From 7ea4668ff732f22c0d686ed35fd6ff1a0c431736 Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 2 Feb 2016 11:53:38 -0500 Subject: [PATCH] Remove former populate_state --- .../scripts/mvc/form/form-parameters.js | 103 ++-- .../galaxy/scripts/mvc/form/form-section.js | 1 - client/galaxy/scripts/utils/utils.js | 13 +- lib/galaxy/tools/__init__.py | 482 +++++------------- lib/galaxy/tools/parameters/__init__.py | 60 +-- lib/galaxy/tools/parameters/basic.py | 6 - lib/galaxy/webapps/galaxy/api/tools.py | 2 +- lib/galaxy/workflow/modules.py | 16 +- static/maps/mvc/form/form-parameters.js.map | 2 +- static/maps/mvc/form/form-section.js.map | 2 +- static/maps/utils/utils.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 10 +- .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 2 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/mvc/form/form-parameters.js | 2 +- static/scripts/mvc/form/form-section.js | 2 +- static/scripts/utils/utils.js | 2 +- test/qunit/tests/masthead_tests.js | 1 - 19 files changed, 231 insertions(+), 481 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-parameters.js b/client/galaxy/scripts/mvc/form/form-parameters.js index 72d2220579c..567adce09a1 100644 --- a/client/galaxy/scripts/mvc/form/form-parameters.js +++ b/client/galaxy/scripts/mvc/form/form-parameters.js @@ -7,7 +7,7 @@ define(['utils/utils', 'mvc/ui/ui-select-library', 'mvc/ui/ui-select-ftp', 'mvc/ui/ui-color-picker'], - function(Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker) { + function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker ) { // create form view return Backbone.Model.extend({ @@ -31,50 +31,30 @@ define(['utils/utils', 'ftpfile' : '_fieldFtp' }, - // initialize - initialize: function(app, options) { + initialize: function( app, options ) { this.app = app; }, /** Returns an input field for a given field type */ - create: function(input_def) { - // add regular/default value if missing - if (input_def.value === undefined) { - input_def.value = null; - } - if (input_def.default_value === undefined) { - input_def.default_value = input_def.value; - } - - // create field wrapper - var field = null; - var fieldClass = this.types[input_def.type]; - if (fieldClass && typeof(this[fieldClass]) === 'function') { - field = this[fieldClass].call(this, input_def); - } - - // match unavailable field types - if (!field) { + create: function( input_def ) { + var fieldClass = this.types[ input_def.type ]; + var field = typeof( this[ fieldClass ] ) === 'function' ? this[ fieldClass ].call( this, input_def ) : null; + if ( !field ) { this.app.incompatible = true; - if (input_def.options) { - field = this._fieldSelect(input_def); - } else { - field = this._fieldText(input_def); - } + field = input_def.options ? this._fieldSelect( input_def ) : this._fieldText( input_def ); Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').'); } - - // set initial field value - input_def.value !== undefined && ( field.value( input_def.value ) ); + input_def.value === undefined && ( input_def.value = null ); + field.value( input_def.value ); return field; }, /** Data input field */ - _fieldData: function(input_def) { + _fieldData: function( input_def ) { var self = this; - return new SelectContent.View(this.app, { + return new SelectContent.View( this.app, { id : 'field-' + input_def.id, extensions : input_def.extensions, optional : input_def.optional, @@ -82,37 +62,33 @@ define(['utils/utils', type : input_def.type, data : input_def.options, onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); }, /** Select/Checkbox/Radio options field */ - _fieldSelect: function (input_def) { + _fieldSelect: function ( input_def ) { // show text field e.g. in workflow editor if( input_def.is_workflow ) { return this._fieldText( input_def ); } // customize properties - if (input_def.type == 'data_column') { + if ( input_def.type == 'data_column' ) { input_def.error_text = 'Missing columns in referenced dataset.' } // configure options fields var options = []; - for (var i in input_def.options) { - var option = input_def.options[i]; - options.push({ - label: option[0], - value: option[1] - }); - } + _.each( input_def.options, function( option ) { + options.push( { label: option[ 0 ], value: option[ 1 ] } ); + }); // identify display type var SelectClass = Ui.Select; - switch (input_def.display) { + switch ( input_def.display ) { case 'checkboxes': SelectClass = Ui.Checkbox; break; @@ -127,19 +103,18 @@ define(['utils/utils', id : 'field-' + input_def.id, data : options, error_text : input_def.error_text || 'No options available', - optional : input_def.optional && input_def.default_value === null, multiple : input_def.multiple, optional : input_def.optional, searchable : input_def.searchable, onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); }, /** Drill down options field */ - _fieldDrilldown: function (input_def) { + _fieldDrilldown: function ( input_def ) { // show text field e.g. in workflow editor if( input_def.is_workflow ) { return this._fieldText( input_def ); @@ -152,25 +127,25 @@ define(['utils/utils', data : input_def.options, display : input_def.display, onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); }, /** Text input field */ - _fieldText: function(input_def) { + _fieldText: function( input_def ) { // field replaces e.g. a select field - if (input_def.options) { + if ( input_def.options ) { input_def.area = input_def.multiple; - if (!Utils.validate(input_def.value)) { + if ( !Utils.validate( input_def.value ) ) { input_def.value = null; } else { - if ($.isArray(input_def.value)) { + if ( $.isArray( input_def.value ) ) { var str_value = ''; - for (var i in input_def.value) { - str_value += String(input_def.value[i]); - if (!input_def.multiple) { + for ( var i in input_def.value ) { + str_value += String( input_def.value[ i ] ); + if ( !input_def.multiple ) { break; } str_value += '\n'; @@ -192,7 +167,7 @@ define(['utils/utils', /** Slider field */ - _fieldSlider: function(input_def) { + _fieldSlider: function( input_def ) { var self = this; return new Ui.Slider.View({ id : 'field-' + input_def.id, @@ -201,14 +176,14 @@ define(['utils/utils', min : input_def.min, max : input_def.max, onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); }, /** Hidden field */ - _fieldHidden: function(input_def) { + _fieldHidden: function( input_def ) { return new Ui.Hidden({ id : 'field-' + input_def.id, info : input_def.info @@ -217,54 +192,54 @@ define(['utils/utils', /** Boolean field */ - _fieldBoolean: function(input_def) { + _fieldBoolean: function( input_def ) { var self = this; return new Ui.RadioButton.View({ id : 'field-' + input_def.id, data : [ { label : 'Yes', value : 'true' }, { label : 'No', value : 'false' }], onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); }, /** Color picker field */ - _fieldColor: function(input_def) { + _fieldColor: function( input_def ) { var self = this; return new ColorPicker({ id : 'field-' + input_def.id, onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); }, /** Library dataset field */ - _fieldLibrary: function(input_def) { + _fieldLibrary: function( input_def ) { var self = this; return new SelectLibrary.View({ id : 'field-' + input_def.id, optional : input_def.optional, multiple : input_def.multiple, onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); }, /** FTP file field */ - _fieldFtp: function(input_def) { + _fieldFtp: function( input_def ) { var self = this; return new SelectFtp.View({ id : 'field-' + input_def.id, optional : input_def.optional, multiple : input_def.multiple, onchange : function() { - self.app.trigger('change'); + self.app.trigger( 'change' ); } }); } diff --git a/client/galaxy/scripts/mvc/form/form-section.js b/client/galaxy/scripts/mvc/form/form-section.js index f3a37dad204..88c9653f478 100644 --- a/client/galaxy/scripts/mvc/form/form-section.js +++ b/client/galaxy/scripts/mvc/form/form-section.js @@ -231,7 +231,6 @@ define(['utils/utils', name : input_def.name, label : input_def.label || input_def.name, value : input_def.value, - default_value : input_def.default_value, text_value : input_def.text_value || input_def.value, collapsible_value : input_def.collapsible_value, collapsible_preview : input_def.collapsible_preview, diff --git a/client/galaxy/scripts/utils/utils.js b/client/galaxy/scripts/utils/utils.js index e581fbea5bb..cc5e05aa19b 100644 --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -48,15 +48,12 @@ function sanitize(content) { * usually used for selectable options * @param{String} value - Value or list to be validated */ -function validate (value) { - if (!