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commit/galaxy-central: dan: Comment out igv local external display application link by default, since it is confusing users (most do not have a local igv running).
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3947a9273550/ Changeset: 3947a9273550 User: dan Date: 2015-02-11 20:39:38+00:00 Summary: Comment out igv local external display application link by default, since it is confusing users (most do not have a local igv running). Affected #: 1 file diff -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 -r 3947a92735506923a0f51abe36263bbc0aecfb79 tool-data/shared/igv/igv_build_sites.txt.sample --- a/tool-data/shared/igv/igv_build_sites.txt.sample +++ b/tool-data/shared/igv/igv_build_sites.txt.sample @@ -1,4 +1,4 @@ #site_id site_name site_url dbkey ivg_build_name web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum #web_jnlp_1.5 web 1.5 http://www.broadinstitute.org/igvdata/jws/prod hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum -local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum \ No newline at end of file +#local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: rename the link from toolform to the Tool Shed
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11d7c10c1b5e/ Changeset: 11d7c10c1b5e User: martenson Date: 2015-02-11 19:31:13+00:00 Summary: rename the link from toolform to the Tool Shed Affected #: 3 files diff -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -290,7 +290,7 @@ if (this.options.sharable_url) { menu_button.addMenu({ icon : 'fa-external-link', - title : 'Open in Toolshed', + title : 'See in Tool Shed', tooltip : 'Access the repository', onclick : function() { window.open(self.options.sharable_url); diff -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -290,7 +290,7 @@ if (this.options.sharable_url) { menu_button.addMenu({ icon : 'fa-external-link', - title : 'Open in Toolshed', + title : 'See in Tool Shed', tooltip : 'Access the repository', onclick : function() { window.open(self.options.sharable_url); diff -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l.deferred.reset();l.deferred.execute(function(){l._updateModel(m)})}});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l.deferred.reset();l.deferred.execute(function(){l._updateModel(m)})}});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: UI, history multi-view: pressing enter in the history copy dialog will copy the history and close the dialog
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c6915ffcd27c/ Changeset: c6915ffcd27c User: carlfeberhard Date: 2015-02-11 18:52:40+00:00 Summary: UI, history multi-view: pressing enter in the history copy dialog will copy the history and close the dialog Affected #: 3 files diff -r c171738e365b598c2ea43a0b09dd9c458d4431b1 -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -46,6 +46,11 @@ Galaxy.modal.hide(); }); } + function checkNameAndCopy(){ + var name = Galaxy.modal.$( '#copy-modal-title' ).val(); + if( !validateName( name ) ){ return; } + copyHistory( name ); + } Galaxy.modal.show( _.extend({ title : _l( 'Copying history' ) + ' "' + historyName + '"', @@ -58,14 +63,15 @@ ].join('')), buttons : { 'Cancel' : function(){ Galaxy.modal.hide(); }, - 'Copy' : function(){ - var name = Galaxy.modal.$( '#copy-modal-title' ).val(); - if( !validateName( name ) ){ return; } - copyHistory( name ); - } + 'Copy' : checkNameAndCopy } }, options )); $( '#copy-modal-title' ).focus().select(); + $( '#copy-modal-title' ).on( 'keydown', function( ev ){ + if( ev.keyCode === 13 ){ + checkNameAndCopy(); + } + }); } diff -r c171738e365b598c2ea43a0b09dd9c458d4431b1 -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -46,6 +46,11 @@ Galaxy.modal.hide(); }); } + function checkNameAndCopy(){ + var name = Galaxy.modal.$( '#copy-modal-title' ).val(); + if( !validateName( name ) ){ return; } + copyHistory( name ); + } Galaxy.modal.show( _.extend({ title : _l( 'Copying history' ) + ' "' + historyName + '"', @@ -58,14 +63,15 @@ ].join('')), buttons : { 'Cancel' : function(){ Galaxy.modal.hide(); }, - 'Copy' : function(){ - var name = Galaxy.modal.$( '#copy-modal-title' ).val(); - if( !validateName( name ) ){ return; } - copyHistory( name ); - } + 'Copy' : checkNameAndCopy } }, options )); $( '#copy-modal-title' ).focus().select(); + $( '#copy-modal-title' ).on( 'keydown', function( ev ){ + if( ev.keyCode === 13 ){ + checkNameAndCopy(); + } + }); } diff -r c171738e365b598c2ea43a0b09dd9c458d4431b1 -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){window.HISTORY_MODEL=d;function g(H,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return H.copy()}var F=H.get("name"),C="Copy of '"+F+"'";function D(J){if(!J){if(!Galaxy.modal.$("#invalid-title").size()){var I=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(I)}return false}return J}function G(I){var J=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(J);H.copy(true,I).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){var I=Galaxy.modal.$("#copy-modal-title").val();if(!D(I)){return}G(I)}}},E));$("#copy-modal-title").focus().select()}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',D.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var C=this,D;if(this.model.get("deleted")){D=this.model.undelete()}else{D=this.model._delete()}D.fail(function(G,E,F){alert(_l("Could not delete the history")+":\n"+F)}).done(function(E){C.render()})},"click .copy-history.btn":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.template(C.options));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},template:function w(C){C=C||{};var D=[];if(this.options.headerHeight){D=D.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}D=D.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(D.join(""))},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")}},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var D=this;D.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(D.includeDeletedHistories,D)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(D.excludeDeletedHistories,D)}]});D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});D.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowDeleted(E,false)},F*200)})});D.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowHidden(E,false)},F*200)})});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){window.HISTORY_MODEL=d;function g(I,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var F=I.get("name"),C="Copy of '"+F+"'";function D(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function G(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}function H(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!D(J)){return}G(J)}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:H}},E));$("#copy-modal-title").focus().select();$("#copy-modal-title").on("keydown",function(J){if(J.keyCode===13){H()}})}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',D.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var C=this,D;if(this.model.get("deleted")){D=this.model.undelete()}else{D=this.model._delete()}D.fail(function(G,E,F){alert(_l("Could not delete the history")+":\n"+F)}).done(function(E){C.render()})},"click .copy-history.btn":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.template(C.options));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},template:function w(C){C=C||{};var D=[];if(this.options.headerHeight){D=D.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}D=D.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(D.join(""))},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")}},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var D=this;D.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(D.includeDeletedHistories,D)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(D.excludeDeletedHistories,D)}]});D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});D.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowDeleted(E,false)},F*200)})});D.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowHidden(E,false)},F*200)})});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:m}}); \ 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.

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commit/galaxy-central: carlfeberhard: UI, history multi-view: use Galaxy.options.root or galaxy_config.root for 'Done' button if available
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c171738e365b/ Changeset: c171738e365b User: carlfeberhard Date: 2015-02-11 18:42:12+00:00 Summary: UI, history multi-view: use Galaxy.options.root or galaxy_config.root for 'Done' button if available Affected #: 5 files diff -r bc6a54c340fb81096d73ea76122eca3675117df8 -r c171738e365b598c2ea43a0b09dd9c458d4431b1 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -390,6 +390,7 @@ return paired; }, + /** autopair by exact match */ autopairSimple : autoPairFnBuilder({ scoreThreshold: function(){ return 1.0; }, match : function _match( params ){ @@ -404,6 +405,7 @@ } }), + /** autopair by levenshtein edit distance scoring */ autopairLevenshtein : autoPairFnBuilder({ scoreThreshold: function(){ return this.matchPercentage; }, match : function _matches( params ){ @@ -420,6 +422,7 @@ } }), + /** autopair by longest common substrings scoring */ autopairLCS : autoPairFnBuilder({ scoreThreshold: function(){ return this.matchPercentage; }, match : function _matches( params ){ diff -r bc6a54c340fb81096d73ea76122eca3675117df8 -r c171738e365b598c2ea43a0b09dd9c458d4431b1 client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -504,16 +504,6 @@ return this.collection.create({ current: true }); }, - ///** delete the current history */ - //deleteCurrent : function deleteCurrent(){ - // var multipanel = this, - // currentColumn = multipanel.columnMap[ multipanel.currentHistoryId ]; - // currentColumn.model._delete() - // .done( function(){ - // multipanel.create(); - // }); - //}, - // ------------------------------------------------------------------------ columns /** create columns from collection */ createColumns : function createColumns( columnOptions ){ @@ -877,7 +867,7 @@ /** */ events : { // will move to the server root (gen. Analyze data) - 'click .done.btn' : function(){ window.location = '/'; }, + 'click .done.btn' : 'close', //TODO:?? could just go back - but that's not always correct/desired behav. //'click .done.btn' : function(){ window.history.back(); }, // creates a new empty history and makes it current @@ -890,6 +880,17 @@ //'dragstart .list-item .title-bar' : function( e ){ console.debug( 'ok' ); } }, + close : function( ev ){ + //TODO: switch to pushState/router + var destination = '/'; + if( Galaxy && Galaxy.options && Galaxy.options.root ){ + destination = Galaxy.options.root; + } else if( galaxy_config && galaxy_config.root ){ + destination = galaxy_config.root; + } + window.location = destination; + }, + /** Include deleted histories in the collection */ includeDeletedHistories : function(){ //TODO: better through API/limit+offset diff -r bc6a54c340fb81096d73ea76122eca3675117df8 -r c171738e365b598c2ea43a0b09dd9c458d4431b1 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -390,6 +390,7 @@ return paired; }, + /** autopair by exact match */ autopairSimple : autoPairFnBuilder({ scoreThreshold: function(){ return 1.0; }, match : function _match( params ){ @@ -404,6 +405,7 @@ } }), + /** autopair by levenshtein edit distance scoring */ autopairLevenshtein : autoPairFnBuilder({ scoreThreshold: function(){ return this.matchPercentage; }, match : function _matches( params ){ @@ -420,6 +422,7 @@ } }), + /** autopair by longest common substrings scoring */ autopairLCS : autoPairFnBuilder({ scoreThreshold: function(){ return this.matchPercentage; }, match : function _matches( params ){ diff -r bc6a54c340fb81096d73ea76122eca3675117df8 -r c171738e365b598c2ea43a0b09dd9c458d4431b1 static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -504,16 +504,6 @@ return this.collection.create({ current: true }); }, - ///** delete the current history */ - //deleteCurrent : function deleteCurrent(){ - // var multipanel = this, - // currentColumn = multipanel.columnMap[ multipanel.currentHistoryId ]; - // currentColumn.model._delete() - // .done( function(){ - // multipanel.create(); - // }); - //}, - // ------------------------------------------------------------------------ columns /** create columns from collection */ createColumns : function createColumns( columnOptions ){ @@ -877,7 +867,7 @@ /** */ events : { // will move to the server root (gen. Analyze data) - 'click .done.btn' : function(){ window.location = '/'; }, + 'click .done.btn' : 'close', //TODO:?? could just go back - but that's not always correct/desired behav. //'click .done.btn' : function(){ window.history.back(); }, // creates a new empty history and makes it current @@ -890,6 +880,17 @@ //'dragstart .list-item .title-bar' : function( e ){ console.debug( 'ok' ); } }, + close : function( ev ){ + //TODO: switch to pushState/router + var destination = '/'; + if( Galaxy && Galaxy.options && Galaxy.options.root ){ + destination = Galaxy.options.root; + } else if( galaxy_config && galaxy_config.root ){ + destination = galaxy_config.root; + } + window.location = destination; + }, + /** Include deleted histories in the collection */ includeDeletedHistories : function(){ //TODO: better through API/limit+offset diff -r bc6a54c340fb81096d73ea76122eca3675117df8 -r c171738e365b598c2ea43a0b09dd9c458d4431b1 static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){window.HISTORY_MODEL=d;function g(H,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return H.copy()}var F=H.get("name"),C="Copy of '"+F+"'";function D(J){if(!J){if(!Galaxy.modal.$("#invalid-title").size()){var I=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(I)}return false}return J}function G(I){var J=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(J);H.copy(true,I).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){var I=Galaxy.modal.$("#copy-modal-title").val();if(!D(I)){return}G(I)}}},E));$("#copy-modal-title").focus().select()}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',D.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var C=this,D;if(this.model.get("deleted")){D=this.model.undelete()}else{D=this.model._delete()}D.fail(function(G,E,F){alert(_l("Could not delete the history")+":\n"+F)}).done(function(E){C.render()})},"click .copy-history.btn":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.template(C.options));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},template:function w(C){C=C||{};var D=[];if(this.options.headerHeight){D=D.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}D=D.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(D.join(""))},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":function(){window.location="/"},"click .create-new.btn":"create","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")}},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var D=this;D.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(D.includeDeletedHistories,D)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(D.excludeDeletedHistories,D)}]});D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});D.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowDeleted(E,false)},F*200)})});D.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowHidden(E,false)},F*200)})});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue","ui/mode-button","ui/search-input"],function(d,l,z,a){window.HISTORY_MODEL=d;function g(H,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return H.copy()}var F=H.get("name"),C="Copy of '"+F+"'";function D(J){if(!J){if(!Galaxy.modal.$("#invalid-title").size()){var I=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(I)}return false}return J}function G(I){var J=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(J);H.copy(true,I).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){var I=Galaxy.modal.$("#copy-modal-title").val();if(!D(I)){return}G(I)}}},E));$("#copy-modal-title").focus().select()}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',D.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var C=this,D;if(this.model.get("deleted")){D=this.model.undelete()}else{D=this.model._delete()}D.fail(function(G,E,F){alert(_l("Could not delete the history")+":\n"+F)}).done(function(E){C.render()})},"click .copy-history.btn":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.template(C.options));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},template:function w(C){C=C||{};var D=[];if(this.options.headerHeight){D=D.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}D=D.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(D.join(""))},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":"close","click .create-new.btn":"create","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")}},close:function(D){var C="/";if(Galaxy&&Galaxy.options&&Galaxy.options.root){C=Galaxy.options.root}else{if(galaxy_config&&galaxy_config.root){C=galaxy_config.root}}window.location=C},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var D=this;D.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(D.includeDeletedHistories,D)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(D.excludeDeletedHistories,D)}]});D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});D.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowDeleted(E,false)},F*200)})});D.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowHidden(E,false)},F*200)})});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:m}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fdb5e1329ef2/ Changeset: fdb5e1329ef2 User: carlfeberhard Date: 2015-02-11 18:15:53+00:00 Summary: UI, paired collection creator: add metrics for init, creation, and filter-change Affected #: 3 files diff -r 86ac99a2896b87915e35b81db1320fdfe73bf556 -r fdb5e1329ef2de9a712f5139bcd71ee4ac278f24 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -188,6 +188,7 @@ /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */ initialize : function( attributes ){ + this.metric( 'PairedCollectionCreator.initialize', attributes ); //this.debug( '-- PairedCollectionCreator:', attributes ); attributes = _.defaults( attributes, { @@ -584,6 +585,7 @@ .done( function( response, message, xhr ){ //this.info( 'ok', response, message, xhr ); creator.trigger( 'collection:created', response, message, xhr ); + creator.metric( 'collection:created', response ); if( typeof creator.oncreate === 'function' ){ creator.oncreate.call( this, response, message, xhr ); } @@ -883,6 +885,7 @@ this.$( '.forward-unpaired-filter input' ).val(), this.$( '.reverse-unpaired-filter input' ).val() ]; + this.metric( 'filter-change', this.filters ); this._renderFilters(); this._renderUnpaired(); }); @@ -1028,12 +1031,14 @@ /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */ _clickUnpairAll : function( ev ){ + this.metric( 'unpairAll' ); this.unpairAll(); }, /** attempt to autopair */ _clickAutopair : function( ev ){ - this.autoPair(); + var paired = this.autoPair(); + this.metric( 'autopair', paired.length, this.unpaired.length ); this.trigger( 'autopair' ); }, diff -r 86ac99a2896b87915e35b81db1320fdfe73bf556 -r fdb5e1329ef2de9a712f5139bcd71ee4ac278f24 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -188,6 +188,7 @@ /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */ initialize : function( attributes ){ + this.metric( 'PairedCollectionCreator.initialize', attributes ); //this.debug( '-- PairedCollectionCreator:', attributes ); attributes = _.defaults( attributes, { @@ -584,6 +585,7 @@ .done( function( response, message, xhr ){ //this.info( 'ok', response, message, xhr ); creator.trigger( 'collection:created', response, message, xhr ); + creator.metric( 'collection:created', response ); if( typeof creator.oncreate === 'function' ){ creator.oncreate.call( this, response, message, xhr ); } @@ -883,6 +885,7 @@ this.$( '.forward-unpaired-filter input' ).val(), this.$( '.reverse-unpaired-filter input' ).val() ]; + this.metric( 'filter-change', this.filters ); this._renderFilters(); this._renderUnpaired(); }); @@ -1028,12 +1031,14 @@ /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */ _clickUnpairAll : function( ev ){ + this.metric( 'unpairAll' ); this.unpairAll(); }, /** attempt to autopair */ _clickAutopair : function( ev ){ - this.autoPair(); + var paired = this.autoPair(); + this.metric( 'autopair', paired.length, this.unpaired.length ); this.trigger( 'autopair' ); }, diff -r 86ac99a2896b87915e35b81db1320fdfe73bf556 -r fdb5e1329ef2de9a712f5139bcd71ee4ac278f24 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,b,f,c){var i=Backbone.View.extend(f.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(l){this.pair=l.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(l){l.currentTarget.style.opacity="0.4";if(l.originalEvent){l=l.originalEvent}l.dataTransfer.effectAllowed="move";l.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(l){l.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(l){this.$el.parent().trigger(l)},toString:function(){return"PairView("+this.pair.name+")"}});function g(m){m=m||{};m.createPair=m.createPair||function l(r){this.debug("creating pair:",r.listA[r.indexA].name,r.listB[r.indexB].name);r=r||{};return this._pair(r.listA.splice(r.indexA,1)[0],r.listB.splice(r.indexB,1)[0],{silent:true})};var o=[];function q(){if(!o.length){o=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]}return o}m.preprocessMatch=m.preprocessMatch||function n(s){var r=q.call(this);return _.extend(s,{matchTo:s.matchTo.name.replace(r[0],""),possible:s.possible.name.replace(r[1],"")})};return function p(t){this.debug("autopair _strategy ---------------------------");t=t||{};var r=t.listA,A=t.listB,z=0,y,v={score:0,index:null},x=[];this.debug("starting list lens:",r.length,A.length);this.debug("bestMatch (starting):",JSON.stringify(v,null," "));while(z<r.length){var w=r[z];v.score=0;for(y=0;y<A.length;y++){var u=A[y];this.debug(z+":"+w.name);this.debug(y+":"+u.name);if(r[z]!==A[y]){v=m.match.call(this,m.preprocessMatch.call(this,{matchTo:w,possible:u,index:y,bestMatch:v}));this.debug("bestMatch:",JSON.stringify(v,null," "));if(v.score===1){this.debug("breaking early due to perfect match");break}}}var s=m.scoreThreshold.call(this);this.debug("scoreThreshold:",s);this.debug("bestMatch.score:",v.score);if(v.score>=s){this.debug("creating pair");x.push(m.createPair.call(this,{listA:r,indexA:z,listB:A,indexB:v.index}));this.debug("list lens now:",r.length,A.length)}else{z+=1}if(!r.length||!A.length){return x}}this.debug("paired:",JSON.stringify(x,null," "));this.debug("autopair _strategy ---------------------------");return x}}var k=Backbone.View.extend(f.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(l){l=_.defaults(l,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,strategy:"lcs",matchPercentage:0.9,twoPassAutopairing:true});this.initialList=l.datasets;this.historyId=l.historyId;this.filters=this.commonFilters[l.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(l.filters)){this.filters=l.filters}this.automaticallyPair=l.automaticallyPair;this.strategy=this.strategies[l.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(l.strategy)){this.strategy=l.strategy}this.matchPercentage=l.matchPercentage;this.twoPassAutopairing=l.twoPassAutopairing;this.removeExtensions=true;this.oncancel=l.oncancel;this.oncreate=l.oncreate;this.autoscrollDist=l.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(l){l.sort(function(n,m){return b(n.name,m.name)});return l},_ensureIds:function(){this.initialList.forEach(function(l){if(!l.hasOwnProperty("id")){l.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(){var o=this.filters.map(function(p){return new RegExp(p)}),m=[[],[]];function n(p,q){return q.test(p.name)}this.unpaired.forEach(function l(p){o.forEach(function(r,q){if(n(p,r)){m[q].push(p)}})});return m},_addToUnpaired:function(m){var l=function(n,p){if(n===p){return n}var o=Math.floor((p-n)/2)+n,q=b(m.name,this.unpaired[o].name);if(q<0){return l(n,o)}else{if(q>0){return l(o+1,p)}}while(this.unpaired[o]&&this.unpaired[o].name===m.name){o++}return o}.bind(this);this.unpaired.splice(l(0,this.unpaired.length),0,m)},autoPair:function(n){var m=this._splitByFilters(),l=[];if(this.twoPassAutopairing){l=this.autopairSimple({listA:m[0],listB:m[1]});m=this._splitByFilters()}n=n||this.strategy;m=this._splitByFilters();l=l.concat(this[n].call(this,{listA:m[0],listB:m[1]}));return l},autopairSimple:g({scoreThreshold:function(){return 1},match:function j(l){l=l||{};if(l.matchTo===l.possible){return{index:l.index,score:1}}return l.bestMatch}}),autopairLevenshtein:g({scoreThreshold:function(){return this.matchPercentage},match:function e(m){m=m||{};var n=h(m.matchTo,m.possible),l=1-(n/(Math.max(m.matchTo.length,m.possible.length)));if(l>m.bestMatch.score){return{index:m.index,score:l}}return m.bestMatch}}),autopairLCS:g({scoreThreshold:function(){return this.matchPercentage},match:function e(n){n=n||{};var l=this._naiveStartingAndEndingLCS(n.matchTo,n.possible).length,m=l/(Math.max(n.matchTo.length,n.possible.length));if(m>n.bestMatch.score){return{index:n.index,score:m}}return n.bestMatch}}),_naiveStartingAndEndingLCS:function(o,m){var p="",q="",n=0,l=0;while(n<o.length&&n<m.length){if(o[n]!==m[n]){break}p+=o[n];n+=1}if(n===o.length){return o}if(n===m.length){return m}n=(o.length-1);l=(m.length-1);while(n>=0&&l>=0){if(o[n]!==m[l]){break}q=[o[n],q].join("");n-=1;l-=1}return p+q},_pair:function(n,l,m){m=m||{};var o=this._createPair(n,l,m.name);this.paired.push(o);this.unpaired=_.without(this.unpaired,n,l);if(!m.silent){this.trigger("pair:new",o)}return o},_createPair:function(n,l,m){if(!(n&&l)||(n===l)){throw new Error("Bad pairing: "+[JSON.stringify(n),JSON.stringify(l)])}m=m||this._guessNameForPair(n,l);return{forward:n,name:m,reverse:l}},_guessNameForPair:function(o,m,q){q=(q!==undefined)?(q):(this.removeExtensions);var l=o.name,p=m.name,n=this._naiveStartingAndEndingLCS(l.replace(this.filters[0],""),p.replace(this.filters[1],""));if(q){var r=n.lastIndexOf(".");if(r>0){var s=n.slice(r,n.length);n=n.replace(s,"");l=l.replace(s,"");p=p.replace(s,"")}}return n||(l+" & "+p)},_unpair:function(m,l){l=l||{};if(!m){throw new Error("Bad pair: "+JSON.stringify(m))}this.paired=_.without(this.paired,m);this._addToUnpaired(m.forward);this._addToUnpaired(m.reverse);if(!l.silent){this.trigger("pair:unpair",[m])}return m},unpairAll:function(){var l=[];while(this.paired.length){l.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",l)},_pairToJSON:function(m,l){l=l||"hda";return{collection_type:"paired",src:"new_collection",name:m.name,element_identifiers:[{name:"forward",id:m.forward.id,src:l},{name:"reverse",id:m.reverse.id,src:l}]}},createList:function(n){var o=this,m="/api/histories/"+this.historyId+"/contents/dataset_collections";var l={type:"dataset_collection",collection_type:"list:paired",name:_.escape(n||o.$(".collection-name").val()),element_identifiers:o.paired.map(function(p){return o._pairToJSON(p)})};return jQuery.ajax(m,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(l)}).fail(function(r,p,q){o._ajaxErrHandler(r,p,q)}).done(function(p,q,r){o.trigger("collection:created",p,q,r);if(typeof o.oncreate==="function"){o.oncreate.call(this,p,q,r)}})},_ajaxErrHandler:function(o,l,n){this.error(o,l,n);var m=c("An error occurred while creating this collection");if(o){if(o.readyState===0&&o.status===0){m+=": "+c("Galaxy could not be reached and may be updating.")+c(" Try again in a few minutes.")}else{if(o.responseJSON){m+="<br /><pre>"+JSON.stringify(o.responseJSON)+"</pre>"}else{m+=": "+n}}}creator._showAlert(m,"alert-danger")},render:function(l,m){this.$el.empty().html(k.templates.main());this._renderHeader(l);this._renderMiddle(l);this._renderFooter(l);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(m,n){var l=this.$(".header").empty().html(k.templates.header()).find(".help-content").prepend($(k.templates.helpContent()));this._renderFilters();return l},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(m,n){var l=this.$(".middle").empty().html(k.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return l},_renderUnpaired:function(q,r){var o=this,p,m,l=[],n=this._splitByFilters();this.$(".forward-column .title").text([n[0].length,c("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[0].length));this.$(".reverse-column .title").text([n[1].length,c("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}m=n[1].map(function(t,s){if((n[0][s]!==undefined)&&(n[0][s]!==t)){l.push(o._renderPairButton())}return o._renderUnpairedDataset(t)});p=n[0].map(function(s){return o._renderUnpairedDataset(s)});if(!p.length&&!m.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(p).add(this.$(".unpaired-columns .paired-column .column-datasets").append(l)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(m));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(l){return["(",l," ",c("filtered out"),")"].join("")},_renderUnpairedDataset:function(l){return $("<li/>").attr("id","dataset-"+l.id).addClass("dataset unpaired").attr("draggable",true).addClass(l.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(l.name)).data("dataset",l)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(c("Pair these datasets")))},_renderUnpairedEmpty:function(){var l=$('<div class="empty-message"></div>').text("("+c("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(l);return l},_renderUnpairedNotShown:function(){var l=$('<div class="empty-message"></div>').text("("+c("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(l);return l},_adjUnpairedOnScrollbar:function(){var o=this.$(".unpaired-columns").last(),p=this.$(".unpaired-columns .reverse-column .dataset").first();if(!p.size()){return}var l=o.offset().left+o.outerWidth(),n=p.offset().left+p.outerWidth(),m=Math.floor(l)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",(m>0)?m:0)},_renderPaired:function(m,n){this.$(".paired-column-title .title").text([this.paired.length,c("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var l=this;this.paired.forEach(function(q,o){var p=new i({pair:q});l.$(".paired-columns .column-datasets").append(p.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',c("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var l=$('<div class="empty-message"></div>').text("("+c("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(l);return l},_renderFooter:function(m,n){var l=this.$(".footer").empty().html(k.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return l},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(l){function m(p,o){return['<button class="filter-choice btn" ','data-forward="',p,'" data-reverse="',o,'">',c("Forward"),": ",p,", ",c("Reverse"),": ",o,"</button>"].join("")}var n=$(_.template(['<div class="choose-filters">','<div class="help">',c("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",_.values(this.commonFilters).map(function(o){return m(o[0],o[1])}).join(""),"</div>"].join(""))({}));return this.$(l).popover({container:".collection-creator",placement:"bottom",html:true,content:n})},_validationWarning:function(m,l){var n="validation-warning";if(m==="name"){m=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(l){m=m||this.$("."+n);m.removeClass(n)}else{m.addClass(n)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(l){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var l,m=null;if(this.paired.length){m="alert-success";l=this.paired.length+" "+c("pairs created");if(!this.unpaired.length){l+=": "+c("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{l=c("Could not automatically create any pairs from the given dataset names")}this._showAlert(l,m)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(l){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(l){$(l.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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.remove-extensions":function(l){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(l){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(l){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(l){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(m,l){l=l||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(l).show().find(".alert-message").html(m)},_hideAlert:function(l){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(l){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(l){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(l,m){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(l,m)},hidePaired:function(l,m){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(l,m)},splitView:function(l,m){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(l,m);return this},_clickUnpairAll:function(l){this.unpairAll()},_clickAutopair:function(l){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(m){var l=$(m.currentTarget);this.