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Merge branch 'dev' into ui_pref_routing

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This commit is contained in:
guerler
2017-03-01 12:59:48 -05:00
parent f0b03a59b5 d3840c5c41
commit c281dd87ed
25 changed files with 135 additions and 200 deletions
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client/galaxy/scripts/mvc/form/form-input.js
+4 -7
View File
@@ -46,22 +46,19 @@ define([], function() {
});
},
/** Set backdrop for input element
*/
/** Set backdrop for input element */
backdrop: function() {
this.model.set( 'backdrop', true );
},
/** Set error text
*/
/** Set error text */
error: function( text ) {
this.model.set( 'error_text', text );
},
/** Reset this view
*/
/** Reset this view */
reset: function() {
this.model.set( 'error_text', null );
!this.model.get( 'fixed' ) && this.model.set( 'error_text', null );
},
render: function() {
client/galaxy/scripts/mvc/form/form-section.js
+1
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@@ -156,6 +156,7 @@ function( Utils, Ui, Portlet, Repeat, InputElement, Parameters ) {
style : input_def.style,
backdrop : input_def.backdrop,
hidden : input_def.hidden,
fixed : input_def.fixed,
field : field
});
this.app.element_list[ id ] = input_element;
client/galaxy/scripts/mvc/tool/tool-form-composite.js
+1 -1
View File
@@ -306,7 +306,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
var is_simple_input = ([ 'data_input', 'data_collection_input' ]).indexOf( step.step_type ) != -1;
_.each( step.inputs, function( input ) { input.flavor = 'module'; input.hide_label = is_simple_input; } );
form = new Form( Utils.merge({
title : '<b>' + step.name + '</b>' + step.description,
title : step.title,
onchange : function() { _.each( self.links[ step.index ], function( link ) { self._refreshStep( link ) } ) },
inputs : step.inputs && step.inputs.length > 0 ? step.inputs : [ { type: 'hidden', name: 'No options available.', ignore: null } ]
}, step ) );
client/galaxy/scripts/mvc/tool/tool-form-workflow.js → client/galaxy/scripts/mvc/workflow/workflow-forms.js
+14 -16
View File
@@ -1,12 +1,18 @@
/** This is the workflow tool form. */
define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
function( Utils, ToolFormBase ) {
var View = Backbone.View.extend({
define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], function( Utils, Form, ToolFormBase ) {
/** Default form wrapper for non-tool modules in the workflow editor. */
var Default = Backbone.View.extend({
initialize: function( options ) {
this.form = new Form( options );
}
});
/** Tool form wrapper for the workflow editor. */
var Tool = Backbone.View.extend({
initialize: function( options ) {
var self = this;
this.workflow = options.workflow;
this.node = options.node;
this.setElement( '<div/>' );
if ( this.node ) {
this.post_job_actions = this.node.post_job_actions || {};
Utils.deepeach( options.inputs, function( input ) {
@@ -15,7 +21,7 @@ define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
input.type = 'hidden';
input.info = 'Data input \'' + input.name + '\' (' + Utils.textify( input.extensions ) + ')';
input.value = { '__class__': 'RuntimeValue' };
} else {
} else if ( !input.fixed ) {
input.collapsible_value = { '__class__': 'RuntimeValue' };
input.is_workflow = ( input.options && input.options.length == 0 ) ||
( [ 'integer', 'float' ].indexOf( input.type ) != -1 );
@@ -64,7 +70,6 @@ define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
});
},
}));
this.$el.append( this.form.$el );
} else {
Galaxy.emit.debug('tool-form-workflow::initialize()', 'Node not found in workflow.');
}
@@ -74,14 +79,6 @@ define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
_makeSections: function( options ){
var inputs = options.inputs;
var datatypes = options.datatypes;
inputs.push({
label : 'Annotation / Notes',
name : '__annotation',
type : 'text',
area : true,
help : 'Add an annotation or note for this step. It will be shown with the workflow.',
value : this.node.annotation
});
var output_id = this.node.output_terminals && Object.keys( this.node.output_terminals )[ 0 ];
if ( output_id ) {
inputs.push({
@@ -256,6 +253,7 @@ define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
});
return {
View: View
Default: Default,
Tool: Tool
};
});
client/galaxy/scripts/mvc/workflow/workflow-view.js
+54 -53
View File
@@ -6,13 +6,12 @@ define([
'mvc/workflow/workflow-canvas',
'mvc/workflow/workflow-node',
'mvc/workflow/workflow-icons',
'mvc/tool/tool-form-workflow',
'mvc/form/form-view',
'mvc/workflow/workflow-forms',
'mvc/ui/ui-misc',
'utils/async-save-text',
'libs/toastr',
'ui/editable-text'
], function( Utils, Globals, Workflow, WorkflowCanvas, Node, WorkflowIcons, ToolForm, Form, Ui, async_save_text, Toastr ){
], function( Utils, Globals, Workflow, WorkflowCanvas, Node, WorkflowIcons, FormWrappers, Ui, async_save_text, Toastr ){
// Reset tool search to start state.
