def mutate(self, args, context, info):
index = args.get('index')
name = args.get('name')
sample_group_id = args.get('sample_group_id')
plant = PlantModel(index, name, sample_group_id)
try:
db.session.add(plant)
db.session.flush()
except IntegrityError as err:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
except DBAPIError:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
db.session.commit()
return CreatePlant(id=plant.id,
index=plant.index,
name=plant.name,
sample_group_id=plant.sample_group_id)
def mutate(self, args, context, info):
exp_data = args.get('experiment_data')
sample_group_data = exp_data.get('sample_group_data')
try:
experiment = ExperimentModel(
exp_data.get('name'), exp_data.get('description'),
exp_data.get('scientist'), exp_data.get('group_name'),
exp_data.get('start_date'),
exp_data.get('start_of_experimentation'))
db.session.add(experiment)
db.session.flush()
for group_data in sample_group_data:
group = SampleGroupModel.fromdict(group_data, experiment.id)
db.session.add(group)
db.session.flush()
for plant_data in group_data.get('plants'):
plant = PlantModel(plant_data.get('index'),
plant_data.get('name'), group.id)
db.session.add(plant)
except DBAPIError as err:
#TODO add unique constraint checks
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
db.session.commit()
return ConstructExperiment(
id=to_global_id('Experiment', experiment.id))
def mutate(self, args, context, info):
identity = get_jwt_identity()
proj_data = args.get('project_data')
_, exp_id = from_global_id(proj_data.pop('id'))
with db.session.no_autoflush:
try:
experiment = db.session.query(ExperimentModel).get(exp_id)
if experiment.scientist == identity.get(
'username') or is_admin(identity):
EditProject._edit_experiment(proj_data, experiment)
else:
raise ForbiddenActionError(
"Unable to edit experiment {} by user {}. Insufficient privileges."
.format(experiment.name, identity.get('username')),
identity.get('username'))
# User is not allowed to edit this project
db.session.commit()
return EditProject(experiment=experiment)
except IntegrityError as err:
db.session.rollback()
#TODO add experiment name constraint
if err.orig.diag.constraint_name == u'uq_sample_groups_treatment_experiment_id':
raise ConstraintViolationError(
'It is not allowed to have two sample groups with the same '
'treatment.')
elif err.orig.diag.constraint_name == u'sample_group_name_experiment_id_key':
raise ConstraintViolationError(
'It is not allowed to have two sample groups with the same '
'name.')
except DBAPIError as err:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
def mutate(self, args, context, info):
plant_id = args.get('plant_id')
_, plant_db_id = from_global_id(plant_id)
plant = db.session.query(PlantModel).get(plant_db_id)
experiment_id = plant.sample_group.experiment_id
timestamp, created = TimestampModel.get_or_create(experiment_id)
snapshot = SnapshotModel(plant_id=plant_db_id,
timestamp_id=timestamp.id,
camera_position=args.get('camera_position'),
measurement_tool=args.get('measurement_tool'),
phenobox_id=args.get('phenobox_id'))
try:
db.session.add(snapshot)
db.session.flush()
except IntegrityError as err:
db.session.rollback()
if err.orig.diag.constraint_name == u'uq_snapshot_plant_id_timestamp_id':
raise ConflictingDataError(
'There already exists a snapshot for this plant and timestamp'
)
except DBAPIError as err:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
db.session.commit()
return CreateSnapshot(id=to_global_id('Snapshot', snapshot.id),
timestamp_id=to_global_id(
'Timestamp', timestamp.id),
new_timestamp=created)
def mutate(self, args, context, info):
ql_id = args.get('id')
_, id = from_global_id(ql_id)
try:
db.session.delete(db.session.query(PostprocessModel).get(id))
db.session.commit()
except DBAPIError:
logging.getLogger(__name__).exception("An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
return DeletePostprocess(id=ql_id)
def mutate(self, args, context, info):
try:
timestamp_id = args.get('timestamp_id')
_, timestamp_db_id = from_global_id(timestamp_id)
timestamp = db.session.query(TimestampModel).get(timestamp_db_id)
setattr(timestamp, 'completed', True)
db.session.flush()
db.session.commit()
return CompleteTimestamp(id=timestamp_id)
except DBAPIError:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
def mutate(self, args, context, info):
ql_id = args.get('id')
_, db_id = from_global_id(ql_id)
snapshot = db.session.query(SnapshotModel).get(db_id)
if snapshot is None:
return # Exception to indicate this entry does not exist
try:
snapshot.purge()
except DBAPIError as err:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
return DeleteSnapshot(id=ql_id)
def mutate(self, args, context, info):
sample_group = SampleGroupModel.fromdict(args.get('group_data'), args.get('experiment_id'))
try:
db.session.add(sample_group)
db.session.flush()
except IntegrityError as err:
logging.getLogger(__name__).exception("An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
db.session.commit()
return CreateSampleGroup(id=sample_group.id, name=sample_group.name, treatment=sample_group.treatment,
description=sample_group.description,
species=sample_group.speciesm, genotype=sample_group.genotype,
variety=sample_group.variety,
growth_conditions=sample_group.growth_conditions, is_control=sample_group.is_control,
experiment_id=sample_group.experiment_id)
def mutate(self, args, context, info):
snapshot_id = args.get('snapshot_id')
_, snapshot_db_id = from_global_id(snapshot_id)
try:
snapshot = db.session.query(SnapshotModel).get(snapshot_db_id)
snapshot.excluded = args.get('exclude')
db.session.add(snapshot)
db.session.flush()
except DBAPIError as err:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
db.session.commit()
return ChangeSnapshotExclusion(id=snapshot_id,
excluded=args.get('exclude'))
def mutate(self, args, context, info):
ql_id = args.get('id')
_, id = from_global_id(ql_id)
try:
experiment = db.session.query(ExperimentModel).get(id)
if len(experiment.timestamps) > 0:
raise UnableToDeleteError(
"Experiment could not be deleted because there are timestamps associated with it"
)
db.session.delete(experiment)
db.session.commit()
except DBAPIError as err:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
return DeleteExperiment(id=ql_id)
def mutate(self, args, context, info):
name = args.get('name')
description = args.get('description')
scientist = args.get('scientist')
group_name = args.get('group_name')
experiment = ExperimentModel(name, description, scientist, group_name)
try:
db.session.add(experiment)
db.session.flush()
except DBAPIError as err:
logging.getLogger(__name__).exception(
"An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
db.session.commit()
return CreateExperiment(id=experiment.id,
name=experiment.name,
description=experiment.description,
scientist=experiment.scientist,
group_name=group_name)
def mutate(self, args, context, info):
snapshot_id = args.get('snapshot_id')
_, snapshot_db_id = from_global_id(snapshot_id)
t = args.get('type')
if t is not None and t.strip() == '':
t = None
image = ImageModel(snapshot_id=snapshot_db_id, path=args.get('path'), filename=args.get('filename'),
angle=args.get('angle'),
image_type=t)
try:
db.session.add(image)
db.session.flush()
except IntegrityError as err:
print(err.message)
db.session.rollback()
raise ConflictingDataError("Image already exists")
except DBAPIError:
logging.getLogger(__name__).exception("An unexpected DB error occured")
db.session.rollback()
raise UnknownDataError("An unexpected DB error occured")
db.session.commit()
return AddImage(id=to_global_id('Image', image.id))