$(".forward-unpaired-filter input").val(l.data("forward"));this.$(".reverse-unpaired-filter input").val(l.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(l){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(l){l.stopPropagation();return this.toggleSelectUnpaired($(l.currentTarget))},toggleSelectUnpaired:function(n,m){m=m||{};var o=n.data("dataset"),l=m.force!==undefined?m.force:!n.hasClass("selected");if(!n.size()||o===undefined){return n}if(l){n.addClass("selected");if(!m.waitToPair){this.pairAllSelected()}}else{n.removeClass("selected")}return n},pairAllSelected:function(m){m=m||{};var n=this,o=[],l=[],p=[];n.$(".unpaired-columns .forward-column .dataset.selected").each(function(){o.push($(this).data("dataset"))});n.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){l.push($(this).data("dataset"))});o.length=l.length=Math.min(o.length,l.length);o.forEach(function(r,q){try{p.push(n._pair(r,l[q],{silent:true}))}catch(s){n.error(s)}});if(p.length&&!m.silent){this.trigger("pair:new",p)}return p},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(n){if(n.shiftKey){var m=this,l=$(n.target).addClass("selected"),o=function(p){m.$(p.target).filter(".dataset").addClass("selected")};l.parent().on("mousemove",o);$(document).one("mouseup",function(p){l.parent().off("mousemove",o);m.pairAllSelected()})}},_clickPairRow:function(n){var o=$(n.currentTarget).index(),m=$(".unpaired-columns .forward-column .dataset").eq(o).data("dataset"),l=$(".unpaired-columns .reverse-column .dataset").eq(o).data("dataset");this._pair(m,l)},_startPartitionDrag:function(m){var l=this,p=m.pageY;$("body").css("cursor","ns-resize");l.$(".flexible-partition-drag").css("color","black");function o(q){l.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",n)}function n(q){var r=q.pageY-p;if(!l.adjPartition(r)){$("body").trigger("mouseup")}l._adjUnpairedOnScrollbar();p+=r}$("body").mousemove(n);$("body").one("mouseup",o)},adjPartition:function(m){var l=this.$(".unpaired-columns"),n=this.$(".paired-columns"),o=parseInt(l.css("height"),10),p=parseInt(n.css("height"),10);o=Math.max(10,o+m);p=p-m;var q=m<0;if(q){if(this.unpairedPanelHidden){return false}else{if(o<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){l.show();this.unpairedPanelHidden=false}}if(!q){if(this.pairedPanelHidden){return false}else{if(p<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){n.show();this.pairedPanelHidden=false}}l.css({height:o+"px",flex:"0 0 auto"});return true},selectPair:function(l){l.stopPropagation();$(l.currentTarget).toggleClass("selected")},clearSelectedPaired:function(l){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(o){o.stopPropagation();var q=$(o.currentTarget),n=q.parent().parent(),m=n.index(".dataset.paired"),p=this.paired[m],l=prompt("Enter a new name for the pair:",p.name);if(l){p.name=l;p.customizedName=true;q.text(p.name)}},_clickUnpair:function(m){var l=Math.floor($(m.currentTarget).index(".unpair-btn"));this._unpair(this.paired[l])},_dragoverPairedColumns:function(o){o.preventDefault();var m=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(m,o.originalEvent.clientY);var n=this._getNearestPairedDatasetLi(o.originalEvent.clientY);$(".paired-drop-placeholder").remove();var l=$('<div class="paired-drop-placeholder"></div>');if(!n.size()){m.append(l)}else{n.before(l)}},_checkForAutoscroll:function(l,r){var p=2;var q=l.offset(),o=l.scrollTop(),m=r-q.top,n=(q.top+l.outerHeight())-r;if(m>=0&&m<this.autoscrollDist){l.scrollTop(o-p)}else{if(n>=0&&n<this.autoscrollDist){l.scrollTop(o+p)}}},_getNearestPairedDatasetLi:function(r){var o=4,m=this.$(".paired-columns .column-datasets li").toArray();for(var n=0;n<m.length;n++){var q=$(m[n]),p=q.offset().top,l=Math.floor(q.outerHeight()/2)+o;if(p+l>r&&p-l<r){return q}}return $()},_dropPairedColumns:function(m){m.preventDefault();m.dataTransfer.dropEffect="move";var l=this._getNearestPairedDatasetLi(m.originalEvent.clientY);if(l.size()){this.$dragging.insertBefore(l)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var l=[];this.$(".paired-columns .dataset.paired").each(function(){l.push($(this).data("pair"))});this.paired=l;this._renderPaired()},_pairDragstart:function(m,n){n.$el.addClass("selected");var l=this.$(".paired-columns 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function l(n,m){n=n||"body";if(!this.size()){return this}$(this).each(function(){var p=$(this),o=p.data("target");if(o){p.mouseover(function(q){$(o,n).css({background:m})}).mouseout(function(q){$(o).css({background:""})})}});return this}})}());var d=function a(n,l){l=_.defaults(l||{},{datasets:n,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var m=new k(l);Galaxy.modal.show({title:"Create a collection of paired datasets",body:m.$el,width:"80%",height:"800px",closing_events:true});m.render();window.PCC=m;return m};return{PairedCollectionCreator:k,pairedCollectionCreatorModal:d}}); \ No newline at end of file +define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,b,f,c){var i=Backbone.View.extend(f.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(l){this.pair=l.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(l){l.currentTarget.style.opacity="0.4";if(l.originalEvent){l=l.originalEvent}l.dataTransfer.effectAllowed="move";l.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(l){l.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(l){this.$el.parent().trigger(l)},toString:function(){return"PairView("+this.pair.name+")"}});function g(m){m=m||{};m.createPair=m.createPair||function l(r){this.debug("creating pair:",r.listA[r.indexA].name,r.listB[r.indexB].name);r=r||{};return this._pair(r.listA.splice(r.indexA,1)[0],r.listB.splice(r.indexB,1)[0],{silent:true})};var o=[];function q(){if(!o.length){o=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]}return o}m.preprocessMatch=m.preprocessMatch||function n(s){var r=q.call(this);return _.extend(s,{matchTo:s.matchTo.name.replace(r[0],""),possible:s.possible.name.replace(r[1],"")})};return function p(t){this.debug("autopair _strategy ---------------------------");t=t||{};var r=t.listA,A=t.listB,z=0,y,v={score:0,index:null},x=[];this.debug("starting list lens:",r.length,A.length);this.debug("bestMatch (starting):",JSON.stringify(v,null," "));while(z<r.length){var w=r[z];v.score=0;for(y=0;y<A.length;y++){var u=A[y];this.debug(z+":"+w.name);this.debug(y+":"+u.name);if(r[z]!==A[y]){v=m.match.call(this,m.preprocessMatch.call(this,{matchTo:w,possible:u,index:y,bestMatch:v}));this.debug("bestMatch:",JSON.stringify(v,null," "));if(v.score===1){this.debug("breaking early due to perfect match");break}}}var s=m.scoreThreshold.call(this);this.debug("scoreThreshold:",s);this.debug("bestMatch.score:",v.score);if(v.score>=s){this.debug("creating pair");x.push(m.createPair.call(this,{listA:r,indexA:z,listB:A,indexB:v.index}));this.debug("list lens now:",r.length,A.length)}else{z+=1}if(!r.length||!A.length){return x}}this.debug("paired:",JSON.stringify(x,null," "));this.debug("autopair _strategy ---------------------------");return x}}var k=Backbone.View.extend(f.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(l){this.metric("PairedCollectionCreator.initialize",l);l=_.defaults(l,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,strategy:"lcs",matchPercentage:0.9,twoPassAutopairing:true});this.initialList=l.datasets;this.historyId=l.historyId;this.filters=this.commonFilters[l.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(l.filters)){this.filters=l.filters}this.automaticallyPair=l.automaticallyPair;this.strategy=this.strategies[l.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(l.strategy)){this.strategy=l.strategy}this.matchPercentage=l.matchPercentage;this.twoPassAutopairing=l.twoPassAutopairing;this.removeExtensions=true;this.oncancel=l.oncancel;this.oncreate=l.oncreate;this.autoscrollDist=l.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(l){l.sort(function(n,m){return b(n.name,m.name)});return l},_ensureIds:function(){this.initialList.forEach(function(l){if(!l.hasOwnProperty("id")){l.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(){var o=this.filters.map(function(p){return new RegExp(p)}),m=[[],[]];function n(p,q){return q.test(p.name)}this.unpaired.forEach(function l(p){o.forEach(function(r,q){if(n(p,r)){m[q].push(p)}})});return m},_addToUnpaired:function(m){var l=function(n,p){if(n===p){return n}var o=Math.floor((p-n)/2)+n,q=b(m.name,this.unpaired[o].name);if(q<0){return l(n,o)}else{if(q>0){return l(o+1,p)}}while(this.unpaired[o]&&this.unpaired[o].name===m.name){o++}return o}.bind(this);this.unpaired.splice(l(0,this.unpaired.length),0,m)},autoPair:function(n){var m=this._splitByFilters(),l=[];if(this.twoPassAutopairing){l=this.autopairSimple({listA:m[0],listB:m[1]});m=this._splitByFilters()}n=n||this.strategy;m=this._splitByFilters();l=l.concat(this[n].call(this,{listA:m[0],listB:m[1]}));return l},autopairSimple:g({scoreThreshold:function(){return 1},match:function j(l){l=l||{};if(l.matchTo===l.possible){return{index:l.index,score:1}}return l.bestMatch}}),autopairLevenshtein:g({scoreThreshold:function(){return this.matchPercentage},match:function e(m){m=m||{};var n=h(m.matchTo,m.possible),l=1-(n/(Math.max(m.matchTo.length,m.possible.length)));if(l>m.bestMatch.score){return{index:m.index,score:l}}return m.bestMatch}}),autopairLCS:g({scoreThreshold:function(){return this.matchPercentage},match:function e(n){n=n||{};var l=this._naiveStartingAndEndingLCS(n.matchTo,n.possible).length,m=l/(Math.max(n.matchTo.length,n.possible.length));if(m>n.bestMatch.score){return{index:n.index,score:m}}return n.bestMatch}}),_naiveStartingAndEndingLCS:function(o,m){var p="",q="",n=0,l=0;while(n<o.length&&n<m.length){if(o[n]!==m[n]){break}p+=o[n];n+=1}if(n===o.length){return o}if(n===m.length){return 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l=this.$(".header").empty().html(k.templates.header()).find(".help-content").prepend($(k.templates.helpContent()));this._renderFilters();return l},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(m,n){var l=this.$(".middle").empty().html(k.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return l},_renderUnpaired:function(q,r){var o=this,p,m,l=[],n=this._splitByFilters();this.$(".forward-column .title").text([n[0].length,c("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[0].length));this.$(".reverse-column .title").text([n[1].length,c("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}m=n[1].map(function(t,s){if((n[0][s]!==undefined)&&(n[0][s]!==t)){l.push(o._renderPairButton())}return o._renderUnpairedDataset(t)});p=n[0].map(function(s){return o._renderUnpairedDataset(s)});if(!p.length&&!m.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(p).add(this.$(".unpaired-columns .paired-column .column-datasets").append(l)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(m));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(l){return["(",l," ",c("filtered out"),")"].join("")},_renderUnpairedDataset:function(l){return $("<li/>").attr("id","dataset-"+l.id).addClass("dataset 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l=o.offset().left+o.outerWidth(),n=p.offset().left+p.outerWidth(),m=Math.floor(l)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",(m>0)?m:0)},_renderPaired:function(m,n){this.$(".paired-column-title .title").text([this.paired.length,c("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var l=this;this.paired.forEach(function(q,o){var p=new i({pair:q});l.$(".paired-columns .column-datasets").append(p.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',c("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var l=$('<div class="empty-message"></div>').text("("+c("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(l);return l},_renderFooter:function(m,n){var l=this.$(".footer").empty().html(k.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return l},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(l){function m(p,o){return['<button class="filter-choice btn" ','data-forward="',p,'" data-reverse="',o,'">',c("Forward"),": ",p,", ",c("Reverse"),": ",o,"</button>"].join("")}var n=$(_.template(['<div class="choose-filters">','<div class="help">',c("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",_.values(this.commonFilters).map(function(o){return m(o[0],o[1])}).join(""),"</div>"].join(""))({}));return 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l,m=null;if(this.paired.length){m="alert-success";l=this.paired.length+" "+c("pairs created");if(!this.unpaired.length){l+=": "+c("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{l=c("Could not automatically create any pairs from the given dataset names")}this._showAlert(l,m)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(l){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(l){$(l.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',c("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',c("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',c("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',c("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',c("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',c("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',c("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',c("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',c("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>",'<div class="flexible-partition">','<div class="flexible-partition-drag" title="',c("Drag to change"),'"></div>','<div class="column-header">','<div class="column-title paired-column-title">','<span class="title"></span>',"</div>",'<a class="unpair-all-link" href="javascript:void(0);">',c("Unpair all"),"</a>","</div>","</div>",'<div class="paired-columns flex-column-container scroll-container flex-row">','<ol class="column-datasets"></ol>',"</div>"].join("")),footer:_.template(['<div class="attributes clear">','<div class="clear">','<label class="remove-extensions-prompt pull-right">',c("Remove file extensions from pair names"),"?",'<input class="remove-extensions pull-right" type="checkbox" />',"</label>","</div>",'<div class="clear">','<input class="collection-name form-control pull-right" ','placeholder="',c("Enter a name for your new list"),'" />','<div class="collection-name-prompt pull-right">',c("Name"),":</div>","</div>","</div>",'<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',c("Cancel"),"</button>",'<div class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',c("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',c("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',c("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',c("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",c(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",c(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",c(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",c(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",c(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",c(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function l(n,m){n=n||"body";if(!this.size()){return this}$(this).each(function(){var p=$(this),o=p.data("target");if(o){p.mouseover(function(q){$(o,n).css({background:m})}).mouseout(function(q){$(o).css({background:""})})}});return this}})}());var d=function a(n,l){l=_.defaults(l||{},{datasets:n,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var m=new k(l);Galaxy.modal.show({title:"Create a collection of paired datasets",body:m.$el,width:"80%",height:"800px",closing_events:true});m.render();window.PCC=m;return m};return{PairedCollectionCreator:k,pairedCollectionCreatorModal:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/bc6a54c340fb/ Changeset: bc6a54c340fb User: carlfeberhard Date: 2015-02-11 18:16:20+00:00 Summary: Merge Affected #: 1 file diff -r fdb5e1329ef2de9a712f5139bcd71ee4ac278f24 -r bc6a54c340fb81096d73ea76122eca3675117df8 test/base/test_data.py --- a/test/base/test_data.py +++ b/test/base/test_data.py @@ -75,7 +75,7 @@ def __init__(self, repository, environ): self.repository = repository self.updated = False - repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-repos") + repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-cache") m = hashlib.md5() m.update(repository) repo_path = os.path.join(repo_cache, m.hexdigest()) 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: jmchilton: Fix incorrect constant pointed out by Nicola.
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d9da5a9edfa/ Changeset: 1d9da5a9edfa User: jmchilton Date: 2015-02-11 18:15:21+00:00 Summary: Fix incorrect constant pointed out by Nicola. https://bitbucket.org/galaxy/galaxy-central/pull-request/664/remove-test-da…. Affected #: 1 file diff -r 86ac99a2896b87915e35b81db1320fdfe73bf556 -r 1d9da5a9edfa536e8755ecafdb9f7a23694d6761 test/base/test_data.py --- a/test/base/test_data.py +++ b/test/base/test_data.py @@ -75,7 +75,7 @@ def __init__(self, repository, environ): self.repository = repository self.updated = False - repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-repos") + repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-cache") m = hashlib.md5() m.update(repository) repo_path = os.path.join(repo_cache, m.hexdigest()) 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: guerler: ToolForm: Reduce number of refresh events
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/86ac99a2896b/ Changeset: 86ac99a2896b User: guerler Date: 2015-02-11 18:12:06+00:00 Summary: ToolForm: Reduce number of refresh events Affected #: 9 files diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -93,7 +93,7 @@ this._renderForm(options); // rebuild the underlying data structure - this.tree.finalize(); + var current_state = this.tree.finalize(); // show errors on startup if (options.initial_errors) { @@ -102,9 +102,15 @@ // add refresh listener this.on('refresh', function() { - // by using/resetting the deferred ajax queue the number of redundant calls is reduced - self.deferred.reset(); - self.deferred.execute(function(){self._updateModel()}); + var new_state = self.tree.finalize(); + if (!_.isEqual(new_state, current_state)) { + // backup current state + current_state = new_state; + + // by using/resetting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel(current_state)}); + } }); // add reset listener diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -274,15 +274,15 @@ /** Request a new model for an already created tool form and updates the form inputs */ - _updateModel: function() { + _updateModel: function(current_state) { // link self var self = this; // create the request dictionary - var current_state = { + current_state = { tool_id : this.options.id, tool_version : this.options.version, - inputs : this.tree.finalize() + inputs : current_state } // log tool state diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -115,7 +115,7 @@ }); // log tool state - console.debug('tools-form::_refreshForm() - Refreshing states.'); + console.debug('tools-form::_refreshForm() - Sending current state (see below).'); console.debug(current_state); // activates/disables spinner for dynamic fields to indicate that they are currently being updated @@ -188,7 +188,7 @@ self.deferred.done(process_id); // log success - console.debug('tools-form::_refreshForm() - States refreshed.'); + console.debug('tools-form::_refreshForm() - Received new model (see below).'); console.debug(new_model); }, error : function(response) { diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -93,7 +93,7 @@ this._renderForm(options); // rebuild the underlying data structure - this.tree.finalize(); + var current_state = this.tree.finalize(); // show errors on startup if (options.initial_errors) { @@ -102,9 +102,15 @@ // add refresh listener this.on('refresh', function() { - // by using/resetting the deferred ajax queue the number of redundant calls is reduced - self.deferred.reset(); - self.deferred.execute(function(){self._updateModel()}); + var new_state = self.tree.finalize(); + if (!_.isEqual(new_state, current_state)) { + // backup current state + current_state = new_state; + + // by using/resetting the deferred ajax queue the number of redundant calls is reduced + self.deferred.reset(); + self.deferred.execute(function(){self._updateModel(current_state)}); + } }); // add reset listener diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -274,15 +274,15 @@ /** Request a new model for an already created tool form and updates the form inputs */ - _updateModel: function() { + _updateModel: function(current_state) { // link self var self = this; // create the request dictionary - var current_state = { + current_state = { tool_id : this.options.id, tool_version : this.options.version, - inputs : this.tree.finalize() + inputs : current_state } // log tool state diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -115,7 +115,7 @@ }); // log tool state - console.debug('tools-form::_refreshForm() - Refreshing states.'); + console.debug('tools-form::_refreshForm() - Sending current state (see below).'); console.debug(current_state); // activates/disables spinner for dynamic fields to indicate that they are currently being updated @@ -188,7 +188,7 @@ self.deferred.done(process_id); // log success - console.debug('tools-form::_refreshForm() - States refreshed.'); + console.debug('tools-form::_refreshForm() - Received new model (see below).'); console.debug(new_model); }, error : function(response) { diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l.deferred.reset();l.deferred.execute(function(){l._updateModel(m)})}});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e={tool_id:this.options.id,tool_version:this.options.version,inputs:this.tree.finalize()};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(e){var d=this;e={tool_id:this.options.id,tool_version:this.options.version,inputs:e};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(){var f=this;var g=this.tree.finalize({data:function(l){try{if(l&&l.values[0].src==="hda"){return f.content.get({id:l.values[0].id,src:"hda"}).id_uncoded}}catch(k){console.debug("tools-form::_updateModel - Invalid or empty data input value.")}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(g);function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);f.deferred.done(i);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(k)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(){var f=this;var g=this.tree.finalize({data:function(l){try{if(l&&l.values[0].src==="hda"){return f.content.get({id:l.values[0].id,src:"hda"}).id_uncoded}}catch(k){console.debug("tools-form::_updateModel - Invalid or empty data input value.")}return null}});console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);f.deferred.done(i);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(k)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: UI, paired collection creator: in-file TODO's, cleanup, change modal/creator render order to allow auto focus on name input
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43b1d5b62c62/ Changeset: 43b1d5b62c62 User: carlfeberhard Date: 2015-02-11 17:55:25+00:00 Summary: UI, paired collection creator: in-file TODO's, cleanup, change modal/creator render order to allow auto focus on name input Affected #: 3 files diff -r d00255be341d2b08af3fceeb2c8f46d3d6ce610b -r 43b1d5b62c62bfd40c86ac201d6cf8a6f388e29b client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -6,10 +6,6 @@ ], function( levenshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: - _adjPairedOnScrollBar - parition drag now doesn't stop when dragging down - can push footer out of modal - only *after* partition is all the way down once? PROGRAMMATICALLY: @@ -84,6 +80,7 @@ }); +// ============================================================================ /** returns an autopair function that uses the provided options.match function */ function autoPairFnBuilder( options ){ options = options || {}; @@ -182,6 +179,7 @@ } +// ============================================================================ /** An interface for building collections of paired datasets. */ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ @@ -254,8 +252,8 @@ /** map of common filter pairs by name */ commonFilters : { - none : [ '', '' ], - illumina : [ '_1', '_2' ] + illumina : [ '_1', '_2' ], + Rs : [ '_R1', '_R2' ] }, /** which commonFilter to use by default */ DEFAULT_FILTERS : 'illumina', @@ -469,7 +467,6 @@ /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */ _pair : function( fwd, rev, options ){ options = options || {}; - //TODO: eventing, options //this.debug( '_pair:', fwd, rev ); var pair = this._createPair( fwd, rev, options.name ); this.paired.push( pair ); @@ -493,19 +490,22 @@ /** try to find a good pair name for the given fwd and rev datasets */ _guessNameForPair : function( fwd, rev, removeExtensions ){ removeExtensions = ( removeExtensions !== undefined )?( removeExtensions ):( this.removeExtensions ); - var lcs = this._naiveStartingAndEndingLCS( -//TODO: won't work with regex - fwd.name.replace( this.filters[0], '' ), - rev.name.replace( this.filters[1], '' ) - ); + var fwdName = fwd.name, + revName = rev.name, + lcs = this._naiveStartingAndEndingLCS( + fwdName.replace( this.filters[0], '' ), + revName.replace( this.filters[1], '' ) + ); if( removeExtensions ){ var lastDotIndex = lcs.lastIndexOf( '.' ); if( lastDotIndex > 0 ){ - lcs = lcs.slice( 0, lastDotIndex ); + var extension = lcs.slice( lastDotIndex, lcs.length ); + lcs = lcs.replace( extension, '' ); + fwdName = fwdName.replace( extension, '' ); + revName = revName.replace( extension, '' ); } } - //TODO: optionally remove extension - return lcs || ( fwd.name + ' & ' + rev.name ); + return lcs || ( fwdName + ' & ' + revName ); }, /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */ @@ -535,7 +535,8 @@ // ------------------------------------------------------------------------ API /** convert a pair into JSON compatible with the collections API */ - _pairToJSON : function( pair ){ + _pairToJSON : function( pair, src ){ + src = src || 'hda'; //TODO: consider making this the pair structure when created instead return { collection_type : 'paired', @@ -544,13 +545,11 @@ element_identifiers : [{ name : 'forward', id : pair.forward.id, - //TODO: isn't necessarily true - src : 'hda' + src : src }, { name : 'reverse', id : pair.reverse.id, - //TODO: isn't necessarily true - src : 'hda' + src : src }] }; }, @@ -560,14 +559,9 @@ */ createList : function( name ){ var creator = this, - url; - if( creator.historyId ){ url = '/api/histories/' + this.historyId + '/contents/dataset_collections'; - //} else { - // - } -//TODO:?? Can't we use ListPairedCollection.create() + //TODO: use ListPairedCollection.create() var ajaxData = { type : 'dataset_collection', collection_type : 'list:paired', @@ -647,7 +641,6 @@ var $middle = this.$( '.middle' ).empty().html( PairedCollectionCreator.templates.middle() ); // (re-) hide the un/paired panels based on instance vars - //TODO: use replaceWith if( this.unpairedPanelHidden ){ this.$( '.unpaired-columns' ).hide(); } else if( this.pairedPanelHidden ){ @@ -701,7 +694,8 @@ return; } // add to appropo cols - //TODO: not the best way to render + //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment + // and swapping out that this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd ) .add( this.$( '.unpaired-columns .paired-column .column-datasets' ).append( $prd ) ) .add( this.$( '.unpaired-columns .reverse-column .column-datasets' ).append( $rev ) ); @@ -776,12 +770,11 @@ this.$( '.paired-columns .column-datasets' ).empty(); var creator = this; this.paired.forEach( function( pair, i ){ -//TODO: cache these? + //TODO: cache these? var pairView = new PairView({ pair: pair }); creator.$( '.paired-columns .column-datasets' ) .append( pairView.render().$el ) .append([ -//TODO: data-index="i" '<button class="unpair-btn">', '<span class="fa fa-unlink" title="', _l( 'Unpair' ), '"></span>', '</button>' @@ -828,9 +821,9 @@ '<div class="help">', _l( 'Choose from the following filters to change which unpaired reads are shown in the display' ), ':</div>', - //TODO: connect with common filters - filterChoice( '_1', '_2' ), - filterChoice( '_R1', '_R2' ), + _.values( this.commonFilters ).map( function( filterSet ){ + return filterChoice( filterSet[0], filterSet[1] ); + }).join( '' ), '</div>' ].join(''))({})); @@ -927,7 +920,7 @@ 'click .forward-column .column-title' : '_clickShowOnlyUnpaired', 'click .reverse-column .column-title' : '_clickShowOnlyUnpaired', 'click .unpair-all-link' : '_clickUnpairAll', - //TODO: this seems kinda backasswards + //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly? 'change .forward-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); }, 'focus .forward-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); }, 'click .autopair-link' : '_clickAutopair', @@ -995,7 +988,6 @@ this.$( '.header .alert' ).hide(); }, - //TODO: consolidate these /** toggle between showing only unpaired and split view */ _clickShowOnlyUnpaired : function( ev ){ //this.debug( 'click unpaired', ev.currentTarget ); @@ -1107,7 +1099,6 @@ fwds = [], revs = [], pairs = []; - //TODO: could be made more concise creator.$( '.unpaired-columns .forward-column .dataset.selected' ).each( function(){ fwds.push( $( this ).data( 'dataset' ) ); }); @@ -1163,12 +1154,10 @@ fwd = $( '.unpaired-columns .forward-column .dataset' ).eq( rowIndex ).data( 'dataset' ), rev = $( '.unpaired-columns .reverse-column .dataset' ).eq( rowIndex ).data( 'dataset' ); //this.debug( 'row:', rowIndex, fwd, rev ); - //TODO: animate this._pair( fwd, rev ); }, // ........................................................................ divider/partition -//TODO: simplify /** start dragging the visible divider/partition between unpaired and paired panes */ _startPartitionDrag : function( ev ){ var creator = this, @@ -1208,7 +1197,6 @@ unpairedHi = Math.max( 10, unpairedHi + adj ); pairedHi = pairedHi - adj; -//TODO: seems like shouldn't need this (it should be part of the hide/show/splitView) var movingUpwards = adj < 0; // when the divider gets close to the top - lock into hiding the unpaired section if( movingUpwards ){ @@ -1272,7 +1260,7 @@ pair.name = response; // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these // when adding/removing extensions - //TODO: kinda hacky + //hackish pair.customizedName = true; $name.text( pair.name ); } @@ -1281,10 +1269,8 @@ /** unpair this pair */ _clickUnpair : function( ev ){ //if( !ev.currentTarget ){ return true; } - //TODO: this is a hack bc each paired rev now has two elems (dataset, button) var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) ); //this.debug( 'pair:', pairIndex ); - //TODO: animate this._unpair( this.paired[ pairIndex ] ); }, @@ -1367,7 +1353,7 @@ /** resync the creator's list of paired based on the DOM order of pairs */ _syncPairsToDom : function(){ var newPaired = []; -//TODO: ugh + //TODO: doesn't seem wise to use the dom to store these - can't we sync another way? this.$( '.paired-columns .dataset.paired' ).each( function(){ newPaired.push( $( this ).data( 'pair' ) ); }); @@ -1702,7 +1688,7 @@ throw new Error( 'Galaxy or Galaxy.modal not found' ); } - var creator = new PairedCollectionCreator( options ).render(); + var creator = new PairedCollectionCreator( options ); Galaxy.modal.show({ title : 'Create a collection of paired datasets', body : creator.$el, @@ -1710,6 +1696,7 @@ height : '800px', closing_events: true }); + creator.render(); //TODO: remove modal header window.PCC = creator; return creator; diff -r d00255be341d2b08af3fceeb2c8f46d3d6ce610b -r 43b1d5b62c62bfd40c86ac201d6cf8a6f388e29b static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -6,10 +6,6 @@ ], function( levenshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: - _adjPairedOnScrollBar - parition drag now doesn't stop when dragging down - can push footer out of modal - only *after* partition is all the way down once? PROGRAMMATICALLY: @@ -84,6 +80,7 @@ }); +// ============================================================================ /** returns an autopair function that uses the provided options.match function */ function autoPairFnBuilder( options ){ options = options || {}; @@ -182,6 +179,7 @@ } +// ============================================================================ /** An interface for building collections of paired datasets. */ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ @@ -254,8 +252,8 @@ /** map of common filter pairs by name */ commonFilters : { - none : [ '', '' ], - illumina : [ '_1', '_2' ] + illumina : [ '_1', '_2' ], + Rs : [ '_R1', '_R2' ] }, /** which commonFilter to use by default */ DEFAULT_FILTERS : 'illumina', @@ -469,7 +467,6 @@ /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */ _pair : function( fwd, rev, options ){ options = options || {}; - //TODO: eventing, options //this.debug( '_pair:', fwd, rev ); var pair = this._createPair( fwd, rev, options.name ); this.paired.push( pair ); @@ -493,19 +490,22 @@ /** try to find a good pair name for the given fwd and rev datasets */ _guessNameForPair : function( fwd, rev, removeExtensions ){ removeExtensions = ( removeExtensions !