From 3a9e1571458f931b6d6a268ad628bfac88655df3 Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 21 Jun 2016 09:43:29 -0400 Subject: [PATCH 1/3] Fix saving visualizations --- lib/galaxy/webapps/galaxy/api/visualizations.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py index 7f40a214d1f..8d768c2b4c3 100644 --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -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 } From 41baf5d107b23b1761bfc5f4769f08f7b68c692e Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 21 Jun 2016 10:26:02 -0400 Subject: [PATCH 2/3] Fix library common json loads call --- lib/galaxy/webapps/galaxy/controllers/library_common.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/library_common.py b/lib/galaxy/webapps/galaxy/controllers/library_common.py index 02050585bf6..49cbfcc1790 100644 --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/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' ) From ac902304ae6f64dc9c9f313a12572bcfb7769d06 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 16 Jun 2016 16:10:36 -0400 Subject: [PATCH 3/3] Fix two errors in sff_extract.py detected by flake8 -- either of these code paths would have thrown an exception and failed prior to this. --- tools/filters/sff_extract.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py index 06158434f19..2268442463e 100644 --- a/tools/filters/sff_extract.py +++ b/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 :-)