diff --git a/src/sssom/util.py b/src/sssom/util.py index f9e77e7a..bd457c25 100644 --- a/src/sssom/util.py +++ b/src/sssom/util.py @@ -27,7 +27,6 @@ COLUMN_INVERT_DICTIONARY, COMMENT, CONFIDENCE, - CURIE_MAP, MAPPING_JUSTIFICATION, MAPPING_SET_ID, MAPPING_SET_SOURCE, @@ -68,7 +67,7 @@ get_converter, ) from .sssom_document import MappingSetDocument -from .typehints import MetadataType, PrefixMap, get_default_metadata +from .typehints import MetadataType, get_default_metadata logging = _logging.getLogger(__name__) @@ -149,8 +148,7 @@ def from_mapping_set_document(cls, doc: MappingSetDocument) -> "MappingSetDataFr return cls(df=pd.DataFrame(), converter=doc.converter) df = pd.DataFrame(get_dict_from_mapping(mapping) for mapping in doc.mapping_set.mappings) - meta = extract_global_metadata(doc) - meta.pop(CURIE_MAP, None) + meta = _extract_global_metadata(doc) # remove columns where all values are blank. df.replace("", np.nan, inplace=True) @@ -1010,14 +1008,13 @@ def get_file_extension(file: Union[str, Path, TextIO]) -> str: return "tsv" -def extract_global_metadata(msdoc: MappingSetDocument) -> Dict[str, PrefixMap]: +def _extract_global_metadata(msdoc: MappingSetDocument) -> MetadataType: """Extract metadata. :param msdoc: MappingSetDocument object :return: Dictionary containing metadata """ - # TODO mark as private - meta = {CURIE_MAP: msdoc.prefix_map} + meta = {} ms_meta = msdoc.mapping_set for key in [ slot