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resolves spatialdata_io.xenium() capability to read in xeniumranger v3.0.1.1 resegemented data #244

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resolves spatialdata_io.xenium() capability to read in xeniumranger v3.0.1.1 resegemented data #244

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7a369fa
Update xenium.py - fix version detection after resegment for proper b…
Pancreas-Pratik Nov 30, 2024
d69b750
Update _constants.py - add spec needed for correct xenium ranger vers…
Pancreas-Pratik Nov 30, 2024
36ffab2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 30, 2024
05ece63
Update _constants.py - fixed formatting of spec addition
Pancreas-Pratik Nov 30, 2024
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2 changes: 2 additions & 0 deletions src/spatialdata_io/_constants/_constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -145,6 +145,8 @@ class XeniumKeys(ModeEnum):

# specs keys
ANALYSIS_SW_VERSION = "analysis_sw_version"
# spec which contains xeniumranger version (after resegment is run from xenium-3.0.1.1)
XENIUM_RANGER = "xenium_ranger"

# zarr file with labels file and cell summary keys
CELLS_ZARR = "cells.zarr.zip"
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11 changes: 10 additions & 1 deletion src/spatialdata_io/readers/xenium.py
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Expand Up @@ -719,7 +719,16 @@ def _parse_version_of_xenium_analyzer(
specs: dict[str, Any],
hide_warning: bool = True,
) -> packaging.version.Version | None:
string = specs[XeniumKeys.ANALYSIS_SW_VERSION]

# After using xeniumranger 3.0.1.1 to resegment data from xenium-1.6.0.7, a new dict is added to `specs`, named 'xenium_ranger',
# which contains the key 'version' and it's value pair 'xenium-3.0.1.1' for the resegmented,
# which contains a new 'version' key and value is added in specs, using this version (rather than the original 'analysis_sw_version'),
# corrects branching and parsing when using xenium() on the xeniumranger resegmented /outs/ folder path
if specs.get(XeniumKeys.XENIUM_RANGER):
string = specs[XeniumKeys.XENIUM_RANGER]["version"]
else:
string = specs[XeniumKeys.ANALYSIS_SW_VERSION]

pattern = r"^(?:x|X)enium-(\d+\.\d+\.\d+(\.\d+-\d+)?)"

result = re.search(pattern, string)
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