galaxy-commits September 2013

galaxy-commits@lists.galaxyproject.org

1 participants
149 discussions

commit/galaxy-central: carlfeberhard: History panel: remove sessionStorage for panel when user logs out
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c4b5f082ead5/ Changeset: c4b5f082ead5 User: carlfeberhard Date: 2013-09-26 21:08:42 Summary: History panel: remove sessionStorage for panel when user logs out Affected #: 5 files diff -r 4dc1714a5a0a9f2dde02dea061eb45b0aae1e08d -r c4b5f082ead51a655f24fe5a2478996ee3bde95c static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -212,6 +212,14 @@ this.log( this + ' (init\'d) storage:', this.storage.get() ); }, + clearWebStorage : function(){ + for( var key in sessionStorage ){ + if( key.indexOf( 'HistoryView.' ) === 0 ){ + sessionStorage.removeItem( key ); + } + } + }, + /** Add an hda to this history's collection * @param {HistoryDatasetAssociation} hda hda to add to the collection */ diff -r 4dc1714a5a0a9f2dde02dea061eb45b0aae1e08d -r c4b5f082ead51a655f24fe5a2478996ee3bde95c static/scripts/mvc/user/user-model.js --- a/static/scripts/mvc/user/user-model.js +++ b/static/scripts/mvc/user/user-model.js @@ -70,6 +70,17 @@ return BaseModel.prototype.fetch.call( this, options ); }, + /** Clears all data from the sessionStorage. + */ + clearSessionStorage : function(){ + for( var key in sessionStorage ){ + //TODO: currently only history + if( key.indexOf( 'HistoryView.' ) === 0 ){ + sessionStorage.removeItem( key ); + } + } + }, + /** string representation */ toString : function(){ var userInfo = [ this.get( 'username' ) ]; diff -r 4dc1714a5a0a9f2dde02dea061eb45b0aae1e08d -r c4b5f082ead51a655f24fe5a2478996ee3bde95c static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistentStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find("[title]").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistentStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find("[title]").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 4dc1714a5a0a9f2dde02dea061eb45b0aae1e08d -r c4b5f082ead51a655f24fe5a2478996ee3bde95c static/scripts/packed/mvc/user/user-model.js --- a/static/scripts/packed/mvc/user/user-model.js +++ b/static/scripts/packed/mvc/user/user-model.js @@ -1,1 +1,1 @@ -var User=Backbone.Model.extend(LoggableMixin).extend({urlRoot:"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(a){this.log("User.initialize:",a);this.on("loaded",function(b,c){this.log(this+" has loaded:",b,c)});this.on("change",function(b,c){this.log(this+" has changed:",b,c.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(d,b){d=d||User.CURRENT_ID_STR;b=b||{};var a=this,c=b.success;b.success=function(f,e){a.trigger("loaded",f,e);if(c){c(f,e)}};if(d===User.CURRENT_ID_STR){b.url=this.urlRoot+"/"+User.CURRENT_ID_STR}return BaseModel.prototype.fetch.call(this,b)},toString:function(){var a=[this.get("username")];if(this.get("id")){a.unshift(this.get("id"));a.push(this.get("email"))}return"User("+a.join(":")+")"}});User.CURRENT_ID_STR="current";User.getCurrentUserFromApi=function(b){var a=new User();a.loadFromApi(User.CURRENT_ID_STR,b);return a};var UserCollection=Backbone.Collection.extend(LoggableMixin).extend({model:User,urlRoot:"api/users"}); \ No newline at end of file +var User=Backbone.Model.extend(LoggableMixin).extend({urlRoot:"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(a){this.log("User.initialize:",a);this.on("loaded",function(b,c){this.log(this+" has loaded:",b,c)});this.on("change",function(b,c){this.log(this+" has changed:",b,c.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(d,b){d=d||User.CURRENT_ID_STR;b=b||{};var a=this,c=b.success;b.success=function(f,e){a.trigger("loaded",f,e);if(c){c(f,e)}};if(d===User.CURRENT_ID_STR){b.url=this.urlRoot+"/"+User.CURRENT_ID_STR}return BaseModel.prototype.fetch.call(this,b)},clearSessionStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},toString:function(){var a=[this.get("username")];if(this.get("id")){a.unshift(this.get("id"));a.push(this.get("email"))}return"User("+a.join(":")+")"}});User.CURRENT_ID_STR="current";User.getCurrentUserFromApi=function(b){var a=new User();a.loadFromApi(User.CURRENT_ID_STR,b);return a};var UserCollection=Backbone.Collection.extend(LoggableMixin).extend({model:User,urlRoot:"api/users"}); \ No newline at end of file diff -r 4dc1714a5a0a9f2dde02dea061eb45b0aae1e08d -r c4b5f082ead51a655f24fe5a2478996ee3bde95c templates/user/logout.mako --- a/templates/user/logout.mako +++ b/templates/user/logout.mako @@ -39,6 +39,14 @@ </%def><%def name="body()"> + <script type="text/javascript"> + $(function(){ + //HACK: should happen before we get to this page - _before_ logged out of session + if( top.Galaxy && top.Galaxy.currUser ){ + top.Galaxy.currUser.clearSessionStorage(); + } + }); + </script> %if message: ${render_msg( message, status )} %endif 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.

