Merge branch 'feat-run-name-service' into feat-post-process-all

Author: diitaz93

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_")

cg/services/run_devices/run_names/pacbio.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 
-from cg.services.run_devices.run_names.service import RunNamesService
+from cg.services.run_devices.run_names.service import RunDirectoryNamesService
 
 
-class PacbioRunNamesService(RunNamesService):
+class PacbioRunDirectoryNamesService(RunDirectoryNamesService):
 
     def get_run_names(self) -> list[str]:
         """

cg/services/run_devices/run_names/service.py

@@ -1,7 +1,7 @@
 from abc import ABC, abstractmethod
 
 
-class RunNamesService(ABC):
+class RunDirectoryNamesService(ABC):
 
     def __init__(self, run_directory: str):
         self.run_directory = run_directory

tests/fixture_plugins/pacbio_fixtures/service_fixtures.py

@@ -22,7 +22,7 @@
 )
 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 PacbioRunNamesService
+from cg.services.run_devices.run_names.pacbio import PacbioRunDirectoryNamesService
 from cg.store.store import Store
 
 # Mocked services
@@ -51,8 +51,8 @@ def pac_bio_run_file_manager() -> PacBioRunFileManager:
 
 
 @pytest.fixture
-def pacbio_run_names_service(pac_bio_runs_dir: Path) -> PacbioRunNamesService:
-    return PacbioRunNamesService(run_directory=pac_bio_runs_dir.as_posix())
+def pacbio_run_names_service(pac_bio_runs_dir: Path) -> PacbioRunDirectoryNamesService:
+    return PacbioRunDirectoryNamesService(run_directory=pac_bio_runs_dir.as_posix())
 
 
 @pytest.fixture

tests/services/run_names/test_pacbio_run_names_service.py

@@ -1,10 +1,10 @@
 from pathlib import Path
 
-from cg.services.run_devices.run_names.pacbio import PacbioRunNamesService
+from cg.services.run_devices.run_names.pacbio import PacbioRunDirectoryNamesService
 
 
 def test_pacbio_get_run_names(
-    pacbio_run_names_service: PacbioRunNamesService, pacbio_run_names: set
+    pacbio_run_names_service: PacbioRunDirectoryNamesService, pacbio_run_names: set
 ):
     """Test that getting PacBio run names works."""
     # GIVEN a PacBio run names service
@@ -18,7 +18,7 @@ def test_pacbio_get_run_names(
 
 def test_pacbio_get_run_names_empty(tmp_path: Path):
     # GIVEN a run directory with no run folders and a PacBio run names service
-    pacbio_run_names_service: PacbioRunNamesService = PacbioRunNamesService(
+    pacbio_run_names_service: PacbioRunDirectoryNamesService = PacbioRunDirectoryNamesService(
         run_directory=tmp_path.as_posix()
     )
 
@@ -35,7 +35,7 @@ def test_pacbio_get_run_names_with_files_return_emty(tmp_path: Path):
     run_dir.mkdir()
     Path(run_dir, "file1").touch()
     Path(run_dir, "file2").touch()
-    pacbio_run_names_service: PacbioRunNamesService = PacbioRunNamesService(
+    pacbio_run_names_service: PacbioRunDirectoryNamesService = PacbioRunDirectoryNamesService(
         run_directory=run_dir.as_posix()
     )
 
@@ -52,7 +52,7 @@ def test_pacbio_get_run_names_with_subfolders_return_empty(tmp_path: Path):
     run_dir.mkdir()
     subfolder = Path(run_dir, "subfolder")
     subfolder.mkdir()
-    pacbio_run_names_service: PacbioRunNamesService = PacbioRunNamesService(
+    pacbio_run_names_service: PacbioRunDirectoryNamesService = PacbioRunDirectoryNamesService(
         run_directory=run_dir.as_posix()
     )