Mercurial > repos > sh477 > data_manager_vep_cache_downloader
view data_manager/data_manager_vep_cache_download.py @ 7:7890790d2afd draft
Fully working now and improved several things
author | sh477 |
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date | Tue, 01 Mar 2022 18:12:26 +0000 |
parents | a3dba0440f08 |
children |
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#!/usr/bin/env python import datetime import json import os import re from urllib.request import urlretrieve import sys import tarfile def main(): # Read in given out_file and create target directory for file download with open(sys.argv[1]) as fh: params = json.load(fh) target_directory = params['output_data'][0]['extra_files_path'] os.mkdir(target_directory) # Process parameters for metadata and file download url = params['param_dict']['url'].rstrip("/") + "/" + params['param_dict']['file_name'].lstrip("/") m = re.search(r"(.*?)(merged|refseq)?_vep_(\d+?)_", params['param_dict']['file_name']) version = str(m.group(3)) cache_type = m.group(2) if m.group(2) else "default" species = m.group(1).rstrip("_") display_name = f"{species.capitalize().replace('_', ' ')} {params['param_dict']['dbkey']} (V{version}{'' if cache_type == 'default' else ', ' + cache_type.capitalize()})" # Download and extract given cache archive, remove archive afterwards final_file, headers = urlretrieve(url, os.path.join(target_directory, params['param_dict']['file_name'])) tar = tarfile.open(final_file, "r:gz") tar.extractall(target_directory) tar.close() os.remove(final_file) # Construct metadata for the new data table entry data_manager_dict = { 'data_tables': { 'vep_versioned_annotation_cache': [ { 'value': params['param_dict']['file_name'].strip(".tar.gz"), 'dbkey': params['param_dict']['dbkey'], 'version': version, 'cachetype': cache_type, 'name': display_name, 'species': species, 'path': './%s' % params['param_dict']['file_name'].strip(".tar.gz") } ] } } # Save metadata to out_file with open(sys.argv[1], 'w') as fh: json.dump(data_manager_dict, fh, sort_keys=True) if __name__ == "__main__": main()