Merge dev, resolve conflicts from console re-enablement.

client/grunt-tasks/scripts.js

@@ -7,35 +7,17 @@ module.exports = function( grunt ){
     "use strict";
 
     var app = grunt.config.get( 'app' ),
-        paths = grunt.config.get( 'paths' );
-
-    grunt.config( 'uglify', {
-        target : {
-            files: [{
-                expand : true,
-                cwd : paths.srcSymlink,
-                src : '**/*.js',
-                dest : paths.dist
-            }],
-        }
-    });
-
-    if (grunt.option('develop')){
-        grunt.config( 'uglify.options', {
+        paths = grunt.config.get( 'paths' ),
+        // uglify settings used when scripts are decompressed/not-minified
+        decompressedSettings = {
+            mangle   : false,
             beautify : true,
             compress : {
                 drop_debugger : false
             }
-        });
-    } else {
-        grunt.config( 'uglify.target.options', {
-            sourceMap : true,
-            sourceMapName : function( path ){
-                // rewrite name to have all source maps in 'static/maps'
-                return path.replace( paths.dist, paths.maps ) + '.map';
-            }
-        });
-        grunt.config( 'uglify.options', {
+        },
+        // uglify settings used when scripts are compressed/minified
+        compressedSettings = {
             mangle : {
                 screw_ie8 : true
             },
@@ -55,16 +37,39 @@ module.exports = function( grunt ){
                 if_return : true,
                 join_vars : true,
                 cascade : true,
-                drop_console : true
+            }
+        };
+
+    grunt.config( 'uglify', {
+        target : {
+            files: [{
+                expand : true,
+                cwd : paths.srcSymlink,
+                src : '**/*.js',
+                dest : paths.dist
+            }],
+        }
+    });
+
+
+    if (grunt.option( 'develop' )){
+        grunt.config( 'uglify.options', decompressedSettings );
+
+    } else {
+        grunt.config( 'uglify.target.options', {
+            sourceMap : true,
+            sourceMapName : function( path ){
+                // rewrite name to have all source maps in 'static/maps'
+                return path.replace( paths.dist, paths.maps ) + '.map';
             }
         });
+        grunt.config( 'uglify.options', compressedSettings );
     }
 
-
     // -------------------------------------------------------------------------- decompress for easier debugging
     grunt.registerTask( 'decompress', function(){
         grunt.log.writeln( "decompressing... (don't forget to call 'grunt' again before committing)" );
-        grunt.config( 'uglify.options', { beautify: true });
+        grunt.config( 'uglify.options', decompressedSettings );
         grunt.config( 'uglify.target.options', {});
         grunt.task.run( 'uglify' );
     });

lib/galaxy/tools/errors.py

@@ -11,9 +11,9 @@ GALAXY TOOL ERROR REPORT
 This error report was sent from the Galaxy instance hosted on the server
 "${host}"
 -----------------------------------------------------------------------------
-This is in reference to dataset id ${dataset_id} from history id ${history_id}
+This is in reference to dataset id ${dataset_id} (${dataset_id_encoded}) from history id ${history_id} (${history_id_encoded})
 -----------------------------------------------------------------------------
-You should be able to view the history containing the related history item
+You should be able to view the history containing the related history item (${hda_id_encoded})
 
 ${hid}: ${history_item_name}
 
@@ -26,7 +26,8 @@ The user ${email_str} provided the following information:
 
 ${message}
 -----------------------------------------------------------------------------
-job id: ${job_id}
+info url: ${hda_show_params_link}
+job id: ${job_id} (${job_id_encoded})
 tool id: ${job_tool_id}
 tool version: ${tool_version}
 job pid or drm id: ${job_runner_external_id}
@@ -81,7 +82,10 @@ class ErrorReporter( object ):
         hda = self.hda
         job = self.job
         host = web.url_for( '/', qualified=True )
-        history_view_link = web.url_for( controller="history", action="view", id=self.app.security.encode_id( hda.history_id ), qualified=True )
+        history_id_encoded = self.app.security.encode_id( hda.history_id )
+        history_view_link = web.url_for( controller="history", action="view", id=history_id_encoded, qualified=True )
+        hda_id_encoded = self.app.security.encode_id( hda.id )
+        hda_show_params_link = web.url_for( controller="dataset", action="show_params", dataset_id=hda_id_encoded, qualified=True )
         # Build the email message
         if user and user.email != email:
             email_str = "'%s' (providing preferred contact email '%s')" % (user.email, email)
@@ -89,11 +93,16 @@ class ErrorReporter( object ):
             email_str = "'%s'" % (email or 'anonymously')
         self.report = string.Template( error_report_template ) \
             .safe_substitute( host=host,
+                              dataset_id_encoded=self.app.security.encode_id( hda.dataset_id ),
                               dataset_id=hda.dataset_id,
+                              history_id_encoded=history_id_encoded,
                               history_id=hda.history_id,
+                              hda_id_encoded=hda_id_encoded,
                               hid=hda.hid,
                               history_item_name=hda.get_display_name(),
                               history_view_link=history_view_link,
+                              hda_show_params_link=hda_show_params_link,
+                              job_id_encoded=self.app.security.encode_id( job.id ),
                               job_id=job.id,
                               tool_version=job.tool_version,
                               job_tool_id=job.tool_id,

