Merge pull request #1387 from mvdbeek/skipped_state

Support for testing workflows with conditional steps

planemo/galaxy/activity.py

@@ -223,7 +223,7 @@ def _execute(  # noqa C901
 
         if not kwds.get("no_wait"):
             final_state = _wait_for_invocation_jobs(ctx, user_gi, invocation_id, polling_backoff)
-            if final_state != "ok":
+            if final_state not in ("ok", "skipped"):
                 msg = "Failed to run workflow final history state is [%s]." % final_state
                 error_message = msg if not error_message else f"{error_message}. {msg}"
                 ctx.vlog(msg)
@@ -698,7 +698,7 @@ def _invocation(self):
 
     @property
     def was_successful(self):
-        return self.history_state in ["ok", None] and self.invocation_state == "scheduled"
+        return self.history_state in ["ok", "skipped", None] and self.invocation_state == "scheduled"
 
 
 def _tool_id(tool_path):
@@ -740,7 +740,7 @@ def _retry_on_timeouts(ctx, gi, f):
             except RequestException:
                 end_time = time.time()
                 if end_time - start_time > 45 and (try_num + 1) < try_count:
-                    ctx.vlog("Galaxy seems to have timedout, retrying to fetch status.")
+                    ctx.vlog("Galaxy seems to have timed out, retrying to fetch status.")
                     continue
                 else:
                     raise
@@ -815,6 +815,8 @@ def get_state():
                 return terminal_state
         if current_non_terminal_states:
             return None
+        if len(current_states) > 1:
+            current_states = current_states - {"skipped"}
         assert len(current_states) == 1, f"unexpected state(s) found: {current_states}"
         return current_states.pop()
 

tests/data/wf18_simple_conditional-test.yml

@@ -0,0 +1,7 @@
+- doc: Simple conditional concat workflow test
+  job:
+    some_file:
+      class: File
+      path: hello.txt
+    should_run: false
+  outputs: {}

tests/data/wf18_simple_conditional.yml

@@ -0,0 +1,13 @@
+class: GalaxyWorkflow
+inputs:
+  should_run:
+    type: boolean
+  some_file:
+    type: data
+steps:
+  cat1:
+    tool_id: cat1
+    in:
+      input1: some_file
+      should_run: should_run
+    when: $(inputs.should_run)

tests/test_cmd_test.py

@@ -358,3 +358,13 @@ def test_workflow_test_output_sanitization(self):
             test_command = self.append_profile_argument_if_needed(test_command)
             test_command.append(test_artifact)
             self._check_exit_code(test_command, exit_code=0)
+
+    @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    def test_workflow_test_skipped_invocation(self):
+        cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
+        with self._isolate():
+            test_artifact = os.path.join(TEST_DATA_DIR, "wf18_simple_conditional.yml")
+            test_command = self._test_command("--extra_tools", cat)
+            test_command = self.append_profile_argument_if_needed(test_command)
+            test_command.append(test_artifact)
+            self._check_exit_code(test_command, exit_code=0)