From b06ffc8a72249f18ec08d40c19d6a96ba66e80c2 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Tue, 14 Jan 2025 00:13:45 -0500 Subject: [PATCH] Moved duckdb files into a separate directory root. --- src/snakefiles/duckdb.snakefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/snakefiles/duckdb.snakefile b/src/snakefiles/duckdb.snakefile index 110a4c0d..96693176 100644 --- a/src/snakefiles/duckdb.snakefile +++ b/src/snakefiles/duckdb.snakefile @@ -7,7 +7,7 @@ import os # Write all compendia files to DuckDB and Parquet, then create `babel_outputs/duckdb/compendia_done` to signal that we're done. rule export_all_compendia_to_duckdb: input: - nodes_files=expand("{od}/duckdb/parquet/filename={fn}/compendium.duckdb", + nodes_files=expand("{od}/duckdb/duckdbs/filename={fn}/compendium.duckdb", od=config['output_directory'], fn=map(lambda fn: os.path.splitext(fn)[0], get_all_compendia(config)) ) @@ -30,7 +30,7 @@ rule export_compendia_to_duckdb: # Write all synonyms files to Parquet via DuckDB, then create `babel_outputs/duckdb/synonyms_done` to signal that we're done. rule export_all_synonyms_to_duckdb: input: - sapbert_training_file=expand("{od}/duckdb/parquet/filename={fn}/synonyms.duckdb", + sapbert_training_file=expand("{od}/duckdb/duckdbs/filename={fn}/synonyms.duckdb", od=config['output_directory'], fn=map(lambda fn: os.path.splitext(fn)[0], get_all_synonyms_with_drugchemicalconflated(config)) ) @@ -45,7 +45,7 @@ rule export_synonyms_to_duckdb: input: synonyms_file=config['output_directory'] + "/synonyms/{filename}.txt", output: - duckdb_filename=config['output_directory'] + "/duckdb/parquet/filename={filename}/synonyms.duckdb" + duckdb_filename=config['output_directory'] + "/duckdb/duckdbs/filename={filename}/synonyms.duckdb" run: duckdb_exporters.export_synonyms_to_parquet(input.synonyms_file, output.duckdb_filename)