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1.0.2
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- Bugfix: Special RxNorm BioPortal operations made much more explicit via parameter. Previous logic was handling other instances of RxNorm.
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joeflack4 committed Oct 7, 2023
1 parent d1809ff commit edc2e86
Showing 1 changed file with 5 additions and 3 deletions.
8 changes: 5 additions & 3 deletions owl_on_fhir/__main__.py
Original file line number Diff line number Diff line change
Expand Up @@ -199,9 +199,11 @@ def owl_to_fhir(
retain_intermediaries=False, intermediary_type=['obographs', 'semsql'][0], use_cached_intermediaries=False,
intermediary_outdir: str = None, convert_intermediaries_only=False, native_uri_stems: List[str] = None,
code_system_id: str = None, code_system_url: str = None, dev_oak_path: str = None,
dev_oak_interpreter_path: str = None
dev_oak_interpreter_path: str = None, rxnorm_bioportal=False
) -> str:
"""Run conversion"""
"""Run conversion
:param rxnorm_bioportal: Special custom case. Set True if the file being processed is RxNorm.ttl from BioPortal."""
include_all_predicates = not include_only_critical_predicates

if not os.path.exists(CACHE_DIR):
Expand Down Expand Up @@ -233,7 +235,7 @@ def owl_to_fhir(
intermediary_outdir = intermediary_outdir if intermediary_outdir else out_dir

# Preprocessing: Special cases
if 'rxnorm' in input_path.lower() or 'rxnorm' in out_filename.lower():
if rxnorm_bioportal:
input_path = _preprocess_rxnorm(input_path)

# Convert
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