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Add back the "print" lint rule #791

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Merged
merged 1 commit into from
May 23, 2024
Merged

Add back the "print" lint rule #791

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1 change: 0 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@ ignore = [
"FBT", # flake-boolean-trap... disallows boolean args to functions... fixing this code will require refactors.
"ANN", # flake8-annotations is for typed code
"DJ", # django specific
"T20", # forbids print, we print quite a bit
"PYI", # pyi is typing stub files
"PT", # pytest specific
"PTH", # pathlib is preferred, but we're not using it yet
Expand Down
93 changes: 0 additions & 93 deletions v03_pipeline/bin/write_cached_reference_dataset_query_ht.py
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12 changes: 8 additions & 4 deletions v03_pipeline/lib/misc/sample_ids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,10 @@

import hail as hl

from v03_pipeline.lib.logger import get_logger

logger = get_logger(__name__)


class MatrixTableSampleSetError(Exception):
def __init__(self, message, missing_samples):
Expand Down Expand Up @@ -42,15 +46,15 @@ def remap_sample_ids(
f'All callset sample IDs:{mt.s.collect()}'
)
if ignore_missing_samples_when_remapping:
print(message)
logger.info(message)
else:
raise MatrixTableSampleSetError(message, missing_samples)

mt = mt.annotate_cols(**project_remap_ht[mt.s])
remap_expr = hl.if_else(hl.is_missing(mt.seqr_id), mt.s, mt.seqr_id)
mt = mt.annotate_cols(seqr_id=remap_expr, vcf_id=mt.s)
mt = mt.key_cols_by(s=mt.seqr_id)
print(f'Remapped {remap_count} sample ids...')
logger.info(f'Remapped {remap_count} sample ids...')
return mt


Expand All @@ -77,9 +81,9 @@ def subset_samples(
if (
subset_count > anti_join_ht_count
) and ignore_missing_samples_when_subsetting:
print(message)
logger.info(message)
else:
raise MatrixTableSampleSetError(message, missing_samples)
print(f'Subsetted to {subset_count} sample ids')
logger.info(f'Subsetted to {subset_count} sample ids')
mt = mt.semi_join_cols(sample_subset_ht)
return mt.filter_rows(hl.agg.any(hl.is_defined(mt.GT)))
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