patch - Concatenate Microbial fastq files

cg/cli/deliver/base.py

@@ -18,9 +18,7 @@
 from cg.services.deliver_files.deliver_files_service.deliver_files_service_factory import (
     DeliveryServiceFactory,
 )
-from cg.services.deliver_files.rsync.service import (
-    DeliveryRsyncService,
-)
+from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.store.models import Analysis, Case
 
 LOG = logging.getLogger(__name__)
@@ -90,8 +88,8 @@ def deliver_case(
         LOG.error(f"Could not find case with id {case_id}")
         return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
-        delivery_type=delivery_type if delivery_type else case.data_delivery,
-        workflow=case.data_analysis,
+        case=case,
+        delivery_type=delivery_type,
     )
     delivery_service.deliver_files_for_case(
         case=case, delivery_base_path=Path(inbox), dry_run=dry_run
@@ -100,8 +98,8 @@ def deliver_case(
 
 @deliver.command(
     name="ticket",
-    help="Deliver all case files for cases in a ticket based on delivery type to the customer inbox on the HPC "
-    "and start an Rsync job to clinical-delivery. "
+    help="Deliver all case files for cases in a ticket based on delivery type to the customer"
+    "inbox on the HPC and start an Rsync job to clinical-delivery. "
     "NOTE: the dry-run flag will copy files to the customer inbox on Hasta, "
     "but will not perform the Rsync job.",
 )
@@ -116,7 +114,8 @@ def deliver_ticket(
     dry_run: bool,
 ):
     """
-    Deliver all case files based on delivery type to the customer inbox on the HPC for cases connected to a ticket.
+    Deliver all case files based on delivery type to the customer inbox on the HPC for cases
+    connected to a ticket.
     """
     inbox: str = context.delivery_path
     service_builder: DeliveryServiceFactory = context.delivery_service_factory
@@ -125,8 +124,8 @@ def deliver_ticket(
         LOG.error(f"Could not find case connected to ticket {ticket}")
         return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
-        delivery_type=delivery_type if delivery_type else cases[0].data_delivery,
-        workflow=cases[0].data_analysis,
+        case=cases[0],
+        delivery_type=delivery_type,
     )
     delivery_service.deliver_files_for_ticket(
         ticket_id=ticket, delivery_base_path=Path(inbox), dry_run=dry_run
@@ -173,8 +172,8 @@ def deliver_sample_raw_data(
         LOG.error(f"Could not find case with id {case_id}")
         return
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
+        case=case,
         delivery_type=delivery_type,
-        workflow=case.data_analysis,
     )
     delivery_service.deliver_files_for_sample(
         case=case, sample_id=sample_id, delivery_base_path=Path(inbox), dry_run=dry_run
@@ -186,7 +185,8 @@ def deliver_sample_raw_data(
 @DRY_RUN
 def deliver_auto_raw_data(context: CGConfig, dry_run: bool):
     """
-    Deliver all case files for the raw data workflow to the customer inbox on the HPC and start a Rsync job.
+    Deliver all case files for the raw data workflow to the customer inbox on the HPC and start a
+    Rsync job.
     1. get all cases with analysis type fastq that need to be delivered
     2. check if their upload has started
     3. if not, start the upload

cg/cli/deliver/utils.py

@@ -2,7 +2,6 @@
 from datetime import datetime
 from pathlib import Path
 
-from cg.constants import Workflow
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
 )
@@ -27,8 +26,8 @@ def deliver_raw_data_for_analyses(
         try:
             case: Case = analysis.case
             delivery_service: DeliverFilesService = service_builder.build_delivery_service(
+                case=case,
                 delivery_type=case.data_delivery,
-                workflow=Workflow.RAW_DATA,
             )
 
             delivery_service.deliver_files_for_case(

cg/constants/constants.py

@@ -258,6 +258,13 @@ class MicrosaltAppTags(StrEnum):
     PREP_CATEGORY: str = "mic"
 
