change constants for fetching app tags from statusdb

cg/services/deliver_files/deliver_files_service/deliver_files_service.py

@@ -9,21 +9,13 @@
 from cg.services.deliver_files.deliver_files_service.error_handling import (
     handle_no_delivery_files_error,
 )
-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.models import DeliveryFiles
 from cg.services.deliver_files.file_filter.abstract import FilterDeliveryFilesService
-from cg.services.deliver_files.file_formatter.abstract import (
-    DeliveryFileFormattingService,
-)
-from cg.services.deliver_files.file_formatter.models import (
-    FormattedFiles,
-)
+from cg.services.deliver_files.file_formatter.abstract import DeliveryFileFormattingService
+from cg.services.deliver_files.file_formatter.models import FormattedFiles
 from cg.services.deliver_files.file_mover.service import DeliveryFilesMover
-from cg.services.deliver_files.rsync.service import (
-    DeliveryRsyncService,
-)
+from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.store.exc import EntryNotFoundError
 from cg.store.models import Case
 from cg.store.store import Store

cg/services/deliver_files/deliver_files_service/deliver_files_service_factory.py

@@ -5,7 +5,7 @@
 from cg.apps.housekeeper.hk import HousekeeperAPI
 from cg.apps.tb import TrailblazerAPI
 from cg.constants import DataDelivery, Workflow
-from cg.constants.constants import MICROBIAL_APP_TAGS
+from cg.constants.constants import MICROBIAL_APP_TAGS, PrepCategory
 from cg.services.analysis_service.analysis_service import AnalysisService
 from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
     DeliverFilesService,
@@ -134,14 +134,19 @@ def build_delivery_service(
             analysis_service=self.analysis_service,
         )
 
-    @staticmethod
-    def _convert_workflow(case: Case) -> Workflow:
+    def _convert_workflow(self, 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:
+        microbial_tags: list[str] = [
+            application.tag
+            for application in self.store.get_active_applications_by_prep_category(
+                prep_category=PrepCategory.MICROBIAL
+            )
+        ]
+        if case.data_analysis == Workflow.RAW_DATA and tag in microbial_tags:
             return Workflow.MICROSALT
         return case.data_analysis
 

cg/services/deliver_files/file_formatter/service.py

@@ -2,28 +2,14 @@
 import os
 from pathlib import Path
 
-from cg.constants.delivery import INBOX_NAME
-from cg.services.deliver_files.file_fetcher.models import (
-    CaseFile,
-    DeliveryFiles,
-    SampleFile,
-)
-from cg.services.deliver_files.file_formatter.abstract import (
-    DeliveryFileFormattingService,
-)
-from cg.services.deliver_files.file_formatter.models import (
-    FormattedFile,
-    FormattedFiles,
-)
-from cg.services.deliver_files.file_formatter.utils.case_service import (
-    CaseFileFormatter,
-)
+from cg.services.deliver_files.file_fetcher.models import CaseFile, DeliveryFiles, SampleFile
+from cg.services.deliver_files.file_formatter.abstract import DeliveryFileFormattingService
+from cg.services.deliver_files.file_formatter.models import FormattedFile, FormattedFiles
+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_formatter.utils.sample_service import SampleFileFormatter
 
 LOG = logging.getLogger(__name__)
 

cg/store/crud/read.py

@@ -862,6 +862,19 @@ def get_current_application_version_by_tag(self, tag: str) -> ApplicationVersion
             valid_from=dt.datetime.now(),
         ).first()
 
+    def get_active_applications_by_prep_category(
+        self, prep_category: PrepCategory
+    ) -> list[Application]:
+        """Return all active applications by prep category."""
+        return apply_application_filter(
+            applications=self._get_query(table=Application),
+            filter_functions=[
+                ApplicationFilter.BY_PREP_CATEGORIES,
+                ApplicationFilter.IS_NOT_ARCHIVED,
+            ],
+            prep_categories=[prep_category],
+        ).all()
+
     def get_bed_version_by_file_name(self, bed_version_file_name: str) -> BedVersion:
         """Return bed version with file name."""
         return apply_bed_version_filter(

cg/store/filters/status_application_filters.py

@@ -3,7 +3,7 @@
 
 from sqlalchemy.orm import Query
 
-from cg.constants import PrepCategory, Workflow
+from cg.constants import PrepCategory
 from cg.store.models import Application
 
