Merge branch 'tags_in_history' into dev

client/galaxy/scripts/mvc/history/hda-li.js

@@ -43,6 +43,12 @@ HDAListItemView.prototype.templates = (function(){
                 '<span class="hid"><%- dataset.hid %></span> ',
                 '<span class="name"><%- dataset.name %></span>',
             '</div>',
+            '</br>',
+            '<span class="nametags">',
+                '<% _.each(dataset.nametags, function(tag){ %>',
+                    '<span class="label label-info"><%- tag %></span>',
+                '<% }); %>',
+            '</span>',
         '</div>'
     ], 'dataset' );
 

client/galaxy/style/less/history.less

@@ -221,6 +221,13 @@
                 }
             }
         }
+        span.nametags {
+            span.label {
+                display: inline-block;
+                margin-right: 2px;
+                text-decoration: none;
+            }
+        }
     }
 }
 

lib/galaxy/managers/hdas.py

@@ -254,13 +254,18 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
             'id',
             'type_id',
             'name',
-            'history_id', 'hid',
+            'history_id',
+            'hid',
             'history_content_type',
             'dataset_id',
-            'state', 'extension',
+            'state',
+            'extension',
             'deleted', 'purged', 'visible',
-            'type', 'url',
-            'create_time', 'update_time',
+            'nametags',
+            'type',
+            'url',
+            'create_time',
+            'update_time',
         ])
         self.add_view( 'detailed', [
             'model_class',
@@ -281,6 +286,7 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
             'creating_job',
             'rerunnable',
 
+            'tags',
             'uuid',
             'permissions',
             'file_name',
@@ -292,7 +298,7 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
             # 'url',
             'download_url',
 
-            'annotation', 'tags',
+            'annotation',
 
             'api_type'
         ], include_keys_from='summary' )
@@ -326,7 +332,7 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
             'misc_blurb'    : self._remap_from( 'blurb' ),
             'file_ext'      : self._remap_from( 'extension' ),
             'file_path'     : self._remap_from( 'file_name' ),
-
+            'nametags'      : self.serialize_nametags,
             'resubmitted'   : lambda i, k, **c: self.hda_manager.has_been_resubmitted( i ),
             'display_apps'  : self.serialize_display_apps,
             'display_types' : self.serialize_old_display_applications,
@@ -380,6 +386,17 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
 
         return display_apps
 
+    def serialize_nametags( self, hda, key, trans=None, **context ):
+        """
+        Return list of 'name.' child tags attached to this dataset.
+        TODO: investigate faster ways to fetch children of .name
+        """
+        nametags = []
+        for tag in hda.tags:
+            if tag.user_tname.startswith('name.'):
+                nametags.append(tag.user_tname[5:])
+        return nametags
+
     def serialize_old_display_applications( self, hda, key, trans=None, **context ):
         """
         Return dictionary containing old-style display app urls.

lib/galaxy/tools/actions/__init__.py

@@ -214,6 +214,7 @@ class DefaultToolAction( object ):
         # format.
         input_ext = 'data' if tool.profile < 16.04 else "input"
         input_dbkey = incoming.get( "dbkey", "?" )
+        preserved_tags = []
         for name, data in reversed(inp_data.items()):
             if not data:
                 data = NoneDataset( datatypes_registry=app.datatypes_registry )
@@ -234,6 +235,9 @@ class DefaultToolAction( object ):
             if identifier is not None:
                 incoming[ "%s|__identifier__" % name ] = identifier
 
+            for tag in data.tags:
+                preserved_tags.append(tag)
+
         # Collect chromInfo dataset and add as parameters to incoming
         ( chrom_info, db_dataset ) = app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id != 'CONVERTER_fasta_to_len' )
         if db_dataset:
@@ -303,6 +307,9 @@ class DefaultToolAction( object ):
                 trans.sa_session.add( data )
                 trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions, new=True )
 
+            for tag in preserved_tags:
+                data.tags.append(tag.copy())
+
             # Must flush before setting object store id currently.
             # TODO: optimize this.
             trans.sa_session.flush()

static/maps/analysis.js.map

@@ -0,0 +1 @@
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static/maps/app.js.map

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static/maps/app/analysis.js.map

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static/maps/mvc/history/hda-li.js.map

