move new validation service to orders (#4110)

Move the service in cg/services/order_validation_service/ to cg/services/orders/validation/. Similarly done in the tests
Clinical-Genomics · Jan 17, 2025 · dea27c5 · dea27c5
1 parent f91d98e
commit dea27c5
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Showing 183 changed files with 646 additions and 760 deletions.
diff --git a/cg/meta/orders/api.py b/cg/meta/orders/api.py
@@ -12,10 +12,10 @@
 from cg.apps.lims import LimsAPI
 from cg.meta.orders.ticket_handler import TicketHandler
 from cg.models.orders.constants import OrderType
-from cg.services.order_validation_service.models.order import Order
-from cg.services.order_validation_service.order_validation_service import OrderValidationService
-from cg.services.orders.store_order_services.store_order_service import StoreOrderService
-from cg.services.orders.store_order_services.storing_service_registry import StoringServiceRegistry
+from cg.services.orders.storing.service import StoreOrderService
+from cg.services.orders.storing.service_registry import StoringServiceRegistry
+from cg.services.orders.validation.models.order import Order
+from cg.services.orders.validation.service import OrderValidationService
 from cg.store.models import User
 
 LOG = logging.getLogger(__name__)

diff --git a/cg/meta/orders/ticket_handler.py b/cg/meta/orders/ticket_handler.py
@@ -6,10 +6,10 @@
 from cg.clients.freshdesk.freshdesk_client import FreshdeskClient
 from cg.clients.freshdesk.models import TicketCreate, TicketResponse
 from cg.models.orders.constants import OrderType
-from cg.services.order_validation_service.models.order import Order
-from cg.services.order_validation_service.models.order_with_cases import OrderWithCases
-from cg.services.order_validation_service.models.order_with_samples import OrderWithSamples
 from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
+from cg.services.orders.validation.models.order import Order
+from cg.services.orders.validation.models.order_with_cases import OrderWithCases
+from cg.services.orders.validation.models.order_with_samples import OrderWithSamples
 from cg.store.models import Customer, Sample
 from cg.store.store import Store
 

diff --git a/cg/server/ext.py b/cg/server/ext.py
@@ -12,13 +12,13 @@
 from cg.server.app_config import app_config
 from cg.services.application.service import ApplicationsWebService
 from cg.services.delivery_message.delivery_message_service import DeliveryMessageService
-from cg.services.order_validation_service.order_validation_service import OrderValidationService
 from cg.services.orders.order_service.order_service import OrderService
 from cg.services.orders.order_summary_service.order_summary_service import OrderSummaryService
-from cg.services.orders.store_order_services.storing_service_registry import (
+from cg.services.orders.storing.service_registry import (
     StoringServiceRegistry,
     setup_storing_service_registry,
 )
+from cg.services.orders.validation.service import OrderValidationService
 from cg.services.sample_run_metrics_service.sample_run_metrics_service import (
     SampleRunMetricsService,
 )

