add tests, redirect to rna-scout when using upload

cg/cli/upload/scout.py

@@ -50,6 +50,12 @@ def upload_to_scout(context, re_upload: bool, print_console: bool, case_id: str)
         suggest_cases_to_upload(status_db=status_db)
         return
 
+    case_obj: Case = status_db.get_case_by_internal_id(internal_id=case_id)
+    if case_obj.analyses == Workflow.TOMTE:
+        context.invoke(
+            upload_rna_to_scout, case_id=case_id, re_upload=re_upload, analysis=case_obj.analyses
+        )
+
     context.invoke(
         create_scout_load_config, case_id=case_id, print_console=print_console, re_upload=re_upload
     )

cg/meta/upload/scout/uploadscoutapi.py

@@ -539,13 +539,6 @@ def get_config_builder(self, analysis, hk_version) -> ScoutConfigBuilder:
             Workflow.RNAFUSION: RnafusionConfigBuilder(
                 hk_version_obj=hk_version, analysis_obj=analysis, lims_api=self.lims
             ),
-            Workflow.TOMTE: TomteConfigBuilder(
-                hk_version_obj=hk_version,
-                analysis_obj=analysis,
-                mip_analysis_api=self.mip_analysis_api,
-                lims_api=self.lims,
-                madeline_api=self.madeline_api,
-            ),
         }
 
         return config_builders[analysis.workflow]

tests/cli/upload/test_cli_scout.py

@@ -1,53 +1,86 @@
 import logging
 
 import mock
+import pytest
 from click.testing import CliRunner, Result
 
 from cg.cli.upload.scout import create_scout_load_config, get_upload_api
 from cg.constants import EXIT_SUCCESS, Workflow
 from cg.meta.upload.scout.uploadscoutapi import UploadScoutAPI
 from cg.meta.upload.upload_api import UploadAPI
+from cg.meta.workflow.analysis import AnalysisAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
+from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
+from cg.meta.workflow.mip_rna import MipRNAAnalysisAPI
+from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
+from cg.meta.workflow.tomte import TomteAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.store.models import Case
 from cg.store.store import Store
 from tests.mocks.scout import MockScoutLoadConfig
 from tests.store_helpers import StoreHelpers
 
+WORKFLOWS_TO_TEST: list = [
+    Workflow.BALSAMIC,
+    Workflow.MIP_DNA,
+    Workflow.MIP_RNA,
+    Workflow.RNAFUSION,
+    Workflow.TOMTE,
+]
 
-def test_get_upload_api(cg_context: CGConfig, case_id: str, helpers: StoreHelpers):
+ANALYSIS_API: dict[Workflow, UploadAPI] = [
+    (Workflow.BALSAMIC, BalsamicAnalysisAPI)(Workflow.MIP_DNA, MipDNAAnalysisAPI)(
+        Workflow.MIP_RNA, MipRNAAnalysisAPI
+    )(Workflow.RNAFUSION, RnafusionAnalysisAPI)(Workflow.TOMTE, TomteAnalysisAPI)
+]
+
+
+@pytest.mark.parametrize(
+    "workflow,analysis_api",
+    ANALYSIS_API,
+)
+def test_get_upload_api(
+    cg_context: CGConfig,
+    case_id: str,
+    helpers: StoreHelpers,
+    workflow: Workflow,
+    analysis_api: AnalysisAPI,
+):
     """Test to get the correct upload API for a BALSAMIC case."""
     status_db: Store = cg_context.status_db
 
     # GIVEN a case with a balsamic analysis
     case: Case = helpers.ensure_case(
         store=status_db, data_analysis=Workflow.BALSAMIC, case_id=case_id
     )
-    helpers.add_analysis(store=status_db, case=case, workflow=Workflow.BALSAMIC)
+    helpers.add_analysis(store=status_db, case=case, workflow=workflow)
 
     # WHEN getting the upload API
     upload_api: UploadAPI = get_upload_api(cg_config=cg_context, case=case)
 
     # THEN assert that the type of upload API is correct
-    assert type(upload_api.analysis_api) == BalsamicAnalysisAPI
+    assert type(upload_api.analysis_api) is analysis_api
 
 
+@pytest.mark.parametrize(
+    "workflow",
+    WORKFLOWS_TO_TEST,
+)
 def test_create_scout_load_config(
     caplog,
     cli_runner: CliRunner,
     cg_context: CGConfig,
     case_id: str,
     helpers: StoreHelpers,
+    workflow: Workflow,
 ):
     """Test to create a scout load config for a BALSAMIC case."""
     caplog.set_level(logging.DEBUG)
     status_db: Store = cg_context.status_db
 
     # GIVEN a case with a balsamic analysis
-    case: Case = helpers.ensure_case(
-        store=status_db, data_analysis=Workflow.BALSAMIC, case_id=case_id
-    )
-    helpers.add_analysis(store=status_db, case=case, workflow=Workflow.BALSAMIC)
+    case: Case = helpers.ensure_case(store=status_db, data_analysis=workflow, case_id=case_id)
+    helpers.add_analysis(store=status_db, case=case, workflow=workflow)
 
     with mock.patch.object(UploadScoutAPI, "generate_config", return_value=MockScoutLoadConfig()):
         # WHEN creating the scout load config