Improve usage of SSSOM-py

pyproject.toml

@@ -16,7 +16,7 @@ linkml-runtime = ">=1.5.3"
 linkml-renderer = ">=0.3.0"
 networkx = ">=2.7.1"
 sssom-schema = ">=0.11.0"
-sssom = ">=0.3.38"
+sssom = ">=0.4.0"
 ratelimit = ">=2.2.1"
 appdirs = ">=1.4.4"
 semsql = ">=0.3.1"

src/oaklib/utilities/lexical/lexical_indexer.py

@@ -7,19 +7,20 @@
 """
 import logging
 import re
+import typing as t
 from collections import defaultdict
 from pathlib import Path
 from typing import Collection, Dict, List, Optional, Tuple, Union
 
+import curies
+from curies import Converter
 from linkml_runtime.dumpers import json_dumper, yaml_dumper
 from linkml_runtime.loaders import json_loader, yaml_loader
 from linkml_runtime.utils.metamodelcore import URIorCURIE
-from sssom.constants import LICENSE, MAPPING_SET_ID
-from sssom.context import get_default_metadata
-from sssom.sssom_document import MappingSetDocument
+from sssom.context import ensure_converter
 from sssom.typehints import Metadata
-from sssom.util import MappingSetDataFrame, to_mapping_set_dataframe
-from sssom_schema import Mapping, MappingSet
+from sssom.util import MappingSetDataFrame
+from sssom_schema import Mapping
 
 from oaklib.datamodels.lexical_index import (
     LexicalGrouping,
@@ -245,7 +246,7 @@ def lexical_index_to_sssom(
     lexical_index: LexicalIndex,
     ruleset: MappingRuleCollection = None,
     meta: Metadata = None,
-    prefix_map: dict = None,
+    prefix_map: Union[None, Converter, t.Mapping[str, str]] = None,
     subjects: Collection[CURIE] = None,
     objects: Collection[CURIE] = None,
     symmetric: bool = False,
@@ -310,24 +311,19 @@ def lexical_index_to_sssom(
         #            mappings.append(create_mapping(oi, term, r1, r2))
     logging.info("Done creating SSSOM mappings")
 
-    if meta is None:
-        meta = get_default_metadata()
-    if prefix_map:
-        meta.prefix_map.update(
-            {k: v for k, v in prefix_map.items() if k not in meta.prefix_map.keys()}
-        )
-    mapping_set_id = meta.metadata[MAPPING_SET_ID]
-    license = meta.metadata[LICENSE]
-
-    mset = MappingSet(mapping_set_id=mapping_set_id, mappings=mappings, license=license)
-    # doc = MappingSetDocument(prefix_map=oi.prefix_map(), mapping_set=mset)
-    doc = MappingSetDocument(prefix_map=meta.prefix_map, mapping_set=mset)
-    msdf = to_mapping_set_dataframe(doc)
-    num_mappings = len(msdf.df.index)
-    if ensure_strict_prefixes:
-        msdf.clean_prefix_map()
-        if len(msdf.df.index) < num_mappings:
-            raise ValueError("Mappings included prefixes that were not in the prefix map")
+    # TODO what's the business logic for combining these three
+    #  different streams of prefix maps?
+    converter = curies.chain(
+        [
+            Converter.from_prefix_map(meta.prefix_map) if meta is not None else Converter([]),
+            oi.converter,
+            ensure_converter(prefix_map, use_defaults=False),
+        ]
+    )
+    msdf = MappingSetDataFrame.from_mappings(
+        mappings=mappings, metadata=meta and meta.metadata, converter=converter
+    )
+    msdf.clean_prefix_map(strict=ensure_strict_prefixes)
     return msdf
 
 

src/oaklib/utilities/mapping/sssom_utils.py

@@ -2,10 +2,9 @@
 from typing import Iterable, List, Optional, Tuple
 
 from linkml_runtime.utils.metamodelcore import URIorCURIE
-from sssom.sssom_document import MappingSetDocument
-from sssom.util import to_mapping_set_dataframe
+from sssom.util import MappingSetDataFrame
 from sssom.writers import write_table
-from sssom_schema import Mapping, MappingSet
+from sssom_schema import Mapping
 
 from oaklib.io.streaming_writer import StreamingWriter
 from oaklib.types import CURIE
@@ -74,14 +73,7 @@ def emit(self, obj: Mapping):
         self.mappings.append(obj)
 
     def finish(self):
-        mset = MappingSet(
-            mapping_set_id="temp", mappings=self.mappings, license=UNSPECIFIED_MAPPING_SET_ID
-        )
-        if self.ontology_interface:
-            prefix_map = self.ontology_interface.prefix_map()
-        else:
-            prefix_map = {}
-        doc = MappingSetDocument(prefix_map=prefix_map, mapping_set=mset)
-        msdf = to_mapping_set_dataframe(doc)
+        converter = self.ontology_interface.converter if self.ontology_interface else None
+        msdf = MappingSetDataFrame.from_mappings(self.mappings, converter=converter)
         msdf.clean_prefix_map(strict=False)
         write_table(msdf, self.file)