Re-organise metrics_parser.

cg/meta/workflow/mutant/metrics_parser/metrics_parser.py

@@ -52,7 +52,26 @@ class MetricsParser:
     }
 
     @classmethod
-    def get_raw_results(cls, results_file_path: Path) -> list[dict[str, Any]]:
+    def parse_samples_results(cls, case: Case, results_file_path: Path) -> dict[str, SampleResults]:
+        try:
+            raw_results: list[dict[str, Any]] = cls._get_raw_results(
+                results_file_path=results_file_path
+            )
+        except Exception as exception_object:
+            raise CgError from exception_object
+
+        validated_results_list: list[SampleResults] = cls._get_validated_results_list(
+            raw_results=raw_results
+        )
+
+        samples_results: dict[str, SampleResults] = cls._get_samples_results(
+            case=case, results_list=validated_results_list
+        )
+
+        return samples_results
+
+    @classmethod
+    def _get_raw_results(cls, results_file_path: Path) -> list[dict[str, Any]]:
         """Parses raw_results from the results file."""
         try:
             raw_results: list[dict[Any, Any]] = [
@@ -66,7 +85,7 @@ def get_raw_results(cls, results_file_path: Path) -> list[dict[str, Any]]:
         return raw_results
 
     @classmethod
-    def get_altered_sample_result(cls, sample_result: dict[str, Any]) -> dict[str, Any]:
+    def _get_altered_sample_result(cls, sample_result: dict[str, Any]) -> dict[str, Any]:
         """Takes a raw_sample_result with headers from the results file (MutantResultsHeaderRawData)
         and returns an altered_sample_result with the corrected headers from MutantResultsHeaderData.
         """
@@ -77,54 +96,35 @@ def get_altered_sample_result(cls, sample_result: dict[str, Any]) -> dict[str, A
         return altered_sample_result
 
     @classmethod
-    def get_validated_results_list(cls, raw_results: list[dict[str, Any]]) -> list[SampleResults]:
+    def _get_validated_results_list(cls, raw_results: list[dict[str, Any]]) -> list[SampleResults]:
         """Takes raw_results and returns a list of validated SampleResults with the corrected headers."""
         validated_results_list = []
         for sample_result in raw_results:
-            altered_sample_result: dict[str, Any] = cls.get_altered_sample_result(
+            altered_sample_result: dict[str, Any] = cls._get_altered_sample_result(
                 sample_result=sample_result
             )
             validated_result: SampleResults = SampleResults.model_validate(altered_sample_result)
             validated_results_list.append(validated_result)
         return validated_results_list
 
     @classmethod
-    def get_sample_name_to_id_mapping(cls, case: Case) -> dict[str, str]:
+    def _get_sample_name_to_id_mapping(cls, case: Case) -> dict[str, str]:
         sample_name_to_id_mapping: dict[str, str] = {}
         for sample in case.samples:
             sample_name_to_id_mapping[sample.name] = sample.internal_id
         return sample_name_to_id_mapping
 
     @classmethod
-    def get_samples_results(
+    def _get_samples_results(
         cls, case: Case, results_list: list[SampleResults]
     ) -> dict[str, SampleResults]:
         """Takes a Case object and a list of SampleResults and builds a dict[str, SampleResults] with
         sample_internal_ids as keys."""
 
-        sample_name_to_id_mapping: dict[str, str] = cls.get_sample_name_to_id_mapping(case=case)
+        sample_name_to_id_mapping: dict[str, str] = cls._get_sample_name_to_id_mapping(case=case)
 
         samples_results: dict[str, SampleResults] = {}
         for result in results_list:
             sample_internal_id = sample_name_to_id_mapping[result.sample_name]
             samples_results[sample_internal_id] = result
         return samples_results
-
-    @classmethod
-    def parse_samples_results(cls, case: Case, results_file_path: Path) -> dict[str, SampleResults]:
-        try:
-            raw_results: list[dict[str, Any]] = cls.get_raw_results(
-                results_file_path=results_file_path
-            )
-        except Exception as exception_object:
-            raise CgError from exception_object
-
-        validated_results_list: list[SampleResults] = cls.get_validated_results_list(
-            raw_results=raw_results
-        )
-
-        samples_results: dict[str, SampleResults] = cls.get_samples_results(
-            case=case, results_list=validated_results_list
-        )
-
-        return samples_results

