Clean up print statements (#1442)

* Removed print statements from test_data, test_enhancements and test_generators

* Replace some print statements with TODO comments, since that looks like it was the intent

* More print -> TODO:

* Removed print statements (as long as there's an assert) in test_issues

* Most print statements removed from test_rewrite_rules, test_scripts, test_utils and test_validation. Definitely some methods that need assertions so we can remove the print statements.

tests/test_data/test_sqlite.py

@@ -69,14 +69,7 @@ def test_sqlite_store(self):
         q = session.query(endpoint.module.Person)
         all_objs = q.all()
         self.assertEqual(2, len(all_objs))
-        for p in all_objs:
-            print(p)
-            for rel in p.has_familial_relationships:
-                print(rel)
-                print(rel.type)
         q = session.query(endpoint.module.FamilialRelationship)
-        for r in q.all():
-            print(r)
         session.close()
         # step 4: test loading from SQLStore
         # 4a: first test load_all, diff to original data should be empty
@@ -120,15 +113,13 @@ def test_mixin(self):
         b.add_class("my_abstract", slots=["my_abstract_slot"], abstract=True)
         b.add_class("my_class1", is_a="my_abstract", mixins=["my_mixin"])
         b.add_class("my_class2", slots=["ref_to_c1"])
-        # print(yaml_dumper.dumps(b.schema))
         endpoint = SQLStore(b.schema, database_path=TMP_DB)
         endpoint.db_exists(force=True)
         mod = endpoint.compile_native()
         i1 = mod.MyClass1(my_mixin_slot="v1", my_abstract_slot="v2")
         i2 = mod.MyClass2(ref_to_c1=i1)
         endpoint.dump(i2)
         i2_recap = endpoint.load(target_class=mod.MyClass2)
-        # print(yaml_dumper.dumps(i2_recap))
         diff = compare_objs(i2, i2_recap)
         self.assertEqual(diff, "")
 

tests/test_data/test_sqlite_pydantic.py

@@ -71,14 +71,7 @@ def test_sqlite_store(self):
         q = session.query(endpoint.module.Person)
         all_objs = q.all()
         self.assertEqual(2, len(all_objs))
-        for p in all_objs:
-            print(p)
-            for rel in p.has_familial_relationships:
-                print(rel)
-                print(rel.type)
         q = session.query(endpoint.module.FamilialRelationship)
-        for r in q.all():
-            print(r)
         # step 4: test loading from SQLStore
         # 4a: first test load_all, diff to original data should be empty
         [returned_container] = endpoint.load_all(target_class=Container)

tests/test_enhancements/test_enumeration.py

@@ -213,7 +213,6 @@ def test_notebook_model_2(self):
             "Something",
             [module.UnusualEnumPatterns.M, module.UnusualEnumPatterns["% ! -- whoo"]],
         )
-        print(str(t))
 
     def test_notebook_model_3(self):
         file = "notebook_model_3"

tests/test_generators/test_contextgen.py

@@ -26,7 +26,6 @@ def test_context(self):
         json_dumper.dump(element=inst, to_file=DATA_JSON)
         with open(CONTEXT_OUT, "w") as stream:
             stream.write(ContextGenerator(SCHEMA).serialize())
-        print(rdf_dumper.dumps(inst, CONTEXT_OUT))
 
 
 if __name__ == "__main__":

tests/test_generators/test_owlgen.py

@@ -46,7 +46,6 @@ def test_owlgen(self):
         self.assertGreater(len(owl_classes), 10)
         for c in owl_classes:
             types = list(g.objects(c, RDF.type))
-            # print(f'Class={c} {types}')
             self.assertCountEqual(types, [OWL.Class])
         assert KS.MedicalEvent in owl_classes
         # test that enums are treated as classes
@@ -55,13 +54,11 @@ def test_owlgen(self):
         assert len(owl_object_properties) > 10
         for p in owl_object_properties:
             types = list(g.objects(p, RDF.type))
-            # print(f'Class={c} {types}')
             self.assertCountEqual(types, [OWL.ObjectProperty])
         owl_datatype_properties = list(g.subjects(RDF.type, OWL.DatatypeProperty))
         assert len(owl_datatype_properties) > 10
         for p in owl_datatype_properties:
             types = list(g.objects(p, RDF.type))
-            # print(f'Class={c} {types}')
             self.assertCountEqual(types, [OWL.DatatypeProperty])
         # check that definitions are present, and use the default profile
         self.assertIn(
@@ -123,8 +120,6 @@ def test_definition_uris(self):
              URIRef('http://www.w3.org/2004/02/skos/core#exactMatch'),
              URIRef('http://schema.org/Person'))
         ]
-        #for t in triples:
-        #    print(t)
         for t in expected:
             self.assertIn(t, triples)
 

