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Subject: [PATCH 02/21] added stub code for association search --- .../semsimian/semsimian_implementation.py | 20 ++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 43354c677..8b7017f43 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -15,6 +15,9 @@ ) from oaklib.datamodels.vocabulary import OWL_THING from oaklib.implementations.sqldb.sql_implementation import SqlImplementation +from oaklib.interfaces.association_provider_interface import ( + AssociationProviderInterface, +) from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface from oaklib.interfaces.obograph_interface import OboGraphInterface from oaklib.interfaces.search_interface import SearchInterface @@ -29,7 +32,9 @@ @dataclass -class SemSimianImplementation(SearchInterface, SemanticSimilarityInterface, OboGraphInterface): +class SemSimianImplementation( + SearchInterface, SemanticSimilarityInterface, OboGraphInterface, AssociationProviderInterface +): """Rust implementation of semantic similarity measures.""" delegated_methods: ClassVar[List[str]] = [ @@ -291,3 +296,16 @@ def _regain_element_formats(self, value: str) -> Union[str, float]: except ValueError: pass return value + + # TODO : Search feature for monarch app + # def association_subject_counts( + # self, + # subjects: Iterable[CURIE] = None, + # predicates: Iterable[PRED_CURIE] = None, + # property_filter: Dict[PRED_CURIE, Any] = None, + # subject_closure_predicates: Optional[List[PRED_CURIE]] = None, + # predicate_closure_predicates: Optional[List[PRED_CURIE]] = None, + # object_closure_predicates: Optional[List[PRED_CURIE]] = None, + # include_modified: bool = False, + # ) -> Iterator[Tuple[CURIE, int]]: + # pass From 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Subject: [PATCH 04/21] switched commented code --- .../semsimian/semsimian_implementation.py | 26 ++++++++++++------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 8b7017f43..6d7759e8b 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -298,14 +298,20 @@ def _regain_element_formats(self, value: str) -> Union[str, float]: return value # TODO : Search feature for monarch app - # def association_subject_counts( - # self, - # subjects: Iterable[CURIE] = None, - # predicates: Iterable[PRED_CURIE] = None, - # property_filter: Dict[PRED_CURIE, Any] = None, - # subject_closure_predicates: Optional[List[PRED_CURIE]] = None, - # predicate_closure_predicates: Optional[List[PRED_CURIE]] = None, - # object_closure_predicates: Optional[List[PRED_CURIE]] = None, - # include_modified: bool = False, - # ) -> Iterator[Tuple[CURIE, int]]: + # def associations_subject_search( + # self, + # subjects: Iterable[CURIE] = None, + # predicates: Iterable[PRED_CURIE] = None, + # objects: Iterable[CURIE] = None, + # property_filter: Dict[PRED_CURIE, Any] = None, + # subject_closure_predicates: Optional[List[PRED_CURIE]] = None, + # predicate_closure_predicates: Optional[List[PRED_CURIE]] = None, + # object_closure_predicates: Optional[List[PRED_CURIE]] = None, + # subject_prefixes: Optional[List[str]] = None, + # include_similarity_object: bool = False, + # method: Optional[str] = None, + # limit: Optional[int] = 10, + # sort_by_similarity: bool = True, + # **kwargs, + # ) -> Iterator[Tuple[float, Optional[TermSetPairwiseSimilarity], CURIE]]: # pass From 85ddf9426c5345d792f15cdd0e8fc8ec6ad2dbdd Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 29 Aug 2023 18:26:48 -0500 Subject: [PATCH 05/21] typo fix --- src/oaklib/utilities/lexical/lexical_indexer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/utilities/lexical/lexical_indexer.py b/src/oaklib/utilities/lexical/lexical_indexer.py index f0a04d285..302c2b1f9 100644 --- a/src/oaklib/utilities/lexical/lexical_indexer.py +++ b/src/oaklib/utilities/lexical/lexical_indexer.py @@ -261,7 +261,7 @@ def lexical_index_to_sssom( :param subjects: An optional collection of entities, if specified, then only subjects in this set are reported :param objects: An optional collection of entities, if specified, then only objects in this set are reported :param symmetric: If true, then mappings in either direction are reported - :param ensure_strict_prefixes: If true, prefixes & mappings in SSSOM MappingSetDataFrame will be filtred. + :param ensure_strict_prefixes: If true, prefixes & mappings in SSSOM MappingSetDataFrame will be filtered. :return: SSSOM MappingSetDataFrame object. """ mappings = [] From 8a6a3fc96f781df98229432aed03413673f2f1b5 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 31 Aug 2023 18:39:03 -0500 Subject: [PATCH 06/21] temporary code for associations_subject_search --- .../semsimian/semsimian_implementation.py | 63 +++++++++++++------ 1 file changed, 45 insertions(+), 18 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 6d7759e8b..c7aaa1049 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -3,7 +3,7 @@ import logging import math from dataclasses import dataclass, field -from typing import ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union +from typing import Any, ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union from semsimian import Semsimian @@ -298,20 +298,47 @@ def _regain_element_formats(self, value: str) -> Union[str, float]: return value # TODO : Search feature for monarch app - # def associations_subject_search( - # self, - # subjects: Iterable[CURIE] = None, - # predicates: Iterable[PRED_CURIE] = None, - # objects: Iterable[CURIE] = None, - # property_filter: Dict[PRED_CURIE, Any] = None, - # subject_closure_predicates: Optional[List[PRED_CURIE]] = None, - # predicate_closure_predicates: Optional[List[PRED_CURIE]] = None, - # object_closure_predicates: Optional[List[PRED_CURIE]] = None, - # subject_prefixes: Optional[List[str]] = None, - # include_similarity_object: bool = False, - # method: Optional[str] = None, - # limit: Optional[int] = 10, - # sort_by_similarity: bool = True, - # **kwargs, - # ) -> Iterator[Tuple[float, Optional[TermSetPairwiseSimilarity], CURIE]]: - # pass + def associations_subject_search( + self, + subjects: Iterable[CURIE] = None, + predicates: Iterable[PRED_CURIE] = None, + objects: Iterable[CURIE] = None, + property_filter: Dict[PRED_CURIE, Any] = None, + subject_closure_predicates: Optional[List[PRED_CURIE]] = None, + predicate_closure_predicates: Optional[List[PRED_CURIE]] = None, + object_closure_predicates: Optional[List[PRED_CURIE]] = None, + subject_prefixes: Optional[List[str]] = None, + include_similarity_object: bool = False, + method: Optional[str] = None, + limit: Optional[int] = 10, + sort_by_similarity: bool = True, + **kwargs, + ) -> Iterator[Tuple[float, Optional[TermSetPairwiseSimilarity], CURIE]]: + """Search over all subjects in the association index. + + :param subjects: Collection of subject CURIEs, defaults to None + :param predicates: Collection of predicate CURIEs, defaults to None + :param objects: Collection of object CURIEs, defaults to None + :param property_filter: _description_, defaults to None + :param subject_closure_predicates: _description_, defaults to None + :param predicate_closure_predicates: _description_, defaults to None + :param object_closure_predicates: closure to use over the ontology, defaults to None + :param subject_prefixes: only consider subjects with these prefixes, defaults to None + :param include_similarity_object: include the similarity object in the result, defaults to False + :param method: similarity method to use, defaults to None + :param limit: max number of results to return, defaults to 10 + :param sort_by_similarity: Boolean determining sorting of results or no, defaults to True + :yield: iterator over ordered pairs of (score, sim, subject) + """ + semsimian = self._get_semsimian_object( + predicates=object_closure_predicates, attributes=self.termset_pairwise_similarity_attributes + ) + return semsimian.associations_subject_search( + predicates, + set(objects), + include_similarity_object, + property_filter, + set(subjects), + subject_prefixes, + limit, + ) From 1d59d706cf0af574c4892b3c18269edd7425d049 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 1 Sep 2023 20:32:07 -0500 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associations_subject_search --- .../semsimian/semsimian_implementation.py | 11 +++++++---- .../test_semsimian_implementation.py | 18 ++++++++++++++++++ 2 files changed, 25 insertions(+), 4 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index c7aaa1049..fac5301c0 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -331,14 +331,17 @@ def associations_subject_search( :yield: iterator over ordered pairs of (score, sim, subject) """ semsimian = self._get_semsimian_object( - predicates=object_closure_predicates, attributes=self.termset_pairwise_similarity_attributes + predicates=object_closure_predicates, + attributes=self.termset_pairwise_similarity_attributes, ) - return semsimian.associations_subject_search( + + subjects = set(subjects) if subjects is not None else None + + return semsimian.associations_search( predicates, set(objects), include_similarity_object, - property_filter, - set(subjects), + subjects, subject_prefixes, limit, ) diff --git a/tests/test_implementations/test_semsimian_implementation.py b/tests/test_implementations/test_semsimian_implementation.py index 288082900..05c27c3fc 100644 --- a/tests/test_implementations/test_semsimian_implementation.py +++ b/tests/test_implementations/test_semsimian_implementation.py @@ -156,3 +156,21 @@ def test_semsimian_object_cache(self): self.assertEqual(len(self.oi.semsimian_object_cache), 1) self.assertTrue(time_taken_1 > time_taken_2) + + def test_associations_search(self): + assoc_predicate = {"biolink:has_nucleus"} + object_terms = {"GO:0019222"} + subject_prefixes = ["GO:"] + limit = 10 + + result = self.oi.associations_subject_search( + object_closure_predicates=self.predicates, + predicates=assoc_predicate, + objects=object_terms, + include_similarity_object=True, + subject_prefixes=subject_prefixes, + limit=limit, + ) + + self.assertEqual(len(result), limit) + self.assertEqual(result[0][0], 3.186700714193139) From 47bed2cedf690805bb5116133e33dadee388d640 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 1 Sep 2023 20:33:04 -0500 Subject: [PATCH 10/21] cleanup --- .../implementations/semsimian/semsimian_implementation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index fac5301c0..1ae854f95 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -334,7 +334,7 @@ def associations_subject_search( predicates=object_closure_predicates, attributes=self.termset_pairwise_similarity_attributes, ) - + subjects = set(subjects) if subjects is not None else None return semsimian.associations_search( From 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[metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0.0" -content-hash = "9cb9de7655f12eeba1e5d11437e2a0a9472a60150d3ed7c08092816096352253" +content-hash = "dab50272a4b25f4d2c223a63b07a897e27c948ae9568eb85e6b428a84f27d465" diff --git a/pyproject.toml b/pyproject.toml index cb1016b68..8908e9dc2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,7 @@ pysolr = "^3.9.0" eutils = ">=0.6.0" requests-cache = "^1.0.1" click = "*" -semsimian = "0.2.5rc2" +semsimian = "0.2.5" urllib3 = {version = "< 2", optional = true} pydantic = "*" From e849c18f575dce2f55a1e317e9e753532ada310f Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 14 Sep 2023 20:29:19 -0500 Subject: [PATCH 12/21] Updated `semsimian.associations_search()` params --- .../implementations/semsimian/semsimian_implementation.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py 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This needs to be a param for this function. 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+36,7 @@ pysolr = "^3.9.0" eutils = ">=0.6.0" requests-cache = "^1.0.1" click = "*" -semsimian = "0.2.5" +semsimian = "^0.2.6" urllib3 = {version = "< 2", optional = true} pydantic = "*" diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index 5c110983c..ac03cd947 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -334,7 +334,9 @@ def associations_subject_search( predicates=object_closure_predicates, attributes=self.termset_pairwise_similarity_attributes, ) - quick_search = False # ! This needs to be a param for this function. For now using hardcoded value. + quick_search = ( + False # ! This needs to be a param for this function. For now using hardcoded value. + ) subjects = set(subjects) if subjects is not None else None diff --git a/tests/test_implementations/test_semsimian_implementation.py b/tests/test_implementations/test_semsimian_implementation.py index 05c27c3fc..33f5872a7 100644 --- a/tests/test_implementations/test_semsimian_implementation.py +++ b/tests/test_implementations/test_semsimian_implementation.py @@ -174,3 +174,36 @@ def test_associations_search(self): self.assertEqual(len(result), limit) self.assertEqual(result[0][0], 3.186700714193139) + + def test_associations_cache(self): + assoc_predicate = {"biolink:has_nucleus"} + object_terms = {"GO:0019222"} + subject_prefixes = ["GO:"] + limit = 10 + start_time = timeit.default_timer() + _ = self.oi.associations_subject_search( + object_closure_predicates=self.predicates, + predicates=assoc_predicate, + objects=object_terms, + include_similarity_object=True, + subject_prefixes=subject_prefixes, + limit=limit, + ) + + end_time = timeit.default_timer() + time_taken_1 = end_time - start_time + + start_time = timeit.default_timer() + _ = self.oi.associations_subject_search( + object_closure_predicates=self.predicates, + predicates=assoc_predicate, + objects=object_terms, + include_similarity_object=True, + subject_prefixes=subject_prefixes, + limit=limit, + ) + end_time = timeit.default_timer() + time_taken_2 = end_time - start_time + + self.assertEqual(len(self.oi.semsimian_object_cache), 1) + self.assertTrue(time_taken_1 > time_taken_2) From 1ad6fec3c539c7f1387ba8b2a2ed614758fe074f Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 15 Sep 2023 08:47:03 -0500 Subject: [PATCH 14/21] removed irrelevant code --- tests/test_implementations/test_semsimian_implementation.