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commit/galaxy-central: guerler: ToolForm: Show/hide single dataset selection field
by commits-noreply＠bitbucket.org 12 Nov '14

12 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7450b2567fb/ Changeset: d7450b2567fb User: guerler Date: 2014-11-12 08:13:37+00:00 Summary: ToolForm: Show/hide single dataset selection field Affected #: 3 files diff -r 4231a77fe8946110b2c56efd436000b864b06a84 -r d7450b2567fb56f93ccc0191a7059ebb46b23cc5 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -14,15 +14,62 @@ // add element this.setElement('<div/>'); - // current selection - this.current = 'single'; + // list of select fields + this.list = {}; + + // radio button options + var radio_buttons = []; + + // set initial state + if (!options.multiple) { + this.current = 'single'; + } else { + this.current = 'multiple'; + } + + // add single dataset selector + if (!options.multiple) { + radio_buttons.push({icon: 'fa-file-o', label : 'Single dataset', value : 'single'}); + this.select_single = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + this.list['single'] = { + field: this.select_single, + type : 'hda' + }; + } + + // add multiple dataset selector + radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); + this.select_multiple = new Ui.Select.View({ + multiple : true, + onchange : function() { + self.trigger('change'); + } + }); + this.list['multiple'] = { + field: this.select_multiple, + type : 'hda' + }; + + // add collection selector + radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); + this.select_collection = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + this.list['collection'] = { + field: this.select_collection, + type : 'hdca' + }; // create button this.button_type = new Ui.RadioButton.View({ value : this.current, - data : [ { icon: 'fa-file-o', label : 'Single dataset', value : 'single' }, - { icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }, - { icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }], + data : radio_buttons, onchange: function(value) { self.current = value; self.refresh(); @@ -30,44 +77,6 @@ } }); - // single dataset select field - this.select_single = new Ui.Select.View({ - onchange : function() { - self.trigger('change'); - } - }); - - // multiple datasets select field - this.select_multiple = new Ui.Select.View({ - multiple : true, - onchange : function() { - self.trigger('change'); - } - }); - - // collection select field - this.select_collection = new Ui.Select.View({ - onchange : function() { - self.trigger('change'); - } - }); - - // list of all select fields - this.list = { - 'single' : { - field: this.select_single, - type : 'hda' - }, - 'multiple' : { - field: this.select_multiple, - type : 'hda' - }, - 'collection' : { - field: this.select_collection, - type : 'hdca' - } - }; - // add batch mode information this.$batch = $(ToolTemplate.batchMode()); @@ -129,7 +138,7 @@ } // update selection fields - this.select_single.update(dataset_options); + this.select_single && this.select_single.update(dataset_options); this.select_multiple.update(dataset_options); this.select_collection.update(collection_options); @@ -153,7 +162,7 @@ this.current = 'collection'; this.select_collection.value(list[0]); } else { - if (list.length > 1) { + if (list.length > 1 || this.options.multiple) { this.current = 'multiple'; this.select_multiple.value(list); } else { diff -r 4231a77fe8946110b2c56efd436000b864b06a84 -r d7450b2567fb56f93ccc0191a7059ebb46b23cc5 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -14,15 +14,62 @@ // add element this.setElement('<div/>'); - // current selection - this.current = 'single'; + // list of select fields + this.list = {}; + + // radio button options + var radio_buttons = []; + + // set initial state + if (!options.multiple) { + this.current = 'single'; + } else { + this.current = 'multiple'; + } + + // add single dataset selector + if (!options.multiple) { + radio_buttons.push({icon: 'fa-file-o', label : 'Single dataset', value : 'single'}); + this.select_single = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + this.list['single'] = { + field: this.select_single, + type : 'hda' + }; + } + + // add multiple dataset selector + radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); + this.select_multiple = new Ui.Select.View({ + multiple : true, + onchange : function() { + self.trigger('change'); + } + }); + this.list['multiple'] = { + field: this.select_multiple, + type : 'hda' + }; + + // add collection selector + radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); + this.select_collection = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + this.list['collection'] = { + field: this.select_collection, + type : 'hdca' + }; // create button this.button_type = new Ui.RadioButton.View({ value : this.current, - data : [ { icon: 'fa-file-o', label : 'Single dataset', value : 'single' }, - { icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }, - { icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }], + data : radio_buttons, onchange: function(value) { self.current = value; self.refresh(); @@ -30,44 +77,6 @@ } }); - // single dataset select field - this.select_single = new Ui.Select.View({ - onchange : function() { - self.trigger('change'); - } - }); - - // multiple datasets select field - this.select_multiple = new Ui.Select.View({ - multiple : true, - onchange : function() { - self.trigger('change'); - } - }); - - // collection select field - this.select_collection = new Ui.Select.View({ - onchange : function() { - self.trigger('change'); - } - }); - - // list of all select fields - this.list = { - 'single' : { - field: this.select_single, - type : 'hda' - }, - 'multiple' : { - field: this.select_multiple, - type : 'hda' - }, - 'collection' : { - field: this.select_collection, - type : 'hdca' - } - }; - // add batch mode information this.$batch = $(ToolTemplate.batchMode()); @@ -129,7 +138,7 @@ } // update selection fields - this.select_single.update(dataset_options); + this.select_single && this.select_single.update(dataset_options); this.select_multiple.update(dataset_options); this.select_collection.update(collection_options); @@ -153,7 +162,7 @@ this.current = 'collection'; this.select_collection.value(list[0]); } else { - if (list.length > 1) { + if (list.length > 1 || this.options.multiple) { this.current = 'multiple'; this.select_multiple.value(list); } else { diff -r 4231a77fe8946110b2c56efd436000b864b06a84 -r d7450b2567fb56f93ccc0191a7059ebb46b23cc5 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(j,g){this.app=j;this.options=g;var f=this;this.setElement("<div/>");this.current="single";this.button_type=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Single dataset",value:"single"},{icon:"fa-files-o",label:"Multiple datasets",value:"multiple"},{icon:"fa-folder-o",label:"List of datasets",value:"collection"}],onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list={single:{field:this.select_single,type:"hda"},multiple:{field:this.select_multiple,type:"hda"},collection:{field:this.select_collection,type:"hdca"}};this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m!==undefined){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m!==undefined){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});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: guerler: ToolForm: Match and sort datasets and collections through API, add single selection as default option
by commits-noreply＠bitbucket.org 12 Nov '14

