def checkParameterSets(self, data, allowTermination, name, isTool):
success = True
# Define the allowed attributes.
allowedAttributes = {}
allowedAttributes['id'] = (str, True, True, 'id')
allowedAttributes['description'] = (str, True, True, 'description')
allowedAttributes['data'] = (list, True, False, None)
# Define the allowed attributes in the data section of the parameter set.
allowedDataAttributes = {}
allowedDataAttributes['id'] = (str, True, True, 'id')
allowedDataAttributes['values'] = (list, True, True, 'values')
# The parameter set definitions differ slightly between tools and pipelines. For tools, the argument is
# provided as the means of identifying the node for which the supplied values apply. For pipelines, it is
# the node within the pipeline that is supplied.
if isTool: allowedDataAttributes['argument'] = (str, True, True, 'argument')
else: allowedDataAttributes['node'] = (str, True, True, 'nodeId')
# Loop over all of the defined parameter sets.
for parameterSet in data:
# Check that the supplied structure is a dictionary.
if not methods.checkIsDictionary(parameterSet, allowTermination): return False
# Check that the node has a valid ID. This is required for help messages.
id = methods.checkForId(parameterSet, name, 'parameter sets', allowTermination, isTool)
if not id: return False
# Define a set of information to be used in help messages.
helpInfo = (name, 'parameter sets', id)
# Define a structure to hold the data.
attributes = parameterSetData()
# Check the attributes.
success, attributes = methods.checkAttributes(parameterSet, allowedAttributes, attributes, allowTermination, helpInfo)
# Loop over all of the data supplied with the parameter set and check the validity.
for dataSet in parameterSet['data']:
# Check that the supplied structure is a dictionary.
if not methods.checkIsDictionary(dataSet, allowTermination): return False
# Define a structure to hold the information for each argument.
dataAttributes = parameterSetArguments()
# Check the attributes.
success, dataAttributes = methods.checkAttributes(dataSet, allowedDataAttributes, dataAttributes, allowTermination, helpInfo)
# Append this argument to the main parameter set attributes.
attributes.data.append(dataAttributes)
# Store the parameter set data.
#TODO RROR
if attributes.id in self.sets: print('parameterSets.checkParameterSets - REPEAT', attributes.id); exit(0)
self.sets[attributes.id] = attributes
return success
def checkDefinedEdges(self, data):
if 'connect nodes' not in data: return True
# Define the allowed attributes.
allowedAttributes = {}
allowedAttributes['argument'] = (str, True, False, None)
allowedAttributes['source'] = (str, True, False, None)
allowedAttributes['target'] = (str, True, False, None)
# Loop over all the defined definitions.
for i, information in enumerate(data['connect nodes']):
# Define a set of information to be used in help messages.
helpInfo = (self.name, 'connect nodes', str(i))
# Check that the supplied structure is a dictionary.
if not methods.checkIsDictionary(information, self.allowTermination): return
# Define the attributes object.
attributes = edgeDefinitions()
# Check the attributes conform to expectations.
self.success, attributes = methods.checkAttributes(information, allowedAttributes, attributes, self.allowTermination, helpInfo)
# Store the connection.
attributes.source = str(information['source'])
attributes.target = str(information['target'])
attributes.argument = str(information['argument'])
self.connections.append(attributes)
def checkSharedNodeTasks(self):
# Define the allowed nodes attributes.
allowedAttributes = {}
allowedAttributes['node id'] = (str, False, True, 'externalNodeId')
allowedAttributes['stub extension'] = (str, False, True, 'stubExtension')
allowedAttributes['task'] = (str, True, True, 'task')
allowedAttributes['task argument'] = (str, False, True, 'taskArgument')
# Loop over all of the defined nodes.
for nodeId in self.sharedNodeAttributes:
for node in self.sharedNodeAttributes[nodeId].nodes:
# Define a set of information to be used in help messages.
helpInfo = (self.name, 'shared nodes', nodeId)
# Check that the supplied structure is a dictionary.
if not methods.checkIsDictionary(node, self.allowTermination): return
# Define the attributes object.
attributes = nodeTaskAttributes()
# Check that the supplied attributes are valid.
self.success, attributes = methods.checkAttributes(node, allowedAttributes, attributes, self.allowTermination, helpInfo)
#TODO INCLUDE A CHECK TO ENSURE THAT AN ALLOWED COMBINATION OF FIELDS IS PRESENT. IN PARTICULAR,
# IF THE TASK POINTS TO A PIPELINE RATHER THAN A TOOL, ENSURE THAT THE NODE ID IS PRESENT AND NOT
# THE TASK ARGUMENT.
# Store the attributes.
self.sharedNodeAttributes[nodeId].sharedNodeTasks.append(attributes)
def checkArguments(self, data):
# If there is not information on unique graph nodes, return.
if 'arguments' not in data: return
# Define the allowed nodes attributes.
allowedAttributes = {}
allowedAttributes['description'] = (str, True, True, 'description')
allowedAttributes['hide in help'] = (bool, False, True, 'hideInHelp')
allowedAttributes['linked argument'] = (str, False, True, 'linkedArgument')
allowedAttributes['long form argument'] = (str, True, True, 'longFormArgument')
allowedAttributes['node id'] = (str, True, True, 'nodeId')
allowedAttributes['required'] = (bool, False, True, 'isRequired')
allowedAttributes['short form argument'] = (str, True, True, 'shortFormArgument')
# Loop over all of the argument categories.
for category in data['arguments']:
# Loop over all arguments in the category.
for argumentInformation in data['arguments'][category]:
# Check that the supplied structure is a dictionary.
if not methods.checkIsDictionary(argumentInformation, self.allowTermination): return
# Check that the node has a long form argument. This is required for help messages.
longFormArgument = methods.checkForLongFormArgument(argumentInformation, self.allowTermination)
if not longFormArgument: return
# Define a set of information to be used in help messages.
helpInfo = (self.name, 'arguments -> ' + category, longFormArgument)
# Define the attributes object and add the help category.
attributes = pipelineArguments()
attributes.category = category
# Check the attributes conform to expectations.
self.success, attributes = methods.checkAttributes(argumentInformation, allowedAttributes, attributes, self.allowTermination, helpInfo)
# If the long form argument already exists, there is a problem. All arguments must be unique.
if longFormArgument in self.longFormArguments: self.errors.repeatedLongFormArgument(helpInfo)
# Also check that the node id is not the name of a task.
shortFormArgument = attributes.shortFormArgument
if shortFormArgument in self.shortFormArguments: self.errors.repeatedShortFormArgument(helpInfo)
# If the argument shares a name with a pipeline task.
if longFormArgument.strip('-') in self.pipelineTasks: self.errors.argumentIsTask(longFormArgument, shortFormArgument, isLongForm = True)
if shortFormArgument.strip('-') in self.pipelineTasks: self.errors.argumentIsTask(longFormArgument, shortFormArgument, isLongForm = False)
# Store the attributes.
self.longFormArguments[longFormArgument] = attributes
self.shortFormArguments[shortFormArgument] = longFormArgument
def checkReplaceSubstring(self, arguments):
allowedFields = {}
allowedFields['replace'] = (str, True)
allowedFields['with'] = (str, True)
# Loop over all the arguments.
for category in arguments.keys():
for argumentAttributes in arguments[category]:
# Check if the argument has instructions on replacing substrings.
if 'replace substring' in argumentAttributes:
# Get the long form argument.
argument = argumentAttributes['long form argument']
replace = argumentAttributes['replace substring']
# Loop over the list and check that each entry is a dictionary with the correct attributes.
for data in replace:
if not methods.checkIsDictionary(data, self.allowTermination):
if self.allowTermination: self.errors.invalidReplaceSubstring(self.name, category, argument)
else: return False
# Check the contained values.
observedFields = []
toReplace = None
replaceWith = None
for key in data:
value = data[key]
if key not in allowedFields:
if self.allowTermination: self.errors.invalidReplaceSubstring(self.name, category, argument)
else: return False
# Store the value.
if key == 'replace': toReplace = value
elif key == 'with': replaceWith = value
# Record the field as having been observed.
observedFields.append(key)
# Store the values.
self.arguments[argument].isReplaceSubstring = True
self.arguments[argument].replaceSubstring.append((str(toReplace), str(replaceWith)))
# Check that all required fields have been set.
for field in allowedFields.keys():
if allowedFields[field][1] and field not in observedFields:
if self.allowTermination: self.errors.invalidReplaceSubstring(self.name, category, argument)
else: return False
# Return success.
return True
def checkUniqueNodes(self, data):
# If there is not information on unique graph nodes, return.
if 'unique graph nodes' not in data: return
# Define the allowed nodes attributes.
allowedAttributes = {}
allowedAttributes['delete files'] = (bool, False, True, 'isDelete')
allowedAttributes['evaluate command'] = (dict, False, True, 'evaluateCommand')
allowedAttributes['id'] = (str, True, True, 'id')
allowedAttributes['omit from reduced plot'] = (bool, False, True, 'omitFromReducedPlot')
allowedAttributes['node id'] = (str, False, True, 'nodeId')
allowedAttributes['task'] = (str, True, True, 'task')
allowedAttributes['task argument'] = (str, False, True, 'taskArgument')
# Loop over all of the defined nodes.
for uniqueNode in data['unique graph nodes']:
# Check that the supplied structure is a dictionary.
if not methods.checkIsDictionary(uniqueNode, self.allowTermination): return
# Check that the node has a valid ID. This is required for help messages.
id = methods.checkForId(uniqueNode, self.name, 'unique graph nodes', self.allowTermination, isTool = False)
if not id: return
# Define a set of information to be used in help messages.
helpInfo = (self.name, 'unique graph nodes', id)
# Define the attributes object.
attributes = uniqueGraphNodes()
# Check the attributes conform to expectations.
self.success, attributes = methods.checkAttributes(uniqueNode, allowedAttributes, attributes, self.allowTermination, helpInfo)
# If the nodeId already exists in the attributes, a node of this name has already been seen. All
#nodes must have a unique name.
if attributes.id in self.uniqueNodeAttributes: self.errors.repeatedNodeId(helpInfo)
# Also check that the node id is not the name of a task.
if attributes.id in self.allTasks: self.errors.nodeIdIsTaskId('unique', helpInfo)
# Store the attributes.
self.uniqueNodeAttributes[attributes.id] = attributes
