def basic_setup(self):
global log, M
if self.args[0]:
# Probably being called from the command line - load the config file
self.config = conf = appconfig("config:%s" % self.args[0], relative_to=os.getcwd())
# ... logging does not understand section#subsection syntax
logging_config = self.args[0].split("#")[0]
logging.config.fileConfig(logging_config, disable_existing_loggers=False)
log = logging.getLogger("allura.command")
log.info("Initialize command with config %r", self.args[0])
load_environment(conf.global_conf, conf.local_conf)
self.setup_globals()
from allura import model
M = model
ming.configure(**conf)
activitystream.configure(**conf)
pylons.tmpl_context.user = M.User.anonymous()
else:
# Probably being called from another script (websetup, perhaps?)
log = logging.getLogger("allura.command")
conf = pylons.config
self.tools = pylons.app_globals.entry_points["tool"].values()
for ep in iter_entry_points("allura.command_init"):
log.info("Running command_init for %s", ep.name)
ep.load()(conf)
log.info("Loaded tools")
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", required=True, help="provide name for experiment, to be used as prefix for database collections")
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--dryrun", help="Do the calculations but do not change the database (handiest with --debug 1 to see the results", action="store_true")
parser.add_argument("--configuration", help="Configuration file for experiment", required=True)
args = parser.parse_args()
simconfig = utils.TreeStructuredConfiguration(args.configuration)
if int(args.debug) == 1:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("CALCULATING GRAPH SYMMETRY STATS - Experiment: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def setUp(self):
data.set_database_port("27017")
data.set_database_hostname("localhost")
data.set_experiment_name("testupdate")
config = data.getMingConfiguration()
ming.configure(**config)
# clean out the collection
data.PerGenerationStatsPostclassification.m.remove()
self.data = dict(
simulation_time=1000,
classification_id=ObjectId("52056c3b3f07d50754eec1a3"),
classification_type="EVEN",
classification_dim=2,
classification_coarseness=4,
replication=0,
sample_size=50,
population_size=2000,
mutation_rate=0.01,
simulation_run_id="urn:uuid:07f75571-6f6b-4113-84c5-46cb8114cb72",
mode_richness=[5,3],
class_richness=2,
mode_evenness_iqv=[0.5,0.3],
class_evenness_iqv=0.25,
design_space_occupation=None,
class_innovation_interval_times=None
)
def basic_setup(self):
global log, M
if self.args[0]:
# Probably being called from the command line - load the config file
self.config = conf = appconfig('config:%s' % self.args[0],
relative_to=os.getcwd())
# Configure logging
try:
# ... logging does not understand section#subsection syntax
logging_config = self.args[0].split('#')[0]
logging.config.fileConfig(logging_config,
disable_existing_loggers=False)
except Exception: # pragma no cover
print >> sys.stderr, (
'Could not configure logging with config file %s' %
self.args[0])
log = logging.getLogger('allura.command')
log.info('Initialize command with config %r', self.args[0])
load_environment(conf.global_conf, conf.local_conf)
self.setup_globals()
from allura import model
M = model
ming.configure(**conf)
pylons.c.user = M.User.anonymous()
else:
# Probably being called from another script (websetup, perhaps?)
log = logging.getLogger('allura.command')
conf = pylons.config
self.tools = pylons.g.entry_points['tool'].values()
for ep in iter_entry_points('allura.command_init'):
log.info('Running command_init for %s', ep.name)
ep.load()(conf)
log.info('Loaded tools')
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment", required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Configuration file for experiment", required=True)
parser.add_argument("--filename", help="path to file for export", required=True)
args = parser.parse_args()
simconfig = utils.TreeStructuredConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
#### main program ####
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", required=True, help="provide name for experiment, to be used as prefix for database collections")
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--finalized", help="Only export runs which finalized after convergence", action="store_true")
parser.add_argument("--action", choices=["sample", "single", "bulk"])
parser.add_argument("--ssize", help="Sample size of graphs to export", default="100")
parser.add_argument("--id", help="Export trait graphs with this object id")
parser.add_argument("--idfile", help="Export trait graphs for ids in file")
parser.add_argument("--directory", help="Directory to which DOT files are written")
args = parser.parse_args()
if int(args.debug) == 1:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("EXPORT TRAIT GRAPHS AS DOT - Experiment: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def basic_setup(self):
global log, M
if self.args[0]:
# Probably being called from the command line - load the config
# file
self.config = conf = appconfig('config:%s' %
self.args[0], relative_to=os.getcwd())
# ... logging does not understand section#subsection syntax
logging_config = self.args[0].split('#')[0]
logging.config.fileConfig(
logging_config, disable_existing_loggers=False)
log = logging.getLogger('allura.command')
log.info('Initialize command with config %r', self.args[0])
load_environment(conf.global_conf, conf.local_conf)
self.setup_globals()
from allura import model
M = model
ming.configure(**conf)
if asbool(conf.get('activitystream.recording.enabled', False)):
activitystream.configure(**h.convert_bools(conf, prefix='activitystream.'))
pylons.tmpl_context.user = M.User.anonymous()
else:
