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https://github.com/galaxyproject/galaxy.git
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Merge pull request #115 from guerler/revise_validation
Revise late validation of tool parameters
This commit is contained in:
Dannon Baker
@@ -84,7 +84,7 @@ define(['utils/utils',
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/** Data input field
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*/
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_fieldData: function(input_def) {
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if (!this.app.options.is_dynamic) {
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if (this.app.options.is_workflow) {
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input_def.info = 'Data input \'' + input_def.name + '\' (' + Utils.textify(input_def.extensions.toString()) + ')';
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input_def.value = null;
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return this._fieldHidden(input_def);
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@@ -107,7 +107,7 @@ define(['utils/utils',
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*/
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_fieldSelect: function (input_def) {
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// show text field in if dynamic fields are disabled e.g. in workflow editor
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if (!this.app.options.is_dynamic && input_def.is_dynamic) {
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if (input_def.options.length == 0 && this.app.options.is_workflow) {
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return this._fieldText(input_def);
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}
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@@ -157,10 +157,10 @@ define(['utils/utils',
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*/
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_fieldDrilldown: function (input_def) {
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// show text field in if dynamic fields are disabled e.g. in workflow editor
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if (!this.app.options.is_dynamic && input_def.is_dynamic) {
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if (input_def.options.length == 0 && this.app.options.is_workflow) {
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return this._fieldText(input_def);
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}
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// create drill down field
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var self = this;
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return new Ui.Drilldown.View({
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@@ -185,13 +185,16 @@ define(['utils/utils',
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if (!Utils.validate(input_def.value)) {
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input_def.value = '';
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} else {
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if (input_def.value instanceof Array) {
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input_def.value = value.toString();
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} else {
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input_def.value = String(input_def.value).replace(/[\[\]'"\s]/g, '');
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if (input_def.multiple) {
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input_def.value = input_def.value.replace(/,/g, '\n');
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if ($.isArray(input_def.value)) {
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var str_value = '';
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for (var i in input_def.value) {
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str_value += String(input_def.value[i]);
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if (!input_def.multiple) {
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break;
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}
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str_value += '\n';
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}
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input_def.value = str_value;
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}
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}
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}
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@@ -11,8 +11,8 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
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initialize: function(options) {
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// options
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this.optionsDefault = {
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// uses dynamic fields instead of text fields
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is_dynamic : true,
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// uses workflow editor mode i.e. text instead of select fields
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is_workflow : false,
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// shows form in narrow view mode
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narrow : false,
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// shows errors on start
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@@ -24,7 +24,7 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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text_disable : 'Set at Runtime',
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// configure workflow style
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is_dynamic : false,
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is_workflow : true,
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narrow : true,
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initial_errors : true,
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cls : 'ui-portlet-narrow',
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@@ -37,13 +37,6 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
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}
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});
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// declare fields as optional
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Utils.deepeach(options.inputs, function(item) {
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if (item.type) {
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item.optional = (['data', 'data_hidden', 'hidden', 'repeat', 'conditional']).indexOf(item.type) == -1;
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}
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});
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// declare conditional fields as not optional
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Utils.deepeach(options.inputs, function(item) {
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if (item.type) {
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@@ -2257,7 +2257,7 @@ class Tool( object, Dictifiable ):
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return tool_dict
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def to_json (self, trans, kwd={}, is_dynamic=True):
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def to_json (self, trans, kwd={}, is_workflow=False):
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"""
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Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
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"""
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@@ -2369,7 +2369,7 @@ class Tool( object, Dictifiable ):
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error = 'State validation failed.'