@@ -1 +1 @@
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+{"version":3,"file":"hda-li.js","sources":["../../../src/mvc/history/hda-li.js"],"names":["define","DATASET_LI","BASE_MVC","_l","_super","DatasetListItemView","HDAListItemView","extend","className","prototype","initialize","attributes","options","call","this","toString","modelString","model","templates","titleBarTemplate","wrapTemplate","warnings","_","hidden","titleBar"],"mappings":"AAAAA,QACI,yBACA,eACA,sBACD,SAAUC,EAAYC,EAAUC,GAEnC,YAGA,IAAIC,GAASH,EAAWI,oBAMpBC,EAAkBF,EAAOG,QAGzBC,UAAcJ,EAAOK,UAAUD,UAAY,mBAE3CE,WAAa,SAAUC,EAAYC,GAC/BR,EAAOK,UAAUC,WAAWG,KAAMC,KAAMH,EAAYC,IAKxDG,SAAW,WACP,GAAIC,GAAgBF,KAAW,MAAIA,KAAKG,MAAQ,GAAK,YACrD,OAAO,mBAAqBD,EAAc,MA8C9C,OAxCJV,GAAgBG,UAAUS,UAAa,WAEnC,GAAIC,GAAmBjB,EAASkB,cAE5B,6CACI,mCACA,sBAEI,+CACA,gDACJ,SACA,QACA,0BACI,gDACI,mDACJ,YACJ,UACJ,UACD,WAECC,EAAWC,EAAEf,UAAYH,EAAOK,UAAUS,UAAUG,UACpDE,OAASrB,EAASkB,cAEd,gCACI,+CACIjB,EAAI,gCACR,SACJ,WACD,YAGP,OAAOmB,GAAEf,UAAYH,EAAOK,UAAUS,WAClCM,SAAWL,EACXE,SAAWA,QAQXf,gBAAmBA"}

static/scripts/analysis.js

@@ -0,0 +1,2 @@
+var jQuery=require("jquery"),$=jQuery,GalaxyApp=require("galaxy").GalaxyApp,QUERY_STRING=require("utils/query-string-parsing"),PANEL=require("layout/panel"),ToolPanel=require("./tool-panel"),HistoryPanel=require("./history-panel"),PAGE=require("layout/page"),ToolForm=require("mvc/tool/tool-form"),UserPreferences=require("mvc/user/user-preferences");Tours=require("mvc/tours"),window.app=function(a,b){window.Galaxy=new GalaxyApp(a,b),Galaxy.debug("analysis app");var c=a.config,d=new ToolPanel({el:"#left",userIsAnonymous:Galaxy.user.isAnonymous(),toolbox:c.toolbox,toolbox_in_panel:c.toolbox_in_panel,stored_workflow_menu_entries:c.stored_workflow_menu_entries,nginx_upload_path:c.nginx_upload_path,ftp_upload_site:c.ftp_upload_site,default_genome:c.default_genome,default_extension:c.default_extension}),e=new PANEL.CenterPanel({el:"#center"}),f=new HistoryPanel({el:"#right",galaxyRoot:Galaxy.root,userIsAnonymous:Galaxy.user.isAnonymous(),allow_user_dataset_purge:c.allow_user_dataset_purge}),g=new PAGE.PageLayoutView(_.extend(a,{el:"body",left:d,center:e,right:f}));Galaxy.page=g,Galaxy.params=Galaxy.config.params,Galaxy.toolPanel=d.tool_panel,Galaxy.upload=d.uploadButton,Galaxy.currHistoryPanel=f.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.app={display:function(a){$(".select2-hidden-accessible").remove(),e.display(a)}},Galaxy.router=new(Backbone.Router.extend({initialize:function(a){this.options=a},execute:function(a,b,c){Galaxy.debug("router execute:",a,b,c);var d=QUERY_STRING.parse(b.pop());b.push(d),a&&a.apply(this,b)},routes:{"(/)":"home","(/)root*":"home","(/)tours(/)(:tour_id)":"show_tours","(/)users(/)":"show_users"},show_tours:function(a){a?Tours.giveTour(a):e.display(new Tours.ToursView)},show_users:function(){e.display(new UserPreferences.View)},home:function(a){a.tool_id||a.job_id?"upload1"===a.tool_id?(Galaxy.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(a):this._loadCenterIframe(a.workflow_id?"workflow/run?id="+a.workflow_id:a.m_c?a.m_c+"/"+a.m_a:"welcome")},_loadToolForm:function(a){a.id=a.tool_id,e.display(new ToolForm.View(a))},_loadCenterIframe:function(a,b){b=b||Galaxy.root,a=b+a,e.$("#galaxy_main").prop("src",a)}}))(a),$(function(){g.render(),g.right.historyView.loadCurrentHistory(),Galaxy.listenTo(g.right.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})}),g.right.historyView.connectToQuotaMeter(g.masthead.quotaMeter),Backbone.history.start({root:Galaxy.root,pushState:!0})})};
+//# sourceMappingURL=../maps/analysis.js.map

