mirror of
https://github.com/galaxyproject/galaxy.git
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Merge branch 'release_16.07' into dev
Conflicts: doc/source/admin/conda_faq.rst static/maps/mvc/ui/ui-modal.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-modal.js
This commit is contained in:
Nicola Soranzo
@@ -1,5 +1,8 @@
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define([], function() {
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var View = Backbone.View.extend({
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className: "ui-modal",
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// defaults
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optionsDefault : {
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container : 'body',
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@@ -19,18 +22,8 @@ var View = Backbone.View.extend({
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// initialize
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initialize: function( options ) {
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this.setElement( this._template() );
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this.options = _.defaults( options || {}, this.optionsDefault );
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$( this.options.container ).prepend( this.el );
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// link elements
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this.$header = this.$( '.modal-header' );
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this.$dialog = this.$( '.modal-dialog' );
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this.$body = this.$( '.modal-body' );
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this.$footer = this.$( '.modal-footer' );
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this.$backdrop = this.$( '.modal-backdrop' );
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this.$buttons = this.$( '.buttons' );
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// optional render
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options && this.render();
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},
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@@ -70,6 +63,16 @@ var View = Backbone.View.extend({
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*/
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render: function() {
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var self = this;
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this.$el.html( this._template() );
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// link elements
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this.$header = this.$( '.modal-header' );
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this.$dialog = this.$( '.modal-dialog' );
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this.$body = this.$( '.modal-body' );
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this.$footer = this.$( '.modal-footer' );
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this.$backdrop = this.$( '.modal-backdrop' );
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this.$buttons = this.$( '.buttons' );
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if (this.options.body == 'progress') {
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this.options.body = $( '<div class="progress progress-striped active">' +
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'<div class="progress-bar progress-bar-info" style="width:100%"/>' +
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@@ -164,17 +167,15 @@ var View = Backbone.View.extend({
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* Returns the modal template
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*/
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_template: function() {
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return '<div class="ui-modal">' +
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'<div class="modal-backdrop fade"/>' +
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'<div class="modal-dialog">' +
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'<div class="modal-content">' +
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'<div class="modal-header">' +
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'<h4 class="title"/>' +
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'</div>' +
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'<div class="modal-body"/>' +
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'<div class="modal-footer">' +
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'<div class="buttons"/>' +
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'</div>' +
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return '<div class="modal-backdrop fade"/>' +
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'<div class="modal-dialog">' +
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'<div class="modal-content">' +
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'<div class="modal-header">' +
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'<h4 class="title"/>' +
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'</div>' +
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'<div class="modal-body"/>' +
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'<div class="modal-footer">' +
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'<div class="buttons"/>' +
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'</div>' +
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'</div>' +
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'</div>';
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@@ -50,13 +50,17 @@ Below we answer some common questions (collected by Lance Parsons):
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Galaxy's dependency job resolution is managed via
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``dependency_resolvers_conf.xml`` configuration file. Most Galaxy administrators
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have not set up a dependency resolvers configuration file, which means they are
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using Galaxy's default ( ``dependency_resolvers_conf.xml.sample`` ). With
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release 16.04, Galaxy has enabled Conda dependency resolution by default when
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should be using Galaxy's default dependency resolvers configuration file
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( ``dependency_resolvers_conf.xml.sample`` ). With
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release 16.04, Galaxy has enabled Conda dependency resolution by default when
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Conda was already installed on the system. Having Conda enabled in
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``dependency_resolvers_conf.xml`` means that Galaxy will look for job
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``dependency_resolvers_conf.xml`` means that Galaxy can look for job
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dependencies using the Conda system when it attempts to run tools.
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Note that the order of resolvers in the file matters and the ``<tool_shed_packages />``
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entry should remain first. This means that tools that have specified Tool Shed packages
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as their dependencies will work without a change.
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The most common configuration settings related to Conda are listed in Table 1.
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See `galaxy.ini.sample`_ for the complete list.
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@@ -101,7 +105,7 @@ See `galaxy.ini.sample`_ for the complete list.
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2. How do Conda dependencies work? Where do things get installed?
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*********************************************************************************
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In contrast to the old dependency system, which was used exclusively by Galaxy,
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In contrast to the TS dependency system, which was used exclusively by Galaxy,
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Conda is a pre-existing, independent project. With Conda, it is possible for an
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admin to install and manage packages without touching Galaxy at all. Galaxy can
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handle these dependencies for you, but admins are not required to use Galaxy for
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@@ -170,19 +174,28 @@ systems newer than 2007.
