = ActiveSupport::HashWithIndifferentAccess.new YAML::load(workflow.definition)
         rescue => e
           logger.error "Error converting definition yaml to json: #{e.message}"
           raise ArgumentError, "Error converting definition yaml to json: #{e.message}"
@@ -77,11 +77,21 @@ class WorkUnitsController < ApplicationController
       attrs['cwd'] = "/var/spool/cwl"
       attrs['output_path'] = "/var/spool/cwl"
 
+      input_defaults = {}
+      if wf_json
+        inputs = get_cwl_inputs(wf_json)
+        inputs.each do |input|
+          if input[:default]
+            input_defaults[cwl_shortname(input[:id])] = input[:default]
+          end
+        end
+      end
+
       # mounts
       mounts = {
         "/var/lib/cwl/cwl.input.json" => {
           "kind" => "json",
-          "content" => {}
+          "content" => input_defaults
         },
         "stdout" => {
           "kind" => "file",

diff --git a/apps/workbench/test/integration/work_units_test.rb b/apps/workbench/test/integration/work_units_test.rb
index 3f551a012ea62a692b5fdfcf0c99de0208b359bd..5b5848ee7766580003ee10be1c28ba944070bf36 100644 (file)
--- a/apps/workbench/test/integration/work_units_test.rb
+++ b/apps/workbench/test/integration/work_units_test.rb
@@ -109,8 +109,8 @@ class WorkUnitsTest < ActionDispatch::IntegrationTest
   end
 
   [
-    ['Two Part Pipeline Template', 'part-one', 'Provide a value for the following'],
-    ['Workflow with input specifications', 'this workflow has inputs specified', 'Provide a value for the following'],
+    ['Pipeline with default input specifications', 'part-one', 'Provide values for the following'],
+    ['Workflow with default input specifications', 'this workflow has inputs specified', 'Provide a value for the following'],
   ].each do |template_name, preview_txt, process_txt|
     test "run a process using template #{template_name} from dashboard" do
       visit page_with_token('admin')
@@ -131,6 +131,10 @@ class WorkUnitsTest < ActionDispatch::IntegrationTest
       # in the process page now
       assert_text process_txt
       assert_selector 'a', text: template_name
+
+      assert_equal "Set value for ex_string_def", find('div.form-group > div > p.form-control-static > a', text: "hello-testing-123")[:"data-title"]
+
+      page.assert_selector 'a.disabled,button.disabled', text: 'Run'
     end
   end
 

diff --git a/services/api/test/fixtures/pipeline_templates.yml b/services/api/test/fixtures/pipeline_templates.yml
index cbd82de9241101a72cc1c263903b9a403a8234fa..49503c971236af12a936085d92084a79e2dfc0ba 100644 (file)
--- a/services/api/test/fixtures/pipeline_templates.yml
+++ b/services/api/test/fixtures/pipeline_templates.yml
@@ -243,3 +243,25 @@ template_in_asubproject_with_same_name_as_one_in_active_user_home:
         dataclass: Collection
         title: "Foo/bar pair"
         description: "Provide a collection containing at least two files."
+
+workflow_with_input_defaults:
+  uuid: zzzzz-p5p6p-aox0k0ofxrystg2
+  owner_uuid: zzzzz-j7d0g-v955i6s2oi1cbso
+  created_at: 2014-04-14 12:35:04 -0400
+  updated_at: 2014-04-14 12:35:04 -0400
+  modified_at: 2014-04-14 12:35:04 -0400
+  modified_by_client_uuid: zzzzz-ozdt8-brczlopd8u8d0jr
+  modified_by_user_uuid: zzzzz-tpzed-xurymjxw79nv3jz
+  name: Pipeline with default input specifications
+  components:
+    part-one:
+      script: foo
+      script_version: master
+      script_parameters:
+        ex_string:
+          required: true
+          dataclass: string
+        ex_string_def:
+          required: true
+          dataclass: string
+          default: hello-testing-123
\ No newline at end of file

diff --git a/services/api/test/fixtures/workflows.yml b/services/api/test/fixtures/workflows.yml
index 4badf9e175f21c1fb521befa6d6c6bbe8024af5b..f79320e907801cae499cdcbf809a4602194656f4 100644 (file)
--- a/services/api/test/fixtures/workflows.yml
+++ b/services/api/test/fixtures/workflows.yml
@@ -44,3 +44,22 @@ workflow_with_input_specifications:
       inputBinding:
         position: 1
     outputs: []
+
+workflow_with_input_defaults:
+  uuid: zzzzz-7fd4e-validwithinput2
+  owner_uuid: zzzzz-j7d0g-zhxawtyetzwc5f0
+  name: Workflow with default input specifications
+  description: this workflow has inputs specified
+  created_at: <%= 1.minute.ago.to_s(:db) %>
+  definition: |
+    cwlVersion: v1.0
+    class: CommandLineTool
+    baseCommand:
+    - echo
+    inputs:
+    - type: string
+      id: ex_string
+    - type: string
+      id: ex_string_def
+      default: hello-testing-123
+    outputs: []