diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js index 42989b861d7..f094425b24f 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js @@ -23,7 +23,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' _refresh: function() { var margin = _.reduce( this.$el.children(), function( memo, child ) { return memo + $( child ).outerHeight(); - }, 0 ) - this.$steps.height() + 30; + }, 0 ) - this.$steps.height() + 25; this.$steps.css( 'height', $( window ).height() - margin ); }, @@ -56,7 +56,9 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' errors : step.messages, initial_errors : true, cls : 'ui-portlet-narrow', - hide_operations : true + hide_operations : true, + needs_refresh : false, + always_refresh : step.step_type != 'tool' }, step ); self.steps[ i ] = step; self.links[ i ] = []; @@ -167,7 +169,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' this._renderHistory(); _.each ( this.steps, function( step, i ) { self._renderStep( step, i ) } ); this.deferred.execute( function() { self.execute_btn.unwait(); - self.execute_btn.model.set( { wait_text: 'Sending...', percentage: -1 } ) } ); + self.execute_btn.model.set( { wait_text: 'Sending...', percentage: -1 } ); } ); }, /** Render header */ @@ -193,7 +195,8 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' this.$message.append( new Ui.Message( { message : 'Some tools in this workflow may have changed since it was last saved or some errors were found. The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.', status : 'warning', - persistent : true + persistent : true, + fade : false } ).$el ); } }, @@ -205,9 +208,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' if ( !_.isEmpty( this.wp_inputs ) ) { this.wp_form = new Form({ title: 'Workflow Parameters', inputs: this.wp_inputs, cls: 'ui-portlet-narrow', onchange: function() { _.each( self.wp_form.input_list, function( input_def, i ) { - _.each( input_def.links, function( step ) { - self._refreshStep( step ); - }); + _.each( input_def.links, function( step ) { self._refreshStep( step ) } ); }); } }); @@ -266,17 +267,16 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' }, '' ) ) ) ); } - self._append( self.$steps, form.$el ); } else { _.each( step.inputs, function( input ) { input.flavor = 'module' } ); form = new Form( Utils.merge({ title : '' + step.name + '', onchange : function() { _.each( self.links[ i ], function( link ) { self._refreshStep( link ) } ) } }, step ) ); - self._append( self.$steps, form.$el ); } self.forms[ i ] = form; - self._refreshStep( step ); + self._append( self.$steps, form.$el ); + step.needs_refresh && self._refreshStep( step ); self._resolve( form.deferred, promise ); self.execute_btn.model.set( 'percentage', ( i + 1 ) * 100.0 / self.steps.length ); Galaxy.emit.debug( 'tool-form-composite::initialize()', i + ' : Workflow step state ready.', step ); @@ -327,6 +327,8 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' } }); form.trigger( 'change' ); + } else { + step.needs_refresh = true; } }, diff --git a/client/galaxy/scripts/mvc/ui/ui-misc.js b/client/galaxy/scripts/mvc/ui/ui-misc.js index 4ecc4308e65..5fb397def4a 100644 --- a/client/galaxy/scripts/mvc/ui/ui-misc.js +++ b/client/galaxy/scripts/mvc/ui/ui-misc.js @@ -42,7 +42,8 @@ define(['utils/utils', message : null, status : 'info', cls : '', - persistent : false + persistent : false, + fade : true }).set( options ); this.listenTo( this.model, 'change', this.render, this ); this.render(); @@ -62,7 +63,7 @@ define(['utils/utils', } if ( this.model.get( 'message' ) ) { this.$el.html( this.model.get( 'message' ) ); - this.$el.fadeIn(); + this.$el[ this.model.get( 'fade' ) ? 'fadeIn' : 'show' ](); this.timeout && window.clearTimeout( this.timeout ); if ( !this.model.get( 'persistent' ) ) { var self = this; diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 1f997843a0d..efae3382977 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3309,6 +3309,15 @@ class HistoryDatasetCollectionAssociation( DatasetCollectionInstance, UsesAnnota return (( type_coerce( cls.content_type, types.Unicode ) + u'-' + type_coerce( cls.id, types.Unicode ) ).label( 'type_id' )) + def to_hda_representative( self, multiple=False ): + rval = [] + for dataset in self.collection.dataset_elements: + rval.append( dataset.dataset_instance ) + if multiple is False: + break + if len( rval ) > 0: + return rval if multiple else rval[ 0 ] + def to_dict( self, view='collection' ): dict_value = dict( hid=self.hid, diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index db15dc640e7..ef88eceee8f 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -114,16 +114,6 @@ class ToolParameter( object, Dictifiable ): """ return None - def get_initial_value_from_history_prevent_repeats( self, trans, other_values, already_used ): - """ - Get the starting value for the parameter, but if fetching from the history, try - to find a value that has not yet been used. already_used is a list of objects that - tools must manipulate (by adding to it) to store a memento that they can use to detect - if a value has already been chosen from the history. This is to support the capability to - choose each dataset once - """ - return self.get_initial_value( trans, other_values ) - def get_required_enctype( self ): """ If this parameter needs the form to have a specific encoding @@ -1202,10 +1192,12 @@ class ColumnListParameter( SelectToolParameter ): return [] column_list = None for dataset in util.listify( dataset ): + # Use representative dataset if a dataset collection is parsed + if isinstance( dataset, trans.app.model.HistoryDatasetCollectionAssociation ): + dataset = dataset.to_hda_representative() # Columns can only be identified if metadata is available if not hasattr( dataset, 'metadata' ) or not hasattr( dataset.metadata, 'columns' ) or not dataset.metadata.columns: return [] - # Build up possible columns for this dataset this_column_list = [] if self.numerical: @@ -1216,7 +1208,6 @@ class ColumnListParameter( SelectToolParameter ): else: for i in range( 0, dataset.metadata.columns ): this_column_list.append( str( i + 1 ) ) - # Take the intersection of these columns with the other columns. if column_list is None: column_list = this_column_list @@ -1668,6 +1659,25 @@ class BaseDataToolParameter( ToolParameter ): self.options_filter_attribute = options_elem.get( 'options_filter_attribute', None ) self.is_dynamic = self.options is not None + def get_initial_value( self, trans, other_values ): + if trans.workflow_building_mode is workflow_building_modes.ENABLED or trans.app.name == 'tool_shed': + return RuntimeValue() + if self.optional: + return None + history = trans.history + if history is not None: + dataset_matcher = DatasetMatcher( trans, self, None, other_values ) + if isinstance( self, DataToolParameter ): + for hda in reversed( history.active_datasets_children_and_roles ): + match = dataset_matcher.hda_match( hda ) + if match: + return match.hda + else: + dataset_collection_matcher = DatasetCollectionMatcher( dataset_matcher ) + for hdca in reversed( history.active_dataset_collections ): + if dataset_collection_matcher.hdca_match( hdca, reduction=self.multiple ): + return hdca + def to_json( self, value, app ): def single_to_json( value ): src = None @@ -1681,7 +1691,6 @@ class BaseDataToolParameter( ToolParameter ): src = 'hda' if src is not None: return { 'id' : app.security.encode_id( value.id ), 'src' : src } - if value not in [ None, '', 'None' ]: if isinstance( value, list ) and len( value ) > 0: values = [ single_to_json( v ) for v in value ] @@ -1830,44 +1839,6 @@ class DataToolParameter( BaseDataToolParameter ): for item in dataset_collector( history.active_datasets_children_and_roles, None ): yield item - def get_initial_value( self, trans, other_values ): - return self.get_initial_value_from_history_prevent_repeats(trans, other_values, None ) - - def get_initial_value_from_history_prevent_repeats( self, trans, other_values, already_used ): - """ - NOTE: This is wasteful since dynamic options and dataset collection - happens twice (here and when generating HTML). - """ - # Can't look at history in workflow mode. Tool shed has no histories. - if trans.workflow_building_mode is workflow_building_modes.ENABLED or trans.app.name == 'tool_shed': - return RuntimeValue() - history = self._get_history( trans ) - dataset_matcher = DatasetMatcher( trans, self, None, other_values ) - if self.optional: - return None - most_recent_dataset = [] - - def dataset_collector( datasets ): - for data in datasets: - if data.visible and dataset_matcher.hda_accessible( data, check_security=False ): - match = dataset_matcher.valid_hda_match( data, check_security=False ) - if not match or dataset_matcher.filter( match.hda ): - continue - data = match.hda - most_recent_dataset.append(data) - # Also collect children via association object - dataset_collector( data.children ) - dataset_collector( history.active_datasets_children_and_roles ) - most_recent_dataset.reverse() - if already_used is not None: - for val in most_recent_dataset: - if val is not None and val not in already_used: - already_used.append(val) - return val - if len(most_recent_dataset) > 0: - return most_recent_dataset[0] - return '' - def from_json( self, value, trans, other_values={} ): if trans.workflow_building_mode is workflow_building_modes.ENABLED: return None diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py index 2f754950492..248301781d2 100644 --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -7,7 +7,7 @@ import logging import os import validation from galaxy.util import string_as_bool -from galaxy.model import User +from galaxy.model import User, HistoryDatasetAssociation, HistoryDatasetCollectionAssociation import galaxy.tools log = logging.getLogger(__name__) @@ -125,10 +125,12 @@ class DataMetaFilter( Filter ): return dataset_value in file_value.split( self.separator ) return file_value == dataset_value ref = other_values.get( self.ref_name, None ) + if isinstance( ref, HistoryDatasetCollectionAssociation ): + ref = ref.to_hda_representative( self.multiple ) is_data = isinstance( ref, galaxy.tools.wrappers.DatasetFilenameWrapper ) is_data_list = isinstance( ref, galaxy.tools.wrappers.DatasetListWrapper ) or isinstance( ref, list ) is_data_or_data_list = is_data or is_data_list - if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not is_data_or_data_list: + if not isinstance( ref, HistoryDatasetAssociation ) and not is_data_or_data_list: return [] # not a valid dataset if is_data_list: @@ -398,7 +400,9 @@ class RemoveValueFilter( Filter ): value = other_values.get( self.ref_name ) else: data_ref = other_values.get( self.meta_ref ) - if not isinstance( data_ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ) and not isinstance( data_ref, galaxy.tools.wrappers.DatasetFilenameWrapper ): + if isinstance( data_ref, HistoryDatasetCollectionAssociation ): + data_ref = data_ref.to_hda_representative() + if not isinstance( data_ref, HistoryDatasetAssociation ) and not isinstance( data_ref, galaxy.tools.wrappers.DatasetFilenameWrapper ): return options # cannot modify options value = data_ref.metadata.get( self.metadata_key, None ) return [ ( disp_name, optval, selected ) for disp_name, optval, selected in options if not compare_value( optval, value ) ] diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py index 63f5399297f..3381b569654 100644 --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1135,7 +1135,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix trans.workflow_building_mode = workflow_building_modes.USE_HISTORY for step in workflow.steps: try: - module_injector.inject( step ) + module_injector.inject( step, steps=workflow.steps ) except MissingToolException: if step.tool_id not in missing_tools: missing_tools.append(step.tool_id) diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index 0769cea9182..2dc98a6469d 100644 --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -21,7 +21,7 @@ from galaxy.tools.parameters.basic import ( from