static/scripts/app.js

@@ -0,0 +1,2 @@
+define(["utils/utils","layout/masthead","mvc/ui/ui-modal","mvc/ui/ui-modal","mvc/user/user-quotameter"],function(a,b,c,d){return Backbone.View.extend({initialize:function(a){Galaxy.app=this,Galaxy.modal=new c.View,Galaxy.masthead=new b.View(a),this.setElement(this._template(a)),this.$el.append(Galaxy.masthead.$el),$("body").append(this.$el),this.render()},render:function(){require(["app/analysis"],function(a){window.console.log(a)},function(a){console.debug(a)})},initialize2:function(e){this.options=a.merge(e,{}),this.params=this.options.params,this.setElement(this._template(e)),Galaxy.app=this,$("body").append(this.$el);var f=$(this.$el.parent()).attr("scroll","no").addClass("full-content");this.options.message_box_visible&&(f.addClass("has-message-box"),this.$("#messagebox").show()),this.options.show_inactivity_warning&&(f.addClass("has-inactivity-box"),this.$("#inactivebox").show()),Galaxy.masthead||(Galaxy.masthead=new b.View(e),Galaxy.modal=new c.View,Galaxy.menu=new Menu.GalaxyMenu({masthead:Galaxy.masthead,config:e}),Galaxy.quotaMeter=new d.UserQuotaMeter({model:Galaxy.user,el:Galaxy.masthead.$(".quota-meter-container")}).render())},display:function(a,b){$(".select2-hidden-accessible").remove(),this.panels&&this.panels[b||"center"].display(a)},_buildPanels:function(b,c){this.panels=[];var d=["left","center","right"];for(var e in d){var f=d[e],g=this.panels[f]=new b[f](c);if("center"==f)this.$("#center").append(g.$el);else{var h=a.merge(g.components,{header:{title:"",cls:"",buttons:[]},body:{cls:""}}),i=$(this._templatePanel(f));i.find(".panel-header-text").html(h.header.title),i.find(".unified-panel-header-inner").addClass(h.header.cls);for(var e in h.header.buttons)i.find(".panel-header-buttons").append(h.header.buttons[e].$el);i.find(".unified-panel-body").addClass(h.body.cls).append(g.$el);{new Panel({center:this.$("#center"),panel:i,drag:i.find(".unified-panel-footer > .drag"),toggle:i.find(".unified-panel-footer > .panel-collapse"),right:"right"==f})}this.$el.append(i)}}},_templatePanel:function(a){return'<div id="'+a+'"><div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"><div class="panel-header-buttons" style="float: right"/><div class="panel-header-text"/></div></div><div class="unified-panel-body"/><div class="unified-panel-footer"><div class="panel-collapse '+a+'"/><div class="drag"/></div></div>'},_template:function(){return'<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"><div id="background"/><div id="messagebox" class="panel-'+Galaxy.config.message_box_class+'-message" style="display: none;">'+Galaxy.config.message_box_content+'</div><div id="inactivebox" class="panel-warning-message" style="display: none;">'+Galaxy.config.inactivity_box_content+' <a href="'+Galaxy.root+'user/resend_verification">Resend verification.</a></div><div id="center" class="inbound"/></div>'}})});
+//# sourceMappingURL=../maps/app.js.map

