add service to config

Clinical-Genomics · Oct 11, 2024 · 9d08561 · 9d08561
1 parent 4e1977f
commit 9d08561
Showing 1 changed file with 25 additions and 13 deletions.
diff --git a/cg/models/cg_config.py b/cg/models/cg_config.py
@@ -2,7 +2,7 @@
 from pathlib import Path
 from typing import Any
 
-from pydantic import BaseModel, EmailStr, Field, ConfigDict
+from pydantic import BaseModel, ConfigDict, EmailStr, Field
 from typing_extensions import Literal
 
 from cg.apps.coverage import ChanjoAPI
@@ -47,21 +47,14 @@
 from cg.services.run_devices.pacbio.housekeeper_service.pacbio_houskeeper_service import (
     PacBioHousekeeperService,
 )
-from cg.services.run_devices.pacbio.metrics_parser.metrics_parser import (
-    PacBioMetricsParser,
-)
-from cg.services.run_devices.pacbio.post_processing_service import (
-    PacBioPostProcessingService,
-)
+from cg.services.run_devices.pacbio.metrics_parser.metrics_parser import PacBioMetricsParser
+from cg.services.run_devices.pacbio.post_processing_service import PacBioPostProcessingService
 from cg.services.run_devices.pacbio.run_data_generator.pacbio_run_data_generator import (
     PacBioRunDataGenerator,
 )
-from cg.services.run_devices.pacbio.run_file_manager.run_file_manager import (
-    PacBioRunFileManager,
-)
-from cg.services.run_devices.pacbio.run_validator.pacbio_run_validator import (
-    PacBioRunValidator,
-)
+from cg.services.run_devices.pacbio.run_file_manager.run_file_manager import PacBioRunFileManager
+from cg.services.run_devices.pacbio.run_validator.pacbio_run_validator import PacBioRunValidator
+from cg.services.run_devices.run_names.pacbio import PacbioRunDirectoryNamesService
 from cg.services.sequencing_qc_service.sequencing_qc_service import SequencingQCService
 from cg.services.slurm_service.slurm_cli_service import SlurmCLIService
 from cg.services.slurm_service.slurm_service import SlurmService
@@ -360,6 +353,13 @@ class RunInstruments(BaseModel):
     illumina: IlluminaConfig
 
 
+class RunDirectoryNamesServices(BaseModel):
+    pacbio: PacbioRunDirectoryNamesService
+
+    class Config:
+        arbitrary_types_allowed = True
+
+
 class PostProcessingServices(BaseModel):
     pacbio: PacBioPostProcessingService
 
@@ -427,6 +427,7 @@ class CGConfig(BaseModel):
     pdc_service_: PdcService | None = None
     post_processing_services_: PostProcessingServices | None = None
     pigz: CommonAppConfig | None = None
+    run_directory_names_services_: RunDirectoryNamesServices | None = None
     sample_sheet_api_: IlluminaSampleSheetService | None = None
     scout: CommonAppConfig = None
     scout_api_: ScoutAPI = None
@@ -633,6 +634,17 @@ def pdc_service(self) -> PdcService:
             self.pdc_service_ = service
         return service
 
+    @property
+    def run_directory_names_services(self) -> RunDirectoryNamesServices:
+        services = self.__dict__.get("run_directory_names_services_")
+        if services is None:
+            LOG.debug("Instantiating run directory names services")
+            services = RunDirectoryNamesServices(
+                pacbio=PacbioRunDirectoryNamesService(self.run_instruments.pacbio.data_dir)
+            )
+            self.run_directory_names_services_ = services
+        return services
+
     @property
     def sample_sheet_api(self) -> IlluminaSampleSheetService:
         sample_sheet_api = self.__dict__.get("sample_sheet_api_")