1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4971f90034e8/
changeset: 4971f90034e8
user: inithello
date: 2012-12-20 22:33:19
summary: Fix server error when attempting to install a repository that has already been installed.
affected #: 2 files
diff -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 -r 4971f90034e88ff9397adcc2cf406d20f09c2714 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -223,6 +223,7 @@
message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's "
message += "<b>Repository Actions</b> pop-up menu. "
if len( repo_info_dicts ) == 1:
+ created_or_updated_tool_shed_repositories.append( installed_tool_shed_repository )
return created_or_updated_tool_shed_repositories, all_repo_info_dicts, filtered_repo_info_dicts, message
else:
# A tool shed repository is being installed into a Galaxy instance for the first time. We may have the case where a repository
diff -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 -r 4971f90034e88ff9397adcc2cf406d20f09c2714 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1138,6 +1138,7 @@
created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \
shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False )
if message and len( repo_info_dicts ) == 1:
+ installed_tool_shed_repository = created_or_updated_tool_shed_repositories[ 0 ]
message+= 'Click <a href="%s">here</a> to manage the repository. ' % \
( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( installed_tool_shed_repository.id ) ) )
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/3c4600ee9bdf/
changeset: 3c4600ee9bdf
user: carlfeberhard
date: 2012-12-20 21:20:42
summary: functional tests, tags: fix test_005_add_tag_to_history to check for tag using get_tagging_elt_async; twilltestcase: add get_tags (get_tagging_elt_async)
affected #: 2 files
diff -r 5d4372b6e2855a69758716fc20440071d3f19fbf -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 test/base/twilltestcase.py
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -2474,3 +2474,6 @@
def add_tag( self, item_id, item_class, context, new_tag ):
self.visit_url( "%s/tag/add_tag_async?item_id=%s&item_class=%s&context=%s&new_tag=%s" % \
( self.url, item_id, item_class, context, new_tag ) )
+ def get_tags( self, item_id, item_class ):
+ self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" % \
+ ( self.url, item_id, item_class ) )
diff -r 5d4372b6e2855a69758716fc20440071d3f19fbf -r 3c4600ee9bdf65737f3c9e2bb77d6749102b98a3 test/functional/test_tags.py
--- a/test/functional/test_tags.py
+++ b/test/functional/test_tags.py
@@ -33,6 +33,7 @@
assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database'
global admin_user_private_role
admin_user_private_role = get_private_role( admin_user )
+
def test_005_add_tag_to_history( self ):
"""Testing adding a tag to a history"""
# Logged in as admin_user
@@ -45,7 +46,9 @@
'History',
'history.mako',
'hello' )
- self.check_history_for_string( 'tags : {"hello"' )
+ self.get_tags( self.security.encode_id( history1.id ), 'History' )
+ self.check_page_for_string( 'tags : {"hello": ""}' )
+
def test_010_add_tag_to_history_item( self ):
"""Testing adding a tag to a history item"""
# Logged in as admin_user
@@ -56,6 +59,7 @@
'edit_attributes.mako',
'goodbye' )
self.check_hda_attribute_info( 'tags : {"goodbye"' )
+
def test_999_reset_data_for_later_test_runs( self ):
"""Reseting data to enable later test runs to to be valid"""
# logged in as admin_user
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/276c47b70c28/
changeset: 276c47b70c28
user: carlfeberhard
date: 2012-12-20 19:42:45
summary: expose_api: add Cache-Control response headers to prevent some browsers from caching api calls
affected #: 1 file
diff -r 1073bded37116da144e4e292462346fb7b035bca -r 276c47b70c285fe9bee6aef86e65ca9463b661ae lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -155,6 +155,8 @@
error_message = 'Your request did not appear to be valid JSON, please consult the API documentation'
return error
trans.response.set_content_type( "application/json" )
+ # send 'do not cache' headers to handle IE's caching of ajax get responses
+ trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store"
# Perform api_run_as processing, possibly changing identity
if 'payload' in kwargs and 'run_as' in kwargs['payload']:
if not trans.user_can_do_run_as():
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/a53fe9c93956/
changeset: a53fe9c93956
user: carlfeberhard
date: 2012-12-20 18:25:09
summary: base-mvc: fix to handle IE console methods being objects; history panel: handle workflow hide on finish using state:ready event
affected #: 3 files
diff -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 -r a53fe9c9395621e0c9376ee7109274612f735cb9 static/scripts/mvc/base-mvc.js