function reset_tool_search( initValue ) {
@@ -661,62 +660,64 @@ define([
var $container = $( '#' + cls );
if ( content && $container.find( '#' + id ).length == 0 ) {
var $el = $( '<div id="' + id + '" class="' + cls + '"/>' );
var form = null;
var form_wrapper = null;
content.node = node;
content.workflow = this.workflow;
content.datatypes = this.datatypes;
content.icon = WorkflowIcons[ node.type ];
content.cls = 'ui-portlet-narrow';
if ( node.type == 'tool' ) {
content.node = node;
content.workflow = this.workflow;
content.datatypes = this.datatypes;
form = new ToolForm.View( content );
} else {
content.inputs.unshift({
type : 'text',
name : '__label',
label : 'Label',
value : node.label,
help : 'Add a step label.',
onchange: function( new_label ) {
var duplicate = false;
for ( var i in self.workflow.nodes ) {
var n = self.workflow.nodes[ i ];
if ( n.label && n.label == new_label && n.id != node.id ) {
duplicate = true;
break;
}
content.inputs.unshift({
type : 'text',
name : '__annotation',
label : 'Annotation',
fixed : true,
value : node.annotation,
area : true,
help : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.'
});
content.inputs.unshift({
type : 'text',
name : '__label',
label : 'Label',
value : node.label,
help : 'Add a step label.',
fixed : true,
onchange: function( new_label ) {
var duplicate = false;
for ( var i in self.workflow.nodes ) {
var n = self.workflow.nodes[ i ];
if ( n.label && n.label == new_label && n.id != node.id ) {
duplicate = true;
break;
}
var input_id = form.data.match( '__label' );
var input_element = form.element_list[ input_id ];
input_element.model.set( 'error_text', duplicate && 'Duplicate label. Please fix this before saving the workflow.' );
form.trigger( 'change' );
}
var input_id = form_wrapper.form.data.match( '__label' );
var input_element = form_wrapper.form.element_list[ input_id ];
input_element.model.set( 'error_text', duplicate && 'Duplicate label. Please fix this before saving the workflow.' );
form_wrapper.form.trigger( 'change' );
}
});
content.onchange = function() {
Utils.request({
type : 'POST',
url : Galaxy.root + 'api/workflows/build_module',
data : {
id : node.id,
type : node.type,
content_id : node.content_id,
inputs : form_wrapper.form.data.create()
},
success : function( data ) {
node.update_field_data( data );
}
});
content.inputs.push({
type : 'text',
name : '__annotation',
label : 'Annotation',
value : node.annotation,
area : true,
help : 'Add an annotation or notes to this step. Annotations are available when a workflow is viewed.'