galaxy.tools.parameters.wrapped import make_dict_copy from galaxy.tools import DefaultToolState from galaxy.tools import ToolInputsNotReadyException -from galaxy.util import odict +from galaxy.util import odict, listify from galaxy.util.bunch import Bunch from galaxy.web.framework import formbuilder from tool_shed.util import common_util @@ -132,7 +132,7 @@ class WorkflowModule( object ): """ pass - def add_dummy_datasets( self, connections=None): + def add_dummy_datasets( self, connections=None, steps=None ): # Replaced connected inputs with DummyDataset values. pass @@ -417,7 +417,7 @@ class SubWorkflowModule( WorkflowModule ): """ return None - def add_dummy_datasets( self, connections=None): + def add_dummy_datasets( self, connections=None, steps=None ): # Replaced connected inputs with DummyDataset values. return None @@ -1139,11 +1139,10 @@ class ToolModule( WorkflowModule ): if flush_required: self.trans.sa_session.flush() - def add_dummy_datasets( self, connections=None): + def add_dummy_datasets( self, connections=None, steps=None ): if connections: # Store onnections by input name - input_connections_by_name = \ - dict( ( conn.input_name, conn ) for conn in connections ) + input_connections_by_name = dict( ( conn.input_name, conn ) for conn in connections ) else: input_connections_by_name = {} @@ -1151,10 +1150,24 @@ class ToolModule( WorkflowModule ): # are not persisted so we need to do it every time) def callback( input, prefixed_name, context, **kwargs ): if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ): - if connections is None or prefixed_name in input_connections_by_name: + if self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY: + if connections is None or prefixed_name in input_connections_by_name: + if steps: + connection = input_connections_by_name[ prefixed_name ] + output_step = next( output_step for output_step in steps if connection.output_step_id == output_step.id ) + if output_step.type.startswith( 'data' ): + output_inputs = output_step.module.get_runtime_inputs() + output_value = output_inputs[ 'input' ].get_initial_value( self.trans, context ) + if isinstance( input, DataToolParameter ): + for v in listify( output_value ): + if isinstance( v, self.trans.app.model.HistoryDatasetCollectionAssociation ): + return v.to_hda_representative() + return output_value + return RuntimeValue() + else: + return input.get_initial_value( self.trans, context ) + elif connections is None or prefixed_name in input_connections_by_name: return RuntimeValue() - elif self.trans.workflow_building_mode is workflow_building_modes.USE_HISTORY: - return input.get_initial_value( self.trans, context ) visit_input_values( self.tool.inputs, self.state.inputs, callback ) @@ -1289,7 +1302,7 @@ class WorkflowModuleInjector(object): self.trans = trans self.allow_tool_state_corrections = allow_tool_state_corrections - def inject( self, step, step_args=None ): + def inject( self, step, step_args=None, steps=None ): """ Pre-condition: `step` is an ORM object coming from the database, if supplied `step_args` is the representation of the inputs for that step supplied via web form. @@ -1319,7 +1332,7 @@ class WorkflowModuleInjector(object): # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) - module.add_dummy_datasets( connections=step.input_connections ) + module.add_dummy_datasets( connections=step.input_connections, steps=steps ) state, step_errors = module.compute_runtime_state( self.trans, step_args ) step.state = state if step.type == "subworkflow": diff --git a/static/maps/mvc/tool/tool-form-composite.js.map b/static/maps/mvc/tool/tool-form-composite.js.map index cc24d64df76..724ef2e3576 100644 --- a/static/maps/mvc/tool/tool-form-composite.js.map +++ b/static/maps/mvc/tool/tool-form-composite.js.map @@ -1 +1 @@ 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"].join("")}});return{CitationView:n,CitationListView:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(42),i(32),i(6),i(5)],s=function(t,e,i,n){"use strict";var s=t.FoldoutListItemView,l=t.ListItemView,c=s.extend({className:s.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(t){this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,s.prototype.initialize.call(this,t)},_setUpListeners:function(){s.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,e){o.has(t.changed,"deleted")?this.render():o.has(t.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=s.prototype._getFoldoutPanelOptions.call(this);return o.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCListItemView("+t+")"}});c.prototype.templates=function(){var t=o.extend({},s.prototype.templates.warnings,{error:i.wrapTemplate(["<% if( model.error ){ %>",'
',n("There was an error getting the data for this collection"),": <%- model.error %>","
","<% } %>"]),purged:i.wrapTemplate(["<% if( model.purged ){ %>",'
',n("This collection has been deleted and removed from disk"),"
","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',n("This collection has been deleted"),"
","<% } %>"])}),e=i.wrapTemplate(['
','
','<%- collection.element_identifier || collection.name %>',"
",'
',"
"],"collection"),a=i.wrapTemplate(['
','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<% if( collection.collection_type === "list" ){ %>',n("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',n("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',n("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',n("a list of <%- countText %>dataset lists"),"<% } %>","
"],"collection");return o.extend({},s.prototype.templates,{warnings:t,titleBar:e,subtitle:a})}();var d=l.extend({className:l.prototype.className+" dataset-collection-element",initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log("DCEListItemView.initialize:",t),l.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCEListItemView("+t+")"}});d.prototype.templates=function(){var t=i.wrapTemplate(['
','
','<%- element.element_identifier %>',"
",'
',"
