- Add: TestWrite.test_missing_entries()

Author: joeflack4

tests/test_writers.py

@@ -5,6 +5,7 @@
 import unittest
 from typing import Any, Dict
 
+import curies
 import pandas as pd
 from curies import Converter
 
@@ -191,3 +192,65 @@ def test_write_sssom_ontoportal_json(self):
             self.mapping_count,
             f"{path} has the wrong number of mappings.",
         )
+
+    # TODO: Determine assertions that should pass
+    # TODO: Fix failing assertions that should pass
+    # TODO: before merging, remove pass/fail comments at end of assertion lines
+    def test_missing_entries(self):
+        """Test to make sure that missing entires do not appear"""
+        df = pd.DataFrame([{
+            'subject_id': 'Orphanet:58',
+            'subject_label': 'Alexander disease',
+            'predicate_id': 'skos:exactMatch',
+            'object_id': 'icd11.foundation:2023359698',
+            'object_label': 'Alexander disease',
+            'mapping_justification': 'semapv:UnspecifiedMatching'
+        }])
+        metadata = {
+            'creator_id': 'orcid:0000-0002-2906-7319',
+            'curie_map': {
+                'MONDO': 'http://purl.obolibrary.org/obo/MONDO_',
+                'Orphanet': 'http://www.orpha.net/ORDO/Orphanet_',
+                'icd11.foundation': 'http://id.who.int/icd/entity/',
+                'oboInOwl': 'http://www.geneontology.org/formats/oboInOwl#',
+                'orcid': 'https://orcid.org/',
+                'owl': 'http://www.w3.org/2002/07/owl#',
+                'rdf': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#',
+                'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
+                'semapv': 'https://w3id.org/semapv/',
+                'skos': 'http://www.w3.org/2004/02/skos/core#',
+                'sssom': 'https://w3id.org/sssom/'
+            },
+            'license': 'http://w3id.org/sssom/license/unspecified',
+            'mapping_provider': 'https://www.orpha.net/'
+        }
+
+        # When passing Converter
+        msdf: MappingSetDataFrame = MappingSetDataFrame(
+            converter=curies.Converter.from_prefix_map(metadata['curie_map']),
+            df=df,
+            metadata=metadata
+        )
+        self.assertIn('curie_map', msdf.metadata)  # pass
+        self.assertIn('icd11.foundation', msdf.metadata['curie_map'])  # pass
+        self.assertIn('icd11.foundation', msdf.prefix_map)  # pass
+        tmp_file = os.path.join(test_out_dir, "test_missing_entries.sssom.tsv")
+        with open(tmp_file, 'w') as f:
+            write_table(msdf, f)
+        msdf2 = parse_sssom_table(tmp_file)
+        self.assertIn('curie_map', msdf2.metadata)  # fail
+        self.assertIn('icd11.foundation', msdf2.metadata['curie_map'])  # KeyError
+        self.assertIn('icd11.foundation', msdf2.prefix_map)  # pass
+
+        # When no passed Converter
+        msdf: MappingSetDataFrame = MappingSetDataFrame(df=df, metadata=metadata)
+        self.assertIn('curie_map', msdf.metadata)  # pass
+        self.assertIn('icd11.foundation', msdf.metadata['curie_map'])  # pass
+        self.assertIn('icd11.foundation', msdf.prefix_map)  # fail
+        tmp_file = os.path.join(test_out_dir, "test_missing_entries.sssom.tsv")
+        with open(tmp_file, 'w') as f:
+            write_table(msdf, f)
+        msdf2 = parse_sssom_table(tmp_file)
+        self.assertIn('curie_map', msdf2.metadata)  # fail
+        self.assertIn('icd11.foundation', msdf2.metadata['curie_map'])  # KeyError
+        self.assertIn('icd11.foundation', msdf2.prefix_map)  # fail