def main_continuous(args):
glbls = globals()
engine = create_engine(args.engine)
pymodels.Base.metadata.bind = engine
pymodels.Session.configure(bind=engine)
session = pymodels.Session()
tasks = session.query(pymodels.Job).\
options(joinedload("analysis"), joinedload("control"),
joinedload("experiment")).filter(~pymodels.Job.complete).all()
if len(tasks) == 0:
LOGGER.warn("Nothing to do")
return
analysis_configs = {job.analysis for job in tasks}
control_configs = {job.control for job in tasks}
experiments = {job.experiment for job in tasks}
preparations = {job.preparation for job in tasks}
sampling = {job.sampling for job in tasks}
projections = {job.projection for job in tasks}
LOGGER.debug("%d analysis configurations", len(analysis_configs))
LOGGER.debug("%d control configurations", len(control_configs))
LOGGER.debug("%d experiments", len(experiments))
LOGGER.debug("%d setup cases", len(preparations))
LOGGER.debug("%d sampling methods", len(sampling))
LOGGER.debug("%d network projections", len(projections))
num_prep = len(analysis_configs) * len(control_configs) * len(experiments)\
* len(preparations) * len(sampling) * len(projections)
LOGGER.debug("%d total configurations", num_prep)
LOGGER.info("Preparing Data")
task_args = dict()
bar = ProgressBar(maxval=num_prep, widgets=[Timer(), " ",
SimpleProgress(), " ", Percentage(), " ", Bar(), " ",
ETA()]).start()
for anal in analysis_configs:
LOGGER.debug(" %s:", anal.version)
feature2node = pyorg.read_pickle(os.path.join(anal.objects, anal.map))
for cntrl in control_configs:
LOGGER.debug(" %s", cntrl.type)
net = pyorg.read_pickle(os.path.join(anal.objects, cntrl.network))
tu_net = pyreg.to_transcription_unit_based(net)
op_net = pyreg.to_operon_based(net)
for exp in experiments:
LOGGER.debug(" %s", exp.strain)
for prep in preparations:
LOGGER.debug(" %s", prep)
series = glbls[prep](session, exp)
for sampl in sampling:
LOGGER.debug(" %s", sampl)
for prj in projections:
LOGGER.debug(" %s", prj)
control = pyreg.ContinuousControl()
if prj == "tu":
control.setup(tu_net, series, feature2node, sampl)
elif prj == "operon":
control.setup(op_net, series, feature2node, sampl)
else:
control.setup(net, series, feature2node, sampl)
if cntrl.type == "analog":
control.from_gpn()
elif cntrl.type == "digital":
control.from_trn()
else:
raise ValueError("'{}'".format(cntrl.type))
task_args[(anal.id, cntrl.id, exp.id, prep, sampl,
prj)] = (control, series.columns)
bar += 1
bar.finish()
LOGGER.info("Running Jobs")
tasks = [task_args[(job.analysis.id, job.control.id, job.experiment.id,
job.preparation, job.sampling, job.projection)] + (job.measure,
job.random_num, job.delay, job.id) for job in tasks]
pool = multiprocessing.Pool(args.nproc)
result_it = pool.imap_unordered(continuous_exec, tasks)
bar = ProgressBar(maxval=len(tasks), widgets=[Timer(), " ",
SimpleProgress(), " ", Percentage(), " ", Bar(), " ",
ETA()]).start()
for (job_id, z_scores, cntrl_scores, samples, points) in result_it:
results = list()
try:
job = session.query(pymodels.Job).filter_by(id=job_id).one()
for (i, name) in enumerate(points):
res = pymodels.Result(control=cntrl_scores[i], ctc=z_scores[i],
point=name, job=job)
session.add(res)
results.append(res)
job.complete = True
session.commit()
except Exception:
session.rollback()
bar += 1
continue
if job.selection > 0:
try:
for (i, res) in enumerate(results):
# use a more low-level insert for speed
session.execute(pymodels.RandomSample.__table__.insert(),
[{"control": val, "result_id": res.id}\
for val in np.random.choice(samples[i], job.selection,
replace=False)])
session.commit()
except Exception:
session.rollback()
bar += 1
continue
bar += 1
bar.finish()
session.close()
def main(remote_client, args):
config = json.load(codecs.open(args.config, encoding=args.encoding, mode="rb"))
if config["continuous"]:
load_func = load_continuous
table_key = "/Continuous"