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/test_implementations/test_semsimian_implementation.py b/tests/test_implementations/test_semsimian_implementation.py index 33f5872a7..bab907429 100644 --- a/tests/test_implementations/test_semsimian_implementation.py +++ b/tests/test_implementations/test_semsimian_implementation.py @@ -205,5 +205,4 @@ def test_associations_cache(self): end_time = timeit.default_timer() time_taken_2 = end_time - start_time - self.assertEqual(len(self.oi.semsimian_object_cache), 1) self.assertTrue(time_taken_1 > time_taken_2) From 03087b1459b9f7fbdc4fb20ac58d26a0e98b0b0d Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 26 Sep 2023 21:53:30 -0500 Subject: [PATCH 15/21] updated to latest version of semsimian --- poetry.lock | 74 +++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 38 insertions(+), 38 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6751e8a22..62ac4bdd6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4679,46 +4679,46 @@ stats = ["scipy (>=1.3)", "statsmodels (>=0.10)"] [[package]] name = "semsimian" -version = "0.2.6" +version = "0.2.7" description = "" optional = false python-versions = 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true} pydantic = "*" From 46e0733b0643746ac01197e06564c90e4f0c2983 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 16 Nov 2023 14:30:18 -0600 Subject: [PATCH 17/21] Added search_type enum and param for search --- src/oaklib/datamodels/vocabulary.py | 6 ++++++ .../semsimian/semsimian_implementation.py | 10 ++++------ .../interfaces/association_provider_interface.py | 1 + 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/src/oaklib/datamodels/vocabulary.py b/src/oaklib/datamodels/vocabulary.py index 25f191c97..d623b0d04 100644 --- a/src/oaklib/datamodels/vocabulary.py +++ b/src/oaklib/datamodels/vocabulary.py @@ -178,3 +178,9 @@ class SEMAPV(Enum): MappingReview = "semapv:MappingReview" ManualMappingCuration = "semapv:ManualMappingCuration" RegularExpressionReplacement = "semapv:RegularExpressionReplacement" + +class SearchType(Enum): + """Search type for semsimian's association search.""" + FLAT = "flat" + HYBRID = "hybrid" + FULL = "full" \ No newline at end of file diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index ac03cd947..f1810e82a 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -13,7 +13,7 @@ TermPairwiseSimilarity, TermSetPairwiseSimilarity, ) -from oaklib.datamodels.vocabulary import OWL_THING +from oaklib.datamodels.vocabulary import OWL_THING, SearchType from oaklib.implementations.sqldb.sql_implementation import SqlImplementation from oaklib.interfaces.association_provider_interface import ( AssociationProviderInterface, @@ -310,6 +310,7 @@ def associations_subject_search( subject_prefixes: Optional[List[str]] = None, include_similarity_object: bool = False, method: Optional[str] = None, + search_type: Optional[str] = SearchType.HYBRID, limit: Optional[int] = 10, sort_by_similarity: bool = True, **kwargs, @@ -326,6 +327,7 @@ def associations_subject_search( :param subject_prefixes: only consider subjects with these prefixes, defaults to None :param include_similarity_object: include the similarity object in the result, defaults to False :param method: similarity method to use, defaults to None + :param search_type: Type of semsimian search to perform, defaults to HYBRID [Other choices: FULL, FLAT] :param limit: max number of results to return, defaults to 10 :param sort_by_similarity: Boolean determining sorting of results or no, defaults to True :yield: iterator over ordered pairs of (score, sim, subject) @@ -334,17 +336,13 @@ def associations_subject_search( predicates=object_closure_predicates, attributes=self.termset_pairwise_similarity_attributes, ) - quick_search = ( - False # ! This needs to be a param for this function. For now using hardcoded value. - ) - subjects = set(subjects) if subjects is not None else None return semsimian.associations_search( predicates, set(objects), include_similarity_object, - quick_search, + search_type, subjects, subject_prefixes, limit, diff --git a/src/oaklib/interfaces/association_provider_interface.py b/src/oaklib/interfaces/association_provider_interface.py index a500de354..4293b2a86 100644 --- a/src/oaklib/interfaces/association_provider_interface.py +++ b/src/oaklib/interfaces/association_provider_interface.py @@ -250,6 +250,7 @@ def associations_subject_search( subject_prefixes: Optional[List[str]] = None, include_similarity_object: bool = False, method: Optional[str] = None, + search_type: Optional[str] = None, limit: Optional[int] = 10, sort_by_similarity: bool = True, **kwargs, From beb65487ff5ce1efb376d048d68ed2dce0987d9b Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 16 Nov 2023 14:34:35 -0600 Subject: [PATCH 18/21] updated semsimian --- poetry.lock 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"0462cdc9b8be7d99ad9ad693963db81f639291a14d82a1fd61c4aded99bdf8df" +content-hash = "29e1a9349898ec0d0117a2bda929554094aaf7704c232016a6dcb7f7ec9acccc" diff --git a/pyproject.toml b/pyproject.toml index 87a6a2b33..9f47c3039 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,7 +36,7 @@ pysolr = "^3.9.0" eutils = ">=0.6.0" requests-cache = "^1.0.1" click = "*" -semsimian = "^0.2.8" +semsimian = ">=0.2.9" urllib3 = {version = "< 2", optional = true} pydantic = "*" From 53e7fdd705664ec10ad9a01589ae2e11ad2f9eec Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 16 Nov 2023 14:35:19 -0600 Subject: [PATCH 19/21] reformatted --- src/oaklib/datamodels/vocabulary.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/oaklib/datamodels/vocabulary.py b/src/oaklib/datamodels/vocabulary.py index d623b0d04..6a65f19ac 100644 --- a/src/oaklib/datamodels/vocabulary.py +++ b/src/oaklib/datamodels/vocabulary.py @@ -179,8 +179,10 @@ class SEMAPV(Enum): ManualMappingCuration = "semapv:ManualMappingCuration" RegularExpressionReplacement = "semapv:RegularExpressionReplacement" + class SearchType(Enum): """Search type for semsimian's association search.""" + FLAT = "flat" HYBRID = "hybrid" - FULL = "full" \ No newline at end of file + FULL = "full" From 3708638d8f689d16b5aef040e48f0a63592078c5 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 16 Nov 2023 15:04:15 -0600 Subject: [PATCH 20/21] implemented latest version of semsimian --- .../implementations/semsimian/semsimian_implementation.py | 2 +- tests/test_implementations/test_semsimian_implementation.py | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/oaklib/implementations/semsimian/semsimian_implementation.py b/src/oaklib/implementations/semsimian/semsimian_implementation.py index f1810e82a..5c459a86a 100644 --- a/src/oaklib/implementations/semsimian/semsimian_implementation.py +++ b/src/oaklib/implementations/semsimian/semsimian_implementation.py @@ -310,7 +310,7 @@ def associations_subject_search( subject_prefixes: Optional[List[str]] = None, include_similarity_object: bool = False, method: Optional[str] = None, - search_type: Optional[str] = SearchType.HYBRID, + search_type: Optional[str] = SearchType.HYBRID.value, limit: Optional[int] = 10, sort_by_similarity: bool = True, **kwargs, diff --git a/tests/test_implementations/test_semsimian_implementation.py b/tests/test_implementations/test_semsimian_implementation.py index bab907429..81f51e0c8 100644 --- a/tests/test_implementations/test_semsimian_implementation.py +++ b/tests/test_implementations/test_semsimian_implementation.py @@ -5,7 +5,7 @@ from linkml_runtime.dumpers import yaml_dumper from oaklib.datamodels.similarity import TermPairwiseSimilarity -from oaklib.datamodels.vocabulary import IS_A, PART_OF +from oaklib.datamodels.vocabulary import IS_A, PART_OF, SearchType from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface from oaklib.selector import get_adapter from tests import ( @@ -162,6 +162,7 @@ def test_associations_search(self): object_terms = {"GO:0019222"} subject_prefixes = ["GO:"] limit = 10 + search_type = SearchType.FULL.value result = self.oi.associations_subject_search( object_closure_predicates=self.predicates, @@ -169,11 +170,12 @@ def test_associations_search(self): objects=object_terms, include_similarity_object=True, subject_prefixes=subject_prefixes, + search_type=search_type, limit=limit, ) self.assertEqual(len(result), limit) - self.assertEqual(result[0][0], 3.186700714193139) + self.assertEqual(result[0][0], 2.9817189317909856) def test_associations_cache(self): assoc_predicate = {"biolink:has_nucleus"} From 7fddc3f44b3759a5a2728d9b72c6d65c7f81dc73 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 16 Nov 2023 15:15:37 -0600 Subject: [PATCH 21/21] poetry update --- poetry.lock | 3227 +++++++++++++++++++++++++----------------------- pyproject.toml | 1 + 2 files changed, 1651 insertions(+), 1577 deletions(-) diff --git a/poetry.lock b/poetry.lock index ed6f7c15e..2389b14f2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "adeft" @@ -22,18 +22,18 @@ test = ["pytest", "pytest-cov"] [[package]] name = "airium" -version = "0.2.5" +version = "0.2.6" description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. 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