Add job resume test with HDCA input to paused dataset

I am slightly surprised that this worked without change, but it appears that the remapping occurs via the HDAs that the HDCA is composed of.
galaxyproject · Dec 31, 2017 · 9fdf0a6 · 9fdf0a6
1 parent 2610341
commit 9fdf0a6
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Showing 2 changed files with 52 additions and 13 deletions.
diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
@@ -676,20 +676,53 @@ def test_workflow_resume_from_failed_step(self):
         history_id = self.dataset_populator.new_history()
         invocation_id = self.__invoke_workflow(history_id, workflow_id)
         self.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id, assert_ok=False)
-        failed_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=False)
-        assert failed_dataset['state'] == 'error', failed_dataset
-        paused_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=False)
+        failed_dataset_one = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=False)
+        assert failed_dataset_one['state'] == 'error', failed_dataset_one
+        paused_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=5, wait=True, assert_ok=False)
         assert paused_dataset['state'] == 'paused', paused_dataset
         inputs = {"thebool": "false",
                   "failbool": "false",
-                  "rerun_remap_job_id": failed_dataset['creating_job']}
+                  "rerun_remap_job_id": failed_dataset_one['creating_job']}
         self.dataset_populator.run_tool(tool_id='job_properties',
                                         inputs=inputs,
                                         history_id=history_id,
                                         assert_ok=True)
-        unpaused_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=2, wait=True, assert_ok=False)
+        unpaused_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=5, wait=True, assert_ok=False)
         assert unpaused_dataset['state'] == 'ok'
 
+    @skip_without_tool("job_properties")
+    @skip_without_tool("identifier_multiple_in_conditional")
+    def test_workflow_resume_from_failed_step_with_hdca_input(self):
+        workflow_id = self._upload_yaml_workflow("""
+class: GalaxyWorkflow
+steps:
+  - tool_id: job_properties
+    state:
+      thebool: true
+      failbool: true
+  - tool_id: identifier_collection
+    state:
+      input1:
+        $link: 0#list_output
+""")
+        with self.dataset_populator.test_history() as history_id:
+            invocation_id = self.__invoke_workflow(history_id, workflow_id)
+            self.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id, assert_ok=False)
+            failed_dataset_one = self.dataset_populator.get_history_dataset_details(history_id, hid=1, wait=True, assert_ok=False)
+            assert failed_dataset_one['state'] == 'error', failed_dataset_one
+            paused_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=5, wait=True, assert_ok=False)
+            assert paused_dataset['state'] == 'paused', paused_dataset
+            inputs = {"thebool": "false",
+                      "failbool": "false",
+                      "rerun_remap_job_id": failed_dataset_one['creating_job']}
+            self.dataset_populator.run_tool(tool_id='job_properties',
+                                            inputs=inputs,
+                                            history_id=history_id,
+                                            assert_ok=True)
+            unpaused_dataset = self.dataset_populator.get_history_dataset_details(history_id, hid=5, wait=True,
+                                                                                  assert_ok=False)
+            assert unpaused_dataset['state'] == 'ok'
+
     @skip_without_tool("collection_creates_pair")
     def test_workflow_run_output_collection_mapping(self):
         workflow_id = self._upload_yaml_workflow("""

diff --git a/test/functional/tools/job_properties.xml b/test/functional/tools/job_properties.xml
@@ -1,26 +1,32 @@
 <tool id="job_properties" name="Test Job Properties">
-    <command>
+    <command><![CDATA[
         #if $thebool
-            echo "The bool is true";
-            echo "The bool is really true" 1>&amp;2;
-            echo "This is a line of text." > $out_file1
+            echo "The bool is true" &&
+            echo "The bool is really true" 1>&2 &&
+            echo "This is a line of text." > '$out_file1' &&
+            cp '$out_file1' $one &&
+            cp '$out_file1' $two
         #else
-            echo "The bool is not true";
-            echo "The bool is very not true" 1>&amp;2;
-            echo "This is a different line of text." > $out_file1;
+            echo "The bool is not true" &&
+            echo "The bool is very not true" 1>&2 &&
+            echo "This is a different line of text." > '$out_file1' &&
             sh -c "exit 2"
         #end if
         #if $failbool
             ; sh -c "exit 127"
         #end if
 
-    </command>
+    ]]></command>
     <inputs>
         <param name="thebool" type="boolean" label="The boolean property" />
         <param name="failbool" type="boolean" label="The failure property" checked="false" />
     </inputs>
     <outputs>
         <data name="out_file1" />
+        <collection name="list_output" type="list" label="A list output">
+            <data name="one" format="txt" />
+            <data name="two" format="txt" />
+        </collection>
     </outputs>
     <stdio>
         <exit_code range="127"   level="fatal"   description="Failing exit code." />