def __getitem__(self, key):
if key == 'tracknumber':
return str(self.tags['trkn'][0][0])
elif key == 'key':
warn('Keys are not supported for M4A files')
return ''
return self.tags[self.translate_key(key)][0]
def save_image():
password = request.forms.get('password')
if password != config['Password']:
end(403, "wrong password!")
upfile = request.files.get('upfile')
if not upfile:
end(401, "no file in the request!")
path = os.path.join(config['MediaRoot'], upfile.raw_filename)
if not os.path.exists(path):
filesize = -1
try:
filesize = int(request.forms.get('filesize'))
except TypeError:
end(400, "missing file size in the request!")
# save file
info("upfile path: " + path)
upfile.save(path)
# check file size in request against written file size
if filesize != os.stat(path).st_size:
end(411, "file sizes do not match!")
else:
warn("file " + path + " already exists")
def test_single(sample, location, expected, profile, threshold, gene):
expected = [r for r in expected if not pd.isnull(r)]
message = '{} - {}'.format(sample, ' or '.join(expected))
message = colorize('{:30}'.format(message, 'teal'))
if '' not in expected:
expected = [[str(x).strip() for x in re.split('[/\+]', r)] for r in expected]
expected = set(tuple(sorted(r, key=sortkey)) for r in expected)
else:
expected = set()
try:
solutions = genotype.genotype(location, gene, profile, threshold)
except:
logbook.error('{} {}', message, colorize('CRASH ', 'red'))
exit(1)
def fix(s):
return re.split('(\d+)', s)[1]
orig_solutions = solutions
solutions = set(tuple(sorted((fix(p) for p in s), key=sortkey)) for s in solutions)
expected = set(tuple(sorted((fix(p) for p in s), key=sortkey)) for s in expected)
if solutions == expected:
logbook.info('{} {} {}', message, colorize('OK ', 'green'), list(orig_solutions))
return 1
elif solutions <= expected and len(solutions) != 0:
logbook.info('{} {} {}', message, colorize('OK< ', 'green'), list(orig_solutions))
return 2
elif len(expected & solutions) > 0:
logbook.warn('{} {} {}', message, colorize('MULTI', 'yellow'), list(orig_solutions))
return 3
else:
logbook.error('{} {} {}', message, colorize('FAIL ', 'red'), list(orig_solutions))
return 0
def test_samples(samples, location, profile, threshold, gene='cyp2d6'):
from pathos.multiprocessing import ProcessingPool as Pool
pool = Pool(processes=16)
def f(s):
global counter
sample, expected = s[0], s[1:]
# if sample not in T: continue
loc = location.format(sample)
if not os.path.exists(loc): # or sample == 'PGXT122':
return 0
try:
res = test_single(sample, loc, expected, profile, threshold, gene)
except Exception as e:
print(s, e)
res = 0
# sys.stderr.write('-')
return res
# sys.stderr.write(' ' * len(samples) + '|\r')
result = pool.map(f, samples)
logbook.warn(
'Passed {} out of {} ({} subset, {} multi)\n',
colorize(str(len([x for x in result if x > 0])), 'green'),
colorize(str(len(result)), 'blue'),
colorize(str(len([x for x in result if x == 2])), 'yellow'),
colorize(str(len([x for x in result if x == 3])), 'yellow')
)
def send_back():
handler = MultiProcessingHandler(queue)
handler.push_thread()
try:
logbook.warn(message)
finally:
handler.pop_thread()
def test_calling_frame(self):
handler = logbook.TestHandler()
handler.push_thread()
try:
logbook.warn('test')
finally:
handler.pop_thread()
self.assertEqual(handler.records[0].calling_frame, sys._getframe())
def __call__(self):
from logbook.queues import MultiProcessingHandler
handler = MultiProcessingHandler(self.queue)
handler.push_thread()
try:
logbook.warn('Hello World')
finally:
handler.pop_thread()
def __call__(self):
from logbook.queues import MultiProcessingHandler
handler = MultiProcessingHandler(self.queue)
handler.push_thread()
try:
logbook.warn('Hello World')
finally:
handler.pop_thread()
def __setitem__(self, key, value):
if key == 'tracknumber':
k, n = self.tags['trkn'][0]
self.tags['trkn'][0] = (int(value), n)
elif key == 'key':
warn('Keys are not supported for M4A files')
pass
else:
self.tags[self.translate_key(key)] = [value]
def test_blackhole_setting(self):
null_handler = logbook.NullHandler()
heavy_init = logbook.LogRecord.heavy_init
try:
def new_heavy_init(self):
raise RuntimeError('should not be triggered')
logbook.LogRecord.heavy_init = new_heavy_init
with null_handler:
logbook.warn('Awesome')
finally:
logbook.LogRecord.heavy_init = heavy_init
def scrapeRuns():
runs = []
today = datetime.now()
for meetingURL in RPTodayRaces(today).cardurls:
try:
race_card = RPRaceCard(meetingURL)
for nag in race_card.runners:
runs.append(
Run(nag["name"], race_card.location, race_card.time))
except Exception, e:
warn("url=" + meetingURL + " " + str(e))
def parse_nutrition_str(self, nutrition_str):
nutrition_infos = {}
nutrition_str = nutrition_str.replace(u" \u2013 pro durchschnittlicher Portion", "")
nutrition_arr = nutrition_str.split()
for i in xrange(0, len(nutrition_arr), 2):
try:
nutrition_infos[nutrition_arr[i]] = nutrition_arr[i+1]
except IndexError:
warn("Malformatted nutrition string: '%s'" % nutrition_str)
return nutrition_infos
def scrapeRuns():
runs = []
today = datetime.now()
for meetingURL in RPTodayRaces(today).cardurls:
try:
race_card = RPRaceCard(meetingURL)
for nag in race_card.runners:
runs.append(
Run( nag["name"] , race_card.location, race_card.time)
)
except Exception, e:
warn("url=" + meetingURL + " " + str(e))
def save_image():
password = request.forms.get("password")
if password != PASSWORD:
abort(403, "ERROR: wrong password!")
upfile = request.files.get("upfile")
if not upfile:
abort(401, "ERROR: no file in the request!")
