def __init__(self, pipeline):
# Define errors.
self.pipelineErrors = pce.pipelineErrors()
# Record the name of the top level pipeline, e.g. that defined on the command line.
self.pipeline = None
# The number of tiers in the super pipeline.
self.numberOfTiers = 1
# Store all of the pipeline configuration files comprising the superpipeline in a
# dictionary, indexed by the name of the pipeline.
self.pipelineConfigurationData = {}
# Store information on all the constituent tools.
self.toolConfigurationData = {}
# Store all the tasks in the superpipeline along with the tools,
self.tools = []
self.tasks = {}
# Store the unique and shared node IDs in all the pipeline.
self.uniqueNodeIds = []
self.sharedNodeIds = []
# Store all of the constituent pipeline with their tier and also all the pipelines indexed
# by tier.
self.pipelinesByTier = {}
self.tiersByPipeline = {}
# Keep track of the tasks that should be included in a plot.
self.tasksInPlot = {}
# Associate a random string with the graph. This will be used in any makefiles and intermediate
# files to ensure simultaneous executions of gkno will not produced filename conflicts.
self.randomString = strOps.getRandomString(8)
def __init__(self, allowTermination = True):
# Handle errors.
self.errors = errors.pipelineErrors()
# Store the name of the pipeline.
self.name = None
# Store the path to the configuration file.
self.path = None
# Store the id for this pipeline.
self.id = None
# The pipeline description.
self.description = 'No description'
# The categories the pipeline is included in for help messages.
self.categories = []
# The parameter set information for this pipeline.
self.parameterSets = parameterSets.parameterSets()
# The tasks that the pipeline comprises. Also store all of the tasks and all of the tools
# that are executed by the pipeline.
self.pipelineTasks = {}
self.allTasks = []
self.allTools = []
# The pipeline graph nodes that are shared between different tasks in the pipeline.
self.sharedNodeAttributes = {}
# Pipeline graph nodes that are kept as unique for a specific task,
self.uniqueNodeAttributes = {}
# The connections that need to be made between nodes and tasks.
self.connections = []
# Store all of the valid top level pipeline arguments.
self.longFormArguments = {}
self.shortFormArguments = {}
# If the pipeline contains tasks that are themselves pipelines. Store all of the pipelines
# used in this pipeline.
self.hasPipelineAsTask = False
self.requiredPipelines = []
# If there is a request to import argument from a tool, store the name of the tool. This tool
# will not be checked for validity, that is left to the methods that use the tool.
self.importArgumentsFromTool = None
# If the pipeline is nested within other pipelines, the nodes associated with this pipeline
# have an address to locate them within the graph structure. For example, if the main pipeline
# has a task 'run' which is a pipeline, all the nodes created for this pipeline are prepended
# with 'run.' etc. Store this address.
self.address = None
# It is sometimes desirable to allow all steps to be processed without termination. Other
# times, if a problem is encountered, execution should terminate. Keep track of this.
self.allowTermination = allowTermination
# Flag if this pipeline contains instructions for building tasks that generate multiple output
# file nodes.
self.generatesMultipleNodes = False
# Pipelines can be marked as developmental. This will keep them out of help messages and not include
# them in the web json.
self.isDevelopment = False
# As pipeline configuration files are processed, success will identify whether a problem was
# encountered.
self.success = True