From 966d8caa7cbd2e51b6e6759bafc650d798849e91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pawe=C5=82=20Srokosz?= Date: Tue, 5 Apr 2022 16:07:49 +0200 Subject: [PATCH 1/2] Use Poetry for dependency management --- poetry.lock | 1284 ++++++++++++++++++++++++++++++++ pyproject.toml | 63 ++ requirements.txt | 30 - setup.py | 29 - tests/backend/requirements.txt | 6 - 5 files changed, 1347 insertions(+), 65 deletions(-) create mode 100644 poetry.lock delete mode 100644 requirements.txt delete mode 100644 setup.py delete mode 100644 tests/backend/requirements.txt diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 000000000..b4176d03c --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1284 @@ +[[package]] +name = "alembic" +version = "1.4.2" +description = "A database migration tool for SQLAlchemy." +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + +[package.dependencies] +Mako = "*" +python-dateutil = "*" +python-editor = ">=0.3" +SQLAlchemy = ">=1.1.0" + +[[package]] +name = "aniso8601" +version = "9.0.1" +description = "A library for parsing ISO 8601 strings." +category = "main" +optional = false +python-versions = "*" + +[package.extras] +dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] + +[[package]] +name = "apispec" +version = "3.3.1" +description = "A pluggable API specification generator. 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"sha256:88ab9867d8973d8ae84719cf233b7dafc54326fcaec89683c3f9f77c002cdff9"}, +] +werkzeug = [ + {file = "Werkzeug-2.0.3-py3-none-any.whl", hash = "sha256:1421ebfc7648a39a5c58c601b154165d05cf47a3cd0ccb70857cbdacf6c8f2b8"}, + {file = "Werkzeug-2.0.3.tar.gz", hash = "sha256:b863f8ff057c522164b6067c9e28b041161b4be5ba4d0daceeaa50a163822d3c"}, +] +zipp = [ + {file = "zipp-3.8.0-py3-none-any.whl", hash = "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"}, + {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"}, +] diff --git a/pyproject.toml b/pyproject.toml index 118dd16ad..d2dfa2a5c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,3 +5,66 @@ force_grid_wrap = 0 use_parentheses = true ensure_newline_before_comments = true line_length = 88 + +[tool.poetry] +name = "mwdb-core" +version = "2.7.0" +description = "MWDB Core malware database" +authors = ["CERT Polska "] +license = "AGPLv3" +readme = "README.md" +repository = "https://github.com/CERT-Polska/mwdb-core" +documentation = "https://mwdb.readthedocs.io/en/latest/" +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: 3" +] + +[tool.poetry.dependencies] +python = "^3.7" +Werkzeug = "2.0.3" +uwsgi = "2.0.20" +alembic = "1.4.2" +Flask = "2.0.2" +Flask-SQLAlchemy = "2.5.1" +Flask-Migrate = "3.1.0" +Flask-RESTful = "0.3.9" +SQLAlchemy = "1.3.18" +marshmallow = "3.7.1" +ssdeep = "3.4" +psycopg2-binary = "2.8.5" +requests = "2.26.0" +apispec = {version = "3.3.1", extras = ["yaml", "validation"]} +bcrypt = "3.1.4" +python-magic = "0.4.18" +luqum = "0.7.4" +python-json-logger = "2.0.2" +click = "7.1.2" +click-default-group = "1.2.2" +PyYAML = "5.4" +redis = "3.2.1" +minio = "7.1.0" +typed-config = "0.2.1" +karton-core = "^4.3.0" +Authlib = "0.15.4" +regex = "2021.7.6" +pyJWT = "2.3.0" +Flask-Limiter = "2.1.3" +python-dateutil = "2.8.2" + +[tool.poetry.dev-dependencies] +isort = "5.10.1" +black = "22.3.0" +flake8 = "3.8.4" +mypy = "0.940" +pytest = "*" +pytest-rerunfailures = "*" +python-baseconv = "*" + +[tool.poetry.scripts] +mwdb-core = "mwdb.cli:cli" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index f16e5d61f..000000000 --- a/requirements.txt +++ /dev/null @@ -1,30 +0,0 @@ -Werkzeug==2.0.3 -uwsgi==2.0.20 -alembic==1.4.2 -Flask==2.0.2 -Flask-SQLAlchemy==2.5.1 -Flask-Migrate==3.1.0 -Flask-RESTful==0.3.9 -SQLAlchemy==1.3.18 -marshmallow==3.7.1 -ssdeep==3.4 -psycopg2-binary==2.8.5 -requests==2.26.0 -apispec[yaml,validation]==3.3.1 -bcrypt==3.1.4 -python-magic==0.4.18 -luqum==0.7.4 -python-json-logger==2.0.2 -click==7.1.2 -click-default-group==1.2.2 -PyYAML==5.4 -redis==3.2.1 -minio==7.1.0 -typed-config==0.2.1 -karton-core==4.3.0 -Authlib==0.15.4 -prance==0.21.8.0 # apispec unpinned dependency -regex==2021.7.6 -pyJWT==2.3.0 -Flask-Limiter==2.1.3 -python-dateutil==2.8.2 diff --git a/setup.py b/setup.py deleted file mode 100644 index ca9149338..000000000 --- a/setup.py +++ /dev/null @@ -1,29 +0,0 @@ -from setuptools import setup, find_packages - -LONG_DESCRIPTION = """ -Malware repository component for automated malware collection/analysis systems. - -Under the hood of mwdb.cert.pl service hosted by CERT.pl. -""" - -setup(name="mwdb-core", - version="2.7.0", - description="MWDB Core malware database", - long_description=LONG_DESCRIPTION, - author="CERT Polska", - author_email="info@cert.pl", - packages=find_packages(), - include_package_data=True, - url="https://github.com/CERT-Polska/mwdb-core", - install_requires=open("requirements.txt").read().splitlines(), - python_requires='>=3.7', - entry_points={ - 'console_scripts': [ - 'mwdb-core=mwdb.cli:cli' - ], - }, - classifiers=[ - "Development Status :: 5 - Production/Stable", - "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 3" - ]) diff --git a/tests/backend/requirements.txt b/tests/backend/requirements.txt deleted file mode 100644 index d384487bc..000000000 --- a/tests/backend/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -python-dateutil==2.7.0 -pyJWT==2.3.0 -pytest -pytest-rerunfailures -requests -python-baseconv From 11f9619a13c3f33c3d88f516cc605214bde7b892 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pawe=C5=82=20Srokosz?= Date: Thu, 7 Apr 2022 17:22:59 +0200 Subject: [PATCH 2/2] Added Poetry to core Dockerfile --- deploy/docker/Dockerfile | 37 ++-- docker/start.sh | 2 +- poetry.lock | 413 ++++++++++++++++++++++++++++++++++++++- poetry.toml | 2 + pyproject.toml | 5 +- 5 files changed, 439 insertions(+), 20 deletions(-) create mode 100644 poetry.toml diff --git a/deploy/docker/Dockerfile b/deploy/docker/Dockerfile index 8c2a85134..63b806875 100644 --- a/deploy/docker/Dockerfile +++ b/deploy/docker/Dockerfile @@ -1,22 +1,35 @@ -FROM python:3.8-alpine +FROM python:3.8-alpine as base LABEL maintainer="info@cert.pl" -RUN apk add --no-cache postgresql-client postgresql-dev libmagic +ENV PIP_DEFAULT_TIMEOUT=100 \ + PIP_DISABLE_PIP_VERSION_CHECK=1 \ + PIP_NO_CACHE_DIR=1 \ + POETRY_VERSION=1.1.13 -COPY requirements.txt docker/plugins/requirements-*.txt /tmp/ -RUN apk add --no-cache -t build libffi libffi-dev py3-cffi build-base python3-dev automake m4 autoconf libtool gcc g++ musl-dev libffi-dev openssl-dev cargo \ - && BUILD_LIB=1 pip --no-cache-dir install -r /tmp/requirements.txt \ - && ls /tmp/requirements-*.txt | xargs -i,, pip --no-cache-dir install -r ,, \ - && apk del build +FROM base as builder -# Copy backend files -COPY docker/ setup.py MANIFEST.in requirements.txt /app/ +WORKDIR /app +# Install build-time Alpine dependencies +RUN apk add --no-cache postgresql-client postgresql-dev libmagic && \ + apk add --no-cache libffi libffi-dev py3-cffi build-base python3-dev automake m4 autoconf libtool gcc g++ musl-dev libffi-dev openssl-dev cargo && \ + pip install "poetry==$POETRY_VERSION" +# Create virtualenv and install build-time Python dependencies +RUN python3 -m venv /app/.venv && /app/.venv/bin/pip install wheel +# Copy MWDB Core code +COPY pyproject.toml poetry.lock poetry.toml README.md /app/ COPY