tests/test_generators/test_pydanticgen.py

@@ -49,24 +49,20 @@ def test_dynamic():
             # NOTE: generated pydantic doesn't yet do validation
             e1 = EmploymentEvent(is_current=True)
             p1 = Person(id="x", has_employment_history=[e1])
-            print(p1)
             assert p1.id == "x"
             assert p1.name is None
             json = {"id": "P1", "has_employment_history": [{"is_current": True}]}
             p2 = Person(**json)
-            print(p2)
             p2 = Person(**dataset_dict["persons"][0])
             print(dataset_dict)
             ds1 = Dataset(**dataset_dict)
-            print(ds1)
             assert len(ds1.persons) == 2
 
         test_dynamic()
 
     def test_compile_pydantic(self):
         """Generate and compile pydantic classes"""
         gen = PydanticGenerator(SCHEMA, package=PACKAGE)
-        print(gen.allow_extra)
         code = gen.serialize()
         mod = compile_python(code, PACKAGE)
         p = mod.Person(id="P:1")

tests/test_generators/test_pythongen.py

@@ -57,7 +57,6 @@ def test_pythongen(self):
         # however, inline in a non-list context does not
         p2dict = {"id": "P:2", "has_birth_event": {"started_at_time": "1981-01-01"}}
         p2 = json_loader.loads(p2dict, kitchen_module.Person)
-        print(p2)
         self.assertEqual(
             "Person(id='P:1', name=None, has_employment_history=[EmploymentEvent(started_at_time=None, ended_at_time=None, is_current=None, metadata=None, employed_at='ROR:1', type=None)], has_familial_relationships=[], has_medical_history=[], age_in_years=None, addresses=[], has_birth_event=None, species_name=None, stomach_count=None, is_living=None, aliases=[])",
             str(p),
@@ -71,7 +70,6 @@ def test_pythongen(self):
 
         diagnosis = kitchen_module.DiagnosisConcept(id="CODE:D0001", name="headache")
         event = kitchen_module.MedicalEvent(in_location="GEO:1234", diagnosis=diagnosis)
-        print(str(event))
         self.assertEqual(
             "MedicalEvent(started_at_time=None, ended_at_time=None, is_current=None, metadata=None, in_location='GEO:1234', diagnosis=DiagnosisConcept(id='CODE:D0001', name='headache', in_code_system=None), procedure=None)",
             str(event),

tests/test_generators/test_rdfgen.py

@@ -42,7 +42,6 @@ def test_rdf_type_in_jsonld(self):
         graph = Graph()
         graph.parse(data=JSONLD, format="json-ld", prefix=True)
         ttl_str = graph.serialize(format='turtle').decode()
-        print(ttl_str)
         graph.parse(data=ttl_str, format="turtle")
 
 

tests/test_generators/test_shexgen.py

@@ -45,10 +45,8 @@ def test_shex(self):
                     )
                     return
                 raise e
-            # print(g)
             nodes = set()
             for s, p, o in g.triples((None, None, None)):
-                # print(f'{s} {p} {o}')
                 nodes.add(s)
             for node in nodes:
                 r = evaluate(g, shexstr, focus=node)

tests/test_generators/test_sqlalchemygen.py

@@ -139,7 +139,6 @@ def test_sqla_declarative_on_metamodel(self):
         """
         sv = package_schemaview("linkml_runtime.linkml_model.meta")
         gen = SQLAlchemyGenerator(sv.schema)
-        print(f"SQLAGEN: ****")
         code = gen.generate_sqla(template=TemplateEnum.DECLARATIVE)
         assert "class ClassDefinition(" in code
         assert "class Annotation(" in code
@@ -211,8 +210,6 @@ def test_sqla_imperative_dataclasses_exec(self):
         session.add(p1)
         q = session.query(mod.Person).where(mod.Person.name == p1.name)
         persons = q.all()
-        # for person in persons:
-        #    print(f'Person={person}')
         assert len(persons) == 1
         assert p1 in persons
         p1 = persons[0]
@@ -235,8 +232,6 @@ def test_sqla_imperative_dataclasses_exec(self):
         session.commit()
         q = session.query(mod.Person).where(mod.Person.id == p2.id)
         persons = q.all()
-        # for person in persons:
-        #    print(f'Person={person}')
         assert len(persons) == 1
         p2_recap = persons[0]
         p2mh = p2_recap.has_medical_history
@@ -285,8 +280,6 @@ def test_sqla_imperative_pydantic_exec(self):
         q = session.query(mod.Person).where(mod.Person.name == p1.name)
         # q = session.query(mod.Person)
         persons = q.all()
-        for person in persons:
-            print(f"Person={person}")
         self.assertEqual(1, len(persons))
         assert p1 in persons
         p1 = persons[0]
@@ -302,8 +295,6 @@ def test_sqla_imperative_pydantic_exec(self):
         q = session.query(mod.Person).where(mod.Person.id == p2.id)
         persons = q.all()
         assert len(persons) == 1
-        # for person in persons:
-        #    print(f'Person={person.has_medical_history}')
         p2_recap = persons[0]
         p2mh = p2_recap.has_medical_history
         assert p2mh[0].duration == e1.duration
@@ -361,7 +352,6 @@ def test_sqla_declarative_exec(self):
         session.add(mod.Person(id="P2", aliases=["Fred"], has_news_events=[news_event]))
         # session.add(mod.Person(id='P3', has_familial_relationships=[{"related_to": "P4"}]))
         session.commit()
-        # print(f'QUERYING::  {mod.NewsEvent} // {type(mod.NewsEvent)}')
         q = session.query(mod.NewsEvent)
         all_news = q.all()
         # ensure news object is shared between persons
@@ -371,7 +361,6 @@ def test_sqla_declarative_exec(self):
         for person in persons:
             assert isinstance(person, mod.NamedThing)
             logging.info(f"Person={person}")
-            # print(f' Person.address={person.current_address}')
             for a in person.aliases:
                 logging.info(f"  ALIAS={a}")
             for e in person.has_medical_history:

tests/test_generators/test_sqlddlgen.py

@@ -90,9 +90,6 @@ def test_sqlddl(self):
         gen = SQLDDLGenerator(SCHEMA, mergeimports=True, rename_foreign_keys=True)
         ddl = gen.serialize()
         with open(SQLDDLLOG, "w") as log:
-            # with open(DDL_PATH, 'w') as stream:
-            #     stream.write(ddl)
-            # print(ddl)
             try:
                 os.remove(DB)
             except OSError:
@@ -116,11 +113,9 @@ def test_sqlddl(self):
             log.write(f"{cur.fetchall()}\n")
             con.commit()
             con.close()
-            # print(gen.to_sqla_python())
             # output = StringIO()
             # with redirect_stdout(output):
             #    gen.write_sqla_python_imperative('output.kitchen_sink')
-            # print(output.getvalue())
             # with open(SQLA_CODE, 'w') as stream:
             #    stream.write(output.getvalue())
             kitchen_module = create_and_compile_sqla_bindings(gen, SQLA_CODE)
@@ -134,8 +129,6 @@ def test_sqlddl(self):
                 kitchen_module.Person.name == NAME
             )
             log.write(f"Q={q}\n")
-            # for row in q.all():
-            #    print(f'Row={row}')
             agent = kitchen_module.Agent(id="Agent03")
             log.write(f"Agent={agent}\n")
             activity = kitchen_module.Activity(id="Act01", was_associated_with=agent)
@@ -181,8 +174,6 @@ def test_sqlddl(self):
                     log.write(f"  Address={a}\n")
                     # if a.city == CITY:
                     #    is_found_address = True
-                # for alias in p.aliases:
-                #    print(f'  AKA={a}')
             # assert is_found_address
             session.commit()
 

tests/test_generators/test_sqltablegen.py

@@ -41,7 +41,6 @@ def test_inject_primary_key(self):
         b.add_defaults()
         gen = SQLTableGenerator(b.schema)
         ddl = gen.generate_ddl()
-        # print(ddl)
         assert "PRIMARY KEY (id)" in ddl
         assert "full_name TEXT" in ddl
         assert 'CREATE TABLE "dummy class"' in ddl
@@ -56,7 +55,6 @@ def test_no_injection(self):
         b.add_defaults()
         gen = SQLTableGenerator(b.schema, use_foreign_keys=False)
         ddl = gen.generate_ddl()
-        # print(ddl)
         assert "PRIMARY KEY (id)" not in ddl
         assert "full_name TEXT" in ddl
         assert 'CREATE TABLE "dummy class"' in ddl
@@ -80,7 +78,7 @@ def test_dialect(self):
         for dialect in ["postgresql", "sqlite", "mysql"]:
             gen = SQLTableGenerator(b.schema, dialect=dialect)
             ddl = gen.generate_ddl()
-            # print(f"DIALECT: {dialect}\n SQL:\n{ddl}")
+
             if dialect == "postgresql":
                 assert "id SERIAL" in ddl
                 assert "COMMENT ON TABLE" in ddl
@@ -218,7 +216,6 @@ def test_sqlddl_basic(self):
         with open(SQLDDLLOG, "w") as log:
             # with open(DDL_PATH, 'w') as stream:
             #     stream.write(ddl)
-            # print(ddl)
             try:
                 os.remove(DB)
             except OSError:

