def get_phenotype_evidence(locus_id, phenotype_id, observable_id, chemical_id, reference_id, with_children):
query = DBSession.query(Phenotypeevidence)
if locus_id is not None:
query = query.filter_by(locus_id=locus_id)
if reference_id is not None:
query = query.filter_by(reference_id=reference_id)
if phenotype_id is not None:
query = query.filter_by(phenotype_id=phenotype_id)
if observable_id is not None:
if with_children:
phenotype_ids = set()
for new_observable_id in list(get_all_bioconcept_children(observable_id)):
phenotype_ids.update([x.id for x in DBSession.query(Phenotype.id).filter_by(observable_id=new_observable_id).all()])
else:
phenotype_ids = set([x.id for x in DBSession.query(Phenotype.id).filter_by(observable_id=observable_id).all()])
phenotype_ids = list(phenotype_ids)
num_chunks = int(ceil(1.0*len(phenotype_ids)/500))
evidences = []
for i in range(num_chunks):
subquery = query.filter(Phenotypeevidence.phenotype_id.in_(phenotype_ids[i*500:(i+1)*500]))
if len(evidences) + subquery.count() > query_limit:
return None
evidences.extend(subquery.all())
return evidences
if chemical_id is not None:
chemical_evidence_ids = list(set([x.evidence_id for x in DBSession.query(Chemicalproperty).filter_by(bioitem_id=chemical_id).all()]))
num_chunks = int(ceil(1.0*len(chemical_evidence_ids)/500))
evidences = []
for i in range(num_chunks):
subquery = query.filter(Phenotypeevidence.id.in_(chemical_evidence_ids[i*500:(i+1)*500]))
if len(evidences) + subquery.count() > query_limit:
return None
evidences.extend(subquery.all())
return evidences
else:
if query.count() > query_limit:
return None
return query.all()
def get_go_evidence(locus_id, go_id, reference_id, with_children):
query = DBSession.query(Goevidence)
if locus_id is not None:
query = query.filter_by(locus_id=locus_id)
if reference_id is not None:
query = query.filter_by(reference_id=reference_id)
if go_id is not None:
if with_children:
child_ids = list(get_all_bioconcept_children(go_id))
num_chunks = int(ceil(1.0*len(child_ids)/500))
evidences = []
for i in range(num_chunks):
subquery = query.filter(Goevidence.go_id.in_(child_ids[i*500:(i+1)*500]))
if len(evidences) + subquery.count() > query_limit:
return None
evidences.extend([x for x in subquery.all()])
return evidences
else:
query = query.filter_by(go_id=go_id)
if query.count() > query_limit:
return None
return query.all()
