def implementation(logger, args):
list_of_files = {}
if path_exists(args.sg_local_path, logger=logger, force=True):
for (dirpath, dirnames, filenames) in os.walk(args.sg_local_path):
for filename in filenames:
list_of_files[filename] = os.sep.join([dirpath, filename])
logger.debug(list_of_files)
gi = GalaxyInstance(args.url, key=args.key)
tools = gi.tools.get_tools()
counter_singularity = 0
counter_docker = 0
match = {}
unmatch = []
for t in tools:
t_id = t['id']
t_xml_file = gi.tools.show_tool(t['id'])['config_file']
container_name = None
try:
tool_xml = load(t_xml_file)
requirements, containers = parse_requirements_from_xml(tool_xml)
conda_targets = requirements_to_conda_targets(requirements)
mulled_targets = [
build_target(c.package, c.version) for c in conda_targets
]
container_name = mulled_container_name("biocontainers",
mulled_targets)
except Exception as ex:
logger.exception('Caught an error at {} with tid: {}'.format(
args.url, t_id))
pass
singularity = 'not_found'
if container_name:
container_name = container_name.lower()
counter_docker += 1
if os.path.basename(container_name) in list_of_files:
singularity = os.path.join(args.sg_local_path,
os.path.basename(container_name))
counter_singularity += 1
match[t_id] = {
'docker': "docker://{}".format(container_name),
'singularity': singularity
}
unmatch.append(t_id)
print(t_id, container_name, singularity)
dump(match, "{}_{}".format(args.url.split('/')[2], args.matched))
dump(unmatch, "{}_{}".format(args.url.split('/')[2], args.notmatched))
print("number of tools {}".format(len(tools)))
print("number of docker images matched {}".format(counter_docker))
print("number of singularity images in CVMFS {}".format(
len(list_of_files)))
print(
"number of singularity images matched {}".format(counter_singularity))
def parse_file(self, xml_filepath):
"""
Parse the given XML file for visualizations data.
:returns: visualization config dictionary
"""
xml_tree = load(xml_filepath)
visualization = self.parse_visualization(xml_tree.getroot())
return visualization
def parse_file(self, xml_filepath):
"""
Parse the given XML file for visualizations data.
:returns: visualization config dictionary
"""
xml_tree = load(xml_filepath)
visualization = self.parse_visualization(xml_tree.getroot())
return visualization
def __init_schedulers(self):
config_file = self.app.config.workflow_schedulers_config_file
use_default_scheduler = False
if not config_file or (not os.path.exists(config_file) and not self.app.config.is_set('workflow_schedulers_config_file')):
log.info("No workflow schedulers plugin config file defined, using default scheduler.")
use_default_scheduler = True
elif not os.path.exists(config_file):
log.info(f"Cannot find workflow schedulers plugin config file '{config_file}', using default scheduler.")
use_default_scheduler = True
if use_default_scheduler:
self.__init_default_scheduler()
else:
self.DEFAULT_BASE_HANDLER_POOLS = ('workflow-schedulers',)
plugins_element = load(config_file).getroot()
self.__init_schedulers_for_element(plugins_element)
if not self.__handlers_configured and self.__stack_has_pool:
# Stack has a pool for us so override inherited config and use the pool
self.__init_handlers()
self.__handlers_configured = True
elif use_default_scheduler:
self._set_default_handler_assignment_methods()