tests/meta/workflow/mutant/conftest.py

@@ -11,8 +11,6 @@
 )
 
 from cg.meta.workflow.mutant.quality_controller.quality_controller import QualityController
-from cg.meta.workflow.mutant.quality_controller.report_generator_utils import ReportGenerator
-from cg.meta.workflow.mutant.quality_controller.result_logger_utils import ResultLogger
 # from cg.meta.workflow.mutant.quality_controller.utils import get_quality_metrics, get_report_path
 
 
@@ -210,12 +208,12 @@ def mutant_results_file_path_qc_pass(mutant_analysis_dir_case_qc_pass: Path) ->
 
 @pytest.fixture
 def mutant_raw_results_qc_pass(mutant_results_file_path_qc_pass: Path) -> list[dict[str, Any]]:
-    return MetricsParser.get_raw_results(results_file_path=mutant_results_file_path_qc_pass)
+    return MetricsParser._get_raw_results(results_file_path=mutant_results_file_path_qc_pass)
 
 
 @pytest.fixture
 def mutant_results_list_qc_pass(mutant_raw_results_qc_pass: list[dict[str, Any]]):
-    return MetricsParser.get_validated_results_list(raw_results=mutant_raw_results_qc_pass)
+    return MetricsParser._get_validated_results_list(raw_results=mutant_raw_results_qc_pass)
 
 
 # @pytest.fixture

tests/meta/workflow/mutant/test_mutant_metrics_parser.py

@@ -4,29 +4,29 @@
 from cg.store.models import Case
 
 
-def test_get_raw_results(mutant_results_file_path_qc_pass: Path):
+def test__get_raw_results(mutant_results_file_path_qc_pass: Path):
     # GIVEN a path to a valid results file
 
     # WHEN parsing the file
-    MetricsParser.get_raw_results(results_file_path=mutant_results_file_path_qc_pass)
+    MetricsParser._get_raw_results(results_file_path=mutant_results_file_path_qc_pass)
 
     # THEN no error is thrown
 
 
-def test_get_validated_results_list(mutant_raw_results_qc_pass):
+def test__get_validated_results_list(mutant_raw_results_qc_pass):
     # GIVEN a valid raw_results: list[dict[str, Any]] objects
 
     # WHEN parsing the file
-    MetricsParser.get_validated_results_list(raw_results=mutant_raw_results_qc_pass)
+    MetricsParser._get_validated_results_list(raw_results=mutant_raw_results_qc_pass)
 
     # THEN no error is thrown
 
 
-def test_get_sample_name_to_id_mapping(mutant_case_qc_pass: Case):
+def test__get_sample_name_to_id_mapping(mutant_case_qc_pass: Case):
     # GIVEN a case
 
     # WHEN creating a sample_name_to_id_mapping dict
-    sample_name_to_id_mapping: dict[str, str] = MetricsParser.get_sample_name_to_id_mapping(
+    sample_name_to_id_mapping: dict[str, str] = MetricsParser._get_sample_name_to_id_mapping(
         case=mutant_case_qc_pass
     )
 
@@ -36,13 +36,13 @@ def test_get_sample_name_to_id_mapping(mutant_case_qc_pass: Case):
     assert sample_name_to_id_mapping["0PROVSEK"] == "external_negative_control_qc_pass"
 
 
-def test_get_samples_results(
+def test__get_samples_results(
     mutant_case_qc_pass: Case, mutant_results_list_qc_pass: list[SampleResults]
 ):
     # GIVEN a case and corresponding results_list
 
     # WHEN creating a sample_name_to_id_mapping dict
-    MetricsParser.get_samples_results(
+    MetricsParser._get_samples_results(
         case=mutant_case_qc_pass, results_list=mutant_results_list_qc_pass
     )