(value instanceof Array)) { - value = [value]; +function validate ( value ) { + if ( !( value instanceof Array ) ) { + value = [ value ]; } - if (value.length === 0) { - return false; - } - for (var i in value) { - if (['__null__', '__undefined__', null, undefined].indexOf(value[i]) > -1) { + for( var i in value ) { + if ( [ '__null__', '__undefined__', null, undefined ].indexOf( value[ i ] ) > -1 ) { return false; } } diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index aa58c698ed3..a0d1be510ae 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1108,7 +1108,7 @@ class Tool( object, Dictifiable ): else: input.visit_inputs( "", value[input.name], callback ) - def handle_input( self, trans, incoming, history=None, source='html' ): + def handle_input( self, trans, incoming, history=None ): """ Process incoming parameters for this tool from the dict `incoming`, update the tool state (or create if none existed), and either return @@ -1135,32 +1135,31 @@ class Tool( object, Dictifiable ): if rerun_remap_job_id and len( expanded_incomings ) > 1: raise exceptions.MessageException( 'Failure executing tool (cannot create multiple jobs when remapping existing job).' ) + # Process incoming data validation_timer = ExecutionTimer() all_errors = [] all_params = [] - validate_input = self.get_hook( 'validate_input' ) for expanded_incoming in expanded_incomings: - expanded_state = self.new_state( request_context ) - # Process incoming data + params = {} + errors = {} if not self.check_values: # If `self.check_values` is false we don't do any checking or # processing on input This is used to pass raw values # through to/from external sites. - errors = {} - params = expanded_incoming + state_inputs = expanded_incoming else: # Update state for all inputs on the current page taking new # values from `incoming`. - errors = self.populate_state( request_context, self.inputs, expanded_state.inputs, expanded_incoming, source=source ) + self._populate_state( request_context, self.inputs, expanded_incoming, params, errors ) + # If the tool provides a `validate_input` hook, call it. + validate_input = self.get_hook( 'validate_input' ) if validate_input: - validate_input( trans, errors, expanded_state.inputs, self.inputs ) - params = expanded_state.inputs + validate_input( request_context, errors, params, self.inputs ) all_errors.append( errors ) all_params.append( params ) - log.debug("Validated and populated state for tool request %s" % validation_timer) - # If there were errors, we stay on the same page and display - # error messages + log.debug( 'Validated and populated state for tool request %s' % validation_timer ) + # If there were errors, we stay on the same page and display them if any( all_errors ): raise exceptions.MessageException( err_data=all_errors[ 0 ] ) else: @@ -1175,6 +1174,7 @@ class Tool( object, Dictifiable ): else: raise exceptions.MessageException( execution_tracker.execution_errors[ 0 ] ) + def handle_single_execution( self, trans, rerun_remap_job_id, params, history, mapping_over_collection, execution_cache=None ): """ Return a pair with whether execution is successful as well as either @@ -1199,6 +1199,7 @@ class Tool( object, Dictifiable ): message = 'Failure executing tool (invalid data returned from tool execution)' return False, message + def find_fieldstorage( self, x ): if isinstance( x, FieldStorage ): raise InterruptedUpload( None ) @@ -1207,145 +1208,6 @@ class Tool( object, Dictifiable ): elif isinstance(x, list): [ self.find_fieldstorage( y ) for y in x ] - def populate_state( self, trans, inputs, state, incoming, source="html", prefix="", context=None ): - errors = dict() - # Push this level onto the context stack - context = ExpressionContext( state, context ) - for input in inputs.itervalues(): - key = prefix + input.name - if isinstance( input, Repeat ): - group_state = state[input.name] - # Create list of empty errors for each previously existing state - group_errors = [ ] - any_group_errors = False - rep_index = 0 - del group_state[:] # Clear prepopulated defaults if repeat.min set. - while True: - rep_name = "%s_%d" % ( key, rep_index ) - if not any( [ incoming_key.startswith(rep_name) for incoming_key in incoming.keys() ] ): - break - if rep_index < input.max: - new_state = {} - new_state['__index__'] = rep_index - self.fill_in_new_state( trans, input.inputs, new_state, context ) - group_state.append( new_state ) - group_errors.append( {} ) - rep_errors = self.populate_state( trans, - input.inputs, - new_state, - incoming, - source, - prefix=rep_name + "|", - context=context ) - if rep_errors: - any_group_errors = True - group_errors[rep_index].update( rep_errors ) - - else: - group_errors[-1] = { '__index__': 'Cannot add repeat (max size=%i).' % input.max } - any_group_errors = True - rep_index += 1 - if any_group_errors: - errors[ input.name ] = group_errors - elif isinstance( input, Conditional ): - group_state = state[input.name] - group_prefix = "%s|" % ( key ) - # Deal with the 'test' element and see if its value changed - if input.value_ref and not input.value_ref_in_group: - # We are referencing an existent parameter, which is not - # part of this group - test_param_key = prefix + input.test_param.name - else: - test_param_key = group_prefix + input.test_param.name - # Get value of test param and determine current case - value, test_param_error = check_param_from_incoming( trans, - group_state, - input.test_param, - incoming, - test_param_key, - context, - source ) - - if test_param_error: - errors[ input.name ] = [ test_param_error ] - # Store the value of the test element - group_state[ input.test_param.name ] = value - else: - current_case = input.get_current_case( value, trans ) - # Current case has changed, throw away old state - group_state = state[input.name] = {} - # TODO: we should try to preserve values if we can - self.fill_in_new_state( trans, input.cases[current_case].inputs, group_state, context ) - group_errors = self.populate_state( trans, - input.cases[current_case].inputs, - group_state, - incoming, - source, - prefix=group_prefix, - context=context) - if group_errors: - errors[ input.name ] = group_errors - # Store the current case in a special value - group_state['__current_case__'] = current_case - # Store the value of the test element - group_state[ input.test_param.name ] = value - elif isinstance( input, Section ): - group_state = state[input.name] - group_prefix = "%s|" % ( key ) - self.fill_in_new_state( trans, input.inputs, group_state, context ) - group_errors = self.populate_state( trans, - input.inputs, - group_state, - incoming, - source, - prefix=group_prefix, - context=context ) - if group_errors: - errors[ input.name ] = group_errors - elif isinstance( input, UploadDataset ): - group_state = state[input.name] - group_errors = [] - any_group_errors = False - d_type = input.get_datatype( trans, context ) - writable_files = d_type.writable_files - # remove extra files - while len( group_state ) > len( writable_files ): - del group_state[-1] - - # Add new fileupload as needed - while len( writable_files ) > len( group_state ): - new_state = {} - new_state['__index__'] = len( group_state ) - self.fill_in_new_state( trans, input.inputs, new_state, context ) - group_state.append( new_state ) - if any_group_errors: - group_errors.append( {} ) - - # Update state - for i, rep_state in enumerate( group_state ): - rep_index = rep_state['__index__'] - rep_prefix = "%s_%d|" % ( key, rep_index ) - rep_errors = self.populate_state( trans, - input.inputs, - rep_state, - incoming, - source, - prefix=rep_prefix, - context=context) - if rep_errors: - any_group_errors = True - group_errors.append( rep_errors ) - else: - group_errors.append( {} ) - # Were there *any* errors for any repetition? - if any_group_errors: - errors[input.name] = group_errors - else: - value, error = check_param_from_incoming( trans, state, input, incoming, key, context, source ) - if error: - errors[ input.name ] = error - state[ input.name ] = value - return errors def update_state( self, trans, inputs, state, incoming, source='html', prefix="", context=None, update_only=False, old_errors={}, item_callback=None ): @@ -1663,7 +1525,7 @@ class Tool( object, Dictifiable ): if input.min: messages[ input.name ] = [] for i in range( input.min ): - rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 ) + rep_prefix = prefix + '%s %d > ' % ( input.title, i + 1 ) rep_dict = dict() messages[ input.name ].append( rep_dict ) self.check_and_update_param_values_helper( input.inputs, {}, trans, rep_dict, context, rep_prefix, update_values=update_values ) @@ -1677,13 +1539,13 @@ class Tool( object, Dictifiable ): else: if isinstance( input, Repeat ): for i, d in enumerate( values[ input.name ] ): - rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 ) + rep_prefix = prefix + '%s %d > ' % ( input.title, i + 1 ) self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix, update_values=update_values ) elif isinstance( input, Conditional ): group_values = values[ input.name ] use_initial_value = False if '__current_case__' in group_values: - if int( group_values['__current_case__'] ) >= len( input.cases ): + if int( group_values[ '__current_case__' ] ) >= len( input.cases ): use_initial_value = True else: use_initial_value = True @@ -1691,11 +1553,11 @@ class Tool( object, Dictifiable ): # No test param invalidates the whole conditional values[ input.name ] = group_values = input.get_initial_value( trans, context ) messages[ input.test_param.name ] = "No value found for '%s%s', using default" % ( prefix, input.test_param.label ) - current_case = group_values['__current_case__'] + current_case = group_values[ '__current_case__' ] for child_input in input.cases[current_case].inputs.itervalues(): messages[ child_input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, child_input.label ) else: - current = group_values["__current_case__"] + current = group_values[ '__current_case__' ] self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix, update_values=update_values ) elif isinstance( input, Section ): messages[ input.name ] = {} @@ -1710,14 +1572,14 @@ class Tool( object, Dictifiable ): else: # skip check if is workflow parameters ck_param = True - search = input.type in ["text"] + search = input.type in [ 'text' ] if trans.workflow_building_mode and contains_workflow_parameter( values[ input.name ], search=search ): ck_param = False # this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input if ck_param: input.value_from_basic( input.value_to_basic( value, self.app ), self.app, ignore_errors=False ) except: - log.info("Parameter validation failed.", exc_info=True) + log.info( "Parameter validation failed.", exc_info=True ) messages[ input.name ] = "Value no longer valid for '%s%s', replacing with default" % ( prefix, input.label ) if update_values: values[ input.name ] = input.get_initial_value( trans, context ) @@ -2018,7 +1880,7 @@ class Tool( object, Dictifiable ): # If an admin user, expose the path to the actual tool config XML file. if trans.user_is_admin(): - tool_dict['config_file'] = os.path.abspath(self.config_file) + tool_dict[ 'config_file' ] = os.path.abspath( self.config_file ) # Add link details. if link_details: @@ -2042,11 +1904,11 @@ class Tool( object, Dictifiable ): return tool_dict - def to_json(self, trans, kwd={}, job=None, workflow_mode=False): + def to_json( self, trans, kwd={}, job=None, workflow_mode=False ): """ Recursively creates a tool dictionary containing repeats, dynamic options and updated states. """ - history_id = kwd.get('history_id', None) + history_id = kwd.get( 'history_id', None ) history = None try: if history_id is not None: @@ -2070,7 +1932,7 @@ class Tool( object, Dictifiable ): self._map_source_to_history( request_context, self.inputs, job_params ) tool_message = self._compare_tool_version( job ) params_to_incoming( kwd, self.inputs, job_params, self.app ) - except Exception, e: + except Exception as e: raise exceptions.MessageException( str( e ) ) # create parameter object @@ -2116,7 +1978,7 @@ class Tool( object, Dictifiable ): return None # ensures that input dictionary is jsonifiable - def sanitize(dict, key='value'): + def sanitize( dict, key='value' ): # get current value value = dict[key] if key in dict else None @@ -2138,142 +2000,52 @@ class Tool( object, Dictifiable ): # update and return dict[key] = value - # check the current state of a value and update it if necessary - def check_state( input, value, context ): - error = 'State validation failed.' - if isinstance( value, galaxy.tools.parameters.basic.DummyDataset ): - return [ None, None ] - elif isinstance( value, galaxy.tools.parameters.basic.RuntimeValue ): - return [ { '__class__' : 'RuntimeValue' }, None ] - elif isinstance( value, dict ): - if value.get( '__class__' ) == 'RuntimeValue': - return [ value, None ] - try: - value, error = check_param( request_context, input, value, context, boolean_fix=True ) - except Exception, err: - log.error( 'Checking parameter %s failed. %s', input.name, str( err ) ) - pass - return [ value, error ] - - # populates state with incoming url parameters - def populate_state( inputs, state, errors, incoming, prefix="", context=None ): - context = ExpressionContext(state, context) - for input in inputs.itervalues(): - state[input.name] = input.get_initial_value( request_context, context ) - key = prefix + input.name - if input.type == 'repeat': - group_state = state[input.name] - rep_index = 0 - del group_state[:] - while True: - rep_name = "%s_%d" % (key, rep_index) - if not any([incoming_key.startswith(rep_name) for incoming_key in incoming.keys()]) and rep_index >= input.min: - break - if rep_index < input.max: - new_state = {} - new_state['__index__'] = rep_index - group_state.append(new_state) - populate_state( input.inputs, new_state, errors, incoming, prefix=rep_name + "|", context=context ) - rep_index += 1 - elif input.type == 'conditional': - group_state = state[input.name] - group_prefix = "%s|" % ( key ) - test_param_key = group_prefix + input.test_param.name - default_value = incoming.get(test_param_key, group_state.get(input.test_param.name, None)) - value, error = check_state( input.test_param, default_value, context ) - if error: - errors[test_param_key] = error - else: - try: - current_case = input.get_current_case( value, request_context ) - group_state = state[input.name] = {} - populate_state( input.cases[current_case].inputs, group_state, errors, incoming, prefix=group_prefix, context=context ) - group_state['__current_case__'] = current_case - except Exception: - errors[test_param_key] = 'The selected case is unavailable/invalid.' - pass - group_state[input.test_param.name] = value - elif input.type == 'section': - group_state = state[input.name] - group_prefix = "%s|" % ( key ) - populate_state( input.inputs, group_state, errors, incoming, prefix=group_prefix, context=context ) - else: - default_value = incoming.get(key, state.get(input.name, None)) - value, error = check_state( input, default_value, context ) - if error: - errors[key] = error - state[input.name] = value - - # builds tool model including all attributes - def iterate( group_inputs, inputs, state_inputs, other_values=None ): + # populates model from state + def populate_model( inputs, state_inputs, group_inputs, other_values=None ): other_values = ExpressionContext( state_inputs, other_values ) for input_index, input in enumerate( inputs.itervalues() ): tool_dict = None - group_state = state_inputs.get(input.name, {}) + group_state = state_inputs.get( input.name, {} ) if input.type == 'repeat': tool_dict = input.to_dict( request_context ) - group_cache = tool_dict['cache'] = {} + group_cache = tool_dict[ 'cache' ] = {} for i in range( len( group_state ) ): - group_cache[i] = {} - iterate( group_cache[i], input.inputs, group_state[i], other_values ) + group_cache[ i ] = {} + populate_model( input.inputs, group_state[ i ], group_cache[ i ], other_values ) elif input.type == 'conditional': tool_dict = input.to_dict( request_context ) if 'test_param' in tool_dict: - test_param = tool_dict['test_param'] - test_param['default_value'] = jsonify( input.test_param.get_initial_value( request_context, other_values ) ) - test_param['value'] = jsonify(group_state.get(test_param['name'], test_param['default_value'])) - test_param['text_value'] = input.test_param.value_to_display_text(test_param['value'], self.app) - for i in range(len( tool_dict['cases'] ) ): + test_param = tool_dict[ 'test_param' ] + test_param[ 'value' ] = jsonify( group_state.get( test_param[ 'name' ], input.test_param.get_initial_value( request_context, other_values ) ) ) + test_param[ 'text_value' ] = input.test_param.value_to_display_text( test_param[ 'value' ], self.app ) + for i in range( len( tool_dict['cases'] ) ): current_state = {} - if i == group_state.get('__current_case__', None): + if i == group_state.get( '__current_case__' ): current_state = group_state - iterate( tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values ) + populate_model( input.cases[ i ].inputs, current_state, tool_dict[ 'cases' ][ i ][ 'inputs' ], other_values ) elif input.type == 'section': tool_dict = input.to_dict( request_context ) - iterate( tool_dict['inputs'], input.inputs, group_state, other_values ) + populate_model( tool_dict[ 'inputs' ], input.inputs, group_state, other_values ) else: - # expand input dictionary, resolve dynamic parameters - try: - tool_dict = input.to_dict( request_context, other_values=other_values ) - except Exception: - tool_dict = input.to_dict( request_context ) - log.exception('tools::to_json() - Skipping parameter expansion for %s.' % input.name) - pass - - # backup default value - try: - tool_dict['default_value'] = input.get_initial_value( request_context, other_values ) - except Exception: - tool_dict['default_value'] = None - log.exception('tools::to_json() - Getting initial value failed %s.' % input.name) - pass - - # update input value from tool state - tool_dict['value'] = state_inputs.get(input.name, tool_dict['default_value']) - - # add text value + tool_dict = input.to_dict( request_context, other_values=other_values ) + tool_dict[ 'value' ] = state_inputs.get( input.name, input.get_initial_value( request_context, other_values ) ) tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ], self.app ) + sanitize( tool_dict, 'value' ) + group_inputs[ input_index ] = tool_dict - # sanitize values - sanitize(tool_dict, 'value') - sanitize(tool_dict, 'default_value') - - # backup final input dictionary - group_inputs[input_index] = tool_dict - - # sanatization for the final tool state - def sanitize_state(state): + # sanatizes tool state + def sanitize_state( state ): keys = None - if isinstance(state, dict): + if isinstance( state, dict ): keys = state - elif isinstance(state, list): - keys = range( len(state) ) + elif isinstance( state, list ): + keys = range( len( state ) ) if keys: for k in keys: - if isinstance(state[k], dict) or isinstance(state[k], list): - sanitize_state(state[k]) + if isinstance( state[ k ], dict ) or isinstance( state[ k ], list ): + sanitize_state( state[ k ] ) else: - state[k] = jsonify(state[k]) + state[ k ] = jsonify( state[ k ] ) # expand incoming parameters (parameters might trigger multiple tool executions, # here we select the first execution only in order to resolve dynamic parameters) @@ -2284,75 +2056,110 @@ class Tool( object, Dictifiable ): if self.input_translator: self.input_translator.translate( params ) - # initialize and populate tool state + # create tool state state_inputs = {} state_errors = {} - populate_state( self.inputs, state_inputs, state_errors, params.__dict__ ) + self._populate_state( request_context, self.inputs, params.__dict__, state_inputs, state_errors ) - # create basic tool model + # create tool model tool_model = self.to_dict( request_context ) - tool_model['inputs'] = {} - - # build tool model and tool state - iterate( tool_model['inputs'], self.inputs, state_inputs, '' ) + tool_model[ 'inputs' ] = {} + populate_model( self.inputs, state_inputs, tool_model[ 'inputs' ] ) # sanitize tool state - sanitize_state(state_inputs) + sanitize_state( state_inputs ) - # load tool help + # create tool help tool_help = '' if self.help: - tool_help = self.help - tool_help = tool_help.render( static_path=url_for( '/static' ), host_url=url_for('/', qualified=True) ) + tool_help = self.help.render( static_path=url_for( '/static' ), host_url=url_for( '/', qualified=True ) ) if type( tool_help ) is not unicode: - tool_help = unicode( tool_help, 'utf-8') + tool_help = unicode( tool_help, 'utf-8' ) - # check if citations exist - tool_citations = False - if self.citations: - tool_citations = True - - # get tool versions + # create tool versions tool_versions = [] - tools = self.app.toolbox.get_loaded_tools_by_lineage(self.id) + tools = self.app.toolbox.get_loaded_tools_by_lineage( self.id ) for t in tools: if t.version not in tool_versions: - tool_versions.append(t.version) + tool_versions.append( t.version ) - # add information with underlying requirements and their versions - tool_requirements = [] - if self.requirements: - for requirement in self.requirements: - tool_requirements.append({ - 'name' : requirement.name, - 'version' : requirement.version - }) - - # add toolshed url - sharable_url = None - if self.tool_shed_repository: - sharable_url = self.tool_shed_repository.get_sharable_url( self.app ) - - # add additional properties + # update tool model tool_model.update({ 'id' : self.id, 'help' : tool_help, - 'citations' : tool_citations, + 'citations' : bool( self.citations ), 'biostar_url' : self.app.config.biostar_url, - 'sharable_url' : sharable_url, + 'sharable_url' : self.tool_shed_repository.get_sharable_url( self.app ) if self.tool_shed_repository else None, 'message' : tool_message, 'versions' : tool_versions, - 'requirements' : tool_requirements, + 'requirements' : [ { 'name' : r.name, 'version' : r.version } for r in self.requirements ], 'errors' : state_errors, 'state_inputs' : state_inputs, 'job_id' : trans.security.encode_id( job.id ) if job else None, 'job_remap' : self._get_job_remap( job ), 'history_id' : trans.security.encode_id( history.id ) }) - - # return enriched tool model return tool_model + # populates state from incoming parameters + def _populate_state( self, request_context, inputs, incoming, state, errors, prefix='', context=None ): + context = ExpressionContext( state, context ) + for input in inputs.itervalues(): + state[ input.name ] = input.get_initial_value( request_context, context ) + key = prefix + input.name + group_state = state[ input.name ] + group_prefix = '%s|' % ( key ) + if input.type == 'repeat': + rep_index = 0 + del group_state[:] + while True: + rep_prefix = '%s_%d' % ( key, rep_index ) + if not any( [ incoming_key.startswith( rep_prefix ) for incoming_key in incoming.keys() ] ) and rep_index >= input.min: + break + if rep_index < input.max: + new_state = { '__index__' : rep_index } + group_state.append( new_state ) + self._populate_state( request_context, input.inputs, incoming, new_state, errors, prefix=rep_prefix + '|', context=context ) + rep_index += 1 + elif input.type == 'conditional': + test_param_key = group_prefix + input.test_param.name + test_param_value = incoming.get( test_param_key, group_state.get( input.test_param.name ) ) + value, error = check_param( request_context, input.test_param, test_param_value, context ) + if error: + errors[ test_param_key ] = error + else: + try: + current_case = input.get_current_case( value, request_context ) + group_state = state[ input.name ] = {} + self._populate_state( request_context, input.cases[ current_case ].inputs, incoming, group_state, errors, prefix=group_prefix, context=context ) + group_state[ '__current_case__' ] = current_case + except Exception: + errors[ test_param_key ] = 'The selected case is unavailable/invalid.' + pass + group_state[ input.test_param.name ] = value + elif input.type == 'section': + self._populate_state( request_context, input.inputs, incoming, group_state, errors, prefix=group_prefix, context=context ) + elif input.type == 'upload_dataset': + d_type = input.get_datatype( request_context, context=context ) + writable_files = d_type.writable_files + while len( group_state ) > len( writable_files ): + del group_state[ -1 ] + while len( writable_files ) > len( group_state ): + new_state = { '__index__' : len( group_state ) } + for upload_item in input.inputs.itervalues(): + new_state[ upload_item.name ] = upload_item.get_initial_value( request_context, context ) + group_state.append( new_state ) + for i, rep_state in enumerate( group_state ): + rep_index = rep_state[ '__index__' ] + rep_prefix = '%s_%d|' % ( key, rep_index ) + self._populate_state( request_context, input.inputs, incoming, rep_state, errors, prefix=rep_prefix, context=context ) + else: + param_value = incoming.get( key, state.get( input.name ) ) + value, error = check_param( request_context, input, param_value, context ) + if error: + errors[ key ] = error + state[ input.name ] = value + def _get_job_remap( self, job): if job: if job.state == job.states.ERROR: @@ -2373,28 +2180,28 @@ class Tool( object, Dictifiable ): # Create index for hdas. hda_source_dict = {} for hda in history.datasets: - key = '%s_%s' % (hda.hid, hda.dataset.id) + key = '%s_%s' % ( hda.hid, hda.dataset.id ) hda_source_dict[ hda.dataset.id ] = hda_source_dict[ key ] = hda # Ditto for dataset collections. hdca_source_dict = {} for hdca in history.dataset_collections: - key = '%s_%s' % (hdca.hid, hdca.collection.id) + key = '%s_%s' % ( hdca.hid, hdca.collection.id ) hdca_source_dict[ hdca.collection.id ] = hdca_source_dict[ key ] = hdca # Map dataset or collection to current history - def map_to_history(value): + def map_to_history( value ): id = None source = None - if isinstance(value, self.app.model.HistoryDatasetAssociation): + if isinstance( value, self.app.model.HistoryDatasetAssociation ): id = value.dataset.id source = hda_source_dict - elif isinstance(value, self.app.model.HistoryDatasetCollectionAssociation): + elif isinstance( value, self.app.model.HistoryDatasetCollectionAssociation ): id = value.collection.id source = hdca_source_dict else: return None - key = '%s_%s' % (value.hid, id) + key = '%s_%s' % ( value.hid, id ) if key in source: return source[ key ] elif id in source: @@ -2442,16 +2249,15 @@ class Tool( object, Dictifiable ): else: message += 'You can re-run the job with this tool version, which is a different version of the original tool.' else: - new_tool_shed_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + '/%s/' % tool.tool_shed_repository.changeset_revision - old_tool_shed = tool_id.split( "/repos/" )[0] - old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, old_tool_shed ) - old_tool_shed_url = old_tool_shed_url + "/view/%s/%s/" % (tool.repository_owner, tool.repository_name) - message = 'This job was run with tool id \"%s\", version "%s", which is not available. ' % (old_tool_shed_url, tool_id, tool_version) + new_tool_shed_url = '%s/%s/' % ( tool.tool_shed_repository.get_sharable_url( tool.app ), tool.tool_shed_repository.changeset_revision ) + old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_id.split( '/repos/' )[ 0 ] ) + old_tool_shed_url = '%s/view/%s/%s/' % ( old_tool_shed_url, tool.repository_owner, tool.repository_name ) + message = 'This job was run with tool id \"%s\", version "%s", which is not available. ' % ( old_tool_shed_url, tool_id, tool_version ) if len( tools ) > 1: - message += 'You can re-run the job with the selected tool id \"%s\" or choose another derivation of the tool.' % (new_tool_shed_url, self.id) + message += 'You can re-run the job with the selected tool id \"%s\" or choose another derivation of the tool.' % ( new_tool_shed_url, self.id ) else: - message += 'You can re-run the job with tool id \"%s\", which is a derivation of the original tool.' % (new_tool_shed_url, self.id) - except Exception, e: + message += 'You can re-run the job with tool id \"%s\", which is a derivation of the original tool.' % ( new_tool_shed_url, self.id ) + except Exception as e: raise exceptions.MessageException( str( e ) ) return message @@ -2787,18 +2593,6 @@ def json_fix( val ): return val -def check_param_from_incoming( trans, state, input, incoming, key, context, source ): - """ - Unlike "update" state, this preserves default if no incoming value found. - This lets API user specify just a subset of params and allow defaults to be - used when available. - """ - default_input_value = state.get( input.name, None ) - incoming_value = get_incoming_value( incoming, key, default_input_value ) - value, error = check_param( trans, input, incoming_value, context, source=source ) - return value, error - - def get_incoming_value( incoming, key, default ): """ Fetch value from incoming dict directly or check