Add basic_search and fix node() for external refs in FunOwlImplementation

src/oaklib/implementations/funowl/funowl_implementation.py

@@ -38,6 +38,7 @@
 )
 
 from oaklib.datamodels import obograph
+from oaklib.datamodels.search import SearchConfiguration, SearchProperty, SearchTermSyntax
 from oaklib.datamodels.vocabulary import (
     DEPRECATED_PREDICATE,
     EQUIVALENT_CLASS,
@@ -413,6 +414,57 @@ def entity_alias_map(self, curie: CURIE) -> Dict[PRED_CURIE, List[str]]:
             alias_map[predicate].extend(metadata.get(predicate, []))
         return dict(alias_map)
 
+    def basic_search(
+        self, search_term: str, config: Optional[SearchConfiguration] = None
+    ) -> Iterable[CURIE]:
+        if config is None:
+            config = SearchConfiguration()
+        properties = list(config.properties or [])
+        if config.syntax == SearchTermSyntax(SearchTermSyntax.STARTS_WITH):
+            matcher = lambda text: str(text).startswith(search_term)
+        elif config.syntax == SearchTermSyntax(SearchTermSyntax.REGULAR_EXPRESSION):
+            prog = re.compile(search_term)
+            matcher = lambda text: prog.search(str(text))
+        elif config.is_partial:
+            matcher = lambda text: search_term in str(text)
+        else:
+            matcher = lambda text: str(text) == search_term
+        search_all = SearchProperty(SearchProperty.ANYTHING) in properties
+        search_label = search_all or not properties or SearchProperty(SearchProperty.LABEL) in properties
+        search_identifier = search_all or SearchProperty(SearchProperty.IDENTIFIER) in properties
+        search_alias = search_all or SearchProperty(SearchProperty.ALIAS) in properties
+        search_mapped = search_all or SearchProperty(SearchProperty.MAPPED_IDENTIFIER) in properties
+        seen: Set[CURIE] = set()
+        for curie in self.entities(filter_obsoletes=False):
+            if search_label:
+                label = self.label(curie)
+                if label and matcher(label):
+                    if curie not in seen:
+                        seen.add(curie)
+                        yield curie
+                    continue
+            if search_identifier and matcher(curie):
+                if curie not in seen:
+                    seen.add(curie)
+                    yield curie
+                continue
+            if search_alias:
+                for alias in self.entity_aliases(curie):
+                    if alias and matcher(alias):
+                        if curie not in seen:
+                            seen.add(curie)
+                            yield curie
+                        break
+                if curie in seen:
+                    continue
+            if search_mapped:
+                for xref in self.entity_metadata_map(curie).get(HAS_DBXREF, []):
+                    if matcher(xref):
+                        if curie not in seen:
+                            seen.add(curie)
+                            yield curie
+                        break
+
     def terms_subsets(self, curies: Iterable[CURIE]) -> Iterable[tuple[CURIE, CURIE]]:
         for curie in curies:
             for subset in self.entity_metadata_map(curie).get(IN_SUBSET, []):
@@ -434,10 +486,11 @@ def node(
     ) -> Optional[obograph.Node]:
         entity_types = set(self.owl_type(curie))
         label = self.label(curie)
+        node_id = cast(CURIE, self.curie_to_uri(curie)) if expand_curies else curie
         if not entity_types and label is None:
             if strict:
                 raise ValueError(f"Unknown entity: {curie}")
-            return None
+            return obograph.Node(id=node_id, type="CLASS")
         if any(
             owl_type in entity_types
             for owl_type in [OWL_OBJECT_PROPERTY, OWL_ANNOTATION_PROPERTY, OWL_DATATYPE_PROPERTY]
@@ -447,7 +500,6 @@ def node(
             node_type = "INDIVIDUAL"
         else:
             node_type = "CLASS"
-        node_id = cast(CURIE, self.curie_to_uri(curie)) if expand_curies else curie
         meta = None
         if include_metadata:
             meta = obograph.Meta()

tests/test_cli.py

@@ -66,6 +66,18 @@
 TEST_SYNONYMIZER_OBO = "simpleobo:" + str(INPUT_DIR / "synonym-test.obo")
 RULES_FILE = INPUT_DIR / "matcher_rules.yaml"
 SYNONYMIZER_RULES_FILE = INPUT_DIR / "cli-synonymizer-rules.yaml"
+EXTERNAL_REFERENCE_OFN = """\
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+Prefix(CL:=<http://purl.obolibrary.org/obo/CL_>)
+Prefix(BFO:=<http://purl.obolibrary.org/obo/BFO_>)
+Prefix(GO:=<http://purl.obolibrary.org/obo/GO_>)
+Ontology(
+Declaration(Class(CL:0000540))
+AnnotationAssertion(rdfs:label CL:0000540 "neuron")
+SubClassOf(CL:0000540 GO:0008150)
+SubClassOf(CL:0000540 ObjectSomeValuesFrom(BFO:0000050 GO:0008150))
+)
+"""
 
 
 def _outpath(test: str, fmt: str = "tmp") -> str:
@@ -115,6 +127,35 @@ def test_input_type_and_sniff_for_functional_owl_suffix(self):
                 self.assertEqual(0, result.exit_code, result.output)
                 self.assertIn("nucleus", result.stdout)
 