path = os.path.join(MEDIA_ROOT, upfile.raw_filename)
if not os.path.exists(path):
debug("upfile path: " + path)
upfile.save(path)
else:
warn("file " + path + " already exists")
def test_single(sample, location, expected, profile, gene, solver):
expected = [r for r in expected if not pd.isnull(r)]
message = '{}::{}::{}'.format(sample, solver[:2], gene)
expected = [[
str(x).strip() for x in re.split(r'[/\+]', r) if str(x).strip() != ''
] for r in expected]
expected = [tuple(sorted(r, key=sortkey)) for r in expected]
def fix(s):
return re.split(r'(\d+)', s)[1]
expected = [
tuple(sorted((fix(p) for p in s), key=sortkey)) for s in expected
]
expected, expected_new = set(expected), set(expected[1:])
solutions = genotype.genotype(
location,
'tmp/{}_{}_{}.out'.format(sample, gene, profile),
'tmp/{}_{}_{}.log'.format(sample, gene, profile),
gene,
profile,
0.5,
solver,
cn_solution=None,
reference='/data/cb/inumanag/aldy/cram-genome.fa',
cn_neutral_region=None)
orig_solutions = '; '.join(','.join(s[1]) for s in solutions)
orig_expected = '; '.join(','.join(s) for s in expected)
solutions = set(
tuple(sorted((fix(p) for p in s[1]), key=sortkey)) for s in solutions)
if solutions == expected:
logbook.warn('{:20} {} {:25} == {}', message,
colorize('OK ', 'green'), orig_solutions, orig_expected)
return 1
elif solutions <= expected and len(solutions) != 0:
if solutions == expected_new:
logbook.warn('{:20} {} {:25} == {}', message,
colorize('OK= ', 'green'), orig_solutions,
orig_expected)
else:
logbook.warn('{:20} {} {:25} <= {}', message,
colorize('OK? ', 'green'), orig_solutions,
orig_expected)
return 2
elif len(expected & solutions) > 0:
logbook.warn('{:20} {} {:25} =~ {}', message,
colorize('MULT ', 'yellow'), orig_solutions,
orig_expected)
return 3
else:
logbook.error('{:20} {} {:25} != {}', message,
colorize('FAIL ', 'red'), orig_solutions, orig_expected)
return 0
def save_tags(filepath, fragments, genome=None,
re_offset=0):
def get_tag_intervals():
for frag in fragments:
# rev primer
rname = frag.left_primer.name
if rname.endswith('_fwd') or rname.endswith('_rev'):
rname = rname[:-4]
rname += '_rev'
rev_tag = get_tag_interval(frag.left_primer,
frag.left_rsite, name=rname,
re_offset=re_offset)
yield ('left_primer', rev_tag)
# fwd primer
fname = frag.right_primer.name
if fname.endswith('_fwd') or fname.endswith('_rev'):
fname = fname[:-4]
fname += '_fwd'
fwd_tag = get_tag_interval(frag.right_primer,
frag.right_rsite, name=fname,
re_offset=re_offset)
yield ('right_primer', fwd_tag)
notice('called')
if genome is None:
with open(filepath, 'w') as f:
for prim_loc, x in get_tag_intervals():
f.write(bedentry_as_string(x, extra=prim_loc))
return
z = collections.defaultdict(set)
for prim_loc, x in get_tag_intervals():
seq = genome[x.chrom][x.start:x.end]
if prim_loc == 'left_primer':
assert x.strand == '-'
seq = seq.reverse_complement()
else:
assert x.strand == '+'
seq = seq.seq.tostring()
if seq in z[x.name]:
warn('%s has multiple identical tag sequences.' % x.name)
else:
z[x.name].add(seq)
with open(filepath, 'w') as f:
for name in sorted(z):
v = z[name]
while len(v):
f.write('>%s\n' % name)
f.write('%s\n' % v.pop())
def test_blackhole_setting(self):
null_handler = logbook.NullHandler()
heavy_init = logbook.LogRecord.heavy_init
try:
def new_heavy_init(self):
raise RuntimeError('should not be triggered')
logbook.LogRecord.heavy_init = new_heavy_init
with null_handler:
logbook.warn('Awesome')
finally:
logbook.LogRecord.heavy_init = heavy_init
null_handler.bubble = True
with capture_stderr() as captured:
logbook.warning('Not a blockhole')
self.assertNotEqual(captured.getvalue(), '')
def test_blackhole_setting(self):
null_handler = logbook.NullHandler()
heavy_init = logbook.LogRecord.heavy_init
try:
def new_heavy_init(self):
raise RuntimeError('should not be triggered')
logbook.LogRecord.heavy_init = new_heavy_init
with null_handler:
logbook.warn('Awesome')
finally:
logbook.LogRecord.heavy_init = heavy_init
null_handler.bubble = True
with capture_stderr() as captured:
logbook.warning('Not a blockhole')
self.assertNotEqual(captured.getvalue(), '')
def count(doc):
phone_num = doc['phone']
if len(phone_num) > 12 or not phone_num.isdigit():
logbook.warn('anomaly phone num: {}'.format(phone_num))
return
phone_position = int(phone_num[:7])
position_doc = m_phone.phone.find_one({'_id':phone_position})
if not position_doc:
logbook.warn('can not select the num: {}'.format(phone_num))
return
key_list = [
'province:{}'.format(position_doc['province'].encode('utf8')),
'city:{}'.format(position_doc['city'].encode('utf8')),]
msetnx_dict = {item: 0 for item in key_list}
r_db.msetnx(msetnx_dict)
incr = lambda key: r_db.incr(key)
map(incr, key_list)
def test_blackhole_setting(activation_strategy):
null_handler = logbook.NullHandler()
heavy_init = logbook.LogRecord.heavy_init
with activation_strategy(null_handler):
def new_heavy_init(self):
raise RuntimeError('should not be triggered')
logbook.LogRecord.heavy_init = new_heavy_init
try:
with activation_strategy(null_handler):
logbook.warn('Awesome')
finally:
logbook.LogRecord.heavy_init = heavy_init
null_handler.bubble = True
with capturing_stderr_context() as captured:
logbook.warning('Not a blockhole')
assert captured.getvalue() != ''
def count(doc):
phone_num = doc['phone']
if len(phone_num) > 12 or not phone_num.isdigit():
logbook.warn('anomaly phone num: {}'.format(phone_num))
return
phone_position = int(phone_num[:7])
position_doc = m_phone.phone.find_one({'_id': phone_position})
if not position_doc:
logbook.warn('can not select the num: {}'.format(phone_num))
return
key_list = [
'province:{}'.format(position_doc['province'].encode('utf8')),
'city:{}'.format(position_doc['city'].encode('utf8')),
]
msetnx_dict = {item: 0 for item in key_list}
r_db.msetnx(msetnx_dict)
incr = lambda key: r_db.incr(key)
map(incr, key_list)
def create_settings_file():
filename = 'photobackup_settings.py'
global input
# Python2 compatibility for input()
try:
input = raw_input
except NameError:
pass
# ask for the upload directory (should be writable by the server)
media_root = input("The directory where to put the pictures" +
" (should be writable by the server you use): ")
if not os.path.isdir(media_root):
notice("Directory {} does not exist, creating it".format(media_root))
os.mkdir(media_root)
server_user = input("Owner of the directory [www-data]: ")
if not server_user:
server_user = '******'
try:
server_user_uid = pwd.getpwnam(server_user).pw_uid
if os.stat(media_root).st_uid != server_user_uid:
notice("Changing owner to: ".format(server_user))
try:
shutil.chown(media_root, server_user, server_user)
except AttributeError:
warn("Can't change directory's owner, please do it correctly!")
except KeyError:
warn("User {} not found, please check the directory's rights."
.format(server_user))
# ask a password for the server
text = "The server password that you use in the mobile app: "
password = getpass.getpass(prompt=text)
passhash = hashlib.sha512(password.encode('utf-8')).hexdigest()
with open(filename, 'w') as settings:
settings.write("# generated settings for PhotoBackup Bottle server\n")
settings.write("MEDIA_ROOT = '{}'\n".format(media_root))
settings.write("PASSWORD = '******'\n".format(passhash))
notice("Settings file is created, please launch me again!")
return media_root, passhash
def test_blackhole_setting(activation_strategy):
null_handler = logbook.NullHandler()
heavy_init = logbook.LogRecord.heavy_init
with activation_strategy(null_handler):
def new_heavy_init(self):
raise RuntimeError('should not be triggered')
logbook.LogRecord.heavy_init = new_heavy_init
try:
with activation_strategy(null_handler):
logbook.warn('Awesome')
finally:
logbook.LogRecord.heavy_init = heavy_init
null_handler.bubble = True
with capturing_stderr_context() as captured:
logbook.warning('Not a blockhole')
assert captured.getvalue() != ''
def simple_pkg_ver(pkg, ver):
u"""
pip справшивает где скачать пакет такой-то версии — даём ссылку на самих себя
"""
from pygift.tools import version_validate
if tools.can_be_proxied(pkg):
return proxy.simple_pkg_ver(pkg, ver)
# если пакет публичный - его могут попробовать поставить по обычному номеру версии
if not version_validate(ver):
if not tools.is_public(pkg):
warn("unsupported version requested: {!r}=={!r}", pkg, ver)
return '<!-- unsupported version format --!>'
else:
debug("unsupported version format, yet public pkg, simulating proxy: {!r}=={!r}", pkg, ver)
return proxy.json2simple_pkg_ver(pkg, ver)
url = url_for('pkg_generate', pkg=pkg, ver=ver)
return '<a href="{url}">{pkg}-{ver}</a>'.format(url=escape(url), pkg=escape(pkg), ver=escape(ver))
def save(line):
'''
save the code-position to mongo
'''
# format the fileline
info = line.strip('\r\n').strip(' ').split(' ')
info[0] = int(info[0])
info[1] = info[1].decode('gb2312').encode('utf8')
if len(info) > 2:
logbook.warn(info)
# save the info to mongo
try:
doc = {'_id': info[0], 'position':info[1]}
ret = m.position.save(doc)
except StandardError, error_info:
logbook.error(error_info)
logbook.warn('code:{}, position:{}, original:'.format(
info[0], info[1], info,
))
def test_global_functions(activation_strategy):
with activation_strategy(logbook.TestHandler()) as handler:
logbook.debug('a debug message')
logbook.info('an info message')
logbook.warn('warning part 1')
logbook.warning('warning part 2')
logbook.notice('notice')
logbook.error('an error')
logbook.critical('pretty critical')
logbook.log(logbook.CRITICAL, 'critical too')
assert handler.has_debug('a debug message')
assert handler.has_info('an info message')
assert handler.has_warning('warning part 1')
assert handler.has_warning('warning part 2')
assert handler.has_notice('notice')
assert handler.has_error('an error')
assert handler.has_critical('pretty critical')
assert handler.has_critical('critical too')
assert handler.records[0].channel == 'Generic'
assert handler.records[0].dispatcher is None
def test_global_functions(self):
handler = logbook.TestHandler()
with handler:
logbook.debug('a debug message')
logbook.info('an info message')
logbook.warn('warning part 1')
logbook.warning('warning part 2')
logbook.notice('notice')
logbook.error('an error')
logbook.critical('pretty critical')
logbook.log(logbook.CRITICAL, 'critical too')
self.assert_(handler.has_debug('a debug message'))
self.assert_(handler.has_info('an info message'))
self.assert_(handler.has_warning('warning part 1'))
self.assert_(handler.has_warning('warning part 2'))
self.assert_(handler.has_notice('notice'))
self.assert_(handler.has_error('an error'))
self.assert_(handler.has_critical('pretty critical'))
self.assert_(handler.has_critical('critical too'))
self.assertEqual(handler.records[0].logger_name, 'generic')
self.assertEqual(handler.records[0].channel, None)
def test_global_functions(self):
handler = logbook.TestHandler()
with handler:
logbook.debug('a debug message')
logbook.info('an info message')
logbook.warn('warning part 1')
logbook.warning('warning part 2')
logbook.notice('notice')
logbook.error('an error')
logbook.critical('pretty critical')
logbook.log(logbook.CRITICAL, 'critical too')
self.assert_(handler.has_debug('a debug message'))
self.assert_(handler.has_info('an info message'))
self.assert_(handler.has_warning('warning part 1'))
self.assert_(handler.has_warning('warning part 2'))
self.assert_(handler.has_notice('notice'))
self.assert_(handler.has_error('an error'))
self.assert_(handler.has_critical('pretty critical'))
self.assert_(handler.has_critical('critical too'))
self.assertEqual(handler.records[0].channel, 'Generic')
self.assertEqual(handler.records[0].dispatcher, None)
def save_county():
while r_db.randomkey:
key = r_db.randomkey()
if not key.isdigit():
logbook.warn(key)
continue
count = int(r_db.get(key))
parent_id = int(key) / 100 * 100
parent = m_db.card.city.find_one({'_id': parent_id})
if not parent:
parent = {'_id': int(parent_id), 'position': '未知'.decode('utf8')}
self_doc = m_db.position.find_one({'_id': key})
if not self_doc:
self_doc = {'_id': int(key), 'position': '未知'.decode('utf8')}
self_doc['count'] = count
self_doc['position'] = '{parent} {self}'.format(
parent=parent['position'].encode('utf8'),
self=self_doc['position'].encode('utf8'),
)
ret = m_db.card.county.save(self_doc)
logbook.info(ret)
r_db.delete(key)
def save(line):
'''
save the code-position to mongo
'''
# format the fileline
info = line.strip('\r\n').strip(' ').split(' ')
info[0] = int(info[0])
info[1] = info[1].decode('gb2312').encode('utf8')
if len(info) > 2:
logbook.warn(info)
# save the info to mongo
try:
doc = {'_id': info[0], 'position': info[1]}
ret = m.position.save(doc)
except StandardError, error_info:
logbook.error(error_info)
logbook.warn('code:{}, position:{}, original:'.format(
info[0],
info[1],
info,
))
def _reread(self):
conf_name = 'pygift.json'
conf_dirs = (
os.path.dirname(os.path.abspath(__file__)),