special nginx upload diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py index c05063b7d82..534a5a66159 100644 --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -19,47 +19,43 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr and a display label. If the callback returns a value, it will be replace the old value. - - FIXME: There is redundancy between this and the visit_inputs methods of - Repeat and Group. This tracks labels and those do not. It would - be nice to unify all the places that recursively visit inputs. """ context = ExpressionContext( input_values, context ) for input in inputs.itervalues(): if isinstance( input, Repeat ) or isinstance( input, UploadDataset ): for i, d in enumerate( input_values[ input.name ] ): index = d['__index__'] - new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index ) - new_label_prefix = label_prefix + "%s %d > " % ( input.title, i + 1 ) + new_name_prefix = name_prefix + '%s_%d|' % ( input.name, index ) + new_label_prefix = label_prefix + '%s %d > ' % ( input.title, i + 1 ) visit_input_values( input.inputs, d, callback, new_name_prefix, new_label_prefix, no_replacement_value=no_replacement_value, context=context, details=details ) elif isinstance( input, Conditional ): values = input_values[ input.name ] - current = values["__current_case__"] - new_name_prefix = name_prefix + input.name + "|" + current = values[ '__current_case__' ] + new_name_prefix = name_prefix + input.name + '|' visit_input_values( input.cases[current].inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details ) elif isinstance( input, Section ): values = input_values[ input.name ] - new_name_prefix = name_prefix + input.name + "|" + new_name_prefix = name_prefix + input.name + '|' visit_input_values( input.inputs, values, callback, new_name_prefix, label_prefix, no_replacement_value=no_replacement_value, context=context, details=details ) else: args = { 'input' : input, 'value' : input_values.get( input.name ), - 'prefixed_name' : "%s%s" % ( name_prefix, input.name ), - 'prefixed_label' : "%s%s" % ( label_prefix, input.label ) + 'prefixed_name' : '%s%s' % ( name_prefix, input.name ), + 'prefixed_label' : '%s%s' % ( label_prefix, input.label ) } if details: args[ 'context' ] = context new_value = callback( **args ) if no_replacement_value is REPLACE_ON_TRUTHY: - replace = bool(new_value) + replace = bool( new_value ) else: replace = new_value != no_replacement_value if replace: - input_values[input.name] = new_value + input_values[ input.name ] = new_value -def check_param( trans, param, incoming_value, param_values, source='html', boolean_fix=False ): +def check_param( trans, param, incoming_value, param_values ): """ Check the value of a single parameter `param`. The value in `incoming_value` is converted from its HTML encoding and validated. @@ -70,20 +66,16 @@ def check_param( trans, param, incoming_value, param_values, source='html', bool value = incoming_value error = None try: - # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code - if boolean_fix and param.type == 'boolean' and isinstance( value, basestring ): - return [ string_as_bool( value ), None ] - if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ): - # Convert value from HTML representation - if source == 'html': - value = param.from_html( value, trans, param_values ) - else: - value = param.from_json( value, trans, param_values ) - # Then do any further validation on the value - param.validate( value, trans ) - elif value is None and isinstance( param, SelectToolParameter ): - # An empty select list or column list - param.validate( value, trans ) + if trans.workflow_building_mode: + if isinstance( value, galaxy.tools.parameters.basic.DummyDataset ): + return [ None, None ] + if isinstance( value, galaxy.tools.parameters.basic.RuntimeValue ): + return [ { '__class__' : 'RuntimeValue' }, None ] + if isinstance( value, dict ): + if value.get( '__class__' ) == 'RuntimeValue': + return [ value, None ] + value = param.from_html( value, trans, param_values ) + param.validate( value, trans ) except ValueError, e: error = str( e ) return value, error @@ -116,7 +108,7 @@ def params_from_strings( params, param_values, app, ignore_errors=False ): for key, value in param_values.iteritems(): value = json_fix( loads( value ) ) if key in params: - value = params[key].value_from_basic( value, app, ignore_errors ) + value = params[ key ].value_from_basic( value, app, ignore_errors ) rval[ key ] = value return rval @@ -131,18 +123,18 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ): for input in inputs.itervalues(): if isinstance( input, Repeat ) or isinstance( input, UploadDataset ): for d in input_values[ input.name ]: - index = d['__index__'] - new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index ) + index = d[ '__index__' ] + new_name_prefix = name_prefix + '%s_%d|' % ( input.name, index ) params_to_incoming( incoming, input.inputs, d, app, new_name_prefix ) elif isinstance( input, Conditional ): values = input_values[ input.name ] - current = values["__current_case__"] - new_name_prefix = name_prefix + input.name + "|" + current = values[ '__current_case__' ] + new_name_prefix = name_prefix + input.name + '|' incoming[ new_name_prefix + input.test_param.name ] = values[ input.test_param.name ] params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix ) elif isinstance( input, Section ): values = input_values[ input.name ] - new_name_prefix = name_prefix + input.name + "|" + new_name_prefix = name_prefix + input.name + '|' params_to_incoming( incoming, input.inputs, values, app, new_name_prefix ) else: value = input_values.get( input.name ) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 55889d268a9..6c72f719de5 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -111,9 +111,6 @@ class ToolParameter( object, Dictifiable ): """ return value - def from_json( self, value, trans=None, other_values={} ): - return self.from_html( value, trans, other_values ) - def get_initial_value( self, trans, other_values ): """ Return the starting value of the parameter @@ -481,9 +478,6 @@ class BooleanToolParameter( ToolParameter ): return form_builder.CheckboxField( self.name, checked, refresh_on_change=self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): - return form_builder.CheckboxField.is_checked( value ) - - def from_json( self, value, trans=None, other_values={} ): return string_as_bool( value ) def to_python( self, value, app ): diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index dfa2febb1e8..7c40846f87e 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -255,7 +255,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): # TODO: handle dbkeys params = util.Params( inputs, sanitize=False ) incoming = params.__dict__ - vars = tool.handle_input( trans, incoming, history=target_history, source='json' ) + vars = tool.handle_input( trans, incoming, history=target_history ) # TODO: check for errors and ensure that output dataset(s) are available. output_datasets = vars.get( 'out_data', [] ) diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index 7d1ccda8892..9ca51130579 100644 --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -163,7 +163,7 @@ class WorkflowModule( object ): """ raise TypeError( "Abstract method" ) - def compute_runtime_state( self, trans, step_updates=None, source="html" ): + def compute_runtime_state( self, trans, step_updates=None ): """ Determine the runtime state (potentially different from self.state which describes configuration state). This (again unlike self.state) is currently always a `DefaultToolState` object. @@ -278,7 +278,7 @@ class SimpleWorkflowModule( WorkflowModule ): errors[ name ] = error return errors - def compute_runtime_state( self, trans, step_updates=None, source="html" ): + def compute_runtime_state( self, trans, step_updates=None ): if step_updates and "tool_state" in step_updates: # Fix this for multiple inputs state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) ) @@ -441,7 +441,7 @@ class SubWorkflowModule( WorkflowModule ): errors[ name ] = error return errors - def compute_runtime_state( self, trans, step_updates=None, source="html" ): + def compute_runtime_state( self, trans, step_updates=None ): state = self.get_runtime_state() step_errors = {} return state, step_errors @@ -1084,7 +1084,7 @@ class ToolModule( WorkflowModule ): inputs = self.state.inputs return self.tool.check_and_update_param_values( inputs, self.trans, workflow_building_mode=True ) - def compute_runtime_state( self, trans, step_updates=None, source="html" ): + def compute_runtime_state( self, trans, step_updates=None ): # Warning: This method destructively modifies existing step state. step_errors = None state = self.state @@ -1097,7 +1097,7 @@ class ToolModule( WorkflowModule ): # Update the state self.runtime_post_job_actions = step_updates.get(RUNTIME_POST_JOB_ACTIONS_KEY, {}) step_errors = tool.update_state( trans, tool.inputs, state.inputs, step_updates, - update_only=True, old_errors=old_errors, source=source ) + update_only=True, old_errors=old_errors ) step_metadata_runtime_state = self.__step_meta_runtime_state() if step_metadata_runtime_state: state.inputs[ RUNTIME_STEP_META_STATE_KEY ] = step_metadata_runtime_state @@ -1385,7 +1385,7 @@ class WorkflowModuleInjector(object): self.trans = trans self.allow_tool_state_corrections = allow_tool_state_corrections - def inject( self, step, step_args=None, source="html" ): + def inject( self, step, step_args=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. @@ -1421,7 +1421,7 @@ class WorkflowModuleInjector(object): # are not persisted so we need to do it every time) module.add_dummy_datasets( connections=step.input_connections ) - state, step_errors = module.compute_runtime_state( trans, step_args, source=source ) + state, step_errors = module.compute_runtime_state( trans, step_args ) step.state = state @@ -1440,7 +1440,7 @@ def populate_module_and_state( trans, workflow, param_map, allow_tool_state_corr module_injector = WorkflowModuleInjector( trans, allow_tool_state_corrections ) for step in workflow.steps: step_args = param_map.get( step.id, {} ) - step_errors = module_injector.inject( step, step_args=step_args, source="json" ) + step_errors = module_injector.inject( step, step_args=step_args ) if step.type == 'tool' or step.type is None: if step_errors: message = "Workflow cannot be run because of validation errors in some steps: %s" % step_errors diff --git a/static/maps/mvc/form/form-parameters.js.map b/static/maps/mvc/form/form-parameters.js.map index 7c07a7da0cf..2f621eea3f7 100644 --- a/static/maps/mvc/form/form-parameters.js.map +++ b/static/maps/mvc/form/form-parameters.js.map @@ -1 +1 @@ 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    '},_templateRow:function(t){return'
    '+t.name+"
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  • '+t.title_new+"
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this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5},this.DATA_={},this.CALLBACK_=t,this.CHAR_=0,this.LINE_=1,this.CHAR_IN_LINE_=0,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0,this.PARSETMP_={},this.SKIPTILLEOL_=!1,this.VALBRACES_=null,this.BRACETYPE_=null,this.BRACECOUNT_=0,this.STATE_=this.STATES_.ENTRY_OR_JUNK,this.ERRORS_=[],this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,online:998,data:999},this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"},this.getErrors=function(){return this.ERRORS_},this.parse=function(t){for(var e=0;en;n++){var l=i[n],c=!1;"\\"==l&&a-1>n?l=i[++n]:("{"==l||"}"==l)&&(c=!0),c||(r+=l)}t.Fields[e]=r}if("string"==t.ObjectType)for(var e in t.Fields)this.MACROS_[e]=t.Fields[e];else this.CALLBACK_(t)},this.processCharacter_=function(t){if(this.CHAR_++,this.CHAR_IN_LINE_++,"\n"==t&&(this.LINE_++,this.CHAR_IN_LINE_=1),this.SKIPTILLEOL_)return void("\n"==t&&(this.SKIPTILLEOL_=!1));if(this.SKIPCOMMENT_&&"%"==t)return void(this.SKIPTILLEOL_=!0);if(!this.SKIPWS_||!/\s/.test(t)){this.SKIPWS_=!1,this.SKIPCOMMENT_=!1,this.SKIPTILLEOL_=!1;for(var e=!0;e;)switch(e=!1,this.STATE_){case this.STATES_.ENTRY_OR_JUNK:"@"==t&&(this.STATE_=this.STATES_.OBJECT_TYPE,this.DATA_={ObjectType:""}),this.BRACETYPE_=null,this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(t))this.DATA_.ObjectType+=t.toLowerCase(),this.SKIPWS_=!0,this.SKIPCOMMENT_=!0;else{var 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    ","<% } %>"])},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(2),i(1),i(3))},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},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].$el.attr("tour_id",t)}function e(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var g=p.indexOf(d);-1!=g&&(g+=d.length,h.push(parseInt(p.substr(g))),u||(u=p.substr(0,g)))}h.sort(function(t,e){return t-e});var a=0;for(var f in h)e(c+"_"+a++,r[u+h[f]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$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){return s(t.inputs,this.flat_dict,e)},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,i,s){s=a.extend(!0,{},s),r.each(t,function(t){t&&t.type&&(s[t.name]=t)}),r.each(t,function(t){r.isObject(t)&&(t.type&&s[t[e]]?i(t,s[t[e]]):n(t,e,i,s))})},s=function(t,e,n){function s(t,o){for(var a in o){var r=o[a],l=r.name;switch(""!=t&&(l=t+"|"+l),r.type){case"repeat":for(var c in r.cache)s(l+"_"+c,r.cache[c]);break;case"conditional":var d=i(r,r.test_param&&r.test_param.value);-1!=d&&s(l,r.cases[d].inputs);break;case"section":s(l,r.inputs);break;default:var h=e[l];h&&n(h,r)}}}var o={};return s("",t),o};return{Manager:e,matchIds:s,matchContext:n}}.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(i){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.field=e.field,this.text_enable=t.options.text_enable||"Enable",this.text_disable=t.options.text_disable||"Disable",this.cls_enable=t.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=t.options.cls_disable||"fa fa-caret-square-o-up",this.setElement(this._template(e)),this.$field=this.$(".ui-form-field"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_icon=this.$(".ui-form-collapsible").find(".icon"),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),this.field.collapsed=void 0!==e.collapsible_value&&JSON.stringify(e.value)==JSON.stringify(e.collapsible_value),this._refresh();var i=this;this.$collapsible.on("click",function(){i.field.collapsed=!i.field.collapsed,i._refresh()})},disable:function(t){this.$backdrop.show(),t&&this.$backdrop.css({opacity:0,cursor:"default"})},error:function(t){this.$error_text.html(t),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$collapsible_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this.$preview.show(),this._tooltip(this.text_enable,this.cls_enable)):(this.$field.fadeIn("fast"),this.$preview.hide(),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change")},_tooltip:function(t,e){this.$collapsible_icon.addClass(e).tooltip({placement:"bottom"}).attr("data-original-title",t).tooltip("fixTitle").tooltip("hide")},_template:function(t){var e='
