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Merge branch 'release_16.04' into dev

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This commit is contained in:
Dannon Baker
2016-06-21 14:57:09 -04:00
parent a5cc0081f7 15a4734aed
commit d722dd34af
3 changed files with 14 additions and 8 deletions
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lib/galaxy/webapps/galaxy/api/visualizations.py
+2 -2
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@@ -15,7 +15,7 @@ from galaxy.web import _future_expose_api as expose_api
from galaxy import web
from galaxy import util
from galaxy import exceptions
import json
import logging
log = logging.getLogger( __name__ )
@@ -136,7 +136,7 @@ class VisualizationsController( BaseAPIController, UsesVisualizationMixin, Shara
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
+1 -1
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@@ -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
+11 -5
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@@ -847,11 +847,17 @@ class MoveDirectoryFiles( RecipeStep ):
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">