def test_get_job_categories():
session_name = generate_random_string()
js = JobSession(session_name)
job_categories = js.get_job_categories()
assert (type(job_categories) == type([]))
print('\nThere are %s job categories: %s' %
(len(job_categories), job_categories))
def test_run_job():
session_name = generate_random_string()
js = JobSession(session_name)
j = js.run_job({'remote_command': '/bin/sleep', 'args': ['5']})
j_id = j.id
assert (len(j_id) > 0)
print('\nSubmitted job id: %s' % j_id)
def test_get_job_array():
session_name = generate_random_string()
js = JobSession(session_name)
ja = js.run_bulk_jobs({'remote_command': '/bin/sleep', 'args': ['5']}, 1, 10, 5, 2)
ja2 = js.get_job_array(ja.id)
assert (ja.id == ja2.id)
print('\nRetrieved job array: %s' % ja2)
def test_new_session():
session_name = generate_random_string()
existing_session_names = JobSession.list_session_names()
js = JobSession(session_name)
session_names = JobSession.list_session_names()
assert (len(session_names) == len(existing_session_names) + 1)
print('\nCreated new session: %s' % (session_name))
def test_run_bulk_jobs():
session_name = generate_random_string()
js = JobSession(session_name)
ja = js.run_bulk_jobs({'remote_command': '/bin/sleep', 'args': ['5']}, 1, 10, 5, 2)
jl = ja.job_list
ja_id = ja.id
assert (len(ja_id) > 0)
assert (len(jl) == 2)
print('\nSubmitted job array id: %s' % ja_id)
def test_job_info_from_job():
session_name = generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {'remote_command': '/bin/sleep', 'args': ['10'], 'job_name': job_name}
j = js.run_job(d)
ji = j.get_info()
assert (ji.job_name == job_name)
print('\nJob info from job: %s' % (ji))
def test_destroy_session():
session_names = JobSession.list_session_names()
print('\nExisting session names: %s' % session_names)
for name in session_names:
print('Destroying session: %s' % name)
JobSession.destroy_by_name(name)
session_names = JobSession.list_session_names()
print('Remaining session names: %s' % session_names)
assert (len(session_names) == 0)
def test_get_info():
session_name = 'drmaa2python-%s' % generate_random_string()
js = JobSession(session_name)
jn = 'drmaa2python-%s' % generate_random_string()
d = {'remote_command': '/bin/sleep', 'args': ['10'], 'job_name': jn, 'output_path': '/dev/null', 'join_files': True}
j = js.run_job(d)
ji = j.get_info()
assert (ji.job_name == jn)
print('\nGet info: %s' % (ji))
def test_get_template():
session_name = generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {'remote_command': '/bin/sleep', 'args': ['5'], 'job_name': job_name, 'output_path': '/dev/null', 'join_files': True}
ja = js.run_bulk_jobs(d, 1, 10, 3, 2)
jt = ja.get_template()
assert (jt.job_name == job_name)
print('\nGet template: %s' % (jt))
def test_wait_any_started():
session_name = generate_random_string()
js = JobSession(session_name)
ja = js.run_bulk_jobs({'remote_command': '/bin/sleep', 'args': ['5']}, 1, 10, 5, 2)
jl = ja.job_list
jl_ids = list(map(lambda j: j.id, jl))
print('\nWaiting on start of any job with id from %s' % jl_ids)
j = js.wait_any_started(jl)
assert (j.id in jl_ids)
print('Job %s started' % j)
def test_get_jobs():
js = JobSession('js-01')
j_name = 'drmaa2python-%s' % int(random.uniform(0, 1000))
