From f2629e43f09dfccf58c38707228f3186bcb5e10f Mon Sep 17 00:00:00 2001
From: Daven Quinn <code@davenquinn.com>
Date: Mon, 23 Dec 2024 18:24:38 -0500
Subject: [PATCH 1/2] Updated query printing, added a refresh_schema method

- Database.refresh_schema
- updated query
- formatted code
---
 .idea/misc.xml                                |   1 -
 app-frame/macrostrat/app_frame/__init__.py    |   3 +-
 .../macrostrat/app_frame/compose/__init__.py  |   5 +-
 .../macrostrat/app_frame/control_command.py   |   4 +-
 app-frame/macrostrat/app_frame/core.py        |   2 +-
 .../app_frame/subsystems/__init__.py          |   4 +-
 .../macrostrat/app_frame/utils/__init__.py    |   2 -
 app-frame/poetry.lock                         | 176 +++++++-
 .../macrostrat/auth_system/core/__init__.py   |   4 +-
 .../macrostrat/auth_system/core/database.py   |   6 +-
 .../macrostrat/auth_system/core/schema.py     |  56 +--
 .../macrostrat/auth_system/legacy/api.py      |   7 +-
 .../macrostrat/auth_system/legacy/backend.py  |   8 +-
 .../macrostrat/auth_system/legacy/identity.py |   2 +-
 .../auth_system/legacy/test_auth.py           |   2 +-
 database/macrostrat/database/__init__.py      |  26 +-
 .../database/transfer/dump_database.py        |   1 +
 .../database/transfer/move_tables.py          |   1 +
 .../database/transfer/restore_database.py     |   1 +
 .../database/transfer/stream_utils.py         |   1 +
 .../macrostrat/database/transfer/utils.py     |   2 +-
 database/macrostrat/database/utils.py         | 117 +++---
 database/tests/test_database.py               |  16 +-
 .../dinosaur/upgrade_cluster/utils.py         |   8 +-
 dinosaur/poetry.lock                          |   2 +-
 dinosaur/tests/test_upgrade_cluster.py        |  24 +-
 poetry.lock                                   | 384 ++++++++++--------
 utils/macrostrat/utils/__init__.py            |   2 +-
 28 files changed, 575 insertions(+), 292 deletions(-)

diff --git a/.idea/misc.xml b/.idea/misc.xml
index 7a009cf..3a2a2ad 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -1,4 +1,3 @@
-<?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="Black">
     <option name="enabledOnReformat" value="true" />
diff --git a/app-frame/macrostrat/app_frame/__init__.py b/app-frame/macrostrat/app_frame/__init__.py
index b1374b2..6aca365 100644
--- a/app-frame/macrostrat/app_frame/__init__.py
+++ b/app-frame/macrostrat/app_frame/__init__.py
@@ -1,5 +1,6 @@
 from macrostrat.app_frame.compose.base import compose
+
+from .control_command import BackendType, CommandBase, ControlCommand
 from .core import Application
 from .exc import ApplicationError
 from .subsystems import Subsystem, SubsystemError, SubsystemManager
-from .control_command import ControlCommand, CommandBase, BackendType
diff --git a/app-frame/macrostrat/app_frame/compose/__init__.py b/app-frame/macrostrat/app_frame/compose/__init__.py
index 7b1837c..ad24cf5 100644
--- a/app-frame/macrostrat/app_frame/compose/__init__.py
+++ b/app-frame/macrostrat/app_frame/compose/__init__.py
@@ -10,10 +10,11 @@
 from typer import Context, Typer
 
 from macrostrat.utils import get_logger
-from .base import check_status, compose
-from .follow_logs import Result, command_stream, follow_logs
+
 from ..core import Application
 from ..utils import add_click_command
+from .base import check_status, compose
+from .follow_logs import Result, command_stream, follow_logs
 
 # Typer command-line application
 
diff --git a/app-frame/macrostrat/app_frame/control_command.py b/app-frame/macrostrat/app_frame/control_command.py
index 01d0dc9..fabaad1 100644
--- a/app-frame/macrostrat/app_frame/control_command.py
+++ b/app-frame/macrostrat/app_frame/control_command.py
@@ -3,11 +3,11 @@
 from enum import Enum
 from os import environ
 
-from typer import Context, Option
-from typer import rich_utils
+from typer import Context, Option, rich_utils
 from typer.models import TyperInfo
 
 from macrostrat.utils import get_logger
+
 from .compose import add_docker_compose_commands
 from .core import Application
 from .utils import CommandBase, ControlCommandGroup  # noqa
diff --git a/app-frame/macrostrat/app_frame/core.py b/app-frame/macrostrat/app_frame/core.py
index deede40..23988db 100644
--- a/app-frame/macrostrat/app_frame/core.py
+++ b/app-frame/macrostrat/app_frame/core.py
@@ -83,7 +83,7 @@ def load_dotenv(self):
 
     def setup_environment(self, env: EnvironmentDependency):
         environ["DOCKER_SCAN_SUGGEST"] = "false"
-        #environ["DOCKER_BUILDKIT"] = "1"
+        # environ["DOCKER_BUILDKIT"] = "1"
 
         # Set up environment for docker-compose
         # We may need to move this to a context where it is only
diff --git a/app-frame/macrostrat/app_frame/subsystems/__init__.py b/app-frame/macrostrat/app_frame/subsystems/__init__.py
index 6b6369e..b47c9b5 100644
--- a/app-frame/macrostrat/app_frame/subsystems/__init__.py
+++ b/app-frame/macrostrat/app_frame/subsystems/__init__.py
@@ -97,7 +97,9 @@ def order_plugins(self, store=None):
     def __load_plugin(self, plugin, app: ApplicationBase):
         if isinstance(plugin, Subsystem):
             if plugin.app is not app:
-                raise SubsystemError(f"Subsystem {plugin.name} was initialized against the wrong app")
+                raise SubsystemError(
+                    f"Subsystem {plugin.name} was initialized against the wrong app"
+                )
             return plugin
         if issubclass(plugin, Subsystem):
             return plugin(app)
diff --git a/app-frame/macrostrat/app_frame/utils/__init__.py b/app-frame/macrostrat/app_frame/utils/__init__.py
index 813e9e8..a676d50 100644
--- a/app-frame/macrostrat/app_frame/utils/__init__.py
+++ b/app-frame/macrostrat/app_frame/utils/__init__.py
@@ -39,7 +39,6 @@ def command(self, name=None, **kwargs):
         _name = self._name_modifier(name, kwargs.pop("aliases", None))
         return super().command(_name, **kwargs)
 
