def mp_process_assays(settings, batch_id, login, user_id, ns):
""" this function will be started in different process, so it must initialize
everything from scratch, including database connection
"""
pid = os.getpid()
cerr('mp_process_assays()[%d]: connecting to db' % pid)
dbh = get_dbhandler_notsafe()
if dbh is None:
dbh = get_dbhandler(settings)
dbh.session().global_user = dbh.get_user(user_id)
cerr('mp_process_assays()[%d]: processing...' % pid)
result = process_assays(batch_id, login, ns)
dbh.session().global_user = None
return result
def mp_run_callback( settings, callback, params, user, mode, ns=None):
""" run analyis """
if ns:
ns.start_time = int(time())
ns.status = 'R'
ns.msg = 'Processing...'
ns.cerr += 'mp_run_callback(): connecting to db...\n'
dbh = get_dbhandler_notsafe()
if dbh is None:
dbh = get_dbhandler(settings)
# user authorization should be performed by Query
q = Query( params, dbh )
# callback needs to return result (a dictionary object)
# { 'custom': data, 'options': options,
# 'html': html_or_None, 'jscode': jscode_or_None }
if ns:
ns.cerr += 'mp_run_callback(): processing callback...\n'
result = callback( q, user )
if type(result) != dict:
return result
#result['sample_filtering'] = sample_summary( q.get_sample_summary(mode))
#result['marker_filtering'] = marker_summary( q )
result['sample_filtering'] = format_sample_summary( q.get_sample_summary(mode) )
result['marker_filtering'] = format_marker_summary( q )
if ns:
ns.finish_time = int(time())
ns.status = 'D'
ns.msg = 'Finished...'
ns.cerr += 'mp_run_callback(): callback finished...\n'
return result
