Test upgrade of linkml-runtime to 1.9.1-rc1

Makefile

@@ -3,6 +3,9 @@ RUN = poetry run
 test:
 	$(RUN) python -m unittest tests/test_*py tests/*/test_*py
 
+lint-fix:
+	$(RUN) tox -e format
+
 # not yet deployed
 doctest:
 	find src docs -type f \( -name "*.rst" -o -name "*.md" -o -name "*.py" \) -print0 | xargs -0 $(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE

pyproject.toml

@@ -12,7 +12,7 @@ curies = ">=0.6.6"
 pronto = ">=2.5.0"
 SPARQLWrapper = "*"
 SQLAlchemy = ">=1.4.32"
-linkml-runtime = ">=1.5.3"
+linkml-runtime = "1.9.1-rc1"
 linkml-renderer = ">=0.3.0"
 networkx = ">=2.7.1"
 sssom = "^0.4.4"

src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py

@@ -11,7 +11,14 @@
 from prefixmaps.io.parser import load_multi_context
 from sssom_schema import Mapping
 
-from oaklib.datamodels.obograph import DefinitionPropertyValue, Edge, Graph, Meta, Node, SynonymPropertyValue
+from oaklib.datamodels.obograph import (
+    DefinitionPropertyValue,
+    Edge,
+    Graph,
+    Meta,
+    Node,
+    SynonymPropertyValue,
+)
 from oaklib.datamodels.search import SearchConfiguration
 from oaklib.datamodels.text_annotator import TextAnnotation, TextAnnotationConfiguration
 from oaklib.datamodels.vocabulary import LABEL_PREDICATE, SEMAPV
@@ -552,6 +559,7 @@ def entity_alias_map(self, curie: CURIE) -> ALIAS_MAP:
         if meta is not None:
             for syn in meta.synonyms:
                 from oaklib.converters.obo_graph_to_rdf_owl_converter import SCOPE_MAP
+
                 pred = SCOPE_MAP.get(syn.pred, None)
                 m[pred].append(syn.val)
         return m

tests/test_cli.py

@@ -87,7 +87,7 @@ def _out(self, path: Optional[str] = TEST_OUT) -> str:
     def test_main_help(self):
         result = self.runner.invoke(main, ["--help"])
         out = result.stdout
-        print("STDERR", result.stderr)
+        logging.info("STDERR", result.stderr)
         self.assertIn("search", out)
         self.assertIn("subset", out)
         self.assertIn("validate", out)
@@ -138,8 +138,8 @@ def test_info(self):
                 main,
                 ["-i", str(input_arg), "info", NUCLEUS, "-o", TEST_OUT, "-D", "x,d"],
             )
-            print("STDERR", result.stdout)
-            print("STDERR", result.stderr)
+            logging.info("STDERR", result.stdout)
+            logging.info("STDERR", result.stderr)
             self.assertEqual(0, result.exit_code)
             with open(TEST_OUT) as file:
                 contents = "\n".join(file.readlines())
@@ -149,8 +149,8 @@ def test_info(self):
             result = self.runner.invoke(
                 main, ["-i", str(input_arg), "info", NUCLEUS, "-o", TEST_OUT, "-D", "x"]
             )
-            print("STDERR", result.stdout)
-            print("STDERR", result.stderr)
+            logging.info("STDERR", result.stdout)
+            logging.info("STDERR", result.stderr)
             self.assertEqual(0, result.exit_code)
             with open(TEST_OUT) as file:
                 contents = "\n".join(file.readlines())
@@ -383,8 +383,8 @@ def test_gap_fill(self):
                 TEST_OUT,
             ],
         )
-        print("STDERR", result.stdout)
-        print("STDERR", result.stderr)
+        logging.info("STDERR", result.stdout)
+        logging.info("STDERR", result.stderr)
         self.assertEqual(0, result.exit_code)
         contents = self._out()
         self.assertIn(NUCLEUS, contents)
@@ -428,7 +428,7 @@ def test_paths(self):
                 result = self.runner.invoke(main, all_args, catch_exceptions=False)
                 self.assertEqual(0, result.exit_code)
                 out = result.stdout
-                # print(input_arg, case, out)
+                # logging.info(input_arg, case, out)
                 self.assertIn(expected, out)
                 if unexpected:
                     self.assertNotIn(unexpected, out)
@@ -610,8 +610,8 @@ def test_dump(self):
                 cmd.extend(["-c", conf_path])
             result = self.runner.invoke(main, cmd)
             if result.exit_code != 0:
-                print("STDOUT", result.stdout)
-                print("STDERR", result.stderr)
+                logging.info("STDOUT", result.stdout)
+                logging.info("STDERR", result.stderr)
             self.assertEqual(0, result.exit_code, f"input={input}, output_format={output_format}")
             if output_format == "obojson":
                 obj: obograph.GraphDocument
@@ -722,7 +722,7 @@ def test_extract(self):
                     "-O",
                     output_format,
                 ] + query
-                # print(cmd)
+                # logging.info(cmd)
                 if dangling:
                     cmd += ["--dangling"]
                 result = self.runner.invoke(main, cmd)
@@ -736,7 +736,7 @@ def test_extract(self):
                     nucleus_node = [n for n in g.nodes if n.lbl == "nucleus"][0]
                     self.assertTrue(nucleus_node is not None)
                     # TODO
-                    # print(nucleus_node)
+                    # logging.info(nucleus_node)
                     # self.assertTrue(nucleus_node.meta.definition.val.startswith("A membrane-bounded organelle"))
                 elif output_format == "fhirjson":
                     obj: fhir.CodeSystem
@@ -1040,8 +1040,8 @@ def test_query(self):
 
