From 16aa5b423ed4a7e6c6c8890aa5dd7750871dbb6a Mon Sep 17 00:00:00 2001 From: Jawad Qureshi Date: Wed, 4 Sep 2024 15:59:53 -0500 Subject: [PATCH 1/9] Add new AL2 based image and gunicorn --- .gitignore | 1 - .secrets.baseline | 41 +- Dockerfile | 134 +-- deployment/nginx/nginx.conf | 44 + deployment/uwsgi/uwsgi.ini | 37 - deployment/wsgi/gunicorn.conf.py | 9 + deployment/{uwsgi => wsgi}/wsgi.py | 0 dockerrun.bash | 5 +- fence/jwt/keys.py | 21 +- keys/key/README.md | 1 + poetry.lock | 1220 +++++++++++++++------------- pyproject.toml | 3 +- 12 files changed, 803 insertions(+), 713 deletions(-) create mode 100644 deployment/nginx/nginx.conf delete mode 100644 deployment/uwsgi/uwsgi.ini create mode 100644 deployment/wsgi/gunicorn.conf.py rename deployment/{uwsgi => wsgi}/wsgi.py (100%) create mode 100644 keys/key/README.md diff --git a/.gitignore b/.gitignore index 4a76c3a3e..c760e0ad2 100644 --- a/.gitignore +++ b/.gitignore @@ -102,7 +102,6 @@ ENV/ .mypy_cache/ # jwt keys -keys tests/resources/keys/*.pem .DS_Store diff --git a/.secrets.baseline b/.secrets.baseline index 82a2c6b2a..469ed8bfc 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -115,13 +115,13 @@ } ], "results": { - ".github/workflows/ci.yaml": [ + ".github/workflows/buildpipeline.yaml": [ { "type": "Secret Keyword", - "filename": ".github/workflows/ci.yaml", + "filename": ".github/workflows/buildpipeline.yaml", "hashed_secret": "3e26d6750975d678acb8fa35a0f69237881576b0", "is_verified": false, - "line_number": 13 + "line_number": 17 } ], "deployment/scripts/postgresql/postgresql_init.sql": [ @@ -210,22 +210,13 @@ "line_number": 137 } ], - "fence/resources/storage/storageclient/cleversafe.py": [ - { - "type": "Secret Keyword", - "filename": "fence/resources/storage/storageclient/cleversafe.py", - "hashed_secret": "7cb6efb98ba5972a9b5090dc2e517fe14d12cb04", - "is_verified": false, - "line_number": 274 - } - ], "fence/utils.py": [ { "type": "Secret Keyword", "filename": "fence/utils.py", "hashed_secret": "8318df9ecda039deac9868adf1944a29a95c7114", "is_verified": false, - "line_number": 129 + "line_number": 128 } ], "migrations/versions/a04a70296688_non_unique_client_name.py": [ @@ -268,14 +259,14 @@ "filename": "tests/conftest.py", "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9", "is_verified": false, - "line_number": 1570 + "line_number": 1556 }, { "type": "Base64 High Entropy String", "filename": "tests/conftest.py", "hashed_secret": "227dea087477346785aefd575f91dd13ab86c108", "is_verified": false, - "line_number": 1594 + "line_number": 1579 } ], "tests/credentials/google/test_credentials.py": [ @@ -394,24 +385,6 @@ "line_number": 300 } ], - "tests/storageclient/storage_client_mock.py": [ - { - "type": "Secret Keyword", - "filename": "tests/storageclient/storage_client_mock.py", - "hashed_secret": "37bbea9557f9efd1eeadb25dda9ab6514f08fde9", - "is_verified": false, - "line_number": 158 - } - ], - "tests/storageclient/test_cleversafe_api_client.py": [ - { - "type": "Secret Keyword", - "filename": "tests/storageclient/test_cleversafe_api_client.py", - "hashed_secret": "f683c485d521c2e45830146dd570111770baea29", - "is_verified": false, - "line_number": 130 - } - ], "tests/test-fence-config.yaml": [ { "type": "Basic Auth Credentials", @@ -422,5 +395,5 @@ } ] }, - "generated_at": "2024-08-22T19:43:39Z" + "generated_at": "2023-10-20T20:37:17Z" } diff --git a/Dockerfile b/Dockerfile index f103e44f9..51d8a8ba6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,56 +1,86 @@ -# To run: docker run --rm -d -v /path/to/fence-config.yaml:/var/www/fence/fence-config.yaml --name=fence -p 80:80 fence -# To check running container do: docker exec -it fence /bin/bash +ARG