'/etc',
)
conf_paths = (
os.path.join(conf_dir, conf_name)
for conf_dir in conf_dirs
)
self._path = next(
(path for path in conf_paths if os.path.exists(path)),
None
)
if not self._path:
self._data = {}
warn('config not found')
else:
info('using config {!r}', self._path)
self._mtime = os.path.getmtime(self._path)
with open(self._path) as f:
self._data = demjson.decode(f.read())
self._initialized = True
def save_county():
while r_db.randomkey:
key = r_db.randomkey()
if not key.isdigit():
logbook.warn(key)
continue
count = int(r_db.get(key))
parent_id = int(key) / 100 * 100
parent = m_db.card.city.find_one({'_id': parent_id})
if not parent:
parent = {
'_id': int(parent_id), 'position': '未知'.decode('utf8')}
self_doc = m_db.position.find_one({'_id': key})
if not self_doc:
self_doc = {
'_id': int(key), 'position': '未知'.decode('utf8')}
self_doc['count'] = count
self_doc['position'] = '{parent} {self}'.format(
parent=parent['position'].encode('utf8'),
self=self_doc['position'].encode('utf8'),)
ret = m_db.card.county.save(self_doc)
logbook.info(ret)
r_db.delete(key)
def test_global_functions(self):
handler = logbook.TestHandler()
handler.push_thread()
try:
logbook.debug('a debug message')
logbook.info('an info message')
logbook.warn('warning part 1')
logbook.warning('warning part 2')
logbook.notice('notice')
logbook.error('an error')
logbook.critical('pretty critical')
logbook.log(logbook.CRITICAL, 'critical too')
finally:
handler.pop_thread()
self.assert_(handler.has_debug('a debug message'))
self.assert_(handler.has_info('an info message'))
self.assert_(handler.has_warning('warning part 1'))
self.assert_(handler.has_warning('warning part 2'))
self.assert_(handler.has_notice('notice'))
self.assert_(handler.has_error('an error'))
self.assert_(handler.has_critical('pretty critical'))
self.assert_(handler.has_critical('critical too'))
self.assertEqual(handler.records[0].channel, 'Generic')
self.assertEqual(handler.records[0].dispatcher, None)
def main():
start = time.time()
args = parse_args()
wwise_dir = Path(args.wwise_dir)
out_dir = Path(args.out_dir)
out_dir.mkdir(exist_ok=True)
id_to_filename_path = out_dir / ID_TO_FILENAME
manager = mp.Manager()
queue = manager.Queue()
id_queue = manager.Queue()
setup_logging(queue)
target_handlers = logbook.NestedSetup([
logbook.NullHandler(),
logbook.StreamHandler(sys.stdout, level=logbook.INFO, bubble=True),
logbook.FileHandler("extract.log",
mode="w",
level=logbook.INFO,
bubble=True),
])
sub = MultiProcessingSubscriber(queue)
controller = sub.dispatch_in_background(target_handlers)
quickbms_log_lock = manager.Lock()
quickbms_log = out_dir / "quickbms.log"
try:
id_to_filename_path.unlink()
logbook.info("removed old {id_file}",
id_file=id_to_filename_path.absolute())
except FileNotFoundError:
pass
logbook.info("QuickBMS log: '{qlog}'", qlog=quickbms_log.absolute())
try:
quickbms_log.unlink()
logbook.info("removed old {f}", f=quickbms_log.absolute())
except FileNotFoundError:
pass
id_to_filename_path.touch()
logbook.info("writing old ID -> new filename info in '{id_file}'",
id_file=id_to_filename_path.absolute())
id_to_filename_p = mp.Process(target=id_to_filename_worker,
args=(id_queue, id_to_filename_path, queue))
id_to_filename_p.start()
logbook.info("processing audio files in '{wd}'", wd=wwise_dir.absolute())
fut2func = {}
# Parse .bnk files and metadata.
with ProcessPoolExecutor(max_workers=MAX_WORKERS) as executor:
fut2func[executor.submit(parse_banks_metadata, wwise_dir,
queue)] = parse_banks_metadata
fut2func[executor.submit(decode_banks, wwise_dir, out_dir,
quickbms_log, quickbms_log_lock,
queue)] = decode_banks
memory_bnk_meta_file2metadata = {}
streamed_bnk_meta_file2metadata = {}
orig_bnk2decode_info = {}
for completed_fut in futures.as_completed(fut2func):
if fut2func[completed_fut] == parse_banks_metadata:
result = completed_fut.result()
memory_bnk_meta_file2metadata = result[0]
streamed_bnk_meta_file2metadata = result[1]
elif fut2func[completed_fut] == decode_banks:
orig_bnk2decode_info = completed_fut.result()
if len(memory_bnk_meta_file2metadata) != len(orig_bnk2decode_info):
logbook.warning(
"Amount of Bank and metadata files "
"do not match ({first}) != {second})",
first=len(orig_bnk2decode_info),
second=len(memory_bnk_meta_file2metadata))
s1 = memory_bnk_meta_file2metadata.keys()
s2 = set([key.stem for key in orig_bnk2decode_info])
to_del = []
diff = s2.difference(s1)
for d in diff:
# TODO: expensive!
for key in orig_bnk2decode_info:
if key.stem == d:
logbook.warn("ignoring {f}", f=str(key))
to_del.append(key)
for td in to_del:
del orig_bnk2decode_info[td]
wem_src2wem_dst = {}
# Move .wem files to out_dir in correct places.
with ProcessPoolExecutor(max_workers=MAX_WORKERS) as executor:
for bnk_meta_file, meta in streamed_bnk_meta_file2metadata.items():
for m in meta:
src_dir = bnk_meta_file.parent
src = src_dir / Path(m.generated_audio_file)
if src.exists():
wwise_path = Path(m.wwise_object_path)
dst = out_dir / wwise_path.relative_to(
wwise_path.anchor).with_suffix(".wem")
executor.submit(copy, src, dst, queue, id_queue)
wem_src2wem_dst[src] = dst
else:
logbook.warning(
"found references to {src} in metadata, but "
"the file cannot be found in wwise_dir",
src=src)
decoded_file2metas = {}
for orig_bnk_file, decode_info in orig_bnk2decode_info.items():
orig_bnk_file = orig_bnk_file.stem
meta = memory_bnk_meta_file2metadata[orig_bnk_file]
if len(decode_info) != len(meta):
logbook.error(
"decode_info and meta length mismatch: "
"{len1} != {len2} for bnk: '{bnk}'",
len1=len(decode_info),
len2=len(meta),
bnk=orig_bnk_file)
# print(decode_info)
# print(meta)
continue
# raise ValueError(f"decode_info and meta length mismatch "
# f"{len(decode_info)} != {len(meta)}")
for m, (decoded_stem, decoded_size) in zip(meta, decode_info.items()):
if m.data_size != decoded_size:
# raise ValueError(f"{m.data_size} != {decoded_size}")
logbook.error(
"metadata size and decoded data size length mismatch: "
"{len1} != {len2}",
len1=m.data_size,
len2=decoded_size)
continue
decoded_file2metas[decoded_stem] = m
fs = []
# Move output from decoding .bnk files to correct places in out_dir.
executor = ProcessPoolExecutor(max_workers=MAX_WORKERS)
for decoded_file, meta in decoded_file2metas.items():
src = out_dir / f"{decoded_file}.bin"
wwise_path = Path(meta.wwise_object_path)
dst = out_dir / wwise_path.relative_to(
wwise_path.anchor).with_suffix(".bin")
fs.append(executor.submit(move, src, dst, queue, id_queue))
futures.wait(fs, return_when=futures.ALL_COMPLETED)
fs = []
# Convert all .wem and .bin files to .ogg.
executor = ProcessPoolExecutor(max_workers=MAX_WORKERS)
for bin_file in out_dir.rglob("*.bin"):
fs.append(executor.submit(ww2ogg, bin_file, queue))
for wem_file in out_dir.rglob("*.wem"):
fs.append(executor.submit(ww2ogg, wem_file, queue))
futures.wait(fs, return_when=futures.ALL_COMPLETED)
done_wems_stems = set([ws.stem for ws in wem_src2wem_dst.keys()])
source_wems = [w for w in wwise_dir.rglob("*.wem")]
source_wems_stems = set([w.stem for w in source_wems])
wem_diff = source_wems_stems.difference(done_wems_stems)
if wem_diff:
logbook.warn("failed to determine filename for "
"{num} files",
num=len(wem_diff))
for ws in source_wems:
if str(ws.stem) in wem_diff:
logbook.info("couldn't determine filename for: {ws}", ws=ws)
copy_seq(ws, out_dir, id_to_filename_queue=None)
# Convert leftovers.
leftovers_fs = []
with ProcessPoolExecutor(max_workers=MAX_WORKERS) as executor:
for wem_file in out_dir.rglob("*.wem"):
leftovers_fs.append(executor.submit(ww2ogg, wem_file, queue))
futures.wait(leftovers_fs, return_when=futures.ALL_COMPLETED)
id_queue.put(SENTINEL)
id_to_filename_p.join()
secs = time.time() - start
logbook.info("finished successfully in {secs:.2f} seconds", secs=secs)
controller.stop()
def test_calling_frame(self):
handler = logbook.TestHandler()
with handler:
logbook.warn('test')
self.assertEqual(handler.records[0].calling_frame, sys._getframe())
def convert_latlon_arr(in_lat, in_lon, height, dtime, code="G2A"):
"""Converts between geomagnetic coordinates and AACGM coordinates.
Parameters
------------
in_lat : (np.ndarray or list or float)
Input latitude in degrees N (code specifies type of latitude)
in_lon : (np.ndarray or list or float)
Input longitude in degrees E (code specifies type of longitude)
height : (np.ndarray or list or float)
Altitude above the surface of the earth in km
dtime : (datetime)
Single datetime object for magnetic field
code : (int or str)
Bit code or string denoting which type(s) of conversion to perform
G2A - geographic (geodetic) to AACGM-v2
A2G - AACGM-v2 to geographic (geodetic)
TRACE - use field-line tracing, not coefficients
ALLOWTRACE - use trace only above 2000 km
BADIDEA - use coefficients above 2000 km
GEOCENTRIC - assume inputs are geocentric w/ RE=6371.2
(default = "G2A")
Returns
-------
out_lat : (np.ndarray)
Output latitudes in degrees N
out_lon : (np.ndarray)
Output longitudes in degrees E
out_r : (np.ndarray)
Geocentric radial distance (R_Earth) or altitude above the surface of
the Earth (km)
Notes
-------
At least one of in_lat, in_lon, and height must be a list or array.
"""
import aacgmv2._aacgmv2 as c_aacgmv2
# If a list was entered instead of a numpy array, recast it here
if isinstance(in_lat, list):
in_lat = np.array(in_lat)
if isinstance(in_lon, list):
in_lon = np.array(in_lon)
if isinstance(height, list):
height = np.array(height)
# If one or two of these elements is a float or int, create an array
test_array = np.array([
hasattr(in_lat, "shape"),
hasattr(in_lon, "shape"),
hasattr(height, "shape")
])
if not test_array.all():
if test_array.any():
arr_shape = in_lat.shape if test_array.argmax() == 0 else \
(in_lon.shape if test_array.argmax() == 1 else
height.shape)
if not test_array[0]:
in_lat = np.ones(shape=arr_shape, dtype=float) * in_lat
if not test_array[1]:
in_lon = np.ones(shape=arr_shape, dtype=float) * in_lon
if not test_array[2]:
height = np.ones(shape=arr_shape, dtype=float) * height
else:
logging.info(
"for a single location, consider using convert_latlon")
in_lat = np.array([in_lat])
in_lon = np.array([in_lon])
height = np.array([height])
# Ensure that lat, lon, and height are the same length or if the lengths
# differ that the different ones contain only a single value
if not (in_lat.shape == in_lon.shape and in_lat.shape == height.shape):
ulen = np.unique([in_lat.shape, in_lon.shape, height.shape])
if ulen.min() != (1, ):
logging.error("mismatched input arrays")
return None, None, None
# Test time
if isinstance(dtime, dt.date):
dtime = dt.datetime.combine(dtime, dt.time(0))
assert isinstance(dtime, dt.datetime), \
logging.error('time must be specified as datetime object')
# Test height
if np.min(height) < 0:
logging.warn('conversion not intended for altitudes < 0 km')
# Initialise output
lat_out = np.empty(shape=in_lat.shape, dtype=float) * np.nan
lon_out = np.empty(shape=in_lon.shape, dtype=float) * np.nan
r_out = np.empty(shape=height.shape, dtype=float) * np.nan
# Test code
try:
code = code.upper()
if (np.nanmax(height) > 2000 and code.find("TRACE") < 0
and code.find("ALLOWTRACE") < 0 and code.find("BADIDEA") < 0):
estr = 'coefficients are not valid for altitudes above 2000 km. You'
estr += ' must either use field-line tracing (trace=True '
estr += 'or allowtrace=True) or indicate you know this '
estr += 'is a bad idea'
logging.error(estr)
return lat_out, lon_out, r_out
# make flag
bit_code = convert_str_to_bit(code)
except AttributeError:
bit_code = code
assert isinstance(bit_code, int), \
logging.error("unknown code {:}".format(bit_code))
# Test latitude range
if np.abs(in_lat).max() > 90.0:
assert np.abs(in_lat).max() <= 90.1, \
logging.error('unrealistic latitude')
in_lat = np.clip(in_lat, -90.0, 90.0)
# Constrain longitudes between -180 and 180
in_lon = ((in_lon + 180.0) % 360.0) - 180.0
# Set current date and time
try:
c_aacgmv2.set_datetime(dtime.year, dtime.month, dtime.day, dtime.hour,
dtime.minute, dtime.second)
except:
raise RuntimeError("unable to set time for {:}".format(dtime))
# Vectorise the AACGM code
convert_vectorised = np.vectorize(c_aacgmv2.convert)
# convert
try:
lat_out, lon_out, r_out = convert_vectorised(in_lat, in_lon, height,
bit_code)
except:
pass
return lat_out, lon_out, r_out
def send_back():
with MultiProcessingHandler(queue):