== undefined )?( removeExtensions ):( this.removeExtensions ); - var lcs = this._naiveStartingAndEndingLCS( -//TODO: won't work with regex - fwd.name.replace( this.filters[0], '' ), - rev.name.replace( this.filters[1], '' ) - ); + var fwdName = fwd.name, + revName = rev.name, + lcs = this._naiveStartingAndEndingLCS( + fwdName.replace( this.filters[0], '' ), + revName.replace( this.filters[1], '' ) + ); if( removeExtensions ){ var lastDotIndex = lcs.lastIndexOf( '.' ); if( lastDotIndex > 0 ){ - lcs = lcs.slice( 0, lastDotIndex ); + var extension = lcs.slice( lastDotIndex, lcs.length ); + lcs = lcs.replace( extension, '' ); + fwdName = fwdName.replace( extension, '' ); + revName = revName.replace( extension, '' ); } } - //TODO: optionally remove extension - return lcs || ( fwd.name + ' & ' + rev.name ); + return lcs || ( fwdName + ' & ' + revName ); }, /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */ @@ -535,7 +535,8 @@ // ------------------------------------------------------------------------ API /** convert a pair into JSON compatible with the collections API */ - _pairToJSON : function( pair ){ + _pairToJSON : function( pair, src ){ + src = src || 'hda'; //TODO: consider making this the pair structure when created instead return { collection_type : 'paired', @@ -544,13 +545,11 @@ element_identifiers : [{ name : 'forward', id : pair.forward.id, - //TODO: isn't necessarily true - src : 'hda' + src : src }, { name : 'reverse', id : pair.reverse.id, - //TODO: isn't necessarily true - src : 'hda' + src : src }] }; }, @@ -560,14 +559,9 @@ */ createList : function( name ){ var creator = this, - url; - if( creator.historyId ){ url = '/api/histories/' + this.historyId + '/contents/dataset_collections'; - //} else { - // - } -//TODO:?? Can't we use ListPairedCollection.create() + //TODO: use ListPairedCollection.create() var ajaxData = { type : 'dataset_collection', collection_type : 'list:paired', @@ -647,7 +641,6 @@ var $middle = this.$( '.middle' ).empty().html( PairedCollectionCreator.templates.middle() ); // (re-) hide the un/paired panels based on instance vars - //TODO: use replaceWith if( this.unpairedPanelHidden ){ this.$( '.unpaired-columns' ).hide(); } else if( this.pairedPanelHidden ){ @@ -701,7 +694,8 @@ return; } // add to appropo cols - //TODO: not the best way to render + //TODO: not the best way to render - consider rendering the entire unpaired-columns section in a fragment + // and swapping out that this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd ) .add( this.$( '.unpaired-columns .paired-column .column-datasets' ).append( $prd ) ) .add( this.$( '.unpaired-columns .reverse-column .column-datasets' ).append( $rev ) ); @@ -776,12 +770,11 @@ this.$( '.paired-columns .column-datasets' ).empty(); var creator = this; this.paired.forEach( function( pair, i ){ -//TODO: cache these? + //TODO: cache these? var pairView = new PairView({ pair: pair }); creator.$( '.paired-columns .column-datasets' ) .append( pairView.render().$el ) .append([ -//TODO: data-index="i" '<button class="unpair-btn">', '<span class="fa fa-unlink" title="', _l( 'Unpair' ), '"></span>', '</button>' @@ -828,9 +821,9 @@ '<div class="help">', _l( 'Choose from the following filters to change which unpaired reads are shown in the display' ), ':</div>', - //TODO: connect with common filters - filterChoice( '_1', '_2' ), - filterChoice( '_R1', '_R2' ), + _.values( this.commonFilters ).map( function( filterSet ){ + return filterChoice( filterSet[0], filterSet[1] ); + }).join( '' ), '</div>' ].join(''))({})); @@ -927,7 +920,7 @@ 'click .forward-column .column-title' : '_clickShowOnlyUnpaired', 'click .reverse-column .column-title' : '_clickShowOnlyUnpaired', 'click .unpair-all-link' : '_clickUnpairAll', - //TODO: this seems kinda backasswards + //TODO: this seems kinda backasswards - re-sending jq event as a backbone event, can we listen directly? 'change .forward-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); }, 'focus .forward-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); }, 'click .autopair-link' : '_clickAutopair', @@ -995,7 +988,6 @@ this.$( '.header .alert' ).hide(); }, - //TODO: consolidate these /** toggle between showing only unpaired and split view */ _clickShowOnlyUnpaired : function( ev ){ //this.debug( 'click unpaired', ev.currentTarget ); @@ -1107,7 +1099,6 @@ fwds = [], revs = [], pairs = []; - //TODO: could be made more concise creator.$( '.unpaired-columns .forward-column .dataset.selected' ).each( function(){ fwds.push( $( this ).data( 'dataset' ) ); }); @@ -1163,12 +1154,10 @@ fwd = $( '.unpaired-columns .forward-column .dataset' ).eq( rowIndex ).data( 'dataset' ), rev = $( '.unpaired-columns .reverse-column .dataset' ).eq( rowIndex ).data( 'dataset' ); //this.debug( 'row:', rowIndex, fwd, rev ); - //TODO: animate this._pair( fwd, rev ); }, // ........................................................................ divider/partition -//TODO: simplify /** start dragging the visible divider/partition between unpaired and paired panes */ _startPartitionDrag : function( ev ){ var creator = this, @@ -1208,7 +1197,6 @@ unpairedHi = Math.max( 10, unpairedHi + adj ); pairedHi = pairedHi - adj; -//TODO: seems like shouldn't need this (it should be part of the hide/show/splitView) var movingUpwards = adj < 0; // when the divider gets close to the top - lock into hiding the unpaired section if( movingUpwards ){ @@ -1272,7 +1260,7 @@ pair.name = response; // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these // when adding/removing extensions - //TODO: kinda hacky + //hackish pair.customizedName = true; $name.text( pair.name ); } @@ -1281,10 +1269,8 @@ /** unpair this pair */ _clickUnpair : function( ev ){ //if( !ev.currentTarget ){ return true; } - //TODO: this is a hack bc each paired rev now has two elems (dataset, button) var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) ); //this.debug( 'pair:', pairIndex ); - //TODO: animate this._unpair( this.paired[ pairIndex ] ); }, @@ -1367,7 +1353,7 @@ /** resync the creator's list of paired based on the DOM order of pairs */ _syncPairsToDom : function(){ var newPaired = []; -//TODO: ugh + //TODO: doesn't seem wise to use the dom to store these - can't we sync another way? this.$( '.paired-columns .dataset.paired' ).each( function(){ newPaired.push( $( this ).data( 'pair' ) ); }); @@ -1702,7 +1688,7 @@ throw new Error( 'Galaxy or Galaxy.modal not found' ); } - var creator = new PairedCollectionCreator( options ).render(); + var creator = new PairedCollectionCreator( options ); Galaxy.modal.show({ title : 'Create a collection of paired datasets', body : creator.$el, @@ -1710,6 +1696,7 @@ height : '800px', closing_events: true }); + creator.render(); //TODO: remove modal header window.PCC = creator; return creator; diff -r d00255be341d2b08af3fceeb2c8f46d3d6ce610b -r 43b1d5b62c62bfd40c86ac201d6cf8a6f388e29b static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,b,f,c){var i=Backbone.View.extend(f.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(l){this.pair=l.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(l){l.currentTarget.style.opacity="0.4";if(l.originalEvent){l=l.originalEvent}l.dataTransfer.effectAllowed="move";l.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(l){l.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(l){this.$el.parent().trigger(l)},toString:function(){return"PairView("+this.pair.name+")"}});function g(m){m=m||{};m.createPair=m.createPair||function l(r){this.debug("creating pair:",r.listA[r.indexA].name,r.listB[r.indexB].name);r=r||{};return this._pair(r.listA.splice(r.indexA,1)[0],r.listB.splice(r.indexB,1)[0],{silent:true})};var o=[];function q(){if(!o.length){o=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]}return o}m.preprocessMatch=m.preprocessMatch||function n(s){var r=q.call(this);return _.extend(s,{matchTo:s.matchTo.name.replace(r[0],""),possible:s.possible.name.replace(r[1],"")})};return function p(t){this.debug("autopair _strategy ---------------------------");t=t||{};var r=t.listA,A=t.listB,z=0,y,v={score:0,index:null},x=[];this.debug("starting list lens:",r.length,A.length);this.debug("bestMatch (starting):",JSON.stringify(v,null," "));while(z<r.length){var w=r[z];v.score=0;for(y=0;y<A.length;y++){var u=A[y];this.debug(z+":"+w.name);this.debug(y+":"+u.name);if(r[z]!==A[y]){v=m.match.call(this,m.preprocessMatch.call(this,{matchTo:w,possible:u,index:y,bestMatch:v}));this.debug("bestMatch:",JSON.stringify(v,null," "));if(v.score===1){this.debug("breaking early due to perfect match");break}}}var s=m.scoreThreshold.call(this);this.debug("scoreThreshold:",s);this.debug("bestMatch.score:",v.score);if(v.score>=s){this.debug("creating pair");x.push(m.createPair.call(this,{listA:r,indexA:z,listB:A,indexB:v.index}));this.debug("list lens now:",r.length,A.length)}else{z+=1}if(!r.length||!A.length){return x}}this.debug("paired:",JSON.stringify(x,null," "));this.debug("autopair _strategy ---------------------------");return x}}var k=Backbone.View.extend(f.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(l){l=_.defaults(l,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,strategy:"lcs",matchPercentage:0.9,twoPassAutopairing:true});this.initialList=l.datasets;this.historyId=l.historyId;this.filters=this.commonFilters[l.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(l.filters)){this.filters=l.filters}this.automaticallyPair=l.automaticallyPair;this.strategy=this.strategies[l.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(l.strategy)){this.strategy=l.strategy}this.matchPercentage=l.matchPercentage;this.twoPassAutopairing=l.twoPassAutopairing;this.removeExtensions=true;this.oncancel=l.oncancel;this.oncreate=l.oncreate;this.autoscrollDist=l.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(l){l.sort(function(n,m){return b(n.name,m.name)});return l},_ensureIds:function(){this.initialList.forEach(function(l){if(!l.hasOwnProperty("id")){l.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(){var o=this.filters.map(function(p){return new RegExp(p)}),m=[[],[]];function n(p,q){return q.test(p.name)}this.unpaired.forEach(function l(p){o.forEach(function(r,q){if(n(p,r)){m[q].push(p)}})});return m},_addToUnpaired:function(m){var l=function(n,p){if(n===p){return n}var o=Math.floor((p-n)/2)+n,q=b(m.name,this.unpaired[o].name);if(q<0){return l(n,o)}else{if(q>0){return l(o+1,p)}}while(this.unpaired[o]&&this.unpaired[o].name===m.name){o++}return o}.bind(this);this.unpaired.splice(l(0,this.unpaired.length),0,m)},autoPair:function(n){var m=this._splitByFilters(),l=[];if(this.twoPassAutopairing){l=this.autopairSimple({listA:m[0],listB:m[1]});m=this._splitByFilters()}n=n||this.strategy;m=this._splitByFilters();l=l.concat(this[n].call(this,{listA:m[0],listB:m[1]}));return l},autopairSimple:g({scoreThreshold:function(){return 1},match:function j(l){l=l||{};if(l.matchTo===l.possible){return{index:l.index,score:1}}return l.bestMatch}}),autopairLevenshtein:g({scoreThreshold:function(){return this.matchPercentage},match:function e(m){m=m||{};var n=h(m.matchTo,m.possible),l=1-(n/(Math.max(m.matchTo.length,m.possible.length)));if(l>m.bestMatch.score){return{index:m.index,score:l}}return m.bestMatch}}),autopairLCS:g({scoreThreshold:function(){return this.matchPercentage},match:function e(n){n=n||{};var l=this._naiveStartingAndEndingLCS(n.matchTo,n.possible).length,m=l/(Math.max(n.matchTo.length,n.possible.length));if(m>n.bestMatch.score){return{index:n.index,score:m}}return n.bestMatch}}),_naiveStartingAndEndingLCS:function(o,m){var p="",q="",n=0,l=0;while(n<o.length&&n<m.length){if(o[n]!==m[n]){break}p+=o[n];n+=1}if(n===o.length){return o}if(n===m.length){return m}n=(o.length-1);l=(m.length-1);while(n>=0&&l>=0){if(o[n]!==m[l]){break}q=[o[n],q].join("");n-=1;l-=1}return p+q},_pair:function(n,l,m){m=m||{};var o=this._createPair(n,l,m.name);this.paired.push(o);this.unpaired=_.without(this.unpaired,n,l);if(!m.silent){this.trigger("pair:new",o)}return o},_createPair:function(n,l,m){if(!(n&&l)||(n===l)){throw new Error("Bad pairing: "+[JSON.stringify(n),JSON.stringify(l)])}m=m||this._guessNameForPair(n,l);return{forward:n,name:m,reverse:l}},_guessNameForPair:function(n,l,o){o=(o!==undefined)?(o):(this.removeExtensions);var m=this._naiveStartingAndEndingLCS(n.name.replace(this.filters[0],""),l.name.replace(this.filters[1],""));if(o){var p=m.lastIndexOf(".");if(p>0){m=m.slice(0,p)}}return m||(n.name+" & "+l.name)},_unpair:function(m,l){l=l||{};if(!m){throw new Error("Bad pair: "+JSON.stringify(m))}this.paired=_.without(this.paired,m);this._addToUnpaired(m.forward);this._addToUnpaired(m.reverse);if(!l.silent){this.trigger("pair:unpair",[m])}return m},unpairAll:function(){var l=[];while(this.paired.length){l.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",l)},_pairToJSON:function(l){return{collection_type:"paired",src:"new_collection",name:l.name,element_identifiers:[{name:"forward",id:l.forward.id,src:"hda"},{name:"reverse",id:l.reverse.id,src:"hda"}]}},createList:function(n){var o=this,m;if(o.historyId){m="/api/histories/"+this.historyId+"/contents/dataset_collections"}var l={type:"dataset_collection",collection_type:"list:paired",name:_.escape(n||o.$(".collection-name").val()),element_identifiers:o.paired.map(function(p){return o._pairToJSON(p)})};return jQuery.ajax(m,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(l)}).fail(function(r,p,q){o._ajaxErrHandler(r,p,q)}).done(function(p,q,r){o.trigger("collection:created",p,q,r);if(typeof o.oncreate==="function"){o.oncreate.call(this,p,q,r)}})},_ajaxErrHandler:function(o,l,n){this.error(o,l,n);var m=c("An error occurred while creating this collection");if(o){if(o.readyState===0&&o.status===0){m+=": "+c("Galaxy could not be reached and may be updating.")+c(" Try again in a few minutes.")}else{if(o.responseJSON){m+="<br /><pre>"+JSON.stringify(o.responseJSON)+"</pre>"}else{m+=": "+n}}}creator._showAlert(m,"alert-danger")},render:function(l,m){this.$el.empty().html(k.templates.main());this._renderHeader(l);this._renderMiddle(l);this._renderFooter(l);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(m,n){var l=this.$(".header").empty().html(k.templates.header()).find(".help-content").prepend($(k.templates.helpContent()));this._renderFilters();return l},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(m,n){var l=this.$(".middle").empty().html(k.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return l},_renderUnpaired:function(q,r){var o=this,p,m,l=[],n=this._splitByFilters();this.$(".forward-column .title").text([n[0].length,c("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[0].length));this.$(".reverse-column .title").text([n[1].length,c("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}m=n[1].map(function(t,s){if((n[0][s]!==undefined)&&(n[0][s]!==t)){l.push(o._renderPairButton())}return o._renderUnpairedDataset(t)});p=n[0].map(function(s){return o._renderUnpairedDataset(s)});if(!p.length&&!m.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(p).add(this.$(".unpaired-columns .paired-column .column-datasets").append(l)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(m));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(l){return["(",l," ",c("filtered out"),")"].join("")},_renderUnpairedDataset:function(l){return $("<li/>").attr("id","dataset-"+l.id).addClass("dataset unpaired").attr("draggable",true).addClass(l.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(l.name)).data("dataset",l)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(c("Pair these datasets")))},_renderUnpairedEmpty:function(){var l=$('<div class="empty-message"></div>').text("("+c("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(l);return l},_renderUnpairedNotShown:function(){var l=$('<div class="empty-message"></div>').text("("+c("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(l);return l},_adjUnpairedOnScrollbar:function(){var o=this.$(".unpaired-columns").last(),p=this.$(".unpaired-columns .reverse-column .dataset").first();if(!p.size()){return}var l=o.offset().left+o.outerWidth(),n=p.offset().left+p.outerWidth(),m=Math.floor(l)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",(m>0)?m:0)},_renderPaired:function(m,n){this.$(".paired-column-title .title").text([this.paired.length,c("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var l=this;this.paired.forEach(function(q,o){var p=new i({pair:q});l.$(".paired-columns .column-datasets").append(p.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',c("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var l=$('<div class="empty-message"></div>').text("("+c("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(l);return l},_renderFooter:function(m,n){var l=this.$(".footer").empty().html(k.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return l},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(l){function m(p,o){return['<button class="filter-choice btn" ','data-forward="',p,'" data-reverse="',o,'">',c("Forward"),": ",p,", ",c("Reverse"),": ",o,"</button>"].join("")}var n=$(_.template(['<div class="choose-filters">','<div class="help">',c("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",m("_1","_2"),m("_R1","_R2"),"</div>"].join(""))({}));return this.$(l).popover({container:".collection-creator",placement:"bottom",html:true,content:n})},_validationWarning:function(m,l){var n="validation-warning";if(m==="name"){m=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(l){m=m||this.$("."+n);m.removeClass(n)}else{m.addClass(n)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(l){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var l,m=null;if(this.paired.length){m="alert-success";l=this.paired.length+" "+c("pairs created");if(!this.unpaired.length){l+=": "+c("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{l=c("Could not automatically create any pairs from the given dataset names")}this._showAlert(l,m)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(l){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(l){$(l.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(l){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(l){$(l.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(l){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(l){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(l){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(l){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(m,l){l=l||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(l).show().find(".alert-message").html(m)},_hideAlert:function(l){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(l){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(l){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(l,m){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(l,m)},hidePaired:function(l,m){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(l,m)},splitView:function(l,m){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(l,m);return this},_clickUnpairAll:function(l){this.unpairAll()},_clickAutopair:function(l){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(m){var l=$(m.currentTarget);this.$(".forward-unpaired-filter input").val(l.data("forward"));this.$(".reverse-unpaired-filter input").val(l.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(l){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(l){l.stopPropagation();return this.toggleSelectUnpaired($(l.currentTarget))},toggleSelectUnpaired:function(n,m){m=m||{};var o=n.data("dataset"),l=m.force!==undefined?m.force:!n.hasClass("selected");if(!n.size()||o===undefined){return n}if(l){n.addClass("selected");if(!m.waitToPair){this.pairAllSelected()}}else{n.removeClass("selected")}return n},pairAllSelected:function(m){m=m||{};var n=this,o=[],l=[],p=[];n.$(".unpaired-columns .forward-column .dataset.selected").each(function(){o.push($(this).data("dataset"))});n.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){l.push($(this).data("dataset"))});o.length=l.length=Math.min(o.length,l.length);o.forEach(function(r,q){try{p.push(n._pair(r,l[q],{silent:true}))}catch(s){n.error(s)}});if(p.length&&!m.silent){this.trigger("pair:new",p)}return p},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(n){if(n.shiftKey){var m=this,l=$(n.target).addClass("selected"),o=function(p){m.$(p.target).filter(".dataset").addClass("selected")};l.parent().on("mousemove",o);$(document).one("mouseup",function(p){l.parent().off("mousemove",o);m.pairAllSelected()})}},_clickPairRow:function(n){var o=$(n.currentTarget).index(),m=$(".unpaired-columns .forward-column .dataset").eq(o).data("dataset"),l=$(".unpaired-columns .reverse-column .dataset").eq(o).data("dataset");this._pair(m,l)},_startPartitionDrag:function(m){var l=this,p=m.pageY;$("body").css("cursor","ns-resize");l.$(".flexible-partition-drag").css("color","black");function o(q){l.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",n)}function n(q){var r=q.pageY-p;if(!l.adjPartition(r)){$("body").trigger("mouseup")}l._adjUnpairedOnScrollbar();p+=r}$("body").mousemove(n);$("body").one("mouseup",o)},adjPartition:function(m){var l=this.$(".unpaired-columns"),n=this.$(".paired-columns"),o=parseInt(l.css("height"),10),p=parseInt(n.css("height"),10);o=Math.max(10,o+m);p=p-m;var q=m<0;if(q){if(this.unpairedPanelHidden){return false}else{if(o<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){l.show();this.unpairedPanelHidden=false}}if(!q){if(this.pairedPanelHidden){return false}else{if(p<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){n.show();this.pairedPanelHidden=false}}l.css({height:o+"px",flex:"0 0 auto"});return true},selectPair:function(l){l.stopPropagation();$(l.currentTarget).toggleClass("selected")},clearSelectedPaired:function(l){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(o){o.stopPropagation();var q=$(o.currentTarget),n=q.parent().parent(),m=n.index(".dataset.paired"),p=this.paired[m],l=prompt("Enter a new name for the pair:",p.name);if(l){p.name=l;p.customizedName=true;q.text(p.name)}},_clickUnpair:function(m){var l=Math.floor($(m.currentTarget).index(".unpair-btn"));this._unpair(this.paired[l])},_dragoverPairedColumns:function(o){o.preventDefault();var m=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(m,o.originalEvent.clientY);var n=this._getNearestPairedDatasetLi(o.originalEvent.clientY);$(".paired-drop-placeholder").remove();var l=$('<div class="paired-drop-placeholder"></div>');if(!n.size()){m.append(l)}else{n.before(l)}},_checkForAutoscroll:function(l,r){var p=2;var 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+define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,b,f,c){var i=Backbone.View.extend(f.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(l){this.pair=l.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(l){l.currentTarget.style.opacity="0.4";if(l.originalEvent){l=l.originalEvent}l.dataTransfer.effectAllowed="move";l.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(l){l.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(l){this.$el.parent().trigger(l)},toString:function(){return"PairView("+this.pair.name+")"}});function g(m){m=m||{};m.createPair=m.createPair||function l(r){this.debug("creating pair:",r.listA[r.indexA].name,r.listB[r.indexB].name);r=r||{};return this._pair(r.listA.splice(r.indexA,1)[0],r.listB.splice(r.indexB,1)[0],{silent:true})};var o=[];function q(){if(!o.length){o=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]}return o}m.preprocessMatch=m.preprocessMatch||function n(s){var r=q.call(this);return 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b(n.name,m.name)});return l},_ensureIds:function(){this.initialList.forEach(function(l){if(!l.hasOwnProperty("id")){l.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(){var o=this.filters.map(function(p){return new RegExp(p)}),m=[[],[]];function n(p,q){return q.test(p.name)}this.unpaired.forEach(function l(p){o.forEach(function(r,q){if(n(p,r)){m[q].push(p)}})});return m},_addToUnpaired:function(m){var l=function(n,p){if(n===p){return n}var o=Math.floor((p-n)/2)+n,q=b(m.name,this.unpaired[o].name);if(q<0){return l(n,o)}else{if(q>0){return l(o+1,p)}}while(this.unpaired[o]&&this.unpaired[o].name===m.name){o++}return o}.bind(this);this.unpaired.splice(l(0,this.unpaired.length),0,m)},autoPair:function(n){var m=this._splitByFilters(),l=[];if(this.twoPassAutopairing){l=this.autopairSimple({listA:m[0],listB:m[1]});m=this._splitByFilters()}n=n||this.strategy;m=this._splitByFilters();l=l.concat(this[n].call(this,{listA:m[0],listB:m[1]}));return l},autopairSimple:g({scoreThreshold:function(){return 1},match:function j(l){l=l||{};if(l.matchTo===l.possible){return{index:l.index,score:1}}return l.bestMatch}}),autopairLevenshtein:g({scoreThreshold:function(){return this.matchPercentage},match:function e(m){m=m||{};var n=h(m.matchTo,m.possible),l=1-(n/(Math.max(m.matchTo.length,m.possible.length)));if(l>m.bestMatch.score){return{index:m.index,score:l}}return m.bestMatch}}),autopairLCS:g({scoreThreshold:function(){return this.matchPercentage},match:function e(n){n=n||{};var l=this._naiveStartingAndEndingLCS(n.matchTo,n.possible).length,m=l/(Math.max(n.matchTo.length,n.possible.length));if(m>n.bestMatch.score){return{index:n.index,score:m}}return n.bestMatch}}),_naiveStartingAndEndingLCS:function(o,m){var p="",q="",n=0,l=0;while(n<o.length&&n<m.length){if(o[n]!==m[n]){break}p+=o[n];n+=1}if(n===o.length){return o}if(n===m.length){return 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"+JSON.stringify(m))}this.paired=_.without(this.paired,m);this._addToUnpaired(m.forward);this._addToUnpaired(m.reverse);if(!l.silent){this.trigger("pair:unpair",[m])}return m},unpairAll:function(){var l=[];while(this.paired.length){l.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",l)},_pairToJSON:function(m,l){l=l||"hda";return{collection_type:"paired",src:"new_collection",name:m.name,element_identifiers:[{name:"forward",id:m.forward.id,src:l},{name:"reverse",id:m.reverse.id,src:l}]}},createList:function(n){var o=this,m="/api/histories/"+this.historyId+"/contents/dataset_collections";var l={type:"dataset_collection",collection_type:"list:paired",name:_.escape(n||o.$(".collection-name").val()),element_identifiers:o.paired.map(function(p){return o._pairToJSON(p)})};return jQuery.ajax(m,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(l)}).fail(function(r,p,q){o._ajaxErrHandler(r,p,q)}).done(function(p,q,r){o.trigger("collection:created",p,q,r);if(typeof o.oncreate==="function"){o.oncreate.call(this,p,q,r)}})},_ajaxErrHandler:function(o,l,n){this.error(o,l,n);var m=c("An error occurred while creating this collection");if(o){if(o.readyState===0&&o.status===0){m+=": "+c("Galaxy could not be reached and may be updating.")+c(" Try again in a few minutes.")}else{if(o.responseJSON){m+="<br /><pre>"+JSON.stringify(o.responseJSON)+"</pre>"}else{m+=": "+n}}}creator._showAlert(m,"alert-danger")},render:function(l,m){this.$el.empty().html(k.templates.main());this._renderHeader(l);this._renderMiddle(l);this._renderFooter(l);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(m,n){var l=this.$(".header").empty().html(k.templates.header()).find(".help-content").prepend($(k.templates.helpContent()));this._renderFilters();return l},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(m,n){var l=this.$(".middle").empty().html(k.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return l},_renderUnpaired:function(q,r){var o=this,p,m,l=[],n=this._splitByFilters();this.$(".forward-column .title").text([n[0].length,c("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[0].length));this.$(".reverse-column .title").text([n[1].length,c("unpaired reverse")].join(" "));this.$(".reverse-column 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l=this.$(".footer").empty().html(k.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return l},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(l){function m(p,o){return['<button class="filter-choice btn" ','data-forward="',p,'" data-reverse="',o,'">',c("Forward"),": ",p,", ",c("Reverse"),": ",o,"</button>"].join("")}var n=$(_.template(['<div class="choose-filters">','<div class="help">',c("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",_.values(this.commonFilters).map(function(o){return m(o[0],o[1])}).join(""),"</div>"].join(""))({}));return 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l=this,p=m.pageY;$("body").css("cursor","ns-resize");l.$(".flexible-partition-drag").css("color","black");function o(q){l.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",n)}function n(q){var r=q.pageY-p;if(!l.adjPartition(r)){$("body").trigger("mouseup")}l._adjUnpairedOnScrollbar();p+=r}$("body").mousemove(n);$("body").one("mouseup",o)},adjPartition:function(m){var l=this.$(".unpaired-columns"),n=this.$(".paired-columns"),o=parseInt(l.css("height"),10),p=parseInt(n.css("height"),10);o=Math.max(10,o+m);p=p-m;var q=m<0;if(q){if(this.unpairedPanelHidden){return false}else{if(o<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){l.show();this.unpairedPanelHidden=false}}if(!q){if(this.pairedPanelHidden){return false}else{if(p<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){n.show();this.pairedPanelHidden=false}}l.css({height:o+"px",flex:"0 0 auto"});return true},selectPair:function(l){l.stopPropagation();$(l.currentTarget).toggleClass("selected")},clearSelectedPaired:function(l){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(o){o.stopPropagation();var q=$(o.currentTarget),n=q.parent().parent(),m=n.index(".dataset.paired"),p=this.paired[m],l=prompt("Enter a new name for the pair:",p.name);if(l){p.name=l;p.customizedName=true;q.text(p.name)}},_clickUnpair:function(m){var l=Math.floor($(m.currentTarget).index(".unpair-btn"));this._unpair(this.paired[l])},_dragoverPairedColumns:function(o){o.preventDefault();var m=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(m,o.originalEvent.clientY);var n=this._getNearestPairedDatasetLi(o.originalEvent.clientY);$(".paired-drop-placeholder").remove();var l=$('<div class="paired-drop-placeholder"></div>');if(!n.size()){m.append(l)}else{n.before(l)}},_checkForAutoscroll:function(l,r){var p=2;var q=l.offset(),o=l.scrollTop(),m=r-q.top,n=(q.top+l.outerHeight())-r;if(m>=0&&m<this.autoscrollDist){l.scrollTop(o-p)}else{if(n>=0&&n<this.autoscrollDist){l.scrollTop(o+p)}}},_getNearestPairedDatasetLi:function(r){var o=4,m=this.$(".paired-columns .column-datasets li").toArray();for(var n=0;n<m.length;n++){var q=$(m[n]),p=q.offset().top,l=Math.floor(q.outerHeight()/2)+o;if(p+l>r&&p-l<r){return q}}return $()},_dropPairedColumns:function(m){m.preventDefault();m.dataTransfer.dropEffect="move";var l=this._getNearestPairedDatasetLi(m.originalEvent.clientY);if(l.size()){this.$dragging.insertBefore(l)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var l=[];this.$(".paired-columns .dataset.paired").each(function(){l.push($(this).data("pair"))});this.paired=l;this._renderPaired()},_pairDragstart:function(m,n){n.$el.addClass("selected");var l=this.$(".paired-columns 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flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',c("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',c("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',c("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',c("Filter this list"),'" 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","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",c(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function l(n,m){n=n||"body";if(!this.size()){return this}$(this).each(function(){var p=$(this),o=p.data("target");if(o){p.mouseover(function(q){$(o,n).css({background:m})}).mouseout(function(q){$(o).css({background:""})})}});return this}})}());var d=function a(n,l){l=_.defaults(l||{},{datasets:n,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var m=new k(l);Galaxy.modal.show({title:"Create a collection of paired datasets",body:m.$el,width:"80%",height:"800px",closing_events:true});m.render();window.PCC=m;return m};return{PairedCollectionCreator:k,pairedCollectionCreatorModal:d}}); \ 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.