 
+MICROBIAL_APP_TAGS = [
+    MicrosaltAppTags.MWRNXTR003,
+    MicrosaltAppTags.MWXNXTR003,
+    MicrosaltAppTags.VWGNXTR001,
+]
+
+
 class MutantQC:
     EXTERNAL_NEGATIVE_CONTROL_READS_THRESHOLD: int = 100000
     INTERNAL_NEGATIVE_CONTROL_READS_THRESHOLD: int = 2000

cg/meta/upload/upload_api.py

@@ -97,8 +97,8 @@ def upload_files_to_customer_inbox(self, case: Case) -> None:
         """Uploads the analysis files to the customer inbox."""
         factory_service: DeliveryServiceFactory = self.config.delivery_service_factory
         delivery_service: DeliverFilesService = factory_service.build_delivery_service(
+            case=case,
             delivery_type=case.data_delivery,
-            workflow=case.data_analysis,
         )
         delivery_service.deliver_files_for_case(
             case=case, delivery_base_path=Path(self.config.delivery_path)

cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py

@@ -1,61 +1,41 @@
 """Module for the factory of the deliver files service."""
 
 from typing import Type
+
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.apps.tb import TrailblazerAPI
-from cg.constants import Workflow, DataDelivery
+from cg.constants import DataDelivery, Workflow
+from cg.constants.constants import MICROBIAL_APP_TAGS
 from cg.services.analysis_service.analysis_service import AnalysisService
-from cg.services.deliver_files.file_filter.sample_service import SampleFileFilter
-from cg.services.deliver_files.tag_fetcher.bam_service import (
-    BamDeliveryTagsFetcher,
-)
-from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
-    FastqConcatenationService,
-)
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
 )
 from cg.services.deliver_files.deliver_files_service.exc import DeliveryTypeNotSupported
-from cg.services.deliver_files.tag_fetcher.abstract import (
-    FetchDeliveryFileTagsService,
-)
-from cg.services.deliver_files.tag_fetcher.sample_and_case_service import (
-    SampleAndCaseDeliveryTagsFetcher,
-)
-from cg.services.deliver_files.file_fetcher.analysis_service import (
-    AnalysisDeliveryFileFetcher,
-)
-from cg.services.deliver_files.file_fetcher.abstract import (
-    FetchDeliveryFilesService,
-)
+from cg.services.deliver_files.file_fetcher.abstract import FetchDeliveryFilesService
 from cg.services.deliver_files.file_fetcher.analysis_raw_data_service import (
     RawDataAndAnalysisDeliveryFileFetcher,
 )
-from cg.services.deliver_files.file_fetcher.raw_data_service import (
-    RawDataDeliveryFileFetcher,
-)
-from cg.services.deliver_files.file_formatter.service import (
-    DeliveryFileFormatter,
-)
-
-from cg.services.deliver_files.file_formatter.abstract import (
-    DeliveryFileFormattingService,
-)
-from cg.services.deliver_files.file_formatter.utils.case_service import (
-    CaseFileFormatter,
-)
+from cg.services.deliver_files.file_fetcher.analysis_service import AnalysisDeliveryFileFetcher
+from cg.services.deliver_files.file_fetcher.raw_data_service import RawDataDeliveryFileFetcher
+from cg.services.deliver_files.file_filter.sample_service import SampleFileFilter
+from cg.services.deliver_files.file_formatter.abstract import DeliveryFileFormattingService
+from cg.services.deliver_files.file_formatter.service import DeliveryFileFormatter
+from cg.services.deliver_files.file_formatter.utils.case_service import CaseFileFormatter
 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_mover.service import (
-    DeliveryFilesMover,
+from cg.services.deliver_files.file_formatter.utils.sample_service import SampleFileFormatter
+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
+from cg.services.deliver_files.tag_fetcher.bam_service import BamDeliveryTagsFetcher
+from cg.services.deliver_files.tag_fetcher.sample_and_case_service import (
+    SampleAndCaseDeliveryTagsFetcher,
 )
-from cg.services.deliver_files.rsync.service import (
-    DeliveryRsyncService,
+from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
+    FastqConcatenationService,
 )
+from cg.store.models import Case
 from cg.store.store import Store
 
