Simplify parsing SSSOM w/ curies.chain

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 +56,7 @@
 
 from .context import HINT, ensure_converter
 from .sssom_document import MappingSetDocument
-from .typehints import Metadata, MetadataType, generate_mapping_set_id
+from .typehints import Metadata, MetadataType, generate_mapping_set_id, get_default_metadata
 from .util import (
     PREFIX_MAP_KEY,
     SSSOM_DEFAULT_RDF_SERIALISATION,
@@ -193,44 +194,35 @@ 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 PREFIX_MAP_KEY 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`` (handled with ensure_converter)
+    #  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),
+        ]
+    )
+
+    # 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(),
+        )
+    )
 
-    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)
+    msdf = from_sssom_dataframe(df, prefix_map=converter, meta=combine_meta)
     return msdf
 
 

src/sssom/writers.py

@@ -441,7 +441,7 @@ def to_fhir_json(msdf: MappingSetDataFrame) -> Dict:
 def to_json(msdf: MappingSetDataFrame) -> JsonObj:
     """Convert a mapping set dataframe to a JSON object."""
     doc = to_mapping_set_document(msdf)
-    data = JSONDumper().dumps(doc.mapping_set, contexts=doc.prefix_map)
+    data = JSONDumper().dumps(doc.mapping_set, contexts={"@context": doc.prefix_map})
     json_obj = json.loads(data)
     return json_obj
 

tests/test_collapse.py

@@ -73,6 +73,7 @@ def test_diff(self):
     def test_reconcile_prefix(self):
         """Test curie reconciliation is performing as expected."""
         msdf = parse_sssom_table(data_dir / "basic3.tsv")
+        msdf.clean_prefix_map()
 
         self.assertEqual(
             {

tests/test_conversion.py

@@ -146,9 +146,10 @@ def _test_to_dataframe(self, mdoc, test):
             test.ct_data_frame_rows,
             f"The pandas data frame has less elements than the orginal one for {test.filename}",
         )
-        df.to_csv(test.get_out_file("roundtrip.tsv"), sep="\t")
-        # data = pd.read_csv(test.get_out_file("roundtrip.tsv"), sep="\t")
-        data = parse_sssom_table(test.get_out_file("roundtrip.tsv")).df
+        path = test.get_out_file("roundtrip.tsv")
+        with open(path, "w") as file:
+            write_table(msdf, file=file)
+        data = parse_sssom_table(path).df
         self.assertEqual(
             len(data),
             test.ct_data_frame_rows,

tests/test_utils.py

@@ -129,16 +129,10 @@ def test_clean_prefix_map_strict(self):
     def test_clean_prefix_map_not_strict(self):
         """Test clean prefix map with 'strict'=False."""
         msdf = parse_sssom_table(f"{data_dir}/test_clean_prefix.tsv")
-        original_curie_map = msdf.prefix_map
-        self.assertEqual(
-            {"a", "b", "c", "d", "orcid"}.union(SSSOM_BUILT_IN_PREFIXES),
-            set(original_curie_map),
-        )
         msdf.clean_prefix_map(strict=False)
-        new_curie_map = msdf.prefix_map
         self.assertEqual(
             {"a", "b", "c", "d", "orcid", "x1", "y1", "z1"}.union(SSSOM_BUILT_IN_PREFIXES),
-            set(new_curie_map),
+            set(msdf.prefix_map),
         )
 
     def test_invert_nodes(self):

tests/test_validate.py

@@ -29,6 +29,22 @@ def test_validate_json(self):
         """
         self.assertIsNone(validate(self.correct_msdf1, self.validation_types))
 
+    @unittest.skip(
+        reason="""\
+
+    This test did not previously do what was expected. It was raising a validation error
+    not because of the text below suggesting the validator was able to identify an issue
+    with the `mapping_justification` slot, but because `orcid` was missing from the prefix map.
+    The error actually thrown was::
+
+      jsonschema.exceptions.ValidationError: The prefixes in {'orcid'} are missing from 'curie_map'.
+
+    With updates in https://github.com/mapping-commons/sssom-py/pull/431, the default prefix map
+    which includes `orcid` is added on parse, and this error goes away. Therefore, this test
+    now fails, but again, this is a sporadic failure since the test was not correct in the first
+    place. Therefore, this test is now skipped and marked for FIXME.
+    """
+    )
     def test_validate_json_fail(self):
         """
         Test if JSONSchemaValidation fail is as expected.