patch - Concatenate Microbial fastq files

cg/cli/deliver/base.py

@@ -6,7 +6,7 @@
 import click
 
 from cg.apps.tb import TrailblazerAPI
-from cg.cli.deliver.utils import deliver_raw_data_for_analyses
+from cg.cli.deliver.utils import deliver_raw_data_for_analyses, get_pseudo_workflow
 from cg.cli.utils import CLICK_CONTEXT_SETTINGS
 from cg.constants import Workflow
 from cg.constants.cli_options import DRY_RUN
@@ -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__)
@@ -89,9 +87,10 @@ def deliver_case(
     if not case:
         LOG.error(f"Could not find case with id {case_id}")
         return
+    pseudo_workflow: str = get_pseudo_workflow(case=cases[0])
     delivery_service: DeliverFilesService = service_builder.build_delivery_service(
         delivery_type=delivery_type if delivery_type else case.data_delivery,
-        workflow=case.data_analysis,
+        workflow=pseudo_workflow,
     )
     delivery_service.deliver_files_for_case(
         case=case, delivery_base_path=Path(inbox), dry_run=dry_run
@@ -124,9 +123,10 @@ def deliver_ticket(
     if not cases:
         LOG.error(f"Could not find case connected to ticket {ticket}")
         return
+    pseudo_workflow: str = get_pseudo_workflow(case=cases[0])
     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,
+        workflow=pseudo_workflow,
     )
     delivery_service.deliver_files_for_ticket(
         ticket_id=ticket, delivery_base_path=Path(inbox), dry_run=dry_run

cg/cli/deliver/utils.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 
 from cg.constants import Workflow
+from cg.constants.constants import MICROBIAL_APP_TAGS
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
 )
@@ -43,3 +44,11 @@ def deliver_raw_data_for_analyses(
             )
             LOG.error(f"Could not deliver files for analysis {analysis.id}: {error}")
             continue
+
+
+def get_pseudo_workflow(case: Case) -> str:
+    """Return the literal '' if the case is Microbial-fastq, otherwise return the case workflow."""
+    tag: str = case.samples[0].application_version.application.tag
+    if case.data_analysis == Workflow.RAW_DATA and tag in MICROBIAL_APP_TAGS:
+        return "microbial-fastq"
+    return case.data_analysis

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/services/deliver_files/deliver_files_service/deliver_files_service_factory.py

@@ -1,60 +1,38 @@
 """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.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.store import Store
 
@@ -104,10 +82,10 @@ def _get_file_fetcher(self, delivery_type: DataDelivery) -> FetchDeliveryFilesSe
 
     @staticmethod
     def _get_sample_file_formatter(
-        workflow: Workflow,
+        workflow: str,
     ) -> SampleFileFormatter | SampleFileConcatenationFormatter:
         """Get the file formatter service based on the workflow."""
-        if workflow in [Workflow.MICROSALT]:
+        if workflow in [Workflow.MICROSALT, "microbial-fastq"]:
             return SampleFileConcatenationFormatter(FastqConcatenationService())
         return SampleFileFormatter()
 
@@ -126,7 +104,7 @@ def _validate_delivery_type(delivery_type: DataDelivery):
         )
 
     def build_delivery_service(
-        self, workflow: Workflow, delivery_type: DataDelivery
+        self, workflow: str, delivery_type: DataDelivery
     ) -> DeliverFilesService:
         """Build a delivery service based on the workflow and delivery type."""
         delivery_type: DataDelivery = self._sanitise_delivery_type(delivery_type)