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Polars load fix #39

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merged 2 commits into from
Oct 11, 2024
Merged

Polars load fix #39

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9078ec6
bug fix
Miking98 Oct 11, 2024
37162fe
Merge remote-tracking branch 'origin/main' into polars_load_fix
Miking98 Oct 11, 2024
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6 changes: 3 additions & 3 deletions src/meds_etl/omop.py
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Original file line number Diff line number Diff line change
Expand Up @@ -451,7 +451,7 @@ def extract_metadata(path_to_src_omop_dir: str, path_to_decompressed_dir: str, v
# from (concept ID -> concept code) and (concept ID -> concept name)
print("Generating metadata from OMOP `concept` table")
for concept_file in tqdm(itertools.chain(*get_table_files(path_to_src_omop_dir, "concept")),
total=len(get_table_files(path_to_src_omop_dir, "concept")[0]),
total=len(get_table_files(path_to_src_omop_dir, "concept")[0]) + len(get_table_files(path_to_src_omop_dir, "concept")[1]),
desc="Generating metadata from OMOP `concept` table"):
# Note: Concept table is often split into gzipped shards by default
if verbose:
Expand Down Expand Up @@ -493,7 +493,7 @@ def extract_metadata(path_to_src_omop_dir: str, path_to_decompressed_dir: str, v
# Include map from custom concepts to normalized (ie standard ontology)
# parent concepts, where possible, in the code_metadata dictionary
for concept_relationship_file in tqdm(itertools.chain(*get_table_files(path_to_src_omop_dir, "concept_relationship")),
total=len(get_table_files(path_to_src_omop_dir, "concept_relationship")),
total=len(get_table_files(path_to_src_omop_dir, "concept_relationship")[0]) + len(get_table_files(path_to_src_omop_dir, "concept_relationship")[1]),
desc="Generating metadata from OMOP `concept_relationship` table"):
with load_file(path_to_decompressed_dir, concept_relationship_file) as f:
# This table has `concept_id_1`, `concept_id_2`, `relationship_id` columns
Expand Down Expand Up @@ -522,7 +522,7 @@ def extract_metadata(path_to_src_omop_dir: str, path_to_decompressed_dir: str, v
datasets: List[str] = []
dataset_versions: List[str] = []
for cdm_source_file in tqdm(itertools.chain(*get_table_files(path_to_src_omop_dir, "cdm_source")),
total=get_table_files(path_to_src_omop_dir, "cdm_source"),
total=len(get_table_files(path_to_src_omop_dir, "cdm_source")[0]) + len(get_table_files(path_to_src_omop_dir, "cdm_source")[1]),
desc="Extracting dataset metadata"):
with load_file(path_to_decompressed_dir, cdm_source_file) as f:
cdm_source = read_polars_df(f.name)
Expand Down
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