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 test_add_optical_image(self, fill_db, sm_config, ds_config):
db = DB(sm_config['db'])
action_queue_mock = MagicMock(spec=QueuePublisher)
es_mock = MagicMock(spec=ESExporter)
img_store_mock = MagicMock(ImageStoreServiceWrapper)
img_store_mock.post_image.side_effect = [
'opt_img_id1', 'opt_img_id2', 'opt_img_id3', 'thumbnail_id'
]
img_store_mock.get_image_by_id.return_value = Image.new(
'RGB', (100, 100))
ds_man = create_ds_man(sm_config=sm_config,
db=db,
es=es_mock,
img_store=img_store_mock,
action_queue=action_queue_mock,
sm_api=True)
ds_man._annotation_image_shape = MagicMock(return_value=(100, 100))
ds_id = '2000-01-01'
ds = create_ds(ds_id=ds_id, ds_config=ds_config)
zoom_levels = [1, 2, 3]
raw_img_id = 'raw_opt_img_id'
ds_man.add_optical_image(ds,
raw_img_id, [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
zoom_levels=zoom_levels)
assert db.select('SELECT * FROM optical_image') == [
('opt_img_id{}'.format(i + 1), ds.id, zoom)
for i, zoom in enumerate(zoom_levels)
]
assert db.select('SELECT optical_image FROM dataset where id = %s',
params=(ds_id, )) == [(raw_img_id, )]
assert db.select('SELECT thumbnail FROM dataset where id = %s',
params=(ds_id, )) == [('thumbnail_id', )]
def fill_db(test_db, sm_config, ds_config):
upload_dt = '2000-01-01 00:00:00'
ds_id = '2000-01-01'
meta = {'Data_Type': 'Imaging MS'}
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)])
def fill_db(test_db, sm_config, ds_config):
upload_dt = '2000-01-01 00:00:00'
ds_id = '2000-01-01'
meta = {'Data_Type': 'Imaging MS'}
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'])])
def fill_db(test_db, sm_config, ds_config):
upload_dt = '2000-01-01 00:00:00'
ds_id = '2000-01-01'
metadata = {"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(metadata), json.dumps(ds_config), DatasetStatus.FINISHED,
True, ['HMDB-v4'], ['+H', '+Na', '+K'])])
def create_ds_man(sm_config,
db=None,
es=None,
img_store=None,
action_queue=None,
status_queue=None,
sm_api=False):
db = db or DB(sm_config['db'])
es_mock = es or MagicMock(spec=ESExporter)
action_queue_mock = action_queue or MagicMock(QueuePublisher)
status_queue_mock = status_queue or MagicMock(QueuePublisher)
img_store_mock = img_store or MagicMock(spec=ImageStoreServiceWrapper)
if sm_api:
return SMapiDatasetManager(db=db,
es=es_mock,
mode='queue',
image_store=img_store_mock,
action_queue=action_queue_mock,
status_queue=status_queue_mock)
else:
return SMDaemonDatasetManager(db=db,
es=es_mock,
img_store=img_store_mock,
mode=None,
status_queue=status_queue_mock)
def reindex_results(ds_id, ds_mask):
assert ds_id or ds_mask
conf = SMConfig.get_conf()
if ds_mask == '_all_':
_reindex_all(conf)
else:
db = DB(conf['db'])
es_exp = ESExporter(db)
if ds_id:
rows = db.select("select id, name, config from dataset where id = '{}'".format(ds_id))
elif ds_mask:
rows = db.select("select id, name, config from dataset where name like '{}%'".format(ds_mask))
else:
rows = []
_reindex_datasets(rows, es_exp)
def test_delete_ds(self, fill_db, sm_config, ds_config):
db = DB(sm_config['db'])
action_queue_mock = MagicMock(spec=QueuePublisher)
es_mock = MagicMock(spec=ESExporter)
img_store_service_mock = MagicMock(spec=ImageStoreServiceWrapper)
ds_man = create_ds_man(sm_config, db=db, es=es_mock, img_store=img_store_service_mock,
action_queue=action_queue_mock, sm_api=False)
ds_id = '2000-01-01'
ds = create_ds(ds_id=ds_id, ds_config=ds_config)
ds_man.delete(ds)
ids = ['iso_image_{}_id'.format(id) for id in range(1, 3)]
img_store_service_mock.delete_image_by_id.assert_has_calls(
[call('fs', 'iso_image', ids[0]), call('fs', 'iso_image', ids[1])])
es_mock.delete_ds.assert_called_with(ds_id)
assert db.select_one('SELECT * FROM dataset WHERE id = %s', params=(ds_id,)) == []
def _reindex_all(conf):
es_config = conf['elasticsearch']
alias = es_config['index']
es_man = ESIndexManager(es_config)
new_index = es_man.another_index_name(es_man.internal_index_name(alias))
es_man.create_index(new_index)
try:
tmp_es_config = deepcopy(es_config)
tmp_es_config['index'] = new_index
db = DB(conf['db'])
es_exp = ESExporter(db, tmp_es_config)