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# skip dynamic fields if deactivated
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if not is_dynamic and input.is_dynamic:
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if is_workflow and input.is_dynamic:
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return [value, None]
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# validate value content
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@@ -2463,29 +2463,31 @@ class Tool( object, Dictifiable ):
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elif input.type == 'section':
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iterate( tool_dict['inputs'], input.inputs, group_state, other_values )
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else:
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# create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options
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# identify name
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input_name = tool_dict.get('name')
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# expand input dictionary incl. repeats and dynamic_parameters
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try:
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tool_dict = input.to_dict(trans, other_values=other_values)
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except Exception:
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log.exception('tools::to_json() - Skipping parameter expansion for %s.' % input_name)
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pass
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# identify name
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input_name = tool_dict.get('name')
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if input_name:
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# backup default value
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try:
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tool_dict['default_value'] = input.get_initial_value(trans, other_values)
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except Exception:
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# get initial value failed due to improper late validation
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tool_dict['default_value'] = None
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pass
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# backup default value
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try:
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tool_dict['default_value'] = input.get_initial_value(trans, other_values)
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except Exception:
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log.exception('tools::to_json() - Getting initial value failed %s.' % input_name)
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# get initial value failed due to improper late validation
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tool_dict['default_value'] = None
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pass
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# update input value from tool state
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tool_dict['value'] = state_inputs.get(input_name, tool_dict['default_value'])
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# update input value from tool state
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tool_dict['value'] = state_inputs.get(input_name, tool_dict['default_value'])
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# sanitize values
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sanitize(tool_dict, 'value')
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sanitize(tool_dict, 'default_value')
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# sanitize values
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sanitize(tool_dict, 'value')
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sanitize(tool_dict, 'default_value')
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# backup final input dictionary
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group_inputs[input_index] = tool_dict
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@@ -64,12 +64,10 @@ def check_param( trans, param, incoming_value, param_values, source='html' ):
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value = param.from_html( value, trans, param_values )
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else:
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value = param.from_json( value, trans, param_values )
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# Only validate if late validation is not needed
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if not param.need_late_validation( trans, param_values ):
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# Allow the value to be converted if necessary
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filtered_value = param.filter_value( value, trans, param_values )
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# Then do any further validation on the value
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param.validate( filtered_value, trans.history )
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# Allow the value to be converted if necessary
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filtered_value = param.filter_value( value, trans, param_values )
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# Then do any further validation on the value
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param.validate( filtered_value, trans.history )
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elif value is None and isinstance( param, SelectToolParameter ):
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# An empty select list or column list
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param.validate( value, trans.history )
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@@ -203,10 +203,7 @@ class ToolParameter( object, Dictifiable ):
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for validator in self.validators:
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validator.validate( value, history )
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def need_late_validation( self, trans, context ):
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return False
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def to_dict( self, trans, view='collection', value_mapper=None ):
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def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
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""" to_dict tool parameter. This can be overridden by subclasses. """
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tool_dict = super( ToolParameter, self ).to_dict()
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#TODO: wrapping html as it causes a lot of errors on subclasses - needs histories, etc.
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@@ -290,7 +287,7 @@ class TextToolParameter( ToolParameter ):
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def get_initial_value( self, trans, context, history=None ):
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return self.value
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def to_dict( self, trans, view='collection', value_mapper=None ):
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def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
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d = super(TextToolParameter, self).to_dict(trans)
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d['area'] = self.area
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d['size'] = self.size
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@@ -495,7 +492,7 @@ class BooleanToolParameter( ToolParameter ):
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else:
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return self.falsevalue
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def to_dict( self, trans, view='collection', value_mapper=None ):
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def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
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d = super(BooleanToolParameter, self).to_dict(trans)
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d['value'] = self.checked
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d['truevalue'] = self.truevalue
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@@ -705,7 +702,7 @@ class BaseURLToolParameter( ToolParameter ):
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# BaseURLToolParameters are ultimately "hidden" parameters
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return None
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def to_dict( self, trans, view='collection', value_mapper=None ):
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def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
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d = super( BaseURLToolParameter, self ).to_dict( trans )
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d['value'] = self.get_value( trans )
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return d
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@@ -852,9 +849,9 @@ class SelectToolParameter( ToolParameter ):
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def get_html_field( self, trans=None, value=None, context={} ):
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# Dynamic options are not yet supported in workflow, allow
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# specifying the value as text for now.
