def secret_new(request):
"""
New secret view for the new chromosome viewer.
This is most probably used for uploading the new images ?
"""
# fn = db.secret_file("%(name)s%(suffix)s" % request.matchdict)
# return FileResponse(fn, request=request)
profileName = request.matchdict["profile_name"]
chr_num = request.matchdict["chr_num"]
file_name = "%(name)s%(suffix)s" % request.matchdict
fn = db.secret_file(file_name, chr_num)
return FileResponse(fn, request=request)
def secret_new(request):
"""
New secret view for the new chromosome viewer.
This is most probably used for uploading the new images ?
"""
# fn = db.secret_file("%(name)s%(suffix)s" % request.matchdict)
# return FileResponse(fn, request=request)
profileName = request.matchdict["profile_name"]
chr_num = request.matchdict["chr_num"]
file_name = "%(name)s%(suffix)s" % request.matchdict
fn = db.secret_file(file_name, chr_num)
return FileResponse(fn, request=request)
def secret(request):
fn = db.secret_file("%(name)s%(suffix)s" % request.matchdict)
return FileResponse(fn, request=request)
# thus we need to check to make sure there are no NaN
# logratios, and stop with an error if there are.
nan_probes = numpy.isnan(probes["logratio"]).sum()
if 0 < nan_probes:
return {"error": "%d nan probes on chr%s" % (nan_probes, cname)}
r = db.ChromProbes(info["name"], cname)
r.put(probes)
r = db.Profile(info["name"])
info.update(probeInfo)
info["uploader"] = userid
info["uploaded_on"] = datetime.now()
info["ready"] = False
r.put(info)
# save gz profile to disk.
f.seek(0)
out_name = db.secret_file("%(name)s.bedGraph.gz" % info)
saved = gzip.open(out_name, "w")
for data in f:
saved.write(data)
saved.close()
# add profile to user lists.
uprofs = [db.UserProfiles(u) for u in db_users]
to_update = [r for r in uprofs if r.compatible(info)]
for r in to_update:
r.add(info["name"])
# add profile to processing queue.
db.ProfileQueue.db.append(info["name"])
# need to return error none to avoid template nameError.
info["error"] = None
return info
def secret(request):
fn = db.secret_file("%(name)s%(suffix)s" % request.matchdict)
return FileResponse(fn, request=request)
# thus we need to check to make sure there are no NaN
# logratios, and stop with an error if there are.
nan_probes = numpy.isnan(probes["logratio"]).sum()
if 0 < nan_probes:
return {"error": "%d nan probes on chr%s" % (nan_probes, cname)}
r = db.ChromProbes(info["name"], cname)
r.put(probes)
r = db.Profile(info["name"])
info.update(probeInfo)
info["uploader"] = userid
info["uploaded_on"] = datetime.now()
info["ready"] = False
r.put(info)
# save gz profile to disk.
f.seek(0)
out_name = db.secret_file("%(name)s.bedGraph.gz" % info)
saved = gzip.open(out_name, "w")
for data in f:
saved.write(data)
saved.close()
# add profile to user lists.
uprofs = [db.UserProfiles(u) for u in db_users]
to_update = [r for r in uprofs if r.compatible(info)]
for r in to_update:
r.add(info["name"])
# add profile to processing queue.
db.ProfileQueue.db.append(info["name"])
# need to return error none to avoid template nameError.
info["error"] = None
return info
