error messages simplified #81

Author: hkir-dev

src/dosdp/validator.py

@@ -27,7 +27,7 @@ def test_jschema(validator, pattern):
     if not validator.is_valid(pattern):
         es = validator.iter_errors(pattern)
         for e in es:
-            warnings.warn(" => ".join([str(e.schema_path), str(e.message), str(e.context)]))
+            warnings.warn(str(e.message))
             is_valid = False
 
     return is_valid
@@ -262,7 +262,8 @@ def validate(pattern):
 
     stat = True
     for pattern_doc in pattern_docs:
-        logging.info("Checking %s" % pattern_doc)
+        if len(pattern_docs) > 1:
+            logging.info("Checking %s" % pattern_doc)
         with open(pattern_doc, "r") as stream:
             try:
                 pattern = ryaml.load(stream)

src/schema/test/generic_test/validator_test.py

@@ -30,6 +30,8 @@
                                                          "../negative_test_set/multi_clause_with_multi_list2.yaml")
 NEGATIVE_PATTERN_UNDECLARED_ANNOT_PROP = os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                                       "../negative_test_set/undeclared_annotation_prop.yaml")
+NEGATIVE_PATTERN_SCHEMA = os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                       "../negative_test_set/not_schema_compliant.yaml")
 
 
 class ValidatorTest(unittest.TestCase):
@@ -65,3 +67,6 @@ def test_single_list_per_multi_clause(self):
 
     def test_undeclared_annotation_prop(self):
         self.assertFalse(validate(NEGATIVE_PATTERN_UNDECLARED_ANNOT_PROP))
+
+    def test_schema_validation(self):
+        self.assertFalse(validate(NEGATIVE_PATTERN_SCHEMA))

src/schema/test/negative_test_set/not_schema_compliant.yaml

@@ -0,0 +1,55 @@
+pattern_name: acute
+
+pattern_iri: http://purl.obolibrary.org/obo/mondo/patterns/acute.yaml
+
+description: 'This pattern is applied to diseases that are described as having an acute onset, i.e. the sudden appearance of disease manifestations over a short period of time.
+
+Examples: [acute bronchiolitis](http://purl.obolibrary.org/obo/MONDO_0020680),
+  [acute liver failure](http://purl.obolibrary.org/obo/MONDO_0019542)'
+
+contributors:
+- https://orcid.org/0000-0002-6601-2165
+- https://orcid.org/0000-0001-5208-3432
+
+classes:
+  acute: PATO:0000389
+  disease: MONDO:0000001
+
+relations:
+  has modifier: RO:0002573
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+  related_synonym: oio:hasRelatedSynonym
+
+vars:
+  disease: '''disease'''
+
+name:
+  text: acute %s
+  vars:
+  - disease
+
+# axioms is not valid
+axioms:
+- annotationProperty: exact_synonym
+  text: '%s, acute'
+  vars:
+  - disease
+
+annotations:
+#  property is not valid
+- property: exact_synonym
+  text: '%s, acute'
+  vars:
+  - disease
+
+def:
+  text: Acute form of %s.
+  vars:
+  - disease
+
+equivalentTo:
+  text: '%s and ''has modifier'' some ''acute'''
+  vars:
+  - disease