def test_hello_world_job(self):
r = C.load_installed_cluster_templates_by_name('sge')
log.debug(r)
job_name = "int_job_hello"
output_dir = get_temp_cluster_dir(job_name)
cmd = "pbsmrtpipe --help"
def _to_p(x_):
return os.path.join(output_dir, x_)
sh_script = _to_p('qsub_test.sh')
with open(sh_script, 'w') as f:
f.write(cmd + "\n")
# qsub output
stdout = _to_p('stdout')
stderr = _to_p('stderr')
for x in [stdout, stderr]:
with open(x, 'w') as f:
f.write("")
log.info(sh_script)
cmd = r.render("start",
sh_script,
'test_job_01',
stdout=stdout,
stderr=stderr,
nproc=1)
log.debug("Running qsub command '{c}'".format(c=cmd))
time_out = 60 * 5
rcode, stdout, stderr, run_time = run_command(cmd,
None,
None,
time_out=time_out)
log.debug((rcode, stdout, stderr, run_time))
if rcode != 0:
log.info(stdout)
log.error(stderr)
log.error("Failed Integration Job {i} with exit code {r}".format(
i=job_name, r=rcode))
if os.path.exists(stderr):
with open(stderr, 'r') as f:
log.error(f.read())
else:
try:
shutil.rmtree(output_dir)
except Exception as e:
log.warn("Unable to cleanup testdir {o}. {m}".format(
o=output_dir, m=e.message))
self.assertEqual(rcode, 0, stderr)
def test_hello_world_job(self):
r = C.load_installed_cluster_templates_by_name('sge')
log.debug(r)
job_name = "int_job_hello"
output_dir = get_temp_cluster_dir(job_name)
cmd = "pbsmrtpipe --help"
def _to_p(x_):
return os.path.join(output_dir, x_)
sh_script = _to_p('qsub_test.sh')
with open(sh_script, 'w') as f:
f.write(cmd + "\n")
# qsub output
stdout = _to_p('stdout')
stderr = _to_p('stderr')
for x in [stdout, stderr]:
with open(x, 'w') as f:
f.write("")
log.info(sh_script)
cmd = r.render("start", sh_script, 'test_job_01', stdout=stdout, stderr=stderr, nproc=1)
log.debug("Running qsub command '{c}'".format(c=cmd))
time_out = 60 * 5
with tempfile.TemporaryFile() as stdout_tmp:
with tempfile.TemporaryFile() as stderr_tmp:
rcode, stdout, stderr, run_time = run_command(cmd, stdout_tmp, stderr_tmp, time_out=time_out)
log.debug((rcode, stdout, stderr, run_time))
if rcode != 0:
log.info(stdout)
log.error(stderr)
log.error("Failed Integration Job {i} with exit code {r}".format(i=job_name, r=rcode))
if os.path.exists(stderr):
with open(stderr, 'r') as f:
log.error(f.read())
else:
try:
shutil.rmtree(output_dir)
except Exception as e:
log.warn("Unable to cleanup testdir {o}. {m}".format(o=output_dir, m=e.message))
self.assertEqual(rcode, 0, stderr)
def _get_root_temp_dir(self):
return get_temp_cluster_dir(self.JOB_NAME)
def _get_root_temp_dir(self):
"""Override me to set the shared tmp dir"""
return get_temp_cluster_dir(self.JOB_NAME)
def _get_root_temp_dir(self):
return get_temp_cluster_dir(self.JOB_NAME)
def _get_root_temp_dir(self):
"""Override me to set the shared tmp dir"""
return get_temp_cluster_dir(self.JOB_NAME)