# Probably being called from another script (websetup, perhaps?)
log = logging.getLogger('allura.command')
conf = pylons.config
self.tools = pylons.app_globals.entry_points['tool'].values()
for ep in h.iter_entry_points('allura.command_init'):
log.info('Running command_init for %s', ep.name)
ep.load()(conf)
log.info('Loaded tools')
def setup(parser):
config = parser.parse_args()
sim_id = uuid.uuid1().urn
script = __file__
if config.debug == '1':
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
data.set_experiment_name(config.experiment)
data.set_database_hostname(config.dbhost)
data.set_database_port(config.dbport)
dbconfig = data.getMingConfiguration(data.modules)
ming.configure(**dbconfig)
# set up parallelism. At the moment, this doesn't do anything on OSX
# but should provide parallelism on Linux across the replicates at least
if config.cores is not None:
cores = config.cores
else:
cores = utils.get_parallel_cores(config.devel)
log.info("Setting up %s cores for parallel simulation", cores)
import simuOpt
if(config.debug == 1):
simuOpt.setOptions(alleleType='long',optimized=True,quiet=False,numThreads = cores)
else:
simuOpt.setOptions(alleleType='long',optimized=True,quiet=False,numThreads = cores)
return (config,sim_id,script, cores)
def setup():
global args, simconfig
permitted_stage_tags = data.get_experiment_stage_tags()
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment", required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Configuration file for experiment", required=True)
parser.add_argument("--collections", choices=['postclassification', 'traits', 'both'], help="Collections to retrofit ", required=True)
args = parser.parse_args()
simconfig = utils.CTPyConfiguration(args.configuration)
if args.debug:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration()
ming.configure(**config)
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment, to be used as prefix for database collections")
parser.add_argument("--simid", help="simulation ID to export from database")
parser.add_argument("--debug", type=int, help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--outputdirectory", help="path to directory for exported data files", required=True)
args = parser.parse_args()
if args.debug == 1:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("EXPORT DATA TO CSV - Experiment: %s SimulationID: %s", args.experiment, args.simid)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment", required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Configuration file for experiment", required=True)
parser.add_argument("--parallelism", help="Number of concurrent processes to run", default="4")
parser.add_argument("--diagram", help="Draw a diagram when complete", default=False)
args = parser.parse_args()
simconfig = utils.AxelrodExtensibleConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def configure(args=None):
'''Load the options and configure the system'''
if args is None: args = sys.argv
options, args = get_options(args)
if options.verbose:
log.info('Settings:')
for k,v in sorted(options.__dict__.items()):
log.info(' %s: %r', k, v)
ming_config = {
'ming.zarkov.master':options.mongo_uri,
'ming.zarkov.database':options.mongo_database,
'ming.zarkov.use_gevent':True}
for dbinfo in options.extra_dbs:
dbinfo = dict(dbinfo)
prefix = 'ming.%s.' % dbinfo.pop('name')
for k,v in dbinfo.items():
ming_config[prefix + k] = v
if options.mongo_username:
ming_config['ming.zarkov.authenticate.name'] = options.mongo_username
if options.mongo_username:
ming_config['ming.zarkov.authenticate.password'] = options.mongo_password
ming.configure(**ming_config)
if options.pdb:
sys.excepthook = postmortem_hook
return options, args
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment", required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Configuration file for experiment", required=True)
parser.add_argument("--popsize", help="Population size", required=True)
parser.add_argument("--numloci", help="Number of loci per individual", required=True)
parser.add_argument("--maxinittraits", help="Max initial number of traits per locus for initialization", required=True)
parser.add_argument("--conformismstrength", help="Strength of conformist bias [0.0 - 1.0]", required=True)
parser.add_argument("--anticonformismstrength", help="Strength of conformist bias [0.0 - 1.0]", required=True)
parser.add_argument("--innovationrate", help="Theta value rate at which innovations occur in population", required=True)
parser.add_argument("--periodic", help="Periodic boundary condition", choices=['1','0'], required=True)
parser.add_argument("--kandlerinterval", help="Interval for Kandler remaining traits sample, taken before maxtime, in generations (will be scaled to timesteps)", default="1000")
parser.add_argument("--simulationendtime", help="Time at which simulation and sampling end, defaults to 2M steps", default="2000000")
args = parser.parse_args()
simconfig = utils.MixtureConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
simconfig.num_features = int(args.numloci)
simconfig.num_traits = int(args.maxinittraits)
simconfig.popsize = int(args.popsize)
mut = pg.moran_mutation_rate_from_theta(float(args.popsize), float(args.innovationrate))
simconfig.innovation_rate = float(args.numloci) * mut
simconfig.configured_innovation_rate = float(args.innovationrate)
log.debug("configured theta = %s, using numloci %s * per-locus mutation rate %s = all-loci innovation rate: %s", args.innovationrate, args.numloci, mut, simconfig.innovation_rate)
simconfig.maxtime = int(args.simulationendtime)
simconfig.script = __file__
simconfig.conformism_strength = float(args.conformismstrength)
simconfig.anticonformism_strength = float(args.anticonformismstrength)
simconfig.maxtime = int(args.simulationendtime)
simconfig.model_class_label = simconfig.MODEL_CLASS_LABEL
log.debug("Equifinality model class: %s", simconfig.model_class_label)
simconfig.sim_id = uuid.uuid4().urn
if args.periodic == '1':
simconfig.periodic = 1
else:
simconfig.periodic = 0
def setUp(self):
setup_unit_test()
config = {
'ming.main.uri': 'mim://host/allura_test',
}
ming.configure(**config)
for i in range(10):
M.User.upsert('sample-user-%d' % i)
