def test_add_ds(self, test_db, sm_config, ds_config):
action_queue_mock = MagicMock(spec=QueuePublisher)
es_mock = MagicMock(spec=ESExporter)
db = DB(sm_config['db'])
try:
ds_man = create_ds_man(sm_config,
db=db,
es=es_mock,
action_queue=action_queue_mock,
sm_api=False)
ds_id = '2000-01-01'
ds_name = 'ds_name'
input_path = 'input_path'
upload_dt = datetime.now()
metadata = {}
ds = create_ds(ds_id=ds_id,
ds_name=ds_name,
input_path=input_path,
upload_dt=upload_dt,
metadata=metadata,
ds_config=ds_config)
ds_man.add(ds, search_job_factory=self.SearchJob)
DS_SEL = 'select name, input_path, upload_dt, metadata, config from dataset where id=%s'
assert db.select_one(DS_SEL,
params=(ds_id, )) == (ds_name, input_path,
upload_dt, metadata,
ds_config)
finally:
db.close()
def fill_db(test_db, sm_config, ds_config):
upload_dt = '2000-01-01 00:00:00'
ds_id = '2000-01-01'
meta = {"meta": "data"}
db = DB(sm_config['db'])
db.insert('INSERT INTO dataset (id, name, input_path, upload_dt, metadata, config, '
'status, is_public, mol_dbs, adducts) values (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s)',
rows=[(ds_id, 'ds_name', 'input_path', upload_dt,
json.dumps(meta), json.dumps(ds_config), DatasetStatus.FINISHED,
True, ['HMDB-v4'], ['+H'])])
db.insert("INSERT INTO job (id, db_id, ds_id) VALUES (%s, %s, %s)",
rows=[(0, 0, ds_id)])
db.insert("INSERT INTO sum_formula (id, db_id, sf) VALUES (%s, %s, %s)",
rows=[(1, 0, 'H2O')])
db.insert(("INSERT INTO iso_image_metrics (job_id, db_id, sf, adduct, iso_image_ids) "
"VALUES (%s, %s, %s, %s, %s)"),
rows=[(0, 0, 'H2O', '+H', ['iso_image_1_id', 'iso_image_2_id'])])
db.close()
def fill_db(test_db, sm_config, ds_config):
upload_dt = '2000-01-01 00:00:00'
ds_id = '2000-01-01'
meta = {"meta": "data"}
db = DB(sm_config['db'])
db.insert('INSERT INTO dataset values (%s, %s, %s, %s, %s, %s, %s)',
rows=[(ds_id, 'ds_name',
'input_path', upload_dt, json.dumps(meta),
json.dumps(ds_config), DatasetStatus.FINISHED)])
db.insert("INSERT INTO job (id, db_id, ds_id) VALUES (%s, %s, %s)",
rows=[(0, 0, ds_id)])
db.insert("INSERT INTO sum_formula (id, db_id, sf) VALUES (%s, %s, %s)",
rows=[(1, 0, 'H2O')])
db.insert((
"INSERT INTO iso_image_metrics (job_id, db_id, sf, adduct, iso_image_ids) "
"VALUES (%s, %s, %s, %s, %s)"),
rows=[(0, 0, 'H2O', '+H', ['iso_image_1_id', 'iso_image_2_id'])])
db.close()
def test_add_ds(self, test_db, sm_config, ds_config):
action_queue_mock = MagicMock(spec=QueuePublisher)
es_mock = MagicMock(spec=ESExporter)
db = DB(sm_config['db'])
try:
ds_man = create_ds_man(sm_config, db=db, es=es_mock, action_queue=action_queue_mock, sm_api=False)
ds_id = '2000-01-01'
ds_name = 'ds_name'
input_path = 'input_path'
upload_dt = datetime.now()
metadata = {}
ds = create_ds(ds_id=ds_id, ds_name=ds_name, input_path=input_path, upload_dt=upload_dt,
metadata=metadata, ds_config=ds_config)
ds_man.add(ds, search_job_factory=self.SearchJob)
DS_SEL = 'select name, input_path, upload_dt, metadata, config from dataset where id=%s'
assert db.select_one(DS_SEL, params=(ds_id,)) == (ds_name, input_path, upload_dt, metadata, ds_config)
finally:
db.close()
def _callback(self, msg):
log_msg = " SM daemon received a message: {}".format(msg)
logger.info(log_msg)
self._post_to_slack('new', " [v] Received: {}".format(json.dumps(msg)))
db = DB(self._sm_config['db'])
try:
ds_man = self._dataset_manager_factory(
db=db, es=ESExporter(db),
img_store=ImageStoreServiceWrapper(self._sm_config['services']['img_service_url']),
mode='queue',
status_queue=QueuePublisher(config=self._sm_config['rabbitmq'],
qdesc=SM_DS_STATUS,
logger=logger)
)
ds_man.process(ds=Dataset.load(db, msg['ds_id']),
action=msg['action'],
search_job_factory=SearchJob,
del_first=msg.get('del_first', False))
finally:
if db:
db.close()
def _callback(self, msg):
log_msg = " SM daemon received a message: {}".format(msg)
logger.info(log_msg)
self._post_to_slack('new', " [v] Received: {}".format(json.dumps(msg)))
db = DB(self._sm_config['db'])
try:
ds_man = self._dataset_manager_factory(
db=db,
es=ESExporter(db),
img_store=ImageStoreServiceWrapper(
self._sm_config['services']['img_service_url']),
mode='queue',
status_queue=QueuePublisher(config=self._sm_config['rabbitmq'],
qdesc=SM_DS_STATUS,
logger=logger))
ds_man.process(ds=Dataset.load(db, msg['ds_id']),
action=msg['action'],
search_job_factory=SearchJob,
del_first=msg.get('del_first', False))
finally:
if db:
db.close()