1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/447e69511115/
Changeset: 447e69511115
User: guerler
Date: 2014-12-02 17:05:53+00:00
Summary: Merge
Affected #: 0 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/98a6cad91c3a/
Changeset: 98a6cad91c3a
Branch: next-stable
User: guerler
Date: 2014-12-01 04:40:38+00:00
Summary: ToolForm: Add drill down element
Affected #: 25 files
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -211,7 +211,7 @@
this.tree.matchModel(new_model, function(input_id, node) {
var input = self.input_list[input_id];
if (input && input.options) {
- if (JSON.stringify(input.options) != JSON.stringify(node.options)) {
+ if (!_.isEqual(input.options, node.options)) {
// backup new options
input.options = node.options;
@@ -223,6 +223,9 @@
case 'data':
new_options = input.options;
break;
+ case 'drill_down':
+ new_options = input.options;
+ break;
default:
for (var i in node.options) {
var opt = node.options[i];
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -337,7 +337,12 @@
input_def.searchable = true;
field = this._fieldSelect(input_def);
break;
-
+
+ // drill down field
+ case 'drill_down':
+ field = this._fieldDrilldown(input_def);
+ break;
+
// field not found
default:
// flag
@@ -417,6 +422,20 @@
});
},
+ /** Drill down options field
+ */
+ _fieldDrilldown : function (input_def) {
+ var self = this;
+ return new Ui.Drilldown.View({
+ id : 'field-' + input_def.id,
+ data : input_def.options,
+ display : input_def.display,
+ onchange : function() {
+ self.app.refresh();
+ }
+ });
+ },
+
/** Text input field
*/
_fieldText : function(input_def) {
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/tools/tools-select-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-select-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js
@@ -90,6 +90,11 @@
// update options
this.update(options.data);
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// refresh view
this.refresh();
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-drilldown.js
--- /dev/null
+++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js
@@ -0,0 +1,102 @@
+// dependencies
+define(['utils/utils', 'mvc/ui/ui-options'], function(Utils, Options) {
+
+/**
+ * This class creates/wraps a drill down element.
+ */
+var View = Options.Base.extend({
+ // initialize
+ initialize: function(options) {
+ this.display = options.display || 'checkbox';
+ options.multiple = (this.display == 'checkbox');
+ Options.Base.prototype.initialize.call(this, options);
+ },
+
+ /** Template for input field
+ */
+ _templateOption: function(name, value, selected) {
+ return '<div>' +
+ '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' +
+ Utils.sanitize(name) +
+ '<div/>';
+ },
+
+ /** Template to create options tree
+ */
+ _templateOptions: function(data, current) {
+ // link this
+ var self = this;
+
+ // attach show/hide event
+ function attachEvents($button, $subgroup) {
+ function setVisibility (visible) {
+ if (visible) {
+ $subgroup.fadeIn('fast')
+ $button.removeClass('toggle-expand');
+ $button.addClass('toggle');
+ $button.is_expanded = true;
+ } else {
+ $subgroup.hide();
+ $button.removeClass('toggle');
+ $button.addClass('toggle-expand');
+ $button.is_expanded = false;
+ }
+ };
+ $button.on('click', function() {
+ setVisibility(!$button.is_expanded);
+ });
+ }
+
+ // recursive function which iterates through options
+ function iterate ($tmpl, data) {
+ for (i in data) {
+ // current option level in hierarchy
+ var level = data[i];
+
+ // check for options
+ var has_options = level.options.length > 0;
+
+ // build template
+ var $group = $('<div/>');
+ if (has_options) {
+ // create button and add flag
+ var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');
+
+ // add expand group
+ var $buttongroup = $('<div/>');
+ $buttongroup.append($button);
+ $buttongroup.append(self._templateOption(level.name, level.value));
+ $group.append($buttongroup);
+
+ // add sub group
+ var $subgroup = $('<div style="display: none; margin-left: 25px;"/>');
+ iterate($subgroup, level.options);
+ $group.append($subgroup);
+
+ // attach click event to collapse/expand hierarchy
+ attachEvents($button, $subgroup);
+ } else {
+ $group.append(self._templateOption(level.name, level.value));
+ }
+ $tmpl.append($group);
+ }
+ }
+
+ // iterate through options and create dom
+ var $tmpl = $('<div/>');
+ iterate($tmpl, data);
+ return $tmpl;
+ },
+
+ /** Template for drill down view
+ */
+ _template: function(options) {
+ return '<div class="ui-options drilldown-container" id="' + options.id + '"/>';
+ }
+});
+
+return {
+ View: View
+}
+
+});
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-misc.js
--- a/client/galaxy/scripts/mvc/ui/ui-misc.js
+++ b/client/galaxy/scripts/mvc/ui/ui-misc.js
@@ -1,6 +1,6 @@
// dependencies
-define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'],
- function(Utils, Select, Slider, Options, ButtonMenu, Modal) {
+define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'],
+ function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) {
/**
* This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.
@@ -339,7 +339,6 @@
var Input = Backbone.View.extend({
// options
optionsDefault: {
- value : '',
type : 'text',
placeholder : '',
disabled : false,
@@ -356,6 +355,11 @@
// create new element
this.setElement(this._template(this.options));
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// disable input field
if (this.options.disabled) {
this.$el.prop('disabled', true);
@@ -395,18 +399,18 @@
// plugin
var Hidden = Backbone.View.extend({
- // options
- optionsDefault: {
- value : ''
- },
-
// initialize
initialize : function(options) {
// configure options
- this.options = Utils.merge(options, this.optionsDefault);
+ this.options = options;
// create new element
this.setElement(this._template(this.options));
+
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
},
// value
@@ -441,6 +445,7 @@
Searchbox : Searchbox,
Select : Select,
Hidden : Hidden,
- Slider : Slider
+ Slider : Slider,
+ Drilldown : Drilldown
}
});
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-options.js
--- a/client/galaxy/scripts/mvc/ui/ui-options.js
+++ b/client/galaxy/scripts/mvc/ui/ui-options.js
@@ -2,7 +2,7 @@
define(['utils/utils'], function(Utils) {
/** Base class for options based ui elements **/
-var OptionsBase = Backbone.View.extend({
+var Base = Backbone.View.extend({
// initialize
initialize: function(options) {
// options
@@ -56,16 +56,19 @@
var current = this._getValue();
// remove all options
- this.$el.find('.ui-option').remove();
+ this.$options.empty();
- // add new options
- for (var key in options) {
- // load option template
- var $option = $(this._templateOption(options[key]));
- $option.addClass('ui-option');
-
- // append to dom
- this.$options.append($option);
+ // add new options using single option templates or full template
+ if (this._templateOptions) {
+ // rebuild options using full template
+ this.$options.append(this._templateOptions(options));
+ } else {
+ // rebuild options using single option templates
+ for (var key in options) {
+ var $option = $(this._templateOption(options[key]));
+ $option.addClass('ui-option');
+ this.$options.append($option);
+ }
}
// add change events
@@ -82,6 +85,29 @@
this.value(current);
},
+ /** Return/Set current value
+ */
+ value: function (new_value) {
+ // check if its an array
+ if (typeof new_value === 'string') {
+ new_value = [new_value];
+ }
+
+ // set new value
+ if (new_value !== undefined) {
+ // reset selection
+ this.$el.find('input').prop('checked', false);
+
+ // update to new selection
+ for (var i in new_value) {
+ this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true);
+ };
+ }
+
+ // get and return value
+ return this._getValue();
+ },
+
/** Check if selected value exists (or any if multiple)
*/
exists: function(value) {
@@ -198,46 +224,6 @@
*/
_messageHide: function() {
this.$message.hide();
- }
-});
-
-/** Radio button field **/
-var Radio = {};
-Radio.View = OptionsBase.extend({
- // initialize
- initialize: function(options) {
- OptionsBase.prototype.initialize.call(this, options);
- },
-
- /** Return/Set current value
- */
- value: function (new_val) {
- // check if its an array
- if (typeof new_val === 'string') {
- new_val = [new_val];
- }
-
- // set new value
- if (new_val !== undefined) {
- // reset selection
- this.$el.find('input').prop('checked', false);
-
- // update to new selection
- for (var i in new_val) {
- this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true);
- };
- }
-
- // get and return value
- return this._getValue();
- },
-
- /** Template for options
- */
- _templateOption: function(pair) {
- return '<div>' +
- '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
- '</div>';
},
/** Main template function
@@ -247,16 +233,33 @@
}
});
+/** Radio button field **/
+var Radio = {};
+Radio.View = Base.extend({
+ // initialize
+ initialize: function(options) {
+ Base.prototype.initialize.call(this, options);
+ },
+
+ /** Template for a single option
+ */
+ _templateOption: function(pair) {
+ return '<div>' +
+ '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
+ '</div>';
+ }
+});
+
/** Checkbox options field **/
var Checkbox = {};
-Checkbox.View = Radio.View.extend({
+Checkbox.View = Base.extend({
// initialize
initialize: function(options) {
options.multiple = true;
- Radio.View.prototype.initialize.call(this, options);
+ Base.prototype.initialize.call(this, options);
},
- /** Template for options
+ /** Template for a single option
*/
_templateOption: function(pair) {
return '<div>' +
@@ -267,27 +270,27 @@
/** Radio button options field styled as classic buttons **/
var RadioButton = {};
-RadioButton.View = OptionsBase.extend({
+RadioButton.View = Base.extend({
// initialize
initialize: function(options) {
- OptionsBase.prototype.initialize.call(this, options);
+ Base.prototype.initialize.call(this, options);
},
/** Return/Set current value
*/
- value: function (new_val) {
+ value: function (new_value) {
// set new value
- if (new_val !== undefined) {
+ if (new_value !== undefined) {
this.$el.find('input').prop('checked', false);
this.$el.find('label').removeClass('active');
- this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active');
+ this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active');
}
// get and return value
return this._getValue();
},
- /** Template for options
+ /** Template for a single option
*/
_templateOption: function(pair) {
var tmpl = '<label class="btn btn-default">';
@@ -307,6 +310,7 @@
});
return {
+ Base : Base,
Radio : Radio,
RadioButton : RadioButton,
Checkbox : Checkbox
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-select-default.js
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -41,6 +41,11 @@
// refresh
this.update(this.options.data);
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// show/hide
if (!this.options.visible) {
this.hide();
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 client/galaxy/scripts/mvc/ui/ui-slider.js
--- a/client/galaxy/scripts/mvc/ui/ui-slider.js
+++ b/client/galaxy/scripts/mvc/ui/ui-slider.js
@@ -5,7 +5,6 @@
var View = Backbone.View.extend({
// options
optionsDefault: {
- value : '',
min : null,
max : null,
step : null,
@@ -49,6 +48,11 @@
// link text input field
this.$text = this.$el.find('#text');
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// add text field event
this.$text.on('change', function () {
self.value($(this).val());
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1606,19 +1606,20 @@
"""
return self.filtered.keys()
- def to_dict( self, trans, view='collection', value_mapper=None ):
+ def to_dict( self, trans, view='collection', value_mapper=None, context={} ):
# skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
d = ToolParameter.to_dict( self, trans )
options = []
try:
- options = self.get_options( trans, {} )
+ options = self.get_options( trans, context )
except KeyError:
# will sometimes error if self.is_dynamic and self.filtered
# bc we dont/cant fill out other_values above ({})
pass
-
d[ 'options' ] = options
+ d[ 'display' ] = self.display
+ d[ 'is_dynamic' ] = self.is_dynamic
return d
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -211,7 +211,7 @@
this.tree.matchModel(new_model, function(input_id, node) {
var input = self.input_list[input_id];
if (input && input.options) {
- if (JSON.stringify(input.options) != JSON.stringify(node.options)) {
+ if (!_.isEqual(input.options, node.options)) {
// backup new options
input.options = node.options;
@@ -223,6 +223,9 @@
case 'data':
new_options = input.options;
break;
+ case 'drill_down':
+ new_options = input.options;
+ break;
default:
for (var i in node.options) {
var opt = node.options[i];
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -337,7 +337,12 @@
input_def.searchable = true;
field = this._fieldSelect(input_def);
break;
-
+
+ // drill down field
+ case 'drill_down':
+ field = this._fieldDrilldown(input_def);
+ break;
+
// field not found
default:
// flag
@@ -417,6 +422,20 @@
});
},
+ /** Drill down options field
+ */
+ _fieldDrilldown : function (input_def) {
+ var self = this;
+ return new Ui.Drilldown.View({
+ id : 'field-' + input_def.id,
+ data : input_def.options,
+ display : input_def.display,
+ onchange : function() {
+ self.app.refresh();
+ }
+ });
+ },
+
/** Text input field
*/
_fieldText : function(input_def) {
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/tools/tools-select-content.js
--- a/static/scripts/mvc/tools/tools-select-content.js
+++ b/static/scripts/mvc/tools/tools-select-content.js
@@ -90,6 +90,11 @@
// update options
this.update(options.data);
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// refresh view
this.refresh();
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-drilldown.js
--- /dev/null
+++ b/static/scripts/mvc/ui/ui-drilldown.js
@@ -0,0 +1,102 @@
+// dependencies
+define(['utils/utils', 'mvc/ui/ui-options'], function(Utils, Options) {
+
+/**
+ * This class creates/wraps a drill down element.
+ */
+var View = Options.Base.extend({
+ // initialize
+ initialize: function(options) {
+ this.display = options.display || 'checkbox';
+ options.multiple = (this.display == 'checkbox');
+ Options.Base.prototype.initialize.call(this, options);
+ },
+
+ /** Template for input field
+ */
+ _templateOption: function(name, value, selected) {
+ return '<div>' +
+ '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' +
+ Utils.sanitize(name) +
+ '<div/>';
+ },
+
+ /** Template to create options tree
+ */
+ _templateOptions: function(data, current) {
+ // link this
+ var self = this;
+
+ // attach show/hide event
+ function attachEvents($button, $subgroup) {
+ function setVisibility (visible) {
+ if (visible) {
+ $subgroup.fadeIn('fast')
+ $button.removeClass('toggle-expand');
+ $button.addClass('toggle');
+ $button.is_expanded = true;
+ } else {
+ $subgroup.hide();
+ $button.removeClass('toggle');
+ $button.addClass('toggle-expand');
+ $button.is_expanded = false;
+ }
+ };
+ $button.on('click', function() {
+ setVisibility(!$button.is_expanded);
+ });
+ }
+
+ // recursive function which iterates through options
+ function iterate ($tmpl, data) {
+ for (i in data) {
+ // current option level in hierarchy
+ var level = data[i];
+
+ // check for options
+ var has_options = level.options.length > 0;
+
+ // build template
+ var $group = $('<div/>');
+ if (has_options) {
+ // create button and add flag
+ var $button = $('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');
+
+ // add expand group
+ var $buttongroup = $('<div/>');
+ $buttongroup.append($button);
+ $buttongroup.append(self._templateOption(level.name, level.value));
+ $group.append($buttongroup);
+
+ // add sub group
+ var $subgroup = $('<div style="display: none; margin-left: 25px;"/>');
+ iterate($subgroup, level.options);
+ $group.append($subgroup);
+
+ // attach click event to collapse/expand hierarchy
+ attachEvents($button, $subgroup);
+ } else {
+ $group.append(self._templateOption(level.name, level.value));
+ }
+ $tmpl.append($group);
+ }
+ }
+
+ // iterate through options and create dom
+ var $tmpl = $('<div/>');
+ iterate($tmpl, data);
+ return $tmpl;
+ },
+
+ /** Template for drill down view
+ */
+ _template: function(options) {
+ return '<div class="ui-options drilldown-container" id="' + options.id + '"/>';
+ }
+});
+
+return {
+ View: View
+}
+
+});
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-misc.js
--- a/static/scripts/mvc/ui/ui-misc.js
+++ b/static/scripts/mvc/ui/ui-misc.js
@@ -1,6 +1,6 @@
// dependencies
-define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'],
- function(Utils, Select, Slider, Options, ButtonMenu, Modal) {
+define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-drilldown', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'],
+ function(Utils, Select, Slider, Options, Drilldown, ButtonMenu, Modal) {
/**
* This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.
