add test for validation pool

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

@@ -27,7 +27,7 @@ class FluffySample(Sample):
     well_position_rml: str | None = None
 
     @model_validator(mode="after")
-    def set_default_index_sequence(self):
+    def set_default_index_sequence(self) -> "FluffySample":
         """Set a default index_sequence from the index and index_number."""
         if not self.index_sequence and (self.index and self.index_number):
             try:

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

@@ -23,11 +23,12 @@ class RmlSample(Sample):
     pool: str
     priority: PriorityEnum
     rml_plate_name: str | None = None
+
     volume: int
     well_position_rml: str | None = None
 
     @model_validator(mode="after")
-    def set_default_index_sequence(self):
+    def set_default_index_sequence(self) -> "RmlSample":
         """Set a default index_sequence from the index and index_number."""
         if not self.index_sequence and (self.index and self.index_number):
             try:

tests/conftest.py

@@ -123,6 +123,7 @@
     "tests.fixture_plugins.orders_fixtures.order_form_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_to_submit_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_fixtures",
+    "tests.fixture_plugins.orders_fixtures.path_fixtures",
     "tests.fixture_plugins.orders_fixtures.services_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_service_fixtures",
@@ -745,12 +746,6 @@ def apps_dir(fixtures_dir: Path) -> Path:
     return Path(fixtures_dir, "apps")
 
 
-@pytest.fixture(scope="session")
-def cgweb_orders_dir(fixtures_dir: Path) -> Path:
-    """Return the path to the cgweb_orders dir."""
-    return Path(fixtures_dir, "cgweb_orders")
-
-
 @pytest.fixture(scope="session")
 def data_dir(fixtures_dir: Path) -> Path:
     """Return the path to the data dir."""

tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py

@@ -129,5 +129,23 @@ def tomte_order_to_submit(cgweb_orders_dir: Path) -> dict:
 def invalid_balsamic_order_to_submit(cgweb_orders_dir: Path) -> dict:
     """Load an invalid example Balsamic order."""
     return ReadFile.get_content_from_file(
-        file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "FAIL_balsamic.json")
+        file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "balsamic_FAIL.json")
+    )
+
+
+@pytest.fixture(scope="session")
+def fluffy_order_to_submit_without_index_sequence(invalid_cgweb_orders_dir) -> dict:
+    """Load an invalid example Fluffy order."""
+    return ReadFile.get_content_from_file(
+        file_format=FileFormat.JSON,
+        file_path=Path(invalid_cgweb_orders_dir, "fluffy_no_index_sequence.json"),
+    )
+
+
+@pytest.fixture(scope="session")
+def rml_order_to_submit_without_index_sequence(invalid_cgweb_orders_dir) -> dict:
+    """Load an invalid example RML order."""
+    return ReadFile.get_content_from_file(
+        file_format=FileFormat.JSON,
+        file_path=Path(invalid_cgweb_orders_dir, "rml_no_index_sequence.json"),
     )

tests/fixture_plugins/orders_fixtures/path_fixtures.py

@@ -0,0 +1,15 @@
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture(scope="session")
+def cgweb_orders_dir(fixtures_dir: Path) -> Path:
+    """Return the path to the cgweb_orders dir."""
+    return Path(fixtures_dir, "cgweb_orders")
+
+
+@pytest.fixture(scope="session")
+def invalid_cgweb_orders_dir(fixtures_dir: Path) -> Path:
+    """Return the path to the invalid_cgweb_orders dir."""
+    return Path(fixtures_dir, "invalid_cgweb_orders")

tests/fixture_plugins/orders_fixtures/services_fixtures.py

@@ -7,6 +7,7 @@
 )
 from cg.services.orders.submitter.service import OrderSubmitter
 from cg.services.orders.submitter.ticket_handler import TicketHandler
+from cg.services.orders.validation.model_validator.model_validator import ModelValidator
 from cg.services.orders.validation.service import OrderValidationService
 from cg.store.store import Store
 from tests.mocks.limsmock import MockLimsAPI
@@ -17,6 +18,11 @@ def freshdesk_client() -> FreshdeskClient:
     return FreshdeskClient(base_url="https://mock.freshdesk.com", api_key="mock_api_key")
 
 
+@pytest.fixture
+def model_validator() -> ModelValidator:
+    return ModelValidator()
+
+
 @pytest.fixture
 def order_validation_service(store_to_submit_and_validate_orders: Store) -> OrderValidationService:
     return OrderValidationService(store_to_submit_and_validate_orders)
@@ -35,15 +41,15 @@ def order_submitter(
     )
 
 
-@pytest.fixture
-def ticket_handler(store: Store, freshdesk_client: FreshdeskClient) -> TicketHandler:
-    return TicketHandler(db=store, client=freshdesk_client, system_email_id=12345, env="production")
-
-
 @pytest.fixture
 def storing_service_registry(
     store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
 ) -> StoringServiceRegistry:
     return setup_storing_service_registry(
         lims=lims_api, status_db=store_to_submit_and_validate_orders
     )
+
+
+@pytest.fixture
+def ticket_handler(store: Store, freshdesk_client: FreshdeskClient) -> TicketHandler:
+    return TicketHandler(db=store, client=freshdesk_client, system_email_id=12345, env="production")