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commit/galaxy-central: jmchilton: Merged in dan/galaxy-central-prs/stable (pull request #666)
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/577b270034b4/ Changeset: 577b270034b4 Branch: stable User: jmchilton Date: 2015-02-11 17:54:36+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #666) [STABLE] Several Fixes for Tool Data Tables Affected #: 1 file diff -r 32e4527bab2d79f0797c28500a379b6b6c7a3900 -r 577b270034b48d90e58ffbea296e700d229545c9 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -335,11 +335,13 @@ def get_named_fields_list( self ): rval = [] - named_colums = self.get_column_name_list() + named_columns = self.get_column_name_list() for fields in self.get_fields(): field_dict = {} for i, field in enumerate( fields ): - field_name = named_colums[i] + if i == len( named_columns ): + break + field_name = named_columns[i] if field_name is None: field_name = i #check that this is supposed to be 0 based. field_dict[ field_name ] = field @@ -366,6 +368,7 @@ self.columns[ name ] = index self.largest_index = index else: + self.largest_index = 0 for column_elem in config_element.findall( 'column' ): name = column_elem.get( 'name', None ) assert name is not None, "Required 'name' attribute missing from column def" @@ -495,7 +498,7 @@ try: data_table_fh = open( filename, 'r+b' ) except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e ) + log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e ) data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d61e421e06c/ Changeset: 0d61e421e06c Branch: stable User: dan Date: 2015-02-11 17:33:49+00:00 Summary: Fix for Data Tables persisting when .loc file doesn't exist. Affected #: 1 file diff -r 0b9127ab708d7d8497e80169a3b8636aea1e37c6 -r 0d61e421e06c25f7658b8405574a2aafa63d04f0 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -495,7 +495,7 @@ try: data_table_fh = open( filename, 'r+b' ) except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e ) + log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e ) data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line https://bitbucket.org/galaxy/galaxy-central/commits/7df1519a9fbe/ Changeset: 7df1519a9fbe Branch: stable User: dan Date: 2015-02-11 17:37:59+00:00 Summary: Fix for TabularToolDataTable.get_named_fields_list() when a data line has extra columns. Affected #: 1 file diff -r 0d61e421e06c25f7658b8405574a2aafa63d04f0 -r 7df1519a9fbecfc8c07e0dde3bf9845714c9a2ac lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -335,11 +335,13 @@ def get_named_fields_list( self ): rval = [] - named_colums = self.get_column_name_list() + named_columns = self.get_column_name_list() for fields in self.get_fields(): field_dict = {} for i, field in enumerate( fields ): - field_name = named_colums[i] + if i == len( named_columns ): + break + field_name = named_columns[i] if field_name is None: field_name = i #check that this is supposed to be 0 based. field_dict[ field_name ] = field https://bitbucket.org/galaxy/galaxy-central/commits/ca653e8d044d/ Changeset: ca653e8d044d Branch: stable User: dan Date: 2015-02-11 17:40:33+00:00 Summary: Fix for parsing Tool Data Table columns that are defined as individual xml elements. Affected #: 1 file diff -r 7df1519a9fbecfc8c07e0dde3bf9845714c9a2ac -r ca653e8d044d29e15d4ff3266e333aa75c09e5d7 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -368,6 +368,7 @@ self.columns[ name ] = index self.largest_index = index else: + self.largest_index = 0 for column_elem in config_element.findall( 'column' ): name = column_elem.get( 'name', None ) assert name is not None, "Required 'name' attribute missing from column def" https://bitbucket.org/galaxy/galaxy-central/commits/577b270034b4/ Changeset: 577b270034b4 Branch: stable User: jmchilton Date: 2015-02-11 17:54:36+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #666) [STABLE] Several Fixes for Tool Data Tables Affected #: 1 file diff -r 32e4527bab2d79f0797c28500a379b6b6c7a3900 -r 577b270034b48d90e58ffbea296e700d229545c9 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -335,11 +335,13 @@ def get_named_fields_list( self ): rval = [] - named_colums = self.get_column_name_list() + named_columns = self.get_column_name_list() for fields in self.get_fields(): field_dict = {} for i, field in enumerate( fields ): - field_name = named_colums[i] + if i == len( named_columns ): + break + field_name = named_columns[i] if field_name is None: field_name = i #check that this is supposed to be 0 based. field_dict[ field_name ] = field @@ -366,6 +368,7 @@ self.columns[ name ] = index self.largest_index = index else: + self.largest_index = 0 for column_elem in config_element.findall( 'column' ): name = column_elem.get( 'name', None ) assert name is not None, "Required 'name' attribute missing from column def" @@ -495,7 +498,7 @@ try: data_table_fh = open( filename, 'r+b' ) except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e ) + log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e ) data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line 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: dan: Fix for parsing Tool Data Table columns that are defined as individual xml elements.
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d00255be341d/ Changeset: d00255be341d User: dan Date: 2015-02-11 17:40:33+00:00 Summary: Fix for parsing Tool Data Table columns that are defined as individual xml elements. Affected #: 1 file diff -r da99d403f3375c31e8d784a91d430fe7068de1ab -r d00255be341d2b08af3fceeb2c8f46d3d6ce610b lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -386,6 +386,7 @@ self.columns[ name ] = index self.largest_index = index else: + self.largest_index = 0 for column_elem in config_element.findall( 'column' ): name = column_elem.get( 'name', None ) assert name is not None, "Required 'name' attribute missing from column def" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Fix for TabularToolDataTable.get_named_fields_list() when a data line has extra columns.
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da99d403f337/ Changeset: da99d403f337 User: dan Date: 2015-02-11 17:37:59+00:00 Summary: Fix for TabularToolDataTable.get_named_fields_list() when a data line has extra columns. Affected #: 1 file diff -r 70caaa5b7ff7dd4a11ddead7d946cb145e58686a -r da99d403f3375c31e8d784a91d430fe7068de1ab lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -353,11 +353,13 @@ def get_named_fields_list( self ): rval = [] - named_colums = self.get_column_name_list() + named_columns = self.get_column_name_list() for fields in self.get_fields(): field_dict = {} for i, field in enumerate( fields ): - field_name = named_colums[i] + if i == len( named_columns ): + break + field_name = named_columns[i] if field_name is None: field_name = i # check that this is supposed to be 0 based. field_dict[ field_name ] = field Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for Data Tables persisting when .loc file doesn't exist.
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70caaa5b7ff7/ Changeset: 70caaa5b7ff7 User: dan Date: 2015-02-11 17:33:49+00:00 Summary: Fix for Data Tables persisting when .loc file doesn't exist. Affected #: 1 file diff -r 75d1aa0e7663ec42f004a785ece731fd992f979d -r 70caaa5b7ff7dd4a11ddead7d946cb145e58686a lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -513,7 +513,7 @@ try: data_table_fh = open( filename, 'r+b' ) except IOError, e: - log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e ) + log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e ) data_table_fh = open( filename, 'wb' ) if os.stat( filename )[6] != 0: # ensure last existing line ends with new line 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: guerler: ToolForm: Move debug output
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75d1aa0e7663/ Changeset: 75d1aa0e7663 User: guerler Date: 2015-02-11 17:27:18+00:00 Summary: ToolForm: Move debug output Affected #: 6 files diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d client/galaxy/scripts/mvc/tools/tools-content.js --- a/client/galaxy/scripts/mvc/tools/tools-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-content.js @@ -15,9 +15,6 @@ this.summary[c.id + '_' + c.src] = c; } } - - // log - console.debug('tools-content::initialize() - Completed.'); }, /** Returns matched content from summary. diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -350,6 +350,9 @@ message : options.message }); } + + // log + console.debug('tools-form-base::initialize() - Completed.'); } }); }); diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d static/scripts/mvc/tools/tools-content.js --- a/static/scripts/mvc/tools/tools-content.js +++ b/static/scripts/mvc/tools/tools-content.js @@ -15,9 +15,6 @@ this.summary[c.id + '_' + c.src] = c; } } - - // log - console.debug('tools-content::initialize() - Completed.'); }, /** Returns matched content from summary. diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -350,6 +350,9 @@ message : options.message }); } + + // log + console.debug('tools-form-base::initialize() - Completed.'); } }); }); diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d static/scripts/packed/mvc/tools/tools-content.js --- a/static/scripts/packed/mvc/tools/tools-content.js +++ b/static/scripts/packed/mvc/tools/tools-content.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.summary={}},add:function(e){for(var d in e){for(var b in e[d]){var f=e[d][b];this.summary[f.id+"_"+f.src]=f}}console.debug("tools-content::initialize() - Completed.")},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.summary={}},add:function(e){for(var d in e){for(var b in e[d]){var f=e[d][b];this.summary[f.id+"_"+f.src]=f}}},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})}})}); \ No newline at end of file diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ 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: guerler: ToolForm: Update select validation, remove spaces
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bbd5375d27aa/ Changeset: bbd5375d27aa User: guerler Date: 2015-02-11 17:20:06+00:00 Summary: ToolForm: Update select validation, remove spaces Affected #: 6 files diff -r 52e80be61a360ea2cf1387920ebdffdff5c0218c -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -105,7 +105,7 @@ if (new_value !== undefined) { // reset selection this.$('input').prop('checked', false); - + // set value if (new_value !== null) { // check if its an array @@ -122,7 +122,7 @@ // refresh this._refresh(); - + // get and return value return this._getValue(); }, @@ -146,7 +146,7 @@ /** Return first available option */ first: function() { - var options = this.$('input'); + var options = this.$('input').first(); if (options.length > 0) { return options.val(); } else { diff -r 52e80be61a360ea2cf1387920ebdffdff5c0218c -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -87,21 +87,17 @@ } // validate and return value - var val = this.$select.val(); - if (!Utils.validate(val)) { - return null; - } - return val; + return this._getValue(); }, /** Return the first select option */ first: function() { - var options = this.$select.find('option'); + var options = this.$select.find('option').first(); if (options.length > 0) { return options.val(); } else { - return undefined; + return null; } }, @@ -182,7 +178,7 @@ */ update: function(options) { // backup current value - var current = this.$select.val(); + var current = this._getValue(); // remove all options this.$select.find('option').remove(); @@ -204,7 +200,7 @@ this.$select.val(current); // check if any value was set - if (!this.$select.val()) { + if (this._getValue() === null) { this.$select.val(this.first()); } @@ -232,10 +228,19 @@ */ _change: function() { if (this.options.onchange) { - this.options.onchange(this.$select.val()); + this.options.onchange(this._getValue()); } }, + /** Validate */ + _getValue: function() { + var val = this.$select.val(); + if (!Utils.validate(val)) { + return null; + } + return val; + }, + /** Refresh the select view */ _refresh: function() { diff -r 52e80be61a360ea2cf1387920ebdffdff5c0218c -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -105,7 +105,7 @@ if (new_value !== undefined) { // reset selection this.$('input').prop('checked', false); - + // set value if (new_value !== null) { // check if its an array @@ -122,7 +122,7 @@ // refresh this._refresh(); - + // get and return value return this._getValue(); }, @@ -146,7 +146,7 @@ /** Return first available option */ first: function() { - var options = this.$('input'); + var options = this.$('input').first(); if (options.length > 0) { return options.val(); } else { diff -r 52e80be61a360ea2cf1387920ebdffdff5c0218c -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -87,21 +87,17 @@ } // validate and return value - var val = this.$select.val(); - if (!Utils.validate(val)) { - return null; - } - return val; + return this._getValue(); }, /** Return the first select option */ first: function() { - var options = this.$select.find('option'); + var options = this.$select.find('option').first(); if (options.length > 0) { return options.val(); } else { - return undefined; + return null; } }, @@ -182,7 +178,7 @@ */ update: function(options) { // backup current value - var current = this.$select.val(); + var current = this._getValue(); // remove all options this.$select.find('option').remove(); @@ -204,7 +200,7 @@ this.$select.val(current); // check if any value was set - if (!this.$select.val()) { + if (this._getValue() === null) { this.$select.val(this.first()); } @@ -232,10 +228,19 @@ */ _change: function() { if (this.options.onchange) { - this.options.onchange(this.$select.val()); + this.options.onchange(this._getValue()); } }, + /** Validate */ + _getValue: function() { + var val = this.$select.val(); + if (!Utils.validate(val)) { + return null; + } + return val; + }, + /** Refresh the select view */ _refresh: function() { diff -r 52e80be61a360ea2cf1387920ebdffdff5c0218c -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this.value(l)},value:function(j){if(j!==undefined){this.$("input").prop("checked",false);if(j!==null){if(!(j instanceof Array)){j=[j]}for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}}this._refresh();return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return null}},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_getValue:function(){var h=[];this.$(":checked").each(function(){h.push($(this).val())});if(!c.validate(h)){return null}if(this.options.multiple){return h}else{return h[0]}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this.value(l)},value:function(j){if(j!==undefined){this.$("input").prop("checked",false);if(j!==null){if(!(j instanceof Array)){j=[j]}for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}}this._refresh();return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input").first();if(h.length>0){return h.val()}else{return null}},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_getValue:function(){var h=[];this.$(":checked").each(function(){h.push($(this).val())});if(!c.validate(h)){return null}if(this.options.multiple){return h}else{return h[0]}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file diff -r 52e80be61a360ea2cf1387920ebdffdff5c0218c -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:false,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}var d=this.$select.val();if(!a.validate(d)){return null}return d},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();if(this.options.optional&&!this.options.multiple){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find('option[value="__undefined__"]').remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"__undefined__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:false,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(this.options.optional&&!this.options.multiple){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(this._getValue()===null){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){this.$select.find('option[value="__undefined__"]').remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"__undefined__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ 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: guerler: ToolForm: Remove brackets
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/52e80be61a36/ Changeset: 52e80be61a36 User: guerler Date: 2015-02-11 16:19:29+00:00 Summary: ToolForm: Remove brackets Affected #: 3 files diff -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 -r 52e80be61a360ea2cf1387920ebdffdff5c0218c client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -34,9 +34,9 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - ((v === null || (v == this.default_value) || - (Number(v) == Number(this.default_value)) || - (JSON.stringify(v) == JSON.stringify(this.default_value))))); + (v === null || v == this.default_value || + Number(v) == Number(this.default_value) || + JSON.stringify(v) == JSON.stringify(this.default_value))); // refresh view this._refresh(); diff -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 -r 52e80be61a360ea2cf1387920ebdffdff5c0218c static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -34,9 +34,9 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - ((v === null || (v == this.default_value) || - (Number(v) == Number(this.default_value)) || - (JSON.stringify(v) == JSON.stringify(this.default_value))))); + (v === null || v == this.default_value || + Number(v) == Number(this.default_value) || + JSON.stringify(v) == JSON.stringify(this.default_value))); // refresh view this._refresh(); diff -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 -r 52e80be61a360ea2cf1387920ebdffdff5c0218c static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((b===null||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh();a.app.trigger("refresh")})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(b===null||b==this.default_value||Number(b)==Number(this.default_value)||JSON.stringify(b)==JSON.stringify(this.default_value)));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh();a.app.trigger("refresh")})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ 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: guerler: ToolForm: Move forward with drill down element, simplify validation
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/15cd0c4f1a40/ Changeset: 15cd0c4f1a40 User: guerler Date: 2015-02-11 16:03:22+00:00 Summary: ToolForm: Move forward with drill down element, simplify validation Affected #: 21 files diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -34,9 +34,9 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - (((this.field.validate && !this.field.validate()) || !v || - (v == this.default_value) || (Number(v) == Number(this.default_value)) || - (JSON.stringify(v) == JSON.stringify(this.default_value))))); + ((v === null || (v == this.default_value) || + (Number(v) == Number(this.default_value)) || + (JSON.stringify(v) == JSON.stringify(this.default_value))))); // refresh view this._refresh(); diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -233,18 +233,28 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value('__null__'); - this.select_multiple && this.select_multiple.value('__null__'); - this.select_collection && this.select_collection.value('__null__'); + this.select_single && this.select_single.value(null); + this.select_multiple && this.select_multiple.value(null); + this.select_collection && this.select_collection.value(null); } this.refresh(); } + // validate value + var id_list = this._select().value(); + if (id_list === null) { + return null; + } + // transform into an array - var id_list = this._select().value(); if (!(id_list instanceof Array)) { id_list = [id_list]; } + + // check if value exists + if (id_list.length === 0) { + return null; + } // prepare result dict var result = { @@ -264,12 +274,6 @@ return result; }, - /** Validate current selection - */ - validate: function() { - return this._select().validate(); - }, - /** Refreshes data selection view */ refresh: function() { this.button_type.value(this.current); diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -118,9 +118,6 @@ if (field && field.value) { // validate field value var value = field.value(); - if (field.validate && !field.validate()) { - value = null; - } // get and patch field value if (patch[input.type]) { @@ -128,7 +125,7 @@ } // ignore certain values - if (input.ignore === undefined || (value !== null && input.ignore != value)) { + if (input.ignore === undefined || input.ignore != value) { // add value to submission add (job_input_id, input.id, value); diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 client/galaxy/scripts/mvc/ui/ui-drilldown.js --- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -12,33 +12,44 @@ Options.BaseIcons.prototype.initialize.call(this, options); }, + /** Expand/collapse a sub group + */ + _setState: function (header_id, is_expanded) { + var $button = this.$('#button-' + header_id); + var $subgroup = this.$('#subgroup-' + header_id); + $button.data('is_expanded', is_expanded); + if (is_expanded) { + $subgroup.fadeIn('fast') + $button.removeClass('toggle-expand'); + $button.addClass('toggle'); + } else { + $subgroup.hide(); + $button.removeClass('toggle'); + $button.addClass('toggle-expand'); + } + }, + /** Template to create options tree */ _templateOptions: function(options) { // link this var self = this; - // attach show/hide event - function attachEvents($button, $subgroup) { - function setVisibility (visible) { - if (visible) { - $subgroup.fadeIn('fast') - $button.removeClass('toggle-expand'); - $button.addClass('toggle'); - $button.is_expanded = true; - } else { - $subgroup.hide(); - $button.removeClass('toggle'); - $button.addClass('toggle-expand'); - $button.is_expanded = false; - } - }; + + // link data + this.header_index = {}; + this.header_list = []; + + // attach event handler + function attach($el, header_id) { + var $button = $el.find('#button-' + header_id); $button.on('click', function() { - setVisibility(!$button.is_expanded); + self._setState(header_id, !$button.data('is_expanded')); }); } // recursive function which iterates through options - function iterate ($tmpl, options) { + function iterate ($tmpl, options, header) { + header = header || []; for (i in options) { // current option level in hierarchy var level = options[i]; @@ -46,13 +57,21 @@ // check for options var has_options = level.options.length > 0; + // copy current header list + var new_header = header.slice(0); + // build template var $group = $('<div/>'); if (has_options) { - // create button and add flag - var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'); + // create button and subgroup + var header_id = Utils.uuid(); + var $button = $('<span id="button-' + header_id + '" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'); + var $subgroup = $('<div id="subgroup-' + header_id + '" style="display: none; margin-left: 25px;"/>'); - // add expand group + // keep track of button and subgroup + new_header.push(header_id); + + // create expandable header section var $buttongroup = $('<div/>'); $buttongroup.append($button); $buttongroup.append(self._templateOption({ @@ -60,19 +79,17 @@ value: level.value })); $group.append($buttongroup); - - // add sub group - var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); - iterate($subgroup, level.options); + iterate($subgroup, level.options, new_header); $group.append($subgroup); - - // attach click event to collapse/expand hierarchy - attachEvents($button, $subgroup); } else { + // append child options $group.append(self._templateOption({ label: level.name, value: level.value })); + + // keep track of header list + self.header_index[level.value] = new_header; } $tmpl.append($group); } @@ -81,6 +98,18 @@ // iterate through options and create dom var $tmpl = $('<div/>'); iterate($tmpl, options); + + // merge index to create a non-duplicate list of headers + for (var i in this.header_index) { + this.header_list = _.uniq(this.header_list.concat(this.header_index[i])); + } + + // attach expand/collapse events + for (var i in this.header_list) { + attach($tmpl, this.header_list[i]); + } + + // return template return $tmpl; }, diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -101,19 +101,22 @@ /** Return/Set current value */ value: function (new_value) { - // set new value if provided + // set new value if available if (new_value !== undefined) { - // check if its an array - if (!(new_value instanceof Array)) { - new_value = [new_value]; - } - // reset selection this.$('input').prop('checked', false); + + // set value + if (new_value !== null) { + // check if its an array + if (!(new_value instanceof Array)) { + new_value = [new_value]; + } - // update to new selection - for (var i in new_value) { - this.$('input[value="' + new_value[i] + '"]').first().prop('checked', true); + // update to new selection + for (var i in new_value) { + this.$('input[value="' + new_value[i] + '"]').first().prop('checked', true); + } }; } @@ -147,16 +150,10 @@ if (options.length > 0) { return options.val(); } else { - return undefined; + return null; } }, - /** Validate the selected option/options - */ - validate: function() { - return Utils.validate(this.value()); - }, - /** Wait message during request processing */ wait: function() { @@ -213,21 +210,22 @@ /** Return current selection */ _getValue: function() { - // get selected values - var selected = this.$(':checked'); - if (selected.length == 0) { - return '__null__'; + // track values in array + var selected = []; + this.$(':checked').each(function() { + selected.push($(this).val()); + }); + + // get selected elements + if (!Utils.validate(selected)) { + return null; } - + // return multiple or single value if (this.options.multiple) { - var values = []; - selected.each(function() { - values.push($(this).val()); - }); - return values; + return selected; } else { - return selected.val(); + return selected[0]; } }, diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -75,13 +75,23 @@ /** Return/Set current selection */ value : function (new_value) { + // set new value if (new_value !== undefined) { + if (new_value === null) { + new_value = '__null__'; + } this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); } } - return this.$select.val(); + + // validate and return value + var val = this.$select.val(); + if (!Utils.validate(val)) { + return null; + } + return val; }, /** Return the first select option @@ -95,12 +105,6 @@ } }, - /** Validate the current selection - */ - validate: function() { - return Utils.validate(this.value()); - }, - /** Return the label/text of the current selection */ text : function () { diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 client/galaxy/scripts/utils/utils.js --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -35,6 +35,9 @@ if (!(value instanceof Array)) { value = [value]; } + if (value.length === 0) { + return false; + } for (var i in value) { if (['__null__', '__undefined__', 'None', null, undefined].indexOf(value[i]) > -1) { return false; diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -34,9 +34,9 @@ this.field.skip = false; var v = this.field.value && this.field.value(); this.field.skip = Boolean(options.optional && - (((this.field.validate && !this.field.validate()) || !v || - (v == this.default_value) || (Number(v) == Number(this.default_value)) || - (JSON.stringify(v) == JSON.stringify(this.default_value))))); + ((v === null || (v == this.default_value) || + (Number(v) == Number(this.default_value)) || + (JSON.stringify(v) == JSON.stringify(this.default_value))))); // refresh view this._refresh(); diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -233,18 +233,28 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.select_single && this.select_single.value('__null__'); - this.select_multiple && this.select_multiple.value('__null__'); - this.select_collection && this.select_collection.value('__null__'); + this.select_single && this.select_single.value(null); + this.select_multiple && this.select_multiple.value(null); + this.select_collection && this.select_collection.value(null); } this.refresh(); } + // validate value + var id_list = this._select().value(); + if (id_list === null) { + return null; + } + // transform into an array - var id_list = this._select().value(); if (!(id_list instanceof Array)) { id_list = [id_list]; } + + // check if value exists + if (id_list.length === 0) { + return null; + } // prepare result dict var result = { @@ -264,12 +274,6 @@ return result; }, - /** Validate current selection - */ - validate: function() { - return this._select().validate(); - }, - /** Refreshes data selection view */ refresh: function() { this.button_type.value(this.current); diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -118,9 +118,6 @@ if (field && field.value) { // validate field value var value = field.value(); - if (field.validate && !field.validate()) { - value = null; - } // get and patch field value if (patch[input.type]) { @@ -128,7 +125,7 @@ } // ignore certain values - if (input.ignore === undefined || (value !== null && input.ignore != value)) { + if (input.ignore === undefined || input.ignore != value) { // add value to submission add (job_input_id, input.id, value); diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/mvc/ui/ui-drilldown.js --- a/static/scripts/mvc/ui/ui-drilldown.js +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -12,33 +12,44 @@ Options.BaseIcons.prototype.initialize.call(this, options); }, + /** Expand/collapse a sub group + */ + _setState: function (header_id, is_expanded) { + var $button = this.