--- a/static/scripts/mvc/base-mvc.js
+++ b/static/scripts/mvc/base-mvc.js
@@ -78,7 +78,11 @@
*/
log : function(){
if( this.logger ){
- return this.logger.log.apply( this.logger, arguments );
+ var log = this.logger.log;
+ if( typeof this.logger.log == 'object' ){
+ log = Function.prototype.bind.call( this.logger.log, this.logger );
+ }
+ return log.apply( this.logger, arguments );
}
return undefined;
}
diff -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 -r a53fe9c9395621e0c9376ee7109274612f735cb9 static/scripts/mvc/dataset/hda-model.js
--- a/static/scripts/mvc/dataset/hda-model.js
+++ b/static/scripts/mvc/dataset/hda-model.js
@@ -82,7 +82,7 @@
this.on( 'change:state', function( currModel, newState ){
this.log( this + ' has changed state:', currModel, newState );
if( this.inReadyState() ){
- this.trigger( 'state:ready', this.get( 'id' ), newState, this.previous( 'state' ), currModel );
+ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) );
}
});
diff -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 -r a53fe9c9395621e0c9376ee7109274612f735cb9 static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -5,55 +5,6 @@
Backbone.js implementation of history panel
TODO:
- refactoring on for_editing:
- uhoh: purge link in warning message in history_common.mako conditional on trans.app.config.allow_user_dataset_purge
- bug: rerun still doesn't take encoded ids
-
- anon user, mako template init:
- BUG: shouldn't have tag/anno buttons (on hdas)
- Check for user in hdaView somehow
-
- logged in, mako template:
- bug: rename not being changed locally - render() shows old name, refresh: new name
- TODO: editable text to MV, might also just use REST.update on history
- BUG: meter is not updating RELIABLY on change:nice_size
- BUG: am able to start upload even if over quota - 'runs' forever
- bug: quotaMeter bar rendering square in chrome
-
- from loadFromApi:
-
- fixed:
- BUG: not loading deleted datasets
- FIXED: history_contents, show: state_ids returns all ids now (incl. deleted)
- BUG: upload, history size, doesn't change
- FIXED: using change:nice_size to trigger re-render of history size
- BUG: delete uploading hda - now in state 'discarded'! ...new state to handle
- FIXED: handled state
- BUG: historyItem, error'd ds show display, download?
- FIXED: removed
- bug: loading hdas (alt_hist)
- FIXED: added anon user api request ( trans.user == None and trans.history.id == requested id )
- bug: quota meter not updating on upload/tool run
- FIXED: quotaMeter now listens for 'state:ready' from glx_history in alternate_history.mako
- bug: use of new HDACollection with event listener in init doesn't die...keeps reporting
- FIXED: change getVisible to return an array
- BUG: history, broken intial hist state (running, updater, etc.)
- ??: doesn't seem to happen anymore
- BUG: collapse all should remove all expanded from storage
- FIXED: hideAllItemBodies now resets storage.expandedItems
- BUG: historyItem, shouldn't allow tag, annotate, peek on purged datasets
- FIXED: ok state now shows only: info, rerun
- BUG: history?, some ids aren't returning encoded...
- FIXED:???
- BUG: history, showing deleted ds
- FIXED
- UGH: historyItems have to be decorated with history_ids (api/histories/:history_id/contents/:id)
- FIXED by adding history_id to history_contents.show
- BUG: history, if hist has err'd ds, hist has perm state 'error', updater on following ds's doesn't run
- FIXED by reordering history state from ds' states here and histories
- BUG: history, broken annotation on reload (can't get thru api (sets fine, tho))
- FIXED: get thru api for now
-
replication:
show_deleted/hidden:
use storage
@@ -61,9 +12,6 @@
need urls
change template
move histview fadein/out in render to app?
- don't draw body until it's first expand event
- localize all
- ?: render url templates on init or render?
?: history, annotation won't accept unicode
RESTful:
@@ -167,13 +115,11 @@
//TODO??: purged
//TODO??: could be more selective here
this.model.hdas.bind( 'change:deleted', this.handleHdaDeletionChange, this );
- this.model.hdas.bind( 'change:hidden', this.render, this );
// if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state,
// then: remove it from the collection if the panel is set to NOT show hidden datasets
- this.model.hdas.bind( 'change:state', function( hda, newState, changedList ){
- if( ( hda.inReadyState() )
- && ( !hda.get( 'visible' ) )
+ this.model.hdas.bind( 'state:ready', function( hda, newState, oldState ){
+ if( ( !hda.get( 'visible' ) )
&& ( !this.storage.get( 'show_hidden' ) ) ){
this.removeHdaView( hda.get( 'id' ) );
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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