Test mutant validator (#4134)

add tests for mutant validator

Author: diitaz93

cg/services/orders/validation/workflows/mutant/models/sample.py

@@ -39,7 +39,7 @@ class MutantSample(Sample):
 
     @model_validator(mode="before")
     @classmethod
-    def set_original_lab_address(cls, data: any):
+    def set_original_lab_address(cls, data: any) -> any:
         if isinstance(data, dict):
             is_set = bool(data.get("original_lab_address"))
             if not is_set:
@@ -48,7 +48,7 @@ def set_original_lab_address(cls, data: any):
 
     @model_validator(mode="before")
     @classmethod
-    def set_region_code(cls, data: any):
+    def set_region_code(cls, data: any) -> any:
         if isinstance(data, dict):
             is_set = bool(data.get("region_code"))
             if not is_set:

tests/fixtures/cgweb_orders/sarscov2.json

@@ -39,7 +39,7 @@
 			"organism": "SARS-CoV-2",
 			"organism_other": "",
 			"original_lab": "Karolinska University Hospital Solna",
-			"original_lab_address": "171 76 Solna",
+			"original_lab_address": "",
 			"phenotype_groups": null,
 			"phenotype_terms": null,
 			"pool": null,
@@ -51,7 +51,7 @@
 			"reagent_label": null,
 			"reference_genome": "NC_111",
 			"region": "Stockholm",
-			"region_code": "01",
+			"region_code": "",
 			"require_qc_ok": null,
 			"rml_plate_name": null,
 			"selection_criteria": "Allmän övervakning",

tests/services/orders/lims_service/test_order_lims_service.py

@@ -164,7 +164,7 @@ def test_to_lims_sarscov2(mutant_order: MutantOrder):
     assert first_sample["udfs"]["lab_code"] == "SE100 Karolinska"
     assert first_sample["udfs"]["organism"] == "SARS-CoV-2"
     assert first_sample["udfs"]["original_lab"] == "Karolinska University Hospital Solna"
-    assert first_sample["udfs"]["original_lab_address"] == "171 76 Solna"
+    assert first_sample["udfs"]["original_lab_address"] == "171 76 Stockholm"
     assert first_sample["udfs"]["pre_processing_method"] == "COVIDSeq"
     assert first_sample["udfs"]["priority"] == "research"
     assert first_sample["udfs"]["reference_genome"] == "NC_111"

tests/services/orders/validation_service/test_model_validator.py

@@ -3,7 +3,9 @@
 from cg.services.orders.validation.model_validator.model_validator import ModelValidator
 from cg.services.orders.validation.models.order import Order
 from cg.services.orders.validation.workflows.fluffy.models.order import FluffyOrder
+from cg.services.orders.validation.workflows.mutant.models.order import MutantOrder
 from cg.services.orders.validation.workflows.rml.models.order import RmlOrder
+from cg.services.orders.validation.workflows.tomte.models.order import TomteOrder
 
 
 @pytest.mark.parametrize(
@@ -21,12 +23,110 @@ def test_validate_pool_sample_default_index(
     model_validator: ModelValidator,
     request: pytest.FixtureRequest,
 ):
+    """Test the default index sequence is set for a pool sample without index sequence."""
     # GIVEN a pool raw order with a sample without index sequence but correct index and index number
     raw_order: dict = request.getfixturevalue(order_fixture)
-    assert raw_order["samples"][0]["index_sequence"] == ""
+    assert not raw_order["samples"][0]["index_sequence"]
 
     # WHEN validating the order
     order, _ = model_validator.validate(order=raw_order, model=order_model)
 
     # THEN the index sequence should be set to the default index sequence
     assert order.samples[0].index_sequence == expected_index_sequence
+
+
+def test_validate_mutant_sample_gets_lab_and_region(
+    sarscov2_order_to_submit: dict, model_validator: ModelValidator
+):
+    """Test the lab address and region code are set for a mutant sample without these fields."""
+    # GIVEN a Mutant order with a sample without lab address and region code
+    assert not sarscov2_order_to_submit["samples"][0]["original_lab_address"]
+    assert not sarscov2_order_to_submit["samples"][0]["region_code"]
+
+    # WHEN validating the order
+    order, _ = model_validator.validate(order=sarscov2_order_to_submit, model=MutantOrder)
+
+    # THEN the lab address and region code should be set
+    assert order.samples[0].original_lab_address == "171 76 Stockholm"
+    assert order.samples[0].region_code == "01"
+
+
+def test_order_field_error(valid_order: TomteOrder, model_validator: ModelValidator):
+    # GIVEN a Tomte order with an order field error
+    valid_order.name = ""
+    raw_order: dict = valid_order.model_dump(by_alias=True)
+
+    # WHEN validating the order
+    _, errors = model_validator.validate(order=raw_order, model=TomteOrder)
+
+    # THEN there should be an order error
+    assert errors.order_errors
+
+    # THEN the error should concern the missing name
+    assert errors.order_errors[0].field == "name"
+
+
+def test_case_field_error(valid_order: TomteOrder, model_validator: ModelValidator):
+    # GIVEN a Tomte order with a case field error
+    valid_order.cases[0].priority = None
+    raw_order: dict = valid_order.model_dump()
+
+    # WHEN validating the order
+    _, errors = model_validator.validate(order=raw_order, model=TomteOrder)
+
+    # THEN there should be a case error
+    assert errors.case_errors
+
+    # THEN the error should concern the missing name
+    assert errors.case_errors[0].field == "priority"
+
+
+def test_case_sample_field_error(valid_order: TomteOrder, model_validator: ModelValidator):
+
+    # GIVEN a Tomte order with a case sample error
+    valid_order.cases[0].samples[0].well_position = 1.8
+    raw_order: dict = valid_order.model_dump()
+
+    # WHEN validating the order
+    _, errors = model_validator.validate(order=raw_order, model=TomteOrder)
+
+    # THEN a case sample error should be returned
+    assert errors.case_sample_errors
+
+    # THEN the case sample error should concern the invalid data type
+    assert errors.case_sample_errors[0].field == "well_position"
+
+
+def test_order_case_and_case_sample_field_error(
+    valid_order: TomteOrder, model_validator: ModelValidator
+):
+    # GIVEN a Tomte order with an order, case and case sample error
+    valid_order.name = None
+    valid_order.cases[0].priority = None
+    valid_order.cases[0].samples[0].well_position = 1.8
+    raw_order: dict = valid_order.model_dump(by_alias=True)
+
+    # WHEN validating the order
+    _, errors = model_validator.validate(order=raw_order, model=TomteOrder)
+
+    # THEN all errors should be returned
+    assert errors.order_errors
+    assert errors.case_errors
+    assert errors.case_sample_errors
+
+    # THEN the errors should concern the relevant fields
+    assert errors.order_errors[0].field == "name"
+    assert errors.case_errors[0].field == "priority"
+    assert errors.case_sample_errors[0].field == "well_position"
+
+
+def test_null_conversion(valid_order: TomteOrder, model_validator: ModelValidator):
+    # GIVEN a Tomte order with a sample with empty concentration
+    valid_order.cases[0].samples[0].concentration_ng_ul = ""
+    raw_order: dict = valid_order.model_dump(by_alias=True)
+
+    # WHEN validating the order
+    order, _ = model_validator.validate(order=raw_order, model=TomteOrder)
+
+    # THEN the empty concentration should be converted to None
+    assert order.cases[0].samples[0].concentration_ng_ul is None