--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datamanager_create_reference.py	Sun Jan 17 14:11:06 2016 -0500
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+
+import sys
+import os
+import re
+import tempfile
+import subprocess
+import fileinput
+import shutil
+import optparse
+import urllib2
+from ftplib import FTP
+import tarfile
+
+from galaxy.util.json import from_json_string, to_json_string
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+
+def get_config_dict(config,dataset_directory=None):
+    keys = ['dataset_directory','ensembl_organism','ensembl_prefix','ensembl_version','ensembl_genome_version','ucsc_genome_version','ncbi_organism','ncbi_prefix','chromosomes','mt_chromosome','gene_sources','ig_gene_sources','rrna_gene_sources']
+    pat = '^([^=]+?)\s*=\s*(.*)$'
+    config_dict = {}
+    try:
+        fh = open(config)
+        for i,l in enumerate(fh):
+           line = l.strip() 
+           if line.startswith('#'):
+               continue
+           m = re.match(pat,line)
+           if m and len(m.groups()) == 2:
+               (k,v) = m.groups()
+               if k in keys:
+                   config_dict[k] = v
+    except Exception, e:
+        stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
+    else:
+        fh.close()
+    if dataset_directory:
+        config_dict['dataset_directory'] = dataset_directory
+    return config_dict
+
+def run_defuse_script(data_manager_dict, params, target_directory, dbkey, description, config, script):
+    if not os.path.isdir(target_directory):
+        os.makedirs(target_directory)
+    ## Name the config consistently with data_manager_conf.xml
+    #  copy the config file to the target_directory
+    #  when DataManager moves files to there tool-data location, the config will get moved as well,
+    #   and the value_translation in data_manager_conf.xml will tell us the new location
+    #  defuse.xml will use the path to this config file to set the dataset_directory
+    config_name = '%s.config' % dbkey
+    defuse_config = os.path.join( target_directory, config_name)
+    shutil.copyfile(config,defuse_config) 
+    cmd = "/bin/bash %s %s" % (script,target_directory)
+    # Run
+    try:
+        tmp_out = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp_out, 'wb' )
+        tmp_err = tempfile.NamedTemporaryFile().name
+        tmp_stderr = open( tmp_err, 'wb' )
+        proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        # get stderr, allowing for case where it's very large
+        tmp_stderr = open( tmp_err, 'rb' )
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stdout.close()
+        tmp_stderr.close()
+        if returncode != 0:
+            raise Exception, stderr
+
+        # TODO: look for errors in program output.
+    except Exception, e:
+        stop_err( 'Error creating defuse reference:\n' + str( e ) )
+    config_dict = get_config_dict(config, dataset_directory=target_directory)
+    data_table_entry = dict(value=dbkey, dbkey=dbkey, name=description, path=config_name)
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+def _add_data_table_entry( data_manager_dict, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables']['defuse_reference'] = data_manager_dict['data_tables'].get( 'defuse_reference', [] )
+    data_manager_dict['data_tables']['defuse_reference'].append( data_table_entry )
+    return data_manager_dict
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-k', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='dbkey' )
+    parser.add_option( '-d', '--description', dest='description', action='store', type="string", default=None, help='description' )
+    parser.add_option( '-c', '--defuse_config', dest='defuse_config', action='store', type="string", default=None, help='defuse_config' )
+    parser.add_option( '-s', '--defuse_script', dest='defuse_script', action='store', type="string", default=None, help='defuse_script' )
+    (options, args) = parser.parse_args()
+
+    filename = args[0]
+
+    params = from_json_string( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+
+     
+    #Create Defuse Reference Data
+    run_defuse_script( data_manager_dict, params, target_directory, options.dbkey, options.description,options.defuse_config,options.defuse_script)
+
+    #save info to json file
+    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+
+if __name__ == "__main__": main()
+