def test_flowgramAli_bin(self):
"""Check if we have a working FlowgramAligner"""
ali_exe = get_flowgram_ali_exe()
self.assertTrue(which(ali_exe) is not None, "The alignment program %s "
"is not accessible via the PATH environment variable."
% ali_exe)
# test if its callable and actually works
command = "%s -h" % ali_exe
proc = Popen(command, shell=True, universal_newlines=True,
stdout=PIPE, stderr=STDOUT)
if (proc.wait() != 0):
self.fail("Calling %s failed. Check permissions and that it is in fact an executable."
% ali_exe)
result = proc.stdout.read()
# check that the help string looks correct
self.assertTrue(result.startswith("Usage"))
def test_denoise_worker(self):
"""denoiser_worker.py is where it belongs and is callable."""
DENOISE_WORKER = "denoiser_worker.py"
self.assertTrue(which(DENOISE_WORKER) is not None,
"%s is not accessible via the PATH environment "
"variable." % DENOISE_WORKER)
# test if its callable and actually works
command = "%s -h" % DENOISE_WORKER
proc = Popen(command, shell=True, universal_newlines=True,
stdout=PIPE, stderr=STDOUT)
if (proc.wait() != 0):
self.fail("Calling %s failed. Check permissions and that it is in fact an executable."
% DENOISE_WORKER)
result = proc.stdout.read()
# check that the help string looks correct
self.assertTrue(result.startswith("Usage"))
def check_flowgram_ali_exe():
"""Check if we have a working FlowgramAligner"""
ali_exe = get_flowgram_ali_exe()
if which(ali_exe) is None:
raise ApplicationNotFoundError("The alignment program %s is not "
"accessible via the PATH environment "
"variable." % ali_exe)
# test if its callable and actually works
command = "%s -h" % ali_exe
proc = Popen(command, shell=True, universal_newlines=True,
stdout=PIPE, stderr=STDOUT)
if (proc.wait() != 0):
raise ApplicationError("Calling %s failed. Check permissions and that it is in fact an executable."
% ali_exe)
result = proc.stdout.read()
# check that the help string looks correct
if (not result.startswith("Usage")):
raise ApplicationError("Calling %s failed. Check permissions and that it is in fact an executable."
% ali_exe)
return True