def delete_region(request):
md = request.matchdict
userid = authenticated_userid(request)
table = db.REGION_TABLES_DICT[md["trackType"]]
db.AnnotationCounts(userid, md["name"]).put(None)
regions = table(userid, md["name"], md["chr"])
removed, after = regions.remove(int(request.matchdict["id"]))
result = {}
# if md["trackType"] == "breakpoints":
# evec = db.ModelError(userid, md["name"], md["chr"])
# err_removed, err_after = evec.remove(removed["error"])
# chroms = update_model(db.Models(md["name"], md["chr"]).get(),
# err_after,
# after,
# md["name"],
# md["chr"],
# userid)
# else:
res = db.DisplayedProfile(userid, md["name"])
chroms = res.remove(removed, md["chr"])
result["updates"] = [
{
"profile_id": md["name"],
"chromosome": ch,
# "update": model,
} for ch in chroms.iteritems()
]
#, model in chroms.iteritems()]
return result
def table_profiles(names, userid):
profiles = []
for pname in names:
p = db.Profile(pname).get_export(userid)
# add info for how many annotations for this user.
counts = db.AnnotationCounts(userid, pname).get()
p.update(counts)
profiles.append(p)
return profiles
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 add_region(request):
md = request.matchdict
userid = authenticated_userid(request)
table = db.REGION_TABLES_DICT[md["trackType"]]
regions = table(userid, md["name"], md["chr"])
# TODO: check if the region that we add has the same min value as
# an existing annotation. In that case the SegAnnot segmentation
# is undefined and so we should reject the new annotation.
db.AnnotationCounts(userid, md["name"]).put(None)
reg = {
"min": int(md["min"]),
"max": int(md["max"]),
"annotation": md["annotation"],
}
# first calculate error of this region.
###if md["trackType"] == "breakpoints":
# models = db.Models(md["name"], md["chr"]).get()
# breaks = numpy.array([
# ((reg["min"] < m["breaks"]) & (m["breaks"] < reg["max"])).sum()
# for m in models
# ])
# error = breaks != TARGET_BREAKS[reg["annotation"]]
# reg["error"] = error.astype(int)
added, after = regions.add(reg)
# then add to the total error.
result = {}
#if md["trackType"] == "breakpoints":
# evec = db.ModelError(userid, md["name"], md["chr"])
# err_added, err_after = evec.add(reg["error"])
# chroms = update_model(models,
# err_after,
# after,
# md["name"],
# md["chr"],
# userid)
#else:
res = db.DisplayedProfile(userid, md["name"])
chroms = res.add(added, md["chr"])
# do not send numpy error.
if "error" in added:
added.pop("error")
result["updates"] = [
{
"profile_id": md["name"],
"chromosome": ch,
# "update": model,
} for ch in chroms.iteritems()
]
#, models in chroms.iteritems()]
result["region"] = added
#return {}
return result