def test_persist_with_location(self, nested_session, tube_rack_fac,
barcoded_location_c127s8):
tr = tube_rack_fac()
tr.location = barcoded_location_c127s8
kw = tube_rack_fac.init_kw.copy()
kw['location'] = barcoded_location_c127s8
persist(nested_session, tr, kw, True)
def test_persist_all_attributes(
self, request, nested_session, iso_fac_name, iso_job_fac,
iso_stock_rack_fac, iso_sector_stock_rack_fac,
iso_preparation_plate_fac, iso_plate1, iso_plate2, iso_plate3,
iso_aliquot_plate_fac, iso_sector_preparation_plate_fac,
rack_layout_fac):
iso_fac = request.getfuncargvalue(iso_fac_name)
rl1 = rack_layout_fac.new()
iso = iso_fac(rack_layout=rl1)
iso_job = iso_job_fac(isos=[iso])
assert iso.iso_job.label == iso_job.label
kw = iso_fac.init_kw
kw['rack_layout'] = rl1
iso_stock_rack = iso_stock_rack_fac(iso=iso,
rack_layout=rack_layout_fac.new())
assert len(iso.iso_stock_racks) == 1
kw['iso_stock_racks'] = [iso_stock_rack]
iso_sector_stock_rack = iso_sector_stock_rack_fac(
iso=iso, rack_layout=rack_layout_fac.new())
assert len(iso.iso_sector_stock_racks) == 1
kw['iso_sector_stock_racks'] = [iso_sector_stock_rack]
iso_preparation_plate = iso_preparation_plate_fac(
iso=iso, rack=iso_plate1, rack_layout=rack_layout_fac.new())
assert len(iso.iso_preparation_plates) == 1
kw['iso_preparation_plates'] = [iso_preparation_plate]
iso_aliquot_plate = iso_aliquot_plate_fac(iso=iso, rack=iso_plate2)
assert len(iso.iso_aliquot_plates) == 1
kw['iso_aliquot_plates'] = [iso_aliquot_plate]
if iso_fac_name == 'stock_sample_creation_iso_fac':
iso_sector_prep_plate = iso_sector_preparation_plate_fac(
iso=iso, rack=iso_plate3, rack_layout=rack_layout_fac.new())
assert len(iso.iso_sector_preparation_plates) == 1
kw['iso_sector_preparation_plates'] = [iso_sector_prep_plate]
persist(nested_session, iso, kw, True)
def test_persist(self, request, nested_session, fac_name):
fac = request.getfuncargvalue(fac_name)
md = fac()
# The attribute check fails occasionally for molecules with more than
# one chemical structure because the structures are kept in a list
# and the retrieval order is undefined.
persist(nested_session, md, fac.init_kw, False)
def test_persist(self, nested_session, worklist_series_fac,
planned_worklist_fac):
ws = worklist_series_fac()
pwl = planned_worklist_fac()
ws.add_worklist(0, pwl)
attrs = dict(planned_worklists=[pwl])
persist(nested_session, ws, attrs, True)
def test_persist(self, request, nested_session,
planned_liquid_transfer_fac_name):
planned_liquid_transfer_fac = \
request.getfuncargvalue(planned_liquid_transfer_fac_name)
plt = planned_liquid_transfer_fac()
persist(nested_session, plt, planned_liquid_transfer_fac.init_kw,
True)
def test_persist(self, nested_session, worklist_series_fac,
planned_worklist_fac):
ws = worklist_series_fac()
pwl = planned_worklist_fac()
ws.add_worklist(0, pwl)
attrs = dict(planned_worklists=[pwl])
persist(nested_session, ws, attrs, True)
def test_persist(self, request, nested_session, fac_name):
fac = request.getfuncargvalue(fac_name)
md = fac()
# The attribute check fails occasionally for molecules with more than
# one chemical structure because the structures are kept in a list
# and the retrieval order is undefined.
persist(nested_session, md, fac.init_kw, False)
def test_persist(self, nested_session, experiment_fac, experiment_job_fac):
exp = experiment_fac()
# FIXME: Working around the circular dependency of experiment and
# experiment job here.
exp_job = experiment_job_fac(experiments=[exp])
kw = experiment_fac.init_kw
kw['job'] = exp.job
exp.job = exp_job
persist(nested_session, exp, kw, True)
def test_persist(self, nested_session, experiment_fac,
experiment_job_fac):
exp = experiment_fac()
