fix: Scout files logs for delivery report & remove outdated UDF access (

#2923)

### Fixed:
- File retrieval logging for Scout upload files to be specific to its respective pipeline (delivery report generation).
- Removed outdated UDF usage for retrieving the application version (delivery report generation).

cg/meta/report/balsamic.py

@@ -33,7 +33,7 @@
     BalsamicTargetedSampleMetadataModel,
     BalsamicWGSSampleMetadataModel,
 )
-from cg.models.report.report import CaseModel
+from cg.models.report.report import CaseModel, ScoutReportFiles
 from cg.models.report.sample import SampleModel
 from cg.store.models import Bed, BedVersion, Case, Sample
 
@@ -91,8 +91,9 @@ def get_panel_metadata(
             gc_dropout=sample_metrics.gc_dropout if sample_metrics else None,
         )
 
+    @staticmethod
     def get_wgs_metadata(
-        self, million_read_pairs: float, sample_metrics: BalsamicWGSQCMetrics
+        million_read_pairs: float, sample_metrics: BalsamicWGSQCMetrics
     ) -> BalsamicWGSSampleMetadataModel:
         """Return report metadata for Balsamic WGS analysis."""
         return BalsamicWGSSampleMetadataModel(
@@ -162,6 +163,17 @@ def is_report_accredited(
             return True
         return False
 
+    def get_scout_uploaded_files(self, case: Case) -> ScoutReportFiles:
+        """Return files that will be uploaded to Scout."""
+        return ScoutReportFiles(
+            snv_vcf=self.get_scout_uploaded_file_from_hk(
+                case_id=case.internal_id, scout_tag="snv_vcf"
+            ),
+            sv_vcf=self.get_scout_uploaded_file_from_hk(
+                case_id=case.internal_id, scout_tag="sv_vcf"
+            ),
+        )
+
     def get_required_fields(self, case: CaseModel) -> dict:
         """Return a dictionary with the delivery report required fields for Balsamic."""
         analysis_type: str = case.data_analysis.type

cg/meta/report/mip_dna.py

@@ -24,7 +24,7 @@
 from cg.models.mip.mip_analysis import MipAnalysis
 from cg.models.mip.mip_metrics_deliverables import get_sample_id_metric
 from cg.models.report.metadata import MipDNASampleMetadataModel
-from cg.models.report.report import CaseModel
+from cg.models.report.report import CaseModel, ScoutReportFiles
 from cg.models.report.sample import SampleModel
 from cg.store.models import Case, Sample
 
@@ -88,6 +88,23 @@ def is_report_accredited(
                 return False
         return True
 
+    def get_scout_uploaded_files(self, case: Case) -> ScoutReportFiles:
+        """Return files that will be uploaded to Scout."""
+        return ScoutReportFiles(
+            snv_vcf=self.get_scout_uploaded_file_from_hk(
+                case_id=case.internal_id, scout_tag="snv_vcf"
+            ),
+            sv_vcf=self.get_scout_uploaded_file_from_hk(
+                case_id=case.internal_id, scout_tag="sv_vcf"
+            ),
+            vcf_str=self.get_scout_uploaded_file_from_hk(
+                case_id=case.internal_id, scout_tag="vcf_str"
+            ),
+            smn_tsv=self.get_scout_uploaded_file_from_hk(
+                case_id=case.internal_id, scout_tag="smn_tsv"
+            ),
+        )
+
     def get_required_fields(self, case: CaseModel) -> dict:
         """Return dictionary with the delivery report required fields for MIP DNA."""
         return {

cg/meta/report/report_api.py

@@ -260,7 +260,9 @@ def get_samples_data(self, case: Case, analysis_metadata: AnalysisModel) -> list
                     gender=sample.sex,
                     source=lims_sample.get("source") if lims_sample else None,
                     tumour=sample.is_tumour,
-                    application=self.get_sample_application_data(lims_sample=lims_sample),
+                    application=self.get_sample_application_data(
+                        sample=sample, lims_sample=lims_sample
+                    ),
                     methods=self.get_sample_methods_data(sample_id=sample.internal_id),
                     status=case_sample.status,
                     metadata=self.get_sample_metadata(
@@ -289,15 +291,15 @@ def get_workflow_accreditation_limitation(self, application_tag: str) -> str | N
         )
         return application_limitation.limitations if application_limitation else None
 
