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 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 init_env(p):
global redis_key
env = bootstrap(p)
redis_key = "cfront-{0}:job:hits".format("dev" if cfront_settings.get("debug_mode",False) else "prod")
redis_key = "cfront-{0}:job:hits".format("dev" if cfront_settings.get("debug_mode",False) else "prod")
def __init__(self, request):
print cfront_settings.get("maintenance_mode", False)
if "job_key" in request.matchdict:
set_request_job(request)
if cfront_settings.get("maintenance_mode", False):
if not "sorry" in request.url:
raise exc.HTTPFound(request.route_url("maintainance"))
def __init__(self,request):
print cfront_settings.get("maintenance_mode", False)
if "job_key" in request.matchdict:
set_request_job(request)
if cfront_settings.get("maintenance_mode", False):
if not "sorry" in request.url:
raise exc.HTTPFound(request.route_url("maintainance"))
def spacer_retrieve_regions(request):
import twobitreader
spacer_id = request.matchdict['spacer_id']
spacer= Session.query(Spacer).get(spacer_id)
genome = spacer.job.genome_name
genome_root = cfront_settings.get("gfport_root")
genome_path = os.path.join(genome_root,"{0}.2bit".format(spacer.job.genome_name))
print genome_path
print "CHECK THIS CODE!!"
tbf = twobitreader.TwoBitFile(genome_path)
hits = spacer.hits
return [{"sequence":tbf.get(h.chr)[h.start:h.start+100]} for h in hits[:100]]
def spacer_retrieve_regions(request):
import twobitreader
spacer_id = request.matchdict['spacer_id']
spacer = Session.query(Spacer).get(spacer_id)
genome = spacer.job.genome_name
genome_root = cfront_settings.get("gfport_root")
genome_path = os.path.join(genome_root,
"{0}.2bit".format(spacer.job.genome_name))
print genome_path
print "CHECK THIS CODE!!"
tbf = twobitreader.TwoBitFile(genome_path)
hits = spacer.hits
return [{
"sequence": tbf.get(h.chr)[h.start:h.start + 100]
} for h in hits[:100]]
def job_post_new(request):
sequence = request.params["query"].upper()
sequence = re.sub("\s","",sequence)
if cfront_settings.get("debug_mode",False): print sequence
if re.compile("[^AGTCN]").search(sequence) is not None:
return {"status":"error",
"message":"Ambiguous or invalid characters found in input sequene.",
"matches":None,
"job_key":None}
if len(sequence)<23 or len(sequence) > 250 :
return {"status":"error",
"message":"Sequence length not within allowed range (23 - 250bp)",
"matches":None,
"job_key":None}
genome = request.params.get("genome","hg19")
matches = webserver_db.check_genome(sequence,genome)
infos = webserver_db.compute_spacers(sequence)
if cfront_settings.get("debug_mode",False): print "lmatches: {0}".format(len(matches))
if cfront_settings.get("debug_mode",False): print "linfos: {0}".format(len(infos))
print request.params.get("inputRadios")
if ( request.params.get("inputRadios",None) == "unique_genomic" ) and len(matches) == 0:
raise JobERR(Job.ERR_NOGENOME,None)
if request.params.get("inputRadios",None) == "unique_genomic" and len(matches) > 1:
raise JobERR(Job.ERR_MULTIPLE_GENOME,None)
elif len(infos) == 0:
raise JobERR(Job.NOSPACERS,None)
else:
params = dict(date_submitted = datetime.datetime.utcnow(),
sequence = sequence,
name = request.params["name"],
email = request.params["email"],
genome = Job.GENOMES[genome],
query_type = request.params.get("inputRadios"))
if len(matches) > 0:
params.update(dict(chr=matches[0]["tName"],
start=matches[0]["tStart"],
strand=1 if matches[0]["strand"] == "+" else -1))
if "key" in request.params:
params["key"] = request.params.get("key")
job = Job(**params)
Session.add(job)
for spacer_info in infos:
Session.add(Spacer(job = job,**spacer_info))
job.computed_spacers = True
Session.flush()
mail.mail_new_job(request,job)
return {"status":"success",
"message":None,
"job_key":job.key}
def job_from_spacers(request):
spacer_lines = request.params["query"].strip().splitlines()
spacer_row_lists = [re.compile("\s+").split(l.strip()) for l in spacer_lines]
spacers = [dict(sequence = rl[0].upper(),
strand_input = rl[2] if len(rl) > 2 else "+",
name = rl[1] if len(rl) > 1 else None) for rl in spacer_row_lists]
#checks input for strand and sequence
for i,s in enumerate(spacers):
if s["strand_input"] == "+":
s["strand"] = 1
elif s["strand_input"] == "-":
s["strand"] = -1
else:
raise JobERR(Job.ERR_BADINPUT + "unrecognized character for strand ({0})".format(s["strand_input"]),None)
strand = s["strand"]
seq = s["sequence"]
if s["strand"] == 1:
if len(seq) != 23 or (seq[-2:] != "AG" and seq[-2:] != "GG"):
raise JobERR(Job.ERR_BADINPUT + " no forward strand guide found in sequence {0}: {1}"\
.format(i,s["sequence"]),None)
else:
if len(seq) != 23 or (seq[:2] != "CT" and seq[:2] != "CC"):
raise JobERR(Job.ERR_BADINPUT + " no reverse strand guide found in sequence {0}: {1}"\
.format(i,s["sequence"]),None)
job_sequence = ""
spacer_infos = []
for i,s in enumerate(spacers):
job_sequence += "NN"
si = dict(name = s["name"],
sequence = s["sequence"],
position = len(job_sequence),
strand = s["strand"])
if len(s["sequence"]) != 23:
raise JobERR(Job.BADSPACER_LENGTH,None)
spacer_infos.append(si)
job_sequence += si["sequence"]
job_sequence += "NN"
if cfront_settings.get("debug_mode",False): print job_sequence
if re.compile("[^AGTCN]").search(job_sequence) is not None:
return {"status":"error",
"message":"Ambiguous or invalid characters found in input sequene.",
"matches":None,
"job_key":None}
if len(job_sequence) > 500 :
return {"status":"error",
"message":"Sequence length not within allowed range (23 - 500bp)",
"matches":None,
"job_key":None}
print "GENOME: {0}".format(request.params.get("genome","hg19"))
if len(spacer_infos) == 0:
raise JobERR(Job.NOSPACERS,None)
else:
params = dict(date_submitted = datetime.datetime.utcnow(),
sequence = job_sequence,
genome = Job.GENOMES[request.params.get("genome","hg19")],
name = request.params["name"],
email = request.params["email"],
twostrand = False,
query_type = "guides_list")
if "key" in request.params:
params["key"] = request.params.get("key")
job = Job(**params)
Session.add(job)
for spacer_info in spacer_infos:
Session.add(Spacer(job = job,**spacer_info))
job.computed_spacers = True
Session.flush()
mail.mail_new_job(request,job)
return {"status":"success",
"message":None,
"job_key":job.key}
def job_post_new(request):
sequence = request.params["query"].upper()
sequence = re.sub("\s", "", sequence)
if cfront_settings.get("debug_mode", False): print sequence
if re.compile("[^AGTCN]").search(sequence) is not None:
return {
"status": "error",
"message":
"Ambiguous or invalid characters found in input sequene.",
"matches": None,
"job_key": None
}
if len(sequence) < 23 or len(sequence) > 250:
return {
"status": "error",
"message": "Sequence length not within allowed range (23 - 250bp)",
"matches": None,
"job_key": None
}
genome = request.params.get("genome", "hg19")
matches = webserver_db.check_genome(sequence, genome)
infos = webserver_db.compute_spacers(sequence)
if cfront_settings.get("debug_mode", False):
print "lmatches: {0}".format(len(matches))
if cfront_settings.get("debug_mode", False):
print "linfos: {0}".format(len(infos))
print request.params.get("inputRadios")
if (request.params.get("inputRadios", None)
== "unique_genomic") and len(matches) == 0:
raise JobERR(Job.ERR_NOGENOME, None)
if request.params.get("inputRadios",
None) == "unique_genomic" and len(matches) > 1:
raise JobERR(Job.ERR_MULTIPLE_GENOME, None)
elif len(infos) == 0:
raise JobERR(Job.NOSPACERS, None)
else:
params = dict(date_submitted=datetime.datetime.utcnow(),
sequence=sequence,
name=request.params["name"],
email=request.params["email"],
genome=Job.GENOMES[genome],
query_type=request.params.get("inputRadios"))
if len(matches) > 0:
params.update(
dict(chr=matches[0]["tName"],
start=matches[0]["tStart"],
strand=1 if matches[0]["strand"] == "+" else -1))
if "key" in request.params:
params["key"] = request.params.get("key")
job = Job(**params)
Session.add(job)
for spacer_info in infos:
Session.add(Spacer(job=job, **spacer_info))
job.computed_spacers = True
Session.flush()
mail.mail_new_job(request, job)
return {"status": "success", "message": None, "job_key": job.key}
def job_from_spacers(request):
spacer_lines = request.params["query"].strip().splitlines()
spacer_row_lists = [
re.compile("\s+").split(l.strip()) for l in spacer_lines
]
spacers = [
dict(sequence=rl[0].upper(),
strand_input=rl[2] if len(rl) > 2 else "+",
name=rl[1] if len(rl) > 1 else None) for rl in spacer_row_lists
]
#checks input for strand and sequence
for i, s in enumerate(spacers):
if s["strand_input"] == "+":
s["strand"] = 1
elif s["strand_input"] == "-":
s["strand"] = -1
else:
raise JobERR(
Job.ERR_BADINPUT +
"unrecognized character for strand ({0})".format(
s["strand_input"]), None)
strand = s["strand"]
seq = s["sequence"]
if s["strand"] == 1:
if len(seq) != 23 or (seq[-2:] != "AG" and seq[-2:] != "GG"):
raise JobERR(Job.ERR_BADINPUT + " no forward strand guide found in sequence {0}: {1}"\
.format(i,s["sequence"]),None)
else:
if len(seq) != 23 or (seq[:2] != "CT" and seq[:2] != "CC"):
raise JobERR(Job.ERR_BADINPUT + " no reverse strand guide found in sequence {0}: {1}"\
.format(i,s["sequence"]),None)
job_sequence = ""
spacer_infos = []
for i, s in enumerate(spacers):
job_sequence += "NN"
si = dict(name=s["name"],
sequence=s["sequence"],
position=len(job_sequence),
strand=s["strand"])
if len(s["sequence"]) != 23:
raise JobERR(Job.BADSPACER_LENGTH, None)
spacer_infos.append(si)
job_sequence += si["sequence"]
job_sequence += "NN"
if cfront_settings.get("debug_mode", False): print job_sequence
if re.compile("[^AGTCN]").search(job_sequence) is not None:
return {
"status": "error",
"message":
"Ambiguous or invalid characters found in input sequene.",
"matches": None,
"job_key": None
}
if len(job_sequence) > 500:
return {
"status": "error",
"message": "Sequence length not within allowed range (23 - 500bp)",
"matches": None,
"job_key": None
}
print "GENOME: {0}".format(request.params.get("genome", "hg19"))
if len(spacer_infos) == 0:
raise JobERR(Job.NOSPACERS, None)
else:
params = dict(date_submitted=datetime.datetime.utcnow(),
sequence=job_sequence,
genome=Job.GENOMES[request.params.get("genome", "hg19")],
name=request.params["name"],
email=request.params["email"],
twostrand=False,
query_type="guides_list")
if "key" in request.params:
params["key"] = request.params.get("key")
job = Job(**params)
Session.add(job)
for spacer_info in spacer_infos:
Session.add(Spacer(job=job, **spacer_info))
job.computed_spacers = True
Session.flush()
mail.mail_new_job(request, job)
return {"status": "success", "message": None, "job_key": job.key}
def init_env(p):
global redis_key
env = bootstrap(p)
redis_key = "cfront-{0}:job:hits".format("dev" if cfront_settings.get("debug_mode",False) else "prod")
