Cleanup Metadata usages (#447)

- Standardizes additional handling of prefix maps and metadata
- Deletes the no longer used `Metadata` class
- Deletes `sssom.typehints` module (which was not named aptly for how it
was used) and moves its remaining functionality into `sssom.constants`

src/sssom/__init__.py

@@ -9,6 +9,7 @@
 
 from sssom_schema import Mapping, MappingSet, slots  # noqa:401
 
+from sssom.io import get_metadata_and_prefix_map  # noqa:401
 from sssom.sssom_document import MappingSetDocument  # noqa:401
 from sssom.util import (  # noqa:401
     MappingSetDataFrame,
@@ -20,3 +21,5 @@
     parse,
     reconcile_prefix_and_data,
 )
+
+from .constants import generate_mapping_set_id, get_default_metadata  # noqa:401

src/sssom/constants.py

@@ -1,9 +1,10 @@
 """Constants."""
 
 import pathlib
+import uuid
 from enum import Enum
 from functools import lru_cache
-from typing import List
+from typing import Any, Dict, List
 
 import pkg_resources
 import yaml
@@ -271,3 +272,41 @@ def _get_sssom_schema_object() -> SSSOMSchemaView:
 
 SSSOM_URI_PREFIX = "https://w3id.org/sssom/"
 DEFAULT_LICENSE = f"{SSSOM_URI_PREFIX}license/unspecified"
+
+#: The type for metadata that gets passed around in many places
+MetadataType = Dict[str, Any]
+
+
+def generate_mapping_set_id() -> str:
+    """Generate a mapping set ID."""
+    return f"{SSSOM_URI_PREFIX}mappings/{uuid.uuid4()}"
+
+
+def get_default_metadata() -> MetadataType:
+    """Get default metadata.
+
+    :returns: A metadata dictionary containing a default
+        license with value :data:`DEFAULT_LICENSE` and an
+        auto-generated mapping set ID
+
+    If you want to combine some metadata you loaded
+    but ensure that there is also default metadata,
+    the best tool is :class:`collections.ChainMap`.
+    You can do:
+
+    .. code-block:: python
+
+        my_metadata: dict | None = ...
+
+        from collections import ChainMap
+        from sssom import get_default_metadata
+
+        metadata = dict(ChainMap(
+            my_metadata or {},
+            get_default_metadata()
+        ))
+    """
+    return {
+        "mapping_set_id": generate_mapping_set_id(),
+        "license": DEFAULT_LICENSE,
+    }

src/sssom/io.py

@@ -3,8 +3,9 @@
 import logging
 import os
 import re
+from collections import ChainMap
 from pathlib import Path
-from typing import List, Optional, TextIO, Union
+from typing import List, Optional, TextIO, Tuple, Union
 
 import curies
 import pandas as pd
@@ -16,15 +17,15 @@
 
 from .constants import (
     CURIE_MAP,
-    DEFAULT_LICENSE,
     PREFIX_MAP_MODE_MERGED,
     PREFIX_MAP_MODE_METADATA_ONLY,
     PREFIX_MAP_MODE_SSSOM_DEFAULT_ONLY,
+    MetadataType,
     SchemaValidationType,
+    get_default_metadata,
 )
 from .context import get_converter
 from .parsers import get_parsing_function, parse_sssom_table, split_dataframe
-from .typehints import Metadata, generate_mapping_set_id
 from .util import (
     MappingSetDataFrame,
     are_params_slots,
@@ -134,34 +135,25 @@ def split_file(input_path: str, output_directory: Union[str, Path]) -> None:
 
 
 def get_metadata_and_prefix_map(
-    metadata_path: Union[None, str, Path] = None, prefix_map_mode: Optional[str] = None
-) -> Metadata:
+    metadata_path: Union[None, str, Path] = None, *, prefix_map_mode: Optional[str] = None
+) -> Tuple[Converter, MetadataType]:
     """
-    Load SSSOM metadata from a file, and then augments it with default prefixes.
+    Load SSSOM metadata from a YAML file, and then augment it with default prefixes.
 
     :param metadata_path: The metadata file in YAML format
     :param prefix_map_mode: one of metadata_only, sssom_default_only, merged
-    :return: a prefix map dictionary and a metadata object dictionary
+    :return: A converter and remaining metadata from the YAML file
     """
     if metadata_path is None:
-        return Metadata.default()
+        return get_converter(), get_default_metadata()
 
     with Path(metadata_path).resolve().open() as file:
         metadata = yaml.safe_load(file)
-    if not metadata.get("mapping_set_id"):
-        metadata["mapping_set_id"] = generate_mapping_set_id()
-    if not metadata.get("license"):
-        metadata["license"] = DEFAULT_LICENSE
-        logging.warning(f"No License provided, using {DEFAULT_LICENSE}")
-
-    if CURIE_MAP in metadata:
-        prefix_map = metadata.pop(CURIE_MAP)
-    else:
-        prefix_map = {}
-    converter = Converter.from_prefix_map(prefix_map)
-    converter = _merge_converter(converter, prefix_map_mode=prefix_map_mode)
 
-    return Metadata(converter=converter, metadata=metadata)
+    metadata = dict(ChainMap(metadata, get_default_metadata()))
+    converter = Converter.from_prefix_map(metadata.pop(CURIE_MAP, {}))
+    converter = _merge_converter(converter, prefix_map_mode=prefix_map_mode)
+    return converter, metadata
 
 
 def _merge_converter(converter: Converter, prefix_map_mode: str = None) -> Converter:

src/sssom/parsers.py

@@ -8,7 +8,7 @@
 import typing
 from collections import ChainMap, Counter
 from pathlib import Path
-from typing import Any, Callable, Dict, Iterable, List, Optional, TextIO, Union, cast
+from typing import Any, Callable, Dict, Iterable, List, Optional, TextIO, Tuple, Union, cast
 from xml.dom import Node, minidom
 from xml.dom.minidom import Document
 
@@ -48,12 +48,13 @@
     SUBJECT_LABEL,
     SUBJECT_SOURCE,
     SUBJECT_SOURCE_ID,
+    MetadataType,
     _get_sssom_schema_object,
+    get_default_metadata,
 )
 
 from .context import ConverterHint, _get_built_in_prefix_map, ensure_converter
 from .sssom_document import MappingSetDocument
-from .typehints import Metadata, MetadataType, get_default_metadata
 from .util import (
     SSSOM_DEFAULT_RDF_SERIALISATION,
     URI_SSSOM_MAPPINGS,
@@ -298,17 +299,17 @@ def parse_obographs_json(
 
 def _get_prefix_map_and_metadata(
     prefix_map: ConverterHint = None, meta: Optional[MetadataType] = None
-) -> Metadata:
-    if prefix_map and meta and CURIE_MAP in meta:
-        logging.info(
-            "Prefix map provided as parameter, but SSSOM file provides its own prefix map. "
-            "Prefix map provided externally is disregarded in favour of the prefix map in the SSSOM file."
-        )
-        prefix_map = meta[CURIE_MAP]
-    converter = ensure_converter(prefix_map)
+) -> Tuple[Converter, MetadataType]:
     if meta is None:
-        meta = Metadata.default().metadata
-    return Metadata(converter=converter, metadata=meta)
+        meta = get_default_metadata()
+    converter = curies.chain(
+        [
+            _get_built_in_prefix_map(),
+            Converter.from_prefix_map(meta.pop(CURIE_MAP, {})),
+            ensure_converter(prefix_map, use_defaults=False),
+        ]
+    )
+    return converter, meta
 
 
 def _address_multivalued_slot(k: str, v: Any) -> Union[str, List[str]]:

src/sssom/sssom_document.py

@@ -1,12 +1,11 @@
 """Additional SSSOM object models."""
 
 from dataclasses import dataclass
+from typing import Dict
 
 from curies import Converter
 from sssom_schema import MappingSet
 
-from .typehints import PrefixMap
-
 __all__ = [
     "MappingSetDocument",
 ]
@@ -28,6 +27,6 @@ class MappingSetDocument:
     converter: Converter
 
     @property
-    def prefix_map(self) -> PrefixMap:
+    def prefix_map(self) -> Dict[str, str]:
         """Get a prefix map."""
         return dict(self.converter.bimap)

src/sssom/util.py

@@ -57,7 +57,9 @@
     SUBJECT_LABEL,
     SUBJECT_SOURCE,
     UNKNOWN_IRI,
+    MetadataType,
     _get_sssom_schema_object,
+    get_default_metadata,
 )
 from .context import (
     SSSOM_BUILT_IN_PREFIXES,
@@ -67,7 +69,6 @@
     get_converter,
 )
 from .sssom_document import MappingSetDocument
-from .typehints import MetadataType, get_default_metadata
 
 logging = _logging.getLogger(__name__)
 

tests/test_parsers.py

@@ -16,7 +16,7 @@
 from curies import Converter
 from rdflib import Graph
 
-from sssom.constants import CURIE_MAP, DEFAULT_LICENSE, SSSOM_URI_PREFIX
+from sssom.constants import CURIE_MAP, DEFAULT_LICENSE, SSSOM_URI_PREFIX, get_default_metadata
 from sssom.context import SSSOM_BUILT_IN_PREFIXES, ensure_converter, get_converter
 from sssom.io import parse_file
 from sssom.parsers import (
@@ -29,7 +29,6 @@
     from_sssom_rdf,
     parse_sssom_table,
 )
-from sssom.typehints import get_default_metadata
 from sssom.util import MappingSetDataFrame, sort_df_rows_columns
 from sssom.writers import write_table
 from tests.test_data import data_dir as test_data_dir