});
content.onchange = function() {
Utils.request({
type : 'POST',
url : Galaxy.root + 'api/workflows/build_module',
data : {
id : node.id,
type : node.type,
content_id : node.content_id,
inputs : form.data.create()
},
success : function( data ) {
node.update_field_data( data );
}
});
};
form = new Form( content );
};
if ( node.type == 'tool' ) {
form_wrapper = new FormWrappers.Tool( content );
} else {
form_wrapper = new FormWrappers.Default( content );
}
$el.append( form.$el );
$el.append( form_wrapper.form.$el );
$container.append( $el );
}
$( '.' + cls ).hide();
lib/galaxy/managers/workflows.py
+12 -2
View File
@@ -412,8 +412,6 @@ class WorkflowContentsManager(UsesAnnotations):
}
def _workflow_to_dict_editor(self, trans, stored):
"""
"""
workflow = stored.latest_workflow
# Pack workflow data into a dictionary and return
data = {}
@@ -426,6 +424,8 @@ class WorkflowContentsManager(UsesAnnotations):
module = module_factory.from_workflow_step( trans, step )
if not module:
raise exceptions.MessageException( 'Unrecognized step type: %s' % step.type )
# Load label from state of data input modules, necessary for backward compatibility
self.__set_default_label( module, step.tool_inputs )
# Fix any missing parameters
upgrade_message = module.check_and_update_state()
if upgrade_message:
@@ -835,6 +835,7 @@ class WorkflowContentsManager(UsesAnnotations):
step_dict["subworkflow"] = subworkflow
module = module_factory.from_dict( trans, step_dict, **kwds )
self.__set_default_label( module, step_dict.get( 'tool_state' ) )
module.save_to_step( step )
annotation = step_dict[ 'annotation' ]
@@ -924,6 +925,15 @@ class WorkflowContentsManager(UsesAnnotations):
del step.temp_input_connections
def __set_default_label( self, module, state ):
""" Previously data input modules had a `name` attribute to rename individual steps. Here, this value is transferred
to the actual `label` attribute which is available for all module types, unique, and mapped to its own database column.
"""
if not module.label and module.type in [ 'data_input', 'data_collection_input' ] and isinstance( state, dict ):
default_label = state.get( 'name' )
if str( default_label ).lower() not in [ 'input dataset', 'input dataset collection' ]:
module.label = default_label
class MissingToolsException(exceptions.MessageException):
lib/galaxy/webapps/galaxy/api/workflows.py
+1
View File
@@ -369,6 +369,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
return {
'label' : inputs.get( '__label', '' ),
'annotation' : inputs.get( '__annotation', '' ),
'name' : module.get_name(),
'tool_state' : module.get_state(),
'data_inputs' : module.get_data_inputs(),
'data_outputs' : module.get_data_outputs(),
lib/galaxy/workflow/modules.py
+7 -21
View File
@@ -236,7 +236,7 @@ class SubWorkflowModule( WorkflowModule ):
@classmethod
def from_dict( Class, trans, d, **kwds ):
module = Class( trans )
module = super( SubWorkflowModule, Class ).from_dict( trans, d, **kwds )
if "subworkflow" in d:
module.subworkflow = d[ "subworkflow" ]
elif "content_id" in d:
@@ -244,14 +244,12 @@ class SubWorkflowModule( WorkflowModule ):
module.subworkflow = WorkflowsManager( trans.app ).get_owned_workflow( trans, d[ "content_id" ] )
else:
raise Exception( "Step associated subworkflow could not be found." )
module.label = d.get( "label" )
return module
@classmethod
def from_workflow_step( Class, trans, step, **kwds ):
module = Class( trans )
module = super( SubWorkflowModule, Class ).from_workflow_step( trans, step, **kwds )
module.subworkflow = step.subworkflow
module.label = step.label
return module
def save_to_step( self, step ):
@@ -274,11 +272,9 @@ class SubWorkflowModule( WorkflowModule ):
if hasattr( self.subworkflow, 'input_steps' ):
for step in self.subworkflow.input_steps:
name = step.label
if name is None:
step_module = module_factory.from_workflow_step( self.trans, step )
name = step_module.state.inputs.get( "name" )
if not name:
raise Exception( "Failed to find name for workflow module." )
step_module = module_factory.from_workflow_step( self.trans, step )
name = step_module.get_name()
step_type = step.type
assert step_type in step_to_input_type
input = dict(
@@ -379,11 +375,6 @@ class InputModule( WorkflowModule ):
class InputDataModule( InputModule ):
type = "data_input"
name = "Input dataset"
default_name = "Input Dataset"
def get_inputs( self ):
