| Previous changeset 41:2dbaaa6e8344 (2016-07-08) Next changeset 43:e42284a13168 (2016-07-08) |
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Commit message:
planemo upload |
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modified:
data_manager_gene_annotation/data_manager/data_manager.py |
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| diff -r 2dbaaa6e8344 -r bf05cda04e1f data_manager_gene_annotation/data_manager/data_manager.py --- a/data_manager_gene_annotation/data_manager/data_manager.py Fri Jul 08 11:47:55 2016 -0400 +++ b/data_manager_gene_annotation/data_manager/data_manager.py Fri Jul 08 14:33:30 2016 -0400 |
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| @@ -1,6 +1,5 @@ import os import sys -import uuid import json import argparse import requests @@ -42,7 +41,7 @@ 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' + default=None, help='Data table entry unique ID' ) parser.add_argument('--url', dest='url', action='store', help='Url to download gtf file from') @@ -54,13 +53,18 @@ # Attempt to download gene annotation file from given url gene_annotation_file_name = url_download(args.url) + name = str(args.name) + + if not name: + name = gene_annotation_file_name.split(".")[0] + # Update Data Manager JSON and write to file data_manager_entry = { 'data_tables': { 'gene_annotation': { - 'value': gene_annotation_file_name, + 'value': gene_annotation_file_name.split(".")[0], 'dbkey': gene_annotation_file_name.split(".")[0], - 'name': str(args.name), + 'name': name, 'path': os.path.join(work_dir, gene_annotation_file_name) } } |