AZLINUX_BASE_VERSION=master -FROM quay.io/cdis/python:python3.9-buster-2.0.0 +# Base stage with python-build-base +FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} as base + +# Comment this in, and comment out the line above, if quay is down +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base ENV appname=fence +ENV POETRY_NO_INTERACTION=1 \ + POETRY_VIRTUALENVS_IN_PROJECT=1 \ + POETRY_VIRTUALENVS_CREATE=1 + +WORKDIR /${appname} + +# create gen3 user +# Create a group 'gen3' with GID 1000 and a user 'gen3' with UID 1000 +RUN groupadd -g 1000 gen3 && \ + useradd -m -s /bin/bash -u 1000 -g gen3 gen3 && \ + chown -R gen3:gen3 /$appname && \ + mkdir -p /var/www/$appname && \ + chown -R gen3:gen3 /var/www/$appname && \ + chown -R gen3:gen3 /venv + + +# Builder stage +FROM base as builder + +USER gen3 + + +RUN python -m venv /venv + + +COPY poetry.lock pyproject.toml /${appname}/ + +RUN pip install poetry && \ + poetry install -vv --only main --no-interaction + +COPY --chown=gen3:gen3 . /$appname +COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py + +# Run poetry again so this app itself gets installed too +RUN poetry install --without dev --no-interaction + +RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \ + && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py + +# Final stage +FROM base + +COPY --from=builder /venv /venv +COPY --from=builder /$appname /$appname + +# install tar +RUN yum install tar -y + +# install nginx +RUN yum install nginx -y + +RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx + +# chown nginx directories +RUN chown -R gen3:gen3 /var/log/nginx + +# pipe nginx logs to stdout and stderr +RUN ln -sf /dev/stdout /var/log/nginx/access.log && ln -sf /dev/stderr /var/log/nginx/error.log + +# create /var/lib/nginx/tmp/client_body to allow nginx to write to fence +RUN mkdir -p /var/lib/nginx/tmp/client_body +RUN chown -R gen3:gen3 /var/lib/nginx/ + +# copy nginx config +COPY ./deployment/nginx/nginx.conf /etc/nginx/nginx.conf + + +# Switch to non-root user 'gen3' for the serving process +USER gen3 + +RUN source /venv/bin/activate + +ENV PYTHONUNBUFFERED=1 \ +PYTHONIOENCODING=UTF-8 + -RUN pip install --upgrade pip -RUN pip install --upgrade poetry -RUN apt-get update \ - && apt-get install -y --no-install-recommends curl bash git \ - && apt-get -y install vim \ - libmcrypt4 mcrypt \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/ - -RUN mkdir -p /var/www/$appname \ - && mkdir -p /var/www/.cache/Python-Eggs/ \ - && mkdir /run/nginx/ \ - && ln -sf /dev/stdout /var/log/nginx/access.log \ - && ln -sf /dev/stderr /var/log/nginx/error.log \ - && chown nginx -R /var/www/.cache/Python-Eggs/ \ - && chown nginx /var/www/$appname - -# aws cli v2 - needed for storing files in s3 during usersync k8s job -RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" \ - && unzip awscliv2.zip \ - && ./aws/install \ - && /bin/rm -rf awscliv2.zip ./aws - -WORKDIR /$appname - -# copy ONLY poetry artifact, install the dependencies but not fence -# this will make sure than the dependencies is cached -COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-root --no-dev --no-interaction \ - && poetry show -v - -# copy source code ONLY after installing dependencies -COPY . /$appname -COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini -COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py -COPY clear_prometheus_multiproc /$appname/clear_prometheus_multiproc - -# install fence -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-dev --no-interaction \ - && poetry show -v - -RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \ - && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py - -WORKDIR /var/www/$appname - -CMD ["sh","-c","bash /fence/dockerrun.bash && /dockerrun.sh"] +CMD ["/fence/dockerrun.bash"] diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf new file mode 100644 index 000000000..c64485a90 --- /dev/null +++ b/deployment/nginx/nginx.conf @@ -0,0 +1,44 @@ +user gen3; +worker_processes auto; +error_log /var/log/nginx/error.log notice; +pid /var/lib/nginx/nginx.pid; + +# Load dynamic modules. See /usr/share/doc/nginx/README.dynamic. +include /usr/share/nginx/modules/*.conf; + +events { + worker_connections 1024; +} + +http { + log_format main '$remote_addr - $remote_user [$time_local] "$request" ' + '$status $body_bytes_sent "$http_referer" ' + '"$http_user_agent" "$http_x_forwarded_for"'; + + access_log /var/log/nginx/access.log main; + + sendfile on; + tcp_nopush on; + keepalive_timeout 65; + types_hash_max_size 4096; + + include /etc/nginx/mime.types; + default_type application/octet-stream; + + # Load modular configuration files from the /etc/nginx/conf.d directory. + # See http://nginx.org/en/docs/ngx_core_module.html#include + # for more information. + include /etc/nginx/conf.d/*.conf; + + server { + + listen 80; + server_name localhost; + + location / { + proxy_pass http://127.0.0.1:8000; + proxy_set_header Host $host; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + } + } +} diff --git a/deployment/uwsgi/uwsgi.ini b/deployment/uwsgi/uwsgi.ini deleted file mode 100644 index 0ebedb7ce..000000000 --- a/deployment/uwsgi/uwsgi.ini +++ /dev/null @@ -1,37 +0,0 @@ -[uwsgi] -protocol = uwsgi -socket = /var/run/gen3/uwsgi.sock -buffer-size = 32768 -uid = nginx -gid = nginx -chown-socket = nginx:nginx -chmod-socket = 666 -master = true -harakiri-verbose = true -# No global HARAKIRI, using only user HARAKIRI, because export overwrites it -# Cannot overwrite global HARAKIRI with user's: https://git.io/fjYuD -# harakiri = 45 -http-timeout = 45 -socket-timeout = 45 -worker-reload-mercy = 45 -reload-mercy = 45 -mule-reload-mercy = 45 -disable-logging = true -wsgi-file=/fence/wsgi.py -plugins = python3 -vacuum = true -pythonpath = /var/www/fence/ -pythonpath = /fence/ -# poetry installs git dependencies at /usr/local/src -pythonpath = /usr/local/src/* - -# metrics setup -stats = 127.0.0.1:9191 -stats-http = true -env = prometheus_multiproc_dir=/var/tmp/uwsgi_flask_metrics -exec-asap = /fence/clear_prometheus_multiproc /var/tmp/uwsgi_flask_metrics - -# Initialize application in worker processes, not master. This prevents the -# workers from all trying to open the same database connections at startup. -lazy = true -lazy-apps = true diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py new file mode 100644 index 000000000..1eaa94a1e --- /dev/null +++ b/deployment/wsgi/gunicorn.conf.py @@ -0,0 +1,9 @@ +wsgi_app = "deployment.wsgi.wsgi:application" +bind = "0.0.0.0:8000" +workers = 4 +preload_app = True +user = "gen3" +group = "gen3" +timeout = 300 +keepalive = 2 +keepalive_timeout = 5 diff --git a/deployment/uwsgi/wsgi.py b/deployment/wsgi/wsgi.py similarity index 100% rename from deployment/uwsgi/wsgi.py rename to deployment/wsgi/wsgi.py diff --git a/dockerrun.bash b/dockerrun.bash index ce7150731..9c9a67313 100755 --- a/dockerrun.bash +++ b/dockerrun.bash @@ -4,7 +4,7 @@ # Update certificate authority index - # environment may have mounted more authorities # -update-ca-certificates +# update-ca-certificates # # Kubernetes may mount jwt-keys as a tar ball # @@ -15,6 +15,9 @@ if [ -f /fence/jwt-keys.tar ]; then if [ -d jwt-keys ]; then mkdir -p keys mv jwt-keys/* keys/ + rm -rf /fence/keys/key/ fi ) fi +nginx +gunicorn -c /fence/deployment/wsgi/gunicorn.conf.py diff --git a/fence/jwt/keys.py b/fence/jwt/keys.py