Stop sending tower_ids.yaml path to Trailblazer

cg/apps/tb/api.py

@@ -134,7 +134,7 @@ def add_pending_analysis(
         self,
         case_id: str,
         analysis_type: str,
-        config_path: str,
+        config_path: str | None,
         out_dir: str,
         priority: TrailblazerPriority,
         workflow: Workflow,

cg/services/analysis_starter/tracker/implementations/balsamic.py

@@ -14,6 +14,9 @@ def _workflow_manager(self):
     def _get_job_ids_path(self, case_id: str) -> Path:
         return Path(self.workflow_root, case_id, "analysis", "slurm_jobids.yaml")
 
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return self._get_job_ids_path(case_id).parent
+
     def _get_workflow_version(self, case_config: BalsamicCaseConfig) -> str:
         config_data: dict = read_json(case_config.sample_config)
         return config_data["analysis"]["BALSAMIC_version"]

cg/services/analysis_starter/tracker/implementations/microsalt.py

@@ -34,6 +34,9 @@ def _get_job_ids_path(self, case_id: str) -> Path:
             f"{project_id}_slurm_ids{FileExtensions.YAML}",
         )
 
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return self._get_job_ids_path(case_id).parent
+
     def _get_file_name_start(self, case_id: str) -> str:
         """Returns the LIMS project id if the case contains multiple samples, else the sample id."""
         case: Case = self.store.get_case_by_internal_id(case_id)

cg/services/analysis_starter/tracker/implementations/mip_dna.py

@@ -14,6 +14,9 @@ def _workflow_manager(self) -> WorkflowManager:
     def _get_job_ids_path(self, case_id: str) -> Path:
         return Path(self.workflow_root, case_id, "analysis", "slurm_job_ids.yaml")
 
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return self._get_job_ids_path(case_id).parent
+
     def _get_sample_info_path(self, case_id: str) -> Path:
         return Path(self.workflow_root, case_id, "analysis", f"{case_id}_qc_sample_info.yaml")
 

cg/services/analysis_starter/tracker/implementations/nextflow.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from cg.constants.constants import FileExtensions, WorkflowManager
+from cg.constants.constants import WorkflowManager
 from cg.services.analysis_starter.configurator.models.nextflow import NextflowCaseConfig
 from cg.services.analysis_starter.tracker.tracker import Tracker
 
@@ -9,9 +9,11 @@ class NextflowTracker(Tracker):
     def _workflow_manager(self) -> WorkflowManager:
         return WorkflowManager.Tower
 
-    def _get_job_ids_path(self, case_id: str) -> Path:
-        """Return the path to a Trailblazer config file containing Tower IDs."""
-        return Path(self.workflow_root, case_id, "tower_ids").with_suffix(FileExtensions.YAML)
+    def _get_job_ids_path(self, case_id: str) -> Path | None:
+        return None
+
+    def _get_out_dir_path(self, case_id: str) -> Path:
+        return Path(self.workflow_root, case_id)
 
     def _get_workflow_version(self, case_config: NextflowCaseConfig) -> str:
         return case_config.revision

cg/services/analysis_starter/tracker/tracker.py

@@ -6,7 +6,7 @@
 from cg.apps.environ import environ_email
 from cg.apps.tb import TrailblazerAPI
 from cg.apps.tb.models import TrailblazerAnalysis
-from cg.constants.constants import CaseActions, CustomerId, Workflow
+from cg.constants.constants import CaseActions, CustomerId, Workflow, WorkflowManager
 from cg.constants.priority import TrailblazerPriority
 from cg.constants.sequencing import SeqLibraryPrepCategory
 from cg.constants.tb import AnalysisType
@@ -62,25 +62,25 @@ def _track_in_trailblazer(
         self, case_id: str, tower_workflow_id: int | None
     ) -> TrailblazerAnalysis:
         analysis_type: str = self._get_analysis_type(case_id)
-        config_path: Path = self._get_job_ids_path(case_id)
+        config_path: Path | None = self._get_job_ids_path(case_id)
         email: str = environ_email()
         order_id: int = self.store.get_case_by_internal_id(case_id).latest_order.id
-        out_dir: str = config_path.parent.as_posix()
+        out_dir: Path = self._get_out_dir_path(case_id)
         priority: TrailblazerPriority = self._get_trailblazer_priority(case_id)
         ticket: str = self.store.get_latest_ticket_from_case(case_id)
         is_case_for_development: bool = self._is_case_for_development(case_id)
         return self.trailblazer_api.add_pending_analysis(
             analysis_type=analysis_type,
             case_id=case_id,
-            config_path=config_path.as_posix(),
+            config_path=config_path.as_posix() if config_path else None,
             email=email,
             order_id=order_id,
-            out_dir=out_dir,
+            out_dir=out_dir.as_posix(),
             priority=priority,
             ticket=ticket,
             workflow=self.store.get_case_workflow(case_id),
             workflow_manager=self._workflow_manager(),
-            tower_workflow_id=tower_workflow_id,
+            tower_workflow_id=str(tower_workflow_id) if tower_workflow_id else None,
             is_hidden=is_case_for_development,
         )
 
@@ -133,11 +133,15 @@ def _is_case_for_development(self, case_id: str) -> bool:
         return case.customer.internal_id == CustomerId.CG_INTERNAL_CUSTOMER
 
     @abstractmethod
-    def _workflow_manager(self):
+    def _workflow_manager(self) -> WorkflowManager:
         pass
 
     @abstractmethod
-    def _get_job_ids_path(self, case_id: str):
+    def _get_job_ids_path(self, case_id: str) -> Path | None:
+        pass
+
+    @abstractmethod
+    def _get_out_dir_path(self, case_id: str) -> Path:
         pass
 
     @abstractmethod

tests/services/analysis_starter/test_nextflow_tracker.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from typing import cast
 
 import mock
 import pytest
@@ -7,7 +7,7 @@
 from cg.apps.tb import TrailblazerAPI
 from cg.constants.constants import Workflow, WorkflowManager
 from cg.constants.tb import AnalysisType
-from cg.models.cg_config import CGConfig
+from cg.models.cg_config import CGConfig, RarediseaseConfig
 from cg.models.orders.sample_base import StatusEnum
 from cg.services.analysis_starter.configurator.models.nextflow import NextflowCaseConfig
 from cg.services.analysis_starter.tracker.implementations.nextflow import NextflowTracker
@@ -35,13 +35,15 @@ def nextflow_tracker(cg_context: CGConfig, helpers: StoreHelpers, raredisease_ca
     return NextflowTracker(
         store=cg_context.status_db,
         trailblazer_api=cg_context.trailblazer_api,
-        workflow_root=cg_context.raredisease.root,
+        workflow_root=cast(RarediseaseConfig, cg_context.raredisease).root,
     )
 
 
-def test_nextflow_tracker(nextflow_tracker: NextflowTracker, raredisease_case_id: str):
+def test_nextflow_tracker(
+    cg_context: CGConfig, nextflow_tracker: NextflowTracker, raredisease_case_id: str
+):
     # GIVEN a raredisease case
-    case: Case = nextflow_tracker.store.get_case_by_internal_id(raredisease_case_id)
+    case: Case = cast(Case, nextflow_tracker.store.get_case_by_internal_id(raredisease_case_id))
     case_config = NextflowCaseConfig(
         case_id=raredisease_case_id,
         workflow=Workflow.RAREDISEASE,
@@ -55,6 +57,9 @@ def test_nextflow_tracker(nextflow_tracker: NextflowTracker, raredisease_case_id
         work_dir="work/dir",
     )
 
+    # GIVEN a root directory is set
+    root_directory: str = cast(RarediseaseConfig, cg_context.raredisease).root
+
     # WHEN wanting to track the started microSALT analysis
     with mock.patch.object(
         TrailblazerAPI,
@@ -71,14 +76,13 @@ def test_nextflow_tracker(nextflow_tracker: NextflowTracker, raredisease_case_id
         nextflow_tracker.track(case_config=case_config, tower_workflow_id="1")
 
     # THEN the appropriate POST should have been sent
-    config_path: Path = nextflow_tracker._get_job_ids_path(raredisease_case_id)
     expected_request_body: dict = {
         "case_id": raredisease_case_id,
         "email": environ_email(),
         "type": AnalysisType.WGS,
-        "config_path": config_path.as_posix(),
+        "config_path": None,
         "order_id": case.latest_order.id,
-        "out_dir": config_path.parent.as_posix(),
+        "out_dir": f"{root_directory}/{raredisease_case_id}",
         "priority": nextflow_tracker._get_trailblazer_priority(raredisease_case_id),
         "workflow": Workflow.RAREDISEASE.upper(),
         "ticket": str(case.latest_order.ticket_id),