Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[24.0] Fix get_content_as_text for compressed text datatypes #17976

Merged
merged 1 commit into from
Apr 12, 2024
Merged

[24.0] Fix get_content_as_text for compressed text datatypes #17976

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 6 additions & 3 deletions lib/galaxy/managers/hdas.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,7 @@
MinimalManagerApp,
StructuredApp,
)
from galaxy.util.compression_utils import get_fileobj

log = logging.getLogger(__name__)

Expand Down Expand Up @@ -303,11 +304,13 @@ def text_data(self, hda, preview=True):
# 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
Expand Down
10 changes: 10 additions & 0 deletions lib/galaxy_test/api/test_datasets.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
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 (
Expand Down Expand Up @@ -356,6 +357,15 @@ def test_get_content_as_text(self, history_id):
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)
Expand Down
Loading