def setUp(self):
ming.configure(**{
'ming.zarkov.master':'mim:///',
'ming.zarkov.database':'zarkov'})
self.options = mock.Mock()
self.options.journal_file_size = 1024
self.options.journal_min_files = 4
self.journal_dir = tempfile.mkdtemp('.journal', 'zarkov-test')
self.j = JournalWriter(self.options, self.journal_dir, start_greenlets=False)
def test_configure_optional_params(self, Connection):
ming.configure(**{
'ming.main.uri':'mongodb://localhost:27017/test_db',
'ming.main.replicaSet': 'foobar',
'ming.main.w': 2,
'ming.main.ssl': True,
})
session = Session.by_name('main')
assert session.bind.conn is not None
assert session.bind.db is not None
def test_configure_optional_params(self, Connection):
ming.configure(**{
'ming.main.uri':'mongodb://localhost:27017/test_db',
'ming.main.replicaSet': 'foobar',
'ming.main.w': 2,
'ming.main.ssl': True,
})
session = Session.by_name('main')
assert session.bind.conn is not None
assert session.bind.db is not None
def connection_configure():
from ming import configure
from ming.odm import ThreadLocalODMSession
configure(**{'ming.mysession.uri': 'mongodb://localhost:27017/tutorial'})
session = ThreadLocalODMSession.by_name('mysession')
session.db
ThreadLocalODMSession.by_name('mysession') is session
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument(
"--experiment",
help=
"provide name for experiment, to be used as prefix for database collections"
)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost",
help="database hostname, defaults to localhost",
default="localhost")
parser.add_argument("--dbport",
help="database port, defaults to 27017",
default="27017")
parser.add_argument("--configuration", help="Path to configuration file")
parser.add_argument("--model",
choices=['axelrod', 'extensible', 'treestructured'],
required=True)
parser.add_argument(
"--finalized",
help="Only export runs which finalized after convergence",
action="store_true")
parser.add_argument("--filename",
help="path to file for export",
required=True)
args = parser.parse_args()
simconfig = utils.TreeStructuredConfiguration(args.configuration)
if args.model == 'axelrod':
simconfig = utils.AxelrodConfiguration(args.configuration)
elif args.model == 'extensible':
simconfig = utils.AxelrodExtensibleConfiguration(args.configuration)
elif args.model == 'treestructured':
simconfig = utils.TreeStructuredConfiguration(args.configuration)
else:
log.error("This shouldn't happen - args.model = %s", args.model)
if args.debug == 1:
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("EXPORT DATA TO CSV - Experiment: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def test_configure(self, Connection):
ming.configure(**{
'ming.main.uri':'mongodb://localhost:27017/test_db',
'ming.main.connect_retry': 1,
'ming.main.tz_aware': False,
})
session = Session.by_name('main')
assert session.bind.conn is not None
assert session.bind.db is not None
args, kwargs = Connection.call_args
assert 'database' not in kwargs
def test_configure(self):
ming.configure(**{
'ming.main.master':'mongodb://localhost:27017/',
'ming.main.database':'test_db',
'ming.main.network_timeout':'0.1',
'ming.main.connect_retry': 1,
'ming.main.tz_aware': False,
})
session = Session.by_name('main')
assert session.bind.conn is not None
assert session.bind.db is not None
def main(global_config, **settings):
""" This function returns a Pyramid WSGI application.
"""
import ming
update_settings_from_environ(settings)
ming.configure(**settings)
config = Configurator(settings=settings)
add_routes(config)
config.scan()
return config.make_wsgi_app()
def setUp(self):
class TestDoc(Document):
class __mongometa__:
name='test_doc'
session = Session.by_name('main')
_id=Field(S.ObjectId, if_missing=None)
a=Field(S.Int, if_missing=None)
b=Field(S.Object, dict(a=S.Int(if_missing=None)))
config = {
'ming.main.master':'mongo://localhost:27017/test_db' }
ming.configure(**config)
self.session = TestDoc.__mongometa__.session
def setup_schema(command, conf, vars):
"""Place any commands to setup allura here"""
import ming
import allura
REGISTRY.prepare()
REGISTRY.register(pylons.c, EmptyClass())
REGISTRY.register(pylons.g, config['pylons.app_globals'])
REGISTRY.register(allura.credentials, allura.lib.security.Credentials())
ming.configure(**conf)
# Nothing to do
log.info('setup_schema called')
def setup_schema(command, conf, vars):
"""Place any commands to setup allura here"""
import ming
import allura
REGISTRY.prepare()
REGISTRY.register(pylons.c, EmptyClass())
REGISTRY.register(pylons.g, config["pylons.app_globals"])
REGISTRY.register(allura.credentials, allura.lib.security.Credentials())
ming.configure(**conf)
# Nothing to do
log.info("setup_schema called")
def test_configure(self, Connection):
ming.configure(**{
'ming.main.uri':'mongodb://localhost:27017/test_db',
'ming.main.connect_retry': 1,
'ming.main.tz_aware': False,
})
session = Session.by_name('main')
assert session.bind.conn is not None
assert session.bind.db is not None
assert session.bind.bind._auto_ensure_indexes
args, kwargs = Connection.call_args
assert 'database' not in kwargs
def setup_schema(command, conf, vars):
"""Place any commands to setup allura here"""
import ming
import allura
REGISTRY.prepare()
REGISTRY.register(pylons.tmpl_context, EmptyClass())
REGISTRY.register(pylons.app_globals, config['pylons.app_globals'])
REGISTRY.register(allura.credentials, allura.lib.security.Credentials())
ming.configure(**conf)
if asbool(conf.get('activitystream.recording.enabled', False)):
activitystream.configure(**h.convert_bools(conf, prefix='activitystream.'))
# Nothing to do
log.info('setup_schema called')
def setup_schema(command, conf, vars):
"""Place any commands to setup allura here"""
import ming
import allura
REGISTRY.prepare()
REGISTRY.register(pylons.tmpl_context, EmptyClass())
REGISTRY.register(pylons.app_globals, config['pylons.app_globals'])
REGISTRY.register(allura.credentials, allura.lib.security.Credentials())
ming.configure(**conf)
if asbool(conf.get('activitystream.recording.enabled', False)):
activitystream.configure(**conf)
# Nothing to do
log.info('setup_schema called')
def main(global_config, **settings):
""" This function returns a Pyramid WSGI application.
