Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
diff data_manager_gene_annotation/data_manager/data_manager.py @ 22:b47ce1c4373e draft
planemo upload
author | scottx611x |
---|---|
date | Thu, 23 Jun 2016 15:11:30 -0400 |
parents | 7662f6a989c9 |
children | cb42506ae8ce |
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--- a/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 14:25:15 2016 -0400 +++ b/data_manager_gene_annotation/data_manager/data_manager.py Thu Jun 23 15:11:30 2016 -0400 @@ -12,7 +12,6 @@ dest='output', action='store', help='JSON filename', - default="gene_annotation.json" ) parser.add_argument('--name', dest='name', @@ -30,10 +29,12 @@ def url_download(url, name): + # Good to note here that requests will automatically handle + # content_encoding types: "gzip" and "deflate" response = requests.get(url=url, stream=True) - # Create path that we will write the file to - file_path = 'download_{}.dat'.format(name) + # Generate file_name + file_path = 'gene_annotation_{}'.format(name) block_size = 10 * 1024 * 1024 # 10MB chunked download with open(file_path, 'w+') as f: @@ -53,11 +54,11 @@ # Attempt to download gene annotation file from given url gene_annotation_file_path = url_download(args.url, args.name) - # Update Data Manager Json and write out + # Update Data Manager JSON and write to file data_manager_entry = { 'data_tables': { 'gene_annotation': { - 'date': str(datetime.datetime.now()), + 'value': str(datetime.datetime.now()), 'dbkey': str(args.name), 'name': str(args.name), 'path': gene_annotation_file_path,