static/scripts/app/analysis.js

@@ -0,0 +1,2 @@
+define([],function(){Backbone.View.extend({initialize:function(a){this.options=Utils.merge(a,{}),this.setElement(this._template());var b=this.options.params;this.$("#galaxy_main").prop("src",Galaxy.root+(b.tool_id&&"tool_runner?"+$.param(b)||b.workflow_id&&"workflow/run?id="+b.workflow_id||b.m_c&&b.m_c+"/"+b.m_a||Galaxy.config.require_login&&!Galaxy.user.id&&"user/login"||"root/welcome"));var c=this;this.$("#galaxy_main").on("load",function(){$(this).show(),c.$("#center-panel").empty().hide()})},display:function(a){this.$("#galaxy_main").hide(),this.$("#center-panel").empty().scrollTop(0).append(a).show()},_template:function(){return'<div style="position: absolute; width: 100%; height: 100%"><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;"/><div id="center-panel" style="position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/></div>'}}),Backbone.View.extend({initialize:function(a){if(this.options=Utils.merge(a,{}),this.setElement(this._template()),Galaxy.user.id||!Galaxy.config.require_login){var b=new Tools.ToolSearch({spinner_url:a.spinner_url,search_url:a.search_url,hidden:!1}),c=new Tools.ToolCollection(a.toolbox),d=new Tools.ToolPanel({tool_search:b,tools:c,layout:a.toolbox_in_panel});tool_panel_view=new Tools.ToolPanelView({model:d}),Galaxy.toolPanel=d,d.get("layout").size()>0&&(tool_panel_view.render(),this.$(".toolMenu").show()),this.$el.prepend(tool_panel_view.$el),this.$("#internal-workflows").append(this._templateTool({title:"All workflows",href:"workflow/list_for_run"}));for(var e in a.stored_workflow_menu_entries){var f=a.stored_workflow_menu_entries[e];this.$("#internal-workflows").append(this._templateTool({title:f.stored_workflow.name,href:"workflow/run?id="+f.encoded_stored_workflow_id}))}this.$("a[minsizehint]").click(function(){parent.handle_minwidth_hint&&parent.handle_minwidth_hint($(this).attr("minsizehint"))}),Galaxy.upload=new Upload(a),this.components={header:{title:"Tools",buttons:[Galaxy.upload]}}}},_templateTool:function(a){return'<div class="toolTitle"><a href="'+Galaxy.root+a.href+'" target="galaxy_main">'+a.title+"</a></div>"},_template:function(){return'<div class="toolMenuContainer"><div class="toolMenu" style="display: none"><div id="search-no-results" style="display: none; padding-top: 5px"><em><strong>Search did not match any tools.</strong></em></div></div><div class="toolSectionPad"/><div class="toolSectionPad"/><div class="toolSectionTitle" id="title_XXinternalXXworkflow"><span>Workflows</span></div><div id="internal-workflows" class="toolSectionBody"><div class="toolSectionBg"/></div></div>'}}),Backbone.View.extend({initialize:function(a){this.options=Utils.merge(a,{}),this.setElement(this._template());var b=new Ui.ButtonLink({id:"history-refresh-button",title:"Refresh history",cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){top.Galaxy&&top.Galaxy.currHistoryPanel&&top.Galaxy.currHistoryPanel.loadCurrentHistory()}}),c=new Ui.ButtonLink({id:"history-options-button",title:"History options",cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:Galaxy.root+"root/history_options"}),d=new Ui.ButtonLink({id:"history-view-multi-button",title:"View all histories",cls:"panel-header-button",icon:"fa fa-columns",href:Galaxy.root+"history/view_multiple"});this.components={header:{title:"History",cls:"history-panel-header",buttons:[b,c,d]},body:{cls:"unified-panel-body-background"}},Galaxy.historyOptionsMenu=optionsMenu(c.$el,{anonymous:Galaxy.user.id&&"true"||"false",purgeAllowed:Galaxy.config.allow_user_dataset_purge&&"true"||"false",root:Galaxy.root}),Galaxy.currHistoryPanel=new HistoryPanel.CurrentHistoryPanel({el:this.$el,purgeAllowed:Galaxy.config.allow_user_dataset_purge,linkTarget:"galaxy_main",$scrollContainer:function(){return this.$el.parent()}}),Galaxy.currHistoryPanel.connectToQuotaMeter(Galaxy.quotaMeter),Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),Galaxy.currHistoryPanel.loadCurrentHistory()},_template:function(){return'<div id="current-history-panel" class="history-panel"/>'}});return{left:Backbone.View.extend({initialize:function(){}})}});
+//# sourceMappingURL=../../maps/app/analysis.js.map

static/scripts/mvc/history/hda-li.js

@@ -1,2 +1,2 @@
-define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c){"use strict";var d=a.DatasetListItemView,e=d.extend({className:d.prototype.className+" history-content",initialize:function(a,b){d.prototype.initialize.call(this,a,b)},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAListItemView("+a+")"}});return e.prototype.templates=function(){var a=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- dataset.hid %></span> ','<span class="name"><%- dataset.name %></span>',"</div>","</div>"],"dataset"),e=_.extend({},d.prototype.templates.warnings,{hidden:b.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',c("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return _.extend({},d.prototype.templates,{titleBar:a,warnings:e})}(),{HDAListItemView:e}});
+define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c){"use strict";var d=a.DatasetListItemView,e=d.extend({className:d.prototype.className+" history-content",initialize:function(a,b){d.prototype.initialize.call(this,a,b)},toString:function(){var a=this.model?this.model+"":"(no model)";return"HDAListItemView("+a+")"}});return e.prototype.templates=function(){var a=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="hid"><%- dataset.hid %></span> ','<span class="name"><%- dataset.name %></span>',"</div>","</br>",'<span class="nametags">',"<% _.each(dataset.nametags, function(tag){ %>",'<span class="label label-info"><%- tag %></span>',"<% }); %>","</span>","</div>"],"dataset"),e=_.extend({},d.prototype.templates.warnings,{hidden:b.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',c("This dataset has been hidden"),"</div>","<% } %>"],"dataset")});return _.extend({},d.prototype.templates,{titleBar:a,warnings:e})}(),{HDAListItemView:e}});
 //# sourceMappingURL=../../../maps/mvc/history/hda-li.js.map