def add_samples(body):
"""
Creates a new sample following the Sample schema,
only adding Sample level information.
:param body: POST request body
:type body: object
:returns: message, 201 on success, error code on failure
:rtype: object, int
.. note::
Refer to the OpenAPI Spec for a proper schemas of Sample objects.
"""
db_session = get_session()
print(body)
if not body.get("patient_id"):
err = dict(message="No patient_id provided", code=400)
return err, 400
if not body.get("sample_id"):
err = dict(message="No sample_id provided", code=400)
return err, 400
if not body.get("description"):
err = dict(message="No description provided", code=400)
return err, 400
body["created"] = datetime.datetime.utcnow()
try:
orm_sample = Sample(**body)
except TypeError as e:
err = _report_conversion_error("sample", e, **body)
return err, 400
try:
db_session.add(orm_sample)
db_session.commit()
except exc.IntegrityError as ie:
if ie.args[0].find("FOREIGN KEY constraint failed"):
db_session.rollback()
err = _report_foreign_key("sample: " + body["sample_id"], **body)
return err, 400
db_session.rollback()
err = _report_object_exists("sample: " + body["sample_id"], **body)
return err, 400
except ORMException as e:
db_session.rollback()
err = _report_write_error("sample", e, **body)
return err, 500
return {"code": 201, "message": "Sample successfully added"}, 201
def add_segments(body):
"""
Creates a new CNV following the CNV schema attached to an
existing sample.
:param body: POST request body
:type body: object
:returns: message, 201 on success, error code on failure
:rtype: object, int
.. note::
Refer to the OpenAPI Spec for a proper schemas of CNV objects.
"""
db_session = get_session()
if not body.get("patient_id"):
err = dict(message="No patient_id provided", code=400)
return err, 400
if not body.get("sample_id"):
err = dict(message="No sample_id provided", code=400)
return err, 400
segments = body["segments"]
for segment in segments:
segment["sample_id"] = body["sample_id"]
print(segment)
try:
orm_segment = CNV(**segment)
except TypeError as e:
err = _report_conversion_error("segment", e, **body)
return err, 400
try:
db_session.add(orm_segment)
db_session.commit()
except exc.IntegrityError as ie:
if ie.args[0].find("FOREIGN KEY constraint failed"):
db_session.rollback()
err = _report_foreign_key("segment: " + body["sample_id"],
**body)
return err, 400
db_session.rollback()
err = _report_object_exists("segment: " + body["sample_id"],
**body)
return err, 400
except ORMException as e:
db_session.rollback()
err = _report_write_error("segment", e, **body)
return err, 500
return {"code": 201, "message": "Segments successfully added"}, 201
def get_patients():
"""
Return all individuals
"""
db_session = get_session()
try:
q = db_session.query(Patient)
except orm.ORMException as e:
err = _report_search_failed("patient", e, patient_id="all")
return err, 500
patient_ids_dict = [orm.dump(p) for p in q]
return [d["patient_id"] for d in patient_ids_dict], 200
def get_samples(patient_id, tags=None, description=None):
"""
Return samples of a patient.
:param patient_id: Id of patient
:type patient_id = string
:param tags: List of tags
:type tags: list
:returns: samples, 200 on sucess, error code on failure
:rtype: object, int
"""
db_session = get_session()
if not patient_id:
err = dict(message="No patient_id provided", code=400)
return err, 400
try:
q = db_session.query(Sample).filter_by(patient_id=patient_id)
if tags:
q = q.filter(or_(*[Sample.tags.contains(tag) for tag in tags]))
if description:
q = q.filter(Sample.description.contains(description))
except orm.ORMException as e:
err = _report_search_failed("sample", e, patient_id=patient_id)
return err, 500
response = {}
dump = [orm.dump(p) for p in q]
for d in dump:
response["patient_id"] = d["patient_id"]
samples = response.get("samples", [])
samples_dict = dict(sample_id=d["sample_id"])
if d.get("tags"):
samples_dict["tags"] = d["tags"]
samples_dict["created"] = d["created"]
samples_dict["description"] = d["description"]
samples.append(samples_dict)
response["samples"] = samples
return response, 200
def add_patients(body):
"""
Creates a new patient following the Patient schema,
only adding Patient level information.
:param body: POST request body
:type body: object
:returns: message, 201 on success, error code on failure
:rtype: object, int
.. note::
Refer to the OpenAPI Spec for a proper schemas of Patient objects.
"""
db_session = get_session()
try:
orm_patient = Patient(patient_id=body.get("patient_id"))
except TypeError as e:
err = _report_conversion_error("patient", e, **body)
return err, 400
try:
db_session.add(orm_patient)
db_session.commit()
except exc.IntegrityError:
db_session.rollback()
err = _report_object_exists("patient: " + body["patient_id"], **body)
return err, 400
except ORMException as e:
db_session.rollback()
err = _report_write_error("patient", e, **body)
return err, 500
return {"code": 201, "message": "Patient successfully added"}, 201
def get_segments(patient_id, sample_id, chromosome_number, start_position,
end_position):
"""
Return segments within the specified region
:param: patient_id: Id of patient
:type: string
:param: sample_id: Id of sample
:type: string
:param: chromosome_number: Chromosome number
:type: string
:param: start_position: Start position
:type: integer
:param: end_position: End position
:type: integer
:returns: segments, 200 on sucess, error code on failure
:rtype: object, int
"""
db_session = get_session()
try:
validate_uuid_string("patient_id", str(patient_id))
except IdentifierFormatError as e:
err = _report_search_failed(
"cnv",
e,
patient_id=patient_id,
)
return err, 500
if isinstance(sample_id, int):
sample_id = str(sample_id)
if isinstance(chromosome_number, int):
chromosome_number = str(chromosome_number)
try:
q = (db_session.query(CNV).join(Sample).filter(
CNV.chromosome_number == chromosome_number,
Sample.sample_id == sample_id,
Sample.patient_id == patient_id,
))
except orm.ORMException as e:
err = _report_search_failed(
"cnv",
e,
patient_id=patient_id,
sample_id=sample_id,
chromosome_number=chromosome_number,
)
return err, 400
response = []
segments = [orm.dump(p) for p in q]
for segment in segments:
if ((segment["start_position"] >= start_position
and segment["end_position"] <= end_position)
or (segment["start_position"] <= start_position <=
segment["end_position"])
or (segment["start_position"] <= end_position <=
segment["end_position"])
or (start_position <= segment["start_position"]
and segment["end_position"] <= end_position)):
del segment["sample_id"]
response.append(segment)
print(response)
return response, 200