lib/galaxy/tools/parameters/basic.py

@@ -1764,6 +1764,22 @@ class DataToolParameter( BaseDataToolParameter ):
             self.validators.append( validation.MetadataValidator() )
         self._parse_formats( trans, tool, input_source )
         self.multiple = input_source.get_bool('multiple', False)
+        self.min = input_source.get( 'min' )
+        self.max = input_source.get( 'max' )
+        if self.min:
+            try:
+                self.min = int( self.min )
+            except:
+                raise ValueError( "An integer is required for min property." )
+        if self.max:
+            try:
+                self.max = int( self.max )
+            except:
+                raise ValueError( "An integer is required for max property." )
+        if not self.multiple and (self.min is not None):
+            raise ValueError( "Cannot specify min property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name )
+        if not self.multiple and (self.max is not None):
+            raise ValueError( "Cannot specify max property on single data parameter '%s'. Set multiple=\"true\" to enable this option." % self.name )
         self.is_dynamic = True
         self._parse_options( input_source )
         # Load conversions required for the dataset input
@@ -2052,17 +2068,31 @@ class DataToolParameter( BaseDataToolParameter ):
         return "No dataset"
 
     def validate( self, value, history=None ):
+        dataset_count = 0
         for validator in self.validators:
             if value and self.multiple:
-                if isinstance(value, list):
-                    for v in value:
-                        validator.validate( v, history )
-                elif isinstance(value, galaxy.model.HistoryDatasetCollectionAssociation):
-                    for v in value.collection.dataset_instances:
+                if not isinstance( value, list ):
+                    value = [ value ]
+                for v in value:
+                    if isinstance(v, galaxy.model.HistoryDatasetCollectionAssociation):
+                        for dataset_instance in v.collection.dataset_instances:
+                            dataset_count += 1
+                            validator.validate( dataset_instance, history )
+                    else:
+                        dataset_count += 1
                         validator.validate( v, history )
             else:
+                if value:
+                    dataset_count += 1
                 validator.validate( value, history )
 
+        if self.min is not None:
+            if self.min > dataset_count:
+                raise ValueError( "At least %d datasets are required." % self.min )
+        if self.max is not None:
+            if self.max < dataset_count:
+                raise ValueError( "At most %d datasets are required." % self.max )
+
     def get_dependencies( self ):
         """
         Get the *names* of the other params this param depends on.
@@ -2124,6 +2154,10 @@ class DataToolParameter( BaseDataToolParameter ):
         d['extensions'] = extensions
         d['edam_formats'] = edam_formats
         d['multiple'] = self.multiple
+        if self.multiple:
+            # For consistency, should these just always be in the dict?
+            d['min'] = self.min
+            d['max'] = self.max
         d['options'] = {'hda': [], 'hdca': []}
 
         # return default content if context is not available

lib/galaxy/web/base/interactive_environments.py

@@ -67,7 +67,7 @@ class InteractiveEnviornmentRequest(object):
         # their defaults dictionary instead.
         default_dict['command_inject'] = '--sig-proxy=true'
         default_dict['docker_hostname'] = 'localhost'
-        default_dict['wx_tempdir'] = False
+        default_dict['wx_tempdir'] = 'False'
         viz_config = ConfigParser.SafeConfigParser(default_dict)
         conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" )
         if not os.path.exists( conf_path ):

static/maps/galaxy.interactive_environments.js.map

@@ -1 +1 @@
-{"version":3,"file":"galaxy.interactive_environments.js","sources":["../src/galaxy.interactive_environments.js"],"names":["append_notebook","url","clear_main_area","$","append","remove","children","display_spinner","galaxy_root","test_ie_availability","success_callback","request_count","interval","setInterval","ajax","xhrFields","withCredentials","type","timeout","success","clearInterval","error","toastr","closeButton","timeOut","tapToDismiss"],"mappings":"AAIA,QAASA,iBAAgBC,GACrBC,kBACAC,EAAE,SAASC,OAAO,uHAAwHH,EAAK,eAInJ,QAASC,mBACLC,EAAE,YAAYE,SACdF,EAAE,SAASG,WAAWD,SAG1B,QAASE,mBACDJ,EAAE,SAASC,OAAO,0BAA4BI,YAAc,wGAWpE,QAASC,sBAAqBR,EAAKS,GAC/B,GAAIC,GAAgB,CACpBJ,mBACAK,SAAWC,YAAY,WACnBV,EAAEW,MACEb,IAAKA,EACLc,WACIC,iBAAiB,GAErBC,KAAM,MACNC,QAAS,IACTC,QAAS,WAELC,cAAcR,UACdF,KAEJW,MAAO,WACHV,IAEGA,EAAgB,KACfS,cAAcR,UACdV,kBACAoB,OAAOD,MACH,sDACA,SACCE,aAAe,EAAMC,QAAW,IAAOC,cAAgB,SAKzE"}
+{"version":3,"file":"galaxy.interactive_environments.js","sources":["../src/galaxy.interactive_environments.js"],"names":["append_notebook","url","clear_main_area","$","append","remove","children","display_spinner","galaxy_root","test_ie_availability","success_callback","request_count","interval","setInterval","ajax","xhrFields","withCredentials","type","timeout","success","console","log","clearInterval","error","toastr","closeButton","timeOut","tapToDismiss"],"mappings":"AAIA,QAASA,iBAAgBC,GACrBC,kBACAC,EAAE,SAASC,OAAO,uHAAwHH,EAAK,eAInJ,QAASC,mBACLC,EAAE,YAAYE,SACdF,EAAE,SAASG,WAAWD,SAG1B,QAASE,mBACDJ,EAAE,SAASC,OAAO,0BAA4BI,YAAc,wGAWpE,QAASC,sBAAqBR,EAAKS,GAC/B,GAAIC,GAAgB,CACpBJ,mBACAK,SAAWC,YAAY,WACnBV,EAAEW,MACEb,IAAKA,EACLc,WACIC,iBAAiB,GAErBC,KAAM,MACNC,QAAS,IACTC,QAAS,WACLC,QAAQC,IAAI,8BACZC,cAAcV,UACdF,KAEJa,MAAO,WACHZ,IACAS,QAAQC,IAAI,WAAaV,GACtBA,EAAgB,KACfW,cAAcV,UACdV,kBACAsB,OAAOD,MACH,sDACA,SACCE,aAAe,EAAMC,QAAW,IAAOC,cAAgB,SAKzE"}

static/maps/libs/toastr.js.map

@@ -1 +1 @@
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static/maps/mvc/form/form-parameters.js.map