name = self.state.inputs.get( 'name', self.default_name )
return dict( name=TextToolParameter( None, Element( "param", name="name", label="Name", type="text", value=name ) ) )
def get_data_outputs( self ):
return [ dict( name='output', extensions=['input'] ) ]
@@ -400,21 +391,17 @@ class InputDataModule( InputModule ):
return ', '.join( filter_set )
def get_runtime_inputs( self, connections=None ):
label = self.state.inputs.get( "name", "Input Dataset" )
return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=False, type="data", format=self.get_filter_set( connections ) ), self.trans ) )
return dict( input=DataToolParameter( None, Element( "param", name="input", label=self.label, multiple=False, type="data", format=self.get_filter_set( connections ) ), self.trans ) )
class InputDataCollectionModule( InputModule ):
type = "data_collection_input"
name = "Input dataset collection"
default_name = "Input Dataset Collection"
default_collection_type = "list"
collection_type = default_collection_type
def get_inputs( self ):
name = self.state.inputs.get( "name", self.default_name )
collection_type = self.state.inputs.get( "collection_type", self.default_collection_type )
input_name = TextToolParameter( None, Element( "param", name="name", label="Name", type="text", value=name ) )
input_collection_type = TextToolParameter( None, XML(
'''
<param name="collection_type" label="Collection type" type="text" value="%s">
@@ -423,12 +410,11 @@ class InputDataCollectionModule( InputModule ):
<option value="list:paired">List of Dataset Pairs</option>
</param>
''' % collection_type ) )
return odict( [ ( "name", input_name ), ( "collection_type", input_collection_type ) ] )
return dict( collection_type=input_collection_type )
def get_runtime_inputs( self, **kwds ):
label = self.state.inputs.get( "name", self.default_name )
collection_type = self.state.inputs.get( "collection_type", self.default_collection_type )
input_element = Element( "param", name="input", label=label, type="data_collection", collection_type=collection_type )
input_element = Element( "param", name="input", label=self.label, type="data_collection", collection_type=collection_type )
return dict( input=DataCollectionToolParameter( None, input_element, self.trans ) )
def get_data_outputs( self ):
static/maps/mvc/form/form-input.js.map
+1 -1
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@@ -1,2 +1,2 @@
define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.app_options=a.model?a.model.attributes:{},this.field=b&&b.field||new Backbone.View,this.model=b&&b.model||new Backbone.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up"}).set(b),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var c=this.model.get("collapsible_value");this.field.collapsed=void 0!==c&&JSON.stringify(this.model.get("value"))==JSON.stringify(c),this.listenTo(this.model,"change",this.render,this),this.render();var d=this;this.$collapsible.on("click",function(){d.field.collapsed=!d.field.collapsed,a.trigger&&a.trigger("change"),d.render()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(a){this.model.set("error_text",a)},reset:function(){this.model.set("error_text",null)},render:function(){$(".tooltip").hide();var a=this.model.get("help",""),b=this.model.get("argument");b&&-1==a.indexOf("("+b+")")&&(a+=" ("+b+")"),this.$info.html(a),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(_.escape(this.model.get("text_value")));var c=this.model.get("error_text");if(this.$error[c?"show":"hide"](),this.$el[c?"addClass":"removeClass"]("ui-error"),this.$error_text.html(c),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var d=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+d)).attr("data-original-title",this.model.get("text_"+d)).tooltip({placement:"bottom"})}},_template:function(){return $("<div/>").addClass("ui-form-element").append($("<div/>").addClass("ui-form-error ui-error").append($("<span/>").addClass("fa fa-arrow-down")).append($("<span/>").addClass("ui-form-error-text"))).append($("<div/>").addClass("ui-form-title").append($("<div/>").addClass("ui-form-collapsible").append($("<i/>").addClass("ui-form-collapsible-icon")).append($("<span/>").addClass("ui-form-collapsible-text"))).append($("<span/>").addClass("ui-form-title-text"))).append($("<div/>").addClass("ui-form-field").append($("<span/>").addClass("ui-form-info")).append($("<div/>").addClass("ui-form-backdrop"))).append($("<div/>").addClass("ui-form-preview"))}})});