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This depends on your ``galaxy.ini`` setting. Starting with release 16.07, Galaxy
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can automatically install the Conda package manager for you if you have enabled
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``conda_auto_init``. Galaxy can then install Trinity along with its dependencies
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using one of the methods listed in question 2 above. Further, if
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``conda_auto_install`` is enabled, Galaxy will install Trinity via Conda only
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when a Trinity job is launched and Trinity is not yet installed.
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using one of the methods listed in question 2 above. In particular, if
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``conda_auto_install`` is True and Trinity is not installed yet, Galaxy will try
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to install it via Conda when a Trinity job is launched.
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With release 16.07 you can see which dependencies are being used
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in the “Manage installed tools” section of the Admin panel and you can select
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whether or not to install Conda packages or Tool Shed package recipes when you
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install new tools there, even if ``conda_auto_install`` is disabled.
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More improvements to the UI will be coming in future releases. To see if Galaxy
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has created a Trinity environment for you have a look at folder under
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During a tool installation, the Galaxy admin has control over which systems will be used to
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install the tool requirements. The default settings will trigger installation
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of both TS and Conda packages (if Conda is present), thus depending on the
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dependency resolvers configuration with regards to what will actually be used during
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the tool execution.
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To check if Galaxy has created a Trinity environment, have a look at folders under
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``<tool_dependency_dir>/_conda/envs/``(or ``<conda_prefix>/envs`` if you have changed `conda_prefix` in your galaxy.ini file).
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We recommend to use Conda on a tool-per-tool basis, by unchecking the checkbox
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for TS dependencies during the tool installation, and for tools where there
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are no available TS dependencies.
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5. Can I mix traditional Galaxy packages and Conda packages?
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*********************************************************************************
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@@ -198,7 +211,8 @@ The order in which resolvers are tried is listed in the
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- Packages manually installed by administrators
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- Conda packages
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The first system that satisfies a requirement will be used.
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The first system that satisfies a requirement will be used. See
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`resolver docs`_ for detailed documentation.
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6. How do I know what system is being used by a given tool?
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@@ -206,10 +220,7 @@ The first system that satisfies a requirement will be used.
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The Galaxy log will show which dependency resolution system is used
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to satisfy each tool dependency and you can specify priorities using the
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``dependency_resolution_conf.xml`` file. If you put Conda on
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top, Galaxy will first try to use Conda to resolve a tool dependency;
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if this does not work, the following dependency resolver is used, as
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listed. See `resolver docs`_ for detailed documentation. Starting from Galaxy
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``dependency_resolvers_conf.xml`` file (see question 5 above). Starting from Galaxy
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release 16.07, you can see which dependency will be used (“resolved”) in the
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Admin panel.
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@@ -24,6 +24,7 @@ EXTRA_CONFIG_KWDS = {
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'conda_ensure_channels': 'r,bioconda,iuc',
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'conda_auto_install': False,
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'conda_auto_init': False,
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'conda_copy_dependencies': False,
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}
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CONFIG_VAL_NOT_FOUND = object()
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@@ -322,8 +322,8 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
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continue
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optional = params.get("is_" + name, None)
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other = params.get("or_" + name, None)
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if optional and optional == 'true':
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# optional element... == 'true' actually means it is NOT checked (and therefore omitted)
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if optional and optional == '__NOTHING__':
