diff data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.py @ 0:715bc9aeef69 draft

planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.py	Wed Feb 27 09:08:21 2019 -0500
@@ -0,0 +1,47 @@
+import argparse
+import datetime
+import json
+import os
+import shutil
+import sys
+import tarfile
+import urllib.request, urllib.error, urllib.parse
+import zipfile
+from import_data import run, _main
+
+parser = argparse.ArgumentParser(description='Create data manager json.')
+parser.add_argument('--url', dest='url', action='store', help='Url for CARD data')
+parser.add_argument('--out', dest='output', action='store', help='JSON filename')
+parser.add_argument('--name', dest='name', action='store', default='CARD_data-' + str(datetime.datetime.now().strftime('%Y-%B-%d-%H:%M:%S')), help='Data table database name')
+args = parser.parse_args()
+
+print('[rgi_database_builder] Importing...')
+
+_main(args)
+
+def main(args):
+    print('[rgi_database_builder] Building......')
+
+    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(rgi_databases=data_manager_entry))
+
+    params = json.loads(open(args.output,'r').read())
+
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+    output_path = os.path.join(os.getcwd(), 'rgi-database')
+
+    for filename in os.listdir(output_path):
+        print('[rgi_database_builder] move file: {} from {} to {}'.format(filename, output_path, target_directory))
+        shutil.move(os.path.join(output_path, filename), target_directory)
+
+    print(args.output)
+    print('[rgi_database_builder] write file: {}'.format(args.output))
+    open(args.output, 'w').write(json.dumps(data_manager_json))
+
+if __name__ == '__main__':
+    main(args)