+    def test_funowl_info_search_and_graph_outputs(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            ontology_path = Path(tmpdir) / "external-ref.ofn"
+            ontology_path.write_text(EXTERNAL_REFERENCE_OFN)
+            viz_out = Path(tmpdir) / "viz.json"
+            for args, expected in (
+                (["-I", "ofn", "-i", str(ontology_path), "info", "neuron"], "CL:0000540 ! neuron"),
+                (
+                    ["-I", "ofn", "-i", str(ontology_path), "info", "l~neur"],
+                    "CL:0000540 ! neuron",
+                ),
+                (
+                    ["-I", "ofn", "-i", str(ontology_path), "info", "CL:0000540", "-O", "obo"],
+                    "id: CL:0000540",
+                ),
+            ):
+                result = self.runner.invoke(main, args)
+                self.assertEqual(0, result.exit_code, result.output)
+                self.assertIn(expected, result.stdout)
+            result = self.runner.invoke(
+                main,
+                ["-I", "ofn", "-i", str(ontology_path), "viz", "CL:0000540", "-O", "json", "-o", str(viz_out)],
+            )
+            self.assertEqual(0, result.exit_code, result.output)
+            obj = json.load(open(viz_out))
+            node_ids = {node["id"] for node in obj["nodes"]}
+            self.assertIn("CL:0000540", node_ids)
+            self.assertIn("GO:0008150", node_ids)
+
     def test_multilingual(self):
         for input_arg in [INPUT_DIR / "hp-international-test.db"]:
             results = self.runner.invoke(main, ["-i", str(input_arg), "languages"])

tests/test_implementations/test_funowl.py

@@ -1,9 +1,12 @@
 import logging
+import tempfile
 import unittest
+from pathlib import Path
 
 from kgcl_schema.datamodel import kgcl
 from pyhornedowl.model import EquivalentClasses, SubClassOf
 
+from oaklib.datamodels.search import SearchConfiguration
 from oaklib.implementations.funowl.funowl_implementation import FunOwlImplementation
 from oaklib.interfaces.obograph_interface import OboGraphInterface
 from oaklib.interfaces.owl_interface import AxiomFilter
@@ -16,6 +19,18 @@
 TEST_GRAPH_PROJECTION_ONT = INPUT_DIR / "graph_projection.owl"
 TEST_INST_ONT = INPUT_DIR / "inst.ofn"
 NEW_NAME = "new name"
+EXTERNAL_REFERENCE_OFN = """\
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+Prefix(CL:=<http://purl.obolibrary.org/obo/CL_>)
+Prefix(BFO:=<http://purl.obolibrary.org/obo/BFO_>)
+Prefix(GO:=<http://purl.obolibrary.org/obo/GO_>)
+Ontology(
+Declaration(Class(CL:0000540))
+AnnotationAssertion(rdfs:label CL:0000540 "neuron")
+SubClassOf(CL:0000540 GO:0008150)
+SubClassOf(CL:0000540 ObjectSomeValuesFrom(BFO:0000050 GO:0008150))
+)
+"""
 
 
 class TestFunOwlImplementation(unittest.TestCase):
@@ -92,6 +107,21 @@ def test_logical_definitions(self):
     def test_ancestors_descendants(self):
         self.compliance_tester.test_ancestors_descendants(self.oi)
 
+    def test_basic_search(self):
+        self.assertIn(NUCLEUS, list(self.oi.basic_search("nucleus")))
+        cfg = SearchConfiguration(is_partial=True)
+        self.assertIn(NUCLEUS, list(self.oi.basic_search("nucl", config=cfg)))
+
+    def test_stub_nodes_for_unresolved_external_references(self):
+        with tempfile.TemporaryDirectory() as tmpdir:
+            path = Path(tmpdir) / "external-ref.ofn"
+            path.write_text(EXTERNAL_REFERENCE_OFN)
+            oi = FunOwlImplementation(OntologyResource(str(path)))
+            graph = oi.direct_graph("CL:0000540")
+            node_ids = {node.id for node in graph.nodes}
+            self.assertIn("CL:0000540", node_ids)
+            self.assertIn("GO:0008150", node_ids)
+
     def test_patcher(self):
         oi = self.oi
         anns = list(oi.annotation_assertion_axioms(NUCLEUS))