12 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4231a77fe894/ Changeset: 4231a77fe894 User: guerler Date: 2014-11-12 02:46:38+00:00 Summary: ToolForm: Match and sort datasets and collections through API, add single selection as default option Affected #: 21 files diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 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 @@ -1,96 +1,23 @@ define(['utils/utils'], function(Utils){ return Backbone.Model.extend({ // initialize - initialize: function(options) { - // backup basic url - this.base_url = galaxy_config.root + 'api/histories/' + options.history_id + '/contents'; - - // prepare content obects - this.datatypes = {}; + initialize: function(app) { this.summary = {}; - - // link this - var self = this; - - // request datatypes - Utils.get({ - url : galaxy_config.root + 'api/datatypes/mapping', - cache : true, - success : function(response) { - // backup datatype dictionary - self.datatypes = response; - - // get history summary - Utils.get({ - url : self.base_url + '?deleted=false', - success : function(response) { - // backup summary - self.summary = response; - - // sort by id - self.summary.sort(function(a, b) { - return a.hid > b.hid ? -1 : (a.hid < b.hid ? 1 : 0); - }); - - // log - console.debug('tools-content::initialize() - Completed.'); - - // callback - options.success && options.success(); - }, - error : function(response) { - // log request failure - console.debug('tools-content::initialize() - Ajax request for summary failed.'); - console.debug(response); - } - }); - }, - error : function(response) { - // log request failure - console.debug('tools-content::initialize() - Ajax request for datatypes failed.'); - console.debug(response); - } - }); }, - /** - * Filters contents by data type. + /** Add new content elements */ - filterType: function(options) { - // initialize parameters - options = options || {}; - var result = []; - - // identify content type - var history_content_type = 'dataset'; - if (options.src== 'hdca') { - history_content_type = 'dataset_collection'; + add: function(content_list) { + // add/update content in summary list + for (var i in content_list) { + for (var j in content_list[i]) { + var c = content_list[i][j]; + this.summary[c.id + '_' + c.src] = c; + } } - // search in summary - for (var i in this.summary) { - var content = this.summary[i]; - - // check ok state (TODO: should be implemented in the api) - if (content.history_content_type === 'dataset' && content.state !== 'ok') { - continue; - } - - // match datatypes - var found = false; - for (var i in options.extensions) { - if (this._matchType(options.extensions[i], content.extension)) { - found = true; - break; - } - } - - // final match result - if ((content.history_content_type === history_content_type) && (found || !options.extensions)) { - result.push(content); - } - } - return result; + // log + console.debug('tools-content::initialize() - Completed.'); }, /** Returns matched content from summary. @@ -126,33 +53,6 @@ console.debug(response); } }); - }, - - /** Check if datatypes match - */ - _matchType: function(target, reference) { - // check if target class is available - var target_class = this.datatypes.ext_to_class_name[target]; - if (!target_class) { - console.debug('tools-content::_matchType() - Specific target class unavailable. Accepting all formats.'); - return true; - } - - // check if reference class is available - var reference_class = this.datatypes.ext_to_class_name[reference]; - if (!reference_class) { - console.debug('tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.'); - return true; - } - - // check reference group - var reference_group = this.datatypes.class_to_classes[reference_class]; - if (reference_group[target_class]) { - return true; - } - - // classes do not match - return false; } }); }); \ No newline at end of file diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 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 @@ -21,11 +21,19 @@ var self = this; // link galaxy modal or create one - if (parent.Galaxy && parent.Galaxy.modal) { - this.modal = parent.Galaxy.modal; + var galaxy = parent.Galaxy; + if (galaxy && galaxy.modal) { + this.modal = galaxy.modal; } else { this.modal = new Ui.Modal.View(); } + + // check if the user is an admin + if (galaxy && galaxy.currUser) { + this.is_admin = galaxy.currUser.get('is_admin') + } else { + this.is_admin = false; + } // link options this.options = options; @@ -47,12 +55,10 @@ this.job_handler = new ToolJobs(this); // request history content and build form - this.content = new ToolContent({ - history_id : self.options.history_id, - success : function() { - self._buildForm(self.options); - } - }); + this.content = new ToolContent(this); + + // build this form + this._buildForm(options); }, // message @@ -72,7 +78,7 @@ // this happens i.e. when repeat blocks are added or removed and on initialization rebuild: function() { this.tree.refresh(); - console.debug('tools-form::refresh() - Refreshed form structure.'); + console.debug('tools-form::rebuild() - Rebuilding data structures.'); }, // refreshes input states i.e. for dynamic parameters @@ -142,7 +148,7 @@ var current_state = this.tree.finalize({ data : function(dict) { if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { - return self.content.get({id: dict.values[0].id}).dataset_id; + return self.content.get({id: dict.values[0].id, src: 'hda'}).dataset_id; } return null; } @@ -215,16 +221,22 @@ // get/update field var field = self.field_list[input_id]; - if (field.update && input.type != 'data') { + if (field.update) { var new_options = []; - for (var i in node.options) { - var opt = node.options[i]; - if (opt.length > 2) { - new_options.push({ - 'label': opt[0], - 'value': opt[1] - }); - } + switch (input.type) { + case 'data': + new_options = input.options; + break; + default: + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } } field.update(new_options); console.debug('Updating options for ' + input_id); @@ -292,7 +304,7 @@ }); // add admin operations - if (Galaxy.currUser.get('is_admin')) { + if (this.is_admin) { // create download button menu.addMenu({ icon : 'fa-download', diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -142,8 +142,8 @@ if (batch_n === -1) { batch_n = n; } else { - if (batch_n !== n && n != 1) { - this._foundError(input_id, 'Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -372,6 +372,7 @@ id : 'field-' + input_def.id, extensions : input_def.extensions, multiple : input_def.multiple, + data : input_def.options, onchange : function() { self.app.refresh(); } diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -4,7 +4,8 @@ var View = Backbone.View.extend({ // initialize initialize : function(app, options) { - // configure options + // link app and options + this.app = app; this.options = options; // link this @@ -14,13 +15,14 @@ this.setElement('<div/>'); // current selection - this.current = 'hda'; + this.current = 'single'; // create button - this.button_new = new Ui.RadioButton.View({ + this.button_type = new Ui.RadioButton.View({ value : this.current, - data : [ { icon: 'fa-file-o', label : 'Select datasets', value : 'hda' }, - { icon: 'fa-files-o', label : 'Select a collection', value : 'hdca' }], + data : [ { icon: 'fa-file-o', label : 'Single dataset', value : 'single' }, + { icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }, + { icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }], onchange: function(value) { self.current = value; self.refresh(); @@ -28,68 +30,56 @@ } }); - // - // datasets - // - var datasets = app.content.filterType({ - src : 'hda', - extensions : options.extensions - }); - - // configure options fields - var dataset_options = []; - for (var i in datasets) { - dataset_options.push({ - label: datasets[i].hid + ': ' + datasets[i].name, - value: datasets[i].id - }); - } - - // select field - this.select_datasets = new Ui.Select.View({ - multiple : true, - data : dataset_options, - value : dataset_options[0] && dataset_options[0].value, + // single dataset select field + this.select_single = new Ui.Select.View({ onchange : function() { self.trigger('change'); } }); - // - // collections - // - var collections = app.content.filterType({ - src : 'hdca', - extensions : options.extensions - }); - - // configure options fields - var collection_options = []; - for (var i in collections) { - collection_options.push({ - label: collections[i].hid + ': ' + collections[i].name, - value: collections[i].id - }); - } - - // create select field for collections - this.select_collection = new Ui.Select.View({ - data : collection_options, - value : collection_options[0] && collection_options[0].value, + // multiple datasets select field + this.select_multiple = new Ui.Select.View({ + multiple : true, onchange : function() { self.trigger('change'); } }); + // collection select field + this.select_collection = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + + // list of all select fields + this.list = { + 'single' : { + field: this.select_single, + type : 'hda' + }, + 'multiple' : { + field: this.select_multiple, + type : 'hda' + }, + 'collection' : { + field: this.select_collection, + type : 'hdca' + } + }; + + // add batch mode information + this.$batch = $(ToolTemplate.batchMode()); + // add elements to dom - this.$el.append(Utils.wrap(this.button_new.$el)); - this.$el.append(this.select_datasets.$el); - this.$el.append(this.select_collection.$el); + this.$el.append(Utils.wrap(this.button_type.$el)); + for (var i in this.list) { + this.$el.append(this.list[i].field.$el); + } + this.$el.append(this.$batch); - // check for batch mode - if (!this.options.multiple) { - this.$el.append(ToolTemplate.batchMode()); - } + // update options + this.update(options.data); // refresh view this.refresh(); @@ -102,31 +92,77 @@ }); }, + /** Indicate that select fields are being updated */ + wait: function() { + for (var i in this.list) { + this.list[i].field.wait(); + } + }, + + /** Indicate that the options update has been completed */ + unwait: function() { + for (var i in this.list) { + this.list[i].field.unwait(); + } + }, + + /** Update content selector */ + update: function(options) { + // identify dataset options + var dataset_options = []; + for (var i in options.hda) { + var hda = options.hda[i]; + dataset_options.push({ + label: hda.hid + ': ' + hda.name, + value: hda.id + }); + } + + // identify collection options + var collection_options = []; + for (var i in options.hdca) { + var hdca = options.hdca[i]; + collection_options.push({ + label: hdca.hid + ': ' + hdca.name, + value: hdca.id + }); + } + + // update selection fields + this.select_single.update(dataset_options); + this.select_multiple.update(dataset_options); + this.select_collection.update(collection_options); + + // add to content list + this.app.content.add(options); + }, + /** Return the currently selected dataset values */ value : function (dict) { // update current value if (dict !== undefined) { try { - // set source - this.current = dict.values[0].src; - this.refresh(); - // create list var list = []; for (var i in dict.values) { list.push(dict.values[i].id); } - // identify select element - switch(this.current) { - case 'hda': - this.select_datasets.value(list); - break; - case 'hdca': - this.select_collection.value(list[0]); - break; + // identify suitable select field + if (dict && dict.values.length > 0 && dict.values[0].src == 'hcda') { + this.current = 'collection'; + this.select_collection.value(list[0]); + } else { + if (list.length > 1) { + this.current = 'multiple'; + this.select_multiple.value(list); + } else { + this.current = 'single'; + this.select_single.value(list[0]); + } } - + this.refresh(); + // check if value has been set var select = this._select(); if (!select.validate()) { @@ -153,7 +189,7 @@ for (var i in id_list) { result.values.push({ id : id_list[i], - src : this.current + src : this.list[this.current].type }); } @@ -169,26 +205,24 @@ /** Refreshes data selection view */ refresh: function() { - switch (this.current) { - case 'hda': - this.select_datasets.$el.fadeIn(); - this.select_collection.$el.hide(); - break; - case 'hdca': - this.select_datasets.$el.hide(); - this.select_collection.$el.fadeIn(); - break; + for (var i in this.list) { + var $el = this.list[i].field.$el; + if (this.current == i) { + $el.show(); + } else { + $el.hide(); + } + } + if (this.current != 'single' && !this.options.multiple) { + this.$batch.show(); + } else { + this.$batch.hide(); } }, /** Assists in selecting the current field */ _select: function() { - switch(this.current) { - case 'hdca': - return this.select_collection; - default: - return this.select_datasets; - } + return this.list[this.current].field; } }); diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -56,7 +56,7 @@ batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + - 'This is a batch mode input field. A separate job will be triggered for each dataset.' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; } }; diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2067,22 +2067,49 @@ return ref def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): + # create dictionary and fill default parameters d = super( DataToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions d['multiple'] = self.multiple + d['is_dynamic'] = True + d['options'] = {'hda': [], 'hdca': []} + + # return default content if context is not available if other_values is None: - # No need to produce lists of datasets for history. return d + # prepare dataset/collection matching dataset_matcher = DatasetMatcher( trans, self, None, other_values ) history = trans.history multiple = self.multiple - for hda_match, hid in self.match_datasets( history, dataset_matcher ): - # hda_match not an hda - it is a description of the match, may - # describe match after implicit conversion. - pass - for history_dataset_collection in self.match_collections( history, dataset_matcher, reduction=multiple ): - pass + + # add datasets + for hda in history.active_datasets_children_and_roles: + if dataset_matcher.hda_match( hda ): + d['options']['hda'].append({ + 'id' : trans.security.encode_id( hda.id ), + 'hid' : hda.hid, + 'name' : hda.name, + 'src' : 'hda', + 'dataset_id' : hda.dataset_id + }) + + # add dataset collections + dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) + for hdca in history.active_dataset_collections: + if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ): + d['options']['hdca'].append({ + 'id' : trans.security.encode_id( hdca.id ), + 'hid' : hdca.hid, + 'name' : hdca.name, + 'src' : 'hdca' + }) + + # sort both lists + d['options']['hda'] = sorted(d['options']['hda'], key=lambda k: k['hid'], reverse=True) + d['options']['hdca'] = sorted(d['options']['hdca'], key=lambda k: k['hid'], reverse=True) + + # return final dictionary return d diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -131,12 +131,13 @@ """ api_type = "file" encoded_id = trans.security.encode_id( hda.id ) + encoded_dataset_id = trans.security.encode_id( hda.dataset_id ); # TODO: handle failed_metadata here as well return { 'id' : encoded_id, 'history_id' : encoded_history_id, - 'dataset_id' : hda.dataset_id, + 'dataset_id' : encoded_dataset_id, 'name' : hda.name, 'type' : api_type, 'state' : hda.dataset.state, diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -575,11 +575,13 @@ dict['value'] = value return dict - # populate state + # initialize state using default parameters def initialize_state(trans, inputs, state, context=None): context = ExpressionContext(state, context) for input in inputs.itervalues(): state[input.name] = input.get_initial_value(trans, context) + + # populates state with incoming url parameters def populate_state(trans, inputs, state, incoming, prefix="", context=None ): errors = dict() context = ExpressionContext(state, context) @@ -630,12 +632,14 @@ state[input.name] = value return errors - # build model + # builds tool model including all attributes def iterate(group_inputs, inputs, tool_state, errors, other_values=None): other_values = ExpressionContext( tool_state, other_values ) for input_index, input in enumerate( inputs.itervalues() ): # create model dictionary group_inputs[input_index] = input.to_dict(trans) + if group_inputs[input_index] is None: + continue # identify stat for subsection/group group_state = tool_state[input.name] diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/mvc/tools/tools-content.js --- a/static/scripts/mvc/tools/tools-content.js +++ b/static/scripts/mvc/tools/tools-content.js @@ -1,96 +1,23 @@ define(['utils/utils'], function(Utils){ return Backbone.Model.extend({ // initialize - initialize: function(options) { - // backup basic url - this.base_url = galaxy_config.root + 'api/histories/' + options.history_id + '/contents'; - - // prepare content obects - this.datatypes = {}; + initialize: function(app) { this.summary = {}; - - // link this - var self = this; - - // request datatypes - Utils.get({ - url : galaxy_config.root + 'api/datatypes/mapping', - cache : true, - success : function(response) { - // backup datatype dictionary - self.datatypes = response; - - // get history summary - Utils.get({ - url : self.base_url + '?deleted=false', - success : function(response) { - // backup summary - self.summary = response; - - // sort by id - self.summary.sort(function(a, b) { - return a.hid > b.hid ? -1 : (a.hid < b.hid ? 1 : 0); - }); - - // log - console.debug('tools-content::initialize() - Completed.'); - - // callback - options.success && options.success(); - }, - error : function(response) { - // log request failure - console.debug('tools-content::initialize() - Ajax request for summary failed.'); - console.debug(response); - } - }); - }, - error : function(response) { - // log request failure - console.debug('tools-content::initialize() - Ajax request for datatypes failed.'); - console.debug(response); - } - }); }, - /** - * Filters contents by data type. + /** Add new content elements */ - filterType: function(options) { - // initialize parameters - options = options || {}; - var result = []; - - // identify content type - var history_content_type = 'dataset'; - if (options.src== 'hdca') { - history_content_type = 'dataset_collection'; + add: function(content_list) { + // add/update content in summary list + for (var i in content_list) { + for (var j in content_list[i]) { + var c = content_list[i][j]; + this.summary[c.id + '_' + c.src] = c; + } } - // search in summary - for (var i in this.summary) { - var content = this.summary[i]; - - // check ok state (TODO: should be implemented in the api) - if (content.history_content_type === 'dataset' && content.state !== 'ok') { - continue; - } - - // match datatypes - var found = false; - for (var i in options.extensions) { - if (this._matchType(options.extensions[i], content.extension)) { - found = true; - break; - } - } - - // final match result - if ((content.history_content_type === history_content_type) && (found || !options.extensions)) { - result.push(content); - } - } - return result; + // log + console.debug('tools-content::initialize() - Completed.'); }, /** Returns matched content from summary. @@ -126,33 +53,6 @@ console.debug(response); } }); - }, - - /** Check if datatypes match - */ - _matchType: function(target, reference) { - // check if target class is available - var target_class = this.datatypes.ext_to_class_name[target]; - if (!target_class) { - console.debug('tools-content::_matchType() - Specific target class unavailable. Accepting all formats.'); - return true; - } - - // check if reference class is available - var reference_class = this.datatypes.ext_to_class_name[reference]; - if (!reference_class) { - console.debug('tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.'); - return true; - } - - // check reference group - var reference_group = this.datatypes.class_to_classes[reference_class]; - if (reference_group[target_class]) { - return true; - } - - // classes do not match - return false; } }); }); \ No newline at end of file diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -21,11 +21,19 @@ var self = this; // link galaxy modal or create one - if (parent.Galaxy && parent.Galaxy.modal) { - this.modal = parent.Galaxy.modal; + var galaxy = parent.Galaxy; + if (galaxy && galaxy.modal) { + this.modal = galaxy.modal; } else { this.modal = new Ui.Modal.View(); } + + // check if the user is an admin + if (galaxy && galaxy.currUser) { + this.is_admin = galaxy.currUser.get('is_admin') + } else { + this.is_admin = false; + } // link options this.options = options; @@ -47,12 +55,10 @@ this.job_handler = new ToolJobs(this); // request history content and build form - this.content = new ToolContent({ - history_id : self.options.history_id, - success : function() { - self._buildForm(self.options); - } - }); + this.content = new ToolContent(this); + + // build this form + this._buildForm(options); }, // message @@ -72,7 +78,7 @@ // this happens i.e. when repeat blocks are added or removed and on initialization rebuild: function() { this.tree.refresh(); - console.debug('tools-form::refresh() - Refreshed form structure.'); + console.debug('tools-form::rebuild() - Rebuilding data structures.'); }, // refreshes input states i.e. for dynamic parameters @@ -142,7 +148,7 @@ var current_state = this.tree.finalize({ data : function(dict) { if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { - return self.content.get({id: dict.values[0].id}).dataset_id; + return self.content.get({id: dict.values[0].id, src: 'hda'}).dataset_id; } return null; } @@ -215,16 +221,22 @@ // get/update field var field = self.field_list[input_id]; - if (field.update && input.type != 'data') { + if (field.update) { var new_options = []; - for (var i in node.options) { - var opt = node.options[i]; - if (opt.length > 2) { - new_options.push({ - 'label': opt[0], - 'value': opt[1] - }); - } + switch (input.type) { + case 'data': + new_options = input.options; + break; + default: + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } } field.update(new_options); console.debug('Updating options for ' + input_id); @@ -292,7 +304,7 @@ }); // add admin operations - if (Galaxy.currUser.get('is_admin')) { + if (this.is_admin) { // create download button menu.addMenu({ icon : 'fa-download', diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -142,8 +142,8 @@ if (batch_n === -1) { batch_n = n; } else { - if (batch_n !== n && n != 1) { - this._foundError(input_id, 'Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); + if (batch_n !== n) { + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + batch_n + '</b>.'); return false; } } diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -372,6 +372,7 @@ id : 'field-' + input_def.id, extensions : input_def.extensions, multiple : input_def.multiple, + data : input_def.options, onchange : function() { self.app.refresh(); } diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -4,7 +4,8 @@ var View = Backbone.View.extend({ // initialize initialize : function(app, options) { - // configure options + // link app and options + this.app = app; this.options = options; // link this @@ -14,13 +15,14 @@ this.setElement('<div/>'); // current selection - this.current = 'hda'; + this.current = 'single'; // create button - this.button_new = new Ui.RadioButton.View({ + this.button_type = new Ui.RadioButton.View({ value : this.current, - data : [ { icon: 'fa-file-o', label : 'Select datasets', value : 'hda' }, - { icon: 'fa-files-o', label : 'Select a collection', value : 'hdca' }], + data : [ { icon: 'fa-file-o', label : 'Single dataset', value : 'single' }, + { icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }, + { icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }], onchange: function(value) { self.current = value; self.refresh(); @@ -28,68 +30,56 @@ } }); - // - // datasets - // - var datasets = app.content.filterType({ - src : 'hda', - extensions : options.extensions - }); - - // configure options fields - var dataset_options = []; - for (var i in datasets) { - dataset_options.push({ - label: datasets[i].hid + ': ' + datasets[i].name, - value: datasets[i].id - }); - } - - // select field - this.select_datasets = new Ui.Select.View({ - multiple : true, - data : dataset_options, - value : dataset_options[0] && dataset_options[0].value, + // single dataset select field + this.select_single = new Ui.Select.View({ onchange : function() { self.trigger('change'); } }); - // - // collections - // - var collections = app.content.filterType({ - src : 'hdca', - extensions : options.extensions - }); - - // configure options fields - var collection_options = []; - for (var i in collections) { - collection_options.push({ - label: collections[i].hid + ': ' + collections[i].name, - value: collections[i].id - }); - } - - // create select field for collections - this.select_collection = new Ui.Select.View({ - data : collection_options, - value : collection_options[0] && collection_options[0].value, + // multiple datasets select field + this.select_multiple = new Ui.Select.View({ + multiple : true, onchange : function() { self.trigger('change'); } }); + // collection select field + this.select_collection = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + + // list of all select fields + this.list = { + 'single' : { + field: this.select_single, + type : 'hda' + }, + 'multiple' : { + field: this.select_multiple, + type : 'hda' + }, + 'collection' : { + field: this.select_collection, + type : 'hdca' + } + }; + + // add batch mode information + this.$batch = $(ToolTemplate.batchMode()); + // add elements to dom - this.$el.append(Utils.wrap(this.button_new.$el)); - this.$el.append(this.select_datasets.$el); - this.$el.append(this.select_collection.$el); + this.$el.append(Utils.wrap(this.button_type.$el)); + for (var i in this.list) { + this.$el.append(this.list[i].field.$el); + } + this.$el.append(this.$batch); - // check for batch mode - if (!this.options.multiple) { - this.$el.append(ToolTemplate.batchMode()); - } + // update options + this.update(options.data); // refresh view this.refresh(); @@ -102,31 +92,77 @@ }); }, + /** Indicate that select fields are being updated */ + wait: function() { + for (var i in this.list) { + this.list[i].field.wait(); + } + }, + + /** Indicate that the options update has been completed */ + unwait: function() { + for (var i in this.list) { + this.list[i].field.unwait(); + } + }, + + /** Update content selector */ + update: function(options) { + // identify dataset options + var dataset_options = []; + for (var i in options.hda) { + var hda = options.hda[i]; + dataset_options.push({ + label: hda.hid + ': ' + hda.name, + value: hda.id + }); + } + + // identify collection options + var collection_options = []; + for (var i in options.hdca) { + var hdca = options.hdca[i]; + collection_options.push({ + label: hdca.hid + ': ' + hdca.name, + value: hdca.id + }); + } + + // update selection fields + this.select_single.update(dataset_options); + this.select_multiple.update(dataset_options); + this.select_collection.update(collection_options); + + // add to content list + this.app.content.add(options); + }, + /** Return the currently selected dataset values */ value : function (dict) { // update current value if (dict !== undefined) { try { - // set source - this.current = dict.values[0].src; - this.refresh(); - // create list var list = []; for (var i in dict.values) { list.push(dict.values[i].id); } - // identify select element - switch(this.current) { - case 'hda': - this.select_datasets.value(list); - break; - case 'hdca': - this.select_collection.value(list[0]); - break; + // identify suitable select field + if (dict && dict.values.length > 0 && dict.values[0].src == 'hcda') { + this.current = 'collection'; + this.select_collection.value(list[0]); + } else { + if (list.length > 1) { + this.current = 'multiple'; + this.select_multiple.value(list); + } else { + this.current = 'single'; + this.select_single.value(list[0]); + } } - + this.refresh(); + // check if value has been set var select = this._select(); if (!select.validate()) { @@ -153,7 +189,7 @@ for (var i in id_list) { result.values.push({ id : id_list[i], - src : this.current + src : this.list[this.current].type }); } @@ -169,26 +205,24 @@ /** Refreshes data selection view */ refresh: function() { - switch (this.current) { - case 'hda': - this.select_datasets.$el.fadeIn(); - this.select_collection.$el.hide(); - break; - case 'hdca': - this.select_datasets.$el.hide(); - this.select_collection.$el.fadeIn(); - break; + for (var i in this.list) { + var $el = this.list[i].field.$el; + if (this.current == i) { + $el.show(); + } else { + $el.hide(); + } + } + if (this.current != 'single' && !this.options.multiple) { + this.$batch.show(); + } else { + this.$batch.hide(); } }, /** Assists in selecting the current field */ _select: function() { - switch(this.current) { - case 'hdca': - return this.select_collection; - default: - return this.select_datasets; - } + return this.list[this.current].field; } }); diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -56,7 +56,7 @@ batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + - 'This is a batch mode input field. A separate job will be triggered for each dataset.' + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; } }; diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 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(c){this.base_url=galaxy_config.root+"api/histories/"+c.history_id+"/contents";this.datatypes={};this.summary={};var b=this;a.get({url:galaxy_config.root+"api/datatypes/mapping",cache:true,success:function(d){b.datatypes=d;a.get({url:b.base_url+"?deleted=false",success:function(e){b.summary=e;b.summary.sort(function(g,f){return g.hid>f.hid?-1:(g.hid<f.hid?1:0)});console.debug("tools-content::initialize() - Completed.");c.success&&c.success()},error:function(e){console.debug("tools-content::initialize() - Ajax request for summary failed.");console.debug(e)}})},error:function(d){console.debug("tools-content::initialize() - Ajax request for datatypes failed.");console.debug(d)}})},filterType:function(c){c=c||{};var b=[];var g="dataset";if(c.src=="hdca"){g="dataset_collection"}for(var d in this.summary){var e=this.summary[d];if(e.history_content_type==="dataset"&&e.state!=="ok"){continue}var f=false;for(var d in c.extensions){if(this._matchType(c.extensions[d],e.extension)){f=true;break}}if((e.history_content_type===g)&&(f||!c.extensions)){b.push(e)}}return b},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)}})},_matchType:function(f,b){var c=this.datatypes.ext_to_class_name[f];if(!c){console.debug("tools-content::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var d=this.datatypes.ext_to_class_name[b];if(!d){console.debug("tools-content::_matchType() - Specific reference class unavailable. Accepting all formats.");return true}var e=this.datatypes.class_to_classes[d];if(e[c]){return true}return false}})}); \ 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}}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 diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 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","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","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:n.options.history_id,success:function(){n._buildForm(n.options)}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::refresh() - Refreshed form structure.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update&&p.type!="data"){var t=[];for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}v.update(t);console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.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="+o.options.id)}});if(Galaxy.currUser.get("is_admin")){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.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="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g&&g!=1){this._foundError(l,"Please make sure that you select a single input or the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f]);break}}else{console.debug(e);c.app.modal.show({title:"Job submission failed",body:a.error(d),buttons:{Close:function(){c.app.modal.hide()}}})}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(h){var d=h.inputs;var m=-1;var i=null;for(var k in d){var f=d[k];var l=this.app.tree.match(k);var e=this.app.field_list[l];var j=this.app.input_list[l];if(j&&e&&e.validate&&!e.validate()){this._foundError(l);return false}if(f.batch){var g=f.values.length;var c=null;if(g>0){c=f.values[0]&&f.values[0].src}if(c){if(i===null){i=c}else{if(i!==c){this._foundError(l,"Please select either dataset or dataset list fields for all batch mode fields.");return false}}}if(m===-1){m=g}else{if(m!==g){this._foundError(l,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+m+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.content.filterType({src:"hda",extensions:h.extensions});var k=[];for(var j in l){k.push({label:l[j].hid+": "+l[j].name,value:l[j].id})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.content.filterType({src:"hdca",extensions:h.extensions});var f=[];for(var j in m){f.push({label:m[j].hid+": "+m[j].name,value:m[j].id})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(m){if(m!==undefined){try{this.current=m.values[0].src;this.refresh();var l=[];for(var h in m.values){l.push(m.values[h].id)}switch(this.current){case"hda":this.select_datasets.value(l);break;case"hdca":this.select_collection.value(l[0]);break}var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.current})}return f},validate:function(){return this._select().validate()},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}},_select:function(){switch(this.current){case"hdca":return this.select_collection;default:return this.select_datasets}}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(j,g){this.app=j;this.options=g;var f=this;this.setElement("<div/>");this.current="single";this.button_type=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Single dataset",value:"single"},{icon:"fa-files-o",label:"Multiple datasets",value:"multiple"},{icon:"fa-folder-o",label:"List of datasets",value:"collection"}],onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list={single:{field:this.select_single,type:"hda"},multiple:{field:this.select_multiple,type:"hda"},collection:{field:this.select_collection,type:"hdca"}};this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m!==undefined){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file diff -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 -r 4231a77fe8946110b2c56efd436000b864b06a84 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}}}); \ 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: Small fix for e4c9f0b.