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if self.need_late_validation( trans, context ):
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if value is not None:
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assert isinstance( value, UnvalidatedValue ), "Late validation needed for '%s', but provided value (%s) is not of type UnvalidatedValue (%s)." % ( self.name, value, type( value ) )
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options = list(self.get_options( trans, context ))
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if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
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if isinstance( value, UnvalidatedValue ):
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value = value.value
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if self.multiple:
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if value is None:
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@@ -870,7 +867,6 @@ class SelectToolParameter( ToolParameter ):
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# We could have an unvalidated value here when e.g. running a workflow.
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value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ]
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field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values )
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options = self.get_options( trans, context )
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for text, optval, selected in options:
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if isinstance( optval, UnvalidatedValue ):
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optval = optval.value
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@@ -881,7 +877,8 @@ class SelectToolParameter( ToolParameter ):
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return field
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def from_html( self, value, trans=None, context={} ):
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if self.need_late_validation( trans, context ):
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legal_values = self.get_legal_values( trans, context )
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if len(list(legal_values)) == 0 and (trans is None or trans.workflow_building_mode):
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if self.multiple:
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# While it is generally allowed that a select value can be '',
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# we do not allow this to be the case in a dynamically
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@@ -896,7 +893,6 @@ class SelectToolParameter( ToolParameter ):
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# use \r\n to separate lines.
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value = value.split()
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return UnvalidatedValue( value )
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legal_values = self.get_legal_values( trans, context )
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if not legal_values and self.optional:
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return None
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if not legal_values:
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@@ -963,61 +959,12 @@ class SelectToolParameter( ToolParameter ):
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return UnvalidatedValue( value["value"] )
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return super( SelectToolParameter, self ).value_from_basic( value, app, ignore_errors=ignore_errors )
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def need_late_validation( self, trans, context ):
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"""
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Determine whether we need to wait to validate this parameters value
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given the current state. For parameters with static options this is
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always false (can always validate immediately). For parameters with
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dynamic options, we need to check whether the other parameters which
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determine what options are valid have been set. For the old style
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dynamic options which do not specify dependencies, this is always true
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(must validate at runtime).
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"""
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# Option list is statically defined, never need late validation
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if not self.is_dynamic:
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return False
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# Old style dynamic options, no dependency information so there isn't
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# a lot we can do: if we're dealing with workflows, have to assume
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# late validation no matter what.
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if self.dynamic_options is not None and ( trans is None or trans.workflow_building_mode ):
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return True
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# If we got this far, we can actually look at the dependencies
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# to see if their values will not be available until runtime.
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for dep_name in self.get_dependencies():
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# This may not be completely correct, but it's possible to go
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# through the layers indicated below without assigning dep_value,
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# which is even worse. TODO fix it?
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dep_value = None
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if dep_name in context:
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dep_value = context[ dep_name ]
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else:
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# Quick hack to check deeper in the context.
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# TODO: Context should really be scoped and the correct subset passed along.
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# This happens specifically in all the GATK tools, the way the reference genome is handled.
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for layer in context.itervalues():
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if isinstance( layer, dict ) and self.name in layer and dep_name in layer:
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dep_value = layer[dep_name]
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# Dependency on a dataset that does not yet exist
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if isinstance( dep_value, DummyDataset ):
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return True
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# Dependency on a value that has not been checked
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if isinstance( dep_value, UnvalidatedValue ):
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return True
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# Dependency on a value that does not yet exist
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if isinstance( dep_value, RuntimeValue ):
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return True
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#dataset not ready yet
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if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not dep_value.datatype.matches_any( self.ref_input.formats ) ):
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return True
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# Dynamic, but all dependenceis are known and have values
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return False
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def get_initial_value( self, trans, context, history=None ):
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# More working around dynamic options for workflow
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if self.need_late_validation( trans, context ):
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options = list( self.get_options( trans, context ) )
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if len(options) == 0 and (trans is None or trans.workflow_building_mode):
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# Really the best we can do?