"""
config = Configurator(settings=settings)
# MongoDB connection configuration
url_str = settings.get('mongo_uri', 'mongodb://localhost:27017/default')
ming_config = {'ming.default.uri': url_str}
ming.configure(**ming_config)
config.add_static_view('static', 'static', cache_max_age=3600)
config.add_route('home', '/')
config.scan()
return config.make_wsgi_app()
def setUp(self):
config = {
'ming.main.uri': 'mim://allura',
'ming.project.uri': 'mim://project-data',
}
ming.configure(**config)
setup_unit_test()
self.session = session(File)
self.conn = M.session.main_doc_session.db._connection
self.db = M.session.main_doc_session.db
self.db.fs.remove()
self.db.fs.files.remove()
self.db.fs.chunks.remove()
def test_configure_with_database(self):
ming.configure(
**{
"ming.main.uri": "mongodb://localhost:27017/test_db",
"ming.main.database": "another_test_db",
"ming.main.connect_retry": 1,
"ming.main.tz_aware": False,
})
session = Session.by_name("main")
assert session.bind.conn is not None
assert session.bind.db is not None
assert session.bind.bind._auto_ensure_indexes
args, kwargs = self.MockConn.call_args
assert "database" in kwargs
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment", required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Configuration file for experiment", required=True)
parser.add_argument("--popsize", help="Population size", required=True)
parser.add_argument("--maxinittraits", help="Max initial number of traits per indiv", required=True)
parser.add_argument("--additionrate", help="Rate at which traits are added during interactions", required=True)
parser.add_argument("--maxtraitvalue", help="Maximum integer token for traits in the trait space", required=True)
parser.add_argument("--periodic", help="Periodic boundary condition", choices=['1','0'], required=True)
parser.add_argument("--diagram", help="Draw a diagram of the converged model", action="store_true")
parser.add_argument("--drift_rate", help="Rate of drift")
args = parser.parse_args()
simconfig = utils.AxelrodExtensibleConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
if args.drift_rate:
simconfig.drift_rate = float(args.drift_rate)
simconfig.popsize = int(args.popsize)
simconfig.maxtraits = int(args.maxinittraits)
simconfig.add_rate = float(args.additionrate)
simconfig.max_trait_value = int(args.maxtraitvalue)
simconfig.sim_id = uuid.uuid4().urn
if args.periodic == '1':
simconfig.periodic = 1
elif args.periodic == '0':
simconfig.periodic = 0
def ming_config(**conf):
"""Temporarily swap in a new ming configuration, restoring the previous
one when the contextmanager exits.
:param \*\*conf: keyword arguments defining the new ming configuration
"""
import ming
from ming.session import Session
datastores = Session._datastores
try:
ming.configure(**conf)
yield
finally:
Session._datastores = datastores
for name, session in Session._registry.iteritems():
session.bind = datastores.get(name, None)
session._name = name
def ming_config(**conf):
"""Temporarily swap in a new ming configuration, restoring the previous
one when the contextmanager exits.
:param \*\*conf: keyword arguments defining the new ming configuration
"""
import ming
from ming.session import Session
datastores = Session._datastores
try:
ming.configure(**conf)
yield
finally:
Session._datastores = datastores
for name, session in Session._registry.iteritems():
session.bind = datastores.get(name, None)
session._name = name
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument(
"--experiment",
required=True,
help=
"provide name for experiment, to be used as prefix for database collections"
)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost",
help="database hostname, defaults to localhost",
default="localhost")
parser.add_argument("--dbport",
help="database port, defaults to 27017",
default="27017")
parser.add_argument(
"--dryrun",
help=
"Do the calculations but do not change the database (handiest with --debug 1 to see the results",
action="store_true")
parser.add_argument("--configuration",
help="Configuration file for experiment",
required=True)
args = parser.parse_args()
simconfig = utils.TreeStructuredConfiguration(args.configuration)
if int(args.debug) == 1:
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("CALCULATING GRAPH SYMMETRY STATS - Experiment: %s",
args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def setup_schema(command, conf, vars):
"""Place any commands to setup allura here"""
import ming
import allura
# turbogears has its own special magic wired up for its globals, can't use a regular Registry
tgl = RequestLocals()
tgl.tmpl_context = EmptyClass()
tgl.app_globals = config['tg.app_globals']
tg.request_local.context._push_object(tgl)
REGISTRY.prepare()
REGISTRY.register(allura.credentials, allura.lib.security.Credentials())
ming.configure(**conf)
if asbool(conf.get('activitystream.recording.enabled', False)):
activitystream.configure(**h.convert_bools(conf, prefix='activitystream.'))
# Nothing to do
log.info('setup_schema called')
def http_main(global_config, **local_settings):
""" This function returns a (minimal) Pyramid WSGI application.
"""
settings = dict(global_config)
settings.update(local_settings)
config = Configurator(settings=settings)
config.add_renderer(None, 'pyramid.renderers.json_renderer_factory')
config.add_route('chapman.1_0.queue', '/1.0/q/{qname}/')
config.add_route('chapman.1_0.message', '/1.0/m/{message_id}/')
config.add_subscriber(
RequireHeader('Authorization', 'chapman %s' % settings['chapman.secret']),
NewRequest)
config.scan('chapman.views')
if not ming.Session._datastores:
ming.configure(**settings)
app = config.make_wsgi_app()
db = ming.Session.by_name('chapman').db
app = MongoMiddleware(app, db.connection)
return app
def setup():
global sargs, config, simconfig
sargs = utils.ScriptArgs()
if sargs.debug:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
simconfig = utils.CTPyConfiguration(sargs.configuration)
log.debug("experiment name: %s", sargs.experiment_name)
data.set_experiment_name(sargs.experiment_name)
data.set_database_hostname(sargs.database_hostname)
data.set_database_port(sargs.database_port)
#### main program ####
log.info("INITIALIZE_EXPERIMENT - Starting program")
config = data.getMingConfiguration()
ming.configure(**config)
def setup():
global sargs, config, simconfig
sargs = utils.ScriptArgs()
if sargs.debug == 1:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
simconfig = utils.CTPyConfiguration(sargs.configuration)
log.debug("experiment name: %s", sargs.experiment_name)
data.set_experiment_name(sargs.experiment_name)
data.set_database_hostname(sargs.database_hostname)
data.set_database_port(sargs.database_port)
log.info("CALCULATE_PERSIMRUN_STATISTICS - Starting program")
config = data.getMingConfiguration()
ming.configure(**config)
def http_main(global_config, **local_settings):
""" This function returns a (minimal) Pyramid WSGI application.
