Enable retrieving synonyms on get_prefixes and implement `get_uri_p…

…refixes` (#100)

docs/source/tutorial.rst

@@ -251,6 +251,52 @@ This works with both :class:`pathlib.Path` and vanilla strings.
     urlretrieve(url, path)
     converter = curies.load_shacl(path)
 
+Introspecting on a Context
+--------------------------
+After loading a context, it's possible to get certain information out of the converter. For example, if you want to
+get all of the CURIE prefixes from the converter, you can use :meth:`Converter.get_prefixes`:
+
+.. code-block:: python
+
+    import curies
+
+    converter = curies.get_bioregistry_converter()
+    prefixes = converter.get_prefixes()
+    assert 'chebi' in prefixes
+    assert 'CHEBIID' not in prefixes, "No synonyms are included by default"
+
+    prefixes = converter.get_prefixes(include_synonyms=True)
+    assert 'chebi' in prefixes
+    assert 'CHEBIID' in prefixes
+
+Similarly, the URI prefixes can be extracted with :meth:`Converter.get_uri_prefixes` like in:
+
+.. code-block:: python
+
+    import curies
+
+    converter = curies.get_bioregistry_converter()
+    uri_prefixes = converter.get_uri_prefixes()
+    assert 'http://purl.obolibrary.org/obo/CHEBI_'' in prefixes
+    assert 'https://bioregistry.io/chebi:' not in prefixes, "No synonyms are included by default"
+
+    uri_prefixes = converter.get_uri_prefixes(include_synonyms=True)
+    assert 'http://purl.obolibrary.org/obo/CHEBI_'' in prefixes
+    assert 'https://bioregistry.io/chebi:' in prefixes
+
+It's also possible to get a bijective prefix map, i.e., a dictionary from primary CURIE prefixes
+to primary URI prefixes. This is useful for compatibility with legacy systems which assume simple prefix maps.
+This can be done with the ``bimap`` property like in the following:
+
+.. code-block:: python
+
+    import curies
+
+    converter = curies.get_bioregistry_converter()
+    prefix_map = converter.bimap
+    >>> prefix_map['chebi']
+    'http://purl.obolibrary.org/obo/CHEBI_'
+
 Modifying a Context
 -------------------
 Incremental Converters

src/curies/api.py

@@ -965,9 +965,41 @@ def from_shacl(
         ]
         return cls(records, **kwargs)
 
-    def get_prefixes(self) -> Set[str]:
-        """Get the set of prefixes covered by this converter."""
-        return {record.prefix for record in self.records}
+    def get_prefixes(self, *, include_synonyms: bool = False) -> Set[str]:
+        """Get the set of prefixes covered by this converter.
+
+        :param include_synonyms: If true, include secondary prefixes.
+        :return:
+            A set of primary prefixes covered by the converter. If ``include_synonyms`` is
+            set to ``True``, secondary prefixes (i.e., ones in :data:`Record.prefix_synonyms`
+            are also included
+        """
+        rv = {record.prefix for record in self.records}
+        if include_synonyms:
+            rv.update(
+                prefix_synonym
+                for record in self.records
+                for prefix_synonym in record.prefix_synonyms
+            )
+        return rv
+
+    def get_uri_prefixes(self, *, include_synonyms: bool = False) -> Set[str]:
+        """Get the set of URI prefixes covered by this converter.
+
+        :param include_synonyms: If true, include secondary prefixes.
+        :return:
+            A set of primary URI prefixes covered by the converter. If ``include_synonyms`` is
+            set to ``True``, secondary URI prefixes (i.e., ones in :data:`Record.uri_prefix_synonyms`
+            are also included
+        """
+        rv = {record.uri_prefix for record in self.records}
+        if include_synonyms:
+            rv.update(
+                uri_prefix_synonym
+                for record in self.records
+                for uri_prefix_synonym in record.uri_prefix_synonyms
+            )
+        return rv
 
     def format_curie(self, prefix: str, identifier: str) -> str:
         """Format a prefix and identifier into a CURIE string."""

tests/test_api.py

@@ -67,6 +67,24 @@ def test_duplicate_failure(self):
         with self.assertRaises(ValueError):
             self.converter.add_record(Record(prefix="GO", uri_prefix=CHEBI_URI_PREFIX))
 
+    def test_get_prefix_synonyms(self):
+        """Test getting prefix synonyms."""
+        self.assertEqual({self.prefix}, self.converter.get_prefixes())
+        self.assertEqual({self.prefix}, self.converter.get_prefixes(include_synonyms=False))
+        self.assertEqual(
+            {self.prefix, self.prefix_synonym},
+            self.converter.get_prefixes(include_synonyms=True),
+        )
+
+    def test_get_uri_prefix_synonyms(self):
+        """Test getting URI prefix synonyms."""
+        self.assertEqual({self.uri_prefix}, self.converter.get_uri_prefixes())
+        self.assertEqual({self.uri_prefix}, self.converter.get_uri_prefixes(include_synonyms=False))
+        self.assertEqual(
+            {self.uri_prefix, self.uri_prefix_synonym},
+            self.converter.get_uri_prefixes(include_synonyms=True),
+        )
+
     def test_extend_on_prefix_match(self):
         """Test adding a new prefix in merge mode."""
         s1, s2, s3 = "s1", "s2", "s3"
@@ -259,6 +277,9 @@ def test_subset(self):
         new_converter = self.converter.get_subconverter(["CHEBI"])
         self.assertEqual(1, len(new_converter.records))
         self.assertEqual({"CHEBI"}, new_converter.get_prefixes())
+        self.assertEqual(
+            {"http://purl.obolibrary.org/obo/CHEBI_"}, new_converter.get_uri_prefixes()
+        )
         self.assertEqual({"CHEBI"}, set(new_converter.bimap))
         self.assertEqual({"CHEBI"}, set(new_converter.prefix_map))
         self.assertEqual(
@@ -282,6 +303,15 @@ def test_predicates(self):
     def test_convert(self):
         """Test compression."""
         self.assertEqual({"CHEBI", "MONDO", "GO", "OBO"}, self.converter.get_prefixes())
+        self.assertEqual(
+            {
+                "http://purl.obolibrary.org/obo/CHEBI_",
+                "http://purl.obolibrary.org/obo/MONDO_",
+                "http://purl.obolibrary.org/obo/GO_",
+                "http://purl.obolibrary.org/obo/",
+            },
+            self.converter.get_uri_prefixes(),
+        )
         self._assert_convert(self.converter)
 
     def _assert_convert(self, converter: Converter):
@@ -556,7 +586,7 @@ def test_combine_with_synonyms(self):
         self.assertIn("GO", c3.bimap)
 
     def test_combine_ci(self):
-        """Test combining case insensitive."""
+        """Test combining case-insensitive."""
         c1 = Converter.from_priority_prefix_map(
             {
                 "CHEBI": [
@@ -573,6 +603,8 @@ def test_combine_ci(self):
         )
         converter = chain([c1, c2], case_sensitive=False)
         self.assertEqual({"CHEBI"}, converter.get_prefixes())
+        self.assertEqual({"CHEBI"}, converter.get_prefixes(include_synonyms=False))
+        self.assertEqual({"CHEBI", "chebi"}, converter.get_prefixes(include_synonyms=True))
         for url in [
             "http://purl.obolibrary.org/obo/CHEBI_138488",
             "http://identifiers.org/chebi/138488",