logbook.warn(message)
from logbook import warn, StreamHandler
import sys
from termcc.cc import cc
my_handler = StreamHandler(sys.stdout)
my_handler.push_application()
warn(cc(':red: :yin_yang: This is a warning :reset:'))
import os
from logbook import Processor
def inject_cwd(record):
record.extra['cwd'] = os.getcwd()
with my_handler.applicationbound():
with Processor(inject_cwd).applicationbound():
warn(cc(':blue: :yin_yang: This is a warning'))
def fetch(self):
canteens = []
for canteen in self.urls:
mid, url = canteen
weeks_to_parse = [""]
parsed_weeks = []
while len(weeks_to_parse) > 0:
week_to_parse = weeks_to_parse.pop(0)
if week_to_parse in parsed_weeks:
continue
parsed_weeks.append(week_to_parse)
# Fetch data
if week_to_parse:
params = urlencode({"WA": week_to_parse})
else:
params = urlencode({})
try:
content = urlopen(url, params).read()
except URLError:
error("Request failed for URL %s." % url)
continue
# Build lxml tree
tree = html.fromstring(content)
# Look for further weeks to parse
wboxh_elements = tree.cssselect("div#wbox > input")
for wbox in wboxh_elements:
week_value = wbox.get("value")
if wbox.get("class") == "wboxh":
if not week_value in weeks_to_parse\
and not week_value in parsed_weeks:
weeks_to_parse.append(week_value)
else:
if not week_value in parsed_weeks:
parsed_weeks.append(week_value)
week_to_parse = week_value
# Parse canteen infos
canteen = {}
canteen["mid"] = mid
# Name
canteen["name"] = beautify_string(tree.cssselect("div.WoHSName")[0].text)
canteen["short_name"] = canteen["name"].split(",", 1)[0]
# Address
canteen["address"] = beautify_string(tree.cssselect("div.WoAdr")[0].text)
canteen["address"] = canteen["address"].replace(")", "")
canteen["address"] = canteen["address"].replace("(", "")
# Period
canteen["period_value"] = week_to_parse
canteen["period"] = beautify_string(tree.cssselect("div.WoDate")[0].text)
# Year
try:
canteen["year"] = int(canteen["period"].rsplit(".", 1)[1])
except (IndexError, ValueError):
error("%s: Failed to parse year from period" % canteen["short_name"])
canteen["year"] = date.today().year
# Week
try:
canteen["week"] = int(canteen["period"][canteen["period"].find("KW")+3:canteen["period"].find(",")])
except ValueError:
error('%s: Failed to parse week number from "%s"' % (canteen["short_name"], canteen["period"]))
continue
# Opening times
opening_times = beautify_string(tree.cssselect("div.WoTime")[0].text_content())
opening_times = opening_times[opening_times.find(":")+1:].strip()
canteen["opening_times"] = opening_times
# Main note
main_note_e = tree.cssselect("div.Meldung_std")
if main_note_e:
canteen["main_note"] = main_note_e[0].text_content()
else:
canteen["main_note"] = ""
# Additives
try:
canteen["additives"] = beautify_string(tree.cssselect("table.zusatz_std")[0].text_content(), False)
except IndexError:
warn("%s: Cannot parse additives" % canteen["short_name"])
# Parse meals
# Subtree for better speed
sub_trees = tree.cssselect("table.wo_std")
if sub_trees:
sub_tree = sub_trees[0]
# Bars (table heads)
bars = []
for th in sub_tree.cssselect("th.bli_0"):
bar = beautify_string(th.getchildren()[0].text_content())
if bar:
bars.append(bar)
# Side dishes
side_dishes = []
for td in sub_tree.cssselect("td.bli_1.sw.bto"):
side_dish = self.parse_side_dish(td)
side_dishes.append(side_dish)
current_side_dish = 0
# Days
days = []
for i, tr in enumerate(sub_tree.cssselect("tr.bto")):
day = {}
# Date
date_s = beautify_string([e for e in tr.cssselect("td.bre_1")[0].itertext()][1])
# Make sure date has correct format
try:
day["date"] = str(date(*(strptime(date_s, "%d.%m.%Y")[0:3])))
except ValueError:
error("%s: %s has invalid date format" % (canteen["short_name"], date_s))
continue
# Note
note_td = tr.cssselect("td.Meld_TgStd")
if not note_td:
day["note"] = ""
# Side dish
try:
day["side_dish"] = side_dishes[current_side_dish]
current_side_dish = current_side_dish + 1
except IndexError:
warn("%s: Failed to parse side dish for day %s" % (canteen["short_name"], day["date"]))
day["side_dish"] = ""
# Prices
prices = []
for td in tr.cssselect("td.re"):
price = beautify_string(td.text_content())
if price:
prices.append(price)
# Meals
meals = []
for j, td in enumerate(tr.cssselect("td.bli_1.abst_o")):
description = beautify_string(td.text_content())
if description:
meal = {}
try:
if (j <= len(bars) - 1):
meal["bar"] = bars[j]
else:
meal["bar"] = ""
meal["description"] = description
if (j <= len(prices) - 1):
meal["price"] = prices[j]
else:
meal["price"] = ""
except IndexError:
error("%s: IndexError while parsing meals" % canteen["short_name"])
nutrition_infos = self.parse_nutrition_infos(td)
if nutrition_infos != None:
meal["nutrition_infos"] = nutrition_infos
meals.append(meal)
day["meals"] = meals
else:
day["note"] = beautify_string(note_td[0].text_content())
days.append(day)
canteen["days"] = days
canteens.append(canteen)
return canteens
return [(s[0], gene, tuple(s[1:]), samples_path.format(s[0]), profile,
solver) for s in samples]
samples = []
for gene in 'CYP2D6 CYP2A6 CYP2C19 CYP2C8 CYP2C9 CYP3A4 CYP3A5 CYP4F2 TPMT DPYD'.split(
):
loc = '/data/cb/inumanag/aldy/cdc/pgrnseq-v1/bams/{}.cram'
samples += get_samples('PGRNseq-v1 (CDC)', gene, loc, 'pgrnseq-v1',
'gurobi')
for gene in ['CYP2D6']:
loc = '/data/cb/inumanag/aldy/baylor/pgrnseq-v2/bams/{}.cram'
samples += get_samples('PGRNseq-v2', gene, loc, 'pgrnseq-v2', 'gurobi')
pool = Pool(processes=np)
result = pool.map(
f, samples
) #[y for y in samples if y[0] == 'NA17012' and y[1] == 'CYP2D6'])
result = list(result)
logbook.warn('Passed {} out of {} ({} subset, {} multi)',
sum(1 for _, x in result if x > 0), len(result),
sum(1 for x in result if x == 2),
sum(1 for x in result if x == 3))
fails = [':'.join(s) for s, x in result if x == 0]
if len(fails) > 0:
logbook.warn('Fail:\n{}', '\n '.join(fails))
# get_samples('PGRNseq-v2 (Old)', gene='CYP2D6', samples_path='/../data/pgrnseq-old/{}.dz', profile='pgrnseq-v2', threshold=.5)
# get_samples('Illumina', gene='CYP2D6', samples_path='/../data/illumina/{}.bam', profile='illumina', threshold=.5)
# get_samples('Illumina (IU)', gene='CYP2D6', samples_path='/../data/illumina-milan/{}.bam', profile='illumina', threshold=.5)
warn("Can't change directory's owner, please do it correctly!")
except KeyError:
warn("User {} not found, please check the directory's rights."
.format(server_user))
# ask a password for the server
text = "The server password that you use in the mobile app: "
password = getpass.getpass(prompt=text)
passhash = hashlib.sha512(password.encode('utf-8')).hexdigest()
with open(filename, 'w') as settings:
settings.write("# generated settings for PhotoBackup Bottle server\n")
settings.write("MEDIA_ROOT = '{}'\n".format(media_root))
settings.write("PASSWORD = '******'\n".format(passhash))
notice("Settings file is created, please launch me again!")
return media_root, passhash
MEDIA_ROOT, PASSWORD = None, None
# import user-created settings for this specific server
try:
from photobackup_settings import MEDIA_ROOT, PASSWORD
if os.path.isdir(MEDIA_ROOT) and os.path.exists(MEDIA_ROOT):
notice("pictures directory is " + MEDIA_ROOT)
else:
sys.exit("pictures directory " + MEDIA_ROOT + "does not exist!")
except ImportError:
warn("Can't find photobackup_settings.py file, creating it")
MEDIA_ROOT, PASSWORD = create_settings_file()
def __call__(self):
from logbook.queues import MultiProcessingHandler
with MultiProcessingHandler(self.queue):
logbook.warn(self.message)
def __call__(self):
from logbook.queues import MultiProcessingHandler
with MultiProcessingHandler(self.queue):
logbook.warn(self.message)
def send_back():
with MultiProcessingHandler(queue):
logbook.warn('Hello World')
def save_image(username, domain):
debug("got a POST root call.")
# app.logger.debug('Query:'+pp.pformat(request))
# app.logger.debug('Query:'+pp.pformat(request.form))
password = request.form.get('password')
if password != config['Password']:
error("password NOT ok.")
end(403, "wrong password!")
debug("ok: password")
# app.logger.debug('File:'+pp.pformat(request.files))
try:
debug("ok: getlist %s." % (pp.pformat(request.getlists)))
except Exception as e:
debug("getlist failed %s." % (str(e)))
try:
upfile = request.files.get('upfile')
# upfile = request.files['upfile']
except Exception as e:
debug("upfile request get failed %s." % (str(e)))
if not upfile:
error("no file in the request.")
end(401, "no file in the request!")
upfile1 = upfile
debug("ok: file present in request.")
# remove anypath inside the filename to insure against injection.
# ex: upfil.raw_filename should not contain any '..'
# already done by secure_filename
# filename = os.path.basename(filename)
try:
filename = secure_filename(upfile.filename)
except Exception as e:
debug("secure_filename failed: %s:%s" % (upfile.filename, str(e)))
debug("ok: secure_filename succeed %s" % filename)
# Prevent uploading file with more than 1 dot.
dotCount = filename.count('.')
if dotCount != 1:
error("file do contains more than 1 dot.")
end(403, "file contains more than 1 dot!")
debug("ok: file do not contains more than 1 dot.")
# Prevent uploading from unwanted file which can be used for injection
extension = os.path.splitext(filename)[1].lower()
if extension not in allowed_extention:
error("file extension NOT allowed '%s'." % extension)
debug("error: allowed %s." % (pp.pformat(allowed_extention)))
end(403, "file extension not allowed!")
debug("ok: file extension allowed.")
# app.logger.debug('Query:'+pp.pformat(upfile))
# extract the exif date, to get the date
try:
tags = exifread.process_file(upfile)
# for tag in tags.keys():
# if tag not in ('JPEGThumbnail', 'TIFFThumbnail', 'Filename', 'EXIF MakerNote'):
# debug("Key: %s, value %s" % (tag, tags[tag]))
except Exception as e:
debug("exif not working %s" % str(e))
debug("ok: got the img exif content")
# EXIF DateTimeOriginal
# value 2015:09:14 15:37:03
try:
if 'EXIF DateTimeOriginal' in tags:
debug("ok: got exif EXIF DateTimeOriginal")
date = str(tags['EXIF DateTimeOriginal'])
elif 'Image DateTime' in tags:
# generated PANO file
debug("ok: got exif Image DateTime")
date = str(tags['Image DateTime'])
else:
debug("hum, no date found in exif tag")
date = ''
for tag in tags.keys():
if tag not in ('JPEGThumbnail', 'TIFFThumbnail', 'Filename', 'EXIF MakerNote'):
debug("Key: %s, value %s" % (tag, tags[tag]))
debug("ok, no exception up to now")
except Exception as e:
for tag in tags.keys():
if tag not in ('JPEGThumbnail', 'TIFFThumbnail', 'Filename', 'EXIF MakerNote'):
debug("Key: %s, value %s" % (tag, tags[tag]))
debug("error: failed to read date from read tags from array.")
end(400, "oups, read tags from array")
debug("ok: got exif date '%s'" % date)
if username is not None and domain is not None:
username = secure_filename(urllib.parse.quote_plus(username).lower())
domain = secure_filename(urllib.parse.quote_plus(domain).lower())
debug("username %s, domain %s" % (username, domain))
basepath = os.path.join(config['MediaRoot'], domain, username)
else:
basepath = os.path.join(config['MediaRoot'])
res = False
try:
res = re_date.match(date)
except Exception as e:
debug("error: failed to apply regex: %s " % str(e))
if res:
date_folder = res.group(1) + '_' + res.group(2) + '_' + res.group(3)
debug("ok: exif passed '%s'." % date_folder)
filedir = os.path.join(basepath, date_folder)
else:
debug("error: could not find date in string '%s'" % date)
filedir = os.path.join(basepath)
debug("ok: using folder '%s'." % filedir)
filepath = os.path.join(filedir, filename)
if not os.path.isdir(filedir):
debug("Need to create folder %s on system." % (filedir))
try:
os.makedirs(filedir)
except Exception as e:
debug("error: Cannot create folder %s" % str(e))
end(400, "oups, cannot create directory '%s'." % (str(e)))
if not os.path.isfile(filepath):
debug("Storing file %s on system." % (filepath))
filesize = -1
try:
filesize = int(request.form.get('filesize'))
except TypeError as e:
debug("error: %s" % str(e))
end(400, "missing file size in the request!")
except Exception as e:
debug("error: %s" % str(e))
end(400, "missing file size in the request!")
