def sample():
"""Set up a set of samples for testing using the factory boy factories.
The sample factory cascades to all related tables.
"""
# create_all is already in test/database__init__.py.
# I don't know why I have to call it here again, but I do.
Base.metadata.create_all(bind=dal.engine)
# Add some data here
print("Hey, here come some samples...")
session = dal.Session()
samples = SampleFactory.create_batch(5)
for s in samples:
fids = [f.id for f in s.sem_files]
s.primary_sem_file_id = fids[random.randint(0, len(fids) - 1)]
for f in s.sem_files:
ids = [a.id for a in f.analyses]
lids = len(ids)
f.default_analysis_id = ids[random.randint(0, lids - 1)]
rs = RamanSet(sample_id=s.id, experiment_date=s.experiment_date)
session.add(rs)
session.flush()
for rf in s.raman_files:
rf.raman_spectrum.set_id = rs.id
session.commit()
SoftwareFactory.create_batch(5)
yield samples
# Drop and ditch
print("Tearing down test samples and DB")
with dal.session_scope(autocommit=True) as sess:
for s in sess.query(Sample).all():
sess.delete(s)
Base.metadata.drop_all(bind=dal.engine)
import os
from gresq.config import Config
from gresq.database import dal, Base
from gresq.database.models import Sample
import logging
logging.basicConfig(level=logging.DEBUG)
config_prefix = "DEV_DATABASE"
config_suffix = "_ADMIN"
conf = Config(prefix=config_prefix,
suffix=config_suffix,
debug=True,
try_secrets=False)
dal.init_db(conf, privileges={"read": True, "write": True, "validate": True})
with dal.session_scope(autocommit=True) as sess:
for s in sess.query(Sample).all():
sess.delete(s)
dal.Session().close()
#print(Base.metadata.tables)
ret = Base.metadata.drop_all(bind=dal.engine)
print(f"ret: {ret}")
def test_delete__1stsample_cascade(self, sample):
with dal.session_scope(autocommit=True) as sess:
smpl = sess.query(Sample).filter(Sample.id == 1).one()
assert smpl.id == 1
sess.delete(smpl)
print(sess.query(Sample.id).all()[0][0])
import os
from gresq.config import Config
from gresq.database import dal
from gresq.util.csv2db3 import build_db
import logging
logging.basicConfig(level=logging.DEBUG)
config_prefix = "DEV_DATABASE"
config_suffix = "_ADMIN"
conf = Config(prefix=config_prefix,
suffix=config_suffix,
debug=True,
try_secrets=False)
dal.init_db(conf, privileges={"read": True, "write": True, "validate": True})
BOX_CONFIG_PATH = os.environ["BOX_CONFIG_PATH"]
csv2db_file = os.path.join(os.getcwd(), "data", "SEM_Raman_Test")
with dal.session_scope() as session:
build_db(
session,
os.path.join(os.getcwd(), "data"),
csv2db_file,
box_config_path=BOX_CONFIG_PATH,
)