1 0

commit/galaxy-central: natefoo: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a477486bf18e/ Changeset: a477486bf18e Branch: stable User: natefoo Date: 2013-09-26 17:02:58 Summary: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased. Affected #: 1 file diff -r 4b1c7ad464ea5b181d9d5d95e8751518b170fca8 -r a477486bf18eafdd14dd7ba1e91e17f1b05e8121 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -179,7 +179,7 @@ if tools is not None: for tool in self.__findall_with_required(tools, 'tool'): # There can be multiple definitions with identical ids, but different params - id = tool.get('id') + id = tool.get('id').lower() if id not in self.tools: self.tools[id] = list() self.tools[id].append(JobToolConfiguration(**dict(tool.items()))) 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.

1 0

commit/galaxy-central: carlfeberhard: History panel: fix race condition when setting updater
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4dc1714a5a0a/ Changeset: 4dc1714a5a0a User: carlfeberhard Date: 2013-09-26 18:38:18 Summary: History panel: fix race condition when setting updater Affected #: 2 files diff -r a7e3721795d6c480d4e116f1054235450102d725 -r 4dc1714a5a0a9f2dde02dea061eb45b0aae1e08d static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -49,6 +49,8 @@ /** HDACollection of the HDAs contained in this history. */ this.hdas = new HDACollection(); + this.updateTimeoutId = null; + // if we've got hdas passed in the constructor, load them and set up updates if needed if( initialHdas && _.isArray( initialHdas ) ){ this.hdas.add( initialHdas ); @@ -63,11 +65,7 @@ // then: refresh the panel this.hdas.bind( 'state:ready', function( hda, newState, oldState ){ if( hda.get( 'force_history_refresh' ) ){ - //TODO: could poll jobs here... - var history = this; - setTimeout( function(){ - history.stateUpdater(); - }, History.UPDATE_DELAY ); + this.updateAfterDelay(); } }, this ); @@ -87,13 +85,21 @@ }); }, + updateAfterDelay : function(){ + var history = this; + this.updateTimeoutId = setTimeout( function(){ + history.stateUpdater(); + }, History.UPDATE_DELAY ); + return this.updateTimeoutId; + }, + // get the history's state from it's cummulative ds states, delay + update if needed // events: ready checkForUpdates : function(){ // get overall History state from collection, run updater if History has running/queued hdas // boiling it down on the client to running/not if( this.hdas.running().length ){ - this.stateUpdater(); + this.updateAfterDelay(); } else { this.trigger( 'ready' ); @@ -105,6 +111,7 @@ // set up to run this again in some interval of time // events: ready stateUpdater : function(){ + //TODO: we need to get states from one location: history_contents (right now it's both history and contents) var history = this, oldState = this.get( 'state' ), // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state @@ -133,19 +140,28 @@ // send the changed ids (if any) to dataset collection to have them fetch their own model changes if( changedIds.length ){ - history.fetchHdaUpdates( changedIds ); + history.fetchHdaUpdates( changedIds ) + .done( function(){ + furtherUpdatesOrReady( history ); + }); + } else { + furtherUpdatesOrReady( history ); } - // set up to keep pulling if this history in run/queue state - if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ - setTimeout( function(){ - history.stateUpdater(); - }, History.UPDATE_DELAY ); + function furtherUpdatesOrReady( history ){ + var timeout; + // set up to keep pulling if this history in run/queue state + if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + //|| ( history.hdas.running() ) ){ + timeout = history.updateAfterDelay(); - // otherwise, we're now in a 'ready' state (no hdas running) - } else { - history.trigger( 'ready' ); + // otherwise, we're now in a 'ready' state (no hdas running) + } else { + this.updateTimeoutId = null; + history.trigger( 'ready' ); + } + return timeout; } }).error( function( xhr, status, error ){ @@ -176,8 +192,8 @@ */ fetchHdaUpdates : function( hdaIds ){ //TODO:?? move to collection? still need proper url - var history = this; - jQuery.ajax({ + var history = this, + xhr = jQuery.ajax({ url : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }), /** @@ -218,6 +234,7 @@ history.updateHdas( hdaDataList ); } }); + return xhr; }, /** Update the models in the hdas collection from the data given. diff -r a7e3721795d6c480d4e116f1054235450102d725 -r 4dc1714a5a0a9f2dde02dea061eb45b0aae1e08d static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,g,d){if(e.get("force_history_refresh")){var f=this;setTimeout(function(){f.stateUpdater()},History.UPDATE_DELAY)}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{a.log("Error updating hdas from api history contents",b,h,c,d,f);var g=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",g,h,c,d)}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file 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.

