Merge branch 'refs/heads/improve-order-flow-main' into add-pool-rules

tests/conftest.py

@@ -118,11 +118,10 @@
     "tests.fixture_plugins.observations_fixtures.observations_api_fixtures",
     "tests.fixture_plugins.observations_fixtures.observations_input_files_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_form_fixtures",
-    "tests.fixture_plugins.orders_fixtures.order_store_service_fixtures",
     "tests.fixture_plugins.orders_fixtures.order_to_submit_fixtures",
-    "tests.fixture_plugins.orders_fixtures.orders_fixtures",
-    "tests.fixture_plugins.orders_fixtures.status_data_fixtures",
+    "tests.fixture_plugins.orders_fixtures.order_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.pacbio_fixtures.dto_fixtures",
     "tests.fixture_plugins.pacbio_fixtures.file_data_fixtures",

tests/fixture_plugins/orders_fixtures/status_data_fixtures.py → tests/fixture_plugins/orders_fixtures/order_fixtures.py

@@ -1,66 +1,71 @@
+"""Fixtures for orders parsed into their respective models."""
+
 import pytest
 
-from cg.models.orders.constants import OrderType
-from cg.services.order_validation_service.order_validation_service import OrderValidationService
 from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
 from cg.services.order_validation_service.workflows.fastq.models.order import FastqOrder
 from cg.services.order_validation_service.workflows.fluffy.models.order import FluffyOrder
 from cg.services.order_validation_service.workflows.metagenome.models.order import MetagenomeOrder
+from cg.services.order_validation_service.workflows.microbial_fastq.models.order import (
+    MicrobialFastqOrder,
+)
 from cg.services.order_validation_service.workflows.microsalt.models.order import MicrosaltOrder
 from cg.services.order_validation_service.workflows.mip_dna.models.order import MipDnaOrder
 from cg.services.order_validation_service.workflows.mip_rna.models.order import MipRnaOrder
+from cg.services.order_validation_service.workflows.pacbio_long_read.models.order import PacbioOrder
 from cg.services.order_validation_service.workflows.rml.models.order import RmlOrder
-from cg.services.orders.store_order_services.store_metagenome_order import (
-    StoreMetagenomeOrderService,
-)
-from cg.store.store import Store
-from tests.store_helpers import StoreHelpers
 
 
 @pytest.fixture
-def metagenome_order(
-    metagenome_order_to_submit: dict, store_metagenome_order_service: StoreMetagenomeOrderService
-) -> MetagenomeOrder:
-    """Parse metagenome order example."""
-    order_validation_service = OrderValidationService(store_metagenome_order_service.status_db)
-    order: MetagenomeOrder = order_validation_service.parse_and_validate(
-        raw_order=metagenome_order_to_submit, order_type=OrderType.METAGENOME
-    )
-    order._generated_ticket_id = 123456
-    return order
+def balsamic_order(balsamic_order_to_submit: dict) -> BalsamicOrder:
+    balsamic_order_to_submit["user_id"] = 1
+    balsamic_order = BalsamicOrder.model_validate(balsamic_order_to_submit)
+    balsamic_order._generated_ticket_id = 123456
+    for case_index, sample_index, sample in balsamic_order.enumerated_new_samples:
+        sample._generated_lims_id = f"ACC{case_index}-{sample_index}"
+    return balsamic_order
 
 
 @pytest.fixture
-def valid_rml_order(rml_order_to_submit: dict, ticket_id_as_int: int) -> RmlOrder:
-    """Parse rml order example."""
-    rml_order = RmlOrder.model_validate(rml_order_to_submit)
-    rml_order._generated_ticket_id = ticket_id_as_int
-    return rml_order
+def fastq_order(fastq_order_to_submit: dict) -> FastqOrder:
+    fastq_order = FastqOrder.model_validate(fastq_order_to_submit)
+    fastq_order._generated_ticket_id = 123456
+    return fastq_order
 
 
 @pytest.fixture
-def valid_fluffy_order(fluffy_order_to_submit: dict, ticket_id_as_int: int) -> FluffyOrder:
+def fluffy_order(fluffy_order_to_submit: dict, ticket_id_as_int: int) -> FluffyOrder:
     """Parse Fluffy order example."""
     fluffy_order = FluffyOrder.model_validate(fluffy_order_to_submit)
     fluffy_order._generated_ticket_id = ticket_id_as_int
     return fluffy_order
 
 
 @pytest.fixture
-def fastq_order(fastq_order_to_submit: dict) -> FastqOrder:
-    fastq_order = FastqOrder.model_validate(fastq_order_to_submit)
-    fastq_order._generated_ticket_id = 123456
-    return fastq_order
+def metagenome_order(
+    metagenome_order_to_submit: dict,
+    ticket_id_as_int: int,
+) -> MetagenomeOrder:
+    """Parse metagenome order example."""
+    order = MetagenomeOrder.model_validate(metagenome_order_to_submit)
+    order._generated_ticket_id = ticket_id_as_int
+    return order
 
 
 @pytest.fixture
-def mip_rna_order(mip_rna_order_to_submit: dict) -> MipRnaOrder:
-    mip_rna_order_to_submit["user_id"] = 1
-    mip_rna_order = MipRnaOrder.model_validate(mip_rna_order_to_submit)
-    for case_index, sample_index, sample in mip_rna_order.enumerated_new_samples:
-        sample._generated_lims_id = f"ACC{case_index}-{sample_index}"
-    mip_rna_order._generated_ticket_id = 123456
-    return mip_rna_order
+def microbial_fastq_order(
+    microbial_fastq_order_to_submit: dict, ticket_id_as_int: int
+) -> MicrobialFastqOrder:
+    order = MicrobialFastqOrder.model_validate(microbial_fastq_order_to_submit)
+    order._generated_ticket_id = ticket_id_as_int
+    return order
+
+
+@pytest.fixture
+def microsalt_order(microbial_order_to_submit: dict) -> MicrosaltOrder:
+    order = MicrosaltOrder.model_validate(microbial_order_to_submit)
+    order._generated_ticket_id = 123456
+    return order
 
 
 @pytest.fixture
@@ -74,45 +79,25 @@ def mip_dna_order(mip_dna_order_to_submit: dict) -> MipDnaOrder:
 
 
 @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 balsamic_order(balsamic_order_to_submit: dict) -> BalsamicOrder:
-    balsamic_order_to_submit["user_id"] = 1
-    balsamic_order = BalsamicOrder.model_validate(balsamic_order_to_submit)
-    balsamic_order._generated_ticket_id = 123456
-    for case_index, sample_index, sample in balsamic_order.enumerated_new_samples:
+def mip_rna_order(mip_rna_order_to_submit: dict) -> MipRnaOrder:
+    mip_rna_order_to_submit["user_id"] = 1
+    mip_rna_order = MipRnaOrder.model_validate(mip_rna_order_to_submit)
+    for case_index, sample_index, sample in mip_rna_order.enumerated_new_samples:
         sample._generated_lims_id = f"ACC{case_index}-{sample_index}"
-    return balsamic_order
+    mip_rna_order._generated_ticket_id = 123456
+    return mip_rna_order
 
 
 @pytest.fixture
-def balsamic_submit_store(
-    base_store: Store, balsamic_order: BalsamicOrder, helpers: StoreHelpers
-) -> 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
+def pacbio_order(pacbio_order_to_submit: dict, ticket_id_as_int: int) -> PacbioOrder:
+    order = PacbioOrder.model_validate(pacbio_order_to_submit)
+    order._generated_ticket_id = ticket_id_as_int
+    return order
 
 
 @pytest.fixture
-def microsalt_order(microbial_order_to_submit: dict) -> MicrosaltOrder:
-    order = MicrosaltOrder.model_validate(microbial_order_to_submit)
-    order._generated_ticket_id = 123456
-    return order
+def rml_order(rml_order_to_submit: dict, ticket_id_as_int: int) -> RmlOrder:
+    """Parse rml order example."""
+    rml_order = RmlOrder.model_validate(rml_order_to_submit)
+    rml_order._generated_ticket_id = ticket_id_as_int
+    return rml_order

tests/fixture_plugins/orders_fixtures/order_to_submit_fixtures.py

@@ -1,3 +1,5 @@
+"""Fixtures for orders parsed from JSON files into dictionaries."""
+
 from pathlib import Path
 
 import pytest

tests/fixture_plugins/orders_fixtures/store_fixtures.py

@@ -1,10 +1,30 @@
+"""Store fixtures for the order services tests."""
+
 import pytest
 
 from cg.constants.sequencing import SeqLibraryPrepCategory
+from cg.models.orders.constants import OrderType
+from cg.services.order_validation_service.workflows.balsamic.models.order import BalsamicOrder
+from cg.services.order_validation_service.workflows.mip_dna.models.order import MipDnaOrder
+from cg.store.models import Application
 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
+) -> 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"]
@@ -16,3 +36,32 @@ def store_with_rml_applications(store: Store, helpers: StoreHelpers) -> Store:
         )
     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

tests/fixture_plugins/orders_fixtures/order_store_service_fixtures.py → tests/fixture_plugins/orders_fixtures/store_service_fixtures.py

@@ -1,6 +1,5 @@
 import pytest
 
-from cg.models.orders.constants import OrderType
 from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
 from cg.services.orders.store_order_services.store_case_order import StoreCaseOrderService
 from cg.services.orders.store_order_services.store_fastq_order_service import StoreFastqOrderService
@@ -15,7 +14,6 @@
     StorePacBioOrderService,
 )
 from cg.services.orders.store_order_services.store_pool_order import StorePoolOrderService
-from cg.store.models import Application
 from cg.store.store import Store
 from tests.mocks.limsmock import MockLimsAPI
 from tests.store_helpers import StoreHelpers
@@ -45,21 +43,6 @@ def store_pacbio_order_service(base_store: Store, lims_api: MockLimsAPI) -> Stor
     return StorePacBioOrderService(status_db=base_store, lims_service=OrderLimsService(lims_api))
 
 
-@pytest.fixture
-def metagenome_storing_store(base_store: Store, helpers: StoreHelpers):
-    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 store_metagenome_order_service(
     metagenome_storing_store: Store, lims_api: MockLimsAPI, helpers: StoreHelpers

tests/fixtures/cgweb_orders/microbial_fastq.json

@@ -1,6 +1,9 @@
 {
     "name": "Microbial Fastq order",
-    "customer": "cust002",
+    "customer": "cust000",
+    "delivery_type": "fastq",
+    "project_type": "microbial-fastq",
+    "user_id": 0,
     "comment": "",
     "samples": [
         {