define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.app_options=a.model?a.model.attributes:{},this.field=b&&b.field||new Backbone.View,this.model=b&&b.model||new Backbone.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up"}).set(b),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var c=this.model.get("collapsible_value");this.field.collapsed=void 0!==c&&JSON.stringify(this.model.get("value"))==JSON.stringify(c),this.listenTo(this.model,"change",this.render,this),this.render();var d=this;this.$collapsible.on("click",function(){d.field.collapsed=!d.field.collapsed,a.trigger&&a.trigger("change"),d.render()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(a){this.model.set("error_text",a)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){$(".tooltip").hide();var a=this.model.get("help",""),b=this.model.get("argument");b&&-1==a.indexOf("("+b+")")&&(a+=" ("+b+")"),this.$info.html(a),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(_.escape(this.model.get("text_value")));var c=this.model.get("error_text");if(this.$error[c?"show":"hide"](),this.$el[c?"addClass":"removeClass"]("ui-error"),this.$error_text.html(c),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var d=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+d)).attr("data-original-title",this.model.get("text_"+d)).tooltip({placement:"bottom"})}},_template:function(){return $("<div/>").addClass("ui-form-element").append($("<div/>").addClass("ui-form-error ui-error").append($("<span/>").addClass("fa fa-arrow-down")).append($("<span/>").addClass("ui-form-error-text"))).append($("<div/>").addClass("ui-form-title").append($("<div/>").addClass("ui-form-collapsible").append($("<i/>").addClass("ui-form-collapsible-icon")).append($("<span/>").addClass("ui-form-collapsible-text"))).append($("<span/>").addClass("ui-form-title-text"))).append($("<div/>").addClass("ui-form-field").append($("<span/>").addClass("ui-form-info")).append($("<div/>").addClass("ui-form-backdrop"))).append($("<div/>").addClass("ui-form-preview"))}})});
//# sourceMappingURL=../../../maps/mvc/form/form-input.js.map
static/scripts/mvc/form/form-section.js
+1 -1
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@@ -1,2 +1,2 @@
define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f){var g=Backbone.View.extend({initialize:function(a,b){this.app=a,this.inputs=b.inputs,this.parameters=new f,this.setElement($("<div/>")),this.render()},render:function(){var a=this;this.$el.empty(),_.each(this.inputs,function(b){a.add(b)})},add:function(b){var c=jQuery.extend(!0,{},b);switch(c.id=b.id=a.uid(),this.app.input_list[c.id]=c,c.type){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id,this.app.model.get("sustain_conditionals")&&(a.test_param.disabled=!0);var c=this._addRow(a.test_param);c.model&&c.model.set("onchange",function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=b.$("#"+a.id+"-section-"+e),h=!1;for(var i in f.inputs)if(!f.inputs[i].hidden){h=!0;break}e==d&&h?g.fadeIn("fast"):g.hide()}b.app.trigger("change")});for(var d in a.cases){var e=new g(this.app,{inputs:a.cases[d].inputs});this._append(e.$el.addClass("ui-form-section"),a.id+"-section-"+d)}c.trigger("change")},_addRepeat:function(a){function b(b){var d=a.id+"-section-"+f++,e=new g(c.app,{inputs:b});h.add({id:d,$el:e.$el,ondel:function(){h.del(d),c.app.trigger("change")}})}for(var c=this,f=0,h=new d.View({title:a.title||"Repeat",min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=_.size(a.cache),j=0;j<Math.max(Math.max(i,a.min||0),a.default||0);j++)b(i>j?a.cache[j]:a.inputs);this.app.model.get("sustain_repeats")&&h.hideOptions();var k=new e(this.app,{label:a.title||a.name,help:a.help,field:h});this._append(k.$el,a.id)},_addSection:function(a){var b=new c.View({title:a.title||a.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!a.expanded});b.append(new g(this.app,{inputs:a.inputs}).$el),b.append($("<div/>").addClass("ui-form-info").html(a.help)),this.app.on("expand",function(a){b.$("#"+a).length>0&&b.expand()}),this._append(b.$el,a.id)},_addRow:function(a){var b=this,c=a.id;a.onchange=a.onchange||function(){b.app.trigger("change",c)};var d=this.parameters.create(a);this.app.field_list[c]=d;var f=new e(this.app,{name:a.name,label:a.hide_label?"":a.label||a.name,value:a.value,text_value:a.text_value,collapsible_value:a.collapsible_value,collapsible_preview:a.collapsible_preview,help:a.help,argument:a.argument,disabled:a.disabled,color:a.color,style:a.style,backdrop:a.backdrop,hidden:a.hidden,field:d});return this.app.element_list[c]=f,this._append(f.$el,a.id),d},_append:function(a,b){this.$el.append(a.addClass("section-row").attr("id",b))}});return{View:g}});