1 0

commit/galaxy-central: Dave Bouvier: Explicitly require paramiko before loading the Fabric egg, in order to resolve a version conflict in cases where the system paramiko version is older than 1.10.0.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7e3721795d6/ Changeset: a7e3721795d6 User: Dave Bouvier Date: 2013-09-26 18:15:02 Summary: Explicitly require paramiko before loading the Fabric egg, in order to resolve a version conflict in cases where the system paramiko version is older than 1.10.0. Affected #: 1 file diff -r 736555674763159f1422c1c822e93019ed6a62ed -r a7e3721795d6c480d4e116f1054235450102d725 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -11,10 +11,9 @@ from galaxy.util.template import fill_template from galaxy import eggs -import pkg_resources - -pkg_resources.require('ssh' ) -pkg_resources.require( 'Fabric' ) +eggs.require( 'ssh' ) +eggs.require( 'paramiko' ) +eggs.require( 'Fabric' ) from fabric.api import env from fabric.api import lcd 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.

1 0

commit/galaxy-central: Dave Bouvier: Eliminate use of features that are specific to ElementTree 1.3, introduced in python 2.7.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/736555674763/ Changeset: 736555674763 User: Dave Bouvier Date: 2013-09-26 18:03:54 Summary: Eliminate use of features that are specific to ElementTree 1.3, introduced in python 2.7. Affected #: 1 file diff -r 0b955e54451cf22a1a7c8fa0f92beb9e375f1f1e -r 736555674763159f1422c1c822e93019ed6a62ed lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -264,11 +264,13 @@ in_actions_group = True # Record the number of <actions> elements so we can filter out any <action> elements that precede <actions> elements. actions_elem_count = len( elem.findall( 'actions' ) ) - # Record the number of <actions> elements that have architecture and os specified, in order to filter out any platform-independent - # <actions> elements that come before platform-specific <actions> elements. This call to elem.findall is filtered by tags that have - # both the os and architecture specified. For more details, see http://docs.python.org/2/library/xml.etree.elementtree.html Section - # 19.7.2.1. - platform_actions_element_count = len( elem.findall( 'actions[@architecture][@os]' ) ) + # Record the number of <actions> elements that have both architecture and os specified, in order to filter out any + # platform-independent <actions> elements that come before platform-specific <actions> elements. + platform_actions_elements = [] + for actions_elem in elem.findall( 'actions' ): + if actions_elem.get( 'architecture' ) is not None and actions_elem.get( 'os' ) is not None: + platform_actions_elements.append( actions_elem ) + platform_actions_element_count = len( platform_actions_elements ) platform_actions_elements_processed = 0 actions_elems_processed = 0 # The tag sets that will go into the after_install_actions list are <action> tags instead of <actions> tags. These will be processed 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.

