From 79bf428db25e8344ca301bc2d77808b2bdae008e Mon Sep 17 00:00:00 2001 From: Kieron Taylor Date: Thu, 15 Jun 2023 13:03:02 +0000 Subject: [PATCH 01/29] SQLAlchemy compatibility warnings are non-entities. Update deps and remove future flags --- lang_qc/db/mlwh_connection.py | 2 +- lang_qc/db/qc_connection.py | 2 +- poetry.lock | 816 +++++++++++++++++----------------- pyproject.toml | 3 +- tests/conftest.py | 4 +- 5 files changed, 413 insertions(+), 414 deletions(-) diff --git a/lang_qc/db/mlwh_connection.py b/lang_qc/db/mlwh_connection.py index 7734bc70..bcbedc71 100644 --- a/lang_qc/db/mlwh_connection.py +++ b/lang_qc/db/mlwh_connection.py @@ -36,7 +36,7 @@ def get_mlwh_db() -> Session: url = os.environ.get("DB_URL") if url is None or url == "": raise Exception("ENV['DB_URL'] must be set with a database URL") - engine = create_engine(url, future=True, pool_recycle=3600) + engine = create_engine(url, pool_recycle=3600) if session_factory is None: session_factory = sessionmaker(engine) diff --git a/lang_qc/db/qc_connection.py b/lang_qc/db/qc_connection.py index d40c6ec2..d4c2c7a0 100644 --- a/lang_qc/db/qc_connection.py +++ b/lang_qc/db/qc_connection.py @@ -37,7 +37,7 @@ def get_qc_db() -> Session: url = os.environ.get("QCDB_URL") if url is None or url == "": raise Exception("ENV['QCDB_URL'] must be set with a database URL") - engine = create_engine(url, future=True, pool_recycle=3600) + engine = create_engine(url, pool_recycle=3600) if session_factory is None: session_factory = sessionmaker(engine) diff --git a/poetry.lock b/poetry.lock index 35196662..3b243f5a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,6 +1,6 @@ [[package]] name = "alembic" -version = "1.10.4" +version = "1.11.1" description = "A database migration tool for SQLAlchemy." category = "dev" optional = false @@ -16,31 +16,35 @@ tz = ["python-dateutil"] [[package]] name = "anyio" -version = "3.6.2" +version = "3.7.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" category = "main" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7" [package.dependencies] +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" [package.extras] -doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] -trio = ["trio (>=0.16,<0.22)"] +doc = ["packaging", "Sphinx (>=6.1.0)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "sphinx-autodoc-typehints (>=1.2.0)"] +test = ["anyio", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)", "mock (>=4)"] +trio = ["trio (<0.22)"] [[package]] name = "asgiref" -version = "3.6.0" +version = "3.7.2" description = "ASGI specs, helper code, and adapters" category = "main" optional = false python-versions = ">=3.7" +[package.dependencies] +typing-extensions = {version = ">=4", markers = "python_version < \"3.11\""} + [package.extras] -tests = ["mypy (>=0.800)", "pytest", "pytest-asyncio"] +tests = ["pytest", "pytest-asyncio", "mypy (>=0.800)"] [[package]] name = "black" @@ -65,7 +69,7 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "certifi" -version = "2022.12.7" +version = "2023.5.7" description = "Python package for providing Mozilla's CA Bundle." category = "dev" optional = false @@ -122,11 +126,11 @@ cffi = ">=1.12" [package.extras] docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"] -docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"] -pep8test = ["black", "check-manifest", "mypy", "ruff"] +docstest = ["pyenchant (>=1.6.11)", "twine (>=1.12.0)", "sphinxcontrib-spelling (>=4.0.1)"] +pep8test = ["black", "ruff", "mypy", "check-manifest"] sdist = ["setuptools-rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] -test = ["iso8601", "pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-shard (>=0.1.2)", "pytest-subtests", "pytest-xdist"] +test = ["pytest (>=6.2.0)", "pytest-shard (>=0.1.2)", "pytest-benchmark", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601"] test-randomorder = ["pytest-randomly"] tox = ["tox"] @@ -139,10 +143,10 @@ optional = false python-versions = ">=3.7,<4.0" [package.extras] -curio = ["curio (>=1.2,<2.0)", "sniffio (>=1.1,<2.0)"] +doq = ["aioquic (>=0.9.20)"] dnssec = ["cryptography (>=2.6,<40.0)"] +curio = ["curio (>=1.2,<2.0)", "sniffio (>=1.1,<2.0)"] doh = ["h2 (>=4.1.0)", "httpx (>=0.21.1)", "requests (>=2.23.0,<3.0.0)", "requests-toolbelt (>=0.9.1,<0.11.0)"] -doq = ["aioquic (>=0.9.20)"] idna = ["idna (>=2.1,<4.0)"] trio = ["trio (>=0.14,<0.23)"] wmi = ["wmi (>=1.5.1,<2.0.0)"] @@ -163,7 +167,7 @@ idna = ">=2.0.0" name = "exceptiongroup" version = "1.1.1" description = "Backport of PEP 654 (exception groups)" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -192,10 +196,10 @@ ujson = {version = ">=4.0.1,<4.0.2 || >4.0.2,<4.1.0 || >4.1.0,<4.2.0 || >4.2.0,< uvicorn = {version = ">=0.12.0,<0.18.0", extras = ["standard"], optional = true, markers = "extra == \"all\""} [package.extras] -all = ["email_validator (>=1.1.1,<2.0.0)", "itsdangerous (>=1.1.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "orjson (>=3.2.1,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "pyyaml (>=5.3.1,<7.0.0)", "requests (>=2.24.0,<3.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"] -dev = ["autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "pre-commit (>=2.17.0,<3.0.0)", "python-jose[cryptography] (>=3.3.0,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"] -doc = ["mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "typer (>=0.4.1,<0.5.0)"] -test = ["anyio[trio] (>=3.2.1,<4.0.0)", "black (==22.3.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "email_validator (>=1.1.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "flask (>=1.1.2,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "orjson (>=3.2.1,<4.0.0)", "peewee (>=3.13.3,<4.0.0)", "pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "requests (>=2.24.0,<3.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "types-dataclasses (==0.6.5)", "types-orjson (==3.6.2)", "types-ujson (==4.2.1)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)"] +all = ["requests (>=2.24.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<3.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"] +dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)", "pre-commit (>=2.17.0,<3.0.0)"] +doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "typer (>=0.4.1,<0.5.0)", "pyyaml (>=5.3.1,<7.0.0)"] +test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.910)", "flake8 (>=3.8.3,<4.0.0)", "black (==22.3.0)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "flask (>=1.1.2,<3.0.0)", "anyio[trio] (>=3.2.1,<4.0.0)", "types-ujson (==4.2.1)", "types-orjson (==3.6.2)", "types-dataclasses (==0.6.5)"] [[package]] name = "flake8" @@ -219,7 +223,7 @@ optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] -docs = ["Sphinx", "docutils (<0.18)"] +docs = ["sphinx", "docutils (<0.18)"] test = ["objgraph", "psutil"] [[package]] @@ -261,8 +265,8 @@ python-versions = ">=3.7" pydantic = ">=1.9.1" [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["flake8 (<5)", "pygments", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["sphinx (>=3.5)", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "flake8 (<5)", "pytest-cov", "pytest-enabler (>=1.3)", "pygments", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "pytest-flake8"] [[package]] name = "iniconfig" @@ -285,9 +289,9 @@ colorama = {version = ">=0.4.3", optional = true, markers = "extra == \"colors\" [package.extras] colors = ["colorama (>=0.4.3)"] +requirements-deprecated-finder = ["pip-api", "pipreqs"] pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"] plugins = ["setuptools"] -requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "itsdangerous" @@ -323,13 +327,13 @@ python-versions = ">=3.7" MarkupSafe = ">=0.9.2" [package.extras] -babel = ["Babel"] +babel = ["babel"] lingua = ["lingua"] testing = ["pytest"] [[package]] name = "markupsafe" -version = "2.1.2" +version = "2.1.3" description = "Safely add untrusted strings to HTML/XML markup." category = "dev" optional = false @@ -379,11 +383,11 @@ python-versions = ">=3.8" [[package]] name = "orjson" -version = "3.8.11" +version = "3.9.1" description = "Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy" category = "dev" optional = false -python-versions = ">= 3.7" +python-versions = ">=3.7" [[package]] name = "packaging" @@ -422,15 +426,15 @@ python-versions = ">=3.7" [[package]] name = "platformdirs" -version = "3.5.0" +version = "3.5.3" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2023.3.27)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)"] -test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] +docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx-autodoc-typehints (>=1.23,!=1.23.4)", "sphinx (>=7.0.1)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)", "pytest (>=7.3.1)"] [[package]] name = "pluggy" @@ -441,8 +445,8 @@ optional = false python-versions = ">=3.6" [package.extras] -dev = ["pre-commit", "tox"] -testing = ["pytest", "pytest-benchmark"] +testing = ["pytest-benchmark", "pytest"] +dev = ["tox", "pre-commit"] [[package]] name = "pycodestyle" @@ -462,7 +466,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydantic" -version = "1.10.7" +version = "1.10.9" description = "Data validation and settings management using python type hints" category = "main" optional = false @@ -497,7 +501,7 @@ rsa = ["cryptography"] [[package]] name = "pytest" -version = "7.3.1" +version = "7.3.2" description = "pytest: simple powerful testing with Python" category = "dev" optional = false @@ -512,7 +516,7 @@ pluggy = ">=0.12,<2.0" tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] -testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] [[package]] name = "python-dateutil" @@ -565,7 +569,7 @@ python-versions = ">=3.6" [[package]] name = "requests" -version = "2.29.0" +version = "2.31.0" description = "Python HTTP for Humans." category = "dev" optional = false @@ -575,11 +579,11 @@ python-versions = ">=3.7" certifi = ">=2017.4.17" charset-normalizer = ">=2,<4" idna = ">=2.5,<4" -urllib3 = ">=1.21.1,<1.27" +urllib3 = ">=1.21.1,<3" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] -use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "six" @@ -599,7 +603,7 @@ python-versions = ">=3.7" [[package]] name = "sqlacodegen" -version = "3.0.0rc2" +version = "3.0.0rc1" description = "Automatic model code generator for SQLAlchemy" category = "dev" optional = false @@ -607,44 +611,48 @@ python-versions = ">=3.7" [package.dependencies] inflect = ">=4.0.0" -SQLAlchemy = ">=1.4.36,<2.0" +SQLAlchemy = ">=1.4.0" [package.extras] citext = ["sqlalchemy-citext (>=1.7.0)"] -test = ["mysql-connector-python", "psycopg2-binary", "pytest", "pytest-cov", "sqlmodel"] +test = ["pytest", "pytest-cov", "psycopg2-binary", "mysql-connector-python"] [[package]] name = "sqlalchemy" -version = "1.4.45" +version = "2.0.16" description = "Database Abstraction Library" category = "main" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" +python-versions = ">=3.7" [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} -pymysql = {version = "*", optional = true, markers = "python_version >= \"3\" and extra == \"pymysql\""} +greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""} +pymysql = {version = "*", optional = true, markers = "extra == \"pymysql\""} +typing-extensions = ">=4.2.0" [package.extras] -aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] -aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"] +aiomysql = ["greenlet (!=0.4.17)", "aiomysql"] +aiosqlite = ["greenlet (!=0.4.17)", "aiosqlite", "typing-extensions (!=3.10.0.1)"] asyncio = ["greenlet (!=0.4.17)"] -asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"] -mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"] +asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)"] +mariadb_connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"] mssql = ["pyodbc"] -mssql-pymssql = ["pymssql"] -mssql-pyodbc = ["pyodbc"] -mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"] -mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"] -mysql-connector = ["mysql-connector-python"] -oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"] +mssql_pymssql = ["pymssql"] +mssql_pyodbc = ["pyodbc"] +mypy = ["mypy (>=0.910)"] +mysql = ["mysqlclient (>=1.4.0)"] +mysql_connector = ["mysql-connector-python"] +oracle = ["cx-oracle (>=7)"] +oracle_oracledb = ["oracledb (>=1.0.1)"] postgresql = ["psycopg2 (>=2.7)"] -postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"] -postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"] -postgresql-psycopg2binary = ["psycopg2-binary"] -postgresql-psycopg2cffi = ["psycopg2cffi"] -pymysql = ["pymysql", "pymysql (<1)"] -sqlcipher = ["sqlcipher3_binary"] +postgresql_asyncpg = ["greenlet (!=0.4.17)", "asyncpg"] +postgresql_pg8000 = ["pg8000 (>=1.29.1)"] +postgresql_psycopg = ["psycopg (>=3.0.7)"] +postgresql_psycopg2binary = ["psycopg2-binary"] +postgresql_psycopg2cffi = ["psycopg2cffi"] +postgresql_psycopgbinary = ["psycopg[binary] (>=3.0.7)"] +pymysql = ["pymysql"] +sqlcipher = ["sqlcipher3-binary"] [[package]] name = "starlette" @@ -670,7 +678,7 @@ python-versions = ">=3.7" [[package]] name = "typing-extensions" -version = "4.5.0" +version = "4.6.3" description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false @@ -678,24 +686,25 @@ python-versions = ">=3.7" [[package]] name = "ujson" -version = "5.7.0" +version = "5.8.0" description = "Ultra fast JSON encoder and decoder for Python" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [[package]] name = "urllib3" -version = "1.26.15" +version = "2.0.3" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7" [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] -secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] -socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] +socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] +zstd = ["zstandard (>=0.18.0)"] [[package]] name = "uvicorn" @@ -718,7 +727,7 @@ watchgod = {version = ">=0.6", optional = true, markers = "extra == \"standard\" websockets = {version = ">=10.0", optional = true, markers = "extra == \"standard\""} [package.extras] -standard = ["PyYAML (>=5.1)", "colorama (>=0.4)", "httptools (>=0.4.0)", "python-dotenv (>=0.13)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "watchgod (>=0.6)", "websockets (>=10.0)"] +standard = ["websockets (>=10.0)", "httptools (>=0.4.0)", "watchgod (>=0.6)", "python-dotenv (>=0.13)", "PyYAML (>=5.1)", "uvloop (>=0.14.0,!=0.15.0,!=0.15.1)", "colorama (>=0.4)"] [[package]] name = "uvloop" @@ -729,9 +738,9 @@ optional = false 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extras = ["standard"] } uvicorn = { version = "^0.17", extras = ["standard"] } cryptography = { version = "^40.0.2" } -SQLAlchemy = { version = ">=1.4.35, < 1.4.46", extras = ["pymysql"] } -# langqc will be incompatible with sqlalchemy 2.0. Pin version just before the deprecation warnings start +SQLAlchemy = { version = "^2.0.1", extras = ["pymysql"] } pydantic = "^1.9.0" npg_id_generation = { git = "https://github.com/wtsi-npg/npg_id_generation.git", tag="3.0.0" } diff --git a/tests/conftest.py b/tests/conftest.py index 9b2f4342..b4588056 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -85,7 +85,7 @@ def create_mlwhdb_test_sessionfactory(config): url = mysql_url( config, "MySQL MLWH", "test", "test", "127.0.0.1", "3306", "mlwarehouse" ) - engine = create_engine(url, future=True) + engine = create_engine(url) TestingSessionLocal = sessionmaker(bind=engine) with engine.connect() as conn: # Workaround for invalid default values for dates. @@ -118,7 +118,7 @@ def create_qcdb_test_sessionfactory(config): """ url = mysql_url(config, "MySQL QCDB", "test", "test", "127.0.0.1", "3307", "langqc") - engine = create_engine(url, future=True) + engine = create_engine(url) TestingSessionLocal = sessionmaker(bind=engine) with engine.connect() as conn: # Workaround for invalid default values for dates. From 33d76347997313480e25995f0507d434c52fe832 Mon Sep 17 00:00:00 2001 From: Kieron Taylor Date: Thu, 15 Jun 2023 15:31:10 +0000 Subject: [PATCH 02/29] Update MLWH pac_bio_run_well_metrics with multiplex-relevant columns --- lang_qc/db/mlwh_schema.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/lang_qc/db/mlwh_schema.py b/lang_qc/db/mlwh_schema.py index 47ca43f8..e18858d7 100644 --- a/lang_qc/db/mlwh_schema.py +++ b/lang_qc/db/mlwh_schema.py @@ -350,6 +350,9 @@ class PacBioRunWellMetrics(Base): index=True, comment="The PacBio ccs exection mode e.g. OnInstument, OffInstument or None", ) + demultiplex_mode = Column( + String(32), comment="Demultiplexing mode e.g. OnInstument, OffInstument or None" + ) include_kinetics = Column( mysqlTINYINT(1, unsigned=True), comment="Include kinetics information where ccs is run", @@ -498,6 +501,14 @@ class PacBioRunWellMetrics(Base): mysqlSMALLINT(5, unsigned=True), comment="The median base quality of HiFi bases filtered due to low quality ( Date: Mon, 19 Jun 2023 12:53:57 +0000 Subject: [PATCH 03/29] Remove defunct sqlacodegen dependency. 