def main():
parser = argparse.ArgumentParser(description='Simple RPC code generator.')
parser.add_argument("-n", "--name", help="name of the RPC server code",
type=str)
parser.add_argument('filepath', type=str, nargs='*',
help='path to C++ header files that are scanned for prototypes')
parser.add_argument('--functions', type=str,
help='comma separated list of functions to be wrapped')
parser.add_argument('--include-dir', action='store_true')
args = parser.parse_args()
if args.include_dir:
print os.path.join(os.path.dirname (__file__), 'include')
return
prototypes = defaultdict(list)
for filename in args.filepath:
original_filename = os.path.basename(filename)
prototypes[original_filename] += parse_prototypes(filename, args.functions)
special_list = [
('set_debug_level', 'void', [('debug_level', 'const int &')], '%(srpc)sdebug_level = debug_level;'),
('get_counter', 'uint64_t', [('', 'void')], '%(srpc)sreturn_value = %(srpc)scounter;'),
]
for original_filename, prototype_list in prototypes.iteritems():
source_info = dict(FILENAME=os.path.basename(original_filename).upper().replace('.','_'),
original_filename=os.path.basename(original_filename),
namespace = os.path.splitext(os.path.basename(original_filename))[0],
)
server_name = source_info['namespace']
source_info['NAMESPACE'] = source_info['namespace'].upper()
for prototype in special_list:
interface_dict = make_interface_source(server_name, 'simple_rpc', prototype)
collect(source_info, interface_dict)
for prototype in prototype_list:
interface_dict = make_interface_source(server_name, 'simple_rpc::' + source_info['namespace'], prototype)
del interface_dict['special_prototype']
collect(source_info, interface_dict)
client_filename = os.path.splitext(original_filename)[0] + '-rpc.hpp'
print 'creating file', client_filename
f = open(client_filename, 'w')
f.write(templates.client_header % (source_info))
f.close()
client_filename = os.path.splitext(original_filename)[0] + '-rpc.cpp'
print 'creating file', client_filename
f = open(client_filename, 'w')
f.write(templates.client_source % (source_info))
f.close()
server_filename = os.path.splitext(original_filename)[0] + '-rpc-server.cpp'
print 'creating file', server_filename
f = open(server_filename, 'w')
f.write(templates.server_source % (source_info))
f.close()
def sample(self, batchSize, K=None):
x = torch.zeros([batchSize] + self.nvars)
for no in range(len(self.priorList)):
x_ = self.priorList[no].sample(batchSize)
x = collect(self.factorOutIList[no], self.factorOutJList[no], x,
x_)
return x
def novel_junctions_from_unannotated_exons(dbs, confs):
"""List novel junctions from unannotated exons."""
description = [
('start chr', 'string'),
('end chr', 'string'),
('start', 'number'),
('end', 'number'),
('# Reads', 'number'),
('Replicate Id', 'string'),
('Lane Id', 'string'),
]
chart = {}
chart['table_description'] = description
def strategy(conf, row):
"""Insert replicateid"""
return (row[:-1] + (conf['replicateid'], row[-1]))
stats = collect(dbs, confs['configurations'],
_top_novel_junctions_from_unannotated_exons, strategy)
if stats:
stats = sorted(stats, key=lambda row: row[4])
stats.reverse()
chart['table_data'] = stats[:20]
else:
chart['table_data'] = [[None] * len(chart['table_description'])]
return chart
def novel_junctions_from_unannotated_exons(dbs, confs):
"""List novel junctions from unannotated exons."""
