def setUp(self):
import tempfile
self.root_dir = tempfile.mkdtemp()
self.factory = JobFactory(root_dir=self.root_dir,
submit_url='http://localhost:9998/job',
)
# fill user db
transaction.begin()
engine = create_engine('sqlite:///:memory:')
mu.DBSession.configure(bind=engine)
mu.Base.metadata.create_all(engine) # @UndefinedVariable
mu.DBSession().add(mu.User(u'bob', u'Bob', u'*****@*****.**'))
jobid = uuid.UUID('3ad25048-26f6-11e1-851e-00012e260790')
mu.DBSession().add(mu.JobMeta(jobid, owner=u'bob'))
def setUp(self):
self.command = MagmaCommand()
init_user_db()
self.command.job_factory = JobFactory('/dev/null')
class JobFactoryTestCase(unittest.TestCase):
def setUp(self):
import tempfile
self.root_dir = tempfile.mkdtemp()
self.factory = JobFactory(root_dir=self.root_dir,
submit_url='http://localhost:9998/job',
)
# fill user db
transaction.begin()
engine = create_engine('sqlite:///:memory:')
mu.DBSession.configure(bind=engine)
mu.Base.metadata.create_all(engine) # @UndefinedVariable
mu.DBSession().add(mu.User(u'bob', u'Bob', u'*****@*****.**'))
jobid = uuid.UUID('3ad25048-26f6-11e1-851e-00012e260790')
mu.DBSession().add(mu.JobMeta(jobid, owner=u'bob'))
def tearDown(self):
import shutil
shutil.rmtree(self.root_dir)
mu.DBSession.remove()
def test_hasrootdir(self):
self.assertEqual(self.factory.root_dir, self.root_dir)
def test_id2url(self):
jobid = uuid.UUID('3ad25048-26f6-11e1-851e-00012e260790')
jobdbfn = 'sqlite:///'
jobdbfn += os.path.join(self.root_dir, str(jobid), 'results.db')
self.assertEqual(self.factory.id2url(jobid), jobdbfn)
def test_id2jobdir(self):
jobid = uuid.UUID('3ad25048-26f6-11e1-851e-00012e260790')
jobdir = os.path.join(self.root_dir, str(jobid))
self.assertEqual(self.factory.id2jobdir(jobid), jobdir)
def test_id2db(self):
jobid = uuid.UUID('3ad25048-26f6-11e1-851e-00012e260790')
jobdbfn = os.path.join(self.root_dir, str(jobid), 'results.db')
self.assertEqual(self.factory.id2db(jobid), jobdbfn)
def test_fromdb(self):
# mock/stub private methods which do external calls
self.factory._makeJobDir = Mock(return_value='/mydir')
self.factory._copyFile = Mock()
self.factory._makeJobSession = Mock(return_value=initTestingDB())
dbfile = os.tmpfile()
job = self.factory.fromDb(dbfile, u'bob')
self.assertIsInstance(job.id, uuid.UUID)
self.assertEqual(job.dir, u'/mydir')
self.assertEqual(job.meta.owner, u'bob')
self.assertEqual(job.meta.description, u'My first description')
self.assertEqual(job.meta.ms_filename, u'F123456.mzxml')
self.assertEqual(job.meta.state, u'STOPPED')
self.factory._makeJobDir.assert_called_with(job.id)
self.factory._copyFile.assert_called_with(dbfile, job.id)
o = mu.DBSession().query(mu.JobMeta.owner
).filter(mu.JobMeta.jobid == job.id).scalar()
self.assertEqual(o, u'bob', 'job meta has been inserted')
def test_fromid(self):
jobid = uuid.UUID('3ad25048-26f6-11e1-851e-00012e260790')
self.factory._makeJobSession = Mock(return_value=456)
self.factory.id2jobdir = Mock(return_value=789)
job = self.factory.fromId(jobid)
self.assertEqual(job.owner, u'bob')
self.assertEqual(job.db.session, 456)
self.assertEqual(job.dir, 789)
self.factory._makeJobSession.assert_called_with(jobid)
self.factory.id2jobdir.assert_called_with(jobid)
def test_fromid_notfoundindb(self):
jobid = uuid.UUID('11111111-1111-1111-1111-111111111111')
self.factory._makeJobSession = Mock()
self.factory.id2jobdir = Mock()
with self.assertRaises(JobNotFound) as exc:
self.factory.fromId(jobid)
self.assertEqual(exc.exception.jobid, jobid)
self.assertEqual(exc.exception.message, "Job not found in database")
def test_fromid_notfoundasdb(self):
jobid = uuid.UUID('11111111-1111-1111-1111-111111111111')
self.factory._getJobMeta = Mock(mu.JobMeta)
with self.assertRaises(JobNotFound) as exc:
self.factory.fromId(jobid)
self.assertEqual(exc.exception.jobid, jobid)
self.assertEqual(exc.exception.message, "Data of job not found")
def test_submitQuery(self):
self.factory.init_script = "# make magma available"
job = self.factory.fromScratch(u'bob')
self.factory.script_fn = 'script.sh'
cmd = "magma add_structures -t smiles structures.dat results.db\n"
jobquery = JobQuery(job.dir, cmd, ['structures.dat'])
status_cb_url = 'http://example.com/status/{}.json'.format(job.id)
jobquery.status_callback_url = status_cb_url
launcher_url = 'http://*****:*****@patch('requests.post')
def test_submitJob2Launcher(self, ua):
from requests import Response
create_url = 'http://*****:*****@patch('requests.delete')
def test_cancel(self, ua):
job = self.factory.fromScratch(u'ed')
url = 'http://*****:*****@patch('os.stat')
def test_dbSize(self, stat):
class Mystat(object):
st_size = 1234
mystat = Mystat()
stat.return_value = mystat
jobid = uuid.UUID('11111111-1111-1111-1111-111111111111')
result = self.factory.dbSize(jobid)
self.assertEqual(result, 1234)
@patch('os.stat')
def test_dbSize_noresultdbfile(self, stat):
stat.side_effect = OSError()
jobid = uuid.UUID('11111111-1111-1111-1111-111111111111')
result = self.factory.dbSize(jobid)
self.assertEqual(result, 0)
