From aeab88be4d226975bc577af243928fc9abe71070 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 17 Apr 2024 15:06:25 +0200 Subject: [PATCH] Raise MessageException when report references invalid workflow output Marginally better than an uncaught exception IMO. Fixes https://sentry.galaxyproject.org/share/issue/45391593603042799ef5ac5b18d22440/: ``` Exception: Failed to find workflow output named [Fasta Statistics on input dataset(s): Fasta summary stats], workflow doesn't define output by that name - valid names are ['Flye assembly on input dataset(s) (consensus)', 'Flye assembly on input dataset(s) (assembly_graph)', 'Flye assembly on input dataset(s) (Graphical Fragment Assembly)', 'Flye assembly on input dataset(s) (assembly_info)', 'Flye assembly on input dataset(s) (log)', None, 'Bandage Image on input dataset(s): Assembly Graph Image', 'Quast on input dataset(s): PDF report', 'Quast on input dataset(s): HTML report', 'Quast on input dataset(s): tabular report', 'Quast on input dataset(s): Log', 'Bar chart showing contig sizes']. File "starlette/applications.py", line 123, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/middleware/errors.py", line 186, in __call__ raise exc File "starlette/middleware/errors.py", line 164, in __call__ await self.app(scope, receive, _send) File "starlette_context/middleware/raw_middleware.py", line 92, in __call__ await self.app(scope, receive, send_wrapper) File "starlette/middleware/base.py", line 189, in __call__ with collapse_excgroups(): File "contextlib.py", line 155, in __exit__ self.gen.throw(typ, value, traceback) File "starlette/_utils.py", line 93, in collapse_excgroups raise exc File "starlette/middleware/base.py", line 191, in __call__ response = await self.dispatch_func(request, call_next) File "galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options response = await call_next(request) File "starlette/middleware/base.py", line 165, in call_next raise app_exc File "starlette/middleware/base.py", line 151, in coro await self.app(scope, receive_or_disconnect, send_no_error) File "starlette/middleware/exceptions.py", line 62, in __call__ await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 758, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/routing.py", line 778, in app await route.handle(scope, receive, send) File "starlette/routing.py", line 299, in handle await self.app(scope, receive, send) File "starlette/routing.py", line 79, in app await wrap_app_handling_exceptions(app, request)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 74, in app response = await func(request) File "fastapi/routing.py", line 278, in app raw_response = await run_endpoint_function( File "fastapi/routing.py", line 193, in run_endpoint_function return await run_in_threadpool(dependant.call, **values) File "starlette/concurrency.py", line 42, in run_in_threadpool return await anyio.to_thread.run_sync(func, *args) File "anyio/to_thread.py", line 56, in run_sync return await get_async_backend().run_sync_in_worker_thread( File "anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread return await future File "anyio/_backends/_asyncio.py", line 851, in run result = context.run(func, *args) File "galaxy/webapps/galaxy/api/workflows.py", line 1485, in show_invocation_report return self.invocations_service.show_invocation_report(trans, invocation_id) File "galaxy/webapps/galaxy/services/invocations.py", line 143, in show_invocation_report wfi_report = self._workflows_manager.get_invocation_report(trans, invocation_id, format=format) File "galaxy/managers/workflows.py", line 428, in get_invocation_report return generate_report( File "galaxy/workflow/reports/__init__.py", line 14, in generate_report return plugin.generate_report_json(trans, invocation, runtime_report_config_json=runtime_report_config_json) File "galaxy/workflow/reports/generators/__init__.py", line 43, in generate_report_json internal_markdown = self._generate_internal_markdown( File "galaxy/workflow/reports/generators/__init__.py", line 73, in _generate_internal_markdown internal_markdown = resolve_invocation_markdown(trans, invocation, workflow_markdown) File "galaxy/managers/markdown_util.py", line 958, in resolve_invocation_markdown galaxy_markdown = _remap_galaxy_markdown_calls(_remap, workflow_markdown) File "galaxy/managers/markdown_util.py", line 1012, in _remap_galaxy_markdown_calls return _remap_galaxy_markdown_containers(_remap_container, markdown) File "galaxy/managers/markdown_util.py", line 971, in _remap_galaxy_markdown_containers (replacement, whole_block) = func(replace) File "galaxy/managers/markdown_util.py", line 1008, in _remap_container return func(match.group(1), f"{matching_line}\n") File "galaxy/managers/markdown_util.py", line 926, in _remap ref_object = invocation.get_output_object(name) File "galaxy/model/__init__.py", line 8593, in get_output_object raise Exception( ``` --- lib/galaxy/model/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 7e582782e911..672d2cb12ea3 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -8576,11 +8576,11 @@ def get_output_object(self, label): # That probably isn't good. workflow_output = self.workflow.workflow_output_for(label) if workflow_output: - raise Exception( + raise galaxy.exceptions.MessageException( f"Failed to find workflow output named [{label}], one was defined but none registered during execution." ) else: - raise Exception( + raise galaxy.exceptions.MessageException( f"Failed to find workflow output named [{label}], workflow doesn't define output by that name - valid names are {self.workflow.workflow_output_labels}." )