From 4d28f77a38e69774c03bf5c9d8f8fd60a3e2a2d5 Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Fri, 12 Jul 2024 03:05:51 -0500 Subject: [PATCH 01/21] Start upgrading for psycopg3 --- database/macrostrat/database/__init__.py | 20 ++++++- database/macrostrat/database/postgresql.py | 3 +- database/macrostrat/database/utils.py | 2 +- database/poetry.lock | 67 +++++++++++++++++++++- database/pyproject.toml | 1 + database/tests/test_database.py | 4 +- database/tests/test_database_fixtures.py | 2 +- dinosaur/poetry.lock | 64 +++++++++++++++++++++ poetry.lock | 35 +++++++++++ 9 files changed, 187 insertions(+), 11 deletions(-) diff --git a/database/macrostrat/database/__init__.py b/database/macrostrat/database/__init__.py index 9bb7cf2..f009271 100644 --- a/database/macrostrat/database/__init__.py +++ b/database/macrostrat/database/__init__.py @@ -4,8 +4,8 @@ from pathlib import Path from typing import Optional, Union -from psycopg2.errors import InvalidSavepointSpecification -from psycopg2.sql import Identifier +from psycopg.errors import InvalidSavepointSpecification +from psycopg.sql import Identifier from sqlalchemy import URL, MetaData, create_engine, inspect, text from sqlalchemy.exc import IntegrityError, InternalError from sqlalchemy.ext.compiler import compiles @@ -57,12 +57,26 @@ def __init__(self, db_conn: Union[str, URL], *, echo_sql=False, **kwargs): pass to queries and other database operations. """ + compiles(Insert, "postgresql")(prefix_inserts) self.instance_params = kwargs.pop("instance_params", {}) log.info(f"Setting up database connection '{db_conn}'") - self.engine = create_engine(db_conn, echo=echo_sql, **kwargs) + + url = db_conn + if not isinstance(url, URL): + url = URL(url) + if url.drivername == "postgresql": + # Use the psycopg3 driver if available + try: + from psycopg3 import connect + except ImportError: + pass + else: + url.drivername = "postgresql+psycopg" + + self.engine = create_engine(url, echo=echo_sql, **kwargs) self.metadata = kwargs.get("metadata", metadata) # Scoped session for database diff --git a/database/macrostrat/database/postgresql.py b/database/macrostrat/database/postgresql.py index cf3ec2b..e3f7ff2 100644 --- a/database/macrostrat/database/postgresql.py +++ b/database/macrostrat/database/postgresql.py @@ -4,7 +4,6 @@ from contextvars import ContextVar from typing import TYPE_CHECKING -import psycopg2 from sqlalchemy.dialects import postgresql from sqlalchemy.exc import CompileError from sqlalchemy.ext.compiler import compiles @@ -63,7 +62,7 @@ def prefix_inserts(insert, compiler, **kw): def table_exists(db: Database, table_name: str, schema: str = "public") -> bool: """Check if a table exists in a PostgreSQL database.""" sql = """SELECT EXISTS ( - SELECT FROM information_schema.tables + SELECT FROM information_schema.tables WHERE table_schema = :schema AND table_name = :table_name );""" diff --git a/database/macrostrat/database/utils.py b/database/macrostrat/database/utils.py index ec23961..0e640a2 100644 --- a/database/macrostrat/database/utils.py +++ b/database/macrostrat/database/utils.py @@ -8,7 +8,7 @@ from click import echo, secho from psycopg2.extensions import set_wait_callback from psycopg2.extras import wait_select -from psycopg2.sql import SQL, Composable, Composed +from psycopg.sql import SQL, Composable, Composed import psycopg2.errors from rich.console import Console from sqlalchemy import MetaData, create_engine, text diff --git a/database/poetry.lock b/database/poetry.lock index 510f697..03065b7 100644 --- a/database/poetry.lock +++ b/database/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "aiofiles" @@ -11,6 +11,34 @@ files = [ {file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"}, ] +[[package]] +name = "backports-zoneinfo" +version = "0.2.1" +description = "Backport of the standard library zoneinfo module" +optional = false +python-versions = ">=3.6" +files = [ + {file = "backports.zoneinfo-0.2.1-cp36-cp36m-macosx_10_14_x86_64.whl", hash = "sha256:da6013fd84a690242c310d77ddb8441a559e9cb3d3d59ebac9aca1a57b2e18bc"}, + {file = "backports.zoneinfo-0.2.1-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:89a48c0d158a3cc3f654da4c2de1ceba85263fafb861b98b59040a5086259722"}, + {file = "backports.zoneinfo-0.2.1-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:1c5742112073a563c81f786e77514969acb58649bcdf6cdf0b4ed31a348d4546"}, + {file = "backports.zoneinfo-0.2.1-cp36-cp36m-win32.whl", hash = "sha256:e8236383a20872c0cdf5a62b554b27538db7fa1bbec52429d8d106effbaeca08"}, + {file = 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"sha256:8961c0f32cd0336fb8e8ead11a1f8cd99ec07145ec2931122faaac1c8f7fd987"}, + {file = "backports.zoneinfo-0.2.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:e81b76cace8eda1fca50e345242ba977f9be6ae3945af8d46326d776b4cf78d1"}, + {file = "backports.zoneinfo-0.2.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:7b0a64cda4145548fed9efc10322770f929b944ce5cee6c0dfe0c87bf4c0c8c9"}, + {file = "backports.zoneinfo-0.2.1-cp38-cp38-win32.whl", hash = "sha256:1b13e654a55cd45672cb54ed12148cd33628f672548f373963b0bff67b217328"}, + {file = "backports.zoneinfo-0.2.1-cp38-cp38-win_amd64.whl", hash = "sha256:4a0f800587060bf8880f954dbef70de6c11bbe59c673c3d818921f042f9954a6"}, + {file = "backports.zoneinfo-0.2.1.tar.gz", hash = "sha256:fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2"}, +] + +[package.extras] +tzdata = ["tzdata"] + [[package]] name = "click" version = "8.1.3" @@ -211,6 +239,30 @@ files = [ {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"}, ] +[[package]] +name = "psycopg" +version = "3.2.1" +description = "PostgreSQL database adapter for Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "psycopg-3.2.1-py3-none-any.whl", hash = "sha256:ece385fb413a37db332f97c49208b36cf030ff02b199d7635ed2fbd378724175"}, + {file = "psycopg-3.2.1.tar.gz", hash = "sha256:dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7"}, +] + +[package.dependencies] +"backports.zoneinfo" = {version = ">=0.2.0", markers = "python_version < \"3.9\""} +typing-extensions = ">=4.4" +tzdata = {version = "*", markers = "sys_platform == \"win32\""} + +[package.extras] +binary = ["psycopg-binary (==3.2.1)"] +c = ["psycopg-c (==3.2.1)"] +dev = ["ast-comments (>=1.1.2)", "black (>=24.1.0)", "codespell (>=2.2)", "dnspython (>=2.1)", "flake8 (>=4.0)", "mypy (>=1.6)", "types-setuptools (>=57.4)", "wheel (>=0.37)"] +docs = ["Sphinx (>=5.0)", "furo (==2022.6.21)", "sphinx-autobuild (>=2021.3.14)", "sphinx-autodoc-typehints (>=1.12)"] +pool = ["psycopg-pool"] +test = ["anyio (>=4.0)", "mypy (>=1.6)", "pproxy (>=2.7)", "pytest (>=6.2.5)", "pytest-cov (>=3.0)", "pytest-randomly (>=3.5)"] + [[package]] name = "psycopg2-binary" version = "2.9.6" @@ -510,7 +562,18 @@ files = [ {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"}, ] +[[package]] +name = "tzdata" +version = "2024.1" +description = "Provider of IANA time zone data" +optional = false +python-versions = ">=2" +files = [ + {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, + {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, +] + [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "b340b0f3df2c27f453d2b4696a460c3ad8dc5366ebd04ef7c7991842d26da2e8" +content-hash = "a59022f89375f1cced7c4c87820c3dbedf8eedc46c4274f2226502cf38a46d1b" diff --git a/database/pyproject.toml b/database/pyproject.toml index 0532363..e705beb 100644 --- a/database/pyproject.toml +++ b/database/pyproject.toml @@ -16,6 +16,7 @@ python = "^3.8" sqlparse = "^0.4.4" aiofiles = "^23.2.1" rich = "^13.7.1" +psycopg = "^3.2.1" [tool.poetry.dev-dependencies] "macrostrat.utils" = { path = "../utils", develop = true } diff --git a/database/tests/test_database.py b/database/tests/test_database.py