change to staticmethod and clean up sonarcloud issue

cg/meta/workflow/raredisease.py

@@ -107,7 +107,8 @@ def get_pipeline_parameters(self, case_id: str) -> PipelineParameters:
             outdir=self.get_case_path(case_id=case_id),
         )
 
-    def get_phenotype_code(self, phenotype: str) -> int:
+    @staticmethod
+    def get_phenotype_code(phenotype: str) -> int:
         """Return Raredisease phenotype code."""
         LOG.debug("Translate phenotype to int")
         if phenotype == "unaffected":
@@ -117,23 +118,22 @@ def get_phenotype_code(self, phenotype: str) -> int:
         else:
             return 0
 
-    def get_sex_code(self, sex: str) -> int:
-        """Return Raredisease phenotype code."""
-        LOG.debug("Translate phenotype to int")
+    @staticmethod
+    def get_sex_code(sex: str) -> int:
+        """Return Raredisease sex code."""
+        LOG.debug("Translate sex to int")
         if sex == "male":
             return 1
         elif sex == "female":
             return 2
         else:
             return 0
 
-    def get_parental_id(self, parent: CaseSample) -> str:
-        """Return Raredisease phenotype code."""
-        LOG.debug("Translate phenotype to int")
-        if parent:
-            return parent.internal_id
-        else:
-            return ""
+    @staticmethod
+    def get_parental_id(parent: CaseSample) -> str:
+        """Return Raredisease parental id."""
+        LOG.debug("Return parental id")
+        return parent.internal_id if parent else ""
 
     @property
     def root(self) -> str:

tests/meta/workflow/test_prepare_fastq_api.py

@@ -190,7 +190,11 @@ def test_add_decompressed_sample_loops_through_spring(
     case = analysis_store.get_case_by_internal_id(case_id)
     sample = case.samples[0]
 
-    with mock.patch.object(files, "get_hk_files_dict", return_value={},), mock.patch.object(
+    with mock.patch.object(
+        files,
+        "get_hk_files_dict",
+        return_value={},
+    ), mock.patch.object(
         files,
         "get_spring_paths",
         return_value=[CompressionData(spring_file.with_suffix(""))],