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 checkArguments(self, category, arguments, allowedAttributes, isInput, isOutput):
# Loop over all of the input arguments and check their validity.
for argumentInformation in arguments:
# Define a set of information to be used in help messages.
helpInfo = (self.name, 'arguments', category)
# Define a class to store task attribtues.
attributes = argumentAttributes()
# Check all the supplied attributes.
self.success, attributes = methods.checkAttributes(argumentInformation, allowedAttributes, attributes, self.allowTermination, helpInfo)
# Check that the argument name is unique.
if attributes.longFormArgument in self.arguments:
if self.allowTermination: self.errors.repeatedLongFormArgument(helpInfo, attributes.longFormArgument)
else:
self.success = False
return
# Define the argument category.
attributes.category = category
# Store the attributes for the argument.
if isInput: attributes.isInput = True
elif isOutput: attributes.isOutput = True
self.arguments[attributes.longFormArgument] = attributes
def checkTopLevelInformation(self, data):
# Define the allowed general attributes.
allowedAttributes = {}
allowedAttributes['arguments'] = (dict, True, False, None)
allowedAttributes['argument delimiter'] = (str, False, True, 'delimiter')
allowedAttributes['argument order'] = (list, False, True, 'argumentOrder')
allowedAttributes['categories'] = (list, True, True, 'categories')
allowedAttributes['configuration type'] = (str, True, False, None)
allowedAttributes['description'] = (str, True, True, 'description')
allowedAttributes['developmental'] = (bool, False, True, 'isDevelopmental')
allowedAttributes['executable'] = (str, True, True, 'executable')
allowedAttributes['hide tool'] = (bool, False, True, 'isHidden')
allowedAttributes['id'] = (str, True, True, 'id')
allowedAttributes['parameter sets'] = (list, True, False, None)
allowedAttributes['modifier'] = (str, False, True, 'modifier')
allowedAttributes['path'] = (str, True, True, 'path')
allowedAttributes['precommand'] = (str, False, True, 'precommand')
allowedAttributes['R packages'] = (list, False, True, 'rPackages')
allowedAttributes['tools'] = (list, True, True, 'requiredCompiledTools')
allowedAttributes['url'] = (str, False, True, 'url')
allowedAttributes['web page'] = (dict, False, True, 'webPage')
# Define a set of information to be used in help messages.
helpInfo = (self.name, None, None)
# Check the attributes against the allowed attributes and make sure everything is ok.
self = methods.checkAttributes(data, allowedAttributes, self, self.allowTermination, helpInfo)
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 validate(self, data):
# Define the allowed input argument attributes.
allowedAttributes = {}
allowedAttributes['data type'] = (str, True, True, 'dataType')
allowedAttributes['description'] = (str, False, True, 'description')
allowedAttributes['long form argument'] = (str, True, True, 'longFormArgument')
allowedAttributes['short form argument'] = (str, True, True, 'shortFormArgument')
allowedAttributes['values'] = (list, True, True, 'values')
# Loop over all of the defined gkno arguments.
for identifier in data:
# Define a set of information to be used in help messages.
helpInfo = ('gknoConfiguration', 'gkno options', identifier)
# Check all the supplied attributes.
attributes = gknoArgumentAttributes()
success, attributes = methods.checkAttributes(data[identifier], allowedAttributes, attributes, True, helpInfo)
# Check that the argument name is unique.
#TODO ERROR
if attributes.longFormArgument in self.arguments: print('gknoConfiguration.validate - 1', attributes.longFormArgument); exit(0)
if attributes.shortFormArgument in self.shortForms: print('gknoConfiguration.validate - 2', attributes.shortFormArgument); exit(0)
# Store the attributes for the argument.
self.arguments[attributes.longFormArgument] = attributes
self.shortForms[attributes.shortFormArgument] = attributes.longFormArgument
self.options[str(identifier)] = gknoArgumentAttributes()
self.options[identifier].longFormArgument = attributes.longFormArgument
self.options[identifier].shortFormArgument = attributes.shortFormArgument
def checkPipelineTasks(self, data):
