From 54edbfd663d55f96aa06d54bf77a0bd26251bdfc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Jun 2024 22:40:32 +0000 Subject: [PATCH 1/3] Bump urllib3 from 2.1.0 to 2.2.2 Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.1.0 to 2.2.2. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/2.1.0...2.2.2) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index bed0cdb..7e969ee 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1450,17 +1450,18 @@ files = [ [[package]] name = "urllib3" -version = "2.1.0" +version = "2.2.2" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" files = [ - {file = "urllib3-2.1.0-py3-none-any.whl", hash = "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3"}, - {file = "urllib3-2.1.0.tar.gz", hash = "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"}, + {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, + {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, ] [package.extras] brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] From 54804224ac95c1d4e603667770af97a9a8ca50bc Mon Sep 17 00:00:00 2001 From: Richard Bruskiewich Date: Tue, 18 Jun 2024 10:04:27 -0700 Subject: [PATCH 2/3] Code checks in get_associations() to ignore unknown (or invalid) subject/object categories or predicates, return empty matches (with log warnings) --- bmt/toolkit.py | 87 +++++++++++++++++++++++++++++++------- tests/unit/test_toolkit.py | 29 ++++++++++++- 2 files changed, 100 insertions(+), 16 deletions(-) diff --git a/bmt/toolkit.py b/bmt/toolkit.py index b61da7a..a17ad7a 100644 --- a/bmt/toolkit.py +++ b/bmt/toolkit.py @@ -421,6 +421,11 @@ def get_associations( This method returns a list of names or (optionally formatted) curies designating classes that are descendants of the class biolink:Association. + Note that the method does not attempt to continue matching input constraints + if any category or predicate is deemed unknown to the current Biolink Model: + The caller should know well enough to check these, *before* calling this method! + But log warnings are issued as a courtesys to inform them! + Parameters ---------- subject_categories: Optional[List[str]] @@ -441,34 +446,68 @@ def get_associations( A list of elements """ - filtered_elements: List[str] = list() + + filtered_elements: List[str] = [] inverse_predicates: Optional[List[str]] = None subject_categories_formatted = [] object_categories_formatted = [] predicates_formatted = [] association_elements = self.get_descendants("association") + if subject_categories: for sc in subject_categories: - sc_formatted = format_element(self.get_element(sc)) + sc_elem = self.get_element(sc) + if not sc_elem: + logger.warning( + f"get_associations(): could not find subject category " + + f"element '{str(sc)}' in current Biolink Model release?" + ) + return [] + sc_formatted = format_element(sc_elem) subject_categories_formatted.append(sc_formatted) + if object_categories: for oc in object_categories: - oc_formatted = format_element(self.get_element(oc)) + oc_elem = self.get_element(oc) + if not oc_elem: + logger.warning( + f"get_associations(): could not find object category " + + f"element '{str(oc)}' in current Biolink Model release?" + ) + return [] + oc_formatted = format_element(oc_elem) object_categories_formatted.append(oc_formatted) + if predicates: for pred in predicates: - pred_formatted = format_element(self.get_element(pred)) + p_elem = self.get_element(pred) + if not p_elem: + logger.warning( + f"get_associations(): could not find predicate " + + f"element '{str(pred)}' in current Biolink Model release?" + ) + return [] + pred_formatted = format_element(p_elem) predicates_formatted.append(pred_formatted) + inverse_predicates = list() for pred_curie in predicates_formatted: - predicate = self.get_element(pred_curie) - if predicate: - inverse_p = self.get_inverse(predicate.name) - if inverse_p: - inverse_predicates.append(inverse_p) - inverse_predicates = self._format_all_elements(elements=inverse_predicates, formatted=True) - - + p_elem = self.get_element(pred_curie) + if not p_elem: + # Not too worried here about predictes missing + # their inverse, so we just skip them + continue + inverse_p = self.get_inverse(p_elem.name) + if inverse_p: + # TODO: unsure that this test is needed, if the + # existence of 'p_elem' is vetted above, since + # all predicates in the model ought to have names? + logger.warning( + f"get_associations(): inverse predicate name '{str(p_elem.name)}' " + + f"does not match any element in the current Biolink Model release?" + ) + inverse_predicates.append(inverse_p) + inverse_predicates = self._format_all_elements(elements=inverse_predicates, formatted=True) if subject_categories_formatted or predicates_formatted or object_categories_formatted: # This feels like a bit of a brute force approach as an implementation, @@ -480,17 +519,35 @@ def get_associations( # the association_elements all come from # get_descendants(), hence are assumed to be extant association: Element = self.get_element(name) + if not association: + # TODO: unsure that this test is needed, since all + # known association classes ought to have names? + logger.warning( + f"get_associations(): association name '{str(name)}' " + + f"does not match any element in the current Biolink Model release?" + ) + continue # sanity checks, probably not necessary # assert association, f"'{name}' not a Biolink Element?" # assert isinstance(association, ClassDefinition), f"'{name}' not a ClassDefinition?" # Try to match associations in the forward direction - if not( - self.match_association(association, subject_categories_formatted, predicates_formatted, object_categories_formatted) or + if not ( + self.match_association( + association, + subject_categories_formatted, + predicates_formatted, + object_categories_formatted + ) or ( match_inverses and - self.match_association(association, object_categories, inverse_predicates, subject_categories_formatted) + self.match_association( + association, + object_categories, + inverse_predicates, + subject_categories_formatted + ) ) ): continue diff --git a/tests/unit/test_toolkit.py b/tests/unit/test_toolkit.py index dd976e0..2be5b07 100644 --- a/tests/unit/test_toolkit.py +++ b/tests/unit/test_toolkit.py @@ -558,7 +558,7 @@ def test_get_associations_without_parameters(toolkit): "biolink:ChemicalAffectsGeneAssociation" ] ), - ( # Q8 - Check if "biolink:Gene -- biolink:affected -> biolink:SmallMolecule" - still no direct match + ( # Q9 - Check if "biolink:Gene -- biolink:affected -> biolink:SmallMolecule" - still no direct match [GENE_OR_GENE_PRODUCT], ["biolink:affected_by"], ["biolink:ChemicalEntity"], @@ -568,6 +568,33 @@ def test_get_associations_without_parameters(toolkit): "biolink:Association", "biolink:ChemicalAffectsGeneAssociation" ] + ), + ( # Q10 - Check if "biolink:not-a-category -- biolink:affects -> biolink:SmallMolecule" - + # has no direct match (and issues a log warning?) + ["biolink:not-a-category"], + ["biolink:affects"], + ["biolink:ChemicalEntity"], + False, # match_inverses + [], # there is no direct match for a nonsense subject category + ["biolink:Association"] + ), + ( # Q11 - Check if "biolink:Gene -- biolink:not-a-predicate -> biolink:SmallMolecule" - + # has no direct match (and issues a log warning?) + [GENE_CURIE], + ["biolink:not-a-predicate"], + ["biolink:ChemicalEntity"], + False, # match_inverses + [], # there is no direct match for a nonsense predicate + ["biolink:Association"] + ), + ( # Q12 - Check if "biolink:Gene -- biolink:affects -> biolink:not-a-category" - + # has no direct match (and issues a log warning?) + [GENE_CURIE], + ["biolink:affects"], + ["biolink:not-a-category"], + False, # match_inverses + [], # there is no direct match for a nonsense object category + ["biolink:Association"] ) ] ) From f3182a00ca563246e11b533c20f27e903162f72c Mon Sep 17 00:00:00 2001 From: Richard Bruskiewich Date: Tue, 18 Jun 2024 10:44:50 -0700 Subject: [PATCH 3/3] poetry update --- poetry.lock | 864 ++++++++++++++++++++----------------------------- pyproject.toml | 2 +- 2 files changed, 346 insertions(+), 520 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7e969ee..023f7c9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,90 +1,69 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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Taylor Moxon "] license = "BSD"