index f30d564..4732f5f 100644 --- a/database/tests/test_database.py +++ b/database/tests/test_database.py @@ -8,9 +8,9 @@ from sys import stdout from dotenv import load_dotenv -from psycopg2.errors import SyntaxError +from psycopg.errors import SyntaxError from psycopg2.extensions import AsIs -from psycopg2.sql import SQL, Identifier, Literal, Placeholder +from psycopg.sql import SQL, Identifier, Literal, Placeholder from pytest import fixture, mark, raises, warns from sqlalchemy.exc import ProgrammingError from sqlalchemy.sql import text diff --git a/database/tests/test_database_fixtures.py b/database/tests/test_database_fixtures.py index dc31f62..2ee1ac9 100644 --- a/database/tests/test_database_fixtures.py +++ b/database/tests/test_database_fixtures.py @@ -1,6 +1,6 @@ from pathlib import Path -from psycopg2.sql import Literal +from psycopg.sql import Literal from pytest import fixture, mark, raises from sqlalchemy.exc import StatementError diff --git a/dinosaur/poetry.lock b/dinosaur/poetry.lock index 22fa961..9b728d4 100644 --- a/dinosaur/poetry.lock +++ b/dinosaur/poetry.lock @@ -11,6 +11,34 @@ files = [ {file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"}, ] +[[package]] +name = "backports-zoneinfo" +version = "0.2.1" +description = "Backport of the standard library zoneinfo module" +optional = false +python-versions = 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"backports.zoneinfo-0.2.1-cp38-cp38-win32.whl", hash = "sha256:1b13e654a55cd45672cb54ed12148cd33628f672548f373963b0bff67b217328"}, + {file = "backports.zoneinfo-0.2.1-cp38-cp38-win_amd64.whl", hash = "sha256:4a0f800587060bf8880f954dbef70de6c11bbe59c673c3d818921f042f9954a6"}, + {file = "backports.zoneinfo-0.2.1.tar.gz", hash = "sha256:fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2"}, +] + +[package.extras] +tzdata = ["tzdata"] + [[package]] name = "certifi" version = "2023.5.7" @@ -289,6 +317,7 @@ aiofiles = "^23.2.1" click = "^8.1.3" GeoAlchemy2 = "^0.14.0" "macrostrat.utils" = "^1.0.0" +psycopg = "^3.2.1" psycopg2-binary = "^2.9.6" rich = "^13.7.1" SQLAlchemy = "^2.0.18" @@ -381,6 +410,30 @@ files = [ {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"}, ] +[[package]] +name = "psycopg" +version = "3.2.1" +description = "PostgreSQL database adapter for Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "psycopg-3.2.1-py3-none-any.whl", hash = "sha256:ece385fb413a37db332f97c49208b36cf030ff02b199d7635ed2fbd378724175"}, + {file = "psycopg-3.2.1.tar.gz", hash = "sha256:dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7"}, +] + +[package.dependencies] +"backports.zoneinfo" = {version = ">=0.2.0", markers = "python_version < \"3.9\""} +typing-extensions = ">=4.4" +tzdata = {version = "*", markers = "sys_platform == \"win32\""} + +[package.extras] +binary = ["psycopg-binary (==3.2.1)"] +c = ["psycopg-c (==3.2.1)"] +dev = ["ast-comments (>=1.1.2)", "black (>=24.1.0)", "codespell (>=2.2)", "dnspython (>=2.1)", "flake8 (>=4.0)", "mypy (>=1.6)", "types-setuptools (>=57.4)", "wheel (>=0.37)"] +docs = ["Sphinx (>=5.0)", "furo (==2022.6.21)", "sphinx-autobuild (>=2021.3.14)", "sphinx-autodoc-typehints (>=1.12)"] +pool = ["psycopg-pool"] +test = ["anyio (>=4.0)", "mypy (>=1.6)", "pproxy (>=2.7)", "pytest (>=6.2.5)", "pytest-cov (>=3.0)", "pytest-randomly (>=3.5)"] + [[package]] name = "psycopg2-binary" version = "2.9.6" @@ -770,6 +823,17 @@ files = [ {file = "typing_extensions-4.5.0.tar.gz", hash = "sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb"}, ] +[[package]] +name = "tzdata" +version = "2024.1" +description = "Provider of IANA time zone data" +optional = false +python-versions = ">=2" +files = [ + {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, + {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, +] + [[package]] name = "urllib3" version = "2.0.2" diff --git a/poetry.lock