rows = db.select('select id, name, config from dataset')
_reindex_datasets(rows, es_exp)
es_man.remap_alias(tmp_es_config['index'], alias=alias)
except Exception as e:
es_man.delete_index(new_index)
raise e
def _reindex_all(conf):
es_config = conf['elasticsearch']
alias = es_config['index']
es_man = ESIndexManager(es_config)
new_index = es_man.another_index_name(es_man.internal_index_name(alias))
es_man.create_index(new_index)
try:
tmp_es_config = deepcopy(es_config)
tmp_es_config['index'] = new_index
db = DB(conf['db'])
es_exp = ESExporter(db, tmp_es_config)
rows = db.select('select id, name, config from dataset')
_reindex_datasets(rows, es_exp)
es_man.remap_alias(tmp_es_config['index'], alias=alias)
except Exception as e:
es_man.delete_index(new_index)
raise e
def test_dataset_load_existing_ds_works(fill_db, sm_config, ds_config):
db = DB(sm_config['db'])
upload_dt = datetime.strptime('2000-01-01 00:00:00', "%Y-%m-%d %H:%M:%S")
ds_id = '2000-01-01'
meta = {"meta": "data"}
ds = Dataset.load(db, ds_id)
assert (ds.id == ds_id and ds.name == 'ds_name'
and ds.input_path == 'input_path' and ds.upload_dt == upload_dt
and ds.meta == meta and ds.config == ds_config
and ds.status == DatasetStatus.FINISHED)
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 reindex_results(ds_id, ds_mask):
assert ds_id or ds_mask
conf = SMConfig.get_conf()
if ds_mask == '_all_':
_reindex_all(conf)
else:
db = DB(conf['db'])
es_exp = ESExporter(db)
if ds_id:
rows = db.select(
"select id, name, config from dataset where id = '{}'".format(
ds_id))
elif ds_mask:
rows = db.select(
"select id, name, config from dataset where name like '{}%'".
format(ds_mask))
else:
rows = []
_reindex_datasets(rows, es_exp)
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()
def test_add_optical_image(self, fill_db, sm_config, ds_config):
db = DB(sm_config['db'])
action_queue_mock = MagicMock(spec=QueuePublisher)
es_mock = MagicMock(spec=ESExporter)
img_store_mock = MagicMock(ImageStoreServiceWrapper)
img_store_mock.post_image.side_effect = ['opt_img_id1', 'opt_img_id2', 'opt_img_id3', 'thumbnail_id']
img_store_mock.get_image_by_id.return_value = Image.new('RGB', (100, 100))
ds_man = create_ds_man(sm_config=sm_config, db=db, es=es_mock,
img_store=img_store_mock, action_queue=action_queue_mock, sm_api=True)
ds_man._annotation_image_shape = MagicMock(return_value=(100, 100))
ds_id = '2000-01-01'
ds = create_ds(ds_id=ds_id, ds_config=ds_config)
zoom_levels = [1, 2, 3]
raw_img_id = 'raw_opt_img_id'
ds_man.add_optical_image(ds, raw_img_id, [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
zoom_levels=zoom_levels)
assert db.select('SELECT * FROM optical_image') == [
('opt_img_id{}'.format(i + 1), ds.id, zoom)
for i, zoom in enumerate(zoom_levels)]
assert db.select('SELECT optical_image FROM dataset where id = %s', params=(ds_id,)) == [(raw_img_id,)]
assert db.select('SELECT thumbnail FROM dataset where id = %s', params=(ds_id,)) == [('thumbnail_id',)]
def test_delete_ds(self, fill_db, sm_config, ds_config):
db = DB(sm_config['db'])
action_queue_mock = MagicMock(spec=QueuePublisher)
es_mock = MagicMock(spec=ESExporter)
img_store_service_mock = MagicMock(spec=ImageStoreServiceWrapper)
ds_man = create_ds_man(sm_config,
db=db,
es=es_mock,
img_store=img_store_service_mock,
action_queue=action_queue_mock,
sm_api=False)
ds_id = '2000-01-01'
ds = create_ds(ds_id=ds_id, ds_config=ds_config)
ds_man.delete(ds)
ids = ['iso_image_{}_id'.format(id) for id in range(1, 3)]
img_store_service_mock.delete_image_by_id.assert_has_calls(
[call('fs', 'iso_image', ids[0]),
call('fs', 'iso_image', ids[1])])
es_mock.delete_ds.assert_called_with(ds_id)
assert db.select_one('SELECT * FROM dataset WHERE id = %s',
params=(ds_id, )) == []
def create_api_ds_man(db=None,
es=None,
img_store=None,
action_queue=None,
sm_config=None):
db = db or DB(sm_config['db'])
es = es or ESExporter(db)
img_store = img_store or MagicMock(spec=ImageStoreServiceWrapper)
action_queue = action_queue or QueuePublisher(sm_config['rabbitmq'],
ACTION_QDESC)
action_queue.queue_args = {'x-max-priority': 3}
return SMapiDatasetManager(db=db,
es=es,
image_store=img_store,
mode='queue',
action_queue=action_queue)
