Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
diff data_manager/data_manager.py @ 46:9346d2955707 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
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date | Tue, 04 Apr 2017 18:07:39 -0400 |
parents | |
children | 3a02b8ab423a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager.py Tue Apr 04 18:07:39 2017 -0400 @@ -0,0 +1,74 @@ +import argparse +import datetime +import json +import os +import sys +import uuid + +import requests +from requests.exceptions import ContentDecodingError + + +def url_download(url): + """Attempt to download gene annotation file from a given url + :param url: full url to gene annotation file + :type url: str. + :returns: name of downloaded gene annotation file + :raises: ContentDecodingError, IOError + """ + response = requests.get(url=url, stream=True) + + # Generate file_name + file_name = response.url.split("/")[-1] + + block_size = 10 * 1024 * 1024 # 10MB chunked download + with open(file_name, 'w+') as f: + try: + # Good to note here that requests' iter_content() will + # automatically handle decoding "gzip" and "deflate" encoding + # formats + 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_name) + + return file_name + + +def main(): + parser = argparse.ArgumentParser(description='Create data manager JSON.') + parser.add_argument('--out', dest='output', action='store', + help='JSON filename') + 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='Url to download gtf file from') + + args = parser.parse_args() + + work_dir = os.getcwd() + + # Attempt to download gene annotation file from given url + gene_annotation_file_name = url_download(args.url) + + # Update Data Manager JSON and write to file + data_manager_entry = { + 'data_tables': { + 'gff_gene_annotations': { + 'value': str(datetime.datetime.now()), + 'dbkey': str(args.name), + 'name': gene_annotation_file_name, + 'path': os.path.join(work_dir, gene_annotation_file_name) + } + } + } + + with open(os.path.join(args.output), "w+") as f: + f.write(json.dumps(data_manager_entry)) + + +if __name__ == '__main__': + main()