description = [('start chr', 'string'),
('end chr', 'string'),
('start', 'number'),
('end', 'number'),
('# Reads', 'number'),
('Replicate Id', 'string'),
('Lane Id', 'string'),
]
chart = {}
chart['table_description'] = description
def strategy(conf, row):
"""Insert replicateid"""
return (row[:-1] + (conf['replicateid'], row[-1]))
stats = collect(dbs,
confs['configurations'],
_top_novel_junctions_from_unannotated_exons,
strategy)
if stats:
stats = sorted(stats, key=lambda row: row[4])
stats.reverse()
chart['table_data'] = stats[:20]
else:
chart['table_data'] = [[None] * len(chart['table_description'])]
return chart
def collect(request):
success = utils.collect()
end = datetime.datetime.now()
if success:
html = "<html><body>Collection Complete at %s</body></html>" % (end)
else:
html = "<html><body>Collection Failed</body></html>"
print("request received")
return HttpResponse(html)
def collect(request):
success = utils.collect()
end = datetime.datetime.now()
if success:
html = "<html><body>Collection Complete at %s</body></html>" % (end)
else:
html = "<html><body>Collection Failed</body></html>"
print("request received")
return HttpResponse(html)
def inverse(self, z):
batch_size = z.shape[0]
inv_ldj = z.new_zeros(batch_size)
for layer, indexI, indexJ in reversed(
list(zip(self.layers, self.indexI, self.indexJ))):
z, z_ = utils.dispatch(indexI, indexJ, z)
z_ = utils.stackRGblock(z_)
z_, log_prob = layer.inverse(z_)
inv_ldj = inv_ldj + log_prob.view(batch_size, -1).sum(dim=1)
z_ = utils.unstackRGblock(z_, batch_size)
z = utils.collect(indexI, indexJ, z, z_)
return z, inv_ldj
def get_action(self, gamestate: G) -> A:
"""
Send this gamestate to redis, wait <timeout> seconds and return
whatever action ends up in redis
"""
gamestate_id = random.getrandbits(64)
utils.write_chan(
self.r,
"commands",
ctypes.NewGamestate(
command_type="new-gamestate",
game_type=self.game_type,
gamestate_id=gamestate_id,
gamestate=gamestate.__dict__,
),
)
def event_stream(interval):
while True:
yield utils.read_chan(self.pubsub, interval)
msg_stream = (
msg
for msg in event_stream(interval=0.1)
if msg is None or msg["gamestate_id"] == gamestate_id
)
messages = utils.collect(
msg_stream, min_time=self.timeout, max_time=max(self.timeout, 5)
)
if messages is None:
utils.print_err(
f"Failed to receive message from engineservers "
f"after timeout of {max(self.timeout, 5)}",
exit=True,
)
actions = [
a["best_move"]
for a in messages
if a["gamestate_id"] == gamestate_id
]
print([a["gamestate_id"] for a in messages])
assert (
len(actions) > 0
), f"No engineserver responded with actions for gamestate id {gamestate_id}"
return actions[-1]
def forward(self, x):
# dim(x) = (B, C, H, W)
batch_size = x.shape[0]
ldj = x.new_zeros(batch_size)
for layer, indexI, indexJ in zip(self.layers, self.indexI,
self.indexJ):
x, x_ = utils.dispatch(indexI, indexJ, x)
# dim(x_) = (B, C, num_RG_blocks, K*K)
x_ = utils.stackRGblock(x_)
# dim(x_) = (B*num_RG_blocks, C, K, K)
x_, log_prob = layer.forward(x_)
ldj = ldj + log_prob.view(batch_size, -1).sum(dim=1)
x_ = utils.unstackRGblock(x_, batch_size)
x = utils.collect(indexI, indexJ, x, x_)
return x, ldj
def read_input(self):
"""Reads the input data from source given in arguments.
Returns:
A list of (hash, count, size) tuples.
"""
print("+++ Reading data from %s" % self.args.input, file=sys.stderr)
def convert(tokens):
"""A helper that converts tokens on a line to integers."""
return (int(tokens[0], 16), int(tokens[1]), int(tokens[2]))
with fileinput.input(self.args.input) as lines:
# Tokenize the lines on two spaces
tokenised = map(lambda line: line.split(" "), lines)
# Parse the tokenized data
data = map(convert, tokenised)
# Collect the data to a list since he file is closed when we leave
# this with block
return utils.collect(data)
def start(message):
response = utils.collect()
if response.get('error'):
return bot.send_message(chat_id=message.chat.id, text='Error: {}'.format(response['error']))
text = '\n'.join([f'{i}: {j}%' for i, j in response.items()])
bot.send_message(chat_id=message.chat.id, text=text)
def test_hierarchyPrior():
class UniTestPrior(source.Source):
def __init__(self, nvars, element, name="UniTestPrior"):
super(UniTestPrior, self).__init__(nvars, 1.0, name)
self.element = torch.nn.Parameter(torch.tensor(element), requires_grad=False)
def sample(self, batchSize):
return torch.ones([batchSize] + self.nvars).to(self.element).float() * self.element
def _energy(self, z):
return (torch.tensor([2])**self.element * np.prod(z.shape[2:]))
length = 32
channel = 3
decimal = flow.ScalingNshifting(256, -128)
