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[24.0] Fix get_content_as_text for compressed text datatypes #17976
[24.0] Fix get_content_as_text for compressed text datatypes #17976
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Fixes: ``` UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte 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/datasets.py", line 192, in get_content_as_text return self.service.get_content_as_text(trans, dataset_id) File "galaxy/webapps/galaxy/services/datasets.py", line 643, in get_content_as_text truncated, dataset_data = self.hda_manager.text_data(hda, preview=True) File "galaxy/managers/hdas.py", line 310, in text_data hda_data = open(hda.get_file_name()).read(MAX_PEEK_SIZE) File "<frozen codecs>", line 322, in decode ``` from https://sentry.galaxyproject.org/share/issue/9eb8e5b692b94700ac9b304b6d1c2418/
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Looks good! thank you!
Hmm, that API test error looks ... well, not likely caused by this PR, but it does happen on reruns of the action and in https://github.com/galaxyproject/galaxy/actions/runs/8665751645/job/23765082220#step:10:861 |
yeah, suspicious for sure, but seemed unrelated to this change |
the test passes for me before and after this PR locally |
Fixes:
from https://sentry.galaxyproject.org/share/issue/9eb8e5b692b94700ac9b304b6d1c2418/
(Please replace this header with a description of your pull request. Please include BOTH what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
(If fixing a bug, please add any relevant error or traceback)
(For UI components, it is recommended to include screenshots or screencasts)
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