galaxy-commits April 2014

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261 discussions

commit/galaxy-central: davebgx: Remove stray debug output.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cd73af9c02e7/ Changeset: cd73af9c02e7 User: davebgx Date: 2014-04-16 15:23:09 Summary: Remove stray debug output. Affected #: 1 file diff -r f3c5d9a5ed95956442dbd39e9ce97367cdc0d93b -r cd73af9c02e7f94d76239c010da12fcf1f91d1d4 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -637,7 +637,6 @@ # for the compute server. def metadata_path_on_compute(path): compute_path = path - log.info(compute_tmp_dir) if compute_tmp_dir and tmp_dir and in_directory(path, tmp_dir): path_relative = os.path.relpath(path, tmp_dir) compute_path = os.path.join(compute_tmp_dir, path_relative) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Modify test framework to account for recent UI changes.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3c5d9a5ed95/ Changeset: f3c5d9a5ed95 User: davebgx Date: 2014-04-16 15:18:56 Summary: Modify test framework to account for recent UI changes. Affected #: 2 files diff -r 6f698dec58950f0f56421a13474df0359c0777d7 -r f3c5d9a5ed95956442dbd39e9ce97367cdc0d93b test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -385,12 +385,6 @@ return value == hda[ key ] return False - def clear_history( self ): - """Empties a history of all datasets""" - self.visit_page( "clear_history" ) - self.check_history_for_string( 'Your history is empty' ) - self.home() - def delete_history( self, id ): """Deletes one or more histories""" history_list = self.get_histories_as_data_list() @@ -466,7 +460,8 @@ self.visit_url( "%s/history_new?name=%s" % ( self.url, name ) ) else: self.visit_url( "%s/history_new" % self.url ) - self.check_history_for_string('Your history is empty') + self.check_page_for_string( 'New history created' ) + assert self.is_history_empty(), 'Creating new history did not result in an empty history.' self.home() def rename_history( self, id, old_name, new_name ): diff -r 6f698dec58950f0f56421a13474df0359c0777d7 -r f3c5d9a5ed95956442dbd39e9ce97367cdc0d93b test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -98,7 +98,7 @@ if not historyB.deleted: raise AssertionError( "Problem deleting history id %d" % historyB.id ) # Since we deleted the current history, make sure the history frame was refreshed - self.check_history_for_string( 'Your history is empty.' ) + assert self.is_history_empty(), 'Deleting active history did not result in a new empty history being created.' # We'll now test deleting a list of histories # After deleting the current history, a new one should have been created global history1 @@ -121,7 +121,7 @@ ids = '%s,%s' % ( self.security.encode_id( history1.id ), self.security.encode_id( history2.id ) ) self.delete_history( ids ) # Since we deleted the current history, make sure the history frame was refreshed - self.check_history_for_string( 'Your history is empty.' ) + assert self.is_history_empty(), 'Deleting active history did not result in a new empty history being created.' try: self.view_stored_active_histories( strings_displayed=[ history1.name ] ) raise AssertionError( "History %s is displayed in the active history list after it was deleted" % history1.name ) @@ -790,7 +790,7 @@ self.check_page_for_string( 'hg15' ) self.assertEqual( len( self.get_history_as_data_list() ), 1 ) # Delete the history item - self.delete_history_item( str( latest_hda.id ), strings_displayed=[ "Your history is empty" ] ) + self.delete_history_item( str( latest_hda.id ), strings_displayed=[] ) self.assertEqual( len( self.get_history_as_data_list() ), 0 ) # Try deleting an invalid hid try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Client App: factor out config serializer, move defensive programming
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6f698dec5895/ Changeset: 6f698dec5895 User: carlfeberhard Date: 2014-04-15 22:06:26 Summary: Client App: factor out config serializer, move defensive programming Affected #: 1 file diff -r 1da9460ee1d0d5f3f89a767e41c40b5188af988c -r 6f698dec58950f0f56421a13474df0359c0777d7 templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -3,27 +3,10 @@ <%def name="bootstrap()"> ## Bootstap dictionaries for GalaxyApp object's JSON, create GalaxyApp, ## and steal existing attributes from plain objects already created - <% - config_dict = {} - user_dict = {} - try: - if 'configuration' in trans.webapp.api_controllers: - config_dict = ( trans.webapp.api_controllers[ 'configuration' ] - .get_config_dict( trans.app.config, trans.user_is_admin() ) ) - - if 'users' in trans.webapp.api_controllers: - user_dict = self.get_user_dict() - - except Exception, exc: - pass - - # genomes - # datatypes - %><script type="text/javascript"> require([ 'galaxy-app-base' ], function( app ){ galaxy = new app.GalaxyApp({ - config : ${ h.to_json_string( config_dict ) }, + config : ${ get_config_json() }, userJSON : ${ get_user_json() }, root : '${h.url_for( "/" )}', //TODO: get these options from the server @@ -48,34 +31,64 @@ </script></%def> + +## ---------------------------------------------------------------------------- +<%def name="get_config_dict()"> + ## Return a dictionary of universe_wsgi.ini settings + <% + config_dict = {} + try: + if 'configuration' in trans.webapp.api_controllers: + config_dict = ( trans.webapp.api_controllers[ 'configuration' ] + .get_config_dict( trans.app.config, trans.user_is_admin() ) ) + except Exception, exc: + pass + + return config_dict + %> +</%def> + +<%def name="get_config_json()"> + ## Conv. fn to write as JSON +${ h.to_json_string( get_config_dict() )} +</%def> + + ## ---------------------------------------------------------------------------- <%def name="get_user_dict()"> ## Return a dictionary of user or anonymous user data including: ## email, id, disk space used, quota percent, and tags used <% - if trans.user: - user_dict = trans.user.to_dict( view='element', - value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) - user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) + user_dict = {} + try: + if trans.user: + user_dict = trans.user.to_dict( view='element', + value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) + user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) - # tags used - users_api_controller = trans.webapp.api_controllers[ 'users' ] - user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user ) - return user_dict + # tags used + users_api_controller = trans.webapp.api_controllers[ 'users' ] + user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user ) + return user_dict - usage = 0 - percent = None - try: - usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) - percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) - except AssertionError, assertion: - # no history for quota_agent.get_usage assertion + usage = 0 + percent = None + try: + usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) + percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) + except AssertionError, assertion: + # no history for quota_agent.get_usage assertion + pass + return { + 'total_disk_usage' : int( usage ), + 'nice_total_disk_usage' : util.nice_size( usage ), + 'quota_percent' : percent + } + + except Exception, exc: pass - return { - 'total_disk_usage' : int( usage ), - 'nice_total_disk_usage' : util.nice_size( usage ), - 'quota_percent' : percent - } + + return user_dict %></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix to dcc0c19 when user controller isn't present, gen. defensive programming
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1da9460ee1d0/ Changeset: 1da9460ee1d0 User: carlfeberhard Date: 2014-04-15 21:40:48 Summary: Fix to dcc0c19 when user controller isn't present, gen. defensive programming Affected #: 1 file diff -r 5e079414e9f9ca489229816553e5133f5b3d5c0e -r 1da9460ee1d0d5f3f89a767e41c40b5188af988c templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -5,11 +5,17 @@ ## and steal existing attributes from plain objects already created <% config_dict = {} - if 'configuration' in trans.webapp.api_controllers: - config_dict = ( trans.webapp.api_controllers[ 'configuration' ] - .get_config_dict( trans.app.config, trans.user_is_admin() ) ) + user_dict = {} + try: + if 'configuration' in trans.webapp.api_controllers: + config_dict = ( trans.webapp.api_controllers[ 'configuration' ] + .get_config_dict( trans.app.config, trans.user_is_admin() ) ) - user_dict = self.get_user_dict() + if 'users' in trans.webapp.api_controllers: + user_dict = self.get_user_dict() + + except Exception, exc: + pass # genomes # datatypes Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix to dcc0c19 when configuration controller isn't present
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e079414e9f9/ Changeset: 5e079414e9f9 User: carlfeberhard Date: 2014-04-15 21:27:18 Summary: Fix to dcc0c19 when configuration controller isn't present Affected #: 1 file diff -r b8c2e002769773350c8bc729f099110cc26d9d01 -r 5e079414e9f9ca489229816553e5133f5b3d5c0e templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -4,13 +4,12 @@ ## Bootstap dictionaries for GalaxyApp object's JSON, create GalaxyApp, ## and steal existing attributes from plain objects already created <% - config_dict = ( trans.webapp.api_controllers[ 'configuration' ] - .get_config_dict( trans.app.config, trans.user_is_admin() ) ) - #import pprint - #pprint.pprint( config_dict ) + config_dict = {} + if 'configuration' in trans.webapp.api_controllers: + config_dict = ( trans.webapp.api_controllers[ 'configuration' ] + .get_config_dict( trans.app.config, trans.user_is_admin() ) ) user_dict = self.get_user_dict() - #pprint.pprint( user_dict ) # genomes # datatypes Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Temporary fix to galaxy.panels.mako to ensure AMD order