-
     def _name_modifier(self, name, aliases: list[str] = None):
         """Return a function that modifies the name for a command to include aliases
         https://github.com/fastapi/typer/issues/132
@@ -69,7 +68,6 @@ def get_command(self, ctx, cmd_name):
         cmd_name = self._group_cmd_name(cmd_name)
         return super().get_command(ctx, cmd_name)
 
-
     def _group_cmd_name(self, default_name):
         for cmd in self.commands.values():
             name = cmd.name
diff --git a/app-frame/poetry.lock b/app-frame/poetry.lock
index 5ec9a44..8130e5d 100644
--- a/app-frame/poetry.lock
+++ b/app-frame/poetry.lock
@@ -1,5 +1,16 @@
 # This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
 [[package]]
 name = "click"
 version = "8.1.7"
@@ -26,17 +37,36 @@ files = [
 ]
 
 [[package]]
-name = "macrostrat.utils"
+name = "colorlog"
+version = "6.9.0"
+description = "Add colours to the output of Python's logging module."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "colorlog-6.9.0-py3-none-any.whl", hash = "sha256:5906e71acd67cb07a71e779c47c4bcb45fb8c2993eebe9e5adcd6a6f1b283eff"},
+    {file = "colorlog-6.9.0.tar.gz", hash = "sha256:bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+
+[package.extras]
+development = ["black", "flake8", "mypy", "pytest", "types-colorama"]
+
+[[package]]
+name = "macrostrat-utils"
 version = "1.3.0"
 description = "Core utilities for Macrostrat and Sparrow"
 optional = false
-python-versions = "*"
-files = []
-develop = true
+python-versions = "<4.0,>=3.8"
+files = [
+    {file = "macrostrat_utils-1.3.0-py3-none-any.whl", hash = "sha256:596681457b5bf02c827f075a381d7036242cd4aa21293965a1b9ca1dc9421bd6"},
+    {file = "macrostrat_utils-1.3.0.tar.gz", hash = "sha256:c8b2fd708ca5db54689e899b030b0b7b8ce5b24b76a2a9758e4583be53dc06e2"},
+]
 
-[package.source]
-type = "directory"
-url = "../utils"
+[package.dependencies]
+colorlog = ">=6.5.0,<7.0.0"
+pydantic = ">=1.10.4,<3.0.0"
 
 [[package]]
 name = "markdown-it-py"
@@ -84,6 +114,138 @@ files = [
     {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"},
 ]
 
+[[package]]
+name = "pydantic"
+version = "2.10.4"
+description = "Data validation using Python type hints"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pydantic-2.10.4-py3-none-any.whl", hash = "sha256:597e135ea68be3a37552fb524bc7d0d66dcf93d395acd93a00682f1efcb8ee3d"},
+    {file = "pydantic-2.10.4.tar.gz", hash = "sha256:82f12e9723da6de4fe2ba888b5971157b3be7ad914267dea8f05f82b28254f06"},
+]
+
+[package.dependencies]
+annotated-types = ">=0.6.0"
+pydantic-core = "2.27.2"
+typing-extensions = ">=4.12.2"
+
+[package.extras]
+email = ["email-validator (>=2.0.0)"]
+timezone = ["tzdata"]
+
+[[package]]
+name = "pydantic-core"
+version = "2.27.2"
+description = "Core functionality for Pydantic validation and serialization"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pydantic_core-2.27.2-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:2d367ca20b2f14095a8f4fa1210f5a7b78b8a20009ecced6b12818f455b1e9fa"},
+    {file = "pydantic_core-2.27.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:491a2b73db93fab69731eaee494f320faa4e093dbed776be1a829c2eb222c34c"},
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+]
+
+[package.dependencies]
+typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
+
 [[package]]
 name = "pygments"
 version = "2.18.0"
diff --git a/auth-system/macrostrat/auth_system/core/__init__.py b/auth-system/macrostrat/auth_system/core/__init__.py
index 3eb872a..cb4ec90 100644
--- a/auth-system/macrostrat/auth_system/core/__init__.py
+++ b/auth-system/macrostrat/auth_system/core/__init__.py
@@ -1,7 +1,7 @@
 from .main import (
+    get_groups,
     get_groups_from_header_token,
+    get_user_id,
     get_user_token_from_cookie,
-    get_groups,
     has_access,
-    get_user_id
 )
diff --git a/auth-system/macrostrat/auth_system/core/database.py b/auth-system/macrostrat/auth_system/core/database.py
index 8fbb431..45fa086 100644
--- a/auth-system/macrostrat/auth_system/core/database.py
+++ b/auth-system/macrostrat/auth_system/core/database.py
@@ -2,11 +2,11 @@
 from contextvars import ContextVar
 from typing import Optional
 
-from sqlalchemy import Engine
-from sqlalchemy import select, update
-from sqlalchemy.orm import sessionmaker, declarative_base, Session
+from sqlalchemy import Engine, select, update
+from sqlalchemy.orm import Session, declarative_base, sessionmaker
 
 from macrostrat.database import Database
+
 from .schema import Token
 
 
diff --git a/auth-system/macrostrat/auth_system/core/schema.py b/auth-system/macrostrat/auth_system/core/schema.py
index f1e015d..25ef4a0 100644
--- a/auth-system/macrostrat/auth_system/core/schema.py
+++ b/auth-system/macrostrat/auth_system/core/schema.py
@@ -1,8 +1,24 @@
+import datetime
 import enum
 from typing import List
-import datetime
-from sqlalchemy import ForeignKey, func, DateTime, Enum, PrimaryKeyConstraint, UniqueConstraint
-from sqlalchemy.dialects.postgresql import VARCHAR, TEXT, INTEGER, ARRAY, BOOLEAN, JSON, JSONB
+
+from sqlalchemy import (
+    DateTime,
+    Enum,
+    ForeignKey,
+    PrimaryKeyConstraint,
+    UniqueConstraint,
+    func,
+)
+from sqlalchemy.dialects.postgresql import (
+    ARRAY,
+    BOOLEAN,
+    INTEGER,
+    JSON,
+    JSONB,
+    TEXT,
+    VARCHAR,
+)
 from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, relationship
 