1 0

commit/galaxy-central: natefoo: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0b955e54451c/ Changeset: 0b955e54451c User: natefoo Date: 2013-09-26 17:02:58 Summary: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased. Affected #: 1 file diff -r 870b10eaa4cf2c4045988425685175dcaabe625b -r 0b955e54451cf22a1a7c8fa0f92beb9e375f1f1e lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -179,7 +179,7 @@ if tools is not None: for tool in self.__findall_with_required(tools, 'tool'): # There can be multiple definitions with identical ids, but different params - id = tool.get('id') + id = tool.get('id').lower() if id not in self.tools: self.tools[id] = list() self.tools[id].append(JobToolConfiguration(**dict(tool.items()))) 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8e782b7becb6/ Changeset: 8e782b7becb6 User: dannon Date: 2013-09-26 15:49:26 Summary: Correct distributedobjectstore parent in another place. Affected #: 1 file diff -r 47b5784396f7bbd83cb4867e824980e9d6cdf55b -r 8e782b7becb6769ad59d8bb3d75e1ed0f8f517af lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -432,7 +432,7 @@ return default -class DistributedObjectStore(ObjectStore): +class DistributedObjectStore(NestedObjectStore): """ ObjectStore that defers to a list of backends, for getting objects the first store where the object exists is used, objects are created in a https://bitbucket.org/galaxy/galaxy-central/commits/0dbc9501b7e7/ Changeset: 0dbc9501b7e7 User: dannon Date: 2013-09-26 15:49:50 Summary: Merge. Affected #: 2 files diff -r 8e782b7becb6769ad59d8bb3d75e1ed0f8f517af -r 0dbc9501b7e7943cf68df987ee528e142c892311 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -378,7 +378,7 @@ return True else: try: - return { "psycopg2": lambda: self.config.get( "app:main", "database_connection" ).startswith( "postgres://" ), + return { "psycopg2": lambda: self.config.get( "app:main", "database_connection" ).startswith( "postgres" ), "MySQL_python": lambda: self.config.get( "app:main", "database_connection" ).startswith( "mysql://" ), "DRMAA_python": lambda: "sge" in self.config.get( "app:main", "start_job_runners" ).split(","), "drmaa": lambda: "drmaa" in self.config.get( "app:main", "start_job_runners" ).split(","), diff -r 8e782b7becb6769ad59d8bb3d75e1ed0f8f517af -r 0dbc9501b7e7943cf68df987ee528e142c892311 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -76,7 +76,7 @@ sa_session.refresh( user ) current = user.get_disk_usage() print user.username, '<' + user.email + '>:', - if engine != 'postgres': + if engine not in ( 'postgres', 'postgresql' ): new = user.calculate_disk_usage() sa_session.refresh( user ) # usage changed while calculating, do it again @@ -94,7 +94,7 @@ print '+%s' % ( nice_size( new - current ) ) else: print '-%s' % ( nice_size( current - new ) ) - if not options.dryrun and engine != 'postgres': + if not options.dryrun and engine not in ( 'postgres', 'postgresql' ): user.set_disk_usage( new ) sa_session.add( user ) sa_session.flush() 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.