define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f){var g=Backbone.View.extend({initialize:function(a,b){this.app=a,this.inputs=b.inputs,this.parameters=new f,this.setElement($("<div/>")),this.render()},render:function(){var a=this;this.$el.empty(),_.each(this.inputs,function(b){a.add(b)})},add:function(b){var c=jQuery.extend(!0,{},b);switch(c.id=b.id=a.uid(),this.app.input_list[c.id]=c,c.type){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id,this.app.model.get("sustain_conditionals")&&(a.test_param.disabled=!0);var c=this._addRow(a.test_param);c.model&&c.model.set("onchange",function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=b.$("#"+a.id+"-section-"+e),h=!1;for(var i in f.inputs)if(!f.inputs[i].hidden){h=!0;break}e==d&&h?g.fadeIn("fast"):g.hide()}b.app.trigger("change")});for(var d in a.cases){var e=new g(this.app,{inputs:a.cases[d].inputs});this._append(e.$el.addClass("ui-form-section"),a.id+"-section-"+d)}c.trigger("change")},_addRepeat:function(a){function b(b){var d=a.id+"-section-"+f++,e=new g(c.app,{inputs:b});h.add({id:d,$el:e.$el,ondel:function(){h.del(d),c.app.trigger("change")}})}for(var c=this,f=0,h=new d.View({title:a.title||"Repeat",min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=_.size(a.cache),j=0;j<Math.max(Math.max(i,a.min||0),a.default||0);j++)b(i>j?a.cache[j]:a.inputs);this.app.model.get("sustain_repeats")&&h.hideOptions();var k=new e(this.app,{label:a.title||a.name,help:a.help,field:h});this._append(k.$el,a.id)},_addSection:function(a){var b=new c.View({title:a.title||a.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!a.expanded});b.append(new g(this.app,{inputs:a.inputs}).$el),b.append($("<div/>").addClass("ui-form-info").html(a.help)),this.app.on("expand",function(a){b.$("#"+a).length>0&&b.expand()}),this._append(b.$el,a.id)},_addRow:function(a){var b=this,c=a.id;a.onchange=a.onchange||function(){b.app.trigger("change",c)};var d=this.parameters.create(a);this.app.field_list[c]=d;var f=new e(this.app,{name:a.name,label:a.hide_label?"":a.label||a.name,value:a.value,text_value:a.text_value,collapsible_value:a.collapsible_value,collapsible_preview:a.collapsible_preview,help:a.help,argument:a.argument,disabled:a.disabled,color:a.color,style:a.style,backdrop:a.backdrop,hidden:a.hidden,fixed:a.fixed,field:d});return this.app.element_list[c]=f,this._append(f.$el,a.id),d},_append:function(a,b){this.$el.append(a.addClass("section-row").attr("id",b))}});return{View:g}});
//# sourceMappingURL=../../../maps/mvc/form/form-section.js.map
static/scripts/mvc/tool/tool-form-composite.js
+1 -1
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static/scripts/mvc/tool/tool-form-workflow.js
-2
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static/scripts/mvc/workflow/workflow-forms.js
+2
View File
@@ -0,0 +1,2 @@
define(["utils/utils","mvc/form/form-view","mvc/tool/tool-form-base"],function(a,b,c){var d=Backbone.View.extend({initialize:function(a){this.form=new b(a)}}),e=Backbone.View.extend({initialize:function(b){var d=this;this.workflow=b.workflow,this.node=b.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},a.deepeach(b.inputs,function(b){b.type&&(-1!=["data","data_collection"].indexOf(b.type)?(b.type="hidden",b.info="Data input '"+b.name+"' ("+a.textify(b.extensions)+")",b.value={__class__:"RuntimeValue"}):b.fixed||(b.collapsible_value={__class__:"RuntimeValue"},b.is_workflow=b.options&&0==b.options.length||-1!=["integer","float"].indexOf(b.type)))}),a.deepeach(b.inputs,function(a){"conditional"==a.type&&(a.test_param.collapsible_value=void 0)}),this._makeSections(b),this.form=new c(a.merge(b,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,sustain_version:!0,cls:"ui-portlet-narrow",postchange:function(b,c){var e=c.model.attributes,f={tool_id:e.id,tool_version:e.version,type:"tool",inputs:$.extend(!0,{},c.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",f),a.