Implement running tests against exisiting invocation

Addresses #1290

docs/commands.rst

@@ -67,5 +67,6 @@ documentation describes these commands.
 .. include:: commands/workflow_edit.rst
 .. include:: commands/workflow_job_init.rst
 .. include:: commands/workflow_lint.rst
+.. include:: commands/workflow_test_check.rst
 .. include:: commands/workflow_test_init.rst
 .. include:: commands/workflow_upload.rst

docs/planemo.commands.rst

@@ -500,6 +500,14 @@ planemo.commands.cmd\_workflow\_lint module
    :undoc-members:
    :show-inheritance:
 
+planemo.commands.cmd\_workflow\_test\_check module
+--------------------------------------------------
+
+.. automodule:: planemo.commands.cmd_workflow_test_check
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 planemo.commands.cmd\_workflow\_test\_init module
 -------------------------------------------------
 

planemo/galaxy/activity.py

@@ -152,6 +152,7 @@ def _execute(  # noqa C901
 ) -> "GalaxyBaseRunResponse":
     user_gi = config.user_gi
     admin_gi = config.gi
+    run_response = None
 
     start_datetime = datetime.now()
     try:
@@ -205,46 +206,31 @@ def _execute(  # noqa C901
             allow_tool_state_corrections=True,
             inputs_by="name",
         )
-        invocation_id = invocation["id"]
-
-        ctx.vlog("Waiting for invocation [%s]" % invocation_id)
-        polling_backoff = kwds.get("polling_backoff", 0)
-        no_wait = kwds.get("no_wait", False)
-
-        final_invocation_state, job_state, error_message = wait_for_invocation_and_jobs(
+        run_response = invocation_to_run_response(
             ctx,
-            invocation_id=invocation_id,
-            history_id=history_id,
-            user_gi=user_gi,
-            no_wait=no_wait,
-            polling_backoff=polling_backoff,
+            config.user_gi,
+            runnable,
+            invocation,
+            polling_backoff=kwds.get("polling_backoff", 0),
+            no_wait=kwds.get("no_wait", False),
+            start_datetime=start_datetime,
+            log=log_contents_str(config),
         )
-        if final_invocation_state not in ("ok", "skipped"):
-            msg = f"Failed to run workflow [{workflow_id}], at least one job is in [{final_invocation_state}] state."
-            ctx.vlog(msg)
-            summarize_history(ctx, user_gi, history_id)
-
-        response_kwds = {
-            "workflow_id": workflow_id,
-            "invocation_id": invocation_id,
-            "history_state": job_state if not no_wait else None,
-            "invocation_state": final_invocation_state,
-            "error_message": error_message,
-        }
 
     else:
         raise NotImplementedError()
 
-    run_response = response_class(
-        ctx=ctx,
-        runnable=runnable,
-        user_gi=user_gi,
-        history_id=history_id,
-        log=log_contents_str(config),
-        start_datetime=start_datetime,
-        end_datetime=datetime.now(),
-        **response_kwds,
-    )
+    if not run_response:
+        run_response = response_class(
+            ctx=ctx,
+            runnable=runnable,
+            user_gi=user_gi,
+            history_id=history_id,
+            log=log_contents_str(config),
+            start_datetime=start_datetime,
+            end_datetime=datetime.now(),
+            **response_kwds,
+        )
     if kwds.get("download_outputs"):
         output_directory = kwds.get("output_directory", None)
         ctx.vlog("collecting outputs from run...")
@@ -253,6 +239,45 @@ def _execute(  # noqa C901
     return run_response
 
 
+def invocation_to_run_response(
+    ctx, user_gi, runnable, invocation, polling_backoff=0, no_wait=False, start_datetime=None, log=None
+):
+    start_datetime = start_datetime or datetime.now()
+    invocation_id = invocation["id"]
+    history_id = invocation["history_id"]
+    workflow_id = invocation["workflow_id"]
+
+    ctx.vlog("Waiting for invocation [%s]" % invocation_id)
+
+    final_invocation_state, job_state, error_message = wait_for_invocation_and_jobs(
+        ctx,
+        invocation_id=invocation_id,
+        history_id=history_id,
+        user_gi=user_gi,
+        no_wait=no_wait,
+        polling_backoff=polling_backoff,
+    )
+    if final_invocation_state not in ("ok", "skipped"):
+        msg = f"Failed to run workflow [{workflow_id}], at least one job is in [{final_invocation_state}] state."
+        ctx.vlog(msg)
+        summarize_history(ctx, user_gi, history_id)
+
+    return GalaxyWorkflowRunResponse(
+        ctx,
+        runnable=runnable,
+        user_gi=user_gi,
+        history_id=history_id,
+        workflow_id=workflow_id,
+        invocation_id=invocation_id,
+        history_state=job_state if not no_wait else None,
+        invocation_state=final_invocation_state,
+        error_message=error_message,
+        log=log,
+        start_datetime=start_datetime,
+        end_datetime=datetime.now(),
+    )
+
+
 def stage_in(
     ctx: "PlanemoCliContext", runnable: Runnable, config: "BaseGalaxyConfig", job_path: str, **kwds
 ) -> Tuple[Dict[str, Any], str]:

planemo/options.py

@@ -467,12 +467,13 @@ def docker_extra_volume_option():
     )
 
