Fix file read sentinel. Use simplejson for python2.5 compatibility in genome index.

lib/galaxy/tools/genome_index/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import with_statement
 
-import os, shutil, logging, tempfile, json, tarfile
+import os, shutil, logging, tempfile, tarfile
 
 from galaxy import model, util
 from galaxy.web.framework.helpers import to_unicode
@@ -9,6 +9,10 @@ from galaxy.util.json import *
 from galaxy.web.base.controller import UsesHistoryMixin
 from galaxy.tools.data import ToolDataTableManager
 
+import pkg_resources
+pkg_resources.require("simplejson")
+import simplejson
+
 log = logging.getLogger(__name__)
 
 def load_genome_index_tools( toolbox ):
@@ -70,7 +74,7 @@ class GenomeIndexToolWrapper( object ):
             fp = open( gitd.dataset.get_file_name(), 'r' )
             deferred = sa_session.query( model.DeferredJob ).filter_by( id=gitd.deferred_job_id ).first()
             try:
-                logloc = json.load( fp )
+                logloc = simplejson.load( fp )
             except ValueError:
                 deferred.state = app.model.DeferredJob.states.ERROR
                 sa_session.add( deferred )
@@ -211,7 +215,7 @@ class GenomeIndexToolWrapper( object ):
         import hashlib
         md5 = hashlib.md5()
         with open( filename, 'rb' ) as f: 
-            for chunk in iter( lambda: f.read( 8192 ), b'' ): 
+            for chunk in iter( lambda: f.read( 8192 ), '' ):
                  md5.update( chunk )
         return md5.digest()