Merge pull request #7458 from mvdbeek/fix_broken_hidden_parameter

[19.01] Fix hidden parameter use in workflows

lib/galaxy/workflow/modules.py

@@ -33,6 +33,7 @@ from galaxy.tools.parameters.basic import (
     ConnectedValue,
     DataCollectionToolParameter,
     DataToolParameter,
+    HiddenToolParameter,
     is_runtime_value,
     parameter_types,
     runtime_to_json,
@@ -889,6 +890,8 @@ class ToolModule(WorkflowModule):
                     skip = not visible or not is_data
                 elif connectable_only:
                     skip = not visible or not (is_data or is_connectable)
+                elif isinstance(input, HiddenToolParameter):
+                    skip = False
                 else:
                     skip = not visible
                 if not skip:

run_tests.sh

@@ -270,7 +270,7 @@ exists() {
     type "$1" >/dev/null 2>/dev/null
 }
 
-DOCKER_DEFAULT_IMAGE='mvdbeek/testing-base:19.01.3'
+DOCKER_DEFAULT_IMAGE='galaxy/testing-base:19.01.0'
 
 test_script="./scripts/functional_tests.py"
 report_file="run_functional_tests.html"

test/api/test_workflows.py

@@ -2074,6 +2074,23 @@ outer_input:
         content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
         assert content["name"] == "foo was replaced"
 
+    @skip_without_tool("hidden_param")
+    def test_hidden_param_in_workflow(self):
+        with self.dataset_populator.test_history() as history_id:
+            run_object = self._run_jobs("""
+class: GalaxyWorkflow
+steps:
+  step1:
+    tool_id: hidden_param
+""", test_data={}, history_id=history_id, wait=False)
+            self.wait_for_invocation_and_jobs(history_id, run_object.workflow_id, run_object.invocation_id)
+            contents = self.__history_contents(history_id)
+            assert len(contents) == 1
+            okay_dataset = contents[0]
+            assert okay_dataset["state"] == "ok"
+            content = self.dataset_populator.get_history_dataset_content(history_id, hid=1)
+            assert content == '1\n'
+
     @skip_without_tool("output_filter")
     def test_optional_workflow_output(self):
         with self.dataset_populator.test_history() as history_id:

test/functional/tools/hidden_param.xml

@@ -0,0 +1,23 @@
+<tool id="hidden_param" name="Hidden Parameter" version="0.1.0">
+    <description>Hidden Parameter</description>
+    <command><![CDATA[
+echo '$hidden_param' > '$out_file1'
+    ]]></command>
+    <inputs>
+        <param name="hidden_param" type="hidden" value="1" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+    </help>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -91,6 +91,7 @@
   <tool file="column_param.xml" />
   <tool file="column_param_configfile.xml" />
   <tool file="column_multi_param.xml" />
+  <tool file="hidden_param.xml" />
   <tool file="special_params.xml" />
   <tool file="section.xml" />
   <tool file="sam_to_unsorted_bam.xml" />