From f67cbe72d571f87a87e868161650e5965e681881 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 1 Mar 2016 14:09:22 -0500 Subject: [PATCH 01/19] revert escaping added in a24e206ff7762d5b86d3dc7240190f043dc532b5 that prevented line endings and spaces to be rendered properly --- templates/webapps/tool_shed/repository/view_repository.mako | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/templates/webapps/tool_shed/repository/view_repository.mako b/templates/webapps/tool_shed/repository/view_repository.mako index 5dffa956ede..496c877a510 100644 --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -25,7 +25,7 @@ tip_str = '' sharable_link_label = 'Link to this repository revision:' sharable_link_changeset_revision = changeset_revision - + if heads: multiple_heads = len( heads ) > 1 else: @@ -119,8 +119,7 @@ %if repository.long_description:
-

${repository.long_description|h}

- ## ${render_long_description( to_html_string( repository.long_description ) )} + ${render_long_description( to_html_string( repository.long_description ) )}
%endif %if repository.homepage_url: From 9daf348770bc5ff7576db297bd3f959b8a35d006 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 1 Mar 2016 15:51:58 -0500 Subject: [PATCH 02/19] Basic routing bypass for known client routes, instead of 404ing. --- lib/galaxy/webapps/galaxy/controllers/root.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index b0c950bb96f..c0f2f04b6a2 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -31,8 +31,21 @@ class RootController( controller.JSAppLauncher, UsesAnnotations ): @web.expose def default(self, trans, target1=None, target2=None, **kwd): - """Called on any url that does not match a controller method. """ + Called on any url that does not match a controller method. + """ + # "dumb" option for handling valid clientside routes. + # What else might be in kwd that we'd ever want to handle here? Safest + # to just prune it and return a 'naked' index and let the client handle + # the rest? + # TODO: unified routing file between client/framework specifying what + # the client can/will handle. + cmp_path = trans.request.path.strip('/') + client_handled_paths = ['tours', + 'noop'] # Does nothing, remove me. + for path in client_handled_paths: + if cmp_path.startswith(path): + return self.index( trans ) raise HTTPNotFound( 'This link may not be followed from within Galaxy.' ) def _get_extended_config( self, trans ): From a49401189735daa55e44dec7af6b84a646e8bbc9 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Wed, 2 Mar 2016 11:40:45 -0500 Subject: [PATCH 03/19] Improve dataset error log message --- lib/galaxy/jobs/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index be0577f90ae..688c0ccfc46 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1262,7 +1262,7 @@ class JobWrapper( object ): dataset.extension = 'txt' self.sa_session.add( dataset ) if job.states.ERROR == final_job_state: - log.debug( "setting dataset state to ERROR" ) + log.debug( "(%s) setting dataset %s state to ERROR", job.id, dataset_assoc.dataset.dataset.id ) # TODO: This is where the state is being set to error. Change it! dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR # Pause any dependent jobs (and those jobs' outputs) From 4992684d1fc58d4774e5d6a6c1df9c193218c460 Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Wed, 2 Mar 2016 11:41:20 -0500 Subject: [PATCH 04/19] Hide tools that have been replaced. --- config/tool_conf.xml.main | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/config/tool_conf.xml.main b/config/tool_conf.xml.main index b4db4af7c7a..4575f630f5e 100644 --- a/config/tool_conf.xml.main +++ b/config/tool_conf.xml.main @@ -28,18 +28,18 @@
- +