$('#button-' + header_id); + var $subgroup = this.$('#subgroup-' + header_id); + $button.data('is_expanded', is_expanded); + if (is_expanded) { + $subgroup.fadeIn('fast') + $button.removeClass('toggle-expand'); + $button.addClass('toggle'); + } else { + $subgroup.hide(); + $button.removeClass('toggle'); + $button.addClass('toggle-expand'); + } + }, + /** Template to create options tree */ _templateOptions: function(options) { // link this var self = this; - // attach show/hide event - function attachEvents($button, $subgroup) { - function setVisibility (visible) { - if (visible) { - $subgroup.fadeIn('fast') - $button.removeClass('toggle-expand'); - $button.addClass('toggle'); - $button.is_expanded = true; - } else { - $subgroup.hide(); - $button.removeClass('toggle'); - $button.addClass('toggle-expand'); - $button.is_expanded = false; - } - }; + + // link data + this.header_index = {}; + this.header_list = []; + + // attach event handler + function attach($el, header_id) { + var $button = $el.find('#button-' + header_id); $button.on('click', function() { - setVisibility(!$button.is_expanded); + self._setState(header_id, !$button.data('is_expanded')); }); } // recursive function which iterates through options - function iterate ($tmpl, options) { + function iterate ($tmpl, options, header) { + header = header || []; for (i in options) { // current option level in hierarchy var level = options[i]; @@ -46,13 +57,21 @@ // check for options var has_options = level.options.length > 0; + // copy current header list + var new_header = header.slice(0); + // build template var $group = $('<div/>'); if (has_options) { - // create button and add flag - var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'); + // create button and subgroup + var header_id = Utils.uuid(); + var $button = $('<span id="button-' + header_id + '" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'); + var $subgroup = $('<div id="subgroup-' + header_id + '" style="display: none; margin-left: 25px;"/>'); - // add expand group + // keep track of button and subgroup + new_header.push(header_id); + + // create expandable header section var $buttongroup = $('<div/>'); $buttongroup.append($button); $buttongroup.append(self._templateOption({ @@ -60,19 +79,17 @@ value: level.value })); $group.append($buttongroup); - - // add sub group - var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); - iterate($subgroup, level.options); + iterate($subgroup, level.options, new_header); $group.append($subgroup); - - // attach click event to collapse/expand hierarchy - attachEvents($button, $subgroup); } else { + // append child options $group.append(self._templateOption({ label: level.name, value: level.value })); + + // keep track of header list + self.header_index[level.value] = new_header; } $tmpl.append($group); } @@ -81,6 +98,18 @@ // iterate through options and create dom var $tmpl = $('<div/>'); iterate($tmpl, options); + + // merge index to create a non-duplicate list of headers + for (var i in this.header_index) { + this.header_list = _.uniq(this.header_list.concat(this.header_index[i])); + } + + // attach expand/collapse events + for (var i in this.header_list) { + attach($tmpl, this.header_list[i]); + } + + // return template return $tmpl; }, diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -101,19 +101,22 @@ /** Return/Set current value */ value: function (new_value) { - // set new value if provided + // set new value if available if (new_value !== undefined) { - // check if its an array - if (!(new_value instanceof Array)) { - new_value = [new_value]; - } - // reset selection this.$('input').prop('checked', false); + + // set value + if (new_value !== null) { + // check if its an array + if (!(new_value instanceof Array)) { + new_value = [new_value]; + } - // update to new selection - for (var i in new_value) { - this.$('input[value="' + new_value[i] + '"]').first().prop('checked', true); + // update to new selection + for (var i in new_value) { + this.$('input[value="' + new_value[i] + '"]').first().prop('checked', true); + } }; } @@ -147,16 +150,10 @@ if (options.length > 0) { return options.val(); } else { - return undefined; + return null; } }, - /** Validate the selected option/options - */ - validate: function() { - return Utils.validate(this.value()); - }, - /** Wait message during request processing */ wait: function() { @@ -213,21 +210,22 @@ /** Return current selection */ _getValue: function() { - // get selected values - var selected = this.$(':checked'); - if (selected.length == 0) { - return '__null__'; + // track values in array + var selected = []; + this.$(':checked').each(function() { + selected.push($(this).val()); + }); + + // get selected elements + if (!Utils.validate(selected)) { + return null; } - + // return multiple or single value if (this.options.multiple) { - var values = []; - selected.each(function() { - values.push($(this).val()); - }); - return values; + return selected; } else { - return selected.val(); + return selected[0]; } }, diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -75,13 +75,23 @@ /** Return/Set current selection */ value : function (new_value) { + // set new value if (new_value !== undefined) { + if (new_value === null) { + new_value = '__null__'; + } this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); } } - return this.$select.val(); + + // validate and return value + var val = this.$select.val(); + if (!Utils.validate(val)) { + return null; + } + return val; }, /** Return the first select option @@ -95,12 +105,6 @@ } }, - /** Validate the current selection - */ - validate: function() { - return Utils.validate(this.value()); - }, - /** Return the label/text of the current selection */ text : function () { diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh();a.app.trigger("refresh")})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((b===null||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh();a.app.trigger("refresh")})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value("__null__");this.select_multiple&&this.select_multiple.value("__null__");this.select_collection&&this.select_collection.value("__null__")}this.refresh()}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value(null);this.select_multiple&&this.select_multiple.value(null);this.select_collection&&this.select_collection.value(null)}this.refresh()}var j=this._select().value();if(j===null){return null}if(!(j instanceof Array)){j=[j]}if(j.length===0){return null}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(t.validate&&!t.validate()){v=null}if(g[u.type]){v=g[u.type](v)}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(u.ignore===undefined||u.ignore!=v){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/packed/mvc/ui/ui-drilldown.js --- a/static/scripts/packed/mvc/ui/ui-drilldown.js +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.BaseIcons.extend({initialize:function(d){d.type=d.display||"checkbox";d.multiple=(d.display=="checkbox");a.BaseIcons.prototype.initialize.call(this,d)},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption({label:q.name,value:q.value}));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption({label:q.name,value:q.value}))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options-list drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.BaseIcons.extend({initialize:function(d){d.type=d.display||"checkbox";d.multiple=(d.display=="checkbox");a.BaseIcons.prototype.initialize.call(this,d)},_setState:function(d,e){var f=this.$("#button-"+d);var g=this.$("#subgroup-"+d);f.data("is_expanded",e);if(e){g.fadeIn("fast");f.removeClass("toggle-expand");f.addClass("toggle")}else{g.hide();f.removeClass("toggle");f.addClass("toggle-expand")}},_templateOptions:function(g){var f=this;this.header_index={};this.header_list=[];function e(k,i){var l=k.find("#button-"+i);l.on("click",function(){f._setState(i,!l.data("is_expanded"))})}function d(r,t,o){o=o||[];for(h in t){var k=t[h];var l=k.options.length>0;var q=o.slice(0);var s=$("<div/>");if(l){var n=b.uuid();var i=$('<span id="button-'+n+'" class="ui-drilldown-button form-toggle icon-button toggle-expand"/>');var m=$('<div id="subgroup-'+n+'" style="display: none; margin-left: 25px;"/>');q.push(n);var p=$("<div/>");p.append(i);p.append(f._templateOption({label:k.name,value:k.value}));s.append(p);d(m,k.options,q);s.append(m)}else{s.append(f._templateOption({label:k.name,value:k.value}));f.header_index[k.value]=q}r.append(s)}}var j=$("<div/>");d(j,g);for(var h in this.header_index){this.header_list=_.uniq(this.header_list.concat(this.header_index[h]))}for(var h in this.header_list){e(j,this.header_list[h])}return j},_template:function(d){return'<div class="ui-options-list drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this.value(l)},value:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}this.$("input").prop("checked",false);for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}this._refresh();return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return undefined}},validate:function(){return c.validate(this.value())},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_getValue:function(){var i=this.$(":checked");if(i.length==0){return"__null__"}if(this.options.multiple){var h=[];i.each(function(){h.push($(this).val())});return h}else{return i.val()}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this.value(l)},value:function(j){if(j!==undefined){this.$("input").prop("checked",false);if(j!==null){if(!(j instanceof Array)){j=[j]}for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}}this._refresh();return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return null}},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_getValue:function(){var h=[];this.$(":checked").each(function(){h.push($(this).val())});if(!c.validate(h)){return null}if(this.options.multiple){return h}else{return h[0]}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:false,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){return a.validate(this.value())},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();if(this.options.optional&&!this.options.multiple){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find('option[value="__undefined__"]').remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"__undefined__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:false,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}var d=this.$select.val();if(!a.validate(d)){return null}return d},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();if(this.options.optional&&!this.options.multiple){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find('option[value="__undefined__"]').remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"__undefined__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(l){function m(q,p){for(var n in q){var o=q[n];if(o&&typeof(o)=="object"){p(o);m(o,p)}}}function c(n){return $("<div/>").text(n).html()}function k(o){if(!(o instanceof Array)){o=[o]}for(var n in o){if(["__null__","__undefined__","None",null,undefined].indexOf(o[n])>-1){return false}}return true}function g(n){var n=n.toString();if(n){n=n.replace(/,/g,", ");var o=n.lastIndexOf(", ");if(o!=-1){n=n.substr(0,o)+" or "+n.substr(o+1)}return n}return""}function d(n){top.__utils__get__=top.__utils__get__||{};if(n.cache&&top.__utils__get__[n.url]){n.success&&n.success(top.__utils__get__[n.url]);console.debug("utils.js::get() - Fetching from cache ["+n.url+"].")}else{h({url:n.url,data:n.data,success:function(o){top.__utils__get__[n.url]=o;n.success&&n.success(o)},error:function(o){n.error&&n.error(o)}})}}function h(o){var n={contentType:"application/json",type:o.type||"GET",data:o.data||{},url:o.url};if(n.type=="GET"||n.type=="DELETE"){if(n.url.indexOf("?")==-1){n.url+="?"}else{n.url+="&"}n.url=n.url+$.param(n.data,true);n.data=null}else{n.dataType="json";n.url=n.url;n.data=JSON.stringify(n.data)}$.ajax(n).done(function(p){if(typeof p==="string"){try{p=p.replace("Infinity,",'"Infinity",');p=jQuery.parseJSON(p)}catch(q){console.debug(q)}}o.success&&o.success(p)}).fail(function(q){var p=null;try{p=jQuery.parseJSON(q.responseText)}catch(r){p=q.responseText}o.error&&o.error(p,q)})}function i(q,n){var o=$('<div class="'+q+'"></div>');o.appendTo(":eq(0)");var p=o.css(n);o.remove();return p}function f(n){if(!$('link[href^="'+n+'"]').length){$('<link href="'+galaxy_config.root+n+'" rel="stylesheet">').appendTo("head")}}function j(n,o){if(n){return l.defaults(n,o)}else{return o}}function b(o,q){var p="";if(o>=100000000000){o=o/100000000000;p="TB"}else{if(o>=100000000){o=o/100000000;p="GB"}else{if(o>=100000){o=o/100000;p="MB"}else{if(o>=100){o=o/100;p="KB"}else{if(o>0){o=o*10;p="b"}else{return"<strong>-</strong>"}}}}}var n=(Math.round(o)/10);if(q){return n+" "+p}else{return"<strong>"+n+"</strong> "+p}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function e(){var p=new Date();var n=(p.getHours()<10?"0":"")+p.getHours();var o=(p.getMinutes()<10?"0":"")+p.getMinutes();var q=p.getDate()+"/"+(p.getMonth()+1)+"/"+p.getFullYear()+", "+n+":"+o;return q}return{cssLoadFile:f,cssGetAttribute:i,get:d,merge:j,bytesToString:b,uuid:a,time:e,request:h,sanitize:c,textify:g,validate:k,deepeach:m}}); \ No newline at end of file +define(["libs/underscore"],function(l){function m(q,p){for(var n in q){var o=q[n];if(o&&typeof(o)=="object"){p(o);m(o,p)}}}function c(n){return $("<div/>").text(n).html()}function k(o){if(!(o instanceof Array)){o=[o]}if(o.length===0){return false}for(var n in o){if(["__null__","__undefined__","None",null,undefined].indexOf(o[n])>-1){return false}}return true}function g(n){var n=n.toString();if(n){n=n.replace(/,/g,", ");var o=n.lastIndexOf(", ");if(o!=-1){n=n.substr(0,o)+" or "+n.substr(o+1)}return n}return""}function d(n){top.__utils__get__=top.__utils__get__||{};if(n.cache&&top.__utils__get__[n.url]){n.success&&n.success(top.__utils__get__[n.url]);console.debug("utils.js::get() - Fetching from cache 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j(n,o){if(n){return l.defaults(n,o)}else{return o}}function b(o,q){var p="";if(o>=100000000000){o=o/100000000000;p="TB"}else{if(o>=100000000){o=o/100000000;p="GB"}else{if(o>=100000){o=o/100000;p="MB"}else{if(o>=100){o=o/100;p="KB"}else{if(o>0){o=o*10;p="b"}else{return"<strong>-</strong>"}}}}}var n=(Math.round(o)/10);if(q){return n+" "+p}else{return"<strong>"+n+"</strong> "+p}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function e(){var p=new Date();var n=(p.getHours()<10?"0":"")+p.getHours();var o=(p.getMinutes()<10?"0":"")+p.getMinutes();var q=p.getDate()+"/"+(p.getMonth()+1)+"/"+p.getFullYear()+", "+n+":"+o;return q}return{cssLoadFile:f,cssGetAttribute:i,get:d,merge:j,bytesToString:b,uuid:a,time:e,request:h,sanitize:c,textify:g,validate:k,deepeach:m}}); \ No newline at end of file diff -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 -r 15cd0c4f1a402d96c4d243b38ae71cb1c87978a0 static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -35,6 +35,9 @@ if (!(value instanceof Array)) { value = [value]; } + if (value.length === 0) { + return false; + } for (var i in value) { if (['__null__', '__undefined__', 'None', null, undefined].indexOf(value[i]) > -1) { return false; 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: guerler: ToolForm: Place requirements into pulldown menu, add toolshed link, remove spaces
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1bb9dcb87c49/ Changeset: 1bb9dcb87c49 User: guerler Date: 2015-02-11 03:13:42+00:00 Summary: ToolForm: Place requirements into pulldown menu, add toolshed link, remove spaces Affected #: 4 files diff -r 0afbc9b476c5cd7ebf827b834628c877f75fe3e6 -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -22,13 +22,13 @@ // portlet style cls_portlet : 'ui-portlet-limited' }; - + // configure options this.options = Utils.merge(options, this.optionsDefault); - + // log options console.debug(this.options); - + // link galaxy modal or create one var galaxy = parent.Galaxy; if (galaxy && galaxy.modal) { @@ -36,84 +36,84 @@ } else { this.modal = new Ui.Modal.View(); } - + // check if the user is an admin if (galaxy && galaxy.currUser) { this.is_admin = galaxy.currUser.get('is_admin'); } else { this.is_admin = false; } - + // link container this.container = this.options.container || 'body'; - + // create deferred processing queue handler // this handler reduces the number of requests to the api by filtering redundant requests this.deferred = new Deferred(); - + // set element this.setElement('<div/>'); - + // add to main element $(this.container).append(this.$el); - + // build this form this.build(this.options); }, - + /** Main tool form build function. This function is called once a new model is available. */ build: function(options) { // link this var self = this; - + // reset events this.off('refresh'); this.off('reset'); - + // reset field list, which contains the input field elements this.field_list = {}; - + // reset sequential input definition list, which contains the input definitions as provided from the api this.input_list = {}; - + // reset input element list, which contains the dom elements of each input element (includes also the input field) this.element_list = {}; - + // creates a tree/json data structure from the input form this.tree = new ToolTree(this); - + // request history content and build form this.content = new ToolContent(this); - + // update model data self.options.inputs = options && options.inputs; - + // create ui elements this._renderForm(options); - + // rebuild the underlying data structure this.tree.finalize(); - + // show errors on startup if (options.initial_errors) { this._errors(options); } - + // add refresh listener this.on('refresh', function() { // by using/resetting the deferred ajax queue the number of redundant calls is reduced self.deferred.reset(); self.deferred.execute(function(){self._updateModel()}); }); - + // add reset listener this.on('reset', function() { for (var i in this.element_list) { this.element_list[i].reset(); } }); - + // refresh this.trigger('refresh'); }, @@ -124,7 +124,7 @@ $(this.container).empty(); $(this.container).append($el); }, - + /** Highlight and scroll to input element (currently only used for error notifications) */ highlight: function (input_id, message, silent) { @@ -144,7 +144,7 @@ } } }, - + /** Highlights errors */ _errors: function(options) { @@ -168,35 +168,10 @@ _renderForm: function(options) { // link this var self = this; - + // create message view this.message = new Ui.Message(); - - // button for version selection - var requirements_button = new Ui.ButtonIcon({ - icon : 'fa-info-circle', - title : (!options.narrow && 'Requirements') || null, - tooltip : 'Display tool requirements', - onclick : function() { - if (!this.visible) { - this.visible = true; - self.message.update({ - persistent : true, - message : ToolTemplate.requirements(options), - status : 'info' - }); - } else { - this.visible = false; - self.message.update({ - message : '' - }); - } - } - }); - if (!options.requirements || options.requirements.length == 0) { - requirements_button.$el.hide(); - } - + // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', @@ -226,14 +201,14 @@ } else { versions_button.$el.hide(); } - + // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', title : (!options.narrow && 'Options') || null, tooltip : 'View available options' }); - + // configure button selection if(options.biostar_url) { // add question option @@ -256,7 +231,7 @@ } }); }; - + // create share button menu_button.addMenu({ icon : 'fa-share', @@ -266,7 +241,7 @@ prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + galaxy_config.root + 'root?tool_id=' + options.id); } }); - + // add admin operations if (this.is_admin) { // create download button @@ -279,47 +254,83 @@ } }); } - + + // button for version selection + if (options.requirements && options.requirements.length > 0) { + menu_button.addMenu({ + icon : 'fa-info-circle', + title : 'Requirements', + tooltip : 'Display tool requirements', + onclick : function() { + if (!this.visible) { + this.visible = true; + self.message.update({ + persistent : true, + message : ToolTemplate.requirements(options), + status : 'info' + }); + } else { + this.visible = false; + self.message.update({ + message : '' + }); + } + } + }); + } + + + // add toolshed url + if (this.options.sharable_url) { + menu_button.addMenu({ + icon : 'fa-external-link', + title : 'Open in Toolshed', + tooltip : 'Access the repository', + onclick : function() { + window.open(self.options.sharable_url); + } + }); + } + // create tool form section this.section = new ToolSection.View(self, { inputs : options.inputs }); - + // switch to classic tool form mako if the form definition is incompatible if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; } - + // create portlet this.portlet = new Portlet.View({ icon : 'fa-wrench', title : '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Tool Version ' + options.version + ')', cls : this.options.cls_portlet, operations: { - requirements : requirements_button, - menu : menu_button, - versions : versions_button + menu : menu_button, + versions : versions_button }, buttons : this.buttons }); - + // append message this.portlet.append(this.message.$el.addClass('ui-margin-top')); - + // append tool section this.portlet.append(this.section.$el); - + // start form this.$el.empty(); this.$el.append(this.portlet.$el); - + // append help if (options.help != '') { this.$el.append(ToolTemplate.help(options.help)); } - + // append citations if (options.citations) { var $citations = $('<div/>'); @@ -330,7 +341,7 @@ citations.fetch(); this.$el.append($citations); } - + // show message if available in model if (options.message) { this.message.update({ diff -r 0afbc9b476c5cd7ebf827b834628c877f75fe3e6 -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2520,7 +2520,7 @@ for t in tools: tool_versions.append(t.version) - ## add information with underlying requirements and their versions + # add information with underlying requirements and their versions tool_requirements = [] if self.requirements: for requirement in self.requirements: @@ -2529,11 +2529,17 @@ 'version' : requirement.version }) + # add toolshed url + sharable_url = None + if self.tool_shed_repository: + sharable_url = self.tool_shed_repository.get_sharable_url( trans.app ) + # add additional properties tool_model.update({ 'help' : tool_help, 'citations' : tool_citations, 'biostar_url' : trans.app.config.biostar_url, + 'sharable_url' : sharable_url, 'message' : tool_message, 'versions' : tool_versions, 'requirements' : tool_requirements, diff -r 0afbc9b476c5cd7ebf827b834628c877f75fe3e6 -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -22,13 +22,13 @@ // portlet style cls_portlet : 'ui-portlet-limited' }; - + // configure options this.options = Utils.merge(options, this.optionsDefault); - + // log options console.debug(this.options); - + // link galaxy modal or create one var galaxy = parent.Galaxy; if (galaxy && galaxy.modal) { @@ -36,84 +36,84 @@ } else { this.modal = new Ui.Modal.View(); } - + // check if the user is an admin if (galaxy && galaxy.currUser) { this.is_admin = galaxy.currUser.get('is_admin'); } else { this.is_admin = false; } - + // link container this.container = this.options.container || 'body'; - + // create deferred processing queue handler // this handler reduces the number of requests to the api by filtering redundant requests this.deferred = new Deferred(); - + // set element this.setElement('<div/>'); - + // add to main element $(this.container).append(this.$el); - + // build this form this.build(this.options); }, - + /** Main tool form build function. This function is called once a new model is available. */ build: function(options) { // link this var self = this; - + // reset events this.off('refresh'); this.off('reset'); - + // reset field list, which contains the input field elements this.field_list = {}; - + // reset sequential input definition list, which contains the input definitions as provided from the api this.input_list = {}; - + // reset input element list, which contains the dom elements of each input element (includes also the input field) this.element_list = {}; - + // creates a tree/json data structure from the input form this.tree = new ToolTree(this); - + // request history content and build form this.content = new ToolContent(this); - + // update model data self.options.inputs = options && options.inputs; - + // create ui elements this._renderForm(options); - + // rebuild the underlying data structure this.tree.finalize(); - + // show errors on startup if (options.initial_errors) { this._errors(options); } - + // add refresh listener this.on('refresh', function() { // by using/resetting the deferred ajax queue the number of redundant calls is reduced self.deferred.reset(); self.deferred.execute(function(){self._updateModel()}); }); - + // add reset listener this.on('reset', function() { for (var i in this.element_list) { this.element_list[i].reset(); } }); - + // refresh this.trigger('refresh'); }, @@ -124,7 +124,7 @@ $(this.container).empty(); $(this.container).append($el); }, - + /** Highlight and scroll to input element (currently only used for error notifications) */ highlight: function (input_id, message, silent) { @@ -144,7 +144,7 @@ } } }, - + /** Highlights errors */ _errors: function(options) { @@ -168,35 +168,10 @@ _renderForm: function(options) { // link this var self = this; - + // create message view this.message = new Ui.Message(); - - // button for version selection - var requirements_button = new Ui.ButtonIcon({ - icon : 'fa-info-circle', - title : (!options.narrow && 'Requirements') || null, - tooltip : 'Display tool requirements', - onclick : function() { - if (!this.visible) { - this.visible = true; - self.message.update({ - persistent : true, - message : ToolTemplate.requirements(options), - status : 'info' - }); - } else { - this.visible = false; - self.message.update({ - message : '' - }); - } - } - }); - if (!options.requirements || options.requirements.length == 0) { - requirements_button.$el.hide(); - } - + // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', @@ -226,14 +201,14 @@ } else { versions_button.$el.hide(); } - + // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', title : (!options.narrow && 'Options') || null, tooltip : 'View available options' }); - + // configure button selection if(options.biostar_url) { // add question option @@ -256,7 +231,7 @@ } }); }; - + // create share button menu_button.addMenu({ icon : 'fa-share', @@ -266,7 +241,7 @@ prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + galaxy_config.root + 'root?tool_id=' + options.id); } }); - + // add admin operations if (this.is_admin) { // create download button @@ -279,47 +254,83 @@ } }); } - + + // button for version selection + if (options.requirements && options.requirements.length > 0) { + menu_button.addMenu({ + icon : 'fa-info-circle', + title : 'Requirements', + tooltip : 'Display tool requirements', + onclick : function() { + if (!this.visible) { + this.visible = true; + self.message.update({ + persistent : true, + message : ToolTemplate.requirements(options), + status : 'info' + }); + } else { + this.visible = false; + self.message.update({ + message : '' + }); + } + } + }); + } + + + // add toolshed url + if (this.options.sharable_url) { + menu_button.addMenu({ + icon : 'fa-external-link', + title : 'Open in Toolshed', + tooltip : 'Access the repository', + onclick : function() { + window.open(self.options.sharable_url); + } + }); + } + // create tool form section this.section = new ToolSection.View(self, { inputs : options.inputs }); - + // switch to classic tool form mako if the form definition is incompatible if (this.incompatible) { this.$el.hide(); $('#tool-form-classic').show(); return; } - + // create portlet this.portlet = new Portlet.View({ icon : 'fa-wrench', title : '<b>' + options.name + '</b> ' + options.description + ' (Galaxy Tool Version ' + options.version + ')', cls : this.options.cls_portlet, operations: { - requirements : requirements_button, - menu : menu_button, - versions : versions_button + menu : menu_button, + versions : versions_button }, buttons : this.buttons }); - + // append message this.portlet.append(this.message.$el.addClass('ui-margin-top')); - + // append tool section this.portlet.append(this.section.$el); - + // start form this.$el.empty(); this.$el.append(this.portlet.$el); - + // append help if (options.help != '') { this.$el.append(ToolTemplate.help(options.help)); } - + // append citations if (options.citations) { var $citations = $('<div/>'); @@ -330,7 +341,7 @@ citations.fetch(); this.$el.append($citations); } - + // show message if available in model if (options.message) { this.message.update({ diff -r 0afbc9b476c5cd7ebf827b834628c877f75fe3e6 -r 1bb9dcb87c4994b81a7dcdd825dd3ed91c767219 static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!u.narrow&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!u.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){t.options.id=t.options.id.replace(t.options.version,this.version);t.options.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!u.narrow&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:this.options.cls_portlet,operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}}})}); \ 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.

