diff data_manager/vsnp_dnaprints_fetcher.py @ 0:19c6d9c66c75 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vsnp_dnaprints_fetcher.py	Fri May 08 15:25:21 2020 -0400
@@ -0,0 +1,66 @@
+import argparse
+import json
+import os
+import sys
+try:
+    # For Python 3.0 and later
+    from urllib.request import Request, urlopen
+except ImportError:
+    # Fall back to Python 2 imports
+    from urllib2 import Request, urlopen
+
+
+def url_download(url, workdir):
+    file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
+    src = None
+    dst = None
+    try:
+        req = Request(url)
+        src = urlopen(req)
+        with open(file_path, 'wb') as dst:
+            while True:
+                chunk = src.read(2**10)
+                if chunk:
+                    dst.write(chunk)
+                else:
+                    break
+    except Exception as e:
+        sys.exit(str(e))
+    finally:
+        if src:
+            src.close()
+    return file_path
+
+
+def download(dbkey, name, url, out_file):
+
+    with open(out_file) as fh:
+        params = json.loads(fh.read())
+
+    workdir = params['output_data'][0]['extra_files_path']
+    os.makedirs(workdir)
+    file_path = url_download(url, workdir)
+    entry_name = os.path.basename(file_path)
+
+    data_manager_json = {"data_tables": {}}
+    data_manager_entry = {}
+    data_manager_entry['value'] = dbkey
+    data_manager_entry['name'] = entry_name
+    data_manager_entry['path'] = file_path
+    data_manager_entry['description'] = "DNAprints file for %s" % name
+    data_manager_json["data_tables"]["vsnp_dnaprints"] = data_manager_entry
+
+    with open(out_file, 'w') as fh:
+        fh.write(json.dumps(data_manager_json, sort_keys=True))
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--dbkey', dest='dbkey', help='Genome reference dbkey')
+parser.add_argument('--name', dest='name', help='Reference display name')
+parser.add_argument('--url', dest='url', help='URL to download DNAprints file')
+parser.add_argument('--out_file', dest='out_file', help='JSON output file')
+
+args = parser.parse_args()
+
+download(args.dbkey, args.name, args.url, args.out_file)