Make tests fail, not print

tests/__init__.py

@@ -24,7 +24,7 @@
 # Action on mismatch.  One of 'Ignore', 'Report' or 'Fail'
 #  If 'Fail', the expected file will be saved in the appropriate temp directory
 #  NOTE: Before setting this back to Report or Ignore, you need to run cleartemp.sh in this directory
-DEFAULT_MISMATCH_ACTION = eval(test_settings.get('DEFAULT_MISMATCH_ACTION', 'MismatchAction.Report'))
+DEFAULT_MISMATCH_ACTION = eval(test_settings.get('DEFAULT_MISMATCH_ACTION', 'MismatchAction.Fail'))
 
 # Use local import map.  If True, tests/input/local_import_map.json is used to create the test files.  Note that this
 #  will result in local path names being recorded in jsonld files.  This should always be set to False before generating

tests/support/clicktestcase.py

@@ -80,10 +80,13 @@ def closein_comparison(expected_txt: str, actual_txt: str) -> None:
                 nt = nt[window:]
                 ot = ot[window:]
             offset = max(offset-view, 0)
-            print("   - - EXPECTED - -")
-            print(ow[offset:offset+view+view])
-            print("\n   - - ACTUAL - -")
-            print(nw[offset:offset+view+view])
+            msg = '\n'.join([
+                "   - - EXPECTED - -",
+                str(ow[offset:offset+view+view]),
+                "   - - ACTUAL - -",
+                str(nw[offset:offset+view+view])
+            ])
+            raise ValueError(msg)
 
     def do_test(self,
                 args: Union[str, List[str]],

tests/support/test_environment.py

@@ -65,7 +65,7 @@ def __init__(self, filedir: str) -> None:
     @staticmethod
     def _check_changed(test_file: str, runtime_file: str) -> None:
         if not filecmp.cmp(test_file, runtime_file):
-            print(
+            raise Exception(
                 f"WARNING: Test file {test_file} does not match {runtime_file}.  "
                 f"You may want to update the test version and rerun")
         from tests import USE_LOCAL_IMPORT_MAP
@@ -112,7 +112,7 @@ def fail_on_error(self) -> bool:
 
     @property
     def report_errors(self) -> bool:
-        return self.mismatch_action != MismatchAction.Ignore
+        return self.mismatch_action == MismatchAction.Report
 
     def __str__(self):
         """ Return the current state of the log file """
@@ -175,10 +175,12 @@ def generate_directory(self, dirname: Union[str, List[str]], generator: Callable
 
         diffs = are_dir_trees_equal(expected_output_directory, temp_output_directory)
         if diffs:
-            self.log(expected_output_directory, diffs)
             if not self.fail_on_error:
+                self.log(expected_output_directory, diffs)
                 shutil.rmtree(expected_output_directory)
                 os.rename(temp_output_directory, expected_output_directory)
+            else:
+                raise Exception(f'Diffs found in {expected_output_directory}:\n{diffs}')
         else:
             shutil.rmtree(temp_output_directory)
 
@@ -237,12 +239,13 @@ def eval_single_file(self, expected_file_path: str, actual_text: str, filtr: Cal
             cmsg = comparator(actual_text, actual_text)
             if cmsg:
                 msg = msg + '\n' + cmsg
-        if msg:
-            self.log(expected_file_path, msg)
+
         if msg and not self.fail_on_error:
             self.make_temp_dir(os.path.dirname(expected_file_path), clear=False)
             with open(expected_file_path, 'w', encoding='UTF-8') as outf:
                 outf.write(actual_text)
+        elif msg is not None:
+            raise Exception(msg)
         return not msg
 
 

tests/test_issues/test_issue_368_enums.py

@@ -27,9 +27,6 @@ def test_issue_368_enums(self):
         def dump_and_load(dumper: Callable, sfx: str) -> None:
             fname = env.actual_path(f'issue_368_1.{sfx}')
             dumper(example, fname)
-            with open(fname) as f:
-                print(f'\n----- {sfx} -----')
-                print(f.read())
 
         dump_and_load(json_dumper.dump, 'json')
         dump_and_load(yaml_dumper.dump, 'yaml')

tests/test_issues/test_linkml_issue_478.py

@@ -14,12 +14,8 @@ class Issue478TestCase(TestCase):
 
     def test_issue_478(self):
         view = SchemaView(env.input_path('linkml_issue_478.yaml'))
-        for c in view.all_classes():
-            print(f'c={c}')
         cnames = list(view.class_name_mappings().keys())
         snames = list(view.slot_name_mappings().keys())
-        print(cnames)
-        print(snames)
         cnames.remove("5'Sequencing")  ## TODO
         self.assertCountEqual(['FooBar', 'NamedThing', 'BiosampleProcessing', 'TooMuchWhitespace'], cnames)
         snames.remove("5'_sequence")  ## TODO

tests/test_issues/test_linkml_issue_576.py

@@ -23,8 +23,6 @@ def test_issue_no_namespace(self):
         s = rdflib_dumper.dumps(inst, view, 'turtle', prefix_map={"@base": "http://example.org/default/"})
         self.assertIn("@base <http://example.org/default/> .", s)
         g = rdflib.Graph().parse(data=s, format='turtle')
-        for t in g.triples((None, None, None)):
-            print(t)
         cases = [
             (None,
              rdflib.term.URIRef('https://w3id.org/linkml/personinfo/source'),

tests/test_loaders_dumpers/test_enum.py

@@ -18,20 +18,13 @@ def test_enum(self):
         * https://github.com/linkml/linkml/issues/119
         """
         i = Organism(state='LIVING')
-        print(i)
-        print(i.state)
-        print(i.state.code)
-        print(i.state.code.text)
-        print(type(i.state))
-        print(StateEnum.LIVING)
         assert str(i.state) == 'LIVING'
         assert i.state.code == StateEnum.LIVING
         obj = json.loads(json_dumper.dumps(i))
         assert obj['state'] == 'LIVING'
         obj = yaml.safe_load(yaml_dumper.dumps(i))
         assert obj['state'] == 'LIVING'
         reconstituted = json_loader.loads(json_dumper.dumps(i), target_class=Organism)
-        print(f'RECONSTITUTED = {reconstituted}')
         assert reconstituted.state.code == StateEnum.LIVING
 
