Trailblazer priority control samples (#3991)(patch)

### Fixed

- Controls ran with slurm qos express have the priority in trailblazer corresponding to the priority in statusDB

cg/apps/demultiplex/demultiplex_api.py

@@ -12,7 +12,7 @@
 from cg.apps.tb import TrailblazerAPI
 from cg.constants.constants import FileFormat, Workflow
 from cg.constants.demultiplexing import DemultiplexingDirsAndFiles
-from cg.constants.priority import SlurmQos
+from cg.constants.priority import SlurmQos, TrailblazerPriority
 from cg.constants.tb import AnalysisType
 from cg.exc import HousekeeperFileMissingError
 from cg.io.controller import WriteFile
@@ -49,6 +49,11 @@ def slurm_quality_of_service(self) -> Literal[SlurmQos.HIGH, SlurmQos.LOW]:
         """Return SLURM quality of service."""
         return SlurmQos.LOW if self.environment == "stage" else SlurmQos.HIGH
 
+    @property
+    def trailblazer_priority(self) -> Literal[TrailblazerPriority.HIGH, TrailblazerPriority.LOW]:
+        """Return Trailblazer quality of service."""
+        return TrailblazerPriority.LOW if self.environment == "stage" else TrailblazerPriority.HIGH
+
     def set_dry_run(self, dry_run: bool) -> None:
         """Set dry run."""
         LOG.debug(f"DemultiplexingAPI: Set dry run to {dry_run}")
@@ -213,7 +218,7 @@ def add_to_trailblazer(
             analysis_type=AnalysisType.OTHER,
             config_path=sequencing_run.trailblazer_config_path.as_posix(),
             out_dir=sequencing_run.trailblazer_config_path.parent.as_posix(),
-            slurm_quality_of_service=self.slurm_quality_of_service,
+            priority=self.trailblazer_priority,
             email=self.mail,
             workflow=Workflow.DEMULTIPLEX,
         )

cg/apps/tb/api.py

@@ -12,7 +12,7 @@
 from cg.apps.tb.models import AnalysesResponse, TrailblazerAnalysis
 from cg.constants import Workflow
 from cg.constants.constants import APIMethods, FileFormat, JobType, WorkflowManager
-from cg.constants.priority import SlurmQos
+from cg.constants.priority import TrailblazerPriority
 from cg.constants.tb import AnalysisStatus
 from cg.exc import (
     AnalysisNotCompletedError,
@@ -21,6 +21,7 @@
 )
 from cg.io.controller import APIRequest, ReadStream
 
+
 LOG = logging.getLogger(__name__)
 
 
@@ -112,7 +113,7 @@ def add_pending_analysis(
         analysis_type: str,
         config_path: str,
         out_dir: str,
-        slurm_quality_of_service: SlurmQos,
+        priority: TrailblazerPriority,
         email: str = None,
         order_id: int | None = None,
         workflow: Workflow = None,
@@ -128,7 +129,7 @@ def add_pending_analysis(
             "config_path": config_path,
             "order_id": order_id,
             "out_dir": out_dir,
-            "priority": slurm_quality_of_service,
+            "priority": priority,
             "workflow": workflow.upper(),
             "ticket": ticket,
             "workflow_manager": workflow_manager,

cg/cli/workflow/raw_data/raw_data_service.py

@@ -4,6 +4,7 @@
 from cg.constants.constants import Workflow
 from cg.constants.tb import AnalysisStatus, AnalysisType
 from cg.exc import CaseNotFoundError
+from cg.meta.workflow.utils.utils import MAP_TO_TRAILBLAZER_PRIORITY
 from cg.store.models import Analysis, Case
 from cg.store.store import Store
 
@@ -41,7 +42,7 @@ def _add_analysis_to_trailblazer(self, case: Case) -> None:
             config_path="",
             order_id=case.latest_order.id,
             out_dir="",
-            slurm_quality_of_service=case.slurm_priority,
+            priority=MAP_TO_TRAILBLAZER_PRIORITY[case.priority],
             workflow=Workflow.RAW_DATA,
             ticket=case.latest_ticket,
         )

cg/constants/priority.py

@@ -11,6 +11,13 @@ class SlurmQos(StrEnum):
     EXPRESS: str = "express"
 