# save file
debug("upfile path: '%s'." % (filepath))
upfile.seek(0, os.SEEK_SET)
upfile.save(filepath)
# check file size in request against written file size
if filesize != os.stat(filepath).st_size:
debug("error: file sizes do not match '%s' <> '%s'." % (filesize, os.stat(filepath).st_size))
end(411, "file sizes do not match!")
return ('', 200)
else:
warn("file " + filepath + " already exists")
filesize = -1
try:
filesize = int(request.form.get('filesize'))
except TypeError as e:
debug("error: %s" % str(e))
end(400, "missing file size in the request!")
except Exception as e:
debug("error: %s" % str(e))
end(400, "missing file size in the request!")
debug("ok: got filesize from header '%s'." % filesize)
# check file size in request against written file size
if filesize != os.stat(filepath).st_size:
debug("error: file sizes do not match '%s' <> '%s'" % (filesize, os.stat(filepath).st_size))
end(411, "file sizes do not match!")
return ('', 200)
def convert_latlon(in_lat, in_lon, height, dtime, code="G2A"):
"""Converts between geomagnetic coordinates and AACGM coordinates
Parameters
------------
in_lat : (float)
Input latitude in degrees N (code specifies type of latitude)
in_lon : (float)
Input longitude in degrees E (code specifies type of longitude)
height : (float)
Altitude above the surface of the earth in km
dtime : (datetime)
Datetime for magnetic field
code : (str or int)
Bit code or string denoting which type(s) of conversion to perform
G2A - geographic (geodetic) to AACGM-v2
A2G - AACGM-v2 to geographic (geodetic)
TRACE - use field-line tracing, not coefficients
ALLOWTRACE - use trace only above 2000 km
BADIDEA - use coefficients above 2000 km
GEOCENTRIC - assume inputs are geocentric w/ RE=6371.2
(default is "G2A")
Returns
-------
out_lat : (float)
Output latitude in degrees N
out_lon : (float)
Output longitude in degrees E
out_r : (float)
Geocentric radial distance (R_Earth) or altitude above the surface of
the Earth (km)
"""
import aacgmv2._aacgmv2 as c_aacgmv2
# Test time
if isinstance(dtime, dt.date):
dtime = dt.datetime.combine(dtime, dt.time(0))
assert isinstance(dtime, dt.datetime), \
logging.error('time must be specified as datetime object')
# Test height
if height < 0:
logging.warn('conversion not intended for altitudes < 0 km')
# Initialise output
lat_out = np.nan
lon_out = np.nan
r_out = np.nan
# Test code
try:
code = code.upper()
if (height > 2000 and code.find("TRACE") < 0
and code.find("ALLOWTRACE") < 0 and code.find("BADIDEA") < 0):
estr = 'coefficients are not valid for altitudes above 2000 km. You'
estr += ' must either use field-line tracing (trace=True '
estr += 'or allowtrace=True) or indicate you know this '
estr += 'is a bad idea'
logging.error(estr)
return lat_out, lon_out, r_out
# make flag
bit_code = convert_str_to_bit(code)
except AttributeError:
bit_code = code
assert isinstance(bit_code, int), \
logging.error("unknown code {:}".format(bit_code))
# Test latitude range
if abs(in_lat) > 90.0:
assert abs(in_lat) <= 90.1, logging.error('unrealistic latitude')
in_lat = np.sign(in_lat) * 90.0
# Constrain longitudes between -180 and 180
in_lon = ((in_lon + 180.0) % 360.0) - 180.0
# Set current date and time
try:
c_aacgmv2.set_datetime(dtime.year, dtime.month, dtime.day, dtime.hour,
dtime.minute, dtime.second)
except:
raise RuntimeError("unable to set time for {:}".format(dtime))
# convert location
try:
lat_out, lon_out, r_out = c_aacgmv2.convert(in_lat, in_lon, height,
bit_code)
except:
pass
return lat_out, lon_out, r_out
def put(path):
debug("PUT with path '%s'" % (path))
# remove anypath inside the filename to insure against injection.
# ex: upfil.raw_filename should not contain any '..'
# already done by secure_filename
# filename = os.path.basename(filename)
try:
filename = secure_filename(path)
except Exception as e:
debug("secure_filename failed: %s:%s" % (path, str(e)))
debug("ok: secure_filename succeed %s" % filename)
# Prevent uploading file with more than 1 dot.
dotCount = filename.count('.')
if dotCount != 2:
error("file do not contains more than 2 dot.")
end(403, "file do not contains 2 dot!")
debug("ok: file contains just 2 dot.")
# Prevent uploading from unwanted file which can be used for injection
root, ext = os.path.splitext(filename)
first_ext = os.path.splitext(root)[1].lower()
extension = first_ext + ext
extension = extension.lower()
if extension not in allowed_extention:
error("file extension NOT allowed '%s'." % extension)
debug("error: allowed %s." % (pp.pformat(allowed_extention)))
end(403, "file extension not allowed!")
debug("ok: file extension '%s' allowed." % (extension))
basepath = os.path.join(config['MediaRoot'])
filepath = os.path.join(basepath, filename)
if not os.path.isdir(basepath):
debug("Need to create folder '%s' on system." % (basepath))
try:
os.makedirs(basepath)
except Exception as e:
debug("error: Cannot create folder %s" % str(e))
end(400, "oups, cannot create directory '%s'." % (str(e)))
if not os.path.isfile(filepath):
debug("Storing file %s on system." % (filepath))
filesize = -1
try:
filesize = int(request.headers.get('Content-Length'))
except TypeError as e:
debug("error: %s" % str(e))
end(400, "missing file size in the request!")
except Exception as e:
debug("error: %s" % str(e))
end(400, "missing file size in the request!")
upfile = request.data
# save file
debug("upfile path: '%s'." % (filepath))
with open(filepath, "wb") as fo:
fo.write(upfile)
# check file size in request against written file size
if filesize != os.stat(filepath).st_size:
debug("error: file sizes do not match '%s' <> '%s'." % (filesize, os.stat(filepath).st_size))
end(411, "file sizes do not match!")
return ('', 201)
else:
warn("file " + filepath + " already exists")
end(400, "file already exist!")
def test_calling_frame(self):
handler = logbook.TestHandler()
with handler:
logbook.warn('test')
self.assertEqual(handler.records[0].calling_frame, sys._getframe())
