def loadProject(self, mcProject, fileStore=None):
self.inGraph = NX.DiGraph()
globTree = mcProject.mcTree
self.maxParallelSubtrees = None
leafEvents = [globTree.getName(i) for i in globTree.getLeaves()]
expMap = None
if fileStore:
expMap = dict()
for name in mcProject.expIDMap:
expMap[name] = fileStore.readGlobalFile(
mcProject.expIDMap[name])
else:
expMap = mcProject.expMap
for name, expPath in expMap.items():
exp = ExperimentWrapper(ET.parse(expPath).getroot())
tree = exp.getTree()
self.inGraph.add_node(name)
# Go through the species tree and add the correct
# dependencies (i.e. to the outgroups and the ingroups,
# but not to the other nodes that are just there because
# they are needed to form the correct paths).
for node in tree.postOrderTraversal():
nodeName = tree.getName(node)
# we don't add edges for leaves (in the global tree)
# as they are input sequences and do not form dependencies
# (it would be clever to maybe do the same with existing
# references when --overwrite is not specified but for now
# we just do the leaves)
if nodeName not in leafEvents and nodeName in exp.getSequenceMap(
):
self.inGraph.add_edge(name, nodeName)
configFile = fileStore.readGlobalFile(exp.getConfigID())
configElem = ET.parse(configFile).getroot()
conf = ConfigWrapper(configElem)
# load max parellel subtrees from the node's config
if self.maxParallelSubtrees is None:
self.maxParallelSubtrees = conf.getMaxParallelSubtrees()
else:
assert self.maxParallelSubtrees == conf.getMaxParallelSubtrees(
)
assert NX.is_directed_acyclic_graph(self.inGraph)
def loadProject(self, mcProject, fileStore = None):
self.inGraph = NX.DiGraph()
globTree = mcProject.mcTree
self.maxParallelSubtrees = None
leafEvents = [globTree.getName(i) for i in globTree.getLeaves()]
expMap = None
if fileStore:
expMap = dict()
for name in mcProject.expIDMap:
expMap[name] = fileStore.readGlobalFile(mcProject.expIDMap[name])
else:
expMap = mcProject.expMap
for name, expPath in expMap.items():
exp = ExperimentWrapper(ET.parse(expPath).getroot())
tree = exp.getTree()
self.inGraph.add_node(name)
# Go through the species tree and add the correct
# dependencies (i.e. to the outgroups and the ingroups,
# but not to the other nodes that are just there because
# they are needed to form the correct paths).
for node in tree.postOrderTraversal():
nodeName = tree.getName(node)
# we don't add edges for leaves (in the global tree)
# as they are input sequences and do not form dependencies
# (it would be clever to maybe do the same with existing
# references when --overwrite is not specified but for now
# we just do the leaves)
if nodeName not in leafEvents and nodeName in exp.getSequenceMap():
self.inGraph.add_edge(name, nodeName)
configFile = fileStore.readGlobalFile(exp.getConfigID())
configElem = ET.parse(configFile).getroot()
conf = ConfigWrapper(configElem)
# load max parellel subtrees from the node's config
if self.maxParallelSubtrees is None:
self.maxParallelSubtrees = conf.getMaxParallelSubtrees()
else:
assert self.maxParallelSubtrees == conf.getMaxParallelSubtrees()
assert NX.is_directed_acyclic_graph(self.inGraph)
