commit/galaxy-central: guerler: ToolForm/Workflow: Add payload, use default value to collapse/expand sections, fix styles
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf6b51623d29/ Changeset: bf6b51623d29 User: guerler Date: 2015-01-14 03:39:17+00:00 Summary: ToolForm/Workflow: Add payload, use default value to collapse/expand sections, fix styles Affected #: 25 files diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -111,7 +111,7 @@ this.tree.finalize(); // show errors - if (!this.workflow && options.errors) { + if (options.errors) { var error_messages = this.tree.matchResponse(options.errors); for (var input_id in error_messages) { this.highlight(input_id, error_messages[input_id], true); @@ -145,7 +145,7 @@ // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', - title : 'Requirements', + title : (!self.workflow && 'Requirements') || null, tooltip : 'Display tool requirements', onclick : function() { if (!this.visible) { @@ -170,7 +170,7 @@ // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', - title : 'Versions', + title : (!self.workflow && 'Versions') || null, tooltip : 'Select another tool version' }); if (options.versions && options.versions.length > 1) { @@ -200,7 +200,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', - title : 'Options', + title : (!self.workflow && 'Options') || null, tooltip : 'View available options' }); diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -9,6 +9,7 @@ initialize: function(options) { // link with node representation in workflow module this.node = workflow.active_node; + if (!this.node) { console.debug('FAILED - tools-form-workflow:initialize() - Node not found in workflow.'); return; @@ -18,6 +19,13 @@ this.workflow = true; this.options = options; + // traverse through dictionary + Utils.deepeach(options.inputs, function(item) { + if (item.type && (['data', 'data_hidden', 'hidden']).indexOf(item.type) == -1) { + item.optional = true; + } + }); + // load extension var self = this; Utils.get({ @@ -38,6 +46,7 @@ inputs[Utils.uuid()] = { label : 'Edit Step Attributes', type : 'section', + expand : this.node.annotation, inputs : [{ label : 'Annotation / Notes', name : 'annotation', @@ -160,7 +169,10 @@ type : 'boolean', value : 'false', ignore : 'false', - help : 'This action will send an email notifying you when the job is done.' + help : 'This action will send an email notifying you when the job is done.', + payload : { + 'host' : window.location.host + } },{ action : 'DeleteIntermediatesAction', label : 'Delete non-outputs', @@ -173,31 +185,51 @@ // visit input nodes and enrich by name/value pairs from server data var self = this; - function visit (inputs) { - for (var i in inputs) { - var input = inputs[i]; + function visit (head, head_list) { + head_list = head_list || []; + head_list.push(head); + for (var i in head.inputs) { + var input = head.inputs[i]; if (input.action) { + // construct identifier as expected by backend input.name = 'pja__' + output_id + '__' + input.action; if (input.argument) { input.name += '__' + input.argument; } + + // modify names of payload arguments + if (input.payload) { + for (var p_id in input.payload) { + var p = input.payload[p_id]; + input.payload[input.name + '__' + p_id] = p; + delete p; + } + } + + // access/verify existence of value var d = self.post_job_actions[input.action + output_id]; if (d) { + // mark as expanded + for (var j in head_list) { + head_list[j].expand = true; + } + + // update input field value if (input.argument) { input.value = d.action_arguments && d.action_arguments[input.argument] || input.value; } else { input.value = 'true'; } } - } else { - if (input.inputs) { - visit(input.inputs); - } + } + // continue with sub section + if (input.inputs) { + visit(input, head_list.slice(0)); } } } - visit(input_config.inputs); - + visit(input_config); + // return final configuration return input_config; }, @@ -205,6 +237,15 @@ /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { + Galaxy.modal.show({ + title : 'Coming soon...', + body : 'This feature has not been implemented yet.', + buttons : { + 'Close' : function() { + Galaxy.modal.hide(); + } + } + }); }, /** Request a new model for an already created tool form and updates the form inputs diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -12,6 +12,7 @@ // link field this.field = options.field; + this.defaultvalue = options.defaultvalue; // set element this.setElement(this._template(options)); @@ -25,9 +26,17 @@ // add field element this.$field.prepend(this.field.