tests/fixtures/invalid_cgweb_orders/fluffy_no_index_sequence.json

@@ -0,0 +1,72 @@
+{
+	"cases": [],
+	"comment": null,
+	"customer": "cust000",
+	"data_delivery": null,
+	"delivery_type": "statina",
+	"name": "1604.19.rml",
+	"project_type": "fluffy",
+	"samples": [
+		{
+			"age_at_sampling": null,
+			"application": "RMLP15R100",
+			"capture_kit": null,
+			"collection_date": null,
+			"comment": "comment",
+			"concentration": "2",
+			"concentration_ng_ul": null,
+			"concentration_sample": "4",
+			"container": null,
+			"container_name": null,
+			"control": "positive",
+			"custom_index": null,
+			"customer": "cust000",
+			"data_analysis": "FLUFFY",
+			"data_delivery": "statina",
+			"elution_buffer": null,
+			"extraction_method": null,
+			"family_name": null,
+			"father": null,
+			"formalin_fixation_time": null,
+			"index": "IDT DupSeq 10 bp Set B",
+			"index_number": "3",
+			"index_sequence": "",
+			"internal_id": null,
+			"lab_code": null,
+			"mother": null,
+			"name": "fluffysample1",
+			"organism": null,
+			"organism_other": null,
+			"original_lab": null,
+			"original_lab_address": null,
+			"phenotype_groups": null,
+			"phenotype_terms": null,
+			"pool": "pool1",
+			"post_formalin_fixation_time": null,
+			"pre_processing_method": null,
+			"primer": null,
+			"priority": "research",
+			"quantity": null,
+			"reagent_label": "C01 IDT_10nt_568 (TGTGAGCGAA-AACTCCGATC)",
+			"reference_genome": null,
+			"region": null,
+			"region_code": null,
+			"require_qc_ok": false,
+			"rml_plate_name": "plate1",
+			"selection_criteria": null,
+			"sex": null,
+			"source": null,
+			"status": null,
+			"subject_id": null,
+			"tissue_block_size": null,
+			"tumour": null,
+			"tumour_purity": null,
+			"verified_organism": null,
+			"volume": "20",
+			"well_position": null,
+			"well_position_rml": "A:1"
+		}
+	],
+	"ticket": null,
+	"user_id": 1
+}

tests/fixtures/invalid_cgweb_orders/rml_no_index_sequence.json

@@ -0,0 +1,72 @@
+{
+	"cases": [],
+	"comment": null,
+	"customer": "cust000",
+	"data_delivery": null,
+	"delivery_type": "fastq",
+	"name": "1604.19.rml",
+	"project_type": "rml",
+	"samples": [
+		{
+			"age_at_sampling": null,
+			"application": "RMLP15R500",
+			"capture_kit": null,
+			"collection_date": null,
+			"comment": "",
+			"concentration": "2",
+			"concentration_ng_ul": null,
+			"concentration_sample": null,
+			"container": null,
+			"container_name": null,
+			"control": "",
+			"custom_index": null,
+			"customer": "cust000",
+			"data_analysis": "RAW-DATA",
+			"data_delivery": "fastq",
+			"elution_buffer": null,
+			"extraction_method": null,
+			"family_name": null,
+			"father": null,
+			"formalin_fixation_time": null,
+			"index": "NEXTflex® v2 UDI Barcodes 1 - 96",
+			"index_number": "3",
+			"index_sequence": "",
+			"internal_id": null,
+			"lab_code": null,
+			"mother": null,
+			"name": "rmlsample4",
+			"organism": null,
+			"organism_other": null,
+			"original_lab": null,
+			"original_lab_address": null,
+			"phenotype_groups": null,
+			"phenotype_terms": null,
+			"pool": "pool4",
+			"post_formalin_fixation_time": null,
+			"pre_processing_method": null,
+			"primer": null,
+			"priority": "priority",
+			"quantity": null,
+			"reagent_label": "UDI 3 (CGCTGCTC-GGCAGATC)",
+			"reference_genome": null,
+			"region": null,
+			"region_code": null,
+			"require_qc_ok": false,
+			"rml_plate_name": "rmplate4",
+			"selection_criteria": null,
+			"sex": null,
+			"source": null,
+			"status": null,
+			"subject_id": null,
+			"tissue_block_size": null,
+			"tumour": null,
+			"tumour_purity": null,
+			"verified_organism": null,
+			"volume": "23",
+			"well_position": null,
+			"well_position_rml": "A:1"
+		}
+	],
+	"ticket": null,
+	"user_id": 1
+}

tests/services/orders/validation_service/test_model_validator.py

@@ -0,0 +1,35 @@
+import pytest
+
+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.rml.models.order import RmlOrder
+
+
+@pytest.mark.parametrize(
+    "order_fixture, expected_index_sequence, order_model",
+    [
+        (
+            "fluffy_order_to_submit_without_index_sequence",
+            "C01 IDT_10nt_568 (TGTGAGCGAA-AACTCCGATC)",
+            FluffyOrder,
+        ),
+        ("rml_order_to_submit_without_index_sequence", "UDI 3 (CGCTGCTC-GGCAGATC)", RmlOrder),
+    ],
+    ids=["fluffy", "rml"],
+)
+def test_validate_pool_sample_default_index(
+    order_fixture: str,
+    expected_index_sequence: str,
+    order_model: type[Order],
+    model_validator: ModelValidator,
+    request: pytest.FixtureRequest,
+):
+    # GIVEN a pool raw order with a sample without index sequence but correct index and index number
+    raw_order: dict = request.getfixturevalue(order_fixture)
+
+    # 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