for cseq in amp.cached_sequences:
job_queue.add(JOB_ID_PROCESS_SNPS, ProcessSNPMessage(cached_sequence_id=cseq.id),
parent_job=job.parent)
job_queue.finish(job, None)
class AmpliconWorker(PasterDaemonContextProcess):
def run(self, config_path, as_daemon=False):
global process_assay_job, process_amplicon_job
mgr = get_manager(config_path)
jobqueue = mgr.jobqueue()
sequence_source = mgr.sequence_source()
tm_calc = mgr.tm_calc(mgr)
dg_calc = mgr.dg_calc(mgr)
# does the thread knock it out?
assay_thread = LogExcRepeatedThread(10, process_assay_job, LOGGER_NAME, jobqueue, tm_calc, dg_calc)
sequence_thread = LogExcRepeatedThread(15, process_amplicon_job, LOGGER_NAME, jobqueue, sequence_source, dg_calc)
if as_daemon:
assay_thread.daemon = True
sequence_thread.daemon = True
assay_thread.start()
sequence_thread.start()
if __name__ == "__main__":
worker = PasterLikeProcess('amplicons.pid')
worker.run(AmpliconWorker)
logger.exception("Error from Reprocess worker [job %s]: Non-zero result status (%d)" % job.id, result )
job_queue.abort(job, JSONErrorMessage("Unable add to qtools: Non-zero result status (%d)" % result))
continue
# this is key; otherwise, the SQL connection pool will be sucked up.
Session.close()
class ReprocessWorker(PasterDaemonContextProcess):
def run(self, config_path, as_daemon=False):
global process_reprocess_job
mgr = get_manager(config_path)
jobqueue = mgr.jobqueue()
config = mgr.pylons_config
# TODO add as runtime argument
reprocess_thread = LogExcRepeatedThread(10, process_reprocess_job, LOGGER_NAME, jobqueue, config )
if as_daemon:
reprocess_thread.daemon = True
reprocess_thread.start()
if __name__ == "__main__":
worker = PasterLikeProcess('reprocess.pid')
worker.run(ReprocessWorker)
start = snp['chromStart']
else:
start = snp['chromStart']+1
end = snp['chromEnd']
message = ProcessSNPAmpliconMessage(sequence_group_id, chromosome, start, end)
job_queue.add(JOB_ID_PROCESS_SNP_AMPLICON, message, parent_job=job)
# TODO: need to be in transaction?
job_queue.progress(job)
Session.close()
class SNPWorker(PasterDaemonContextProcess):
def run(self, config_path, as_daemon=False):
global process_snp_job
snp_table = 'snp131'
mgr = get_manager(config_path)
jobqueue = mgr.jobqueue()
# TODO add as runtime argument
snp_source = mgr.snp_source(snp_table='snp131')
snp_thread = LogExcRepeatedThread(10, process_snp_job, LOGGER_NAME, jobqueue, snp_source, snp_table)
if as_daemon:
snp_thread.daemon = True
snp_thread.start()
if __name__ == "__main__":
worker = PasterLikeProcess('snps.pid')
worker.run(SNPWorker)
