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Prevent Overwriting of Existing Sample Sheets (#3915) #4012

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merged 3 commits into from
Dec 11, 2024
Merged

Prevent Overwriting of Existing Sample Sheets (#3915) #4012

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fb3bdbf
Add sample sheet overwrite check
ahdamin Dec 10, 2024
5adf5d2
Add sample sheet paths logging
ahdamin Dec 11, 2024
a7e1241
Merge branch 'master' into prevent-overwriting-existing-sheets
diitaz93 Dec 11, 2024
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12 changes: 11 additions & 1 deletion cg/apps/demultiplex/sample_sheet/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,8 @@
from cg.apps.demultiplex.sample_sheet.sample_sheet_creator import SampleSheetCreator
from cg.apps.demultiplex.sample_sheet.sample_sheet_validator import SampleSheetValidator
from cg.apps.demultiplex.sample_sheet.utils import (
delete_sample_sheet_from_housekeeper,
add_and_include_sample_sheet_path_to_housekeeper,
delete_sample_sheet_from_housekeeper,
)
from cg.apps.housekeeper.hk import HousekeeperAPI
from cg.apps.lims import LimsAPI
Expand Down Expand Up @@ -160,6 +160,16 @@ def _use_sample_sheet_from_housekeeper(
"would have copied it to sequencing run directory"
)
return

try:
if sample_sheet_path.samefile(run_directory_data.sample_sheet_path):
LOG.info(
"Sample sheet from Housekeeper already matches the target location. Skipping."
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)
return
except FileNotFoundError:
LOG.warning("Sample sheet or target path does not exist.")
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LOG.info("Sample sheet from Housekeeper is valid. Copying it to sequencing run directory")
link_or_overwrite_file(src=sample_sheet_path, dst=run_directory_data.sample_sheet_path)

Expand Down
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