     def test_validate_help(self):
         result = self.runner.invoke(main, ["validate", "--help"])
-        print("STDERR", result.stdout)
-        print("STDERR", result.stderr)
+        logging.info("STDERR", result.stdout)
+        logging.info("STDERR", result.stderr)
         self.assertEqual(0, result.exit_code)
 
     def test_validate_bad_ontology(self):
@@ -1179,7 +1179,7 @@ def test_lexmatch_owl(self):
                 "--no-ensure-strict-prefixes",
             ],
         )
-        print("STDERR", result.stdout)
+        logging.info("STDERR", result.stdout)
         err = result.stderr
         self.assertEqual(0, result.exit_code)
         with open(outfile) as stream:
@@ -1207,7 +1207,7 @@ def test_lexmatch_sqlite(self):
                 "--no-ensure-strict-prefixes",
             ],
         )
-        print("STDERR", result.stdout)
+        logging.info("STDERR", result.stdout)
         err = result.stderr
         self.assertEqual("", err)
         self.assertEqual(0, result.exit_code)
@@ -1495,7 +1495,7 @@ def test_statistics(self):
                 args = ["-i", str(input_arg), "statistics", "-o", str(out_path)] + opts
                 result = self.runner.invoke(main, args)
                 err = result.stderr
-                # print(" ".join(args))
+                # logging.info(" ".join(args))
                 logging.info(f"ERR={err}")
                 self.assertEqual(0, result.exit_code)
                 with open(out_path) as file:
@@ -1521,7 +1521,7 @@ def test_annotate_file(self):
                 outfile,
             ],
         )
-        print("STDERR", result.stdout)
+        logging.info("STDERR", result.stdout)
         err = "\n".join(
             [line for line in result.stderr.split("\n") if not line.startswith("WARNING")]
         )
@@ -1550,7 +1550,7 @@ def test_annotate_words(self):
                 outfile,
             ],
         )
-        print("STDERR", result.stdout)
+        logging.info("STDERR", result.stdout)
         err = result.stderr
         self.assertEqual("", err)
         self.assertEqual(0, result.exit_code)

tests/test_converters/test_obo_graph_to_cx.py

@@ -1,4 +1,5 @@
 import json
+import logging
 import unittest
 
 import curies
@@ -27,7 +28,7 @@ def test_convert(self):
         """Tests parsing then converting to cx document."""
         gd: GraphDocument = json_loader.load(str(ONT), target_class=GraphDocument)
         doc = self.converter.convert(gd)
-        print(doc)
+        logging.info(doc)
         with open(OUT, "w", encoding="UTF-8") as f:
             json.dump(doc, f)
         cxn = create_nice_cx_from_file(OUT)

tests/test_implementations/__init__.py

@@ -464,7 +464,7 @@ def test_skos_mappings(self, oi: MappingProviderInterface):
             mappings = [
                 (m.subject_id, m.predicate_id, m.object_id) for m in oi.sssom_mappings(curies)
             ]
-            print(mappings)
+            logging.info(mappings)
             expected = [
                 ("X:0000001", "oio:hasDbXref", "Y:1"),
                 ("X:0000001", "skos:exactMatch", "schema:Person"),
@@ -873,13 +873,13 @@ def test_chains(self, oi: OboGraphInterface):
         ]
 
         for chain_query, included, excluded in cases:
-            print(f"Q={chain_query} I={included} E={excluded}")
+            logging.info(f"Q={chain_query} I={included} E={excluded}")
             chains = list(oi.chains(chain_query))
-            print(f". RESULTS={chains}")
-            # print(len(chains))
+            logging.info(f". RESULTS={chains}")
+            # logging.info(len(chains))
             tuples_chains = []
             for chain in chains:
-                # print(chain)
+                # logging.info(chain)
                 tuple_chain = []
                 for e in chain:
                     tuple_chain.append((e.sub, e.pred, e.obj))
@@ -1080,7 +1080,7 @@ def test_merge(self, target: MergeInterface, source: BasicOntologyInterface):
         merged_entities = set(target.entities(owl_type=OWL_CLASS))
         diff = merged_entities.difference(target_entities.union(source_entities))
         for x in diff:
-            print(x)
+            logging.info(x)
         test.assertCountEqual(target_entities.union(source_entities), merged_entities)
         in_both = target_entities.intersection(source_entities)
         test.assertIn(CELL, in_both)
@@ -1184,8 +1184,8 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
                 n_unexpected += 1
             ch.type = type(ch).__name__
         for e in expected:
-            print("Expected not found:")
-            print(yaml_dumper.dumps(e))
+            logging.info("Expected not found:")
+            logging.info(yaml_dumper.dumps(e))
         test.assertEqual(0, len(expected), f"Expected changes not found: {expected}")
         expected_rev = [
             kgcl.NewSynonym(
@@ -1235,8 +1235,8 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
                     n_unexpected += 1
             ch.type = type(ch).__name__
         for e in expected_rev:
-            print("Expected (reversed) not found:")
-            print(yaml_dumper.dumps(e))
+            logging.info("Expected (reversed) not found:")
+            logging.info(yaml_dumper.dumps(e))
         test.assertEqual(0, len(expected_rev), f"Expected changes not found: {expected_rev}")
         test.assertEqual(0, n_unexpected, f"Unexpected changes: {n_unexpected}")
         # test diff summary
@@ -1252,7 +1252,7 @@ def test_diff(self, oi: DifferInterface, oi_modified: DifferInterface):
             ("EdgeDeletion", 5),
         ]
         for typ, expected in cases:
-            print(typ)
+            logging.info(typ)
             test.assertEqual(expected, residual[typ])
 
     def test_as_obograph(self, oi: OboGraphInterface):
@@ -1726,7 +1726,7 @@ def test_patcher_obsoletion_chains(self, get_adapter_function: Callable):
                 continue
             # expanded_changes = oi.expand_changes(changes, apply=False)
             # for change in expanded_changes:
-            #    print(json_dumper.dumps(change))
+            #    logging.info(json_dumper.dumps(change))
             expanded_changes = oi.expand_changes(changes, apply=True)
             logging.info(f"Expanded changes: {len(expanded_changes)}")
             test.assertGreater(len(expanded_changes), 1)
@@ -2150,7 +2150,7 @@ def test_information_content_scores(
             use_associations=use_associations,
         ):
             m[curie] = score
-            print(f"{curie} IC= {score}")
+            logging.info(f"{curie} IC= {score}")
         test.assertGreater(len(m), 0)
         if use_associations:
             # test.assertEqual(m[CELLULAR_COMPONENT], 0.0, "all genes are under cell component")
@@ -2159,7 +2159,7 @@ def test_information_content_scores(
             test.assertLess(m[NUCLEAR_ENVELOPE], 1.0)
         # universal root node always has zero information content
         for k, v in m.items():
-            print(f"{k} IC= {v}")
+            logging.info(f"{k} IC= {v}")
         test.assertEqual(m[OWL_THING], 0.0)
         for child, parent in posets:
             if use_associations:
@@ -2272,7 +2272,7 @@ def test_annotate_text(self, oi: TextAnnotatorInterface):
             anns = sorted(anns, key=lambda x: x.subject_start)
             test.assertEqual(n, len(anns))
             for i, ann in enumerate(anns):
-                print(ann)
+                logging.info(ann)
                 object_id, object_label, subject_start, subject_end = expected[i]
                 test.assertEqual(object_id, ann.object_id)
                 test.assertEqual(object_label, ann.object_label)

tests/test_implementations/test_sqldb.py

@@ -611,7 +611,7 @@ def test_create_from_input_specification(self):
     def test_integration_create_from_hpo_input_specification(self):
         spec = yaml_loader.load(str(CONF_DIR_PATH / "hpoa-input-spec.yaml"), InputSpecification)
         oi = get_adapter(spec)
-        print(oi)
+        logging.info(oi)
 
     def test_store_associations(self):
         shutil.copyfile(DB, MUTABLE_DB)