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static/maps/mvc/form/form-repeat.js.map

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static/maps/mvc/form/form-select-content.js.map

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static/maps/mvc/form/form-view.js.map

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static/maps/mvc/history/options-menu.js.map

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static/maps/mvc/job/job-model.js.map

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static/maps/mvc/tools/tools-jobs.js.map

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static/maps/mvc/ui/ui-select.js.map

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static/maps/utils/deferred.js.map

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static/maps/utils/uploadbox.js.map

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static/scripts/galaxy.interactive_environments.js

@@ -1,2 +1,2 @@
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+function append_notebook(a){clear_main_area(),$("#main").append('<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="'+a+'"></iframe>')}function clear_main_area(){$("#spinner").remove(),$("#main").children().remove()}function display_spinner(){$("#main").append('<img id="spinner" src="'+galaxy_root+'static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">')}function test_ie_availability(a,b){var c=0;display_spinner(),interval=setInterval(function(){$.ajax({url:a,xhrFields:{withCredentials:!0},type:"GET",timeout:500,success:function(){console.log("Connected to IE, returning"),clearInterval(interval),b()},error:function(){c++,console.log("Request "+c),c>30&&(clearInterval(interval),clear_main_area(),toastr.error("Could not connect to IE, contact your administrator","Error",{closeButton:!0,timeOut:2e4,tapToDismiss:!1}))}})},1e3)}
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static/scripts/libs/toastr.js

@@ -1,2 +1,2 @@
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static/scripts/mvc/dataset/dataset-choice.js

@@ -1,2 +1,2 @@
-define(["mvc/dataset/dataset-model","mvc/dataset/dataset-list","mvc/ui/ui-modal","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){function f(a,b,c){function d(a,b){for(var c in b)if(b.hasOwnProperty(c)&&a[c]!==b[c])return!1;return!0}return a.filter(function(a){return!a.deleted&&a.visible&&(!c||void 0===a.collection_type)&&d(a,b)})}var g=function(d,g){function h(){l.resolve(j.getSelectedModels().map(function(a){return a.toJSON()}))}g=_.defaults(g||{},{datasetsOnly:!0,where:{state:"ok"},multiselect:!1,selected:[]}),g.title=g.title||e(g.multiselect?"Choose datasets:":"Choose a dataset:");var i,j,k,l=jQuery.Deferred(),m=g.filter||f;return d=m(d,g.where,g.datasetsOnly),d.length?(g.multiselect&&(k={},k[e("Ok")]=h),i=new c.View({height:"auto",buttons:k,closing_events:!0,closing_callback:function(){l.resolve(null)},body:['<div class="list-panel"></div>'].join("")}),i.$(".modal-header").remove(),i.$(".modal-footer").css("margin-top","0px"),j=new b.DatasetList({title:g.title,subtitle:g.subtitle||e(["Click the checkboxes on the right to select datasets. ","Click the datasets names to see their details. "].join("")),el:i.$body.find(".list-panel"),selecting:!0,selected:g.selected,collection:new a.DatasetAssociationCollection(d)}),j.once("rendered:initial",function(){i.show(),i.$el.addClass("dataset-choice-modal")}),g.multiselect||(j.on("rendered",function(){j.$(".list-actions").hide()}),j.on("view:selected",function(a){l.resolve([a.model.toJSON()])})),j.render(0),l.always(function(){i.hide()})):l.reject("No matches found")},h=Backbone.View.extend(d.LoggableMixin).extend({className:"dataset-choice",initialize:function(a){this.debug(this+"(DatasetChoice).initialize:",a),this.label=void 0!==a.label?e(a.label):"",this.where=a.where,this.datasetsOnly=void 0!==a.datasetsOnly?a.datasetsOnly:!0,this.datasetJSON=a.datasetJSON||[],this.selected=a.selected||[],this._setUpListeners()},_setUpListeners:function(){},render:function(){var a=this.toJSON();return this.$el.html(this._template(a)),this.$(".selected").replaceWith(this._renderSelected(a)),this},_template:function(a){return _.template(["<label>",'<span class="prompt"><%= label %></span>','<div class="selected"></div>',"</label>"].join(""))(a)},_renderSelected:function(a){return $(a.selected.length?_.template(['<div class="selected">','<span class="title"><%= selected.hid %>: <%= selected.name %></span>','<span class="subtitle">',"<i><%= selected.misc_blurb %></i>","<i>",e("format")+": ","<%= selected.file_ext %></i>","<i><%= selected.misc_info %></i>","</span>","</div>"].join(""),{variable:"selected"})(a.selected[0]):['<span class="none-selected-msg">(',e("click to select a dataset"),")</span>"].join(""))},toJSON:function(){var a=this;return{label:a.label,datasets:a.datasetJSON,selected:_.compact(_.map(a.selected,function(b){return _.findWhere(a.datasetJSON,{id:b})}))}},events:{click:"chooseWithModal"},chooseWithModal:function(){var a=this;return this._createModal().done(function(b){b?(a.selected=_.pluck(b,"id"),a.trigger("selected",a,b),a.render()):a.trigger("cancelled",a)}).fail(function(){a.trigger("error",a,arguments)})},_createModal:function(){return new g(this.datasetJSON,this._getModalOptions())},_getModalOptions:function(){return{title:this.label,multiselect:!1,selected:this.selected,where:this.where,datasetsOnly:this.datasetsOnly}},toString:function(){return"DatasetChoice("+this.selected+")"}}),i=h.extend({className:h.prototype.className+" multi",cells:{hid:e("History #"),name:e("Name"),misc_blurb:e("Summary"),file_ext:e("Format"),genome_build:e("Genome"),tags:e("Tags"),annotation:e("Annotation")},initialize:function(a){this.showHeaders=void 0!==a.showHeaders?a.showHeaders:!0,this.cells=a.cells||this.cells,h.prototype.initialize.call(this,a)},_renderSelected:function(a){return $(a.selected.length?_.template(['<table class="selected">',"<% if( json.showHeaders ){ %>","<thead><tr>","<% _.map( json.cells, function( val, key ){ %>","<th><%= val %></th>","<% }); %>","</tr></thead>","<% } %>","<tbody>","<% _.map( json.selected, function( selected ){ %>","<tr>","<% _.map( json.cells, function( val, key ){ %>",'<td class="cell-<%= key %>"><%= selected[ key ] %></td>',"<% }) %>","</tr>","<% }); %>","</tbody>","</table>"].join(""),{variable:"json"})(a):['<span class="none-selected-msg">(',e("click to select a dataset"),")</span>"].join(""))},toJSON:function(){return _.extend(h.prototype.toJSON.call(this),{showHeaders:this.showHeaders,cells:this.cells})},_getModalOptions:function(){return _.extend(h.prototype._getModalOptions.call(this),{multiselect:!0})},toString:function(){return"DatasetChoice("+this.selected+")"}});return{DatasetChoiceModal:g,DatasetChoice:h,MultiDatasetChoice:i}});
+define(["mvc/dataset/dataset-model","mvc/dataset/dataset-list","mvc/ui/ui-modal","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){function f(a,b,c){function d(a,b){for(var c in b)if(b.hasOwnProperty(c)&&a[c]!==b[c])return!1;return!0}return a.filter(function(a){return console.debug(a),!a.deleted&&a.visible&&(!c||void 0===a.collection_type)&&d(a,b)})}var g=function(d,g){function h(){l.resolve(j.getSelectedModels().map(function(a){return a.toJSON()}))}g=_.defaults(g||{},{datasetsOnly:!0,where:{state:"ok"},multiselect:!1,selected:[]}),g.title=g.title||e(g.multiselect?"Choose datasets:":"Choose a dataset:");var i,j,k,l=jQuery.Deferred(),m=g.filter||f;return d=m(d,g.where,g.datasetsOnly),d.length?(g.multiselect&&(k={},k[e("Ok")]=h),i=new c.View({height:"auto",buttons:k,closing_events:!0,closing_callback:function(){l.resolve(null)},body:['<div class="list-panel"></div>'].join("")}),i.$(".modal-header").remove(),i.$(".modal-footer").css("margin-top","0px"),j=new b.DatasetList({title:g.title,subtitle:g.subtitle||e(["Click the checkboxes on the right to select datasets. ","Click the datasets names to see their details. "].join("")),el:i.$body.find(".list-panel"),selecting:!0,selected:g.selected,collection:new a.DatasetAssociationCollection(d)}),j.once("rendered:initial",function(){i.show(),i.$el.addClass("dataset-choice-modal")}),g.multiselect||(j.on("rendered",function(){j.$(".list-actions").hide()}),j.on("view:selected",function(a){l.resolve([a.model.toJSON()])})),j.render(0),l.always(function(){i.hide()})):l.reject("No matches found")},h=Backbone.View.extend(d.LoggableMixin).extend({className:"dataset-choice",initialize:function(a){this.debug(this+"(DatasetChoice).initialize:",a),this.label=void 0!==a.label?e(a.label):"",this.where=a.where,this.datasetsOnly=void 0!==a.datasetsOnly?a.datasetsOnly:!0,this.datasetJSON=a.datasetJSON||[],this.selected=a.selected||[],this._setUpListeners()},_setUpListeners:function(){},render:function(){var a=this.toJSON();return this.$el.html(this._template(a)),this.$(".selected").replaceWith(this._renderSelected(a)),this},_template:function(a){return _.template(["<label>",'<span class="prompt"><%= label %></span>','<div class="selected"></div>',"</label>"].join(""))(a)},_renderSelected:function(a){return $(a.selected.length?_.template(['<div class="selected">','<span class="title"><%= selected.hid %>: <%= selected.name %></span>','<span class="subtitle">',"<i><%= selected.misc_blurb %></i>","<i>",e("format")+": ","<%= selected.file_ext %></i>","<i><%= selected.misc_info %></i>","</span>","</div>"].join(""),{variable:"selected"})(a.selected[0]):['<span class="none-selected-msg">(',e("click to select a dataset"),")</span>"].join(""))},toJSON:function(){var a=this;return{label:a.label,datasets:a.datasetJSON,selected:_.compact(_.map(a.selected,function(b){return _.findWhere(a.datasetJSON,{id:b})}))}},events:{click:"chooseWithModal"},chooseWithModal:function(){var a=this;return this._createModal().done(function(b){b?(a.selected=_.pluck(b,"id"),a.trigger("selected",a,b),a.render()):a.trigger("cancelled",a)}).fail(function(){a.trigger("error",a,arguments)})},_createModal:function(){return new g(this.datasetJSON,this._getModalOptions())},_getModalOptions:function(){return{title:this.label,multiselect:!1,selected:this.selected,where:this.where,datasetsOnly:this.datasetsOnly}},toString:function(){return"DatasetChoice("+this.selected+")"}}),i=h.extend({className:h.prototype.className+" multi",cells:{hid:e("History #"),name:e("Name"),misc_blurb:e("Summary"),file_ext:e("Format"),genome_build:e("Genome"),tags:e("Tags"),annotation:e("Annotation")},initialize:function(a){this.showHeaders=void 0!==a.showHeaders?a.showHeaders:!0,this.cells=a.cells||this.cells,h.prototype.initialize.call(this,a)},_renderSelected:function(a){return $(a.selected.length?_.template(['<table class="selected">',"<% if( json.showHeaders ){ %>","<thead><tr>","<% _.map( json.cells, function( val, key ){ %>","<th><%= val %></th>","<% }); %>","</tr></thead>","<% } %>","<tbody>","<% _.map( json.selected, function( selected ){ %>","<tr>","<% _.map( json.cells, function( val, key ){ %>",'<td class="cell-<%= key %>"><%= selected[ key ] %></td>',"<% }) %>","</tr>","<% }); %>","</tbody>","</table>"].join(""),{variable:"json"})(a):['<span class="none-selected-msg">(',e("click to select a dataset"),")</span>"].join(""))},toJSON:function(){return _.extend(h.prototype.toJSON.call(this),{showHeaders:this.showHeaders,cells:this.cells})},_getModalOptions:function(){return _.extend(h.prototype._getModalOptions.call(this),{multiselect:!0})},toString:function(){return"DatasetChoice("+this.selected+")"}});return{DatasetChoiceModal:g,DatasetChoice:h,MultiDatasetChoice:i}});
 //# sourceMappingURL=../../../maps/mvc/dataset/dataset-choice.js.map

