def test_query_pi(db: Session):
study1 = fakes.StudyFactory(id="study1",
principal_investigator__name="John Doe")
study2 = fakes.StudyFactory(id="study2",
principal_investigator__name="Jane Doe")
fakes.BiosampleFactory(id="sample1", study=study1)
fakes.BiosampleFactory(id="sample2", study=study2)
db.commit()
q = query.StudyQuerySchema()
assert q.facet(db, "principal_investigator_name") == {
"John Doe": 1,
"Jane Doe": 1,
}
q = query.StudyQuerySchema(conditions=[{
"table": "study",
"field": "principal_investigator_name",
"value": "John Doe",
}])
assert ["study1"] == [r.id for r in q.execute(db)]
qp = query.BiosampleQuerySchema(conditions=[{
"table": "study",
"field": "principal_investigator_name",
"value": "John Doe",
}])
assert ["sample1"] == [r.id for r in qp.execute(db)]
def binned_facet_study(
db: Session,
attribute: str,
conditions: List[query.ConditionSchema],
**kwargs,
) -> query.BinnedFacetResponse:
bins, facets = query.StudyQuerySchema(conditions=conditions).binned_facet(
db, attribute, **kwargs)
return query.BinnedFacetResponse(bins=bins, facets=facets)
def test_distinct_results(db: Session):
study = fakes.StudyFactory(id="study1")
fakes.BiosampleFactory(id="sample1", study=study)
fakes.BiosampleFactory(id="sample2", study=study)
fakes.BiosampleFactory(id="sample3", study=study)
fakes.BiosampleFactory(id="sample4", study=study)
db.commit()
q = query.StudyQuerySchema(conditions=[])
assert len(q.execute(db).all()) == 1
def test_facet_foreign_table(db: Session):
env_local1 = fakes.EnvoTermFactory(label="local1")
env_local2 = fakes.EnvoTermFactory(label="local2")
fakes.BiosampleFactory(id="sample1", env_local_scale=env_local1)
fakes.BiosampleFactory(id="sample2", env_local_scale=env_local2)
fakes.BiosampleFactory(id="sample3", env_local_scale=env_local2)
db.commit()
q = query.StudyQuerySchema(conditions=[])
assert q.facet(db, "env_local_scale") == {}
assert q.facet(db, "sample_id") == {}
def test_indirect_join(db: Session):
study = fakes.StudyFactory(id="study1")
fakes.OmicsProcessingFactory(id="omics_processing1",
biosample__study=study)
db.commit()
q = query.StudyQuerySchema(conditions=[{
"table": "omics_processing",
"field": "id",
"value": "omics_processing1",
"op": "=="
}])
assert {s.id for s in q.execute(db)} == {"study1"}
def test_basic_query(db: Session, table):
tests: Dict[str, Tuple[fakes.AnnotatedFactory, query.BaseQuerySchema]] = {
"study": (fakes.StudyFactory(), query.StudyQuerySchema()),
"omics_processing":
(fakes.OmicsProcessingFactory(), query.OmicsProcessingQuerySchema()),
"biosample": (fakes.BiosampleFactory(), query.BiosampleQuerySchema()),
"reads_qc": (fakes.ReadsQCFactory(), query.ReadsQCQuerySchema()),
"metagenome_assembly": (
fakes.MetagenomeAssemblyFactory(),
query.MetagenomeAssemblyQuerySchema(),
),
"metagenome_annotation": (
fakes.MetagenomeAnnotationFactory(),
query.MetagenomeAnnotationQuerySchema(),
),
"metaproteomic_analysis": (
fakes.MetaproteomicAnalysisFactory(),
query.MetaproteomicAnalysisQuerySchema(),
),
}
db.commit()
q = tests[table][1].execute(db)
assert tests[table][0].id in {r.id for r in q.all()}
def facet_study(
db: Session, attribute: str,
conditions: List[query.ConditionSchema]) -> query.FacetResponse:
facets = query.StudyQuerySchema(conditions=conditions).facet(db, attribute)
return query.FacetResponse(facets=facets)
def search_study(db: Session,
conditions: List[query.ConditionSchema]) -> Query:
return query.StudyQuerySchema(conditions=conditions).execute(db)