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Use alt functions for readers and writers #2

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merged 1 commit into from
May 21, 2024
Merged

Use alt functions for readers and writers #2

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8 changes: 4 additions & 4 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -49,10 +49,10 @@ python_requires = >=3.8
# For more information, check out https://semver.org/.
install_requires =
importlib-metadata; python_version<"3.8"
dolomite_base>=0.2.0
dolomite_sce>=0.1.0
dolomite_se>=0.1.0
multiassayexperiment>=0.4.2,<0.5.0
dolomite_base>=0.2.4
dolomite_sce>=0.1.2
dolomite_se>=0.1.3
multiassayexperiment>=0.4.2
biocutils
pandas
numpy
Expand Down
14 changes: 7 additions & 7 deletions src/dolomite_mae/read_multi_assay_experiment.py
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Expand Up @@ -7,9 +7,9 @@
from dolomite_base.read_object import read_object_registry
from multiassayexperiment import MultiAssayExperiment

read_object_registry[
"multi_sample_dataset"
] = "dolomite_mae.read_multi_assay_experiment"
read_object_registry["multi_sample_dataset"] = (
"dolomite_mae.read_multi_assay_experiment"
)


def read_multi_assay_experiment(
Expand All @@ -30,7 +30,7 @@ def read_multi_assay_experiment(
Metadata for the object.

kwargs:
Further arguments, ignored.
Further arguments.

Returns:
A
Expand All @@ -41,7 +41,7 @@ def read_multi_assay_experiment(
_sample_path = os.path.join(path, "sample_data")
_sample_data = None
if os.path.exists(_sample_path):
_sample_data = dl.read_object(_sample_path)
_sample_data = dl.alt_read_object(_sample_path, **kwargs)

if _sample_data is None:
raise RuntimeError("Cannot read 'sample_data'.")
Expand Down Expand Up @@ -70,7 +70,7 @@ def read_multi_assay_experiment(
_expt_read_path = os.path.join(_expts_path, str(_aidx))

try:
_expts[_aname] = dl.read_object(_expt_read_path)
_expts[_aname] = dl.alt_read_object(_expt_read_path, **kwargs)
except Exception as ex:
raise RuntimeError(
f"failed to load experiment '{_aname}' from '{path}'; "
Expand All @@ -95,7 +95,7 @@ def read_multi_assay_experiment(

_meta_path = os.path.join(path, "other_data")
if os.path.exists(_meta_path):
_meta = dl.read_object(_meta_path)
_meta = dl.alt_read_object(_meta_path, **kwargs)
mae = mae.set_metadata(_meta.as_dict())

return mae
16 changes: 8 additions & 8 deletions src/dolomite_mae/save_multi_assay_experiment.py
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Expand Up @@ -36,7 +36,8 @@ def save_multi_assay_experiment(
Further arguments to pass to the ``save_object`` method for the
assays.

kwargs: Further arguments, ignored.
kwargs:
Further arguments.

Returns:
``x`` is saved to path.
Expand All @@ -49,14 +50,12 @@ def save_multi_assay_experiment(
if assay_args is None:
assay_args = {}

with open(os.path.join(path, "OBJECT"), "w", encoding="utf-8") as handle:
handle.write(
'{ "type": "multi_sample_dataset", "multi_sample_dataset": { "version": "1.0" } }'
)
_info = {"multi_sample_dataset": {"version": "1.0"}}
dl.save_object_file(path, "multi_sample_dataset", _info)

# sample/column data
_sample_path = os.path.join(path, "sample_data")
dl.save_object(x.get_column_data(), _sample_path, **data_frame_args)
dl.alt_save_object(x.get_column_data(), _sample_path, **data_frame_args, **kwargs)

# save alt expts.
_expt_names = x.get_experiment_names()
Expand All @@ -70,11 +69,12 @@ def save_multi_assay_experiment(
for _aidx, _aname in enumerate(_expt_names):
_expt_save_path = os.path.join(_expt_path, str(_aidx))
try:
dl.save_object(
dl.alt_save_object(
x.experiment(_aname),
path=_expt_save_path,
data_frame_args=data_frame_args,
assay_args=assay_args,
**kwargs,
)
except Exception as ex:
raise RuntimeError(
Expand Down Expand Up @@ -125,6 +125,6 @@ def save_multi_assay_experiment(

_meta = x.get_metadata()
if _meta is not None and len(_meta) > 0:
dl.save_object(_meta, path=os.path.join(path, "other_data"))
dl.alt_save_object(_meta, path=os.path.join(path, "other_data"), **kwargs)

return
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