1 0

commit/galaxy-central: natefoo: Fix a few postgres dialect renaming misses.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1385bc4954ac/ Changeset: 1385bc4954ac User: natefoo Date: 2013-09-26 15:34:27 Summary: Fix a few postgres dialect renaming misses. Affected #: 2 files diff -r 47b5784396f7bbd83cb4867e824980e9d6cdf55b -r 1385bc4954acdabc2cd59d54db947c8cce615a84 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -378,7 +378,7 @@ return True else: try: - return { "psycopg2": lambda: self.config.get( "app:main", "database_connection" ).startswith( "postgres://" ), + return { "psycopg2": lambda: self.config.get( "app:main", "database_connection" ).startswith( "postgres" ), "MySQL_python": lambda: self.config.get( "app:main", "database_connection" ).startswith( "mysql://" ), "DRMAA_python": lambda: "sge" in self.config.get( "app:main", "start_job_runners" ).split(","), "drmaa": lambda: "drmaa" in self.config.get( "app:main", "start_job_runners" ).split(","), diff -r 47b5784396f7bbd83cb4867e824980e9d6cdf55b -r 1385bc4954acdabc2cd59d54db947c8cce615a84 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -76,7 +76,7 @@ sa_session.refresh( user ) current = user.get_disk_usage() print user.username, '<' + user.email + '>:', - if engine != 'postgres': + if engine not in ( 'postgres', 'postgresql' ): new = user.calculate_disk_usage() sa_session.refresh( user ) # usage changed while calculating, do it again @@ -94,7 +94,7 @@ print '+%s' % ( nice_size( new - current ) ) else: print '-%s' % ( nice_size( current - new ) ) - if not options.dryrun and engine != 'postgres': + if not options.dryrun and engine not in ( 'postgres', 'postgresql' ): user.set_disk_usage( new ) sa_session.add( user ) sa_session.flush() 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.