 
@@ -12,9 +28,7 @@ class Base(DeclarativeBase):
 
 class GroupMembers(Base):
     __tablename__ = "group_members"
-    __table_args__ = {
-        'schema': 'macrostrat_auth'
-    }
+    __table_args__ = {"schema": "macrostrat_auth"}
     id: Mapped[int] = mapped_column(primary_key=True, autoincrement=True)
     group_id: Mapped[int] = mapped_column(ForeignKey("macrostrat_auth.group.id"))
     user_id: Mapped[int] = mapped_column(ForeignKey("macrostrat_auth.user.id"))
@@ -22,26 +36,26 @@ class GroupMembers(Base):
 
 class Group(Base):
     __tablename__ = "group"
-    __table_args__ = {
-        'schema': 'macrostrat_auth'
-    }
+    __table_args__ = {"schema": "macrostrat_auth"}
     id: Mapped[int] = mapped_column(primary_key=True, autoincrement=True)
     name: Mapped[str] = mapped_column(VARCHAR(255))
-    users: Mapped[List["User"]] = relationship(secondary="macrostrat_auth.group_members", lazy="joined",
-                                               back_populates="groups")
+    users: Mapped[List["User"]] = relationship(
+        secondary="macrostrat_auth.group_members",
+        lazy="joined",
+        back_populates="groups",
+    )
 
 
 class User(Base):
     __tablename__ = "user"
-    __table_args__ = {
-        'schema': 'macrostrat_auth'
-    }
+    __table_args__ = {"schema": "macrostrat_auth"}
     id: Mapped[int] = mapped_column(primary_key=True, autoincrement=True)
     sub: Mapped[str] = mapped_column(VARCHAR(255))
     name: Mapped[str] = mapped_column(VARCHAR(255))
     email: Mapped[str] = mapped_column(VARCHAR(255))
-    groups: Mapped[List[Group]] = relationship(secondary="macrostrat_auth.group_members", lazy="joined",
-                                               back_populates="users")
+    groups: Mapped[List[Group]] = relationship(
+        secondary="macrostrat_auth.group_members", lazy="joined", back_populates="users"
+    )
     created_on: Mapped[datetime.datetime] = mapped_column(
         DateTime(timezone=True), server_default=func.now()
     )
@@ -52,20 +66,14 @@ class User(Base):
 
 class Token(Base):
     __tablename__ = "token"
-    __table_args__ = {
-        'schema': 'macrostrat_auth'
-    }
+    __table_args__ = {"schema": "macrostrat_auth"}
     id: Mapped[int] = mapped_column(primary_key=True, autoincrement=True)
     token: Mapped[str] = mapped_column(VARCHAR(255), unique=True)
     group: Mapped[Group] = mapped_column(ForeignKey("macrostrat_auth.group.id"))
     used_on: Mapped[datetime.datetime] = mapped_column(
         DateTime(timezone=True), nullable=True
     )
-    expires_on: Mapped[datetime.datetime] = mapped_column(
-        DateTime(timezone=True)
-    )
+    expires_on: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True))
     created_on: Mapped[datetime.datetime] = mapped_column(
         DateTime(timezone=True), server_default=func.now()
     )
-
-
diff --git a/auth-system/macrostrat/auth_system/legacy/api.py b/auth-system/macrostrat/auth_system/legacy/api.py
index 7add0a6..a5f1a61 100644
--- a/auth-system/macrostrat/auth_system/legacy/api.py
+++ b/auth-system/macrostrat/auth_system/legacy/api.py
@@ -1,9 +1,10 @@
-from starlette.routing import Route, Router
+from starlette.authentication import AuthenticationError, requires
 from starlette.responses import JSONResponse
-from starlette.authentication import requires, AuthenticationError
+from starlette.routing import Route, Router
+from webargs_starlette import use_annotations
+
 from macrostrat.utils import get_logger
 
-from webargs_starlette import use_annotations
 from .context import get_backend, get_identity_provider
 
 log = get_logger(__name__)
diff --git a/auth-system/macrostrat/auth_system/legacy/backend.py b/auth-system/macrostrat/auth_system/legacy/backend.py
index 36d2f48..6afa65b 100644
--- a/auth-system/macrostrat/auth_system/legacy/backend.py
+++ b/auth-system/macrostrat/auth_system/legacy/backend.py
@@ -4,15 +4,15 @@
 """
 import time
 import warnings
-from typing import Tuple, Any
+from typing import Any, Tuple
 
 import jwt
 from starlette.authentication import (
-    BaseUser,
-    SimpleUser,
-    AuthenticationBackend,
     AuthCredentials,
+    AuthenticationBackend,
     AuthenticationError,
+    BaseUser,
+    SimpleUser,
     UnauthenticatedUser,
 )
 from starlette.requests import Request
diff --git a/auth-system/macrostrat/auth_system/legacy/identity.py b/auth-system/macrostrat/auth_system/legacy/identity.py
index 10ead36..b04ee1e 100644
--- a/auth-system/macrostrat/auth_system/legacy/identity.py
+++ b/auth-system/macrostrat/auth_system/legacy/identity.py
@@ -1,4 +1,4 @@
-from werkzeug.security import generate_password_hash, check_password_hash
+from werkzeug.security import check_password_hash, generate_password_hash
 
