Simplify parsing SSSOM

This provides an alternative to #429 that makes more explicit the chaining operations done on the metadata and prefix maps

This is also a good change to carefully document the way that this is handled, since I might not have captured it accurately

src/sssom/parsers.py

@@ -6,12 +6,13 @@
 import logging as _logging
 import re
 import typing
-from collections import Counter
+from collections import ChainMap, Counter
 from pathlib import Path
 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
 
+import curies
 import numpy as np
 import pandas as pd
 import requests
@@ -55,7 +56,13 @@
 
 from .context import HINT, ensure_converter
 from .sssom_document import MappingSetDocument
-from .typehints import Metadata, MetadataType, PrefixMap, generate_mapping_set_id
+from .typehints import (
+    Metadata,
+    MetadataType,
+    PrefixMap,
+    generate_mapping_set_id,
+    get_default_metadata,
+)
 from .util import (
     PREFIX_MAP_KEY,
     SSSOM_DEFAULT_RDF_SERIALISATION,
@@ -193,44 +200,36 @@ def parse_sssom_table(
     stream: io.StringIO = _open_input(file_path)
     sep_new = _get_seperator_symbol_from_file_path(file_path)
     df, sssom_metadata = _read_pandas_and_metadata(stream, sep_new)
-    # if mapping_predicates:
-    #     # Filter rows based on presence of predicate_id list provided.
-    #     df = df[df["predicate_id"].isin(mapping_predicates)]
-
-    # If SSSOM external metadata is provided, merge it with the internal metadata
-
-    if sssom_metadata:
-        if meta:
-            for k, v in meta.items():
-                if k in sssom_metadata:
-                    if sssom_metadata[k] != v:
-                        logging.warning(
-                            f"SSSOM internal metadata {k} ({sssom_metadata[k]}) "
-                            f"conflicts with provided ({meta[k]})."
-                        )
-                else:
-                    logging.info(f"Externally provided metadata {k}:{v} is added to metadata set.")
-                    sssom_metadata[k] = v
-        meta = sssom_metadata
-
-        if "curie_map" in sssom_metadata:
-            if prefix_map:
-                for k, v in prefix_map.items():
-                    if k in sssom_metadata[CURIE_MAP]:
-                        if sssom_metadata[CURIE_MAP][k] != v:
-                            logging.warning(
-                                f"SSSOM prefix map {k} ({sssom_metadata[CURIE_MAP][k]}) "
-                                f"conflicts with provided ({prefix_map[k]})."
-                            )
-                    else:
-                        logging.info(
-                            f"Externally provided metadata {k}:{v} is added to metadata set."
-                        )
-                        sssom_metadata[CURIE_MAP][k] = v
-            prefix_map = sssom_metadata[CURIE_MAP]
+    if meta is None:
+        meta = {}
+
+    # The priority order for combining prefix maps are:
+    #  1. Internal prefix map inside the document
+    #  2. Prefix map passed through this function inside the ``meta``
+    #  3. Prefix map passed through this function to ``prefix_map``
+    #  4. Default prefix map (handled with ensure_converter)
+    converter = curies.chain(
+        [
+            Converter.from_prefix_map(sssom_metadata.pop(CURIE_MAP, {})),
+            Converter.from_prefix_map(meta.pop(CURIE_MAP, {})),
+            ensure_converter(prefix_map),
+        ]
+    )
 
-    meta_all = _get_prefix_map_and_metadata(prefix_map=prefix_map, meta=meta)
-    msdf = from_sssom_dataframe(df, prefix_map=meta_all.prefix_map, meta=meta_all.metadata)
+    # The priority order for combining metadata is:
+    #  1. Metadata appearing in the SSSOM document
+    #  2. Metadata passed through ``meta`` to this function
+    #  3. Default metadata
+    combine_meta = dict(
+        ChainMap(
+            sssom_metadata,
+            meta,
+            get_default_metadata(),
+        )
+    )
+
+    msdf = from_sssom_dataframe(df, prefix_map=converter, meta=combine_meta)
+    msdf.clean_prefix_map()
     return msdf
 
 
@@ -394,7 +393,7 @@ def parse_alignment_xml(
 
 def from_sssom_dataframe(
     df: pd.DataFrame,
-    prefix_map: Optional[PrefixMap] = None,
+    prefix_map: HINT = None,
     meta: Optional[MetadataType] = None,
 ) -> MappingSetDataFrame:
     """Convert a dataframe to a MappingSetDataFrame.