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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.

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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 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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 _.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 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 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 .dataset.selected");this.$dragging=l},_pairDragend:function(l,m){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(m){var l=this;l.removeExtensions=(m!==undefined)?(m):(!l.removeExtensions);_.each(l.paired,function(n){if(n.customizedName){return}n.name=l._guessNameForPair(n.forward,n.reverse)});l._renderPaired();l._renderFooter()},_changeName:function(l){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(l){if(l.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(m){var l=this._getName();if(!l){this._validationWarning("name")}else{this.createList()}},_printList:function(m){var l=this;_.each(m,function(n){if(m===l.paired){l._printPair(n)}else{}})},_printPair:function(l){this.debug(l.forward.name,l.reverse.name,": ->",l.name)},toString:function(){return"PairedCollectionCreator"}});k.templates=k.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)">',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 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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). 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','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 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: 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.

1 0

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.

1 0

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. 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