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)
def all_sample_query():
"""Provide a query with all current samples
Returns:
Query: All samples
"""
sesh = dal.Session()
return sesh.query(Sample).all()
def test_get_or_add_software_row_new(self):
session = dal.Session()
name = fake.last_name()
version = fake.first_name()
row = get_or_add_software_row(session, name, version)
assert row.name == name
assert row.version == version
print(row)
def test_check_software_version_exists(self,sample):
session = dal.Session()
rows = session.query(Software).all()
#for r in rows:
# print(r)
name = rows[0].name
version = rows[0].version
print()
print(f"name: {name}")
print(f"version: {version}")
row = check_software_version(session, name, version)
print(row)
assert row.name == name
assert row.version == version
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_prop__uses_helium_query(self, sample, all_sample_query):
sesh = dal.Session()
query = sesh.query(Recipe.uses_helium).all()
for r in query:
print(r)
def test_prop__carbon_source_query(self, sample, all_sample_query):
sesh = dal.Session()
query = sesh.query(Recipe.carbon_source).all()
for r in query:
print(r)
def test_prop__average_carbon_flow_rate_query(self, sample,
all_sample_query):
sesh = dal.Session()
query = sesh.query(Recipe.average_carbon_flow_rate).all()
for r in query:
print(r)
def test_prop__maximum_pressure_query(self, sample):
sesh = dal.Session()
query = sesh.query(Recipe.maximum_pressure).all()
for r in query:
print(r)
def test_check_software_version_none(self,sample):
row = check_software_version(dal.Session(), 'testsoft', '0.0.1')
assert row==None
