dev:minimal WoRMS compatibility: mypy fix

Author: grololo06

py/API_operations/TaxoManager.py

@@ -598,9 +598,12 @@ def pull_updates(self) -> Dict[str, Any]:
             for a_col in self.UpdatableCols:
                 setattr(taxon, a_col, a_json_taxon[a_col])
             taxon.lastupdate_datetime = lastupdate_datetime
+            # TODO: Below is mandatory as we alter trigger for fast deletion
+            # But we lose, in case of failure, the facility to re-sync, which is based on last
+            # updated date of taxonomy entries, nothing for deletes here.
+            self.session.commit()
         if len(to_delete) > 0:
             TaxonomyBO.do_deletes(self.session, to_delete)
-        self.session.commit()
 
         # if gvp('updatestat') == 'Y':
         #     msg = DoSyncStatUpdate()

py/BO/Taxonomy.py

@@ -432,24 +432,27 @@ def do_deletes(cls, session: Session, to_delete: List[ClassifIDT]) -> None:
         # *   **`taxonomy.parent_id`**: Although not explicitly defined with a `ForeignKey` constraint in the SQLAlchemy model (it is a simple `INTEGER` column), it logically points to `taxonomy.id` to represent the taxonomic tree structure.
         # *   **`taxonomy.rename_to`**: Similarly, this `INTEGER` column is used to store an "advised" target taxon for mass category changes, logically referring to another `taxonomy.id`.
         # *   **`taxo_recast.transforms`**: This `JSONB` column stores mapping in the form `{from:to}`, where both values are taxonomic IDs, though they are not enforced by database-level foreign key constraints.
-
+        sql = text("SELECT DISTINCT id FROM taxonomy")
+        res: Result = session.execute(sql, {"een": list(to_delete)})
+        present = {an_id for an_id, in res}
+        final_delete = present.intersection(to_delete)
         # We want to protect 1. and 2.
-        logger.info("Taxo delete, list: %s", to_delete)
+        logger.info("Taxo delete, list: %s", final_delete)
         sql = text("SELECT DISTINCT objid FROM obj_head WHERE classif_id = ANY (:een)")
-        res: Result = session.execute(sql, {"een": list(to_delete)})
-        prevent_obj_head = {an_id for an_id, in res}
+        res2: Result = session.execute(sql, {"een": list(final_delete)})
+        prevent_obj_head = {an_id for an_id, in res2}
         if len(prevent_obj_head) > 0:
             logger.error("Unsafe deletion due to objects %s", prevent_obj_head)
         sql = text("SELECT DISTINCT objid FROM objectsclassifhisto WHERE classif_id = ANY (:een)")
-        res: Result = session.execute(sql, {"een": list(to_delete)})
-        prevent_obj_histo = {an_id for an_id, in res}
+        res3: Result = session.execute(sql, {"een": list(final_delete)})
+        prevent_obj_histo = {an_id for an_id, in res3}
         if len(prevent_obj_histo) > 0:
             logger.error("Unsafe deletion due to objects history %s", prevent_obj_histo)
         # assert len(prevent_obj_head) == 0 and len(prevent_obj_histo) == 0, "Cannot achieve safe deletion"
         logger.info("deleting categories")
         session.execute(text("alter table taxonomy disable trigger all"))
         try:
-            for a_taxon in to_delete:
+            for a_taxon in final_delete:
                 logger.info("deleting category %s", a_taxon)
                 taxon = session.query(Taxonomy).get(a_taxon)
                 session.delete(taxon)