by commits-noreply＠bitbucket.org 11 Nov '14

11 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7cdccd6e7573/ Changeset: 7cdccd6e7573 User: jmchilton Date: 2014-11-11 20:56:18+00:00 Summary: Small fix for e4c9f0b. Affected #: 1 file diff -r e4c9f0b5a73851ab2d8644889d305aaab80208d9 -r 7cdccd6e757315f66bada94b85cf046ff5f8edc1 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2268,6 +2268,8 @@ subcollection_type = self._history_query( trans ).collection_type_description.collection_type pass + return d + class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Nov '14

11 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2f7780bd1b1/ Changeset: d2f7780bd1b1 User: jmchilton Date: 2014-11-11 18:41:00+00:00 Summary: Refactor dataset matcher stuff for use outside of field generation. (i.e. for reuse in filtering datasets on the client side) Affected #: 2 files diff -r d519ad65435883112008e90ec06ebf44a91586e7 -r d2f7780bd1b1d5b545c6c222fb383d6a35833855 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1796,26 +1796,52 @@ field_name = "%s%s" % ( self.name, suffix ) field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + for history_dataset_collection in self.match_collections( history, dataset_matcher, reduction=reduction ): + name = history_dataset_collection.name + hid = str( history_dataset_collection.hid ) + hidden_text = "" # TODO + id = value_modifier( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ) ) + selected = value and history_dataset_collection in value + text = "%s:%s %s" % ( hid, hidden_text, name ) + field.add_option( text, id, selected ) + + return field + + def _get_select_dataset_field( self, history, dataset_matcher, multiple=False, suffix="" ): + field_name = "%s%s" % ( self.name, suffix ) + field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + + for hda_match, hid in self.match_datasets( history, dataset_matcher ): + if not hda_match.implicit_conversion: + hda = hda_match.hda + hda_name = hda.name + selected = dataset_matcher.selected( hda ) + if hda.visible: + hidden_text = "" + else: + hidden_text = " (hidden)" + field.add_option( "%s:%s %s" % ( hid, hidden_text, hda_name ), hda.id, selected ) + else: + hda_name = hda_match.original_hda.name + hda = hda_match.hda # Get converted dataset + target_ext = hda_match.target_ext + selected = dataset_matcher.selected( hda ) + field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) + + self._ensure_selection( field ) + return field + + def match_collections( self, history, dataset_matcher, reduction=True ): dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) for history_dataset_collection in history.active_dataset_collections: if dataset_collection_matcher.hdca_match( history_dataset_collection, reduction=reduction ): - name = history_dataset_collection.name - hid = str( history_dataset_collection.hid ) - hidden_text = "" # TODO - id = value_modifier( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ) ) - selected = value and history_dataset_collection in value - text = "%s:%s %s" % ( hid, hidden_text, name ) - field.add_option( text, id, selected ) + yield history_dataset_collection - return field + def match_datasets( self, history, dataset_matcher ): - def _get_select_dataset_field( self, history, dataset_matcher, multiple=False, suffix="" ): - - # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): for i, hda in enumerate( hdas ): - hda_name = hda.name if parent_hid is not None: hid = "%s.%d" % ( parent_hid, i + 1 ) else: @@ -1823,27 +1849,13 @@ hda_match = dataset_matcher.hda_match( hda ) if not hda_match: continue - if not hda_match.implicit_conversion: - selected = dataset_matcher.selected( hda ) - if hda.visible: - hidden_text = "" - else: - hidden_text = " (hidden)" - field.add_option( "%s:%s %s" % ( hid, hidden_text, hda_name ), hda.id, selected ) - else: - hda = hda_match.hda # Get converted dataset - target_ext = hda_match.target_ext - selected = dataset_matcher.selected( hda ) - field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) + yield (hda_match, hid) # Also collect children via association object - dataset_collector( hda.children, hid ) + for item in dataset_collector( hda.children, hid ): + yield item - field_name = "%s%s" % ( self.name, suffix ) - field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) - - dataset_collector( history.active_datasets_children_and_roles, None ) - self._ensure_selection( field ) - return field + for item in dataset_collector( history.active_datasets_children_and_roles, None ): + yield item def get_initial_value( self, trans, context, history=None ): return self.get_initial_value_from_history_prevent_repeats(trans, context, None, history=history) @@ -2098,15 +2110,31 @@ return self._switch_fields( fields, default_field=default_field ) - def _get_single_collection_field( self, trans, history, value, other_values ): - field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + def match_collections( self, trans, history, dataset_matcher ): dataset_collections = trans.app.dataset_collections_service.history_dataset_collections( history, self._history_query( trans ) ) - dataset_matcher = DatasetMatcher( trans, self, value, other_values ) dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) for dataset_collection_instance in dataset_collections: if not dataset_collection_matcher.hdca_match( dataset_collection_instance ): continue + yield dataset_collection_instance + + def match_multirun_collections( self, trans, history, dataset_matcher ): + dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) + + for history_dataset_collection in history.active_dataset_collections: + if not self._history_query( trans ).can_map_over( history_dataset_collection ): + continue + + datasets_match = dataset_collection_matcher.hdca_match( history_dataset_collection ) + if datasets_match: + yield history_dataset_collection + + def _get_single_collection_field( self, trans, history, value, other_values ): + field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) + dataset_matcher = DatasetMatcher( trans, self, value, other_values ) + + for dataset_collection_instance in self.match_collections( trans, history, dataset_matcher ): instance_id = dataset_collection_instance.hid instance_name = dataset_collection_instance.name selected = ( value and ( dataset_collection_instance == value ) ) @@ -2122,22 +2150,16 @@ field_name = "%s%s" % ( self.name, suffix ) field = form_builder.SelectField( field_name, multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) dataset_matcher = DatasetMatcher( trans, self, value, other_values ) - dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) - for history_dataset_collection in history.active_dataset_collections: - if not self._history_query( trans ).can_map_over( history_dataset_collection ): - continue + for history_dataset_collection in self.match_multirun_collections( trans, history, dataset_matcher ): + name = history_dataset_collection.name + hid = str( history_dataset_collection.hid ) + hidden_text = "" # TODO + subcollection_type = self._history_query( trans ).collection_type_description.collection_type + id = "%s|%s" % ( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ), subcollection_type ) + text = "%s:%s %s" % ( hid, hidden_text, name ) - datasets_match = dataset_collection_matcher.hdca_match( history_dataset_collection ) - if datasets_match: - name = history_dataset_collection.name - hid = str( history_dataset_collection.hid ) - hidden_text = "" # TODO - subcollection_type = self._history_query( trans ).collection_type_description.collection_type - id = "%s|%s" % ( dataset_matcher.trans.security.encode_id( history_dataset_collection.id ), subcollection_type ) - text = "%s:%s %s" % ( hid, hidden_text, name ) - - field.add_option( text, id, False ) + field.add_option( text, id, False ) return field diff -r d519ad65435883112008e90ec06ebf44a91586e7 -r d2f7780bd1b1d5b545c6c222fb383d6a35833855 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -53,11 +53,12 @@ return False target_ext, converted_dataset = hda.find_conversion_destination( formats ) if target_ext: + original_hda = hda if converted_dataset: hda = converted_dataset if check_security and not self.