@@ -339,7 +339,6 @@
var Input = Backbone.View.extend({
// options
optionsDefault: {
- value : '',
type : 'text',
placeholder : '',
disabled : false,
@@ -356,6 +355,11 @@
// create new element
this.setElement(this._template(this.options));
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// disable input field
if (this.options.disabled) {
this.$el.prop('disabled', true);
@@ -395,18 +399,18 @@
// plugin
var Hidden = Backbone.View.extend({
- // options
- optionsDefault: {
- value : ''
- },
-
// initialize
initialize : function(options) {
// configure options
- this.options = Utils.merge(options, this.optionsDefault);
+ this.options = options;
// create new element
this.setElement(this._template(this.options));
+
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
},
// value
@@ -441,6 +445,7 @@
Searchbox : Searchbox,
Select : Select,
Hidden : Hidden,
- Slider : Slider
+ Slider : Slider,
+ Drilldown : Drilldown
}
});
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-options.js
--- a/static/scripts/mvc/ui/ui-options.js
+++ b/static/scripts/mvc/ui/ui-options.js
@@ -2,7 +2,7 @@
define(['utils/utils'], function(Utils) {
/** Base class for options based ui elements **/
-var OptionsBase = Backbone.View.extend({
+var Base = Backbone.View.extend({
// initialize
initialize: function(options) {
// options
@@ -56,16 +56,19 @@
var current = this._getValue();
// remove all options
- this.$el.find('.ui-option').remove();
+ this.$options.empty();
- // add new options
- for (var key in options) {
- // load option template
- var $option = $(this._templateOption(options[key]));
- $option.addClass('ui-option');
-
- // append to dom
- this.$options.append($option);
+ // add new options using single option templates or full template
+ if (this._templateOptions) {
+ // rebuild options using full template
+ this.$options.append(this._templateOptions(options));
+ } else {
+ // rebuild options using single option templates
+ for (var key in options) {
+ var $option = $(this._templateOption(options[key]));
+ $option.addClass('ui-option');
+ this.$options.append($option);
+ }
}
// add change events
@@ -82,6 +85,29 @@
this.value(current);
},
+ /** Return/Set current value
+ */
+ value: function (new_value) {
+ // check if its an array
+ if (typeof new_value === 'string') {
+ new_value = [new_value];
+ }
+
+ // set new value
+ if (new_value !== undefined) {
+ // reset selection
+ this.$el.find('input').prop('checked', false);
+
+ // update to new selection
+ for (var i in new_value) {
+ this.$el.find('input[value="' + new_value[i] + '"]').first().prop('checked', true);
+ };
+ }
+
+ // get and return value
+ return this._getValue();
+ },
+
/** Check if selected value exists (or any if multiple)
*/
exists: function(value) {
@@ -198,46 +224,6 @@
*/
_messageHide: function() {
this.$message.hide();
- }
-});
-
-/** Radio button field **/
-var Radio = {};
-Radio.View = OptionsBase.extend({
- // initialize
- initialize: function(options) {
- OptionsBase.prototype.initialize.call(this, options);
- },
-
- /** Return/Set current value
- */
- value: function (new_val) {
- // check if its an array
- if (typeof new_val === 'string') {
- new_val = [new_val];
- }
-
- // set new value
- if (new_val !== undefined) {
- // reset selection
- this.$el.find('input').prop('checked', false);
-
- // update to new selection
- for (var i in new_val) {
- this.$el.find('input[value="' + new_val[i] + '"]').prop('checked', true);
- };
- }
-
- // get and return value
- return this._getValue();
- },
-
- /** Template for options
- */
- _templateOption: function(pair) {
- return '<div>' +
- '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
- '</div>';
},
/** Main template function
@@ -247,16 +233,33 @@
}
});
+/** Radio button field **/
+var Radio = {};
+Radio.View = Base.extend({
+ // initialize
+ initialize: function(options) {
+ Base.prototype.initialize.call(this, options);
+ },
+
+ /** Template for a single option
+ */
+ _templateOption: function(pair) {
+ return '<div>' +
+ '<input type="radio" name="' + this.options.id + '" value="' + pair.value + '"/>' + pair.label + '<br>' +
+ '</div>';
+ }
+});
+
/** Checkbox options field **/
var Checkbox = {};
-Checkbox.View = Radio.View.extend({
+Checkbox.View = Base.extend({
// initialize
initialize: function(options) {
options.multiple = true;
- Radio.View.prototype.initialize.call(this, options);
+ Base.prototype.initialize.call(this, options);
},
- /** Template for options
+ /** Template for a single option
*/
_templateOption: function(pair) {
return '<div>' +
@@ -267,27 +270,27 @@
/** Radio button options field styled as classic buttons **/
var RadioButton = {};
-RadioButton.View = OptionsBase.extend({
+RadioButton.View = Base.extend({
// initialize
initialize: function(options) {
- OptionsBase.prototype.initialize.call(this, options);
+ Base.prototype.initialize.call(this, options);
},
/** Return/Set current value
*/
- value: function (new_val) {
+ value: function (new_value) {
// set new value
- if (new_val !== undefined) {
+ if (new_value !== undefined) {
this.$el.find('input').prop('checked', false);
this.$el.find('label').removeClass('active');
- this.$el.find('[value="' + new_val + '"]').prop('checked', true).closest('label').addClass('active');
+ this.$el.find('[value="' + new_value + '"]').prop('checked', true).closest('label').addClass('active');
}
// get and return value
return this._getValue();
},
- /** Template for options
+ /** Template for a single option
*/
_templateOption: function(pair) {
var tmpl = '<label class="btn btn-default">';
@@ -307,6 +310,7 @@
});
return {
+ Base : Base,
Radio : Radio,
RadioButton : RadioButton,
Checkbox : Checkbox
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-select-default.js
--- a/static/scripts/mvc/ui/ui-select-default.js
+++ b/static/scripts/mvc/ui/ui-select-default.js
@@ -41,6 +41,11 @@
// refresh
this.update(this.options.data);
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// show/hide
if (!this.options.visible) {
this.hide();
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/mvc/ui/ui-slider.js
--- a/static/scripts/mvc/ui/ui-slider.js
+++ b/static/scripts/mvc/ui/ui-slider.js
@@ -5,7 +5,6 @@
var View = Backbone.View.extend({
// options
optionsDefault: {
- value : '',
min : null,
max : null,
step : null,
@@ -49,6 +48,11 @@
// link text input field
this.$text = this.$el.find('#text');
+ // set initial value
+ if (this.options.value !== undefined) {
+ this.value(this.options.value);
+ }
+
// add text field event
this.$text.on('change', function () {
self.value($(this).val());
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(!_.isEqual(p.options,u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;case"drill_down":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/tools/tools-select-content.js
--- a/static/scripts/packed/mvc/tools/tools-select-content.js
+++ b/static/scripts/packed/mvc/tools/tools-select-content.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}});
\ No newline at end of file
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-drilldown.js
--- /dev/null
+++ b/static/scripts/packed/mvc/ui/ui-drilldown.js
@@ -0,0 +1,1 @@
+define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(g,h){var e=this;function f(l,m){function k(n){if(n){m.fadeIn("fast");l.removeClass("toggle-expand");l.addClass("toggle");l.is_expanded=true}else{m.hide();l.removeClass("toggle");l.addClass("toggle-expand");l.is_expanded=false}}l.on("click",function(){k(!l.is_expanded)})}function d(q,o){for(i in o){var r=o[i];var m=r.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var k=$("<div/>");k.append(n);k.append(e._templateOption(r.name,r.value));l.append(k);var p=$('<div style="display: none; margin-left: 25px;"/>');d(p,r.options);l.append(p);f(n,p)}else{l.append(e._templateOption(r.name,r.value))}q.append(l)}}var j=$("<div/>");d(j,g);return j},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}});
\ No newline at end of file
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-misc.js
--- a/static/scripts/packed/mvc/ui/ui-misc.js
+++ b/static/scripts/packed/mvc/ui/ui-misc.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,n,p,l){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(q){return'<img class="ui-image '+q.cls+'" src="'+q.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},title:function(q){this.$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=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:q.tooltip,placement:"bottom"})},_template:function(q){return'<div><span class="fa '+q.icon+'" class="ui-icon"/> '+q.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(q.onclick){q.onclick()}});$(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="'+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:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var q=this;$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick&&!q.disabled){r.onclick()}});$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(q){var r="";if(q.title){r="width: auto;"}var s='<div id="'+q.id+'" style="float: '+q.floating+"; "+r+'" class="'+q.cls+'">';if(q.title){s+='<div class="button"><i class="icon fa '+q.icon+'"/> <span class="title">'+q.title+"</span></div>"}else{s+='<i class="icon fa '+q.icon+'"/>'}s+="</div>";return s}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options));$(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 m=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement("<div></div>")},update:function(r){this.options=k.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.$el.fadeOut()}},_template:function(q){return'<div class="ui-message alert alert-'+q.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));var q=this;if(this.options.onclick){this.$el.on("submit",function(t){var s=q.$el.find("#search");q.options.onclick(s.val())})}},_template:function(q){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+q.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.disabled){this.$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.$el.val()},_template:function(q){if(q.area){return'<textarea id="'+q.id+'" class="ui-textarea '+q.cls+'"></textarea>'}else{return'<input id="'+q.id+'" type="'+q.type+'" value="'+q.value+'" placeholder="'+q.placeholder+'" class="ui-input '+q.cls+'">'}}});var o=Backbone.View.extend({optionsDefault:{value:""},initialize:function(q){this.options=k.merge(q,this.optionsDefault);this.setElement(this._template(this.options))},value:function(q){if(q!==undefined){this.$el.val(q)}return this.$el.val()},_template:function(q){return'<hidden id="'+q.id+'" value="'+q.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:p,Icon:c,Image:d,Input:i,Label:j,Message:m,Modal:l,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Searchbox:a,Select:b,Hidden:o,Slider:e}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-drilldown","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(k,b,e,o,l,q,m){var d=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},_template:function(r){return'<img class="ui-image '+r.cls+'" src="'+r.url+'"/>'}});var j=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options))},title:function(r){this.$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=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).tooltip({title:r.tooltip,placement:"bottom"})},_template:function(r){return'<div><span class="fa '+r.icon+'" class="ui-icon"/> '+r.title+"</div>"}});var g=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(this.el).on("click",function(){$(".tooltip").hide();if(r.onclick){r.onclick()}});$(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="'+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:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));this.$button=this.$el.find(".button");var r=this;$(this.el).on("click",function(){$(".tooltip").hide();if(s.onclick&&!r.disabled){s.onclick()}});$(this.el).tooltip({title:s.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled");this.disabled=true},enable:function(){this.$button.removeClass("disabled");this.disabled=false},_template:function(r){var s="";if(r.title){s="width: auto;"}var t='<div id="'+r.id+'" style="float: '+r.floating+"; "+s+'" class="'+r.cls+'">';if(r.title){t+='<div class="button"><i class="icon fa '+r.icon+'"/> <span class="title">'+r.title+"</span></div>"}else{t+='<i class="icon fa '+r.icon+'"/>'}t+="</div>";return t}});var f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement(this._template(this.options));$(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 n=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:false},initialize:function(r){this.options=k.merge(r,this.optionsDefault);this.setElement("<div></div>")},update:function(s){this.options=k.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.$el.fadeOut()}},_template:function(r){return'<div class="ui-message alert alert-'+r.status+'"/>'}});var a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));var r=this;if(this.options.onclick){this.$el.on("submit",function(u){var t=r.$el.find("#search");r.options.onclick(t.val())})}},_template:function(r){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+r.searchword+'"><button type="submit" class="btn search-btn"><i class="fa fa-search"></i></button></form></div>'}});var i=Backbone.View.extend({optionsDefault:{type:"text",placeholder:"",disabled:false,visible:true,cls:"",area:false},initialize:function(s){this.options=k.merge(s,this.optionsDefault);this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}if(this.options.disabled){this.$el.prop("disabled",true)}if(!this.options.visible){this.$el.hide()}var r=this;this.$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.$el.val()},_template:function(r){if(r.area){return'<textarea id="'+r.id+'" class="ui-textarea '+r.cls+'"></textarea>'}else{return'<input id="'+r.id+'" type="'+r.type+'" value="'+r.value+'" placeholder="'+r.placeholder+'" class="ui-input '+r.cls+'">'}}});var p=Backbone.View.extend({initialize:function(r){this.options=r;this.setElement(this._template(this.options));if(this.options.value!==undefined){this.value(this.options.value)}},value:function(r){if(r!==undefined){this.$el.val(r)}return this.$el.val()},_template:function(r){return'<hidden id="'+r.id+'" value="'+r.value+'"/>'}});return{Anchor:f,Button:g,ButtonIcon:h,ButtonMenu:q,Icon:c,Image:d,Input:i,Label:j,Message:n,Modal:m,RadioButton:o.RadioButton,Checkbox:o.Checkbox,Radio:o.Radio,Searchbox:a,Select:b,Hidden:p,Slider:e,Drilldown:l}});
\ No newline at end of file
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-options.js
--- a/static/scripts/packed/mvc/ui/ui-options.js
+++ b/static/scripts/packed/mvc/ui/ui-options.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find('input[value="'+f[g]+'"]').prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}});
\ No newline at end of file
+define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(typeof g==="string"){g=[g]}if(g!==undefined){this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}});
\ No newline at end of file
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-select-default.js
--- a/static/scripts/packed/mvc/ui/ui-select-default.js
+++ b/static/scripts/packed/mvc/ui/ui-select-default.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}});
\ No newline at end of file
diff -r 20e0db2511e555b9a168a96dee1ff75180aabbdf -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 static/scripts/packed/mvc/ui/ui-slider.js
--- a/static/scripts/packed/mvc/ui/ui-slider.js
+++ b/static/scripts/packed/mvc/ui/ui-slider.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");if(this.options.value!==undefined){this.value(this.options.value)}this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/8fefb0715524/
Changeset: 8fefb0715524
Branch: next-stable
User: guerler
Date: 2014-12-01 05:21:40+00:00
Summary: ToolForm: Fix select2 value selection
Affected #: 9 files
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 client/galaxy/scripts/mvc/ui/ui-drilldown.js
--- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js
+++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js
@@ -23,7 +23,7 @@
/** Template to create options tree
*/
- _templateOptions: function(data, current) {
+ _templateOptions: function(options) {
// link this
var self = this;
@@ -48,10 +48,10 @@
}
// recursive function which iterates through options
- function iterate ($tmpl, data) {
- for (i in data) {
+ function iterate ($tmpl, options) {
+ for (i in options) {
// current option level in hierarchy
- var level = data[i];
+ var level = options[i];
// check for options
var has_options = level.options.length > 0;
@@ -84,7 +84,7 @@
// iterate through options and create dom
var $tmpl = $('<div/>');
- iterate($tmpl, data);
+ iterate($tmpl, options);
return $tmpl;
},
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 client/galaxy/scripts/mvc/ui/ui-options.js
--- a/client/galaxy/scripts/mvc/ui/ui-options.js
+++ b/client/galaxy/scripts/mvc/ui/ui-options.js
@@ -7,7 +7,6 @@
initialize: function(options) {
// options
this.optionsDefault = {
- value : [],
visible : true,
data : [],
id : Utils.uuid(),
@@ -38,7 +37,7 @@
this.update(this.options.data);
// set initial value
- if (this.options.value) {
+ if (this.options.value !== undefined) {
this.value(this.options.value);
}
@@ -88,13 +87,13 @@
/** Return/Set current value
*/
value: function (new_value) {
- // check if its an array
- if (typeof new_value === 'string') {
- new_value = [new_value];
- }
-
- // set new value
+ // set new value if provided
if (new_value !== undefined) {
+ // check if its an array
+ if (!(new_value instanceof Array)) {
+ new_value = [new_value];
+ }
+
// reset selection
this.$el.find('input').prop('checked', false);
@@ -111,12 +110,14 @@
/** Check if selected value exists (or any if multiple)
*/
exists: function(value) {
- if (typeof value === 'string') {
- value = [value];
- }
- for (var i in value) {
- if (this.$el.find('input[value="' + value[i] + '"]').length > 0) {
- return true;
+ if (value !== undefined) {
+ if (!(value instanceof Array)) {
+ value = [value];
+ }
+ for (var i in value) {
+ if (this.$el.find('input[value="' + value[i] + '"]').length > 0) {
+ return true;
+ }
}
}
return false;
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 client/galaxy/scripts/mvc/ui/ui-select-default.js
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -75,6 +75,9 @@
value : function (new_value) {
if (new_value !== undefined) {
this.$select.val(new_value);
+ if (this.$select.select2) {
+ this.$select.select2('val', new_value);
+ }
}
return this.$select.val();
},
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/mvc/ui/ui-drilldown.js
--- a/static/scripts/mvc/ui/ui-drilldown.js
+++ b/static/scripts/mvc/ui/ui-drilldown.js
@@ -23,7 +23,7 @@
/** Template to create options tree
*/
- _templateOptions: function(data, current) {
+ _templateOptions: function(options) {
// link this
var self = this;
@@ -48,10 +48,10 @@
}
// recursive function which iterates through options
- function iterate ($tmpl, data) {
- for (i in data) {
+ function iterate ($tmpl, options) {
+ for (i in options) {
// current option level in hierarchy
- var level = data[i];
+ var level = options[i];
// check for options
var has_options = level.options.length > 0;
@@ -84,7 +84,7 @@
// iterate through options and create dom
var $tmpl = $('<div/>');
- iterate($tmpl, data);
+ iterate($tmpl, options);
return $tmpl;
},
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/mvc/ui/ui-options.js
--- a/static/scripts/mvc/ui/ui-options.js
+++ b/static/scripts/mvc/ui/ui-options.js
@@ -7,7 +7,6 @@
initialize: function(options) {
// options
this.optionsDefault = {
- value : [],
visible : true,
data : [],
id : Utils.uuid(),
@@ -38,7 +37,7 @@
this.update(this.options.data);
// set initial value
- if (this.options.value) {
+ if (this.options.value !== undefined) {
this.value(this.options.value);
}
@@ -88,13 +87,13 @@
/** Return/Set current value
*/
value: function (new_value) {
- // check if its an array
- if (typeof new_value === 'string') {
- new_value = [new_value];
- }
-
- // set new value
+ // set new value if provided
if (new_value !== undefined) {
+ // check if its an array
+ if (!(new_value instanceof Array)) {
+ new_value = [new_value];
+ }
+
// reset selection
this.$el.find('input').prop('checked', false);
@@ -111,12 +110,14 @@
/** Check if selected value exists (or any if multiple)
*/
exists: function(value) {
- if (typeof value === 'string') {
- value = [value];
- }
- for (var i in value) {
- if (this.$el.find('input[value="' + value[i] + '"]').length > 0) {
- return true;
+ if (value !== undefined) {
+ if (!(value instanceof Array)) {
+ value = [value];
+ }
+ for (var i in value) {
+ if (this.$el.find('input[value="' + value[i] + '"]').length > 0) {
+ return true;
+ }
}
}
return false;
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/mvc/ui/ui-select-default.js
--- a/static/scripts/mvc/ui/ui-select-default.js
+++ b/static/scripts/mvc/ui/ui-select-default.js
@@ -75,6 +75,9 @@
value : function (new_value) {
if (new_value !== undefined) {
this.$select.val(new_value);
+ if (this.$select.select2) {
+ this.$select.select2('val', new_value);
+ }
}
return this.$select.val();
},
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/packed/mvc/ui/ui-drilldown.js
--- a/static/scripts/packed/mvc/ui/ui-drilldown.js
+++ b/static/scripts/packed/mvc/ui/ui-drilldown.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(g,h){var e=this;function f(l,m){function k(n){if(n){m.fadeIn("fast");l.removeClass("toggle-expand");l.addClass("toggle");l.is_expanded=true}else{m.hide();l.removeClass("toggle");l.addClass("toggle-expand");l.is_expanded=false}}l.on("click",function(){k(!l.is_expanded)})}function d(q,o){for(i in o){var r=o[i];var m=r.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var k=$("<div/>");k.append(n);k.append(e._templateOption(r.name,r.value));l.append(k);var p=$('<div style="display: none; margin-left: 25px;"/>');d(p,r.options);l.append(p);f(n,p)}else{l.append(e._templateOption(r.name,r.value))}q.append(l)}}var j=$("<div/>");d(j,g);return j},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}});