 
 class IdentityProvider:
diff --git a/auth-system/macrostrat/auth_system/legacy/test_auth.py b/auth-system/macrostrat/auth_system/legacy/test_auth.py
index 0feebd7..8e40fda 100644
--- a/auth-system/macrostrat/auth_system/legacy/test_auth.py
+++ b/auth-system/macrostrat/auth_system/legacy/test_auth.py
@@ -12,7 +12,7 @@
 
 from . import get_backend
 from .api import AuthAPI
-from .context import create_backend, set_identity_provider, get_identity_provider
+from .context import create_backend, get_identity_provider, set_identity_provider
 from .identity import BaseUser, IdentityProvider
 
 
diff --git a/database/macrostrat/database/__init__.py b/database/macrostrat/database/__init__.py
index 9dc07ac..2e43812 100644
--- a/database/macrostrat/database/__init__.py
+++ b/database/macrostrat/database/__init__.py
@@ -5,13 +5,14 @@
 
 from psycopg2.errors import InvalidSavepointSpecification
 from psycopg2.sql import Identifier
-from sqlalchemy import URL, MetaData, create_engine, inspect, Engine
+from sqlalchemy import URL, Engine, MetaData, create_engine, inspect
 from sqlalchemy.exc import IntegrityError, InternalError
 from sqlalchemy.ext.compiler import compiles
 from sqlalchemy.orm import Session, scoped_session, sessionmaker
 from sqlalchemy.sql.expression import Insert
 
 from macrostrat.utils import get_logger
+
 from .mapper import DatabaseMapper
 from .postgresql import on_conflict, prefix_inserts  # noqa
 from .utils import (  # noqa
@@ -184,6 +185,29 @@ def inspector(self):
             self.__inspector__ = inspect(self.engine)
         return self.__inspector__
 
+    def refresh_schema(self, *, automap=None):
+        """
+        Refresh the current database connection
+
+        - closes the session and flushes
+        - removes the inspector
+
+        If automap is True, will automap the database after refreshing.
+        If automap is False, will not automap the database after refreshing.
+        If automap is None, it will re-map the database if it was previously mapped.
+        """
+        # Close the session
+        self.session.flush()
+        self.session.close()
+        # Remove the inspector
+        self.__inspector__ = None
+
+        if automap is None:
+            automap = self.mapper is not None
+
+        if automap:
+            self.automap()
+
     def entity_names(self, **kwargs):
         """
         Returns an iterator of names of *schema objects*
diff --git a/database/macrostrat/database/transfer/dump_database.py b/database/macrostrat/database/transfer/dump_database.py
index 101d7c9..0e28fdf 100644
--- a/database/macrostrat/database/transfer/dump_database.py
+++ b/database/macrostrat/database/transfer/dump_database.py
@@ -7,6 +7,7 @@
 from sqlalchemy.engine import Engine
 
 from macrostrat.utils import get_logger
+
 from .stream_utils import print_stdout, print_stream_progress
 from .utils import _create_command
 
diff --git a/database/macrostrat/database/transfer/move_tables.py b/database/macrostrat/database/transfer/move_tables.py
index 2e6d586..769da14 100644
--- a/database/macrostrat/database/transfer/move_tables.py
+++ b/database/macrostrat/database/transfer/move_tables.py
@@ -3,6 +3,7 @@
 from sqlalchemy.engine import Engine
 
 from macrostrat.utils import get_logger
+
 from .dump_database import pg_dump
 from .restore_database import pg_restore
 from .stream_utils import print_stdout, print_stream_progress
diff --git a/database/macrostrat/database/transfer/restore_database.py b/database/macrostrat/database/transfer/restore_database.py
index 269f3b2..a8327d4 100644
--- a/database/macrostrat/database/transfer/restore_database.py
+++ b/database/macrostrat/database/transfer/restore_database.py
@@ -7,6 +7,7 @@
 from sqlalchemy.engine import Engine
 
 from macrostrat.utils import get_logger
+
 from .stream_utils import print_stdout, print_stream_progress
 from .utils import _create_command, _create_database_if_not_exists
 
diff --git a/database/macrostrat/database/transfer/stream_utils.py b/database/macrostrat/database/transfer/stream_utils.py
index 94fdf87..a34f502 100644
--- a/database/macrostrat/database/transfer/stream_utils.py
+++ b/database/macrostrat/database/transfer/stream_utils.py
@@ -5,6 +5,7 @@
 from aiofiles.threadpool import AsyncBufferedIOBase
 
 from macrostrat.utils import get_logger
+
 from .utils import console
 
 log = get_logger(__name__)
diff --git a/database/macrostrat/database/transfer/utils.py b/database/macrostrat/database/transfer/utils.py
index f570795..ed68459 100644
--- a/database/macrostrat/database/transfer/utils.py
+++ b/database/macrostrat/database/transfer/utils.py
@@ -5,7 +5,7 @@
 from sqlalchemy.engine.url import URL
 from sqlalchemy_utils import create_database, database_exists, drop_database
 
-from macrostrat.utils import get_logger, ApplicationError
+from macrostrat.utils import ApplicationError, get_logger
 
 console = Console()
 
diff --git a/database/macrostrat/database/utils.py b/database/macrostrat/database/utils.py
index 4821c22..0c3c607 100644
--- a/database/macrostrat/database/utils.py
+++ b/database/macrostrat/database/utils.py
@@ -1,6 +1,8 @@
 from contextlib import contextmanager
+from enum import Enum
 from pathlib import Path
 from re import search
+from sys import stderr
 from time import sleep
 from typing import IO, Union
 from warnings import warn
@@ -17,8 +19,8 @@
     IntegrityError,
     InternalError,
     InvalidRequestError,
-    ProgrammingError,
     OperationalError,
+    ProgrammingError,
 )
 from sqlalchemy.orm import sessionmaker
 from sqlalchemy.schema import Table
@@ -46,23 +48,11 @@ def infer_is_sql_text(_string: str) -> bool:
     if isinstance(_string, bytes):
         _string = _string.decode("utf-8")
 
-    keywords = [
-        "SELECT",
-        "INSERT",
-        "UPDATE",
-        "CREATE",
-        "DROP",
-        "DELETE",
-        "ALTER",
-        "SET",
-        "GRANT",
-        "WITH",
-    ]
     lines = _string.split("\n")
     if len(lines) > 1:
         return True
     _string = _string.lower()
-    for i in keywords:
+    for i in _sql_keywords:
         if _string.strip().startswith(i.lower() + " "):
             return True
     return False
@@ -97,26 +87,40 @@ def get_dataframe(connectable, filename_or_query, **kwargs):
 
 
 def pretty_print(sql, **kwargs):
+    """Print and optionally summarize an SQL query"""
+    summarize = kwargs.pop("summarize", True)
+    if summarize:
+        sql = summarize_statement(sql)
+    secho(sql, **kwargs)
+
+
+_sql_keywords = [
+    "SELECT",
+    "INSERT",
+    "UPDATE",
+    "CREATE",
+    "DROP",
+    "DELETE",
+    "ALTER",
+    "SET",
+    "GRANT",
+    "WITH",
+    "NOTIFY",
+    "COPY",
+]
+
+
+def summarize_statement(sql):
     for line in sql.split("\n"):
-        for i in [
-            "SELECT",
-            "INSERT",
-            "UPDATE",
-            "CREATE",
-            "DROP",
-            "DELETE",
-            "ALTER",
-            "SET",
-            "GRANT",
-            "WITH",
-            "NOTIFY",
-            "COPY",
-        ]:
+        for i in _sql_keywords:
             if not line.startswith(i):
                 continue
-            start = line.split("(")[0].strip().rstrip(";").replace(" AS", "")
-            secho(start, **kwargs)
-            return
+            return line.split("(")[0].strip().rstrip(";").replace(" AS", "")
+
+
+class DevNull(object):
+    def write(self, *_):
+        pass
 
 
 def get_sql_text(sql, interpret_as_file=None, echo_file_name=True):
@@ -235,6 +239,13 @@ def infer_has_server_binds(sql):
 _default_statement_filter = lambda sql_text, params: True
 
 
+class PrintMode(Enum):
+    NONE = "none"
+    ERRORS = "errors"
+    SUMMARY = "summary"
+    ALL = "all"
+
+
 def _run_sql(connectable, sql, params=None, **kwargs):
     """
     Internal function for running a query on a SQLAlchemy connectable,
@@ -251,6 +262,11 @@ def _run_sql(connectable, sql, params=None, **kwargs):
     has_server_binds = kwargs.pop("has_server_binds", None)
     ensure_single_query = kwargs.pop("ensure_single_query", False)
     statement_filter = kwargs.pop("statement_filter", _default_statement_filter)
+    output_mode = kwargs.pop("output_mode", PrintMode.SUMMARY)
+    output_file = kwargs.pop("output_file", stderr)
+
+    if output_mode == PrintMode.NONE:
+        output_file = DevNull()
 
     if stop_on_error:
         raise_errors = True
@@ -283,6 +299,7 @@ def _run_sql(connectable, sql, params=None, **kwargs):
             query = _render_query(query, connectable)
 
         sql_text = str(query)
+
         if isinstance(query, str):
             sql_text = format(query, strip_comments=True).strip()
             if sql_text == "":
@@ -293,8 +310,18 @@ def _run_sql(connectable, sql, params=None, **kwargs):
                 has_server_binds = infer_has_server_binds(sql_text)
 
         should_run = statement_filter(sql_text, params)
+
+        # Shorten summary text for printing
+        if output_mode != PrintMode.ALL:
+            sql_text = summarize_statement(sql_text)
+
         if not should_run:
-            pretty_print(sql_text, dim=True, strikethrough=True)
+            secho(
+                sql_text,
+                dim=True,
+                strikethrough=True,
+                file=output_file,
+            )
             continue
 
         # This only does something for postgresql, but it's harmless to run it for other engines
@@ -318,7 +345,7 @@ def _run_sql(connectable, sql, params=None, **kwargs):
                 trans.commit()
             elif hasattr(connectable, "commit"):
                 connectable.commit()
-            pretty_print(sql_text, dim=True)
+            secho(sql_text, dim=True, file=output_file)
         except Exception as err:
             if trans is not None:
                 trans.rollback()
@@ -327,7 +354,7 @@ def _run_sql(connectable, sql, params=None, **kwargs):
             if raise_errors or _should_raise_query_error(err):
                 raise err
 
-            _print_error(sql_text, err)
+            _print_error(sql_text, err, file=output_file)
         finally:
             set_wait_callback(None)
 
@@ -356,17 +383,18 @@ def _should_raise_query_error(err):
     return False
 
 
-def _print_error(sql_text, err):
+def _print_error(sql_text, err, **kwargs):
     if orig := getattr(err, "orig", None):
         _err = str(orig)
     else:
         _err = str(err)
     _err = _err.strip()
-    dim = "already exists" in _err
-    pretty_print(sql_text, fg=None if dim else "red", dim=True)
+    # Decide whether error should be dimmed
+    dim = kwargs.pop("dim", "already exists" in _err)
+    secho(sql_text, fg=None if dim else "red", dim=True, **kwargs)
     if dim:
         _err = "  " + _err
-    secho(_err, fg="red", dim=dim)
+    secho(_err, fg="red", dim=dim, **kwargs)
     log.error(err)
 
 
@@ -468,7 +496,9 @@ def run_sql(*args, **kwargs):
     return list(res)
 
 
-def execute(connectable, sql, params=None, stop_on_error=False):
+def execute(connectable, sql, params=None, stop_on_error=False, **kwargs):
+    output_file = kwargs.pop("output_file", None)
+    output_mode = kwargs.pop("output_mode", None)
     sql = format(sql, strip_comments=True).strip()
     if sql == "":
         return
@@ -477,17 +507,12 @@ def execute(connectable, sql, params=None, stop_on_error=False):
         res = connectable.execute(text(sql), params=params)
         if hasattr(connectable, "commit"):
             connectable.commit()
-        pretty_print(sql, dim=True)
+        pretty_print(sql, dim=True, file=output_file, mode=output_mode)
         return res
     except (ProgrammingError, IntegrityError) as err:
-        err = str(err.orig).strip()
-        dim = "already exists" in err
         if hasattr(connectable, "rollback"):
             connectable.rollback()
-        pretty_print(sql, fg=None if dim else "red", dim=True)
-        if dim:
-            err = "  " + err
-        secho(err, fg="red", dim=dim)
+        _print_error(sql, dim=True, file=output_file, mode=output_mode)
         if stop_on_error:
             return
     finally:
diff --git a/database/tests/test_database.py b/database/tests/test_database.py
index 37d88c0..7bad61c 100644
--- a/database/tests/test_database.py
+++ b/database/tests/test_database.py
@@ -17,7 +17,7 @@
 
 from macrostrat.database import Database, run_sql
 from macrostrat.database.postgresql import table_exists
-from macrostrat.database.utils import infer_is_sql_text, temp_database
+from macrostrat.database.utils import _print_error, infer_is_sql_text, temp_database
 from macrostrat.utils import get_logger, relative_path
 
 load_dotenv()
@@ -398,3 +398,17 @@ def test_check_table_exists(db):
 def test_check_table_exists_postgresql(db):
     assert table_exists(db, "sample")
     assert not table_exists(db, "samplea")
+
+
+def test_database_schema_refresh(db):
+    # Create a new table
+    sql = "CREATE TABLE new_table (name TEXT)"
+    db.run_sql(sql)
+    names = db.inspector.get_table_names()
+    assert "new_table" not in names
+    db.refresh_schema(automap=False)
+    assert "new_table" in db.inspector.get_table_names()
+
+
+def test_print_error():
+    _print_error("SELECT * FROM test", Exception("Test error"))
diff --git a/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py b/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py
index 0e52862..2a518cd 100644
--- a/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py
+++ b/dinosaur/macrostrat/dinosaur/upgrade_cluster/utils.py
@@ -121,12 +121,10 @@ def wait_for_cluster(container: Container, url: str):
         else:
             time_running = 0
 
-
-
     if container.status == "exited":
-            raise RuntimeError(
-                "Container exited unexpectedly:\n" + container.logs().decode("utf-8")
-            )
+        raise RuntimeError(
+            "Container exited unexpectedly:\n" + container.logs().decode("utf-8")
+        )
 
     wait_for_ready(create_engine(url))
     print("Database cluster is ready")
diff --git a/dinosaur/poetry.lock b/dinosaur/poetry.lock
index 2049dac..fc7703f 100644
--- a/dinosaur/poetry.lock
+++ b/dinosaur/poetry.lock
@@ -278,7 +278,7 @@ files = [
 
 [[package]]
 name = "macrostrat-database"
-version = "3.5.0"
+version = "3.5.1"
 description = "A SQLAlchemy-based database toolkit."
 optional = false
 python-versions = "^3.10"
diff --git a/dinosaur/tests/test_upgrade_cluster.py b/dinosaur/tests/test_upgrade_cluster.py
index c51415e..82fba0e 100644
--- a/dinosaur/tests/test_upgrade_cluster.py
+++ b/dinosaur/tests/test_upgrade_cluster.py
@@ -45,9 +45,11 @@
 version_images = {}
 # Extract versions from image names
 
+
 def get_major_version(image_name):
     return int(match(r".*:(\d+)", image_name).group(1))
 
+
 old_postgres_major_version = get_major_version(old_postgres_image)
 new_postgres_major_version = get_major_version(new_postgres_image)
 
@@ -113,7 +115,9 @@ def test_schema_clone(postgres_11_db):
     url_clone = url.set(database="test_schema_clone")
 
     with create_schema_clone(
-        postgres_11_db.engine, url_clone, image_name=version_images[old_postgres_major_version]
+        postgres_11_db.engine,
+        url_clone,
+        image_name=version_images[old_postgres_major_version],
     ) as clone:
         conn = clone.connect()
         assert conn.execute(text("SELECT 1")).fetchone()[0] == 1
@@ -126,8 +130,20 @@ def test_schema_clone(postgres_11_db):
 def test_upgrade_cluster(postgres_11_cluster_volume):
     """Test upgrade of a PostgreSQL cluster."""
 
-    assert check_database_cluster_version(client, postgres_11_cluster_volume) == old_postgres_major_version
+    assert (
+        check_database_cluster_version(client, postgres_11_cluster_volume)
+        == old_postgres_major_version
+    )
 
-    upgrade_database_cluster(client, postgres_11_cluster_volume, new_postgres_major_version, ["test_database"], version_images)
+    upgrade_database_cluster(
+        client,
+        postgres_11_cluster_volume,
+        new_postgres_major_version,
+        ["test_database"],
+        version_images,
+    )
 
-    assert check_database_cluster_version(client, postgres_11_cluster_volume) == new_postgres_major_version
+    assert (
+        check_database_cluster_version(client, postgres_11_cluster_volume)
+        == new_postgres_major_version
+    )
diff --git a/poetry.lock b/poetry.lock
index 7c91aa7..d9c8688 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -131,13 +131,13 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2024.8.30"
+version = "2024.12.14"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
-    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
+    {file = "certifi-2024.12.14-py3-none-any.whl", hash = "sha256:1275f7a45be9464efc1173084eaa30f866fe2e47d389406136d332ed4967ec56"},
+    {file = "certifi-2024.12.14.tar.gz", hash = "sha256:b650d30f370c2b724812bee08008be0c4163b163ddaec3f2546c1caf65f191db"},
 ]
 
 [[package]]
@@ -335,13 +335,13 @@ files = [
 
 [[package]]
 name = "click"
-version = "8.1.7"
+version = "8.1.8"
 description = "Composable command line interface toolkit"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
-    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+    {file = "click-8.1.8-py3-none-any.whl", hash = "sha256:63c132bbbed01578a06712a2d1f497bb62d9c1c0d329b7903a866228027263b2"},
+    {file = "click-8.1.8.tar.gz", hash = "sha256:ed53c9d8990d83c2a27deae68e4ee337473f6330c040a31d4225c9574d16096a"},
 ]
 
 [package.dependencies]
@@ -377,51 +377,51 @@ development = ["black", "flake8", "mypy", "pytest", "types-colorama"]
 
 [[package]]
 name = "cryptography"
-version = "43.0.3"
+version = "44.0.0"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "cryptography-43.0.3-cp37-abi3-macosx_10_9_universal2.whl", hash = "sha256:bf7a1932ac4176486eab36a19ed4c0492da5d97123f1406cf15e41b05e787d2e"},
-    {file = "cryptography-43.0.3-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:63efa177ff54aec6e1c0aefaa1a241232dcd37413835a9b674b6e3f0ae2bfd3e"},
-    {file = "cryptography-43.0.3-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e1ce50266f4f70bf41a2c6dc4358afadae90e2a1e5342d3c08883df1675374f"},
-    {file = "cryptography-43.0.3-cp37-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:443c4a81bb10daed9a8f334365fe52542771f25aedaf889fd323a853ce7377d6"},
-    {file = "cryptography-43.0.3-cp37-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:74f57f24754fe349223792466a709f8e0c093205ff0dca557af51072ff47ab18"},
-    {file = "cryptography-43.0.3-cp37-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:9762ea51a8fc2a88b70cf2995e5675b38d93bf36bd67d91721c309df184f49bd"},
-    {file = "cryptography-43.0.3-cp37-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:81ef806b1fef6b06dcebad789f988d3b37ccaee225695cf3e07648eee0fc6b73"},
-    {file = "cryptography-43.0.3-cp37-abi3-win32.whl", hash = "sha256:cbeb489927bd7af4aa98d4b261af9a5bc025bd87f0e3547e11584be9e9427be2"},
-    {file = "cryptography-43.0.3-cp37-abi3-win_amd64.whl", hash = "sha256:f46304d6f0c6ab8e52770addfa2fc41e6629495548862279641972b6215451cd"},
-    {file = "cryptography-43.0.3-cp39-abi3-macosx_10_9_universal2.whl", hash = "sha256:8ac43ae87929a5982f5948ceda07001ee5e83227fd69cf55b109144938d96984"},
-    {file = "cryptography-43.0.3-cp39-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:846da004a5804145a5f441b8530b4bf35afbf7da70f82409f151695b127213d5"},
-    {file = "cryptography-43.0.3-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0f996e7268af62598f2fc1204afa98a3b5712313a55c4c9d434aef49cadc91d4"},
-    {file = "cryptography-43.0.3-cp39-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:f7b178f11ed3664fd0e995a47ed2b5ff0a12d893e41dd0494f406d1cf555cab7"},
-    {file = "cryptography-43.0.3-cp39-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:c2e6fc39c4ab499049df3bdf567f768a723a5e8464816e8f009f121a5a9f4405"},
-    {file = "cryptography-43.0.3-cp39-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:e1be4655c7ef6e1bbe6b5d0403526601323420bcf414598955968c9ef3eb7d16"},
-    {file = "cryptography-43.0.3-cp39-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:df6b6c6d742395dd77a23ea3728ab62f98379eff8fb61be2744d4679ab678f73"},
-    {file = "cryptography-43.0.3-cp39-abi3-win32.whl", hash = "sha256:d56e96520b1020449bbace2b78b603442e7e378a9b3bd68de65c782db1507995"},
-    {file = "cryptography-43.0.3-cp39-abi3-win_amd64.whl", hash = "sha256:0c580952eef9bf68c4747774cde7ec1d85a6e61de97281f2dba83c7d2c806362"},
-    {file = "cryptography-43.0.3-pp310-pypy310_pp73-macosx_10_9_x86_64.whl", hash = "sha256:d03b5621a135bffecad2c73e9f4deb1a0f977b9a8ffe6f8e002bf6c9d07b918c"},
-    {file = "cryptography-43.0.3-pp310-pypy310_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:a2a431ee15799d6db9fe80c82b055bae5a752bef645bba795e8e52687c69efe3"},
-    {file = "cryptography-43.0.3-pp310-pypy310_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:281c945d0e28c92ca5e5930664c1cefd85efe80e5c0d2bc58dd63383fda29f83"},
-    {file = "cryptography-43.0.3-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:f18c716be16bc1fea8e95def49edf46b82fccaa88587a45f8dc0ff6ab5d8e0a7"},
-    {file = "cryptography-43.0.3-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:4a02ded6cd4f0a5562a8887df8b3bd14e822a90f97ac5e544c162899bc467664"},
-    {file = "cryptography-43.0.3-pp39-pypy39_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:53a583b6637ab4c4e3591a15bc9db855b8d9dee9a669b550f311480acab6eb08"},
-    {file = "cryptography-43.0.3-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:1ec0bcf7e17c0c5669d881b1cd38c4972fade441b27bda1051665faaa89bdcaa"},
-    {file = "cryptography-43.0.3-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:2ce6fae5bdad59577b44e4dfed356944fbf1d925269114c28be377692643b4ff"},
-    {file = "cryptography-43.0.3.tar.gz", hash = "sha256:315b9001266a492a6ff443b61238f956b214dbec9910a081ba5b6646a055a805"},
+python-versions = "!=3.9.0,!=3.9.1,>=3.7"
+files = [
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 [[package]]
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 python-versions = "^3.10"
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 [[package]]
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 [[package]]
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+    {file = "sqlparse-0.5.3-py3-none-any.whl", hash = "sha256:cf2196ed3418f3ba5de6af7e82c694a9fbdbfecccdfc72e281548517081f16ca"},
+    {file = "sqlparse-0.5.3.tar.gz", hash = "sha256:09f67787f56a0b16ecdbde1bfc7f5d9c3371ca683cfeaa8e6ff60b4807ec9272"},
 ]
 
 [package.extras]
@@ -2156,13 +2156,43 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.1.0"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.1.0-py3-none-any.whl", hash = "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391"},
-    {file = "tomli-2.1.0.tar.gz", hash = "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8"},
+    {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"},
+    {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ece47d672db52ac607a3d9599a9d48dcb2f2f735c6c2d1f34130085bb12b112a"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6972ca9c9cc9f0acaa56a8ca1ff51e7af152a9f87fb64623e31d5c83700080ee"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c954d2250168d28797dd4e3ac5cf812a406cd5a92674ee4c8f123c889786aa8e"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:8dd28b3e155b80f4d54beb40a441d366adcfe740969820caf156c019fb5c7ec4"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_i686.whl", hash = "sha256:e59e304978767a54663af13c07b3d1af22ddee3bb2fb0618ca1593e4f593a106"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:33580bccab0338d00994d7f16f4c4ec25b776af3ffaac1ed74e0b3fc95e885a8"},
+    {file = "tomli-2.2.1-cp311-cp311-win32.whl", hash = "sha256:465af0e0875402f1d226519c9904f37254b3045fc5084697cefb9bdde1ff99ff"},
+    {file = "tomli-2.2.1-cp311-cp311-win_amd64.whl", hash = "sha256:2d0f2fdd22b02c6d81637a3c95f8cd77f995846af7414c5c4b8d0545afa1bc4b"},
+    {file = "tomli-2.2.1-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:4a8f6e44de52d5e6c657c9fe83b562f5f4256d8ebbfe4ff922c495620a7f6cea"},
+    {file = "tomli-2.2.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:8d57ca8095a641b8237d5b079147646153d22552f1c637fd3ba7f4b0b29167a8"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4e340144ad7ae1533cb897d406382b4b6fede8890a03738ff1683af800d54192"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:db2b95f9de79181805df90bedc5a5ab4c165e6ec3fe99f970d0e302f384ad222"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:40741994320b232529c802f8bc86da4e1aa9f413db394617b9a256ae0f9a7f77"},
+    {file = "tomli-2.2.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:400e720fe168c0f8521520190686ef8ef033fb19fc493da09779e592861b78c6"},
+    {file = "tomli-2.2.1-cp312-cp312-musllinux_1_2_i686.whl", hash = "sha256:02abe224de6ae62c19f090f68da4e27b10af2b93213d36cf44e6e1c5abd19fdd"},
+    {file = "tomli-2.2.1-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:b82ebccc8c8a36f2094e969560a1b836758481f3dc360ce9a3277c65f374285e"},
+    {file = "tomli-2.2.1-cp312-cp312-win32.whl", hash = "sha256:889f80ef92701b9dbb224e49ec87c645ce5df3fa2cc548664eb8a25e03127a98"},
+    {file = "tomli-2.2.1-cp312-cp312-win_amd64.whl", hash = "sha256:7fc04e92e1d624a4a63c76474610238576942d6b8950a2d7f908a340494e67e4"},
+    {file = "tomli-2.2.1-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:f4039b9cbc3048b2416cc57ab3bda989a6fcf9b36cf8937f01a6e731b64f80d7"},
+    {file = "tomli-2.2.1-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:286f0ca2ffeeb5b9bd4fcc8d6c330534323ec51b2f52da063b11c502da16f30c"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a92ef1a44547e894e2a17d24e7557a5e85a9e1d0048b0b5e7541f76c5032cb13"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9316dc65bed1684c9a98ee68759ceaed29d229e985297003e494aa825ebb0281"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e85e99945e688e32d5a35c1ff38ed0b3f41f43fad8df0bdf79f72b2ba7bc5272"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:ac065718db92ca818f8d6141b5f66369833d4a80a9d74435a268c52bdfa73140"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744"},
+    {file = "tomli-2.2.1-cp313-cp313-win32.whl", hash = "sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec"},
+    {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
+    {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
 
 [[package]]
@@ -2206,13 +2236,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "2.2.3"
+version = "2.3.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"},
-    {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"},
+    {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"},
+    {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"},
 ]
 
 [package.extras]
diff --git a/utils/macrostrat/utils/__init__.py b/utils/macrostrat/utils/__init__.py
index 8d3ef2d..5c696ce 100644
--- a/utils/macrostrat/utils/__init__.py
+++ b/utils/macrostrat/utils/__init__.py
@@ -6,7 +6,7 @@
 from contextlib import contextmanager
 from pathlib import Path
 
-from .exc import BaseError, ApplicationError
+from .exc import ApplicationError, BaseError
 from .logs import get_logger, setup_stderr_logs
 from .shell import cmd, split_args
 

From 9f5751aa0ac508bd952b10f0648fca334efa57e2 Mon Sep 17 00:00:00 2001
From: Daven Quinn <code@davenquinn.com>
Date: Mon, 23 Dec 2024 18:26:32 -0500
Subject: [PATCH 2/2] Updated pyproject

---
 database/pyproject.toml | 2 +-
 dinosaur/poetry.lock    | 2 +-
 poetry.lock             | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/database/pyproject.toml b/database/pyproject.toml
index fd68f06..a2fc613 100644
--- a/database/pyproject.toml
+++ b/database/pyproject.toml
@@ -3,7 +3,7 @@ authors = ["Daven Quinn <dev@davenquinn.com>"]
 description = "A SQLAlchemy-based database toolkit."
 name = "macrostrat.database"
 packages = [{ include = "macrostrat" }]
-version = "3.5.1"
+version = "3.5.2"
 
 [tool.poetry.dependencies]
 GeoAlchemy2 = "^0.15.2"
diff --git a/dinosaur/poetry.lock b/dinosaur/poetry.lock
index fc7703f..b4c3eb0 100644
--- a/dinosaur/poetry.lock
+++ b/dinosaur/poetry.lock
@@ -278,7 +278,7 @@ files = [
 
 [[package]]
 name = "macrostrat-database"
-version = "3.5.1"
+version = "3.5.2"
 description = "A SQLAlchemy-based database toolkit."
 optional = false
 python-versions = "^3.10"
diff --git a/poetry.lock b/poetry.lock
index d9c8688..08c323c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -793,7 +793,7 @@ url = "auth-system"
 
 [[package]]
 name = "macrostrat-database"
-version = "3.5.1"
+version = "3.5.2"
 description = "A SQLAlchemy-based database toolkit."
 optional = false
 python-versions = "^3.10"