# FIXME: Working around the circular dependency of experiment and
# experiment job here.
exp_job = experiment_job_fac(experiments=[exp])
kw = experiment_fac.init_kw
kw['job'] = exp.job
exp.job = exp_job
persist(nested_session, exp, kw, True)
def test_persist(self, nested_session,
stock_sample_creation_iso_request_fac,
molecule_design_library_fac):
ssir1 = stock_sample_creation_iso_request_fac()
persist(nested_session, ssir1,
stock_sample_creation_iso_request_fac.init_kw, True)
kw = stock_sample_creation_iso_request_fac.init_kw
kw['molecule_design_library'] = molecule_design_library_fac()
ssir = stock_sample_creation_iso_request_fac(**kw)
persist(nested_session, ssir, kw, True)
def test_persist(self, nested_session,
stock_sample_creation_iso_request_fac,
molecule_design_library_fac):
ssir1 = stock_sample_creation_iso_request_fac()
persist(nested_session, ssir1,
stock_sample_creation_iso_request_fac.init_kw,
True)
kw = stock_sample_creation_iso_request_fac.init_kw
kw['molecule_design_library'] = molecule_design_library_fac()
ssir = stock_sample_creation_iso_request_fac(**kw)
persist(nested_session, ssir, kw, True)
def test_persist_all_attributes(self, nested_session, iso_job_fac,
iso_job_stock_rack_fac,
iso_job_preparation_plate_fac):
ij = iso_job_fac()
kw = iso_job_fac.init_kw
ijsr = iso_job_stock_rack_fac(iso_job=ij)
assert len(ij.iso_job_stock_racks) == 1
kw['iso_job_stock_racks'] = [ijsr]
ijpp = iso_job_preparation_plate_fac(iso_job=ij)
assert len(ij.iso_job_preparation_plates) == 1
kw['iso_job_preparation_plates'] = [ijpp]
persist(nested_session, ij, kw, True)
def test_persist_all_attributes(self, nested_session, iso_job_fac,
iso_job_stock_rack_fac,
iso_job_preparation_plate_fac):
ij = iso_job_fac()
kw = iso_job_fac.init_kw
ijsr = iso_job_stock_rack_fac(iso_job=ij)
assert len(ij.iso_job_stock_racks) == 1
kw['iso_job_stock_racks'] = [ijsr]
ijpp = iso_job_preparation_plate_fac(iso_job=ij)
assert len(ij.iso_job_preparation_plates) == 1
kw['iso_job_preparation_plates'] = [ijpp]
persist(nested_session, ij, kw, True)
def test_convert_from_sample(self, nested_session, sample_fac, tube_fac,
molecule_fac):
container = tube_fac()
sample = sample_fac(container=container)
molecule = molecule_fac()
sm = sample.make_sample_molecule(molecule, 1e-5)
assert sm in sample.sample_molecules
# Needs to be in the session or else the conversion will fail.
nested_session.add(type(sample), sample)
sample.convert_to_stock_sample()
attrs = dict(id=sample.id,
supplier=sample.supplier,
molecule_design_pool=sample.molecule_design_pool,
concentration=sample.concentration,
molecule_type=sample.molecule_type)
persist(nested_session, sample, attrs, True)
def test_convert_from_sample(self, nested_session,
sample_fac,
tube_fac, molecule_fac):
container = tube_fac()
sample = sample_fac(container=container)
molecule = molecule_fac()
sm = sample.make_sample_molecule(molecule, 1e-5)
assert sm in sample.sample_molecules
# Needs to be in the session or else the conversion will fail.
nested_session.add(type(sample), sample)
sample.convert_to_stock_sample()
attrs = dict(id=sample.id,
supplier=sample.supplier,
molecule_design_pool=sample.molecule_design_pool,
concentration=sample.concentration,
molecule_type=sample.molecule_type
)
persist(nested_session, sample, attrs, True)
def test_persist_all_attributes(self, request, nested_session,
iso_fac_name,
iso_job_fac, iso_stock_rack_fac,
iso_sector_stock_rack_fac,
iso_preparation_plate_fac, iso_plate1,
iso_plate2, iso_plate3,
iso_aliquot_plate_fac,
iso_sector_preparation_plate_fac,
rack_layout_fac):
iso_fac = request.getfuncargvalue(iso_fac_name)
rl1 = rack_layout_fac.new()
iso = iso_fac(rack_layout=rl1)
iso_job = iso_job_fac(isos=[iso])
assert iso.iso_job.label == iso_job.label
kw = iso_fac.init_kw
kw['rack_layout'] = rl1
iso_stock_rack = iso_stock_rack_fac(iso=iso,
rack_layout=rack_layout_fac.new())
assert len(iso.iso_stock_racks) == 1
kw['iso_stock_racks'] = [iso_stock_rack]
iso_sector_stock_rack = iso_sector_stock_rack_fac(
iso=iso,
rack_layout=rack_layout_fac.new())
assert len(iso.iso_sector_stock_racks) == 1
kw['iso_sector_stock_racks'] = [iso_sector_stock_rack]
