feat: ldh linking on publication; car submission only after mapping

- Only perform LDH linkage on score set publication.
- Do not spawn LDH linkage after car submission.
- Test improvements for score set publication; ldh linkage on publication
required better handling of worker call assertions in test cases.
- Test fixes for altered logic.

Author: bencap

src/mavedb/lib/exceptions.py

@@ -186,12 +186,6 @@ class SubmissionEnqueueError(ValueError):
     pass
 
 
-class LinkingEnqueueError(ValueError):
-    """Raised when a linking job fails to be enqueued despite appearing as if it should have been"""
-
-    pass
-
-
 class UniProtIDMappingEnqueueError(Exception):
     """Raised when a UniProt ID mapping job fails to be enqueued despite appearing as if it should have been"""
 

src/mavedb/routers/score_sets.py

@@ -2056,15 +2056,26 @@ async def publish_score_set(
     db.refresh(item)
 
     # await the insertion of this job into the worker queue, not the job itself.
-    job = await worker.enqueue_job("refresh_published_variants_view", correlation_id_for_context())
-    if job is not None:
-        save_to_logging_context({"worker_job_id": job.job_id})
-        logger.info(msg="Enqueud published variant materialized view refresh job.", extra=logging_context())
+    refresh_published_variants_job = await worker.enqueue_job(
+        "refresh_published_variants_view", correlation_id_for_context()
+    )
+    if refresh_published_variants_job is not None:
+        save_to_logging_context({"refresh_published_variants_job_id": refresh_published_variants_job.job_id})
+        logger.info(msg="Enqueued published variant materialized view refresh job.", extra=logging_context())
     else:
         logger.warning(
             msg="Failed to enqueue published variant materialized view refresh job.", extra=logging_context()
         )
 
+    submit_to_ldh_job = await worker.enqueue_job(
+        "submit_score_set_mappings_to_ldh", item.id, correlation_id_for_context()
+    )
+    if submit_to_ldh_job is not None:
+        save_to_logging_context({"submit_to_ldh_job_id": submit_to_ldh_job.job_id})
+        logger.info(msg="Enqueued submit score set mappings to LDH job.", extra=logging_context())
+    else:
+        logger.warning(msg="Failed to enqueue submit score set mappings to LDH job.", extra=logging_context())
+
     enriched_experiment = enrich_experiment_with_num_score_sets(item.experiment, user_data)
     return score_set.ScoreSet.model_validate(item).copy(update={"experiment": enriched_experiment})