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Implemented entities_metadata_statements() for SQLImplementation() #679

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merged 13 commits into from
Nov 16, 2023
Merged

Implemented entities_metadata_statements() for SQLImplementation() #679

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5a79b15
Adde `entities_metadata_statements` to SQLImplementation
hrshdhgd Nov 14, 2023
ed6c3fb
Merge branch 'main' into issue-676
hrshdhgd Nov 14, 2023
9c6a0cd
Moved test to core compliance tests
hrshdhgd Nov 15, 2023
dd85d62
included axiom annotations (optional)
hrshdhgd Nov 15, 2023
ec352f2
refactored to follow format
hrshdhgd Nov 15, 2023
ba367fa
formattted
hrshdhgd Nov 15, 2023
41df720
added expected results
hrshdhgd Nov 15, 2023
777c1e8
formatted
hrshdhgd Nov 15, 2023
07748da
added more cases
hrshdhgd Nov 15, 2023
0df542b
formatted
hrshdhgd Nov 16, 2023
2925ddb
refactor include_all_triples to include_nested_metadata
hrshdhgd Nov 16, 2023
7ac4f19
added kwargs
hrshdhgd Nov 16, 2023
076fd41
Added **kwargs,
hrshdhgd Nov 16, 2023
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28 changes: 28 additions & 0 deletions src/oaklib/implementations/sqldb/sql_implementation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,7 @@
DEFINITION,
LANGUAGE_TAG,
METADATA_MAP,
METADATA_STATEMENT,
PRED_CURIE,
PREFIX_MAP,
RELATIONSHIP,
Expand Down Expand Up @@ -671,6 +672,33 @@ def entity_metadata_map(self, curie: CURIE, include_all_triples=False) -> METADA
self.add_missing_property_values(curie, m)
return dict(m)

def entities_metadata_statements(
self,
curies: Iterable[CURIE],
predicates: Optional[List[PRED_CURIE]] = None,
include_nested_metadata=False,
**kwargs,
) -> Iterator[METADATA_STATEMENT]:
q = self.session.query(Statements)
if not include_nested_metadata:
subquery = self.session.query(RdfTypeStatement.subject).filter(
RdfTypeStatement.object == "owl:AnnotationProperty"
)
annotation_properties = {row.subject for row in subquery}
annotation_properties = annotation_properties.union(STANDARD_ANNOTATION_PROPERTIES)
q = q.filter(Statements.predicate.in_(tuple(annotation_properties)))
q = q.filter(Statements.subject.in_(curies))
if predicates is not None:
q = q.filter(Statements.predicate.in_(predicates))
for row in q:
if row.value is not None:
v = _python_value(row.value, row.datatype)
elif row.object is not None:
v = row.object
else:
v = None
yield row.subject, row.predicate, v, row.datatype, {}
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def ontologies(self) -> Iterable[CURIE]:
for row in self.session.query(OntologyNode):
yield row.id
Expand Down
6 changes: 5 additions & 1 deletion src/oaklib/interfaces/basic_ontology_interface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1419,7 +1419,11 @@ def entity_metadata_map(self, curie: CURIE) -> METADATA_MAP:
raise NotImplementedError

def entities_metadata_statements(
self, curies: Iterable[CURIE], predicates: Optional[List[PRED_CURIE]] = None
self,
curies: Iterable[CURIE],
predicates: Optional[List[PRED_CURIE]] = None,
include_nested_metadata=False,
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**kwargs,
) -> Iterator[METADATA_STATEMENT]:
"""
Retrieve metadata statements (entity annotations) for a collection of entities.
Expand Down
126 changes: 126 additions & 0 deletions tests/test_implementations/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,6 +112,7 @@
INTRACELLULAR,
INTRACELLULAR_ORGANELLE,
MAMMALIA,
MEMBRANE,
NUCLEAR_ENVELOPE,
NUCLEAR_MEMBRANE,
NUCLEUS,
Expand Down Expand Up @@ -1880,3 +1881,128 @@ def test_annotate_text(self, oi: TextAnnotatorInterface):
test.assertEqual(object_label, ann.object_label)
test.assertEqual(subject_start, ann.subject_start)
test.assertEqual(subject_end, ann.subject_end)