"""
settings = dict(global_config)
settings.update(local_settings)
config = Configurator(settings=settings)
config.add_renderer(None, 'pyramid.renderers.json_renderer_factory')
config.add_route('chapman.1_0.queue', '/1.0/q/{qname}/')
config.add_route('chapman.1_0.message', '/1.0/m/{message_id}/')
config.add_subscriber(
RequireHeader('Authorization',
'chapman %s' % settings['chapman.secret']), NewRequest)
config.scan('chapman.views')
if not ming.Session._datastores:
ming.configure(**settings)
app = config.make_wsgi_app()
db = ming.Session.by_name('chapman').db
app = MongoMiddleware(app, db.connection)
return app
def setup():
global sargs, config, simconfig
sargs = utils.ScriptArgs()
if sargs.debug:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
simconfig = utils.CTPyConfiguration(sargs.configuration)
log.debug("experiment name: %s", sargs.experiment_name)
data.set_experiment_name(sargs.experiment_name)
data.set_database_hostname(sargs.database_hostname)
data.set_database_port(sargs.database_port)
#### main program ####
log.info("SUBSAMPLE_INDIVIDUAL_SAMPLES - Starting program")
log.info("Performing subsampling for experiment named: %s", data.experiment_name)
config = data.getMingConfiguration()
ming.configure(**config)
def setup(parser):
config = parser.parse_args()
sim_id = uuid.uuid1().urn
script = __file__
if config.debug == '1':
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
data.set_experiment_name(config.experiment)
data.set_database_hostname(config.dbhost)
data.set_database_port(config.dbport)
dbconfig = data.getMingConfiguration(data.modules)
ming.configure(**dbconfig)
# set up parallelism. At the moment, this doesn't do anything on OSX
# but should provide parallelism on Linux across the replicates at least
if config.cores is not None:
cores = config.cores
else:
cores = utils.get_parallel_cores(config.devel)
log.info("Setting up %s cores for parallel simulation", cores)
import simuOpt
if (config.debug == 1):
simuOpt.setOptions(alleleType='long',
optimized=True,
quiet=False,
numThreads=cores)
else:
simuOpt.setOptions(alleleType='long',
optimized=True,
quiet=False,
numThreads=cores)
return (config, sim_id, script, cores)
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment",
help="provide name for experiment",
required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost",
help="database hostname, defaults to localhost",
default="localhost")
parser.add_argument("--dbport",
help="database port, defaults to 27017",
default="27017")
parser.add_argument("--configuration",
help="Configuration file for experiment",
required=True)
parser.add_argument("--parallelism",
help="Number of concurrent processes to run",
default="4")
parser.add_argument("--diagram",
help="Draw a diagram when complete",
default=False)
args = parser.parse_args()
simconfig = utils.AxelrodExtensibleConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment, to be used as prefix for database collections")
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Path to configuration file")
parser.add_argument("--model", choices=['axelrod', 'extensible', 'treestructured'], required=True)
parser.add_argument("--finalized", help="Only export runs which finalized after convergence", action="store_true")
parser.add_argument("--filename", help="path to file for export", required=True)
args = parser.parse_args()
simconfig = utils.TreeStructuredConfiguration(args.configuration)
if args.model == 'axelrod':
simconfig = utils.AxelrodConfiguration(args.configuration)
elif args.model == 'extensible':
simconfig = utils.AxelrodExtensibleConfiguration(args.configuration)
elif args.model == 'treestructured':
simconfig = utils.TreeStructuredConfiguration(args.configuration)
else:
log.error("This shouldn't happen - args.model = %s", args.model)
if args.debug == 1:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("EXPORT DATA TO CSV - Experiment: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument(
"--experiment",
help=
"provide name for experiment, to be used as prefix for database collections"
)
parser.add_argument("--simid",
help="simulation ID to export from database")
parser.add_argument("--debug", type=int, help="turn on debugging output")
parser.add_argument("--dbhost",
help="database hostname, defaults to localhost",
default="localhost")
parser.add_argument("--dbport",
help="database port, defaults to 27017",
default="27017")
parser.add_argument("--outputdirectory",
help="path to directory for exported data files",
required=True)
args = parser.parse_args()
if args.debug == 1:
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("EXPORT DATA TO CSV - Experiment: %s SimulationID: %s",
args.experiment, args.simid)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
def setup():
global args, config, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment, to be used as prefix for database collections")
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Path to configuration file")
parser.add_argument("--filename", help="path and base filename for exports (DO NOT include *.csv extension)", required=True)
args = parser.parse_args()
if int(args.debug) == 1:
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
#### main program ####
log.info("EXPORT DATA TO CSV - Experiment: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
# Define your item pipelines here
#
# Don't forget to add your pipeline to the ITEM_PIPELINES setting
# See: http://doc.scrapy.org/en/latest/topics/item-pipeline.html
from scrapy import log
from pymongo.errors import DuplicateKeyError
import config
from information_value.models import Document
from information_value.models import odm_session
import ming
ming_config = {'ming.document_store.uri': config.DATABASE_URL}
ming.configure(**ming_config)
class LeninPipeline(object):
def process_item(self, item, spider):
Document(
name=item['name'],
url=item['url'],
text=item['text'],
month=item['month'],
year=int(item['year']),
)
try:
odm_session.flush()
except DuplicateKeyError:
log.msg('Duplicate found', level=log.WARNING)
return
log.msg('Document saved', level=log.INFO)
def _make_core_app(root, global_conf, full_stack=True, **app_conf):
"""
Set allura up with the settings found in the PasteDeploy configuration
file used.
:param root: The controller module containing the TG root
:param global_conf: The global settings for allura (those
defined under the ``[DEFAULT]`` section).
:type global_conf: dict
:param full_stack: Should the whole TG2 stack be set up?
:type full_stack: str or bool
:return: The allura application with all the relevant middleware
loaded.
This is the PasteDeploy factory for the allura application.
