def post(self):
"""
Create a new biospecimen
---
template:
path:
new_resource.yml
properties:
resource:
Biospecimen
"""
body = request.get_json(force=True)
# Deserialize
try:
s = BiospecimenSchema(strict=True).load(body).data
# Request body not valid
except ValidationError as e:
abort(400, 'could not create biospecimen: {}'.format(e.messages))
# Add to and save in database
db.session.add(s)
db.session.commit()
return BiospecimenSchema(201, 'biospecimen {} created'.format(
s.kf_id)).jsonify(s), 201
def patch(self, kf_id):
"""
Update an existing biospecimen. Allows partial update of resource
---
template:
path:
update_by_id.yml
properties:
resource:
Biospecimen
"""
sa = Biospecimen.query.get(kf_id)
if sa is None:
abort(404, 'could not find {} `{}`'.format('biospecimen', kf_id))
# Partial update - validate but allow missing required fields
body = request.get_json(force=True) or {}
try:
sa = BiospecimenSchema(strict=True).load(body,
instance=sa,
partial=True).data
except ValidationError as err:
abort(400, 'could not update biospecimen: {}'.format(err.messages))
db.session.add(sa)
db.session.commit()
return BiospecimenSchema(200, 'biospecimen {} updated'.format(
sa.kf_id)).jsonify(sa), 200
def delete(self, kf_id):
"""
Delete biospecimen by id
Deletes a biospecimen given a Kids First id
---
template:
path:
delete_by_id.yml
properties:
resource:
Biospecimen
"""
# Check if biospecimen exists
sa = Biospecimen.query.get(kf_id)
if sa is None:
abort(404, 'could not find {} `{}`'.format('biospecimen', kf_id))
# Save in database
db.session.delete(sa)
db.session.commit()
return BiospecimenSchema(200, 'biospecimen {} deleted'.format(
sa.kf_id)).jsonify(sa), 200
def get(self, filter_params, after, limit):
"""
Get all biospecimens
---
description: Get all biospecimens
template:
path:
get_list.yml
properties:
resource:
Biospecimen
"""
# Get study id, diagnosis_id and remove from model filter params
study_id = filter_params.pop('study_id', None)
diagnosis_id = filter_params.pop('diagnosis_id', None)
# Apply filter params
q = (Biospecimen.query
.filter_by(**filter_params))
# Apply study_id filter and diagnosis_id filter
from dataservice.api.participant.models import Participant
if study_id:
q = (q.join(Participant.biospecimens)
.filter(Participant.study_id == study_id))
if diagnosis_id:
q = (q.join(BiospecimenDiagnosis)
.filter(BiospecimenDiagnosis.diagnosis_id == diagnosis_id))
return (BiospecimenSchema(many=True)
.jsonify(Pagination(q, after, limit)))
def get(self, kf_id):
"""
Get biospecimens by id
---
template:
path:
get_by_id.yml
properties:
resource:
Biospecimen
"""
sa = Biospecimen.query.get(kf_id)
if sa is None:
abort(404, 'could not find {} `{}`'.format('biospecimen', kf_id))
return BiospecimenSchema().jsonify(sa)
def get(self, filter_params, after, limit):
"""
Get all biospecimens
---
description: Get all biospecimens
template:
path:
get_list.yml
properties:
resource:
Biospecimen
"""
# Get and remove special filter params that are not attributes of model
study_id = filter_params.pop('study_id', None)
diagnosis_id = filter_params.pop('diagnosis_id', None)
genomic_file_id = filter_params.pop('genomic_file_id', None)
# Get and remove any list type filter params that need to be
# handled differently than others
duo_ids = filter_params.pop('duo_ids', None)
# Apply filter params
q = (Biospecimen.query.filter_by(**filter_params))
# Apply duo_ids filter
# Get specimens whose duo ids list includes all values in duo_ids
if duo_ids:
duo_ids = [id_.strip() for id_ in duo_ids[0].split(',')]
q = q.filter(Biospecimen.duo_ids.contains(duo_ids))
# Apply study_id filter and diagnosis_id filter
from dataservice.api.participant.models import Participant
if study_id:
q = (q.join(Participant.biospecimens).filter(
Participant.study_id == study_id))
if diagnosis_id:
q = (q.join(BiospecimenDiagnosis).filter(
BiospecimenDiagnosis.diagnosis_id == diagnosis_id))
if genomic_file_id:
q = (q.join(BiospecimenGenomicFile).filter(
BiospecimenGenomicFile.genomic_file_id == genomic_file_id))
return (BiospecimenSchema(many=True).jsonify(
Pagination(q, after, limit)))