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mvdbeek
aeab88be4d
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( ```
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
.. image:: https://img.shields.io/badge/release-documentation-blue.svg
:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.8 . To check your Python version, run:
.. code:: console
$ python -V
Python 3.8.18
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .