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dax_settings = dax.DAX_Settings()
logger = setup_info_logger()
parser = configure_parser()
parsed_args = parser.parse_args()
logger.info('testing logger')
#argument checks do their own logging
if not check_arguments(logger, parsed_args):
exit(-1)
if not dax_settings.is_cluster_valid(logger):
exit(-1)
launcher = bin.read_settings(parsed_args.settings, logger, exe='patch assessors')
with XnatUtils.get_interface(launcher.xnat_host, launcher.xnat_user,
launcher.xnat_pass) as intf:
print 'intf=', intf
print 'launcher process dict=', launcher.project_process_dict
project_list = set(launcher.project_process_dict.keys())
if parsed_args.projects:
for p in project_list:
if p not in project_list:
msg = "project {} is not in the list of projects defined in {} ({})"
logger.warning(msg.format(p, parsed_args.settings, project_list))
for p in project_list:
project_processors = launcher.project_process_dict.get(p, None)
if project_processors is None:
logger.info("Procject '{}' has no processors - skipping")
def _deserialize_inputs(self, assessor):
return json.loads(
XnatUtils.parse_assessor_inputs(assessor.attrs.get('inputs')))
if filepath.endswith('.py'):
test = imp.load_source('test', filepath)
try:
#print('evaling:' + _tmp.format(os.path.basename(filepath)[:-3]))
return eval(_tmp.format(os.path.basename(filepath)[:-3]))
except AttributeError as e:
#print('attribute error', str(e))
pass
err = '[ERROR] Module or processor NOT FOUND in the python file {}.'
logger.error(err.format(filepath))
elif filepath.endswith('.yaml'):
return processors.load_from_yaml(
XnatUtils, filepath, args, singularity_imagedir)
return None
def check_executable(self, executable, name, version_opt='--version'):
"""Method to check the executable.
:param executable: executable path
:param name: name of Executable
:return: Complete path to the executable
"""
if executable == name:
if not XnatUtils.executable_exists(executable):
raise SpiderError("Executable '%s' not found on your computer."
% name)
else:
executable = os.path.abspath(executable)
if not executable.endswith(name):
if os.path.isdir(executable):
executable = os.path.join(executable, name)
else:
msg = "Error for executable path '%s': Wrong name."
raise SpiderError(msg % executable)
if not os.path.isfile(executable):
msg = "Executable '%s' not found"
raise SpiderError(msg % executable)
self.get_exe_version(executable, version_opt)
return executable
ProcessorParser.parse_inputs(yaml_source)
self.variables_to_inputs = ProcessorParser.parse_variables(self.inputs)
self.csess = None
self.artefacts = None
self.artefacts_by_input = None
self.parameter_matrix = None
self.assessor_parameter_map = None
self.xsitype = yaml_source['attrs'].get('xsitype', 'proc:genProcData')
if proctype:
self.proctype = proctype
else:
self.proctype = XnatUtils.get_proctype(
yaml_source['inputs']['default']['spider_path'])[0]