def close(self):
info("closed game %s after %s turns (played for %s minutes)", self.id,
self.time, self.get_nb_minutes())
self.cancel()
self.server.log_status()
if config.record_games:
self.f.close()
def Closing(self, event): # Cleanup cleanup, everybody do your share
#self.thread.StopThreads()
#self.thread.Destroy()
log.info(_("Cleaning up plugins"))
for name, instance, type, version in plugins.InterfacePluginList: instance.cleanup()
log.info(_("Shutting down"))
self.Destroy()
def coordlink(request):
world = World.objects.get(name=request.POST['namespace'])
if not permissions.can_coordlink(request.user, world):
return response_403()
tileY, tileX = int(request.POST['tileY']), int(request.POST['tileX'])
tile, _ = Tile.objects.get_or_create(world=world, tileY=tileY, tileX=tileX)
if tile.properties.get('protected'):
if not permissions.can_admin(request.user, world):
# TODO: log?
return HttpResponse('')
# Must convert to str because that's how JsonField reads the existing keys
charY = int(request.POST['charY'])
charX = int(request.POST['charX'])
assert charY < Tile.ROWS
assert charX < Tile.COLS
charY, charX = str(charY), str(charX)
link_tileY = str(int(request.POST['link_tileY']))
link_tileX = str(int(request.POST['link_tileX']))
if 'cell_props' not in tile.properties:
tile.properties['cell_props'] = {}
if charY not in tile.properties['cell_props']:
tile.properties['cell_props'][charY] = {}
if charX not in tile.properties['cell_props'][charY]:
tile.properties['cell_props'][charY][charX] = {}
tile.properties['cell_props'][charY][charX]['link'] = {
'type': 'coord',
'link_tileY': link_tileY,
'link_tileX': link_tileX,
}
tile.save()
log.info('ACTION:COORDLINK %s %s %s %s %s %s %s' % (world.id, tileY, tileX, charY, charX, link_tileY, link_tileX))
return HttpResponse('')
def urllink(request):
# TODO: factor out w/above
world = World.objects.get(name=request.POST['namespace'])
if not permissions.can_urllink(request.user, world):
return response_403()
tileY, tileX = int(request.POST['tileY']), int(request.POST['tileX'])
tile, _ = Tile.objects.get_or_create(world=world, tileY=tileY, tileX=tileX)
if tile.properties.get('protected'):
if not permissions.can_admin(request.user, world):
# TODO: log?
return HttpResponse('')
# Must convert to str because that's how JsonField reads the existing keys
charY = int(request.POST['charY'])
charX = int(request.POST['charX'])
assert charY < Tile.ROWS
assert charX < Tile.COLS
charY, charX = str(charY), str(charX)
url = request.POST['url'].strip()
if not urlparse.urlparse(url)[0]: # no scheme
url = 'http://' + url
if 'cell_props' not in tile.properties:
tile.properties['cell_props'] = {}
if charY not in tile.properties['cell_props']:
tile.properties['cell_props'][charY] = {}
if charX not in tile.properties['cell_props'][charY]:
tile.properties['cell_props'][charY][charX] = {}
tile.properties['cell_props'][charY][charX]['link'] = {
'type': 'url',
'url': url,
}
tile.save()
log.info('ACTION:URLLINK %s %s %s %s %s %s' % (world.id, tileY, tileX, charY, charX, url))
return HttpResponse('')
def count_blast_hits(self):
"""Make sure we have blast hits."""
count = db.sra_blast_hits_count(
self.state['cxn'], self.state['iteration'])
log.info('{} blast hits in iteration {}'.format(
count, self.state['iteration']))
return count
def filter_contigs(assembler):
"""Remove junk from the assembled contigs."""
log.info('Saving assembled contigs: iteration {}'.format(
assembler.state['iteration']))
blast_db = blast.temp_db_name(
assembler.state['iter_dir'], assembler.state['blast_db'])
hits_file = blast.output_file_name(
assembler.state['iter_dir'], assembler.state['blast_db'])
blast.create_db(
assembler.state['iter_dir'], assembler.file['output'], blast_db)
blast.against_contigs(
blast_db,
assembler.state['query_target'],
hits_file,
protein=assembler.args['protein'],
db_gencode=assembler.args['db_gencode'],
temp_dir=assembler.args['temp_dir'])
save_blast_against_contigs(assembler, hits_file)
all_hits = {row['contig_id']: row
for row
in db.get_contig_blast_hits(
assembler.state['cxn'],
assembler.state['iteration'])}
return save_contigs(assembler, all_hits)
def _resultConsumer(self, delayedResult):
jobID = delayedResult.getJobID()
assert jobID == self.jobID
try:
result = delayedResult.get()
except Exception, exc:
log.info( "Result for job %s raised exception: %s" % (jobID, exc) )
return
def unregister(self):
try:
info("unregistering server...")
s = urllib.urlopen(UNREGISTER_URL + "?ip=" + self.ip).read()
except:
s = "couldn't access to the metaserver"
if s:
warning("couldn't unregister from the metaserver (%s)", s[:80])
def nothing_assembled(self):
"""Make there is assembler output."""