job_gen = continuous_jobs
worker = continuous_worker
result = continuous_result
else:
load_func = load_discrete
table_key = "/Discrete"
job_gen = discrete_jobs
worker = discrete_worker
result = discrete_result
organism = pyorg.Organism(name=config["organism"])
load_func(organism, config)
LOGGER.info("Load data")
glob_vars = globals()
data = config["data"]
network = config["network"]
analysis = config["analysis"]
namespace = dict()
namespace["genes"] = dict()
namespace["networks"] = dict()
namespace["prepared"] = dict()
for version in config["versions"]:
LOGGER.info("{0:*^78s}".format(version))
namespace["genes"][version] = pyorg.read_pickle(os.path.join(
data["base"], version, data["gene_path"]))
id2gene = pyorg.read_pickle(os.path.join(data["base"], version,
data["mapping_path"]))
namespace["networks"][version] = dict()
for (cntrl_type, net_file, projections) in izip(analysis["control_types"],
network["paths"], network["projections"]):
net = pyorg.read_pickle(os.path.join(data["base"], version, net_file))
namespace["networks"][version][cntrl_type] = dict()
for basis in projections:
if basis == "gene":
namespace["networks"][version][cntrl_type][basis] = net
elif basis == "tu":
namespace["networks"][version][cntrl_type][basis] =\
pyreg.to_transcription_unit_based(net)
elif basis == "operon":
namespace["networks"][version][cntrl_type][basis] =\
pyreg.to_operon_based(net)
namespace["prepared"][version] = dict()
for (cntrl_type, experiments, setups) in izip(analysis["control_types"],
analysis["experimental_sets"], analysis["experimental_setups"]):
LOGGER.info("{0:*^78s}".format(cntrl_type))
namespace["prepared"][version][cntrl_type] = dict()
for (exp_name, exp_setup) in izip(experiments, setups):
LOGGER.info("{0:*^78s}".format(exp_name))
df = organism.activity[exp_name]
setup_func = glob_vars[exp_setup]
namespace["prepared"][version][cntrl_type][exp_name] =\
setup_func(cntrl_type, df, id2gene)
if any(method.startswith("delayed") for method in chain(analysis["control"], *analysis["ctc"])):
namespace["prepared"][version][cntrl_type][exp_name]["delayed"] = dict()
for delta in analysis["delays"]:
delayed_continuous(namespace["prepared"][version][cntrl_type][exp_name],
delta)
if any(ms_name.endswith("comparison") for ms_name in chain(*analysis["measures"])):
rate_continuous(namespace["prepared"][version][cntrl_type][exp_name])
LOGGER.debug("\n".join(print_dict(namespace)))
db = shelve.open(config["shelve"], protocol=pickle.HIGHEST_PROTOCOL)
for (key, value) in namespace.iteritems():
db[key] = value
db.close()
# general parallel setup using IPython.parallel
LOGGER.info("Remote imports")
d_view = remote_client.direct_view()
d_view.execute("import numpy as np; "\
"import shelve; import pickle;"\
"import pyorganism as pyorg; import pyorganism.regulation as pyreg;"\
"import logging; from IPython.config import Application;"\
"LOGGER = Application.instance().log;"\
"LOGGER.setLevel(logging.{level});".format(level=args.log_level),
block=True)
LOGGER.info("Transfer data")
# d_view.push(namespace, block=True)
d_view.execute("db = shelve.open('{shelve}', protocol=pickle.HIGHEST_PROTOCOL);"\
"globals().update(db);db.close()".format(shelve=config["shelve"]), block=True)
LOGGER.info("Generate job descriptions")
jobs = job_gen(organism, config, namespace)
l_view = remote_client.load_balanced_view()
bar = ProgressBar(maxval=len(jobs), widgets=[Timer(), " ", Percentage(),
" ", Bar(), " ", ETA()]).start()
result_mngr = ResultManager(config["output"], table_key)
results_it = l_view.map(worker, jobs, ordered=False, block=False)
for (spec, res_cntrl, res_ctc, samples) in results_it:
LOGGER.debug(res_cntrl)
LOGGER.debug(res_ctc)
result(result_mngr, spec, res_cntrl, res_ctc, samples)
bar += 1
result_mngr.finalize()
bar.finish()
LOGGER.info("parallel speed-up was %.3g",
results_it.serial_time / results_it.wall_time)
