Merge branch 'release_16.04'

lib/galaxy/webapps/galaxy/api/visualizations.py

@@ -15,7 +15,7 @@
 from galaxy import web
 from galaxy import util
 from galaxy import exceptions
-
+import json
 import logging
 log = logging.getLogger( __name__ )
 
@@ -136,7 +136,7 @@ def update( self, trans, id, payload, **kwargs ):
         latest_config = visualization.latest_revision.config
         if( ( title != visualization.latest_revision.title ) or
                 ( dbkey != visualization.latest_revision.dbkey ) or
-                ( util.json.dumps( config ) != util.json.dumps( latest_config ) ) ):
+                ( json.dumps( config ) != json.dumps( latest_config ) ) ):
             revision = self.add_visualization_revision( trans, visualization, config, title, dbkey )
             rval = { 'id' : id, 'revision' : revision.id }
 

lib/galaxy/webapps/galaxy/controllers/library_common.py

@@ -2751,7 +2751,7 @@ def lucene_search( trans, cntrller, search_term, search_url, **kwd ):
     status = kwd.get( 'status', 'done' )
     full_url = "%s/find?%s" % ( search_url, urllib.urlencode( { "kwd" : search_term } ) )
     response = urllib2.urlopen( full_url )
-    ldda_ids = util.json.loads( response.read() )[ "ids" ]
+    ldda_ids = loads( response.read() )[ "ids" ]
     response.close()
     lddas = [ trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) for ldda_id in ldda_ids ]
     return status, message, get_sorted_accessible_library_items( trans, cntrller, lddas, 'name' )

lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py

@@ -847,11 +847,17 @@ def execute_step( self, tool_dependency, package_name, actions, action_dict, fil
 
     def move_directory_files( self, current_dir, source_dir, destination_dir ):
         source_directory = os.path.abspath( os.path.join( current_dir, source_dir ) )
-        destination_directory = os.path.join( destination_dir )
-        destination_parent_directory = os.path.dirname(destination_directory)
-        if not os.path.isdir( destination_parent_directory ):
-            os.makedirs( destination_parent_directory )
-        shutil.move( source_directory, destination_directory )
+        destination_directory = os.path.abspath(os.path.join(destination_dir))
+        if not os.path.isdir(destination_directory):
+            os.makedirs(destination_directory)
+        for dir_entry in os.listdir(source_directory):
+            source_entry = os.path.join(source_directory, dir_entry)
+            if os.path.islink(source_entry):
+                destination_entry = os.path.join(destination_directory, dir_entry)
+                os.symlink(os.readlink(source_entry), destination_entry)
+                os.remove(source_entry)
+            else:
+                shutil.move(source_entry, destination_directory)
 
     def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
         # <action type="move_directory_files">

tools/filters/sff_extract.py

@@ -231,7 +231,7 @@ def sequences(fileh, header):
     while True:
         if fposition == header['index_offset']:
             # we have to skip the index section
-            fposition += index_length
+            fposition += header['index_length']
             continue
         else:
             bytes_read, seq_data = read_sequence(header=header, fileh=fileh,
@@ -276,7 +276,7 @@ def remove_last_xmltag_in_file(fname, tag=None):
 
     # we check that we're removing the asked tag
     if tag is not None and tag != last_tag:
-        etxt = join('The given xml tag (', tag, ') was not the last one in the file')
+        etxt = 'The given xml tag (%s) was not the last one in the file' % tag
         raise RuntimeError(etxt)
 
     # while we are at it: also remove all white spaces in that line :-)