$el); - // start with enabled optional fields + // decide wether to expand or collapse optional fields this.field.skip = false; - + if (options.optional) { + if ((this.field.validate && !this.field.validate()) || + (this.field.value && !this.field.value()) || + (this.field.value && Number(this.field.value()) == Number(this.defaultvalue)) || + (this.field.value && JSON.stringify(this.field.value()) == JSON.stringify(this.defaultvalue))) { + this.field.skip = true; + } + } + // refresh view this._refresh(); @@ -63,11 +72,12 @@ if (!this.field.skip) { this.$field.fadeIn('fast'); this.$title_optional.html('Disable'); - this.app.trigger('refresh'); } else { this.$field.hide(); this.$title_optional.html('Enable'); + this.field.value(this.defaultvalue); } + this.app.trigger('refresh'); }, /** Main Template diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc 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 @@ -232,9 +232,9 @@ // create input field wrapper var input_element = new InputElement(this.app, { - label : input_def.title, - help : input_def.help, - field : repeat + label : input_def.title, + help : input_def.help, + field : repeat }); // displays as grouped subsection @@ -292,6 +292,11 @@ } }); + // show sub section if requested + if (input_def.expand) { + portlet.$header.trigger('click'); + } + // create table row this.table.add(portlet.$el); @@ -313,10 +318,11 @@ // create input field wrapper var input_element = new InputElement(this.app, { - label : input_def.label, - optional : input_def.optional, - help : input_def.help, - field : field + label : input_def.label, + defaultvalue : input_def.defaultvalue, + optional : input_def.optional, + help : input_def.help, + field : field }); // add to element list diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc 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 @@ -4,7 +4,7 @@ // tool form templates return { help: function(content) { - return '<div class="toolHelp">' + + return '<div class="toolHelp" style="overflow: auto;">' + '<div class="toolHelpBody">' + content + '</div>' + diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -122,13 +122,21 @@ value = patch[input.type](value); } - // handle default value + // handle simple value if (!field.skip) { - if (field.validate && !field.validate(value)) { + if (field.validate && !field.validate()) { value = null; } - if (input.ignore === undefined || (value && input.ignore != value)) { + if (input.ignore === undefined || (value !== null && input.ignore != value)) { + // add value to submission add (job_input_id, input.id, value); + + // add payload to submission + if (input.payload) { + for (var p_id in input.payload) { + add (p_id, input.id, input.payload[p_id]); + } + } } } } diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc client/galaxy/scripts/utils/utils.js --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -6,6 +6,18 @@ // dependencies define(["libs/underscore"], function(_) { +/** Traverse through json +*/ +function deepeach(dict, callback) { + for (var i in dict) { + var d = dict[i]; + if (d && typeof(d) == "object") { + callback(d); + deepeach(d, callback); + } + } +} + /** * Sanitize/escape a string * @param{String} content - Content to be sanitized @@ -248,7 +260,8 @@ request: request, sanitize: sanitize, textify: textify, - validate: validate + validate: validate, + deepeach: deepeach }; }); diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -12,8 +12,10 @@ import threading import types import urllib +import copy -from galaxy import eggs +from galaxy import eggs, util + eggs.require( "MarkupSafe" ) # MarkupSafe must load before mako eggs.require( "Mako" ) eggs.require( "elementtree" ) @@ -2150,9 +2152,9 @@ return None # ensures that input dictionary is jsonifiable - def sanitize(dict): + def sanitize(dict, key='value'): # get current value - value = dict['value'] if 'value' in dict else None + value = dict[key] if key in dict else None # jsonify by type if dict['type'] in ['data']: @@ -2167,15 +2169,8 @@ value = jsonify(value) # update and return - dict['value'] = value - return dict + dict[key] = value - # 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) - # check the current state of a value and update it if necessary def check_state(trans, input, default_value, context): value = default_value @@ -2195,6 +2190,7 @@ def populate_state(trans, inputs, state, errors, incoming, prefix="", context=None ): context = ExpressionContext(state, context) for input in inputs.itervalues(): + state[input.name] = input.get_initial_value(trans, context) key = prefix + input.name if input.type == 'repeat': group_state = state[input.name] @@ -2207,7 +2203,6 @@ if rep_index < input.max: new_state = {} new_state['__index__'] = rep_index - initialize_state(trans, input.inputs, new_state, context) group_state.append(new_state) populate_state(trans, input.inputs, new_state, errors, incoming, prefix=rep_name + "|", context=context) rep_index += 1 @@ -2223,7 +2218,6 @@ try: current_case = input.get_current_case(value, trans) group_state = state[input.name] = {} - initialize_state(trans, input.cases[current_case].inputs, group_state, context) populate_state( trans, input.cases[current_case].inputs, group_state, errors, incoming, prefix=group_prefix, context=context) group_state['__current_case__'] = current_case except Exception, e: @@ -2272,13 +2266,17 @@ # identify name input_name = tool_dict.get('name') if input_name: + # backup default value + tool_dict['defaultvalue'] = input.get_initial_value(trans, other_values) + # update input value from tool state if input_name in state_inputs: tool_dict['value'] = state_inputs[input_name] - - # sanitize if value exists - tool_dict = sanitize(tool_dict) - + + # sanitize values + sanitize(tool_dict, 'value') + sanitize(tool_dict, 'defaultvalue') + # backup final input dictionary group_inputs[input_index] = tool_dict @@ -2303,7 +2301,6 @@ # initialize and populate tool state state_inputs = {} state_errors = {} - initialize_state(trans, self.inputs, state_inputs) populate_state(trans, self.inputs, state_inputs, state_errors, params.__dict__) # create basic tool model diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -111,7 +111,7 @@ this.tree.finalize(); // show errors - if (!this.workflow && options.errors) { + if (options.errors) { var error_messages = this.tree.matchResponse(options.errors); for (var input_id in error_messages) { this.highlight(input_id, error_messages[input_id], true); @@ -145,7 +145,7 @@ // button for version selection var requirements_button = new Ui.ButtonIcon({ icon : 'fa-info-circle', - title : 'Requirements', + title : (!self.workflow && 'Requirements') || null, tooltip : 'Display tool requirements', onclick : function() { if (!this.visible) { @@ -170,7 +170,7 @@ // button for version selection var versions_button = new Ui.ButtonMenu({ icon : 'fa-cubes', - title : 'Versions', + title : (!self.workflow && 'Versions') || null, tooltip : 'Select another tool version' }); if (options.versions && options.versions.length > 1) { @@ -200,7 +200,7 @@ // button menu var menu_button = new Ui.ButtonMenu({ icon : 'fa-caret-down', - title : 'Options', + title : (!self.workflow && 'Options') || null, tooltip : 'View available options' }); diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -9,6 +9,7 @@ initialize: function(options) { // link with node representation in workflow module this.node = workflow.active_node; + if (!this.node) { console.debug('FAILED - tools-form-workflow:initialize() - Node not found in workflow.'); return; @@ -18,6 +19,13 @@ this.workflow = true; this.options = options; + // traverse through dictionary + Utils.deepeach(options.inputs, function(item) { + if (item.type && (['data', 'data_hidden', 'hidden']).indexOf(item.type) == -1) { + item.optional = true; + } + }); + // load extension var self = this; Utils.get({ @@ -38,6 +46,7 @@ inputs[Utils.uuid()] = { label : 'Edit Step Attributes', type : 'section', + expand : this.node.annotation, inputs : [{ label : 'Annotation / Notes', name : 'annotation', @@ -160,7 +169,10 @@ type : 'boolean', value : 'false', ignore : 'false', - help : 'This action will send an email notifying you when the job is done.' + help : 'This action will send an email notifying you when the job is done.', + payload : { + 'host' : window.location.host + } },{ action : 'DeleteIntermediatesAction', label : 'Delete non-outputs', @@ -173,31 +185,51 @@ // visit input nodes and enrich by name/value pairs from server data var self = this; - function visit (inputs) { - for (var i in inputs) { - var input = inputs[i]; + function visit (head, head_list) { + head_list = head_list || []; + head_list.push(head); + for (var i in head.inputs) { + var input = head.inputs[i]; if (input.action) { + // construct identifier as expected by backend input.name = 'pja__' + output_id + '__' + input.action; if (input.argument) { input.name += '__' + input.argument; } + + // modify names of payload arguments + if (input.payload) { + for (var p_id in input.payload) { + var p = input.payload[p_id]; + input.payload[input.name + '__' + p_id] = p; + delete p; + } + } + + // access/verify existence of value var d = self.post_job_actions[input.action + output_id]; if (d) { + // mark as expanded + for (var j in head_list) { + head_list[j].expand = true; + } + + // update input field value if (input.argument) { input.value = d.action_arguments && d.action_arguments[input.argument] || input.value; } else { input.value = 'true'; } } - } else { - if (input.inputs) { - visit(input.inputs); - } + } + // continue with sub section + if (input.inputs) { + visit(input, head_list.slice(0)); } } } - visit(input_config.inputs); - + visit(input_config); + // return final configuration return input_config; }, @@ -205,6 +237,15 @@ /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { + Galaxy.modal.show({ + title : 'Coming soon...', + body : 'This feature has not been implemented yet.', + buttons : { + 'Close' : function() { + Galaxy.modal.hide(); + } + } + }); }, /** Request a new model for an already created tool form and updates the form inputs diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -12,6 +12,7 @@ // link field this.field = options.field; + this.defaultvalue = options.defaultvalue; // set element this.setElement(this._template(options)); @@ -25,9 +26,17 @@ // add field element this.$field.prepend(this.field.$el); - // start with enabled optional fields + // decide wether to expand or collapse optional fields this.field.skip = false; - + if (options.optional) { + if ((this.field.validate && !this.field.validate()) || + (this.field.value && !this.field.value()) || + (this.field.value && Number(this.field.value()) == Number(this.defaultvalue)) || + (this.field.value && JSON.stringify(this.field.value()) == JSON.stringify(this.defaultvalue))) { + this.field.skip = true; + } + } + // refresh view this._refresh(); @@ -63,11 +72,12 @@ if (!this.field.skip) { this.$field.fadeIn('fast'); this.$title_optional.html('Disable'); - this.app.trigger('refresh'); } else { this.$field.hide(); this.$title_optional.html('Enable'); + this.field.value(this.defaultvalue); } + this.app.trigger('refresh'); }, /** Main Template diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -232,9 +232,9 @@ // create input field wrapper var input_element = new InputElement(this.app, { - label : input_def.title, - help : input_def.help, - field : repeat + label : input_def.title, + help : input_def.help, + field : repeat }); // displays as grouped subsection @@ -292,6 +292,11 @@ } }); + // show sub section if requested + if (input_def.expand) { + portlet.$header.trigger('click'); + } + // create table row this.table.add(portlet.$el); @@ -313,10 +318,11 @@ // create input field wrapper var input_element = new InputElement(this.app, { - label : input_def.label, - optional : input_def.optional, - help : input_def.help, - field : field + label : input_def.label, + defaultvalue : input_def.defaultvalue, + optional : input_def.optional, + help : input_def.help, + field : field }); // add to element list diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -4,7 +4,7 @@ // tool form templates return { help: function(content) { - return '<div class="toolHelp">' + + return '<div class="toolHelp" style="overflow: auto;">' + '<div class="toolHelpBody">' + content + '</div>' + diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -122,13 +122,21 @@ value = patch[input.type](value); } - // handle default value + // handle simple value if (!field.skip) { - if (field.validate && !field.validate(value)) { + if (field.validate && !field.validate()) { value = null; } - if (input.ignore === undefined || (value && input.ignore != value)) { + if (input.ignore === undefined || (value !== null && input.ignore != value)) { + // add value to submission add (job_input_id, input.id, value); + + // add payload to submission + if (input.payload) { + for (var p_id in input.payload) { + add (p_id, input.id, input.payload[p_id]); + } + } } } } diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){console.debug(l);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.options=l;this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var n=this.options;this._renderForm(n);this.tree.finalize();if(!this.workflow&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in o){this.highlight(m,o[m],true)}}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var p in this.element_list){this.element_list[p].reset()}})},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:"Versions",tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:"Options",tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(this.options.workflow){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){console.debug(l);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.options=l;this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this._buildForm()},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).animate({scrollTop:o.