iso_preparation_plate = iso_preparation_plate_fac(
iso=iso,
rack=iso_plate1,
rack_layout=rack_layout_fac.new())
assert len(iso.iso_preparation_plates) == 1
kw['iso_preparation_plates'] = [iso_preparation_plate]
iso_aliquot_plate = iso_aliquot_plate_fac(iso=iso,
rack=iso_plate2)
assert len(iso.iso_aliquot_plates) == 1
kw['iso_aliquot_plates'] = [iso_aliquot_plate]
if iso_fac_name == 'stock_sample_creation_iso_fac':
iso_sector_prep_plate = iso_sector_preparation_plate_fac(
iso=iso,
rack=iso_plate3,
rack_layout=rack_layout_fac.new())
assert len(iso.iso_sector_preparation_plates) == 1
kw['iso_sector_preparation_plates'] = [iso_sector_prep_plate]
persist(nested_session, iso, kw, True)
def test_persist_all_attributes(self, nested_session,
worklist_series_member_fac,
executed_worklist_fac):
wsm = worklist_series_member_fac()
pwl = wsm.planned_worklist
assert not pwl.worklist_series is None
assert not pwl.index is None
assert len(pwl.executed_worklists) == 0
ewl = executed_worklist_fac(planned_worklist=pwl)
assert ewl.planned_worklist is pwl
assert len(pwl.executed_worklists) == 1
attrs = dict(executed_worklists=pwl.executed_worklists,
index=pwl.index,
worklist_series=pwl.worklist_series)
pwl_from_storage = persist(nested_session, pwl, attrs, True)
assert pwl_from_storage.worklist_series_member == wsm
def test_persist_all_attributes(self, nested_session,
worklist_series_member_fac,
executed_worklist_fac):
wsm = worklist_series_member_fac()
pwl = wsm.planned_worklist
assert not pwl.worklist_series is None
assert not pwl.index is None
assert len(pwl.executed_worklists) == 0
ewl = executed_worklist_fac(planned_worklist=pwl)
assert ewl.planned_worklist is pwl
assert len(pwl.executed_worklists) == 1
attrs = dict(executed_worklists=pwl.executed_worklists,
index=pwl.index,
worklist_series=pwl.worklist_series)
pwl_from_storage = persist(nested_session, pwl, attrs, True)
assert pwl_from_storage.worklist_series_member == wsm
def test_persist_with_iso(self, nested_session, library_plate_fac,
lab_iso_fac):
kw = library_plate_fac.init_kw
kw['lab_iso'] = lab_iso_fac()
lp = library_plate_fac(**kw)
persist(nested_session, lp, kw, True)
def test_persist(self, nested_session, gene_fac):
gene = gene_fac()
# The gene table is a materialized view; we should not be able to
# insert new records here.
with pytest.raises(IntegrityError):
persist(nested_session, gene, gene_fac.init_kw, True)
def test_persist(self, nested_session, tube_transfer_worklist_fac):
ttwl = tube_transfer_worklist_fac()
persist(nested_session, ttwl, tube_transfer_worklist_fac.init_kw,
True)
def test_persist(self, nested_session, molecule_design_library_fac):
mdl = molecule_design_library_fac()
persist(nested_session, mdl, molecule_design_library_fac.init_kw,
True)
def _test_persist(self):
with RdbContextManager() as session:
attrs = self._get_data()
persist(session, self.entity_class, attrs, True)
def test_persist(self, nested_session, item_status_fac):
its = item_status_fac()
persist(nested_session, its, item_status_fac.init_kw, True)
def test_persist(self, nested_session, sample_molecule_fac):
sm = sample_molecule_fac()
persist(nested_session, sm, sample_molecule_fac.init_kw, True)
def test_persist(self, nested_session, rack_position_set_fac):
rps = rack_position_set_fac()
persist(nested_session, rps, rack_position_set_fac.init_kw, True)
def test_persist(self, nested_session, barcoded_location_fac):
bl = barcoded_location_fac()
kw = barcoded_location_fac.init_kw
# FIXME: This should not be necessary.
bl.type = kw['type'] = bl.type.name
persist(nested_session, bl, kw, True)
def test_persist(self, nested_session, lab_iso_request_fac):
lir = lab_iso_request_fac()
persist(nested_session, lir, lab_iso_request_fac.init_kw, True)
def test_persist(self, nested_session, tube_transfer_worklist_fac):
ttwl = tube_transfer_worklist_fac()
persist(nested_session, ttwl, tube_transfer_worklist_fac.init_kw, True)
def test_persist(self, nested_session, tube_transfer_fac):
tt = tube_transfer_fac()
persist(nested_session, tt, tube_transfer_fac.init_kw, True)
def test_persist(self, nested_session, barcoded_location_fac):
bl = barcoded_location_fac()
