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commit/galaxy-central: guerler: ToolForm: Enables hierarchical references and conversion of the tool form into a json/xml tree structure
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8d307a592c72/
Changeset: 8d307a592c72
User: guerler
Date: 2014-08-28 20:03:35
Summary: ToolForm: Enables hierarchical references and conversion of the tool form into a json/xml tree structure
Affected #: 12 files
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -1,8 +1,8 @@
define(['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-datasets', 'mvc/tools/tools-section'],
+ 'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-datasets', 'mvc/tools/tools-section', 'mvc/tools/tools-tree'],
function(Portlet, Ui, CitationModel, CitationView,
- Tools, ToolTemplate, ToolDatasets, ToolSection) {
+ Tools, ToolTemplate, ToolDatasets, ToolSection, ToolTree) {
// create tool model
var Model = Backbone.Model.extend({
@@ -29,6 +29,18 @@
id : options.id
});
+ // creates a tree/json structure from the input form
+ this.tree = new ToolTree(this);
+
+ // reset field list
+ this.field_list = {};
+
+ // reset sequential input definition list
+ this.inputs_sequential = {};
+
+ // create data model
+ this.data = new Backbone.Model();
+
// initialize datasets
this.datasets = new ToolDatasets({
success: function() {
@@ -39,13 +51,6 @@
// initialize tool form
_initializeToolForm: function() {
-
- // reset field list
- this.field_list = {};
-
- // reset sequential input definition list
- this.inputs_sequential = {};
-
// fetch model and render form
var self = this;
this.model.fetch({
@@ -67,6 +72,7 @@
title : 'Execute',
floating : 'clear',
onclick : function() {
+ console.log(self.tree.create(self));
}
})
}
@@ -107,8 +113,25 @@
// append tool section
self.portlet.append(self.section.$el);
+
+ // trigger refresh
+ self.refresh();
}
});
+ },
+
+ // refresh
+ refresh: function() {
+ // recreate tree structure
+ this.tree.refresh();
+
+ // trigger change
+ for (var id in this.field_list) {
+ this.field_list[id].trigger('change');
+ }
+
+ // log
+ console.debug('tools-form::refresh() - Recreated tree structure. Refresh.');
}
});
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -1,4 +1,5 @@
-define(['mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'], function(Table, Ui, Tabs) {
+define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'],
+ function(Utils, Table, Ui, Tabs) {
// create form view
var View = Backbone.View.extend({
@@ -13,6 +14,13 @@
// link datasets
this.datasets = app.datasets;
+ // link data model
+ this.data = app.data;
+
+ // add table class for tr tag
+ // this assist in transforming the form into a json structure
+ options.cls_tr = 'form-row';
+
// create table
this.table = new Table.View(options);
@@ -28,98 +36,115 @@
// reset table
this.table.delAll();
- // model
- var data = new Backbone.Model();
-
// load settings elements into table
- for (var id in this.inputs) {
- this._add(this.inputs[id], data);
- }
-
- // trigger change
- for (var id in this.app.field_list) {
- this.app.field_list[id].trigger('change');
+ for (var i in this.inputs) {
+ this._add(this.inputs[i], this.data);
}
},
// add table row
- _add: function(inputs_def, data) {
+ _add: function(input, data) {
// link this
var self = this;
+ // clone definition
+ var input_def = jQuery.extend(true, {}, input);
+
+ // create unique id
+ input_def.id = Utils.uuid();
+
+ // add to sequential list of inputs
+ this.app.inputs_sequential[input_def.id] = input_def;
+
// identify field type
- var type = inputs_def.type;
+ var type = input_def.type;
switch(type) {
// conditional field
case 'conditional':
// add label to input definition root
- inputs_def.label = inputs_def.test_param.label;
+ input_def.label = input_def.test_param.label;
- // add id to input definition root
- inputs_def.name = inputs_def.test_param.name;
+ // add value to input definition root
+ input_def.value = input_def.test_param.value;
// build options field
- this._addRow('conditional', inputs_def, data);
+ this._addRow('conditional', input_def, data);
// add fields
- for (var i in inputs_def.cases) {
+ for (var i in input_def.cases) {
+ // create id tag
+ var sub_section_id = input_def.id + '-section-' + i;
+
// create sub section
var sub_section = new View(this.app, {
- inputs : inputs_def.cases[i].inputs,
+ inputs : input_def.cases[i].inputs,
cls : 'ui-table-plain'
});
// append sub section
this.table.add('');
this.table.add(sub_section.$el);
- this.table.append(inputs_def.name + '_formsection_' + i);
+ this.table.append(sub_section_id);
}
break;
// repeat block
case 'repeat':
// create tab field
var tabs = new Tabs.View({
- title_new : 'Add Group',
+ title_new : 'Add ' + input_def.title,
onnew : function() {
+ // create id tag
+ var sub_section_id = input_def.id + '-section-' + Utils.uuid();
+
// create sub section
var sub_section = new View(self.app, {
- inputs : inputs_def.inputs,
+ inputs : input_def.inputs,
cls : 'ui-table-plain'
});
- // create id tag
- var sub_section_id = inputs_def.name + '_formsection_' + tabs.size();
-
// add new tab
tabs.add({
id : sub_section_id,
- title : 'Repeat',
+ title : input_def.title,
$el : sub_section.$el,
ondel : function() {
+ // delete tab
tabs.del(sub_section_id);
+
+ // retitle tabs
+ tabs.retitle(input_def.title);
+
+ // trigger refresh
+ self.app.refresh();
}
});
+ // retitle tabs
+ tabs.retitle(input_def.title);
+
// show tab
tabs.show(sub_section_id);
+
+ // trigger refresh
+ self.app.refresh();
}
});
// append sub section
- this.table.add(inputs_def.title);
+ this.table.add('');
this.table.add(tabs.$el);
- this.table.append(inputs_def.name);
+ this.table.append(input_def.id);
break;
// default single element row
default:
- this._addRow(type, inputs_def, data);
+ this._addRow(type, input_def, data);
}
},
// add table row
- _addRow: function(field_type, inputs_def, data) {
+ _addRow: function(field_type, input_def, data) {
// get id
- var id = inputs_def.name;
+ var id = input_def.id;
// field wrapper
var field = null;
@@ -128,37 +153,42 @@
switch(field_type) {
// text input field
case 'text' :
- field = this._field_text(inputs_def, data);
+ field = this._field_text(input_def, data);
break;
// select field
case 'select' :
- field = this._field_select(inputs_def, data);
+ field = this._field_select(input_def, data);
break;
// radiobox field
case 'radiobutton' :
- field = this._field_radio(inputs_def, data);
+ field = this._field_radio(input_def, data);
break;
// dataset
case 'data':
- field = this._field_data(inputs_def, data);
+ field = this._field_data(input_def, data);
break;
// dataset column
case 'data_column':
- field = this._field_column(inputs_def, data);
+ field = this._field_column(input_def, data);
break;
// text area field
case 'textarea' :
- field = this._field_textarea(inputs_def, data);
+ field = this._field_textarea(input_def, data);
break;
// conditional select field
case 'conditional':
- field = this._field_conditional(inputs_def, data);
+ field = this._field_conditional(input_def, data);
+ break;
+
+ // hidden field
+ case 'hidden':
+ field = this._field_hidden(input_def, data);
break;
}
@@ -170,68 +200,37 @@
// set value
if (!data.get(id)) {
- data.set(id, inputs_def.value);
+ data.set(id, input_def.value);
}
field.value(data.get(id));
// add to field list
this.app.field_list[id] = field;
- // add to input definition into sequential list
- this.app.inputs_sequential[id] = inputs_def;
-
// combine field and info
var $input = $('<div/>');
$input.append(field.$el);
- if (inputs_def.help) {
- $input.append('<div class="ui-table-form-info">' + inputs_def.help + '</div>');
+ if (input_def.help) {
+ $input.append('<div class="ui-table-form-info">' + input_def.help + '</div>');
}
- // add row to table
- this.table.add('<span class="ui-table-form-title">' + inputs_def.label + '</span>', '25%');
+ // create table row
+ this.table.add('<span class="ui-table-form-title">' + input_def.label + '</span>', '25%');
this.table.add($input);
- // add to table
+ // append to table
this.table.append(id);
-
- // show/hide
- if (inputs_def.hide) {
- this.table.get(id).hide();
- }
- },
-
- // text input field
- _field_text : function(inputs_def, data) {
- var id = inputs_def.name;
- return new Ui.Input({
- id : 'field-' + id,
- value : data.get(id),
- onchange : function(value) {
- data.set(id, value);
- }
- });
- },
-
- // text area
- _field_textarea : function(inputs_def, data) {
- var id = inputs_def.name;
- return new Ui.Textarea({
- id : 'field-' + id,
- onchange : function() {
- data.set(id, field.value());
- }
- });
},
// conditional input field
- _field_conditional : function(inputs_def, data) {
+ _field_conditional : function(input_def, data) {
// link this
var self = this;
// configure options fields
var options = [];
- for (var i in inputs_def.test_param.options) {
- var option = inputs_def.test_param.options[i];
+ for (var i in input_def.test_param.options) {
+ var option = input_def.test_param.options[i];
options.push({
label: option[0],
value: option[1]
@@ -239,7 +238,7 @@
}
// select field
- var id = inputs_def.name;
+ var id = input_def.id;
return new Ui.Select.View({
id : 'field-' + id,
data : options,
@@ -249,19 +248,29 @@
data.set(id, value);
// check value in order to hide/show options
- for (var i in inputs_def.cases) {
+ for (var i in input_def.cases) {
// get case
- var case_def = inputs_def.cases[i];
+ var case_def = input_def.cases[i];
// identify subsection name
- var section_id = inputs_def.name + '_formsection_' + i;
-
+ var section_id = input_def.id + '-section-' + i;
+
// identify row
var section_row = self.table.get(section_id);
- // check
- if (case_def.value == value) {
- section_row.show();
+ // check if non-hidden elements exist
+ var nonhidden = false;
+ for (var j in case_def.inputs) {
+ var type = case_def.inputs[j].type;
+ if (type && type !== 'hidden') {
+ nonhidden = true;
+ break;
+ }
+ }
+
+ // show/hide sub form
+ if (case_def.value == value && nonhidden) {
+ section_row.fadeIn('fast');
} else {
section_row.hide();
}
@@ -271,12 +280,12 @@
},
// data input field
- _field_data : function(inputs_def, data) {
+ _field_data : function(input_def, data) {
// link this
var self = this;
// get element id
- var id = inputs_def.name;
+ var id = input_def.id;
// get datasets
var datasets = this.datasets.filterType();
@@ -299,11 +308,8 @@
// update value
data.set(id, value);
- // find referenced columns
- var column_list = _.where(self.app.inputs_sequential, {
- data_ref : id,
- type : 'data_column'
- });
+ // get referenced columns
+ var column_list = self.app.tree.findReferences(id);
// find selected dataset
var dataset = self.datasets.filter(value);
@@ -333,7 +339,7 @@
// update referenced columns
for (var i in column_list) {
- var column_field = self.app.field_list[column_list[i].name]
+ var column_field = self.app.field_list[column_list[i]]
if (column_field) {
column_field.update(columns);
column_field.value(column_field.first());
@@ -348,8 +354,8 @@
},
// column selection field
- _field_column : function (inputs_def, data) {
- var id = inputs_def.name;
+ _field_column : function (input_def, data) {
+ var id = input_def.id;
return new Ui.Select.View({
id : 'field-' + id,
value : data.get(id),
@@ -360,11 +366,11 @@
},
// select field
- _field_select : function (inputs_def, data) {
+ _field_select : function (input_def, data) {
// configure options fields
var options = [];
- for (var i in inputs_def.options) {
- var option = inputs_def.options[i];
+ for (var i in input_def.options) {
+ var option = input_def.options[i];
options.push({
label: option[0],
value: option[1]
@@ -373,12 +379,12 @@
// identify display type
var SelectClass = Ui.Select;
- if (inputs_def.display == 'checkboxes') {
+ if (input_def.display == 'checkboxes') {
SelectClass = Ui.Checkbox;
}
// select field
- var id = inputs_def.name;
+ var id = input_def.id;
return new SelectClass.View({
id : 'field-' + id,
data : options,
@@ -389,17 +395,49 @@
});
},
- // radio field
- _field_radio : function(inputs_def, data) {
- var id = inputs_def.name;
- return new Ui.RadioButton({
+ // text input field
+ _field_text : function(input_def, data) {
+ var id = input_def.id;
+ return new Ui.Input({
id : 'field-' + id,
- data : inputs_def.data,
value : data.get(id),
onchange : function(value) {
data.set(id, value);
}
});
+ },
+
+ // text area
+ _field_textarea : function(input_def, data) {
+ var id = input_def.id;
+ return new Ui.Textarea({
+ id : 'field-' + id,
+ onchange : function() {
+ data.set(id, field.value());
+ }
+ });
+ },
+
+ // radio field
+ _field_radio : function(input_def, data) {
+ var id = input_def.id;
+ return new Ui.RadioButton({
+ id : 'field-' + id,
+ data : input_def.data,
+ value : data.get(id),
+ onchange : function(value) {
+ data.set(id, value);
+ }
+ });
+ },
+
+ // hidden field
+ _field_hidden : function(input_def, data) {
+ var id = input_def.id;
+ return new Ui.Hidden({
+ id : 'field-' + id,
+ value : data.get(id)
+ });
}
});
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/mvc/tools/tools-tree.js
--- /dev/null
+++ b/static/scripts/mvc/tools/tools-tree.js
@@ -0,0 +1,135 @@
+// dependencies
+define([], function() {
+
+// tool form tree
+return Backbone.Model.extend({
+ // initialize
+ initialize: function(app) {
+ // link app
+ this.app = app;
+ },
+
+ // creates tree structure
+ refresh: function() {
+ // check if section is available
+ if (!this.app.section) {
+ return {};
+ }
+
+ // create dictionary
+ this.dict = {};
+
+ // create xml object
+ this.xml = $('<div/>');
+
+ // fill dictionary
+ this._iterate(this.app.section.$el, this.dict, this.xml);
+ },
+
+ // iterate
+ _iterate: function(parent, dict, xml) {
+ // get child nodes
+ var self = this;
+ var children = $(parent).children();
+ children.each(function() {
+ // get child element
+ var child = this;
+
+ // get id
+ var id = $(child).attr('id');
+
+ // create new branch
+ if ($(child).hasClass('form-row') || $(child).hasClass('tab-pane')) {
+ // create sub dictionary
+ dict[id] = {};
+
+ // add input element if it exists
+ var input = self.app.inputs_sequential[id];
+ if (input) {
+ dict[id] = {
+ input : input
+ }
+ }
+
+ // create xml element
+ var $el = $('<div id="' + id + '"/>');
+
+ // append xml
+ xml.append($el);
+
+ // fill sub dictionary
+ self._iterate(child, dict[id], $el);
+ } else {
+ self._iterate(child, dict, xml);
+ }
+ });
+ },
+
+ // find referenced elements
+ findReferences: function(identifier) {
+ // referenced elements
+ var referenced = [];
+
+ // link this
+ var self = this;
+
+ // iterate
+ function search (name, parent) {
+ // get child nodes
+ var children = $(parent).children();
+
+ // create sublist
+ var list = [];
+
+ // verify that hierachy level is referenced to identifier
+ children.each(function() {
+ // get child element
+ var child = this;
+
+ // get id
+ var id = $(child).attr('id');
+
+ // skip
+ if (id !== identifier) {
+ // get input element
+ var input = self.app.inputs_sequential[id];
+ if (input) {
+ // check for new reference definition
+ if (input.name == name) {
+ // stop iteration
+ return;
+ }
+
+ // check for referenced element
+ if (input.data_ref == name) {
+ list.push(id);
+ }
+ }
+ }
+ });
+
+ // merge temporary list with result
+ referenced = referenced.concat(list);
+
+ // continue iteration
+ children.each(function() {
+ search(identifier, this);
+ });
+ }
+
+ // get initial node
+ var node = this.xml.find('#' + identifier);
+ if (node.length > 0) {
+ // get parent input element
+ var input = self.app.inputs_sequential[identifier];
+ if (input) {
+ search(input.name, node.parent());
+ }
+ }
+
+ // return
+ return referenced;
+ }
+});
+
+});
\ No newline at end of file
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/mvc/ui/ui-misc.js
--- a/static/scripts/mvc/ui/ui-misc.js
+++ b/static/scripts/mvc/ui/ui-misc.js
@@ -409,6 +409,35 @@
}
});
+// plugin
+var Hidden = Backbone.View.extend({
+ // options
+ optionsDefault: {
+ value : ''
+ },
+
+ // initialize
+ initialize : function(options) {
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create new element
+ this.setElement(this._template(this.options));
+ },
+
+ // value
+ value : function (new_val) {
+ if (new_val !== undefined) {
+ this.$el.val(new_val);
+ }
+ return this.$el.val();
+ },
+
+ // element
+ _template: function(options) {
+ return '<hidden id="' + options.id + '" value="' + options.value + '"/>';
+ }
+});
// return
return {
@@ -426,6 +455,7 @@
Checkbox : Checkbox,
Searchbox : Searchbox,
Select : Select,
- Textarea : Textarea
+ Textarea : Textarea,
+ Hidden : Hidden
}
});
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/mvc/ui/ui-table.js
--- a/static/scripts/mvc/ui/ui-table.js
+++ b/static/scripts/mvc/ui/ui-table.js
@@ -17,7 +17,8 @@
onchange : null,
ondblclick : null,
onconfirm : null,
- cls : 'ui-table'
+ cls : 'ui-table',
+ cls_tr : ''
},
// events
@@ -43,7 +44,7 @@
this.setElement($el);
// initialize row
- this.row = $('<tr></tr>');
+ this.row = this._row();
},
// add header cell
@@ -156,13 +157,18 @@
}
// row
- this.row = $('<tr></tr>');
+ this.row = this._row();
// row count
this.row_count++;
this._refresh();
},
+ // create new row
+ _row: function() {
+ return $('<tr class="' + this.options.cls_tr + '"></tr>');
+ },
+
// onclick
_onclick: function(e) {
// get values
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/mvc/ui/ui-tabs.js
--- a/static/scripts/mvc/ui/ui-tabs.js
+++ b/static/scripts/mvc/ui/ui-tabs.js
@@ -132,7 +132,7 @@
del: function(id) {
// delete tab from dom
this.$el.find('#tab-' + id).remove();
- this.$el.find('#tab-content-' + id).remove();
+ this.$el.find('#' + id).remove();
// check if first tab has been deleted
if (this.first_tab == id) {
@@ -143,14 +143,17 @@
if (this.first_tab != null) {
this.show(this.first_tab);
}
+
+ // delete from list
+ if (this.list[id]) {
+ delete this.list[id];
+ }
},
// delete tab
delRemovable: function() {
for (var id in this.list) {
- if (this.list[id]) {
- this.del(id);
- }
+ this.del(id);
}
},
@@ -165,7 +168,7 @@
this.$el.find('.tab-element').removeClass('active');
this.$el.find('.tab-pane').removeClass('active');
this.$el.find('#tab-' + id).addClass('active');
- this.$el.find('#tab-content-' + id).addClass('active');
+ this.$el.find('#' + id).addClass('active');
}
},
@@ -201,6 +204,14 @@
return $el.html();
},
+ // retitle
+ retitle: function(new_title) {
+ var index = 0;
+ for (var id in this.list) {
+ this.title(id, ++index + ': ' + new_title);
+ }
+ },
+
// fill template
_template: function(options) {
return '<div class="ui-tabs tabbable tabs-left">' +
@@ -224,8 +235,8 @@
// fill template tab
_template_tab: function(options) {
var tmpl = '<li id="tab-' + options.id + '" class="tab-element">' +
- '<a id="tab-title-link-' + options.id + '" title="" href="#tab-content-' + options.id + '" data-original-title="">' +
- '<span id="tab-title-text-' + options.id + '">' + options.title + '</span>';
+ '<a id="tab-title-link-' + options.id + '" title="" href="#' + options.id + '" data-original-title="">' +
+ '<span id="tab-title-text-' + options.id + '" class="tab-title-text">' + options.title + '</span>';
if (options.ondel) {
tmpl += '<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>';
@@ -239,7 +250,7 @@
// fill template tab content
_template_tab_content: function(options) {
- return '<div id="tab-content-' + options.id + '" class="tab-pane"/>';
+ return '<div id="' + options.id + '" class="tab-pane"/>';
}
});
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 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(["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-datasets","mvc/tools/tools-section"],function(f,j,h,a,e,c,g,i){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){this.field_list={};this.inputs_sequential={};var k=this;this.model.fetch({error:function(l){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:"<b>"+k.model.get("name")+"</b> "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.section=new i.View(k,{inputs:k.model.get("inputs")});k.portlet.append(k.section.$el)}})}});return{View:b}});
\ No newline at end of file
+define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,k,i,a,f,d,h,j,c){var e=Backbone.Model.extend({initialize:function(l){this.url=galaxy_config.root+"api/tools/"+l.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(m){var l=this;this.options=m;this.model=new e({id:m.id});this.tree=new c(this);this.field_list={};this.inputs_sequential={};this.data=new Backbone.Model();this.datasets=new h({success:function(){l._initializeToolForm()}})},_initializeToolForm:function(){var l=this;this.model.fetch({error:function(m){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){l.inputs=l.model.get("inputs");l.portlet=new g.View({icon:"fa-wrench",title:"<b>"+l.model.get("name")+"</b> "+l.model.get("description"),buttons:{execute:new k.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){console.log(l.tree.create(l))}})}});l.message=new k.Message();l.portlet.append(l.message.$el);$(l.main_el).append(l.portlet.$el);if(l.options.help!=""){$(l.main_el).append(d.help(l.options.help))}if(l.options.citations){$(l.main_el).append(d.citations());var m=new i.ToolCitationCollection();m.tool_id=l.options.id;var n=new a.CitationListView({collection:m});n.render();m.fetch()}l.setElement(l.portlet.content());l.section=new j.View(l,{inputs:l.model.get("inputs")});l.portlet.append(l.section.$el);l.refresh()}})},refresh:function(){this.tree.refresh();for(var l in this.field_list){this.field_list[l].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")}});return{View:b}});
\ No newline at end of file
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(b,d,a){var c=Backbone.View.extend({initialize:function(f,e){this.app=f;this.inputs=e.inputs;this.datasets=f.datasets;this.table=new b.View(e);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();var e=new Backbone.Model();for(var f in this.inputs){this._add(this.inputs[f],e)}for(var f in this.app.field_list){this.app.field_list[f].trigger("change")}},_add:function(f,k){var e=this;var j=f.type;switch(j){case"conditional":f.label=f.test_param.label;f.name=f.test_param.name;this._addRow("conditional",f,k);for(var h in f.cases){var l=new c(this.app,{inputs:f.cases[h].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(l.$el);this.table.append(f.name+"_formsection_"+h)}break;case"repeat":var g=new a.View({title_new:"Add Group",onnew:function(){var m=new c(e.app,{inputs:f.inputs,cls:"ui-table-plain"});var i=f.name+"_formsection_"+g.size();g.add({id:i,title:"Repeat",$el:m.$el,ondel:function(){g.del(i)}});g.show(i)}});this.table.add(f.title);this.table.add(g.$el);this.table.append(f.name);break;default:this._addRow(j,f,k)}},_addRow:function(h,e,f){var j=e.name;var g=null;switch(h){case"text":g=this._field_text(e,f);break;case"select":g=this._field_select(e,f);break;case"radiobutton":g=this._field_radio(e,f);break;case"data":g=this._field_data(e,f);break;case"data_column":g=this._field_column(e,f);break;case"textarea":g=this._field_textarea(e,f);break;case"conditional":g=this._field_conditional(e,f);break}if(!g){console.debug("tools-form::_addRow() : Unmatched field type ("+h+").");return}if(!f.get(j)){f.set(j,e.value)}g.value(f.get(j));this.app.field_list[j]=g;this.app.inputs_sequential[j]=e;var i=$("<div/>");i.append(g.$el);if(e.help){i.append('<div class="ui-table-form-info">'+e.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+e.label+"</span>","25%");this.table.add(i);this.table.append(j);if(e.hide){this.table.get(j).hide()}},_field_text:function(e,f){var g=e.name;return new d.Input({id:"field-"+g,value:f.get(g),onchange:function(h){f.set(g,h)}})},_field_textarea:function(e,f){var g=e.name;return new d.Textarea({id:"field-"+g,onchange:function(){f.set(g,field.value())}})},_field_conditional:function(g,k){var e=this;var f=[];for(var h in g.test_param.options){var j=g.test_param.options[h];f.push({label:j[0],value:j[1]})}var l=g.name;return new d.Select.View({id:"field-"+l,data:f,value:k.get(l),onchange:function(q){k.set(l,q);for(var p in g.cases){var n=g.cases[p];var o=g.name+"_formsection_"+p;var m=e.table.get(o);if(n.value==q){m.show()}else{m.hide()}}}})},_field_data:function(g,k){var e=this;var l=g.name;var j=this.datasets.filterType();var f=[];for(var h in j){f.push({label:j[h].get("name"),value:j[h].get("id")})}return new d.Select.View({id:"field-"+l,data:f,value:f[0].value,onchange:function(r){k.set(l,r);var n=_.where(e.app.inputs_sequential,{data_ref:l,type:"data_column"});var t=e.datasets.filter(r);if(t&&n.length>0){console.debug("tool-form::field_data() - Selected dataset "+r+".");var s=t.get("metadata_column_types");if(!s){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+r+".")}var q=[];for(var p in s){q.push({label:"Column: "+(parseInt(p)+1)+" ["+s[p]+"]",value:p})}for(var o in n){var m=e.app.field_list[n[o].name];if(m){m.update(q);m.value(m.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+r+".")}}})},_field_column:function(e,f){var g=e.name;return new d.Select.View({id:"field-"+g,value:f.get(g),onchange:function(h){f.set(g,h)}})},_field_select:function(f,k){var e=[];for(var g in f.options){var h=f.options[g];e.push({label:h[0],value:h[1]})}var j=d.Select;if(f.display=="checkboxes"){j=d.Checkbox}var l=f.name;return new j.View({id:"field-"+l,data:e,value:k.get(l),onchange:function(i){k.set(l,i)}})},_field_radio:function(e,f){var g=e.name;return new d.RadioButton({id:"field-"+g,data:e.data,value:f.get(g),onchange:function(h){f.set(g,h)}})}});return{View:c}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(c,b,e,a){var d=Backbone.View.extend({initialize:function(g,f){this.app=g;this.inputs=f.inputs;this.datasets=g.datasets;this.data=g.data;f.cls_tr="form-row";this.table=new b.View(f);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var f in this.inputs){this._add(this.inputs[f],this.data)}},_add:function(n,h){var o=this;var k=jQuery.extend(true,{},n);k.id=c.uuid();this.app.inputs_sequential[k.id]=k;var l=k.type;switch(l){case"conditional":k.label=k.test_param.label;k.value=k.test_param.value;this._addRow("conditional",k,h);for(var j in k.cases){var g=k.id+"-section-"+j;var f=new d(this.app,{inputs:k.cases[j].inputs,cls:"ui-table-plain"});this.table.add("");this.table.add(f.$el);this.table.append(g)}break;case"repeat":var m=new a.View({title_new:"Add "+k.title,onnew:function(){var i=k.id+"-section-"+c.uuid();var p=new d(o.app,{inputs:k.inputs,cls:"ui-table-plain"});m.add({id:i,title:k.title,$el:p.$el,ondel:function(){m.del(i);m.retitle(k.title);o.app.refresh()}});m.retitle(k.title);m.show(i);o.app.refresh()}});this.table.add("");this.table.add(m.$el);this.table.append(k.id);break;default:this._addRow(l,k,h)}},_addRow:function(i,f,g){var k=f.id;var h=null;switch(i){case"text":h=this._field_text(f,g);break;case"select":h=this._field_select(f,g);break;case"radiobutton":h=this._field_radio(f,g);break;case"data":h=this._field_data(f,g);break;case"data_column":h=this._field_column(f,g);break;case"textarea":h=this._field_textarea(f,g);break;case"conditional":h=this._field_conditional(f,g);break;case"hidden":h=this._field_hidden(f,g);break}if(!h){console.debug("tools-form::_addRow() : Unmatched field type ("+i+").");return}if(!g.get(k)){g.set(k,f.value)}h.value(g.get(k));this.app.field_list[k]=h;var j=$("<div/>");j.append(h.$el);if(f.help){j.append('<div class="ui-table-form-info">'+f.help+"</div>")}this.table.add('<span class="ui-table-form-title">'+f.label+"</span>","25%");this.table.add(j);this.table.append(k)},_field_conditional:function(f,l){var g=this;var h=[];for(var j in f.test_param.options){var k=f.test_param.options[j];h.push({label:k[0],value:k[1]})}var m=f.id;return new e.Select.View({id:"field-"+m,data:h,value:l.get(m),onchange:function(u){l.set(m,u);for(var s in f.cases){var o=f.cases[s];var r=f.id+"-section-"+s;var n=g.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(f,l){var g=this;var m=f.id;var k=this.datasets.filterType();var h=[];for(var j in k){h.push({label:k[j].get("name"),value:k[j].get("id")})}return new e.Select.View({id:"field-"+m,data:h,value:h[0].value,onchange:function(s){l.set(m,s);var o=g.app.tree.findReferences(m);var u=g.datasets.filter(s);if(u&&o.length>0){console.debug("tool-form::field_data() - Selected dataset "+s+".");var t=u.get("metadata_column_types");if(!t){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+s+".")}var r=[];for(var q in t){r.push({label:"Column: "+(parseInt(q)+1)+" ["+t[q]+"]",value:q})}for(var p in o){var n=g.app.field_list[o[p]];if(n){n.update(r);n.value(n.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+s+".")}}})},_field_column:function(f,g){var h=f.id;return new e.Select.View({id:"field-"+h,value:g.get(h),onchange:function(i){g.set(h,i)}})},_field_select:function(f,l){var g=[];for(var h in f.options){var j=f.options[h];g.push({label:j[0],value:j[1]})}var k=e.Select;if(f.display=="checkboxes"){k=e.Checkbox}var m=f.id;return new k.View({id:"field-"+m,data:g,value:l.get(m),onchange:function(i){l.set(m,i)}})},_field_text:function(f,g){var h=f.id;return new e.Input({id:"field-"+h,value:g.get(h),onchange:function(i){g.set(h,i)}})},_field_textarea:function(f,g){var h=f.id;return new e.Textarea({id:"field-"+h,onchange:function(){g.set(h,field.value())}})},_field_radio:function(f,g){var h=f.id;return new e.RadioButton({id:"field-"+h,data:f.data,value:g.get(h),onchange:function(i){g.set(h,i)}})},_field_hidden:function(f,g){var h=f.id;return new e.Hidden({id:"field-"+h,value:g.get(h)})}});return{View:d}});
\ No newline at end of file
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/packed/mvc/tools/tools-tree.js
--- /dev/null
+++ b/static/scripts/packed/mvc/tools/tools-tree.js
@@ -0,0 +1,1 @@
+define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){if(!this.app.section){return{}}this.dict={};this.xml=$("<div/>");this._iterate(this.app.section.$el,this.dict,this.xml)},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("form-row")||$(i).hasClass("tab-pane")){e[h]={};var f=a.app.inputs_sequential[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})},findReferences:function(c){var f=[];var b=this;function d(g,i){var h=$(i).children();var j=[];h.each(function(){var m=this;var l=$(m).attr("id");if(l!==c){var k=b.app.inputs_sequential[l];if(k){if(k.name==g){return}if(k.data_ref==g){j.push(l)}}}});f=f.concat(j);h.each(function(){d(c,this)})}var e=this.xml.find("#"+c);if(e.length>0){var a=b.app.inputs_sequential[c];if(a){d(a.name,e.parent())}}return f}})});
\ No newline at end of file
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/packed/mvc/ui/ui-misc.js
--- a/static/scripts/packed/mvc/ui/ui-misc.js
+++ b/static/scripts/packed/mvc/ui/ui-misc.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(l,b,e,m,p,n){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var k=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$el.html(q)},_template:function(q){return'<label class="ui-label '+q.cls+'">'+q.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r='<button id="'+q.id+'" type="submit" style="float: '+q.floating+';" type="button" class="ui-button '+q.cls+'">';if(q.icon){r+='<i class="icon fa '+q.icon+'"></i> '}r+=q.title+"</button>";return r}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick);$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="ui-button-icon '+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",q.onclick)},_template:function(q){return'<div><a href="javascript:void(0)" class="ui-anchor '+q.cls+'">'+q.title+"</a></div>"}});var o=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=l.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=l.merge(r,this.optionsDefault);if(r.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(r.message);this.$el.fadeIn();if(!r.persistent){var q=this;window.setTimeout(function(){if(q.$el.is(":visible")){q.$el.fadeOut()}else{q.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var q=this;this.$el.on("input",function(){if(q.options.onchange){q.options.onchange(q.$el.val())}})},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'" rows="5"></textarea>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:j,Label:k,Message:o,Modal:n,RadioButton:m,Checkbox:e,Searchbox:a,Select:b,Textarea:i}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-checkbox","mvc/ui/ui-radiobutton","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(l,b,e,m,q,n){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var k=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$el.html(r)},_template:function(r){return'<label class="ui-label '+r.cls+'">'+r.title+"</label>"},value:function(){return options.title}});var c=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){return'<div><span class="fa '+r.icon+'" class="ui-icon"/> '+r.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s='<button id="'+r.id+'" type="submit" style="float: '+r.floating+';" type="button" class="ui-button '+r.cls+'">';if(r.icon){s+='<i class="icon fa '+r.icon+'"></i> '}s+=r.title+"</button>";return s}});var h=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick);$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="ui-button-icon '+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",r.onclick)},_template:function(r){return'<div><a href="javascript:void(0)" class="ui-anchor '+r.cls+'">'+r.title+"</a></div>"}});var o=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement("<div></div>")},update:function(s){this.options=l.merge(s,this.optionsDefault);if(s.message!=""){this.$el.html(this._template(this.options));this.$el.find(".alert").append(s.message);this.$el.fadeIn();if(!s.persistent){var r=this;window.setTimeout(function(){if(r.$el.is(":visible")){r.$el.fadeOut()}else{r.$el.hide()}},3000)}}else{this.$el.fadeOut()}},_template:function(r){return'<div class="ui-message alert alert-'+r.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));var r=this;if(this.options.onclick){this.$el.on("submit",function(u){var t=r.$el.find("#search");r.options.onclick(t.val())})}},_template:function(r){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+r.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var j=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$el.on("input",function(){if(r.options.onchange){r.options.onchange(r.$el.val())}})},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:""},initialize:function(s){this.options=l.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$el.on("input",function(){if(r.options.onchange){r.options.onchange(r.$el.val())}})},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'" rows="5"></textarea>'}});var p=Backbone.View.extend({optionsDefault:{value:""},initialize:function(r){this.options=l.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<hidden id="'+r.id+'" value="'+r.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:q,Icon:c,Image:d,Input:j,Label:k,Message:o,Modal:n,RadioButton:m,Checkbox:e,Searchbox:a,Select:b,Textarea:i,Hidden:p}});
\ No newline at end of file
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/packed/mvc/ui/ui-table.js
--- a/static/scripts/packed/mvc/ui/ui-table.js
+++ b/static/scripts/packed/mvc/ui/ui-table.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table"},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);var d=$(this._template(this.options));this.$thead=d.find("thead");this.$tbody=d.find("tbody");this.$tmessage=d.find("tmessage");this.setElement(d);this.row=$("<tr></tr>")},addHeader:function(c){var d=$("<th></th>");d.append(c);this.row.append(d)},appendHeader:function(){this.$thead.append(this.row);this.row=$("<tr></tr>")},add:function(c,d,f){var e=$("<td></td>");if(d){e.css("width",d)}if(f){e.css("text-align",f)}e.append(c);this.row.append(e)},append:function(c){this._commit(c)},prepend:function(c){this._commit(c,true)},get:function(c){return this.$el.find("#"+c)},del:function(d){var c=this.$tbody.find("#"+d);if(c.length>0){c.remove();this.row_count--;this._refresh()}},delAll:function(){this.$tbody.empty();this.row_count=0;this._refresh()},value:function(c){this.before=this.$tbody.find(".current").attr("id");if(c!==undefined){this.$tbody.find("tr").removeClass("current");if(c){this.$tbody.find("#"+c).addClass("current")}}var d=this.$tbody.find(".current").attr("id");if(d===undefined){return null}else{if(d!=this.before&&this.options.onchange){this.options.onchange(c)}return d}},size:function(){return this.$tbody.find("tr").length},_commit:function(d,c){this.del(d);this.row.attr("id",d);if(c){this.$tbody.prepend(this.row)}else{this.$tbody.append(this.row)}this.row=$("<tr></tr>");this.row_count++;this._refresh()},_onclick:function(f){var c=this.value();var d=$(f.target).closest("tr").attr("id");if(d!=""){if(d&&c!=d){if(this.options.onconfirm){this.options.onconfirm(d)}else{this.value(d)}}}},_ondblclick:function(d){var c=this.value();if(c&&this.options.ondblclick){this.options.ondblclick(c)}},_refresh:function(){if(this.row_count==0){this.$tmessage.show()}else{this.$tmessage.hide()}},_template:function(c){return'<div><table class="'+c.cls+'"><thead></thead><tbody></tbody></table><tmessage>'+c.content+"</tmessage><div>"}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);var d=$(this._template(this.options));this.$thead=d.find("thead");this.$tbody=d.find("tbody");this.$tmessage=d.find("tmessage");this.setElement(d);this.row=this._row()},addHeader:function(c){var d=$("<th></th>");d.append(c);this.row.append(d)},appendHeader:function(){this.$thead.append(this.row);this.row=$("<tr></tr>")},add:function(c,d,f){var e=$("<td></td>");if(d){e.css("width",d)}if(f){e.css("text-align",f)}e.append(c);this.row.append(e)},append:function(c){this._commit(c)},prepend:function(c){this._commit(c,true)},get:function(c){return this.$el.find("#"+c)},del:function(d){var c=this.$tbody.find("#"+d);if(c.length>0){c.remove();this.row_count--;this._refresh()}},delAll:function(){this.$tbody.empty();this.row_count=0;this._refresh()},value:function(c){this.before=this.$tbody.find(".current").attr("id");if(c!==undefined){this.$tbody.find("tr").removeClass("current");if(c){this.$tbody.find("#"+c).addClass("current")}}var d=this.$tbody.find(".current").attr("id");if(d===undefined){return null}else{if(d!=this.before&&this.options.onchange){this.options.onchange(c)}return d}},size:function(){return this.$tbody.find("tr").length},_commit:function(d,c){this.del(d);this.row.attr("id",d);if(c){this.$tbody.prepend(this.row)}else{this.$tbody.append(this.row)}this.row=this._row();this.row_count++;this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(f){var c=this.value();var d=$(f.target).closest("tr").attr("id");if(d!=""){if(d&&c!=d){if(this.options.onconfirm){this.options.onconfirm(d)}else{this.value(d)}}}},_ondblclick:function(d){var c=this.value();if(c&&this.options.ondblclick){this.options.ondblclick(c)}},_refresh:function(){if(this.row_count==0){this.$tmessage.show()}else{this.$tmessage.hide()}},_template:function(c){return'<div><table class="'+c.cls+'"><thead></thead><tbody></tbody></table><tmessage>'+c.content+"</tmessage><div>"}});return{View:b}});
\ No newline at end of file
diff -r 419ca68e073e942fe96b450ad6628949948f306b -r 8d307a592c729ffe5e20aed1f33a56ec6aca0ee9 static/scripts/packed/mvc/ui/ui-tabs.js
--- a/static/scripts/packed/mvc/ui/ui-tabs.js
+++ b/static/scripts/packed/mvc/ui/ui-tabs.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.visible=false;this.$nav=null;this.$content=null;this.first_tab=null;this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},size:function(){return _.size(this.list)},add:function(f){var e=this;var h=f.id;var g=$(this._template_tab(f));var d=$(this._template_tab_content(f));this.list[h]=f.ondel?true:false;if(this.options.onnew){this.$nav.find("#new-tab").before(g)}else{this.$nav.append(g)}d.append(f.$el);this.$content.append(d);if(_.size(this.list)==1){g.addClass("active");d.addClass("active");this.first_tab=h}if(f.ondel){var c=g.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el});c.on("click",function(){c.tooltip("destroy");e.$el.find(".tooltip").remove();f.ondel();return false})}g.on("click",function(i){i.preventDefault();if(f.onclick){f.onclick()}else{e.show(h)}})},del:function(c){this.$el.find("#tab-"+c).remove();this.$el.find("#tab-content-"+c).remove();if(this.first_tab==c){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var c in this.list){if(this.list[c]){this.del(c)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.$el.find(".tab-element").removeClass("active");this.$el.find(".tab-pane").removeClass("active");this.$el.find("#tab-"+c).addClass("active");this.$el.find("#tab-content-"+c).addClass("active")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.$el.find("#tab-title-text-"+e);if(d){c.html(d)}return c.html()},_template:function(c){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="tab-'+d.id+'" class="tab-element"><a id="tab-title-link-'+d.id+'" title="" href="#tab-content-'+d.id+'" data-original-title=""><span id="tab-title-text-'+d.id+'">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-content-'+c.id+'" class="tab-pane"/>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.visible=false;this.$nav=null;this.$content=null;this.first_tab=null;this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},size:function(){return _.size(this.list)},add:function(f){var e=this;var h=f.id;var g=$(this._template_tab(f));var d=$(this._template_tab_content(f));this.list[h]=f.ondel?true:false;if(this.options.onnew){this.$nav.find("#new-tab").before(g)}else{this.$nav.append(g)}d.append(f.$el);this.$content.append(d);if(_.size(this.list)==1){g.addClass("active");d.addClass("active");this.first_tab=h}if(f.ondel){var c=g.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el});c.on("click",function(){c.tooltip("destroy");e.$el.find(".tooltip").remove();f.ondel();return false})}g.on("click",function(i){i.preventDefault();if(f.onclick){f.onclick()}else{e.show(h)}})},del:function(c){this.$el.find("#tab-"+c).remove();this.$el.find("#"+c).remove();if(this.first_tab==c){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}if(this.list[c]){delete this.list[c]}},delRemovable:function(){for(var c in this.list){this.del(c)}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.$el.find(".tab-element").removeClass("active");this.$el.find(".tab-pane").removeClass("active");this.$el.find("#tab-"+c).addClass("active");this.$el.find("#"+c).addClass("active")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.$el.find("#tab-title-text-"+e);if(d){c.html(d)}return c.html()},retitle:function(d){var c=0;for(var e in this.list){this.title(e,++c+": "+d)}},_template:function(c){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="tab-'+d.id+'" class="tab-element"><a id="tab-title-link-'+d.id+'" title="" href="#'+d.id+'" data-original-title=""><span id="tab-title-text-'+d.id+'" class="tab-title-text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="'+c.id+'" class="tab-pane"/>'}});return{View:b}});
\ No newline at end of file
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commit/galaxy-central: natefoo: Update tag latest_2014.08.11 for changeset a6cfe95047eb
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dbdef1812eb9/
Changeset: dbdef1812eb9
Branch: stable
User: natefoo
Date: 2014-08-28 20:00:16
Summary: Update tag latest_2014.08.11 for changeset a6cfe95047eb
Affected #: 1 file
diff -r a6cfe95047eb7e85e3d0aa54e8bcce0ce449c880 -r dbdef1812eb95042343a74611946d97a9d895b6e .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,4 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
-109b170188e97fbfc2c998ec174aff9546dd1bd8 latest_2014.08.11
+a6cfe95047eb7e85e3d0aa54e8bcce0ce449c880 latest_2014.08.11
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Fix: remove 'jquery.event.drag.js' from base_panels.mako; Paired collection creator: allow single/multiple pairs to be re-ordered by drag and drop
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/419ca68e073e/
Changeset: 419ca68e073e
User: carlfeberhard
Date: 2014-08-28 18:19:16
Summary: Fix: remove 'jquery.event.drag.js' from base_panels.mako; Paired collection creator: allow single/multiple pairs to be re-ordered by drag and drop
Affected #: 5 files
diff -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 -r 419ca68e073e942fe96b450ad6628949948f306b 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
@@ -27,11 +27,14 @@
className : 'dataset paired',
initialize : function( attributes ){
+ //console.debug( 'PairView.initialize:', attributes );
this.pair = attributes.pair || {};
},
render : function(){
- this.$el.attr( 'draggable', true )
+ this.$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">',
@@ -40,7 +43,51 @@
'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'
].join(''), { pair: this.pair }))
.addClass( 'flex-column-container' );
+
+//TODO: would be good to get the unpair-btn into this view - but haven't found a way with css
+
return this;
+ },
+
+ events : {
+ 'dragstart' : '_dragstart',
+ 'dragend' : '_dragend',
+ 'dragover' : '_sendToParent',
+ 'drop' : '_sendToParent'
+ },
+
+ /** dragging pairs for re-ordering */
+ _dragstart : function( ev ){
+ //console.debug( this, '_dragstartPair', ev );
+ ev.currentTarget.style.opacity = '0.4';
+ if( ev.originalEvent ){ ev = ev.originalEvent; }
+
+ ev.dataTransfer.effectAllowed = 'move';
+ ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.pair ) );
+
+ //ev.dataTransfer.setDragImage( null, 0, 0 );
+
+ // the canvas can be used to create the image
+ //ev.dataTransfer.setDragImage( canvasCrossHairs(), 25, 25 );
+
+ //console.debug( 'ev.dataTransfer:', ev.dataTransfer );
+ this.$el.parent().trigger( 'pair.dragstart', [ this ] );
+ },
+ /** dragging pairs for re-ordering */
+ _dragend : function( ev ){
+ //console.debug( this, '_dragendPair', ev );
+ ev.currentTarget.style.opacity = '1.0';
+ this.$el.parent().trigger( 'pair.dragend', [ this ] );
+ },
+
+ /** manually bubble up an event to the parent/container */
+ _sendToParent : function( ev ){
+ this.$el.parent().trigger( ev );
+ },
+
+ /** string rep */
+ toString : function(){
+ return 'PairView(' + this.pair.name + ')';
}
});
@@ -106,6 +153,9 @@
/** is the paired panel shown? */
this.pairedPanelHidden = false;
+ /** DOM elements currently being dragged */
+ this.$dragging = null;
+
this._dataSetUp();
this._setUpBehaviors();
@@ -929,8 +979,17 @@
'mousedown .flexible-partition-drag' : '_startPartitionDrag',
// paired
'click .paired-columns .dataset.paired' : 'selectPair',
+ 'click .paired-columns' : 'clearSelectedPaired',
'click .paired-columns .pair-name' : '_clickPairName',
'click .unpair-btn' : '_clickUnpair',
+ // paired - drop target
+ //'dragenter .paired-columns' : '_dragenterPairedColumns',
+ //'dragleave .paired-columns .column-datasets': '_dragleavePairedColumns',
+ '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',
// footer
'change .remove-extensions' : function( ev ){ this.toggleExtensions(); },
@@ -1226,9 +1285,15 @@
// ........................................................................ paired
/** select a pair when clicked */
selectPair : function( ev ){
+ ev.stopPropagation();
$( ev.currentTarget ).toggleClass( 'selected' );
},
+ /** deselect all pairs */
+ clearSelectedPaired : function( ev ){
+ this.$( '.paired-columns .dataset.selected' ).removeClass( 'selected' );
+ },
+
/** rename a pair when the pair name is clicked */
_clickPairName : function( ev ){
ev.stopPropagation();
@@ -1255,6 +1320,94 @@
this._unpair( this.paired[ pairIndex ] );
},
+ // ........................................................................ paired - drag and drop re-ordering
+ //_dragenterPairedColumns : function( ev ){
+ // console.debug( '_dragenterPairedColumns:', ev );
+ //},
+ //_dragleavePairedColumns : function( ev ){
+ // //console.debug( '_dragleavePairedColumns:', ev );
+ //},
+ /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */
+ _dragoverPairedColumns : function( ev ){
+ //console.debug( '_dragoverPairedColumns:', ev );
+ ev.preventDefault();
+
+ var $list = this.$( '.paired-columns .column-datasets' ),
+ offset = $list.offset();
+ //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY );
+ var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY );
+ //console.debug( ev.originalEvent.clientX - offset.left, ev.originalEvent.clientY - offset.top );
+
+ $( '.paired-drop-placeholder' ).remove();
+ var $placeholder = $( '<div class="paired-drop-placeholder"></div>')
+ if( !$nearest.size() ){
+ $list.append( $placeholder );
+ } else {
+ $nearest.before( $placeholder );
+ }
+ },
+ /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate.
+ * If the y is at the end of the list, return an empty jQuery object.
+ */
+ _getNearestPairedDatasetLi : function( y ){
+ var WIGGLE = 4,
+ lis = this.$( '.paired-columns .column-datasets li' ).toArray();
+//TODO: better way?
+ for( var i=0; i<lis.length; i++ ){
+ var $li = $( lis[i] ),
+ top = $li.offset().top,
+ halfHeight = Math.floor( $li.outerHeight() / 2 ) + WIGGLE;
+ if( top + halfHeight > y && top - halfHeight < y ){
+ //console.debug( y, top + halfHeight, top - halfHeight )
+ return $li;
+ }
+ }
+ return $();
+ },
+ /** drop (dragged/selected PairViews) onto the list, re-ordering both the DOM and the internal array of pairs */
+ _dropPairedColumns : function( ev ){
+ // both required for firefox
+ ev.preventDefault();
+ ev.dataTransfer.dropEffect = 'move';
+
+ var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY );
+ if( $nearest.size() ){
+ this.$dragging.insertBefore( $nearest );
+
+ } else {
+ // no nearest before - insert after last element (unpair button)
+ this.$dragging.insertAfter( this.$( '.paired-columns .unpair-btn' ).last() );
+ }
+ // resync the creator's list of paired based on the new DOM order
+ this._syncPairsToDom();
+ return false;
+ },
+ /** resync the creator's list of paired based on the DOM order of pairs */
+ _syncPairsToDom : function(){
+ var newPaired = [];
+//TODO: ugh
+ this.$( '.paired-columns .dataset.paired' ).each( function(){
+ newPaired.push( $( this ).data( 'pair' ) );
+ });
+ //console.debug( newPaired );
+ this.paired = newPaired;
+ this._renderPaired();
+ },
+ /** drag communication with pair sub-views: dragstart */
+ _pairDragstart : function( ev, pair ){
+ //console.debug( '_pairDragstart', ev, pair )
+ // auto select the pair causing the event and move all selected
+ pair.$el.addClass( 'selected' );
+ var $selected = this.$( '.paired-columns .dataset.selected' );
+ this.$dragging = $selected;
+ },
+ /** drag communication with pair sub-views: dragend - remove the placeholder */
+ _pairDragend : function( ev, pair ){
+ //console.debug( '_pairDragend', ev, pair )
+ $( '.paired-drop-placeholder' ).remove();
+ this.$dragging = null;
+ },
+
// ........................................................................ footer
toggleExtensions : function( force ){
var creator = this;
diff -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 -r 419ca68e073e942fe96b450ad6628949948f306b 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).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}});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._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 .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","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){$(h.currentTarget).toggleClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(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($(i.currentTarget).index()/2);this._unpair(this.paired[h])},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_getName:function(){return _.escape(this.$(".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" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',d("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',d("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" 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","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'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. 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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 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','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
diff -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 -r 419ca68e073e942fe96b450ad6628949948f306b static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1870,6 +1870,8 @@
.collection-creator .flexible-partition .column-header .remove-extensions-link{display:none}
.collection-creator .paired-columns{height:0;border:1px solid lightgrey;border-width:1px 0 1px 0;margin-bottom:8px}.collection-creator .paired-columns .column-datasets{width:100%;overflow:auto}
.collection-creator .paired-columns .unpair-btn{float:right;margin-top:-32px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator .paired-columns .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE}
+.collection-creator .paired-columns .paired-drop-placeholder{width:60px;height:3px;margin:2px 0px 0px 14px;background:black}.collection-creator .paired-columns .paired-drop-placeholder:before{float:left;font-size:120%;margin:-9px 0 0 -8px;font-family:FontAwesome;content:'\f0da'}
+.collection-creator .paired-columns .paired-drop-placeholder:last-child{margin-bottom:8px}
.collection-creator .paired-columns .empty-message{text-align:center}
.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .attributes .remove-extensions-prompt{line-height:32px}.collection-creator .footer .attributes .remove-extensions-prompt .remove-extensions{display:inline-block;width:24px;height:24px}
.collection-creator .footer .attributes .collection-name-prompt{margin:5px 4px 0 0}
diff -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 -r 419ca68e073e942fe96b450ad6628949948f306b static/style/src/less/ui/paired-collection-creator.less
--- a/static/style/src/less/ui/paired-collection-creator.less
+++ b/static/style/src/less/ui/paired-collection-creator.less
@@ -374,6 +374,22 @@
background: #DEDEDE;
}
}
+ .paired-drop-placeholder {
+ width : 60px;
+ height : 3px;
+ margin : 2px 0px 0px 14px;
+ background : black;
+ &:before {
+ float: left;
+ font-size: 120%;
+ margin: -9px 0px 0px -8px;
+ font-family: FontAwesome;
+ content: '\f0da';
+ }
+ &:last-child {
+ margin-bottom: 8px;
+ }
+ }
.empty-message {
text-align: center;
}
diff -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 -r 419ca68e073e942fe96b450ad6628949948f306b templates/base/base_panels.mako
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -106,7 +106,6 @@
## Scripts can be loaded later since they progressively add features to
## the panels, but do not change layout
${h.js(
- 'libs/jquery/jquery.event.drag',
'libs/jquery/jquery.event.hover',
'libs/jquery/jquery.form',
'libs/jquery/jquery.rating',
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c46f6814f3a8/
Changeset: c46f6814f3a8
User: natefoo
Date: 2014-08-28 17:35:36
Summary: Merge stable.
Affected #: 4 files
diff -r 36bf58f838476e738d2efa893b1318c6f7bde97f -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,4 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
-7e22f35798522100ff03e1fdd4eced962b292360 latest_2014.08.11
+109b170188e97fbfc2c998ec174aff9546dd1bd8 latest_2014.08.11
diff -r 36bf58f838476e738d2efa893b1318c6f7bde97f -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 lib/galaxy/dataset_collections/structure.py
--- a/lib/galaxy/dataset_collections/structure.py
+++ b/lib/galaxy/dataset_collections/structure.py
@@ -35,9 +35,9 @@
return self._walk_collections( dict_map( lambda hdca: hdca.collection, hdca_dict ) )
def _walk_collections( self, collection_dict ):
- for ( identifier, substructure ) in self.children:
+ for index, ( identifier, substructure ) in enumerate( self.children ):
def element( collection ):
- return collection[ identifier ]
+ return collection[ index ]
if substructure.is_leaf:
yield dict_map( element, collection_dict )
diff -r 36bf58f838476e738d2efa893b1318c6f7bde97f -r c46f6814f3a8323dafb92cfc89fd6f615d021bf1 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -27,7 +27,7 @@
from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField
from galaxy.web.form_builder import build_select_field, HistoryField, PasswordField, WorkflowField, WorkflowMappingField
from galaxy.workflow.modules import module_factory, WorkflowModuleInjector, MissingToolException
-from galaxy.model.orm import eagerload, eagerload_all, desc
+from galaxy.model.orm import eagerload, eagerload_all, desc, not_
from galaxy.security.validate_user_input import validate_publicname
from galaxy.util.sanitize_html import sanitize_html
from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
@@ -2683,7 +2683,7 @@
item = self.get_item( trans, id )
if item:
# Only update slug if slug is not already in use.
- if trans.sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() == 0:
+ if trans.sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug ).count() == 0:
item.slug = new_slug
trans.sa_session.flush()
@@ -2718,7 +2718,9 @@
# add integer to end.
new_slug = slug_base
count = 1
- while sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() != 0:
+ # Ensure unique across model class and user and don't include this item
+ # in the check in case it has previously been assigned a valid slug.
+ while sa_session.query( item.__class__ ).filter( item.__class__.user == item.user, item.__class__.slug == new_slug, item.__class__.id != item.id).count() != 0:
# Slug taken; choose a new slug based on count. This approach can
# handle numerous items with the same name gracefully.
new_slug = '%s-%i' % ( slug_base, count )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: library permissions API - check whether payload is present in the kwd and throw exception if it is not, also bugfix
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/36bf58f83847/
Changeset: 36bf58f83847
User: martenson
Date: 2014-08-28 17:01:32
Summary: library permissions API - check whether payload is present in the kwd and throw exception if it is not, also bugfix
Affected #: 1 file
diff -r b7d851e1c64c79f0c75e4a746e127a5c3832129d -r 36bf58f838476e738d2efa893b1318c6f7bde97f lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -386,8 +386,11 @@
action = kwd.get( 'action', None )
if action is None:
- return self.set_permissions_old( trans, library )
- # raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' )
+ payload = kwd.get( 'payload', None )
+ if payload is not None:
+ return self.set_permissions_old( trans, library, payload, **kwd )
+ else:
+ raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' )
elif action == 'remove_restrictions':
trans.app.security_agent.make_library_public( library )
if not trans.app.security_agent.library_is_public( library ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: no need to expose the method through API anymore
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b7d851e1c64c/
Changeset: b7d851e1c64c
User: martenson
Date: 2014-08-28 16:57:30
Summary: no need to expose the method through API anymore
Affected #: 1 file
diff -r 44ed4f6424270850a56c44f85be4a8ad37a2879a -r b7d851e1c64c79f0c75e4a746e127a5c3832129d lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -342,6 +342,7 @@
raise exceptions.InternalServerError( 'Error loading from the database.' + str(e))
return role
+
@expose_api
def set_permissions( self, trans, encoded_library_id, **kwd ):
"""
@@ -485,7 +486,7 @@
return dict( access_library_role_list=access_library_role_list, modify_library_role_list=modify_library_role_list, manage_library_role_list=manage_library_role_list, add_library_item_role_list=add_library_item_role_list )
- @expose_api
+
def set_permissions_old( self, trans, library, payload, **kwd ):
"""
*** old implementation for backward compatibility ***
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: allowing backward compatibility on setting library permissions API as per John's suggestion
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/44ed4f642427/
Changeset: 44ed4f642427
User: martenson
Date: 2014-08-28 16:54:13
Summary: allowing backward compatibility on setting library permissions API as per John's suggestion
Affected #: 2 files
diff -r 03e9b373ec42cf727a5d735876f55ab442f73310 -r 44ed4f6424270850a56c44f85be4a8ad37a2879a lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -385,7 +385,8 @@
action = kwd.get( 'action', None )
if action is None:
- raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' )
+ return self.set_permissions_old( trans, library )
+ # raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' )
elif action == 'remove_restrictions':
trans.app.security_agent.make_library_public( library )
if not trans.app.security_agent.library_is_public( library ):
@@ -397,7 +398,6 @@
invalid_access_roles_names = []
for role_id in new_access_roles_ids:
role = self._load_role( trans, role_id )
- # Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library, is_library_access=True )
if role in valid_roles:
valid_access_roles.append( role )
@@ -411,7 +411,6 @@
invalid_add_roles_names = []
for role_id in new_add_roles_ids:
role = self._load_role( trans, role_id )
- # Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library )
if role in valid_roles:
valid_add_roles.append( role )
@@ -425,7 +424,6 @@
invalid_manage_roles_names = []
for role_id in new_manage_roles_ids:
role = self._load_role( trans, role_id )
- # Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library )
if role in valid_roles:
valid_manage_roles.append( role )
@@ -439,7 +437,6 @@
invalid_modify_roles_names = []
for role_id in new_modify_roles_ids:
role = self._load_role( trans, role_id )
- # Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library )
if role in valid_roles:
valid_modify_roles.append( role )
@@ -454,6 +451,9 @@
permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } )
trans.app.security_agent.set_all_library_permissions( trans, library, permissions )
+ trans.sa_session.refresh( library )
+ # Copy the permissions to the root folder
+ trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder )
else:
raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.'
