Update rest

Author: cthoyt

pyproject.toml

@@ -85,7 +85,7 @@ docs = [
     "texext",
 ]
 biomappings = [
-    "biomappings>=0.4.0",
+    "biomappings>=0.4.1",
 ]
 web = [
     "semra[biomappings]",

src/semra/client.py

@@ -379,7 +379,7 @@ def summarize_concepts(self) -> t.Counter[tuple[str, str]]:
         query = "MATCH (e:concept) WHERE e.prefix <> 'orcid' RETURN e.prefix, count(e.prefix)"
         return Counter(
             {
-                (prefix, t.cast(str, bioregistry.get_name(prefix))): count
+                (prefix, bioregistry.get_name(prefix, strict=True)): count
                 for prefix, count in self.read_query(query)
             }
         )

src/semra/web/flask_components.py

@@ -5,15 +5,19 @@
 import typing as t
 from typing import cast
 
-import bioregistry
 import flask
 import werkzeug
+from bioregistry import NormalizedNamableReference
 from curies import Reference
 from flask import Blueprint, current_app, render_template
 
+from semra import EXACT_MATCH
 from semra.client import BaseClient
 from semra.web.shared import State, _figure_number
 
+if t.TYPE_CHECKING:
+    import biomappings.resources
+
 __all__ = [
     "flask_blueprint",
     "index_biomapping",
@@ -86,31 +90,27 @@ def mark_exact_incorrect(source: str, target: str) -> werkzeug.Response:
         return flask.redirect(flask.url_for(view_concept.__name__, curie=source))
 
     client = _flask_get_client()
+    state = _flask_get_state()
 
     import biomappings.resources
-    from biomappings.wsgi import _manual_source
-
-    source_reference = Reference.from_curie(source)
-    target_reference = Reference.from_curie(target)
-
-    mapping: dict[str, str] = {
-        "source prefix": source_reference.prefix,
-        "source identifier": source_reference.identifier,
-        "target prefix": target_reference.prefix,
-        "target identifier": target_reference.identifier,
-        "relation": "skos:exactMatch",
-        "type": "semapv:ManualMappingCuration",
-        "source": _manual_source(),
-        "prediction_type": "",
-        "prediction_source": "semra",
-        "prediction_confidence": "",
-    }
-    if source_name := client.get_concept_name(source):
-        mapping["source name"] = source_name
-    if target_name := client.get_concept_name(target):
-        mapping["target name"] = target_name
-
-    mapping = biomappings.resources._standardize_mapping(mapping)
+    from biomappings.utils import MANUAL_MAPPING_CURATION
+
+    subject = NormalizedNamableReference.from_curie(source, name=client.get_concept_name(source))
+    target_reference = NormalizedNamableReference.from_curie(
+        target, name=client.get_concept_name(target)
+    )
+
+    mapping = biomappings.resources.SemanticMapping.model_validate(
+        {
+            "subject": subject,
+            "predicate": EXACT_MATCH,
+            "object": target_reference,
+            "mapping_justification": MANUAL_MAPPING_CURATION,
+            "author": state.current_author,
+            "mapping_tool": "semra",
+        }
+    )
+
     biomappings.resources.append_false_mappings([mapping])
     index_biomapping(_flask_get_false_mapping_index(), mapping)
 
@@ -152,15 +152,12 @@ def _flask_get_false_mapping_index() -> set[tuple[str, str]]:
 
 
 def index_biomapping(
-    mapping_index: set[tuple[str, str]], mapping_dict: t.Mapping[str, str]
+    mapping_index: set[tuple[str, str]], mapping: biomappings.resources.SemanticMapping
 ) -> None:
     """Index a mapping from biomappings."""
-    if mapping_dict["relation"] != "skos:exactMatch":
+    if mapping.predicate.curie != "skos:exactMatch":
         return
-    sp, si = mapping_dict["source prefix"], mapping_dict["source identifier"]
-    tp, ti = mapping_dict["target prefix"], mapping_dict["target identifier"]
-    si = bioregistry.standardize_identifier(sp, si)
-    ti = bioregistry.standardize_identifier(tp, ti)
-    s, t = f"{sp}:{si}", f"{tp}:{ti}"
-    mapping_index.add((s, t))
-    mapping_index.add((t, s))
+    subject_curie = mapping.subject.curie
+    object_curie = mapping.object.curie
+    mapping_index.add((subject_curie, object_curie))
+    mapping_index.add((object_curie, subject_curie))

src/semra/web/shared.py

@@ -4,6 +4,8 @@
 
 from dataclasses import dataclass, field
 
+from bioregistry import NormalizedNamedReference
+
 from semra.client import BaseClient, ExampleMapping, FullSummary
 
 __all__ = [
@@ -22,6 +24,7 @@ class State:
     summary: FullSummary
     biomappings_hash: str | None = None
     false_mapping_index: set[tuple[str, str]] = field(default_factory=set)
+    current_author: NormalizedNamedReference | None = None
 
     def example_mappings(self) -> list[ExampleMapping]:
         """Extract example mappings."""

src/semra/wsgi.py

@@ -6,6 +6,7 @@
 from typing import Literal, overload
 
 import fastapi
+from bioregistry import NormalizedNamedReference
 from flask import Flask
 from flask_bootstrap import Bootstrap5
 from starlette.middleware.wsgi import WSGIMiddleware
@@ -45,9 +46,11 @@ def get_app(
 
     biomappings_git_hash: str | None = None
     false_mapping_index: set[tuple[str, str]] = set()
+    current_author: NormalizedNamedReference | None = None
 
     if use_biomappings:
         try:
+            import biomappings.resources
             import biomappings.utils
         except ImportError:
             pass
@@ -56,11 +59,14 @@ def get_app(
             for m in biomappings.load_false_mappings():
                 index_biomapping(false_mapping_index, m)
 
+            current_author = biomappings.resources.get_current_curator(strict=True)
+
     state = State(
         client=client,
         summary=client.get_full_summary(),
         false_mapping_index=false_mapping_index,
         biomappings_hash=biomappings_git_hash,
+        current_author=current_author,
     )
 
     flask_app = Flask(__name__)