Update name

src/sssom/cli.py

@@ -28,7 +28,7 @@
 
 from sssom.constants import (
     DEFAULT_VALIDATION_TYPES,
-    PrefixMapModeType,
+    MergeMode,
     SchemaValidationType,
     _get_sssom_schema_object,
 )
@@ -172,7 +172,7 @@ def convert(input: str, output: TextIO, output_format: str):
     default="metadata_only",
     show_default=True,
     required=True,
-    type=click.Choice(get_args(PrefixMapModeType), case_sensitive=False),
+    type=click.Choice(get_args(MergeMode), case_sensitive=False),
     help="Defines whether the prefix map in the metadata should be extended or replaced with "
     "the SSSOM default prefix map.",
 )
@@ -205,7 +205,7 @@ def parse(
     input: str,
     input_format: str,
     metadata: str,
-    prefix_map_mode: PrefixMapModeType,
+    prefix_map_mode: MergeMode,
     clean_prefixes: bool,
     strict_clean_prefixes: bool,
     output: TextIO,
@@ -218,7 +218,7 @@ def parse(
         output=output,
         input_format=input_format,
         metadata_path=metadata,
-        prefix_map_mode=prefix_map_mode,
+        merge_mode=prefix_map_mode,
         clean_prefixes=clean_prefixes,
         strict_clean_prefixes=strict_clean_prefixes,
         embedded_mode=embedded_mode,

src/sssom/constants.py

@@ -38,10 +38,10 @@
 ]
 
 UNKNOWN_IRI = "http://w3id.org/sssom/unknown_prefix/"
-PrefixMapModeType = Literal["metadata_only", "sssom_default_only", "merged"]
-PREFIX_MAP_MODE_METADATA_ONLY: PrefixMapModeType = "metadata_only"
-PREFIX_MAP_MODE_SSSOM_DEFAULT_ONLY: PrefixMapModeType = "sssom_default_only"
-PREFIX_MAP_MODE_MERGED: PrefixMapModeType = "merged"
+MergeMode = Literal["metadata_only", "sssom_default_only", "merged"]
+PREFIX_MAP_MODE_METADATA_ONLY: MergeMode = "metadata_only"
+PREFIX_MAP_MODE_SSSOM_DEFAULT_ONLY: MergeMode = "sssom_default_only"
+PREFIX_MAP_MODE_MERGED: MergeMode = "merged"
 ENTITY_REFERENCE = "EntityReference"
 
 # Slot Constants

src/sssom/io.py

@@ -20,8 +20,8 @@
     PREFIX_MAP_MODE_MERGED,
     PREFIX_MAP_MODE_METADATA_ONLY,
     PREFIX_MAP_MODE_SSSOM_DEFAULT_ONLY,
+    MergeMode,
     MetadataType,
-    PrefixMapModeType,
     SchemaValidationType,
     get_default_metadata,
 )
@@ -61,7 +61,7 @@ def parse_file(
     output: TextIO,
     input_format: Optional[str] = None,
     metadata_path: Optional[str] = None,
-    prefix_map_mode: Optional[PrefixMapModeType] = None,
+    merge_mode: Optional[MergeMode] = None,
     clean_prefixes: bool = True,
     strict_clean_prefixes: bool = True,
     embedded_mode: bool = True,
@@ -74,15 +74,15 @@ def parse_file(
     :param input_format: The string denoting the input format.
     :param metadata_path: The path to a file containing the sssom metadata (including prefix_map)
         to be used during parse.
-    :param prefix_map_mode: Defines whether the prefix map in the metadata should be extended or replaced with
+    :param merge_mode: Defines whether the prefix map in the metadata should be extended or replaced with
         the SSSOM default prefix map.
     :param clean_prefixes: If True (default), records with unknown prefixes are removed from the SSSOM file.
     :param strict_clean_prefixes: If True (default), clean_prefixes() will be in strict mode.
     :param embedded_mode:If True (default), the dataframe and metadata are exported in one file (tsv), else two separate files (tsv and yaml).
     :param mapping_predicate_filter: Optional list of mapping predicates or filepath containing the same.
     """
     raise_for_bad_path(input_path)
-    converter, meta = read_metadata(path=metadata_path, mode=prefix_map_mode)
+    converter, meta = read_metadata(path=metadata_path, merge_mode=merge_mode)
     parse_func = get_parsing_function(input_format, input_path)
     mapping_predicates = None
     # Get list of predicates of interest.
@@ -134,13 +134,13 @@ def split_file(input_path: str, output_directory: Union[str, Path]) -> None:
 
 
 def read_metadata(
-    path: Union[None, str, Path] = None, *, mode: Optional[PrefixMapModeType] = None
+    path: Union[None, str, Path] = None, *, merge_mode: Optional[MergeMode] = None
 ) -> Tuple[Converter, MetadataType]:
     """
     Load SSSOM metadata from a YAML file, and then augment it with default prefixes.
 
     :param path: The metadata file in YAML format
-    :param mode: one of metadata_only, sssom_default_only, merged
+    :param merge_mode: one of metadata_only, sssom_default_only, merged
     :return: A converter and remaining metadata from the YAML file
     """
     if path is None:
@@ -152,14 +152,14 @@ def read_metadata(
     metadata = dict(ChainMap(metadata, get_default_metadata()))
     converter = Converter.from_prefix_map(metadata.pop(CURIE_MAP, {}))
 
-    if mode is None or mode == PREFIX_MAP_MODE_METADATA_ONLY:
+    if merge_mode is None or merge_mode == PREFIX_MAP_MODE_METADATA_ONLY:
         converter = curies.chain([_get_built_in_prefix_map(), converter])
-    elif mode == PREFIX_MAP_MODE_SSSOM_DEFAULT_ONLY:
+    elif merge_mode == PREFIX_MAP_MODE_SSSOM_DEFAULT_ONLY:
         converter = get_converter()
-    elif mode == PREFIX_MAP_MODE_MERGED:
+    elif merge_mode == PREFIX_MAP_MODE_MERGED:
         converter = curies.chain([_get_built_in_prefix_map(), converter, get_converter()])
     else:
-        raise ValueError(f"Invalid prefix map mode: {mode}")
+        raise ValueError(f"Invalid prefix map mode: {merge_mode}")
 
     return converter, metadata
 

tests/test_parsers.py

@@ -329,7 +329,7 @@ def test_parse_obographs_merged(self):
         with open(outfile, "w") as f:
             parse_file(
                 input_path=hp_json,
-                prefix_map_mode="merged",
+                merge_mode="merged",
                 clean_prefixes=True,
                 input_format="obographs-json",
                 metadata_path=hp_meta,