1 0

commit/galaxy-central: dannon: Wrong superclass in previous refactoring commit.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47b5784396f7/ Changeset: 47b5784396f7 User: dannon Date: 2013-09-26 15:24:45 Summary: Wrong superclass in previous refactoring commit. Affected #: 1 file diff -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc -r 47b5784396f7bbd83cb4867e824980e9d6cdf55b lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -497,9 +497,8 @@ self.weighted_backend_ids.append(id) self.original_weighted_backend_ids = self.weighted_backend_ids - def shutdown(self): - super(NestedObjectStore, self).shutdown() + super(DistributedObjectStore, self).shutdown() if self.sleeper is not None: self.sleeper.wake() 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7e148067d62/ Changeset: b7e148067d62 User: dannon Date: 2013-09-26 15:13:32 Summary: Correctly shutdown HierarchicalObjectStore and DistributedObjectStore Affected #: 1 file diff -r ff806b8e5f18791641fa49a20d9bea9e65215310 -r b7e148067d62e0153a15d4c46f70eece3c938a7e lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -381,9 +381,8 @@ self.backends = {} def shutdown(self): - [b.shutdown() for b in self.backends.values()] - if self.sleeper is not None: - self.sleeper.wake() + for store in self.backends.values(): + store.shutdown() super(NestedObjectStore, self).shutdown() def exists(self, obj, **kwargs): @@ -452,11 +451,8 @@ self.original_weighted_backend_ids = [] self.max_percent_full = {} self.global_max_percent_full = 0.0 - random.seed() - self.__parse_distributed_config(config, config_xml) - self.sleeper = None if fsmon and ( self.global_max_percent_full or filter( lambda x: x != 0.0, self.max_percent_full.values() ) ): self.sleeper = Sleeper() @@ -501,6 +497,12 @@ self.weighted_backend_ids.append(id) self.original_weighted_backend_ids = self.weighted_backend_ids + + def shutdown(self): + super(NestedObjectStore, self).shutdown() + if self.sleeper is not None: + self.sleeper.wake() + def __filesystem_monitor(self): while self.running: new_weighted_backend_ids = self.original_weighted_backend_ids @@ -570,10 +572,6 @@ for b in config_xml.find('backends'): self.backends[int(b.get('order'))] = build_object_store_from_config(config, fsmon=fsmon, config_xml=b) - def shutdown(self): - for store in self.backends.values(): - store.shutdown() - super(HierarchicalObjectStore, self).shutdown() def exists(self, obj, **kwargs): """ https://bitbucket.org/galaxy/galaxy-central/commits/e890cd2464ac/ Changeset: e890cd2464ac User: dannon Date: 2013-09-26 15:13:50 Summary: merge Affected #: 11 files diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -172,6 +172,7 @@ self.job_stop_queue = self.job_manager.job_stop_queue # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self ) + self.model.engine.dispose() def shutdown( self ): self.job_manager.shutdown() diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -9,7 +9,12 @@ grep -v '^#' $input | sort -k1,1 | ## Generate coverage bedgraph. - bedtools genomecov -bg -split -i stdin -g $chromInfo + bedtools genomecov -bg -i stdin -g $chromInfo + + ## Only use split option for bed and gff/gff3/gtf. + #if $input.ext in [ 'bed', 'gff', 'gff3', 'gtf' ]: + -split + #end if ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this ## should only be used on systems with large RAM. diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -226,7 +226,13 @@ if state == drmaa.JobState.RUNNING and not ajs.running: ajs.running = True ajs.job_wrapper.change_state( model.Job.states.RUNNING ) - if state in ( drmaa.JobState.DONE, drmaa.JobState.FAILED ): + if state == drmaa.JobState.FAILED: + if ajs.job_wrapper.get_state() != model.Job.states.DELETED: + ajs.stop_job = False + ajs.fail_message = "The cluster DRM system terminated this job" + self.work_queue.put( ( self.fail_job, ajs ) ) + continue + if state == drmaa.JobState.DONE: if ajs.job_wrapper.get_state() != model.Job.states.DELETED: self.work_queue.put( ( self.finish_job, ajs ) ) continue diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -121,12 +121,12 @@ for exported_workflow_dict in exported_workflows: workflow_name = exported_workflow_dict[ 'workflow_name' ] workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) - if status == 'error': - log.error( message, exc_info=True ) - trans.response.status = 500 - return message - else: - imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) + if status == 'error': + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + else: + imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) return imported_workflow_dicts @web.expose_api diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -705,9 +705,10 @@ if 'display_url' not in kwd or 'redirect_url' not in kwd: return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' ) try: - redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) + redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) except: - redirect_url = kwd['redirect_url'] # not all will need custom text + redirect_url = kwd['redirect_url'] # not all will need custom text + redirect_url = redirect_url.encode( 'utf-8' ) current_user_roles = trans.get_current_user_roles() if trans.app.security_agent.dataset_is_public( data.dataset ): return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -1,16 +1,17 @@ import logging from galaxy.web.framework.helpers import time_ago +from galaxy import eggs from galaxy import web from galaxy import util from galaxy.web.base.controller import BaseAPIController import tool_shed.util.shed_util_common as suc from tool_shed.galaxy_install import repository_util -from galaxy import eggs -import pkg_resources +eggs.require( 'mercurial' ) -pkg_resources.require( 'mercurial' ) -from mercurial import hg, ui, commands +from mercurial import commands +from mercurial import hg +from mercurial import ui log = logging.getLogger( __name__ ) diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -1,15 +1,19 @@ -import os, logging -from galaxy.web.framework.helpers import time_ago, grids +import logging +import os +from galaxy.web.framework.helpers import grids +from galaxy.web.framework.helpers import time_ago from galaxy.webapps.tool_shed import model from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc -from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid +from tool_shed.grids.repository_grids import CategoryGrid +from tool_shed.grids.repository_grids import RepositoryGrid from galaxy import eggs -import pkg_resources +eggs.require( 'mercurial' ) -pkg_resources.require( 'mercurial' ) -from mercurial import hg, ui, commands +from mercurial import commands +from mercurial import hg +from mercurial import ui log = logging.getLogger( __name__ ) diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -573,27 +573,23 @@ def build_readme_files_folder( trans, folder_id, readme_files_dict, label='Readme files' ): """Return a folder hierarchy containing readme text files.""" if readme_files_dict: - multiple_readme_files = len( readme_files_dict ) > 1 readme_id = 0 folder_id += 1 readme_files_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) - if multiple_readme_files: - folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) - readme_files_root_folder.folders.append( readme_files_folder ) + folder_id += 1 + readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) + multiple_readme_files = len( readme_files_dict ) > 1 + readme_files_root_folder.folders.append( readme_files_folder ) for readme_file_name, readme_file_text in readme_files_dict.items(): readme_id += 1 readme = ReadMe( id=readme_id, name=readme_file_name, text=readme_file_text ) if multiple_readme_files: folder_id += 1 - folder = Folder( id=folder_id, key=readme.name, label=readme.name, parent=readme_files_folder ) + folder = Folder( id=folder_id, key=readme_file_name, label=readme_file_name, parent=readme_files_folder ) folder.readme_files.append( readme ) readme_files_folder.folders.append( folder ) else: - folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=readme.name, parent=readme_files_root_folder ) readme_files_folder.readme_files.append( readme ) - readme_files_root_folder.folders.append( readme_files_folder ) else: readme_files_root_folder = None return folder_id, readme_files_root_folder diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -589,7 +589,7 @@ original_repository_metadata = repository.metadata else: original_repository_metadata = None - readme_file_names = get_readme_file_names( repository.name ) + readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) if app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } @@ -1046,16 +1046,6 @@ # The tool did not change through all of the changeset revisions. return old_id -def get_readme_file_names( repository_name ): - """Creates a list of valid filenames.""" - readme_files = [ 'readme', 'read_me', 'install' ] - valid_filenames = map( lambda f: '%s.txt' % f, readme_files ) - valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) - valid_filenames.extend( readme_files ) - valid_filenames.append( '%s.txt' % repository_name ) - valid_filenames.append( '%s.rst' % repository_name ) - return valid_filenames - def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ): if resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -70,3 +70,13 @@ raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) readme_files_dict = json.from_json_string( raw_text ) return readme_files_dict + +def get_readme_file_names( repository_name ): + """Return a list of file names that will be categorized as README files for the received repository_name.""" + readme_files = [ 'readme', 'read_me', 'install' ] + valid_filenames = map( lambda f: '%s.txt' % f, readme_files ) + valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) + valid_filenames.extend( readme_files ) + valid_filenames.append( '%s.txt' % repository_name ) + valid_filenames.append( '%s.rst' % repository_name ) + return valid_filenames diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -425,7 +425,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rd-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${datatype.extension | h}</${cell_type}><${cell_type}>${datatype.type | h}</${cell_type}><${cell_type}>${datatype.mimetype | h}</${cell_type}> @@ -440,15 +440,15 @@ <%def name="render_failed_test( failed_test, pad, parent, row_counter, row_is_header=False )"><% from tool_shed.util.shed_util_common import to_html_string - encoded_id = trans.security.encode_id( failed_test.id ) + encoded_id = trans.security.encode_id( failed_test.id ) %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rft-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="failed_test_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> @@ -475,7 +475,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-ridm-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${data_manager.index | h}</${cell_type}><${cell_type}>${data_manager.error | h}</${cell_type}></tr> @@ -493,7 +493,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rird-${encoded_id}"><td style="padding-left: ${pad+20}px;"> ${ invalid_repository_dependency.error | h } </td> @@ -510,7 +510,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rit-${encoded_id}"><td style="padding-left: ${pad+20}px;"> %if trans.webapp.name == 'tool_shed' and invalid_tool.repository_id and invalid_tool.tool_config and invalid_tool.changeset_revision: <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision, render_repository_actions_for=render_repository_actions_for )}"> @@ -545,7 +545,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-ritd-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="invalid_td_table"><tr><td>${ invalid_tool_dependency.error | h }</td></tr> @@ -559,14 +559,16 @@ </%def><%def name="render_missing_test_component( missing_test_component, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( missing_test_component.id ) %> + <% + encoded_id = trans.security.encode_id( missing_test_component.