j = js.run_job({'remote_command': '/bin/sleep', 'args': ['10'], 'job_name': j_name})
print('\nSubmitted job: %s' % j)
ji = j.get_info()
print('Retrieving jobs matching job info %s' % ji)
j_list = js.get_jobs(ji)
print('Got jobs: %s' % j_list)
assert (len(j_list) >= 1)
def test_wait_terminated():
session_name = 'drmaa2python-%s' % generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {'remote_command': '/bin/sleep', 'args': ['10'], 'job_name': job_name}
j = js.run_job(d)
j.wait_terminated()
s, ss = j.get_state()
assert (s == JobState.DONE)
print('\nWait terminated for job: %s' % (j))
ji = j.get_info()
print('\nGet info: %s' % (ji))
def test_wait_all_terminated():
session_name = generate_random_string()
js = JobSession(session_name)
ja = js.run_bulk_jobs({'remote_command': '/bin/sleep', 'args': ['5']}, 1, 10, 5, 2)
jl = ja.job_list
jl_ids = list(map(lambda j: j.id, jl))
jl_ids.sort()
print('\nWaiting on termination of all jobs: %s' % jl_ids)
jl2 = js.wait_all_terminated(jl)
jl2_ids = list(map(lambda j: j.id, jl2))
jl2_ids.sort()
assert (jl_ids == jl2_ids)
print('Jobs terminated: ' % jl2_ids)
def test_get_job_array():
session_name = generate_random_string()
js = JobSession(session_name)
d = {
'remote_command': '/bin/sleep',
'args': ['5'],
'output_path': '/dev/null',
'join_files': True
}
ja = js.run_bulk_jobs(d, 1, 10, 5, 2)
ja2 = js.get_job_array(ja.id)
assert (ja.id == ja2.id)
print('\nRetrieved job array: %s' % ja2)
def test_get_template():
session_name = generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
ja = js.run_bulk_jobs(
{
'remote_command': '/bin/sleep',
'args': ['5'],
'job_name': job_name
}, 1, 10, 3, 2)
jt = ja.get_template()
assert (jt.job_name == job_name)
print('\nGet template: %s' % (jt))
def test_run_job():
session_name = generate_random_string()
js = JobSession(session_name)
d = {
'remote_command': '/bin/sleep',
'args': ['5'],
'output_path': '/dev/null',
'join_files': True
}
j = js.run_job(d)
j_id = j.id
assert (len(j_id) > 0)
print('\nSubmitted job id: %s' % j_id)
def test_terminate():
session_name = generate_random_string()
js = JobSession(session_name)
d = {'remote_command': '/bin/sleep', 'args': ['10'], 'output_path': '/dev/null', 'join_files': True}
ja = js.run_bulk_jobs(d, 1, 10, 3, 2)
ja.terminate()
j_list = ja.job_list
failed_jobs = []
for j in j_list:
s, ss = j.get_state()
if s == JobState.FAILED:
failed_jobs.append(j)
assert (len(failed_jobs) > 0)
print('\nTerminate job array: %s' % (ja))
def test_run_bulk_jobs():
session_name = generate_random_string()
js = JobSession(session_name)
d = {
'remote_command': '/bin/sleep',
'args': ['5'],
'output_path': '/dev/null',
'join_files': True
}
ja = js.run_bulk_jobs(d, 1, 10, 5, 2)
jl = ja.job_list
ja_id = ja.id
assert (len(ja_id) > 0)
assert (len(jl) == 2)
print('\nSubmitted job array id: %s' % ja_id)
def test_get_state():
session_name = 'drmaa2python-%s' % generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {
'remote_command': '/bin/sleep',
'args': ['10'],
'job_name': job_name,
'output_path': '/dev/null',
'join_files': True
}
j = js.run_job(d)
(j_state, j_sub_state) = j.get_state()
assert (isinstance(j_state, JobState))
print('\nGet state %s for job %s' % (j_state, j))
def test_wait_any_terminated():