 
@@ -122,18 +102,23 @@ def _validate_delivery_type(delivery_type: DataDelivery):
         ]:
             return
         raise DeliveryTypeNotSupported(
-            f"Delivery type {delivery_type} is not supported. Supported delivery types are {DataDelivery.FASTQ}, {DataDelivery.ANALYSIS_FILES}, {DataDelivery.FASTQ_ANALYSIS}, {DataDelivery.BAM}."
+            f"Delivery type {delivery_type} is not supported. Supported delivery types are"
+            f" {DataDelivery.FASTQ}, {DataDelivery.ANALYSIS_FILES},"
+            f" {DataDelivery.FASTQ_ANALYSIS}, {DataDelivery.BAM}."
         )
 
     def build_delivery_service(
-        self, workflow: Workflow, delivery_type: DataDelivery
+        self, case: Case, delivery_type: DataDelivery | None = None
     ) -> DeliverFilesService:
-        """Build a delivery service based on the workflow and delivery type."""
-        delivery_type: DataDelivery = self._sanitise_delivery_type(delivery_type)
+        """Build a delivery service based on a case."""
+        delivery_type: DataDelivery = self._sanitise_delivery_type(
+            delivery_type if delivery_type else case.data_delivery
+        )
         self._validate_delivery_type(delivery_type)
         file_fetcher: FetchDeliveryFilesService = self._get_file_fetcher(delivery_type)
+        converted_workflow: Workflow = self._convert_workflow(case)
         sample_file_formatter: SampleFileFormatter | SampleFileConcatenationFormatter = (
-            self._get_sample_file_formatter(workflow)
+            self._get_sample_file_formatter(converted_workflow)
         )
         file_formatter: DeliveryFileFormattingService = DeliveryFileFormatter(
             case_file_formatter=CaseFileFormatter(), sample_file_formatter=sample_file_formatter
@@ -149,6 +134,17 @@ def build_delivery_service(
             analysis_service=self.analysis_service,
         )
 
+    @staticmethod
+    def _convert_workflow(case: Case) -> Workflow:
+        """Converts a workflow with the introduction of the microbial-fastq delivery type an
+        unsupported combination of delivery type and workflow setup is required. This function
+        makes sure that a raw data workflow with microbial fastq delivery type is treated as a
+        microsalt workflow so that the microbial-fastq sample files can be concatenated."""
+        tag: str = case.samples[0].application_version.application.tag
+        if case.data_analysis == Workflow.RAW_DATA and tag in MICROBIAL_APP_TAGS:
+            return Workflow.MICROSALT
+        return case.data_analysis
+
     @staticmethod
     def _sanitise_delivery_type(delivery_type: DataDelivery) -> DataDelivery:
         """Sanitise the delivery type."""

tests/services/file_delivery/delivery_file_service/test_service_builder.py

@@ -1,73 +1,76 @@
-import pytest
 from unittest.mock import MagicMock
 
-from cg.constants import Workflow, DataDelivery
+import pytest
+from pydantic import BaseModel
+
+from cg.constants import DataDelivery, Workflow
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
 )
 from cg.services.deliver_files.deliver_files_service.deliver_files_service_factory import (
     DeliveryServiceFactory,
 )
-from cg.services.deliver_files.tag_fetcher.sample_and_case_service import (
-    SampleAndCaseDeliveryTagsFetcher,
-)
-from cg.services.deliver_files.file_fetcher.analysis_service import (
-    AnalysisDeliveryFileFetcher,
-)
+from cg.services.deliver_files.file_fetcher.abstract import FetchDeliveryFilesService
 from cg.services.deliver_files.file_fetcher.analysis_raw_data_service import (
     RawDataAndAnalysisDeliveryFileFetcher,
 )
-from cg.services.deliver_files.file_fetcher.raw_data_service import (
-    RawDataDeliveryFileFetcher,
-)
+from cg.services.deliver_files.file_fetcher.analysis_service import AnalysisDeliveryFileFetcher
+from cg.services.deliver_files.file_fetcher.raw_data_service import RawDataDeliveryFileFetcher
 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_mover.service import (
-    DeliveryFilesMover,
+from cg.services.deliver_files.file_formatter.utils.sample_service import SampleFileFormatter
+from cg.services.deliver_files.file_mover.service import DeliveryFilesMover
+from cg.services.deliver_files.tag_fetcher.abstract import FetchDeliveryFileTagsService
+from cg.services.deliver_files.tag_fetcher.sample_and_case_service import (
+    SampleAndCaseDeliveryTagsFetcher,
 )
 