"],"element");return o.extend({},l.prototype.templates,{titleBar:t})}();var h=e.DatasetListItemView.extend({className:e.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log("DatasetDCEListItemView.initialize:",t),e.DatasetListItemView.prototype.initialize.call(this,t)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):r.when()},toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+t+")"}});h.prototype.templates=function(){var t=i.wrapTemplate(['
','','
','<%- element.element_identifier %>',"
","
"],"element");return o.extend({},e.DatasetListItemView.prototype.templates,{titleBar:t})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(t){c.prototype._swapNewRender.call(this,t);var e=this.model.get("state")||"ok";return this.$el.addClass("state-"+e),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+t+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(70),i(6),i(5)],s=function(t,e,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return o.extend(t,t.object,{element_id:t.id}),delete 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t=this.get("element_identifier");return["DatasetDCE(",t,")"].join("")}})),d=l.extend({model:c,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=a.Model.extend(e.LoggableMixin).extend(e.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(t,e){this.debug(this+"(DatasetCollection).initialize:",t,e,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var t=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(t),this.elements},toJSON:function(){var t=a.Model.prototype.toJSON.call(this);return this.elements&&(t.elements=this.elements.toJSON()),t},inReadyState:function(){var t=this.get("populated");return this.isDeletedOrPurged()||t},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(t){return this.elements},parse:function(t,e){var i=a.Model.prototype.parse.call(this,t,e);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var t=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+t.join(",")+")"}}),u=h.extend({collectionClass:d,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),g=h.extend(e.mixin(n,{constructor:function(t,e){this.debug("\t NestedDCDCE.constructor:",t,e),n.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",t,")"].join("")}})),f=l.extend({model:g,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(e.mixin(n,{constructor:function(t,e){this.debug("\t NestedPairDCDCE.constructor:",t,e),n.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",t,")"].join("")}})),v=f.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(e.mixin(n,{constructor:function(t,e){this.debug("\t NestedListDCDCE.constructor:",t,e),n.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",t,")"].join("")}})),w=f.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),b=h.extend({collectionClass:w,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:b}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(39),i(12),i(6),i(8),i(87),i(5),i(84)],s=function(t,e,i,n,s,c){"use strict";function d(t){var e=t.toJSON(),i=f(e,{creationFn:function(e,i){return e=e.map(function(t){return{id:t.id,name:t.name,src:"dataset"===t.history_content_type?"hda":"hdca"}}),t.createHDCA(e,"list",i)}});return i}var h="collections",u=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"collection-element",initialize:function(t){this.element=t.element||{},this.selected=t.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:a.template(['',"<%- element.name %>","",'"].join("")),select:function(t){this.$el.toggleClass("selected",t),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var t=this,e=this.$el.parent().width();this.$el.animate({"margin-right":e},"fast",function(){t.trigger("discard",{source:t}),t.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(t){t.stopPropagation(),this.select(t)},_clickName:function(t){t.stopPropagation(),t.preventDefault();var e=([c("Enter a new name for the element"),":\n(",c("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(c("Enter a new name for the 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creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},initialize:function(t){this.metric("ListCollectionCreator.initialize",t);var e=this;a.each(this.defaultAttributes,function(i,n){i=t[n]||i,e[n]=i}),e.initialElements=t.elements||[],this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(t){t.hasOwnProperty("id")||(t.id=a.uniqueId())}),this.workingElements},_validateElements:function(){var t=this;return t.invalidElements=[],this.workingElements=this.workingElements.filter(function(e){var i=t._isElementInvalid(e);return i&&t.invalidElements.push({element:e,text:i}),!i}),this.workingElements},_isElementInvalid:function(t){return"dataset"!==t.history_content_type?c("is not a dataset"):t.state!==e.OK?c(a.contains(e.NOT_READY_STATES,t.state)?"hasn't finished running yet":"has errored, is paused, or is not accessible"):t.deleted||t.purged?c("has been deleted or purged"):null},_mangleDuplicateNames:function(){var t=900,e=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+e+")",e+=1,e>=t)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(t){},render:function(t,e){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(t,e){var i=this,n=l("
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":content+=": "+n}e._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(t){"function"==typeof this.oncancel&&this.oncancel.call(this)},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(t){t.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(t){t.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(t){t.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(t,e){e=e||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(e).show().find(".alert-message").html(t)},_hideAlert:function(t){this.$(".main-help").show(),this.$(".header .alert").hide()},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(t){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(t){t.preventDefault();var e=this.$list();this._checkForAutoscroll(e,t.originalEvent.clientY);var i=this._getNearestElement(t.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var n=r('
