def enrichDict(file, mid):
dict = loadOldDict(file)
if mid == '-':
patient = json.loads(sys.stdin.read())
else:
with open(mid, 'r') as pfile:
patient = json.loads(pfile.read())
extractEntries(dict, patient)
with util.OutWrapper(file) as out:
print(json.dumps(dict, indent=2, sort_keys=True), file=out)
"v_spans": []
}
if lineFile is not None:
with open(lineFile, 'r') as lf:
for line in lf:
processLine(obj, line)
addInfo(obj, "pid", "Patient", id)
if len(allPaths) == 0:
print('warning: no path given', file=sys.stderr)
for (path, isfile) in allPaths:
if isfile:
processFile(path, id, obj)
else:
processDirectory(path, id, obj)
min_time = sys.maxint
max_time = -sys.maxint - 1
for e in obj["events"]:
time = e["time"]
if time < min_time:
min_time = time
if time > max_time:
max_time = time
obj["start"] = min_time
obj["end"] = max_time
addInfo(obj, "event_count", "Events", len(obj["events"]))
if output != '-' and not os.path.exists(os.path.dirname(output)):
os.makedirs(os.path.dirname(output))
with util.OutWrapper(output) as out:
print(json.dumps(obj, indent=2), file=out)
if __name__ == '__main__':
(settings, settingsFile, info, lookupMode, rest) = interpretArgs()
dictionary.init(settings, settingsFile)
if lookupMode:
edict = {}
def addEntry(e):
spl = e.split('__', 1)
if len(spl) != 2:
print("shorthand format is '${group_id}__${type_id}': " + e,
file=sys.stderr)
sys.exit(1)
dictionary.createEntry(edict, spl[0].strip(), spl[1].strip())
for e in rest:
if e == "-":
for eid in sys.stdin.read().split(" "):
if len(
eid
) > 0 and eid != "id" and eid != "outcome" and eid != "test":
addEntry(eid)
else:
addEntry(e)
ofile = info['output']
with util.OutWrapper(ofile) as out:
print(json.dumps(edict, indent=2, sort_keys=True), file=out)
else:
enrichDict(info['output'], info['mid'])
usage()
info['pid'] = args.pop(0)
elif val == '--all':
info['pid'] = '--all'
elif val == '-c':
if not args:
print('-c requires argument', file=sys.stderr)
usage()
readConfig(settings, args.pop(0))
elif val == '-o':
if not args:
print('-o requires argument', file=sys.stderr)
usage()
info['output'] = args.pop(0)
else:
print('illegal argument ' + val, file=sys.stderr)
usage()
if do_list:
printList(settings)
sys.exit(0)
if info['pid'] == '':
print('patient id required', file=sys.stderr)
usage()
return (settings, info)
if __name__ == '__main__':
(settings, info) = interpretArgs()
with util.OutWrapper(info['output']) as output:
readShelve(info['pid'], settings, output)