Use bioregistry as a resource for external prefix map via curies (#396)

* Use bioregistry as a resource for external prefix map via `curies`

* removed unnecessary variable

* Added a todo

* commented

* linted

Author: hrshdhgd

Diff for: Makefile

@@ -1,10 +1,10 @@
 PYTHON=python
 SSSOM_VERSION_TAG=0.12.0
-DEFAULT_PREFIX_MAP="https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/obo.context.jsonld"
 SSSOM_PY="https://raw.githubusercontent.com/mapping-commons/sssom/$(SSSOM_VERSION_TAG)/src/sssom_schema/datamodel/sssom_schema.py"
 SSSOM_YAML="https://raw.githubusercontent.com/mapping-commons/sssom/$(SSSOM_VERSION_TAG)/src/sssom_schema/schema/sssom_schema.yaml"
 SSSOM_JSON_SCHEMA="https://raw.githubusercontent.com/mapping-commons/sssom/$(SSSOM_VERSION_TAG)/project/jsonschema/sssom_schema.schema.json"
 SSSOM_JSONLD_CONTEXT="https://raw.githubusercontent.com/mapping-commons/sssom/$(SSSOM_VERSION_TAG)/project/jsonld/sssom_schema.context.jsonld"
+OBO_EPM_JSON="https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/obo.epm.json"
 
 all: test
 
@@ -20,8 +20,8 @@ schema/cliquesummary.py: schema/cliquesummary.yaml
 	gen-py-classes $< > $@
 schema/%.schema.json: .FORCE
 	wget $(SSSOM_JSON_SCHEMA) -O $@
-src/sssom/sssom.external.context.jsonld:
-	wget $(DEFAULT_PREFIX_MAP) -O $@
+src/sssom/obo.epm.json:
+	wget $(OBO_EPM_JSON) -O $@
 schema/%.context.jsonld: .FORCE
 	wget $(SSSOM_JSONLD_CONTEXT) -O $@
 schema/%.yaml sssom/%.yaml: .FORCE
@@ -33,7 +33,7 @@ test:
 	tox
 	sh tests/tests.sh
 
-deploy-dm: src/sssom/sssom.external.context.jsonld
+deploy-dm: src/sssom/obo.epm.json
 
 install:
 	pip install .[test,docs]

Diff for: src/sssom/constants.py

@@ -9,12 +9,15 @@
 from linkml_runtime.utils.schema_as_dict import schema_as_dict
 from linkml_runtime.utils.schemaview import SchemaView
 
+# from curies import Converter
+
+
 # from linkml_runtime.utils.introspection import package_schemaview
 
 HERE = pathlib.Path(__file__).parent.resolve()
 
 SCHEMA_YAML = pkg_resources.resource_filename("sssom_schema", "schema/sssom_schema.yaml")
-EXTERNAL_CONTEXT = HERE / "sssom.external.context.jsonld"
+EXTENDED_PREFIX_MAP = HERE / "obo.epm.json"
 
 # SCHEMA_VIEW = package_schemaview("sssom_schema")
 
@@ -173,6 +176,9 @@
     OBJECT_SOURCE_VERSION: SUBJECT_SOURCE_VERSION,
 }
 
+# TODO: Implement this for all CURIE prefix <=> URI prefix conversions.
+# OBO_EXTENDED_PREFIX_MAP_CONVERTER = Converter.from_extended_prefix_map(EXTENDED_PREFIX_MAP)
+
 
 class SEMAPV(Enum):
     """SEMAPV Enum containing different mapping_justification."""

Diff for: src/sssom/context.py

@@ -6,14 +6,15 @@
 from typing import Optional
 
 import pkg_resources
+from curies import Converter
 
-from sssom.constants import EXTERNAL_CONTEXT
+from sssom.constants import EXTENDED_PREFIX_MAP
 
 from .typehints import Metadata, MetadataType, PrefixMap
 
 # HERE = pathlib.Path(__file__).parent.resolve()
 # DEFAULT_CONTEXT_PATH = HERE / "sssom.context.jsonld"
-# EXTERNAL_CONTEXT_PATH = HERE / "sssom.external.context.jsonld"
+# EXTERNAL_CONTEXT_PATH = HERE / "obo.epm.json"
 
 SSSOM_URI_PREFIX = "https://w3id.org/sssom/"
 SSSOM_BUILT_IN_PREFIXES = ("sssom", "owl", "rdf", "rdfs", "skos", "semapv")
@@ -37,14 +38,13 @@ def get_jsonld_context():
     return context
 
 
-def get_external_jsonld_context():
-    """Get JSON-LD form of sssom_external_context variable from auto-generated 'external_context.py' file.
+def get_extended_prefix_map():
+    """Get prefix map from bioregistry (obo.epm.json).
 
-    :return: JSON-LD context
+    :return: Prefix map.
     """
-    with open(str(EXTERNAL_CONTEXT), "r") as f:
-        data = json.load(f, strict=False)
-    return data
+    converter = Converter.from_extended_prefix_map(EXTENDED_PREFIX_MAP)
+    return converter.prefix_map
 
 
 def get_built_in_prefix_map() -> PrefixMap:
@@ -97,7 +97,7 @@ def get_default_metadata() -> Metadata:
     :return: Metadata
     """
     contxt = get_jsonld_context()
-    contxt_external = get_external_jsonld_context()
+    contxt_external = get_extended_prefix_map()
     prefix_map = {}
     metadata_dict: MetadataType = {}
     for key in contxt["@context"]:
@@ -108,16 +108,8 @@ def get_default_metadata() -> Metadata:
             if "@id" in v and "@prefix" in v:
                 if v["@prefix"]:
                     prefix_map[key] = v["@id"]
-    for key in contxt_external["@context"]:
-        v = contxt_external["@context"][key]
-        if isinstance(v, str):
-            if key not in prefix_map:
-                prefix_map[key] = v
-            else:
-                if prefix_map[key] != v:
-                    logging.warning(
-                        f"{key} is already in prefix map ({prefix_map[key]}, but with a different value than {v}"
-                    )
+
+    prefix_map.update({(k, v) for k, v in contxt_external.items() if k not in prefix_map})
 
     metadata = Metadata(prefix_map=prefix_map, metadata=metadata_dict)
     metadata.metadata["mapping_set_id"] = DEFAULT_MAPPING_SET_ID