diff --git a/cg/services/order_validation_service/models/case_aliases.py b/cg/services/order_validation_service/models/case_aliases.py
diff --git a/cg/services/order_validation_service/models/order_aliases.py b/cg/services/order_validation_service/models/order_aliases.py
diff --git a/cg/services/order_validation_service/models/sample_aliases.py b/cg/services/order_validation_service/models/sample_aliases.py
diff --git a/cg/services/order_validation_service/rules/case_sample/pedigree/validate_pedigree.py b/cg/services/order_validation_service/rules/case_sample/pedigree/validate_pedigree.py
diff --git a/cg/services/order_validation_service/workflows/balsamic_umi/models/case.py b/cg/services/order_validation_service/workflows/balsamic_umi/models/case.py
diff --git a/cg/services/order_validation_service/workflows/balsamic_umi/models/sample.py b/cg/services/order_validation_service/workflows/balsamic_umi/models/sample.py
diff --git a/cg/services/order_validation_service/workflows/fastq/models/order.py b/cg/services/order_validation_service/workflows/fastq/models/order.py
diff --git a/cg/services/order_validation_service/workflows/metagenome/models/order.py b/cg/services/order_validation_service/workflows/metagenome/models/order.py
diff --git a/cg/services/order_validation_service/workflows/microsalt/models/order.py b/cg/services/order_validation_service/workflows/microsalt/models/order.py
diff --git a/cg/services/order_validation_service/workflows/mip_dna/models/order.py b/cg/services/order_validation_service/workflows/mip_dna/models/order.py
diff --git a/cg/services/order_validation_service/workflows/mip_rna/models/order.py b/cg/services/order_validation_service/workflows/mip_rna/models/order.py
diff --git a/cg/services/order_validation_service/workflows/mutant/models/order.py b/cg/services/order_validation_service/workflows/mutant/models/order.py
diff --git a/cg/services/order_validation_service/workflows/pacbio_long_read/models/order.py b/cg/services/order_validation_service/workflows/pacbio_long_read/models/order.py
diff --git a/cg/services/order_validation_service/workflows/rna_fusion/models/order.py b/cg/services/order_validation_service/workflows/rna_fusion/models/order.py
diff --git a/cg/services/order_validation_service/workflows/taxprofiler/models/order.py b/cg/services/order_validation_service/workflows/taxprofiler/models/order.py
diff --git a/cg/services/order_validation_service/workflows/tomte/models/order.py b/cg/services/order_validation_service/workflows/tomte/models/order.py
diff --git a/.../order_lims_service/order_lims_service.py → cg/services/orders/lims_service/service.py b/.../order_lims_service/order_lims_service.py → cg/services/orders/lims_service/service.py
@@ -3,9 +3,9 @@
 from cg.apps.lims import LimsAPI
 from cg.constants import DataDelivery, Workflow
 from cg.models.lims.sample import LimsSample
-from cg.services.order_validation_service.models.sample import Sample
-from cg.services.order_validation_service.workflows.microsalt.models.sample import MicrosaltSample
-from cg.services.order_validation_service.workflows.mutant.models.sample import MutantSample
+from cg.services.orders.validation.models.sample import Sample
+from cg.services.orders.validation.workflows.microsalt.models.sample import MicrosaltSample
+from cg.services.orders.validation.workflows.mutant.models.sample import MutantSample
 
 LOG = logging.getLogger(__name__)
 

diff --git a/...der_validation_service/errors/__init__.py → cg/services/orders/storing/__init__.py b/...der_validation_service/errors/__init__.py → cg/services/orders/storing/__init__.py
diff --git a/.../orders/store_order_services/constants.py → cg/services/orders/storing/constants.py b/.../orders/store_order_services/constants.py → cg/services/orders/storing/constants.py
diff --git a/...ation_service/model_validator/__init__.py → ...rders/storing/implementations/__init__.py b/...ation_service/model_validator/__init__.py → ...rders/storing/implementations/__init__.py
diff --git a/...vices/implementations/store_case_order.py → ...ing/implementations/case_order_service.py b/...vices/implementations/store_case_order.py → ...ing/implementations/case_order_service.py
@@ -3,13 +3,13 @@
 
 from cg.constants.constants import CaseActions, DataDelivery, Workflow
 from cg.constants.pedigree import Pedigree
-from cg.services.order_validation_service.models.case import Case
-from cg.services.order_validation_service.models.existing_case import ExistingCase
-from cg.services.order_validation_service.models.order_with_cases import OrderWithCases
-from cg.services.order_validation_service.models.sample_aliases import SampleInCase
 from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
-from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.store_order_services.store_order_service import StoreOrderService
+from cg.services.orders.lims_service.service import OrderLimsService
+from cg.services.orders.storing.service import StoreOrderService
+from cg.services.orders.validation.models.case import Case
+from cg.services.orders.validation.models.existing_case import ExistingCase
+from cg.services.orders.validation.models.order_with_cases import OrderWithCases
+from cg.services.orders.validation.models.sample_aliases import SampleInCase
 from cg.store.models import ApplicationVersion
 from cg.store.models import Case as DbCase
 from cg.store.models import CaseSample, Customer