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return UnvalidatedValue( None )
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options = list( self.get_options( trans, context ) )
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value = [ optval for _, optval, selected in options if selected ]
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if len( value ) == 0:
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if not self.multiple and options:
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@@ -1143,7 +1090,7 @@ class GenomeBuildParameter( SelectToolParameter ):
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def get_legal_values( self, trans, other_values ):
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return set( dbkey for dbkey, _ in self._get_dbkey_names( trans=trans ) )
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def to_dict( self, trans, view='collection', value_mapper=None ):
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def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
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# skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
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d = ToolParameter.to_dict( self, trans )
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@@ -1266,8 +1213,12 @@ class ColumnListParameter( SelectToolParameter ):
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return []
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column_list = None
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for dataset in util.listify( dataset ):
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# Handle columns not available.
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if not dataset.metadata.columns:
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unavailable = False
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if not hasattr(dataset, 'metadata'):
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unavailable = True
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elif not dataset.metadata.columns:
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unavailable = True
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if unavailable:
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default_column_list = []
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if self.accept_default:
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default_column_list.append( self.default_value or '1' )
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@@ -1327,9 +1278,6 @@ class ColumnListParameter( SelectToolParameter ):
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def get_initial_value( self, trans, context, history=None ):
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if self.default_value is not None:
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# dataset not ready / in workflow / etc
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if self.need_late_validation( trans, context ):
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return UnvalidatedValue( self.default_value )
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return self.default_value
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return SelectToolParameter.get_initial_value( self, trans, context )
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@@ -1339,33 +1287,6 @@ class ColumnListParameter( SelectToolParameter ):
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def get_dependencies( self ):
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return [ self.data_ref ]
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def need_late_validation( self, trans, context ):
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if super( ColumnListParameter, self ).need_late_validation( trans, context ):
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return True
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if self.data_ref not in context:
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return False
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# Get the selected dataset if selected
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referent = context[ self.data_ref ]
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if getattr( referent, 'history_content_type', None ) == "dataset_collection":
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# TODO: also check datasets have been populated.
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referent = referent.collection.dataset_instances
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datasets = util.listify( referent )
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for dataset in datasets:
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if dataset:
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# Check if metadata is available
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if not hasattr(dataset, 'metadata'):
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return True
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# Check if the dataset does not have the expected metadata for columns
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if not dataset.metadata.columns:
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# Only allow late validation if the dataset is not yet ready
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# (since we have reason to expect the metadata to be ready eventually)
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if dataset.is_pending or not dataset.datatype.matches_any( self.ref_input.formats ):
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return True
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# No late validation
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return False
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def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
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# call parent to_dict
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d = super( ColumnListParameter, self ).to_dict( trans, other_values=other_values)
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@@ -1569,9 +1490,9 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
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def get_html_field( self, trans=None, value=None, other_values={} ):
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# Dynamic options are not yet supported in workflow, allow
|
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# specifying the value as text for now.