if not exists(self.file['output']) \
or not getsize(self.file['output']):
log.info('No new assemblies in iteration {}'.format(
self.state['iteration']))
return True
return False
def start_server_and_connect(parameters):
info("active threads: %s", threading.enumerate())
ServerInAThread(parameters).start()
time.sleep(.01) # Linux needs a small delay (at least on the Eee PC 4G)
revision_checker.start_if_needed()
connect_and_play()
info("active threads: %s", threading.enumerate())
sys.exit()
def handle_message(message):
if 'text' in message and message['entities']:
return handle_message_with_entities(message)
elif 'friends' in message:
log.info('Got %d friends on startup', len(message['friends']))
elif 'delete' in message:
pass
else:
log.warn('Skipping message: %r', message)
def initialize(self):
do('rm -f %s/*' % config.config['main']['populationPath'])
do('mkdir %s' % config.config['main']['populationPath'])
do('echo > %s' % config.config['main']['logPath'])
for i in range(0, config.config['ga']['populationSize']):
genome = self.genomeType()
genome.create()
self.genomes.append(genome)
log.info('initialized population of %d genomes' % config.config['ga']['populationSize'])
def check_count_limit(self, type_name):
t = self.world.unit_class(type_name)
if t is None:
info("couldn't check count_limit for %r", type_name)
return False
if t.count_limit == 0:
return True
if self.future_count(t.type_name) >= t.count_limit:
return False
return True
def _delay(self):
max_delay = max([p.delay for p in self.human_players])
if max_delay > .6:
info("max_delay=%s => max_delay=.6")
max_delay = .6
turn_duration = VIRTUAL_TIME_INTERVAL / 1000.0 / float(self.speed)
nb_turns = int(max_delay / turn_duration) + 1
info("max_delay=%s turn_duration=%s => %s buffered turns", max_delay,
turn_duration, nb_turns)
return nb_turns
def quit_game(self, client): # called by a client already out of the game interface
info("%s has quit from game %s after %s turns", client.login, self.id, self.time)
self.human_players.remove(client)
client.state = InTheLobby()
if self.human_players:
# remove the queue, and update the orders
del self.all_orders[client]
self._dispatch_orders_if_needed()
else:
self.close()
def queue_command(self, player, s):
if player not in self.player.world.players:
info("didn't send the order for player %s: %s", player, s)
return
if self.game_session.record_replay:
player_index = self.player.world.players.index(player)
self.game_session.replay_write(" ".join(map(str, (self.player.world.time, player_index, s))))
if not hasattr(self, "_orders"):
self._orders = []
self._orders.append((player, s))
def refresh_tweetstream( tweetstream_key ):
log.info("refreshing tweetstream %s" % tweetstream_key )
# the stream to update
stream = twitter.TweetStream.get_by_urlsafe(tweetstream_key)
# refresh the query
s = Twitter.search( qs = stream.stream_query ) # based on the query string
s.fetch(process_tweets, {"stream-key":tweetstream_key})
def _play(self):
if not self._plan: return
if self.watchdog and self.world.time > \
self._previous_linechange + self.watchdog * 1000:
self._line_nb += 1
self._line_nb %= len(self._plan)
line = self._plan[self._line_nb]
cmd = line.split()
if cmd:
if cmd[0] == "goto":
if re.match("^[+-][0-9]+$", cmd[1]):
self._line_nb += int(cmd[1])
elif "label " + cmd[1] in self._plan:
self._line_nb = self._plan.index("label " + cmd[1])
elif re.match("^[0-9]+$", cmd[1]):
self._line_nb = int(cmd[1])
else:
warning("goto: wrong destination: %s", cmd[1])
self._line_nb += 1
elif cmd[0] == "label":
self._line_nb += 1
info(cmd[1])
elif cmd[0] == "goto_random":
dest = worldrandom.choice(cmd[1:])
if "label " + dest in self._plan:
self._line_nb = self._plan.index("label " + dest)
else:
warning("goto_random: label not found: %s", dest)
self._line_nb += 1
elif cmd[0] == "attack":
self.attack()
self._line_nb += 1
elif cmd[0] in ("retaliate", "watchdog", "constant_attacks",
"research", "teleportation", "send_soldiers_to_base", "raise_dead"):
setattr(self, cmd[0], int(cmd[1]))
self._line_nb += 1
elif cmd[0] == "get":
n = 1
done = True
for w in cmd[1:]:
if re.match("^[0-9]+$", w):
n = int(w)
elif w in rules.classnames():
if not self.get(n, self.equivalent(w)):
done = False
break
n = 1
else:
warning("get: unknown unit: '%s' (in ai.txt)", w)
n = 1
if done:
self._line_nb += 1
else:
warning("unknown command: '%s' (in ai.txt)", cmd[0])
self._line_nb += 1
def protect(request):
world = World.objects.get(name=request.POST['namespace'])
if not permissions.can_admin(request.user, world):
return response_403()
tileY, tileX = request.POST['tileY'], request.POST['tileX']
# TODO: select for update
tile, _ = Tile.objects.get_or_create(world=world, tileY=tileY, tileX=tileX)
tile.properties['protected'] = True
tile.save()
log.info('ACTION:PROTECT %s %s %s' % (world.id, tileY, tileX))
return HttpResponse('')
def load(self):
genome_files = glob.glob(config.config['main']['populationPath'] + '*_genome.obj')
if len(genome_files) == 0:
raise Exception('no genomes found under '+config.config['main']['populationPath'])
for genome_file in genome_files:
try:
genome = pickle.load(open(genome_file))
self.genomes.append(genome)
except EOFError:
log.error("could not load genome from file %s" % genome_file)
log.info('loaded %d genomes' % len(self.genomes))
def _register(self):
try:
s = urllib.urlopen(REGISTER_URL + "?version=%s&login=%s&ip=%s&port=%s" %
(VERSION, self.login, self.ip,
options.port)).read()
except:
s = "couldn't access to the metaserver"
if s:
warning("couldn't register to the metaserver (%s)", s[:80])
else:
info("server registered")
def handleGet(self, event):
"""Compute result in separate thread, doesn't affect GUI response."""
