From 709d2e1292e617504cf5ab0470c8ea5ffc0491e7 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 26 Mar 2008 20:55:18 +0000
Subject: [PATCH] Fix for get_microbial_data tool.

---
 tools/data_source/microbial_import.py      | 2 +-
 tools/data_source/microbial_import_code.py | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/tools/data_source/microbial_import.py b/tools/data_source/microbial_import.py
index f540a94e4e6..faddf729c79 100644
--- a/tools/data_source/microbial_import.py
+++ b/tools/data_source/microbial_import.py
@@ -24,7 +24,7 @@ while have_none:
 #create dictionary keyed by uid of tuples of (displayName,filePath,build) for all files
 available_files = {}
 try:
-    filename = sys.argv[9]
+    filename = sys.argv[-1]
     for i, line in enumerate( file( filename ) ):
         if not line or line[0:1] == "#" : continue
         fields = line.split('\t')
diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py
index 431b4c5b317..ab784a4487d 100644
--- a/tools/data_source/microbial_import_code.py
+++ b/tools/data_source/microbial_import_code.py
@@ -1,12 +1,12 @@
 
-def load_microbial_data( GALAXY_INDEX_DATA_DIR, sep='\t' ):
+def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
     # FIXME: this function is duplicated in the DynamicOptions class.  It is used here only to
     # set data.name in exec_after_process(). 
     microbe_info= {}
     orgs = {}
     
     filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR
-    for i, line in enumerate( file( filename ) ):
+    for i, line in enumerate( open( filename ) ):
         line = line.rstrip( '\r\n' )
         if line and not line.startswith( '#' ):
             fields = line.split( sep )
@@ -96,7 +96,8 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
     if not (kingdom or org):
         print "Parameters are not available."
     
-    microbe_info = load_microbial_data( param_dict.get( 'GALAXY_INDEX_DATA_DIR' ), sep='\t' )
+    GALAXY_DATA_INDEX_DIR = app.config.tool_data_path
+    microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' )
     new_stdout = ""
     split_stdout = stdout.split("\n")
     basic_name = ""