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','',c("Less"),"","
","
",'
','','',"
"].join("")),middle:a.template(['
','',c("Start over"),"",'',c("Clear selected"),"","
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',"
"].join("")),footer:a.template(['
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','','
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","
","
",'
','
','",'
','",'","
","
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','","
","
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","
    ","
  • ",c(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
    • ","
  • ",c(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
    • ","
  • ",c(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
    • ","
  • ",c(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
    • ","
  • ",c(['Click the "Cancel" button to exit the interface.'].join("")),"
    • ","

","

",c(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

"].join("")),invalidElements:a.template([c("The following selections could not be included due to problems:"),"
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  • <%- problem.element.name %>: <%- problem.text %>
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"].join("")),noElementsLeft:a.template(['
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    ','
    ','',"<% if( _.size( problems ) ){ %>",c("The following selections could not be included due to problems"),":","
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    • <%- problem.element.name %>: <%- problem.text %>
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    ","<% } else if( _.size( elements ) < 1 ){ %>",c("No datasets were selected"),".","<% } %>","
    ",c("At least one element is needed for the collection"),". ",c("You may need to "),'',c("cancel")," ",c("and reselect new elements"),".","    ","
    ","
    ",'
    ','
    ','
    ','","
    ","
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    "].join(""))},toString:function(){return"ListCollectionCreator"}}),g=function(t,e,i){var s,o=l.Deferred(),r=Galaxy.modal||new n.View;return e=a.defaults(e||{},{elements:t,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(t,e){r.hide(),o.resolve(e)}}),s=new i(e),r.show({title:e.title||c("Create a collection"),body:s.$el,width:"80%",height:"100%",closing_events:!0}),s.render(),window._collectionCreator=s,o},f=function(t,e){return e=e||{},e.title=c("Create a collection from a list of datasets"),g(t,e,p)};return{DatasetCollectionElementView:u,ListCollectionCreator:p,collectionCreatorModal:g,listCollectionCreatorModal:f,createListCollection:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(42),i(12),i(23),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var c="dataset",d=t.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger), this.log(this+".initialize:",t),d.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(e,i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):t.render()}})},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},remove:function(t,e){var i=this;t=t||this.fxSpeed,this.$el.fadeOut(t,function(){a.View.prototype.remove.call(i),e&&e.call(i)})},_swapNewRender:function(t){return d.prototype._swapNewRender.call(this,t),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var t=this.model.get("state");if(t===e.NOT_VIEWABLE||t===e.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(t===e.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(t===e.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),t.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===e.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var t=d.prototype._renderDetails.call(this);return t.find(".actions .left").empty().append(this._renderSecondaryActions()),t.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),t.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(t),t},_renderSummary:function(){var t=this.model.toJSON(),e=this.templates.summaries[t.state];return(e=e||this.templates.summaries.unknown)(t,this)},_renderDetailMessages:function(){var t=this,e=r('
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    ","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'
    ',s("There was an error getting the data for this dataset"),": <%- model.error %>","
    ","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'
    ',s("This dataset has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',s("This dataset has been deleted"),"
    ","<% } %>"])}),i=n.wrapTemplate(['
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    ','
    ','
    ','
    ',"
    ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
    ','
    ','
    ',"<% if( dataset.peek ){ %>",'
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    ',"<% } %>","<% } %>","
    "],"dataset"),o=n.wrapTemplate(['
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    ',s("You do not have permission to view this dataset"),"
    ","
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    ","<% } %>","<% if( dataset.file_ext ){ %>",'
    ','",'<%- dataset.file_ext %>',"
    ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
    ','",'',"<%- dataset.metadata_dbkey %>","","
    ","<% } %>","<% if( dataset.misc_info ){ %>",'
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    ","<% } %>"],"dataset"),a[e.NEW]=n.wrapTemplate(["
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    "],"dataset"),a[e.DISCARDED]=n.wrapTemplate(["
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    "],"dataset"),a[e.QUEUED]=n.wrapTemplate(["
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    ",s("This job is currently running"),"
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    ',s("The job creating this dataset has been resubmitted"),"
    ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
    ','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
