def prune_pp_platform_args(conf, keep_opts = POST_PROCESS_OPTS):
"""Rewrite platform args of a post_process file.
:param conf: post process config object
:param keep_opts: options to keep in platform args
:returns: updated post process object
"""
newconf = copy.deepcopy(conf)
if conf.get("distributed", {}).get("platform_args"):
opt_d = opt_to_dict(conf['distributed']['platform_args'].split())
keys = list(set(keep_opts) & set(opt_d.keys()))
platform_args = ["{}={}".format(x, opt_d[x]) if x.startswith("--") else "{} {}".format(x, opt_d[x]) for x in keys]
newconf['distributed']['platform_args'] = " ".join(platform_args)
return newconf
def test_platform_args(self):
"""Test making platform args and changing them on the fly. """
from scilifelab.pm.ext.ext_distributed import make_job_template_args
pp = os.path.join(j_doe_00_05, SAMPLES[1], FLOWCELL, "{}-post_process.yaml".format(SAMPLES[1]))
with open(pp) as fh:
config = yaml.load(fh)
platform_args = config["distributed"]["platform_args"].split()
self.assertIn("core", platform_args)
pargs = opt_to_dict(platform_args)
self.assertEqual("P001_102_index6-bcbb.log", pargs['-o'])
kw = {'time':'00:01:00', 'jobname':'test', 'partition':'devel'}
pargs = make_job_template_args(pargs, **kw)
self.assertEqual("devel", pargs['partition'])
nativeSpec = "-t {time} -p {partition} -A {account}".format(**pargs)
self.assertEqual("00:01:00", nativeSpec[3:11])
def test_platform_args(self):
"""Test making platform args and changing them on the fly. """
from scilifelab.pm.ext.ext_distributed import make_job_template_args
pp = os.path.join(j_doe_00_05, SAMPLES[1], FLOWCELL,
"{}-post_process.yaml".format(SAMPLES[1]))
with open(pp) as fh:
config = yaml.load(fh)
platform_args = config["distributed"]["platform_args"].split()
self.assertIn("core", platform_args)
pargs = opt_to_dict(platform_args)
self.assertEqual("P001_102_index6-bcbb.log", pargs['-o'])
kw = {'time': '00:01:00', 'jobname': 'test', 'partition': 'devel'}
pargs = make_job_template_args(pargs, **kw)
self.assertEqual("devel", pargs['partition'])
nativeSpec = "-t {time} -p {partition} -A {account}".format(**pargs)
self.assertEqual("00:01:00", nativeSpec[3:11])
def update_pp_platform_args(conf, **kw):
"""Update post process platform args with keys given in kw.
:param conf: post process configuration
:param kw: keywords with platform arg keys
"""
newconf = copy.deepcopy(conf)
opt_d = opt_to_dict(conf.get("distributed", {}).get("platform_args", []).split())
for k in kw.keys():
if not k in POST_PROCESS_OPT_GROUPS.keys():
LOG.warn("Trying to update disallowed key {}; skipping".format(k))
else:
for x in POST_PROCESS_OPT_GROUPS[k]:
if x in opt_d.keys():
del opt_d[x]
opt_d[POST_PROCESS_OPT_GROUPS[k][0]] = kw[k]
platform_args = ["{}={}".format(x, opt_d[x]) if x.startswith("--") else "{} {}".format(x, opt_d[x]) for x in opt_d.keys()]
newconf["distributed"]["platform_args"] = " ".join(platform_args)
return newconf
def prune_pp_platform_args(conf, keep_opts=POST_PROCESS_OPTS):
"""Rewrite platform args of a post_process file.
:param conf: post process config object
:param keep_opts: options to keep in platform args
:returns: updated post process object
"""
newconf = copy.deepcopy(conf)
if conf.get("distributed", {}).get("platform_args"):
opt_d = opt_to_dict(conf['distributed']['platform_args'].split())
keys = list(set(keep_opts) & set(opt_d.keys()))
platform_args = [
"{}={}".format(x, opt_d[x])
if x.startswith("--") else "{} {}".format(x, opt_d[x])
for x in keys
]
newconf['distributed']['platform_args'] = " ".join(platform_args)
return newconf
def update_pp_platform_args(conf, **kw):
"""Update post process platform args with keys given in kw.
:param conf: post process configuration
:param kw: keywords with platform arg keys
"""
newconf = copy.deepcopy(conf)
opt_d = opt_to_dict(
conf.get("distributed", {}).get("platform_args", []).split())
for k in kw.keys():
if not k in POST_PROCESS_OPT_GROUPS.keys():
LOG.warn("Trying to update disallowed key {}; skipping".format(k))
else:
for x in POST_PROCESS_OPT_GROUPS[k]:
if x in opt_d.keys():
del opt_d[x]
opt_d[POST_PROCESS_OPT_GROUPS[k][0]] = kw[k]
platform_args = [
"{}={}".format(x, opt_d[x]) if x.startswith("--") else "{} {}".format(
x, opt_d[x]) for x in opt_d.keys()
]
newconf["distributed"]["platform_args"] = " ".join(platform_args)
return newconf