diff --git a/...lementations/store_fastq_order_service.py → ...ng/implementations/fastq_order_service.py b/...lementations/store_fastq_order_service.py → ...ng/implementations/fastq_order_service.py
@@ -5,11 +5,11 @@
 from cg.constants.constants import CustomerId
 from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.models.orders.sample_base import SexEnum, StatusEnum
-from cg.services.order_validation_service.workflows.fastq.models.order import FastqOrder
-from cg.services.order_validation_service.workflows.fastq.models.sample import FastqSample
-from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.store_order_services.constants import MAF_ORDER_ID
-from cg.services.orders.store_order_services.store_order_service import StoreOrderService
+from cg.services.orders.lims_service.service import OrderLimsService
+from cg.services.orders.storing.constants import MAF_ORDER_ID
+from cg.services.orders.storing.service import StoreOrderService
+from cg.services.orders.validation.workflows.fastq.models.order import FastqOrder
+from cg.services.orders.validation.workflows.fastq.models.sample import FastqSample
 from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store
 

diff --git a/...implementations/store_metagenome_order.py → ...plementations/metagenome_order_service.py b/...implementations/store_metagenome_order.py → ...plementations/metagenome_order_service.py
@@ -3,15 +3,13 @@
 
 from cg.constants import DataDelivery, Sex
 from cg.models.orders.sample_base import PriorityEnum, StatusEnum
-from cg.services.order_validation_service.workflows.metagenome.models.order import MetagenomeOrder
-from cg.services.order_validation_service.workflows.metagenome.models.sample import MetagenomeSample
-from cg.services.order_validation_service.workflows.taxprofiler.models.order import TaxprofilerOrder
-from cg.services.order_validation_service.workflows.taxprofiler.models.sample import (
-    TaxprofilerSample,
-)
 from cg.services.orders.constants import ORDER_TYPE_WORKFLOW_MAP
-from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.store_order_services.store_order_service import StoreOrderService
+from cg.services.orders.lims_service.service import OrderLimsService
+from cg.services.orders.storing.service import StoreOrderService
+from cg.services.orders.validation.workflows.metagenome.models.order import MetagenomeOrder
+from cg.services.orders.validation.workflows.metagenome.models.sample import MetagenomeSample
+from cg.services.orders.validation.workflows.taxprofiler.models.order import TaxprofilerOrder
+from cg.services.orders.validation.workflows.taxprofiler.models.sample import TaxprofilerSample
 from cg.store.models import ApplicationVersion
 from cg.store.models import Case as DbCase
 from cg.store.models import CaseSample, Customer

diff --git a/...ns/store_microbial_fastq_order_service.py → ...ntations/microbial_fastq_order_service.py b/...ns/store_microbial_fastq_order_service.py → ...ntations/microbial_fastq_order_service.py
@@ -2,14 +2,12 @@
 
 from cg.constants import DataDelivery, SexOptions, Workflow
 from cg.models.orders.sample_base import StatusEnum
-from cg.services.order_validation_service.workflows.microbial_fastq.models.order import (
-    MicrobialFastqOrder,
-)
-from cg.services.order_validation_service.workflows.microbial_fastq.models.sample import (
+from cg.services.orders.lims_service.service import OrderLimsService
+from cg.services.orders.storing.service import StoreOrderService
+from cg.services.orders.validation.workflows.microbial_fastq.models.order import MicrobialFastqOrder
+from cg.services.orders.validation.workflows.microbial_fastq.models.sample import (
     MicrobialFastqSample,
 )
-from cg.services.orders.order_lims_service.order_lims_service import OrderLimsService
-from cg.services.orders.store_order_services.store_order_service import StoreOrderService
 from cg.store.models import ApplicationVersion, Case, CaseSample, Customer, Order, Sample
 from cg.store.store import Store