static/scripts/mvc/form/form-parameters.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a)),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new f({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})},_fieldFtp:function(a){var b=this;return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
+define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new f({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})},_fieldFtp:function(a){var b=this;return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map

static/scripts/mvc/form/form-repeat.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("<div/>");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("<div/>").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(a.id&&!this.list[a.id]){this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()}},del:function(a){if(this.list[a]){this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()}},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}});
+define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("<div/>");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("<div/>").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(!a.id||this.list[a.id])return void console.debug("form-repeat::add - Duplicate repeat block id.");this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(a){if(!this.list[a])return void console.debug("form-repeat::del - Invalid repeat block id.");this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}});
 //# sourceMappingURL=../../../maps/mvc/form/form-repeat.js.map

static/scripts/mvc/form/form-select-content.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d,this.history={};var e=this;this.setElement('<div class="ui-select-content"/>'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var d=[];for(var e in b){var f=b[e];d.push({label:f.hid+": "+f.name,value:f.id}),c.history[f.id+"_"+f.src]=f}a.update(d)}}var c=this;b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=this.history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=this.history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:c}});
+define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d,this.history={};var e=this;this.setElement('<div class="ui-select-content"/>'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var d=[];for(var e in b){var f=b[e];d.push({label:f.hid+": "+f.name,value:f.id}),c.history[f.id+"_"+f.src]=f}a.update(d)}}var c=this;b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){console.debug("tools-select-content::value() - Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=this.history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=this.history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/form/form-select-content.js.map

static/scripts/mvc/form/form-view.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change")}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$el.offset().top-20},500)},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),void(this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message})))}})});
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$el.offset().top-20},500)},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),void console.debug("tools-form-base::initialize() - Completed."))}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map

static/scripts/mvc/history/options-menu.js

@@ -1,2 +1,2 @@
-define(["mvc/ui/popup-menu","mvc/base-mvc","utils/localization"],function(a,b,c){function d(a,b,c){return _.clone(e).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var e=[{html:c("History Lists"),header:!0},{html:c("Saved Histories"),href:"history/list"},{html:c("Histories Shared with Me"),href:"history/list_shared"},{html:c("Current History"),header:!0,anon:!0},{html:c("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:c("Copy History"),href:"history/copy"},{html:c("Copy Datasets"),href:"dataset/copy_datasets"},{html:c("Share or Publish"),href:"history/sharing"},{html:c("Extract Workflow"),href:"workflow/build_from_current_history"},{html:c("Dataset Security"),href:"root/history_set_default_permissions"},{html:c("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:c("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:c("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really unhide all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets")})}}},{html:c("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really delete all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets")})}}},{html:c("Purge Deleted Datasets"),confirm:c("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:c("Show Structure"),href:"history/display_structured",anon:!0},{html:c("Export Citations"),href:"history/citations",anon:!0},{html:c("Export to File"),href:"history/export_archive?preview=True",anon:!0},{html:c("Delete"),confirm:c("Really delete the current history?"),href:"history/delete_current"},{html:c("Delete Permanently"),confirm:c("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:!0,anon:!0},{html:c("Other Actions"),header:!0},{html:c("Import from File"),href:"history/import_archive"}],f=function(b,c){c=c||{};var e=void 0===c.anonymous?!0:c.anonymous,f=c.purgeAllowed||!1,g=c.root||(Galaxy&&Galaxy.options?Galaxy.options.root:"/"),h=d(e,f,g);return new a(b,h)};return f});
+define(["mvc/ui/popup-menu","mvc/base-mvc","utils/localization"],function(a,b,c){function d(a,b,c){return _.clone(e).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var e=[{html:c("History Lists"),header:!0},{html:c("Saved Histories"),href:"history/list"},{html:c("Histories Shared with Me"),href:"history/list_shared"},{html:c("Current History"),header:!0,anon:!0},{html:c("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:c("Copy History"),href:"history/copy"},{html:c("Copy Datasets"),href:"dataset/copy_datasets"},{html:c("Share or Publish"),href:"history/sharing"},{html:c("Extract Workflow"),href:"workflow/build_from_current_history"},{html:c("Dataset Security"),href:"root/history_set_default_permissions"},{html:c("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:c("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:c("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really unhide all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets"),console.error(arguments)})}}},{html:c("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(c("Really delete all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets"),console.error(arguments)})}}},{html:c("Purge Deleted Datasets"),confirm:c("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:c("Show Structure"),href:"history/display_structured",anon:!0},{html:c("Export Citations"),href:"history/citations",anon:!0},{html:c("Export to File"),href:"history/export_archive?preview=True",anon:!0},{html:c("Delete"),confirm:c("Really delete the current history?"),href:"history/delete_current"},{html:c("Delete Permanently"),confirm:c("Really delete the current history permanently? This cannot be undone."),href:"history/delete_current?purge=True",purge:!0,anon:!0},{html:c("Other Actions"),header:!0},{html:c("Import from File"),href:"history/import_archive"}],f=function(b,c){c=c||{};var e=void 0===c.anonymous?!0:c.anonymous,f=c.purgeAllowed||!1,g=c.root||(Galaxy&&Galaxy.options?Galaxy.options.root:"/"),h=d(e,f,g);return new a(b,h)};return f});
 //# sourceMappingURL=../../../maps/mvc/history/options-menu.js.map