__can_access_dataset( hda.dataset ): return False - return HdaImplicitMatch( hda, target_ext ) + return HdaImplicitMatch( hda, target_ext, original_hda ) return False def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): @@ -117,7 +118,8 @@ conversion). """ - def __init__( self, hda, target_ext ): + def __init__( self, hda, target_ext, original_hda ): + self.original_hda = original_hda self.hda = hda self.target_ext = target_ext https://bitbucket.org/galaxy/galaxy-central/commits/e4c9f0b5a738/ Changeset: e4c9f0b5a738 User: jmchilton Date: 2014-11-11 18:41:00+00:00 Summary: Rework ToolDataParameter and ToolDataCollectionParameter to_dict to filter over valid matches. Doesn't do anything with them yet - passing this work off to Sam to populate the dictionaries in whatever manner makes most sense for UI consumption. Affected #: 1 file diff -r d2f7780bd1b1d5b545c6c222fb383d6a35833855 -r e4c9f0b5a73851ab2d8644889d305aaab80208d9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2066,12 +2066,26 @@ ref = ref() return ref - def to_dict( self, trans, view='collection', value_mapper=None ): + def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): d = super( DataToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions d['multiple'] = self.multiple + if other_values is None: + # No need to produce lists of datasets for history. + return d + + dataset_matcher = DatasetMatcher( trans, self, None, other_values ) + history = trans.history + multiple = self.multiple + for hda_match, hid in self.match_datasets( history, dataset_matcher ): + # hda_match not an hda - it is a description of the match, may + # describe match after implicit conversion. + pass + for history_dataset_collection in self.match_collections( history, dataset_matcher, reduction=multiple ): + pass return d + class DataCollectionToolParameter( BaseDataToolParameter ): """ """ @@ -2238,6 +2252,22 @@ def validate( self, value, history=None ): return True # TODO + def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): + d = super( DataCollectionToolParameter, self ).to_dict( trans ) + if other_values is None: + # No need to produce lists of datasets for history. + return d + + dataset_matcher = DatasetMatcher( trans, self, None, other_values ) + history = trans.history + + for hdca in self.match_collections( trans, history, dataset_matcher ): + pass + + for hdca in self.match_multirun_collections( trans, history, dataset_matcher ): + subcollection_type = self._history_query( trans ).collection_type_description.collection_type + pass + class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: Merged in anton/galaxy-central-anton (pull request #539)
by commits-noreply＠bitbucket.org 11 Nov '14

11 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d519ad654358/ Changeset: d519ad654358 User: martenson Date: 2014-11-11 17:26:45+00:00 Summary: Merged in anton/galaxy-central-anton (pull request #539) Initial tweaks to tool_conf.xml sample and one of the tools. Affected #: 2 files diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -104,10 +104,6 @@ <tool file="maf/maf_reverse_complement.xml" /><tool file="maf/maf_filter.xml" /></section> - <section id="scores" name="Get Genomic Scores"> - <tool file="filters/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /> @@ -115,71 +111,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/bar_chart.xml" /><tool file="plotting/boxplot.xml" /> - <tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /></section> - <section id="hyphy" name="Evolution"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - </section> - <section id="motifs" name="Motif Tools"> - <tool file="meme/meme.xml" /> - <tool file="meme/fimo.xml" /> - </section> - <section id="NGS_QC" name="NGS: QC and manipulation"> - - <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> - - <label id="illumina" text="Illumina fastq" /> - - <label id="454" text="Roche-454 data" /> - <label id="solid" text="AB-SOLiD data" /> - <tool file="next_gen_conversion/solid2fastq.xml" /> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - - <label id="generic_fastq" text="Generic FASTQ manipulation" /> - - <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> - </section> -  - <section id="solexa_tools" name="NGS: Mapping"> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml" /> - </section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section> - <section id="samtools" name="NGS: SAM Tools"> - </section> - <section id="ngs-simulation" name="NGS: Simulation"> - <tool file="ngs_simulation/ngs_simulation.xml" /> - </section> - <section id="hgv" name="Phenotype Association"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - <tool file="phenotype_association/sift.xml" /> - <tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml" /> - <tool file="phenotype_association/ldtools.xml" /> - <tool file="phenotype_association/pass.xml" /> - <tool file="phenotype_association/gpass.xml" /> - <tool file="phenotype_association/beam.xml" /> - <tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/master2pg.xml" /> - </section></toolbox> diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 tools/filters/uniq.xml --- a/tools/filters/uniq.xml +++ b/tools/filters/uniq.xml @@ -26,8 +26,7 @@ </test></tests><help> - - .. class:: infomark +.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* 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: 3 new changesets
by commits-noreply＠bitbucket.org 11 Nov '14

11 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26e1a07f9f22/ Changeset: 26e1a07f9f22 User: anton Date: 2014-10-23 16:37:58+00:00 Summary: modification to default tool_conf.xml Affected #: 1 file diff -r ae33952d52dcf4f682b317aaf01dcaa4d79d79b9 -r 26e1a07f9f22035e952344e34cdfa430a7b0ef7d config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -104,10 +104,6 @@ <tool file="maf/maf_reverse_complement.xml" /><tool file="maf/maf_filter.xml" /></section> - <section id="scores" name="Get Genomic Scores"> - <tool file="filters/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /> @@ -115,71 +111,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/bar_chart.xml" /><tool file="plotting/boxplot.xml" /> - <tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /></section> - <section id="hyphy" name="Evolution"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - </section> - <section id="motifs" name="Motif Tools"> - <tool file="meme/meme.xml" /> - <tool file="meme/fimo.xml" /> - </section> - <section id="NGS_QC" name="NGS: QC and manipulation"> - - <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> - - <label id="illumina" text="Illumina fastq" /> - - <label id="454" text="Roche-454 data" /> - <label id="solid" text="AB-SOLiD data" /> - <tool file="next_gen_conversion/solid2fastq.xml" /> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - - <label id="generic_fastq" text="Generic FASTQ manipulation" /> - - <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> - </section> -  - <section id="solexa_tools" name="NGS: Mapping"> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml" /> - </section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section> - <section id="samtools" name="NGS: SAM Tools"> - </section> - <section id="ngs-simulation" name="NGS: Simulation"> - <tool file="ngs_simulation/ngs_simulation.xml" /> - </section> - <section id="hgv" name="Phenotype Association"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - <tool file="phenotype_association/sift.xml" /> - <tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml" /> - <tool file="phenotype_association/ldtools.xml" /> - <tool file="phenotype_association/pass.xml" /> - <tool file="phenotype_association/gpass.xml" /> - <tool file="phenotype_association/beam.xml" /> - <tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/master2pg.xml" /> - </section></toolbox> https://bitbucket.org/galaxy/galaxy-central/commits/addd9cf18318/ Changeset: addd9cf18318 User: anton Date: 2014-10-23 16:42:15+00:00 Summary: uniq.xml edited online with Bitbucket Affected #: 1 file diff -r 26e1a07f9f22035e952344e34cdfa430a7b0ef7d -r addd9cf183181a9c2406c9956ed13b90e6c4558a tools/filters/uniq.xml --- a/tools/filters/uniq.xml +++ b/tools/filters/uniq.xml @@ -26,8 +26,7 @@ </test></tests><help> - - .. class:: infomark +.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* https://bitbucket.org/galaxy/galaxy-central/commits/d519ad654358/ Changeset: d519ad654358 User: martenson Date: 2014-11-11 17:26:45+00:00 Summary: Merged in anton/galaxy-central-anton (pull request #539) Initial tweaks to tool_conf.xml sample and one of the tools. Affected #: 2 files diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 config/tool_conf.xml.sample --- a/config/tool_conf.xml.sample +++ b/config/tool_conf.xml.sample @@ -104,10 +104,6 @@ <tool file="maf/maf_reverse_complement.xml" /><tool file="maf/maf_filter.xml" /></section> - <section id="scores" name="Get Genomic Scores"> - <tool file="filters/wiggle_to_simple.xml" /> - <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> - </section><section id="stats" name="Statistics"><tool file="stats/gsummary.xml" /><tool file="filters/uniq.xml" /> @@ -115,71 +111,6 @@ <section id="plots" name="Graph/Display Data"><tool file="plotting/bar_chart.xml" /><tool file="plotting/boxplot.xml" /> - <tool file="visualization/LAJ.xml" /><tool file="maf/vcf_to_maf_customtrack.xml" /></section> - <section id="hyphy" name="Evolution"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - </section> - <section id="motifs" name="Motif Tools"> - <tool file="meme/meme.xml" /> - <tool file="meme/fimo.xml" /> - </section> - <section