diff --git a/data_managers/data_manager_omamer/data_manager/macros.xml b/data_managers/data_manager_omamer/data_manager/macros.xml deleted file mode 100644 index 0ae6f5e06cf..00000000000 --- a/data_managers/data_manager_omamer/data_manager/macros.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - 2.0.2 - 2 - - - - python - requests - - - diff --git a/data_managers/data_manager_omamer/data_manager/omamer.py b/data_managers/data_manager_omamer/data_manager/omamer.py deleted file mode 100644 index c819f0077e1..00000000000 --- a/data_managers/data_manager_omamer/data_manager/omamer.py +++ /dev/null @@ -1,86 +0,0 @@ -#!/usr/bin/env python - -import argparse -import json -import os -import sys - -import requests - -# URL for downloading OMAmer datasets -OMAMER_DATASETS_URL = "https://omabrowser.org/All/{dataset}" - -# List of OMAmer data sets with versions -OMAMER_DATASETS = { - "Primates_v2.0.0": "Primates-v2.0.0.h5", - "Viridiplantae_v2.0.0": "Viridiplantae-v2.0.0.h5", - "Metazoa_v2.0.0": "Metazoa-v2.0.0.h5", - "LUCA_v0.2.5": "LUCA-v0.2.5.h5", - "LUCA_v2.0.0": "LUCA-v2.0.0.h5", - "Saccharomyceta": "Saccharomyceta.h5", - "Homininae": "Homininae.h5", -} - -DEFAULT_OUTPUT_DIR = "database_omamer" - - -def download_file(url, dest): - try: - with requests.get(url, stream=True) as r: - r.raise_for_status() - with open(dest, 'wb') as f: - for chunk in r.iter_content(chunk_size=8192): - f.write(chunk) - print(f"Downloaded: {url} to {dest}") - except requests.exceptions.RequestException as e: - print(f"Error downloading {url}: {e}") - sys.exit(1) - - -def main(args): - - with open(args.json) as fh: - params = json.load(fh) - target_directory = params["output_data"][0]["extra_files_path"] - - # Create output directory if none exists - if not os.path.exists(target_directory): - os.makedirs(target_directory) - - # Check if the selected dataset exists - if args.name not in OMAMER_DATASETS: - print(f"Error: Selected dataset '{args.name}' not found.") - sys.exit(1) - - # Download the selected OMAmer dataset - dataset = OMAMER_DATASETS[args.name] - url = OMAMER_DATASETS_URL.format(dataset=dataset) - base_name = os.path.splitext(dataset)[0] - destination_path = os.path.join(target_directory, dataset) - download_file(url, destination_path) - - data_manager_entry = { - "value": dataset, - "name": base_name, - "version": args.version, - "path": dataset, - } - - # Creates a JSON dictionary representing the Data Manager configuration - data_manager_json = {"data_tables": {"omamer": [data_manager_entry]}} - - # Writes this JSON dictionary to the specified output file - with open(args.json, "w") as fh: - json.dump(data_manager_json, fh, indent=2, sort_keys=True) - - -if __name__ == "__main__": - # Set up argparse to specify expected command line arguments - parser = argparse.ArgumentParser(description='Download data for OMAmer') - parser.add_argument('--name', default='Primates', choices=OMAMER_DATASETS.keys(), help='Select dataset to download') - parser.add_argument('--json', help='Path to JSON file') - parser.add_argument("--version", help="Omamer version") - - args = parser.parse_args() - - main(args) diff --git a/data_managers/data_manager_omamer/data_manager/omamer.xml b/data_managers/data_manager_omamer/data_manager/omamer.xml index 1359137beaf..dace8599178 100644 --- a/data_managers/data_manager_omamer/data_manager/omamer.xml +++ b/data_managers/data_manager_omamer/data_manager/omamer.xml @@ -1,24 +1,48 @@ - - - macros.xml - + + + wget + + + + - - - - - - - - + + + + + + + + + + @@ -28,10 +52,13 @@ - - + + + + +