static/scripts/mvc/job/job-model.js

@@ -1,2 +1,2 @@
-define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}});
+define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){console.debug(a,b)},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){console.debug(this);var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}});
 //# sourceMappingURL=../../../maps/mvc/job/job-model.js.map

static/scripts/mvc/tools/tools-form-base.js

@@ -1,2 +1,2 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.modal=Galaxy.modal,this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i)},error:function(a){e.deferred.done(i);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),e.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){e.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view","mvc/ui/ui-modal"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){this.options=a.merge(c,{}),this.setElement("<div/>"),this.modal=Galaxy.modal,this.deferred=new b,c.inputs?this._buildForm(c):this._buildModel(c,!0)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:"<b>"+b.name+"</b> "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,c){var e=this;if(this.options.id=b.id,this.options.version=b.version,b.job_id)f=Galaxy.root+"api/jobs/"+b.job_id+"/build_for_rerun";else{var f=Galaxy.root+"api/tools/"+b.id+"/build?";if(b.dataset_id)f+="dataset_id="+b.dataset_id;else{f+="tool_version="+b.version+"&";var g=top.location.href,h=g.indexOf("?");-1!=g.indexOf("tool_id=")&&-1!==h&&(f+=g.slice(h+1))}}var i=this.deferred.register();a.request({type:"GET",url:f,success:function(a){e._buildForm(a.tool_model||a),!c&&e.form.message.update({status:"success",message:"Now you are using '"+e.options.name+"' version "+e.options.version+".",persistent:!1}),e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){e.deferred.done(i),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||a.err_msg||"Uncaught error.";void 0==e.form&&(e.form=new d),e.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){e.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.is_workflow&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("<div/>"),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map

static/scripts/mvc/tools/tools-form-workflow.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;this.node=c.node,this.node&&(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),b.prototype.initialize.call(this,c))},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var f=b.inputs[e];if(f.action){if(f.name="pja__"+a+"__"+f.action,f.pja_arg&&(f.name+="__"+f.pja_arg),f.payload)for(var h in f.payload){var i=f.payload[h];f.payload[f.name+"__"+h]=i,delete i}var j=g.post_job_actions[f.action+a];if(j){for(var k in d)d[k].expanded=!0;f.value=f.pja_arg?j.action_arguments&&j.action_arguments[f.pja_arg]||f.value:"true"}}f.inputs&&c(f,d.slice(0))}}var d=[],e=[];for(key in b)d.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)e.push(this.node.input_terminals[key].name);d.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),d.unshift({0:"Sequences",1:"Sequences"}),d.unshift({0:"Roadmaps",1:"Roadmaps"}),d.unshift({0:"Leave unchanged",1:"__empty__"});var f={title:"Add Actions: '"+a+"'",type:"section",flat:!0,inputs:[{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>'+e.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},g=this;return c(f),f}});return{View:c}});
+define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=c.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!1)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var f=b.inputs[e];if(f.action){if(f.name="pja__"+a+"__"+f.action,f.pja_arg&&(f.name+="__"+f.pja_arg),f.payload)for(var h in f.payload){var i=f.payload[h];f.payload[f.name+"__"+h]=i,delete i}var j=g.post_job_actions[f.action+a];if(j){for(var k in d)d[k].expanded=!0;f.value=f.pja_arg?j.action_arguments&&j.action_arguments[f.pja_arg]||f.value:"true"}}f.inputs&&c(f,d.slice(0))}}var d=[],e=[];for(key in b)d.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)e.push(this.node.input_terminals[key].name);d.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),d.unshift({0:"Sequences",1:"Sequences"}),d.unshift({0:"Roadmaps",1:"Roadmaps"}),d.unshift({0:"Leave unchanged",1:"__empty__"});var f={title:"Add Actions: '"+a+"'",type:"section",flat:!0,inputs:[{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>'+e.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},g=this;return c(f),f}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map

static/scripts/mvc/tools/tools-jobs.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a));var d=[];a.outputs.forEach(function(a){d.push(a.id)}),f._refreshHdas(d)},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}}return!0},_refreshHdas:function(a){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a)}}});
+define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a));var d=[];a.outputs.forEach(function(a){d.push(a.id)}),f._refreshHdas(d)},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+k+"</b> selection(s) while a previous field contains <b>"+d+"</b>."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(a){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(a)}}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map

static/scripts/mvc/ui/ui-select.js

@@ -1,2 +1,2 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.options.container&&(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple)){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),!this.options.container)return void console.log("ui-select::initialize() : container not specified.");if(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}});
 //# sourceMappingURL=../../../maps/mvc/ui/ui-select.js.map

static/scripts/utils/deferred.js

@@ -1,2 +1,2 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})});
+define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,console.debug("Deferred:register() - Register "+b),b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,console.debug("Deferred:done() - Unregister "+a),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})});
 //# sourceMappingURL=../../maps/utils/deferred.js.map