id="NGS_QC" name="NGS: QC and manipulation"> - - <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /> - - <label id="illumina" text="Illumina fastq" /> - - <label id="454" text="Roche-454 data" /> - <label id="solid" text="AB-SOLiD data" /> - <tool file="next_gen_conversion/solid2fastq.xml" /> - <tool file="solid_tools/solid_qual_stats.xml" /> - <tool file="solid_tools/solid_qual_boxplot.xml" /> - - <label id="generic_fastq" text="Generic FASTQ manipulation" /> - - <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /> - </section> -  - <section id="solexa_tools" name="NGS: Mapping"> - <tool file="sr_mapping/bfast_wrapper.xml" /> - <tool file="sr_mapping/PerM.xml" /> - <tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml" /> - </section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section> - <section id="samtools" name="NGS: SAM Tools"> - </section> - <section id="ngs-simulation" name="NGS: Simulation"> - <tool file="ngs_simulation/ngs_simulation.xml" /> - </section> - <section id="hgv" name="Phenotype Association"> - <tool file="evolution/codingSnps.xml" /> - <tool file="evolution/add_scores.xml" /> - <tool file="phenotype_association/sift.xml" /> - <tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml" /> - <tool file="phenotype_association/ldtools.xml" /> - <tool file="phenotype_association/pass.xml" /> - <tool file="phenotype_association/gpass.xml" /> - <tool file="phenotype_association/beam.xml" /> - <tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/master2pg.xml" /> - </section></toolbox> diff -r 932f4bbf2c317fc5dc735777d167765d907a0e0d -r d519ad65435883112008e90ec06ebf44a91586e7 tools/filters/uniq.xml --- a/tools/filters/uniq.xml +++ b/tools/filters/uniq.xml @@ -26,8 +26,7 @@ </test></tests><help> - - .. class:: infomark +.. class:: infomark **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Fix field type output
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/932f4bbf2c31/ Changeset: 932f4bbf2c31 User: guerler Date: 2014-11-10 20:07:04+00:00 Summary: ToolForm: Fix field type output Affected #: 3 files diff -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 -r 932f4bbf2c317fc5dc735777d167765d907a0e0d client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -352,7 +352,7 @@ } // log - console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); + console.debug('tools-form::_addRow() : Auto matched field type (' + input_def.type + ').'); } // set field value diff -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 -r 932f4bbf2c317fc5dc735777d167765d907a0e0d static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -352,7 +352,7 @@ } // log - console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); + console.debug('tools-form::_addRow() : Auto matched field type (' + input_def.type + ').'); } // set field value diff -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 -r 932f4bbf2c317fc5dc735777d167765d907a0e0d static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+field_type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset c9759aa6e40f
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f01e2504095a/ Changeset: f01e2504095a Branch: stable User: natefoo Date: 2014-11-10 20:00:25+00:00 Summary: Update tag latest_2014.10.06 for changeset c9759aa6e40f Affected #: 1 file diff -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de -r f01e2504095a477b16970f9570eb68361f031287 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a1dca14d5b1afbf2b5bde192e3e6b6763836eff8 latest_2014.10.06 +c9759aa6e40f887dec2d27d2f244d6fd7c28e6de latest_2014.10.06 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: Merge stable.
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c92e972a0a3/ Changeset: 1c92e972a0a3 User: jmchilton Date: 2014-11-10 16:43:09+00:00 Summary: Merge stable. Affected #: 4 files diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 latest_2014.10.06 +a1dca14d5b1afbf2b5bde192e3e6b6763836eff8 latest_2014.10.06 diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 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 @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 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 @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r 25f0318f232ff783972c1e3e26fa853c0b9f085b -r 1c92e972a0a38afccfffed8a51be6c63c64969e2 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.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(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return this[h].call(this)},simpleAutoPair:function(){var n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var l=h[m];q=l.name.replace(this.filters[0],"");o=0;for(k=0;k<r.length;k++){var p=r[k];w=p.name.replace(this.filters[1],"");if(l!==p){if(q===w){s=k;o=q.length;break}var n=this._naiveStartingAndEndingLCS(q,w);v=n.length;if(v>o){s=k;o=v}}}var u=o/(Math.min(q.length,w.length));if(u>=this.matchPercentage){this._pair(h.splice(m,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{m+=1}}},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return this[h].call(this)},simpleAutoPair:function(){var n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var l=h[m];q=l.name.replace(this.filters[0],"");o=0;for(k=0;k<r.length;k++){var p=r[k];w=p.name.replace(this.filters[1],"");if(l!==p){if(q===w){s=k;o=q.length;break}var n=this._naiveStartingAndEndingLCS(q,w);v=n.length;if(v>o){s=k;o=v}}}var u=o/(Math.min(q.length,w.length));if(u>=this.matchPercentage){this._pair(h.splice(m,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{m+=1}}},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){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 h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});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(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.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(h){this.toggleExtensions()},"change .collection-name":"_changeName","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(i){var h=this.autoPair();this.trigger("autopair",h)},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return j},pairAllSelected:function(i){i=i||{};var j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column .dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return l},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column .dataset").eq(k).data("dataset"),h=$(".unpaired-columns .reverse-column .dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" 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commit/galaxy-central: jmchilton: Bugfix renaming individual parts of pairs.
by commits-noreply＠bitbucket.org 10 Nov '14

10 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c9759aa6e40f/ Changeset: c9759aa6e40f Branch: stable User: jmchilton Date: 2014-11-10 15:07:56+00:00 Summary: Bugfix renaming individual parts of pairs. >From Carl: "Yeah - that looks fine for stable. A better fix is probably adding the pair index directly into the DOM and getting it there - I'll add that to the 'Iteration 2' card. I'll approve now if you want to do the request." Affected #: 3 files diff -r a16007e4df83c21ff1d9218b3892fae783742fb8 -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de 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 @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r a16007e4df83c21ff1d9218b3892fae783742fb8 -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de 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 @@ -1298,7 +1298,7 @@ _clickPairName : function( ev ){ ev.stopPropagation(); var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().index() ], + pair = this.paired[ $control.parent().parent().index() / 2 ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; diff -r a16007e4df83c21ff1d9218b3892fae783742fb8 -r c9759aa6e40f887dec2d27d2f244d6fd7c28e6de static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.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(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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"+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_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(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" 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.remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header 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h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().index()],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join(""),{pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['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>",d(['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 h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,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 i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal: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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