def test_single_job_fail(tmpdir):
tmpdir = str(tmpdir)
target_file = os.path.join(tmpdir, 'result.txt')
db_file = os.path.join(tmpdir, "test.db")
assert not os.path.exists(target_file)
# create a JIP database and a session
jip.db.init(db_file)
# create the cluster instance
c = cl.LocalCluster()
# create the pipeline
p = jip.Pipeline()
p.job(dir=tmpdir).bash('touch ${input}; exit 1;', outfile=target_file)
p.context(locals())
# create the jobs
jobs = jip.create_jobs(p)
# iterate the executions and pass the session so all jobs are stored
for e in jip.create_executions(jobs, save=True):
jip.submit_job(e.job, cluster=c)
c.wait()
# now the file should be there
assert not os.path.exists(target_file)
# we should also have the log files
assert os.path.exists(os.path.join(tmpdir, "jip-1.out"))
assert os.path.exists(os.path.join(tmpdir, "jip-1.err"))
# and we should have one job in Done state in our database
# we do the query with a fresh session though
job = jip.db.get(1)
assert job is not None
assert job.state == jip.db.STATE_FAILED
def test_job_hierarchy_execution_with_pipes_and_dispatching(tmpdir):
print ">>>", tmpdir
tmpdir = str(tmpdir)
target_file = os.path.join(tmpdir, 'result')
db_file = os.path.join(tmpdir, "test.db")
# create a JIP database and a session
jip.db.init(db_file)
session = jip.db.create_session()
# create the cluster instance
c = cl.LocalCluster()
# create the pipeline
p = jip.Pipeline()
a = p.job(dir=tmpdir).bash('echo "hello world"', output="${target_file}.1")
b = p.job(dir=tmpdir).bash('wc -w ${input}',
input=a,
output="${target_file}.2")
l = p.job(dir=tmpdir).bash('echo "Other" > ${target_file}.3')
a | b
p.context(locals())
# create the jobs
jobs = jip.create_jobs(p)
assert len(jobs) == 3
# iterate the executions and pass the session so all jobs are stored
execs = 0
for e in jip.create_executions(jobs, save=True):
jip.submit_job(e.job, save=True, cluster=c)
execs += 1
assert execs == 2
c.wait()
# now the file should be there
assert os.path.exists(target_file + ".1")
assert os.path.exists(target_file + ".2")
assert os.path.exists(target_file + ".3")
# we should also have the log files
assert os.path.exists(os.path.join(tmpdir, "jip-1.out"))
assert os.path.exists(os.path.join(tmpdir, "jip-1.err"))
assert os.path.exists(os.path.join(tmpdir, "jip-3.out"))
assert os.path.exists(os.path.join(tmpdir, "jip-3.err"))
# and we should have one job in Done state in our database
# we do the query with a fresh session though
find = jip.db.get
assert find(1).state == jip.db.STATE_DONE
assert find(2).state == jip.db.STATE_DONE
assert find(3).state == jip.db.STATE_DONE
# check the content of the output files
assert open(target_file + ".1").read() == "hello world\n"
assert open(target_file + ".2").read().strip() == "2"
assert open(target_file + ".3").read() == "Other\n"
def test_single_dummydirect(tmpdir):
tmpdir = str(tmpdir)
c = cl.LocalCluster()
j = jip.db.Job()
j.stdout = os.path.join(tmpdir, "out.txt")
j.stderr = os.path.join(tmpdir, "err.txt")
j.get_cluster_command = lambda: "echo 'hello world'"
c.submit(j)
c.wait()
with open(os.path.join(tmpdir, 'out.txt')) as of:
assert of.readlines()[0] == "hello world\n"
def test_job_cancelation(tmpdir):
tmpdir = str(tmpdir)
db_file = os.path.join(tmpdir, "test.db")
# create a JIP database and a session
jip.db.init(db_file)
session = jip.db.create_session()
# create the cluster instance
c = cl.LocalCluster()
# create the pipeline
p = jip.Pipeline()
first = p.job(dir=tmpdir).bash('sleep 10')
p.job(dir=tmpdir).bash('sleep 5').depends_on(first)
p.context(locals())
# create the jobs
jobs = jip.create_jobs(p)
# iterate the executions and pass the session so all jobs are stored
for e in jip.create_executions(jobs, save=True):
jip.submit_job(e.job, save=True, cluster=c)
# sleep for a second to give the job time to start
time.sleep(0.1)
# cancel the job
print jobs, jobs[0].id
job = jip.db.get(1)
jip.jobs.cancel(job, cluster=c, save=True)
c.wait()
# and we should have one job in Failed state in our database
# we do the query with a fresh session though
job_1 = jip.db.get(1)
job_2 = jip.db.get(2)
# print the log files
print ">>>JOB 1 STD ERR LOG"
print open(c.resolve_log(job, job_1.stderr)).read()
print ">>>JOB 1 STD OUT LOG"
print open(c.resolve_log(job, job_1.stdout)).read()
assert job_1.state == jip.db.STATE_CANCELED
assert job_2.state == jip.db.STATE_CANCELED
def test_single_job_master_termination(tmpdir):
tmpdir = str(tmpdir)
db_file = os.path.join(tmpdir, "test.db")
# create a JIP database and a session
jip.db.init(db_file)
session = jip.db.create_session()
# create the cluster instance
c = cl.LocalCluster()
# create the pipeline
p = jip.Pipeline()
p.job(dir=tmpdir).bash('sleep 30')
p.context(locals())
# create the jobs
jobs = jip.create_jobs(p)
# iterate the executions and pass the session so all jobs are stored
for e in jip.create_executions(jobs, save=True):
jip.submit_job(e.job, save=True, cluster=c)
# sleep for a second to give the job time to start
time.sleep(1)
c.shutdown()
# and we should have one job in Failed state in our database
# we do the query with a fresh session though
job = jip.db.get(1)
# print the log files
print ">>>STD ERR LOG"
print open(c.resolve_log(job, job.stderr)).read()
print ">>>STD OUT LOG"
print open(c.resolve_log(job, job.stdout)).read()
assert job is not None
assert job.state == jip.db.STATE_FAILED
import jip
import os
import jip.grids as cl
from jip.db import Job
import sys
if __name__ == "__main__":
num_runs = 10 if len(sys.argv) == 1 else int(sys.argv[1])
db_file = os.path.abspath("test.db")
# create a JIP database and a session
jip.db.init(db_file)
session = jip.db.create_session()
# create the cluster instance
c = cl.LocalCluster()
# create the pipeline
for i in range(num_runs):
print("### CREATE RUN", i)
target_file = "result.%d" % i
p = jip.Pipeline()
a = p.bash('echo "hello world" > ${outfile}; sleep 1',
outfile="${target_file}.1.%d" % i)
b = p.bash('wc -w ${input}; sleep 1',
input=a, output="${target_file}.2.%d" % i)
l = p.bash('echo "Other" > ${outfile}; sleep 1',
outfile="${target_file}.3.%d" % i)
p.context(locals())