Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
view data_manager_gene_annotation/data_manager/data_manager.py @ 16:9002c2f64e2a draft
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author | scottx611x |
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date | Wed, 22 Jun 2016 16:35:28 -0400 |
parents | 6261b513ae1b |
children | 6a67977a23da |
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import os import sys import uuid import json import argparse import datetime import requests from requests.exceptions import ContentDecodingError parser = argparse.ArgumentParser(description='Create data manager json.') parser.add_argument('--out', dest='output', action='store', help='JSON filename', default="gene_annotation.json" ) parser.add_argument('--name', dest='name', action='store', default=uuid.uuid4(), help='Data table entry unique ID' ) parser.add_argument('--url', dest='url', action='store', help='Download URL' ) args = parser.parse_args() def url_download(url, name, workdir): response = requests.get(url=url, stream=True) # Create path that we will write the file to file_path = 'download_{}.dat'.format(name) block_size = 10 * 1024 * 1024 # 10MB chunked download with open(file_path, 'w+') as f: try: for buf in response.iter_content(block_size): f.write(buf) except (ContentDecodingError, IOError) as e: sys.stderr.write("Error occured downloading reference file: %s" % e) os.remove(file_path) return file_path def main(args): workdir = os.path.join(os.getcwd(), 'gene_annotation') # Attempt to download gene annotation file from given url gene_annotation_file_path = url_download("http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf", args.name, workdir) # Update Data Manager Json and write out data_manager_entry = { 'data_tables': { 'gene_annotation': { 'date': str(datetime.datetime.now()), 'dbkey': str(args.name), 'name': str(args.name), } } } with open(os.path.join(workdir, args.output), "w+") as f: f.write(json.dumps(data_manager_entry)) if __name__ == '__main__': main(args)