    ';return e+=t.disabled||void 0===t.collapsible_value?t.label:'
    '+t.label+"
    ",e+='
    ',e+='
    ',t.help&&(e+=t.help),t.argument&&-1==t.help.indexOf("("+t.argument+")")&&(e+=" ("+t.argument+")"),e+='
    ',t.collapsible_preview&&(e+='
    '+t.text_value+"
    "),e+="
    "}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(7),i(39),i(53),i(52),i(49)],s=function(t,e,i,n,s,r){return o.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(t,e){this.app=t},create:function(t){void 0===t.value&&(t.value=null),void 0===t.default_value&&(t.default_value=t.value);var e=null,i=this.types[t.type];return i&&"function"==typeof this[i]&&(e=this[i].call(this,t)),e||(this.app.incompatible=!0,e=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0!==t.value&&e.value(t.value),e},_fieldData:function(t){var e=this;return new i.View(this.app,{id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,data:t.options,onchange:function(){e.app.trigger("change")}})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];for(var n in t.options){var s=t.options[n];i.push({label:s[0],value:s[1]})}var o=e.Select;switch(t.display){case"checkboxes":o=e.Checkbox;break;case"radio":o=e.Radio}var a=this;return new o.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",optional:t.optional&&null===t.default_value,multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){a.app.trigger("change")}})},_fieldDrilldown:function(t){if(t.is_workflow)return this._fieldText(t);var i=this;return new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,onchange:function(){i.app.trigger("change")}})},_fieldText:function(i){if(i.options)if(i.area=i.multiple,t.validate(i.value)){if(a.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}}else i.value=null;var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(t){i.onchange?i.onchange(t):o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:function(){i.app.trigger("change")}})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){var i=this;return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){i.app.trigger("change")}})},_fieldColor:function(t){var e=this;return new r({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldLibrary:function(t){var e=this;return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})},_fieldFtp:function(t){var e=this;return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(14),i(9),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("
    "),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:"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.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(14),i(7),i(9),i(37),i(35),i(36)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d(t,i),this.setElement(this.table.$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.options.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;ll?t.cache[l]:t.inputs);this.app.options.sustain_repeats&&o.hideOptions();var d=new c(this.app,{label:t.title||t.name,help:t.help,field:o});this.table.add(d.$el),this.table.append(t.id)},_addSection:function(t){var e=this,s=new h(e.app,{inputs:t.inputs}),o=new i.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),a=new n.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:o}});a.append(s.$el),a.append(l("
    ").addClass("ui-form-info").html(t.help)),a.setOperation("button_visible",function(){a.collapsed?a.expand():a.collapse()}),a.on("expanded",function(){o.setIcon("fa-eye")}),a.on("collapsed",function(){o.setIcon("fa-eye-slash")}),this.app.on("expand",function(t){a.$("#"+t).length>0&&a.expand()}),t.expanded&&a.expand(),this.table.add(a.$el),this.table.append(t.id)},_addRow:function(t){var e=t.id,i=this.parameters.create(t);this.app.field_list[e]=i;var n=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,default_value:t.default_value,text_value:t.text_value||t.value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(27)],s=function(t,e,i){var n=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement('
    '),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var g in this.list)this.$el.append(this.list[g].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({hid:o.hid,label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.add(n,function(t,e){return e.hid-t.hid})}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(38),i(34)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("
    "),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},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)}}},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(){var i=t.data.checksum();i!=e&&(e=i,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(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(31),i(42),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=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(12),i(6),i(5)],s=function(t,e,i){"use strict";var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n -});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(42),i(74),i(41),i(6),i(5)],s=function(t,e,i,n,s){"use strict";var l="history",c=o.Collection.extend(n.LoggableMixin).extend({_logNamespace:l,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)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){var t=[];return this.each(function(e){var i=!e.inReadyState();i&&t.push(e.get("id"))}),t},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new c(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new c(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.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,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.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(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(" 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;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.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({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".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?!0:(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.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.listenTo(t.foldout,"close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['
    ',"
    "],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(57),i(7),i(40),i(20),i(18),i(29)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$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:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,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 o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,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 r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.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/")}}),r.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)}})),r.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")&&r.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&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("
    ").append(s.help(t));if(t.citations){var i=o("
    "),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),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-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new p(this.toJSON());if(t){var i=new 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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");if(t.append(S.tool_link(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}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(['
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