 
+class TrailblazerPriority(StrEnum):
+    LOW: str = "low"
+    NORMAL: str = "normal"
+    HIGH: str = "high"
+    EXPRESS: str = "express"
+
+
 class PriorityTerms(StrEnum):
     EXPRESS: str = "express"
     PRIORITY: str = "priority"

cg/meta/workflow/analysis.py

@@ -20,7 +20,7 @@
     WorkflowManager,
 )
 from cg.constants.gene_panel import GenePanelCombo, GenePanelMasterList
-from cg.constants.priority import SlurmQos
+from cg.constants.priority import SlurmQos, TrailblazerPriority
 from cg.constants.scout import HGNC_ID, ScoutExportFileName
 from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.constants.tb import AnalysisStatus, AnalysisType
@@ -29,7 +29,7 @@
 from cg.meta.archive.archive import SpringArchiveAPI
 from cg.meta.meta import MetaAPI
 from cg.meta.workflow.fastq import FastqHandler
-from cg.meta.workflow.utils.utils import are_all_samples_control
+from cg.meta.workflow.utils.utils import are_all_samples_control, MAP_TO_TRAILBLAZER_PRIORITY
 from cg.models.analysis import AnalysisModel
 from cg.models.cg_config import CGConfig
 from cg.models.fastq import FastqFileMeta
@@ -137,6 +137,12 @@ def get_slurm_qos_for_case(self, case_id: str) -> str:
         priority: int = case.priority or Priority.research
         return Priority.priority_to_slurm_qos().get(priority)
 
+    def get_trailblazer_priority(self, case_id: str) -> int:
+        """Get the priority for the case in Trailblazer."""
+        case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
+        priority: int = case.priority
+        return MAP_TO_TRAILBLAZER_PRIORITY[priority]
+
     def get_workflow_manager(self) -> str:
         """Get workflow manager for a given workflow."""
         return WorkflowManager.Slurm.value
@@ -290,7 +296,7 @@ def add_pending_trailblazer_analysis(
         email: str = environ_email()
         order_id: int = self._get_order_id_from_case_id(case_id)
         out_dir: str = self.get_job_ids_path(case_id).parent.as_posix()
-        slurm_quality_of_service: str = self.get_slurm_qos_for_case(case_id)
+        priority: TrailblazerPriority = self.get_trailblazer_priority(case_id)
         ticket: str = self.status_db.get_latest_ticket_from_case(case_id)
         workflow: Workflow = self.workflow
         workflow_manager: str = self.get_workflow_manager()
@@ -302,7 +308,7 @@ def add_pending_trailblazer_analysis(
             email=email,
             order_id=order_id,
             out_dir=out_dir,
-            slurm_quality_of_service=slurm_quality_of_service,
+            priority=priority,
             ticket=ticket,
             workflow=workflow,
             workflow_manager=workflow_manager,

cg/meta/workflow/utils/utils.py

@@ -1,4 +1,5 @@
 from cg.constants.constants import ControlOptions
+from cg.constants.priority import TrailblazerPriority
 from cg.store.models import Case
 
 
@@ -9,3 +10,12 @@ def are_all_samples_control(case: Case) -> bool:
         sample.control in [ControlOptions.NEGATIVE, ControlOptions.POSITIVE]
         for sample in case.samples
     )
+
+
+MAP_TO_TRAILBLAZER_PRIORITY: dict[int, TrailblazerPriority] = {
+    0: TrailblazerPriority.LOW,
+    1: TrailblazerPriority.NORMAL,
+    2: TrailblazerPriority.HIGH,
+    3: TrailblazerPriority.EXPRESS,
+    4: TrailblazerPriority.NORMAL,
+}

cg/services/deliver_files/deliver_files_service/deliver_files_service.py

@@ -5,6 +5,7 @@
 from cg.apps.tb.models import TrailblazerAnalysis
 from cg.constants import Priority, Workflow
 from cg.constants.tb import AnalysisType
+from cg.meta.workflow.utils.utils import MAP_TO_TRAILBLAZER_PRIORITY
 from cg.services.analysis_service.analysis_service import AnalysisService
 from cg.services.deliver_files.deliver_files_service.error_handling import (
     handle_no_delivery_files_error,
@@ -132,7 +133,7 @@ def _add_trailblazer_tracking(self, case: Case, job_id: int, dry_run: bool) -> N
                 config_path=self.rsync_service.trailblazer_config_path.as_posix(),
                 order_id=case.latest_order.id,
                 out_dir=self.rsync_service.log_dir.as_posix(),
-                slurm_quality_of_service=Priority.priority_to_slurm_qos().get(case.priority),
+                priority=MAP_TO_TRAILBLAZER_PRIORITY[case.priority],
                 workflow=Workflow.RSYNC,
                 ticket=case.latest_ticket,
             )

cg/services/deliver_files/rsync/service.py

@@ -11,7 +11,7 @@
 from cg.constants import Workflow
 from cg.constants.constants import FileFormat
 from cg.constants.delivery import INBOX_NAME
-from cg.constants.priority import SlurmAccount, SlurmQos
+from cg.constants.priority import SlurmAccount, SlurmQos, TrailblazerPriority
 from cg.constants.tb import AnalysisType
 from cg.exc import CgError
 from cg.io.controller import WriteFile
@@ -52,6 +52,15 @@ def slurm_quality_of_service(self) -> str:
         """Return the slurm quality of service depending on the slurm account."""
         return SlurmQos.HIGH if self.account == SlurmAccount.PRODUCTION else SlurmQos.LOW
 
+    @property
+    def trailblazer_priority(self) -> TrailblazerPriority:
+        """Return the trailblazer priority depending on the slurm account."""
+        return (
+            TrailblazerPriority.HIGH
+            if self.account == SlurmAccount.PRODUCTION
+            else TrailblazerPriority.LOW
+        )
+
     @property
     def trailblazer_config_path(self) -> Path:
         """Return Path to trailblazer config."""
@@ -161,7 +170,7 @@ def add_to_trailblazer_api(
             analysis_type=AnalysisType.OTHER,
             config_path=self.trailblazer_config_path.as_posix(),
             out_dir=self.log_dir.as_posix(),
-            slurm_quality_of_service=self.slurm_quality_of_service,
+            priority=self.trailblazer_priority,
             email=self.mail_user,
             workflow=Workflow.RSYNC,
             ticket=ticket,

tests/meta/workflow/test_analysis.py

@@ -9,15 +9,15 @@
 from cg.constants import GenePanelMasterList, Priority, SequencingRunDataAvailability
 from cg.constants.archiving import ArchiveLocations
 from cg.constants.constants import ControlOptions
-from cg.constants.priority import SlurmQos
+from cg.constants.priority import SlurmQos, TrailblazerPriority
 from cg.constants.sequencing import Sequencers
 from cg.exc import AnalysisNotReadyError
 from cg.meta.archive.archive import SpringArchiveAPI
 from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.mip import MipAnalysisAPI
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
 from cg.meta.workflow.prepare_fastq import PrepareFastqAPI
-from cg.meta.workflow.utils.utils import are_all_samples_control
+from cg.meta.workflow.utils.utils import are_all_samples_control, MAP_TO_TRAILBLAZER_PRIORITY
 from cg.models.fastq import FastqFileMeta
 from cg.store.models import Case, Sample, IlluminaSequencingRun
 from cg.store.store import Store
@@ -55,6 +55,39 @@ def test_get_slurm_qos_for_case(
     assert slurm_qos is expected_slurm_qos
 
 
+@pytest.mark.parametrize(
+    "priority,expected_trailblazer_priority",
+    [
+        (Priority.clinical_trials, TrailblazerPriority.NORMAL),
+        (Priority.research, TrailblazerPriority.LOW),
+        (Priority.standard, TrailblazerPriority.NORMAL),
+        (Priority.priority, TrailblazerPriority.HIGH),
+        (Priority.express, TrailblazerPriority.EXPRESS),
+    ],
+)
+def test_get_trailblazer_priority(
+    case_id: str,
+    priority,
+    expected_trailblazer_priority,
+    mip_analysis_api: MipDNAAnalysisAPI,
+    analysis_store: Store,
+):
+    """Test get Trailblazer priority from the case priority"""
+
+    # GIVEN a store with a case with a specific priority
+    mip_analysis_api.status_db = analysis_store
+    case: Case = analysis_store.get_case_by_internal_id(case_id)
+    case.priority = priority
+
+    # WHEN getting the trailblazer priority for the case
+    trailblazer_priority: TrailblazerPriority = mip_analysis_api.get_trailblazer_priority(
+        case_id=case_id
+    )
+
+    # THEN the expected trailblazer priority should be returned
+    assert trailblazer_priority is expected_trailblazer_priority
+
+
 def test_gene_panels_not_part_of_master_list(customer_id: str):
     """Test get only broad non-specific gene panels and custom gene panel list if a supplied gene panels is not part of master list."""
     # GIVEN a customer who is a collaborator on the master list
@@ -624,3 +657,36 @@ def test_case_with_controls_get_correct_slurmqos(
 
     # THEN the result should match the expected QOS
     assert qos == expected_qos
+
+
+@pytest.mark.parametrize(
+    "priority, expected_trailblazer_priority",
+    [
+        (Priority.clinical_trials, TrailblazerPriority.NORMAL),
+        (Priority.research, TrailblazerPriority.LOW),
+        (Priority.standard, TrailblazerPriority.NORMAL),
+        (Priority.priority, TrailblazerPriority.HIGH),
+        (Priority.express, TrailblazerPriority.EXPRESS),
+    ],
+)
+def test_get_trailblazer_priority(
+    case_id: str,
+    priority: Priority,
+    expected_trailblazer_priority: TrailblazerPriority,
+    mip_analysis_api: MipDNAAnalysisAPI,
+    analysis_store: Store,
+):
+    """Test get Trailblazer priority from the case priority"""
+
+    # GIVEN a store with a case with a specific priority
+    mip_analysis_api.status_db = analysis_store
+    case: Case = analysis_store.get_case_by_internal_id(case_id)
+    case.priority = priority
+
+    # WHEN getting the trailblazer priority for the priority
+    trailblazer_priority: TrailblazerPriority = mip_analysis_api.get_trailblazer_priority(
+        case_id=case_id
+    )
+
+    # THEN the expected trailblazer priority should be returned
+    assert trailblazer_priority is expected_trailblazer_priority