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Fix a bug in download_and_rename method #401

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Merged
gregorjerse merged 3 commits into from
Jan 29, 2026
Merged

Fix a bug in download_and_rename method #401

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8185abd
Pin ``pandas`` package version
marcellevstek Jan 29, 2026
3c57ba9
Use uv in e2e tests
gregorjerse Jan 13, 2026
1e18908
Fix a bug in ``download_and_rename`` method
marcellevstek Dec 12, 2025
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6 changes: 3 additions & 3 deletions .github/workflows/e2e.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,8 @@ jobs:

- name: Install ReSDK and its testing dependencies
run: |
python${{ env.PYTHON_VERSION }} -m pip install .[test]
uv venv --python=${{ env.PYTHON_VERSION }}
uv sync --extra=test

- name: Reset Docker credentials store
run: |
Expand Down Expand Up @@ -141,6 +142,5 @@ jobs:
- name: Run tests
run: |
# Make sure `python` refers to the tox environment's Python
export PATH=`pwd`/.tox/py310-e2e-resdk/bin:$PATH
python${{ env.PYTHON_VERSION }} -m pytest --cov=resdk --cov-report=xml:.reports/resdk_e2e_cov.xml \
uv run pytest --cov=resdk --cov-report=xml:.reports/resdk_e2e_cov.xml \
--junit-xml=.reports/resdk_e2e_report.xml tests/functional/**/e2e_*.py
5 changes: 5 additions & 0 deletions docs/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,11 @@ Added
-----
- Add support for ``Python 3.14``

Fixed
-----
- Fix a bug that prevented the downloading and renaming of
a directory from a data object


===================
22.2.1 - 2025-11-19
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -49,7 +49,7 @@ dependencies = [
"wrapt",
"pytz",
"tzlocal",
"pandas",
"pandas<3.0.0",
"tqdm",
"openpyxl",
"xlrd",
Expand Down
42 changes: 30 additions & 12 deletions src/resdk/resources/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,7 @@ def download(
field_name: Optional[str] = None,
download_dir: Optional[str] = None,
show_progress: bool = True,
return_dir_names: bool = False,
) -> list[str]:
"""Download Data object's files and directories.

Expand All @@ -270,6 +271,12 @@ def download(
* re.data.get(42).download(file_name='alignment7.bam')
* re.data.get(42).download(field_name='bam')

The function returns a list of downloaded file names. In case the
Data object contains directories, the user can specify to return directory names
instead of file names contained in those directories via the return_dir_names argument.
WARNING: If neither file_name nor field_name is specified and return_dir_names is set
to True, the method will download both directories and files when the Data object
contains both. However, the returned list will include only the directory names.
"""
if file_name and field_name:
raise ValueError("Only one of file_name or field_name may be given.")
Expand All @@ -281,41 +288,52 @@ def download(
files=files, download_dir=download_dir, show_progress=show_progress
)

return file_names
dir_names = self._files_dirs("dir", file_name, field_name)
if dir_names and return_dir_names:
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Contributor Author

@marcellevstek marcellevstek Jan 13, 2026

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@gregorjerse this works as intended, but if a user does not specify a field or file name, only the directory names get returned. This may seem problematic, if the user expects the file names not contained in the directories to be returned as well.

asset_names = dir_names
else:
asset_names = file_names

return asset_names

def download_and_rename(
self,
custom_file_name: str,
custom_asset_name: str,
overwrite_existing: bool = False,
field_name: Optional[str] = None,
file_name: Optional[str] = None,
download_dir: Optional[str] = None,
):
"""Download and rename a single file from the Data object."""
"""Download and rename an asset from the Data object."""

if not field_name and not file_name:
raise ValueError("Either 'file_name' or 'field_name' must be given.")

if download_dir is None:
download_dir = os.getcwd()
destination_file_path = os.path.join(download_dir, custom_file_name)
if os.path.exists(destination_file_path) and not overwrite_existing:
raise FileExistsError(
f"File with path '{destination_file_path}' already exists. Skipping download."
destination_asset_path = os.path.join(download_dir, custom_asset_name)
if os.path.exists(destination_asset_path) and not overwrite_existing:
logging.warning(
f"File or directory with path '{destination_asset_path}' already exists. "
"Skipping download."
)
return

source_file_name = self.download(
source_asset_name = self.download(
file_name=file_name,
field_name=field_name,
download_dir=download_dir,
return_dir_names=True,
)[0]

source_file_path = os.path.join(download_dir, source_file_name)
source_asset_path = os.path.join(download_dir, source_asset_name)

logging.info(f"Renaming file '{source_file_name}' to '{custom_file_name}'.")
logging.info(
f"Renaming the downloaded asset from '{source_asset_name}' to '{custom_asset_name}'."
)
os.rename(
source_file_path,
destination_file_path,
source_asset_path,
destination_asset_path,
)

def stdout(self) -> str:
Expand Down
7 changes: 5 additions & 2 deletions tests/unit/test_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -209,13 +209,16 @@ def test_download_ok(self, data_mock):
with patch("os.rename") as mock_rename:
Data.download_and_rename(
data_mock,
custom_file_name="text_file1.txt",
custom_asset_name="text_file1.txt",
field_name="txt",
download_dir="/some/path/",
)

data_mock.download.assert_called_once_with(
file_name=None, field_name="txt", download_dir="/some/path/"
file_name=None,
field_name="txt",
download_dir="/some/path/",
return_dir_names=True,
)

mock_rename.assert_called_once()
Expand Down