merging heads

lib/galaxy/web/framework/__init__.py

@@ -105,6 +105,8 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         self.app = app
         self.webapp = webapp
         self.security = webapp.security
+        # FIXME: the following 3 attributes are not currently used
+        #        Remove them if they are not going to be...
         self.__user = NOT_SET
         self.__history = NOT_SET
         self.__galaxy_session = NOT_SET
@@ -178,9 +180,17 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         Support for universe_session and universe_user cookies has been
         removed as of 31 Oct 2008.
         """
+        #log.debug("####In __ensure_valid_session...")
+        #try:
+        #    log.debug("####In __ensure_valid_session, self.galaxy_session: %s" % str( self.galaxy_session ) )
+        #    log.debug("####In __ensure_valid_session, self.galaxy_session.is_valid: %s" % str(self.galaxy_session.is_valid))
+        #except:
+        #    log.debug("####In __ensure_valid_session, self.galaxy_session does not yet exist...")
         sa_session = self.sa_session
         # Try to load an existing session
+        #log.debug("###In __ensure_valid_session, before secure_id = self.get_cookie( name='galaxysession' )...")
         secure_id = self.get_cookie( name='galaxysession' )
+        #log.debug("###In __ensure_valid_session, secure_id: %s" % str( secure_id) )
         galaxy_session = None
         prev_galaxy_session = None
         user_for_new_session = None
@@ -191,8 +201,10 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         if secure_id:
             # Decode the cookie value to get the session_key
             session_key = self.security.decode_session_key( secure_id )
+            #log.debug("###In __ensure_valid_session, session_key: %s" % str( session_key) )
             # Retrive the galaxy_session id via the unique session_key
             galaxy_session = sa_session.query( self.app.model.GalaxySession ).filter_by( session_key=session_key, is_valid=True ).first()
+            #log.debug("###In __ensure_valid_session, galaxy_session: %s" % str( galaxy_session) )
         # If remote user is in use it can invalidate the session, so we need to
         # to check some things now.
         if self.app.config.use_remote_user:
@@ -248,6 +260,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         
         Caller is responsible for flushing the returned session.
         """
+        #log.debug("###In __create_new_session...")
         session_key = self.security.get_new_session_key()
         galaxy_session = self.app.model.GalaxySession(
             session_key=session_key,

test/functional/__init__.py

@@ -24,7 +24,7 @@ log = logging.getLogger( __name__ )
 #       server (for running the tests against a running instance)
 
 default_galaxy_test_host = "localhost"
-default_galaxy_test_port = "9999"
+default_galaxy_test_port = "9879"
 galaxy_test_file_dir = "test-data"
 server = None
 app = None

tools/data_source/gbrowse_datasource.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+#Retreives data from GMOD and stores in a file. GBrowse parameters are provided in the input/output file.
+import urllib, sys, os, gzip, tempfile, shutil
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    filename = sys.argv[1]
+    params = {}
+    
+    for line in open( filename, 'r' ):
+        try:
+            line = line.strip()
+            fields = line.split( '\t' )
+            params[ fields[0] ] = fields[1]
+        except:
+            continue
+    
+    URL = params.get( 'URL', None )
+    if not URL:
+        open( filename, 'w' ).write( "" )
+        stop_err( 'Datasource has not sent back a URL parameter.' )
+
+    for i, param in enumerate( params.keys() ):
+        if i == 0:
+            sep = '?'
+        else:
+            sep = '&'
+        if param != '__collected_datasets__':
+            URL += "%s%s=%s" % ( sep, param, params.get( param ) )
+
+    CHUNK_SIZE = 2**20 # 1Mb 
+    try:
+        page = urllib.urlopen( URL )
+    except Exception, exc:
+        raise Exception( 'Problems connecting to %s (%s)' % ( URL, exc ) )
+        sys.exit( 1 )
+    
+    fp = open( filename, 'wb' )
+    while 1:
+        chunk = page.read( CHUNK_SIZE )
+        if not chunk:
+            break
+        fp.write( chunk )
+    fp.close()      
+    
+if __name__ == "__main__": __main__()