\ No newline at end of file
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/packed/mvc/ui/ui-options.js
--- a/static/scripts/packed/mvc/ui/ui-options.js
+++ b/static/scripts/packed/mvc/ui/ui-options.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(typeof g==="string"){g=[g]}if(g!==undefined){this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}});
\ No newline at end of file
+define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}});
\ No newline at end of file
diff -r 98a6cad91c3ac3825c7f954a0c697c6706ad1d73 -r 8fefb07155242c59a263a785cfef8e0b46560781 static/scripts/packed/mvc/ui/ui-select-default.js
--- a/static/scripts/packed/mvc/ui/ui-select-default.js
+++ b/static/scripts/packed/mvc/ui/ui-select-default.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/1a2ef4a380ff/
Changeset: 1a2ef4a380ff
Branch: next-stable
User: guerler
Date: 2014-12-01 06:18:16+00:00
Summary: ToolForm: Add baseurl, fix dynamic drill down options
Affected #: 7 files
diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 client/galaxy/scripts/mvc/tools/tools-section.js
--- a/client/galaxy/scripts/mvc/tools/tools-section.js
+++ b/client/galaxy/scripts/mvc/tools/tools-section.js
@@ -342,6 +342,11 @@
case 'drill_down':
field = this._fieldDrilldown(input_def);
break;
+
+ // base url field
+ case 'baseurl':
+ field = this._fieldHidden(input_def);
+ break;
// field not found
default:
diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 client/galaxy/scripts/mvc/ui/ui-drilldown.js
--- a/client/galaxy/scripts/mvc/ui/ui-drilldown.js
+++ b/client/galaxy/scripts/mvc/ui/ui-drilldown.js
@@ -16,8 +16,7 @@
*/
_templateOption: function(name, value, selected) {
return '<div>' +
- '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' +
- Utils.sanitize(name) +
+ '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name +
'<div/>';
},
diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -650,6 +650,11 @@
def get_label( self ):
# BaseURLToolParameters are ultimately "hidden" parameters
return None
+
+ def to_dict( self, trans, view='collection', value_mapper=None ):
+ d = super( BaseURLToolParameter, self ).to_dict( trans )
+ d['value'] = self.get_value( trans )
+ return d
DEFAULT_VALUE_MAP = lambda x: x
@@ -1606,13 +1611,13 @@
"""
return self.filtered.keys()
- def to_dict( self, trans, view='collection', value_mapper=None, context={} ):
+ def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
# skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
d = ToolParameter.to_dict( self, trans )
options = []
try:
- options = self.get_options( trans, context )
+ options = self.get_options( trans=trans, other_values=other_values )
except KeyError:
# will sometimes error if self.is_dynamic and self.filtered
# bc we dont/cant fill out other_values above ({})
diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/mvc/tools/tools-section.js
--- a/static/scripts/mvc/tools/tools-section.js
+++ b/static/scripts/mvc/tools/tools-section.js
@@ -342,6 +342,11 @@
case 'drill_down':
field = this._fieldDrilldown(input_def);
break;
+
+ // base url field
+ case 'baseurl':
+ field = this._fieldHidden(input_def);
+ break;
// field not found
default:
diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/mvc/ui/ui-drilldown.js
--- a/static/scripts/mvc/ui/ui-drilldown.js
+++ b/static/scripts/mvc/ui/ui-drilldown.js
@@ -16,8 +16,7 @@
*/
_templateOption: function(name, value, selected) {
return '<div>' +
- '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' +
- Utils.sanitize(name) +
+ '<input name="' + this.options.id + '" class="ui-option" type="' + this.display + '" value="' + value + '">' + name +
'<div/>';
},
diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/packed/mvc/tools/tools-section.js
--- a/static/scripts/packed/mvc/tools/tools-section.js
+++ b/static/scripts/packed/mvc/tools/tools-section.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}});
\ No newline at end of file
diff -r 8fefb07155242c59a263a785cfef8e0b46560781 -r 1a2ef4a380ff35ca7f97ca2c50bab474400c6275 static/scripts/packed/mvc/ui/ui-drilldown.js
--- a/static/scripts/packed/mvc/ui/ui-drilldown.js
+++ b/static/scripts/packed/mvc/ui/ui-drilldown.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+b.sanitize(d)+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}});
\ No newline at end of file
+define(["utils/utils","mvc/ui/ui-options"],function(b,a){var c=a.Base.extend({initialize:function(d){this.display=d.display||"checkbox";d.multiple=(this.display=="checkbox");a.Base.prototype.initialize.call(this,d)},_templateOption:function(d,f,e){return'<div><input name="'+this.options.id+'" class="ui-option" type="'+this.display+'" value="'+f+'">'+d+"<div/>"},_templateOptions:function(f){var e=this;function g(k,l){function j(m){if(m){l.fadeIn("fast");k.removeClass("toggle-expand");k.addClass("toggle");k.is_expanded=true}else{l.hide();k.removeClass("toggle");k.addClass("toggle-expand");k.is_expanded=false}}k.on("click",function(){j(!k.is_expanded)})}function d(p,k){for(i in k){var q=k[i];var m=q.options.length>0;var l=$("<div/>");if(m){var n=$('<span class="ui-drilldown-button form-toggle icon-button toggle-expand" style="position: relative; top: 2px;"/>');var j=$("<div/>");j.append(n);j.append(e._templateOption(q.name,q.value));l.append(j);var o=$('<div style="display: none; margin-left: 25px;"/>');d(o,q.options);l.append(o);g(n,o)}else{l.append(e._templateOption(q.name,q.value))}p.append(l)}}var h=$("<div/>");d(h,f);return h},_template:function(d){return'<div class="ui-options drilldown-container" id="'+d.id+'"/>'}});return{View:c}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/20e0db2511e5/
Changeset: 20e0db2511e5
Branch: next-stable
User: guerler
Date: 2014-12-02 16:47:59+00:00
Summary: Charts: Use most recent select field style
Affected #: 1 file
diff -r 1034c973ec1d2ce424f711d750ecc6de582d02aa -r 20e0db2511e555b9a168a96dee1ff75180aabbdf config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof x)return e;if(!(this instanceof x))return new x(e);this._wrapped=e};typeof exports!="undefined"?(typeof module!="undefined"&&module.exports&&(exports=module.exports=x),exports._=x):e._=x,x.VERSION="1.4.4";var T=x.each=x.forEach=function(e,t,r){if(e==null)return;if(c&&e.forEach===c)e.forEach(t,r);else if(e.length===+e.length){for(var i=0,s=e.length;i<s;i++)if(t.call(r,e[i],i,e)===n)return}else for(var o in e)if(x.has(e,o)&&t.call(r,e[o],o,e)===n)return};x.map=x.collect=function(e,t,n){var r=[];return e==null?r:h&&e.map===h?e.map(t,n):(T(e,function(e,i,s){r.push(t.call(n,e,i,s))}),r)};var N="Reduce of empty array with no initial value";x.reduce=x.foldl=x.inject=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(p&&e.reduce===p)return r&&(t=x.bind(t,r)),i?e.reduce(t,n):e.reduce(t);T(e,function(e,s,o){i?n=t.call(r,n,e,s,o):(n=e,i=!0)});if(!i)throw new TypeError(N);return n},x.reduceRight=x.foldr=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(d&&e.reduceRight===d)return r&&(t=x.bind(t,r)),i?e.reduceRight(t,n):e.reduceRight(t);var s=e.length;if(s!==+s){var o=x.keys(e);s=o.length}T(e,function(u,a,f){a=o?o[--s]:--s,i?n=t.call(r,n,e[a],a,f):(n=e[a],i=!0)});if(!i)throw new TypeError(N);return n},x.find=x.detect=function(e,t,n){var r;return C(e,function(e,i,s){if(t.call(n,e,i,s))return r=e,!0}),r},x.filter=x.select=function(e,t,n){var r=[];return e==null?r:v&&e.filter===v?e.filter(t,n):(T(e,function(e,i,s){t.call(n,e,i,s)&&r.push(e)}),r)},x.reject=function(e,t,n){return x.filter(e,function(e,r,i){return!t.call(n,e,r,i)},n)},x.every=x.all=function(e,t,r){t||(t=x.identity);var i=!0;return 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this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+'<div class="button">'+'<i id="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),errorText:"No data available.",waitText:"Please wait..."},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$message=$("<div/>"),this.$options=$(this._template(t)),this.$el.append(this.$message),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},wait:function(){this._size()==0&&(this._messageShow(this.options.waitText,"info"),this.$options.hide())},unwait:function(){this._messageHide(),this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.errorText,"danger"),this.$options.hide()):(this._messageHide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. 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Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){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(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=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(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart 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h=D.yScale().invert(i.mouseY),p=Math.abs(D.yScale().domain()[0]-D.yScale().domain()[1]),d=.03*p,m=e.nearestValueIndex(c.map(function(e){return e.value}),h,d);m!==null&&(c[m].highlight=!0)}var g=n.tickFormat()(D.x()(s,f),f);o.tooltip.position({left:l+u.left,top:i.mouseY+u.top}).chartContainer(A.parentNode).enabled(v).valueFormatter(function(e,t){return r.tickFormat()(e)}).data({value:g,series:c})(),o.renderGuideLine(l)}),o.dispatch.on("elementMouseout",function(e){k.tooltipHide(),t.clearHighlights()}),k.on("tooltipShow",function(e){v&&_(e,A.parentNode)}),k.on("changeState",function(e){typeof e.disabled!="undefined"&&(b.forEach(function(t,n){t.disabled=e.disabled[n]}),x.disabled=e.disabled),typeof e.index!="undefined"&&(M.i=e.index,M.x=O(M.i),x.index=e.index,tt.data([M])),typeof e.rescaleY!="undefined"&&(y=e.rescaleY),D.update()})}),D}function P(e,n){return n.map(function(n,r){if(!n.values)return n;var i=n.values[e];if(i==null)return n;var s=t.y()(i,e);return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],k.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){k.tooltipHide(e)}),k.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),D.dispatch=k,D.lines=t,D.legend=i,D.xAxis=n,D.yAxis=r,D.interactiveLayer=o,d3.rebind(D,t,"defined","isArea","x","y","xScale","yScale","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id"),D.options=e.utils.optionsFunc.bind(D),D.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,D):u},D.width=function(e){return arguments.length?(f=e,D):f},D.height=function(e){return arguments.length?(l=e,D):l},D.color=function(t){return 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e.y},f=[0],l=e.utils.defaultColor(),c=!1,h=d3.format(",.2f"),p,d,v,m,g=d3.dispatch("chartClick","elementClick","elementDblClick","elementMouseover","elementMouseout"),y="discreteBar",b,w;return E.dispatch=g,E.options=e.utils.optionsFunc.bind(E),E.x=function(e){return arguments.length?(u=e,E):u},E.y=function(e){return arguments.length?(a=e,E):a},E.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,E):t},E.width=function(e){return arguments.length?(n=e,E):n},E.height=function(e){return arguments.length?(r=e,E):r},E.xScale=function(e){return arguments.length?(s=e,E):s},E.yScale=function(e){return arguments.length?(o=e,E):o},E.xDomain=function(e){return arguments.length?(p=e,E):p},E.yDomain=function(e){return arguments.length?(d=e,E):d},E.xRange=function(e){return arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var A=d3.select(this),_=this,D=(a||parseInt(A.style("width"))||960)-u.left-u.right,P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom;M.update=function(){A.call(M)},M.container=this,S.disabled=y.map(function(e){return!!e.disabled});if(!x){var H;x={};for(H in S)S[H]instanceof Array?x[H]=S[H].slice(0):x[H]=S[H]}if(!y||!y.length||!y.filter(function(e){return e.values.length}).length){var B=A.selectAll(".nv-noData").data([T]);return B.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),B.attr("x",u.left+D/2).attr("y",u.top+P/2).text(function(e){return e}),M}A.selectAll(".nv-noData").remove(),b=t.xScale(),w=t.yScale();var j=A.selectAll("g.nv-wrap.nv-stackedAreaChart").data([y]),F=j.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedAreaChart").append("g"),I=j.select("g");F.append("rect").style("opacity",0),F.append("g").attr("class","nv-x nv-axis"),F.append("g").attr("class","nv-y 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U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/d857f25c1114/
Changeset: d857f25c1114
User: guerler
Date: 2014-12-02 16:48:17+00:00
Summary: Merge
Affected #: 1 file
diff -r 82b95de1f7bd2db44900c2d85c14dc49fa683502 -r d857f25c111411359a977366d446cd0a78768595 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
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this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.css("display","inline-block")},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+'<div class="button">'+'<i id="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),errorText:"No data available.",waitText:"Please wait..."},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$message=$("<div/>"),this.$options=$(this._template(t)),this.$el.append(this.$message),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},wait:function(){this._size()==0&&(this._messageShow(this.options.waitText,"info"),this.$options.hide())},unwait:function(){this._messageHide(),this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.errorText,"danger"),this.$options.hide()):(this._messageHide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){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(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=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(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success:function(){n._refreshHdas()}}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request({type:"POST",url:config.root+"api/tools",data:data,success:function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),o.app.storage.save(),o._wait(t,i,s)}},error:function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()}})},_wait:function(t,n,r){var i=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success:function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))}})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function c(i){l._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success:function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success:function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)}})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. 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Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){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(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=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(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart 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h=D.yScale().invert(i.mouseY),p=Math.abs(D.yScale().domain()[0]-D.yScale().domain()[1]),d=.03*p,m=e.nearestValueIndex(c.map(function(e){return e.value}),h,d);m!==null&&(c[m].highlight=!0)}var g=n.tickFormat()(D.x()(s,f),f);o.tooltip.position({left:l+u.left,top:i.mouseY+u.top}).chartContainer(A.parentNode).enabled(v).valueFormatter(function(e,t){return r.tickFormat()(e)}).data({value:g,series:c})(),o.renderGuideLine(l)}),o.dispatch.on("elementMouseout",function(e){k.tooltipHide(),t.clearHighlights()}),k.on("tooltipShow",function(e){v&&_(e,A.parentNode)}),k.on("changeState",function(e){typeof e.disabled!="undefined"&&(b.forEach(function(t,n){t.disabled=e.disabled[n]}),x.disabled=e.disabled),typeof e.index!="undefined"&&(M.i=e.index,M.x=O(M.i),x.index=e.index,tt.data([M])),typeof e.rescaleY!="undefined"&&(y=e.rescaleY),D.update()})}),D}function P(e,n){return n.map(function(n,r){if(!n.values)return n;var i=n.values[e];if(i==null)return n;var s=t.y()(i,e);return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],k.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){k.tooltipHide(e)}),k.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),D.dispatch=k,D.lines=t,D.legend=i,D.xAxis=n,D.yAxis=r,D.interactiveLayer=o,d3.rebind(D,t,"defined","isArea","x","y","xScale","yScale","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id"),D.options=e.utils.optionsFunc.bind(D),D.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,D):u},D.width=function(e){return arguments.length?(f=e,D):f},D.height=function(e){return arguments.length?(l=e,D):l},D.color=function(t){return 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e.y},f=[0],l=e.utils.defaultColor(),c=!1,h=d3.format(",.2f"),p,d,v,m,g=d3.dispatch("chartClick","elementClick","elementDblClick","elementMouseover","elementMouseout"),y="discreteBar",b,w;return E.dispatch=g,E.options=e.utils.optionsFunc.bind(E),E.x=function(e){return arguments.length?(u=e,E):u},E.y=function(e){return arguments.length?(a=e,E):a},E.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,E):t},E.width=function(e){return arguments.length?(n=e,E):n},E.height=function(e){return arguments.length?(r=e,E):r},E.xScale=function(e){return arguments.length?(s=e,E):s},E.yScale=function(e){return arguments.length?(o=e,E):o},E.xDomain=function(e){return arguments.length?(p=e,E):p},E.yDomain=function(e){return arguments.length?(d=e,E):d},E.xRange=function(e){return arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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arguments.length?(n=e,g):n},g.height=function(e){return arguments.length?(r=e,g):r},g.clipEdge=function(e){return arguments.length?(h=e,g):h},g.color=function(t){return arguments.length?(i=e.utils.getColor(t),g):i},g.offset=function(e){return arguments.length?(f=e,g):f},g.order=function(e){return arguments.length?(l=e,g):l},g.style=function(e){if(!arguments.length)return a;a=e;switch(a){case"stack":g.offset("zero"),g.order("default");break;case"stream":g.offset("wiggle"),g.order("inside-out");break;case"stream-center":g.offset("silhouette"),g.order("inside-out");break;case"expand":g.offset("expand"),g.order("default");break;case"stack_percent":g.offset(g.d3_stackedOffset_stackPercent),g.order("default")}return g},g.interpolate=function(e){return arguments.length?(c=e,g):c},g},e.models.stackedAreaChart=function(){function M(y){return y.each(function(y){var A=d3.select(this),_=this,D=(a||parseInt(A.style("width"))||960)-u.left-u.right,P=(f||parseInt(A.style("height"))||400)-u.top-u.bottom;M.update=function(){A.call(M)},M.container=this,S.disabled=y.map(function(e){return!!e.disabled});if(!x){var H;x={};for(H in S)S[H]instanceof Array?x[H]=S[H].slice(0):x[H]=S[H]}if(!y||!y.length||!y.filter(function(e){return e.values.length}).length){var B=A.selectAll(".nv-noData").data([T]);return B.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),B.attr("x",u.left+D/2).attr("y",u.top+P/2).text(function(e){return e}),M}A.selectAll(".nv-noData").remove(),b=t.xScale(),w=t.yScale();var j=A.selectAll("g.nv-wrap.nv-stackedAreaChart").data([y]),F=j.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedAreaChart").append("g"),I=j.select("g");F.append("rect").style("opacity",0),F.append("g").attr("class","nv-x nv-axis"),F.append("g").attr("class","nv-y 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U=I.select(".nv-stackedWrap").datum(y);U.call(t),p&&(n.scale(b).ticks(D/100).tickSize(-P,0),I.select(".nv-x.nv-axis").attr("transform","translate(0,"+P+")"),I.select(".nv-x.nv-axis").call(n)),d&&(r.scale(w).ticks(t.offset()=="wiggle"?0:P/36).tickSize(-D,0).setTickFormat(t.style()=="expand"||t.style()=="stack_percent"?d3.format("%"):E),I.select(".nv-y.nv-axis").call(r)),t.dispatch.on("areaClick.toggle",function(e){y.filter(function(e){return!e.disabled}).length===1?y.forEach(function(e){e.disabled=!1}):y.forEach(function(t,n){t.disabled=n!=e.seriesIndex}),S.disabled=y.map(function(e){return!!e.disabled}),N.stateChange(S),M.update()}),i.dispatch.on("stateChange",function(e){S.disabled=e.disabled,N.stateChange(S),M.update()}),s.dispatch.on("legendClick",function(e,n){if(!e.disabled)return;R=R.map(function(e){return e.disabled=!0,e}),e.disabled=!1,t.style(e.style),S.style=t.style(),N.stateChange(S),M.update()}),o.dispatch.on("elementMousemove",function(i){t.clearHighlights();var s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/pie/config",["plugin/plugins/nvd3/nv.d3"],function(){return $.extend(!0,{},{title:"Pie chart",category:"Area charts",library:"NVD3",tag:"svg",keywords:"small",columns:{label:{title:"Labels",is_label:!0,is_auto:!0},y:{title:"Values",is_numeric:!0}},settings:{main_separator:{type:"separator",title:"Pie chart settings"},donut_ratio:{title:"Donut ratio",info:"Determine how large the donut hole will be.",type:"select",init:"0.5",data:[{label:"50%",value:"0.5"},{label:"25%",value:"0.25"},{label:"10%",value:"0.10"},{label:"0%",value:"0"}]},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},label_separator:{type:"separator",title:"Label settings"},label_type:{title:"Donut label",info:"What would you like to show for each slice?",type:"select",init:"percent",data:[{label:"-- Nothing 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small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{label:"Red-to-Green",value:"redgreen"},{label:"Red-to-green (saturated)",value:"red2green"},{label:"Relief",value:"relief"},{label:"Seismograph",value:"seis"},{label:"Sealand",value:"sealand"},{label:"Split",value:"split"},{label:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. 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\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Merged in BjoernGruening/galaxy-central-1 (pull request #578)
by commits-noreply＠bitbucket.org 02 Dec '14
by commits-noreply＠bitbucket.org 02 Dec '14
02 Dec '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/82b95de1f7bd/
Changeset: 82b95de1f7bd
User: dannon
Date: 2014-12-02 13:26:09+00:00
Summary: Merged in BjoernGruening/galaxy-central-1 (pull request #578)
Update the Dockerfile template to the latest version our Galaxy Docker Container.
