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Improve the database I/O: properly check for existing results #8

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Improve the database I/O: properly check for existing results #8

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33 changes: 21 additions & 12 deletions src/database.py
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Original file line number Diff line number Diff line change
@@ -1,16 +1,14 @@
import argparse
import logging
from pathlib import Path
import sys

import bilby
import pandas as pd
import tqdm

logging.basicConfig(
level=logging.INFO,
datefmt="%H:%M",
format="%(asctime)s %(levelname)-2s: %(message)s",
)

logger = bilby.core.utils.logger
logger.name = "kb"


def main():
Expand All @@ -31,30 +29,36 @@ def main():
database_file = directory.joinpath(args.filename)
if args.clean is False and database_file.exists():
df = pd.read_hdf(database_file, "kb_database")
logging.info(f"Read in database with {len(df)} records")
logger.info(f"Read in database with {len(df)} records")
else:
cols = ["filename", "pulse_number", "n_shapelets", "base_flux_n_polynomial"]
logging.info("Creating new database")
logger.info("Creating new database")
df = pd.DataFrame(columns=cols)

filenames = list(directory.glob("**/*result.json"))
if len(filenames) == 0:
raise ValueError("No results found to create/or add to database")
else:
logger.info(f"Found {len(filenames)} files to add to the database")

# Get all filenames not already in the database
filenames_to_read = []
for filename in filenames:
if filename not in df.filename:
if str(filename) not in df.filename.values:
filenames_to_read.append(filename)

logging.info(f"Adding {len(filenames_to_read)} files to the database")
if len(filenames_to_read) == 0:
logger.info("No new results to add to the database, exiting")
sys.exit()

logger.info(f"Adding {len(filenames_to_read)} files to the database")
for ff in tqdm.tqdm(filenames_to_read):
result = bilby.core.result.read_in_result(ff)
data = dict(
filename=str(ff),
data_file=result.meta_data["args"]["data_file"],
pulse_number=result.meta_data["args"]["pulse_number"],
n_shapelets=result.meta_data["args"]["n_shapelets"],
n_shapelets=str(result.meta_data["args"]["n_shapelets"]),
base_flux_n_polynomial=result.meta_data["args"]["base_flux_n_polynomial"],
maxl_normaltest_pvalue=result.meta_data["maxl_normaltest_pvalue"],
log_evidence=result.log_evidence,
Expand All @@ -74,7 +78,12 @@ def main():
series = pd.Series(data, name=result.label)
df = df.append(series)

df.to_hdf(database_file, "kb_database")
df["pulse_number"] = df["pulse_number"].map(int)
df["data_file"] = df["data_file"].map(str)
df["n_shapelets"] = df["n_shapelets"].map(str)
df["base_flux_n_polynomial"] = df["base_flux_n_polynomial"].map(str)

df.to_hdf(database_file, "kb_database", format="table")


if __name__ == "__main__":
Expand Down