diff --git a/text2term/__main__.py b/text2term/__main__.py index df9863b..9560fac 100644 --- a/text2term/__main__.py +++ b/text2term/__main__.py @@ -17,7 +17,7 @@ "'all' to search all ontologies") parser.add_argument("-o", "--output", required=False, type=str, default="", help="Path to desired output file for the mappings (default=current working directory)") - parser.add_argument("-m", "--mapper", required=False, type=str, default=Mapper.TFIDF, + parser.add_argument("-m", "--mapper", required=False, type=str, default="tfidf", help="Method used to compare source terms with ontology terms. One of: " + str(Mapper.list()) + " (default=tfidf)") parser.add_argument("-csv", "--csv_input", required=False, type=str, default=(), @@ -39,8 +39,10 @@ help="Save vis.js graphs representing the neighborhood of each ontology term (default=False)") parser.add_argument("-c", "--store_in_cache", required=False, type=str, default="", help="Store the target ontology into local cache under acronym") - parser.add_argument("-type", "--term_type", required=False, type=str, default=OntologyTermType.CLASS, + parser.add_argument("-type", "--term_type", required=False, type=str, default="class", help="Define whether to return ontology classes, properties, or both") + parser.add_argument('-u', "--incl_unmapped", required=False, default=False, action="store_true", + help="Include all unmapped terms in the output") arguments = parser.parse_args() if not os.path.exists(arguments.source): @@ -62,4 +64,4 @@ excl_deprecated=arguments.excl_deprecated, mapper=mapper, max_mappings=arguments.top_mappings, min_score=arguments.min_score, base_iris=iris, save_graphs=arguments.save_term_graphs, save_mappings=True, separator=arguments.separator, use_cache=cache_exists(target), - term_type=arguments.term_type) + term_type=arguments.term_type, incl_unmapped=arguments.incl_unmapped)