Merge pull request #1407 from mvdbeek/robust_error_reports

Fix running workflow tests when there are multiple tests
galaxyproject · Nov 16, 2023 · ec3661c · ec3661c
2 parents c36a2fa + 45f5166
commit ec3661c
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Showing 3 changed files with 13 additions and 7 deletions.
diff --git a/planemo/engine/galaxy.py b/planemo/engine/galaxy.py
@@ -54,12 +54,13 @@ def _run(self, runnables, job_paths, output_collectors: Optional[List[Callable]]
         results = []
         if not output_collectors:
             output_collectors = [lambda x: None] * len(runnables)
-        for runnable, job_path, collect_output in zip(runnables, job_paths, output_collectors):
-            self._ctx.vlog(f"Serving artifact [{runnable}] with Galaxy.")
-            with self.ensure_runnables_served([runnable]) as config:
+
+        with self.ensure_runnables_served(runnables) as config:
+            if self._ctx.verbose:
+                self._ctx.log(f"Running Galaxy with API configuration [{config.user_api_config}]")
+            for runnable, job_path, collect_output in zip(runnables, job_paths, output_collectors):
+                self._ctx.vlog(f"Serving artifact [{runnable}] with Galaxy.")
                 self._ctx.vlog(f"Running job path [{job_path}]")
-                if self._ctx.verbose:
-                    self._ctx.log(f"Running Galaxy with API configuration [{config.user_api_config}]")
                 run_response = execute(self._ctx, config, runnable, job_path, **self._kwds)
                 results.append(run_response)
                 if collect_output is not None:

diff --git a/planemo/engine/interface.py b/planemo/engine/interface.py
@@ -116,7 +116,9 @@ def _run_test_cases(self, test_cases, test_timeout):
                 job_paths.append(job_path)
             else:
                 job_paths.append(test_case.job_path)
-            output_collectors.append(lambda run_response: test_case.structured_test_data(run_response))
+            output_collectors.append(
+                lambda run_response, test_case=test_case: test_case.structured_test_data(run_response)
+            )
         try:
             run_responses = self._run(runnables, job_paths, output_collectors)
         finally:

diff --git a/tests/test_cmd_test.py b/tests/test_cmd_test.py
@@ -89,7 +89,7 @@ def test_data_manager_docker_mount(self):
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_workflow_test_simple_yaml(self):
         """Test testing a simple YAML workflow with Galaxy."""
-        with self._isolate():
+        with self._isolate() as test_dir:
             random_lines = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "randomlines.xml")
             cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
             test_artifact = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")
@@ -104,6 +104,9 @@ def test_workflow_test_simple_yaml(self):
                 test_artifact,
             ]
             self._check_exit_code(test_command, exit_code=0)
+            with open(os.path.join(test_dir, "tool_test_output.json")) as test_json:
+                tests_dict = json.load(test_json)
+            assert tests_dict["tests"][0]["id"] != tests_dict["tests"][1]["id"]
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     def test_tool_test_timeout(self):