$el.offset().top-20},500)}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var n=this.options;this._renderForm(n);this.tree.finalize();if(n.errors){var o=this.tree.matchResponse(n.errors);for(var m in o){this.highlight(m,o[m],true)}}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var p in this.element_list){this.element_list[p].reset()}})},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!t.workflow&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.workflow&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.workflow&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(this.options.workflow){this.portlet.$content.css("padding","0px")}this.portlet.append(this.message.$el,true);this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(u.help!=""){this.$el.append(c.help(u.help))}if(u.citations){var s=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=u.id;var n=new a.CitationListView({el:s,collection:l});n.render();l.fetch();this.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.workflow=true;this.options=e;var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done."},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(j){for(var l in j){var k=j[l];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}var m=d.post_job_actions[k.action+h];if(m){if(k.argument){k.value=m.action_arguments&&m.action_arguments[k.argument]||k.value}else{k.value="true"}}}else{if(k.inputs){e(k.inputs)}}}}e(f.inputs);return f},_buildModel:function(){},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id;b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h,true);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.workflow=true;this.options=e;b.deepeach(e.inputs,function(f){if(f.type&&(["data","data_hidden","hidden"]).indexOf(f.type)==-1){f.optional=true}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id;b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h,true);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable");this.app.trigger("refresh")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(c,b){this.app=c;this.field=b.field;this.defaultvalue=b.defaultvalue;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;if(b.optional){if((this.field.validate&&!this.field.validate())||(this.field.value&&!this.field.value())||(this.field.value&&Number(this.field.value())==Number(this.defaultvalue))||(this.field.value&&JSON.stringify(this.field.value())==JSON.stringify(this.defaultvalue))){this.field.skip=true}}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable");this.field.value(this.defaultvalue)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc 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/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs,cls:"ui-table-plain"});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i,cls:"ui-table-plain"});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs,cls:"ui-table-plain"});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(this.app.workflow){var k=e.textify(i.extensions.toString());i.info="Data input '"+i.name+"' ("+k+")";return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(this.app.workflow&&j.is_dynamic){if(!e.validate(j.value)){j.value=""}return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs,cls:"ui-table-plain"});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i,cls:"ui-table-plain"});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs,cls:"ui-table-plain"});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,defaultvalue:i.defaultvalue,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(this.app.workflow){var k=e.textify(i.extensions.toString());i.info="Data input '"+i.name+"' ("+k+")";return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(this.app.workflow&&j.is_dynamic){if(!e.validate(j.value)){j.value=""}return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc 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>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp" style="overflow: auto;"><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>'},requirements:function(a){var d="This tool requires ";for(var b in a.requirements){var c=a.requirements[b];d+=c.name;if(c.version){d+=" (Version "+c.version+")"}if(b<a.requirements.length-2){d+=", "}if(b==a.requirements.length-2){d+=" and "}}return d+'. Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.'}}}); \ No newline at end of file diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(o,r){for(var m in r){var k=r[m];if(k.input){var t=k.input;var n=o;if(o!=""){n+="|"}n+=t.name;switch(t.type){case"repeat":var j="section-";var w=[];var q=null;for(var v in k){var p=v.indexOf(j);if(p!=-1){p+=j.length;w.push(parseInt(v.substr(p)));if(!q){q=v.substr(0,p)}}}w.sort(function(x,i){return x-i});var m=0;for(var l in w){c(n+"_"+m++,k[q+w[l]])}break;case"conditional":var u=b.app.field_list[t.id].value();if(g[t.test_param.type]){u=g[t.test_param.type](u)}d(n+"|"+t.test_param.name,t.id,u);var h=b.matchCase(t,u);if(h!=-1){c(n,r[t.id+"-section-"+h])}break;case"section":c("",k);break;default:var s=b.app.field_list[t.id];if(s&&s.value){var u=s.value();if(g[t.type]){u=g[t.type](u)}if(!s.skip){if(s.validate&&!s.validate(u)){u=null}if(t.ignore===undefined||(u&&t.ignore!=u)){d(n,t.id,u)}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(!t.skip){if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(m){function d(n){return $("<div/>").text(n).html()}function l(o){if(!(o instanceof Array)){o=[o]}for(var n in o){if(["None",null,"null",undefined,"undefined"].indexOf(o[n])>-1){return false}}return true}function h(n){var n=n.toString();if(n){n=n.replace(/,/g,", ");var o=n.lastIndexOf(", ");if(o!=-1){n=n.substr(0,o)+" or "+n.substr(o+1)}return n}return""}function e(n){top.__utils__get__=top.__utils__get__||{};if(n.cache&&top.__utils__get__[n.url]){n.success&&n.success(top.__utils__get__[n.url]);console.debug("utils.js::get() - Fetching from cache ["+n.url+"].")}else{i({url:n.url,data:n.data,success:function(o){top.__utils__get__[n.url]=o;n.success&&n.success(o)},error:function(o){n.error&&n.error(o)}})}}function i(o){var n={contentType:"application/json",type:o.type||"GET",data:o.data||{},url:o.url};if(n.type=="GET"||n.type=="DELETE"){if(n.url.indexOf("?")==-1){n.url+="?"}else{n.url+="&"}n.url=n.url+$.param(n.data);n.data=null}else{n.dataType="json";n.url=n.url;n.data=JSON.stringify(n.data)}$.ajax(n).done(function(p){if(typeof p==="string"){try{p=p.replace("Infinity,",'"Infinity",');p=jQuery.parseJSON(p)}catch(q){console.debug(q)}}o.success&&o.success(p)}).fail(function(q){var p=null;try{p=jQuery.parseJSON(q.responseText)}catch(r){p=q.responseText}o.error&&o.error(p,q)})}function j(q,n){var o=$('<div class="'+q+'"></div>');o.appendTo(":eq(0)");var p=o.css(n);o.remove();return p}function g(n){if(!$('link[href^="'+n+'"]').length){$('<link href="'+galaxy_config.root+n+'" rel="stylesheet">').appendTo("head")}}function k(n,o){if(n){return m.defaults(n,o)}else{return o}}function b(o,q){var p="";if(o>=100000000000){o=o/100000000000;p="TB"}else{if(o>=100000000){o=o/100000000;p="GB"}else{if(o>=100000){o=o/100000;p="MB"}else{if(o>=100){o=o/100;p="KB"}else{if(o>0){o=o*10;p="b"}else{return"<strong>-</strong>"}}}}}var n=(Math.round(o)/10);if(q){return n+" "+p}else{return"<strong>"+n+"</strong> "+p}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(n){var o=$("<p></p>");o.append(n);return o}function f(){var p=new Date();var n=(p.getHours()<10?"0":"")+p.getHours();var o=(p.getMinutes()<10?"0":"")+p.getMinutes();var q=p.getDate()+"/"+(p.getMonth()+1)+"/"+p.getFullYear()+", "+n+":"+o;return q}return{cssLoadFile:g,cssGetAttribute:j,get:e,merge:k,bytesToString:b,uuid:a,time:f,wrap:c,request:i,sanitize:d,textify:h,validate:l}}); \ No newline at end of file +define(["libs/underscore"],function(m){function n(r,q){for(var o in r){var p=r[o];if(p&&typeof(p)=="object"){q(p);n(p,q)}}}function d(o){return $("<div/>").text(o).html()}function l(p){if(!(p instanceof Array)){p=[p]}for(var o in p){if(["None",null,"null",undefined,"undefined"].indexOf(p[o])>-1){return false}}return true}function h(o){var o=o.toString();if(o){o=o.replace(/,/g,", ");var p=o.lastIndexOf(", ");if(p!=-1){o=o.substr(0,p)+" or "+o.substr(p+1)}return o}return""}function e(o){top.__utils__get__=top.__utils__get__||{};if(o.cache&&top.__utils__get__[o.url]){o.success&&o.success(top.__utils__get__[o.url]);console.debug("utils.js::get() - Fetching from cache ["+o.url+"].")}else{i({url:o.url,data:o.data,success:function(p){top.__utils__get__[o.url]=p;o.success&&o.success(p)},error:function(p){o.error&&o.error(p)}})}}function i(p){var o={contentType:"application/json",type:p.type||"GET",data:p.data||{},url:p.url};if(o.type=="GET"||o.type=="DELETE"){if(o.url.indexOf("?")==-1){o.url+="?"}else{o.url+="&"}o.url=o.url+$.param(o.data);o.data=null}else{o.dataType="json";o.url=o.url;o.data=JSON.stringify(o.data)}$.ajax(o).done(function(q){if(typeof q==="string"){try{q=q.replace("Infinity,",'"Infinity",');q=jQuery.parseJSON(q)}catch(r){console.debug(r)}}p.success&&p.success(q)}).fail(function(r){var q=null;try{q=jQuery.parseJSON(r.responseText)}catch(s){q=r.responseText}p.error&&p.error(q,r)})}function j(r,o){var p=$('<div class="'+r+'"></div>');p.appendTo(":eq(0)");var q=p.css(o);p.remove();return q}function g(o){if(!