Properly testing the error regarding the erroneous scoring file

EI-CoreBioinformatics · Mar 12, 2021 · 501704b · 501704b
1 parent 2955ea4
commit 501704b
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Showing 2 changed files with 42 additions and 4 deletions.
diff --git a/Mikado/configuration/configuration.py b/Mikado/configuration/configuration.py
@@ -7,7 +7,7 @@
 from .prepare_config import PrepareConfiguration
 from .serialise_config import SerialiseConfiguration
 from ..utilities.dbutils import DBConfiguration
-from ..utilities.log_utils import LoggingConfiguration, create_null_logger
+from ..utilities.log_utils import LoggingConfiguration, create_null_logger, create_default_logger
 from Mikado._transcripts.scoring_configuration import ScoringFile
 import os
 import yaml
@@ -94,11 +94,11 @@ def load_scoring(self, logger=None):
         """
 
         if logger is None:
-            logger = create_null_logger("check_scoring")
+            logger = create_default_logger("check_scoring", level="WARNING")
         if self.pick.scoring_file is None:
             if self._loaded_scoring != self.pick.scoring_file:            
                 logger.warning(f"Resetting the scoring to its previous value ({self._loaded_scoring})")
-                self.pick.scoring_file = self._loaded_scoring
+                self.pick.scoring_file = self._loaded_scoring = os.path.abspath(self._loaded_scoring)
         elif self._loaded_scoring != self.pick.scoring_file:
             logger.debug("Overwriting the scoring self using '%s' as scoring file", self.pick.scoring_file)
             self.scoring_file = None
@@ -147,7 +147,8 @@ def load_scoring(self, logger=None):
                     self.pick.scoring_file = option
             if found is True:
                 logger.info("Found the correct option: %s", option)
-                self.pick.scoring_file = option
+                self.pick.scoring_file = os.path.abspath(option)
+                self._loaded_scoring = os.path.abspath(option)
                 break
         if not found:
             raise InvalidConfiguration("No scoring configuration file found. Options: {}".format(",".join(options)))

diff --git a/Mikado/tests/test_configurators.py b/Mikado/tests/test_configurators.py
@@ -1,7 +1,13 @@
+import shutil
 import unittest
+from dataclasses import asdict
 
 import marshmallow
+import tempfile
 
+import pkg_resources
+
+from .. import create_default_logger
 from ..configuration import configurator
 from .._transcripts.scoring_configuration import SizeFilter, TargetScore
 from ..configuration.configuration import *
@@ -87,3 +93,34 @@ def test_load_plant_scoring(self):
         self.assertTrue(mammalian.scoring.requirements.compiled == plant.scoring.requirements.compiled
                         != insect.scoring.requirements.compiled)
         self.assertTrue(mammalian.scoring.requirements.parameters != plant.scoring.requirements.parameters)
+
+    def test_load_invalid_scoring(self):
+        erroneous = tempfile.NamedTemporaryFile(suffix=".yaml", mode="wt")
+        plant = MikadoConfiguration(pick=PickConfiguration(scoring_file="plant.yaml"))
+        err_scoring = copy.deepcopy(plant.scoring)
+        key = next(iter(err_scoring.scoring.keys()))
+        err_scoring.scoring[key].rescaling = "invalid"
+        key = next(iter(err_scoring.requirements.parameters.keys()))
+        del err_scoring.requirements.parameters[key]
+        yaml.dump(asdict(err_scoring), erroneous)
+        erroneous.flush()
+        plant.pick.scoring_file = erroneous.name
+        logger = create_default_logger("test_load_invalid_scoring", level="DEBUG")
+        with self.assertRaises(InvalidConfiguration):
+            plant.load_scoring(logger=logger)
+        current = os.getcwd()
+        os.chdir(os.path.dirname(erroneous.name))
+        plant.scoring_file = os.path.basename(erroneous.name)
+        self.assertFalse(os.path.exists("plant.yaml"))
+        os.link(erroneous.name, "plant.yaml")
+        plant._loaded_scoring = None
+        plant.pick.scoring_file = "plant.yaml"
+        with self.assertRaises(InvalidConfiguration):
+            plant.load_scoring(logger=logger)
+        os.remove(os.path.join(tempfile.gettempdir(), "plant.yaml"))
+        plant._loaded_scoring = None
+        plant.load_scoring(logger=logger)
+        self.assertEqual(plant._loaded_scoring,
+                         pkg_resources.resource_filename("Mikado.configuration", os.path.join("scoring_files",
+                                                                                              "plant.yaml")))
+        os.chdir(current)