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frontend/src/views/__tests__/WellsByRun.spec.js | 2 +- frontend/src/views/__tests__/WellsByStatus.spec.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/frontend/src/views/__tests__/WellsByRun.spec.js b/frontend/src/views/__tests__/WellsByRun.spec.js index 51383485..203caad5 100644 --- a/frontend/src/views/__tests__/WellsByRun.spec.js +++ b/frontend/src/views/__tests__/WellsByRun.spec.js @@ -16,7 +16,7 @@ const router = createRouter({ const testWells = [] for (let index = 0; index < 2; index++) { testWells.push({ - label: String.fromCharCode(94 + index) + "1", + label: String.fromCharCode(97 + index) + "1", run_name: "TRACTION-RUN-211", run_start_time: "2023-04-24T10:10:10", run_complete_time: "2023-05-25T02:10:10", diff --git a/frontend/src/views/__tests__/WellsByStatus.spec.js b/frontend/src/views/__tests__/WellsByStatus.spec.js index 5350a704..5ecfff3c 100644 --- a/frontend/src/views/__tests__/WellsByStatus.spec.js +++ b/frontend/src/views/__tests__/WellsByStatus.spec.js @@ -21,7 +21,7 @@ const router = createRouter({ const testWells = [] for (let index = 0; index < 10; index++) { testWells.push({ - label: String.fromCharCode(94 + index) + "1", + label: String.fromCharCode(97 + index) + "1", run_name: `TRACTION-RUN-21${(index / 10).toFixed(0)}`, run_start_time: "2023-04-24T10:10:10", run_complete_time: "2023-05-25T02:10:10", From a05f77ece91ae5ebcf0d31aa45d454397afb4224 Mon Sep 17 00:00:00 2001 From: Kieron Taylor Date: Fri, 2 Jun 2023 15:59:46 +0000 Subject: [PATCH 05/29] Change WellsByRun to accept a list of arguments. --- frontend/src/App.vue | 2 +- frontend/src/router/index.js | 3 +- frontend/src/views/WellsByRun.vue | 32 +++++++++++-------- .../src/views/__tests__/WellsByRun.spec.js | 2 +- 4 files changed, 22 insertions(+), 17 deletions(-) diff --git a/frontend/src/App.vue b/frontend/src/App.vue index a655fda0..7442790b 100644 --- a/frontend/src/App.vue +++ b/frontend/src/App.vue @@ -37,7 +37,7 @@ onMounted(() => { function goToRun(runName) { if (runName != '') { - router.push({ name: 'WellsByRun', params: { runName: runName }}) + router.push({ name: 'WellsByRun', params: { runName: [runName] }}) } } diff --git a/frontend/src/router/index.js b/frontend/src/router/index.js index af6a41f2..fe653940 100644 --- a/frontend/src/router/index.js +++ b/frontend/src/router/index.js @@ -16,7 +16,8 @@ const router = createRouter({ component: WellsByStatus, }, { - path: '/run/:runName', + path: '/run/:runName+', + // + means 1 or more names /run/name1/name2/name3 name: 'WellsByRun', component: WellsByRun, props: true diff --git a/frontend/src/views/WellsByRun.vue b/frontend/src/views/WellsByRun.vue index 6229f492..7c65b91c 100644 --- a/frontend/src/views/WellsByRun.vue +++ b/frontend/src/views/WellsByRun.vue @@ -14,11 +14,11 @@ import { getUserName } from "@/utils/session.js" const route = useRoute() const router = useRouter() -const props = defineProps(["runName"]) +const props = defineProps({"runName": Array}) const focusWell = useWellStore() const serviceClient = new LangQc() -let wellCollection = ref(null) +let wellCollection = ref([]) let user = ref(null) getUserName((email) => { user.value = email }).then(); @@ -32,17 +32,21 @@ watch(() => route.query, (after, before) => { ) watch(() => props.runName, () => { - serviceClient.getWellsForRunPromise(props.runName).then( - (data) => wellCollection.value = data.wells - ).catch(error => { - ElMessage({ - message: error.message, - type: "warning", - duration: 5000 + for (let run of props.runName) { + wellCollection.value = [] + serviceClient.getWellsForRunPromise(run).then( + (data) => wellCollection.value.push(...data.wells) + ).catch(error => { + ElMessage({ + message: error.message, + type: "warning", + duration: 5000 + }) + // Stop table remaining with out of date content + wellCollection.value = [] }) - // Stop table remaining with out of date content - wellCollection.value = null - })}, + } + }, { immediate: true } ) @@ -65,8 +69,8 @@ function wellSelected(well) {