Affected #: 1 file
diff -r 74e82c604d026307fa8d72a7850ddd33c5f9259b -r 82b95de1f7bd2db44900c2d85c14dc49fa683502 lib/tool_shed/util/basic_util.py
--- a/lib/tool_shed/util/basic_util.py
+++ b/lib/tool_shed/util/basic_util.py
@@ -27,24 +27,25 @@
MAINTAINER Bjoern A. Gruning, bjoern.gruening(a)gmail.com
-RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini
-
WORKDIR /galaxy-central
${selected_repositories}
-# Mark one folder as imported from the host.
-VOLUME ["/export/"]
+# Mark folders as imported from the host.
+VOLUME ["/export/", "/data/", "/var/lib/docker"]
-# Expose port 80 to the host
+# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app)
EXPOSE :80
+EXPOSE :21
+EXPOSE :8800
+EXPOSE :9001
# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]
'''
SELECTED_REPOSITORIES_TEMPLATE = '''
-RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker'
+RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}"
'''
def evaluate_template( text, install_environment ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/88d434f15cd4/
Changeset: 88d434f15cd4
User: BjoernGruening
Date: 2014-11-28 19:18:58+00:00
Summary: Update the Dockerfile template to the latest version our Galaxy Docker Container. The new container will be release together with Galaxy next week.
Affected #: 1 file
diff -r 3975b317ffdcbaa6c8dcb4b2b52404bfa34edbc2 -r 88d434f15cd4042df6b4fb22c9861cbd42bb2a77 lib/tool_shed/util/basic_util.py
--- a/lib/tool_shed/util/basic_util.py
+++ b/lib/tool_shed/util/basic_util.py
@@ -27,24 +27,25 @@
MAINTAINER Bjoern A. Gruning, bjoern.gruening(a)gmail.com
-RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini
-
WORKDIR /galaxy-central
${selected_repositories}
-# Mark one folder as imported from the host.
-VOLUME ["/export/"]
+# Mark folders as imported from the host.
+VOLUME ["/export/", "/data/", "/var/lib/docker"]
-# Expose port 80 to the host
+# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app)
EXPOSE :80
+EXPOSE :21
+EXPOSE :8800
+EXPOSE :9001
# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]
'''
SELECTED_REPOSITORIES_TEMPLATE = '''
-RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker'
+RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}"
'''
def evaluate_template( text, install_environment ):
https://bitbucket.org/galaxy/galaxy-central/commits/82b95de1f7bd/
Changeset: 82b95de1f7bd
User: dannon
Date: 2014-12-02 13:26:09+00:00
Summary: Merged in BjoernGruening/galaxy-central-1 (pull request #578)
Update the Dockerfile template to the latest version our Galaxy Docker Container.
Affected #: 1 file
diff -r 74e82c604d026307fa8d72a7850ddd33c5f9259b -r 82b95de1f7bd2db44900c2d85c14dc49fa683502 lib/tool_shed/util/basic_util.py
--- a/lib/tool_shed/util/basic_util.py
+++ b/lib/tool_shed/util/basic_util.py
@@ -27,24 +27,25 @@
MAINTAINER Bjoern A. Gruning, bjoern.gruening(a)gmail.com
-RUN sed -i 's|brand.*|brand = deepTools|g' ~/galaxy-central/universe_wsgi.ini
-
WORKDIR /galaxy-central
${selected_repositories}
-# Mark one folder as imported from the host.
-VOLUME ["/export/"]
+# Mark folders as imported from the host.
+VOLUME ["/export/", "/data/", "/var/lib/docker"]
-# Expose port 80 to the host
+# Expose port 80 (webserver), 21 (FTP server), 8800 (Proxy), 9001 (Galaxy report app)
EXPOSE :80
+EXPOSE :21
+EXPOSE :8800
+EXPOSE :9001
# Autostart script that is invoked during container start
CMD ["/usr/bin/startup"]
'''
SELECTED_REPOSITORIES_TEMPLATE = '''
-RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker'
+RUN install-repository "--url ${tool_shed_url} -o ${repository_owner} --name ${repository_name}"
'''
def evaluate_template( text, install_environment ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1
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18 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1037d12c3005/
Changeset: 1037d12c3005
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: PEP-8 fixes for lib/galaxy/tools/parameters/output_collect.py
Affected #: 1 file
diff -r 5393f6389105d22bc8791f908075c152f11a4d2e -r 1037d12c30058f318014efea19898b209dc8ba8a lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -119,7 +119,8 @@
for root, dirs, files in os.walk( extra_files_path_joined ):
extra_dir = os.path.join( primary_data.extra_files_path, root.replace( extra_files_path_joined, '', 1 ).lstrip( os.path.sep ) )
for f in files:
- app.object_store.update_from_file( primary_data.dataset,
+ app.object_store.update_from_file(
+ primary_data.dataset,
extra_dir=extra_dir,
alt_name=f,
file_name=os.path.join( root, f ),
@@ -127,7 +128,7 @@
dir_only=True,
preserve_symlinks=True
)
- # FIXME:
+ # FIXME:
# since these are placed into the job working dir, let the standard
# Galaxy cleanup methods handle this (for now?)
# there was an extra_files_path dir, attempt to remove it
https://bitbucket.org/galaxy/galaxy-central/commits/fd043fbe00ab/
Changeset: fd043fbe00ab
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Refactor output_collect for reuse.
Reduces cyclomatic complexity slightly as well.
Affected #: 1 file
diff -r 1037d12c30058f318014efea19898b209dc8ba8a -r fd043fbe00abd3f2ee6b6b2f8ffc3271c44cbce0 lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -43,20 +43,8 @@
for filename in glob.glob(os.path.join(app.config.new_file_path, "primary_%i_*" % outdata.id) ):
filenames[ filename ] = DEFAULT_DATASET_COLLECTOR
if 'job_working_directory' in app.config.collect_outputs_from:
- for extra_file_collector in dataset_collectors:
- directory = job_working_directory
- if extra_file_collector.directory:
- directory = os.path.join( directory, extra_file_collector.directory )
- if not util.in_directory( directory, job_working_directory ):
- raise Exception( "Problem with tool configuration, attempting to pull in datasets from outside working directory." )
- if not os.path.isdir( directory ):
- continue
- for filename in sorted( os.listdir( directory ) ):
- path = os.path.join( directory, filename )
- if not os.path.isfile( path ):
- continue
- if extra_file_collector.match( outdata, filename ):
- filenames[ path ] = extra_file_collector
+ for path, extra_file_collector in walk_over_extra_files( dataset_collectors, job_working_directory, outdata ):
+ filenames[ path ] = extra_file_collector
for filename_index, ( filename, extra_file_collector ) in enumerate( filenames.iteritems() ):
fields_match = extra_file_collector.match( outdata, os.path.basename( filename ) )
if not fields_match:
@@ -163,6 +151,22 @@
return primary_datasets
+def walk_over_extra_files( extra_file_collectors, job_working_directory, matchable ):
+ for extra_file_collector in extra_file_collectors:
+ directory = job_working_directory
+ if extra_file_collector.directory:
+ directory = os.path.join( directory, extra_file_collector.directory )
+ if not util.in_directory( directory, job_working_directory ):
+ raise Exception( "Problem with tool configuration, attempting to pull in datasets from outside working directory." )
+ if not os.path.isdir( directory ):
+ continue
+ for filename in sorted( os.listdir( directory ) ):
+ path = os.path.join( directory, filename )
+ if not os.path.isfile( path ):
+ continue
+ if extra_file_collector.match( matchable, filename ):
+ yield path, extra_file_collector
+
# XML can describe custom patterns, but these literals describe named
# patterns that will be replaced.
NAMED_PATTERNS = {
https://bitbucket.org/galaxy/galaxy-central/commits/2022044556ca/
Changeset: 2022044556ca
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Refactor small helper out of get_work_dir_outputs for reuse.
Leave comment about not understanding the complexity :).
Affected #: 1 file
diff -r fd043fbe00abd3f2ee6b6b2f8ffc3271c44cbce0 -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc lib/galaxy/jobs/runners/__init__.py
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -214,23 +214,31 @@
# Walk job's output associations to find and use from_work_dir attributes.
job = job_wrapper.get_job()
job_tool = job_wrapper.tool
+ for (joda, dataset) in self._walk_dataset_outputs( job ):
+ if joda and job_tool:
+ hda_tool_output = job_tool.outputs.get( joda.name, None )
+ if hda_tool_output and hda_tool_output.from_work_dir:
+ # Copy from working dir to HDA.
+ # TODO: move instead of copy to save time?
+ source_file = os.path.join( job_working_directory, hda_tool_output.from_work_dir )
+ destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] )
+ if in_directory( source_file, job_working_directory ):
+ output_pairs.append( ( source_file, destination ) )
+ else:
+ # Security violation.
+ log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) )
+ return output_pairs
+
+ def _walk_dataset_outputs( self, job ):
for dataset_assoc in job.output_datasets + job.output_library_datasets:
for dataset in dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations:
if isinstance( dataset, self.app.model.HistoryDatasetAssociation ):
joda = self.sa_session.query( self.app.model.JobToOutputDatasetAssociation ).filter_by( job=job, dataset=dataset ).first()
- if joda and job_tool:
- hda_tool_output = job_tool.outputs.get( joda.name, None )
- if hda_tool_output and hda_tool_output.from_work_dir:
- # Copy from working dir to HDA.
- # TODO: move instead of copy to save time?
- source_file = os.path.join( job_working_directory, hda_tool_output.from_work_dir )
- destination = job_wrapper.get_output_destination( output_paths[ dataset.dataset_id ] )
- if in_directory( source_file, job_working_directory ):
- output_pairs.append( ( source_file, destination ) )
- else:
- # Security violation.
- log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) )
- return output_pairs
+ yield (joda, dataset)
+ # TODO: why is this not just something easy like:
+ # for dataset_assoc in job.output_datasets + job.output_library_datasets:
+ # yield (dataset_assoc, dataset_assoc.dataset)
+ # I don't understand the reworking it backwards. -John
def _handle_metadata_externally( self, job_wrapper, resolve_requirements=False ):
"""
https://bitbucket.org/galaxy/galaxy-central/commits/691584d72c7c/
Changeset: 691584d72c7c
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Rename variable for clarity post output collections.
After tools can explicitly create collections the term created_collections becomes ambigious - these are history collection instances (HDCA) implicitly created by mapping over collections so renaming this field implicit_collections.
Affected #: 3 files
diff -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc -r 691584d72c7c74e92d5756358a723b8f2064ef91 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2216,7 +2216,7 @@
num_jobs=len( execution_tracker.successful_jobs ),
job_errors=execution_tracker.execution_errors,
jobs=execution_tracker.successful_jobs,
- implicit_collections=execution_tracker.created_collections,
+ implicit_collections=execution_tracker.implicit_collections,
)
else:
template = 'message.mako'
diff -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc -r 691584d72c7c74e92d5756358a723b8f2064ef91 lib/galaxy/tools/execute.py
--- a/lib/galaxy/tools/execute.py
+++ b/lib/galaxy/tools/execute.py
@@ -47,7 +47,7 @@
self.execution_errors = []
self.output_datasets = []
self.outputs_by_output_name = collections.defaultdict(list)
- self.created_collections = {}
+ self.implicit_collections = {}
def record_success( self, job, outputs ):
self.successful_jobs.append( job )
@@ -122,6 +122,6 @@
)
collections[ output_name ] = collection
- self.created_collections = collections
+ self.implicit_collections = collections
__all__ = [ execute ]
diff -r 2022044556ca064d879cacbdeae07f2a8ae6f1fc -r 691584d72c7c74e92d5756358a723b8f2064ef91 lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -784,7 +784,7 @@
workflow_invocation_uuid=invocation.uuid.hex
)
if collection_info:
- step_outputs = dict( execution_tracker.created_collections )
+ step_outputs = dict( execution_tracker.implicit_collections )
else:
step_outputs = dict( execution_tracker.output_datasets )
progress.set_step_outputs( step, step_outputs )
https://bitbucket.org/galaxy/galaxy-central/commits/1e2fbca80715/
Changeset: 1e2fbca80715
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Rename variable for clarity.
This method does not just return datasets.
Affected #: 1 file
diff -r 691584d72c7c74e92d5756358a723b8f2064ef91 -r 1e2fbca807151860c54f84b14ba6285b39aaf6a7 test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -207,12 +207,12 @@
if isinstance(value, list) and len(value) == 1:
inputs_tree[key] = value[0]
- datasets = self.__submit_tool( history_id, tool_id=testdef.tool.id, tool_input=inputs_tree )
- datasets_object = datasets.json()
+ submit_response = self.__submit_tool( history_id, tool_id=testdef.tool.id, tool_input=inputs_tree )
+ submit_response_object = submit_response.json()
try:
- return self.__dictify_outputs( datasets_object ), datasets_object[ 'jobs' ]
+ return self.__dictify_outputs( submit_response_object ), submit_response_object[ 'jobs' ]
except KeyError:
- raise Exception( datasets_object[ 'message' ] )
+ raise Exception( submit_response_object[ 'message' ] )
def _create_collection( self, history_id, collection_def ):
create_payload = dict(
https://bitbucket.org/galaxy/galaxy-central/commits/cd9eb06bb5f7/
Changeset: cd9eb06bb5f7
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Add file missed with pull request 505.
Affected #: 1 file
diff -r 1e2fbca807151860c54f84b14ba6285b39aaf6a7 -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e test/api/test_workflow_map_reduce_pause.ga
--- /dev/null
+++ b/test/api/test_workflow_map_reduce_pause.ga
@@ -0,0 +1,198 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "map_reduce_pause",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 172.83680772781372,
+ "top": 200.96180772781372
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "1": {
+ "annotation": "",
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset Collection"
+ }
+ ],
+ "name": "Input dataset collection",
+ "outputs": [],
+ "position": {
+ "left": 161.46528673171997,
+ "top": 422.5764012336731
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}",
+ "tool_version": null,
+ "type": "data_collection_input",
+ "user_outputs": []
+ },
+ "2": {
+ "annotation": "",
+ "id": 2,
+ "input_connections": {
+ "input": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "name": "Select first",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 410.9444432258606,
+ "top": 195.05903673171997
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "head",
+ "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"lineNum\": \"\\\"1\\\"\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "user_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "id": 3,
+ "input_connections": {
+ "input": {
+ "id": 1,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "name": "Select first",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 632.9756932258606,
+ "top": 360.57988023757935
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "head",
+ "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"lineNum\": \"\\\"1\\\"\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "user_outputs": []
+ },
+ "4": {
+ "annotation": "",
+ "id": 4,
+ "input_connections": {
+ "input": {
+ "id": 2,
+ "output_name": "out_file1"
+ }
+ },
+ "inputs": [],
+ "name": "Pause for dataset review",
+ "outputs": [],
+ "position": {
+ "left": 657.0903172492981,
+ "top": 197.71528673171997
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Pause for Dataset Review\"}",
+ "tool_version": null,
+ "type": "pause",
+ "user_outputs": []
+ },
+ "5": {
+ "annotation": "",
+ "id": 5,
+ "input_connections": {
+ "input1": {
+ "id": 4,
+ "output_name": "output"
+ },
+ "queries_0|input2": {
+ "id": 3,
+ "output_name": "out_file1"
+ }
+ },
+ "inputs": [],
+ "name": "Concatenate datasets (for test workflows)",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 977.8889012336731,
+ "top": 228.01042222976685
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "cat",
+ "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "user_outputs": []
+ },
+ "6": {
+ "annotation": "",
+ "id": 6,
+ "input_connections": {
+ "input1": {
+ "id": 5,
+ "output_name": "out_file1"
+ }
+ },
+ "inputs": [],
+ "name": "Concatenate multiple datasets (for test workflows)",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 1342.545150756836,
+ "top": 233.55210876464844
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "cat_list",
+ "tool_state": "{\"__job_resource\": \"{\\\"__job_resource__select\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "user_outputs": []
+ }
+ },
+ "uuid": "a27044e7-2efe-4661-9a09-00708d3520f1"
+}
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/0a809bab2180/
Changeset: 0a809bab2180
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Refactor dataset collection creation into reusable pieces.
In downstream output collection work this allows creating elements after initial construction - which is useful for output collections composed of dynamically discovered datasets after a job has completed.
Affected #: 5 files
diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/builder.py
--- /dev/null
+++ b/lib/galaxy/dataset_collections/builder.py
@@ -0,0 +1,26 @@
+from galaxy import model
+
+
+def build_collection( type, dataset_instances ):
+ """
+ Build DatasetCollection with populated DatasetcollectionElement objects
+ corresponding to the supplied dataset instances or throw exception if
+ this is not a valid collection of the specified type.
+ """
+ dataset_collection = model.DatasetCollection( )
+ set_collection_elements( dataset_collection, type, dataset_instances )
+ return dataset_collection
+
+
+def set_collection_elements( dataset_collection, type, dataset_instances ):
+ element_index = 0
+ elements = []
+ for element in type.generate_elements( dataset_instances ):
+ element.element_index = element_index
+ element.collection = dataset_collection
+ elements.append( element )
+
+ element_index += 1
+
+ dataset_collection.elements = elements
+ return dataset_collection
diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/types/__init__.py
--- a/lib/galaxy/dataset_collections/types/__init__.py
+++ b/lib/galaxy/dataset_collections/types/__init__.py
@@ -12,10 +12,9 @@
__metaclass__ = ABCMeta
@abstractmethod
- def build_collection( self, dataset_instances ):
- """
- Build DatasetCollection with populated DatasetcollectionElement objects
- corresponding to the supplied dataset instances or throw exception if
+ def generate_elements( self, dataset_instances ):
+ """ Generate DatasetCollectionElements with corresponding
+ to the supplied dataset instances or throw exception if
this is not a valid collection of the specified type.
"""
@@ -24,11 +23,3 @@
def _validation_failed( self, message ):
raise exceptions.ObjectAttributeInvalidException( message )
-
- def _new_collection_for_elements( self, elements ):
- dataset_collection = model.DatasetCollection( )
- for index, element in enumerate( elements ):
- element.element_index = index
- element.collection = dataset_collection
- dataset_collection.elements = elements
- return dataset_collection
diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/types/list.py
--- a/lib/galaxy/dataset_collections/types/list.py
+++ b/lib/galaxy/dataset_collections/types/list.py
@@ -11,13 +11,10 @@
def __init__( self ):
pass
- def build_collection( self, elements ):
- associations = []
+ def generate_elements( self, elements ):
for identifier, element in elements.iteritems():
association = DatasetCollectionElement(
element=element,
element_identifier=identifier,
)
- associations.append( association )
-
- return self._new_collection_for_elements( associations )
+ yield association
diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/dataset_collections/types/paired.py
--- a/lib/galaxy/dataset_collections/types/paired.py
+++ b/lib/galaxy/dataset_collections/types/paired.py
@@ -17,7 +17,7 @@
def __init__( self ):
pass
- def build_collection( self, elements ):
+ def generate_elements( self, elements ):
forward_dataset = elements.get( FORWARD_IDENTIFIER, None )
reverse_dataset = elements.get( REVERSE_IDENTIFIER, None )
if not forward_dataset or not reverse_dataset:
@@ -30,4 +30,5 @@
element=reverse_dataset,
element_identifier=REVERSE_IDENTIFIER,
)
- return self._new_collection_for_elements([left_association, right_association])
+ yield left_association
+ yield right_association
diff -r cd9eb06bb5f7da306031ef62f6c538a5816ef08e -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd lib/galaxy/managers/collections.py
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -1,6 +1,7 @@
from galaxy.dataset_collections.registry import DatasetCollectionTypesRegistry
from galaxy.dataset_collections.matching import MatchingCollections
from galaxy.dataset_collections.type_description import CollectionTypeDescriptionFactory
+from galaxy.dataset_collections import builder
from galaxy import model
from galaxy.exceptions import MessageException
@@ -113,7 +114,7 @@
# else if elements is set, it better be an ordered dict!
type_plugin = collection_type_description.rank_type_plugin()
- dataset_collection = type_plugin.build_collection( elements )
+ dataset_collection = builder.build_collection( type_plugin, elements )
dataset_collection.collection_type = collection_type
return dataset_collection
https://bitbucket.org/galaxy/galaxy-central/commits/9fba811dd8f9/
Changeset: 9fba811dd8f9
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Rearrange verify method to make duplication more obvious.
Affected #: 1 file
diff -r 0a809bab2180137fd7c6cf25a53bfa93fe1b0dcd -r 9fba811dd8f919d6ae24795f17e1f269556cee9e test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -64,6 +64,7 @@
fetcher = self.__dataset_fetcher( history_id )
## TODO: Twill version verifys dataset is 'ok' in here.
self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id )
+ self._verify_metadata( history_id, hid, attributes )
primary_datasets = attributes.get( 'primary_datasets', {} )
if primary_datasets:
@@ -86,8 +87,6 @@
self.twill_test_case.verify_hid( primary_outfile, hda_id=primary_hda_id, attributes=primary_attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id )
self._verify_metadata( history_id, primary_hda_id, primary_attributes )
- self._verify_metadata( history_id, hid, attributes )
-
def _verify_metadata( self, history_id, hid, attributes ):
metadata = attributes.get( 'metadata', {} ).copy()
for key, value in metadata.copy().iteritems():
https://bitbucket.org/galaxy/galaxy-central/commits/4ac25385dfc6/
Changeset: 4ac25385dfc6
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Break up a couple test methods for reuse downstream.
Remove duplication related to verifying a single dataset in tests - allows reuse in downstream when verifying the content of explicitly defined tool output collections.
Refactor out waiting for jobs - seems wrong place to put that logic this should allow easier moving.
Affected #: 1 file
diff -r 9fba811dd8f919d6ae24795f17e1f269556cee9e -r 4ac25385dfc69a72744e8593200696c499d60eaa test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -58,13 +58,10 @@
outfile = output_testdef.outfile
attributes = output_testdef.attributes
name = output_testdef.name
- for job in jobs:
- self.wait_for_job( job[ 'id' ], history_id, maxseconds )
+ self.wait_for_jobs( history_id, jobs, maxseconds )
hid = self.__output_id( output_data )
- fetcher = self.__dataset_fetcher( history_id )
## TODO: Twill version verifys dataset is 'ok' in here.
- self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id )
- self._verify_metadata( history_id, hid, attributes )
+ self.verify_output_dataset( history_id=history_id, hda_id=hid, outfile=outfile, attributes=attributes, shed_tool_id=shed_tool_id )
primary_datasets = attributes.get( 'primary_datasets', {} )
if primary_datasets:
@@ -84,8 +81,16 @@
raise Exception( msg_template % msg_args )
primary_hda_id = primary_output[ "dataset" ][ "id" ]
- self.twill_test_case.verify_hid( primary_outfile, hda_id=primary_hda_id, attributes=primary_attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id )
- self._verify_metadata( history_id, primary_hda_id, primary_attributes )
+ self.verify_output_dataset( history_id, primary_hda_id, primary_outfile, primary_attributes, shed_tool_id=shed_tool_id )
+
+ def wait_for_jobs( self, history_id, jobs, maxseconds ):
+ for job in jobs:
+ self.wait_for_job( job[ 'id' ], history_id, maxseconds )
+
+ def verify_output_dataset( self, history_id, hda_id, outfile, attributes, shed_tool_id ):
+ fetcher = self.__dataset_fetcher( history_id )
+ self.twill_test_case.verify_hid( outfile, hda_id=hda_id, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id )
+ self._verify_metadata( history_id, hda_id, attributes )
def _verify_metadata( self, history_id, hid, attributes ):
metadata = attributes.get( 'metadata', {} ).copy()
https://bitbucket.org/galaxy/galaxy-central/commits/e5be58d2ae87/
Changeset: e5be58d2ae87
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Script to build workflows from simpler YAML description.
Affected #: 3 files
diff -r 4ac25385dfc69a72744e8593200696c499d60eaa -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -8,24 +8,54 @@
from .helpers import DatasetCollectionPopulator
from .helpers import skip_without_tool
+from .yaml_to_workflow import yaml_to_workflow
+
from requests import delete
from requests import put
from galaxy.exceptions import error_codes
+class BaseWorkflowsApiTestCase( api.ApiTestCase ):
+ # TODO: Find a new file for this class.
+
+ def setUp( self ):
+ super( BaseWorkflowsApiTestCase, self ).setUp()
+ self.workflow_populator = WorkflowPopulator( self.galaxy_interactor )
+ self.dataset_populator = DatasetPopulator( self.galaxy_interactor )
+ self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor )
+
+ def _assert_user_has_workflow_with_name( self, name ):
+ names = self._workflow_names()
+ assert name in names, "No workflows with name %s in users workflows <%s>" % ( name, names )
+
+ def _workflow_names( self ):
+ index_response = self._get( "workflows" )
+ self._assert_status_code_is( index_response, 200 )
+ names = map( lambda w: w[ "name" ], index_response.json() )
+ return names
+
+ def _upload_yaml_workflow(self, has_yaml):
+ workflow = yaml_to_workflow(has_yaml)
+ workflow_str = dumps(workflow, indent=4)
+ data = {
+ 'workflow': workflow_str
+ }
+ upload_response = self._post( "workflows", data=data )
+ self._assert_status_code_is( upload_response, 200 )
+ self._assert_user_has_workflow_with_name( "%s (imported from API)" % ( workflow[ "name" ] ) )
+ return upload_response.json()[ "id" ]
+
+
# Workflow API TODO:
# - Allow history_id as param to workflow run action. (hist_id)
# - Allow post to workflows/<workflow_id>/run in addition to posting to
# /workflows with id in payload.
# - Much more testing obviously, always more testing.
-class WorkflowsApiTestCase( api.ApiTestCase ):
+class WorkflowsApiTestCase( BaseWorkflowsApiTestCase ):
def setUp( self ):
super( WorkflowsApiTestCase, self ).setUp()
- self.workflow_populator = WorkflowPopulator( self.galaxy_interactor )
- self.dataset_populator = DatasetPopulator( self.galaxy_interactor )
- self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor )
def test_show_invalid_key_is_400( self ):
show_response = self._get( "workflows/%s" % self._random_key() )
@@ -45,7 +75,7 @@
delete_response = delete( workflow_url )
self._assert_status_code_is( delete_response, 200 )
# Make sure workflow is no longer in index by default.
- assert workflow_name not in self.__workflow_names()
+ assert workflow_name not in self._workflow_names()
def test_other_cannot_delete( self ):
workflow_id = self.workflow_populator.simple_workflow( "test_other_delete" )
@@ -825,10 +855,6 @@
src = 'hdca'
return dict( src=src, id=hda[ "id" ] )
- def _assert_user_has_workflow_with_name( self, name ):
- names = self.__workflow_names()
- assert name in names, "No workflows with name %s in users workflows <%s>" % ( name, names )
-
def __review_paused_steps( self, uploaded_workflow_id, invocation_id, order_index, action=True ):
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
invocation_steps = invocation[ "steps" ]
@@ -863,12 +889,6 @@
else:
return invocation_response
- def __workflow_names( self ):
- index_response = self._get( "workflows" )
- self._assert_status_code_is( index_response, 200 )
- names = map( lambda w: w[ "name" ], index_response.json() )
- return names
-
def __import_workflow( self, workflow_id, deprecated_route=False ):
if deprecated_route:
route = "workflows/import"
diff -r 4ac25385dfc69a72744e8593200696c499d60eaa -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc test/api/test_workflows_from_yaml.py
--- /dev/null
+++ b/test/api/test_workflows_from_yaml.py
@@ -0,0 +1,32 @@
+import json
+
+from .test_workflows import BaseWorkflowsApiTestCase
+
+
+class WorkflowsFromYamlApiTestCase( BaseWorkflowsApiTestCase ):
+
+ def setUp( self ):
+ super( WorkflowsFromYamlApiTestCase, self ).setUp()
+
+ def test_simple_upload(self):
+ workflow_id = self._upload_yaml_workflow("""
+- type: input
+- tool_id: cat1
+ state:
+ input1:
+ $link: 0
+- tool_id: cat1
+ state:
+ input1:
+ $link: 1#out_file1
+- tool_id: random_lines1
+ state:
+ num_lines: 10
+ input:
+ $link: 2#out_file1
+ seed_source:
+ seed_source_selector: set_seed
+ seed: asdf
+ __current_case__: 1
+""")
+ self._get("workflows/%s/download" % workflow_id).content
diff -r 4ac25385dfc69a72744e8593200696c499d60eaa -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc test/api/yaml_to_workflow.py
--- /dev/null
+++ b/test/api/yaml_to_workflow.py
@@ -0,0 +1,220 @@
+import sys
+
+import yaml
+import json
+
+try:
+ from collections import OrderedDict
+except ImportError:
+ from galaxy.util.odict import odict as OrderedDict
+
+
+STEP_TYPE_ALIASES = {
+ 'input': 'data_input',
+ 'input_collection': 'data_collection_input',
+}
+
+
+def yaml_to_workflow(has_yaml):
+ as_python = yaml.load(has_yaml)
+
+ if isinstance(as_python, list):
+ as_python = {"steps": as_python}
+
+ __ensure_defaults(as_python, {
+ "a_galaxy_workflow": "true",
+ "format-version": "0.1",
+ "annotation": "",
+ "name": "Workflow"
+ })
+
+ steps = as_python["steps"]
+
+ conversion_context = ConversionContext()
+ if isinstance(steps, list):
+ steps_as_dict = OrderedDict()
+ for i, step in enumerate(steps):
+ steps_as_dict[ str(i) ] = step
+ if "id" not in step:
+ step["id"] = i
+
+ if "label" in step:
+ label = step["label"]
+ conversion_context.labels[label] = i
+
+ if "position" not in step:
+ # TODO: this really should be optional in Galaxy API.
+ step["position"] = {
+ "left": 10 * i,
+ "top": 10 * i
+ }
+
+ as_python["steps"] = steps_as_dict
+ steps = steps_as_dict
+
+ for i, step in steps.iteritems():
+ step_type = step.get("type", "tool")
+ step_type = STEP_TYPE_ALIASES.get(step_type, step_type)
+ if step_type not in [ "data_input", "data_collection_input", "tool", "pause"]:
+ raise Exception("Unknown step type encountered %s" % step_type)
+ step["type"] = step_type
+ eval("transform_%s" % step_type)(conversion_context, step)
+
+ return as_python
+
+
+def transform_data_input(context, step):
+ transform_input(context, step, default_name="Input dataset")
+
+
+def transform_data_collection_input(context, step):
+ transform_input(context, step, default_name="Input dataset collection")
+
+
+def transform_input(context, step, default_name):
+ default_name = step.get("label", default_name)
+ __ensure_defaults( step, {
+ "annotation": "",
+ })
+
+ __ensure_inputs_connections(step)
+
+ if not "inputs" in step:
+ step["inputs"] = [{}]
+
+ step_inputs = step["inputs"][0]
+ if "name" in step_inputs:
+ name = step_inputs["name"]
+ else:
+ name = default_name
+
+ __ensure_defaults( step_inputs, {
+ "name": name,
+ "description": "",
+ })
+ tool_state = {
+ "name": name
+ }
+ if "collection_type" in step:
+ tool_state["collection_type"] = step["collection_type"]
+
+ __populate_tool_state(step, tool_state)
+
+
+def transform_tool(context, step):
+ if "tool_id" not in step:
+ raise Exception("Tool steps must define a tool_id.")
+
+ __ensure_defaults( step, {
+ "annotation": "",
+ } )
+ __ensure_inputs_connections(step)
+
+ tool_state = {
+ # TODO: Galaxy should not require tool state actually specify a __page__.
+ "__page__": 0,
+ }
+
+ if "connect" not in step:
+ step["connect"] = {}
+
+ connect = step["connect"]
+ del step["connect"]
+
+ def append_link(key, value):
+ if key not in connect:
+ connect[key] = []
+ connect[key].append(value["$link"])
+
+ def replace_links(value, key=""):
+ if __is_link(value):
+ append_link(key, value)
+ return None
+ if isinstance(value, dict):
+ new_values = {}
+ for k, v in value.iteritems():
+ new_key = __join_prefix(key, k)
+ new_values[k] = replace_links(v, new_key)
+ return new_values
+ elif isinstance(value, list):
+ new_values = []
+ for i, v in enumerate(value):
+ # If we are a repeat we need to modify the key
+ # but not if values are actually $links.
+ if __is_link(v):
+ append_link(key, v)
+ new_values.append(None)
+ else:
+ new_key = "%s_%d" % ( key, i )
+ new_values.append(replace_links(v, new_key))
+ return new_values
+ else:
+ return value
+
+ if "state" in step:
+ step_state = step["state"]
+ step_state = replace_links(step_state)
+
+ for key, value in step_state.iteritems():
+ tool_state[key] = json.dumps(value)
+ del step["state"]
+
+ for key, values in connect.iteritems():
+ input_connection_value = []
+ if not isinstance(values, list):
+ values = [ values ]
+ for value in values:
+ if not isinstance(value, dict):
+ value_parts = str(value).split("#")
+ if len(value_parts) == 1:
+ value_parts.append("output")
+ id = value_parts[0]
+ if id in context.labels:
+ id = context.labels[id]
+ value = {"id": int(id), "output_name": value_parts[1]}
+ input_connection_value.append(value)
+ # TODO: this should be a list
+ step["input_connections"][key] = input_connection_value[0]
+
+ __populate_tool_state(step, tool_state)
+
+
+class ConversionContext(object):
+
+ def __init__(self):
+ self.labels = {}
+
+
+def __is_link(value):
+ return isinstance(value, dict) and "$link" in value
+
+
+def __join_prefix(prefix, key):
+ if prefix:
+ new_key = "%s|%s" % (prefix, key)
+ else:
+ new_key = key
+ return new_key
+
+
+def __ensure_inputs_connections(step):
+ if "input_connections" not in step:
+ step["input_connections"] = {}
+
+
+def __ensure_defaults(in_dict, defaults):
+ for key, value in defaults.items():
+ if key not in in_dict:
+ in_dict[ key ] = value
+
+
+def __populate_tool_state(step, tool_state):
+ step["tool_state"] = json.dumps(tool_state)
+
+
+def main(argv):
+ print json.dumps(yaml_to_workflow(argv[0]))
+
+
+if __name__ == "__main__":
+ main(sys.argv)
https://bitbucket.org/galaxy/galaxy-central/commits/c214c2f07f3b/
Changeset: c214c2f07f3b
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Split all workflow extraction testing out of test/api/test_workflows.py.
test_workflows.py was pretty unwieldy and the workflow extraction tests were very different than the other tests in that file (e.g. very different helper functions).
Affected #: 2 files
diff -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc -r c214c2f07f3bf7d86db8ee14188765c9aabdb22e test/api/test_workflow_extraction.py
--- /dev/null
+++ b/test/api/test_workflow_extraction.py
@@ -0,0 +1,269 @@
+from json import dumps, loads
+import operator
+
+from .helpers import skip_without_tool
+from .test_workflows import BaseWorkflowsApiTestCase
+
+
+class WorkflowExtractionApiTestCase( BaseWorkflowsApiTestCase ):
+
+ def setUp( self ):
+ super( WorkflowExtractionApiTestCase, self ).setUp()
+
+ @skip_without_tool( "cat1" )
+ def test_extract_from_history( self ):
+ history_id = self.dataset_populator.new_history()
+ # Run the simple test workflow and extract it back out from history
+ cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=history_id )
+ contents_response = self._get( "histories/%s/contents" % history_id )
+ input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] )
+ downloaded_workflow = self._extract_and_download_workflow(
+ from_history_id=history_id,
+ dataset_ids=dumps( input_hids ),
+ job_ids=dumps( [ cat1_job_id ] ),
+ workflow_name="test import from history",
+ )
+ self.assertEquals( downloaded_workflow[ "name" ], "test import from history" )
+ self.__assert_looks_like_cat1_example_workflow( downloaded_workflow )
+
+ def test_extract_with_copied_inputs( self ):
+ old_history_id = self.dataset_populator.new_history()
+ # Run the simple test workflow and extract it back out from history
+ self.__setup_and_run_cat1_workflow( history_id=old_history_id )
+
+ history_id = self.dataset_populator.new_history()
+
+ # Bug cannot mess up hids or these don't extract correctly. See Trello card here:
+ # https://trello.com/c/mKzLbM2P
+ # # create dummy dataset to complicate hid mapping
+ # self.dataset_populator.new_dataset( history_id, content="dummydataset" )
+ # offset = 1
+
+ offset = 0
+ old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
+ for old_dataset in old_contents:
+ self.__copy_content_to_history( history_id, old_dataset )
+ new_contents = self._get( "histories/%s/contents" % history_id ).json()
+ input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] )
+ cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] )
+ downloaded_workflow = self._extract_and_download_workflow(
+ from_history_id=history_id,
+ dataset_ids=dumps( input_hids ),
+ job_ids=dumps( [ cat1_job_id ] ),
+ workflow_name="test import from history",
+ )
+ self.__assert_looks_like_cat1_example_workflow( downloaded_workflow )
+
+ @skip_without_tool( "random_lines1" )
+ def test_extract_mapping_workflow_from_history( self ):
+ history_id = self.dataset_populator.new_history()
+ hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( history_id )
+ downloaded_workflow = self._extract_and_download_workflow(
+ from_history_id=history_id,
+ dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
+ job_ids=dumps( [ job_id1, job_id2 ] ),
+ workflow_name="test import from mapping history",
+ )
+ self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )
+
+ def test_extract_copied_mapping_from_history( self ):
+ old_history_id = self.dataset_populator.new_history()
+ hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id )
+
+ history_id = self.dataset_populator.new_history()
+ old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
+ for old_content in old_contents:
+ self.__copy_content_to_history( history_id, old_content )
+ # API test is somewhat contrived since there is no good way
+ # to retrieve job_id1, job_id2 like this for copied dataset
+ # collections I don't think.
+ downloaded_workflow = self._extract_and_download_workflow(
+ from_history_id=history_id,
+ dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
+ job_ids=dumps( [ job_id1, job_id2 ] ),
+ workflow_name="test import from history",
+ )
+ self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )
+
+ @skip_without_tool( "random_lines1" )
+ @skip_without_tool( "multi_data_param" )
+ def test_extract_reduction_from_history( self ):
+ history_id = self.dataset_populator.new_history()
+ hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json()
+ hdca_id = hdca[ "id" ]
+ inputs1 = {
+ "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] },
+ "num_lines": 2
+ }
+ implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 )
+ inputs2 = {
+ "f1": { "src": "hdca", "id": implicit_hdca1[ "id" ] },
+ "f2": { "src": "hdca", "id": implicit_hdca1[ "id" ] },
+ }
+ reduction_run_output = self.dataset_populator.run_tool(
+ tool_id="multi_data_param",
+ inputs=inputs2,
+ history_id=history_id,
+ )
+ job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ]
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 )
+ downloaded_workflow = self._extract_and_download_workflow(
+ from_history_id=history_id,
+ dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
+ job_ids=dumps( [ job_id1, job_id2 ] ),
+ workflow_name="test import reduction",
+ )
+ assert len( downloaded_workflow[ "steps" ] ) == 3
+ collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow )
+ tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 )
+ random_lines_map_step = tool_steps[ 0 ]
+ reduction_step = tool_steps[ 1 ]
+ random_lines_input = random_lines_map_step[ "input_connections" ][ "input" ]
+ assert random_lines_input[ "id" ] == collect_step_idx
+ reduction_step_input = reduction_step[ "input_connections" ][ "f1" ]
+ assert reduction_step_input[ "id"] == random_lines_map_step[ "id" ]
+
+ @skip_without_tool( "collection_paired_test" )
+ def test_extract_workflows_with_dataset_collections( self ):
+ history_id = self.dataset_populator.new_history()
+ hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json()
+ hdca_id = hdca[ "id" ]
+ inputs = {
+ "f1": dict( src="hdca", id=hdca_id )
+ }
+ run_output = self.dataset_populator.run_tool(
+ tool_id="collection_paired_test",
+ inputs=inputs,
+ history_id=history_id,
+ )
+ job_id = run_output[ "jobs" ][ 0 ][ "id" ]
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+ downloaded_workflow = self._extract_and_download_workflow(
+ from_history_id=history_id,
+ dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
+ job_ids=dumps( [ job_id ] ),
+ workflow_name="test import from history",
+ )
+ collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )
+ collection_step = collection_steps[ 0 ]
+ collection_step_state = loads( collection_step[ "tool_state" ] )
+ self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
+
+ def __run_random_lines_mapped_over_pair( self, history_id ):
+ hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json()
+ hdca_id = hdca[ "id" ]
+ inputs1 = {
+ "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] },
+ "num_lines": 2
+ }
+ implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 )
+ inputs2 = {
+ "input": { "batch": True, "values": [ { "src": "hdca", "id": implicit_hdca1[ "id" ] } ] },
+ "num_lines": 1
+ }
+ _, job_id2 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs2 )
+ return hdca, job_id1, job_id2
+
+ def __assert_looks_like_randomlines_mapping_workflow( self, downloaded_workflow ):
+ # Assert workflow is input connected to a tool step with one output
+ # connected to another tool step.
+ assert len( downloaded_workflow[ "steps" ] ) == 3
+ collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow )
+ tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 )
+ tool_step_idxs = []
+ tool_input_step_idxs = []
+ for tool_step in tool_steps:
+ self._assert_has_key( tool_step[ "input_connections" ], "input" )
+ input_step_idx = tool_step[ "input_connections" ][ "input" ][ "id" ]
+ tool_step_idxs.append( tool_step[ "id" ] )
+ tool_input_step_idxs.append( input_step_idx )
+
+ assert collect_step_idx not in tool_step_idxs
+ assert tool_input_step_idxs[ 0 ] == collect_step_idx
+ assert tool_input_step_idxs[ 1 ] == tool_step_idxs[ 0 ]
+
+ def __assert_looks_like_cat1_example_workflow( self, downloaded_workflow ):
+ assert len( downloaded_workflow[ "steps" ] ) == 3
+ input_steps = self._get_steps_of_type( downloaded_workflow, "data_input", expected_len=2 )
+ tool_step = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=1 )[ 0 ]
+
+ input1 = tool_step[ "input_connections" ][ "input1" ]
+ input2 = tool_step[ "input_connections" ][ "queries_0|input2" ]
+
+ self.assertEquals( input_steps[ 0 ][ "id" ], input1[ "id" ] )
+ self.assertEquals( input_steps[ 1 ][ "id" ], input2[ "id" ] )
+
+ def __copy_content_to_history( self, history_id, content ):
+ if content[ "history_content_type" ] == "dataset":
+ payload = dict(
+ source="hda",
+ content=content["id"]
+ )
+ response = self._post( "histories/%s/contents/datasets" % history_id, payload )
+
+ else:
+ payload = dict(
+ source="hdca",
+ content=content["id"]
+ )
+ response = self._post( "histories/%s/contents/dataset_collections" % history_id, payload )
+ self._assert_status_code_is( response, 200 )
+ return response.json()
+
+ def __setup_and_run_cat1_workflow( self, history_id ):
+ workflow = self.workflow_populator.load_workflow( name="test_for_extract" )
+ workflow_request, history_id = self._setup_workflow_run( workflow, history_id=history_id )
+ run_workflow_response = self._post( "workflows", data=workflow_request )
+ self._assert_status_code_is( run_workflow_response, 200 )
+
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=10 )
+ return self.__cat_job_id( history_id )
+
+ def _assert_first_step_is_paired_input( self, downloaded_workflow ):
+ collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )
+ collection_step = collection_steps[ 0 ]
+ collection_step_state = loads( collection_step[ "tool_state" ] )
+ self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
+ collect_step_idx = collection_step[ "id" ]
+ return collect_step_idx
+
+ def _extract_and_download_workflow( self, **extract_payload ):
+ create_workflow_response = self._post( "workflows", data=extract_payload )
+ self._assert_status_code_is( create_workflow_response, 200 )
+
+ new_workflow_id = create_workflow_response.json()[ "id" ]
+ download_response = self._get( "workflows/%s/download" % new_workflow_id )
+ self._assert_status_code_is( download_response, 200 )
+ downloaded_workflow = download_response.json()
+ return downloaded_workflow
+
+ def _get_steps_of_type( self, downloaded_workflow, type, expected_len=None ):
+ steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == type ]
+ if expected_len is not None:
+ n = len( steps )
+ assert n == expected_len, "Expected %d steps of type %s, found %d" % ( expected_len, type, n )
+ return sorted( steps, key=operator.itemgetter("id") )
+
+ def __job_id( self, history_id, dataset_id ):
+ url = "histories/%s/contents/%s/provenance" % ( history_id, dataset_id )
+ prov_response = self._get( url, data=dict( follow=False ) )
+ self._assert_status_code_is( prov_response, 200 )
+ return prov_response.json()[ "job_id" ]
+
+ def __cat_job_id( self, history_id ):
+ data = dict( history_id=history_id, tool_id="cat1" )
+ jobs_response = self._get( "jobs", data=data )
+ self._assert_status_code_is( jobs_response, 200 )
+ cat1_job_id = jobs_response.json()[ 0 ][ "id" ]
+ return cat1_job_id
+
+ def _run_tool_get_collection_and_job_id( self, history_id, tool_id, inputs ):
+ run_output1 = self.dataset_populator.run_tool(
+ tool_id=tool_id,
+ inputs=inputs,
+ history_id=history_id,
+ )
+ implicit_hdca = run_output1[ "implicit_collections" ][ 0 ]
+ job_id = run_output1[ "jobs" ][ 0 ][ "id" ]
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 )
+ return implicit_hdca, job_id
diff -r e5be58d2ae874cdeb697e1a367ea18652ca93fdc -r c214c2f07f3bf7d86db8ee14188765c9aabdb22e test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -1,7 +1,5 @@
from base import api
from json import dumps
-from json import loads
-import operator
import time
from .helpers import WorkflowPopulator
from .helpers import DatasetPopulator
@@ -46,6 +44,57 @@
self._assert_user_has_workflow_with_name( "%s (imported from API)" % ( workflow[ "name" ] ) )
return upload_response.json()[ "id" ]
+ def _setup_workflow_run( self, workflow, inputs_by='step_id', history_id=None ):
+ uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
+ if not history_id:
+ history_id = self.dataset_populator.new_history()
+ hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
+ hda2 = self.dataset_populator.new_dataset( history_id, content="4 5 6" )
+ workflow_request = dict(
+ history="hist_id=%s" % history_id,
+ workflow_id=uploaded_workflow_id,
+ )
+ label_map = {
+ 'WorkflowInput1': self._ds_entry(hda1),
+ 'WorkflowInput2': self._ds_entry(hda2)
+ }
+ if inputs_by == 'step_id':
+ ds_map = self._build_ds_map( uploaded_workflow_id, label_map )
+ workflow_request[ "ds_map" ] = ds_map
+ elif inputs_by == "step_index":
+ index_map = {
+ '0': self._ds_entry(hda1),
+ '1': self._ds_entry(hda2)
+ }
+ workflow_request[ "inputs" ] = dumps( index_map )
+ workflow_request[ "inputs_by" ] = 'step_index'
+ elif inputs_by == "name":
+ workflow_request[ "inputs" ] = dumps( label_map )
+ workflow_request[ "inputs_by" ] = 'name'
+
+ return workflow_request, history_id
+
+ def _build_ds_map( self, workflow_id, label_map ):
+ workflow_inputs = self._workflow_inputs( workflow_id )
+ ds_map = {}
+ for key, value in workflow_inputs.iteritems():
+ label = value[ "label" ]
+ if label in label_map:
+ ds_map[ key ] = label_map[ label ]
+ return dumps( ds_map )
+
+ def _ds_entry( self, hda ):
+ src = 'hda'
+ if 'history_content_type' in hda and hda[ 'history_content_type' ] == "dataset_collection":
+ src = 'hdca'
+ return dict( src=src, id=hda[ "id" ] )
+
+ def _workflow_inputs( self, uploaded_workflow_id ):
+ workflow_show_resposne = self._get( "workflows/%s" % uploaded_workflow_id )
+ self._assert_status_code_is( workflow_show_resposne, 200 )
+ workflow_inputs = workflow_show_resposne.json()[ "inputs" ]
+ return workflow_inputs
+
# Workflow API TODO:
# - Allow history_id as param to workflow run action. (hist_id)
@@ -358,109 +407,6 @@
step_map[step_index] = step["inputs"][0]["name"]
return step_map
- @skip_without_tool( "cat1" )
- def test_extract_from_history( self ):
- history_id = self.dataset_populator.new_history()
- # Run the simple test workflow and extract it back out from history
- cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=history_id )
- contents_response = self._get( "histories/%s/contents" % history_id )
- input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] )
- downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
- dataset_ids=dumps( input_hids ),
- job_ids=dumps( [ cat1_job_id ] ),
- workflow_name="test import from history",
- )
- self.assertEquals( downloaded_workflow[ "name" ], "test import from history" )
- self.__assert_looks_like_cat1_example_workflow( downloaded_workflow )
-
- def test_extract_with_copied_inputs( self ):
- old_history_id = self.dataset_populator.new_history()
- # Run the simple test workflow and extract it back out from history
- self.__setup_and_run_cat1_workflow( history_id=old_history_id )
-
- history_id = self.dataset_populator.new_history()
-
- # Bug cannot mess up hids or these don't extract correctly. See Trello card here:
- # https://trello.com/c/mKzLbM2P
- # # create dummy dataset to complicate hid mapping
- # self.dataset_populator.new_dataset( history_id, content="dummydataset" )
- # offset = 1
-
- offset = 0
- old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
- for old_dataset in old_contents:
- self.__copy_content_to_history( history_id, old_dataset )
- new_contents = self._get( "histories/%s/contents" % history_id ).json()
- input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] )
- cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] )
- downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
- dataset_ids=dumps( input_hids ),
- job_ids=dumps( [ cat1_job_id ] ),
- workflow_name="test import from history",
- )
- self.__assert_looks_like_cat1_example_workflow( downloaded_workflow )
-
- def __assert_looks_like_cat1_example_workflow( self, downloaded_workflow ):
- assert len( downloaded_workflow[ "steps" ] ) == 3
- input_steps = self._get_steps_of_type( downloaded_workflow, "data_input", expected_len=2 )
- tool_step = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=1 )[ 0 ]
-
- input1 = tool_step[ "input_connections" ][ "input1" ]
- input2 = tool_step[ "input_connections" ][ "queries_0|input2" ]
-
- self.assertEquals( input_steps[ 0 ][ "id" ], input1[ "id" ] )
- self.assertEquals( input_steps[ 1 ][ "id" ], input2[ "id" ] )
-
- def __setup_and_run_cat1_workflow( self, history_id ):
- workflow = self.workflow_populator.load_workflow( name="test_for_extract" )
- workflow_request, history_id = self._setup_workflow_run( workflow, history_id=history_id )
- run_workflow_response = self._post( "workflows", data=workflow_request )
- self._assert_status_code_is( run_workflow_response, 200 )
-
- self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=10 )
- return self.__cat_job_id( history_id )
-
- def __cat_job_id( self, history_id ):
- data = dict( history_id=history_id, tool_id="cat1" )
- jobs_response = self._get( "jobs", data=data )
- self._assert_status_code_is( jobs_response, 200 )
- cat1_job_id = jobs_response.json()[ 0 ][ "id" ]
- return cat1_job_id
-
- def __job_id( self, history_id, dataset_id ):
- url = "histories/%s/contents/%s/provenance" % ( history_id, dataset_id )
- prov_response = self._get( url, data=dict( follow=False ) )
- self._assert_status_code_is( prov_response, 200 )
- return prov_response.json()[ "job_id" ]
-
- @skip_without_tool( "collection_paired_test" )
- def test_extract_workflows_with_dataset_collections( self ):
- history_id = self.dataset_populator.new_history()
- hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json()
- hdca_id = hdca[ "id" ]
- inputs = {
- "f1": dict( src="hdca", id=hdca_id )
- }
- run_output = self.dataset_populator.run_tool(
- tool_id="collection_paired_test",
- inputs=inputs,
- history_id=history_id,
- )
- job_id = run_output[ "jobs" ][ 0 ][ "id" ]
- self.dataset_populator.wait_for_history( history_id, assert_ok=True )
- downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id ] ),
- workflow_name="test import from history",
- )
- collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )
- collection_step = collection_steps[ 0 ]
- collection_step_state = loads( collection_step[ "tool_state" ] )
- self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
-
def test_empty_create( self ):
response = self._post( "workflows" )
self._assert_status_code_is( response, 400 )
@@ -475,161 +421,6 @@
self._assert_status_code_is( response, 400 )
self._assert_error_code_is( response, error_codes.USER_REQUEST_INVALID_PARAMETER )
- @skip_without_tool( "random_lines1" )
- def test_extract_mapping_workflow_from_history( self ):
- history_id = self.dataset_populator.new_history()
- hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( history_id )
- downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id1, job_id2 ] ),
- workflow_name="test import from mapping history",
- )
- self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )
-
- def test_extract_copied_mapping_from_history( self ):
- old_history_id = self.dataset_populator.new_history()
- hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id )
-
- history_id = self.dataset_populator.new_history()
- old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
- for old_content in old_contents:
- self.__copy_content_to_history( history_id, old_content )
- # API test is somewhat contrived since there is no good way
- # to retrieve job_id1, job_id2 like this for copied dataset
- # collections I don't think.
- downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id1, job_id2 ] ),
- workflow_name="test import from history",
- )
- self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )
-
- @skip_without_tool( "random_lines1" )
- @skip_without_tool( "multi_data_param" )
- def test_extract_reduction_from_history( self ):
- history_id = self.dataset_populator.new_history()
- hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json()
- hdca_id = hdca[ "id" ]
- inputs1 = {
- "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] },
- "num_lines": 2
- }
- implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 )
- inputs2 = {
- "f1": { "src": "hdca", "id": implicit_hdca1[ "id" ] },
- "f2": { "src": "hdca", "id": implicit_hdca1[ "id" ] },
- }
- reduction_run_output = self.dataset_populator.run_tool(
- tool_id="multi_data_param",
- inputs=inputs2,
- history_id=history_id,
- )
- job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ]
- self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 )
- downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id1, job_id2 ] ),
- workflow_name="test import reduction",
- )
- assert len( downloaded_workflow[ "steps" ] ) == 3
- collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow )
- tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 )
- random_lines_map_step = tool_steps[ 0 ]
- reduction_step = tool_steps[ 1 ]
- random_lines_input = random_lines_map_step[ "input_connections" ][ "input" ]
- assert random_lines_input[ "id" ] == collect_step_idx
- reduction_step_input = reduction_step[ "input_connections" ][ "f1" ]
- assert reduction_step_input[ "id"] == random_lines_map_step[ "id" ]
-
- def __copy_content_to_history( self, history_id, content ):
- if content[ "history_content_type" ] == "dataset":
- payload = dict(
- source="hda",
- content=content["id"]
- )
- response = self._post( "histories/%s/contents/datasets" % history_id, payload )
-
- else:
- payload = dict(
- source="hdca",
- content=content["id"]
- )
- response = self._post( "histories/%s/contents/dataset_collections" % history_id, payload )
- self._assert_status_code_is( response, 200 )
- return response.json()
-
- def __run_random_lines_mapped_over_pair( self, history_id ):
- hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json()
- hdca_id = hdca[ "id" ]
- inputs1 = {
- "input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] },
- "num_lines": 2
- }
- implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 )
- inputs2 = {
- "input": { "batch": True, "values": [ { "src": "hdca", "id": implicit_hdca1[ "id" ] } ] },
- "num_lines": 1
- }
- _, job_id2 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs2 )
- return hdca, job_id1, job_id2
-
- def __assert_looks_like_randomlines_mapping_workflow( self, downloaded_workflow ):
- # Assert workflow is input connected to a tool step with one output
- # connected to another tool step.
- assert len( downloaded_workflow[ "steps" ] ) == 3
- collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow )
- tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 )
- tool_step_idxs = []
- tool_input_step_idxs = []
- for tool_step in tool_steps:
- self._assert_has_key( tool_step[ "input_connections" ], "input" )
- input_step_idx = tool_step[ "input_connections" ][ "input" ][ "id" ]
- tool_step_idxs.append( tool_step[ "id" ] )
- tool_input_step_idxs.append( input_step_idx )
-
- assert collect_step_idx not in tool_step_idxs
- assert tool_input_step_idxs[ 0 ] == collect_step_idx
- assert tool_input_step_idxs[ 1 ] == tool_step_idxs[ 0 ]
-
- def _run_tool_get_collection_and_job_id( self, history_id, tool_id, inputs ):
- run_output1 = self.dataset_populator.run_tool(
- tool_id=tool_id,
- inputs=inputs,
- history_id=history_id,
- )
- implicit_hdca = run_output1[ "implicit_collections" ][ 0 ]
- job_id = run_output1[ "jobs" ][ 0 ][ "id" ]
- self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 )
- return implicit_hdca, job_id
-
- def _assert_first_step_is_paired_input( self, downloaded_workflow ):
- collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )
- collection_step = collection_steps[ 0 ]
- collection_step_state = loads( collection_step[ "tool_state" ] )
- self.assertEquals( collection_step_state[ "collection_type" ], u"paired" )
- collect_step_idx = collection_step[ "id" ]
- return collect_step_idx
-
- def _extract_and_download_workflow( self, **extract_payload ):
- create_workflow_response = self._post( "workflows", data=extract_payload )
- self._assert_status_code_is( create_workflow_response, 200 )
-
- new_workflow_id = create_workflow_response.json()[ "id" ]
- download_response = self._get( "workflows/%s/download" % new_workflow_id )
- self._assert_status_code_is( download_response, 200 )
- downloaded_workflow = download_response.json()
- return downloaded_workflow
-
- def _get_steps_of_type( self, downloaded_workflow, type, expected_len=None ):
- steps = [ s for s in downloaded_workflow[ "steps" ].values() if s[ "type" ] == type ]
- if expected_len is not None:
- n = len( steps )
- assert n == expected_len, "Expected %d steps of type %s, found %d" % ( expected_len, type, n )
- return sorted( steps, key=operator.itemgetter("id") )
-
@skip_without_tool( "cat1" )
def test_run_with_pja( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_pja_run", add_pja=True )
@@ -776,45 +567,6 @@
assert len( usages ) == 1
return workflow_id, usages[ 0 ]
- def _setup_workflow_run( self, workflow, inputs_by='step_id', history_id=None ):
- uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
- if not history_id:
- history_id = self.dataset_populator.new_history()
- hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
- hda2 = self.dataset_populator.new_dataset( history_id, content="4 5 6" )
- workflow_request = dict(
- history="hist_id=%s" % history_id,
- workflow_id=uploaded_workflow_id,
- )
- label_map = {
- 'WorkflowInput1': self._ds_entry(hda1),
- 'WorkflowInput2': self._ds_entry(hda2)
- }
- if inputs_by == 'step_id':
- ds_map = self._build_ds_map( uploaded_workflow_id, label_map )
- workflow_request[ "ds_map" ] = ds_map
- elif inputs_by == "step_index":
- index_map = {
- '0': self._ds_entry(hda1),
- '1': self._ds_entry(hda2)
- }
- workflow_request[ "inputs" ] = dumps( index_map )
- workflow_request[ "inputs_by" ] = 'step_index'
- elif inputs_by == "name":
- workflow_request[ "inputs" ] = dumps( label_map )
- workflow_request[ "inputs_by" ] = 'name'
-
- return workflow_request, history_id
-
- def _build_ds_map( self, workflow_id, label_map ):
- workflow_inputs = self._workflow_inputs( workflow_id )
- ds_map = {}
- for key, value in workflow_inputs.iteritems():
- label = value[ "label" ]
- if label in label_map:
- ds_map[ key ] = label_map[ label ]
- return dumps( ds_map )
-
def _setup_random_x2_workflow_steps( self, name ):
workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" )
random_line_steps = self._random_lines_steps( workflow_request )
@@ -843,18 +595,6 @@
)
return workflow_request, history_id
- def _workflow_inputs( self, uploaded_workflow_id ):
- workflow_show_resposne = self._get( "workflows/%s" % uploaded_workflow_id )
- self._assert_status_code_is( workflow_show_resposne, 200 )
- workflow_inputs = workflow_show_resposne.json()[ "inputs" ]
- return workflow_inputs
-
- def _ds_entry( self, hda ):
- src = 'hda'
- if 'history_content_type' in hda and hda[ 'history_content_type' ] == "dataset_collection":
- src = 'hdca'
- return dict( src=src, id=hda[ "id" ] )
-
def __review_paused_steps( self, uploaded_workflow_id, invocation_id, order_index, action=True ):
invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
invocation_steps = invocation[ "steps" ]
https://bitbucket.org/galaxy/galaxy-central/commits/415221281212/
Changeset: 415221281212
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Simplify new test_workflow_extraction.py.
Now makes sense to assume all tests consume a history.
Affected #: 1 file
diff -r c214c2f07f3bf7d86db8ee14188765c9aabdb22e -r 415221281212483cdad6213e284c03e0698dbf63 test/api/test_workflow_extraction.py
--- a/test/api/test_workflow_extraction.py
+++ b/test/api/test_workflow_extraction.py
@@ -9,16 +9,16 @@
def setUp( self ):
super( WorkflowExtractionApiTestCase, self ).setUp()
+ self.history_id = self.dataset_populator.new_history()
@skip_without_tool( "cat1" )
def test_extract_from_history( self ):
- history_id = self.dataset_populator.new_history()
# Run the simple test workflow and extract it back out from history
- cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=history_id )
- contents_response = self._get( "histories/%s/contents" % history_id )
+ cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=self.history_id )
+ contents_response = self._get( "histories/%s/contents" % self.history_id )
input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
+ from_history_id=self.history_id,
dataset_ids=dumps( input_hids ),
job_ids=dumps( [ cat1_job_id ] ),
workflow_name="test import from history",
@@ -31,8 +31,6 @@
# Run the simple test workflow and extract it back out from history
self.__setup_and_run_cat1_workflow( history_id=old_history_id )
- history_id = self.dataset_populator.new_history()
-
# Bug cannot mess up hids or these don't extract correctly. See Trello card here:
# https://trello.com/c/mKzLbM2P
# # create dummy dataset to complicate hid mapping
@@ -42,12 +40,12 @@
offset = 0
old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
for old_dataset in old_contents:
- self.__copy_content_to_history( history_id, old_dataset )
- new_contents = self._get( "histories/%s/contents" % history_id ).json()
+ self.__copy_content_to_history( self.history_id, old_dataset )
+ new_contents = self._get( "histories/%s/contents" % self.history_id ).json()
input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] )
- cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] )
+ cat1_job_id = self.__job_id( self.history_id, new_contents[ (offset + 2) ][ "id" ] )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
+ from_history_id=self.history_id,
dataset_ids=dumps( input_hids ),
job_ids=dumps( [ cat1_job_id ] ),
workflow_name="test import from history",
@@ -56,10 +54,9 @@
@skip_without_tool( "random_lines1" )
def test_extract_mapping_workflow_from_history( self ):
- history_id = self.dataset_populator.new_history()
- hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( history_id )
+ hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( self.history_id )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
+ from_history_id=self.history_id,
dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
job_ids=dumps( [ job_id1, job_id2 ] ),
workflow_name="test import from mapping history",
@@ -70,15 +67,14 @@
old_history_id = self.dataset_populator.new_history()
hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id )
- history_id = self.dataset_populator.new_history()
old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
for old_content in old_contents:
- self.__copy_content_to_history( history_id, old_content )
+ self.__copy_content_to_history( self.history_id, old_content )
# API test is somewhat contrived since there is no good way
# to retrieve job_id1, job_id2 like this for copied dataset
# collections I don't think.
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
+ from_history_id=self.history_id,
dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
job_ids=dumps( [ job_id1, job_id2 ] ),
workflow_name="test import from history",
@@ -88,14 +84,13 @@
@skip_without_tool( "random_lines1" )
@skip_without_tool( "multi_data_param" )
def test_extract_reduction_from_history( self ):
- history_id = self.dataset_populator.new_history()
- hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json()
+ hdca = self.dataset_collection_populator.create_pair_in_history( self.history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json()
hdca_id = hdca[ "id" ]
inputs1 = {
"input": { "batch": True, "values": [ { "src": "hdca", "id": hdca_id } ] },
"num_lines": 2
}
- implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 )
+ implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( self.history_id, "random_lines1", inputs1 )
inputs2 = {
"f1": { "src": "hdca", "id": implicit_hdca1[ "id" ] },
"f2": { "src": "hdca", "id": implicit_hdca1[ "id" ] },
@@ -103,12 +98,12 @@
reduction_run_output = self.dataset_populator.run_tool(
tool_id="multi_data_param",
inputs=inputs2,
- history_id=history_id,
+ history_id=self.history_id,
)
job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ]
- self.dataset_populator.wait_for_history( history_id, assert_ok=True, timeout=20 )
+ self.dataset_populator.wait_for_history( self.history_id, assert_ok=True, timeout=20 )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
+ from_history_id=self.history_id,
dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
job_ids=dumps( [ job_id1, job_id2 ] ),
workflow_name="test import reduction",
@@ -125,8 +120,7 @@
@skip_without_tool( "collection_paired_test" )
def test_extract_workflows_with_dataset_collections( self ):
- history_id = self.dataset_populator.new_history()
- hdca = self.dataset_collection_populator.create_pair_in_history( history_id ).json()
+ hdca = self.dataset_collection_populator.create_pair_in_history( self.history_id ).json()
hdca_id = hdca[ "id" ]
inputs = {
"f1": dict( src="hdca", id=hdca_id )
@@ -134,12 +128,12 @@
run_output = self.dataset_populator.run_tool(
tool_id="collection_paired_test",
inputs=inputs,
- history_id=history_id,
+ history_id=self.history_id,
)
job_id = run_output[ "jobs" ][ 0 ][ "id" ]
- self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+ self.dataset_populator.wait_for_history( self.history_id, assert_ok=True )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=history_id,
+ from_history_id=self.history_id,
dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
job_ids=dumps( [ job_id ] ),
workflow_name="test import from history",
https://bitbucket.org/galaxy/galaxy-central/commits/b8a2150cfea0/
Changeset: b8a2150cfea0
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Simplify interface to test helper _extract_and_download_workflow.
Makes tests in this file marginally more readable.
Affected #: 1 file
diff -r 415221281212483cdad6213e284c03e0698dbf63 -r b8a2150cfea0a925cd21f7de71e1547b3b118025 test/api/test_workflow_extraction.py
--- a/test/api/test_workflow_extraction.py
+++ b/test/api/test_workflow_extraction.py
@@ -18,10 +18,8 @@
contents_response = self._get( "histories/%s/contents" % self.history_id )
input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=self.history_id,
- dataset_ids=dumps( input_hids ),
- job_ids=dumps( [ cat1_job_id ] ),
- workflow_name="test import from history",
+ dataset_ids=input_hids,
+ job_ids=[ cat1_job_id ],
)
self.assertEquals( downloaded_workflow[ "name" ], "test import from history" )
self.__assert_looks_like_cat1_example_workflow( downloaded_workflow )
@@ -45,10 +43,8 @@
input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] )
cat1_job_id = self.__job_id( self.history_id, new_contents[ (offset + 2) ][ "id" ] )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=self.history_id,
- dataset_ids=dumps( input_hids ),
- job_ids=dumps( [ cat1_job_id ] ),
- workflow_name="test import from history",
+ dataset_ids=input_hids,
+ job_ids=[ cat1_job_id ],
)
self.__assert_looks_like_cat1_example_workflow( downloaded_workflow )
@@ -56,10 +52,8 @@
def test_extract_mapping_workflow_from_history( self ):
hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( self.history_id )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=self.history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id1, job_id2 ] ),
- workflow_name="test import from mapping history",
+ dataset_collection_ids=[ hdca[ "hid" ] ],
+ job_ids=[ job_id1, job_id2 ],
)
self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )
@@ -74,10 +68,8 @@
# to retrieve job_id1, job_id2 like this for copied dataset
# collections I don't think.
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=self.history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id1, job_id2 ] ),
- workflow_name="test import from history",
+ dataset_collection_ids=[ hdca[ "hid" ] ],
+ job_ids=[ job_id1, job_id2 ],
)
self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )
@@ -103,10 +95,8 @@
job_id2 = reduction_run_output[ "jobs" ][ 0 ][ "id" ]
self.dataset_populator.wait_for_history( self.history_id, assert_ok=True, timeout=20 )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=self.history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id1, job_id2 ] ),
- workflow_name="test import reduction",
+ dataset_collection_ids=[ hdca[ "hid" ] ],
+ job_ids=[ job_id1, job_id2 ],
)
assert len( downloaded_workflow[ "steps" ] ) == 3
collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow )
@@ -133,10 +123,8 @@
job_id = run_output[ "jobs" ][ 0 ][ "id" ]
self.dataset_populator.wait_for_history( self.history_id, assert_ok=True )
downloaded_workflow = self._extract_and_download_workflow(
- from_history_id=self.history_id,
- dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ),
- job_ids=dumps( [ job_id ] ),
- workflow_name="test import from history",
+ dataset_collection_ids=[ hdca[ "hid" ] ],
+ job_ids=[ job_id ],
)
collection_steps = self._get_steps_of_type( downloaded_workflow, "data_collection_input", expected_len=1 )
collection_step = collection_steps[ 0 ]
@@ -222,6 +210,18 @@
return collect_step_idx
def _extract_and_download_workflow( self, **extract_payload ):
+ if "from_history_id" not in extract_payload:
+ extract_payload[ "from_history_id" ] = self.history_id
+
+ if "workflow_name" not in extract_payload:
+ extract_payload[ "workflow_name" ] = "test import from history"
+
+ for key in "job_ids", "dataset_ids", "dataset_collection_ids":
+ if key in extract_payload:
+ value = extract_payload[ key ]
+ if isinstance(value, list):
+ extract_payload[ key ] = dumps( value )
+
create_workflow_response = self._post( "workflows", data=extract_payload )
self._assert_status_code_is( create_workflow_response, 200 )
https://bitbucket.org/galaxy/galaxy-central/commits/47195be80a9f/
Changeset: 47195be80a9f
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Introduce another helper to simplify test_workflow_extraction.py.
Affected #: 1 file
diff -r b8a2150cfea0a925cd21f7de71e1547b3b118025 -r 47195be80a9fa06c4777103d74dcbb2a18a8c33b test/api/test_workflow_extraction.py
--- a/test/api/test_workflow_extraction.py
+++ b/test/api/test_workflow_extraction.py
@@ -15,8 +15,8 @@
def test_extract_from_history( self ):
# Run the simple test workflow and extract it back out from history
cat1_job_id = self.__setup_and_run_cat1_workflow( history_id=self.history_id )
- contents_response = self._get( "histories/%s/contents" % self.history_id )
- input_hids = map( lambda c: c[ "hid" ], contents_response.json()[ 0:2 ] )
+ contents = self._history_contents()
+ input_hids = map( lambda c: c[ "hid" ], contents[ 0:2 ] )
downloaded_workflow = self._extract_and_download_workflow(
dataset_ids=input_hids,
job_ids=[ cat1_job_id ],
@@ -36,10 +36,10 @@
# offset = 1
offset = 0
- old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
+ old_contents = self._history_contents( old_history_id )
for old_dataset in old_contents:
self.__copy_content_to_history( self.history_id, old_dataset )
- new_contents = self._get( "histories/%s/contents" % self.history_id ).json()
+ new_contents = self._history_contents()
input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] )
cat1_job_id = self.__job_id( self.history_id, new_contents[ (offset + 2) ][ "id" ] )
downloaded_workflow = self._extract_and_download_workflow(
@@ -61,7 +61,7 @@
old_history_id = self.dataset_populator.new_history()
hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id )
- old_contents = self._get( "histories/%s/contents" % old_history_id ).json()
+ old_contents = self._history_contents( old_history_id )
for old_content in old_contents:
self.__copy_content_to_history( self.history_id, old_content )
# API test is somewhat contrived since there is no good way
@@ -175,6 +175,11 @@
self.assertEquals( input_steps[ 0 ][ "id" ], input1[ "id" ] )
self.assertEquals( input_steps[ 1 ][ "id" ], input2[ "id" ] )
+ def _history_contents( self, history_id=None ):
+ if history_id is None:
+ history_id = self.history_id
+ return self._get( "histories/%s/contents" % history_id ).json()
+
def __copy_content_to_history( self, history_id, content ):
if content[ "history_content_type" ] == "dataset":
payload = dict(
https://bitbucket.org/galaxy/galaxy-central/commits/d0dc9272a481/
Changeset: d0dc9272a481
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Fix for running test_extract_workflow.py stand-alone.
Affected #: 1 file
diff -r 47195be80a9fa06c4777103d74dcbb2a18a8c33b -r d0dc9272a4819e2fb8867b45b782ac2e6d3d8861 test/unit/workflows/test_extract_summary.py
--- a/test/unit/workflows/test_extract_summary.py
+++ b/test/unit/workflows/test_extract_summary.py
@@ -1,5 +1,6 @@
import unittest
+import galaxy.model.mapping
from galaxy import model
from galaxy.workflow import extract
https://bitbucket.org/galaxy/galaxy-central/commits/bc4086a04bef/
Changeset: bc4086a04bef
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Remove dated TODO from workflow extraction code.
Affected #: 1 file
diff -r d0dc9272a4819e2fb8867b45b782ac2e6d3d8861 -r bc4086a04beff9b1530e3093a15e15ffd8faa6b0 lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -205,8 +205,6 @@
else:
dataset_collection = content
# TODO: Optimize db call
- # TODO: Ensure this is deterministic, must get same job
- # for each dataset collection.
dataset_instance = dataset_collection.collection.dataset_instances[ 0 ]
if not self.__check_state( dataset_instance ):
# Just checking the state of one instance, don't need more but
https://bitbucket.org/galaxy/galaxy-central/commits/172c82454647/
Changeset: 172c82454647
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: More unit tests for workflow extraction summarize method.
Affected #: 1 file
diff -r bc4086a04beff9b1530e3093a15e15ffd8faa6b0 -r 172c824546478705dfc108310bd5db88254f5798 test/unit/workflows/test_extract_summary.py
--- a/test/unit/workflows/test_extract_summary.py
+++ b/test/unit/workflows/test_extract_summary.py
@@ -46,7 +46,7 @@
assert len( job_dict ) == 1
self.assertEquals( job_dict[ hda.job ], [ ('out1', derived_hda_2 ) ] )
- def test_fake_job( self ):
+ def test_fake_job_hda( self ):
""" Fakes job if creating_job_associations is empty.
"""
hda = MockHda( job=UNDEFINED_JOB )
@@ -59,6 +59,28 @@
datasets = job_dict.values()[ 0 ]
assert datasets == [ ( None, hda ) ]
+ def test_fake_job_hdca( self ):
+ hdca = MockHdca( )
+ self.history.active_datasets.append( hdca )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert len( job_dict ) == 1
+ fake_job = job_dict.keys()[ 0 ]
+ assert fake_job.id.startswith( "fake_" )
+ assert fake_job.is_fake
+ content_instances = job_dict.values()[ 0 ]
+ assert content_instances == [ ( None, hdca ) ]
+
+ def test_implicit_map_job_hdca( self ):
+ creating_job = model.Job()
+ hdca = MockHdca( implicit_output_name="out1", job=creating_job )
+ self.history.active_datasets.append( hdca )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert len( job_dict ) == 1
+ job = job_dict.keys()[ 0 ]
+ assert job is creating_job
+
def test_warns_and_skips_datasets_if_not_finished( self ):
hda = MockHda( state='queued' )
self.history.active_datasets.append( hda )
@@ -102,3 +124,31 @@
self.creating_job_associations = [ assoc ]
else:
self.creating_job_associations = []
+
+
+class MockHdca( object ):
+
+ def __init__( self, implicit_output_name=None, job=None, hid=1 ):
+ self.id = 124
+ self.copied_from_history_dataset_collection_association = None
+ self.history_content_type = "dataset_collection"
+ self.implicit_output_name = implicit_output_name
+ self.hid = 1
+ self.collection = model.DatasetCollection()
+ element = model.DatasetCollectionElement(
+ collection=self.collection,
+ element=model.HistoryDatasetAssociation(),
+ element_index=0,
+ element_identifier="moocow",
+ )
+ element.dataset_instance.dataset = model.Dataset()
+ element.dataset_instance.dataset.state = "ok"
+ creating = model.JobToOutputDatasetAssociation(
+ implicit_output_name,
+ element.dataset_instance,
+ )
+ creating.job = job
+ element.dataset_instance.creating_job_associations = [
+ creating,
+ ]
+ self.collection.elements = [element]
https://bitbucket.org/galaxy/galaxy-central/commits/74e82c604d02/
Changeset: 74e82c604d02
User: jmchilton
Date: 2014-12-02 02:18:56+00:00
Summary: Refactor lib/galaxy/workflow/extract.py to breakup big loop.
Affected #: 1 file
diff -r 172c824546478705dfc108310bd5db88254f5798 -r 74e82c604d026307fa8d72a7850ddd33c5f9259b lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -195,39 +195,48 @@
# needed because cannot allow selection of individual datasets from an implicit
# mapping during extraction - you get the collection or nothing.
for content in self.history.active_contents:
- if content.history_content_type == "dataset_collection":
- hid = content.hid
- content = self.__original_hdca( content )
- self.collection_types[ hid ] = content.collection.collection_type
- if not content.implicit_output_name:
- job = DatasetCollectionCreationJob( content )
- self.jobs[ job ] = [ ( None, content ) ]
+ self.__summarize_content( content )
+
+ def __summarize_content( self, content ):
+ # Update internal state for history content (either an HDA or
+ # an HDCA).
+ if content.history_content_type == "dataset_collection":
+ self.__summarize_dataset_collection( content )
+ else:
+ self.__summarize_dataset( content )
+
+ def __summarize_dataset_collection( self, content ):
+ content = self.__original_hdca( content )
+ dataset_collection = content
+ hid = content.hid
+ self.collection_types[ hid ] = content.collection.collection_type
+ if not content.implicit_output_name:
+ job = DatasetCollectionCreationJob( content )
+ self.jobs[ job ] = [ ( None, content ) ]
+ else:
+ dataset_collection = content
+ # TODO: Optimize db call
+ dataset_instance = dataset_collection.collection.dataset_instances[ 0 ]
+ if not self.__check_state( dataset_instance ):
+ # Just checking the state of one instance, don't need more but
+ # makes me wonder if even need this check at all?
+ return
+
+ job_hda = self.__original_hda( dataset_instance )
+ if not job_hda.creating_job_associations:
+ log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" )
+ job = DatasetCollectionCreationJob( dataset_collection )
+ self.jobs[ job ] = [ ( None, dataset_collection ) ]
+
+ for assoc in job_hda.creating_job_associations:
+ job = assoc.job
+ if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset":
+ self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ]
+ self.implicit_map_jobs.append( job )
else:
- dataset_collection = content
- # TODO: Optimize db call
- dataset_instance = dataset_collection.collection.dataset_instances[ 0 ]
- if not self.__check_state( dataset_instance ):
- # Just checking the state of one instance, don't need more but
- # makes me wonder if even need this check at all?
- continue
+ self.jobs[ job ].append( ( assoc.name, dataset_collection ) )
- job_hda = self.__original_hda( dataset_instance )
- if not job_hda.creating_job_associations:
- log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" )
- job = DatasetCollectionCreationJob( dataset_collection )
- self.jobs[ job ] = [ ( None, dataset_collection ) ]
-
- for assoc in job_hda.creating_job_associations:
- job = assoc.job
- if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset":
- self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ]
- self.implicit_map_jobs.append( job )
- else:
- self.jobs[ job ].append( ( assoc.name, dataset_collection ) )
- else:
- self.__append_dataset( content )
-
- def __append_dataset( self, dataset ):
+ def __summarize_dataset( self, dataset ):
if not self.__check_state( dataset ):
return
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxyproject/usegalaxy-playbook] ecd10d: Update readme w/ instructions for updating Galaxy ...
by GitHub 02 Dec '14
by GitHub 02 Dec '14
02 Dec '14
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: ecd10db580aa8f39812ba06ba977d0ab5df8ba5e
https://github.com/galaxyproject/usegalaxy-playbook/commit/ecd10db580aa8f39…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2014-12-01 (Mon, 01 Dec 2014)
Changed paths:
M README.md
Log Message:
-----------
Update readme w/ instructions for updating Galaxy playbook.
1
0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1034c973ec1d/
Changeset: 1034c973ec1d
Branch: next-stable
User: guerler
Date: 2014-12-01 17:52:01+00:00
Summary: Pages: Sanitize name column in items grid
Affected #: 1 file
diff -r 4569b8f31c883e6f38f6b04c665f93cb2af534ee -r 1034c973ec1d2ce424f711d750ecc6de582d02aa lib/galaxy/webapps/galaxy/controllers/page.py
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -8,6 +8,7 @@
from galaxy import util
from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor
from galaxy.util.json import loads
+from markupsafe import escape
def format_bool( b ):
if b:
@@ -89,9 +90,9 @@
class NameColumn( grids.TextColumn ):
def get_value(self, trans, grid, item):
if hasattr( item, "get_display_name" ):
- return item.get_display_name()
+ return escape(item.get_display_name())
else:
- return item.name
+ return escape(item.name)
# Grid definition.
show_item_checkboxes = True
https://bitbucket.org/galaxy/galaxy-central/commits/5393f6389105/
Changeset: 5393f6389105
User: guerler
Date: 2014-12-01 17:52:17+00:00
Summary: Merge
Affected #: 1 file
diff -r d094b6d5953c1379a69050d4cadef03c55413f06 -r 5393f6389105d22bc8791f908075c152f11a4d2e lib/galaxy/webapps/galaxy/controllers/page.py
--- a/lib/galaxy/webapps/galaxy/controllers/page.py
+++ b/lib/galaxy/webapps/galaxy/controllers/page.py
@@ -8,6 +8,7 @@
from galaxy import util
from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor
from galaxy.util.json import loads
+from markupsafe import escape
def format_bool( b ):
if b:
@@ -89,9 +90,9 @@
class NameColumn( grids.TextColumn ):
def get_value(self, trans, grid, item):
if hasattr( item, "get_display_name" ):
- return item.get_display_name()
+ return escape(item.get_display_name())
else:
- return item.name
+ return escape(item.name)
# Grid definition.
show_item_checkboxes = True
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxyproject/usegalaxy-playbook] 8806f0: Update galaxy role from ansible-galaxy.
by GitHub 02 Dec '14
by GitHub 02 Dec '14
02 Dec '14
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 8806f00147b362ccecca457f346abd1e309338fc
https://github.com/galaxyproject/usegalaxy-playbook/commit/8806f00147b362cc…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2014-12-01 (Mon, 01 Dec 2014)
Changed paths:
M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info
M roles/galaxyprojectdotorg.galaxy/tasks/clone.yml
Log Message:
-----------
Update galaxy role from ansible-galaxy.
1
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Branch: refs/tags/0.4
Home: https://github.com/galaxyproject/ansible-galaxy
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