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fix: [#256] support for multiple studies and multiple assays in sodar_common.py #259

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Feb 13, 2025
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fix: [#256] support for multiple studies and multiple assays in sodar_common.py #259

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9b902ec
fix: [#256] support for multiple studies and multiple assays in sodar…
Feb 13, 2025
52ab943
Merge branch 'main' into 256-sodar_common_support_multiple_assays_and…
slaemmle Feb 13, 2025
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14 changes: 9 additions & 5 deletions src/cubi_tk/sodar_common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,15 +76,15 @@ def get_assay_irods_path(self, assay_uuid=None):
sodar_api_token=self.sodar_api_token,
project_uuid=self.project_uuid,
)

for study in investigation.studies.values():
if assay_uuid:
logger.info(f"Using provided Assay UUID: {assay_uuid}")
try:
#bug fix for rare case that multiple studies and multiple assays exist
if assay_uuid in study.assays.keys():
logger.info(f"Using provided Assay UUID: {assay_uuid}")
assay = study.assays[assay_uuid]
return assay.irods_path
except KeyError:
logger.error("Provided Assay UUID is not present in the Study.")
raise

else:
# Assumption: there is only one assay per study for `snappy` projects.
# If multi-assay project it will only consider the first one and throw a warning.
Expand All @@ -94,6 +94,10 @@ def get_assay_irods_path(self, assay_uuid=None):
for _assay_uuid in assays_:
assay = study.assays[_assay_uuid]
return assay.irods_path

if assay_uuid:
logger.error("Provided Assay UUID is not present in the Ivestifation.")
raise Exception("Cannot find assay with UUID %s" % assay_uuid)
return None

@staticmethod
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