def initial(request):
"""Send user-specific model data as JSON."""
userid = authenticated_userid(request)
result_list = []
for name in request.matchdict["profiles"].split(","):
dp = db.DisplayedProfile(userid, name)
# dp.put(None)
prof = dp.get()
for ch in request.matchdict["chromosomes"].split(","):
if ch in prof:
m = prof[ch] # contains breaks, copy number calls.
m["breakpoints_regions"] = db.Breakpoints(userid, name,
ch).json()
for b in m["breakpoints_regions"]:
# do not send numpy error.
b.pop("error")
m["copies_regions"] = db.Copies(userid, name, ch).json()
result_list.append({
"chromosome": ch,
"profile_id": name,
"update": m,
})
return {
"updates": result_list,
}
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 update_model(models, error, regions, profile, ch, user):
"""Used in add/remove breakpoint regions."""
# store error for learning later.
uerr = db.UserError(user)
uerr.add((profile, ch, error))
model = db.chrom_model(models, error, regions, profile, ch, user)
res = db.DisplayedProfile(user, profile)
chroms = res.get()
chroms[ch] = model
db.infer_gain_loss(chroms)
res.put(chroms)
return chroms
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