-    def get_sample_application_data(self, lims_sample: dict) -> ApplicationModel:
+    def get_sample_application_data(self, sample: Sample, lims_sample: dict) -> ApplicationModel:
         """Retrieves the analysis application attributes."""
         application: Application = self.status_db.get_application_by_tag(
             tag=lims_sample.get("application")
         )
         return (
             ApplicationModel(
                 tag=application.tag,
-                version=lims_sample.get("application_version"),
+                version=sample.application_version.version,
                 prep_category=application.prep_category,
                 description=application.description,
                 details=application.details,
@@ -352,23 +354,7 @@ def get_case_analysis_data(
 
     def get_scout_uploaded_files(self, case: Case) -> ScoutReportFiles:
         """Return files that will be uploaded to Scout."""
-        return ScoutReportFiles(
-            snv_vcf=self.get_scout_uploaded_file_from_hk(
-                case_id=case.internal_id, scout_tag="snv_vcf"
-            ),
-            sv_vcf=self.get_scout_uploaded_file_from_hk(
-                case_id=case.internal_id, scout_tag="sv_vcf"
-            ),
-            vcf_str=self.get_scout_uploaded_file_from_hk(
-                case_id=case.internal_id, scout_tag="vcf_str"
-            ),
-            smn_tsv=self.get_scout_uploaded_file_from_hk(
-                case_id=case.internal_id, scout_tag="smn_tsv"
-            ),
-            vcf_fusion=self.get_scout_uploaded_file_from_hk(
-                case_id=case.internal_id, scout_tag="vcf_fusion"
-            ),
-        )
+        raise NotImplementedError
 
     @staticmethod
     def get_sample_timestamp_data(sample: Sample) -> TimestampModel:

cg/meta/report/rnafusion.py

@@ -23,7 +23,7 @@
 from cg.models.analysis import AnalysisModel
 from cg.models.cg_config import CGConfig
 from cg.models.report.metadata import RnafusionSampleMetadataModel
-from cg.models.report.report import CaseModel
+from cg.models.report.report import CaseModel, ScoutReportFiles
 from cg.models.report.sample import SampleModel
 from cg.models.rnafusion.rnafusion import RnafusionAnalysis, RnafusionQCMetrics
 from cg.store.models import Case, Sample
@@ -88,6 +88,14 @@ def get_template_name(self) -> str:
         """Return template name to render the delivery report."""
         return Workflow.RNAFUSION + "_report.html"
 
+    def get_scout_uploaded_files(self, case: Case) -> ScoutReportFiles:
+        """Return files that will be uploaded to Scout."""
+        return ScoutReportFiles(
+            vcf_fusion=self.get_scout_uploaded_file_from_hk(
+                case_id=case.internal_id, scout_tag="vcf_fusion"
+            )
+        )
+
     def get_required_fields(self, case: CaseModel) -> dict:
         """Return dictionary with the delivery report required fields for Rnafusion."""
         return {

tests/meta/report/test_report_api.py

@@ -24,7 +24,7 @@
     SampleModel,
     TimestampModel,
 )
-from cg.store.models import Analysis, Case, CaseSample
+from cg.store.models import Analysis, Case, CaseSample, Sample
 from cg.store.store import Store
 from tests.meta.report.helper import recursive_assert
 from tests.store_helpers import StoreHelpers
@@ -307,16 +307,17 @@ def test_get_sample_application_data(
     # GIVEN a lims sample instance
 
     # GIVEN the expected application data
-    expected_application_data: dict = case_samples_data[0].sample.to_dict().get("application")
+    sample: Sample = case_samples_data[0].sample
+    expected_application_data: dict = sample.to_dict().get("application")
 
     # WHEN retrieving application data from status DB
     application_data: ApplicationModel = report_api_mip_dna.get_sample_application_data(
-        lims_samples[0]
+        sample=sample, lims_sample=lims_samples[0]
     )
 
     # THEN verify that the application data corresponds to what is expected
     assert application_data.tag == str(expected_application_data.get("tag"))
-    assert application_data.version == str(lims_samples[0].get("application_version"))
+    assert application_data.version == str(sample.application_version.version)
     assert application_data.prep_category == str(expected_application_data.get("prep_category"))
     assert application_data.description == str(expected_application_data.get("description"))
     assert application_data.limitations == str(expected_application_data.get("limitations"))