def __createProc(self, pdag, scmd, stdin, stderr, isLast):
"define one process in the command, return stdout"
if isLast:
stdout = self.__getOutput(pdag, self.stdout)
else:
stdout = Pipeline.Pipe()
# convert arguments
pcmd = []
for a in scmd:
if isinstance(a, FileIn):
pcmd.append(self.__getInput(pdag, a))
elif isinstance(a, FileOut):
pcmd.append(self.__getOutput(pdag, a))
else:
pcmd.append(str(a))
pdag.create(pcmd, stdin, stdout, stderr)
return stdout
def __getOutput(self, pdag, fspec):
"""Get an output file. If fspec can be None, File or FileOut, or any
object that can be converted to a string. Return the appropriate Pout
object, None, or a string. Adds compression process if needed."""
if fspec == None:
return None
if isinstance(fspec, File):
fspec = FileOut(fspec)
if not isinstance(fspec, FileOut):
return str(fspec)
# handle File object, include arg prefix
path = fspec.file.getOutPath()
if fileOps.isCompressed(path) and fspec.autoCompress:
pdev = Pipeline.Pipe()
pdag.create((fileOps.compressCmd(path), ), stdin=pdev, stdout=path)
return Pipeline.POut(pdev, fspec.prefix)
else:
return Pipeline.POut(Pipeline.File(path), fspec.prefix)
