def config_to_dictionary(config):
"""convert the contents of a :py:class:`ConfigParser.ConfigParser`
object to a dictionary
This method works by iterating over all configuration values in a
:py:class:`ConfigParser.ConfigParser` object and inserting values
into a dictionary. Section names are prefixed using and underscore.
Thus::
[sample]
name=12
is entered as ``sample_name=12`` into the dictionary. The sections
``general`` and ``DEFAULT`` are treated specially in that both
the prefixed and the unprefixed values are inserted: ::
[general]
genome=hg19
will be added as ``general_genome=hg19`` and ``genome=hg19``.
Numbers will be automatically recognized as such and converted into
integers or floats.
Returns
-------
config : dict
A dictionary of configuration values
"""
p = defaultdict(lambda: defaultdict(TriggeredDefaultFactory()))
for section in config.sections():
for key, value in config.items(section):
try:
v = iotools.str2val(value)
except TypeError:
E.error("error converting key %s, value %s" % (key, value))
E.error("Possible multiple concurrent attempts to "
"read configuration")
raise
p["%s_%s" % (section, key)] = v
# IMS: new heirarchical format
try:
p[section][key] = v
except TypeError:
# fails with things like genome_dir=abc
# if [genome] does not exist.
continue
if section in ("general", "DEFAULT"):
p["%s" % (key)] = v
for key, value in config.defaults().items():
p["%s" % (key)] = iotools.str2val(value)
return p
def update_params_with_commandline_options(params, options):
"""add and update selected parameters in the parameter
dictionary with command line options.
"""
params["pipeline_name"] = options.pipeline_name
params["dryrun"] = options.dry_run
if options.cluster_queue is not None:
params["cluster_queue"] = options.cluster_queue
if options.cluster_priority is not None:
params["cluster_priority"] = options.cluster_priority
if options.cluster_num_jobs is not None:
params["cluster_num_jobs"] = options.cluster_num_jobs
if options.cluster_options is not None:
params["cluster_options"] = options.cluster_options
if options.cluster_parallel_environment is not None:
params["cluster_parallel_environment"] =\
options.cluster_parallel_environment
if options.without_cluster:
params["without_cluster"] = True
params["shell_logfile"] = options.shell_logfile
params["ruffus_checksums_level"] = options.ruffus_checksums_level
# always create an "input" section
params["input_globs"] = {}
for variable in options.input_globs:
if "=" in variable:
variable, value = variable.split("=")
params["input_globs"][variable.strip()] = value.strip()
else:
params["input_globs"]["default"] = variable.strip()
for variables in options.variables_to_set:
variable, value = variables.split("=")
value = iotools.str2val(value.strip())
# enter old style
params[variable.strip()] = value
# enter new style
parts = variable.split("_")
for x in range(1, len(parts)):
prefix = "_".join(parts[:x])
if prefix in params:
suffix = "_".join(parts[x:])
params[prefix][suffix] = value
if options.work_dir:
params["work_dir"] = os.path.abspath(options.work_dir)
else:
params["work_dir"] = params["start_dir"]
def _convert(key, v):
return iotools.str2val(v)
def conv(v):
return iotools.str2val(re.sub(",", "", v.strip()))