From 686ae08e13fb7069e108b85103340381afa566c0 Mon Sep 17 00:00:00 2001
From: Forrest Collman <forrest.collman@gmail.com>
Date: Wed, 23 Jul 2025 07:09:44 -0700
Subject: [PATCH 1/4] improved session management

---
 dynamicannotationdb/database.py | 52 ++++++++++++++++++++++++++++-----
 1 file changed, 45 insertions(+), 7 deletions(-)

diff --git a/dynamicannotationdb/database.py b/dynamicannotationdb/database.py
index f33e2c7..88f2003 100644
--- a/dynamicannotationdb/database.py
+++ b/dynamicannotationdb/database.py
@@ -55,15 +55,45 @@ def cached_session(self) -> Session:
 
     @contextmanager
     def session_scope(self):
+        session = None
         try:
-            yield self.cached_session
+            # Validate and recreate session if needed
+            if self._cached_session is None or not self._is_session_valid(self._cached_session):
+                if self._cached_session is not None:
+                    try:
+                        self._cached_session.close()
+                    except Exception:
+                        pass
+                self._cached_session = None
+            
+            session = self.cached_session
+            yield session
         except Exception as e:
-            self.cached_session.rollback()
+            if session is not None:
+                try:
+                    session.rollback()
+                except Exception:
+                    pass
             logging.exception(f"SQL Error: {e}")
             raise e
         finally:
-            self.cached_session.close()
-        self._cached_session = None
+            # Don't close the session - let connection pool manage it
+            # The session will be reused for subsequent requests
+            pass
+
+    def _is_session_valid(self, session):
+        """Check if a SQLAlchemy session is valid and can be used."""
+        if session is None:
+            return False
+        try:
+            # Check if session is bound and connection is alive
+            if not hasattr(session, 'bind') or session.bind is None:
+                return False
+            # Try a simple query to test the connection
+            session.execute("SELECT 1")
+            return True
+        except Exception:
+            return False
 
     def commit_session(self):
         try:
@@ -72,9 +102,17 @@ def commit_session(self):
             self.cached_session.rollback()
             logging.exception(f"SQL Error: {e}")
             raise e
-        finally:
-            self.cached_session.close()
-        self._cached_session = None
+        # Don't close or reset the session - keep it for reuse
+
+    def close_session(self):
+        """Explicitly close the cached session (for cleanup/shutdown)."""
+        if self._cached_session is not None:
+            try:
+                self._cached_session.close()
+            except Exception as e:
+                logging.exception(f"Error closing session: {e}")
+            finally:
+                self._cached_session = None
 
     def get_table_sql_metadata(self, table_name: str):
         self.base.metadata.reflect(bind=self.engine)

From 7da8d7ebc0c2147115cded89e7de826f1d743c90 Mon Sep 17 00:00:00 2001
From: Forrest Collman <forrest.collman@gmail.com>
Date: Wed, 23 Jul 2025 07:48:50 -0700
Subject: [PATCH 2/4] Update dynamicannotationdb/database.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 dynamicannotationdb/database.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/dynamicannotationdb/database.py b/dynamicannotationdb/database.py
index 88f2003..3f00292 100644
--- a/dynamicannotationdb/database.py
+++ b/dynamicannotationdb/database.py
@@ -81,8 +81,16 @@ def session_scope(self):
             # The session will be reused for subsequent requests
             pass
 
-    def _is_session_valid(self, session):
-        """Check if a SQLAlchemy session is valid and can be used."""
+    def _is_session_valid(self, session: Session) -> bool:
+        """
+        Check if a SQLAlchemy session is valid and can be used.
+
+        Args:
+            session (Session): The SQLAlchemy session to validate.
+
+        Returns:
+            bool: True if the session is valid, False otherwise.
+        """
         if session is None:
             return False
         try:

From 5c09821dc3790482a4a223d8b5699f21fb24ff03 Mon Sep 17 00:00:00 2001
From: Forrest Collman <forrest.collman@gmail.com>
Date: Wed, 23 Jul 2025 07:49:13 -0700
Subject: [PATCH 3/4] Update dynamicannotationdb/database.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 dynamicannotationdb/database.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dynamicannotationdb/database.py b/dynamicannotationdb/database.py
index 3f00292..6ea86a1 100644
--- a/dynamicannotationdb/database.py
+++ b/dynamicannotationdb/database.py
@@ -98,7 +98,7 @@ def _is_session_valid(self, session: Session) -> bool:
             if not hasattr(session, 'bind') or session.bind is None:
                 return False
             # Try a simple query to test the connection
-            session.execute("SELECT 1")
+            session.get_bind().execute("SELECT 1")
             return True
         except Exception:
             return False

From d89543895631640d8705cabb4cf96f85af65a98f Mon Sep 17 00:00:00 2001
From: Forrest Collman <forrest.collman@gmail.com>
Date: Wed, 23 Jul 2025 07:51:15 -0700
Subject: [PATCH 4/4] update python version to test

---
 .github/workflows/dynamic_annotation_db _ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/dynamic_annotation_db _ci.yml b/.github/workflows/dynamic_annotation_db _ci.yml
index 5995d96..f58677e 100644
--- a/.github/workflows/dynamic_annotation_db _ci.yml	
+++ b/.github/workflows/dynamic_annotation_db _ci.yml	
@@ -30,10 +30,10 @@ jobs:
         
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.7
+    - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.12
 
     - uses: actions/cache@v4
       with: