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, 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_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_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_fac): tt = tube_transfer_fac() persist(nested_session, tt, tube_transfer_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)
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, 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, 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, molecule_type_fac): mt = molecule_type_fac() persist(nested_session, mt, molecule_type_fac.init_kw, True)