 
+class DeliveryScenario(BaseModel):
+    app_tag: str
+    data_analysis: Workflow
+    delivery_type: DataDelivery
+    expected_tag_fetcher: type[FetchDeliveryFileTagsService]
+    expected_file_fetcher: type[FetchDeliveryFilesService]
+    expected_file_mover: type[DeliveryFilesMover]
+    expected_sample_file_formatter: type[SampleFileFormatter]
+
+
 @pytest.mark.parametrize(
-    "workflow,delivery_type,expected_tag_fetcher,expected_file_fetcher,expected_file_mover,expected_sample_file_formatter",
+    "scenario",
     [
-        (
-            Workflow.MICROSALT,
-            DataDelivery.FASTQ,
-            SampleAndCaseDeliveryTagsFetcher,
-            RawDataDeliveryFileFetcher,
-            DeliveryFilesMover,
-            SampleFileConcatenationFormatter,
+        DeliveryScenario(
+            app_tag="MWRNXTR003",
+            data_analysis=Workflow.RAW_DATA,
+            delivery_type=DataDelivery.FASTQ,
+            expected_tag_fetcher=SampleAndCaseDeliveryTagsFetcher,
+            expected_file_fetcher=RawDataDeliveryFileFetcher,
+            expected_file_mover=DeliveryFilesMover,
+            expected_sample_file_formatter=SampleFileConcatenationFormatter,
         ),
-        (
-            Workflow.MUTANT,
-            DataDelivery.ANALYSIS_FILES,
-            SampleAndCaseDeliveryTagsFetcher,
-            AnalysisDeliveryFileFetcher,
-            DeliveryFilesMover,
-            SampleFileFormatter,
+        DeliveryScenario(
+            app_tag="VWGDPTR001",
+            data_analysis=Workflow.MUTANT,
+            delivery_type=DataDelivery.ANALYSIS_FILES,
+            expected_tag_fetcher=SampleAndCaseDeliveryTagsFetcher,
+            expected_file_fetcher=AnalysisDeliveryFileFetcher,
+            expected_file_mover=DeliveryFilesMover,
+            expected_sample_file_formatter=SampleFileFormatter,
         ),
-        (
-            Workflow.BALSAMIC,
-            DataDelivery.FASTQ_ANALYSIS,
-            SampleAndCaseDeliveryTagsFetcher,
-            RawDataAndAnalysisDeliveryFileFetcher,
-            DeliveryFilesMover,
-            SampleFileFormatter,
+        DeliveryScenario(
+            app_tag="PANKTTR020",
+            data_analysis=Workflow.BALSAMIC,
+            delivery_type=DataDelivery.FASTQ_ANALYSIS,
+            expected_tag_fetcher=SampleAndCaseDeliveryTagsFetcher,
+            expected_file_fetcher=RawDataAndAnalysisDeliveryFileFetcher,
+            expected_file_mover=DeliveryFilesMover,
+            expected_sample_file_formatter=SampleFileFormatter,
         ),
     ],
+    ids=["microbial-fastq", "SARS-COV2", "Targeted"],
 )
-def test_build_delivery_service(
-    workflow,
-    delivery_type,
-    expected_tag_fetcher,
-    expected_file_fetcher,
-    expected_file_mover,
-    expected_sample_file_formatter,
-):
+def test_build_delivery_service(scenario: DeliveryScenario):
     # GIVEN a delivery service builder with mocked store and hk_api
     builder = DeliveryServiceFactory(
         store=MagicMock(),
@@ -77,15 +80,22 @@ def test_build_delivery_service(
         analysis_service=MagicMock(),
     )
 
+    # GIVEN a case with mocked sample app tag
+    case_mock = MagicMock()
+    case_mock.data_delivery = scenario.delivery_type
+    case_mock.data_analysis = scenario.data_analysis
+    case_mock.samples = [
+        MagicMock(application_version=MagicMock(application=MagicMock(tag=scenario.app_tag)))
+    ]
+
     # WHEN building a delivery service
-    delivery_service: DeliverFilesService = builder.build_delivery_service(
-        workflow=workflow, delivery_type=delivery_type
-    )
+    delivery_service: DeliverFilesService = builder.build_delivery_service(case=case_mock)
 
     # 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_manager.tags_fetcher, scenario.expected_tag_fetcher)
+    assert isinstance(delivery_service.file_manager, scenario.expected_file_fetcher)
+    assert isinstance(delivery_service.file_mover, scenario.expected_file_mover)
     assert isinstance(
-        delivery_service.file_formatter.sample_file_formatter, expected_sample_file_formatter
+        delivery_service.file_formatter.sample_file_formatter,
+        scenario.expected_sample_file_formatter,
     )