changeset 4:577ff220eaea draft default tip

Uploaded

--- a/data_manager/fetch_mlst_data.py	Mon Jul 11 05:40:29 2016 -0400
+++ b/data_manager/fetch_mlst_data.py	Mon Jul 11 06:15:30 2016 -0400
@@ -36,13 +36,8 @@
 from urlparse import urlparse
 import time
 import subprocess
-
-try:
-    from galaxy.util.json import from_json_string, to_json_string
-    has_galaxy = True
-except ImportError:
-    sys.stderr.write("Will download some stuff to the current dir but can't do Galaxy stuff!")
-    has_galaxy = False
+from json import dumps
+from json import loads
 
 # --------------------------------------------------------------------------------------------------
 
@@ -139,12 +134,8 @@
     species_name_underscores = species_info.name.replace(' ', '_')
     timestamp = time.strftime("%Y%m%d%H%M%S")
 
-    params = None
-    if has_galaxy == True:
-        params = from_json_string(open(args.outfile).read())
-        folder = os.path.join(params['output_data'][0]['extra_files_path'], species_name_underscores, timestamp)
-    else:
-        folder = os.path.join(os.path.dirname(os.path.realpath(__file__)), species_name_underscores, timestamp)
+    params = loads(open(args.outfile).read())
+    folder = os.path.join(params['output_data'][0]['extra_files_path'], species_name_underscores, timestamp)
 
     if not os.path.isdir(folder):
         os.makedirs(folder)
@@ -174,18 +165,17 @@
 
 
     # do Galaxy stuff
-    if has_galaxy == True:
-        data_manager_dict = {}
-        data_manager_dict['data_tables'] = {}
-        name = "%s-%s" % (species_info.name, timestamp)
-        data_manager_dict['data_tables']['mlst_data'] = [dict(value=species_name_underscores,
-                                                              dbkey=species_name_underscores,
-                                                              name=name,
-                                                              time_stamp=timestamp,
-                                                              file_path=folder)]
-        #save info to json file
-        with open(args.outfile, 'wb') as fjson:
-            fjson.write(to_json_string(data_manager_dict))
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = {}
+    name = "%s-%s" % (species_info.name, timestamp)
+    data_manager_dict['data_tables']['mlst_data'] = [dict(value=species_name_underscores,
+                                                          dbkey=species_name_underscores,
+                                                          name=name,
+                                                          time_stamp=timestamp,
+                                                          file_path=folder)]
+    #save info to json file
+    with open(args.outfile, 'wb') as fjson:
+        fjson.write(dumps(data_manager_dict))
 
 # end of main --------------------------------------------------------------------------------------