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commit/galaxy-central: guerler: ToolForm: Modify refresh trigger
by commits-noreply＠bitbucket.org 11 Feb '15

11 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0afbc9b476c5/ Changeset: 0afbc9b476c5 User: guerler Date: 2015-02-11 00:59:03+00:00 Summary: ToolForm: Modify refresh trigger Affected #: 3 files diff -r 581d871b810205f6a02e994983ffe316e206b746 -r 0afbc9b476c5cd7ebf827b834628c877f75fe3e6 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -49,6 +49,9 @@ // refresh view self._refresh(); + + // refresh state + self.app.trigger('refresh'); }); }, @@ -79,7 +82,6 @@ this.$title_optional.html(this.text_enable); this.field.value && this.field.value(this.default_value); } - this.app.trigger('refresh'); }, /** Main Template diff -r 581d871b810205f6a02e994983ffe316e206b746 -r 0afbc9b476c5cd7ebf827b834628c877f75fe3e6 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -49,6 +49,9 @@ // refresh view self._refresh(); + + // refresh state + self.app.trigger('refresh'); }); }, @@ -79,7 +82,6 @@ this.$title_optional.html(this.text_enable); this.field.value && this.field.value(this.default_value); } - this.app.trigger('refresh'); }, /** Main Template diff -r 581d871b810205f6a02e994983ffe316e206b746 -r 0afbc9b476c5cd7ebf827b834628c877f75fe3e6 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh();a.app.trigger("refresh")})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ 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: carlfeberhard: UI, paired collection creator: refactor autopairing and add tests
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/581d871b8102/ Changeset: 581d871b8102 User: carlfeberhard Date: 2015-02-10 23:15:43+00:00 Summary: UI, paired collection creator: refactor autopairing and add tests Affected #: 4 files diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -3,7 +3,7 @@ "utils/natural-sort", "mvc/base-mvc", "utils/localization" -], function( levelshteinDistance, naturalSort, baseMVC, _l ){ +], function( levenshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: _adjPairedOnScrollBar @@ -28,7 +28,6 @@ className : 'dataset paired', initialize : function( attributes ){ - //console.debug( 'PairView.initialize:', attributes ); this.pair = attributes.pair || {}; }, @@ -46,9 +45,6 @@ .data( 'pair', this.pair ) .html( this.template({ pair: this.pair }) ) .addClass( 'flex-column-container' ); - -//TODO: would be good to get the unpair-btn into this view - but haven't found a way with css - return this; }, @@ -61,24 +57,17 @@ /** dragging pairs for re-ordering */ _dragstart : function( ev ){ - //console.debug( this, '_dragstartPair', ev ); ev.currentTarget.style.opacity = '0.4'; if( ev.originalEvent ){ ev = ev.originalEvent; } ev.dataTransfer.effectAllowed = 'move'; ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.pair ) ); - //ev.dataTransfer.setDragImage( null, 0, 0 ); - - // the canvas can be used to create the image - //ev.dataTransfer.setDragImage( canvasCrossHairs(), 25, 25 ); - - //console.debug( 'ev.dataTransfer:', ev.dataTransfer ); this.$el.parent().trigger( 'pair.dragstart', [ this ] ); }, + /** dragging pairs for re-ordering */ _dragend : function( ev ){ - //console.debug( this, '_dragendPair', ev ); ev.currentTarget.style.opacity = '1.0'; this.$el.parent().trigger( 'pair.dragend', [ this ] ); }, @@ -92,8 +81,106 @@ toString : function(){ return 'PairView(' + this.pair.name + ')'; } +}); -}); + +/** returns an autopair function that uses the provided options.match function */ +function autoPairFnBuilder( options ){ + options = options || {}; + options.createPair = options.createPair || function _defaultCreatePair( params ){ + this.debug( 'creating pair:', params.listA[ params.indexA ].name, params.listB[ params.indexB ].name ); + params = params || {}; + return this._pair( + params.listA.splice( params.indexA, 1 )[0], + params.listB.splice( params.indexB, 1 )[0], + { silent: true } + ); + }; + // compile these here outside of the loop + var _regexps = []; + function getRegExps(){ + if( !_regexps.length ){ + _regexps = [ + new RegExp( this.filters[0] ), + new RegExp( this.filters[1] ) + ]; + } + return _regexps; + } + // mangle params as needed + options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch( params ){ + var regexps = getRegExps.call( this ); + return _.extend( params, { + matchTo : params.matchTo.name.replace( regexps[0], '' ), + possible : params.possible.name.replace( regexps[1], '' ) + }); + }; + + return function _strategy( params ){ + this.debug( 'autopair _strategy ---------------------------' ); + params = params || {}; + var listA = params.listA, + listB = params.listB, + indexA = 0, indexB, + bestMatch = { + score : 0.0, + index : null + }, + paired = []; + //console.debug( 'params:', JSON.stringify( params, null, ' ' ) ); + this.debug( 'starting list lens:', listA.length, listB.length ); + this.debug( 'bestMatch (starting):', JSON.stringify( bestMatch, null, ' ' ) ); + + while( indexA < listA.length ){ + var matchTo = listA[ indexA ]; + bestMatch.score = 0.0; + + for( indexB=0; indexB<listB.length; indexB++ ){ + var possible = listB[ indexB ]; + this.debug( indexA + ':' + matchTo.name ); + this.debug( indexB + ':' + possible.name ); + + // no matching with self + if( listA[ indexA ] !== listB[ indexB ] ){ + bestMatch = options.match.call( this, options.preprocessMatch.call( this, { + matchTo : matchTo, + possible: possible, + index : indexB, + bestMatch : bestMatch + })); + this.debug( 'bestMatch:', JSON.stringify( bestMatch, null, ' ' ) ); + if( bestMatch.score === 1.0 ){ + this.debug( 'breaking early due to perfect match' ); + break; + } + } + } + var scoreThreshold = options.scoreThreshold.call( this ); + this.debug( 'scoreThreshold:', scoreThreshold ); + this.debug( 'bestMatch.score:', bestMatch.score ); + + if( bestMatch.score >= scoreThreshold ){ + this.debug( 'creating pair' ); + paired.push( options.createPair.call( this, { + listA : listA, + indexA : indexA, + listB : listB, + indexB : bestMatch.index + })); + this.debug( 'list lens now:', listA.length, listB.length ); + } else { + indexA += 1; + } + if( !listA.length || !listB.length ){ + return paired; + } + } + this.debug( 'paired:', JSON.stringify( paired, null, ' ' ) ); + this.debug( 'autopair _strategy ---------------------------' ); + return paired; + }; +} + /** An interface for building collections of paired datasets. */ @@ -108,15 +195,11 @@ attributes = _.defaults( attributes, { datasets : [], filters : this.DEFAULT_FILTERS, - //automaticallyPair : false, automaticallyPair : true, - matchPercentage : 1.0, - //matchPercentage : 0.9, - //matchPercentage : 0.8, - //strategy : 'levenshtein' - strategy : 'lcs' + strategy : 'lcs', + matchPercentage : 0.9, + twoPassAutopairing : true }); - //this.debug( 'attributes now:', attributes ); /** unordered, original list */ this.initialList = attributes.datasets; @@ -133,15 +216,18 @@ /** try to auto pair the unpaired datasets on load? */ this.automaticallyPair = attributes.automaticallyPair; - /** distance/mismatch level allowed for autopairing */ - this.matchPercentage = attributes.matchPercentage; - /** what method to use for auto pairing (will be passed aggression level) */ this.strategy = this.strategies[ attributes.strategy ] || this.strategies[ this.DEFAULT_STRATEGY ]; if( _.isFunction( attributes.strategy ) ){ this.strategy = attributes.strategy; } + /** distance/mismatch level allowed for autopairing */ + this.matchPercentage = attributes.matchPercentage; + + /** try to autopair using simple first, then this.strategy on the remainder */ + this.twoPassAutopairing = attributes.twoPassAutopairing; + /** remove file extensions (\.*) from created pair names? */ this.removeExtensions = true; //this.removeExtensions = false; @@ -173,12 +259,12 @@ }, /** which commonFilter to use by default */ DEFAULT_FILTERS : 'illumina', - //DEFAULT_FILTERS : 'none', /** map of name->fn for autopairing */ strategies : { - 'lcs' : 'autoPairLCSs', - 'levenshtein' : 'autoPairLevenshtein' + 'simple' : 'autopairSimple', + 'lcs' : 'autopairLCS', + 'levenshtein' : 'autopairLevenshtein' }, /** default autopair strategy name */ DEFAULT_STRATEGY : 'lcs', @@ -191,8 +277,6 @@ this.paired = []; this.unpaired = []; - //this.fwdSelectedIds = []; - //this.revSelectedIds = []; this.selectedIds = []; // sort initial list, add ids if needed, and save new working copy to unpaired @@ -212,7 +296,6 @@ _sortInitialList : function(){ //this.debug( '-- _sortInitialList' ); this._sortDatasetList( this.initialList ); - //this._printList( this.unpaired ); }, /** sort a list of datasets */ @@ -229,39 +312,31 @@ dataset.id = _.uniqueId(); } }); - //this._printList( this.unpaired ); return this.initialList; }, /** split initial list into two lists, those that pass forward filters & those passing reverse */ - _splitByFilters : function( filters ){ - var fwd = [], - rev = []; + _splitByFilters : function(){ + var regexFilters = this.filters.map( function( stringFilter ){ + return new RegExp( stringFilter ); + }), + split = [ [], [] ]; - function _addToFwdOrRev( unpaired ){ - if( this._filterFwdFn( unpaired ) ){ - fwd.push( unpaired ); - } - if( this._filterRevFn( unpaired ) ){ - rev.push( unpaired ); - } + function _filter( unpaired, filter ){ + return filter.test( unpaired.name ); + //return dataset.name.indexOf( filter ) >= 0; } - this.unpaired.forEach( _.bind( _addToFwdOrRev, this ) ); - return [ fwd, rev ]; - }, - - /** filter fn to apply to forward datasets */ - _filterFwdFn : function( dataset ){ -//TODO: this treats *all* strings as regex which may confuse people - var regexp = new RegExp( this.filters[0] ); - return regexp.test( dataset.name ); - //return dataset.name.indexOf( this.filters[0] ) >= 0; - }, - - /** filter fn to apply to reverse datasets */ - _filterRevFn : function( dataset ){ - var regexp = new RegExp( this.filters[1] ); - return regexp.test( dataset.name ); + this.unpaired.forEach( function _filterEach( unpaired ){ + // 90% of the time this seems to work, but: + //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding? + // would need explanation in help as well + regexFilters.forEach( function( filter, i ){ + if( _filter( unpaired, filter ) ){ + split[i].push( unpaired ); + } + }); + }); + return split; }, /** add a dataset to the unpaired list in it's proper order */ @@ -288,202 +363,79 @@ }, // ------------------------------------------------------------------------ auto pairing -//TODO: lots of boiler plate btwn the three auto pair fns /** two passes to automatically create pairs: * use both simpleAutoPair, then the fn mentioned in strategy */ autoPair : function( strategy ){ + // split first using exact matching + var split = this._splitByFilters(), + paired = []; + if( this.twoPassAutopairing ){ + paired = this.autopairSimple({ + listA : split[0], + listB : split[1] + }); + split = this._splitByFilters(); + } + + // uncomment to see printlns while running tests + //this.debug = function(){ console.log.apply( console, arguments ); }; + + // then try the remainder with something less strict strategy = strategy || this.strategy; - //this.debug( '-- autoPair', strategy ); - var paired = this.simpleAutoPair(); - paired = paired.concat( this[ strategy ].call( this ) ); + split = this._splitByFilters(); + paired = paired.concat( this[ strategy ].call( this, { + listA : split[0], + listB : split[1] + })); return paired; }, - /** attempts to pair forward with reverse when names exactly match (after removing filters) */ - simpleAutoPair : function(){ - //this.debug( '-- simpleAutoPair' ); - // simplified auto pair that moves down unpaired lists *in order*, - // removes filters' strings from fwd and rev, - // and, if names w/o filters *exactly* match, creates a pair - // possibly good as a first pass - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - matchFound = false, - paired = []; + autopairSimple : autoPairFnBuilder({ + scoreThreshold: function(){ return 1.0; }, + match : function _match( params ){ + params = params || {}; + if( params.matchTo === params.possible ){ + return { + index: params.index, + score: 1.0 + }; + } + return params.bestMatch; + } + }), - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - matchFound = false; + autopairLevenshtein : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var distance = levenshteinDistance( params.matchTo, params.possible ), + score = 1.0 - ( distance / ( Math.max( params.matchTo.length, params.possible.length ) ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; + } + return params.bestMatch; + } + }), - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev && fwdName === revName ){ - matchFound = true; - // if it is a match, keep i at current, pop fwd, pop rev and break - //this.debug( '---->', fwdName, revName ); - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( j, 1 )[0], - { silent: true } - ); - paired.push( pair ); - break; - } + autopairLCS : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var match = this._naiveStartingAndEndingLCS( params.matchTo, params.possible ).length, + score = match / ( Math.max( params.matchTo.length, params.possible.length ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; } - if( !matchFound ){ i += 1; } + return params.bestMatch; } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ - autoPairLevenshtein : function(){ - //precondition: filters are set, both lists are not empty, and all filenames.length > filters[?].length - //this.debug( '-- autoPairLevenshtein' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - distance, bestIndex, bestDist, - paired = []; - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestDist = Number.MAX_VALUE; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestDist = 0; - break; - } - distance = levenshteinDistance( fwdName, revName ); - //this.debug( '\t\t distance:', distance, 'bestDist:', bestDist ); - if( distance < bestDist ){ - bestIndex = j; - bestDist = distance; - } - } - } - //this.debug( '---->', fwd.name, bestIndex, bestDist ); - //this.debug( '---->', fwd.name, revList[ bestIndex ].name, bestDist ); - - var percentage = 1.0 - ( bestDist / ( Math.max( fwdName.length, revName.length ) ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to auto pair using common substrings from both front and back (after removing filters) */ - autoPairLCSs : function(){ - //precondition: filters are set, both lists are not empty - //this.debug( '-- autoPairLCSs' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - currMatch, bestIndex, bestMatch, - paired = []; - if( !fwdList.length || !revList.length ){ return paired; } - //this.debug( fwdList, revList ); - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestMatch = 0; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestMatch = fwdName.length; - break; - } - var match = this._naiveStartingAndEndingLCS( fwdName, revName ); - currMatch = match.length; - //this.debug( '\t\t match:', match, 'currMatch:', currMatch, 'bestMatch:', bestMatch ); - if( currMatch > bestMatch ){ - bestIndex = j; - bestMatch = currMatch; - } - } - } - //this.debug( '---->', i, fwd.name, bestIndex, revList[ bestIndex ].name, bestMatch ); - - var percentage = bestMatch / ( Math.min( fwdName.length, revName.length ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, + }), /** return the concat'd longest common prefix and suffix from two strings */ _naiveStartingAndEndingLCS : function( s1, s2 ){ @@ -1338,19 +1290,19 @@ // ........................................................................ paired - drag and drop re-ordering //_dragenterPairedColumns : function( ev ){ - // console.debug( '_dragenterPairedColumns:', ev ); + // this.debug( '_dragenterPairedColumns:', ev ); //}, //_dragleavePairedColumns : function( ev ){ - // //console.debug( '_dragleavePairedColumns:', ev ); + // //this.debug( '_dragleavePairedColumns:', ev ); //}, /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */ _dragoverPairedColumns : function( ev ){ - //console.debug( '_dragoverPairedColumns:', ev ); + //this.debug( '_dragoverPairedColumns:', ev ); ev.preventDefault(); var $list = this.$( '.paired-columns .column-datasets' ); this._checkForAutoscroll( $list, ev.originalEvent.clientY ); - //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); + //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY ); $( '.paired-drop-placeholder' ).remove(); @@ -1369,7 +1321,7 @@ scrollTop = $element.scrollTop(), upperDist = y - offset.top, lowerDist = ( offset.top + $element.outerHeight() ) - y; - //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); if( upperDist >= 0 && upperDist < this.autoscrollDist ){ $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ @@ -1388,7 +1340,7 @@ top = $li.offset().top, halfHeight = Math.floor( $li.outerHeight() / 2 ) + WIGGLE; if( top + halfHeight > y && top - halfHeight < y ){ - //console.debug( y, top + halfHeight, top - halfHeight ) + //this.debug( y, top + halfHeight, top - halfHeight ) return $li; } } @@ -1419,13 +1371,13 @@ this.$( '.paired-columns .dataset.paired' ).each( function(){ newPaired.push( $( this ).data( 'pair' ) ); }); - //console.debug( newPaired ); + //this.debug( newPaired ); this.paired = newPaired; this._renderPaired(); }, /** drag communication with pair sub-views: dragstart */ _pairDragstart : function( ev, pair ){ - //console.debug( '_pairDragstart', ev, pair ) + //this.debug( '_pairDragstart', ev, pair ) // auto select the pair causing the event and move all selected pair.$el.addClass( 'selected' ); var $selected = this.$( '.paired-columns .dataset.selected' ); @@ -1433,7 +1385,7 @@ }, /** drag communication with pair sub-views: dragend - remove the placeholder */ _pairDragend : function( ev, pair ){ - //console.debug( '_pairDragend', ev, pair ) + //this.debug( '_pairDragend', ev, pair ) $( '.paired-drop-placeholder' ).remove(); this.$dragging = null; }, @@ -1736,7 +1688,6 @@ //============================================================================= /** a modal version of the paired collection creator */ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){ - console.log( datasets ); options = _.defaults( options || {}, { datasets : datasets, diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -3,7 +3,7 @@ "utils/natural-sort", "mvc/base-mvc", "utils/localization" -], function( levelshteinDistance, naturalSort, baseMVC, _l ){ +], function( levenshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: _adjPairedOnScrollBar @@ -28,7 +28,6 @@ className : 'dataset paired', initialize : function( attributes ){ - //console.debug( 'PairView.initialize:', attributes ); this.pair = attributes.pair || {}; }, @@ -46,9 +45,6 @@ .data( 'pair', this.pair ) .html( this.template({ pair: this.pair }) ) .addClass( 'flex-column-container' ); - -//TODO: would be good to get the unpair-btn into this view - but haven't found a way with css - return this; }, @@ -61,24 +57,17 @@ /** dragging pairs for re-ordering */ _dragstart : function( ev ){ - //console.debug( this, '_dragstartPair', ev ); ev.currentTarget.style.opacity = '0.4'; if( ev.originalEvent ){ ev = ev.originalEvent; } ev.dataTransfer.effectAllowed = 'move'; ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.pair ) ); - //ev.dataTransfer.setDragImage( null, 0, 0 ); - - // the canvas can be used to create the image - //ev.dataTransfer.setDragImage( canvasCrossHairs(), 25, 25 ); - - //console.debug( 'ev.dataTransfer:', ev.dataTransfer ); this.$el.parent().trigger( 'pair.dragstart', [ this ] ); }, + /** dragging pairs for re-ordering */ _dragend : function( ev ){ - //console.debug( this, '_dragendPair', ev ); ev.currentTarget.style.opacity = '1.0'; this.$el.parent().trigger( 'pair.dragend', [ this ] ); }, @@ -92,8 +81,106 @@ toString : function(){ return 'PairView(' + this.pair.name + ')'; } +}); -}); + +/** returns an autopair function that uses the provided options.match function */ +function autoPairFnBuilder( options ){ + options = options || {}; + options.createPair = options.createPair || function _defaultCreatePair( params ){ + this.debug( 'creating pair:', params.listA[ params.indexA ].name, params.listB[ params.indexB ].name ); + params = params || {}; + return this._pair( + params.listA.splice( params.indexA, 1 )[0], + params.listB.splice( params.indexB, 1 )[0], + { silent: true } + ); + }; + // compile these here outside of the loop + var _regexps = []; + function getRegExps(){ + if( !_regexps.length ){ + _regexps = [ + new RegExp( this.filters[0] ), + new RegExp( this.filters[1] ) + ]; + } + return _regexps; + } + // mangle params as needed + options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch( params ){ + var regexps = getRegExps.call( this ); + return _.extend( params, { + matchTo : params.matchTo.name.replace( regexps[0], '' ), + possible : params.possible.name.replace( regexps[1], '' ) + }); + }; + + return function _strategy( params ){ + this.debug( 'autopair _strategy ---------------------------' ); + params = params || {}; + var listA = params.listA, + listB = params.listB, + indexA = 0, indexB, + bestMatch = { + score : 0.0, + index : null + }, + paired = []; + //console.debug( 'params:', JSON.stringify( params, null, ' ' ) ); + this.debug( 'starting list lens:', listA.length, listB.length ); + this.debug( 'bestMatch (starting):', JSON.stringify( bestMatch, null, ' ' ) ); + + while( indexA < listA.length ){ + var matchTo = listA[ indexA ]; + bestMatch.score = 0.0; + + for( indexB=0; indexB<listB.length; indexB++ ){ + var possible = listB[ indexB ]; + this.debug( indexA + ':' + matchTo.name ); + this.debug( indexB + ':' + possible.name ); + + // no matching with self + if( listA[ indexA ] !== listB[ indexB ] ){ + bestMatch = options.match.call( this, options.preprocessMatch.call( this, { + matchTo : matchTo, + possible: possible, + index : indexB, + bestMatch : bestMatch + })); + this.debug( 'bestMatch:', JSON.stringify( bestMatch, null, ' ' ) ); + if( bestMatch.score === 1.0 ){ + this.debug( 'breaking early due to perfect match' ); + break; + } + } + } + var scoreThreshold = options.scoreThreshold.call( this ); + this.debug( 'scoreThreshold:', scoreThreshold ); + this.debug( 'bestMatch.score:', bestMatch.score ); + + if( bestMatch.score >= scoreThreshold ){ + this.debug( 'creating pair' ); + paired.push( options.createPair.call( this, { + listA : listA, + indexA : indexA, + listB : listB, + indexB : bestMatch.index + })); + this.debug( 'list lens now:', listA.length, listB.length ); + } else { + indexA += 1; + } + if( !listA.length || !listB.length ){ + return paired; + } + } + this.debug( 'paired:', JSON.stringify( paired, null, ' ' ) ); + this.debug( 'autopair _strategy ---------------------------' ); + return paired; + }; +} + /** An interface for building collections of paired datasets. */ @@ -108,15 +195,11 @@ attributes = _.defaults( attributes, { datasets : [], filters : this.DEFAULT_FILTERS, - //automaticallyPair : false, automaticallyPair : true, - matchPercentage : 1.0, - //matchPercentage : 0.9, - //matchPercentage : 0.8, - //strategy : 'levenshtein' - strategy : 'lcs' + strategy : 'lcs', + matchPercentage : 0.9, + twoPassAutopairing : true }); - //this.debug( 'attributes now:', attributes ); /** unordered, original list */ this.initialList = attributes.datasets; @@ -133,15 +216,18 @@ /** try to auto pair the unpaired datasets on load? */ this.automaticallyPair = attributes.automaticallyPair; - /** distance/mismatch level allowed for autopairing */ - this.matchPercentage = attributes.matchPercentage; - /** what method to use for auto pairing (will be passed aggression level) */ this.strategy = this.strategies[ attributes.strategy ] || this.strategies[ this.DEFAULT_STRATEGY ]; if( _.isFunction( attributes.strategy ) ){ this.strategy = attributes.strategy; } + /** distance/mismatch level allowed for autopairing */ + this.matchPercentage = attributes.matchPercentage; + + /** try to autopair using simple first, then this.strategy on the remainder */ + this.twoPassAutopairing = attributes.twoPassAutopairing; + /** remove file extensions (\.*) from created pair names? */ this.removeExtensions = true; //this.removeExtensions = false; @@ -173,12 +259,12 @@ }, /** which commonFilter to use by default */ DEFAULT_FILTERS : 'illumina', - //DEFAULT_FILTERS : 'none', /** map of name->fn for autopairing */ strategies : { - 'lcs' : 'autoPairLCSs', - 'levenshtein' : 'autoPairLevenshtein' + 'simple' : 'autopairSimple', + 'lcs' : 'autopairLCS', + 'levenshtein' : 'autopairLevenshtein' }, /** default autopair strategy name */ DEFAULT_STRATEGY : 'lcs', @@ -191,8 +277,6 @@ this.paired = []; this.unpaired = []; - //this.fwdSelectedIds = []; - //this.revSelectedIds = []; this.selectedIds = []; // sort initial list, add ids if needed, and save new working copy to unpaired @@ -212,7 +296,6 @@ _sortInitialList : function(){ //this.debug( '-- _sortInitialList' ); this._sortDatasetList( this.initialList ); - //this._printList( this.unpaired ); }, /** sort a list of datasets */ @@ -229,39 +312,31 @@ dataset.id = _.uniqueId(); } }); - //this._printList( this.unpaired ); return this.initialList; }, /** split initial list into two lists, those that pass forward filters & those passing reverse */ - _splitByFilters : function( filters ){ - var fwd = [], - rev = []; + _splitByFilters : function(){ + var regexFilters = this.filters.map( function( stringFilter ){ + return new RegExp( stringFilter ); + }), + split = [ [], [] ]; - function _addToFwdOrRev( unpaired ){ - if( this._filterFwdFn( unpaired ) ){ - fwd.push( unpaired ); - } - if( this._filterRevFn( unpaired ) ){ - rev.push( unpaired ); - } + function _filter( unpaired, filter ){ + return filter.test( unpaired.name ); + //return dataset.name.indexOf( filter ) >= 0; } - this.unpaired.forEach( _.bind( _addToFwdOrRev, this ) ); - return [ fwd, rev ]; - }, - - /** filter fn to apply to forward datasets */ - _filterFwdFn : function( dataset ){ -//TODO: this treats *all* strings as regex which may confuse people - var regexp = new RegExp( this.filters[0] ); - return regexp.test( dataset.name ); - //return dataset.name.indexOf( this.filters[0] ) >= 0; - }, - - /** filter fn to apply to reverse datasets */ - _filterRevFn : function( dataset ){ - var regexp = new RegExp( this.filters[1] ); - return regexp.test( dataset.name ); + this.unpaired.forEach( function _filterEach( unpaired ){ + // 90% of the time this seems to work, but: + //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding? + // would need explanation in help as well + regexFilters.forEach( function( filter, i ){ + if( _filter( unpaired, filter ) ){ + split[i].push( unpaired ); + } + }); + }); + return split; }, /** add a dataset to the unpaired list in it's proper order */ @@ -288,202 +363,79 @@ }, // ------------------------------------------------------------------------ auto pairing -//TODO: lots of boiler plate btwn the three auto pair fns /** two passes to automatically create pairs: * use both simpleAutoPair, then the fn mentioned in strategy */ autoPair : function( strategy ){ + // split first using exact matching + var split = this._splitByFilters(), + paired = []; + if( this.twoPassAutopairing ){ + paired = this.autopairSimple({ + listA : split[0], + listB : split[1] + }); + split = this._splitByFilters(); + } + + // uncomment to see printlns while running tests + //this.debug = function(){ console.log.apply( console, arguments ); }; + + // then try the remainder with something less strict strategy = strategy || this.strategy; - //this.debug( '-- autoPair', strategy ); - var paired = this.simpleAutoPair(); - paired = paired.concat( this[ strategy ].call( this ) ); + split = this._splitByFilters(); + paired = paired.concat( this[ strategy ].call( this, { + listA : split[0], + listB : split[1] + })); return paired; }, - /** attempts to pair forward with reverse when names exactly match (after removing filters) */ - simpleAutoPair : function(){ - //this.debug( '-- simpleAutoPair' ); - // simplified auto pair that moves down unpaired lists *in order*, - // removes filters' strings from fwd and rev, - // and, if names w/o filters *exactly* match, creates a pair - // possibly good as a first pass - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - matchFound = false, - paired = []; + autopairSimple : autoPairFnBuilder({ + scoreThreshold: function(){ return 1.0; }, + match : function _match( params ){ + params = params || {}; + if( params.matchTo === params.possible ){ + return { + index: params.index, + score: 1.0 + }; + } + return params.bestMatch; + } + }), - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - matchFound = false; + autopairLevenshtein : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var distance = levenshteinDistance( params.matchTo, params.possible ), + score = 1.0 - ( distance / ( Math.max( params.matchTo.length, params.possible.length ) ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; + } + return params.bestMatch; + } + }), - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev && fwdName === revName ){ - matchFound = true; - // if it is a match, keep i at current, pop fwd, pop rev and break - //this.debug( '---->', fwdName, revName ); - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( j, 1 )[0], - { silent: true } - ); - paired.push( pair ); - break; - } + autopairLCS : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var match = this._naiveStartingAndEndingLCS( params.matchTo, params.possible ).length, + score = match / ( Math.max( params.matchTo.length, params.possible.length ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; } - if( !matchFound ){ i += 1; } + return params.bestMatch; } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ - autoPairLevenshtein : function(){ - //precondition: filters are set, both lists are not empty, and all filenames.length > filters[?].length - //this.debug( '-- autoPairLevenshtein' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - distance, bestIndex, bestDist, - paired = []; - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestDist = Number.MAX_VALUE; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestDist = 0; - break; - } - distance = levenshteinDistance( fwdName, revName ); - //this.debug( '\t\t distance:', distance, 'bestDist:', bestDist ); - if( distance < bestDist ){ - bestIndex = j; - bestDist = distance; - } - } - } - //this.debug( '---->', fwd.name, bestIndex, bestDist ); - //this.debug( '---->', fwd.name, revList[ bestIndex ].name, bestDist ); - - var percentage = 1.0 - ( bestDist / ( Math.max( fwdName.length, revName.length ) ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to auto pair using common substrings from both front and back (after removing filters) */ - autoPairLCSs : function(){ - //precondition: filters are set, both lists are not empty - //this.debug( '-- autoPairLCSs' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - currMatch, bestIndex, bestMatch, - paired = []; - if( !fwdList.length || !revList.length ){ return paired; } - //this.debug( fwdList, revList ); - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestMatch = 0; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestMatch = fwdName.length; - break; - } - var match = this._naiveStartingAndEndingLCS( fwdName, revName ); - currMatch = match.length; - //this.debug( '\t\t match:', match, 'currMatch:', currMatch, 'bestMatch:', bestMatch ); - if( currMatch > bestMatch ){ - bestIndex = j; - bestMatch = currMatch; - } - } - } - //this.debug( '---->', i, fwd.name, bestIndex, revList[ bestIndex ].name, bestMatch ); - - var percentage = bestMatch / ( Math.min( fwdName.length, revName.length ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, + }), /** return the concat'd longest common prefix and suffix from two strings */ _naiveStartingAndEndingLCS : function( s1, s2 ){ @@ -1338,19 +1290,19 @@ // ........................................................................ paired - drag and drop re-ordering //_dragenterPairedColumns : function( ev ){ - // console.debug( '_dragenterPairedColumns:', ev ); + // this.debug( '_dragenterPairedColumns:', ev ); //}, //_dragleavePairedColumns : function( ev ){ - // //console.debug( '_dragleavePairedColumns:', ev ); + // //this.debug( '_dragleavePairedColumns:', ev ); //}, /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */ _dragoverPairedColumns : function( ev ){ - //console.debug( '_dragoverPairedColumns:', ev ); + //this.debug( '_dragoverPairedColumns:', ev ); ev.preventDefault(); var $list = this.$( '.paired-columns .column-datasets' ); this._checkForAutoscroll( $list, ev.originalEvent.clientY ); - //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); + //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY ); $( '.paired-drop-placeholder' ).remove(); @@ -1369,7 +1321,7 @@ scrollTop = $element.scrollTop(), upperDist = y - offset.top, lowerDist = ( offset.top + $element.outerHeight() ) - y; - //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); if( upperDist >= 0 && upperDist < this.autoscrollDist ){ $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ @@ -1388,7 +1340,7 @@ top = $li.offset().top, halfHeight = Math.floor( $li.outerHeight() / 2 ) + WIGGLE; if( top + halfHeight > y && top - halfHeight < y ){ - //console.debug( y, top + halfHeight, top - halfHeight ) + //this.debug( y, top + halfHeight, top - halfHeight ) return $li; } } @@ -1419,13 +1371,13 @@ this.$( '.paired-columns .dataset.paired' ).each( function(){ newPaired.push( $( this ).data( 'pair' ) ); }); - //console.debug( newPaired ); + //this.debug( newPaired ); this.paired = newPaired; this._renderPaired(); }, /** drag communication with pair sub-views: dragstart */ _pairDragstart : function( ev, pair ){ - //console.debug( '_pairDragstart', ev, pair ) + //this.debug( '_pairDragstart', ev, pair ) // auto select the pair causing the event and move all selected pair.$el.addClass( 'selected' ); var $selected = this.$( '.paired-columns .dataset.selected' ); @@ -1433,7 +1385,7 @@ }, /** drag communication with pair sub-views: dragend - remove the placeholder */ _pairDragend : function( ev, pair ){ - //console.debug( '_pairDragend', ev, pair ) + //this.debug( '_pairDragend', ev, pair ) $( '.paired-drop-placeholder' ).remove(); this.$dragging = null; }, @@ -1736,7 +1688,6 @@ //============================================================================= /** a modal version of the paired collection creator */ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){ - console.log( datasets ); options = _.defaults( options || {}, { datasets : datasets, diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(i){this.pair=i.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(i){i.currentTarget.style.opacity="0.4";if(i.originalEvent){i=i.originalEvent}i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(i){i.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(i){this.$el.parent().trigger(i)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(i){i=_.defaults(i,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=i.datasets;this.historyId=i.historyId;this.filters=this.commonFilters[i.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(i.filters)){this.filters=i.filters}this.automaticallyPair=i.automaticallyPair;this.matchPercentage=i.matchPercentage;this.strategy=this.strategies[i.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(i.strategy)){this.strategy=i.strategy}this.removeExtensions=true;this.oncancel=i.oncancel;this.oncreate=i.oncreate;this.autoscrollDist=i.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(i){i.sort(function(k,j){return g(k.name,j.name)});return i},_ensureIds:function(){this.initialList.forEach(function(i){if(!i.hasOwnProperty("id")){i.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(l){var k=[],i=[];function j(m){if(this._filterFwdFn(m)){k.push(m)}if(this._filterRevFn(m)){i.push(m)}}this.unpaired.forEach(_.bind(j,this));return[k,i]},_filterFwdFn:function(j){var i=new RegExp(this.filters[0]);return i.test(j.name)},_filterRevFn:function(j){var i=new RegExp(this.filters[1]);return i.test(j.name)},_addToUnpaired:function(j){var i=function(k,m){if(k===m){return k}var l=Math.floor((m-k)/2)+k,n=g(j.name,this.unpaired[l].name);if(n<0){return i(k,l)}else{if(n>0){return i(l+1,m)}}while(this.unpaired[l]&&this.unpaired[l].name===j.name){l++}return l}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,j)},autoPair:function(j){j=j||this.strategy;var i=this.simpleAutoPair();i=i.concat(this[j].call(this));return i},simpleAutoPair:function(){var p=0,n,t=this._splitByFilters(),k=t[0],s=t[1],r,v,l=false,u=[];while(p<k.length){var o=k[p];r=o.name.replace(this.filters[0],"");l=false;for(n=0;n<s.length;n++){var q=s[n];v=q.name.replace(this.filters[1],"");if(o!==q&&r===v){l=true;var m=this._pair(k.splice(p,1)[0],s.splice(n,1)[0],{silent:true});u.push(m);break}}if(!l){p+=1}}return u},autoPairLevenshtein:function(){var q=0,o,v=this._splitByFilters(),k=v[0],t=v[1],s,y,l,u,m,w=[];while(q<k.length){var p=k[q];s=p.name.replace(this.filters[0],"");m=Number.MAX_VALUE;for(o=0;o<t.length;o++){var r=t[o];y=r.name.replace(this.filters[1],"");if(p!==r){if(s===y){u=o;m=0;break}l=levenshteinDistance(s,y);if(l<m){u=o;m=l}}}var x=1-(m/(Math.max(s.length,y.length)));if(x>=this.matchPercentage){var n=this._pair(k.splice(q,1)[0],t.splice(u,1)[0],{silent:true});w.push(n);if(k.length<=0||t.length<=0){return w}}else{q+=1}}return w},autoPairLCSs:function(){var o=0,m,v=this._splitByFilters(),k=v[0],t=v[1],s,z,y,u,q,w=[];if(!k.length||!t.length){return w}while(o<k.length){var n=k[o];s=n.name.replace(this.filters[0],"");q=0;for(m=0;m<t.length;m++){var r=t[m];z=r.name.replace(this.filters[1],"");if(n!==r){if(s===z){u=m;q=s.length;break}var p=this._naiveStartingAndEndingLCS(s,z);y=p.length;if(y>q){u=m;q=y}}}var x=q/(Math.min(s.length,z.length));if(x>=this.matchPercentage){var l=this._pair(k.splice(o,1)[0],t.splice(u,1)[0],{silent:true});w.push(l);if(k.length<=0||t.length<=0){return w}}else{o+=1}}return w},_naiveStartingAndEndingLCS:function(n,l){var o="",p="",m=0,k=0;while(m<n.length&&m<l.length){if(n[m]!==l[m]){break}o+=n[m];m+=1}if(m===n.length){return n}if(m===l.length){return l}m=(n.length-1);k=(l.length-1);while(m>=0&&k>=0){if(n[m]!==l[k]){break}p=[n[m],p].join("");m-=1;k-=1}return o+p},_pair:function(k,i,j){j=j||{};var l=this._createPair(k,i,j.name);this.paired.push(l);this.unpaired=_.without(this.unpaired,k,i);if(!j.silent){this.trigger("pair:new",l)}return l},_createPair:function(k,i,j){if(!(k&&i)||(k===i)){throw new Error("Bad pairing: "+[JSON.stringify(k),JSON.stringify(i)])}j=j||this._guessNameForPair(k,i);return{forward:k,name:j,reverse:i}},_guessNameForPair:function(k,i,l){l=(l!==undefined)?(l):(this.removeExtensions);var j=this._naiveStartingAndEndingLCS(k.name.replace(this.filters[0],""),i.name.replace(this.filters[1],""));if(l){var m=j.lastIndexOf(".");if(m>0){j=j.slice(0,m)}}return j||(k.name+" & "+i.name)},_unpair:function(j,i){i=i||{};if(!j){throw new Error("Bad pair: "+JSON.stringify(j))}this.paired=_.without(this.paired,j);this._addToUnpaired(j.forward);this._addToUnpaired(j.reverse);if(!i.silent){this.trigger("pair:unpair",[j])}return j},unpairAll:function(){var i=[];while(this.paired.length){i.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",i)},_pairToJSON:function(i){return{collection_type:"paired",src:"new_collection",name:i.name,element_identifiers:[{name:"forward",id:i.forward.id,src:"hda"},{name:"reverse",id:i.reverse.id,src:"hda"}]}},createList:function(k){var l=this,j;if(l.historyId){j="/api/histories/"+this.historyId+"/contents/dataset_collections"}var i={type:"dataset_collection",collection_type:"list:paired",name:_.escape(k||l.$(".collection-name").val()),element_identifiers:l.paired.map(function(m){return l._pairToJSON(m)})};return jQuery.ajax(j,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(i)}).fail(function(o,m,n){l._ajaxErrHandler(o,m,n)}).done(function(m,n,o){l.trigger("collection:created",m,n,o);if(typeof l.oncreate==="function"){l.oncreate.call(this,m,n,o)}})},_ajaxErrHandler:function(l,i,k){this.error(l,i,k);var j=d("An error occurred while creating this collection");if(l){if(l.readyState===0&&l.status===0){j+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(l.responseJSON){j+="<br /><pre>"+JSON.stringify(l.responseJSON)+"</pre>"}else{j+=": "+k}}}creator._showAlert(j,"alert-danger")},render:function(i,j){this.$el.empty().html(e.templates.main());this._renderHeader(i);this._renderMiddle(i);this._renderFooter(i);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(j,k){var i=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return i},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(j,k){var i=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return i},_renderUnpaired:function(n,o){var l=this,m,j,i=[],k=this._splitByFilters();this.$(".forward-column .title").text([k[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-k[0].length));this.$(".reverse-column .title").text([k[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-k[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}j=k[1].map(function(q,p){if((k[0][p]!==undefined)&&(k[0][p]!==q)){i.push(l._renderPairButton())}return l._renderUnpairedDataset(q)});m=k[0].map(function(p){return l._renderUnpairedDataset(p)});if(!m.length&&!j.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(m).add(this.$(".unpaired-columns .paired-column .column-datasets").append(i)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(j));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(i){return["(",i," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(i){return $("<li/>").attr("id","dataset-"+i.id).addClass("dataset unpaired").attr("draggable",true).addClass(i.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(i.name)).data("dataset",i)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var i=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(i);return i},_renderUnpairedNotShown:function(){var i=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(i);return i},_adjUnpairedOnScrollbar:function(){var l=this.$(".unpaired-columns").last(),m=this.$(".unpaired-columns .reverse-column .dataset").first();if(!m.size()){return}var i=l.offset().left+l.outerWidth(),k=m.offset().left+m.outerWidth(),j=Math.floor(i)-Math.floor(k);this.$(".unpaired-columns .forward-column").css("margin-left",(j>0)?j:0)},_renderPaired:function(j,k){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var i=this;this.paired.forEach(function(n,l){var m=new f({pair:n});i.$(".paired-columns .column-datasets").append(m.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var i=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(i);return i},_renderFooter:function(j,k){var i=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return i},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(i){function j(m,l){return['<button class="filter-choice btn" ','data-forward="',m,'" data-reverse="',l,'">',d("Forward"),": ",m,", ",d("Reverse"),": ",l,"</button>"].join("")}var k=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",j("_1","_2"),j("_R1","_R2"),"</div>"].join(""))({}));return this.$(i).popover({container:".collection-creator",placement:"bottom",html:true,content:k})},_validationWarning:function(j,i){var k="validation-warning";if(j==="name"){j=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(i){j=j||this.$("."+k);j.removeClass(k)}else{j.addClass(k)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(i){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var i,j=null;if(this.paired.length){j="alert-success";i=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){i+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{i=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(i,j)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(i){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(i){$(i.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(i){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(i){$(i.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(i){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(i){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(i){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(i){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(j,i){i=i||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(i).show().find(".alert-message").html(j)},_hideAlert:function(i){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(i){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(i){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(i,j){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(i,j)},hidePaired:function(i,j){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(i,j)},splitView:function(i,j){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(i,j);return this},_clickUnpairAll:function(i){this.unpairAll()},_clickAutopair:function(i){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(j){var i=$(j.currentTarget);this.$(".forward-unpaired-filter input").val(i.data("forward"));this.$(".reverse-unpaired-filter 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i=this,m=j.pageY;$("body").css("cursor","ns-resize");i.$(".flexible-partition-drag").css("color","black");function l(n){i.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",k)}function k(n){var o=n.pageY-m;if(!i.adjPartition(o)){$("body").trigger("mouseup")}i._adjUnpairedOnScrollbar();m+=o}$("body").mousemove(k);$("body").one("mouseup",l)},adjPartition:function(j){var i=this.$(".unpaired-columns"),k=this.$(".paired-columns"),l=parseInt(i.css("height"),10),m=parseInt(k.css("height"),10);l=Math.max(10,l+j);m=m-j;var n=j<0;if(n){if(this.unpairedPanelHidden){return false}else{if(l<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){i.show();this.unpairedPanelHidden=false}}if(!n){if(this.pairedPanelHidden){return false}else{if(m<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){k.show();this.pairedPanelHidden=false}}i.css({height:l+"px",flex:"0 0 auto"});return true},selectPair:function(i){i.stopPropagation();$(i.currentTarget).toggleClass("selected")},clearSelectedPaired:function(i){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(l){l.stopPropagation();var n=$(l.currentTarget),k=n.parent().parent(),j=k.index(".dataset.paired"),m=this.paired[j],i=prompt("Enter a new name for the pair:",m.name);if(i){m.name=i;m.customizedName=true;n.text(m.name)}},_clickUnpair:function(j){var i=Math.floor($(j.currentTarget).index(".unpair-btn"));this._unpair(this.paired[i])},_dragoverPairedColumns:function(l){l.preventDefault();var j=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(j,l.originalEvent.clientY);var k=this._getNearestPairedDatasetLi(l.originalEvent.clientY);$(".paired-drop-placeholder").remove();var i=$('<div class="paired-drop-placeholder"></div>');if(!k.size()){j.append(i)}else{k.before(i)}},_checkForAutoscroll:function(i,o){var m=2;var n=i.offset(),l=i.scrollTop(),j=o-n.top,k=(n.top+i.outerHeight())-o;if(j>=0&&j<this.autoscrollDist){i.scrollTop(l-m)}else{if(k>=0&&k<this.autoscrollDist){i.scrollTop(l+m)}}},_getNearestPairedDatasetLi:function(p){var m=4,k=this.$(".paired-columns .column-datasets li").toArray();for(var l=0;l<k.length;l++){var o=$(k[l]),n=o.offset().top,j=Math.floor(o.outerHeight()/2)+m;if(n+j>p&&n-j<p){return o}}return $()},_dropPairedColumns:function(j){j.preventDefault();j.dataTransfer.dropEffect="move";var i=this._getNearestPairedDatasetLi(j.originalEvent.clientY);if(i.size()){this.$dragging.insertBefore(i)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var i=[];this.$(".paired-columns .dataset.paired").each(function(){i.push($(this).data("pair"))});this.paired=i;this._renderPaired()},_pairDragstart:function(j,k){k.$el.addClass("selected");var i=this.$(".paired-columns .dataset.selected");this.$dragging=i},_pairDragend:function(i,j){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(j){var i=this;i.removeExtensions=(j!==undefined)?(j):(!i.removeExtensions);_.each(i.paired,function(k){if(k.customizedName){return}k.name=i._guessNameForPair(k.forward,k.reverse)});i._renderPaired();i._renderFooter()},_changeName:function(i){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(i){if(i.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(j){var i=this._getName();if(!i){this._validationWarning("name")}else{this.createList()}},_printList:function(j){var i=this;_.each(j,function(k){if(j===i.paired){i._printPair(k)}else{}})},_printPair:function(i){this.debug(i.forward.name,i.reverse.name,": ->",i.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header 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/>',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',d("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',d("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div 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","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function i(k,j){k=k||"body";if(!this.size()){return this}$(this).each(function(){var m=$(this),l=m.data("target");if(l){m.mouseover(function(n){$(l,k).css({background:j})}).mouseout(function(n){$(l).css({background:""})})}});return this}})}());var b=function c(k,i){console.log(k);i=_.defaults(i||{},{datasets:k,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var j=new e(i).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:j.$el,width:"80%",height:"800px",closing_events:true});window.PCC=j;return j};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,b,f,c){var i=Backbone.View.extend(f.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(l){this.pair=l.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(l){l.currentTarget.style.opacity="0.4";if(l.originalEvent){l=l.originalEvent}l.dataTransfer.effectAllowed="move";l.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(l){l.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(l){this.$el.parent().trigger(l)},toString:function(){return"PairView("+this.pair.name+")"}});function g(m){m=m||{};m.createPair=m.createPair||function l(r){this.debug("creating pair:",r.listA[r.indexA].name,r.listB[r.indexB].name);r=r||{};return this._pair(r.listA.splice(r.indexA,1)[0],r.listB.splice(r.indexB,1)[0],{silent:true})};var o=[];function q(){if(!o.length){o=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]}return o}m.preprocessMatch=m.preprocessMatch||function n(s){var r=q.call(this);return _.extend(s,{matchTo:s.matchTo.name.replace(r[0],""),possible:s.possible.name.replace(r[1],"")})};return function p(t){this.debug("autopair _strategy ---------------------------");t=t||{};var r=t.listA,A=t.listB,z=0,y,v={score:0,index:null},x=[];this.debug("starting list lens:",r.length,A.length);this.debug("bestMatch (starting):",JSON.stringify(v,null," "));while(z<r.length){var w=r[z];v.score=0;for(y=0;y<A.length;y++){var u=A[y];this.debug(z+":"+w.name);this.debug(y+":"+u.name);if(r[z]!==A[y]){v=m.match.call(this,m.preprocessMatch.call(this,{matchTo:w,possible:u,index:y,bestMatch:v}));this.debug("bestMatch:",JSON.stringify(v,null," "));if(v.score===1){this.debug("breaking early due to perfect match");break}}}var s=m.scoreThreshold.call(this);this.debug("scoreThreshold:",s);this.debug("bestMatch.score:",v.score);if(v.score>=s){this.debug("creating pair");x.push(m.createPair.call(this,{listA:r,indexA:z,listB:A,indexB:v.index}));this.debug("list lens now:",r.length,A.length)}else{z+=1}if(!r.length||!A.length){return x}}this.debug("paired:",JSON.stringify(x,null," "));this.debug("autopair _strategy ---------------------------");return x}}var k=Backbone.View.extend(f.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(l){l=_.defaults(l,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,strategy:"lcs",matchPercentage:0.9,twoPassAutopairing:true});this.initialList=l.datasets;this.historyId=l.historyId;this.filters=this.commonFilters[l.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(l.filters)){this.filters=l.filters}this.automaticallyPair=l.automaticallyPair;this.strategy=this.strategies[l.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(l.strategy)){this.strategy=l.strategy}this.matchPercentage=l.matchPercentage;this.twoPassAutopairing=l.twoPassAutopairing;this.removeExtensions=true;this.oncancel=l.oncancel;this.oncreate=l.oncreate;this.autoscrollDist=l.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(l){l.sort(function(n,m){return b(n.name,m.name)});return l},_ensureIds:function(){this.initialList.forEach(function(l){if(!l.hasOwnProperty("id")){l.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(){var o=this.filters.map(function(p){return new RegExp(p)}),m=[[],[]];function n(p,q){return q.test(p.name)}this.unpaired.forEach(function l(p){o.forEach(function(r,q){if(n(p,r)){m[q].push(p)}})});return m},_addToUnpaired:function(m){var l=function(n,p){if(n===p){return n}var o=Math.floor((p-n)/2)+n,q=b(m.name,this.unpaired[o].name);if(q<0){return l(n,o)}else{if(q>0){return l(o+1,p)}}while(this.unpaired[o]&&this.unpaired[o].name===m.name){o++}return o}.bind(this);this.unpaired.splice(l(0,this.unpaired.length),0,m)},autoPair:function(n){var m=this._splitByFilters(),l=[];if(this.twoPassAutopairing){l=this.autopairSimple({listA:m[0],listB:m[1]});m=this._splitByFilters()}n=n||this.strategy;m=this._splitByFilters();l=l.concat(this[n].call(this,{listA:m[0],listB:m[1]}));return l},autopairSimple:g({scoreThreshold:function(){return 1},match:function j(l){l=l||{};if(l.matchTo===l.possible){return{index:l.index,score:1}}return l.bestMatch}}),autopairLevenshtein:g({scoreThreshold:function(){return this.matchPercentage},match:function e(m){m=m||{};var n=h(m.matchTo,m.possible),l=1-(n/(Math.max(m.matchTo.length,m.possible.length)));if(l>m.bestMatch.score){return{index:m.index,score:l}}return m.bestMatch}}),autopairLCS:g({scoreThreshold:function(){return this.matchPercentage},match:function e(n){n=n||{};var l=this._naiveStartingAndEndingLCS(n.matchTo,n.possible).length,m=l/(Math.max(n.matchTo.length,n.possible.length));if(m>n.bestMatch.score){return{index:n.index,score:m}}return n.bestMatch}}),_naiveStartingAndEndingLCS:function(o,m){var p="",q="",n=0,l=0;while(n<o.length&&n<m.length){if(o[n]!==m[n]){break}p+=o[n];n+=1}if(n===o.length){return o}if(n===m.length){return 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",c(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",c(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",c(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function l(n,m){n=n||"body";if(!this.size()){return this}$(this).each(function(){var p=$(this),o=p.data("target");if(o){p.mouseover(function(q){$(o,n).css({background:m})}).mouseout(function(q){$(o).css({background:""})})}});return this}})}());var d=function a(n,l){l=_.defaults(l||{},{datasets:n,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var m=new k(l).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:m.$el,width:"80%",height:"800px",closing_events:true});window.PCC=m;return m};return{PairedCollectionCreator:k,pairedCollectionCreatorModal:d}}); \ No newline at end of file diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 test/qunit/tests/paired-collection-creator.js --- a/test/qunit/tests/paired-collection-creator.js +++ b/test/qunit/tests/paired-collection-creator.js @@ -22,7 +22,7 @@ ok( pcc.hasOwnProperty( 'options' ) && typeof pcc.options === 'object' ); deepEqual( pcc.options.filters, pcc.DEFAULT_FILTERS ); ok( pcc.options.automaticallyPair ); - equal( pcc.options.matchPercentage, 1.0 ); + equal( pcc.options.matchPercentage, 0.9 ); equal( pcc.options.strategy, 'lcs' ); }); @@ -44,6 +44,36 @@ equal( pcc.paired.length, pcc.initialList.length / 2 ); }); + test( "Try easy autopairing with simple exact matching", function() { + var pcc = new PCC({ + datasets : DATA._1, + strategy : 'simple', + twoPassAutopairing : false + }); + equal( pcc.unpaired.length, 0 ); + equal( pcc.paired.length, pcc.initialList.length / 2 ); + }); + + test( "Try easy autopairing with LCS", function() { + var pcc = new PCC({ + datasets : DATA._1, + strategy : 'lcs', + twoPassAutopairing : false + }); + equal( pcc.unpaired.length, 0 ); + equal( pcc.paired.length, pcc.initialList.length / 2 ); + }); + + test( "Try easy autopairing with Levenshtein", function() { + var pcc = new PCC({ + datasets : DATA._1, + strategy : 'levenshtein', + twoPassAutopairing : false + }); + equal( pcc.unpaired.length, 0 ); + equal( pcc.paired.length, pcc.initialList.length / 2 ); + }); + //TODO: // filters: clearing, setting via popover, regex // partition: maximize paired, maximize unpaired, split evenly @@ -69,10 +99,9 @@ ); }); - console.debug( 'requestBody:', JSON.stringify( requestJSON, null, ' ' ) ); + //console.debug( 'requestBody:', JSON.stringify( requestJSON, null, ' ' ) ); pcc.createList( 'Heres a collection' ); server.respond(); deepEqual( requestJSON, DATA._1requestJSON ); }); - }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: guerler: Ui: Update options
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cd41c43e857f/ Changeset: cd41c43e857f User: guerler Date: 2015-02-10 22:09:13+00:00 Summary: Ui: Update options Affected #: 3 files diff -r 82f66cc8b9dc6e68174a23513191c1218299a76a -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -94,9 +94,6 @@ self._change(); }); - // refresh - this._refresh(); - // set previous value this.value(current); }, @@ -120,6 +117,9 @@ }; } + // refresh + this._refresh(); + // get and return value return this._getValue(); }, @@ -163,13 +163,13 @@ if (this._size() == 0) { this._messageShow(this.options.wait_text, 'info'); this.$options.hide(); + this.$menu.hide(); } }, /** Hide wait message */ unwait: function() { - this._messageHide(); this._refresh(); }, @@ -179,6 +179,22 @@ if (this.options.onchange) { this.options.onchange(this._getValue()); } + }, + + /** Refresh options view + */ + _refresh: function() { + // show/hide messages + if (this._size() == 0) { + this._messageShow(this.options.error_text, 'danger'); + this.$options.hide(); + this.$menu.hide(); + } else { + this._messageHide(); + this.$options.css('display', 'inline-block'); + this.$menu.show(); + } + // refresh select/unselect button if (this.select_button) { var total = this._size(); var value = this._getValue(); @@ -194,20 +210,6 @@ } }, - /** Refresh options view - */ - _refresh: function() { - if (this._size() == 0) { - this._messageShow(this.options.error_text, 'danger'); - this.$options.hide(); - this.$menu.hide(); - } else { - this._messageHide(); - this.$options.css('display', 'inline-block'); - this.$menu.show(); - } - }, - /** Return current selection */ _getValue: function() { diff -r 82f66cc8b9dc6e68174a23513191c1218299a76a -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -94,9 +94,6 @@ self._change(); }); - // refresh - this._refresh(); - // set previous value this.value(current); }, @@ -120,6 +117,9 @@ }; } + // refresh + this._refresh(); + // get and return value return this._getValue(); }, @@ -163,13 +163,13 @@ if (this._size() == 0) { this._messageShow(this.options.wait_text, 'info'); this.$options.hide(); + this.$menu.hide(); } }, /** Hide wait message */ unwait: function() { - this._messageHide(); this._refresh(); }, @@ -179,6 +179,22 @@ if (this.options.onchange) { this.options.onchange(this._getValue()); } + }, + + /** Refresh options view + */ + _refresh: function() { + // show/hide messages + if (this._size() == 0) { + this._messageShow(this.options.error_text, 'danger'); + this.$options.hide(); + this.$menu.hide(); + } else { + this._messageHide(); + this.$options.css('display', 'inline-block'); + this.$menu.show(); + } + // refresh select/unselect button if (this.select_button) { var total = this._size(); var value = this._getValue(); @@ -194,20 +210,6 @@ } }, - /** Refresh options view - */ - _refresh: function() { - if (this._size() == 0) { - this._messageShow(this.options.error_text, 'danger'); - this.$options.hide(); - this.$menu.hide(); - } else { - this._messageHide(); - this.$options.css('display', 'inline-block'); - this.$menu.show(); - } - }, - /** Return current selection */ _getValue: function() { diff -r 82f66cc8b9dc6e68174a23513191c1218299a76a -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this._refresh();this.value(l)},value:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}this.$("input").prop("checked",false);for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return undefined}},validate:function(){return c.validate(this.value())},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}},_getValue:function(){var i=this.$(":checked");if(i.length==0){return"__null__"}if(this.options.multiple){var h=[];i.each(function(){h.push($(this).val())});return h}else{return i.val()}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this.value(l)},value:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}this.$("input").prop("checked",false);for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}this._refresh();return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return undefined}},validate:function(){return c.validate(this.value())},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_getValue:function(){var i=this.$(":checked");if(i.length==0){return"__null__"}if(this.options.multiple){var h=[];i.each(function(){h.push($(this).val())});return h}else{return i.val()}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Remove unused variable
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82f66cc8b9dc/ Changeset: 82f66cc8b9dc User: guerler Date: 2015-02-10 21:36:35+00:00 Summary: ToolForm: Remove unused variable Affected #: 3 files diff -r 16593d9d24fe952789835895c532ad246df4346b -r 82f66cc8b9dc6e68174a23513191c1218299a76a client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -176,9 +176,8 @@ /** Trigger custom onchange callback function */ _change: function() { - var current = this._getValue(); if (this.options.onchange) { - this.options.onchange(current); + this.options.onchange(this._getValue()); } if (this.select_button) { var total = this._size(); diff -r 16593d9d24fe952789835895c532ad246df4346b -r 82f66cc8b9dc6e68174a23513191c1218299a76a static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -176,9 +176,8 @@ /** Trigger custom onchange callback function */ _change: function() { - var current = this._getValue(); if (this.options.onchange) { - this.options.onchange(current); + this.options.onchange(this._getValue()); } if (this.select_button) { var total = this._size(); diff -r 16593d9d24fe952789835895c532ad246df4346b -r 82f66cc8b9dc6e68174a23513191c1218299a76a static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this._refresh();this.value(l)},value:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}this.$("input").prop("checked",false);for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return undefined}},validate:function(){return c.validate(this.value())},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){var j=this._getValue();if(this.options.onchange){this.options.onchange(j)}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}},_getValue:function(){var i=this.$(":checked");if(i.length==0){return"__null__"}if(this.options.multiple){var h=[];i.each(function(){h.push($(this).val())});return h}else{return i.val()}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this._refresh();this.value(l)},value:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}this.$("input").prop("checked",false);for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return undefined}},validate:function(){return c.validate(this.value())},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}},_getValue:function(){var i=this.$(":checked");if(i.length==0){return"__null__"}if(this.options.multiple){var h=[];i.each(function(){h.push($(this).val())});return h}else{return i.val()}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Add select/unselect fields, update styles
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/16593d9d24fe/ Changeset: 16593d9d24fe User: guerler Date: 2015-02-10 21:32:59+00:00 Summary: ToolForm: Add select/unselect fields, update styles Affected #: 14 files diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b client/galaxy/scripts/mvc/ui/ui-button-check.js --- /dev/null +++ b/client/galaxy/scripts/mvc/ui/ui-button-check.js @@ -0,0 +1,45 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +return Backbone.View.extend({ + + // default options + optionsDefault: { + icons : ['fa fa-square-o', 'fa fa-minus-square-o', 'fa fa-check-square-o'], + value : 0 + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement($('<div/>')); + + // set initial value + this.value(this.options.value); + + // add event handler + var self = this; + this.$el.on('click', function() { + self.current = (!self.current && 2) || 0; + self.value(self.current); + self.options.onclick && self.options.onclick(); + }); + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.current = new_val; + this.$el.removeClass() + .addClass('ui-checkbutton') + .addClass(this.options.icons[new_val]); + this.options.onchange && this.options.onchange(new_val); + } + return this.current; + } +}); +}); \ No newline at end of file diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b client/galaxy/scripts/mvc/ui/ui-drilldown.js --- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js +++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js @@ -4,28 +4,19 @@ /** * This class creates/wraps a drill down element. */ -var View = Options.Base.extend({ +var View = Options.BaseIcons.extend({ // initialize initialize: function(options) { - this.display = options.display || 'checkbox'; - options.multiple = (this.display == 'checkbox'); - Options.Base.prototype.initialize.call(this, options); + options.type = options.display || 'checkbox'; + options.multiple = (options.display == 'checkbox'); + Options.BaseIcons.prototype.initialize.call(this, options); }, - - /** Template for input field - */ - _templateOption: function(name, value, selected) { - return '<div>' + - '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name + - '<div/>'; - }, - + /** Template to create options tree */ _templateOptions: function(options) { // link this var self = this; - // attach show/hide event function attachEvents($button, $subgroup) { function setVisibility (visible) { @@ -45,52 +36,58 @@ setVisibility(!$button.is_expanded); }); } - + // recursive function which iterates through options function iterate ($tmpl, options) { for (i in options) { // current option level in hierarchy var level = options[i]; - + // check for options var has_options = level.options.length > 0; - + // build template var $group = $('<div/>'); if (has_options) { // create button and add flag - var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>'); - + var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'); + // add expand group var $buttongroup = $('<div/>'); $buttongroup.append($button); - $buttongroup.append(self._templateOption(level.name, level.value)); + $buttongroup.append(self._templateOption({ + label: level.name, + value: level.value + })); $group.append($buttongroup); - + // add sub group var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); iterate($subgroup, level.options); $group.append($subgroup); - + // attach click event to collapse/expand hierarchy attachEvents($button, $subgroup); } else { - $group.append(self._templateOption(level.name, level.value)); + $group.append(self._templateOption({ + label: level.name, + value: level.value + })); } $tmpl.append($group); } } - + // iterate through options and create dom var $tmpl = $('<div/>'); iterate($tmpl, options); return $tmpl; }, - + /** Template for drill down view */ _template: function(options) { - return '<div class="ui-options-input drilldown-container" id="' + options.id + '"/>'; + return '<div class="ui-options-list drilldown-container" id="' + options.id + '"/>'; } }); diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b client/galaxy/scripts/mvc/ui/ui-misc.js --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,13 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) { +define(['utils/utils', + 'mvc/ui/ui-select-default', + 'mvc/ui/ui-slider', + 'mvc/ui/ui-options', + 'mvc/ui/ui-drilldown', + 'mvc/ui/ui-button-menu', + 'mvc/ui/ui-button-check', + 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, ButtonCheck, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -448,59 +455,12 @@ } }); -// plugin -var CheckButton = Backbone.View.extend({ - - // default options - optionsDefault: { - class_add : 'fa fa-square-o', - class_remove : 'fa fa-check-square-o', - class_partial : 'fa fa-minus-square-o', - value : false - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement($('<div/>')); - - // set initial value - this.value(Boolean(this.options.value)); - - // add event handler - var self = this; - this.$el.on('click', function() { - self.value(!self.current); - }); - }, - - // value - value : function (new_val) { - if (new_val !== undefined) { - this.current = new_val; - if (new_val) { - this.$el.removeClass() - .addClass('ui-checkbutton') - .addClass(this.options.class_remove); - } else { - this.