 

tests/test_loaders_dumpers/test_rdflib_dumper.py

@@ -150,17 +150,13 @@ def test_enums(self):
         assert not org1type1.meaning
         assert org1type2.meaning
         org1 = Organization('ROR:1', categories=[org1type1, org1type2])
-        print(org1.categories)
         g = rdflib_dumper.as_rdf_graph(org1, schemaview=view, prefix_map=self.prefix_map)
-        print(g)
         cats = list(g.objects(ROR['1'], INFO['categories']))
-        print(cats)
         self.assertCountEqual([Literal('non profit'), URIRef('https://example.org/bizcodes/001')], cats)
         orgs = rdflib_loader.from_rdf_graph(g, target_class=Organization, schemaview=view)
         assert len(orgs) == 1
         [org1x] = orgs
         catsx = org1x.categories
-        print(catsx)
         self.assertCountEqual([org1type1, org1type2], catsx)
 
     def test_undeclared_prefix(self):
@@ -245,7 +241,6 @@ def test_blank_node(self):
                                              ignore_unmapped_predicates=True)
         self.assertEqual(address.city, 'foo city')
         ttl = rdflib_dumper.dumps(address, schemaview=view)
-        print(ttl)
         g = Graph()
         g.parse(data=ttl, format='ttl')
         INFO = Namespace('https://w3id.org/linkml/examples/personinfo/')

tests/test_processing/test_referencevalidator.py

@@ -148,7 +148,6 @@ def setUpClass(cls):
 
         Sets up a document object that each test will contribute to.
         """
-        print("Setting up class...")
         doc = MarkdownDocument()
         doc.h1("Validation Suite")
         doc.text("This document describes the validation suite for the LinkML model.")
@@ -1154,8 +1153,6 @@ def test_line_number(self):
         """
         obj = yaml.load(s, DupCheckYamlLoader)
         report = validator.validate(obj)
-        for r in report.results_excluding_normalized():
-            print(yaml_dumper.dumps(r))
         self.assertEqual(1, len(report.results_excluding_normalized()))
         r = report.results_excluding_normalized()[0]
         self.assertEqual(3, r.source_line_number)
@@ -1188,8 +1185,6 @@ def test_examples_against_metamodel(self):
         report = Report()
         schema_norm = validator.normalize(schema_dict, target=sdc.name, report=report)
         self.assertEqual(dict, type(schema_norm["prefixes"]))
-        for r in report.results_excluding_normalized():
-            print(yaml_dumper.dumps(r))
         self.assertEqual(len(report.errors()), 0)
         # for r in report.repaired():
         #    print(r)

tests/test_utils/test_dict_utils.py

@@ -40,34 +40,26 @@ def test_as_dict(self):
         assert d['name'] == 'test class'
         assert d['id_prefixes'] == []
         assert d['description'] is None
-        for x in _signature(d):
-            if not _is_python_type(x):
-                print(f'   ****={x} {type(x)}')
         assert all(_is_basic_type(x) for x in _signature(d))
 
         d2 = yutils.as_dict(obj2)
-        print(d2)
         assert d2['slot_usage']['foo']['range'] == 'bar'
         assert all(_is_basic_type(x) for x in _signature(d2))
 
         # as_simple_dict removes nones and empty lists
         d = as_simple_dict(obj)
-        print(d)
         assert isinstance(d, dict)
         assert all(_is_python_type(x) for x in _signature(d))
         assert d == {'name': 'test class'}
 
         d2 = as_simple_dict(obj2)
-        print(d2)
         assert isinstance(d2, dict)
         assert d2 == {'name': 'test class', 'slot_usage': {'foo': {'name': 'foo', 'range': 'bar'}}}
 
         s = yutils.as_yaml(obj)
-        print(s)
         assert(s.strip() == 'name: test class')
 
         s2 = yutils.as_yaml(obj2)
-        print(s2)
         assert(s2.strip().startswith('name: test class'))
 
 

tests/test_utils/test_ruleutils.py

@@ -26,19 +26,13 @@ def test_disjunction(self):
         disj = get_range_as_disjunction(analyte)
         #print(disj)
         self.assertCountEqual(disj, {'MissingValueEnum', 'AnalyteEnum'})
-        for s in view.all_slots().values():
-            disj = get_range_as_disjunction(s)
-            print(f'{s.name} DISJ: {disj}')
 
     def test_roll_up(self):
         # no import schema
         view = SchemaView(SCHEMA)
         c = view.get_class('ProteinCodingGene')
         rules = subclass_to_rules(view, 'ProteinCodingGene', 'SeqFeature')
         rule = rules[0]
-        print(f'IF: {rule.preconditions}')
-        print(f'THEN: {rule.postconditions}')
-        print(yaml_dumper.dumps(rule))