From eb0ff254a59196499e7c714b4fc8d744ef463df9 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 6 Apr 2017 08:37:09 -0400 Subject: [PATCH 1/3] Update to a new Docker test image to fix dependency bugs. Hopefully this will fix tests for #3179. --- run_tests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/run_tests.sh b/run_tests.sh index e17084660b5..6cf42689987 100755 --- a/run_tests.sh +++ b/run_tests.sh @@ -249,7 +249,7 @@ ensure_grunt_for_qunit() { } -DOCKER_DEFAULT_IMAGE='galaxy/testing-base:17.01.0' +DOCKER_DEFAULT_IMAGE='galaxy/testing-base:17.05.0' test_script="./scripts/functional_tests.py" report_file="run_functional_tests.html" From 232e8096925dd7739b98120c172b5cb092192f3e Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 6 Apr 2017 13:52:32 +0100 Subject: [PATCH 2/3] Python3: Use shlex_quote() from six.moves instead of pipes.quote() --- lib/galaxy/tools/wrappers.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py index 7e0631eeff2..72d2fab9be4 100644 --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -1,9 +1,9 @@ import logging import os -import pipes import tempfile from six import string_types +from six.moves import shlex_quote from galaxy import exceptions from galaxy.util import odict @@ -41,7 +41,7 @@ class ToolParameterValueWrapper( object ): """ rval = self.input.value_to_display_text( self.value, self.input.tool.app ) or '' if quote: - return pipes.quote( rval ) or "''" # pipes.quote in Python < 2.7 returns an empty string instead of the expected quoted empty string + return shlex_quote( rval ) return rval From 334f4d7a19882ad97aec75f50b61fda5eb807974 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 6 Apr 2017 13:31:47 -0400 Subject: [PATCH 3/3] Remove old, unused search controller. This would be implemented as a clientside route if we ever pursued development. --- lib/galaxy/webapps/galaxy/buildapp.py | 1 - .../webapps/galaxy/controllers/search.py | 20 ------------------- 2 files changed, 21 deletions(-) delete mode 100644 lib/galaxy/webapps/galaxy/controllers/search.py diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index c20c7541cb0..6bc157dd43a 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -98,7 +98,6 @@ def paste_app_factory( global_conf, **kwargs ): webapp.add_route( '/u/{username}/w/{slug}', controller='workflow', action='display_by_username_and_slug' ) webapp.add_route( '/u/{username}/w/{slug}/{format}', controller='workflow', action='display_by_username_and_slug' ) webapp.add_route( '/u/{username}/v/{slug}', controller='visualization', action='display_by_username_and_slug' ) - webapp.add_route( '/search', controller='search', action='index' ) # TODO: Refactor above routes into external method to allow testing in # isolation as well. diff --git a/lib/galaxy/webapps/galaxy/controllers/search.py b/lib/galaxy/webapps/galaxy/controllers/search.py deleted file mode 100644 index 9fde39e366c..00000000000 --- a/lib/galaxy/webapps/galaxy/controllers/search.py +++ /dev/null @@ -1,20 +0,0 @@ -""" -Contains a basic search interface for Galaxy -""" -import logging - -from galaxy import web -from galaxy.web.base.controller import BaseUIController - -log = logging.getLogger( __name__ ) - - -class SearchController( BaseUIController ): - - @web.expose - def index(self, trans): - """ - Per the message, this is not ready for human consumption, yet. Power - users can still use the search API. - """ - return trans.show_message("Sorry, the search interface isn't quite ready for use, yet. Watch the release notes and check back later!")