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# optional element... == '__NOTHING__' actually means it is NOT checked (and therefore omitted)
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setattr(data.metadata, name, None)
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else:
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if other:
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@@ -521,8 +521,8 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
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if spec.get("readonly"):
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continue
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optional = kwd.get( "is_" + name, None )
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if optional and optional == 'true':
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# optional element... == 'true' actually means it is NOT checked (and therefore ommitted)
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if optional and optional == '__NOTHING__':
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# optional element... == '__NOTHING__' actually means it is NOT checked (and therefore ommitted)
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setattr( ldda.metadata, name, None )
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else:
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setattr( ldda.metadata, name, spec.unwrap( kwd.get( name, None ) ) )
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@@ -1 +1 @@
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|
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File diff suppressed because one or more lines are too long
@@ -1,2 +1,2 @@
|
||||
define([],function(){var a=Backbone.View.extend({optionsDefault:{container:"body",title:"ui-modal",cls:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null,title_separator:!0},buttonList:{},initialize:function(a){this.setElement(this._template()),this.options=_.defaults(a||{},this.optionsDefault),$(this.options.container).prepend(this.el),this.$header=this.$(".modal-header"),this.$dialog=this.$(".modal-dialog"),this.$body=this.$(".modal-body"),this.$footer=this.$(".modal-footer"),this.$backdrop=this.$(".modal-backdrop"),this.$buttons=this.$(".buttons"),a&&this.render()},show:function(a){if(a&&(this.options=_.defaults(a,this.optionsDefault),this.render()),!this.visible&&(this.visible=!0,this.$el.fadeIn("fast"),this.options.closing_events)){var b=this;$(document).on("keyup.ui-modal",function(a){27==a.keyCode&&b.hide(!0)}),this.$backdrop.on("click",function(){b.hide(!0)})}},hide:function(a){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback(a),$(document).off("keyup.ui-modal"),this.$backdrop.off("click")},render:function(){var a=this;if("progress"==this.options.body&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"/></div>')),this.$el.removeClass().addClass("modal").addClass(this.options.cls),this.$header.find(".title").html(this.options.title),this.$body.html(this.options.body),this.$buttons.empty(),this.buttonList={},this.options.buttons){var b=0;$.each(this.options.buttons,function(c,d){var e=$("<button/>").attr("id","button-"+b++).text(c).click(d);a.$buttons.append(e).append(" "),a.buttonList[c]=e})}else this.$footer.hide();this.$backdrop[this.options.backdrop&&"addClass"||"removeClass"]("in"),this.$header[!this.options.title_separator&&"addClass"||"removeClass"]("no-separator"),this.$body.removeAttr("style"),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.$dialog.css("width",this.options.width)},getButton:function(a){return this.buttonList[a]},enableButton:function(a){this.getButton(a).prop("disabled",!1)},disableButton:function(a){this.getButton(a).prop("disabled",!0)},showButton:function(a){this.getButton(a).show()},hideButton:function(a){this.getButton(a).hide()},scrollTop:function(){return this.$body.scrollTop()},_template:function(){return'<div class="ui-modal"><div class="modal-backdrop fade"/><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><h4 class="title"/></div><div class="modal-body"/><div class="modal-footer"><div class="buttons"/></div></div></div></div>'}});return{View:a}});
|
||||
define([],function(){var a=Backbone.View.extend({className:"ui-modal",optionsDefault:{container:"body",title:"ui-modal",cls:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null,title_separator:!0},buttonList:{},initialize:function(a){this.options=_.defaults(a||{},this.optionsDefault),$(this.options.container).prepend(this.el),a&&this.render()},show:function(a){if(a&&(this.options=_.defaults(a,this.optionsDefault),this.render()),!this.visible&&(this.visible=!0,this.$el.fadeIn("fast"),this.options.closing_events)){var b=this;$(document).on("keyup.ui-modal",function(a){27==a.keyCode&&b.hide(!0)}),this.$backdrop.on("click",function(){b.hide(!0)})}},hide:function(a){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback(a),$(document).off("keyup.ui-modal"),this.$backdrop.off("click")},render:function(){var a=this;if(this.$el.html(this._template()),this.$header=this.$(".modal-header"),this.$dialog=this.$(".modal-dialog"),this.$body=this.$(".modal-body"),this.$footer=this.$(".modal-footer"),this.$backdrop=this.$(".modal-backdrop"),this.$buttons=this.$(".buttons"),"progress"==this.options.body&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"/></div>')),this.$el.removeClass().addClass("modal").addClass(this.options.cls),this.$header.find(".title").html(this.options.title),this.$body.html(this.options.body),this.$buttons.empty(),this.buttonList={},this.options.buttons){var b=0;$.each(this.options.buttons,function(c,d){var e=$("<button/>").attr("id","button-"+b++).text(c).click(d);a.$buttons.append(e).append(" "),a.buttonList[c]=e})}else this.$footer.hide();this.$backdrop[this.options.backdrop&&"addClass"||"removeClass"]("in"),this.$header[!this.options.title_separator&&"addClass"||"removeClass"]("no-separator"),this.$body.removeAttr("style"),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.$dialog.css("width",this.options.width)},getButton:function(a){return this.buttonList[a]},enableButton:function(a){this.getButton(a).prop("disabled",!1)},disableButton:function(a){this.getButton(a).prop("disabled",!0)},showButton:function(a){this.getButton(a).show()},hideButton:function(a){this.getButton(a).hide()},scrollTop:function(){return this.$body.scrollTop()},_template:function(){return'<div class="modal-backdrop fade"/><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><h4 class="title"/></div><div class="modal-body"/><div class="modal-footer"><div class="buttons"/></div></div></div>'}});return{View:a}});
|
||||
//# sourceMappingURL=../../../maps/mvc/ui/ui-modal.js.map
|
||||
Reference in New Issue
Block a user