session_name = generate_random_string()
js = JobSession(session_name)
d = {
'remote_command': '/bin/sleep',
'args': ['5'],
'output_path': '/dev/null',
'join_files': True
}
ja = js.run_bulk_jobs(d, 1, 10, 5, 2)
jl = ja.job_list
jl_ids = list(map(lambda j: j.id, jl))
print('\nWaiting on termination of any job with id from %s' % jl_ids)
j = js.wait_any_terminated(jl)
assert (j.id in jl_ids)
print('Job %s terminated' % j)
def test_wait_terminated():
session_name = 'drmaa2python-%s' % generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {
'remote_command': '/bin/sleep',
'args': ['10'],
'job_name': job_name,
'output_path': '/dev/null',
'join_files': True
}
j = js.run_job(d)
j.wait_terminated()
s, ss = j.get_state()
assert (s == JobState.DONE)
print('\nWait terminated for job: %s' % (j))
def run_sagasu_proc(self):
self.session = JobSession()
os.chdir(self.path)
self.job_details = []
Path(self.projname).mkdir(parents=True, exist_ok=True)
i = self.highres
if self.clust == "l":
tot = (self.lowres - self.highres) * (
(self.highsites + 1) - self.lowsites)
pbar = tqdm(desc="SHELXD", total=tot, dynamic_ncols=True)
else:
pass
while not (i >= self.lowres):
Path(os.path.join(self.projname, str(i))).mkdir(parents=True,
exist_ok=True)
i2 = i / 10
j = self.highsites
while not (j <= (self.lowsites - 1)):
os.makedirs(os.path.join(self.projname, str(i), str(j)),
exist_ok=True)
shutil.copy2(self.insin,
(os.path.join(self.projname, str(i), str(j))))
shutil.copy2(self.hklin,
(os.path.join(self.projname, str(i), str(j))))
workpath = os.path.join(self.path, self.projname, str(i),
str(j))
f = os.path.join(self.path, self.projname, str(i), str(j),
self.projname + "_fa.ins")
self.replace(f, "FIND", "FIND " + str(j) + "\n")
self.replace(f, "SHEL", "SHEL 999 " + str(i2) + "\n")
self.replace(f, "NTRY", "NTRY " + str(self.ntry) + "\n")
if self.clust == "l":
os.chdir(workpath)
subprocess.run(["shelxd", self.projname + "_fa"],
stdout=subprocess.PIPE)
pbar.update(1)
pbar.refresh()
os.chdir(self.path)
elif self.clust == "c":
template = self.drmaa2template(workpath)
job = self.session.run_job(template)
self.job_details.append([job])
else:
print("error in input...")
j = j - 1
i = i + 1
def test_get_all_jobs():
js = JobSession('js-01')
j_name = 'drmaa2python-%s' % int(random.uniform(0, 1000))
j = js.run_job({
'remote_command': '/bin/sleep',
'args': ['10'],
'job_name': j_name
})
print('\nSubmitted job: %s' % j)
ji = j.get_info()
j.wait_started()
ms = MonitoringSession('ms-01')
print('Opened monitoring session: %s' % ms.name)
ji2 = JobInfo({'job_id': ji.job_id})
print('Retrieving jobs matching job info %s' % ji2)
j_list = ms.get_all_jobs(ji2)
print('Got all jobs: %s' % j_list)
assert (len(j_list) >= 1)
def test_get_jobs():
js = JobSession('js-01')
j_name = 'drmaa2python-%s' % int(random.uniform(0, 1000))
d = {
'remote_command': '/bin/sleep',
'args': ['10'],
'job_name': j_name,
'output_path': '/dev/null',
'join_files': True
}
j = js.run_job(d)
print('\nSubmitted job: %s' % j)
ji = j.get_info()
print('Retrieving jobs matching job info %s' % ji)
ji2 = JobInfo({'job_id': ji.job_id})
j_list = js.get_jobs(ji2)
print('Got jobs: %s' % j_list)
assert (len(j_list) >= 1)
def test_hold_and_release():
session_name = generate_random_string()