 
-def galaxy_url_option():
+def galaxy_url_option(required: bool = False):
     return planemo_option(
         "--galaxy_url",
         use_global_config=True,
         extra_global_config_vars=["galaxy_url"],
         use_env_var=True,
+        required=required,
         type=str,
         help="Remote Galaxy URL to use with external Galaxy engine.",
     )
@@ -489,12 +490,13 @@ def galaxy_admin_key_option():
     )
 
 
-def galaxy_user_key_option():
+def galaxy_user_key_option(required: bool = False):
     return planemo_option(
         "--galaxy_user_key",
         use_global_config=True,
         extra_global_config_vars=["admin_key"],
         use_env_var=True,
+        required=required,
         type=str,
         help="User key to use with external Galaxy engine.",
     )
@@ -824,7 +826,7 @@ def convert(self, value, param, ctx):
             return super().convert(value, param, ctx)
 
 
-def optional_tools_arg(multiple=False, allow_uris=False):
+def optional_tools_arg(multiple=False, allow_uris=False, metavar="TOOL_PATH"):
     """Decorate click method as optionally taking in the path to a tool
     or directory of tools. If no such argument is given the current working
     directory will be treated as a directory of tools.
@@ -844,7 +846,7 @@ def optional_tools_arg(multiple=False, allow_uris=False):
     nargs = -1 if multiple else 1
     return click.argument(
         name,
-        metavar="TOOL_PATH",
+        metavar=metavar,
         type=arg_type,
         nargs=nargs,
         callback=_optional_tools_default,
@@ -1599,6 +1601,10 @@ def profile_database_options():
     )
 
 
+def test_index_option():
+    return planemo_option("--test_index", default=1, type=int, help="Select which test to run. Counting starts at 1")
+
+
 def test_options():
     return _compose(
         planemo_option(
@@ -1607,7 +1613,6 @@ def test_options():
             help="Update test-data directory with job outputs (normally"
             " written to directory --job_output_files if specified.)",
         ),
-        paste_test_data_paths_option(),
         test_report_options(),
         planemo_option(
             "--test_output_json",

planemo/runnable.py

@@ -265,6 +265,12 @@ def cases(runnable: Runnable) -> List["AbstractTestCase"]:
                 cases.append(ExternalGalaxyToolTestCase(runnable, tool_id, tool_version, i, test_dict))
         return cases
 
+    return definition_to_test_case(tests_path=tests_path, runnable=runnable)
+
+
+def definition_to_test_case(tests_path, runnable):
+    with open(tests_path) as f:
+        tests_def = yaml.safe_load(f)
     tests_directory = os.path.abspath(os.path.dirname(tests_path))
 
     def normalize_to_tests_path(path: str) -> str:
@@ -274,13 +280,11 @@ def normalize_to_tests_path(path: str) -> str:
             absolute_path = path
         return os.path.normpath(absolute_path)
 
-    with open(tests_path) as f:
-        tests_def = yaml.safe_load(f)
-
     if not isinstance(tests_def, list):
         message = TEST_FILE_NOT_LIST_MESSAGE % tests_path
         raise Exception(message)
 
+    cases = []
     for i, test_def in enumerate(tests_def):
         if "job" not in test_def:
             message = TEST_FIELD_MISSING_MESSAGE % (i + 1, tests_path, "job")
@@ -305,7 +309,6 @@ def normalize_to_tests_path(path: str) -> str:
             doc=doc,
         )
         cases.append(case)
-
     return cases
 
 
@@ -434,7 +437,7 @@ def _test_id(self) -> str:
         ]:
             return get_tool_source(self.runnable.path).parse_id()
         else:
-            return os.path.basename(self.runnable.path)
+            return os.path.basename(self.runnable.uri)
 
 
 class ExternalGalaxyToolTestCase(AbstractTestCase):

tests/test_cmds_with_workflow_id.py

@@ -78,3 +78,18 @@ def test_serve_workflow(self):
             with open(output_json_path) as f:
                 output = json.load(f)
             assert "tests" in output
+            test_index = 1
+            invocation_id = output["tests"][test_index]["data"]["invocation_details"]["details"]["invocation_id"]
+            test_path = os.path.join(TEST_DATA_DIR, "wf11-remote.gxwf-test.yml")
+            workflow_test_check_command = [
+                "workflow_test_check",
+                "--galaxy_url",
+                f"http://localhost:{self._port}",
+                "--galaxy_user_key",
+                api.DEFAULT_ADMIN_API_KEY,
+                "--test_index",
+                str(test_index),
+                test_path,
+                invocation_id,
+            ]
+            self._check_exit_code(workflow_test_check_command, exit_code=0)