Merge pull request #5 from Knowledge-Graph-Hub/clean-up

Removed commented code

kg_microbe_merge/merge.py

@@ -101,40 +101,3 @@ def duckdb_merge(
 
     # Tarball all files in a directory
     tarball_files_in_dir(MERGED_DATA_DIR, "merged_kg")
-
-
-# def duckdb_merge(
-#     base_kg_nodes_file, subset_kg_nodes_file, base_kg_edges_file, subset_kg_edges_file
-# ):
-
-#     # Connect to DuckDB
-#     con = duckdb.connect()
-# Merge nodes
-# duckdb_prepare_tables(
-#     con,
-#     base_kg_nodes_file,
-#     subset_kg_nodes_file,
-#     BASE_NODES_TABLE_NAME,
-#     SUBSET_NODES_TABLE_NAME,
-#     NODES_COLUMNS,
-# )
-# merge_kg_nodes,duplicate_nodes = merge_kg_tables(
-#     con, NODES_COLUMNS, BASE_NODES_TABLE_NAME, SUBSET_NODES_TABLE_NAME, "nodes"
-# )
-# write_file(con, NODES_COLUMNS, "merge_kg_nodes.tsv", merge_kg_nodes)
-# write_file(con, NODES_COLUMNS, "duplicate_kg_nodes.tsv", duplicate_nodes)
-
-# # Merge edges
-# duckdb_prepare_tables(
-#     con,
-#     base_kg_edges_file,
-#     subset_kg_edges_file,
-#     BASE_EDGES_TABLE_NAME,
-#     SUBSET_EDGES_TABLE_NAME,
-#     EDGES_COLUMNS,
-# )
-# merge_kg_edges, duplicate_edges = merge_kg_tables(
-#     con, EDGES_COLUMNS, BASE_EDGES_TABLE_NAME, SUBSET_EDGES_TABLE_NAME, "edges"
-# )
-# write_file(con, EDGES_COLUMNS, "merge_kg_edges.tsv", merge_kg_edges)
-# write_file(con, EDGES_COLUMNS, "duplicate_kg_edges.tsv", duplicate_edges)

kg_microbe_merge/run.py

@@ -93,10 +93,6 @@ def download(*args, **kwargs) -> None:
 @click.option("yaml", "-y", type=click.Path(exists=True), required=False)
 @click.option("processes", "-p", default=1, type=int)
 @click.option("--merge-tool", "-m", default="kgx", type=click.Choice(["kgx", "duckdb"]))
-# @click.option("base_nodes", "-base-n", type=click.Path(exists=True), required=False)
-# @click.option("base_edges", "-base-e", type=click.Path(exists=True), required=False)
-# @click.option("subset_nodes", "-subset-n", type=click.Path(exists=True), required=False)
-# @click.option("subset_edges", "-subset-e", type=click.Path(exists=True), required=False)
 @click.option("--data-dir", "-d", type=click.Path(exists=True), default=RAW_DATA_DIR)
 @click.option("--subset-transforms", "-s", multiple=True)
 @click.option("--nodes-batch-size", "-n", type=int, default=100000)
@@ -109,10 +105,6 @@ def merge(
     subset_transforms: tuple,
     nodes_batch_size: int,
     edges_batch_size: int,
-    # base_nodes: str,
-    # base_edges: str,
-    # subset_nodes: str,
-    # subset_edges: str,
 ) -> None:
     """
     Use KGX to load subgraphs to create a merged graph.