def generate_metadata_dataset(study_id, center_id, sample_ids, sample_delim):
mcfg = cm2.get_main_config()
mlog, mlog_handler = cm2.get_logger(cm2.get_client_ip())
process_name = inspect.stack()[1][3]
dataset_name = 'sql_sp_metadata'
if mlog:
mlog.info(
'Processing request from "{}" for generating metadata dataset.'.
format(process_name))
# get the dataset from the database
result, columns, err = rp.get_dataset(mcfg,
mlog,
dataset_name,
study_id=study_id,
center_id=center_id,
sample_ids=sample_ids,
sample_delim=sample_delim)
# check for errors and create an output
if err and not err.exist():
if mlog:
mlog.info(
'Received response from DB, proceeding to render the api response.'
)
cm2.stop_logger(mlog, mlog_handler)
return jsonify(data=result, status=200)
else:
if mlog:
mlog.info('Proceeding to report an error.')
cm2.stop_logger(mlog, mlog_handler)
return jsonify(message='Error retrieving data', status=400)
def generate_view(view_name):
mcfg = cm2.get_main_config()
mlog, mlog_handler = cm2.get_logger(cm2.get_client_ip())
# result = None
# columns = None
# err = None
process_name = inspect.stack()[1][3]
if mlog:
mlog.info(
'Processing request from "{}" for generating "{}" view.'.format(
process_name, view_name))
# get the dataset from the database
result, columns, err = rp.get_veiw_data(mcfg, mlog, view_name)
# check for errors and create an output
if err and not err.exist():
if mlog:
mlog.info(
'Received response from DB, proceeding to render the api response.'
)
cm2.stop_logger(mlog, mlog_handler)
# return jsonify(result), 200
return jsonify(data=result, status=200)
# return json.dumps(result, sort_keys=False)
# {
# 'status': 'OK',
# 'data': json.dumps(result, default=str) # result
# }
else:
mlog.info('Proceeding to report an error.')
cm2.stop_logger(mlog, mlog_handler)
return jsonify(message='Error retrieving data', status=400)
def index():
# verify main app settings and get config and logging references
mcfg = cm2.get_main_config()
# mlog, mlog_handler = cm2.get_logger(cm2.get_client_ip())
env_validated = cm2.check_env_variables(__file__)
if mcfg and env_validated:
request_datetime = datetime.now().strftime("%d/%m/%Y %H:%M:%S")
# if mlog:
# mlog.info('Successful processing of a request, reporting status 200.')
# cm2.stop_logger(mlog, mlog_handler)
r = request
return jsonify(
message='SealfonLab SampleInfo API Up and Running. Date: {}. '
'For more details navigate to {}/api/docs'.format(
request_datetime, request.base_url),
status=200)
else:
# if mlog:
# mlog.info('Errors were reported during validating of environment variables or reading the main config file.')
# cm2.stop_logger(mlog, mlog_handler)
return jsonify(
message=
'SealfonLab SampleInfo API - Errors encountered during retrieving data.',
status=400)
def __init__(self): #, err_obj = None
self.cfg = cm2.get_main_config(
) # ConfigData(gc.MAIN_CONFIG_FILE) # obj_cfg
# self.error = err_obj
self.s_conn = self.prepare_conn_string(
) # self.cfg.get_item_by_key(gc.CFG_DB_CONN).strip()
self.conn = None
def handle_error(error):
code = 500
msg = 'Internal error has occurred'
if isinstance(error, HTTPException):
code = error.code
# url of the request initiated this error
url = request.url
if code == 500:
# if 500 error has occurred, record error in log and send email
# define config and log objects
mcfg = cm2.get_main_config()
mlog, mlog_handler = cm2.get_logger(cm2.get_client_ip())
err = WebError('UNHANDLED ERROR', mcfg, mlog)
_str = 'UNEXPECTED UNHANDLED ERROR "{}" occurred during processing the following URL request: "{}"; ' \
'The original exception that has triggered the error is "{}". ' \
'Here is the traceback: \n{} '.format(
error.name, url, error.original_exception, traceback.format_exc())
err.add_error(_str, code, send_email=True)
if mlog:
mlog.critical(_str)
else:
# just record error in log
msg = error.description
# if mlog:
# mlog.warning('Non-critical error has occurred during processing the following URL request: "{}". '
# 'Code: {}. Error: {}'.format(url, code, error.name))
return jsonify(message=msg, status=code)
def _run_on_start():
# get reference for the main config file
mcfg = cm2.get_main_config()
# get a config value defining if the custom logging should be used
custom_logging = mcfg.get_value('Logging/custom_logging')
if isinstance(custom_logging, bool):
gc.custom_logging = custom_logging
else:
# assign False as a default
gc.custom_logging = False
# start scheduler to delete old log files
scheduler.init_scheduler()
# run first cleaning event on the start up
cm2.clean_log_directory()
def init_scheduler():
app.config.from_object(Scheduler_Config())
mcfg = cm2.get_main_config()
interval_day = mcfg.get_value('Logging/clean_log_frequency_days')
if isinstance(interval_day, int) or isinstance(interval_day, float):
interval_sec = 86400 * interval_day # assign number of days as per config file
else:
interval_sec = 86400 # assign 1 day as default
# define and start scheduler
scheduler = APScheduler()
scheduler.init_app(app)
scheduler.add_job(id='scheduler_clean_log_files',
func=scheduler_clean_log_files,
trigger="interval",
seconds=interval_sec) # 1 day: 86400
scheduler.start()