``app_conf`` contains all the application-specific settings (those defined
under ``[app:main]``.
"""
# Run all the initialization code here
mimetypes.init(
[pkg_resources.resource_filename('allura', 'etc/mime.types')]
+ mimetypes.knownfiles)
patches.apply()
try:
import newrelic
except ImportError:
pass
else:
patches.newrelic()
# Configure MongoDB
ming.configure(**app_conf)
# Configure ActivityStream
if asbool(app_conf.get('activitystream.recording.enabled', False)):
activitystream.configure(**app_conf)
# Configure EW variable provider
ew.render.TemplateEngine.register_variable_provider(get_tg_vars)
# Set FormEncode language to english, as we don't support any other locales
formencode.api.set_stdtranslation(domain='FormEncode', languages=['en'])
# Create base app
base_config = ForgeConfig(root)
load_environment = base_config.make_load_environment()
# Code adapted from tg.configuration, replacing the following lines:
# make_base_app = base_config.setup_tg_wsgi_app(load_environment)
# app = make_base_app(global_conf, full_stack=True, **app_conf)
# Configure the Pylons environment
load_environment(global_conf, app_conf)
if config.get('zarkov.host'):
try:
import zmq
except ImportError:
raise ImportError, "Unable to import the zmq library. Please"\
" check that zeromq is installed or comment out"\
" the zarkov.host setting in your ini file."
app = tg.TGApp()
if asbool(config.get('auth.method', 'local')=='sfx'):
import sfx.middleware
d = h.config_with_prefix(config, 'auth.')
d.update(h.config_with_prefix(config, 'sfx.'))
app = sfx.middleware.SfxMiddleware(app, d)
# Required for pylons
app = RoutesMiddleware(app, config['routes.map'])
# Required for sessions
app = SessionMiddleware(app, config)
# Redirect 401 to the login page
app = LoginRedirectMiddleware(app)
# Add instrumentation
app = AlluraTimerMiddleware(app, app_conf)
# Clear cookies when the CSRF field isn't posted
if not app_conf.get('disable_csrf_protection'):
app = CSRFMiddleware(app, '_session_id')
# Setup the allura SOPs
app = allura_globals_middleware(app)
# Ensure https for logged in users, http for anonymous ones
if asbool(app_conf.get('auth.method', 'local')=='sfx'):
app = SSLMiddleware(app, app_conf.get('no_redirect.pattern'))
# Setup resource manager, widget context SOP
app = ew.WidgetMiddleware(
app,
compress=not asbool(global_conf['debug']),
# compress=True,
script_name=app_conf.get('ew.script_name', '/_ew_resources/'),
url_base=app_conf.get('ew.url_base', '/_ew_resources/'),
extra_headers=eval(app_conf.get('ew.extra_headers', 'None')))
# Handle static files (by tool)
app = StaticFilesMiddleware(app, app_conf.get('static.script_name'))
# Handle setup and flushing of Ming ORM sessions
app = MingMiddleware(app)
# Set up the registry for stacked object proxies (SOPs).
# streaming=true ensures they won't be cleaned up till
# the WSGI application's iterator is exhausted
app = RegistryManager(app, streaming=True)
# Converts exceptions to HTTP errors, shows traceback in debug mode
tg.error.footer_html = '<!-- %s %s -->' # don't use TG footer with extra CSS & images that take time to load
app = tg.error.ErrorHandler(app, global_conf, **config['pylons.errorware'])
# Make sure that the wsgi.scheme is set appropriately when we
# have the funky HTTP_X_SFINC_SSL environ var
if asbool(app_conf.get('auth.method', 'local')=='sfx'):
app = set_scheme_middleware(app)
# Redirect some status codes to /error/document
if config.get('override_root') != 'task':
# "task" wsgi would get a 2nd request to /error/document if we used this middleware
if asbool(config['debug']):
app = StatusCodeRedirect(app, base_config.handle_status_codes)
else:
app = StatusCodeRedirect(app, base_config.handle_status_codes + [500])
return app
def setUp(self):
config = {
'ming.main.uri': 'mim://allura_test',
}
ming.configure(**config)
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment",
help="provide name for experiment",
required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost",
help="database hostname, defaults to localhost",
default="localhost")
parser.add_argument("--dbport",
help="database port, defaults to 27017",
default="27017")
parser.add_argument("--configuration",
help="Configuration file for experiment",
required=True)
parser.add_argument("--popsize", help="Population size", required=True)
parser.add_argument("--maxinittraits",
help="Max initial number of traits per indiv",
required=True)
parser.add_argument(
"--additionrate",
help="Rate at which traits are added during interactions",
required=True)
parser.add_argument(
"--maxtraitvalue",
help="Maximum integer token for traits in the trait space",
required=True)
parser.add_argument("--periodic",
help="Periodic boundary condition",
choices=['1', '0'],
required=True)
parser.add_argument("--diagram",
help="Draw a diagram of the converged model",
action="store_true")
parser.add_argument("--drift_rate", help="Rate of drift")
args = parser.parse_args()
simconfig = utils.AxelrodExtensibleConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
if args.drift_rate:
simconfig.drift_rate = float(args.drift_rate)
simconfig.popsize = int(args.popsize)
simconfig.maxtraits = int(args.maxinittraits)
simconfig.add_rate = float(args.additionrate)
simconfig.max_trait_value = int(args.maxtraitvalue)
simconfig.sim_id = uuid.uuid4().urn
if args.periodic == '1':
simconfig.periodic = 1
elif args.periodic == '0':
simconfig.periodic = 0
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment", help="provide name for experiment", required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost", help="database hostname, defaults to localhost", default="localhost")
parser.add_argument("--dbport", help="database port, defaults to 27017", default="27017")
parser.add_argument("--configuration", help="Configuration file for experiment", required=True)
parser.add_argument("--popsize", help="Population size", required=True)
parser.add_argument("--maxinittraits", help="Max initial number of traits per indiv", required=True)
parser.add_argument("--learningrate", help="Rate at which traits are learned during interactions", required=True)
parser.add_argument("--lossrate", help="Rate at which traits are lost randomly by individuals (0.0 turns this off)", required=True)