static/scripts/utils/uploadbox.js

@@ -1,2 +1,2 @@
-!function(a){jQuery.event.props.push("dataTransfer"),a.uploadpost=function(b){var c=a.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},b),d=c.data;if(d.error_message)return void c.error(d.error_message);var e=new FormData;for(var f in d.payload)e.append(f,d.payload[f]);var g=0;for(var f in d.files){var h=d.files[f];e.append(h.name,h.file,h.file.name),g+=h.file.size}return g>1048576*c.maxfilesize?void c.error(c.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",c.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var a=null;if(xhr.responseText)try{a=jQuery.parseJSON(xhr.responseText)}catch(b){a=xhr.responseText}if(xhr.status<200||xhr.status>299){var d=xhr.statusText;403==xhr.status?d=c.error_login:0==xhr.status?d=c.error_server:d||(d=c.error_default),c.error(d+" ("+xhr.status+")")}else c.success(a)}},xhr.upload.addEventListener("progress",function(a){a.lengthComputable&&c.progress(Math.round(100*a.loaded/a.total))},!1),void xhr.send(e))},a.fn.uploadinput=function(b){var c=this,d=a.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},b),e=a('<input type="file" style="display: none" '+(d.multiple&&"multiple"||"")+"/>");return c.append(e).change(function(b){d.onchange(b.target.files),a(this).val("")}),c.on("drop",function(a){d.ondragleave(a),a.dataTransfer&&(d.onchange(a.dataTransfer.files),a.preventDefault())}),c.on("dragover",function(a){a.preventDefault(),d.ondragover(a)}),c.on("dragleave",function(a){a.stopPropagation(),d.ondragleave(a)}),{dialog:function(){e.trigger("click")}}},a.fn.uploadbox=function(b){function c(a){if(a&&a.length&&!p){for(var b=n,c=0;c<a.length;c++){var d=String(n++);m[d]=a[c],l.announce(d,m[d]),o++}return b}}function d(a){m[a]&&(delete m[a],o--)}function e(){if(0==o||q)return q=!1,p=!1,void l.complete();p=!0;var b=-1;for(var c in m){b=c;break}m[b];d(b),a.uploadpost({url:l.url,data:l.initialize(b),success:function(a){l.success(b,a),e()},error:function(a){l.error(b,a),e()},progress:function(a){l.progress(b,a)}})}function f(){r.dialog()}function g(a){for(a in m)d(a)}function h(){p||(p=!0,e())}function i(){q=!0}function j(b){return l=a.extend({},l,b)}function k(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var l=a.extend({},{dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(a,b){alert(b)},complete:function(){}},b),m={},n=0,o=0,p=!1,q=!1,r=a(this).uploadinput({multiple:!0,onchange:function(a){c(a)},ondragover:b.ondragover,ondragleave:b.ondragleave});return{select:f,add:c,remove:d,start:h,stop:i,reset:g,configure:j,compatible:k}}}(jQuery);
+!function(a){jQuery.event.props.push("dataTransfer"),a.uploadpost=function(b){var c=a.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},b),d=c.data;if(d.error_message)return void c.error(d.error_message);var e=new FormData;for(var f in d.payload)e.append(f,d.payload[f]);var g=0;for(var f in d.files){var h=d.files[f];e.append(h.name,h.file,h.file.name),g+=h.file.size}return g>1048576*c.maxfilesize?void c.error(c.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",c.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var a=null;if(xhr.responseText)try{a=jQuery.parseJSON(xhr.responseText)}catch(b){a=xhr.responseText}if(xhr.status<200||xhr.status>299){var d=xhr.statusText;403==xhr.status?d=c.error_login:0==xhr.status?d=c.error_server:d||(d=c.error_default),c.error(d+" ("+xhr.status+")")}else c.success(a)}},xhr.upload.addEventListener("progress",function(a){a.lengthComputable&&c.progress(Math.round(100*a.loaded/a.total))},!1),console.debug("uploadbox::uploadpost() - Posting following data:"),console.debug(c),void xhr.send(e))},a.fn.uploadinput=function(b){var c=this,d=a.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},b),e=a('<input type="file" style="display: none" '+(d.multiple&&"multiple"||"")+"/>");return c.append(e).change(function(b){d.onchange(b.target.files),a(this).val("")}),c.on("drop",function(a){d.ondragleave(a),a.dataTransfer&&(d.onchange(a.dataTransfer.files),a.preventDefault())}),c.on("dragover",function(a){a.preventDefault(),d.ondragover(a)}),c.on("dragleave",function(a){a.stopPropagation(),d.ondragleave(a)}),{dialog:function(){e.trigger("click")}}},a.fn.uploadbox=function(b){function c(a){if(a&&a.length&&!p){for(var b=n,c=0;c<a.length;c++){var d=String(n++);m[d]=a[c],l.announce(d,m[d]),o++}return b}}function d(a){m[a]&&(delete m[a],o--)}function e(){if(0==o||q)return q=!1,p=!1,void l.complete();p=!0;var b=-1;for(var c in m){b=c;break}m[b];d(b),a.uploadpost({url:l.url,data:l.initialize(b),success:function(a){l.success(b,a),e()},error:function(a){l.error(b,a),e()},progress:function(a){l.progress(b,a)}})}function f(){r.dialog()}function g(a){for(a in m)d(a)}function h(){p||(p=!0,e())}function i(){q=!0}function j(b){return l=a.extend({},l,b)}function k(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var l=a.extend({},{dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(a,b){alert(b)},complete:function(){}},b),m={},n=0,o=0,p=!1,q=!1,r=a(this).uploadinput({multiple:!0,onchange:function(a){c(a)},ondragover:b.ondragover,ondragleave:b.ondragleave});return{select:f,add:c,remove:d,start:h,stop:i,reset:g,configure:j,compatible:k}}}(jQuery);
 //# sourceMappingURL=../../maps/utils/uploadbox.js.map