kw = barcoded_location_fac.init_kw
# FIXME: This should not be necessary.
bl.type = kw['type'] = bl.type.name
persist(nested_session, bl, kw, True)
def test_persist(self, request, nested_session, stock_rack_fac_name):
stock_rack_fac = request.getfuncargvalue(stock_rack_fac_name)
sr = stock_rack_fac()
persist(nested_session, sr, stock_rack_fac.init_kw, True)
def test_persist(self, request, nested_session, iso_fac_name):
iso_fac = request.getfuncargvalue(iso_fac_name)
iso = iso_fac()
persist(nested_session, iso, iso_fac.init_kw, True)
def test_persist(self, nested_session, organization_fac):
org = organization_fac()
persist(nested_session, org, organization_fac.init_kw, True)
def test_persist(self, request, nested_session, fac_name):
fac = request.getfuncargvalue(fac_name)
rack = fac()
persist(nested_session, rack, fac.init_kw, True)
def test_persist(self, nested_session, molecule_fac):
mol = molecule_fac()
persist(nested_session, mol, molecule_fac.init_kw, True)
def test_persist(self, nested_session, user_preferences_fac):
up = user_preferences_fac()
persist(nested_session, up, user_preferences_fac.init_kw, True)
def test_persist(self, nested_session, stock_sample_fac):
sspl = stock_sample_fac()
persist(nested_session, sspl, stock_sample_fac.init_kw, True)
def test_persist(self, nested_session, rack_layout_fac):
rl = rack_layout_fac()
persist(nested_session, rl, rack_layout_fac.init_kw, True)
def test_persist(self, nested_session, user_preferences_fac):
up = user_preferences_fac()
persist(nested_session, up, user_preferences_fac.init_kw, True)
def test_persist(self, nested_session, rack_layout_fac):
rl = rack_layout_fac()
persist(nested_session, rl, rack_layout_fac.init_kw, True)
def test_persist(self, nested_session, device_type_fac):
dev_type = device_type_fac()
persist(nested_session, dev_type, device_type_fac.init_kw, True)
def test_persist(self, nested_session, molecule_design_pool_set_fac):
mdps = molecule_design_pool_set_fac()
persist(nested_session, mdps, molecule_design_pool_set_fac.init_kw,
True)
def test_persist(self, nested_session, tube_transfer_fac):
tt = tube_transfer_fac()
persist(nested_session, tt, tube_transfer_fac.init_kw, True)
def test_persist(self, nested_session, stock_sample_fac):
sspl = stock_sample_fac()
persist(nested_session, sspl, stock_sample_fac.init_kw, True)
def _test_persist(self):
with RdbContextManager() as session:
attrs = self._get_data()
persist(session, self.entity_class, attrs, True)
def test_persist(self, nested_session, experiment_design_fac):
exp_design = experiment_design_fac()
persist(nested_session, exp_design, experiment_design_fac.init_kw,
True)
def test_persist(self, nested_session, library_plate_fac):
lp = library_plate_fac()
persist(nested_session, lp, library_plate_fac.init_kw, True)
def test_persist(self, nested_session, experiment_metadata_fac):
exp_metadata = experiment_metadata_fac()
persist(nested_session, exp_metadata, experiment_metadata_fac.init_kw,
True)
def test_persist(self, nested_session, project_fac):
proj = project_fac()
persist(nested_session, proj, project_fac.init_kw, True)
def test_persist(self, nested_session, species_fac):
spec = species_fac()
persist(nested_session, spec, species_fac.init_kw, True)
def test_persist(self, nested_session, sample_molecule_fac):
sm = sample_molecule_fac()
persist(nested_session, sm, sample_molecule_fac.init_kw, True)
def test_persist(self, nested_session, molecule_type_fac):
mt = molecule_type_fac()
persist(nested_session, mt, molecule_type_fac.init_kw, True)
def test_persist(self, nested_session, lab_iso_request_fac):
lir = lab_iso_request_fac()
persist(nested_session, lir, lab_iso_request_fac.init_kw, True)
def test_persist(self, nested_session, organization_fac):
org = organization_fac()
persist(nested_session, org, organization_fac.init_kw, True)
def test_persist(self, request, nested_session, iso_fac_name):
iso_fac = request.getfuncargvalue(iso_fac_name)
iso = iso_fac()
persist(nested_session, iso, iso_fac.init_kw, True)
def test_persist(self, request, nested_session, stock_rack_fac_name):
stock_rack_fac = request.getfuncargvalue(stock_rack_fac_name)
sr = stock_rack_fac()
persist(nested_session, sr, stock_rack_fac.init_kw, True)