Simplify fixing local curations

biopragmatics · Dec 18, 2024 · 3d18161 · 3d18161
1 parent b5fdc02
commit 3d18161
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Showing 2 changed files with 16 additions and 5 deletions.
diff --git a/src/biomappings/resources/__init__.py b/src/biomappings/resources/__init__.py
@@ -88,7 +88,7 @@ class MappingTuple(NamedTuple):
     prediction_source: Optional[str]
     prediction_confidence: Optional[float]
 
-    def as_dict(self) -> Mapping[str, Any]:
+    def as_dict(self) -> dict[str, Any]:
         """Get the mapping tuple as a dictionary."""
         return dict(zip(MAPPINGS_HEADER, self))  # type:ignore
 
@@ -161,7 +161,7 @@ class PredictionTuple(NamedTuple):
     or can be based off of them.
     """
 
-    def as_dict(self) -> Mapping[str, Any]:
+    def as_dict(self) -> dict[str, Any]:
         """Get the prediction tuple as a dictionary."""
         return dict(zip(PREDICTIONS_HEADER, self))  # type:ignore
 
@@ -218,7 +218,7 @@ def target_curie(self) -> str:
         return f"{self.target_prefix}:{self.target_identifier}"
 
 
-Mappings = Iterable[Mapping[str, str]]
+Mappings = Iterable[dict[str, str]]
 
 
 def get_resource_file_path(fname) -> Path:
@@ -320,6 +320,7 @@ def _lint_curated_mappings(path: Path, *, standardize: bool = False) -> None:
     """Lint the true mappings file."""
     mapping_list = _load_table(path)
     mappings = _remove_redundant(mapping_list, standardize=standardize)
+    mappings = _replace_local_curation_source(mapping_list)
     _write_helper(MAPPINGS_HEADER, mappings, path, mode="w")
 
 
@@ -496,6 +497,17 @@ def _remove_redundant(mappings: Mappings, *, standardize: bool = False) -> Mappi
     return (max(mappings, key=_pick_best) for mappings in dd.values())
 
 
+def _replace_local_curation_source(mappings: Mappings) -> Mappings:
+    """Find `web-` prefixed sources that can be replaced with ORCID CURIEs."""
+    user_to_contributors = {c["user"]: c["orcid"] for c in load_curators()}
+    for mapping in mappings:
+        source = mapping["source"]
+        orcid = user_to_contributors.get(source.removeprefix("web-"))
+        if orcid:
+            mapping["source"] = f"orcid:{orcid}"
+        yield mapping
+
+
 def _pick_best(mapping: Mapping[str, str]) -> int:
     """Assign a value for this mapping.
 

diff --git a/src/biomappings/testing.py b/src/biomappings/testing.py
@@ -167,8 +167,7 @@ def test_contributors(self) -> None:
                             There are some curations that don't have the right metadata
                             in {path}.
 
-                            You can fix this by doing searching for
-                            "{source}" and replacing it with "orcid:{orcid}"
+                            You can fix this by running `biomappings lint` from the console
                             """).rstrip()
                         )
                     else: