def test_dependency():
# Job 2 depends on job 1,
# so job 1 must run first.
global ran1
ran1 = False
global ran2
ran2 = False
class Job1(Job):
def run(self):
global ran1
ran1 = True
class Job2(Job):
def run(self):
ok_(ran1)
global ran2
ran2 = True
j1 = Job1('job1')
j2 = Job2('job2', [j1])
q = Queue(1)
q.put(j2)
q.put(j1)
q.run()
ok_(ran2)
def test_queue():
q = Queue(2)
jobs = []
for i in range(4):
job = TestJob()
q.put(job)
jobs.append(job)
q.run()
for job in jobs:
ok_(job.test_done)
root.addHandler(sh)
root.addHandler(handler)
sh.setLevel(logging.DEBUG)
handler.setLevel(logging.INFO)
root.setLevel(logging.DEBUG)
_log = logging.getLogger(__name__)
if __name__ == "__main__":
lock_path = settings['LOCKFILE']
_log.debug("waiting for lock on %s" % lock_path)
with FileLock(lock_path) as lock:
_log.debug("lock acquired")
queue = Queue(settings["NTHREADS"])
# 1. Download external data.
# 2. Schedule jobs that work with downloaded data.
# 3. run whynot & mrs when all data files have been
# generated/downloaded.
pdb_job = FetchPdbJob()
uniprot_job = FetchUniprotJob()
mmcif_job = FetchMmcifJob()
sf_job = FetchStructureFactorsJob()
pdbredo_job = FetchPdbredoJob()
nmr_job = FetchNmrJob()
queue.put(uniprot_job)
queue.put(pdb_job)
queue.put(mmcif_job)
queue.put(nmr_job)
os.path.join(hssp3_dir, filename)
for filename in os.listdir(hssp3_dir)
]
hghssp_dir = os.path.join(settings['DATADIR'], 'hg-hssp')
hghssp_paths = [
os.path.join(hghssp_dir, filename)
for filename in os.listdir(hghssp_dir)
]
# Oldest files go first:
for path in sorted(hssp3_paths + hghssp_paths, key=os.path.getmtime):
# Not the ones with 9999 hits:
try:
if count_hits(path) >= 9999:
if path.startswith(hssp3_dir):
pdbid = os.path.basename(path).split('.')[0]
self._queue.put(HsspJob(pdbid))
elif path.startswith(hghssp_dir):
seq_id = os.path.basename(path).split('.')[0]
self._queue.put(HgHsspJob(seq_id))
except:
continue
if __name__ == "__main__":
q = Queue(12)
q.put(HsspScheduleJob(q))
q.run()
def test_empty_queue():
q = Queue(2)
q.run()
def test_mmcif_data_dependency():
global uniprot_job
uniprot_job = FetchUniprotJob()
global mmcif_job
mmcif_job = FetchMmcifJob()
global pdb_job
pdb_job = FetchPdbJob()
class TestScheduleMmcifDataJob(ScheduleMmcifDataJob):
def run(self):
global uniprot_job
ok_(uniprot_job.done)
global mmcif_job
ok_(mmcif_job.done)
global pdb_job
ok_(pdb_job.done)
ScheduleMmcifDataJob.run(self)
queue = Queue(32)
data_job = TestScheduleMmcifDataJob(queue, mmcif_job, pdb_job, uniprot_job)
queue.put(data_job)
queue.put(uniprot_job)
queue.put(mmcif_job)
queue.put(pdb_job)
queue.run()
ok_(data_job.done)