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8c2e0027697/ Changeset: b8c2e0027697 User: carlfeberhard Date: 2014-04-15 21:06:40 Summary: Temporary fix to galaxy.panels.mako to ensure AMD order Affected #: 5 files diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 static/scripts/galaxy-app-base.js --- a/static/scripts/galaxy-app-base.js +++ b/static/scripts/galaxy-app-base.js @@ -46,6 +46,11 @@ self._initUser( options.userJSON || {} ); self.debug( 'GalaxyApp.user: ', self.user ); + //TODO: temp + if( typeof options.onload === 'function' ){ + options.onload(); + } + return self; }; @@ -69,6 +74,8 @@ var self = this; self.debug( '_initUser:', userJSON ); self.user = new userModel.User( userJSON ); + //TODO: temp + self.currUser = self.user; return self; }; diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 static/scripts/packed/galaxy-app-base.js --- a/static/scripts/packed/galaxy-app-base.js +++ b/static/scripts/packed/galaxy-app-base.js @@ -1,1 +1,1 @@ -define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,c,f,d){function g(m){var l=this;return l._init(m||{})}f(g,"GalaxyApp");g.defaultOptions={root:"/"};g.prototype._init=function j(m){var l=this;l._processOptions(m);l.debug("GalaxyApp.options: ",l.options);l._initLogger(m.loggerOptions||{});l.debug("GalaxyApp.logger: ",l.logger);l._initLocale();l.debug("GalaxyApp.localize: ",l.localize);l.config=m.config||{};l.debug("GalaxyApp.config: ",l.config);l._initUser(m.userJSON||{});l.debug("GalaxyApp.user: ",l.user);return l};g.prototype._processOptions=function e(n){var m=this,o=g.defaultOptions;m.debug("_processOptions: ",n);m.options={};for(var l in o){if(o.hasOwnProperty(l)){m.options[l]=(n.hasOwnProperty(l))?(n[l]):(o[l])}}return m};g.prototype._initUser=function i(m){var l=this;l.debug("_initUser:",m);l.user=new a.User(m);return l};g.prototype._initLogger=function k(m){var l=this;l.debug("_initLogger:",m);l.logger=new c.MetricsLogger(m);return l};g.prototype._initLocale=function h(m){var l=this;l.debug("_initLocale:",m);l.localize=d;window._l=l.localize;return l};g.prototype.toString=function b(){var l=this.user.get("email")||"(anonymous)";return"GalaxyApp("+l+")"};return{GalaxyApp:g}}); \ No newline at end of file +define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,c,f,d){function g(m){var l=this;return l._init(m||{})}f(g,"GalaxyApp");g.defaultOptions={root:"/"};g.prototype._init=function j(m){var l=this;l._processOptions(m);l.debug("GalaxyApp.options: ",l.options);l._initLogger(m.loggerOptions||{});l.debug("GalaxyApp.logger: ",l.logger);l._initLocale();l.debug("GalaxyApp.localize: ",l.localize);l.config=m.config||{};l.debug("GalaxyApp.config: ",l.config);l._initUser(m.userJSON||{});l.debug("GalaxyApp.user: ",l.user);if(typeof m.onload==="function"){m.onload()}return l};g.prototype._processOptions=function e(n){var m=this,o=g.defaultOptions;m.debug("_processOptions: ",n);m.options={};for(var l in o){if(o.hasOwnProperty(l)){m.options[l]=(n.hasOwnProperty(l))?(n[l]):(o[l])}}return m};g.prototype._initUser=function i(m){var l=this;l.debug("_initUser:",m);l.user=new a.User(m);l.currUser=l.user;return l};g.prototype._initLogger=function k(m){var l=this;l.debug("_initLogger:",m);l.logger=new c.MetricsLogger(m);return l};g.prototype._initLocale=function h(m){var l=this;l.debug("_initLocale:",m);l.localize=d;window._l=l.localize;return l};g.prototype.toString=function b(){var l=this.user.get("email")||"(anonymous)";return"GalaxyApp("+l+")"};return{GalaxyApp:g}}); \ No newline at end of file diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -22,6 +22,7 @@ userJSON : ${ get_user_json() }, root : '${h.url_for( "/" )}', //TODO: get these options from the server + onload : window.Galaxy? window.Galaxy.onload: null, loggerOptions : { } }); diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -85,33 +85,36 @@ 'mvc/user/user-model', 'mvc/user/user-quotameter' ], function( mod_masthead, mod_menu, mod_modal, mod_frame, GalaxyUpload, user, quotameter ){ + if( !Galaxy.currUser ){ + // this doesn't need to wait for the page being readied + Galaxy.currUser = new user.User(${ h.to_json_string( get_user_json(), indent=2 ) }); + } + $(function() { - ## check if masthead is available - if (Galaxy.masthead) + // check if masthead is available + if (Galaxy.masthead){ return; + } - ## get configuration + // get configuration var masthead_config = ${ h.to_json_string( masthead_config ) }; - ## load global galaxy objects + // load global galaxy objects Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); Galaxy.modal = new mod_modal.View(); Galaxy.frame = new mod_frame.GalaxyFrame(); - ## construct default menu options + // construct default menu options Galaxy.menu = new mod_menu.GalaxyMenu({ masthead: Galaxy.masthead, config: masthead_config }); - ## add upload plugin + // add upload plugin Galaxy.upload = new GalaxyUpload(masthead_config); - if( !Galaxy.currUser ){ - Galaxy.currUser = new user.User(${ h.to_json_string( get_user_json(), indent=2 ) }); - } - ## set up the quota meter (And fetch the current user data from trans) - ## add quota meter to masthead + // set up the quota meter (And fetch the current user data from trans) + // add quota meter to masthead Galaxy.quotaMeter = new quotameter.UserQuotaMeter({ model : Galaxy.currUser, el : Galaxy.masthead.$('.quota-meter-container') diff -r a03ea4880a7117156cead39eecb658ca1da301b3 -r b8c2e002769773350c8bc729f099110cc26d9d01 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -1,4 +1,5 @@ <%namespace name="masthead" file="/webapps/galaxy/galaxy.masthead.mako"/> +<%namespace name="galaxy_client" file="../../galaxy_client_app.mako" /><!DOCTYPE HTML> @@ -93,6 +94,7 @@ %endif </style> + ## default script wrapper <script type="text/javascript"> ## configure require @@ -104,27 +106,25 @@ "libs/backbone/backbone": { exports: "Backbone" }, } }); - - ## get configuration + + // load any app configured var galaxy_config = ${ h.to_json_string( self.galaxy_config ) }; - - ## on page load - $(function() - { - ## check if script is defined + Galaxy.onload = function(){ var jscript = galaxy_config.app.jscript; - if (jscript) - { - ## load galaxy app - require([jscript], function(js_lib) - { - ## load galaxy module application - var module = new js_lib.GalaxyApp(); + if( jscript ){ + $( function(){ + require([ jscript ], function( js_lib ){ + ## load galaxy module application + var module = new js_lib.GalaxyApp(); + }); }); - } else + } else { console.log("'galaxy_config.app.jscript' missing."); - }); + } + } </script> + ${ galaxy_client.bootstrap() } + </%def> ## default late-load javascripts @@ -229,4 +229,4 @@ ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout ${self.late_javascripts()} -</html> \ No newline at end of file +</html> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Allow copying Histories directly from the list of Saved Histories.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a03ea4880a71/ Changeset: a03ea4880a71 User: dan Date: 2014-04-15 20:24:14 Summary: Allow copying Histories directly from the list of Saved Histories. Affected #: 1 file diff -r f7983ecf5ea7c15e5c4235f079e86943576fbdba -r a03ea4880a7117156cead39eecb658ca1da301b3 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -91,6 +91,7 @@ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=True ), grids.GridOperation( "View", allow_multiple=False ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), + grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False, inbound=True ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ), grids.GridOperation( "Delete Permanently", condition=( lambda item: not item.purged ), confirm="History contents will be removed from disk, this cannot be undone. Continue?", async_compatible=True ), @@ -237,6 +238,8 @@ show_deleted=history.deleted, use_panels=False ) ) #return self.view( trans, id=kwargs['id'], show_deleted=history.deleted, use_panels=False ) + if operation == 'copy' and kwargs.get( 'id', None ): + return self.copy( trans, id=kwargs.get( 'id', None ) ) history_ids = galaxy.util.listify( kwargs.get( 'id', [] ) ) # Display no message by default status, message = None, None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Provide run and edit links for workflows after extraction from history.