#self.buttonGet.Enable(False)
#self.buttonAbort.Enable(True)
self.abortEvent.clear()
self.jobID += 1
log.info( "Starting job %s in producer thread: GUI remains responsive"
% self.jobID )
delayedresult.startWorker(self._resultConsumer, self._resultProducer,
wargs=(self.jobID,self.abortEvent), jobID=self.jobID)
def no_new_contigs(self, count):
"""Make the are new contigs in the assembler output."""
if count == db.iteration_overlap_count(
self.state['cxn'],
self.state['iteration'],
self.args['bit_score'],
self.args['contig_length']):
log.info('No new contigs were found in iteration {}'.format(
self.state['iteration']))
return True
return False
def installPacks(self, projdir, packnames):
packsdir = os.path.join(projdir, 'packages')
run = self.__runRoot('xterm',
'-e sh -c \"apt-get -y -o dir::cache::archives=\\\"%s\\\" ' \
'--allow-unauthenticated install %s; echo \\\"Press [ENTER] to exit.\\\"; ' \
'read x\"' % (packsdir, packnames))
if run[0] != 0:
log.error(_('exit code:%i\n%s' % (run[0], run[1])))
log.info(_('Failed to start Xterm as root'))
return False
#log.info(_('installCache: success'))
return True
def main():
try:
for i, message in enumerate(streamer.iter_stream(STREAM_URL)):
handle_message(message)
if i and i % 100 == 0:
log.info('Processed %d messages', i)
except KeyboardInterrupt:
log.info('Bye bye!')
except Exception, e:
log.exception('Error handling message: %s', e)
log.warn('Exiting...')
return 1
def start_server_and_connect(parameters):
info("active threads: %s", threading.enumerate())
ServerInAThread(parameters).start()
# TODO: catch exceptions raised by the starting server
# for example: RegisteringError ProbablyNoInternetError
# voice.alert([4049]) # "The server couldn't probably register on the metaserver. check you are connected to the Internet."
# voice.alert([4080]) # "failure: the server couldn't start"
time.sleep(.01) # Linux needs a small delay (at least on the Eee PC 4G)
revision_checker.start_if_needed()
connect_and_play()
info("active threads: %s", threading.enumerate())
sys.exit()
def increase(self):
for param in self.params:
old = param.currentValue
param.increase()
config.config['ga'][param.name] = param.currentValue
if old != param.currentValue:
log.info('changed %s from %s to %s'%(param.name, str(old), str(param.currentValue)))
if param.name == 'genomeSize':
for param2 in self.params:
if param2.name != 'genomeSize':
param2.resetToOriginalValue()
log.info('genomeSize change triggered resetting of the other params')
break
def remove_client(self, client):
info("disconnect: %s" % client.login)
client.is_disconnected = True
if client in self.clients: # not anonymous
self.clients.remove(client)
for c in self.players_not_playing():
c.send_msg([client.login, 4259]) # ... has just disconnected
self.update_menus()
if isinstance(client.state, Playing):
client.cmd_abort_game([])
if self._is_admin(client) and not self.is_standalone:
info("the admin has disconnected => close the server")
sys.exit()
self.log_status()
def walkIndicatorItems(ind):
global level,iocEvalString, cacheItems
cache=False
lastii=ind.findall("./*[local-name()='IndicatorItem']")[-1]
#if we are to look for a filename/registry, then attributes of the hit, save the hit.
searches=walksearches(ind)
if ('FileItem/' in str(searches)) or ('RegistryItem/' in str(searches)):
cache=True
for i in ind.findall("./*[local-name()='IndicatorItem']"):
#do we know how to handle this IOC?
