def openIn(self, autoDecompress=True):
"""open the input file for reading in the ExRun process"""
path = self.__setupIn()
if fileOps.isCompressed(path) and autoDecompress:
return fileOps.openz(path)
else:
return open(path)
def openOut(self, autoCompress=True):
"""open the output file for writing from the ExRun process"""
path = self.__setupOut(autoCompress)
if fileOps.isCompressed(path) and autoCompress:
return fileOps.openz(path, "w")
else:
return open(path, "w")
def openIn(self, autoDecompress=True):
"""open the input file for reading in the ExRun process"""
path = self.__setupIn()
if fileOps.isCompressed(path) and autoDecompress:
return fileOps.openz(path)
else:
return open(path)
def openOut(self, autoCompress=True):
"""open the output file for writing from the ExRun process"""
path = self.__setupOut(autoCompress)
if fileOps.isCompressed(path) and autoCompress:
return fileOps.openz(path, "w")
else:
return open(path, "w")
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)
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)
def __getInput(pdag, fspec):
"""Get an input file. If fspec can be None, File or FileIn, or any
object that can be converted to a string. Return the appropriate PIn
object, None, or a string. Adds decompression process if needed."""
if fspec is None:
return None
if isinstance(fspec, File):
fspec = FileIn(fspec)
if not isinstance(fspec, FileIn):
return str(fspec)
# handle File object, include arg prefix
path = fspec.file.getInPath()
if fileOps.isCompressed(path) and fspec.autoDecompress:
pdev = pipeline.Pipe()
pdag.create((fileOps.decompressCmd(path), path), stdout=pdev)
return pipeline.PIn(pdev, fspec.prefix)
else:
return pipeline.PIn(pipeline.File(path), fspec.prefix)
def _getExt(gxfFile):
if fileOps.isCompressed(gxfFile):
return os.path.splitext(os.path.splitext(gxfFile)[0])[1]
else:
return os.path.splitext(gxfFile)[1]
