def get_sample_details(request_id, sample_id, analysis_id):
"""
swag_from_file: sbs/swagger/sbs_get_individual_sample.yml
"""
params = {}
if not request_id:
return create_json_response(ERROR, REQUIRED_FIELD_REQUEST_ID)
if not sample_id:
return create_json_response(ERROR, REQUIRED_FIELD_SAMPLE_ID)
if not analysis_id:
return create_json_response(ERROR, REQUIRED_FIELD_ANALYSIS_ID)
filter_type = request.args.get('filter_type')
role = user_svc.get_current_user_role_by_access_token()
params['request_id'] = request_id
params['sample_id'] = sample_id
params['analysis_id'] = analysis_id
params['filter_type'] = filter_type
params['role'] = role
try:
result = sample_svc.get_sample_details(params)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, result)
def add_observed_maps():
"""
swag_from_file: sbs/swagger/sbs_post_observed_map_multiple.yml
"""
params = request.get_json(force=True)
request_maps = params['request_maps']
status_list = []
if request_maps:
for request_map_dict in request_maps:
if request_map_dict:
sample_id = request_map_dict['sample_id']
analysis_id = request_map_dict['analysis_id']
map_id = request_map_dict['map_id']
if not sample_id:
return create_json_response(ERROR,
REQUIRED_FIELD_SAMPLE_ID)
if not analysis_id:
return create_json_response(ERROR,
REQUIRED_FIELD_ANALYSIS_ID)
if not map_id:
return create_json_response(ERROR, REQUIRED_FIELD_MAP_ID)
obs_params = {}
obs_params['sample_id'] = sample_id
obs_params['analysis_id'] = analysis_id
obs_params['map_id'] = map_id
try:
status = observed_map_svc.add_observed_map(
obs_params).as_dict()
status_list.append(status)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, status_list)
def get_observed_maps(analysis_id):
"""
swag_from_file: sbs/swagger/sbs_get_observed_maps.yml
"""
if not analysis_id:
return create_json_response(ERROR, REQUIRED_FIELD_ANALYSIS_ID)
try:
result = observed_map_svc.get_observed_maps(analysis_id)
except Exception as e:
logger.error('An error occurred: {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, result)
def delete_sample(sample_id):
"""
swag_from_file: sbs/swagger/sbs_delete_samples.yml
"""
if not sample_id:
return create_json_response(ERROR, REQUIRED_FIELD_SAMPLE_ID)
try:
response = sample_svc.delete_sample(sample_id)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, response)
def update_sample(sample_id):
"""
swag_from_file: sbs/swagger/sbs_put_samples.yml
"""
params = request.get_json(force=True)
params['sample_id'] = sample_id
try:
response = sample_svc.update_sample(params).as_dict()
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, response)
def delete_observed_map(observed_map_id):
"""
swag_from_file: sbs/swagger/sbs_delete_observed_map.yml
"""
if not observed_map_id:
return create_json_response(ERROR,
"Observed Map Id is a required filed")
try:
observed_map_svc.delete_observed_map(observed_map_id)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, None)
def add_sample():
"""
swag_from_file: sbs/swagger/sbs_post_samples.yml
"""
params = request.get_json(force=True)
if 'request_id' not in params or not params['request_id']:
return create_json_response(ERROR, REQUIRED_FIELD_REQUEST_ID)
if 'sample_id' not in params or not params['sample_id']:
return create_json_response(ERROR, REQUIRED_FIELD_SAMPLE_ID)
try:
response = sample_svc.add_sample(params).as_dict()
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, response)
def get_observed_map_comment(observed_map_id):
"""
swag_from_file: sbs/swagger/sbs_get_observed_map_comments.yml
"""
if not observed_map_id:
return create_json_response(ERROR, REQUIRED_FIELD_OBSERVED_MAP_ID)
try:
result = observed_map_svc.get_observed_map_comment(observed_map_id)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
result_list = []
for observed_map_comment in result:
result_list.append(observed_map_comment.as_dict())
return create_json_response(SUCCESS, result_list)
def add_observed_map_comment(observed_map_id):
"""
swag_from_file: sbs/swagger/sbs_post_observed_map_comments.yml
"""
if not observed_map_id:
return create_json_response(ERROR, REQUIRED_FIELD_OBSERVED_MAP_ID)
params = request.get_json(force=True)
params['username'] = get_username()
if 'comment' not in params or not params['comment']:
return create_json_response(ERROR, REQUIRED_FIELD_COMMENT)
try:
result = observed_map_svc.add_observed_map_comments(
observed_map_id, params)
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, result)
def add_observed_map(sample_id, analysis_id, map_id):
"""
swag_from_file: sbs/swagger/sbs_post_observed_map.yml
"""
params = request.get_json(force=True)
if not sample_id:
return create_json_response(ERROR, REQUIRED_FIELD_SAMPLE_ID)
if not analysis_id:
return create_json_response(ERROR, REQUIRED_FIELD_ANALYSIS_ID)
if not map_id:
return create_json_response(ERROR, REQUIRED_FIELD_MAP_ID)
params['sample_id'] = sample_id
params['analysis_id'] = analysis_id
params['map_id'] = map_id
try:
result = observed_map_svc.add_observed_map(params).as_dict()
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
return create_json_response(SUCCESS, result)
def change_tier():
"""
swag_from_file: sbs/swagger/sbs_put_change_tier.yml
"""
result = ""
params = request.get_json(force=True)
if 'variation_list' not in params or not params['variation_list']:
create_json_response(ERROR, REQUIRED_FIELD_VARIATION_LIST)
try:
result = variation_svc.batch_update_tier(params['variation_list'])
except Exception as e:
logger.error('An error occurred : {}'.format(str(e)))
return create_json_response(ERROR, e)
if result:
for variation in result:
variation['is_tier_label_updated'] = "true" if \
variation['is_tier_label_updated'] else "false"
return create_json_response(SUCCESS, result)