def test_query_invalid_attribute(db: Session):
q = query.ReadsQCQuerySchema(conditions=[{
"table": "reads_qc",
"field": "bad value",
"value": ""
}])
with pytest.raises(query.InvalidAttributeException):
q.execute(db)
def binned_facet_reads_qc(
db: Session,
attribute: str,
conditions: List[query.ConditionSchema],
**kwargs,
) -> query.BinnedFacetResponse:
bins, facets = query.ReadsQCQuerySchema(
conditions=conditions).binned_facet(db, attribute, **kwargs)
return query.BinnedFacetResponse(bins=bins, facets=facets)
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_reads_qc(
db: Session, attribute: str,
conditions: List[query.ConditionSchema]) -> query.FacetResponse:
facets = query.ReadsQCQuerySchema(conditions=conditions).facet(
db, attribute)
return query.FacetResponse(facets=facets)
def search_reads_qc(db: Session,
conditions: List[query.ConditionSchema]) -> Query:
return query.ReadsQCQuerySchema(conditions=conditions).execute(db)
def test_facet_invalid_attribute(db: Session):
q = query.ReadsQCQuerySchema()
with pytest.raises(query.InvalidAttributeException):
q.facet(db, "bad value")