def test_dataset_save_overwrite_ds_works(fill_db, sm_config, ds_config):
db = DB(sm_config['db'])
es_mock = MagicMock(spec=ESExporter)
status_queue_mock = MagicMock(spec=QueuePublisher)
upload_dt = datetime.now()
ds_id = '2000-01-01'
ds = Dataset(ds_id, 'ds_name', 'input_path', upload_dt, {}, ds_config)
ds.save(db, es_mock, status_queue_mock)
assert ds == Dataset.load(db, ds_id)
es_mock.sync_dataset.assert_called_once_with(ds_id)
status_queue_mock.publish.assert_called_with({
'ds_id': ds_id,
'status': DatasetStatus.NEW
})
def test_dataset_update_status_works(fill_db, sm_config, ds_config):
db = DB(sm_config['db'])
es_mock = MagicMock(spec=ESExporter)
status_queue_mock = MagicMock(spec=QueuePublisher)
upload_dt = datetime.now()
ds_id = '2000-01-01'
ds = Dataset(ds_id, 'ds_name', 'input_path', upload_dt, {}, ds_config,
DatasetStatus.INDEXING)
ds.set_status(db, es_mock, status_queue_mock, DatasetStatus.FINISHED)
assert DatasetStatus.FINISHED == Dataset.load(db, ds_id).status
status_queue_mock.publish.assert_called_once_with({
'ds_id':
ds_id,
'status':
DatasetStatus.FINISHED
})
def _fetch_ds_metadata(self, ds_id):
db = DB(SMConfig.get_conf()['db'])
res = db.select_one('SELECT name, metadata FROM dataset WHERE id = %s', params=(ds_id,))
return res or ('', {})
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()
from sm.engine.search_job import SearchJob
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='SM process dataset at a remote spark location.')
parser.add_argument('--ds-id', dest='ds_id', type=str, help='Dataset id')
parser.add_argument('--ds-name', dest='ds_name', type=str, help='Dataset name')
parser.add_argument('--input-path', type=str, help='Path to a dataset location')
parser.add_argument('--no-clean', dest='no_clean', action='store_true',
help="Don't clean dataset txt files after job is finished")
parser.add_argument('--config', dest='sm_config_path', default='conf/config.json',
type=str, help='SM config path')
args = parser.parse_args()
SMConfig.set_path(args.sm_config_path)
sm_config = SMConfig.get_conf()
init_loggers(sm_config['logs'])
db = DB(sm_config['db'])
img_store = ImageStoreServiceWrapper(sm_config['services']['img_service_url'])
ds_man = SMDaemonDatasetManager(db, ESExporter(db), img_store, mode='local')
try:
ds = create_ds_from_files(args.ds_id, args.ds_name, args.input_path)
ds_man.add(ds, SearchJob, del_first=True)
except Exception as e:
logging.getLogger('engine').error(e)
sys.exit(1)
sys.exit()
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 set_metadata_thumbnail(db, config, ds_name):
ds_thumb_query = 'SELECT id, transform, thumbnail from dataset {}'.format('WHERE name = %s' if ds_name != ALL_DS_MASK else '')
for id, transform, thumbnail in db.select(ds_thumb_query, params=(ds_name,) if ds_name else None):
if transform != None:
ds = api.Dataset.load(db=db, ds_id=id)
img_store = ImageStoreServiceWrapper(config['services']['img_service_url'])
img_store.storage_type = 'fs'
sm = SMapiDatasetManager(db=db, es=ESExporter(db), image_store=img_store, mode='queue')
ds_opt_img_query = 'SELECT optical_image from dataset {}'.format('WHERE id = %s')
img_id = db.select(ds_opt_img_query, params=(ds.id,))
sm._add_thumbnail_optical_image(ds, f"{img_id[0][0]}", transform)
SMConfig.set_path('conf/config.json')
sm_config = SMConfig.get_conf()
set_metadata_thumbnail(DB(sm_config['db']), sm_config, 'Untreated_3_434')
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Updates thumbnail for a provided dataset")
parser.add_argument('--ds-name', dest='ds_name', type=str, help="Process specific dataset given by its name")
parser.add_argument('--config', dest='sm_config_path', default='conf/config.json', type=str, help='SM config path')
args = parser.parse_args()
SMConfig.set_path(args.sm_config_path)
sm_config = SMConfig.get_conf()
db = DB(sm_config['db'])
if args.ds_name:
set_metadata_thumbnail(db, sm_config, args.ds_name)
else:
def _fetch_ds_metadata(self, ds_id):
db = DB(SMConfig.get_conf()['db'])
res = db.select_one('SELECT name, metadata FROM dataset WHERE id = %s',
params=(ds_id, ))
return res or ('', {})
def _create_db_conn():
config = SMConfig.get_conf()
return DB(config['db'])