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rmtc-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="missing_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr> @@ -587,27 +589,17 @@ encoded_id = trans.security.encode_id( readme.id ) render_rst = readme.name.endswith( '.rst' ) %> - <style type="text/css"> - #readme_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><tr class="datasetRow" %if parent is not None: - parent="${parent}" + parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rr-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="readme_table"> + <table id="readme_files"> %if render_rst: <tr><td>${ rst_to_html( readme.text ) }</td></tr> %else: - <tr><td>${readme.name}<br/>${ to_html_string( readme.text ) }</td></tr> + <tr><td>${ to_html_string( readme.text ) }</td></tr> %endif </table></td> @@ -652,7 +644,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rrd-${encoded_id}"> %if trans.webapp.name == 'galaxy': <${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: @@ -684,28 +676,31 @@ %></%def> -<%def name="render_tool_test_results_css()"> +<%def name="render_table_wrap_style( table_id )"><style type="text/css"> - table.tool_test_results{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } + table.${table_id}{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } </style></%def><%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <% + encoded_id = trans.security.encode_id( installation_error.id ) + %> + ${render_table_wrap_style( "td_install_error_table" )} <tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rtdie-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="td_install_error_table" class="tool_test_results"> + <table id="td_install_error_table"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr> @@ -726,14 +721,17 @@ </%def><%def name="render_repository_installation_error( installation_error, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"> - <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <% + encoded_id = trans.security.encode_id( installation_error.id ) + %> + ${render_table_wrap_style( "rd_install_error_table" )} <tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rrie-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="rd_install_error_table" class="tool_test_results"> + <table id="rd_install_error_table"> %if not is_current_repository: <tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> @@ -757,14 +755,16 @@ </%def><%def name="render_not_tested( not_tested, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( not_tested.id ) %> + <% + encoded_id = trans.security.encode_id( not_tested.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rnt-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="not_tested_table" class="tool_test_results"> + <table id="test_environment"><tr><td>${not_tested.reason | h}</td></tr></table></td> @@ -776,14 +776,16 @@ </%def><%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( passed_test.id ) %> + <% + encoded_id = trans.security.encode_id( passed_test.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rpt-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="passed_tests_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> @@ -808,7 +810,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rt-${encoded_id}"> %if row_is_header: <th style="padding-left: ${pad+20}px;">${tool.name | h}</th> %else: @@ -857,7 +859,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rtd-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${tool_dependency.name | h} @@ -917,9 +919,9 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rte-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table class="grid" id="readme_table"> + <table class="grid" id="test_environment"><tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr><tr><td><b>System:</b> ${test_environment.system | h}</td></tr><tr><td><b>Architecture:</b> ${test_environment.architecture | h}</td></tr> @@ -950,7 +952,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rvdm-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${data_manager.name | h}</${cell_type}><${cell_type}>${data_manager.version | h}</${cell_type}><${cell_type}>${data_manager.data_tables | h}</${cell_type}> @@ -981,7 +983,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rw-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${workflow.workflow_name | h} @@ -1045,6 +1047,8 @@ return str( self.count ) %> %if readme_files_root_folder: + ${render_table_wrap_style( "readme_files" )} + <p/><div class="toolForm"><div class="toolFormTitle">Repository README files - may contain important installation or license information</div><div class="toolFormBody"> @@ -1127,14 +1131,14 @@ %if valid_data_managers_root_folder: <p/><% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="valid_tools"> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="valid_data_managers"> ${render_folder( valid_data_managers_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} </table> %endif %if invalid_data_managers_root_folder: <p/><% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="invalid_tools"> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="invalid_data_managers"> ${render_folder( invalid_data_managers_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} </table> %endif @@ -1156,16 +1160,20 @@ </div> %endif %if tool_test_results_root_folder: - ${render_tool_test_results_css()} + ##${render_table_wrap_style( "failed_test_table" )} + ##${render_table_wrap_style( "missing_table" )} + ##${render_table_wrap_style( "not_tested_table" )} + ##${render_table_wrap_style( "passed_tests_table" )} + ${render_table_wrap_style( "test_environment" )} <p/><div class="toolForm"><div class="toolFormTitle">Automated tool test results</div><div class="toolFormBody"> - <p/> - <% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment"> - ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} - </table> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment"> + ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table></div></div> %endif 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.

1 0

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits September 2013