tests/test_generators/test_sqltransform.py

@@ -44,7 +44,6 @@ def test_inject_primary_key(self):
         b.add_class(DUMMY_CLASS, slots)
         results = self._translate(b)
         rel_schema = self._translate(b).schema
-        # print(yaml_dumper.dumps(rel_schema))
         self.assertCountEqual(
             slots + ["id"], list(rel_schema.classes[DUMMY_CLASS].attributes.keys())
         )
@@ -111,7 +110,6 @@ def test_no_inject_primary_key(self):
         b.add_class(DUMMY_CLASS, slots).set_slot("name", identifier=True)
         results = self._translate(b)
         rel_schema = self._translate(b).schema
-        # print(yaml_dumper.dumps(rel_schema))
         self.assertCountEqual(
             slots, list(rel_schema.classes[DUMMY_CLASS].attributes.keys())
         )
@@ -132,7 +130,6 @@ def test_multivalued_literal(self):
         )
         results = self._translate(b)
         rel_schema = self._translate(b).schema
-        # print(yaml_dumper.dumps(rel_schema))
         rsv = SchemaView(rel_schema)
         c = rsv.get_class("c")
         assert c
@@ -157,7 +154,6 @@ def test_inject_foreign_key(self):
         results = self._translate(b)
         rel_schema = self._translate(b).schema
         rsv = SchemaView(rel_schema)
-        # print(yaml_dumper.dumps(rel_schema))
         c = rsv.get_class("c")
         d = rsv.get_class("d")
         self.assertCountEqual(
@@ -186,7 +182,6 @@ def test_inject_backref_foreign_key(self):
         results = self._translate(b)
         rel_schema = self._translate(b).schema
         rsv = SchemaView(rel_schema)
-        # print(yaml_dumper.dumps(rel_schema))
         c = rsv.get_class("c")
         d = rsv.get_class("d")
         self.assertCountEqual(
@@ -223,7 +218,6 @@ def test_inject_many_to_many(self):
                 results = self._translate(b)
                 rel_schema = self._translate(b).schema
                 rsv = SchemaView(rel_schema)
-                # print(yaml_dumper.dumps(rel_schema))
                 c = rsv.get_class("c")
                 d = rsv.get_class("d")
                 c_has_d = rsv.get_class("c_has_d")
@@ -252,11 +246,9 @@ def test_inject_many_to_many_with_inheritance(self):
             "c1", is_a="c", slot_usage={"has_ds": SlotDefinition("has_ds", range="d1")}
         )
         b.add_class("d1", is_a="d")
-        # print(yaml_dumper.dumps(b.schema))
         results = self._translate(b)
         rel_schema = self._translate(b).schema
         rsv = SchemaView(rel_schema)
-        # print(yaml_dumper.dumps(rel_schema))
         c = rsv.get_class("c")
         d = rsv.get_class("d")
         c1 = rsv.get_class("c1")
@@ -294,7 +286,6 @@ def test_no_foreign_keys(self):
         result = sqltr.transform()
         rel_schema = result.schema
         rsv = SchemaView(rel_schema)
-        print(yaml_dumper.dumps(rel_schema))
         assert "c_has_d" not in rsv.all_classes()
         c1 = rsv.get_class("c1")
         self.assertCountEqual(c1.attributes.keys(), ["name", "description", "has_ds"])
@@ -318,7 +309,6 @@ def test_aliases(self):
         results = self._translate(b)
         rel_schema = self._translate(b).schema
         rsv = SchemaView(rel_schema)
-        # print(yaml_dumper.dumps(rel_schema))
         c = rsv.get_class("c")
         d = rsv.get_class("d")
         c_has_d = rsv.get_class("c_has_d")
@@ -339,7 +329,6 @@ def test_sqlt_on_metamodel(self):
         sqltr = RelationalModelTransformer(sv)
         result = sqltr.transform()
         rschema = result.schema
-        # print(rschema.imports)
         with open(META_OUT_PATH, "w") as stream:
             stream.write(yaml_dumper.dumps(rschema))
         # test Annotation is handled correctly. This has a key annotation_tag with alias 'tag'
@@ -393,7 +382,6 @@ def test_sqlt_complete_example(self):
             "MedicalEvent",
         ]:
             c = sv.get_class(relationship_class)
-            # print(f'RC: {relationship_class} // {c}')
             assert any(
                 a
                 for a in c.attributes.values()
@@ -409,8 +397,6 @@ def test_sqlt_complete_example(self):
 
         for cn in ["Person", "Organization"]:
             c = sv.get_class(f"{cn}_has_news_event")
-            # print(list(c.attributes.keys()))
-            # print(list(c.attributes.values()))
             a1 = c.attributes["has_news_event_id"]
             self.assertEqual(a1.range, "NewsEvent")
             a2 = c.attributes[f"{cn}_id"]