$('link[href^="'+o+'"]').length){$('<link href="'+galaxy_config.root+o+'" rel="stylesheet">').appendTo("head")}}function k(o,p){if(o){return m.defaults(o,p)}else{return p}}function b(p,r){var q="";if(p>=100000000000){p=p/100000000000;q="TB"}else{if(p>=100000000){p=p/100000000;q="GB"}else{if(p>=100000){p=p/100000;q="MB"}else{if(p>=100){p=p/100;q="KB"}else{if(p>0){p=p*10;q="b"}else{return"<strong>-</strong>"}}}}}var o=(Math.round(p)/10);if(r){return o+" "+q}else{return"<strong>"+o+"</strong> "+q}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(o){var p=$("<p></p>");p.append(o);return p}function f(){var q=new Date();var o=(q.getHours()<10?"0":"")+q.getHours();var p=(q.getMinutes()<10?"0":"")+q.getMinutes();var r=q.getDate()+"/"+(q.getMonth()+1)+"/"+q.getFullYear()+", "+o+":"+p;return r}return{cssLoadFile:g,cssGetAttribute:j,get:e,merge:k,bytesToString:b,uuid:a,time:f,wrap:c,request:i,sanitize:d,textify:h,validate:l,deepeach:n}}); \ No newline at end of file diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -6,6 +6,18 @@ // dependencies define(["libs/underscore"], function(_) { +/** Traverse through json +*/ +function deepeach(dict, callback) { + for (var i in dict) { + var d = dict[i]; + if (d && typeof(d) == "object") { + callback(d); + deepeach(d, callback); + } + } +} + /** * Sanitize/escape a string * @param{String} content - Content to be sanitized @@ -248,7 +260,8 @@ request: request, sanitize: sanitize, textify: textify, - validate: validate + validate: validate, + deepeach: deepeach }; }); diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1412,7 +1412,7 @@ .ui-button-icon-plain{border:none !important;background:none !important;height:inherit !important;width:inherit !important;padding-right:3px !important} .ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} .ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} -.ui-portlet,.ui-portlet-slim,.ui-portlet-repeat,.ui-portlet-section,.ui-portlet-slim,.ui-portlet-repeat,.ui-portlet-section{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-slim .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-slim .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-slim .portlet-header .portlet-title .portlet-title-text{vertical-align:middle} +.ui-portlet,.ui-portlet-slim,.ui-portlet-repeat,.ui-portlet-section,.ui-portlet-slim,.ui-portlet-repeat,.ui-portlet-section{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-slim .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title,.ui-portlet-slim .portlet-header .portlet-title{display:inline;vertical-align:middle}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-slim .portlet-header .portlet-title .portlet-title-text{vertical-align:middle;line-height:20px} .ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-slim .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} .ui-portlet .portlet-buttons,.ui-portlet-slim .portlet-buttons{height:50px;padding:10px} .ui-portlet .portlet-content,.ui-portlet-slim .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content,.ui-portlet-slim .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons,.ui-portlet-slim .portlet-content .content .buttons{height:50px;padding:10px} @@ -1765,7 +1765,7 @@ div.toolFormDisabled{border-color:#bfbfbf} div.toolHelp{margin-top:15px;padding:5px} div.toolHelpBody{width:100%} -.toolForm.toolFormInCanvas{border:solid #d6b161 1px;background:#fff}.toolForm.toolFormInCanvas.toolForm-active{border:solid blue 3px;margin:4px} +.toolForm.toolFormInCanvas{border:solid #d6b161 1px;background:#fff}.toolForm.toolFormInCanvas.toolForm-active{border:solid #5f6990 3px;margin:4px} .toolForm.toolFormInCanvas .toolFormTitle{font-size:12px;line-height:1.428571429} div.form,div.toolForm{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px} div.form-title,div.toolFormTitle{padding:5px 10px;background:#ebd9b2;border-bottom:solid #d6b161 1px} diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -586,7 +586,7 @@ border: solid @form-border 1px; background: @white; &.toolForm-active { - border: solid blue 3px; + border: solid @brand-primary 3px; margin: 4px; } .toolFormTitle { diff -r 659fc6822f0afcdf77ba5f8857ba58700ce06b16 -r bf6b51623d29b68ba216d97d99bb1ea200a3e4fc static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -168,6 +168,7 @@ vertical-align: middle; .portlet-title-text { vertical-align: middle; + line-height: 20px; } .icon { font-size: 1.2em; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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