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 commence_file_io(job_id):
print "DEBUG?? ", "{0}".format(cfront_settings.get("debug_mode", False))
if v: print "commencing file io"
job = Session.query(Job).get(job_id)
Session.add(job)
if len(job.good_spacers) == 0 or job.genome_name != 'hg19':
job.files_failed = True
job.date_failed = datetime.datetime.utcnow()
return
write_f4(job_id)
write_f5_f6(job_id)
if len([f for f in job.files if f["ready"] == False]) == 0:
job.files_ready = True
job.date_completed = datetime.datetime.utcnow()
else:
job.files_failed = True
try:
if job.email_complete:
if (not cfront_settings.get("debug_mode",
False)) and cfront_settings.get(
"mails_on_completion", False):
mail.mail_completed_job(None, job)
except mail.MailError as m:
print "writing mail on complete failed for job {0}".format(job.id)
def add_jobs(data_tsv):
cols = ['id', 'sequence', 'date_submitted', 'genome', 'name', 'email', 'date_completed', 'chr', 'start', 'strand', 'computing_spacers', 'computed_spacers', 'files_computing', 'files_ready', 'email_complete', 'key']
rows = []
with open(data_tsv) as f :
for l in f:
rows.append(dict( zip(cols,[e.strip() for e in l.split('\t')]) ))
with transaction.manager:
for r in rows:
sequence = r["sequence"].upper()
sequence = re.sub("\s","",sequence)
if re.compile("[^AGTC]").search(sequence) is not None:
continue
j = Job(key = r['key'],
name = r["name"],
email = r["email"],
chr = r["chr"],
start = r["start"],
strand = r["strand"],
sequence = sequence,
genome = r["genome"],
email_complete=True if r["email_complete"] else False,
date_submitted = datetime.datetime.utcnow())
Session.add(j)
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 commence_file_io(job_id):
print "DEBUG?? ", "{0}".format( cfront_settings.get("debug_mode",False))
if v: print "commencing file io"
job = Session.query(Job).get(job_id)
Session.add(job)
if len(job.good_spacers) == 0 or job.genome_name != 'hg19':
job.files_failed = True
job.date_failed = datetime.datetime.utcnow()
return
write_f4(job_id)
write_f5_f6(job_id)
if len([f for f in job.files if f["ready"] == False]) == 0:
job.files_ready = True
job.date_completed = datetime.datetime.utcnow()
else:
job.files_failed = True
try:
if job.email_complete:
if (not cfront_settings.get("debug_mode",False)) and cfront_settings.get("mails_on_completion",False):
mail.mail_completed_job(None, job)
except mail.MailError as m:
print "writing mail on complete failed for job {0}".format(job.id)
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:
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
