enhance order submission integration tests (#4121)

enhance order submission integration tests

cg/services/orders/storing/service.py

@@ -22,7 +22,7 @@ def store_order(self, order: Order):
         pass
 
     @staticmethod
-    def _fill_in_sample_ids(samples: list[Sample], lims_map: dict):
+    def _fill_in_sample_ids(samples: list[Sample], lims_map: dict) -> None:
         """Fill in LIMS sample ids."""
         for sample in samples:
             LOG.debug(f"{sample.name}: link sample to LIMS")

tests/conftest.py

@@ -123,7 +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.services_and_api_fixtures",
+    "tests.fixture_plugins.orders_fixtures.services_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_fixtures",
     "tests.fixture_plugins.orders_fixtures.store_service_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.context_fixtures",

tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py

@@ -7,18 +7,20 @@
 from cg.constants.constants import FileFormat
 from cg.io.controller import ReadFile
 
+# Valid orders
+
 
 @pytest.fixture(scope="session")
 def balsamic_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example cancer order."""
+    """Load an example Balsamic order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "balsamic.json")
     )
 
 
 @pytest.fixture(scope="session")
 def fastq_order_to_submit(cgweb_orders_dir) -> dict:
-    """Load an example FASTQ order."""
+    """Load an example Fastq order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "fastq.json")
     )
@@ -34,23 +36,23 @@ def fluffy_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def metagenome_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example metagenome order."""
+    """Load an example Metagenome order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "metagenome.json")
     )
 
 
 @pytest.fixture(scope="session")
 def microbial_fastq_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example microbial order."""
+    """Load an example Microbial fastq order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "microbial_fastq.json")
     )
 
 
 @pytest.fixture(scope="session")
 def microbial_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example microbial order."""
+    """Load an example Microsalt order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "microsalt.json")
     )
@@ -66,7 +68,7 @@ def mip_dna_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def mip_rna_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example RNA order."""
+    """Load an example MIP-RNA order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "mip_rna.json")
     )
@@ -90,15 +92,15 @@ def rml_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def rnafusion_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example RNA order."""
+    """Load an example RNA Fusion order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "rnafusion.json")
     )
 
 
 @pytest.fixture(scope="session")
 def sarscov2_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example sarscov2 order."""
+    """Load an example Mutant order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "sarscov2.json")
     )
@@ -114,7 +116,18 @@ def taxprofiler_order_to_submit(cgweb_orders_dir: Path) -> dict:
 
 @pytest.fixture(scope="session")
 def tomte_order_to_submit(cgweb_orders_dir: Path) -> dict:
-    """Load an example TOMTE order."""
+    """Load an example Tomte order."""
     return ReadFile.get_content_from_file(
         file_format=FileFormat.JSON, file_path=Path(cgweb_orders_dir, "tomte.json")
     )
+
+
+# Invalid orders
+
+
+@pytest.fixture(scope="session")
+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")
+    )

tests/fixture_plugins/orders_fixtures/services_and_api_fixtures.py → tests/fixture_plugins/orders_fixtures/services_fixtures.py

@@ -18,8 +18,8 @@ def freshdesk_client() -> FreshdeskClient:
 
 
 @pytest.fixture
-def order_validation_service(store_with_all_test_applications: Store) -> OrderValidationService:
-    return OrderValidationService(store_with_all_test_applications)
+def order_validation_service(store_to_submit_and_validate_orders: Store) -> OrderValidationService:
+    return OrderValidationService(store_to_submit_and_validate_orders)
 
 
 @pytest.fixture(scope="function")
@@ -42,6 +42,8 @@ def ticket_handler(store: Store, freshdesk_client: FreshdeskClient) -> TicketHan
 
 @pytest.fixture
 def storing_service_registry(
-    store_with_all_test_applications: Store, lims_api: MockLimsAPI
+    store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
 ) -> StoringServiceRegistry:
-    return setup_storing_service_registry(lims=lims_api, status_db=store_with_all_test_applications)
+    return setup_storing_service_registry(
+        lims=lims_api, status_db=store_to_submit_and_validate_orders
+    )

tests/fixture_plugins/orders_fixtures/store_fixtures.py

@@ -2,74 +2,17 @@
 
 import pytest
 
-from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.models.orders.constants import OrderType
 from cg.services.orders.storing.constants import MAF_ORDER_ID
-from cg.services.orders.validation.workflows.balsamic.models.order import BalsamicOrder
-from cg.services.orders.validation.workflows.mip_dna.models.order import MipDnaOrder
-from cg.store.models import Application, ApplicationVersion, Customer, Order
+from cg.store.models import ApplicationVersion, Customer, Order
 from cg.store.store import Store
 from tests.store_helpers import StoreHelpers
 
