mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Fix get_content_as_text for compressed text datatypes
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/
This commit is contained in:
@@ -68,6 +68,7 @@ from galaxy.structured_app import (
|
||||
MinimalManagerApp,
|
||||
StructuredApp,
|
||||
)
|
||||
from galaxy.util.compression_utils import get_fileobj
|
||||
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
@@ -303,11 +304,13 @@ class HDAManager(
|
||||
# For now, cannot get data from non-text datasets.
|
||||
if not isinstance(hda.datatype, datatypes.data.Text):
|
||||
return truncated, hda_data
|
||||
if not os.path.exists(hda.get_file_name()):
|
||||
file_path = hda.get_file_name()
|
||||
if not os.path.exists(file_path):
|
||||
return truncated, hda_data
|
||||
|
||||
truncated = preview and os.stat(hda.get_file_name()).st_size > MAX_PEEK_SIZE
|
||||
hda_data = open(hda.get_file_name()).read(MAX_PEEK_SIZE)
|
||||
truncated = preview and os.stat(file_path).st_size > MAX_PEEK_SIZE
|
||||
with get_fileobj(file_path) as fh:
|
||||
hda_data = fh.read(MAX_PEEK_SIZE)
|
||||
return truncated, hda_data
|
||||
|
||||
# .... annotatable
|
||||
|
||||
@@ -12,6 +12,7 @@ from galaxy.model.unittest_utils.store_fixtures import (
|
||||
one_hda_model_store_dict,
|
||||
TEST_SOURCE_URI,
|
||||
)
|
||||
from galaxy.tool_util.verify.test_data import TestDataResolver
|
||||
from galaxy.util.unittest_utils import skip_if_github_down
|
||||
from galaxy_test.base.api_asserts import assert_has_keys
|
||||
from galaxy_test.base.decorators import (
|
||||
@@ -356,6 +357,15 @@ class TestDatasetsApi(ApiTestCase):
|
||||
self._assert_has_key(get_content_as_text_response.json(), "item_data")
|
||||
assert get_content_as_text_response.json().get("item_data") == contents
|
||||
|
||||
def test_get_content_as_text_with_compressed_text_data(self, history_id):
|
||||
test_data_resolver = TestDataResolver()
|
||||
with open(test_data_resolver.get_filename("1.fasta.gz"), mode="rb") as fh:
|
||||
hda1 = self.dataset_populator.new_dataset(history_id, content=fh, ftype="fasta.gz", wait=True)
|
||||
get_content_as_text_response = self._get(f"datasets/{hda1['id']}/get_content_as_text")
|
||||
self._assert_status_code_is(get_content_as_text_response, 200)
|
||||
self._assert_has_key(get_content_as_text_response.json(), "item_data")
|
||||
assert ">hg17" in get_content_as_text_response.json().get("item_data")
|
||||
|
||||
def test_anon_get_content_as_text(self, history_id):
|
||||
contents = "accessible data"
|
||||
hda1 = self.dataset_populator.new_dataset(history_id, content=contents, wait=True)
|
||||
|
||||
Reference in New Issue
Block a user