parser.add_argument("--innovrate", help="Rate at which innovations occur in population", required=True)
parser.add_argument("--periodic", help="Periodic boundary condition", choices=['1','0'], required=True)
parser.add_argument("--diagram", help="Draw a diagram of the converged model", action="store_true")
parser.add_argument("--swrewiring", help="Rewiring probability for Watts-Strogatz population graph", required=False)
parser.add_argument("--numtraittrees", help="Number of trait trees in the design space", required=True)
parser.add_argument("--branchingfactor", help="Value or mean for tree branching factor", required=True)
parser.add_argument("--depthfactor", help="Value or mean for tree depth factor", required=True)
parser.add_argument("--savetraitgraphs", help="Saves a snapshot of trait tree graphs", action="store_true")
parser.add_argument("--samplinginterval", help="Interval between samples, once sampling begins, defaults to 1M steps", default="1000000")
parser.add_argument("--samplingstarttime", help="Time at which sampling begins, defaults to 1M steps", default="6000000")
parser.add_argument("--simulationendtime", help="Time at which simulation and sampling end, defaults to 10000000 steps", default="10000000")
args = parser.parse_args()
simconfig = utils.TreeStructuredConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG, format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO, format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
if args.swrewiring:
simconfig.ws_rewiring = float(args.swrewiring)
simconfig.popsize = int(args.popsize)
simconfig.maxtraits = int(args.maxinittraits)
simconfig.learning_rate = float(args.learningrate)
simconfig.num_trees = int(args.numtraittrees)
simconfig.branching_factor = float(args.branchingfactor)
simconfig.depth_factor = float(args.depthfactor)
simconfig.loss_rate = float(args.lossrate)
simconfig.innov_rate = float(args.innovrate)
simconfig.maxtime = int(args.simulationendtime)
simconfig.script = __file__
simconfig.save_graphs = args.savetraitgraphs
simconfig.sim_id = uuid.uuid4().urn
if args.periodic == '1':
simconfig.periodic = 1
else:
simconfig.periodic = 0
def _make_core_app(root, global_conf, full_stack=True, **app_conf):
"""
Set allura up with the settings found in the PasteDeploy configuration
file used.
:param root: The controller module containing the TG root
:param global_conf: The global settings for allura (those
defined under the ``[DEFAULT]`` section).
:type global_conf: dict
:param full_stack: Should the whole TG2 stack be set up?
:type full_stack: str or bool
:return: The allura application with all the relevant middleware
loaded.
This is the PasteDeploy factory for the allura application.
``app_conf`` contains all the application-specific settings (those defined
under ``[app:main]``.
"""
# Run all the initialization code here
mimetypes.init([pkg_resources.resource_filename('allura', 'etc/mime.types')] + mimetypes.knownfiles)
# Configure MongoDB
ming.configure(**app_conf)
# Configure ActivityStream
if asbool(app_conf.get('activitystream.recording.enabled', False)):
activitystream.configure(**h.convert_bools(app_conf, prefix='activitystream.'))
# Configure EW variable provider
ew.render.TemplateEngine.register_variable_provider(get_tg_vars)
# Set FormEncode language to english, as we don't support any other locales
formencode.api.set_stdtranslation(domain='FormEncode', languages=['en'])
# Create base app
base_config = ForgeConfig(root)
load_environment = base_config.make_load_environment()
# Code adapted from tg.configuration, replacing the following lines:
# make_base_app = base_config.setup_tg_wsgi_app(load_environment)
# app = make_base_app(global_conf, full_stack=True, **app_conf)
# Configure the TG environment
load_environment(global_conf, app_conf)
app = tg.TGApp()
for mw_ep in h.iter_entry_points('allura.middleware'):
Middleware = mw_ep.load()
if getattr(Middleware, 'when', 'inner') == 'inner':
app = Middleware(app, config)
# Required for sessions
app = SessionMiddleware(app, config, data_serializer=BeakerPickleSerializerWithLatin1())
# Handle "Remember me" functionality
app = RememberLoginMiddleware(app, config)
# Redirect 401 to the login page
app = LoginRedirectMiddleware(app)
# Add instrumentation
app = AlluraTimerMiddleware(app, app_conf)
# Clear cookies when the CSRF field isn't posted
if not app_conf.get('disable_csrf_protection'):
app = CSRFMiddleware(app, '_session_id')
if asbool(config.get('cors.enabled', False)):
# Handle CORS requests
allowed_methods = aslist(config.get('cors.methods'))
allowed_headers = aslist(config.get('cors.headers'))
cache_duration = asint(config.get('cors.cache_duration', 0))
app = CORSMiddleware(app, allowed_methods, allowed_headers, cache_duration)
# Setup the allura SOPs
app = allura_globals_middleware(app)
# Ensure http and https used per config
if config.get('override_root') != 'task':
app = SSLMiddleware(app, app_conf.get('no_redirect.pattern'),
app_conf.get('force_ssl.pattern'),
app_conf.get('force_ssl.logged_in'))
# Setup resource manager, widget context SOP
app = ew.WidgetMiddleware(
app,
compress=True,
use_cache=not asbool(global_conf['debug']),
script_name=app_conf.get('ew.script_name', '/_ew_resources/'),
url_base=app_conf.get('ew.url_base', '/_ew_resources/'),
extra_headers=ast.literal_eval(app_conf.get('ew.extra_headers', '[]')),
cache_max_age=asint(app_conf.get('ew.cache_header_seconds', 60*60*24*365)),
# settings to pass through to jinja Environment for EW core widgets
# these are for the easywidgets' own [easy_widgets.engines] entry point
# (the Allura [easy_widgets.engines] entry point is named "jinja" (not jinja2) but it doesn't need
# any settings since it is a class that uses the same jinja env as the rest of allura)
**{
'jinja2.auto_reload': asbool(config['auto_reload_templates']),
'jinja2.bytecode_cache': AlluraJinjaRenderer._setup_bytecode_cache(),
'jinja2.cache_size': asint(config.get('jinja_cache_size', -1)),
}
)
# Handle static files (by tool)
app = StaticFilesMiddleware(app, app_conf.get('static.script_name'))
# Handle setup and flushing of Ming ORM sessions
app = MingMiddleware(app)