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:f,success:function(a){c.update(a.config_form),c.errors(a.config_form),d.node.update_field_data(a),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",a),b.reject()}})}}))):Galaxy.emit.debug("tool-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(a){var b=a.inputs,c=a.datatypes,d=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(d){b.push({name:"pja__"+d+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+d])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),b.push({name:"pja__"+d+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+d])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var e in this.node.output_terminals)b.push(this._makeSection(e,c))}},_makeSection:function(a,b){function c(b,e){e=e||[],e.push(b);for(var f in b.inputs){var g=b.inputs[f],h=g.action;if(h){if(g.name="pja__"+a+"__"+g.action,g.pja_arg&&(g.name+="__"+g.pja_arg),g.payload)for(var i in g.payload){var j=g.payload[i];g.payload[g.name+"__"+i]=j,delete j}var k=d.post_job_actions[g.action+a];if(k){for(var l in e)e[l].expanded=!0;g.value=g.pja_arg?k.action_arguments&&k.action_arguments[g.pja_arg]||g.value:"true"}}g.inputs&&c(g,e.slice(0))}}var d=this,e=[],f=[];for(key in b)e.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)f.push(this.node.input_terminals[key].name);e.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),e.unshift({0:"Sequences",1:"Sequences"}),e.unshift({0:"Roadmaps",1:"Roadmaps"}),e.unshift({0:"Leave unchanged",1:"__empty__"});var g={title:"Configure Output: '"+a+"'",type:"section",flat:!0,inputs:[{label:"Label",type:"text",value:(output=this.node.getWorkflowOutput(a))&&output.label||"",help:"This will provide a short name to describe the output - this must be unique across workflows.",onchange:function(b){d.workflow.attemptUpdateOutputLabel(d.node,a,b)}},{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>'+f.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:e,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return c(g),g}});return{Default:d,Tool:e}});
//# sourceMappingURL=../../../maps/mvc/workflow/workflow-forms.js.map
static/scripts/mvc/workflow/workflow-view.js
+1 -1
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test/unit/workflows/test_modules.py
+25 -83
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@@ -25,99 +25,61 @@ def test_valid_new_tool_has_no_errors():
def test_data_input_default_state():
trans = MockTrans()
module = modules.module_factory.from_dict( trans, { "type": "data_input" } )
module = modules.module_factory.from_dict( trans, { "type": "data_input", "label": "Input Dataset" } )
__assert_has_runtime_input( module, label="Input Dataset" )
def test_data_input_modified_state():
module = __from_state( {
"type": "data_input",
"tool_state": json.dumps({ "name": "Cool Input" }),
} )
module = __from_state( { "type": "data_input", "label": "Cool Input" } )
__assert_has_runtime_input( module, label="Cool Input" )
def test_data_input_step_modified_state():
module = __from_step(
type="data_input",
tool_inputs={
"name": "Cool Input",
},
)
module = __from_step( type="data_input", label="Cool Input" )
__assert_has_runtime_input( module, label="Cool Input" )
def test_data_input_compute_runtime_state_default():
module = __from_step(
type="data_input",
)
module = __from_step( type="data_input" )
state, errors = module.compute_runtime_state( module.trans )
assert not errors
assert 'input' in state.inputs
assert state.inputs[ 'input' ] is None
assert "input" in state.inputs
assert state.inputs[ "input" ] is None
def test_data_input_compute_runtime_state_args():
module = __from_step(
type="data_input",
)
module = __from_step( type="data_input" )
tool_state = module.get_state()
hda = model.HistoryDatasetAssociation()
with mock.patch('galaxy.workflow.modules.check_param') as check_method:
with mock.patch("galaxy.workflow.modules.check_param") as check_method:
check_method.return_value = ( hda, None )
state, errors = module.compute_runtime_state( module.trans, { 'input': 4, 'tool_state': tool_state } )
state, errors = module.compute_runtime_state( module.trans, { "input": 4, "tool_state": tool_state } )
assert not errors
assert 'input' in state.inputs
assert state.inputs[ 'input' ] is hda
assert "input" in state.inputs
assert state.inputs[ "input" ] is hda
def test_data_input_connections():
module = __from_step(
type="data_input",
)
module = __from_step( type="data_input" )
assert len( module.get_data_inputs() ) == 0