b/poetry.lock index 4ef9637..b332787 100644 --- a/poetry.lock +++ b/poetry.lock @@ -465,6 +465,7 @@ aiofiles = "^23.2.1" click = "^8.1.3" GeoAlchemy2 = "^0.14.0" "macrostrat.utils" = "^1.0.0" +psycopg = "^3.2.1" psycopg2-binary = "^2.9.6" rich = "^13.7.1" SQLAlchemy = "^2.0.18" @@ -902,6 +903,29 @@ files = [ dev = ["pre-commit", "tox"] testing = ["pytest", "pytest-benchmark"] +[[package]] +name = "psycopg" +version = "3.2.1" +description = "PostgreSQL database adapter for Python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "psycopg-3.2.1-py3-none-any.whl", hash = "sha256:ece385fb413a37db332f97c49208b36cf030ff02b199d7635ed2fbd378724175"}, + {file = "psycopg-3.2.1.tar.gz", hash = "sha256:dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7"}, +] + +[package.dependencies] +typing-extensions = ">=4.4" +tzdata = {version = "*", markers = "sys_platform == \"win32\""} + +[package.extras] +binary = ["psycopg-binary (==3.2.1)"] +c = ["psycopg-c (==3.2.1)"] +dev = ["ast-comments (>=1.1.2)", "black (>=24.1.0)", "codespell (>=2.2)", "dnspython (>=2.1)", "flake8 (>=4.0)", "mypy (>=1.6)", "types-setuptools (>=57.4)", "wheel (>=0.37)"] +docs = ["Sphinx (>=5.0)", "furo (==2022.6.21)", "sphinx-autobuild (>=2021.3.14)", "sphinx-autodoc-typehints (>=1.12)"] +pool = ["psycopg-pool"] +test = ["anyio (>=4.0)", "mypy (>=1.6)", "pproxy (>=2.7)", "pytest (>=6.2.5)", "pytest-cov (>=3.0)", "pytest-randomly (>=3.5)"] + [[package]] name = "psycopg2-binary" version = "2.9.9" @@ -1683,6 +1707,17 @@ files = [ {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"}, ] +[[package]] +name = "tzdata" +version = "2024.1" +description = "Provider of IANA time zone data" +optional = false +python-versions = ">=2" +files = [ + {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, + {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, +] + [[package]] name = "urllib3" version = "2.2.1" From f29f1dedbc9ceabeb9c89b1bca0beff59936f75a Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Tue, 30 Jul 2024 03:25:32 -0500 Subject: [PATCH 02/21] More tests pass with psycopg3 --- database/macrostrat/database/__init__.py | 12 +++++++++--- database/macrostrat/database/utils.py | 3 +++ 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/database/macrostrat/database/__init__.py b/database/macrostrat/database/__init__.py index f009271..4668b36 100644 --- a/database/macrostrat/database/__init__.py +++ b/database/macrostrat/database/__init__.py @@ -1,4 +1,5 @@ import warnings +import psycopg from contextlib import contextmanager from enum import Enum from pathlib import Path @@ -67,14 +68,19 @@ def __init__(self, db_conn: Union[str, URL], *, echo_sql=False, **kwargs): url = db_conn if not isinstance(url, URL): url = URL(url) - if url.drivername == "postgresql": + + # Prefer the psycopg3 driver for PostgreSQL + + + + if url.drivername.startswith("postgresql"): # Use the psycopg3 driver if available try: - from psycopg3 import connect + from psycopg import connect except ImportError: pass else: - url.drivername = "postgresql+psycopg" + url = url.set(drivername="postgresql+psycopg") self.engine = create_engine(url, echo=echo_sql, **kwargs) self.metadata = kwargs.get("metadata", metadata) diff --git a/database/macrostrat/database/utils.py b/database/macrostrat/database/utils.py index 0e640a2..37fd24a 100644 --- a/database/macrostrat/database/utils.py +++ b/database/macrostrat/database/utils.py @@ -6,6 +6,7 @@ from warnings import warn from click import echo, secho + from psycopg2.extensions import set_wait_callback from psycopg2.extras import wait_select from psycopg.sql import SQL, Composable, Composed @@ -196,6 +197,8 @@ def _get_cursor(connectable): while hasattr(conn, "driver_connection") or hasattr(conn, "connection"): if hasattr(conn, "driver_connection"): conn = conn.driver_connection + elif conn.connection == conn: + break else: conn = conn.connection if callable(conn): From bbcde5a89104e96b316e408e5ce6aa10baa819ea Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Tue, 30 Jul 2024 04:16:16 -0500 Subject: [PATCH 03/21] Fixed some URL handling --- database/macrostrat/database/__init__.py | 3 ++- database/tests/test_database.py | 22 +++++++++++++++++++--- 2 files changed, 21 insertions(+), 4 deletions(-) diff --git a/database/macrostrat/database/__init__.py b/database/macrostrat/database/__init__.py index 4668b36..0cb9734 100644 --- a/database/macrostrat/database/__init__.py +++ b/database/macrostrat/database/__init__.py @@ -11,6 +11,7 @@ from sqlalchemy.exc import IntegrityError, InternalError from sqlalchemy.ext.compiler import compiles from sqlalchemy.orm import Session, scoped_session, sessionmaker +from sqlalchemy.engine.url import make_url from sqlalchemy.sql.expression import Insert from macrostrat.utils import get_logger @@ -67,7 +68,7 @@ def __init__(self, db_conn: Union[str, URL], *, echo_sql=False, **kwargs): url = db_conn if not isinstance(url, URL): - url = URL(url) + url = make_url(url) # Prefer the psycopg3 driver for PostgreSQL diff --git a/database/tests/test_database.py b/database/tests/test_database.py index 4732f5f..ea0821a 100644 --- a/database/tests/test_database.py +++ b/database/tests/test_database.py @@ -6,11 +6,12 @@ from pathlib import Path from sys import stdout +from typing import Any from dotenv import load_dotenv from psycopg.errors import SyntaxError -from psycopg2.extensions import AsIs from psycopg.sql import SQL, Identifier, Literal, Placeholder +#from psycopg2.extensions import AsIs from pytest import fixture, mark, raises, warns from sqlalchemy.exc import ProgrammingError from sqlalchemy.sql import text @@ -209,7 +210,7 @@ def test_server_bound_parameters_mixed(db): def test_server_bound_parameters_invalid(db): sql = "SELECT name FROM %(table_name)s WHERE name = %(name)s" - with raises(KeyError): + with raises(ProgrammingError): db.run_query(sql, {"name": "Test", "table_name": Identifier("sample")}) @@ -238,6 +239,21 @@ def test_server_bound_parameters_dbapi_extensions(db): res = db.run_query(sql, {"name": "Test", "table_name": AsIs("sample")}) assert res.scalar() == "Test" +from psycopg.adapt import Dumper, Buffer + + +class AsIs(Dumper): + adapted: str + + def __init__(self, p_str): + super().__init__(p_str) + + def dump(self, obj: Any): + raise NotImplementedError("AsIs cannot be used as a server-bound parameter") + + def quote(self): + return self.adapted + def test_server_parameters_function_def(db): """Make sure we don't select all % as bound parameters.""" @@ -251,7 +267,7 @@ def test_server_parameters_function_def(db): END; $$ LANGUAGE plpgsql; """ - with raises(TypeError): + with raises(ProgrammingError): db.run_sql(sql, raise_errors=True) # This should not raise db.run_sql(sql, raise_errors=True, has_server_binds=False) From d2bf9925ebf9308ee77baa852533d1c825214c91 Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Tue, 30 Jul 2024 04:38:39 -0500 Subject: [PATCH 04/21] Fixed savepoint errors --- database/macrostrat/database/__init__.py | 5 +++-- database/tests/test_database_fixtures.py | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/database/macrostrat/database/__init__.py b/database/macrostrat/database/__init__.py index 0cb9734..cf095cf 100644 --- a/database/macrostrat/database/__init__.py +++ b/database/macrostrat/database/__init__.py @@ -8,7 +8,7 @@ from psycopg.errors import InvalidSavepointSpecification from psycopg.sql import Identifier from sqlalchemy import URL, MetaData, create_engine, inspect, text -from sqlalchemy.exc import IntegrityError, InternalError +from sqlalchemy.exc import IntegrityError, OperationalError from sqlalchemy.ext.compiler import compiles from sqlalchemy.orm import Session, scoped_session, sessionmaker from sqlalchemy.engine.url import