Windows compatibility issue: Path separator in cloud storage URLs #783
Description
Windows compatibility issue: Path separator in cloud storage URLs
Issue Summary
When running on Windows, tests for pf7, pf8, and pv4 datasets fail with "Invalid bucket name" errors. This is caused by Windows backslashes (\) in cloud storage paths instead of the required forward slashes (/).
Root Cause
In malariagen_data\plasmodium.py, os.path.join() is used to construct cloud storage paths in four methods:
# In sample_metadata() method:
path = os.path.join(self._path, self.CONF["metadata_path"])
# In _open_variant_calls_zarr() method:
path = os.path.join(self._path, self.CONF["variant_calls_zarr_path"])
# In open_genome() method:
path = os.path.join(self._path, self.CONF["reference_path"])
# In genome_features() method:
path = os.path.join(self._path, self.CONF["annotations_path"])On Windows, this produces backslashes which are invalid in cloud storage URLs.
Error Details
Tests fail with similar errors:
gcsfs.retry.HttpError: Invalid bucket name: 'pf7_release\metadata', 400
botocore.exceptions.ParamValidationError: Parameter validation failed: Invalid bucket name
Proposed Fix
Use string formatting with explicit forward slashes:
# In sample_metadata() method:
path = f"{self._path}/{self.CONF['metadata_path']}"
# In _open_variant_calls_zarr() method:
path = f"{self._path}/{self.CONF['variant_calls_zarr_path']}"
# In open_genome() method:
path = f"{self._path}/{self.CONF['reference_path']}"
# In genome_features() method:
path = f"{self._path}/{self.CONF['annotations_path']}"Alternative approach:
# For any of the methods:
path = os.path.join(self._path, self.CONF["metadata_path"]) # or other paths
path = path.replace('\\', '/')Files to Change
malariagen_data\plasmodium.py