 
 @pytest.fixture
-def balsamic_submit_store(
-    base_store: Store, balsamic_order: BalsamicOrder, helpers: StoreHelpers
+def store_to_submit_and_validate_orders(
+    store: Store, helpers: StoreHelpers, customer_id: str
 ) -> Store:
-    for _, _, sample in balsamic_order.enumerated_new_samples:
-        if not base_store.get_application_by_tag(sample.application):
-            application_version = helpers.ensure_application_version(
-                store=base_store, application_tag=sample.application
-            )
-            base_store.session.add(application_version)
-    base_store.session.commit()
-    return base_store
-
-
-@pytest.fixture
-def store_with_rml_applications(store: Store, helpers: StoreHelpers) -> Store:
-    app_tags: list[str] = ["RMLP15R100", "RMLP15R200", "RMLP15R400", "RMLP15R500"]
-    for tag in app_tags:
-        helpers.ensure_application_version(
-            store=store,
-            application_tag=tag,
-            prep_category=SeqLibraryPrepCategory.READY_MADE_LIBRARY,
-        )
-    helpers.ensure_customer(store=store, customer_id="cust000")
-    return store
-
-
-@pytest.fixture
-def metagenome_storing_store(base_store: Store, helpers: StoreHelpers) -> Store:
-    metagenome_application: Application = helpers.ensure_application_version(
-        store=base_store, application_tag="METPCFR030"
-    ).application
-    metagenome_application.order_types = [OrderType.METAGENOME]
-    metagenome_application: Application = helpers.ensure_application_version(
-        store=base_store, application_tag="METWPFR030"
-    ).application
-    metagenome_application.order_types = [OrderType.METAGENOME]
-    customer = base_store.get_customer_by_internal_id("cust000")
-    helpers.ensure_user(store=base_store, customer=customer)
-    return base_store
-
-
-@pytest.fixture
-def mip_dna_submit_store(
-    base_store: Store, mip_dna_order: MipDnaOrder, helpers: StoreHelpers
-) -> Store:
-    for _, _, sample in mip_dna_order.enumerated_new_samples:
-        if not base_store.get_application_by_tag(sample.application):
-            application_version = helpers.ensure_application_version(
-                store=base_store, application_tag=sample.application
-            )
-            base_store.session.add(application_version)
-    base_store.session.commit()
-    return base_store
-
-
-@pytest.fixture
-def store_with_all_test_applications(store: Store, helpers: StoreHelpers) -> Store:
     app_tags: dict[str, list[OrderType]] = {
         "PANKTTR100": [OrderType.BALSAMIC],
         "WGSPCFC030": [OrderType.FASTQ, OrderType.MIP_DNA],
@@ -92,7 +35,7 @@ def store_with_all_test_applications(store: Store, helpers: StoreHelpers) -> Sto
             store=store, application_tag=tag
         )
         application_version.application.order_types = orders
-    customer: Customer = helpers.ensure_customer(store=store, customer_id="cust000")
+    customer: Customer = helpers.ensure_customer(store=store, customer_id=customer_id)
     helpers.ensure_user(store=store, customer=customer)
     helpers.ensure_panel(store=store, panel_abbreviation="AID")
     helpers.ensure_panel(store=store, panel_abbreviation="Ataxi")

tests/fixture_plugins/orders_fixtures/store_service_fixtures.py

@@ -16,57 +16,67 @@
 from cg.services.orders.storing.implementations.pool_order_service import StorePoolOrderService
 from cg.store.store import Store
 from tests.mocks.limsmock import MockLimsAPI
-from tests.store_helpers import StoreHelpers
 
 
 @pytest.fixture
-def store_generic_order_service(base_store: Store, lims_api: MockLimsAPI) -> StoreCaseOrderService:
-    return StoreCaseOrderService(status_db=base_store, lims_service=OrderLimsService(lims_api))
+def store_generic_order_service(
+    store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
+) -> StoreCaseOrderService:
+    return StoreCaseOrderService(
+        status_db=store_to_submit_and_validate_orders, lims_service=OrderLimsService(lims_api)
+    )
 
 
 @pytest.fixture
 def store_pool_order_service(
-    store_with_rml_applications: Store, lims_api: MockLimsAPI
+    store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
 ) -> StorePoolOrderService:
     return StorePoolOrderService(
-        status_db=store_with_rml_applications, lims_service=OrderLimsService(lims_api)
+        status_db=store_to_submit_and_validate_orders, lims_service=OrderLimsService(lims_api)
     )
 
 
 @pytest.fixture
-def store_fastq_order_service(base_store: Store, lims_api: MockLimsAPI) -> StoreFastqOrderService:
-    return StoreFastqOrderService(status_db=base_store, lims_service=OrderLimsService(lims_api))
+def store_fastq_order_service(
+    store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
+) -> StoreFastqOrderService:
+    return StoreFastqOrderService(
+        status_db=store_to_submit_and_validate_orders, lims_service=OrderLimsService(lims_api)
+    )
 
