def process_queue(ofs, stride):
# start a transaction to compute spacers for any jobs which lack them
# NOTE this is the second place in our code where spacers can be created
# this should be fixed as we don't do the same checks here that we do in
# the first -- at views_ajax/post_new.
#
# here we protect against the case where no spacers pass but don't do
# any checking of the input query.
possible_spacer_jobs = Session.query(Job).filter(Job.computed_spacers == False).all()
selected_jobs = [j for j in possible_spacer_jobs if j.id % stride == ofs and j.genome_name != "rn5"]
for j in selected_jobs[:100]:
with transaction.manager:
try:
print "computing spacers {0}".format(j.id)
spacer_infos = webserver_db.compute_spacers(j.sequence)
if (len(spacer_infos)) == 0:
raise JobERR(Job.NOSPACERS, j)
for spacer_info in spacer_infos:
Session.add(Spacer(job=j, **spacer_info))
j.computed_spacers = True
Session.add(j)
except JobERR, e:
print "Excepted a job error during Spacer finding for Job: {0}".format(j.id)
print j.sequence
def process_queue(ofs, stride):
# start a transaction to compute spacers for any jobs which lack them
# NOTE this is the second place in our code where spacers can be created
# this should be fixed as we don't do the same checks here that we do in
# the first -- at views_ajax/post_new.
#
#here we protect against the case where no spacers pass but don't do
# any checking of the input query.
possible_spacer_jobs = Session.query(Job).filter(
Job.computed_spacers == False).all()
selected_jobs = [
j for j in possible_spacer_jobs
if j.id % stride == ofs and j.genome_name != "rn5"
]
for j in selected_jobs[:100]:
with transaction.manager:
try:
print 'computing spacers {0}'.format(j.id)
spacer_infos = webserver_db.compute_spacers(j.sequence)
if (len(spacer_infos)) == 0:
raise JobERR(Job.NOSPACERS, j)
for spacer_info in spacer_infos:
Session.add(Spacer(job=j, **spacer_info))
j.computed_spacers = True
Session.add(j)
except JobERR, e:
print "Excepted a job error during Spacer finding for Job: {0}".format(
j.id)
print j.sequence
def process_queue(ofs, stride):
possible_spacer_jobs = Session.query(Job).filter(Job.computed_spacers == False).all()
selected_jobs = possible_spacer_jobs
for j in selected_jobs[:100]:
with transaction.manager:
try:
print 'computing spacers {0}'.format(j.id)
spacer_infos = webserver_db.compute_spacers(j.sequence)
if(len(spacer_infos)) == 0:
raise JobERR(Job.NOSPACERS, j)
for spacer_info in spacer_infos:
Session.add(Spacer(job = j,**spacer_info))
j.computed_spacers = True
Session.add(j)
print j.id
except JobERR, e:
if e.message == Job.NOSPACERS:
print "No spacers in JOB ID: {0}".format(j.id)
elif e.message == Job.ERR_INVALID_CHARACTERS:
print e.message
else:
print "Excepted a job error during Spacer finding for Job: {0}".format(j.id)
print j.id
print j.sequence
raise e
def process_queue(ofs, stride):
possible_spacer_jobs = Session.query(Job).filter(Job.computed_spacers == False).all()
selected_jobs = possible_spacer_jobs
for j in selected_jobs[:100]:
with transaction.manager:
try:
print 'computing spacers {0}'.format(j.id)
spacer_infos = webserver_db.compute_spacers(j.sequence)
if(len(spacer_infos)) == 0:
raise JobERR(Job.NOSPACERS, j)
for spacer_info in spacer_infos:
Session.add(Spacer(job = j,**spacer_info))
j.computed_spacers = True
Session.add(j)
print j.id
except JobERR, e:
if e.message == Job.NOSPACERS:
j.failed = True
j.computed_spacers = True
Session.add(j)
print "No spacers in JOB ID: {0}".format(j.id)
elif e.message == Job.ERR_INVALID_CHARACTERS:
j.failed = True
j.computed_spacers = True
Session.add(j)
print e.message
else:
print "Excepted a job error during Spacer finding for Job: {0}".format(j.id)
j.failed = True
Session.add(j)
print j.id
print j.sequence
raise e