#split it into category/attribute
itemTarget=i.Context.attrib.get("search")
iocMajorCategory=itemTarget.split('/')[0]
iocAttribute=itemTarget.split('/')[-1]
#some ioc attributes are all lower, 1 upper, then lower, camel case, etc..normalize to lower case.
iocAttribute=iocAttribute.lower()
#optimistic result default. change if you are pessimistic ;-]
iocResult= False
#let python tell us what functions we support by eval'ing our include iocItems modules.
if iocMajorCategory in dir(iocItems):
if iocAttribute in dir(eval(iocMajorCategory)):
#tell the function about items we've cached?
if 'cacheItems' in eval(iocMajorCategory + '.' + iocAttribute + '.func_code.co_varnames'):
#iocResult=eval(iocMajorCategory + '.' + iocAttribute + '("' + str(i.Content) + '")')
if cache:
iocResult=eval("%s.%s(r'%s',cacheItems,True)" %(iocMajorCategory,iocAttribute,i.Content))
debug('cache items: %s' %(str(cacheItems)))
else:
iocResult=eval("%s.%s(r'%s',[],False)" %(iocMajorCategory,iocAttribute,i.Content))
else:
#iocResult=eval(iocMajorCategory + '.' + iocAttribute + '("' + str(i.Content) + '")')
iocResult=eval("%s.%s(r'%s')" %(iocMajorCategory,iocAttribute,i.Content))
else:
debug('cannot evaluate %s'%( (iocMajorCategory + '.' + iocAttribute + '("' + str(i.Content) + '")')))
else:
debug('cannot evaluate %s'%( (iocMajorCategory + '.' + iocAttribute + '("' + str(i.Content) + '")')))
logicOperator=str(i.getparent().attrib.get("operator")).lower()
if i == lastii:
debug('\t'*level + str(iocResult))
info('\t'*level + i.Context.attrib.get("search") + ' ' + i.attrib.get("condition") + ' ' + str(i.Content))
iocEvalString+=' ' + str(iocResult)
else:
debug('\t'*level + str(iocResult) +' ' + str(logicOperator))
info('\t'*level + i.Context.attrib.get("search") + ' ' + i.attrib.get("condition") + ' ' + str(i.Content) + ' ' + str(logicOperator))
iocEvalString+=' ' + str(iocResult) + ' ' + str(logicOperator)
def abort_game(self, client): # called by a client already out of the game interface
info("%s has disconnected from game %s after %s turns", client.login, self.id, self.time)
self.human_players.remove(client)
client.state = InTheLobby() # useful if the client just aborted a game but has not disconnected
if self.human_players:
# give the last order for the other players
for p in self.human_players:
self.all_orders[p].insert(0, ["update" + NEWLINE_REPLACEMENT, None])
self.all_orders[client].insert(0, ["quit" + NEWLINE_REPLACEMENT, None])
self._dispatch_orders_if_needed()
# remove the queue, and update the orders
del self.all_orders[client]
self._dispatch_orders_if_needed()
else:
self.close()
def delete_snap(self):
add_test_info.sub_test_info("6", "Delete VM snap")
snap_to_delete = self.nova_server.snap_delete(self.snap.snap)
assert snap_to_delete.execute, "Snap deletion error"
snapshot = self.nova_server.get_snap(self.snap.snap)
self.timer.wait_for_state_change(snapshot.snap.status, "ACTIVE")
log.info("status: %s" % snapshot.snap.status)
snap_exists = self.nova_server.get_snap(self.snap.snap)
if snap_exists.snap.status == "DELETED":
log.info("VM snap deleted")
else:
log.error("Snap status: %s" % snap_exists.snap.status)
raise AssertionError("VM snap still exists")
add_test_info.sub_test_completed_info()
def write_input_files(self):
"""Write blast hits and matching ends to fasta files."""
log.info('Writing assembler input files: iteration {}'.format(
self.state['iteration']))
with open(self.file['paired_1'], 'w') as end_1, \
open(self.file['paired_2'], 'w') as end_2:
for row in db.get_blast_hits_by_end_count(self.state['db_conn'],
self.state['iteration'],
2):
self.file['paired_count'] += 1
out_file = end_1 if row['seq_end'] == '1' else end_2
out_file.write('>{}/{}\n'.format(row['seq_name'],
row['seq_end']))
out_file.write('{}\n'.format(row['seq']))
with open(self.file['single_1'], 'w') as end_1, \
open(self.file['single_2'], 'w') as end_2, \
open(self.file['single_any'], 'w') as end_any:
for row in db.get_blast_hits_by_end_count(self.state['db_conn'],
self.state['iteration'],
1):
if row['seq_end'] == '1':
out_file = end_1
seq_end = '/1'
self.file['single_1_count'] += 1
elif row['seq_end'] == '2':
out_file = end_2
seq_end = '/2'
self.file['single_2_count'] += 1
else:
out_file = end_any
seq_end = ''
self.file['single_any_count'] += 1
out_file.write('>{}{}\n'.format(row['seq_name'], seq_end))
out_file.write('{}\n'.format(row['seq']))
def handle_upload():
submit = php_get("submit")
if submit == "cancel":
cancel_pending_events()
elif submit == "commit":
commit_pending_events()
elif submit == "submitfile":
ftype = php_get("fieldType")
meta = FILES["fieldFile"]
filename = meta["tmp_name"]
name = meta["name"]
events = None
message = None
log.info("Handling %s file upload: %s", ftype, filename)
if ftype == "varioustxt":
events, sheetcount, rowcount = read_various_text(filename, name)
elif ftype == "storythemes":
events, sheetcount, rowcount = read_storythemes(filename)
elif ftype == "compactstorythemes":
message = expload_compact_storythemes(filename)
elif ftype == "storydefinitions":
events, sheetcount, rowcount = read_stories(filename)
elif ftype == "themedefinitions":
events, sheetcount, rowcount = read_themes(filename)
else:
message = "Type %s is not yet supported" % ftype
if message is None and events is not None:
save_pending_events(events)
message = "" if events else "Nothing to do."
message += " Found %s changes in %s sheets and %s rows." % (
len(events),
sheetcount,
rowcount,
)
return message
def delete_backup(self, backup):
add_test_info.sub_test_info('5', 'delete backup')
backup_to_delete = self.cinder_backup.delete_backup(backup)
assert backup_to_delete.execute, "Backup delete initialize error"
backup_exists = self.cinder_backup.get_backup(backup_to_delete)
self.timer.wait_for_state_change(backup_exists.status, 'deleting')
log.info('status: %s' % backup_exists.status)
backup_exists = self.cinder_backup.get_backup(backup_to_delete)
if not backup_exists.status:
log.info('backup deleted')
else:
log.error('Backup status: %s' % backup_exists.status)
raise AssertionError("Backup still exists")
add_test_info.sub_test_completed_info()
def create_query_from_contigs(args, assembler):
"""Crate a new file with the contigs used as the next query."""
log.info('Creating new query files: iteration {}'.format(
assembler.state['iteration']))
query_dir = join(args['temp_dir'], 'queries')
os.makedirs(query_dir, exist_ok=True)
query_file = assembler.file_prefix() + 'long_reads.fasta'
query = join(query_dir, query_file)
assembler.file['long_reads'] = query
with open(query, 'w') as query_file:
for row in db.get_assembled_contigs(assembler.state['cxn'],
assembler.state['iteration'],
assembler.args['bit_score'],
assembler.args['contig_length']):
util.write_fasta_record(query_file, row[0], row[1])
return query
def remove_client(self, client):
info("disconnect: %s" % client.login)
client.is_disconnected = True
if client in self.clients: # not anonymous
self.clients.remove(client)
for c in self.players_not_playing():
if client.is_compatible(c):
c.send_msg([client.login,
4259]) # ... has just disconnected
self.update_menus()
if isinstance(client.state, Playing):
client.cmd_abort_game([])
elif isinstance(client.state, WaitingForTheGameToStart):
client.cmd_unregister([])
elif isinstance(client.state, OrganizingAGame):
client.cmd_cancel_game([])
if self._is_admin(client) and not self.is_standalone:
info("the admin has disconnected => close the server")
sys.exit()
self.log_status()
def _validate(self, field, force=False):
if not field.input:
return
try:
# self._set_field_status(field, self.STATUS_LOADING, '')
value = field.input.get_value()
if field.validator:
result = field.validator(field, value)
value = value if result is None else result
log.info('Validation passed for %s.%s', self.namespace,
field.name)
self._set_field_status(field, self.STATUS_OK, '')
except Exception as err:
log.warn('Validation Error for %s.%s: %s', self.namespace,
field.name, err)
self._set_field_status(field, self.STATUS_ERROR, str(err))
finally:
log.info('Setting value %s.%s: %s', self.namespace, field.name,
value)
field.value = value
def sign_release(infile):
"""
Signs both the clearsign and the detached signature of a Release file.
Takes a valid path to a release file as an argument.
"""
args = ['gpg', '-q', '--default-key', signingkey, '--batch', '--yes',
'--homedir', gpgdir]
clearargs = args + ['--clearsign', '-a', '-o',
infile.replace('Release', 'InRelease'), infile]
detachargs = args + ['-sb', '-o', infile+'.gpg', infile]
info('Signing Release (clearsign)')
cleargpg = Popen(clearargs)
cleargpg.wait(timeout=5)
info('Signing Release (detached sign)')
detachgpg = Popen(detachargs)
detachgpg.wait(timeout=5)
def delete_vol(self, volume):
add_test_info.sub_test_info('4', 'delete volume')
vol_to_delete = self.cinder_volume.delete_volume(volume=volume)
assert vol_to_delete.execute, "snapshot volume delete initialize error"
volume_exists = self.cinder_volume.get_volume(volume)
self.timer.wait_for_state_change(volume_exists.status, 'deleting')
log.info('status: %s' % volume_exists.status)
volume_exists = self.cinder_volume.get_volume(volume)
if not volume_exists.status:
log.info('snapshot volume deleted')
else:
log.error('volume status: %s' % volume_exists.volume.status)
raise AssertionError("snapshot volume still exists")
add_test_info.sub_test_completed_info()
def blast_query_against_all_shards(assembler):
"""
Blast the query against the SRA databases.
We're using a map-reduce strategy here. We map the blasting of the query
sequences and reduce the output into one fasta file.
"""
log.info('Blasting query against shards: iteration {}'.format(
assembler.state['iteration']))
all_shards = shard_fraction(assembler)
with Pool(processes=assembler.args['cpus']) as pool:
results = [
pool.apply_async(blast_query_against_one_shard,
(assembler.args, assembler.simple_state(), shard))
for shard in all_shards
]
all_results = [result.get() for result in results]
log.info('All {} blast results completed'.format(len(all_results)))
def abort_game(
self,
client): # called by a client already out of the game interface
info("%s has disconnected from game %s after %s turns", client.login,
self.id, self.time)
self.human_players.remove(client)
client.state = InTheLobby(
) # useful if the client just aborted a game but has not disconnected
if self.human_players:
# give the last order for the other players
for p in self.human_players:
self.all_orders[p].insert(
0, ["update" + NEWLINE_REPLACEMENT, None])
self.all_orders[client].insert(
0, ["quit" + NEWLINE_REPLACEMENT, None])
self._dispatch_orders_if_needed()
# remove the queue, and update the orders
del self.all_orders[client]
self._dispatch_orders_if_needed()
else:
self.close()
def create_vol(self, name, size):
add_test_info.sub_test_info('1', 'create volume')
init_create_volume = self.cinder_volume.create_volume(name, size)
assert init_create_volume.status, "Volume Create initialize error"
log.info('volume_name %s' % init_create_volume.vol.name)
self.timer.wait_for_state_change(init_create_volume.vol.status,
'creating')
volume = self.cinder_volume.get_volume(init_create_volume.vol)
assert volume.status, "Volumes Does Exist, hence did not create"
self.volume = volume.volume
log.info('volume exist status: %s' % volume.volume.status)
add_test_info.sub_test_completed_info()
def preprocess(args):
"""Build the databases required by atram."""
log.setup(args['log_file'], args['blast_db'])
with util.make_temp_dir(where=args['temp_dir'],
prefix='atram_preprocessor_',
keep=args['keep_temp_dir']) as temp_dir:
util.update_temp_dir(temp_dir, args)
with db.connect(args['blast_db'], clean=True) as cxn:
db.create_metadata_table(cxn)
db.create_sequences_table(cxn)
load_seqs(args, cxn)
log.info('Creating an index for the sequence table')
db.create_sequences_index(cxn)
shard_list = assign_seqs_to_shards(cxn, args['shard_count'])
create_all_blast_shards(args, shard_list)
def snapshot_delete(self):
add_test_info.sub_test_info('5', 'delete snapshot')
snap_delete = self.cinder_snap.delete_snapshot(self.snapshot)
assert snap_delete, "Snapshot delete initialize error"
snapshot_exists = self.cinder_snap.get_snapshot(self.snapshot)
self.timer.wait_for_state_change(snapshot_exists.snapshot.status,
'deleting')
log.info('status: %s' % snapshot_exists.snapshot.status)
snapshot_exists = self.cinder_snap.get_snapshot(self.snapshot)
if not snapshot_exists.status:
log.info('snapshot deleted')
else:
log.error('snapshot status: %s' % snapshot_exists.snapshot.status)
raise AssertionError("snapshot still exists")
add_test_info.sub_test_completed_info()
def delete_server(self):
add_test_info.sub_test_info("3", "Delete VM")
vm_to_delete = self.nova_server.vm_delete(self.vm.vm)
assert vm_to_delete.execute, "VM deletion error"
vm_exists = self.nova_server.vm_details(self.vm.vm)
self.timer.wait_for_state_change(vm_exists.vm.status, "ACTIVE")
time.sleep(10)
log.info("status: %s" % vm_exists.vm.status)
vm_exists = self.nova_server.vm_details(self.vm.vm)
if not vm_exists.status:
log.info("VM deleted")
else:
log.error("VM status: %s" % vm_exists.vm.status)
raise AssertionError("VM still exists")
add_test_info.sub_test_completed_info()
def delete_server(self, server):
add_test_info.sub_test_info('5', 'Delete VM')
vm_to_delete = self.nova_server.vm_delete(server)
assert vm_to_delete.execute, 'VM deletion error'
vm_exists = self.nova_server.vm_details(server)
self.timer.wait_for_state_change(vm_exists.vm.status, 'ACTIVE')
log.info('status: %s' % vm_exists.vm.status)
time.sleep(10)
vm_exists = self.nova_server.vm_details(server)
if not vm_exists.status:
log.info('VM deleted')
else:
log.error('VM status: %s' % vm_exists.vm.status)
raise AssertionError("VM still exists")
add_test_info.sub_test_completed_info()
def stopRunningJob(status_file,log_dir,lib_dir,branch):
state_obj = status.getState(status_file)
cleaned = False
pid = getPid()
if pid != None:
log.info(u"Job with pid '{}' killed.".format(pid))
os.kill(int(pid), signal.SIGTERM)
cleaned = True
# Prepare file
job.modifyStoppedFile(log_dir, state_obj,branch)
if state_obj["vid"] != None:
if virtualbox.destroyMachine(state_obj["vid"]):
cleaned = True
else:
log.info(u"Cleaning status file.")
