diff --git a/src/semra/landscape/diseases.py b/src/semra/landscape/diseases.py index 6b35ea1..f51bfeb 100644 --- a/src/semra/landscape/diseases.py +++ b/src/semra/landscape/diseases.py @@ -86,6 +86,7 @@ priority_pickle_path=MODULE.join(name="priority.pkl"), priority_sssom_path=MODULE.join(name="priority.sssom.tsv"), configuration_path=MODULE.join(name="configuration.json"), + zenodo_record=11091885, ) @@ -94,6 +95,7 @@ def main(): """Build the mapping database for disease terms.""" # Takes about 2 hours CONFIGURATION.get_mappings(refresh_raw=True, refresh_processed=True) + CONFIGURATION.upload_zenodo() if __name__ == "__main__": diff --git a/src/semra/landscape/genes.py b/src/semra/landscape/genes.py index 2fbbd3e..d6b4b83 100644 --- a/src/semra/landscape/genes.py +++ b/src/semra/landscape/genes.py @@ -59,16 +59,17 @@ Mutation(source="umls", confidence=0.8), Mutation(source="ncit", confidence=0.8), ], - raw_pickle_path=MODULE.join(name="raw.pkl"), - raw_sssom_path=MODULE.join(name="raw.sssom.tsv"), + raw_pickle_path=MODULE.join(name="raw.pkl.gz"), + raw_sssom_path=MODULE.join(name="raw.sssom.tsv.gz"), # raw_neo4j_path=MODULE.join("neo4j_raw"), - processed_pickle_path=MODULE.join(name="processed.pkl"), - processed_sssom_path=MODULE.join(name="processed.sssom.tsv"), + processed_pickle_path=MODULE.join(name="processed.pkl.gz"), + processed_sssom_path=MODULE.join(name="processed.sssom.tsv.gz"), processed_neo4j_path=MODULE.join("neo4j"), processed_neo4j_name="semra-gene", - priority_pickle_path=MODULE.join(name="priority.pkl"), - priority_sssom_path=MODULE.join(name="priority.sssom.tsv"), + priority_pickle_path=MODULE.join(name="priority.pkl.gz"), + priority_sssom_path=MODULE.join(name="priority.sssom.tsv.gz"), configuration_path=MODULE.join(name="configuration.json"), + zenodo_record=11092012, ) @@ -76,6 +77,7 @@ def main(): """Build the mapping database for gene terms.""" CONFIGURATION.get_mappings(refresh_raw=True, refresh_processed=True) + CONFIGURATION.upload_zenodo() if __name__ == "__main__":