 
 @pytest.fixture
-def store_pacbio_order_service(base_store: Store, lims_api: MockLimsAPI) -> StorePacBioOrderService:
-    return StorePacBioOrderService(status_db=base_store, lims_service=OrderLimsService(lims_api))
+def store_pacbio_order_service(
+    store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
+) -> StorePacBioOrderService:
+    return StorePacBioOrderService(
+        status_db=store_to_submit_and_validate_orders, lims_service=OrderLimsService(lims_api)
+    )
 
 
 @pytest.fixture
 def store_metagenome_order_service(
-    metagenome_storing_store: Store, lims_api: MockLimsAPI, helpers: StoreHelpers
+    store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
 ) -> StoreMetagenomeOrderService:
     return StoreMetagenomeOrderService(
-        status_db=metagenome_storing_store, lims_service=OrderLimsService(lims_api)
+        status_db=store_to_submit_and_validate_orders, lims_service=OrderLimsService(lims_api)
     )
 
 
 @pytest.fixture
 def store_microbial_order_service(
-    base_store: Store, lims_api: MockLimsAPI, helpers: StoreHelpers
+    store_to_submit_and_validate_orders: Store,
+    lims_api: MockLimsAPI,
 ) -> StoreMicrobialOrderService:
-    helpers.ensure_application_version(store=base_store, application_tag="MWRNXTR003")
-    helpers.ensure_application_version(store=base_store, application_tag="MWXNXTR003")
-    helpers.ensure_application_version(store=base_store, application_tag="VWGNXTR001")
-
-    return StoreMicrobialOrderService(status_db=base_store, lims_service=OrderLimsService(lims_api))
+    return StoreMicrobialOrderService(
+        status_db=store_to_submit_and_validate_orders, lims_service=OrderLimsService(lims_api)
+    )
 
 
 @pytest.fixture
 def store_microbial_fastq_order_service(
-    base_store: Store, lims_api: MockLimsAPI
+    store_to_submit_and_validate_orders: Store, lims_api: MockLimsAPI
 ) -> StoreMicrobialFastqOrderService:
     return StoreMicrobialFastqOrderService(
-        status_db=base_store, lims_service=OrderLimsService(lims_api)
+        status_db=store_to_submit_and_validate_orders, lims_service=OrderLimsService(lims_api)
     )

tests/fixtures/cgweb_orders/FAIL_balsamic.json

@@ -0,0 +1,61 @@
+{
+	"cases": [
+		{
+			"cohorts": null,
+			"name": "B",
+			"panels": null,
+			"priority": "FAIL",
+			"samples": [
+				{
+					"age_at_sampling": "17.2",
+					"application": "PANKTTR100",
+					"capture_kit": "GMCKsolid",
+					"comment": "This is a sample comment",
+					"concentration_ng_ul": null,
+					"container": "96 well plate",
+					"container_name": "BalsamicPlate",
+					"control": "FAIL",
+					"data_analysis": null,
+					"data_delivery": null,
+					"elution_buffer": "Tris-HCl",
+					"family_name": null,
+					"father": null,
+					"formalin_fixation_time": "15",
+					"mother": null,
+					"name": "BalsamicSample",
+					"phenotype_groups": [
+						"PhGroup"
+					],
+					"phenotype_terms": [
+						"PhTerm"
+					],
+					"post_formalin_fixation_time": "3",
+					"priority": null,
+					"quantity": null,
+					"reference_genome": null,
+					"require_qc_ok": false,
+					"sex": "male",
+					"source": "cytology (FFPE)",
+					"source_comment": null,
+					"status": null,
+					"subject_id": "Subject1",
+					"tissue_block_size": "large",
+					"tumour": true,
+					"tumour_purity": "13",
+					"volume": 42,
+					"well_position": "A:1"
+				}
+			],
+			"synopsis": "A synopsis"
+		}
+	],
+	"comment": null,
+	"customer": "cust000",
+	"data_analysis": "balsamic",
+	"data_delivery": null,
+	"delivery_type": "analysis-scout",
+	"name": "BalsamicOrder",
+	"project_type": "balsamic",
+	"ticket": null,
+	"user_id": 1
+}

tests/fixtures/cgweb_orders/sarscov2.json

@@ -35,7 +35,7 @@
 			"internal_id": null,
 			"lab_code": null,
 			"mother": null,
-			"name": "sarscov2sample1",
+			"name": "control-positive",
 			"organism": "SARS-CoV-2",
 			"organism_other": "",
 			"original_lab": "Karolinska University Hospital Solna",
@@ -94,7 +94,7 @@
 			"internal_id": null,
 			"lab_code": null,
 			"mother": null,
-			"name": "sarscov2sample2",
+			"name": "control-negative",
 			"organism": "SARS-CoV-2",
 			"organism_other": "",
 			"original_lab": "Synlab Medilab",