make_url @@ -329,6 +329,7 @@ def savepoint(self, name=None, rollback="on-error", connection=None): if connection is None: connection = self.session.connection() + params = {"name": Identifier(name)} run_query(connection, "SAVEPOINT {name}", params) should_rollback = rollback == "always" @@ -351,7 +352,7 @@ def _clear_savepoint(connection, name, rollback=True): run_query(connection, "ROLLBACK TO SAVEPOINT {name}", params) else: run_query(connection, "RELEASE SAVEPOINT {name}", params) - except InternalError as err: + except OperationalError as err: if isinstance(err.orig, InvalidSavepointSpecification): log.warning( f"Savepoint {name} does not exist; we may have already rolled back." diff --git a/database/tests/test_database_fixtures.py b/database/tests/test_database_fixtures.py index 2ee1ac9..0692fff 100644 --- a/database/tests/test_database_fixtures.py +++ b/database/tests/test_database_fixtures.py @@ -83,7 +83,7 @@ def test_nested_savepoint(db): def test_savepoint_failing_query(db): """This works to rollback the savepoint, but is awkward.""" - with db.savepoint(): + with db.savepoint(rollback="on-error"): db.run_fixtures(fixture_dir) # This query will fail without a cascade try: From 3b48b7fa14bad969babe207721ce392887cf6c57 Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Tue, 30 Jul 2024 05:04:08 -0500 Subject: [PATCH 05/21] Fix copy command --- database/tests/scripts/test-long-running-query | 12 +++--------- database/tests/test_database.py | 9 +++++---- 2 files changed, 8 insertions(+), 13 deletions(-) diff --git a/database/tests/scripts/test-long-running-query b/database/tests/scripts/test-long-running-query index 24e37bc..eeb5b62 100755 --- a/database/tests/scripts/test-long-running-query +++ b/database/tests/scripts/test-long-running-query @@ -3,9 +3,7 @@ Run a long-running query to test if we can interrupt it. """ -from sys import argv, exit - -from sqlalchemy.exc import OperationalError +from sys import argv from macrostrat.database import Database @@ -14,9 +12,5 @@ print(f"Connecting to {db_conn}") db = Database(db_conn) -try: - db.run_sql("SELECT pg_sleep(10);") -except OperationalError as e: - if "canceling statement due to user request" in str(e): - print("Query canceled due to user request.") - exit(1) +db.run_sql("SELECT pg_sleep(10);") + diff --git a/database/tests/test_database.py b/database/tests/test_database.py index ea0821a..5625a0c 100644 --- a/database/tests/test_database.py +++ b/database/tests/test_database.py @@ -309,7 +309,7 @@ def test_copy_statement(db): pg_conn = db.engine.connect().connection cur = pg_conn.cursor() - cur.copy_expert("COPY sample (name) TO STDOUT", stdout) + cur.copy("COPY sample (name) TO STDOUT", stdout) def test_close_connection(conn): @@ -320,7 +320,7 @@ def test_close_connection(conn): import threading - from psycopg2.extensions import QueryCanceledError + from psycopg.errors import QueryCanceled from sqlalchemy.exc import DBAPIError sql = text("SELECT pg_sleep(10)") @@ -333,7 +333,7 @@ def test_close_connection(conn): conn.execute(sql) assert False except DBAPIError as e: - if type(e.orig) == QueryCanceledError: + if type(e.orig) == QueryCanceled: print("Long running query was cancelled.") assert True t.cancel() @@ -361,14 +361,15 @@ def test_sigint_cancel(db): str(script), db_url, ], + stdout=subprocess.PIPE, ) time.sleep(0.5) p.send_signal(signal.SIGINT) p.wait() - assert p.returncode == 1 # Make sure it didn't take too long dT = time.time() - start assert dT < 2 + assert p.returncode != 0 def test_check_table_exists(db): From a748f8b9c6d00ea8d1af067f628cc0bd91c158f9 Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Thu, 10 Apr 2025 01:56:30 -0500 Subject: [PATCH 06/21] Reformatted all code --- .../app_frame/subsystems/__init__.py | 4 +++- database/macrostrat/database/__init__.py | 7 ++---- database/macrostrat/database/utils.py | 14 +++++++---- database/tests/test_database.py | 6 +++-- .../dinosaur/upgrade_cluster/utils.py | 8 +++---- dinosaur/tests/test_upgrade_cluster.py | 24 +++++++++++++++---- 6 files changed, 41 insertions(+), 22 deletions(-) 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/database/macrostrat/database/__init__.py b/database/macrostrat/database/__init__.py index cf095cf..9a6891a 100644 --- a/database/macrostrat/database/__init__.py +++ b/database/macrostrat/database/__init__.py @@ -1,17 +1,17 @@ import warnings -import psycopg from contextlib import contextmanager from enum import Enum from pathlib import Path from typing import Optional, Union +import psycopg from psycopg.errors import InvalidSavepointSpecification from psycopg.sql import Identifier from sqlalchemy import URL, MetaData, create_engine, inspect, text +from sqlalchemy.engine.url import make_url from sqlalchemy.exc import IntegrityError, OperationalError from sqlalchemy.ext.compiler import compiles from sqlalchemy.orm import Session, scoped_session, sessionmaker -from sqlalchemy.engine.url import make_url from sqlalchemy.sql.expression import Insert from macrostrat.utils import get_logger @@ -59,7 +59,6 @@ def __init__(self, db_conn: Union[str, URL], *, echo_sql=False, **kwargs): pass to queries and other database operations. """ - compiles(Insert, "postgresql")(prefix_inserts) self.instance_params = kwargs.pop("instance_params", {}) @@ -72,8 +71,6 @@ def __init__(self, db_conn: Union[str, URL], *, echo_sql=False, **kwargs): # Prefer the psycopg3 driver for PostgreSQL - - if url.drivername.startswith("postgresql"): # Use the psycopg3 driver if available try: diff --git a/database/macrostrat/database/utils.py b/database/macrostrat/database/utils.py index 37fd24a..18a1c01 100644 --- a/database/macrostrat/database/utils.py +++ b/database/macrostrat/database/utils.py @@ -5,12 +5,11 @@ from typing import IO, Union from warnings import warn +import psycopg2.errors from click import echo, secho - from psycopg2.extensions import set_wait_callback from psycopg2.extras import wait_select from psycopg.sql import SQL, Composable, Composed -import psycopg2.errors from rich.console import Console from sqlalchemy import MetaData, create_engine, text from sqlalchemy.engine import Connection, Engine @@ -18,8 +17,8 @@ IntegrityError, InternalError, InvalidRequestError, + OperationalError, ProgrammingError, - OperationalError ) from sqlalchemy.orm import sessionmaker from sqlalchemy.schema import Table @@ -328,7 +327,9 @@ def _run_sql(connectable, sql, params=None, **kwargs): def _should_raise_query_error(err): """Determine if an error should be raised for a query or not.""" - if not isinstance(err, (ProgrammingError, IntegrityError, InternalError, OperationalError)): + if not isinstance( + err, (ProgrammingError, IntegrityError, InternalError, OperationalError) + ): return True orig_err = getattr(err, "orig", None) @@ -338,7 +339,10 @@ def _should_raise_query_error(err): # If we cancel statements midstream, we should raise the error. # We might want to change this behavior in the future. # Ideally we could handle operational errors more gracefully - if isinstance(orig_err, psycopg2.errors.QueryCanceled) or orig_err.pgcode == "57014": + if ( + isinstance(orig_err, psycopg2.errors.QueryCanceled) + or orig_err.pgcode == "57014" + ): return True return False diff --git a/database/tests/test_database.py b/database/tests/test_database.py index 5625a0c..fbd9fbd 100644 --- a/database/tests/test_database.py +++ b/database/tests/test_database.py @@ -11,7 +11,8 @@ from dotenv import load_dotenv from psycopg.errors import SyntaxError from psycopg.sql import SQL, Identifier, Literal, Placeholder -#from psycopg2.extensions import AsIs + +# from psycopg2.extensions import AsIs from pytest import fixture, mark, raises, warns from sqlalchemy.exc import ProgrammingError