|
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if self.need_late_validation( trans, other_values ):
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if value is not None:
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assert isinstance( value, UnvalidatedValue ), "Late validation needed for '%s', but provided value (%s) is not of type UnvalidatedValue (%s)." % ( self.name, value, type( value ) )
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options = self.get_options( trans, value, other_values )
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if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
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if isinstance( value, UnvalidatedValue ):
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value = value.value
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if self.multiple:
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if value is None:
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@@ -1581,10 +1502,11 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
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return form_builder.TextArea( self.name, value=value )
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else:
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return form_builder.TextField( self.name, value=(value or "") )
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return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, self.get_options( trans, value, other_values ), value, refresh_on_change_values=self.refresh_on_change_values )
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return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, options, value, refresh_on_change_values=self.refresh_on_change_values )
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||||
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||||
def from_html( self, value, trans=None, other_values={} ):
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||||
if self.need_late_validation( trans, other_values ):
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legal_values = self.get_legal_values( trans, other_values )
|
||||
if len(list(legal_values)) == 0 and (trans is None or trans.workflow_building_mode):
|
||||
if self.multiple:
|
||||
if value == '': # No option selected
|
||||
value = None
|
||||
@@ -1600,7 +1522,6 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
|
||||
if not( self.repeat ) and len( value ) > 1:
|
||||
assert self.multiple, "Multiple values provided but parameter %s is not expecting multiple values" % self.name
|
||||
rval = []
|
||||
legal_values = self.get_legal_values( trans, other_values )
|
||||
assert legal_values, "Parameter %s requires a value, but has no legal values defined" % self.name
|
||||
for val in value:
|
||||
if val not in legal_values:
|
||||
@@ -1656,11 +1577,11 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
|
||||
initial_values.append( option['value'] )
|
||||
recurse_options( initial_values, option['options'] )
|
||||
# More working around dynamic options for workflow
|
||||
if self.need_late_validation( trans, context ):
|
||||
# Really the best we can do?
|
||||
options = self.get_options( trans=trans, other_values=context )
|
||||
if len(list(options)) == 0 and (trans is None or trans.workflow_building_mode):
|
||||
return UnvalidatedValue( None )
|
||||
initial_values = []
|
||||
recurse_options( initial_values, self.get_options( trans=trans, other_values=context ) )
|
||||
recurse_options( initial_values, options )
|
||||
if len( initial_values ) == 0:
|
||||
initial_values = None
|
||||
return initial_values
|
||||
@@ -2120,11 +2041,6 @@ class DataToolParameter( BaseDataToolParameter ):
|
||||
else:
|
||||
validator.validate( value, history )
|
||||
|
||||
def need_late_validation( self, trans, context ):
|
||||
if trans is None or trans.workflow_building_mode:
|
||||
return True
|
||||
return False
|
||||
|
||||
def get_dependencies( self ):
|
||||
"""
|
||||
Get the *names* of the other params this param depends on.
|
||||
|
||||
@@ -331,7 +331,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
|
||||
} )
|
||||
|
||||
# create tool model and default tool state (if missing)
|
||||
tool_model = module.tool.to_json(trans, tool_inputs, is_dynamic=False)
|
||||
tool_model = module.tool.to_json(trans, tool_inputs, is_workflow=True)
|
||||
module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
|
||||
return {
|
||||
'tool_model' : tool_model,
|
||||
|
||||
@@ -1 +1 @@
|
||||
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|
||||
@@ -1 +1 @@
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|
||||
@@ -1,2 +1,2 @@
|
||||
define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(a,b,c,d,e){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(!this.app.options.is_dynamic)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){c.options&&(c.area=c.multiple,a.validate(c.value)?c.value instanceof Array?c.value=value.toString():(c.value=String(c.value).replace(/[\[\]'"\s]/g,""),c.multiple&&(c.value=c.value.replace(/,/g,"\n"))):c.value="");var d=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){d.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new e({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