$el.removeClass() - .addClass('ui-checkbutton') - .addClass(this.options.class_add); - } - this.options.onchange && this.options.onchange(new_val); - } - return this.current; - } -}); - // return return { Anchor : Anchor, Button : Button, ButtonIcon : ButtonIcon, + ButtonCheck : ButtonCheck, ButtonMenu : ButtonMenu, Icon : Icon, Image : Image, @@ -511,7 +471,6 @@ RadioButton : Options.RadioButton, Checkbox : Options.Checkbox, Radio : Options.Radio, - CheckButton : CheckButton, Searchbox : Searchbox, Select : Select, Hidden : Hidden, diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -1,5 +1,5 @@ // dependencies -define(['utils/utils'], function(Utils) { +define(['utils/utils', 'mvc/ui/ui-button-check'], function(Utils, ButtonCheck) { /** Base class for options based ui elements **/ var Base = Backbone.View.extend({ @@ -11,7 +11,8 @@ data : [], id : Utils.uuid(), error_text : 'No data available.', - wait_text : 'Please wait...' + wait_text : 'Please wait...', + multiple : false }; // configure options @@ -21,13 +22,28 @@ this.setElement('<div class="ui-options"/>'); // create elements - this.$message = $('<div/>'); - this.$options = $(this._template(options)); + this.$message = $('<div/>'); + this.$options = $(this._template(options)); + this.$menu = $('<div class="ui-options-menu"/>'); // append this.$el.append(this.$message); + this.$el.append(this.$menu); this.$el.append(this.$options); + // add select/unselect all button + if (this.options.multiple) { + this.select_button = new ButtonCheck({ + onclick: function() { + self.$('input').prop('checked', self.select_button.value() !== 0); + self._change(); + } + }); + this.$menu.addClass('ui-margin-bottom'); + this.$menu.append(this.select_button.$el); + this.$menu.append('Select/Unselect all'); + } + // hide input field if (!this.options.visible) { this.$el.hide(); @@ -73,7 +89,7 @@ // add change events var self = this; - this.$el.find('input').on('change', function() { + this.$('input').on('change', function() { self.value(self._getValue()); self._change(); }); @@ -96,11 +112,11 @@ } // reset selection - this.$el.find('input').prop('checked', false); + this.$('input').prop('checked', false); // update to new selection for (var i in new_value) { - this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true); + this.$('input[value="' + new_value[i] + '"]').first().prop('checked', true); }; } @@ -116,7 +132,7 @@ value = [value]; } for (var i in value) { - if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + if (this.$('input[value="' + value[i] + '"]').length > 0) { return true; } } @@ -127,7 +143,7 @@ /** Return first available option */ first: function() { - var options = this.$el.find('input'); + var options = this.$('input'); if (options.length > 0) { return options.val(); } else { @@ -160,8 +176,22 @@ /** Trigger custom onchange callback function */ _change: function() { + var current = this._getValue(); if (this.options.onchange) { - this.options.onchange(this._getValue()); + this.options.onchange(current); + } + if (this.select_button) { + var total = this._size(); + var value = this._getValue(); + if (!(value instanceof Array)) { + this.select_button.value(0); + } else { + if (value.length !== total) { + this.select_button.value(1); + } else { + this.select_button.value(2); + } + } } }, @@ -171,9 +201,11 @@ if (this._size() == 0) { this._messageShow(this.options.error_text, 'danger'); this.$options.hide(); + this.$menu.hide(); } else { this._messageHide(); this.$options.css('display', 'inline-block'); + this.$menu.show(); } }, @@ -181,7 +213,7 @@ */ _getValue: function() { // get selected values - var selected = this.$el.find(':checked'); + var selected = this.$(':checked'); if (selected.length == 0) { return '__null__'; } @@ -201,7 +233,7 @@ /** Returns the number of options */ _size: function() { - return this.$el.find('.ui-option').length; + return this.$('.ui-option').length; }, /** Show message instead if options @@ -222,42 +254,37 @@ /** Main template function */ _template: function() { - return '<div class="ui-options-input"/>'; + return '<div class="ui-options-list"/>'; + } +}); + +/** Iconized **/ +var BaseIcons = Base.extend({ + _templateOption: function(pair) { + var id = Utils.uuid(); + return '<div class="ui-option">' + + '<input id="' + id + '" type="' + this.options.type + '" name="' + this.options.id + '" value="' + pair.value + '"/>' + + '<label class="ui-options-label" for="' + id + '">' + pair.label + '</label>' + + '</div>'; } }); /** Radio button field **/ var Radio = {}; -Radio.View = Base.extend({ - // initialize +Radio.View = BaseIcons.extend({ initialize: function(options) { - Base.prototype.initialize.call(this, options); - }, - - /** Template for a single option - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; + options.type = 'radio'; + BaseIcons.prototype.initialize.call(this, options); } }); /** Checkbox options field **/ var Checkbox = {}; -Checkbox.View = Base.extend({ - // initialize +Checkbox.View = BaseIcons.extend({ initialize: function(options) { options.multiple = true; - Base.prototype.initialize.call(this, options); - }, - - /** Template for a single option - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; + options.type = 'checkbox'; + BaseIcons.prototype.initialize.call(this, options); } }); @@ -274,9 +301,9 @@ value: function (new_value) { // set new value if (new_value !== undefined) { - this.$el.find('input').prop('checked', false); - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); + this.$('input').prop('checked', false); + this.$('label').removeClass('active'); + this.$('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); } // get and return value @@ -294,7 +321,7 @@ if (pair.icon) { tmpl += '<i class="' + cls + '"/>'; } - tmpl += '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">'; + tmpl += '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>'; if (pair.label) { tmpl += pair.label; } @@ -311,6 +338,7 @@ return { Base : Base, + BaseIcons : BaseIcons, Radio : Radio, RadioButton : RadioButton, Checkbox : Checkbox diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/mvc/ui/ui-button-check.js --- /dev/null +++ b/static/scripts/mvc/ui/ui-button-check.js @@ -0,0 +1,45 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +// plugin +return Backbone.View.extend({ + + // default options + optionsDefault: { + icons : ['fa fa-square-o', 'fa fa-minus-square-o', 'fa fa-check-square-o'], + value : 0 + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement($('<div/>')); + + // set initial value + this.value(this.options.value); + + // add event handler + var self = this; + this.$el.on('click', function() { + self.current = (!self.current && 2) || 0; + self.value(self.current); + self.options.onclick && self.options.onclick(); + }); + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.current = new_val; + this.$el.removeClass() + .addClass('ui-checkbutton') + .addClass(this.options.icons[new_val]); + this.options.onchange && this.options.onchange(new_val); + } + return this.current; + } +}); +}); \ No newline at end of file diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/mvc/ui/ui-drilldown.js --- a/static/scripts/mvc/ui/ui-drilldown.js +++ b/static/scripts/mvc/ui/ui-drilldown.js @@ -4,28 +4,19 @@ /** * This class creates/wraps a drill down element. */ -var View = Options.Base.extend({ +var View = Options.BaseIcons.extend({ // initialize initialize: function(options) { - this.display = options.display || 'checkbox'; - options.multiple = (this.display == 'checkbox'); - Options.Base.prototype.initialize.call(this, options); + options.type = options.display || 'checkbox'; + options.multiple = (options.display == 'checkbox'); + Options.BaseIcons.prototype.initialize.call(this, options); }, - - /** Template for input field - */ - _templateOption: function(name, value, selected) { - return '<div>' + - '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name + - '<div/>'; - }, - + /** Template to create options tree */ _templateOptions: function(options) { // link this var self = this; - // attach show/hide event function attachEvents($button, $subgroup) { function setVisibility (visible) { @@ -45,52 +36,58 @@ setVisibility(!$button.is_expanded); }); } - + // recursive function which iterates through options function iterate ($tmpl, options) { for (i in options) { // current option level in hierarchy var level = options[i]; - + // check for options var has_options = level.options.length > 0; - + // build template var $group = $('<div/>'); if (has_options) { // create button and add flag - var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>'); - + var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand"/>'); + // add expand group var $buttongroup = $('<div/>'); $buttongroup.append($button); - $buttongroup.append(self._templateOption(level.name, level.value)); + $buttongroup.append(self._templateOption({ + label: level.name, + value: level.value + })); $group.append($buttongroup); - + // add sub group var $subgroup = $('<div style="display: none; margin-left: 25px;"/>'); iterate($subgroup, level.options); $group.append($subgroup); - + // attach click event to collapse/expand hierarchy attachEvents($button, $subgroup); } else { - $group.append(self._templateOption(level.name, level.value)); + $group.append(self._templateOption({ + label: level.name, + value: level.value + })); } $tmpl.append($group); } } - + // iterate through options and create dom var $tmpl = $('<div/>'); iterate($tmpl, options); return $tmpl; }, - + /** Template for drill down view */ _template: function(options) { - return '<div class="ui-options-input drilldown-container" id="' + options.id + '"/>'; + return '<div class="ui-options-list drilldown-container" id="' + options.id + '"/>'; } }); diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/mvc/ui/ui-misc.js --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,13 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) { +define(['utils/utils', + 'mvc/ui/ui-select-default', + 'mvc/ui/ui-slider', + 'mvc/ui/ui-options', + 'mvc/ui/ui-drilldown', + 'mvc/ui/ui-button-menu', + 'mvc/ui/ui-button-check', + 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, ButtonCheck, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -448,59 +455,12 @@ } }); -// plugin -var CheckButton = Backbone.View.extend({ - - // default options - optionsDefault: { - class_add : 'fa fa-square-o', - class_remove : 'fa fa-check-square-o', - class_partial : 'fa fa-minus-square-o', - value : false - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement($('<div/>')); - - // set initial value - this.value(Boolean(this.options.value)); - - // add event handler - var self = this; - this.$el.on('click', function() { - self.value(!self.current); - }); - }, - - // value - value : function (new_val) { - if (new_val !== undefined) { - this.current = new_val; - if (new_val) { - this.$el.removeClass() - .addClass('ui-checkbutton') - .addClass(this.options.class_remove); - } else { - this.$el.removeClass() - .addClass('ui-checkbutton') - .addClass(this.options.class_add); - } - this.options.onchange && this.options.onchange(new_val); - } - return this.current; - } -}); - // return return { Anchor : Anchor, Button : Button, ButtonIcon : ButtonIcon, + ButtonCheck : ButtonCheck, ButtonMenu : ButtonMenu, Icon : Icon, Image : Image, @@ -511,7 +471,6 @@ RadioButton : Options.RadioButton, Checkbox : Options.Checkbox, Radio : Options.Radio, - CheckButton : CheckButton, Searchbox : Searchbox, Select : Select, Hidden : Hidden, diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -1,5 +1,5 @@ // dependencies -define(['utils/utils'], function(Utils) { +define(['utils/utils', 'mvc/ui/ui-button-check'], function(Utils, ButtonCheck) { /** Base class for options based ui elements **/ var Base = Backbone.View.extend({ @@ -11,7 +11,8 @@ data : [], id : Utils.uuid(), error_text : 'No data available.', - wait_text : 'Please wait...' + wait_text : 'Please wait...', + multiple : false }; // configure options @@ -21,13 +22,28 @@ this.setElement('<div class="ui-options"/>'); // create elements - this.$message = $('<div/>'); - this.$options = $(this._template(options)); + this.$message = $('<div/>'); + this.$options = $(this._template(options)); + this.$menu = $('<div class="ui-options-menu"/>'); // append this.$el.append(this.$message); + this.$el.append(this.$menu); this.$el.append(this.$options); + // add select/unselect all button + if (this.options.multiple) { + this.select_button = new ButtonCheck({ + onclick: function() { + self.$('input').prop('checked', self.select_button.value() !== 0); + self._change(); + } + }); + this.$menu.addClass('ui-margin-bottom'); + this.$menu.append(this.select_button.$el); + this.$menu.append('Select/Unselect all'); + } + // hide input field if (!this.options.visible) { this.$el.hide(); @@ -73,7 +89,7 @@ // add change events var self = this; - this.$el.find('input').on('change', function() { + this.$('input').on('change', function() { self.value(self._getValue()); self._change(); }); @@ -96,11 +112,11 @@ } // reset selection - this.$el.find('input').prop('checked', false); + this.$('input').prop('checked', false); // update to new selection for (var i in new_value) { - this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true); + this.$('input[value="' + new_value[i] + '"]').first().prop('checked', true); }; } @@ -116,7 +132,7 @@ value = [value]; } for (var i in value) { - if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + if (this.$('input[value="' + value[i] + '"]').length > 0) { return true; } } @@ -127,7 +143,7 @@ /** Return first available option */ first: function() { - var options = this.$el.find('input'); + var options = this.$('input'); if (options.length > 0) { return options.val(); } else { @@ -160,8 +176,22 @@ /** Trigger custom onchange callback function */ _change: function() { + var current = this._getValue(); if (this.options.onchange) { - this.options.onchange(this._getValue()); + this.options.onchange(current); + } + if (this.select_button) { + var total = this._size(); + var value = this._getValue(); + if (!(value instanceof Array)) { + this.select_button.value(0); + } else { + if (value.length !== total) { + this.select_button.value(1); + } else { + this.select_button.value(2); + } + } } }, @@ -171,9 +201,11 @@ if (this._size() == 0) { this._messageShow(this.options.error_text, 'danger'); this.$options.hide(); + this.$menu.hide(); } else { this._messageHide(); this.$options.css('display', 'inline-block'); + this.$menu.show(); } }, @@ -181,7 +213,7 @@ */ _getValue: function() { // get selected values - var selected = this.$el.find(':checked'); + var selected = this.$(':checked'); if (selected.length == 0) { return '__null__'; } @@ -201,7 +233,7 @@ /** Returns the number of options */ _size: function() { - return this.$el.find('.ui-option').length; + return this.$('.ui-option').length; }, /** Show message instead if options @@ -222,42 +254,37 @@ /** Main template function */ _template: function() { - return '<div class="ui-options-input"/>'; + return '<div class="ui-options-list"/>'; + } +}); + +/** Iconized **/ +var BaseIcons = Base.extend({ + _templateOption: function(pair) { + var id = Utils.uuid(); + return '<div class="ui-option">' + + '<input id="' + id + '" type="' + this.options.type + '" name="' + this.options.id + '" value="' + pair.value + '"/>' + + '<label class="ui-options-label" for="' + id + '">' + pair.label + '</label>' + + '</div>'; } }); /** Radio button field **/ var Radio = {}; -Radio.View = Base.extend({ - // initialize +Radio.View = BaseIcons.extend({ initialize: function(options) { - Base.prototype.initialize.call(this, options); - }, - - /** Template for a single option - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; + options.type = 'radio'; + BaseIcons.prototype.initialize.call(this, options); } }); /** Checkbox options field **/ var Checkbox = {}; -Checkbox.View = Base.extend({ - // initialize +Checkbox.View = BaseIcons.extend({ initialize: function(options) { options.multiple = true; - Base.prototype.initialize.call(this, options); - }, - - /** Template for a single option - */ - _templateOption: function(pair) { - return '<div>' + - '<input type="checkbox" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' + - '</div>'; + options.type = 'checkbox'; + BaseIcons.prototype.initialize.call(this, options); } }); @@ -274,9 +301,9 @@ value: function (new_value) { // set new value if (new_value !== undefined) { - this.$el.find('input').prop('checked', false); - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); + this.$('input').prop('checked', false); + this.$('label').removeClass('active'); + this.$('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active'); } // get and return value @@ -294,7 +321,7 @@ if (pair.icon) { tmpl += '<i class="' + cls + '"/>'; } - tmpl += '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '">'; + tmpl += '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>'; if (pair.label) { tmpl += pair.label; } @@ -311,6 +338,7 @@ return { Base : Base, + BaseIcons : BaseIcons, Radio : Radio, RadioButton : RadioButton, Checkbox : Checkbox diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/packed/mvc/ui/ui-button-check.js --- /dev/null +++ b/static/scripts/packed/mvc/ui/ui-button-check.js @@ -0,0 +1,1 @@ +define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0},initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement($("<div/>"));this.value(this.options.value);var b=this;this.$el.on("click",function(){b.current=(!b.current&&2)||0;b.value(b.current);b.options.onclick&&b.options.onclick()})},value:function(b){if(b!==undefined){this.current=b;this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.icons[b]);this.options.onchange&&this.options.onchange(b)}return this.current}})}); \ No newline at end of file diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/packed/mvc/ui/ui-drilldown.js --- a/static/scripts/packed/mvc/ui/ui-drilldown.js +++ b/static/scripts/packed/mvc/ui/ui-drilldown.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+d+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options-input drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.BaseIcons.extend({initialize:function(d){d.type=d.display||"checkbox";d.multiple=(d.display=="checkbox");a.BaseIcons.prototype.initialize.call(this,d)},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption({label:q.name,value:q.value}));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption({label:q.name,value:q.value}))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options-list drilldown-container" id="'+d.id+'"/>'}});return{View:c}}); \ No newline at end of file diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/packed/mvc/ui/ui-misc.js --- a/static/scripts/packed/mvc/ui/ui-misc.js +++ b/static/scripts/packed/mvc/ui/ui-misc.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(d,g,h,l,k,r,b){var p=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(s){return'<img class="ui-image '+s.cls+'" src="'+s.url+'"/>'}});var i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},title:function(s){this.$el.html(s)},_template:function(s){return'<label class="ui-label '+s.cls+'">'+s.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){return'<div><span class="fa '+s.icon+'" class="ui-icon"/> '+s.title+"</div>"}});var f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick){s.onclick()}});$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t='<button id="'+s.id+'" type="submit" style="float: '+s.floating+';" type="button" class="'+s.cls+'">';if(s.icon){t+='<i class="icon fa '+s.icon+'"></i> '}t+=s.title+"</button>";return t}});var n=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var s=this;$(this.el).on("click",function(){$(".tooltip").hide();if(t.onclick&&!s.disabled){t.onclick()}});$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},setIcon:function(s){this.$("i").removeClass(this.options.icon).addClass(s);this.options.icon=s},_template:function(s){var t="";if(s.title){t="width: auto;"}var u='<div id="'+s.id+'" style="float: '+s.floating+"; "+t+'" class="'+s.cls+'">';if(s.title){u+='<div class="button"><i class="icon fa '+s.icon+'"/> <span class="title">'+s.title+"</span></div>"}else{u+='<i class="icon fa '+s.icon+'"/>'}u+="</div>";return u}});var o=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick)},_template:function(s){return'<div><a href="javascript:void(0)" class="ui-anchor '+s.cls+'">'+s.title+"</a></div>"}});var a=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:false},initialize:function(s){this.options=d.merge(s,this.optionsDefault);this.setElement("<div></div>");if(this.options.message){this.update(this.options)}},update:function(t){this.options=d.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(t.message);this.$el.fadeIn();if(this.timeout){window.clearTimeout(this.timeout)}if(!t.persistent){var s=this;this.timeout=window.setTimeout(function(){if(s.$el.is(":visible")){s.$el.fadeOut()}else{s.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(s){return'<div class="ui-message alert alert-'+s.status+'"/>'}});var e=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement(this._template(this.options));var s=this;if(this.options.onclick){this.$el.on("submit",function(v){var u=s.$el.find("#search");s.options.onclick(u.val())})}},_template:function(s){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+s.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var m=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var s=this;this.$el.on("input",function(){if(s.options.onchange){s.options.onchange(s.$el.val())}})},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){if(s.area){return'<textarea id="'+s.id+'" class="ui-textarea '+s.cls+'"></textarea>'}else{return'<input id="'+s.id+'" type="'+s.type+'" value="'+s.value+'" placeholder="'+s.placeholder+'" class="ui-input '+s.cls+'">'}}});var j=Backbone.View.extend({initialize:function(s){this.options=s;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(s){if(s!==undefined){this.$("hidden").val(s)}return this.$("hidden").val()},_template:function(t){var s='<div id="'+t.id+'" >';if(t.info){s+="<label>"+t.info+"</label>"}s+='<hidden value="'+t.value+'"/></div>';return s}});var q=Backbone.View.extend({optionsDefault:{class_add:"fa fa-square-o",class_remove:"fa fa-check-square-o",class_partial:"fa fa-minus-square-o",value:false},initialize:function(t){this.options=d.merge(t,this.optionsDefault);this.setElement($("<div/>"));this.value(Boolean(this.options.value));var s=this;this.$el.on("click",function(){s.value(!s.current)})},value:function(s){if(s!==undefined){this.current=s;if(s){this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.class_remove)}else{this.$el.removeClass().addClass("ui-checkbutton").addClass(this.options.class_add)}this.options.onchange&&this.options.onchange(s)}return this.current}});return{Anchor:o,Button:f,ButtonIcon:n,ButtonMenu:r,Icon:c,Image:p,Input:m,Label:i,Message:a,Modal:b,RadioButton:l.RadioButton,Checkbox:l.Checkbox,Radio:l.Radio,CheckButton:q,Searchbox:e,Select:g,Hidden:j,Slider:h,Drilldown:k}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-button-check","mvc/ui/ui-modal"],function(e,h,i,m,l,r,d,b){var q=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(s){return'<img class="ui-image '+s.cls+'" src="'+s.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options))},title:function(s){this.$el.html(s)},_template:function(s){return'<label class="ui-label '+s.cls+'">'+s.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){return'<div><span class="fa '+s.icon+'" class="ui-icon"/> '+s.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick){s.onclick()}});$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},_template:function(s){var t='<button id="'+s.id+'" type="submit" style="float: '+s.floating+';" type="button" class="'+s.cls+'">';if(s.icon){t+='<i class="icon fa '+s.icon+'"></i> '}t+=s.title+"</button>";return t}});var o=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var s=this;$(this.el).on("click",function(){$(".tooltip").hide();if(t.onclick&&!s.disabled){t.onclick()}});$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},setIcon:function(s){this.$("i").removeClass(this.options.icon).addClass(s);this.options.icon=s},_template:function(s){var t="";if(s.title){t="width: auto;"}var u='<div id="'+s.id+'" style="float: '+s.floating+"; "+t+'" class="'+s.cls+'">';if(s.title){u+='<div class="button"><i class="icon fa '+s.icon+'"/> <span class="title">'+s.title+"</span></div>"}else{u+='<i class="icon fa '+s.icon+'"/>'}u+="</div>";return u}});var p=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",s.onclick)},_template:function(s){return'<div><a href="javascript:void(0)" class="ui-anchor '+s.cls+'">'+s.title+"</a></div>"}});var a=Backbone.View.extend({optionsDefault:{message:null,status:"info",persistent:false},initialize:function(s){this.options=e.merge(s,this.optionsDefault);this.setElement("<div></div>");if(this.options.message){this.update(this.options)}},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(t.message);this.$el.fadeIn();if(this.timeout){window.clearTimeout(this.timeout)}if(!t.persistent){var s=this;this.timeout=window.setTimeout(function(){if(s.$el.is(":visible")){s.$el.fadeOut()}else{s.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(s){return'<div class="ui-message alert alert-'+s.status+'"/>'}});var f=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));var s=this;if(this.options.onclick){this.$el.on("submit",function(v){var u=s.$el.find("#search");s.options.onclick(u.val())})}},_template:function(s){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+s.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var n=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(t){this.options=e.merge(t,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var s=this;this.$el.on("input",function(){if(s.options.onchange){s.options.onchange(s.$el.val())}})},value:function(s){if(s!==undefined){this.$el.val(s)}return this.$el.val()},_template:function(s){if(s.area){return'<textarea id="'+s.id+'" class="ui-textarea '+s.cls+'"></textarea>'}else{return'<input id="'+s.id+'" type="'+s.type+'" value="'+s.value+'" placeholder="'+s.placeholder+'" class="ui-input '+s.cls+'">'}}});var k=Backbone.View.extend({initialize:function(s){this.options=s;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(s){if(s!==undefined){this.$("hidden").val(s)}return this.$("hidden").val()},_template:function(t){var s='<div id="'+t.id+'" >';if(t.info){s+="<label>"+t.info+"</label>"}s+='<hidden value="'+t.value+'"/></div>';return s}});return{Anchor:p,Button:g,ButtonIcon:o,ButtonCheck:d,ButtonMenu:r,Icon:c,Image:q,Input:n,Label:j,Message:a,Modal:b,RadioButton:m.RadioButton,Checkbox:m.Checkbox,Radio:m.Radio,Searchbox:f,Select:h,Hidden:k,Slider:i,Drilldown:l}}); \ No newline at end of file diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={visible:true,data:[],id:b.uuid(),error_text:"No data available.",wait_text:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");i.tooltip({title:g[h].tooltip,placement:"bottom"});this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){return b.validate(this.value())},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"__null__"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-input"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(h){var f="fa "+h.icon;if(!h.label){f+=" no-padding"}var g='<label class="btn btn-default">';if(h.icon){g+='<i class="'+f+'"/>'}g+='<input type="radio" name="'+this.options.id+'" value="'+h.value+'">';if(h.label){g+=h.label}g+="</label>";return g},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){this.optionsDefault={visible:true,data:[],id:c.uuid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.select_button=new e({onclick:function(){h.$("input").prop("checked",h.select_button.value()!==0);h._change()}});this.$menu.addClass("ui-margin-bottom");this.$menu.append(this.select_button.$el);this.$menu.append("Select/Unselect all")}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var h=this;this.on("change",function(){h._change()})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h._change()});this._refresh();this.value(l)},value:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}this.$("input").prop("checked",false);for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input");if(h.length>0){return h.val()}else{return undefined}},validate:function(){return c.validate(this.value())},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){var j=this._getValue();if(this.options.onchange){this.options.onchange(j)}if(this.select_button){var h=this._size();var i=this._getValue();if(!(i instanceof Array)){this.select_button.value(0)}else{if(i.length!==h){this.select_button.value(1)}else{this.select_button.value(2)}}}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}},_getValue:function(){var i=this.$(":checked");if(i.length==0){return"__null__"}if(this.options.multiple){var h=[];i.each(function(){h.push($(this).val())});return h}else{return i.val()}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uuid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}}); \ No newline at end of file diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -148,7 +148,7 @@ .form-control::-moz-placeholder{color:#999} .form-control:-ms-input-placeholder{color:#999} .form-control::-webkit-input-placeholder{color:#999} -.form-control,.ui-input,.ui-textarea,.ui-options .ui-options-input,.ui-form-slider .ui-form-slider-text,.ui-select-multiple{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} +.form-control,.ui-input,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select-multiple{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee} textarea.form-control{height:auto} .form-group{margin-bottom:15px} @@ -1435,9 +1435,15 @@ .ui-portlet-limited,.ui-portlet-narrow,.ui-portlet-narrow{max-width:900px} .ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} .ui-popover .popover-title{padding:4px 10px} -.ui-input,.ui-textarea,.ui-options .ui-options-input,.ui-form-slider .ui-form-slider-text,.ui-select-multiple,.ui-textarea,.ui-options .ui-options-input,.ui-form-slider .ui-form-slider-text,.ui-select-multiple{background:transparent} +.ui-input,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select-multiple,.ui-textarea,.ui-options .ui-options-list,.ui-form-slider .ui-form-slider-text,.ui-select-multiple{background:transparent} .ui-textarea{height:100px !important} -.ui-options .ui-options-input{height:100% !important} +.ui-options .ui-options-list{height:100% !important}.ui-options .ui-options-list input[type=checkbox],.ui-options .ui-options-list input[type=radio]{display:none} +.ui-options .ui-options-list label{margin:0px;cursor:pointer} +.ui-options .ui-options-list .ui-drilldown-button{position:relative;top:2px;left:-3px;margin-right:3px;cursor:pointer} +.ui-options .ui-options-list input[type=checkbox]+label:before{font-family:FontAwesome;display:inline-block;font-style:normal;font-size:1.2em;margin-right:5px;position:relative;top:1px;width:10px;content:"\f096"} +.ui-options .ui-options-list input[type=checkbox]:checked+label:before{content:"\f046"} +.ui-options .ui-options-list input[type=radio]+label:before{font-family:FontAwesome;display:inline-block;font-style:normal;font-size:1.2em;margin-right:5px;position:relative;top:1px;width:10px;content:"\f1db"} +.ui-options .ui-options-list input[type=radio]:checked+label:before{content:"\f192"} .ui-form-slider{display:inline-block;width:100%}.ui-form-slider .ui-form-slider-text{width:100px;float:left} .ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px} .ui-radiobutton{width:100%}.ui-radiobutton label{height:23px;line-height:1em} diff -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 -r 16593d9d24fe952789835895c532ad246df4346b static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -321,9 +321,51 @@ } .ui-options { - .ui-options-input { + .ui-options-list { &:extend(.ui-input); height: 100% !important; + input[type=checkbox], input[type=radio] { + display: none; + } + label { + margin: 0px; + cursor: pointer; + } + .ui-drilldown-button { + position: relative; + top: 2px; + left: -3px; + margin-right: 3px; + cursor: pointer; + } + input[type=checkbox] + label:before { + font-family: FontAwesome; + display: inline-block; + font-style: normal; + font-size: 1.2em; + margin-right: 5px; + position: relative; + top: 1px; + width: 10px; + content: "\f096"; + } + input[type=checkbox]:checked + label:before { + content: "\f046"; + } + input[type=radio] + label:before { + font-family: FontAwesome; + display: inline-block; + font-style: normal; + font-size: 1.2em; + margin-right: 5px; + position: relative; + top: 1px; + width: 10px; + content: "\f1db"; + } + input[type=radio]:checked + label:before { + content: "\f192"; + } } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix to 109da69: remove debugging from index.mako
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ba09a5bbe9d/ Changeset: 7ba09a5bbe9d User: carlfeberhard Date: 2015-02-10 20:12:46+00:00 Summary: Fix to 109da69: remove debugging from index.mako Affected #: 1 file diff -r 374318d710755d92b8cea81f34c226ecd60741a5 -r 7ba09a5bbe9d88ca035b44f2178d7d32442cf2e1 templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -152,12 +152,6 @@ currPanel.connectToQuotaMeter( Galaxy.quotaMeter ); currPanel.loadCurrentHistory(); Galaxy.currHistoryPanel = currPanel; - -currPanel.once( 'rendered', function(){ - currPanel.showSelectors(); - currPanel.selectAll(); - _.last( currPanel.actionsPopup.options ).func(); -}); }); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Add reminder for why imports are done this way in s3objectstore for the next time I forget.
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/374318d71075/ Changeset: 374318d71075 User: dannon Date: 2015-02-10 20:06:12+00:00 Summary: Add reminder for why imports are done this way in s3objectstore for the next time I forget. Affected #: 1 file diff -r 2f67cc2049113ace6bccb701c545fd1ec35fb013 -r 374318d710755d92b8cea81f34c226ecd60741a5 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -20,6 +20,7 @@ from ..objectstore import ObjectStore, convert_bytes try: + # Imports are done this way to allow objectstore code to be used outside of Galaxy. import boto from boto.s3.key import Key from boto.s3.connection import S3Connection Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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