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7983ecf5ea7/ Changeset: f7983ecf5ea7 User: dan Date: 2014-04-15 20:01:21 Summary: Provide run and edit links for workflows after extraction from history. Affected #: 1 file diff -r 3a154b52090316dee61f42993eaa5a1fa40116d3 -r f7983ecf5ea7c15e5c4235f079e86943576fbdba lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1201,7 +1201,7 @@ history=history ) else: - extract_workflow( + stored_workflow = extract_workflow( trans, user=user, job_ids=job_ids, @@ -1209,9 +1209,10 @@ workflow_name=workflow_name ) # Index page with message - return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) - ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" - ## % ( workflow_name, web.url_for(controller='workflow', action='editor', id=trans.security.encode_id(stored.id) ) ) ) + workflow_id = trans.security.encode_id( stored_workflow.id ) + return trans.show_message( 'Workflow "%s" created from current history. You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' % + ( workflow_name, url_for( controller='workflow', action='editor', id=workflow_id ), + url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose def run( self, trans, id, history_id=None, multiple_input_mode="product", hide_fixed_params=False, **kwargs ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5813b1de27ae/ Changeset: 5813b1de27ae User: natefoo Date: 2014-04-15 19:32:01 Summary: Update build platforms for dist-scrambling. Affected #: 1 file diff -r 9ea6c8749ab13e8a4e0d917bf3b49d09b43f55e1 -r 5813b1de27ae8bfb0f31db3215162d563ad2becb dist-eggs.ini --- a/dist-eggs.ini +++ b/dist-eggs.ini @@ -8,22 +8,20 @@ ; [hosts] -py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.6 -py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.6 -py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.7 -py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.7 -py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.6 -py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 -py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.7 -py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 -py2.6-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6 -py2.7-macosx-10.3-fat-ucs2 = weyerbacher.bx.psu.edu /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 -py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6 +py2.6-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-i686-ucs2/bin/python2.6 +py2.6-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-i686-ucs4/bin/python2.6 +py2.6-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-x86_64-ucs2/bin/python2.6 +py2.6-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-x86_64-ucs4/bin/python2.6 +py2.7-linux-i686-ucs2 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-i686-ucs2/bin/python2.7 +py2.7-linux-i686-ucs4 = stegmaier.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-i686-ucs4/bin/python2.7 +py2.7-linux-x86_64-ucs2 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs2/bin/python2.7 +py2.7-linux-x86_64-ucs4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs4/bin/python2.7 +py2.6-macosx-10.6-intel-ucs2 = lion.bx.psu.edu /usr/local/bin/python2.6 py2.7-macosx-10.6-intel-ucs2 = lion.bx.psu.edu /usr/local/bin/python2.7 ; ; these hosts are used to build eggs with no C extensions -py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 -py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.7 +py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.6-linux-x86_64-ucs4/bin/python2.6 +py2.7 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/py2.7-linux-x86_64-ucs4/bin/python2.7 [groups] py2.6-linux-i686 = py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 @@ -35,8 +33,8 @@ linux-i686 = py2.6-linux-i686 py2.7-linux-i686 linux-x86_64 = py2.6-linux-x86_64 py2.7-linux-x86_64 linux = linux-i686 linux-x86_64 -py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 -py2.7-macosx = py2.7-macosx-10.3-fat-ucs2 py2.7-macosx-10.6-intel-ucs2 +py2.6-macosx = py2.6-macosx-10.6-intel-ucs2 +py2.7-macosx = py2.7-macosx-10.6-intel-ucs2 macosx = py2.6-macosx py2.7-macosx py2.6-all = py2.6-linux py2.6-macosx py2.7-all = py2.7-linux py2.7-macosx https://bitbucket.org/galaxy/galaxy-central/commits/3a154b520903/ Changeset: 3a154b520903 User: natefoo Date: 2014-04-15 19:32:31 Summary: Update bx-python to 0.7.2 Affected #: 1 file diff -r 5813b1de27ae8bfb0f31db3215162d563ad2becb -r 3a154b52090316dee61f42993eaa5a1fa40116d3 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -12,7 +12,7 @@ no_auto = pbs_python [eggs:platform] -bx_python = 0.7.1 +bx_python = 0.7.2 Cheetah = 2.2.2 MarkupSafe = 0.12 mercurial = 2.2.3 @@ -78,7 +78,6 @@ psycopg2 = _9.2.4_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _7b95ff194725 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 pysam = _kanwei_b10f6e722e9a Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove old platforms and versions from platform string manipulation. Egg compatibility enhancements for OS X. Galaxy's prepackaged OS X eggs should now work on any Python interpreter on Intel versions of OS X 10.6 and newer.
