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Handle invalid BAM locations with fallback and log warnings #8

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Merged
TomCharlesRousseau merged 2 commits into from
Nov 24, 2025
Merged

Handle invalid BAM locations with fallback and log warnings #8

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bc3b0ec
Handle invalid BAM locations with fallback and log warnings
Nov 24, 2025
94d9b5b
Fix ruff formatting issues
Nov 24, 2025
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16 changes: 13 additions & 3 deletions src/sigmabam2openbis/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,13 +137,23 @@ def parse(self, files, collection, logger):
val = self.get_value_as_str(chemical_row.get(col))
if not val:
logger.warning(
f"Missing value for BAM location column '{col}'"
f"Umgang-Id {umgang_id}. Please, check the excel."
f"Missing value for BAM location column '{col}' in row with Umgang-Id {umgang_id}"
)
continue
bam_location_complete.append(val)
if bam_location_complete:
chemical.bam_location_complete = "_".join(bam_location_complete)
location_str = "_".join(bam_location_complete)
try:
# test assignment to catch vocabulary errors
chemical.bam_location_complete = location_str
except ValueError:
fallback = "FB_80_-1_000"
logger.warning(
f"Invalid BAM location '{location_str}'"
f"for Umgang-Id {umgang_id}"
f"Replacing with fallback '{fallback}'."
)
chemical.bam_location_complete = fallback

# Adding chemicals to the collection
collection.add(chemical)