Add multiple value fields to mappings (#64)

* add mappings endpoint to ui * formatting --------- Co-authored-by: Anita Caron <[email protected]>
mapping-commons · Apr 21, 2023 · d1c4952 · d1c4952
1 parent 11bc650
commit d1c4952
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Showing 2 changed files with 51 additions and 4 deletions.
diff --git a/src/database/sparql_implementation.py b/src/database/sparql_implementation.py
@@ -191,19 +191,43 @@ def get_ui_mappings_by_curie(self, search_filter: SearchEntity) -> Iterable[dict
             row["object_id_curie"] = OBO_CURIE_CONVERTER.compress(row["object_id"])
             yield row
 
-    def get_sssom_mappings_query(self, filter: Union[List[dict], None]) -> Iterable[Mapping]:
+    def get_mappings_by_filter(self, filter: Union[List[dict], None]) -> Iterable[dict]:
+        fields_list, fields_single = self._get_fields(
+            slots_type=self.schema_view.mapping_slots.copy()
+        )
+        # Search for single value attributes
         default_query = self.add_filters(
             self.default_query(
                 type=Mapping.class_class_uri,
-                slots=self.schema_view.mapping_slots.copy(),
+                slots=fields_single,
             ),
             filter,
         )
         bindings = self._query(default_query)
         for row in bindings:
             r = self.transform_result(row)
+            # Search for multiple value attributes
+            for field in fields_list:
+                default_query_list = self.add_filters(
+                    self.default_query(
+                        type=Mapping.class_class_uri,
+                        slots={field},
+                        subject=r["_x"],
+                    ),
+                    filter,
+                )
+                results = self._query(default_query_list)
+                bindings_list = self.transform_result_list(results)
+                if len(bindings_list):
+                    r[f"{field}"] = bindings_list
             r.pop("_x")
-            m = create_sssom_mapping(**r)
+            yield r
+
+    def get_sssom_mappings_by_filter(self, filter: Union[List[dict], None]) -> Iterable[Mapping]:
+        bindings = self.get_mappings_by_filter(filter)
+        for row in bindings:
+            row.pop("uuid")
+            m = create_sssom_mapping(**row)
             if m is not None:
                 yield m
 
@@ -338,10 +362,18 @@ def get_mappings_field(imp: SparqlImpl, field: str, value: str) -> Iterable[Mapp
 
 
 def get_mappings_query(imp: SparqlImpl, filter: Union[List[dict], None]) -> Iterable[Mapping]:
-    mappings = imp.get_sssom_mappings_query(filter)
+    mappings = imp.get_sssom_mappings_by_filter(filter)
     return mappings
 
 
+def get_mappings_by_filter_ui(imp: SparqlImpl, filter: Union[List[dict], None]) -> Iterable[dict]:
+    mappings = imp.get_mappings_by_filter(filter)
+    for m in mappings:
+        m["subject_id_curie"] = OBO_CURIE_CONVERTER.compress(m["subject_id"])
+        m["object_id_curie"] = OBO_CURIE_CONVERTER.compress(m["object_id"])
+        yield m
+
+
 def get_mapping_sets(
     request: Request, imp: SparqlImpl, filter: Union[List[dict], None]
 ) -> Iterable[dict]:

diff --git a/src/routers/mappings.py b/src/routers/mappings.py
@@ -6,6 +6,7 @@
 from ..database.sparql_implementation import (
     SparqlImpl,
     get_mapping_by_id,
+    get_mappings_by_filter_ui,
     get_mappings_field,
     get_mappings_query,
     get_ui_mapping_by_id,
@@ -58,3 +59,17 @@ def mappings_by_field(
 @router_ui.get("/{id}", summary="Get mapping by id")
 def mapping_by_id_ui(id: str, sparqlImpl: SparqlImpl = Depends(get_sparql_implementation)):
     return get_ui_mapping_by_id(sparqlImpl, id)
+
+
+@router_ui.get("/", summary="Get mappings with optional filters")
+def mappings_ui(
+    sparqlImpl: SparqlImpl = Depends(get_sparql_implementation),
+    pagination: PaginationParams = Depends(),
+    filter: Union[List[str], None] = Query(default=None),
+):
+    filter_parsed = parser_filter(Mapping, filter)
+    if filter_parsed is None:
+        raise HTTPException(status_code=302, detail="Not valid filter")
+    else:
+        results = get_mappings_by_filter_ui(sparqlImpl, filter_parsed)
+        return paginate(results, **pagination.dict())