def unannotated(userid):
"""Find an un-annotated chromosome."""
names = db.UserProfiles(userid).get()
shuffle(names)
chorder = list(db.ChromLengths.CHROM_ORDER)
shuffle(chorder)
for name in names:
ac = db.AnnotationCounts(userid, name)
counts = ac.get()
for ch in chorder:
if counts[ch] == 0:
return name, ch
def all_profiles(request):
userid = authenticated_userid(request)
profile_names = db.UserProfiles(userid).get()
profiles = table_profiles(profile_names, userid)
urls = [db.COPIES_EXPORT_URL % p for p in profiles if p["copies"] > 0]
info = {
'profile_count': len(profile_names),
"copy_urls": "\n".join(urls),
'profiles': profiles,
'user': userid,
}
return info
def forbidden_userprofiles(request):
userid = authenticated_userid(request)
allowed = db.UserProfiles(userid).get()
md = request.matchdict
looking = md["profiles"].split(',') if "profiles" in md else []
if "name" in md:
for name in md["name"].split(","):
looking.append(name)
# print looking, allowed
for pname in looking:
if pname not in allowed:
raise Forbidden()
def home(request):
userid = authenticated_userid(request)
profile_names = db.UserProfiles(userid).get()
# show only a few of the most recently uploaded profiles.
profiles = table_profiles(profile_names[:5], userid)
info = {
'profile_count': len(profile_names),
'profiles': profiles,
'user': userid,
}
pname = 'nb18'
if pname in profile_names:
info['plot'] = plotJS([pname], ['17'], 'standard')
else:
info["plot"] = None
return info
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
HEADER_TEMPLATES = {
"bed":
'track visibility=%(visibility)s name=%(name)s%(table)s description="%(description)s %(table)s" itemRgb=on',
"bedGraph":
'track type=bedGraph visibility=%(visibility)s alwaysZero=on graphType=points yLineMark=0 yLineOnOff=on name=%(name)s%(table)s description="%(description)s %(table)s"',