from sqlalchemy.sql import text @@ -239,7 +240,8 @@ def test_server_bound_parameters_dbapi_extensions(db): res = db.run_query(sql, {"name": "Test", "table_name": AsIs("sample")}) assert res.scalar() == "Test" -from psycopg.adapt import Dumper, Buffer + +from psycopg.adapt import Buffer, Dumper class AsIs(Dumper): 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/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 + ) From d91695190f54219eec92776a2647ce1e54cbaedb Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Thu, 10 Apr 2025 01:57:39 -0500 Subject: [PATCH 07/21] Formatted code --- database/tests/test_database.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/database/tests/test_database.py b/database/tests/test_database.py index 1e34ed7..b70a2ef 100644 --- a/database/tests/test_database.py +++ b/database/tests/test_database.py @@ -21,8 +21,8 @@ from macrostrat.database.utils import ( _print_error, infer_is_sql_text, - temp_database, run_fixtures, + temp_database, ) from macrostrat.utils import get_logger, relative_path From 9eb3e02ae1f9b670d8e91c1d46137e55c2a2de89 Mon Sep 17 00:00:00 2001 From: Daven Quinn Date: Thu, 10 Apr 2025 02:12:10 -0500 Subject: [PATCH 08/21] Update poetry and psycopg --- poetry.lock | 749 +++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 682 insertions(+), 67 deletions(-) diff --git a/poetry.lock b/poetry.lock index b332787..52049e7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. [[package]] name = "aiofiles" @@ -6,6 +6,7 @@ version = "23.2.1" description = "File support for asyncio." optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "aiofiles-23.2.1-py3-none-any.whl", hash = "sha256:19297512c647d4b27a2cf7c34caa7e405c0d60b5560618a29a9fe027b18b0107"}, {file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"}, @@ -17,17 +18,41 @@ version = "0.6.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] +[[package]] +name = "anyio" +version = "3.7.1" +description = "High level compatibility layer for multiple asynchronous event loop implementations" +optional = false +python-versions = ">=3.7" +groups = ["dev"] +files = [ + {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, + {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"}, +] + +[package.dependencies] +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} +idna = ">=2.8" +sniffio = ">=1.1" + +[package.extras] +doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery"] +test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4) ; python_version < \"3.8\"", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17) ; python_version < \"3.12\" and platform_python_implementation == \"CPython\" and platform_system != \"Windows\""] +trio = ["trio (<0.22)"] + [[package]] name = "babel" version = "2.14.0" 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Markdown parsing, done right!" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"}, {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"}, @@ -583,6 +960,7 @@ version = "2.1.5" description = "Safely add untrusted strings to HTML/XML markup." optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:a17a92de5231666cfbe003f0e4b9b3a7ae3afb1ec2845aadc2bacc93ff85febc"}, {file = "MarkupSafe-2.1.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:72b6be590cc35924b02c78ef34b467da4ba07e4e0f0454a2c5907f473fc50ce5"}, @@ -646,12 +1024,33 @@ files = [ {file = "MarkupSafe-2.1.5.tar.gz", hash = "sha256:d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b"}, ] +[[package]] +name = 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Easy to code. 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+ \ No newline at end of file diff --git a/.idea/python-libraries.iml b/.idea/python-libraries.iml index 92fb703..1d67f67 100644 --- a/.idea/python-libraries.iml +++ b/.idea/python-libraries.iml @@ -1,5 +1,10 @@ + + + + + @@ -18,6 +23,7 @@ +