 
@@ -42,19 +42,15 @@ def apply_application_filter(
     filter_functions: list[Callable],
     applications: Query,
     tag: str = None,
-    prep_category: str = None,
-    prep_categories: list[Workflow] = None,
-    entry_id: int = None,
+    prep_categories: list[PrepCategory] = None,
 ) -> Query:
     """Apply filtering functions to the sample queries and return filtered results."""
 
     for filter_function in filter_functions:
         applications: Query = filter_function(
             applications=applications,
             tag=tag,
-            prep_category=prep_category,
             prep_categories=prep_categories,
-            entry_id=entry_id,
         )
     return applications
 

tests/conftest.py

@@ -30,13 +30,7 @@
 from cg.apps.tb.dto.summary_response import AnalysisSummary, StatusSummary
 from cg.clients.freshdesk.freshdesk_client import FreshdeskClient
 from cg.constants import FileExtensions, SequencingFileTag, Workflow
-from cg.constants.constants import (
-    CaseActions,
-    CustomerId,
-    FileFormat,
-    GenomeVersion,
-    Strandedness,
-)
+from cg.constants.constants import CaseActions, CustomerId, FileFormat, GenomeVersion, Strandedness
 from cg.constants.gene_panel import GenePanelMasterList
 from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG
 from cg.constants.priority import SlurmQos
@@ -57,22 +51,14 @@
 from cg.models import CompressionData
 from cg.models.cg_config import CGConfig, PDCArchivingDirectory
 from cg.models.downsample.downsample_data import DownsampleData
-from cg.models.raredisease.raredisease import (
-    RarediseaseParameters,
-    RarediseaseSampleSheetHeaders,
-)
+from cg.models.raredisease.raredisease import RarediseaseParameters, RarediseaseSampleSheetHeaders
 from cg.models.rnafusion.rnafusion import RnafusionParameters, RnafusionSampleSheetEntry
 from cg.models.run_devices.illumina_run_directory_data import IlluminaRunDirectoryData
-from cg.models.taxprofiler.taxprofiler import (
-    TaxprofilerParameters,
-    TaxprofilerSampleSheetEntry,
-)
+from cg.models.taxprofiler.taxprofiler import TaxprofilerParameters, TaxprofilerSampleSheetEntry
 from cg.models.tomte.tomte import TomteParameters, TomteSampleSheetHeaders
 from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.services.illumina.backup.encrypt_service import IlluminaRunEncryptionService
-from cg.services.illumina.data_transfer.data_transfer_service import (
-    IlluminaDataTransferService,
-)
+from cg.services.illumina.data_transfer.data_transfer_service import IlluminaDataTransferService
 from cg.store.database import create_all_tables, drop_all_tables, initialize_database
 from cg.store.models import (
     Application,
@@ -146,6 +132,7 @@
     "tests.fixture_plugins.pacbio_fixtures.unprocessed_runs_fixtures",
     "tests.fixture_plugins.quality_controller_fixtures.sequencing_qc_check_scenario",
     "tests.fixture_plugins.quality_controller_fixtures.sequencing_qc_fixtures",
+    "tests.fixture_plugins.store_fixtures",
     "tests.fixture_plugins.timestamp_fixtures",
 ]
 