status.setVID(status_file,None)
virtualbox.checkMachines(lib_dir, False)
if cleaned:
if state_obj != None:
status.setState(status_file,u"cleaned")
return status.getState(status_file);
else:
log.info(u"Nothing stopped.")
return None
def exec_test_1():
uuid.set_env()
global add_test_info
add_test_info = AddTestInfo(
4, "Restore Backup of the volume to a new volume of the same size")
try:
add_test_info.started_info()
cinder_auth = CinderAuth()
auth = cinder_auth.auth()
assert auth.status, "Authentication Failed"
cinder_volume = CindeVolumeTest(auth)
volume1 = cinder_volume.create_vol("test_volume1", 1)
backup = cinder_volume.take_backup(volume1, "test_volume1_bkp")
volume2 = cinder_volume.create_vol("test_volume_2", 1)
restore = cinder_volume.restore_backup(backup, volume2)
cinder_volume.delete_vol(volume2)
cinder_volume.delete_backup(backup)
cinder_volume.delete_vol(volume1)
log.info("restore obj %s:" % restore)
add_test_info.success_status("ok")
except AssertionError, e:
log.error(e)
add_test_info.failed_status("error")
sys.exit(1)
def exec_test_2():
uuid.set_env()
global add_test_info
add_test_info = AddTestInfo(
5, 'Restore Backup of the volume to a larger volume ')
try:
add_test_info.started_info()
cinder_auth = CinderAuth()
auth = cinder_auth.auth()
assert auth.status, "Authentication Failed"
cinder_volume = CindeVolumeTest(auth)
volume1 = cinder_volume.create_vol('test_volume1', 1)
backup = cinder_volume.take_backup(volume1, 'test_volume1_bkp2')
volume2 = cinder_volume.create_vol('test_volume2', 2)
restore = cinder_volume.restore_backup(backup, volume2)
cinder_volume.delete_vol(volume2)
cinder_volume.delete_backup(backup)
cinder_volume.delete_vol(volume1)
log.info('restore obj %s:' % restore)
add_test_info.success_status('ok')
except AssertionError, e:
log.error(e)
add_test_info.failed_status('error')
sys.exit(1)
def assembly_loop(args, assembler, blast_db, query):
"""Iterate over the assembly processes."""
for iteration in range(1, assembler.args['iterations'] + 1):
log.info('aTRAM blast DB = "{}", query = "{}", iteration {}'.format(
blast_db,
split(query)[1], iteration))
assembler.init_iteration(blast_db, query, iteration)
with util.make_temp_dir(where=assembler.args['temp_root'],
prefix=assembler.file_prefix(),
keep=args['keep_temp_dir']) as iter_dir:
assembler.setup_files(iter_dir)
query = assembly_loop_iteration(args, assembler)
if not query:
break
else:
log.info('All iterations completed')
def _get(self, nb, types):
self._safe_cnt += 1
if self._safe_cnt > 10:
info("AI has trouble getting: %s %s", nb, types)
self.AI_timer = 100
return False
if isinstance(types, str):
types = [types]
if self.nb(types) >= nb:
return True
for type in types:
if type.__class__ == str:
type = self.world.unit_class(type)
if type is None:
continue
if self.nb(self.world.get_makers(type)) > 0:
self.build_or_train_or_upgradeto(type, nb - self.nb(types))
break
elif self.world.get_makers(type):
self._get(1, self.world.get_makers(type)[0])
return False
return False
def load_one_file(args, cxn, file_name, ends, seq_end_clamp=''):
"""Load sequences from a fasta/fastq file into the atram database."""
log.info('Loading "{}" into sqlite database'.format(file_name))
parser = get_parser(args, file_name)
with util.open_file(args, file_name) as sra_file:
batch = []
for rec in parser(sra_file):
title = rec[0].strip()
seq = rec[1]
seq_name, seq_end = blast.parse_fasta_title(
title, ends, seq_end_clamp)
batch.append((seq_name, seq_end, seq))
if len(batch) >= db.BATCH_SIZE:
db.insert_sequences_batch(cxn, batch)
batch = []
db.insert_sequences_batch(cxn, batch)
def __init__(self, name, bases, dct):
self.__name__ = name
self.type_name = name
self.cls = bases[0]
if "cost" not in dct and hasattr(self.cls, "cost"):
dct["cost"] = [0] * rules.get("parameters", "nb_of_resource_types")
if "sight_range" in dct and dct["sight_range"] == 1 * PRECISION:
dct["sight_range"] = 12 * PRECISION
dct["bonus_height"] = 1
info(
"in %s: replacing sight_range 1 with sight_range 12 and bonus_height 1",
name)
if "special_range" in dct:
del dct["special_range"]
dct["range"] = 12 * PRECISION
dct["minimal_range"] = 4 * PRECISION
dct["is_ballistic"] = 1
info(
"in %s: replacing special_range 1 with range 12, minimal_range 4 and is_ballistic 1",
name)
self.dct = dct
self.init_dict(self)
def sentMessage(self, obj):
item = self.autoMessage.get((self.className, self.method), None)
if not item:
return
userClassHelper = ClassHelper("UserInfo")
userInfo = userClassHelper.find_one({"user": self.userId},
{'nickName': 1})
if not userInfo:
return
obj.update(userInfo)
title = item['title'].format(**obj)
template = item['template'].format(**obj)
# TODO
pushData = {"userid": obj['to'], "title": title, "text": template}
log.info("Push Data:%s", json.dumps(pushData))
try:
res = requests.post(self.pushUrl,
data=json.dumps(pushData),
headers={'X-MeCloud-Debug': '1'})
print res.text
except Exception, ex:
log.err("Push Err:%s", ex)
def add(url, source_id, source_url):
"""Add a URL from a specific source to the datastore. source_id should be
the Twitter user ID of a source and source_url should be the URL to the
specific tweet where the URL was found.
Returns the number of times we've seen the URL.
Under the hood, information about a URL is recorded in a couple of places:
1. The source_url is stored under a key composed of the sha1 hashes of
the source_id and the url. This ensures that we record only the first
source of a given URL shared by a given user.
2. The key from above is added to a set under a key composed of the sha1
hash of the url. The size of this set indicates whether a given link
is over the threshold. The sort value of the key in the set is the
timestamp at which we saw the corresponding URL.
"""
url_hash = sha1_hash(url)
source_hash = sha1_hash(str(source_id))
url_key = 'url:' + url_hash
source_key = 'src:{}:{}'.format(source_hash, url_hash)
ttl = 60 * 60 * 12
pipe = DB.pipeline()
pipe.setnx(source_key, source_url)
pipe.zadd(url_key, source_key, time.time())
pipe.zcount(url_key, '-inf', 'inf')
pipe.expire(url_key, ttl)
pipe.expire(source_key, ttl)
source_key_added, url_key_added, url_key_count, _, _ = pipe.execute()
if not source_key_added:
log.info('URL %s from user %s already in datastore', url, source_id)
return url_key_count
def start_face_cal():
"""
开始计算人脸向量
:return:
"""
media_helper = ClassHelper('Media')
client = RedisDb.get_connection(dbid=1)
redis_key = _build_media_redis_key()
while client.llen(redis_key):
media_id = client.lpop(redis_key)
media = media_helper.get(media_id)
if not media:
log.err('media not found: %s' % media_id)
continue
faces = get_faces_from_media_id(media_id)
face_ids = []
for face_info in faces:
face_info['media'] = media_id
face = create_face_db(face_info)
face_ids.append(face['_id'])
# 没有获取到的话就不更新了
if face_ids:
media_helper.update(media_id, {'$set': {'faces': face_ids}})
log.info('media face calculate finish: %s' % media_id)
def assembly_loop(assembler, blast_db, query):
"""Iterate the assembly processes."""
for iteration in range(1, assembler.args['iterations'] + 1):
log.info('aTRAM blast DB = "{}", query = "{}", iteration {}'.format(
blast_db, query, iteration))
assembler.initialize_iteration(blast_db, query, iteration)
os.makedirs(assembler.iter_dir(), exist_ok=True)
blast_query_against_all_shards(assembler)
if assembler.blast_only or assembler.no_blast_hits():
break
assembler.write_input_files()
assembler.run()
if assembler.nothing_assembled():
break
high_score = filter_contigs(assembler)
count = assembler.assembled_contigs_count(high_score)
if not count:
break
if assembler.no_new_contigs(count):
break
query = create_query_from_contigs(assembler)
else:
log.info('All iterations completed')
def showRunningJobs(lib_dir):
pid = getPid()
if pid != None:
log.info(u"Main process is running with pid '{}'.".format(pid))
else:
log.info(u"Main process is not running.")
processes = []
ci_result = helper.execCommand("ps -alx | grep 'ci_job_handler'")
ci_lines = ci_result.stdout.decode("utf-8").split(u"\n")
formatProcesses(ci_lines,processes)
vm_result = helper.execCommand("ps -alx | grep virtualbox")
vm_lines = vm_result.stdout.decode("utf-8").split(u"\n")
formatProcesses(vm_lines,processes)
if len(processes) > 0:
log.info(u"Following sub processes are running.")
log.info(u"\n".join(processes))
else:
log.info(u"No sub processes are running.")
virtualbox.checkMachines(lib_dir, True)
def fetch_plex_instance(pi_dash, username=None, password=None, host=None):
username = username or pi_dash.config.get('plexserver', 'username', from_keyring=True)
password = password or pi_dash.config.get('plexserver', 'password', from_keyring=True)
host = host or pi_dash.config.get('plexserver', 'host', '')
if username:
log.info('Logging into MyPlex with user %s', username)
user = MyPlexAccount.signin(username, password)
log.info('Connecting to Plex host: %s', host)
return user.resource(host).connect()
log.info('Connecting to Plex host: %s', host)
return PlexServer(host)
def main():
log.info('Starting thresholderbot...')
try:
for i, message in enumerate(streamer.iter_stream(STREAM_URL)):
handle_message(message)
if i and i % 100 == 0:
log.info('Processed %d messages', i)
except KeyboardInterrupt:
log.info('Bye bye!')
except Exception, e:
log.exception('Error handling message: %s', e)
log.warn('Exiting...')
return 1