mwdb /app/mwdb/ +# Install project into /app/.venv (in-project=true) +RUN BUILD_LIB=1 poetry install -n --no-dev -# Install mwdb-core package -RUN pip install /app +FROM base as final +WORKDIR /app +RUN apk add --no-cache postgresql-client postgresql-dev libmagic +# Copy backend files +COPY docker/ /app/ +COPY mwdb /app/mwdb/ +COPY --from=builder /app/.venv /app/.venv # Create a /app/uploads directory # Give +r to everything in /app and +x for directories # Give rwx permissions to /app/uploads for the current user @@ -28,6 +41,4 @@ RUN mkdir -p /app/uploads/ && \ ENV PYTHONPATH=/app ENV FLASK_APP=/app/mwdb/app.py -WORKDIR /app - CMD ["/app/start.sh"] diff --git a/docker/start.sh b/docker/start.sh index f0fa33f68..b05ce59f9 100755 --- a/docker/start.sh +++ b/docker/start.sh @@ -7,6 +7,6 @@ until psql "$MWDB_POSTGRES_URI" -c "\q" ; do done echo "Configuring mwdb-core instance" +. /app/.venv/bin/activate mwdb-core configure --quiet basic - exec uwsgi --ini /app/uwsgi.ini diff --git a/poetry.lock b/poetry.lock index b4176d03c..091fc5f79 100644 --- a/poetry.lock +++ b/poetry.lock @@ -43,6 +43,14 @@ tests = ["PyYAML (>=3.10)", "prance[osv] (>=0.11)", "marshmallow (>=2.19.2)", "p validation = ["prance[osv] (>=0.11)"] yaml = ["PyYAML (>=3.10)"] +[[package]] +name = "atomicwrites" +version = "1.4.0" +description = "Atomic file writes." +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + [[package]] name = "attrs" version = "21.4.0" @@ -86,6 +94,29 @@ six = ">=1.4.1" [package.extras] tests = ["pytest (>=3.2.1)"] +[[package]] +name = "black" +version = "22.3.0" +description = "The uncompromising code formatter." +category = "dev" +optional = false +python-versions = ">=3.6.2" + +[package.dependencies] +click = ">=8.0.0" +mypy-extensions = ">=0.4.3" +pathspec = ">=0.9.0" +platformdirs = ">=2" +tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""} +typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""} +typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} + +[package.extras] +colorama = ["colorama (>=0.4.3)"] +d = ["aiohttp (>=3.7.4)"] +jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] +uvloop = ["uvloop (>=0.15.2)"] + [[package]] name = "certifi" version = "2021.10.8" @@ -126,11 +157,15 @@ unicode_backport = ["unicodedata2"] [[package]] name = "click" -version = "7.1.2" +version = "8.1.2" description = "Composable command line interface toolkit" category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.7" + +[package.dependencies] +colorama = {version = "*", markers = "platform_system == \"Windows\""} +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "click-default-group" @@ -143,6 +178,14 @@ python-versions = "*" [package.dependencies] click = "*" +[[package]] +name = "colorama" +version = "0.4.4" +description = "Cross-platform colored terminal text." +category = "main" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + [[package]] name = "cryptography" version = "36.0.2" @@ -162,6 +205,20 @@ sdist = ["setuptools_rust (>=0.11.4)"] ssh = ["bcrypt (>=3.1.5)"] test = ["pytest (>=6.2.0)", "pytest-cov", "pytest-subtests", "pytest-xdist", "pretend", "iso8601", "pytz", "hypothesis (>=1.11.4,!