def post(self):
"""
Create a new sequencing_experiment
---
template:
path:
new_resource.yml
properties:
resource:
SequencingExperiment
"""
body = request.get_json(force=True)
# Deserialize
try:
se = SequencingExperimentSchema(strict=True).load(body).data
# Request body not valid
except ValidationError as e:
abort(
400, 'could not create sequencing_experiment: {}'.format(
e.messages))
# Add to and save in database
db.session.add(se)
db.session.commit()
return SequencingExperimentSchema(
201, 'sequencing_experiment {} created'.format(
se.kf_id)).jsonify(se), 201
def patch(self, kf_id):
"""
Update an existing sequencing_experiment.
Allows partial update of resource
---
template:
path:
update_by_id.yml
properties:
resource:
SequencingExperiment
"""
se = SequencingExperiment.query.get(kf_id)
if se is None:
abort(
404, 'could not find {} `{}`'.format('sequencing_experiment',
kf_id))
# Partial update - validate but allow missing required fields
body = request.get_json(force=True) or {}
try:
se = (SequencingExperimentSchema(strict=True).load(
body, instance=se, partial=True).data)
except ValidationError as err:
abort(
400, 'could not update sequencing_experiment: {}'.format(
err.messages))
db.session.add(se)
db.session.commit()
return SequencingExperimentSchema(
200, 'sequencing_experiment {} updated'.format(
se.kf_id)).jsonify(se), 200
def get(self, filter_params, after, limit):
"""
Get all sequencing_experiments
---
description: Get all sequencing_experiments
template:
path:
get_list.yml
properties:
resource:
SequencingExperiment
"""
# Get study id and remove from model filter params
study_id = filter_params.pop('study_id', None)
q = (SequencingExperiment.query.filter_by(**filter_params))
# Filter by study
from dataservice.api.participant.models import Participant
from dataservice.api.biospecimen.models import Biospecimen
from dataservice.api.genomic_file.models import GenomicFile
from dataservice.api.biospecimen_genomic_file.models import (
BiospecimenGenomicFile)
if study_id:
q = (q.join(SequencingExperiment.genomic_files).join(
GenomicFile.biospecimen_genomic_files).join(
BiospecimenGenomicFile.biospecimen).join(
Biospecimen.participant).filter(
Participant.study_id == study_id).group_by(
SequencingExperiment.kf_id))
return (SequencingExperimentSchema(many=True).jsonify(
Pagination(q, after, limit)))
def delete(self, kf_id):
"""
Delete sequencing_experiment by id
Deletes a sequencing_experiment given a Kids First id
---
template:
path:
delete_by_id.yml
properties:
resource:
SequencingExperiment
"""
# Check if sequencing_experiment exists
se = SequencingExperiment.query.get(kf_id)
if se is None:
abort(
404, 'could not find {} `{}`'.format('sequencing_experiment',
kf_id))
# Save in database
db.session.delete(se)
db.session.commit()
return SequencingExperimentSchema(
200, 'sequencing_experiment {} deleted'.format(
se.kf_id)).jsonify(se), 200
def get(self, kf_id):
"""
Get a sequencing_experiment by id
---
template:
path:
get_by_id.yml
properties:
resource:
SequencingExperiment
"""
# Get one
se = SequencingExperiment.query.get(kf_id)
if se is None:
abort(404, 'could not find {} `{}`'
.format('sequencing_experiment', kf_id))
return SequencingExperimentSchema().jsonify(se)