    ","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(3),i(1),i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},set:function(t){for(var e in t.attributes){var i=this.match(e);i&&this.app.field_list[i].value(t.get(e))}},create:function(){function t(t,e,i){n.flat_dict[t]=e,o[t]=i,n.app.element_list[e]&&n.app.element_list[e].$el.attr("tour_id",t)}function e(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);g!=-1&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(t,e){return t-e});var a=0;for(var f in h)e(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);v!=-1&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},e("",s),o},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){var i=this;n(t.inputs,function(t,n){i.flat_dict[n]&&e(t,i.flat_dict[n])})},matchResponse:function(t){function e(t,s){if("string"==typeof s){var o=n.flat_dict[t];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==t){var l="|";s instanceof Array&&(l="_"),r=t+l+r}e(r,s[a])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=a(t).children();n.each(function(){var t=this,n=a(t).attr("id");if(a(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,s,o){o=a.extend(!0,{},o),r.each(t,function(t){t&&t.type&&t.name&&(o[t.name]=t)});for(var l in t){var c=t[l],d=s?s+"|"+c.name:c.name;switch(c.type){case"repeat":r.each(c.cache,function(t,i){n(t,e,d+"_"+i,o)});break;case"conditional":if(c.test_param){e(c.test_param,d+"|"+c.test_param.name,o);var h=i(c,c.test_param.value);h!=-1?n(c.cases[h].inputs,e,d,o):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+d+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+d+".");break;case"section":n(c.inputs,e,d,o);break;default:e(c,d,o)}}};return{Manager:e,visitInputs:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2))},function(t,e,i){var n,s;(function(i,o,a){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.app_options=t.options||{},this.field=e&&e.field||new i.View,this.model=e&&e.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up"}).set(e),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,t.trigger&&t.trigger("change"),s.render()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){this.model.set("error_text",null)},render:function(){o(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&t.indexOf("("+e+")")==-1&&(t+=" ("+e+")"),this.$info.html(t),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(a.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.fadeIn("fast"),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var n=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+n)).attr("data-original-title",this.model.get("text_"+n)).tooltip({placement:"bottom"})}},_template:function(){return o("
    ").addClass("ui-form-element").append(o("
    ").addClass("ui-form-error ui-error").append(o("").addClass("fa fa-arrow-down")).append(o("").addClass("ui-form-error-text"))).append(o("
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    ").addClass("ui-form-field").append(o("").addClass("ui-form-info")).append(o("
    ").addClass("ui-form-backdrop"))).append(o("
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    "),this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title_new,tooltip:"Add new "+this.options.title_new+" block",floating:"clear",onclick:function(){i.onnew&&i.onnew()}}),this.table=new e.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append(a("
    ").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(14),i(7),i(9),i(36),i(34),i(35)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d,this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")});for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$el.addClass("ui-table-section"),this.table.add(o.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,a=new h(i.app,{inputs:e});o.add({id:s,$el:a.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=r.size(t.cache),l=0;l").addClass("ui-form-info").html(t.help)),this.app.on("expand",function(t){e.$("#"+t).length>0&&e.expand()}),this.table.add(e.$el),this.table.append(t.id)},_addRow:function(t){var e=this,i=t.id;t.onchange=function(){e.app.trigger("change",i)};var n=this.parameters.create(t);this.app.field_list[i]=n;var s=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,text_value:t.text_value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,color:t.color,style:t.style,backdrop:t.backdrop,field:n});return this.app.element_list[i]=s,this.table.add(s.$el),this.table.append(i),t.hidden&&this.table.get(i).hide(),n}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(37),i(33)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:null,always_refresh:!0}),this.setElement("
    "),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[i];if(n&&n.options&&!a.isEqual(n.options,t.options)){n.options=t.options;var s=e.field_list[i];if(s.update){var o=[];if(["data","data_collection","drill_down"].indexOf(n.type)!=-1)o=n.options;else for(var r in t.options){var l=t.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+i)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.portlet.expand(),this.trigger("expand",t),!i)){var s=this.$el.parents().filter(function(){return["auto","scroll"].indexOf(r(this).css("overflow"))!=-1}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-120},500)}},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},setOnChange:function(t){this.options.onchange=t},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(i){var n=t.input_list[i];if(!n||n.refresh_on_change||t.options.always_refresh){var s=t.data.checksum();s!=e&&(e=s,t.options.onchange&&t.options.onchange())}}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),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}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(o){n=[i(30),i(74),i(5)],s=function(t,e,i){"use strict";function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=t.ListOfListsDatasetCollection,d=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(a.prototype.save),toString:function(){return"History"+a.prototype.toString.call(this)}}),h=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(r.prototype.save),toString:function(){return"History"+r.prototype.toString.call(this)}}),u=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(l.prototype.save),toString:function(){return"History"+l.prototype.toString.call(this)}}),p=c.extend(s).extend({defaults:o.extend(o.clone(c.