refactor(decompose sample file formatter) (#3960) (patch)

# Description
refactoring of the sample file formatters

cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py

@@ -24,7 +24,11 @@
 from cg.services.deliver_files.file_formatter.utils.sample_concatenation_service import (
     SampleFileConcatenationFormatter,
 )
-from cg.services.deliver_files.file_formatter.utils.sample_service import SampleFileFormatter
+from cg.services.deliver_files.file_formatter.utils.sample_service import (
+    SampleFileFormatter,
+    FileManagingService,
+    SampleFileNameFormatter,
+)
 from cg.services.deliver_files.file_mover.service import DeliveryFilesMover
 from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.services.deliver_files.tag_fetcher.abstract import FetchDeliveryFileTagsService
@@ -135,8 +139,14 @@ def _get_sample_file_formatter(
         """Get the file formatter service based on the workflow."""
         converted_workflow: Workflow = self._convert_workflow(case)
         if converted_workflow in [Workflow.MICROSALT]:
-            return SampleFileConcatenationFormatter(FastqConcatenationService())
-        return SampleFileFormatter()
+            return SampleFileConcatenationFormatter(
+                file_manager=FileManagingService(),
+                file_formatter=SampleFileNameFormatter(),
+                concatenation_service=FastqConcatenationService(),
+            )
+        return SampleFileFormatter(
+            file_manager=FileManagingService(), file_name_formatter=SampleFileNameFormatter()
+        )
 
     def build_delivery_service(
         self, case: Case, delivery_type: DataDelivery | None = None

cg/services/deliver_files/file_formatter/utils/sample_concatenation_service.py

@@ -9,26 +9,43 @@
 from cg.services.deliver_files.file_fetcher.models import SampleFile
 from cg.services.deliver_files.file_formatter.models import FormattedFile
 from cg.services.deliver_files.file_formatter.utils.sample_service import (
-    SampleFileFormatter,
+    SampleFileNameFormatter,
+    FileManagingService,
 )
 
 
-class SampleFileConcatenationFormatter(SampleFileFormatter):
+class SampleFileConcatenationFormatter:
     """
     Format the sample files to deliver, concatenate fastq files and return the formatted files.
-    Used for workflows: Microsalt and Mutant.
+    Used for workflows: Microsalt.
     """
 
-    def __init__(self, concatenation_service: FastqConcatenationService):
+    def __init__(
+        self,
+        file_manager: FileManagingService,
+        file_formatter: SampleFileNameFormatter,
+        concatenation_service: FastqConcatenationService,
+    ):
+        self.file_manager = file_manager
+        self.file_name_formatter = file_formatter
         self.concatenation_service = concatenation_service
 
     def format_files(
         self, moved_files: list[SampleFile], ticket_dir_path: Path
     ) -> list[FormattedFile]:
         """Format the sample files to deliver, concatenate fastq files and return the formatted files."""
-        formatted_files: list[FormattedFile] = super().format_files(
-            moved_files=moved_files, ticket_dir_path=ticket_dir_path
+        sample_names: set[str] = self.file_name_formatter.get_sample_names(sample_files=moved_files)
+        for sample_name in sample_names:
+            self.file_manager.create_directories(
+                base_path=ticket_dir_path, directories={sample_name}
+            )
+        formatted_files: list[FormattedFile] = self.file_name_formatter.format_sample_file_names(
+            sample_files=moved_files
         )
+        for formatted_file in formatted_files:
+            self.file_manager.rename_file(
+                src=formatted_file.original_path, dst=formatted_file.formatted_path
+            )
         forward_paths, reverse_path = self._concatenate_fastq_files(formatted_files=formatted_files)
         self._replace_fastq_paths(
             reverse_paths=reverse_path,

cg/services/deliver_files/file_formatter/utils/sample_service.py

@@ -4,54 +4,81 @@
 from cg.services.deliver_files.file_formatter.models import FormattedFile
 
 
-class SampleFileFormatter:
+class FileManagingService:
     """
-    Format the sample files to deliver.
-    Used for all workflows except Microsalt and Mutant.
+    Service to manage files.
+    Handles operations that create or rename files and directories.
     """
 
-    def format_files(
-        self, moved_files: list[SampleFile], ticket_dir_path: Path
-    ) -> list[FormattedFile]:
-        """Format the sample files to deliver and return the formatted files."""
-        sample_names: set[str] = self._get_sample_names(moved_files)
-        self._create_sample_folders(ticket_dir_path=ticket_dir_path, sample_names=sample_names)
-        return self._format_sample_files(moved_files)
-
     @staticmethod
-    def _get_sample_names(sample_files: list[SampleFile]) -> set[str]:
-        return set(sample_file.sample_name for sample_file in sample_files)
+    def create_directories(base_path: Path, directories: set[str]) -> None:
+        """Create directories for given names under the base path."""
+        for directory in directories:
+            Path(base_path, directory).mkdir(exist_ok=True)
 
     @staticmethod
-    def _create_sample_folders(ticket_dir_path: Path, sample_names: set[str]):
-        for sample_name in sample_names:
-            sample_dir_path = Path(ticket_dir_path, sample_name)
-            sample_dir_path.mkdir(exist_ok=True)
+    def rename_file(src: Path, dst: Path) -> None:
+        """Rename a file from src to dst."""
+        os.rename(src, dst)
 