def test_entities_metadata_statements(self, oi: BasicOntologyInterface):
test = self.test

cases = [
(
[MEMBRANE],
[OIO_CREATION_DATE],
[("GO:0016020", "oio:creation_date", "2014-03-06T11:37:54Z", "xsd:string", {})],
),
(
[MEMBRANE],
None,
[
(
"GO:0016020",
"IAO:0000115",
"A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.", # noqa:E501
"xsd:string",
{},
),
("GO:0016020", "oio:creation_date", "2014-03-06T11:37:54Z", "xsd:string", {}),
("GO:0016020", "oio:hasAlternativeId", "GO:0098589", "xsd:string", {}),
("GO:0016020", "oio:hasAlternativeId", "GO:0098805", "xsd:string", {}),
(
"GO:0016020",
"oio:hasDbXref",
"Wikipedia:Biological_membrane",
"xsd:string",
{},
),
("GO:0016020", "oio:hasNarrowSynonym", "membrane region", "xsd:string", {}),
("GO:0016020", "oio:hasNarrowSynonym", "region of membrane", "xsd:string", {}),
("GO:0016020", "oio:hasNarrowSynonym", "whole membrane", "xsd:string", {}),
("GO:0016020", "oio:hasOBONamespace", "cellular_component", "xsd:string", {}),
("GO:0016020", "oio:id", "GO:0016020", "xsd:string", {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_yeast", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_plant", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_pir", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_metagenomics", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_flybase_ribbon", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_chembl", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_candida", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_aspergillus", None, {}),
("GO:0016020", "rdfs:label", "membrane", "xsd:string", {}),
],
),
(
[MEMBRANE],
["oio:inSubset"],
[
("GO:0016020", "oio:inSubset", "obo:go#goslim_yeast", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_plant", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_pir", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_metagenomics", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_flybase_ribbon", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_chembl", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_candida", None, {}),
("GO:0016020", "oio:inSubset", "obo:go#goslim_aspergillus", None, {}),
],
),
(
[NUCLEUS],
None,
[
(
"GO:0005634",
"IAO:0000115",
"A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", # noqa:E501
"xsd:string",
{},
),
(
"GO:0005634",
"oio:hasDbXref",
"NIF_Subcellular:sao1702920020",
"xsd:string",
{},
),
("GO:0005634", "oio:hasDbXref", "Wikipedia:Cell_nucleus", "xsd:string", {}),
("GO:0005634", "oio:hasExactSynonym", "cell nucleus", "xsd:string", {}),
("GO:0005634", "oio:hasNarrowSynonym", "horsetail nucleus", "xsd:string", {}),
("GO:0005634", "oio:hasOBONamespace", "cellular_component", "xsd:string", {}),
("GO:0005634", "oio:id", "GO:0005634", "xsd:string", {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_yeast", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_plant", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_pir", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_mouse", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_metagenomics", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_generic", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_flybase_ribbon", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_drosophila", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_chembl", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_candida", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_aspergillus", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_agr", None, {}),
("GO:0005634", "rdfs:label", "nucleus", "xsd:string", {}),
],
),
(
[NUCLEUS],
["oio:inSubset"],
[
("GO:0005634", "oio:inSubset", "obo:go#goslim_yeast", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_plant", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_pir", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_mouse", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_metagenomics", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_generic", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_flybase_ribbon", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_drosophila", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_chembl", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_candida", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_aspergillus", None, {}),
("GO:0005634", "oio:inSubset", "obo:go#goslim_agr", None, {}),
],
),
]
for case in cases:
curies, predicates, expected_result = case
results = list(oi.entities_metadata_statements(curies=curies, predicates=predicates))
test.assertCountEqual(results, expected_result)
test.assertCountEqual(results[0], expected_result[0])
for idx, result in enumerate(results):
test.assertEqual(result, expected_result[idx])
3 changes: 3 additions & 0 deletions tests/test_implementations/test_sqldb.py
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Expand Up @@ -899,3 +899,6 @@ def test_transitive_object_properties(self):

def test_simple_subproperty_of_chains(self):
self.compliance_tester.test_simple_subproperty_of_chains(self.oi)

def test_entities_metadata_statements(self):
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self.compliance_tester.test_entities_metadata_statements(self.oi)