static/scripts/utils/utils.js

@@ -1,2 +1,2 @@
-define([],function(){function a(b,c){for(var d in b){var e=b[d];e&&"object"==typeof e&&(c(e),a(e,c))}}function b(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function c(a){return $("<div/>").text(a).html()}function d(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function e(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function f(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?a.success&&a.success(top.__utils__get__[a.url]):g({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function g(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function h(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function i(a){$('link[href^="'+a+'"]').length||$('<link href="'+galaxy_config.root+a+'" rel="stylesheet">').appendTo("head")}function j(a,b){return a?_.defaults(a,b):b}function k(a,b){for(var c=1,d=0;b>d;d++)c*=10;return Math.round(a*c)/c}function l(a,b,c){c=void 0!==c?c:1;var d="";if(a>=r)a/=r,d="TB";else if(a>=q)a/=q,d="GB";else if(a>=p)a/=p,d="MB";else if(a>=o)a/=o,d="KB";else{if(!(a>0))return b?"0 b":"<strong>-</strong>";d="b"}var e="b"==d?a:k(a,c);return b?e+" "+d:"<strong>"+e+"</strong> "+d}function m(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function n(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes();return datetime=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c}var o=1024,p=o*o,q=p*o,r=q*o;return{cssLoadFile:i,cssGetAttribute:h,get:f,merge:j,bytesToString:l,uid:m,time:n,request:g,sanitize:c,textify:e,validate:d,deepeach:a,isJSON:b}});
+define([],function(){function a(b,c){for(var d in b){var e=b[d];e&&"object"==typeof e&&(c(e),a(e,c))}}function b(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function c(a){return $("<div/>").text(a).html()}function d(a){if(a instanceof Array||(a=[a]),0===a.length)return!1;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!1;return!0}function e(a){var a=a.toString();if(a){a=a.replace(/,/g,", ");var b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+1)),a}return""}function f(a){top.__utils__get__=top.__utils__get__||{},a.cache&&top.__utils__get__[a.url]?(a.success&&a.success(top.__utils__get__[a.url]),console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):g({url:a.url,data:a.data,success:function(b){top.__utils__get__[a.url]=b,a.success&&a.success(b)},error:function(b){a.error&&a.error(b)}})}function g(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url=b.url+$.param(b.data,!0),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b)})}function h(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function i(a){$('link[href^="'+a+'"]').length||$('<link href="'+galaxy_config.root+a+'" rel="stylesheet">').appendTo("head")}function j(a,b){return a?_.defaults(a,b):b}function k(a,b){for(var c=1,d=0;b>d;d++)c*=10;return Math.round(a*c)/c}function l(a,b,c){c=void 0!==c?c:1;var d="";if(a>=r)a/=r,d="TB";else if(a>=q)a/=q,d="GB";else if(a>=p)a/=p,d="MB";else if(a>=o)a/=o,d="KB";else{if(!(a>0))return b?"0 b":"<strong>-</strong>";d="b"}var e="b"==d?a:k(a,c);return b?e+" "+d:"<strong>"+e+"</strong> "+d}function m(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function n(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes();return datetime=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c}var o=1024,p=o*o,q=p*o,r=q*o;return{cssLoadFile:i,cssGetAttribute:h,get:f,merge:j,bytesToString:l,uid:m,time:n,request:g,sanitize:c,textify:e,validate:d,deepeach:a,isJSON:b}});
 //# sourceMappingURL=../../maps/utils/utils.js.map

templates/webapps/galaxy/root/index.mako

@@ -3,6 +3,7 @@
 ${h.js("libs/bibtex", "libs/jquery/jquery-ui")}
 ${h.css("jquery-ui/smoothness/jquery-ui")}
 ${h.css("base")}
+<%def name="title()">Galaxy</%def>
 <%def name="javascripts()">
     ${parent.javascripts()}
     ${h.templates("tool_link", "panel_section", "tool_search")}

test/api/test_tools.py

@@ -62,6 +62,19 @@ class ToolsTestCase( api.ApiTestCase ):
         self._assert_has_keys( case2_inputs[ 0 ], 'name', 'type', 'label', 'help', 'argument' )
         assert case2_inputs[ 0 ][ "name" ] == "seed"
 
+    @skip_without_tool( "multi_data_param" )
+    def test_show_multi_data( self ):
+        tool_info = self._show_valid_tool( "multi_data_param" )
+
+        f1_info, f2_info = tool_info[ "inputs" ][ 0 ], tool_info[ "inputs" ][ 1 ]
+        self._assert_has_keys( f1_info, "min", "max" )
+        assert f1_info["min"] == 1
+        assert f1_info["max"] == 1235
+
+        self._assert_has_keys( f2_info, "min", "max" )
+        assert f2_info["min"] is None
+        assert f2_info["max"] is None
+
     def _show_valid_tool( self, tool_id ):
         tool_show_response = self._get( "tools/%s" % tool_id, data=dict( io_details=True ) )
         self._assert_status_code_is( tool_show_response, 200 )

test/functional/tools/multi_data_param.xml

@@ -6,7 +6,7 @@
     cat ${" ".join(map(str, $f2))} >> $out2
   </command>
   <inputs>
-    <param name="f1" type="data" format="txt" multiple="true" label="Data 1" />
+    <param name="f1" type="data" format="txt" multiple="true" label="Data 1" min="1" max="1235" />
     <param name="f2" type="data" format="txt" multiple="true" label="Data 2" />
     <conditional name="advanced">
       <param name="full" type="select" label="Parameter Settings">