# Define the allowed general attributes.
allowedAttributes = {}
allowedAttributes['consolidate divisions'] = (bool, False, True, 'consolidate')
allowedAttributes['input is stream'] = (bool, False, True, 'isInputStream')
allowedAttributes['input stream instruction set'] = (str, False, True, 'inputStreamInstructionSet')
allowedAttributes['greedy argument'] = (str, False, True, 'greedyArgument')
allowedAttributes['greedy task'] = (bool, False, True, 'isGreedy')
allowedAttributes['omit from reduced plot'] = (bool, False, True, 'omitFromReducedPlot')
allowedAttributes['output to stream'] = (bool, False, True, 'isOutputStream')
allowedAttributes['output stream instruction set'] = (str, False, True, 'outputStreamInstructionSet')
allowedAttributes['pipeline'] = (str, False, True, 'pipeline')
allowedAttributes['task'] = (str, True, True, 'task')
allowedAttributes['tool'] = (str, False, True, 'tool')
for taskInformation in data:
# Define a set of information to be used in help messages.
#helpInfo = (self.name, 'pipeline tasks', taskInformation)
helpInfo = (self.name, 'pipeline tasks', None)
# Define a class to store task attribtues.
attributes = taskAttributes()
# Check all the supplied attributes.
self.success, attributes = methods.checkAttributes(taskInformation, allowedAttributes, attributes, self.allowTermination, helpInfo)
if not self.success: return False
# Check that the task name is unique.
if attributes.task in self.pipelineTasks:
if self.allowTermination: self.errors.repeatedTaskName(self.name, attributes.task)
else:
self.success = False
return
# Store the attributes for the task.
self.pipelineTasks[attributes.task] = attributes
# Get the tool or pipeline associated with the task.
tool = self.getTaskAttribute(attributes.task, 'tool')
pipeline = self.getTaskAttribute(attributes.task, 'pipeline')
# Each task must define either a tool or a pipeline. Check that one and only one is defined.
#TODO ERROR
if not tool and not pipeline: print('pipeline.checkPipelineTasks - 5'); exit(0)
if tool and pipeline: print('pipeline.checkPipelineTasks - 6'); exit(0)
# If this is a tool, store the tool.
if tool:
self.allTools.append(tool)
self.allTasks.append(attributes.task)
# Checking if the tool or pipeline is valid is performed later when all pipelines
# have been evaluated. If a task points to a pipeline, set the hasPipelineAsTask
# variable to True.
if pipeline:
self.requiredPipelines.append((attributes.task, pipeline))
self.hasPipelineAsTask = True
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 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
def checkTopLevelInformation(self, data):
# Define the allowed general attributes.
allowedAttributes = {}
allowedAttributes['id'] = (str, True, True, 'id')
allowedAttributes['arguments'] = (dict, True, False, None)
allowedAttributes['description'] = (str, True, True, 'description')
allowedAttributes['development'] = (bool, False, True, 'isDevelopment')
allowedAttributes['categories'] = (list, True, True, 'categories')
allowedAttributes['configuration type'] = (str, True, False, None)
allowedAttributes['connect nodes'] = (list, False, False, None)
allowedAttributes['import arguments'] = (str, False, True, 'importArgumentsFromTool')
allowedAttributes['parameter sets'] = (list, True, False, None)
allowedAttributes['pipeline tasks'] = (list, True, False, None)
allowedAttributes['shared graph nodes'] = (list, False, False, None)
allowedAttributes['unique graph nodes'] = (list, False, False, None)
# Define a set of information to be used in help messages.
helpInfo = (self.name, None, None)
# Check the attributes against the allowed attributes and make sure everything is ok.
self.success, self = methods.checkAttributes(data, allowedAttributes, self, self.allowTermination, helpInfo)
def checkTerminationInstructions(self, data):
# If there are not termination instructions, return.
if 'terminate pipeline' not in data: return
# Define the allowed attributes.
allowedAttributes = {}
allowedAttributes['condition'] = (str, False, True, 'condition')
allowedAttributes['consolidating task'] = (str, False, True, 'consolidatingTask')
allowedAttributes['delete tasks'] = (list, False, True, 'deleteTasks')
allowedAttributes['replace nodes'] = (list, False, True, 'replaceNodes')
# Define a set of information to be used in help messages.
helpInfo = (self.name, 'terminate pipeline', None)
# Define the attributes object.
attributes = terminationInstructions()
# Check the attributes conform to expectations.
self.success, attributes = methods.checkAttributes(data['terminate pipeline'], allowedAttributes, attributes, self.allowTermination, helpInfo)
# Store the attributes.
self.terminatePipeline = attributes