'Allowed values are: "remove_restrictions", set_permissions"' )
@@ -485,4 +485,26 @@
return dict( access_library_role_list=access_library_role_list, modify_library_role_list=modify_library_role_list, manage_library_role_list=manage_library_role_list, add_library_item_role_list=add_library_item_role_list )
+ @expose_api
+ def set_permissions_old( self, trans, library, payload, **kwd ):
+ """
+ *** old implementation for backward compatibility ***
+ POST /api/libraries/{encoded_library_id}/permissions
+ Updates the library permissions.
+ """
+ params = galaxy.util.Params( payload )
+ permissions = {}
+ for k, v in trans.app.model.Library.permitted_actions.items():
+ role_params = params.get( k + '_in', [] )
+ in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( trans.security.decode_id( x ) ) for x in galaxy.util.listify( role_params ) ]
+ permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
+ trans.app.security_agent.set_all_library_permissions( trans, library, permissions )
+ trans.sa_session.refresh( library )
+ # Copy the permissions to the root folder
+ trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder )
+ message = "Permissions updated for library '%s'." % library.name
+
+ item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )
+ return item
+
diff -r 03e9b373ec42cf727a5d735876f55ab442f73310 -r 44ed4f6424270850a56c44f85be4a8ad37a2879a lib/galaxy/webapps/galaxy/api/permissions.py
--- a/lib/galaxy/webapps/galaxy/api/permissions.py
+++ /dev/null
@@ -1,52 +0,0 @@
-"""
-API operations on the permissions of a library.
-"""
-import logging, os, string, shutil, urllib, re, socket
-from cgi import escape, FieldStorage
-import galaxy.util
-from galaxy import util, datatypes, jobs, web
-from galaxy.web.base.controller import *
-from galaxy.util.sanitize_html import sanitize_html
-from galaxy.model.orm import *
-
-log = logging.getLogger( __name__ )
-
-
-class PermissionsController( BaseAPIController ):
-
- # Method not ideally named
- @web.expose_api
- def create( self, trans, library_id, payload, **kwd ):
- """
- POST /api/libraries/{encoded_library_id}/permissions
- Updates the library permissions.
- """
- if not trans.user_is_admin():
- trans.response.status = 403
- return "You are not authorized to update library permissions."
-
- params = galaxy.util.Params( payload )
- try:
- decoded_library_id = trans.security.decode_id( library_id )
- except TypeError:
- trans.response.status = 400
- return "Malformed library id ( %s ) specified, unable to decode." % str( library_id )
-
- try:
- library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id )
- except:
- library = None
-
- permissions = {}
- for k, v in trans.app.model.Library.permitted_actions.items():
- role_params = params.get( k + '_in', [] )
- in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( trans.security.decode_id( x ) ) for x in galaxy.util.listify( role_params ) ]
- permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
- trans.app.security_agent.set_all_library_permissions( trans, library, permissions )
- trans.sa_session.refresh( library )
- # Copy the permissions to the root folder
- trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder )
- message = "Permissions updated for library '%s'." % library.name
-
- item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )
- return item
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: nsoranzo: Fix SQlite datatype sniffing for old sqlite3. Remove unused imports.
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/03e9b373ec42/
Changeset: 03e9b373ec42
User: nsoranzo
Date: 2014-08-28 15:09:10
Summary: Fix SQlite datatype sniffing for old sqlite3. Remove unused imports.
Bug fixed: when uploading a gzipped FASTQ file through upload1 tool on a
machine with SQLite 3.3.6, it was detected as 'sqlite' datatype and not
decompressed.
In fact, the sqlite3 command 'pragma schema_version' on any file returns
without error on this SQLite version.
Affected #: 1 file
diff -r 59b6f95bfdd51bcf6c7da17fb9ad2fd4ad7f3133 -r 03e9b373ec42cf727a5d735876f55ab442f73310 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -11,10 +11,7 @@
import struct
import subprocess
import tempfile
-import zipfile
-import sqlite3
-from urllib import urlencode, quote_plus
from galaxy import eggs
eggs.require( "bx-python" )
@@ -22,7 +19,6 @@
from galaxy.datatypes.metadata import MetadataElement,ListParameter,DictParameter
from galaxy.datatypes import metadata
-from galaxy.datatypes.sniff import *
import dataproviders
log = logging.getLogger(__name__)
@@ -580,14 +576,12 @@
except Exception, exc:
pass
- # Connects and runs a query that should work on any real database
- # If the file is not sqlite, an exception will be thrown and the sniffer will return false
def sniff( self, filename ):
+ # The first 16 bytes of any SQLite3 database file is 'SQLite format 3\0', and the file is binary. For details
+ # about the format, see http://www.sqlite.org/fileformat.html
try:
- conn = sqlite3.connect(filename)
- schema_version=conn.cursor().execute("pragma schema_version").fetchone()
- conn.close()
- if schema_version is not None:
+ header = open(filename).read(16)
+ if binascii.b2a_hex(header) == binascii.hexlify('SQLite format 3\0'):
return True
return False
except:
@@ -622,5 +616,5 @@
return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings )
-Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite)
+Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: nsoranzo: Fix SQlite datatype sniffing for old sqlite3. Remove unused imports.
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a6cfe95047eb/
Changeset: a6cfe95047eb
Branch: stable
User: nsoranzo
Date: 2014-08-28 15:09:10
Summary: Fix SQlite datatype sniffing for old sqlite3. Remove unused imports.
Bug fixed: when uploading a gzipped FASTQ file through upload1 tool on a
machine with SQLite 3.3.6, it was detected as 'sqlite' datatype and not
decompressed.
In fact, the sqlite3 command 'pragma schema_version' on any file returns
without error on this SQLite version.
Affected #: 1 file
diff -r 57d1b775b0ca8515fd1fc71cee91e5db41cd9ec1 -r a6cfe95047eb7e85e3d0aa54e8bcce0ce449c880 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -11,10 +11,7 @@
import struct
import subprocess
import tempfile
-import zipfile
-import sqlite3
-from urllib import urlencode, quote_plus
from galaxy import eggs
eggs.require( "bx-python" )
@@ -22,7 +19,6 @@
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes import metadata
-from galaxy.datatypes.sniff import *
import dataproviders
log = logging.getLogger(__name__)
@@ -552,14 +548,12 @@
class SQlite ( Binary ):
file_ext = "sqlite"
- # Connects and runs a query that should work on any real database
- # If the file is not sqlite, an exception will be thrown and the sniffer will return false
def sniff( self, filename ):
+ # The first 16 bytes of any SQLite3 database file is 'SQLite format 3\0', and the file is binary. For details
+ # about the format, see http://www.sqlite.org/fileformat.html
try:
- conn = sqlite3.connect(filename)
- schema_version=conn.cursor().execute("pragma schema_version").fetchone()
- conn.close()
- if schema_version is not None:
+ header = open(filename).read(16)
+ if binascii.b2a_hex(header) == binascii.hexlify('SQLite format 3\0'):
return True
return False
except:
@@ -586,5 +580,5 @@
return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings )
-Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite)
+Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Fix to df2a994: remove debuggging statements
by commits-noreply＠bitbucket.org 28 Aug '14
by commits-noreply＠bitbucket.org 28 Aug '14
28 Aug '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/59b6f95bfdd5/
Changeset: 59b6f95bfdd5
User: carlfeberhard
Date: 2014-08-28 15:49:00
Summary: Fix to df2a994: remove debuggging statements
Affected #: 1 file
diff -r df2a99433e850b7ba594994fece91fdc87c24181 -r 59b6f95bfdd51bcf6c7da17fb9ad2fd4ad7f3133 lib/galaxy/visualization/registry.py
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -229,14 +229,14 @@
Run a visualization's data_source tests to find out if
it can be applied to the target_object.
"""
- log.debug( 'is_object_applicable( self, trans, %s, %s )', target_object, data_source_tests )
+ #log.debug( 'is_object_applicable( self, trans, %s, %s )', target_object, data_source_tests )
for test in data_source_tests:
test_type = test[ 'type' ]
result_type = test[ 'result_type' ]
test_result = test[ 'result' ]
test_fn = test[ 'fn' ]
- log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
- test_type, result_type, test_result, test_fn )
+ #log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
+ # test_type, result_type, test_result, test_fn )
if test_type == 'isinstance':
# parse test_result based on result_type (curr: only datatype has to do this)
@@ -254,7 +254,7 @@
#NOTE: tests are OR'd, if any test passes - the visualization can be applied
if test_fn( target_object, test_result ):
- log.debug( '\t test passed' )
+ #log.debug( '\t test passed' )
return True
return False
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