p1 = source.DiscreteLogistic([channel, 256, 3], decimal, rounding=utils.roundingWidentityGradient)
p2 = source.DiscreteLogistic([channel, 64, 3], decimal, rounding=utils.roundingWidentityGradient)
p3 = source.DiscreteLogistic([channel, 16, 3], decimal, rounding=utils.roundingWidentityGradient)
p4 = source.DiscreteLogistic([channel, 4, 3], decimal, rounding=utils.roundingWidentityGradient)
p5 = source.MixtureDiscreteLogistic([channel, 1, 4], 5, decimal, rounding=utils.roundingWidentityGradient)
P = source.HierarchyPrior(channel, length, [p1, p2, p3, p4, p5], repeat=1)
x = P.sample(100)
logp = P.logProbability(x)
import math
zparts = []
for no in range(int(math.log(length, 2))):
_, parts = utils.dispatch(P.factorOutIList[no], P.factorOutJList[no], x)
zparts.append(parts)
rcnX = torch.zeros_like(x)
for no in range(int(math.log(length, 2))):
part = zparts[no]
rcnX = utils.collect(P.factorOutIList[no], P.factorOutJList[no], rcnX, part)
assert_allclose(x.detach(), rcnX.detach())
length = 8
p1 = UniTestPrior([channel, 16, 3], 1)
p2 = UniTestPrior([channel, 4, 3], 2)
p3 = UniTestPrior([channel, 1, 4], 3)
Pp = source.HierarchyPrior(channel, length, [p1, p2, p3], repeat=2)
x = Pp.sample(1)
logp = Pp.logProbability(x)
target = np.array([[3, 1, 2, 1, 3, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1], [2, 1, 2, 1, 2, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1], [3, 1, 2, 1, 3, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1], [2, 1, 2, 1, 2, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1]])
assert_allclose(x[0, 0].detach().numpy(), target)
assert logp == -(16 * 3 * 2**1 + 4 * 3 * 2**2 + 1 * 4 * 2**3)
p1 = UniTestPrior([channel, 16, 3], 1)
p2 = UniTestPrior([channel, 4, 3], 2)
p3 = UniTestPrior([channel, 1, 4], 3)
Ppodd = source.HierarchyPrior(channel, length, [p1, p2, p3], repeat=1)
x = Ppodd.sample(1)
logp = Ppodd.logProbability(x)
target = np.array([[3, 1, 2, 1, 3, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1], [2, 1, 2, 1, 2, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1], [3, 1, 2, 1, 3, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1], [2, 1, 2, 1, 2, 1, 2, 1], [1, 1, 1, 1, 1, 1, 1, 1]])
assert_allclose(x[0, 0].detach().numpy(), target)
assert logp == -(16 * 3 * 2**1 + 4 * 3 * 2**2 + 1 * 4 * 2**3)
def main():
parser = argparse.ArgumentParser(description='Simple RPC code generator.')
parser.add_argument("-n",
"--name",
help="name of the RPC server code",
type=str)
parser.add_argument(
'filepath',
type=str,
nargs='*',
help='path to C++ header files that are scanned for prototypes')
parser.add_argument('--functions',
type=str,
help='comma separated list of functions to be wrapped')
parser.add_argument('--include-dir', action='store_true')
args = parser.parse_args()
if args.include_dir:
print os.path.join(os.path.dirname(__file__), 'include')
return
prototypes = defaultdict(list)
for filename in args.filepath:
original_filename = os.path.basename(filename)
prototypes[original_filename] += parse_prototypes(
filename, args.functions)
special_list = [
('set_debug_level', 'void', [('debug_level', 'const int &')],
'%(srpc)sdebug_level = debug_level;'),
('get_counter', 'uint64_t', [('', 'void')],
'%(srpc)sreturn_value = %(srpc)scounter;'),
]
for original_filename, prototype_list in prototypes.iteritems():
source_info = dict(
FILENAME=os.path.basename(original_filename).upper().replace(
'.', '_'),
original_filename=os.path.basename(original_filename),
namespace=os.path.splitext(os.path.basename(original_filename))[0],
)
server_name = source_info['namespace']
source_info['NAMESPACE'] = source_info['namespace'].upper()
for prototype in special_list:
interface_dict = make_interface_source(server_name, 'simple_rpc',
prototype)
collect(source_info, interface_dict)
for prototype in prototype_list:
interface_dict = make_interface_source(
server_name, 'simple_rpc::' + source_info['namespace'],
prototype)
del interface_dict['special_prototype']
collect(source_info, interface_dict)
client_filename = os.path.splitext(original_filename)[0] + '-rpc.hpp'
print 'creating file', client_filename
f = open(client_filename, 'w')
f.write(templates.client_header % (source_info))
f.close()
client_filename = os.path.splitext(original_filename)[0] + '-rpc.cpp'
print 'creating file', client_filename
f = open(client_filename, 'w')
f.write(templates.client_source % (source_info))
f.close()
server_filename = os.path.splitext(
original_filename)[0] + '-rpc-server.cpp'
print 'creating file', server_filename
f = open(server_filename, 'w')
f.write(templates.server_source % (source_info))
f.close()