add(delivery service factory)

cg/services/file_delivery/abstract_classes.py → cg/services/file_delivery/deliver_files_service/deliver_files_service.py

@@ -1,30 +1,24 @@
-from abc import abstractmethod, ABC
-
+from pathlib import Path
 from cg.services.file_delivery.fetch_file_service.fetch_delivery_files_service import (
     FetchDeliveryFilesService,
 )
-
+from cg.services.file_delivery.fetch_file_service.models import DeliveryFiles
 from cg.services.file_delivery.file_formatter_service.delivery_file_formatting_service import (
     DeliveryFileFormattingService,
 )
-
 from cg.services.file_delivery.move_files_service.move_delivery_files_service import (
     MoveDeliveryFilesService,
 )
 
 
-class DeliverFilesService(ABC):
+class DeliverFilesService:
     """
-    Abstract class that encapsulates the logic required for delivering files to the customer.
-
+    Deliver files to the customer inbox on hasta.
     1. Get the files to deliver from Housekeeper based on workflow and data delivery
     2. Create a delivery folder structure in the customer folder on Hasta and move the files there
     3. Reformatting of output / renaming of files
-    4. Start a Rsync job to upload the files to Caesar
-    5. Track the status of the Rsync job in Trailblazer
     """
 
-    @abstractmethod
     def __init__(
         self,
         delivery_file_manager_service: FetchDeliveryFilesService,
@@ -35,7 +29,10 @@ def __init__(
         self.file_mover = move_file_service
         self.file_formatter = file_formatter_service
 
-    @abstractmethod
-    def deliver_files_for_case(self, case_id: str) -> None:
+    def deliver_files_for_case(self, case_id: str, delivery_base_path: Path) -> None:
         """Deliver the files to the customer folder."""
-        pass
+        delivery_files: DeliveryFiles = self.file_manager.get_files_to_deliver(case_id)
+        moved_files: DeliveryFiles = self.file_mover.move_files(
+            delivery_files=delivery_files, delivery_base_path=delivery_base_path
+        )
+        self.file_formatter.format_files(moved_files)

cg/services/file_delivery/deliver_files_service/deliver_files_service_factory.py

@@ -0,0 +1,104 @@
+"""Module for the factory of the deliver files service."""
+
+from cg.apps.housekeeper.hk import HousekeeperAPI
+from cg.constants import Workflow, DataDelivery
+from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
+    FastqConcatenationService,
+)
+from cg.services.file_delivery.deliver_files_service.deliver_files_service import (
+    DeliverFilesService,
+)
+from cg.services.file_delivery.fetch_delivery_files_tags.fetch_delivery_file_tags_service import (
+    FetchDeliveryFileTagsService,
+)
+from cg.services.file_delivery.fetch_delivery_files_tags.fetch_sample_and_case_delivery_file_tags_service import (
+    FetchSampleAndCaseDeliveryFileTagsService,
+)
+from cg.services.file_delivery.fetch_file_service.fetch_analysis_files_service import (
+    FetchAnalysisDeliveryFilesService,
+)
+from cg.services.file_delivery.fetch_file_service.fetch_delivery_files_service import (
+    FetchDeliveryFilesService,
+)
+from cg.services.file_delivery.fetch_file_service.fetch_fastq_analysis_files_service import (
+    FetchFastqAndAnalysisDeliveryFilesService,
+)
+from cg.services.file_delivery.fetch_file_service.fetch_fastq_files_service import (
+    FetchFastqDeliveryFilesService,
+)
+from cg.services.file_delivery.file_formatter_service.delivery_file_formatter import (
+    DeliveryFileFormatter,
+)
+
+from cg.services.file_delivery.file_formatter_service.delivery_file_formatting_service import (
+    DeliveryFileFormattingService,
+)
+from cg.services.file_delivery.file_formatter_service.utils.case_file_formatter import (
+    CaseFileFormatter,
+)
+from cg.services.file_delivery.file_formatter_service.utils.sample_file_concatenation_formatter import (
+    SampleFileConcatenationFormatter,
+)
+from cg.services.file_delivery.file_formatter_service.utils.sample_file_formatter import (
+    SampleFileFormatter,
+)
+from cg.services.file_delivery.move_files_service.move_delivery_files_service import (
+    MoveDeliveryFilesService,
+)
+from cg.store.store import Store
+
+
+class DeliveryServiceBuilder:
+    """Class to build the delivery services based on workflow and delivery type."""
+
+    def __init__(self, store: Store, hk_api: HousekeeperAPI):
+        self.store = store
+        self.hk_api = hk_api
+
+    @staticmethod
+    def _get_file_tag_fetcher(delivery_type: DataDelivery) -> FetchDeliveryFileTagsService:
+        """Get the file tag fetcher based on the delivery type."""
+        service_map = {
+            DataDelivery.FASTQ: FetchSampleAndCaseDeliveryFileTagsService,
+            DataDelivery.ANALYSIS_FILES: FetchSampleAndCaseDeliveryFileTagsService,
+            DataDelivery.FASTQ_ANALYSIS: FetchSampleAndCaseDeliveryFileTagsService,
+        }
+        return service_map[delivery_type]()
+
+    def _get_file_fetcher(self, delivery_type: DataDelivery) -> FetchDeliveryFilesService:
+        """Get the file fetcher based on the delivery type."""
+        service_map = {
+            DataDelivery.FASTQ: FetchFastqDeliveryFilesService,
+            DataDelivery.ANALYSIS_FILES: FetchAnalysisDeliveryFilesService,
+            DataDelivery.FASTQ_ANALYSIS: FetchFastqAndAnalysisDeliveryFilesService,
+        }
+        file_tag_fetcher = self._get_file_tag_fetcher(delivery_type)
+        return service_map[delivery_type](
+            status_db=self.store,
+            hk_api=self.hk_api,
+            tags_fetcher=file_tag_fetcher,
+        )
+
+    @staticmethod
+    def _get_sample_file_formatter(
+        workflow: Workflow,
+    ) -> SampleFileFormatter | SampleFileConcatenationFormatter:
+        """Get the file formatter service based on the workflow."""
+        if workflow in [Workflow.MICROSALT, Workflow.MUTANT]:
+            return SampleFileConcatenationFormatter(FastqConcatenationService())
+        return SampleFileFormatter()
+
+    def build_delivery_service(
+        self, workflow: Workflow, delivery_type: DataDelivery
+    ) -> DeliverFilesService:
+        """Build a delivery service based on the workflow and delivery type."""
+        file_fetcher = self._get_file_fetcher(delivery_type)
+        sample_file_formatter = self._get_sample_file_formatter(workflow)
+        file_formatter: DeliveryFileFormattingService = DeliveryFileFormatter(
+            case_file_formatter=CaseFileFormatter(), sample_file_formatter=sample_file_formatter
+        )
+        return DeliverFilesService(
+            delivery_file_manager_service=file_fetcher,
+            move_file_service=MoveDeliveryFilesService(),
+            file_formatter_service=file_formatter,
+        )

cg/services/file_delivery/fetch_file_service/fetch_fastq_analysis_files_service.py

@@ -1,4 +1,7 @@
 from cg.apps.housekeeper.hk import HousekeeperAPI
+from cg.services.file_delivery.fetch_delivery_files_tags.fetch_delivery_file_tags_service import (
+    FetchDeliveryFileTagsService,
+)
 from cg.services.file_delivery.fetch_delivery_files_tags.fetch_sample_and_case_delivery_file_tags_service import (
     FetchSampleAndCaseDeliveryFileTagsService,
 )
@@ -17,30 +20,33 @@
 
 
 class FetchFastqAndAnalysisDeliveryFilesService(FetchDeliveryFilesService):
-    def __init__(self, status_db: Store, hk_api: HousekeeperAPI):
+
+    def __init__(
+        self, status_db: Store, hk_api: HousekeeperAPI, tags_fetcher: FetchDeliveryFileTagsService
+    ):
         self.status_db = status_db
         self.hk_api = hk_api
+        self.tags_fetcher = tags_fetcher
 
     def get_files_to_deliver(self, case_id: str) -> DeliveryFiles:
-        case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
-        fetch_fastq_service = FetchFastqDeliveryFilesService(
-            self.status_db,
-            self.hk_api,
-            tags_fetcher=FetchSampleAndCaseDeliveryFileTagsService(),
-        )
-        fetch_analysis_service = FetchAnalysisDeliveryFilesService(
-            self.status_db,
-            self.hk_api,
-            tags_fetcher=FetchSampleAndCaseDeliveryFileTagsService(),
-        )
-
-        fastq_files: DeliveryFiles = fetch_fastq_service.get_files_to_deliver(case_id)
-        analysis_files: DeliveryFiles = fetch_analysis_service.get_files_to_deliver(case_id)
+        case = self._get_case(case_id)
+        fastq_files = self._fetch_files(FetchFastqDeliveryFilesService, case_id)
+        analysis_files = self._fetch_files(FetchAnalysisDeliveryFilesService, case_id)
         delivery_data = DeliveryMetaData(
             customer_internal_id=case.customer.internal_id, ticket_id=case.latest_ticket
         )
+
         return DeliveryFiles(
             delivery_data=delivery_data,
             case_files=analysis_files.case_files,
             sample_files=analysis_files.sample_files + fastq_files.sample_files,
         )
+
+    def _get_case(self, case_id: str) -> Case:
+        """Fetch the case from the database."""
+        return self.status_db.get_case_by_internal_id(internal_id=case_id)
+
+    def _fetch_files(self, service_class: type, case_id: str) -> DeliveryFiles:
+        """Fetch files using the provided service class."""
+        service = service_class(self.status_db, self.hk_api, tags_fetcher=self.tags_fetcher)
+        return service.get_files_to_deliver(case_id)

