Implemented UnsupportedActionException

snappy_pipeline/base.py

@@ -27,6 +27,10 @@ class MissingConfiguration(InvalidConfiguration):
     """Raised on missing configuration"""
 
 
+class UnsupportedActionException(Exception):
+    """Raised when user try to call action that isn't supported."""
+
+
 def expand_ref(config_path, dict_data, lookup_paths=None, dict_class=OrderedDict):
     """Expand "$ref" in JSON-like data ``dict_data``
 

snappy_pipeline/workflows/somatic_wgs_cnv_calling/__init__.py

@@ -81,6 +81,7 @@
 from biomedsheets.shortcuts import CancerCaseSheet, CancerCaseSheetOptions, is_not_background
 from snakemake.io import expand
 
+from snappy_pipeline.base import UnsupportedActionException
 from ..abstract import BaseStepPart, BaseStep, LinkOutStepPart
 from ..ngs_mapping import NgsMappingWorkflow
 from ...utils import listify, dictify
@@ -381,7 +382,18 @@ class ControlFreecSomaticWgsStepPart(SomaticWgsCnvCallingStepPart):
     name = "control_freec"
 
     def get_output_files(self, action):
+        # Initialise variable
+        valid_action_list = ["run", "transform", "plot"]
         result = {}
+
+        # Validate input
+        if action not in valid_action_list:
+            valid_actions_str = ", ".join(valid_action_list)
+            error_message = "Action {action} is not supported. Valid options: {options}".format(
+                action=action, options=valid_actions_str
+            )
+            raise UnsupportedActionException(error_message)
+
         if action == "run":
             result["ratio"] = self.base_path_out.format(var_caller=self.name, ext=".ratio.txt")
             result["ratio_md5"] = self.base_path_out.format(
@@ -411,8 +423,7 @@ def get_output_files(self, action):
                     expand(self.base_path_out, var_caller=[self.name], ext=plot_ext_values),
                 )
             )
-        else:
-            raise "Unsupported action"
+
         return result
 
     def check_config(self):

tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py

@@ -169,6 +169,16 @@ def test_control_freec_somatic_step_part_get_output_files(somatic_wgs_cnv_callin
     assert actual == expected
 
 
+def test_control_freec_somatic_step_part_get_output_exception(somatic_wgs_cnv_calling_workflow):
+    """Tests if ControlFreecSomaticWgsStepPart::get_output_files() raises exception for invalid
+    action."""
+    # Exception raised cause no RNA mapper defined in config
+    with pytest.raises(Exception) as exec_info:
+        somatic_wgs_cnv_calling_workflow.get_output_files("control_freec", "invalid_action")
+    error_msg = "Called unsupported action, exceptions should have been raised."
+    assert exec_info.value.args[0] is not None, error_msg
+
+
 def test_control_freec_somatic_step_part_get_log_file(somatic_wgs_cnv_calling_workflow):
     # Define expected
     base_name = (