-    def _format_sample_files(self, sample_files: list[SampleFile]) -> list[FormattedFile]:
-        formatted_files: list[FormattedFile] = self._get_formatted_files(sample_files)
-        for formatted_file in formatted_files:
-            os.rename(src=formatted_file.original_path, dst=formatted_file.formatted_path)
-        return formatted_files
+
+class SampleFileNameFormatter:
+    """
+    Class to format sample file names.
+    """
+
+    @staticmethod
+    def get_sample_names(sample_files: list[SampleFile]) -> set[str]:
+        """Extract sample names from the sample files."""
+        return {sample_file.sample_name for sample_file in sample_files}
 
     @staticmethod
-    def _get_formatted_files(sample_files: list[SampleFile]) -> list[FormattedFile]:
+    def format_sample_file_names(sample_files: list[SampleFile]) -> list[FormattedFile]:
         """
-        Returns formatted files:
+        Returns formatted files with original and formatted file names:
         1. Adds a folder with sample name to the path of the sample files.
         2. Replaces sample id by sample name.
         """
-        formatted_files: list[FormattedFile] = []
+        formatted_files = []
         for sample_file in sample_files:
-            replaced_sample_file_name: str = sample_file.file_path.name.replace(
+            replaced_name = sample_file.file_path.name.replace(
                 sample_file.sample_id, sample_file.sample_name
             )
-            formatted_file_path = Path(
-                sample_file.file_path.parent, sample_file.sample_name, replaced_sample_file_name
+            formatted_path = Path(
+                sample_file.file_path.parent, sample_file.sample_name, replaced_name
             )
             formatted_files.append(
-                FormattedFile(
-                    original_path=sample_file.file_path, formatted_path=formatted_file_path
-                )
+                FormattedFile(original_path=sample_file.file_path, formatted_path=formatted_path)
+            )
+        return formatted_files
+
+
+class SampleFileFormatter:
+    """
+    Format the sample files to deliver.
+    Used for all workflows except Microsalt and Mutant.
+    """
+
+    def __init__(
+        self, file_manager: FileManagingService, file_name_formatter: SampleFileNameFormatter
+    ):
+        self.file_manager = file_manager
+        self.file_name_formatter = file_name_formatter
+
+    def format_files(
+        self, moved_files: list[SampleFile], ticket_dir_path: Path
+    ) -> list[FormattedFile]:
+        """Format the sample files to deliver and return the formatted files."""
+        sample_names: set[str] = self.file_name_formatter.get_sample_names(sample_files=moved_files)
+        for sample_name in sample_names:
+            self.file_manager.create_directories(
+                base_path=ticket_dir_path, directories={sample_name}
+            )
+        formatted_files: list[FormattedFile] = self.file_name_formatter.format_sample_file_names(
+            sample_files=moved_files
+        )
+        for formatted_file in formatted_files:
+            self.file_manager.rename_file(
+                src=formatted_file.original_path, dst=formatted_file.formatted_path
             )
         return formatted_files

tests/fixture_plugins/delivery_fixtures/delivery_services_fixtures.py

@@ -27,6 +27,8 @@
 )
 from cg.services.deliver_files.file_formatter.utils.sample_service import (
     SampleFileFormatter,
+    FileManagingService,
+    SampleFileNameFormatter,
 )
 from cg.store.store import Store
 
@@ -119,5 +121,8 @@ def analysis_delivery_service_no_housekeeper_bundle(
 def generic_delivery_file_formatter() -> DeliveryFileFormatter:
     """Fixture to get an instance of GenericDeliveryFileFormatter."""
     return DeliveryFileFormatter(
-        sample_file_formatter=SampleFileFormatter(), case_file_formatter=CaseFileFormatter()
+        sample_file_formatter=SampleFileFormatter(
+            file_manager=FileManagingService(), file_name_formatter=SampleFileNameFormatter()
+        ),
+        case_file_formatter=CaseFileFormatter(),
     )

tests/services/file_delivery/delivery_file_service/test_service_builder.py

@@ -37,7 +37,7 @@ class DeliveryServiceScenario(BaseModel):
     expected_tag_fetcher: type[FetchDeliveryFileTagsService]
     expected_file_fetcher: type[FetchDeliveryFilesService]
     expected_file_mover: type[DeliveryFilesMover]
-    expected_sample_file_formatter: type[SampleFileFormatter]
+    expected_sample_file_formatter: type[SampleFileFormatter | SampleFileConcatenationFormatter]
     store_name: str
 
 

tests/services/file_delivery/file_formatter/utils/test_formatter_utils.py

@@ -6,7 +6,6 @@
     FastqConcatenationService,
 )
 from cg.services.deliver_files.file_fetcher.models import (
-    DeliveryFiles,
     CaseFile,
     SampleFile,
 )
@@ -19,6 +18,8 @@
 )
 from cg.services.deliver_files.file_formatter.utils.sample_service import (
     SampleFileFormatter,
+    FileManagingService,
+    SampleFileNameFormatter,
 )
 
 
@@ -33,12 +34,18 @@
         (
             "expected_moved_analysis_sample_delivery_files",
             "expected_formatted_analysis_sample_files",
-            SampleFileFormatter(),
+            SampleFileFormatter(
+                file_manager=FileManagingService(), file_name_formatter=SampleFileNameFormatter()
+            ),
         ),
         (
             "fastq_concatenation_sample_files",
             "expected_concatenated_fastq_formatted_files",
-            SampleFileConcatenationFormatter(FastqConcatenationService()),
+            SampleFileConcatenationFormatter(
+                file_manager=FileManagingService(),
+                file_formatter=SampleFileNameFormatter(),
+                concatenation_service=FastqConcatenationService(),
+            ),
         ),
     ],
 )