|
||||
define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(a,b,c,d,e){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new e({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
|
||||
//# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map
|
||||
@@ -1,2 +1,2 @@
|
||||
define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),void console.debug("tools-form-base::initialize() - Completed."))}})});
|
||||
define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),void console.debug("tools-form-base::initialize() - Completed."))}})});
|
||||
//# sourceMappingURL=../../../maps/mvc/form/form-view.js.map
|
||||
@@ -1,2 +1,2 @@
|
||||
define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_dynamic:!1,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&(a.optional=-1==["data","data_hidden","hidden","repeat","conditional"].indexOf(a.type))}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),c.unshift({0:"Sequences",1:"Sequences"}),c.unshift({0:"Roadmaps",1:"Roadmaps"}),c.unshift({0:"Leave unchanged",1:"__empty__"});var d={title:"Add Actions: '"+a+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}});
|
||||
define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),c.unshift({0:"Sequences",1:"Sequences"}),c.unshift({0:"Roadmaps",1:"Roadmaps"}),c.unshift({0:"Leave unchanged",1:"__empty__"});var d={title:"Add Actions: '"+a+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}});
|
||||
//# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map
|
||||
@@ -8,7 +8,7 @@
|
||||
from galaxy.tools.parameters import params_to_incoming
|
||||
incoming = {}
|
||||
params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app, to_html=False)
|
||||
self.form_config = tool.to_json(trans, incoming, is_dynamic=False)
|
||||
self.form_config = tool.to_json(trans, incoming, is_workflow=True)
|
||||
self.form_config.update({
|
||||
'id' : tool.id,
|
||||
'job_id' : trans.security.encode_id( job.id ) if job else None,
|
||||
|
||||
@@ -7,31 +7,42 @@ from .test_parameter_parsing import BaseParameterTestCase
|
||||
|
||||
class SelectToolParameterTestCase( BaseParameterTestCase ):
|
||||
|
||||
def test_dep_dummy_datasets_need_late_validation( self ):
|
||||
def test_validated_values( self ):
|
||||
self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
|
||||
assert self.param.need_late_validation( self.trans, { "input_bam": basic.DummyDataset() } )
|
||||
try:
|
||||
self.param.from_html("42", self.trans, { "input_bam": model.HistoryDatasetAssociation() })
|
||||
except ValueError, err:
|
||||
assert str(err) == "An invalid option was selected for my_name, '42', please verify."
|
||||
return
|
||||
assert False
|
||||
|
||||
def test_dep_runtime_values_need_late_validation( self ):
|
||||
def test_validated_values_missing_dependency( self ):
|
||||
self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
|
||||
assert self.param.need_late_validation( self.trans, { "input_bam": basic.RuntimeValue() } )
|
||||
try:
|
||||
self.param.from_html("42", self.trans)
|
||||
except AssertionError, err:
|
||||
assert str(err) == "Required dependency 'input_bam' not found in incoming values"
|
||||
return
|
||||
assert False
|
||||
|
||||
def test_dep_unvalidated_values_need_late_validation( self ):
|
||||
def test_unvalidated_values( self ):
|
||||
self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
|
||||
assert self.param.need_late_validation( self.trans, { "input_bam": basic.UnvalidatedValue( "42" ) } )
|
||||
self.trans.workflow_building_mode = True
|
||||
assert self.param.from_html("42", self.trans).value == "42"
|
||||
|
||||
def test_dep_real_datasets_no_late_validation( self ):
|
||||
def test_validated_datasets( self ):
|
||||
self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
|
||||
assert not self.param.need_late_validation( self.trans, { "input_bam": model.HistoryDatasetAssociation() } )
|
||||
try:
|
||||
self.param.from_html( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } )
|
||||
except ValueError, err:
|
||||
assert str(err) == "Parameter my_name requires a value, but has no legal values defined."
|
||||
return
|
||||
assert False
|
||||
|
||||
def test_nested_context_validation_needed( self ):
|
||||
def test_unvalidated_datasets( self ):
|
||||
self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
|
||||
# Data ref currently must be same level, if not at top level.
|
||||
assert self.param.need_late_validation( self.trans, { "reference_source": { "my_name": "42", "input_bam": basic.RuntimeValue() } } )
|
||||
|
||||
def test_nested_context_validation_not_needed( self ):
|
||||
self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
|
||||
# Data ref currently must be same level, if not at top level.
|
||||
assert not self.param.need_late_validation( self.trans, { "reference_source": { "my_name": "42", "input_bam": model.HistoryDatasetAssociation() } } )
|
||||
self.trans.workflow_building_mode = True
|
||||
assert isinstance( self.param.from_html( model.HistoryDatasetAssociation(), self.trans, { "input_bam": basic.RuntimeValue() } ).value, model.HistoryDatasetAssociation )
|
||||
|
||||
def test_filter_param_value( self ):
|
||||
self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>'''
|
||||
|
||||
Reference in New Issue
Block a user