def test_fetch_uppnexid(self, dbmock):
""" A SampleDeliverer should be able to fetch the Uppnex ID for the
project
"""
# if an uppnexid is given in the configuration, it should be used and the database should not be queried
deliverer = deliver.SampleDeliverer(
self.projectid,
self.sampleid,
rootdir=self.casedir,
uppnexid="this-is-the-uppnexid",
**SAMPLECFG['deliver'])
self.assertEquals(deliverer.uppnexid, "this-is-the-uppnexid")
#called once due to projectname
dbmock.assert_called_once_with(self.projectid)
# if an uppnexid is not supplied in the config, the database should be consulted
dbmock.reset_mock()
prior = dbmock.call_count
deliverer = deliver.SampleDeliverer(
self.projectid,
self.sampleid,
rootdir=self.casedir,
**SAMPLECFG['deliver'])
self.assertEquals(deliverer.uppnexid, PROJECTENTRY['uppnex_id'])
#two calls, one for projectname one for uppnexid
self.assertEquals(dbmock.call_count, 2)
def setUp(self):
with mock.patch.object(deliver.db, 'dbcon', autospec=db.CharonSession):
self.casedir = tempfile.mkdtemp(prefix="case_", dir=self.rootdir)
self.projectid = 'NGIU-P001'
self.sampleid = 'NGIU-S001'
self.deliverer = deliver.SampleDeliverer(self.projectid,
self.sampleid,
rootdir=self.casedir,
**SAMPLECFG['deliver'])
def test_fetch_uppnexid(self, dbmock):
""" A SampleDeliverer should be able to fetch the Uppnex ID for the
project
"""
# if an uppnexid is given in the configuration, it should be used and the database should not be queried
deliverer = deliver.SampleDeliverer(self.projectid,
self.sampleid,
rootdir=self.casedir,
uppnexid="this-is-the-uppnexid",
**SAMPLECFG['deliver'])
self.assertEquals(deliverer.uppnexid, "this-is-the-uppnexid")
self.assertFalse(dbmock.called,
"the database should not have been queried")
# if an uppnexid is not supplied in the config, the database should be consulted
deliverer = deliver.SampleDeliverer(self.projectid,
self.sampleid,
rootdir=self.casedir,
**SAMPLECFG['deliver'])
self.assertEquals(deliverer.uppnexid, PROJECTENTRY['uppnex_id'])
dbmock.assert_called_once_with(self.projectid)
def sample(ctx, projectid, sampleid):
""" Deliver the specified sample to the specified destination
"""
for sid in sampleid:
if not ctx.parent.params['cluster']: # Soft stage case
d = _deliver.SampleDeliverer(projectid, sid, **ctx.parent.params)
elif ctx.parent.params['cluster'] == 'grus':
logger.error(
"When delivering to grus only project can be specified, not sample"
)
return 1
elif ctx.parent.params['cluster'] == 'dds':
logger.error(
"When delivering with DDS only project can be specified, not sample"
)
return 1
_exec_fn(d, d.deliver_sample)