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){c.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(c.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(67),i(72),i(39),i(41),i(6),i(125)],s=function(t,e,i,n,s,l){"use strict";var c=t.PaginatedCollection,d=c.extend(s.LoggableMixin).extend({_logNamespace:"history",model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n);case"list:list":return new i.HistoryListOfListsDatasetCollection(t,n)}var s="Unknown collection_type: "+t.collection_type;return console.warn(s,t),{validationError:s}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(t,e){e=e||{},c.prototype.initialize.call(this,t,e),this.history=e.history||null,this.setHistoryId(e.historyId||null),this.includeDeleted=e.includeDeleted||this.includeDeleted,this.includeHidden=e.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},setHistoryId:function(t){this.historyId=t,this._setUpWebStorage()},_setUpWebStorage:function(t){if(this.historyId)return this.storage=new n.HistoryPrefs({id:n.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(t){this.storage.includeDeleted(t)},"include-hidden":function(t){this.storage.includeHidden(t)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:o.extend(o.clone(c.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),hid:s.buildComparator("hid",{ascending:!1}),"hid-asc":s.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(t){return!t.inReadyState()})},runningAndActive:function(){return this.filter(function(t){return!t.inReadyState()&&t.get("visible")&&!t.get("deleted")})},getByHid:function(t){return this.findWhere({hid:t})},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},hidden:function(){return this.filter(function(t){return t.hidden()})},deleted:function(){return this.filter(function(t){return t.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(t){return t.get("visible")&&!t.get("deleted")})},setIncludeDeleted:function(t,e){if(o.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,o.result(e,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,e){if(o.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,e=e||{},o.result(e,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var e=n.HistoryPrefs.get(this.historyId).toJSON();o.isEmpty(e.expandedIds)||(t.details=o.values(e.expandedIds).join(","))}return c.prototype.fetch.call(this,t)},_buildFetchData:function(t){return o.extend(c.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:c.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var e=c.prototype._buildFetchFilters.call(this,t)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),o.defaults(e,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(t,e){return t&&(e=e||{filters:{}},e.remove=!1,e.filters={"update_time-ge":t.toISOString(),visible:""}),this.fetch(e)},fetchDeleted:function(t){t=t||{};var e=this;return t.filters=o.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,e.trigger("fetching-deleted",e),e.fetch(t).always(function(){e.trigger("fetching-deleted-done",e)})},fetchHidden:function(t){t=t||{};var e=this;return t.filters=o.extend(t.filters,{visible:!1}),t.remove=!1,e.trigger("fetching-hidden",e),e.fetch(t).always(function(){e.trigger("fetching-hidden-done",e)})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=o.extend(t.data||{},e),this.fetch(t)},fetchCollectionCounts:function(t){return t=t||{},t.keys=["type_id","element_count"].join(","),t.filters=o.extend(t.filters||{},{history_content_type:"dataset_collection"}),t.remove=!1,this.fetch(t)},_filterAndUpdate:function(t,e){var i=this,n=i.model.prototype.idAttribute,s=[e]; return i.fetch({filters:t,remove:!1}).then(function(t){return t=t.reduce(function(t,e,s){var o=i.get(e[n]);return o?t.concat(o):t},[]),i.ajaxQueue("save",s,t)})},ajaxQueue:function(t,e,i){return i=i||this.models,new l.AjaxQueue(i.slice().reverse().map(function(i,n){var s=o.isString(t)?i[t]:t;return function(){return s.apply(i,e)}})).deferred},progressivelyFetchDetails:function(t){function i(e){e=e||0;var a=o.extend(o.clone(t),{view:"summary",keys:c,limit:r,offset:e,reset:0===e,remove:!1});o.defer(function(){s.fetch.call(s,a).fail(n.reject).done(function(t){n.notify(t,r,e),t.length!==r?(s.allFetched=!0,n.resolve(t,r,e)):i(e+r)})})}t=t||{};var n=a.Deferred(),s=this,r=t.limitPerCall||s.limitPerProgressiveFetch,l=e.HistoryDatasetAssociation.prototype.searchAttributes,c=l.join(",");return i(),n},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return o.isObject(t)&&t.id&&o.contains(e,t.model_class)},copy:function(t){var e,i,n;o.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,r=a.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:e,source:n,type:i})}).done(function(t){s.add([t],{parse:!0})}).fail(function(t,o,a){s.trigger("error",s,r,{},"Error copying contents",{type:i,id:e,source:n})});return r},createHDCA:function(t,e,i,n){var s=this.model({history_content_type:"dataset_collection",collection_type:e,history_id:this.historyId,name:i,element_identifiers:t});return s.save(n)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return o.has(t.attributes,"annotation")})},matches:function(t){return this.filter(function(e){return e.matches(t)})},clone:function(){var t=r.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o){n=[i(6)],s=function(t){"use strict";var e=t.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(t){var e=this.get("expandedIds");e[t.id]=t.get("id"),this.save("expandedIds",e)},removeExpanded:function(t){var e=this.get("expandedIds");delete e[t.id],this.save("expandedIds",e)},isExpanded:function(t){return o.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return o.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return o.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return o.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(t){if(!t)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+t);return e.storageKeyPrefix+t},get:function(t){return new e({id:e.historyStorageKey(t)})},clearAll:function(t){for(var i in sessionStorage)0===i.indexOf(e.storageKeyPrefix)&&sessionStorage.removeItem(i)}});return{HistoryPrefs:e}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){"use strict";var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;0===e?(i._swapNewRender(t),i.trigger("rendered",i)):a(i).queue("fx",[function(t){i.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){i.$el.fadeIn(e,t)},function(t){i.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown(t.fxSpeed,function(){t.trigger("expanded",t)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp(t.fxSpeed,function(){t.trigger("collapsed",t)})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a('