=3.79.2)"] +[[package]] +name = "flake8" +version = "3.8.4" +description = "the modular source code checker: pep8 pyflakes and co" +category = "dev" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" + +[package.dependencies] +importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} +mccabe = ">=0.6.0,<0.7.0" +pycodestyle = ">=2.6.0a1,<2.7.0" +pyflakes = ">=2.2.0,<2.3.0" + [[package]] name = "flask" version = "2.0.2" @@ -274,6 +331,28 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"] +[[package]] +name = "iniconfig" +version = "1.1.1" +description = "iniconfig: brain-dead simple config-ini parsing" +category = "dev" +optional = false +python-versions = "*" + +[[package]] +name = "isort" +version = "5.10.1" +description = "A Python utility / library to sort Python imports." +category = "dev" +optional = false +python-versions = ">=3.6.1,<4.0" + +[package.extras] +pipfile_deprecated_finder = ["pipreqs", "requirementslib"] +requirements_deprecated_finder = ["pipreqs", "pip-api"] +colors = ["colorama (>=0.4.3,<0.5.0)"] +plugins = ["setuptools"] + [[package]] name = "itsdangerous" version = "2.1.2" @@ -395,6 +474,14 @@ docs = ["sphinx (==3.1.2)", "sphinx-issues (==1.2.0)", "alabaster (==0.7.12)", " lint = ["mypy (==0.782)", "flake8 (==3.8.3)", "flake8-bugbear (==20.1.4)", "pre-commit (>=2.4,<3.0)"] tests = ["pytest", "pytz", "simplejson"] +[[package]] +name = "mccabe" +version = "0.6.1" +description = "McCabe checker, plugin for flake8" +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "minio" version = "7.1.0" @@ -407,6 +494,33 @@ python-versions = "*" certifi = "*" urllib3 = "*" +[[package]] +name = "mypy" +version = "0.940" +description = "Optional static typing for Python" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +mypy-extensions = ">=0.4.3" +tomli = ">=1.1.0" +typed-ast = {version = ">=1.4.0,<2", markers = "python_version < \"3.8\""} +typing-extensions = ">=3.10" + +[package.extras] +dmypy = ["psutil (>=4.0)"] +python2 = ["typed-ast (>=1.4.0,<2)"] +reports = ["lxml"] + +[[package]] +name = "mypy-extensions" +version = "0.4.3" +description = "Experimental type system extensions for programs checked with the mypy typechecker." +category = "dev" +optional = false +python-versions = "*" + [[package]] name = "openapi-schema-validator" version = "0.2.3" @@ -439,6 +553,52 @@ PyYAML = ">=5.1" [package.extras] requests = ["requests"] +[[package]] +name = "packaging" +version = "21.3" +description = "Core utilities for Python packages" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" + +[[package]] +name = "pathspec" +version = "0.9.0" +description = "Utility library for gitignore style pattern matching of file paths." +category = "dev" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" + +[[package]] +name = "platformdirs" +version = "2.5.1" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] + +[[package]] +name = "pluggy" +version = "1.0.0" +description = "plugin and hook calling mechanisms for python" +category = "dev" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""} + +[package.extras] +dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] + [[package]] name = "ply" version = "3.11" @@ -479,6 +639,22 @@ category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +[[package]] +name = "py" +version = "1.11.0" +description = "library with cross-python path, ini-parsing, io, code, log facilities" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" + +[[package]] +name = "pycodestyle" +version = "2.6.0" +description = "Python style guide checker" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + [[package]] name = "pycparser" version = "2.21" @@ -487,6 +663,14 @@ category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +[[package]] +name = "pyflakes" +version = "2.2.0" +description = "passive checker of Python programs" +category = "dev" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" + [[package]] name = "pyjwt" version = "2.3.0" @@ -501,6 +685,17 @@ dev = ["sphinx", "sphinx-rtd-theme", "zope.interface", "cryptography (>=3.3.1)", docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"] tests 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