by commits-noreply＠bitbucket.org 16 Apr '14

16 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9ea6c8749ab1/ Changeset: 9ea6c8749ab1 User: natefoo Date: 2014-04-15 19:27:36 Summary: Remove old platforms and versions from platform string manipulation. Egg compatibility enhancements for OS X. Galaxy's prepackaged OS X eggs should now work on any Python interpreter on Intel versions of OS X 10.6 and newer. Affected #: 1 file diff -r dcc0c19147ead86c6e357c739e0513addfe02cb2 -r 9ea6c8749ab13e8a4e0d917bf3b49d09b43f55e1 lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py +++ b/lib/galaxy/__init__.py @@ -4,24 +4,36 @@ __import__( "pkg_resources" ).declare_namespace( __name__ ) -import os, sys, re -from distutils.sysconfig import get_config_var, get_config_vars +import re +import os +import sys +import platform import pkg_resources # patch get_platform() for better ABI recognition def _get_build_platform(): plat = pkg_resources._get_build_platform() - if sys.version_info[:2] == ( 2, 5 ) and \ - ( ( os.uname()[-1] in ( 'x86_64', 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ - ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ) ): - plat = 'macosx-10.3-fat' - if sys.platform == "sunos5" and not (plat.endswith('_32') or plat.endswith('_64')): - if sys.maxint > 2**31: - plat += '_64' - else: - plat += '_32' - if sys.platform == "linux2" and sys.maxint < 2**31 and plat.endswith( '-x86_64' ): + if sys.platform == 'darwin': + # Assert OS X version is new enough + current_minor_ver = int( platform.mac_ver()[0].split( '.' )[1] ) + assert current_minor_ver >= 6, 'Galaxy is not compatible with Mac OS X < 10.6 (your version is %s)' % platform.mac_ver()[0] + # Python build target may be even older, but this will prevent it from + # fetching our 10.6+ eggs, so fix if necessary (newer versions will be + # fine) + plat_split = plat.split( '-' ) + build_minor_ver = int( plat_split[1].split( '.' )[1] ) + if build_minor_ver < 6: + plat_split[1] = '10.6' + # Our intel (dual arch) eggs will work fine on single-arch builds + if plat_split[-1] in ( 'i386', 'x86_64' ): + plat_split[-1] = 'intel' + # Ditto universal (if you're not on PPC) + if plat_split[-1] == 'universal' and platform.processor() != 'powerpc': + plat_split[-1] = 'intel' + plat = '-'.join( plat_split ) + elif sys.platform == "linux2" and sys.maxint < 2**31 and plat.endswith( '-x86_64' ): + # 32 bit Python on 64 bit Linux plat = plat.replace( '-x86_64', '-i686' ) if not (plat.endswith('-ucs2') or plat.endswith('-ucs4')): if sys.maxunicode > 2**16: @@ -36,34 +48,6 @@ pkg_resources.get_build_platform = _get_build_platform pkg_resources.get_platform = _get_build_platform -# patch compatible_platforms() to allow for Solaris binary compatibility -solarisVersionString = re.compile(r"solaris-(\d)\.(\d+)-(.*)") -def _compatible_platforms(provided,required): - # this is a bit kludgey since we need to know a bit about what happened in - # the original method - if provided is None or required is None or provided==required: - return True # easy case - reqMac = pkg_resources.macosVersionString.match(required) - if reqMac: - return pkg_resources._compatible_platforms(provided,required) - reqSol = solarisVersionString.match(required) - if reqSol: - provSol = solarisVersionString.match(provided) - if not provSol: - return False - if provSol.group(1) != reqSol.group(1) or \ - provSol.group(3) != reqSol.group(3): - return False - if int(provSol.group(2)) > int(reqSol.group(2)): - return False - return True - return False -try: - assert pkg_resources._compatible_platforms -except: - pkg_resources._compatible_platforms = pkg_resources.compatible_platforms - pkg_resources.compatible_platforms = _compatible_platforms - # patch to insert eggs at the beginning of sys.path instead of at the end def _insert_on(self, path, loc = None): """Insert self.location in path before its nearest parent directory""" @@ -108,4 +92,4 @@ pass logging.NullHandler = NullHandler -import galaxy.eggs \ No newline at end of file +import galaxy.eggs Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits April 2014