set_label will INSERT if label not already presented. Fixes #788 (#789)

INCATools · Aug 1, 2024 · 2458242 · 2458242
1 parent a112885
commit 2458242
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Showing 3 changed files with 20 additions and 7 deletions.
diff --git a/src/oaklib/implementations/aggregator/aggregator_implementation.py b/src/oaklib/implementations/aggregator/aggregator_implementation.py
@@ -1,3 +1,4 @@
+import logging
 from collections import defaultdict
 from dataclasses import dataclass
 from io import TextIOWrapper
@@ -140,6 +141,10 @@ def sssom_mappings(self, *args, **kwargs) -> Iterable[Mapping]:
     def label(self, curie: CURIE, **kwargs) -> str:
         return self._delegate_first(lambda i: i.label(curie, **kwargs))
 
+    def set_label(self, curie: CURIE, label: str) -> None:
+        logging.debug(f"Assuming {curie} is in first aggregated resource, label={label}")
+        return self._delegate_first(lambda i: i.set_label(curie, label))
+
     def curies_by_label(self, label: str) -> List[CURIE]:
         return list(self._delegate_iterator(lambda i: i.curies_by_label(label)))
 

diff --git a/src/oaklib/implementations/sqldb/sql_implementation.py b/src/oaklib/implementations/sqldb/sql_implementation.py
@@ -788,11 +788,19 @@ def _execute(self, stmt):
             self.save()
 
     def set_label(self, curie: CURIE, label: str) -> bool:
-        stmt = (
-            update(Statements)
-            .where(and_(Statements.subject == curie, Statements.predicate == LABEL_PREDICATE))
-            .values(value=label)
-        )
+        existing_label = self.label(curie)
+        if existing_label:
+            stmt = (
+                update(Statements)
+                .where(and_(Statements.subject == curie, Statements.predicate == LABEL_PREDICATE))
+                .values(value=label)
+            )
+        else:
+            stmt = (
+                insert(Statements)
+                .values(subject=curie, predicate=LABEL_PREDICATE, value=label)
+                .execution_options(autocommit=True)
+            )
         self._execute(stmt)
 
     def basic_search(self, search_term: str, config: SearchConfiguration = None) -> Iterable[CURIE]:

diff --git a/src/oaklib/utilities/lexical/lexical_indexer.py b/src/oaklib/utilities/lexical/lexical_indexer.py
@@ -79,9 +79,8 @@ def add_labels_from_uris(oi: BasicOntologyInterface):
             if curie.startswith("<http"):
                 label = label.replace(">", "")
             label = " ".join(label.split("_"))
-            # print(f'{curie} ==> {label} // {type(oi)}')
             oi.set_label(curie, label)
-            # print(oi.get_label_by_curie(curie))
+
 
 
 def create_lexical_index(
@@ -127,6 +126,7 @@ def _invert_mapping_pred(mapping_pred: PRED_CURIE) -> PRED_CURIE:
     logging.info("Creating mapping index")
     mapping_pairs_by_curie = defaultdict(list)
     for curie in oi.entities():
+        logging.debug(f"Finding mappings for {curie}")
         pairs = list(oi.simple_mappings_by_curie(curie))
         for pred, object_id in pairs:
             mapping_pairs_by_curie[curie].append((pred, object_id))