Adatps validation behaviour to marshmallow > 3.0. Adds tests

tests/mip/test_mip_config.py

@@ -0,0 +1,149 @@
+"""Tests for the config functionality"""
+import pytest
+
+from trailblazer.mip import config as tb_config
+from trailblazer.exc import ConfigError
+
+def test_validate_config():
+    """Test to validate a correct config"""
+    # GIVEN a correct config
+    sample = dict(
+        sample_id = "sample",
+        analysis_type = 'wes',
+        father = '0',
+        mother = '0',
+        phenotype = 'affected',
+        sex = 'male',
+        expected_coverage = 15,
+        capture_kit = 'agilent_sureselect_cre.v1',
+    )
+
+    config = dict(
+        case = "a_case",
+        default_gene_panels = ["a_panel"],
+        samples = [sample],
+    )
+
+    # WHEN validating the config
+    errors = tb_config.ConfigHandler.validate_config(config)
+
+    # THEN assert the errors is a dict
+    assert isinstance(errors, dict)
+
+    # THEN assert there where no errors
+    assert errors == {}
+
+def test_validate_config_invalid_analysis_type():
+    """Test to validate a invalid config with wrong analysis type"""
+    # GIVEN a correct config
+    sample = dict(
+        sample_id = "sample",
+        analysis_type = 'nonexisting',
+        father = '0',
+        mother = '0',
+        phenotype = 'affected',
+        sex = 'male',
+        expected_coverage = 15,
+        capture_kit = 'agilent_sureselect_cre.v1',
+    )
+
+    config = dict(
+        case = "a_case",
+        default_gene_panels = ["a_panel"],
+        samples = [sample],
+    )
+
+    # WHEN validating the config
+    with pytest.raises(ConfigError):
+    # THEN assert a config error is raised
+        tb_config.ConfigHandler.validate_config(config)
+
+def test_validate_config_unknown_field():
+    """Test to validate a config with a unspecified field.
+
+    This should work since we allow unspecified fields
+    """
+    # GIVEN a correct config with a extra field
+    sample = dict(
+        sample_id = "sample",
+        sample_display_name = "ASAMPLENAME",
+        analysis_type = 'wes',
+        father = '0',
+        mother = '0',
+        phenotype = 'affected',
+        sex = 'male',
+        expected_coverage = 15,
+        capture_kit = 'agilent_sureselect_cre.v1',
+    )
+
+    config = dict(
+        case = "a_case",
+        default_gene_panels = ["a_panel"],
+        samples = [sample],
+    )
+
+    # WHEN validating the config
+    errors = tb_config.ConfigHandler.validate_config(config)
+
+    # THEN assert the errors is a dict
+    assert isinstance(errors, dict)
+
+    # THEN assert there where one error that could pass
+    assert len(errors) == 1
+
+def test_validate_config_unknown_field_and_missing_sample_id():
+    """Test to validate a config with a unspecified field and a missing mandatory field.
+
+    This should raise exception since we do not allow missing mandatory fields
+    """
+    # GIVEN a config with missing sample_id and an extra field
+    sample = dict(
+        sample_display_name = "ASAMPLENAME",
+        analysis_type = 'wes',
+        father = '0',
+        mother = '0',
+        phenotype = 'affected',
+        sex = 'male',
+        expected_coverage = 15,
+        capture_kit = 'agilent_sureselect_cre.v1',
+    )
+
+    config = dict(
+        case = "a_case",
+        default_gene_panels = ["a_panel"],
+        samples = [sample],
+    )
+
+    # WHEN validating the config
+    with pytest.raises(ConfigError):
+    # THEN assert a config error is raised
+        tb_config.ConfigHandler.validate_config(config)
+
+def test_validate_config_unknown_field_and_invalid_analysis_type():
+    """Test to validate a config with a unspecified field and a missing mandatory field.
+
+    This should raise exception since we do not allow wrong analysis types
+    """
+    # GIVEN a config with wrong analysis type and an extra field
+    sample = dict(
+        sample_id = "sample",
+        sample_display_name = "ASAMPLENAME",
+        analysis_type = 'nonexisting',
+        father = '0',
+        mother = '0',
+        phenotype = 'affected',
+        sex = 'male',
+        expected_coverage = 15,
+        capture_kit = 'agilent_sureselect_cre.v1',
+    )
+
+    config = dict(
+        case = "a_case",
+        default_gene_panels = ["a_panel"],
+        samples = [sample],
+    )
+
+    # WHEN validating the config
+    with pytest.raises(ConfigError):
+    # THEN assert a config error is raised
+        tb_config.ConfigHandler.validate_config(config)

trailblazer/mip/config.py

@@ -80,15 +80,25 @@ def validate_config(data: dict, pipeline: str = None) -> dict:
         else:
             errors = ConfigSchema().validate(data)
         if errors:
+            hard_error = False
             for field, messages in errors.items():
                 if isinstance(messages, dict):
                     for level, sample_errors in messages.items():
-                        sample_id = data['samples'][level]['sample_id']
+                        try:
+                            sample_id = data['samples'][level]['sample_id']
+                        except KeyError:
+                            raise ConfigError('missing sample id')
+
                         for sub_field, sub_messages in sample_errors.items():
+                            if sub_messages != ["Unknown field."]:
+                                hard_error = True
                             LOG.error(f"{sample_id} -> {sub_field}: {', '.join(sub_messages)}")
                 else:
+                    hard_error = True
                     LOG.error(f"{field}: {', '.join(messages)}")
-            raise ConfigError('invalid config input', errors=errors)
+            if hard_error:
+                raise ConfigError('invalid config input', errors=errors)
+        return errors
 
     @staticmethod
     def prepare_config(data: dict) -> dict: