| """Rebuild the DuckDB database the pipeline scripts expect, from released files. |
| |
| DATA_DIR=. uv run python bootstrap.py |
| |
| Creates graph.duckdb in DATA_DIR with three tables: |
| |
| edge_ML_expected_ge5 the 2,709,209 filtered edges (from the Parquet file) |
| nodes_ML the 118,422 node property rows (from the TSV) |
| graph_nodes the 18,494 graph nodes with their contiguous indices |
| |
| The released TSV is already UTF-8: the mixed-encoding repair described in the |
| dataset card was applied before upload, so no fallback decoding is needed here. |
| See provenance/import_nodes.py for the code that performed it. |
| """ |
|
|
| import os |
| import pathlib |
|
|
| import duckdb |
|
|
| DATA_DIR = pathlib.Path(os.environ.get( |
| "DATA_DIR", str(pathlib.Path(__file__).resolve().parent))) |
| DB = DATA_DIR / "graph.duckdb" |
| PARQUET = DATA_DIR / "data" / "edge_ML_expected_ge5.parquet" |
| NODES = DATA_DIR / "data" / "nodes_ML_utf8.tsv" |
|
|
| NODE_COLUMNS = ["id", "factor", "Study", "Analytics", "factor1", "factor2", |
| "factor1_org", "factor2_org", "species", "color_group", |
| "color_group_upper1", "color_group_upper2"] |
|
|
| for path in (PARQUET, NODES): |
| if not path.exists(): |
| raise SystemExit(f"missing {path} — download the data/ directory first") |
|
|
| con = duckdb.connect(str(DB)) |
| cols = "{" + ", ".join(f"'{c}': 'VARCHAR'" for c in NODE_COLUMNS) + "}" |
|
|
| con.execute(f""" |
| CREATE OR REPLACE TABLE edge_ML_expected_ge5 AS |
| SELECT * FROM '{PARQUET}' |
| """) |
|
|
| con.execute(f""" |
| CREATE OR REPLACE TABLE nodes_ML AS |
| SELECT * FROM read_csv('{NODES}', delim = '\t', header = false, |
| quote = '', escape = '', columns = {cols}) |
| """) |
|
|
| |
| |
| con.execute(""" |
| CREATE OR REPLACE TABLE graph_nodes AS |
| SELECT id, (row_number() OVER (ORDER BY id) - 1)::BIGINT AS idx |
| FROM ( |
| SELECT DISTINCT id FROM ( |
| SELECT start_id AS id FROM edge_ML_expected_ge5 |
| UNION ALL |
| SELECT end_id FROM edge_ML_expected_ge5 |
| ) |
| ) |
| """) |
|
|
| for table, expected in (("edge_ML_expected_ge5", 2_709_209), |
| ("nodes_ML", 118_422), |
| ("graph_nodes", 18_494)): |
| n = con.execute(f"SELECT count(*) FROM {table}").fetchone()[0] |
| flag = "ok" if n == expected else f"MISMATCH, expected {expected:,}" |
| print(f" {table:<22} {n:>9,} {flag}") |
|
|
| print(f"\nwrote {DB}") |
|
|