tests/fixture_plugins/store_fixtures.py

@@ -0,0 +1,140 @@
+from typing import Generator
+
+import pytest
+
+from cg.constants.constants import ControlOptions
+from cg.store.store import Store
+from tests.store_helpers import StoreHelpers
+
+
+@pytest.fixture
+def applications_store(store: Store, helpers: StoreHelpers) -> Store:
+    """Return a store populated with applications from excel file"""
+    app_tags: list[str] = ["PGOTTTR020", "PGOTTTR030", "PGOTTTR040"]
+    for app_tag in app_tags:
+        helpers.ensure_application(store=store, tag=app_tag)
+    return store
+
+
+@pytest.fixture
+def microbial_store(store: Store, helpers: StoreHelpers) -> Generator[Store, None, None]:
+    """Populate a store with microbial application tags"""
+    microbial_active_apptags = ["MWRNXTR003", "MWGNXTR003", "MWMNXTR003", "MWLNXTR003"]
+    microbial_inactive_apptags = ["MWXNXTR003", "VWGNXTR001", "VWLNXTR001"]
+
+    for app_tag in microbial_active_apptags:
+        helpers.ensure_application(store=store, tag=app_tag, prep_category="mic", is_archived=False)
+
+    for app_tag in microbial_inactive_apptags:
+        helpers.ensure_application(store=store, tag=app_tag, prep_category="mic", is_archived=True)
+
+    return store
+
+
+@pytest.fixture
+def mutant_store(store: Store, helpers: StoreHelpers) -> Store:
+    # Add mutant application and application_version
+    application = helpers.add_application(
+        store=store, application_tag="VWGDPTR001", target_reads=2000000, percent_reads_guaranteed=1
+    )
+
+    # Add cases
+    case_qc_pass = helpers.add_case(store=store, name="case_qc_pass", internal_id="case_qc_pass")
+    case_qc_fail = helpers.add_case(store=store, name="case_qc_fail", internal_id="case_qc_fail")
+
+    case_qc_fail_with_failing_controls = helpers.add_case(
+        store=store,
+        name="case_qc_fail_with_failing_controls",
+        internal_id="case_qc_fail_with_failing_controls",
+    )
+
+    # Add samples
+    sample_qc_pass = helpers.add_sample(
+        store=store,
+        internal_id="sample_qc_pass",
+        name="sample_qc_pass",
+        control=ControlOptions.EMPTY,
+        reads=861966,
+        application_tag=application.tag,
+    )
+
+    sample_qc_fail = helpers.add_sample(
+        store=store,
+        internal_id="sample_qc_fail",
+        name="sample_qc_fail",
+        control=ControlOptions.EMPTY,
+        reads=438776,
+        application_tag=application.tag,
+    )
+
+    external_negative_control_qc_pass = helpers.add_sample(
+        store=store,
+        internal_id="external_negative_control_qc_pass",
+        name="external_negative_control_qc_pass",
+        control=ControlOptions.NEGATIVE,
+        reads=20674,
+        application_tag=application.tag,
+    )
+
+    internal_negative_control_qc_pass = helpers.add_sample(
+        store=store,
+        internal_id="internal_negative_control_qc_pass",
+        name="internal_negative_control_qc_pass",
+        control=ControlOptions.NEGATIVE,
+        reads=0,
+        application_tag=application.tag,
+    )
+
+    sample_qc_pass_with_failing_controls = helpers.add_sample(
+        store=store,
+        internal_id="sample_qc_pass_with_failing_controls",
+        name="sample_qc_pass",
+        control=ControlOptions.EMPTY,
+        reads=861966,
+        application_tag=application.tag,
+    )
+
+    internal_negative_control_qc_fail = helpers.add_sample(
+        store=store,
+        internal_id="internal_negative_control_qc_fail",
+        name="internal_negative_control_qc_fail",
+        control=ControlOptions.NEGATIVE,
+        reads=3000,
+        application_tag=application.tag,
+    )
+
+    external_negative_control_qc_fail = helpers.add_sample(
+        store=store,
+        internal_id="external_negative_control_qc_fail",
+        name="external_negative_control_qc_fail",
+        control=ControlOptions.NEGATIVE,
+        reads=200000,
+        application_tag=application.tag,
+    )
+
+    # Add CaseSample relationships
+    # case_qc_pass
+    helpers.add_relationship(store=store, case=case_qc_pass, sample=sample_qc_pass)
+    helpers.add_relationship(
+        store=store, case=case_qc_pass, sample=external_negative_control_qc_pass
+    )
+
+    # case_qc_fail
+    helpers.add_relationship(store=store, case=case_qc_fail, sample=sample_qc_fail)
+    helpers.add_relationship(
+        store=store, case=case_qc_fail, sample=external_negative_control_qc_pass
+    )
+
+    # case_qc_fail_with_failing_controls
+    helpers.add_relationship(
+        store=store,
+        case=case_qc_fail_with_failing_controls,
+        sample=sample_qc_pass_with_failing_controls,
+    )
+    helpers.add_relationship(
+        store=store,
+        case=case_qc_fail_with_failing_controls,
+        sample=external_negative_control_qc_fail,
+    )
+
+    return store