def view(request):
names = request.matchdict["name"].split(",")
for name in names:
pinfo = db.Profile(name).get()
if pinfo is None or pinfo["export"] == "no":
return forbidden_userprofiles(request)
return fn(request)
def export(request):
"""export annotations and models in plain text formats.
Access rights: for public profiles, everyone can read everyone
else's annotations and models. That way we can have a button for
export to UCSC.
For non-public profiles, deny un-authorized access to annotations
and models as well.
"""
# oldargs=,user_id,profile_id,table,file_format)
# mdkeys user name what format
md = request.matchdict
pro = db.Profile(md["name"])
fun = getattr(pro, md["what"])
# need to
dicts = fun(md["user"])
pinfo = pro.get()
pinfo["table"] = md["what"]
pinfo["visibility"] = EXPORT_VISIBILITY[md["what"]]
for d in dicts:
d["user_id"] = md["user"]
d["profile_id"] = md["name"]
response = respond_bed_csv(md["what"], md["format"], pinfo, dicts)
return response
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 delete_profile(request):
userid = authenticated_userid(request)
profile = db.Profile(request.matchdict["name"])
profile_info = profile.get()
if profile_info["uploader"] != userid:
raise Forbidden("profile can only be deleted by uploader")
try:
pro_msg = profile.delete()
except Exception, e:
pro_msg = "ERROR: " + str(e)
def links(request):
"""Show a list of breakpoints and copy number alterations."""
names = request.matchdict["name"]
namelist = names.split(',')
alterations = []
export = ""
export_db = ""
userid = authenticated_userid(request)
for name in namelist:
pro = db.Profile(name)
copies = pro.copies(userid)
tables = (
#("breaks",pro.breaks(userid)),
("copies", [a for a in copies if a["annotation"] in ALTERED]), )
added = False
for table, dicts in tables:
for d in dicts:
added = True
d["name"] = name
d["type"] = table
d["size"] = d["max"] - d["min"]
d["size_kb"] = d["size"] / 1000
mid = (d["max"] + d["min"]) / 2
d["zoom"] = []
for f in ZOOM_FACTORS:
width = f * d["size"] / 2
d["zoom"].append({
"min": max(mid - width, 1),
"max": mid + width,
})
alterations.append(d)
# If any added for this profile, add it to the export form.
if added:
ex = pro.get_export(userid)
if ex["export"] == "yes":
export_db = ex["db"]
export += ex["ucsc"]
alterations.sort(key=lambda d: (d["name"], db.ChromLengths.CHROM_RANK[d[
"chromosome"]], d["min"]))
return {
"export": export,
"db": export_db,
"alterations": alterations,
"user": userid,
"zoom": ZOOM_FACTORS,
"names": names,
}
def prof_info(name_str, chroms, size):
"""
Parameters -
name-str - name of profile
chroms - number of chromosomes
size - zoom level
Returns -
a dict containing the profile data
"""
out = {"names": name_str}
if "," in name_str:
namelist = name_str.split(",")
out["p"] = None
else:
namelist = [name_str]
out["p"] = db.Profile(name_str).get()
out["plot"] = plotJS(namelist, chroms, size)
return out
def plotJS(profiles, chroms, size):
"""JSON to pass to profilePlot JS code.
A list of list of objects. The first list corresponds to
rows/profiles in the plot table, the second list corresponds to
columns/chroms.
"""
# TODO: when we have multiple genomes, check to make sure we are
# only displaying profiles from one!
pinfo = []
for name in profiles:
pro = db.Profile(name).get()
meta = pro["chrom_meta"]
cinfo = []
for ch in chroms:
d = meta[ch]["plots"][size] if ch in meta else {}
d["profile"] = name
d["chr"] = ch
d["db"] = pro["db"]
cinfo.append(d)
pinfo.append(cinfo)
return json.dumps(pinfo)
return {"error": "profile named '%(name)s' already in db" % info}
probeInfo = read_probes(f, cl)
except ValueError, e:
return {"error": e}
chroms = probeInfo.pop("chroms")
for cname, probes in chroms.iteritems():
# the regexp that we use for validating the logratio column is
# quite permissive: \S+ so it can match 213E-2 and also NaN,
# 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)]