outputs = module.get_data_outputs()
assert len( outputs ) == 1
output = outputs[ 0 ]
assert output[ 'name' ] == 'output'
assert output[ 'extensions' ] == [ 'input' ]
def test_data_input_update():
module = __from_step(
type="data_input",
tool_inputs={
"name": "Cool Input",
},
)
module.recover_state( dict( name="Awesome New Name" ) )
assert module.state.inputs[ 'name' ] == "Awesome New Name"
def test_data_input_get_form():
module = __from_step(
type="data_input",
tool_inputs={
"name": "Cool Input",
},
)
result = module.get_config_form()
assert result[ 'inputs' ][ 0 ][ 'value' ], 'Cool Input'
assert output[ "name" ] == "output"
assert output[ "extensions" ] == [ "input" ]
def test_data_collection_input_default_state():
trans = MockTrans()
module = modules.module_factory.from_dict( trans, { "type": "data_collection_input" } )
module = modules.module_factory.from_dict( trans, { "type": "data_collection_input", "label": "Input Dataset Collection" } )
__assert_has_runtime_input( module, label="Input Dataset Collection", collection_type="list" )
def test_data_input_collection_modified_state():
module = __from_state( {
"type": "data_collection_input",
"tool_state": json.dumps({ "name": "Cool Input Collection", "collection_type": "list:paired" }),
"label": "Cool Input Collection",
"tool_state": json.dumps({ "collection_type": "list:paired" }),
} )
__assert_has_runtime_input( module, label="Cool Input Collection", collection_type="list:paired" )
@@ -125,8 +87,8 @@ def test_data_input_collection_modified_state():
def test_data_input_collection_step_modified_state():
module = __from_step(
type="data_collection_input",
label="Cool Input Collection",
tool_inputs={
"name": "Cool Input Collection",
"collection_type": "list:paired",
},
)
@@ -137,42 +99,27 @@ def test_data_collection_input_connections():
module = __from_step(
type="data_collection_input",
tool_inputs={
'collection_type': 'list:paired'
"collection_type": "list:paired"
}
)
assert len( module.get_data_inputs() ) == 0
outputs = module.get_data_outputs()
assert len( outputs ) == 1
output = outputs[ 0 ]
assert output[ 'name' ] == 'output'
assert output[ 'extensions' ] == [ 'input_collection' ]
assert output[ 'collection_type' ] == 'list:paired'
def test_data_collection_input_update():
module = __from_step(
type="data_collection_input",
tool_inputs={
'name': 'Cool Collection',
'collection_type': 'list:paired',
}
)
module.recover_state( dict( name="New Collection", collection_type="list" ) )
assert module.state.inputs[ 'name' ] == "New Collection"
assert output[ "name" ] == "output"
assert output[ "extensions" ] == [ "input_collection" ]
assert output[ "collection_type" ] == "list:paired"
def test_data_collection_input_config_form():
module = __from_step(
type="data_collection_input",
tool_inputs={
'name': 'Cool Collection',
'collection_type': 'list:paired',
"collection_type": "list:paired",
}
)
result = module.get_config_form()
assert result[ 'inputs' ][ 0 ][ 'value' ], 'Cool Collection'
assert result[ 'inputs' ][ 1 ][ 'value' ], 'list:paired'
assert result[ "inputs" ][ 0 ][ "value" ], "list:paired"
def test_cannot_create_tool_modules_for_missing_tools():
@@ -216,9 +163,8 @@ TEST_WORKFLOW_YAML = """
steps:
- type: "data_input"
label: "input1"
tool_inputs: {"name": "input1"}
- type: "data_collection_input"
tool_inputs: {"name": "input2"}
label: "input2"
- type: "tool"
tool_id: "cat1"
input_connections:
@@ -252,7 +198,6 @@ def test_subworkflow_new_inputs():
input1, input2 = inputs
assert input1["input_type"] == "dataset"
assert input1["name"] == "input1"
assert input2["input_type"] == "dataset_collection"
assert input2["name"] == "input2", input2["name"]
@@ -265,7 +210,6 @@ def test_subworkflow_new_outputs():
assert output1["name"] == "out1"
assert output1["label"] == "out1"
assert output1["extensions"] == ["input"]
assert output2["name"] == "4:out_file1", output2["name"]
assert output2["label"] == "4:out_file1", output2["label"]
@@ -283,7 +227,6 @@ def __assert_has_runtime_input( module, label=None, collection_type=None ):
inputs = module.get_runtime_inputs()
assert len( inputs ) == 1
assert "input" in inputs
input_param = inputs[ "input" ]
if label is not None:
assert input_param.get_label() == label, input_param.get_label()
@@ -318,7 +261,6 @@ def __step( **kwds ):
step = model.WorkflowStep()
for key, value in kwds.items():
setattr( step, key, value )
return step