WIP: Wire up workflow track command

Think we still have some work to do once there are failing jobs.

Author: mvdbeek

planemo/commands/cmd_workflow_track.py

@@ -5,46 +5,22 @@
 from planemo import options
 from planemo.cli import command_function
 from planemo.engine.factory import engine_context
-from planemo.galaxy.invocations.progress import WorkflowProgress
+from planemo.galaxy.activity import wait_for_invocation_and_jobs
 
 
 @click.command("workflow_track")
 @options.invocation_target_options()
 @command_function
 def cli(ctx, invocation_id, **kwds):
     """Run defined tests against existing workflow invocation."""
-    with WorkflowProgress() as workflow_progress:
-        workflow_progress.add_bars()
-        import time
-
-        time.sleep(1)
-        new_step = {"state": "new"}
-        scheduled_step = {"state": "scheduled"}
-        new_steps = [new_step, new_step, new_step]
-        one_scheduled_steps = [scheduled_step, new_step, new_step]
-        two_scheduled_steps = [scheduled_step, scheduled_step, new_step]
-        all_scheduled_steps = [scheduled_step, scheduled_step, scheduled_step]
-        state_pairs = [
-            ({"state": "new"}, {}),
-            ({"state": "ready", "steps": new_steps}, {}),
-            ({"state": "ready", "steps": one_scheduled_steps}, {"states": {"new": 1}}),
-            ({"state": "ready", "steps": two_scheduled_steps}, {"states": {"new": 2}}),
-            ({"state": "ready", "steps": two_scheduled_steps}, {"states": {"new": 1, "running": 1}}),
-            ({"state": "ready", "steps": two_scheduled_steps}, {"states": {"new": 1, "ok": 1}}),
-            ({"state": "ready", "steps": two_scheduled_steps}, {"states": {"ok": 2}}),
-            ({"state": "scheduled", "steps": all_scheduled_steps}, {"states": {"ok": 2, "new": 3}}),
-            ({"state": "scheduled", "steps": all_scheduled_steps}, {"states": {"ok": 2, "running": 1, "new": 2}}),
-            ({"state": "scheduled", "steps": all_scheduled_steps}, {"states": {"ok": 3, "running": 1, "new": 1}}),
-            ({"state": "scheduled", "steps": all_scheduled_steps}, {"states": {"ok": 4, "running": 1}}),
-            ({"state": "scheduled", "steps": all_scheduled_steps}, {"states": {"ok": 5}}),
-        ]
-        for invocation, job_states_summary in state_pairs:
-            workflow_progress.handle_invocation(invocation, job_states_summary)
-            time.sleep(1)
-
     with engine_context(ctx, engine="external_galaxy", **kwds) as engine, engine.ensure_runnables_served([]) as config:
         user_gi = config.user_gi
-        invocation = user_gi.invocations.show_invocation(invocation_id)
-        # https://stackoverflow.com/questions/23113494/double-progress-bar-in-python
+        wait_for_invocation_and_jobs(
+            ctx,
+            invocation_id,
+            history_id=None,
+            user_gi=user_gi,
+            polling_backoff=5,
+        )
 
     ctx.exit(0)

planemo/galaxy/activity.py

@@ -771,7 +771,7 @@ def _history_id(gi, **kwds) -> str:
 
 
 def wait_for_invocation_and_jobs(
-    ctx, invocation_id: str, history_id: str, user_gi: GalaxyInstance, polling_backoff: int
+    ctx, invocation_id: str, history_id: Optional[str], user_gi: GalaxyInstance, polling_backoff: int
 ):
     polling_tracker = PollingTrackerImpl(polling_backoff)
     invocation_api = BioblendInvocationApi(ctx, user_gi)
@@ -780,6 +780,9 @@ def wait_for_invocation_and_jobs(
             ctx, invocation_id, invocation_api, polling_tracker, workflow_progress_display
         )
         if error_message:
+            if not history_id:
+                invocation = invocation_api.get_invocation(invocation_id)
+                history_id = invocation["history_id"]
             summarize_history(ctx, user_gi, history_id)
         return final_invocation_state, job_state, error_message
 

planemo/galaxy/invocations/api.py

@@ -26,6 +26,7 @@ class Invocation(TypedDict, total=False):
     id: str
     state: str
     steps: List[InvocationStep]
+    history_id: Optional[str]
 
 
 class InvocationJobsSummary(TypedDict, total=False):