Pass custom IC map to Semsimian through CLI (#759)

* Pass custom IC map to Semsimian through CLI

* Add test

* Add comment

* Stricter test for equivalence

* Nano-linting

---------

Co-authored-by: Chris Mungall <[email protected]>

src/oaklib/cli.py

@@ -91,6 +91,7 @@
 from oaklib.implementations.obograph.obograph_implementation import (
     OboGraphImplementation,
 )
+from oaklib.implementations.semsimian.semsimian_implementation import SemSimianImplementation
 from oaklib.implementations.sqldb.sql_implementation import SqlImplementation
 from oaklib.interfaces import (
     BasicOntologyInterface,
@@ -2956,7 +2957,10 @@ def similarity(
     if not isinstance(impl, SemanticSimilarityInterface):
         raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}")
     if information_content_file:
-        impl.cached_information_content_map = load_information_content_map(information_content_file)
+        if isinstance(impl, SemSimianImplementation):
+            impl.custom_ic_map_path = information_content_file
+        else:
+            impl.cached_information_content_map = load_information_content_map(information_content_file)
     set1it = None
     set2it = None
     if not (set1_file or set2_file):
@@ -3037,8 +3041,16 @@ def termset_similarity(
     writer.output = output
     if not isinstance(impl, SemanticSimilarityInterface):
         raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}")
+
+    # TODO: @cmungall - one possibility in future is to relieve client of the need for
+    # out of band knowledge about impl details. The generic SemSim interface could have
+    # a load_ic_map method, with the generic impl being to directly load, and the semsimian
+    # impl passing the path through.
     if information_content_file:
-        impl.cached_information_content_map = load_information_content_map(information_content_file)
+        if isinstance(impl, SemSimianImplementation):
+            impl.custom_ic_map_path = information_content_file
+        else:
+            impl.cached_information_content_map = load_information_content_map(information_content_file)
     terms = list(terms)
     ix = terms.index("@")
     set1 = list(query_terms_iterator(terms[0:ix], impl))

src/oaklib/implementations/semsimian/semsimian_implementation.py

@@ -54,6 +54,8 @@ class SemSimianImplementation(
         AssociationProviderInterface.add_associations,
     ]
 
+    custom_ic_map_path: str = None
+
     semsimian_object_cache: Dict[Tuple[PRED_CURIE], Optional["Semsimian"]] = field(default_factory=dict)  # type: ignore # noqa
 
     def __post_init__(self):
@@ -84,6 +86,7 @@ def _get_semsimian_object(
         predicates: List[PRED_CURIE] = None,
         attributes: List[str] = None,
         resource_path: str = None,
+        custom_ic_map_path: str = None,
     ) -> "Semsimian":  # type: ignore # noqa
         """
         Get Semsimian object from "semsimian_object_cache" or add a new one.
@@ -94,6 +97,10 @@ def _get_semsimian_object(
         from semsimian import Semsimian
 
         predicates = tuple(sorted(predicates))
+
+        if custom_ic_map_path is not None:
+            logging.info(f"Using custom IC map with Semsimian: {custom_ic_map_path}")
+
         if predicates not in self.semsimian_object_cache:
             # spo = [
             #     r
@@ -111,6 +118,7 @@ def _get_semsimian_object(
                 predicates=predicates,
                 pairwise_similarity_attributes=attributes,
                 resource_path=self.resource_path,
+                custom_ic_map_path=self.custom_ic_map_path,
             )
 
         return self.semsimian_object_cache[predicates]
@@ -139,7 +147,9 @@ def pairwise_similarity(
         """
         logging.debug(f"Calculating pairwise similarity for {subject} x {object} over {predicates}")
         semsimian = self._get_semsimian_object(
-            predicates=predicates, attributes=self.term_pairwise_similarity_attributes
+            predicates=predicates,
+            attributes=self.term_pairwise_similarity_attributes,
+            custom_ic_map_path=self.custom_ic_map_path
         )
 
         jaccard_val = semsimian.jaccard_similarity(subject, object)
@@ -194,7 +204,9 @@ def all_by_all_pairwise_similarity(
         objects = list(objects)
         logging.info(f"Calculating all-by-all pairwise similarity for {len(objects)} objects")
         semsimian = self._get_semsimian_object(
-            predicates=predicates, attributes=self.term_pairwise_similarity_attributes
+            predicates=predicates,
+            attributes=self.term_pairwise_similarity_attributes,
+            custom_ic_map_path=self.custom_ic_map_path
         )
         all_results = semsimian.all_by_all_pairwise_similarity(
             subject_terms=set(subjects),

tests/input/test_ic.tsv

@@ -0,0 +1,2 @@
+GO:0005773	5.5
+GO:0012505	6.0

tests/test_implementations/test_semsimian_implementation.py

@@ -21,6 +21,8 @@
 
 DB = INPUT_DIR / "go-nucleus.db"
 
+TEST_IC_MAP = INPUT_DIR / "test_ic.tsv"
+
 EXPECTED_ICS = {
     "CARO:0000000": 21.05,
     "BFO:0000002": 0.7069,
@@ -134,6 +136,29 @@ def test_all_by_all_pairwise_similarity(self):
             sem_similarity_object.phenodigm_score, sql_similarity_object.phenodigm_score, places=2
         )
 
+    def test_similarity_with_custom_ic_map(self):
+        adapter = self.oi
+
+        adapter.custom_ic_map_path = TEST_IC_MAP.as_posix()
+
+        if not isinstance(adapter, SemanticSimilarityInterface):
+            raise AssertionError("SemanticSimilarityInterface not implemented")
+        entities = [VACUOLE, ENDOMEMBRANE_SYSTEM]
+
+        for s in entities:
+            for o in entities:
+                for preds in [self.predicates]:
+                    sim = adapter.pairwise_similarity(s, o, predicates=preds)
+                    if sim is not None:
+                        if s == VACUOLE and o == VACUOLE:
+                            self.assertEqual(sim.ancestor_information_content, 5.5)
+                        if s == ENDOMEMBRANE_SYSTEM and o == ENDOMEMBRANE_SYSTEM:
+                            self.assertEqual(sim.ancestor_information_content, 6.0)
+                        if s == VACUOLE and o == ENDOMEMBRANE_SYSTEM:
+                            self.assertEqual(sim.ancestor_information_content, 0)
+                    else:
+                        raise ValueError(f"Did not get similarity for got {s} and {o}")
+
     def test_semsimian_object_cache(self):
         start_time = timeit.default_timer()
         _ = list(