def check_number(value, cast, minv=0, maxv=None):
try:
typed_value = cast(value)
except ValueError:
raise ConfigError("Expected [%s] number. Found [%s]" % (cast, value))
else:
if (minv is not None and typed_value < cast(minv)) or \
(maxv is not None and typed_value > cast(maxv)):
_minv = minv if minv is not None else "any"
_maxv = maxv if maxv is not None else "any"
raise ConfigError("[%s] not in the range (%s,%s)" %
(value, _minv, _maxv))
return typed_value
def is_appset_entry(value):
if not isinstance(value, list) or len(value) != 2:
raise ConfigError(
"unexpected application format [%s]. Expected [appname, maxcpus] format"
% value)
try:
cores = int(value[2])
except ValueError:
raise ConfigError(
"unexpected application format [%s]. Expected [appname, maxcpus] format (maxcpus as integer)"
% value)
return [value[0], cores]
def is_percent(value):
try:
is_float(value.rstrip('%'))
except ConfigError:
raise ConfigError('[%s] should a percentage value (i.e. 0.4%%)' %
value)
return value
def is_boolean(value):
if str(value).lower() in set(["1", "true", "yes"]):
return True
elif str(value).lower() in set(["0", "false", "no"]):
return False
else:
raise ConfigError('[%s] is not a boolean value' % (value))
def is_app_link(value, allow_none=True):
if allow_none and value == 'none':
return value
elif value.startswith('@'):
return value
else:
raise ConfigError('[%s] is not a valid block link' % value)
def is_raxml_bootstrap(value):
try:
return is_integer(value)
except ValueError:
if value == 'alrt' or value == 'alrt_phyml':
return value
else:
raise ConfigError(
'[%s] bootstrap value should an integer, "alrt" or "phyml_alrt"'
% (value))
def is_integer_or_percent(value):
try:
return is_integer(value)
except ConfigError:
try:
is_percent(value)
except ConfigError:
raise ConfigError(
'[%s] should be an integer or a percentage (i.e. 15 or 0.4%%)'
% value)
return value
def check_cores(j, cores_used, cores_total, execution):
if j.cores > cores_total:
raise ConfigError("Job [%s] is trying to be executed using [%d] cores."
" However, the program is limited to [%d] core(s)."
" Use the --multicore option to enable more cores." %
(j, j.cores, cores_total))
elif execution == "insitu" and j.cores > cores_total - cores_used:
log.log(22, "Job [%s] awaiting [%d] core(s)" % (j, j.cores))
return False
else:
return True
def check_config(fname):
conf = ConfigObj(fname, list_values=True)
for k, v in conf.items():
if '_inherits' in v:
base = v['_inherits']
try:
new_dict = dict(conf[base])
except KeyError:
raise ConfigError(
'[%s] config block is referred in [%s] but not present in config file'
% (base, k))
new_dict.update(v)
conf[k] = new_dict
for k in conf.iterkeys():
blocktype = conf[k].get('_app', 'unknown')
for attr, v in conf[k].items():
conf[k][attr] = check_type(blocktype, attr, v)
if isinstance(conf[k][attr], list):
for i in conf[k][attr]:
check_block_link(conf, k, i)
else:
check_block_link(conf, k, conf[k][attr])
for tag, tester in CHECKERS.iteritems():
if tag[0] == blocktype and (tester[2] and tag[1] not in conf[k]):
raise ConfigError('[%s] attribute expected in block [%s]' %
(tag[1], k))
# Check that the number of columns in main workflow definition is the same in all attributes
for flow_name in conf.iterkeys():
if conf[flow_name].get("_app", "") != "main":
continue
npr_config = [
len(v) for k, v in conf[flow_name].iteritems()
if type(v) == list and k != "target_levels"
]
if len(set(npr_config)) != 1:
raise ConfigError(
"List values in [%s] should all have the same length" %
flow_name)
return conf
def is_correlative_integer_list(value, minv=None, maxv=None):
is_list(value)
typed_value = []
last_value = 0
for v in value:
cv = is_integer(v, minv=None, maxv=None)
typed_value.append(cv)
if cv <= last_value:
raise ConfigError("[%s] Numeric values are not correlative" %
value)
last_value = cv
return typed_value
def is_choice(value, choices):
if value in choices:
return value
else:
raise ConfigError('[%s] should be one of %s' % (value, choices))
def is_text(value):
if isinstance(value, str):
return value
else:
raise ConfigError("[%s] is not a valid text string" % value)
def is_list(value):
if not isinstance(value, list):
raise ConfigError("[%s] is not a list" % value)
return value
def is_set(value):
if not isinstance(value, list):
raise ConfigError("Expected a list of values. Found [%s]" % value)
return set(value)
def is_dir(value):
if os.path.isdir(value):
return value
else:
raise ConfigError("Not valid file")
def check_block_link(conf, parent, v):
if isinstance(v, str) and v.startswith('@') and v[1:] not in conf:
raise ConfigError(
'[%s] config block referred in [%s] but not found in config' %
(v, parent))