Move export_history.py script into lib/galaxy/tools/imp_exp so that it's simpler to execute.

export_history.sh

@@ -1,4 +0,0 @@
-#!/bin/sh
-
-cd `dirname $0`
-python ./scripts/export_history.py $@

lib/galaxy/tools/actions/history_imp_exp.py

@@ -54,9 +54,6 @@ class ExportHistoryToolAction( ToolAction ):
         job_wrapper = JobExportHistoryArchiveWrapper( job )
         cmd_line = job_wrapper.setup_job( trans, jeha, include_hidden=incoming[ 'include_hidden' ], \
                                             include_deleted=incoming[ 'include_deleted' ] )
-                                            
-        # Save jeha.
-        trans.sa_session.flush()
         
         #
         # Add parameters to job_parameter table.

lib/galaxy/tools/imp_exp/__init__.py

@@ -199,9 +199,10 @@ class JobExportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ):
         options = ""
         if jeha.compressed:
             options = "-G"
-        return "%s %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ), "export_history.sh" ), \
-                                       options, history_attrs_filename, datasets_attrs_filename, \
-                                       jobs_attrs_filename, jeha.dataset.file_name )
+        return "python %s %s %s %s %s %s" % ( 
+            os.path.join( os.path.abspath( os.getcwd() ), "lib/galaxy/tools/imp_exp/export_history.py" ), \
+            options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename, \
+            jeha.dataset.file_name )
                                     
     def cleanup_after_job( self, db_session ):
         """ Remove temporary directory and attribute files generated during setup for this job. """

lib/galaxy/tools/imp_exp/export_history.py

@@ -2,20 +2,13 @@
 """
 Export a history to an archive file using attribute files.
 
-NOTE: This should not be called directly. Use the set_metadata.sh script in Galaxy's
-top level directly.
-
 usage: %prog history_attrs dataset_attrs job_attrs out_file
     -G, --gzip: gzip archive file
-    -D, --delete_dir: delete attribute files' directory if operation completed successfully
 """
+
 from galaxy import eggs
-import os, pkg_resources, tempfile, tarfile
-pkg_resources.require( "bx-python" )
-import sys, traceback, fileinput
 from galaxy.util.json import *
-from warnings import warn
-from bx.cookbook import doc_optparse
+import optparse, sys, os, tempfile, tarfile
 
 def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ):
     """ Create archive from the given attribute/metadata files and save it to out_file. """
@@ -63,17 +56,15 @@ def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, ou
         # Status.
         return 'Created history archive.'
     except Exception, e:
-        return 'Error creating history archive: %s' + str( e ), sys.stderr
+        return 'Error creating history archive: %s' % str( e ), sys.stderr
 
 if __name__ == "__main__":
     # Parse command line.
-    options, args = doc_optparse.parse( __doc__ )
-    try:
-        gzip = bool( options.gzip )
-        delete_dir = bool( options.delete_dir )
-        history_attrs, dataset_attrs, job_attrs, out_file = args
-    except:
-        doc_optparse.exception()
+    parser = optparse.OptionParser()
+    parser.add_option( '-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.' )
+    (options, args) = parser.parse_args()    
+    gzip = bool( options.gzip )
+    history_attrs, dataset_attrs, job_attrs, out_file = args
     
     # Create archive.
     status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip )