def setUp(self):
"""Set up tests."""
self.inCmpFile = path.join(DATA_DIR, "testsort.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
copyfile(self.inCmpFile, self.outCmpFile)
self.options = Opt()
self.obj = SortService(self.outCmpFile, self.options)
class ForQuiverService(object):
"""
Uses SortService, LoadPulsesService, LoadChemistryService,
RepackService to post process a cmp.h5 file so that the file can
be used by quiver directly.
"""
@property
def name(self):
"""Name of ForQuiverService."""
return "ForQuiverService"
def __init__(self, fileNames, options):
"""Initialize a ForQuiverService object.
Input:
fileNames : pbalign file names
options : pbalign options
"""
self.fileNames = fileNames
self.options = options
self._loadpulsesService = LoadPulsesService(
self.fileNames.pulseFileName,
self.fileNames.outputFileName,
self.options)
self._loadchemistryService = LoadChemistryService(
self.fileNames.pulseFileName,
self.fileNames.outputFileName,
self.options)
self._sortService = SortService(
self.fileNames.outputFileName,
self.options)
self._repackService = RepackService(
self.fileNames.outputFileName,
self.fileNames.outputFileName + ".TMP")
def run(self):
""" Run the ForQuiver service."""
logging.info(self.name + ": Sort.")
self._sortService.checkAvailability()
self._sortService.run()
logging.info(self.name + ": LoadPulses.")
self._loadpulsesService.checkAvailability()
self._loadpulsesService.run()
logging.info(self.name + ": LoadChemistry.")
self._loadchemistryService.checkAvailability()
self._loadchemistryService.run()
logging.info(self.name + ": Repack.")
self._repackService.checkAvailability()
self._repackService.run()
class ForQuiverService(object):
"""
Uses SortService, LoadPulsesService, LoadChemistryService,
RepackService to post process a cmp.h5 file so that the file can
be used by quiver directly.
"""
@property
def name(self):
"""Name of ForQuiverService."""
return "ForQuiverService"
def __init__(self, fileNames, options):
"""Initialize a ForQuiverService object.
Input:
fileNames : pbalign file names
options : pbalign options
"""
self.fileNames = fileNames
self.options = options
self._loadpulsesService = LoadPulsesService(
self.fileNames.pulseFileName, self.fileNames.outputFileName,
self.options)
self._loadchemistryService = LoadChemistryService(
self.fileNames.pulseFileName, self.fileNames.outputFileName,
self.options)
self._sortService = SortService(self.fileNames.outputFileName,
self.options)
self._repackService = RepackService(
self.fileNames.outputFileName,
self.fileNames.outputFileName + ".TMP")
def run(self):
""" Run the ForQuiver service."""
logging.info(self.name + ": Sort.")
self._sortService.checkAvailability()
self._sortService.run()
logging.info(self.name + ": LoadPulses.")
self._loadpulsesService.checkAvailability()
self._loadpulsesService.run()
logging.info(self.name + ": LoadChemistry.")
self._loadchemistryService.checkAvailability()
self._loadchemistryService.run()
logging.info(self.name + ": Repack.")
self._repackService.checkAvailability()
self._repackService.run()
def setUp(self):
"""Set up tests."""
self.rootDir = "/mnt/secondary-siv/" + \
"testdata/BlasrTestData/pbalign"
self.inCmpFile = path.join(self.rootDir, "data/testsort.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
copyfile(self.inCmpFile, self.outCmpFile)
self.options = Opt()
self.obj = SortService(self.outCmpFile, self.options)
def __init__(self, fileNames, options):
"""Initialize a ForQuiverService object.
Input:
fileNames : pbalign file names
options : pbalign options
"""
self.fileNames = fileNames
self.options = options
self._loadpulsesService = LoadPulsesService(
self.fileNames.pulseFileName, self.fileNames.outputFileName,
self.options)
self._loadchemistryService = LoadChemistryService(
self.fileNames.pulseFileName, self.fileNames.outputFileName,
self.options)
self._sortService = SortService(self.fileNames.outputFileName,
self.options)
self._repackService = RepackService(
self.fileNames.outputFileName,
self.fileNames.outputFileName + ".TMP")
class Test_SortService(unittest.TestCase):
"""Test pbalign.forquiverservice.sort."""
def setUp(self):
"""Set up tests."""
self.inCmpFile = path.join(DATA_DIR, "testsort.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
copyfile(self.inCmpFile, self.outCmpFile)
self.options = Opt()
self.obj = SortService(self.outCmpFile, self.options)
def tearDown(self):
remove(self.outCmpFile)
def test_run(self):
"""Test SortService.__init__()."""
print self.obj.cmd
_output, errCode, _errMsg = self.obj.run()
self.assertEqual(errCode, 0)
def __init__(self, fileNames, options):
"""Initialize a ForQuiverService object.
Input:
fileNames : pbalign file names
options : pbalign options
"""
self.fileNames = fileNames
self.options = options
self._loadpulsesService = LoadPulsesService(
self.fileNames.pulseFileName,
self.fileNames.outputFileName,
self.options)
self._loadchemistryService = LoadChemistryService(
self.fileNames.pulseFileName,
self.fileNames.outputFileName,
self.options)
self._sortService = SortService(
self.fileNames.outputFileName,
self.options)
self._repackService = RepackService(
self.fileNames.outputFileName,
self.fileNames.outputFileName + ".TMP")