    '),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i||(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=t.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=t.wrapTemplate(['
    ']),o=t.wrapTemplate(['
    ']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.listenTo(t.foldout,"close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['
    ',"
    "],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(2),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(54),i(7),i(38),i(18),i(28)],s=function(t,e,i,n,s,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?this._buildForm(t):this.deferred.execute(function(e){i._buildModel(e,t,!0)}),t.listen_to_history&&parent.Galaxy&&parent.Galaxy.currHistoryPanel&&this.listenTo(parent.Galaxy.currHistoryPanel.collection,"change",function(){this.refresh()})},refresh:function(){var t=this;t.deferred.reset(),this.deferred.execute(function(e){t._updateModel(e)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:e.icon,title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:!this.options.hide_operations&&this._operations(),onchange:function(){i.refresh()}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.get({url:r,data:l,success:function(t){return t=t.tool_model||t,t.display?(a._buildForm(t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),void e.resolve()):void(window.location=Galaxy.root)},error:function(t,n){var s=t&&t.err_msg||"Uncaught error.";401==n.status?window.location=Galaxy.root+"user/login?"+o.param({redirect:Galaxy.root+"?tool_id="+a.options.id}):a.$el.is(":empty")?a.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var s in e.versions){var o=e.versions[s];o!=e.version&&n.addMenu({title:"Switch to "+o,version:o,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var a=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(a.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),a.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),a.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="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&a.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&a.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){!this.visible||t.portlet.collapsed?(this.visible=!0,t.portlet.expand(),t.message.update({persistent:!0,message:t._templateRequirements(e),status:"info"})):(this.visible=!1,t.message.update({message:""}))}}),e.sharable_url&&a.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:a,versions:n}},_footer:function(){var t=this.options,e=o("
    ").append(this._templateHelp(t));if(t.citations){var i=o("
    "),n=new s.ToolCitationCollection;n.tool_id=t.id;var a=new r.CitationListView({el:i,collection:n});a.render(),n.fetch(),e.append(i)}return e},_templateHelp:function(t){var e=o("
    ").addClass("ui-form-help").append(t.help);return e.find("a").attr("target","_blank"),e},_templateRequirements:function(t){var e=t.requirements.length;if(e>0){var i="This tool requires ";a.each(t.requirements,function(t,n){i+=t.name+(t.version?" (Version "+t.version+")":"")+(n").attr("target","_blank").attr("href","https://wiki.galaxyproject.org/Tools/Requirements").text("here");return o("").append(i+". Click ").append(n).append(" for more information.")}return"No requirements found."}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2))},function(t,e,i){var n,s;(function(o,a){n=[i(2),i(17),i(11),i(19)],s=function(t,e,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(t){this.set("value",parseFloat(t))}}),u=r.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});r.subModelTypes={integer:d,"float":h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new l(t.map(e.inputs,function(t){var e=r.subModelTypes[t.type]||r;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return t.indexOf(e.get("type"))!==-1});e.get("inputs").remove(i)},copy:function(t){var e=new p(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return t.indexOf(e,this.attributes.id)!==-1?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(p.prototype,s);var g=(o.View.extend({}),o.Collection.extend({model:p})),f=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof f?(i=t,i.hide()):t instanceof p&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length");t.append(S.tool_link(this.model.toJSON()));var e=this.model.get("form_style",null);if("upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("regular"===e){var i=this;t.find("a").on("click",function(t){t.preventDefault();var e=new n.View({id:i.model.id,version:i.model.get("version")});e.deferred.execute(function(){Galaxy.app.display(e)})})}return this.$el.append(t),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof p){var i=new w({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof f){var n=new b({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new C({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof m){var i=new x({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof p){var n=new w({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof f){var s=new b({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:t.template(['',' ',''].join("")),panel_section:t.template(['
    ','<%- name %>',"
    ",'