Simplify getting a curies.Converter from a prefixmaps.Context

README.md

@@ -12,8 +12,8 @@ This repository and the corresponding library is designed to satisfy the followi
 - no single authoritative source of either prefixes or prefix-namespace mappings (clash-resilient)
 - preferred semantic namespace is prioritized over web URLs
 - authority preferred prefix is prioritized where possible
-- each individual prefixmap is case-insenstive bijective
-- prefixmap composition and custom ordering of prefixmaps
+- each individual prefix map is case-insensitive bijective
+- prefix map composition and custom ordering of prefixmaps
 - lightweight / low footprint
 - fast (TODO)
 - network-independence / versioned prefix maps
@@ -22,11 +22,11 @@ This repository and the corresponding library is designed to satisfy the followi
 What this is NOT intended for:
 
 - a general source of metadata about either prefixes or namespaces
-- a mechansim for resolving identifiers to web URLs for humans to find information
+- a mechanism for resolving identifiers to web URLs for humans to find information
 
 ## Installation
 
-```
+```shell
 pip install prefixmaps
 ```
 
@@ -39,8 +39,7 @@ from prefixmaps.io.parser import load_multi_context
 from curies import Converter
 
 context = load_multi_context(["obo", "bioregistry.upper", "linked_data", "prefixcc"])
-extended_prefix_map = context.as_extended_prefix_map()
-converter = Converter.from_extended_prefix_map(extended_prefix_map)
+converter: Converter = context.as_converter()
 
 >>> converter.expand("CHEBI:1")
 'http://purl.obolibrary.org/obo/CHEBI_1'
@@ -62,8 +61,7 @@ If we prioritize prefix.cc the OBO prefix is ignored:
 
 ```python
 context = load_multi_context(["prefixcc", "obo"])
-extended_prefix_map = context.as_extended_prefix_map()
-converter = Converter.from_extended_prefix_map(extended_prefix_map)
+converter: Converter = context.as_converter()
 
 >>> converter.expand("GEO:1")
 >>> converter.expand("geo:1")
@@ -76,8 +74,7 @@ If we push `bioregistry` at the start of the list then GEOGEO can be used as the
 
 ```python
 context = load_multi_context(["bioregistry", "prefixcc", "obo"])
-extended_prefix_map = context.as_extended_prefix_map()
-converter = Converter.from_extended_prefix_map(extended_prefix_map)
+converter: Converter = context.as_converter()
 
 >>> converter.expand("geo:1")
 'http://identifiers.org/geo/1'
@@ -92,8 +89,7 @@ We get similar results using the upper-normalized variant of `bioregistry`:
 
 ```python
 context = load_multi_context(["bioregistry.upper", "prefixcc", "obo"])
-extended_prefix_map = context.as_extended_prefix_map()
-converter = Converter.from_extended_prefix_map(extended_prefix_map)
+converter: Converter = context.as_converter()
 
 >>> converter.expand("GEO:1")
 'http://identifiers.org/geo/1'
@@ -106,8 +102,7 @@ Users of OBO ontologies will want to place OBO at the start of the list:
 
 ```python
 context = load_multi_context(["obo", "bioregistry.upper", "prefixcc"])
-extended_prefix_map = context.as_extended_prefix_map()
-converter = Converter.from_extended_prefix_map(extended_prefix_map)
+converter: Converter = context.as_converter()
 
 >>> converter.expand("geo:1")
 >>> converter.expand("GEO:1")
@@ -123,8 +118,7 @@ You can use the ready-made "merged" prefix set, which prioritizes OBO:
 
 ```python
 context = load_context("merged")
-extended_prefix_map = context.as_extended_prefix_map()
-converter = Converter.from_extended_prefix_map(extended_prefix_map)
+converter: Converter = context.as_converter()
 
 >>> converter.expand("GEOGEO:1")
 >>> converter.expand("GEO:1")

pyproject.toml

@@ -36,11 +36,11 @@ typing-extensions = "^4.4.0"
 requests = {version = "^2.28.1", extras = ["refresh"]}
 bioregistry = {version = "^0.8.0", extras = ["refresh"]}
 rdflib = {version = "^6.2.0", extras = ["refresh"]}
+curies = "^0.5.3"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2"
 linkml = "^1.3.1"
-curies = "^0.5.3"
 coverage = "^6.4.4"
 
 [tool.poetry.extras]

src/prefixmaps/datamodel/context.py

@@ -6,7 +6,7 @@
 from enum import Enum
 from typing import List, Mapping, Optional
 
-from typing_extensions import TypedDict
+import curies
 
 __all__ = [
     "StatusType",
@@ -47,15 +47,6 @@ class StatusType(Enum):
     """Both the prefix and the namespace are aliases for existing canonical namespaces."""
 
 
-class RecordDict(TypedDict):
-    """A record that is compatible with :mod:`curies`."""
-
-    prefix: str
-    uri_prefix: str
-    prefix_synonyms: List[str]
-    uri_prefix_synonyms: List[str]
-
-
 @dataclass
 class PrefixExpansion:
     """
@@ -271,8 +262,8 @@ def as_inverted_dict(self) -> INVERSE_PREFIX_EXPANSION_DICT:
         """
         return {pe.namespace: pe.prefix for pe in self.prefix_expansions if pe.canonical()}
 
-    def as_extended_prefix_map(self) -> List[RecordDict]:
-        """Return an extended prfix, appropriate for generating a :class:`curies.Converter`.
+    def as_extended_prefix_map(self) -> List[curies.Record]:
+        """Return an extended prefix, appropriate for generating a :class:`curies.Converter`.
 
         An extended prefix map is a collection of dictionaries, each of which has the following
         fields:
@@ -307,7 +298,7 @@ def as_extended_prefix_map(self) -> List[RecordDict]:
                 prefix_synonyms[reverse_prefix_map[expansion.namespace]].add(expansion.prefix)
 
         return [
-            RecordDict(
+            curies.Record(
                 prefix=prefix,
                 prefix_synonyms=sorted(prefix_synonyms[prefix]),
                 uri_prefix=uri_prefix,
@@ -316,6 +307,11 @@ def as_extended_prefix_map(self) -> List[RecordDict]:
             for prefix, uri_prefix in sorted(prefix_map.items())
         ]
 
+    def as_converter(self) -> curies.Converter:
+        """Get a converter from this prefix map."""
+        extended_prefix_map = self.as_extended_prefix_map()
+        return curies.Converter.from_extended_prefix_map(extended_prefix_map)
+
     def validate(self, canonical_only=True) -> List[str]:
         """
         Validates each prefix expansion in the context.

tests/test_core/test_curies.py

@@ -21,8 +21,8 @@ def test_load(self):
         self.assertIn(uri_prefix_1, context_namespaces)
         self.assertIn(uri_prefix_2, context_namespaces)
 
-        extended_prefix_map = context.as_extended_prefix_map()
-        converter = Converter.from_extended_prefix_map(extended_prefix_map)
+        converter = context.as_converter()
+        self.assertIsInstance(converter, Converter)
 
         # prefix map checks
         self.assertIn(prefix, converter.prefix_map)