def run_pa2checker(annotations):
pa2checker.revert_checker_source()
for annotation, classes in annotations.iteritems():
pa2checker.create_type_annotation(annotation)
pa2checker.update_ontology_utils(annotation, classes)
pa2checker.recompile_checker_framework()
def run_pa2checker(ontology_values):
pa2checker.revert_checker_source()
for ontology_value, classes in ontology_values.iteritems():
pa2checker.insert_ontology_value(ontology_value)
pa2checker.update_ontology_utils(ontology_value, classes)
common.recompile_checker_framework()
def main():
parser = argparse.ArgumentParser(description='command line interface for map2annotation')
parser.add_argument('--type-mapping',dest='type_mapping_file')
parser.add_argument('--field-mapping', dest='field_mapping_file')
parser.add_argument('--project-list', dest='projects', help='project_nameA,project_nameB,...')
args = parser.parse_args()
if args.type_mapping_file is None and args.field_mapping_file is None:
print "error, required at least one mapping file to be indicated."
parser.print_help()
sys.exit(1)
project_list = common.get_project_list()
if args.projects:
arg_projects = args.projects.split(',')
project_list = [project for project in project_list if project in arg_projects]
pa2checker.revert_checker_source()
if not args.type_mapping_file is None:
type_mappings_to_rules(args.type_mapping_file)
if not args.field_mapping_file is None:
field_mappings_to_annotation(project_list, args.field_mapping_file)
for project in project_list:
run_anno_inference(project)
def run_pa2checker(annotations):
pa2checker.revert_checker_source()
for annotation, classes in annotations.iteritems():
pa2checker.create_type_annotation(annotation)
pa2checker.update_ontology_utils(annotation, classes)
pa2checker.recompile_checker_framework()
def convert_2_ontology_value(ontology_set):
""" 1. clean up the ontology source code back to unchanged git version
2. takes the ontology_set, and insert elements into ontology source as new ontologies
3. re-compile ontology to make sure the insertions doesn't break the compilation
"""
pa2checker.revert_checker_source()
for new_ontology in ontology_set:
pa2checker.insert_ontology_value(new_ontology)
common.recompile_checker_framework()