# Set up the registry for stacked object proxies (SOPs).
# streaming=true ensures they won't be cleaned up till
# the WSGI application's iterator is exhausted
app = RegistryManager(app, streaming=True)
# "task" wsgi would get a 2nd request to /error/document if we used this middleware
if config.get('override_root') not in ('task', 'basetest_project_root'):
if asbool(config['debug']):
# Converts exceptions to HTTP errors, shows traceback in debug mode
# don't use TG footer with extra CSS & images that take time to load
tg.error.footer_html = '<!-- %s %s -->'
app = tg.error.ErrorHandler(app, global_conf, **config['tg.errorware'])
else:
app = ErrorMiddleware(app, config, **config['tg.errorware'])
app = SetRequestHostFromConfig(app, config)
# Redirect some status codes to /error/document
if asbool(config['debug']):
app = StatusCodeRedirect(app, base_config.handle_status_codes)
else:
app = StatusCodeRedirect(
app, base_config.handle_status_codes + [500])
for mw_ep in h.iter_entry_points('allura.middleware'):
Middleware = mw_ep.load()
if getattr(Middleware, 'when', 'inner') == 'outer':
app = Middleware(app, config)
return app
config_file = None
simconfig = utils.CTPyConfiguration(config_file)
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment_name)
log.debug(
"NOTE: This interactive simulation always sends data to MongoDB instance on localhost"
)
data.set_experiment_name(args.experiment_name)
data.set_database_hostname("localhost")
data.set_database_port("27017")
config = data.getMingConfiguration()
ming.configure(**config)
sim_id = uuid.uuid4().urn
log.info("Beginning simulation run: %s", sim_id)
beginCollectingData = cpm.expectedIAQuasiStationarityTimeHaploid(
args.popsize, args.mutationrate)
log.info("Starting data collection at generation: %s", beginCollectingData)
totalSimulationLength = beginCollectingData + args.length
log.info("Simulation will sample %s generations after stationarity",
args.length)
data.storeSimulationData(args.popsize, args.mutationrate, sim_id,
args.samplesize, args.replications, args.numloci,
def setup():
global args, simconfig
parser = argparse.ArgumentParser()
parser.add_argument("--experiment",
help="provide name for experiment",
required=True)
parser.add_argument("--debug", help="turn on debugging output")
parser.add_argument("--dbhost",
help="database hostname, defaults to localhost",
default="localhost")
parser.add_argument("--dbport",
help="database port, defaults to 27017",
default="27017")
parser.add_argument("--configuration",
help="Configuration file for experiment",
required=True)
parser.add_argument("--popsize", help="Population size", required=True)
parser.add_argument("--maxinittraits",
help="Max initial number of traits per indiv",
required=True)
parser.add_argument(
"--learningrate",
help="Rate at which traits are learned during interactions",
required=True)
parser.add_argument(
"--lossrate",
help=
"Rate at which traits are lost randomly by individuals (0.0 turns this off)",
required=True)
parser.add_argument("--innovrate",
help="Rate at which innovations occur in population",
required=True)
parser.add_argument("--periodic",
help="Periodic boundary condition",
choices=['1', '0'],
required=True)
parser.add_argument("--diagram",
help="Draw a diagram of the converged model",
action="store_true")
parser.add_argument(
"--swrewiring",
help="Rewiring probability for Watts-Strogatz population graph",
required=False)
parser.add_argument("--numtraittrees",
help="Number of trait trees in the design space",
required=True)
parser.add_argument("--branchingfactor",
help="Value or mean for tree branching factor",
required=True)
parser.add_argument("--depthfactor",
help="Value or mean for tree depth factor",
required=True)
parser.add_argument("--savetraitgraphs",
help="Saves a snapshot of trait tree graphs",
action="store_true")
parser.add_argument(
"--samplinginterval",
help=
"Interval between samples, once sampling begins, defaults to 250K steps",
default="250000")
parser.add_argument(
"--samplingstarttime",
help="Time at which sampling begins, defaults to 1000000 steps",
default="1000000")
args = parser.parse_args()
simconfig = utils.TreeStructuredConfiguration(args.configuration)
if args.debug == '1':
log.basicConfig(level=log.DEBUG,
format='%(asctime)s %(levelname)s: %(message)s')
else:
log.basicConfig(level=log.INFO,
format='%(asctime)s %(levelname)s: %(message)s')
log.debug("experiment name: %s", args.experiment)
data.set_experiment_name(args.experiment)
data.set_database_hostname(args.dbhost)
data.set_database_port(args.dbport)
config = data.getMingConfiguration(data.modules)
ming.configure(**config)
if args.swrewiring:
simconfig.ws_rewiring = float(args.swrewiring)
simconfig.popsize = int(args.popsize)
simconfig.maxtraits = int(args.maxinittraits)
simconfig.learning_rate = float(args.learningrate)
simconfig.num_trees = int(args.numtraittrees)
simconfig.branching_factor = float(args.branchingfactor)
simconfig.depth_factor = float(args.depthfactor)
simconfig.loss_rate = float(args.lossrate)
simconfig.innov_rate = float(args.innovrate)
simconfig.maxtime = simconfig.SIMULATION_CUTOFF_TIME
simconfig.script = __file__
simconfig.save_graphs = args.savetraitgraphs
simconfig.sim_id = uuid.uuid4().urn
if args.periodic == '1':
simconfig.periodic = 1
else:
simconfig.periodic = 0