js = JobSession(session_name)
d = {'remote_command': '/bin/sleep', 'args': ['5'], 'output_path': '/dev/null', 'join_files': True}
ja = js.run_bulk_jobs(d, 1, 10, 3, 2)
ja.hold()
held_jobs = []
j_list = ja.job_list
for j in j_list:
s, ss = j.get_state()
if s.name.endswith('HELD'):
held_jobs.append(j)
assert (len(held_jobs) > 0)
print('\nHold job array: %s' % (ja))
ja.release()
for j in held_jobs:
s, ss = j.get_state()
assert (not s.name.endswith('HELD'))
print('Release job array: %s' % (ja))
def test_wait_all_started():
session_name = generate_random_string()
js = JobSession(session_name)
d = {
'remote_command': '/bin/sleep',
'args': ['5'],
'output_path': '/dev/null',
'join_files': True
}
ja = js.run_bulk_jobs(d, 1, 10, 5, 2)
jl = ja.job_list
jl_ids = list(map(lambda j: j.id, jl))
jl_ids.sort()
print('\nWaiting on start of all jobs: %s' % jl_ids)
jl2 = js.wait_all_started(jl)
jl2_ids = list(map(lambda j: j.id, jl2))
jl2_ids.sort()
assert (jl_ids == jl2_ids)
print('Jobs started: ' % jl2_ids)
def test_terminate():
session_name = 'drmaa2python-%s' % generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {
'remote_command': '/bin/sleep',
'args': ['10'],
'job_name': job_name,
'output_path': '/dev/null',
'join_files': True
}
j = js.run_job(d)
ji = j.get_info()
assert (ji.terminating_signal is None)
j.wait_started()
j.terminate()
j.wait_terminated()
ji = j.get_info()
assert (ji.terminating_signal is not None)
print('\nTerminate job: %s' % (ji))
def test_suspend_and_resume():
session_name = generate_random_string()
js = JobSession(session_name)
d = {'remote_command': '/bin/sleep', 'args': ['5'], 'output_path': '/dev/null', 'join_files': True}
ja = js.run_bulk_jobs(d, 1, 10, 3, 2)
j_list = ja.job_list
js.wait_any_started(j_list)
ja.suspend()
suspended_jobs = []
for j in j_list:
s, ss = j.get_state()
if s == JobState.SUSPENDED:
suspended_jobs.append(j)
assert (len(suspended_jobs) > 0)
print('\nSuspend job array: %s' % (ja))
ja.resume()
for j in suspended_jobs:
s, ss = j.get_state()
assert (s != JobState.SUSPENDED)
print('Resume job array: %s' % (ja))
def test_hold_and_release():
session_name = 'drmaa2python-%s' % generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {
'remote_command': '/bin/sleep',
'args': ['10'],
'job_name': job_name,
'output_path': '/dev/null',
'join_files': True
}
j = js.run_job(d)
ji = j.get_info()
assert (not ji.job_state.endswith('HELD'))
j.hold()
ji = j.get_info()
assert (ji.job_state.endswith('HELD'))
print('\nHold job: %s' % (ji))
j.release()
ji = j.get_info()
assert (not ji.job_state.endswith('HELD'))
print('Release job: %s' % (ji))
def test_suspend_and_resume():
session_name = 'drmaa2python-%s' % generate_random_string()
js = JobSession(session_name)
job_name = 'drmaa2python-%s' % generate_random_string()
d = {
'remote_command': '/bin/sleep',
'args': ['10'],
'job_name': job_name,
'output_path': '/dev/null',
'join_files': True
}
j = js.run_job(d)
j.wait_started()
ji = j.get_info()
assert (ji.job_state != JobState.SUSPENDED.name)
j.suspend()
ji = j.get_info()
assert (ji.job_state == JobState.SUSPENDED.name)
print('\nSuspend job: %s' % (ji))
j.resume()
ji = j.get_info()
assert (ji.job_state != JobState.SUSPENDED.name)
print('Resume job: %s' % (ji))