Add script to update the paths to tool config files in installed repositories' metadata.

scripts/update_shed_config_path.py

@@ -0,0 +1,80 @@
+import os
+import argparse
+import ConfigParser
+import sys
+new_path = [ os.path.join( os.getcwd(), "lib" ) ]
+new_path.extend( sys.path[1:] )
+sys.path = new_path
+
+import logging
+import galaxy.model.tool_shed_install
+import galaxy.model.tool_shed_install.mapping as mapping
+from galaxy.model.orm import *
+from galaxy import eggs
+eggs.require('sqlalchemy')
+import sqlalchemy
+
+def main( opts, session, model ):
+    '''
+    Find all tool shed repositories with the bad path and update with the correct path.
+    '''
+    for row in session.query( model.ToolShedRepository ).all():
+        if 'shed_config_filename' in row.metadata:
+            if row.metadata['shed_config_filename'] == opts.bad_filename:
+                row.metadata['shed_config_filename'] = opts.good_filename
+                session.add( row )
+                session.flush()
+    return 0
+
+def create_database( config_file ):
+    parser = ConfigParser.SafeConfigParser()
+    parser.read( config_file )
+    # Determine which database connection to use.
+    database_connection = parser.get( 'app:main', 'install_database_connection' )
+    if database_connection is None:
+        database_connection = parser.get( 'app:main', 'database_connection' )
+    if database_connection is None:
+        database_connection = 'sqlite:///%s' % parser.get( 'app:main', 'database_file' )
+    if database_connection is None:
+        print 'Unable to determine correct database connection.'
+        exit(1)
+
+    '''Initialize the database file.'''
+    dialect_to_egg = {
+        "sqlite" : "pysqlite>=2",
+        "postgres" : "psycopg2",
+        "postgresql" : "psycopg2",
+        "mysql" : "MySQL_python"
+    }
+    dialect = ( database_connection.split( ':', 1 ) )[0]
+    try:
+        egg = dialect_to_egg[ dialect ]
+        try:
+            eggs.require( egg )
+            print( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
+        except:
+            # If the module is in the path elsewhere (i.e. non-egg), it'll still load.
+            print( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
+    except KeyError:
+        # Let this go, it could possibly work with db's we don't support.
+        print( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
+
+    # Initialize the database connection.
+    engine = create_engine( database_connection )
+    meta = MetaData( bind=engine )
+    install_session = Session = scoped_session( sessionmaker( bind=engine, autoflush=False, autocommit=True ) )
+    model = mapping.init( database_connection )
+    return install_session, model
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument( '--config_file', dest='config_file', required=True, help="The path to your Galaxy configuration .ini file." )
+    parser.add_argument( '--from', dest='bad_filename', required=True, help="The old, invalid path to the shed_tool_conf.xml or migrated_tools_conf.xml file." )
+    parser.add_argument( '--to', dest='good_filename', required=True, help="The updated path to the shed_tool_conf.xml or migrated_tools_conf.xml file." )
+    parser.add_argument( '--force', dest='force', action='store_true', help="Use this flag to set the new path even if the file does not (yet) exist there." )
+    opts = parser.parse_args()
+    if not os.path.exists( opts.good_filename ) and not opts.force:
+        print 'The file %s does not exist, use the --force option to proceed.' % opts.good_filename
+        exit(1)
+    session, model = create_database( opts.config_file )
+    exit( main( opts, session, model ) )