tests/services/file_delivery/delivery_file_service/test_delivery_file_service_builder.py

@@ -0,0 +1,87 @@
+import pytest
+from unittest.mock import MagicMock, patch
+
+from cg.constants import Workflow, DataDelivery
+from cg.services.file_delivery.deliver_files_service.deliver_files_service import (
+    DeliverFilesService,
+)
+from cg.services.file_delivery.deliver_files_service.deliver_files_service_factory import (
+    DeliveryServiceBuilder,
+)
+from cg.services.file_delivery.fetch_delivery_files_tags.fetch_sample_and_case_delivery_file_tags_service import (
+    FetchSampleAndCaseDeliveryFileTagsService,
+)
+from cg.services.file_delivery.fetch_file_service.fetch_analysis_files_service import (
+    FetchAnalysisDeliveryFilesService,
+)
+from cg.services.file_delivery.fetch_file_service.fetch_fastq_analysis_files_service import (
+    FetchFastqAndAnalysisDeliveryFilesService,
+)
+from cg.services.file_delivery.fetch_file_service.fetch_fastq_files_service import (
+    FetchFastqDeliveryFilesService,
+)
+from cg.services.file_delivery.file_formatter_service.utils.sample_file_concatenation_formatter import (
+    SampleFileConcatenationFormatter,
+)
+from cg.services.file_delivery.file_formatter_service.utils.sample_file_formatter import (
+    SampleFileFormatter,
+)
+from cg.services.file_delivery.move_files_service.move_delivery_files_service import (
+    MoveDeliveryFilesService,
+)
+
+
+@pytest.mark.parametrize(
+    "workflow,delivery_type,expected_tag_fetcher,expected_file_fetcher,expected_file_mover,expected_sample_file_formatter",
+    [
+        (
+            Workflow.MICROSALT,
+            DataDelivery.FASTQ,
+            FetchSampleAndCaseDeliveryFileTagsService,
+            FetchFastqDeliveryFilesService,
+            MoveDeliveryFilesService,
+            SampleFileConcatenationFormatter,
+        ),
+        (
+            Workflow.MUTANT,
+            DataDelivery.ANALYSIS_FILES,
+            FetchSampleAndCaseDeliveryFileTagsService,
+            FetchAnalysisDeliveryFilesService,
+            MoveDeliveryFilesService,
+            SampleFileConcatenationFormatter,
+        ),
+        (
+            Workflow.BALSAMIC,
+            DataDelivery.FASTQ_ANALYSIS,
+            FetchSampleAndCaseDeliveryFileTagsService,
+            FetchFastqAndAnalysisDeliveryFilesService,
+            MoveDeliveryFilesService,
+            SampleFileFormatter,
+        ),
+    ],
+)
+def test_build_delivery_service(
+    workflow,
+    delivery_type,
+    expected_tag_fetcher,
+    expected_file_fetcher,
+    expected_file_mover,
+    expected_sample_file_formatter,
+):
+    # GIVEN a delivery service builder with mocked store and hk_api
+    store_mock = MagicMock()
+    hk_api_mock = MagicMock()
+    builder = DeliveryServiceBuilder(store=store_mock, hk_api=hk_api_mock)
+
+    # WHEN building a delivery service
+    delivery_service: DeliverFilesService = builder.build_delivery_service(
+        workflow=workflow, delivery_type=delivery_type
+    )
+
+    # THEN the correct file formatter and file fetcher services are used
+    assert isinstance(delivery_service.file_manager.tags_fetcher, expected_tag_fetcher)
+    assert isinstance(delivery_service.file_manager, expected_file_fetcher)
+    assert isinstance(delivery_service.file_mover, expected_file_mover)
+    assert isinstance(
+        delivery_service.file_formatter.sample_file_formatter, expected_sample_file_formatter
+    )