1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f79c07c4438/ Changeset: 2f79c07c4438 User: carlfeberhard Date: 2014-05-02 21:45:25 Summary: History: cruft removal from controller and associated javascript Affected #: 3 files diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -549,6 +549,7 @@ count += 1 return trans.show_ok_message( "%d datasets have been deleted permanently" % count, refresh_frames=['history'] ) + #TODO: use api instead @web.expose def delete_current( self, trans, purge=False ): """Delete just the active history -- this does not require a logged in user.""" @@ -604,6 +605,7 @@ trans.sa_session.add( history ) trans.sa_session.flush() return trans.show_ok_message( "Your datasets have been unhidden.", refresh_frames=refresh_frames ) + #TODO: used in index.mako @web.expose def resume_paused_jobs( self, trans, current=False, ids=None ): @@ -618,6 +620,7 @@ trans.sa_session.add( history ) trans.sa_session.flush() return trans.show_ok_message( "Your jobs have been resumed.", refresh_frames=refresh_frames ) + #TODO: used in index.mako @web.expose @web.require_login( "rate items" ) @@ -630,34 +633,7 @@ # Rate history. history_rating = self.rate_item( trans.sa_session, trans.get_user(), history, rating ) return self.get_ave_item_rating_data( trans.sa_session, history ) - - @web.expose - def rename_async( self, trans, id=None, new_name=None ): - history = self.get_history( trans, id ) - # Check that the history exists, and is either owned by the current - # user (if logged in) or the current history - assert history is not None - if history.user is None: - assert history == trans.get_history() - else: - assert history.user == trans.user - # Rename - new_name = sanitize_html( new_name ) - history.name = new_name - trans.sa_session.add( history ) - trans.sa_session.flush() - return new_name - - @web.expose - @web.require_login( "use Galaxy histories" ) - def annotate_async( self, trans, id, new_annotation=None, **kwargs ): - history = self.get_history( trans, id ) - if new_annotation: - # Sanitize annotation before adding it. - new_annotation = sanitize_html( new_annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), history, new_annotation ) - trans.sa_session.flush() - return new_annotation + #TODO: used in display_base.mako @web.expose # TODO: Remove require_login when users are warned that, if they are not @@ -686,6 +662,7 @@ self.queue_history_import( trans, archive_type=archive_type, archive_source=archive_source ) return trans.show_message( "Importing history from '%s'. \ This history will be visible when the import is complete" % archive_source ) + #TODO: used in this file and index.mako @web.expose def export_archive( self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False ): @@ -719,6 +696,7 @@ return trans.show_message( "Exporting History '%(n)s'. Use this link to download \ the archive or import it to another Galaxy server: \ <a href='%(u)s'>%(u)s</a>" % ( { 'n' : history.name, 'u' : url } ) ) + #TODO: used in this file and index.mako @web.expose @web.json @@ -733,6 +711,7 @@ "link" : url_for(controller='history', action="display_by_username_and_slug", username=history.user.username, slug=history.slug ) } return return_dict + #TODO: used in page/editor.mako @web.expose @web.require_login( "set history's accessible flag" ) @@ -748,6 +727,7 @@ history.importable = importable trans.sa_session.flush() return + #TODO: used in page/editor.mako @web.expose def get_item_content_async( self, trans, id ): @@ -764,6 +744,7 @@ for dataset in datasets: dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) return trans.stream_template_mako( "/history/item_content.mako", item = history, item_data = datasets ) + #TODO: used in embed_base.mako @web.expose def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): @@ -773,9 +754,12 @@ return ac_data = "" - for history in trans.sa_session.query( model.History ).filter_by( user=user ).filter( func.lower( model.History.name ) .like(q.lower() + "%") ): + for history in ( trans.sa_session.query( model.History ) + .filter_by( user=user ) + .filter( func.lower( model.History.name ).like(q.lower() + "%") ) ): ac_data = ac_data + history.name + "\n" return ac_data + #TODO: used in grid_base.mako @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): @@ -852,6 +836,7 @@ Warning! If you import this history, you will lose your current history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) + #TODO: used in history/view, display, embed @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): @@ -1390,51 +1375,4 @@ def get_item( self, trans, id ): return self.get_history( trans, id ) - - @web.json - def get_display_application_links( self, trans, hda_ids=None ): - """ - Returns external display application JSON data for all/given - HDAs within the current history. - """ - #TODO: fold into API and remove - try: - history = trans.get_history() - #TODO: allow id for more flexibility? (the following doesn't work if anonymous...) - #history = self.get_history( trans, id, check_ownership=True, check_accessible=True, deleted=None ) - if hda_ids: - unencoded_hda_ids = [ trans.security.decode_id( hda_id ) for hda_id in galaxy.util.listify( hda_ids ) ] - #TODO: this gets all - should narrow query by using hda_ids here - no way with this current method - hdas = self.get_history_datasets( trans, history, show_deleted=False, show_hidden=True, show_purged=False ) - - except Exception, exc: - log.error( 'Failed loading data for ids (%s): %s', hda_ids, str( exc ), exc_info=True ) - trans.response.status = 500 - return str( exc ) - - hda_display_links = [] - for hda in hdas: - # only get requested hdas - if hda_ids and hda.id not in unencoded_hda_ids: - continue - - hda_link_data = { 'id': trans.security.encode_id( hda.id ) } - # don't bail on entire list if one hda has an error; record and move on - try: - # 'old style': must be enabled in config (see universe_wsgi.ini) - if trans.app.config.enable_old_display_applications: - hda_link_data[ 'display_types' ] = self.get_old_display_applications( trans, hda ) - - # 'new style' - hda_link_data[ 'display_apps' ] = self.get_display_apps( trans, hda ) - - except Exception, exc: - log.error( 'Failed getting links, hda (%s): %s', hda_link_data[ 'id' ], str( exc ), exc_info=True ) - hda_link_data[ 'error' ] = str( exc ) - - hda_display_links.append( hda_link_data ) - - # send 'do not cache' headers to handle IE's caching of ajax get responses - trans.response.headers[ 'Cache-Control' ] = "max-age=0,no-cache,no-store" - trans.response.set_content_type( 'application/json' ) - return hda_display_links + #TODO: override of base ui controller? diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -34,26 +34,6 @@ // ........................................................................ urls urlRoot: galaxy_config.root + 'api/histories', - /** url for changing the name of the history */ - renameUrl : function(){ -//TODO: just use this.save() - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'history/rename_async?id=' + this.get( 'id' ); - }, - /** url for changing the annotation of the history */ - annotateUrl : function(){ - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'history/annotate_async?id=' + this.get( 'id' ); - }, - /** url for changing the tags of the history */ - tagUrl : function(){ - var id = this.get( 'id' ); - if( !id ){ return undefined; } - return galaxy_config.root + 'tag/get_tagging_elt_async?item_id=' + this.get( 'id' ) + '&item_class=History'; - }, - // ........................................................................ set up/tear down /** Set up the model * @param {Object} historyJSON model data for this History diff -r 3f8e4852623187152ffaea5fd529fac2001c8316 -r 2f79c07c4438b627df03aa3f96dcd51f8b12c641 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 @@ -define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",renameUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"history/rename_async?id="+this.get("id")},annotateUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"history/annotate_async?id="+this.get("id")},tagUrl:function(){var g=this.get("id");if(!g){return undefined}return galaxy_config.root+"tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,r){r=r||{};var l=r.hdaDetailIds||[];var n=jQuery.Deferred(),m=null;function i(s){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(s){if(!s||!s.state_ids){return 0}return _.reduce(s.state_ids,function(t,v,u){return t+v.length},0)}function q(t){if(!g(t)){return[]}if(_.isFunction(l)){l=l(t)}var s=(l.length)?({details:l.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+t.id+"/contents",{data:s})}var p=r.historyFn||i,o=r.hdaFn||q;var k=p(h);k.done(function(s){m=s;n.notify({status:"history data retrieved",historyJSON:m})});k.fail(function(u,s,t){n.reject(u,"loading the history")});var j=k.then(o);j.then(function(s){n.notify({status:"dataset data retrieved",historyJSON:m,hdaJSON:s});n.resolve(m,s)});j.fail(function(u,s,t){n.reject(u,"loading the datasets",{history:m})});return n};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,r){r=r||{};var l=r.hdaDetailIds||[];var n=jQuery.Deferred(),m=null;function i(s){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(s){if(!s||!s.state_ids){return 0}return _.reduce(s.state_ids,function(t,v,u){return t+v.length},0)}function q(t){if(!g(t)){return[]}if(_.isFunction(l)){l=l(t)}var s=(l.length)?({details:l.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+t.id+"/contents",{data:s})}var p=r.historyFn||i,o=r.hdaFn||q;var k=p(h);k.done(function(s){m=s;n.notify({status:"history data retrieved",historyJSON:m})});k.fail(function(u,s,t){n.reject(u,"loading the history")});var j=k.then(o);j.then(function(s){n.notify({status:"dataset data retrieved",historyJSON:m,hdaJSON:s});n.resolve(m,s)});j.fail(function(u,s,t){n.reject(u,"loading the datasets",{history:m})});return n};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}}); 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