feat(refactor): balsamic config (#3885)

### Changed

- Refactor Analysis model for Balsamic

Author: henrikstranneheim

cg/meta/delivery_report/balsamic.py

@@ -28,7 +28,11 @@
     BalsamicTargetedSampleMetadataModel,
     BalsamicWGSSampleMetadataModel,
 )
-from cg.models.delivery_report.report import CaseModel, ReportRequiredFields, ScoutVariantsFiles
+from cg.models.delivery_report.report import (
+    CaseModel,
+    ReportRequiredFields,
+    ScoutVariantsFiles,
+)
 from cg.models.delivery_report.sample import SampleModel
 from cg.store.models import Bed, BedVersion, Case, Sample
 
@@ -76,12 +80,12 @@ def get_panel_metadata(
     ) -> BalsamicTargetedSampleMetadataModel:
         """Return report metadata for Balsamic TGS analysis."""
         bed_version: BedVersion = self.status_db.get_bed_version_by_file_name(
-            analysis_metadata.config.panel.capture_kit
+            analysis_metadata.balsamic_config.panel.capture_kit
         )
         bed: Bed = self.status_db.get_bed_by_entry_id(bed_version.bed_id) if bed_version else None
         return BalsamicTargetedSampleMetadataModel(
             bait_set=bed.name if bed else None,
-            bait_set_version=analysis_metadata.config.panel.capture_kit_version,
+            bait_set_version=analysis_metadata.balsamic_config.panel.capture_kit_version,
             duplicates=sample_metrics.percent_duplication if sample_metrics else None,
             fold_80=sample_metrics.fold_80_base_penalty if sample_metrics else None,
             gc_dropout=sample_metrics.gc_dropout if sample_metrics else None,
@@ -120,11 +124,11 @@ def is_report_accredited(
         self, samples: list[SampleModel], analysis_metadata: BalsamicAnalysis
     ) -> bool:
         """Return whether the Balsamic delivery report is accredited."""
-        if analysis_metadata.config.analysis.sequencing_type == "targeted" and next(
+        if analysis_metadata.balsamic_config.analysis.sequencing_type == "targeted" and next(
             (
                 panel
                 for panel in BALSAMIC_REPORT_ACCREDITED_PANELS
-                if panel in str(analysis_metadata.config.panel.capture_kit)
+                if panel in str(analysis_metadata.balsamic_config.panel.capture_kit)
             ),
             None,
         ):

cg/meta/workflow/balsamic.py

@@ -7,7 +7,7 @@
 from pydantic.v1 import EmailStr, ValidationError
 
 from cg.constants import Workflow
-from cg.constants.constants import FileFormat, SampleType, GenomeVersion
+from cg.constants.constants import FileFormat, GenomeVersion, SampleType
 from cg.constants.housekeeper_tags import BalsamicAnalysisTag
 from cg.constants.observations import ObservationsFileWildcards
 from cg.constants.priority import SlurmQos
@@ -349,7 +349,7 @@ def parse_analysis(self, config_raw: dict, qc_metrics_raw: dict, **kwargs) -> Ba
                 qc_metrics[sample_metric.id] = {sample_metric.name.lower(): sample_metric.value}
 
         return BalsamicAnalysis(
-            config=config_raw,
+            balsamic_config=config_raw,
             sample_metrics=self.cast_metrics_type(sequencing_type, qc_metrics),
         )
 
@@ -615,7 +615,7 @@ def report_deliver(self, case_id: str, dry_run: bool = False) -> None:
     def get_genome_build(self, case_id: str) -> str:
         """Returns the reference genome build version of a Balsamic analysis."""
         analysis_metadata: BalsamicAnalysis = self.get_latest_metadata(case_id)
-        return analysis_metadata.config.reference.reference_genome_version
+        return analysis_metadata.balsamic_config.reference.reference_genome_version
 
     @staticmethod
     def get_variant_caller_version(var_caller_name: str, var_caller_versions: dict) -> str | None:
@@ -631,10 +631,10 @@ def get_variant_callers(self, case_id: str) -> list[str]:
         config.json file.
         """
         analysis_metadata: BalsamicAnalysis = self.get_latest_metadata(case_id)
-        sequencing_type: str = analysis_metadata.config.analysis.sequencing_type
-        analysis_type: str = analysis_metadata.config.analysis.analysis_type
-        var_callers: dict[str, BalsamicVarCaller] = analysis_metadata.config.vcf
-        tool_versions: dict[str, list] = analysis_metadata.config.bioinfo_tools_version
+        sequencing_type: str = analysis_metadata.balsamic_config.analysis.sequencing_type
+        analysis_type: str = analysis_metadata.balsamic_config.analysis.analysis_type
+        var_callers: dict[str, BalsamicVarCaller] = analysis_metadata.balsamic_config.vcf
+        tool_versions: dict[str, list] = analysis_metadata.balsamic_config.bioinfo_tools_version
         analysis_var_callers = []
         for var_caller_name, var_caller_attributes in var_callers.items():
             if (
@@ -653,8 +653,8 @@ def get_pons(self, case_id: str) -> list[str]:
         """Return list of panel of normals used for analysis."""
         pons: list[str] = []
         analysis_metadata: BalsamicAnalysis = self.get_latest_metadata(case_id)
-        if analysis_metadata.config.panel:
-            if pon_cnn := analysis_metadata.config.panel.pon_cnn:
+        if analysis_metadata.balsamic_config.panel:
+            if pon_cnn := analysis_metadata.balsamic_config.panel.pon_cnn:
                 pons.append(pon_cnn)
         return pons
 

cg/models/balsamic/analysis.py

@@ -7,9 +7,9 @@ class BalsamicAnalysis(AnalysisModel):
     """BALSAMIC analysis model
 
     Attributes:
-        config: balsamic config file attributes model
+        balsamic_config: balsamic config file attributes model
         sample_metrics: retrieved QC metrics associated to a sample
     """
 
-    config: BalsamicConfigJSON
+    balsamic_config: BalsamicConfigJSON
     sample_metrics: dict[str, BalsamicQCMetrics]

tests/meta/workflow/test_balsamic.py

@@ -206,7 +206,7 @@ def test_get_variant_caller_version(analysis_api_balsamic: MockBalsamicAnalysis,
     var_caller_name = "manta"
     var_caller_versions: dict[str, list[str]] = analysis_api_balsamic.get_latest_metadata(
         case_id
-    ).config.bioinfo_tools_version
+    ).balsamic_config.bioinfo_tools_version
 
     # GIVEN the tools mock version
     expected_version = "1.6.0"

tests/models/balsamic/test_balsamic_analysis.py

@@ -16,7 +16,7 @@ def test_parse_analysis_tga(cg_context, balsamic_tga_config_raw, balsamic_tga_me
     )
 
     # THEN assert that it was successfully created
-    assert isinstance(balsamic_analysis.config, BalsamicConfigJSON)
+    assert isinstance(balsamic_analysis.balsamic_config, BalsamicConfigJSON)
     assert isinstance(balsamic_analysis.sample_metrics["ACC0000A1"], BalsamicTargetedQCMetrics)
 
 
@@ -33,5 +33,5 @@ def test_parse_analysis_wgs(cg_context, balsamic_wgs_config_raw, balsamic_wgs_me
 
     # THEN assert that it was successfully created
 
-    assert isinstance(balsamic_analysis.config, BalsamicConfigJSON)
+    assert isinstance(balsamic_analysis.balsamic_config, BalsamicConfigJSON)
     assert isinstance(balsamic_analysis.sample_metrics["ACC0000A1"], BalsamicWGSQCMetrics)