From 1f015661fee6ce2243b2c2ac49d5995fc495a5dc Mon Sep 17 00:00:00 2001
From: Kent Pitman <kent_pitman@hms.harvard.edu>
Date: Tue, 31 Jan 2023 12:20:43 -0500
Subject: [PATCH 1/2] Fixes to RDBStorage.update for session hygiene and error
 message.

---
 CHANGELOG.rst       |  9 +++++++++
 pyproject.toml      |  2 +-
 snovault/storage.py | 27 +++++++++++++--------------
 3 files changed, 23 insertions(+), 15 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a67dfe959..fc3c4a4bd 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -6,6 +6,15 @@ snovault
 Change Log
 ----------
 
+7.1.2
+=====
+
+* In ``RDBStorage.update``:
+  * Use session.begin_nested for better stack hygiene.
+  * Better error message on integrity error to acknowledge possibility
+    of both UUID conflit *and* undefined UUID.
+
+
 7.1.1
 =====
 
diff --git a/pyproject.toml b/pyproject.toml
index 643558b2e..e78ded493 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicsnovault"
-version = "7.1.1"
+version = "7.1.1.1b0"  # to become "7.1.2"
 description = "Storage support for 4DN Data Portals."
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
diff --git a/snovault/storage.py b/snovault/storage.py
index 0893519b2..b2cfb4649 100644
--- a/snovault/storage.py
+++ b/snovault/storage.py
@@ -475,19 +475,18 @@ def create(self, item_type, rid):
 
     def update(self, model, properties=None, sheets=None, unique_keys=None, links=None):
         session = self.DBSession()
-        sp = session.begin_nested()
-        try:
-            session.add(model)
-            self._update_properties(model, properties, sheets)
-            if links is not None:
-                self._update_rels(model, links)
-            if unique_keys is not None:
-                keys_add, keys_remove = self._update_keys(model, unique_keys)
-            sp.commit()
-        except (IntegrityError, FlushError):
-            sp.rollback()
-        else:
-            return
+        with session.begin_nested() as sp:
+            try:
+                session.add(model)
+                self._update_properties(model, properties, sheets)
+                if links is not None:
+                    self._update_rels(model, links)
+                if unique_keys is not None:
+                    keys_add, keys_remove = self._update_keys(model, unique_keys)
+                sp.commit()
+                return
+            except (IntegrityError, FlushError):
+                sp.rollback()
 
         # Try again more carefully
         try:
@@ -497,7 +496,7 @@ def update(self, model, properties=None, sheets=None, unique_keys=None, links=No
                 self._update_rels(model, links)
             session.flush()
         except (IntegrityError, FlushError):
-            msg = 'UUID conflict'
+            msg = 'Cannot update because of one or more conflicting (or undefined) UUIDs'
             raise HTTPConflict(msg)
         assert unique_keys is not None
         conflicts = [pk for pk in keys_add if session.query(Key).get(pk) is not None]

From 2430df4013c3cd22d45f4fd9adfe5bafa738b7e5 Mon Sep 17 00:00:00 2001
From: Kent Pitman <kent_pitman@hms.harvard.edu>
Date: Tue, 31 Jan 2023 12:23:40 -0500
Subject: [PATCH 2/2] PEP8

---
 snovault/tests/conftest.py       | 8 ++++----
 snovault/tests/test_embedding.py | 4 +++-
 snovault/tests/test_storage.py   | 2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/snovault/tests/conftest.py b/snovault/tests/conftest.py
index 970f40389..c1e95c840 100644
--- a/snovault/tests/conftest.py
+++ b/snovault/tests/conftest.py
@@ -1,9 +1,9 @@
-import os
-import time
-import tempfile
+# import os
+# import time
+# import tempfile
 import pytest
 import logging
-import subprocess
+# import subprocess
 
 from ..elasticsearch.indexer_queue import QueueManager
 
diff --git a/snovault/tests/test_embedding.py b/snovault/tests/test_embedding.py
index 480365be1..3c1a5a0cc 100644
--- a/snovault/tests/test_embedding.py
+++ b/snovault/tests/test_embedding.py
@@ -1,5 +1,5 @@
 import pytest
-import time
+# import time
 
 from dcicutils.misc_utils import ignored
 from dcicutils.qa_utils import notice_pytest_fixtures, Retry, Eventually
@@ -112,9 +112,11 @@ def test_linked_uuids_object(content, dummy_request, threadlocals):
     # needed to track _linked_uuids
     dummy_request._indexing_view = True
     dummy_request.embed('/testing-link-sources-sno/', sources[0]['uuid'], '@@object')
+
     def my_assertions():
         assert dummy_request._linked_uuids == {('16157204-8c8f-4672-a1a4-14f4b8021fcd', 'TestingLinkSourceSno')}
         assert dummy_request._rev_linked_uuids_by_item == {}
+
     Eventually.call_assertion(my_assertions)
 
 
diff --git a/snovault/tests/test_storage.py b/snovault/tests/test_storage.py
index a78eca505..290381af1 100644
--- a/snovault/tests/test_storage.py
+++ b/snovault/tests/test_storage.py
@@ -1,7 +1,7 @@
 from unittest import mock
 import pytest
 import re
-import transaction as transaction_management
+# import transaction as transaction_management
 import uuid
 import boto3