The new 1.0.0 version of pytest-celery will move towards a Docker-based
approach for smoke and production-like testing, bringing in a number of
dependencies that we don't currently need.
Since the pre-1.0.0 version of pytest-celery was just a shim for
``celery.contrib.pytest``, we can simply load the latter for API,
integration and Selenium tests.
This commit updates the notification creation and sharing logic to include the `galaxy_url` field in the `NotificationCreateRequest` and `SharedItemNotificationFactory` classes. This field is used to generate links in the notification content and is passed as an argument when sending notifications to recipients.
When enabling the `warn_unused_ignores = True` option of mypy, this
was making the `test_galaxy_packages` tests fail with:
```
mypy .
Traceback (most recent call last):
File "/tmp/gxpkgtestenvu3fgDr/bin/mypy", line 8, in <module>
sys.exit(console_entry())
File "/tmp/gxpkgtestenvu3fgDr/lib/python3.10/site-packages/mypy/__main__.py", line 15, in console_entry
main()
File "mypy/main.py", line 100, in main
File "mypy/main.py", line 182, in run_build
File "mypy/build.py", line 192, in build
File "mypy/build.py", line 266, in _build
File "mypy/build.py", line 2942, in dispatch
File "mypy/build.py", line 3333, in process_graph
File "mypy/build.py", line 3414, in process_fresh_modules
File "mypy/build.py", line 2110, in fix_cross_refs
File "mypy/fixup.py", line 52, in fixup_module
File "mypy/fixup.py", line 127, in visit_symbol_table
File "mypy/lookup.py", line 49, in lookup_fully_qualified
AssertionError: Cannot find component 'util' for 'galaxy.util'
make: *** [Makefile:96: mypy] Error 1
```
Moreover, installing packages in editable mode was hiding some issues
with how files from other packages were accessed.
Fixes:
```
ExceptionGroup: unhandled errors in a TaskGroup
File "starlette/_utils.py", line 87, in collapse_excgroups
yield
File "starlette/middleware/base.py", line 190, in __call__
async with anyio.create_task_group() as task_group:
File "anyio/_backends/_asyncio.py", line 678, in __aexit__
raise BaseExceptionGroup(
AttributeError: 'NoneType' object has no attribute 'replace'
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/history_contents.py", line 465, in index
items = self.service.index(
File "galaxy/webapps/galaxy/services/history_contents.py", line 312, in index
return self.__index_v2(trans, history_id, params, serialization_params, filter_query_params, accept)
File "galaxy/webapps/galaxy/services/history_contents.py", line 992, in __index_v2
items = [
File "galaxy/webapps/galaxy/services/history_contents.py", line 993, in <listcomp>
self._serialize_content_item(
File "galaxy/webapps/galaxy/services/history_contents.py", line 1064, in _serialize_content_item
rval = serializer.serialize_to_view(
File "galaxy/managers/base.py", line 785, in serialize_to_view
return self.serialize(item, all_keys, **context)
File "galaxy/managers/hdas.py", line 614, in serialize
return super().serialize(hda, keys, user=user, **context)
File "galaxy/managers/datasets.py", line 770, in serialize
serialized = super().serialize(dataset_assoc, keys, **context)
File "galaxy/managers/base.py", line 698, in serialize
returned[key] = self.serializers[key](item, key, **context)
File "galaxy/managers/datasets.py", line 633, in <lambda>
"peek": lambda item, key, **context: item.display_peek() if item.peek and item.peek != "no peek" else None,
File "galaxy/model/__init__.py", line 4669, in display_peek
return self.datatype.display_peek(self)
File "galaxy/datatypes/qiime2.py", line 57, in display_peek
table += [make_row(pair) for pair in self._peek(dataset, simple=True)]
File "galaxy/datatypes/qiime2.py", line 57, in <listcomp>
table += [make_row(pair) for pair in self._peek(dataset, simple=True)]
File "galaxy/datatypes/qiime2.py", line 54, in make_row
return f"<tr><th>{pair[0]}</th><td>{html.escape(pair[1])}</td></tr>"
File "__init__.py", line 19, in escape
s = s.replace("&", "&") # Must be done first!
```
Marius van den Beek