changeset 6:753ed7c03ea8 draft

Deleted selected files

--- a/data_manager_gene_annotation/data_manager/data_manager.py	Tue Apr 26 12:22:29 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,68 +0,0 @@
-import argparse
-import datetime
-import json
-import os
-import shutil
-import sys
-import tarfile
-import urllib2
-import zipfile
-
-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=str(datetime.date.today()), help='Data table entry unique ID')
-parser.add_argument('--url', dest='url', action='store', help='Download URL', default="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf")
-
-args = parser.parse_args()
-
-def url_download(url, workdir):
-    file_path = os.path.join(workdir, 'download.dat')
-    if not os.path.exists(workdir):
-        os.makedirs(workdir)
-    src = None
-    dst = None
-    try:
-        req = urllib2.Request(url)
-        src = urllib2.urlopen(req)
-        dst = open(file_path, 'wb')
-        while True:
-            chunk = src.read(2**10)
-            if chunk:
-                dst.write(chunk)
-            else:
-                break
-    except Exception, e:
-        print >>sys.stderr, str(e)
-    finally:
-        if src:
-            src.close()
-        if dst:
-            dst.close()
-    if tarfile.is_tarfile(file_path):
-        fh = tarfile.open(file_path, 'r:*')
-    elif zipfile.is_zipfile(file_path):
-        fh = zipfile.ZipFile(file_path, 'r')
-    else:
-        return
-    fh.extractall(workdir)
-    os.remove(file_path)
-
-
-def main(args):
-    workdir = os.path.join(os.getcwd(), 'gene_annotation')
-    url_download(args.url, workdir)
-    data_manager_entry = {}
-    data_manager_entry['value'] = args.name.lower()
-    data_manager_entry['name'] = args.name
-    data_manager_entry['path'] = '.'
-    data_manager_json = dict(data_tables=dict(gene_annotation=data_manager_entry))
-    params = json.loads(open(args.output).read())
-    target_directory = params['output_data'][0]['extra_files_path']
-    os.mkdir(target_directory)
-    output_path = os.path.abspath(os.path.join(os.getcwd(), 'gene_annotation'))
-    for filename in os.listdir(workdir):
-        shutil.move(os.path.join(output_path, filename), target_directory)
-    file(args.output, 'w').write(json.dumps(data_manager_json))
-
-if __name__ == '__main__':
-    main(args)