index d08e9d5f0..f423362fb 100644 --- a/fence/jwt/keys.py +++ b/fence/jwt/keys.py @@ -148,13 +148,26 @@ def from_directory(cls, keys_dir, naming_function=None): prv_filepath = os.path.join(keys_dir, "jwt_private_key.pem") if not os.path.isfile(pub_filepath): - raise EnvironmentError( - "missing public key file; expected file to exist: " + pub_filepath - ) + # Generate public key from private key + with open(prv_filepath, "r") as f: + private_key_file = f.read() + private_key = serialization.load_pem_private_key( + bytes(private_key_file, "utf-8"), + password=None, + backend=default_backend(), + ) + public_key = private_key.public_key() + public_key = public_key.public_bytes( + encoding=serialization.Encoding.PEM, + format=serialization.PublicFormat.SubjectPublicKeyInfo, + ) + public_key = public_key.decode("utf-8") + with open(pub_filepath, "w") as f: + f.write(public_key) if not os.path.isfile(prv_filepath): raise EnvironmentError( - "missing public key file; expected file to exist: " + prv_filepath + "missing private key file; expected file to exist: " + prv_filepath ) with open(pub_filepath, "r") as f: diff --git a/keys/key/README.md b/keys/key/README.md new file mode 100644 index 000000000..cdfd6f26e --- /dev/null +++ b/keys/key/README.md @@ -0,0 +1 @@ +# Need this folder for permission reasons inside the container diff --git a/poetry.lock b/poetry.lock index a91239b85..9e8fde43d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 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 = "addict" @@ -13,13 +13,13 @@ files = [ [[package]] name = "alembic" -version = "1.13.2" +version = "1.12.1" description = "A database migration tool for SQLAlchemy." optional = false -python-versions = ">=3.8" +python-versions = ">=3.7" files = [ - {file = "alembic-1.13.2-py3-none-any.whl", hash = "sha256:6b8733129a6224a9a711e17c99b08462dbf7cc9670ba8f2e2ae9af860ceb1953"}, - {file = "alembic-1.13.2.tar.gz", hash = "sha256:1ff0ae32975f4fd96028c39ed9bb3c867fe3af956bd7bb37343b54c9fe7445ef"}, + {file = "alembic-1.12.1-py3-none-any.whl", hash = "sha256:47d52e3dfb03666ed945becb723d6482e52190917fdb47071440cfdba05d92cb"}, + {file = "alembic-1.12.1.tar.gz", hash = "sha256:bca5877e9678b454706347bc10b97cb7d67f300320fa5c3a94423e8266e2823f"}, ] [package.dependencies] @@ -28,7 +28,7 @@ SQLAlchemy = ">=1.3.0" typing-extensions = ">=4" [package.extras] -tz = ["backports.zoneinfo"] +tz = ["python-dateutil"] [[package]] name = "aniso8601" @@ -46,25 +46,24 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] [[package]] name = "anyio" -version = "4.4.0" +version = "4.0.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, - {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, + {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, + {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" -typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (>=0.23)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.22)"] [[package]] name = "atomicwrites" @@ -78,22 +77,21 @@ files = [ [[package]] name = "attrs" -version = "24.2.0" +version = "23.1.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, - {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, + {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, + {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, ] [package.extras] -benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"] -tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[docs,tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] [[package]] name = "authlib" @@ -151,17 +149,17 @@ wrapt = "*" [[package]] name = "azure-core" -version = "1.30.2" +version = "1.29.5" description = "Microsoft Azure Core Library for Python" optional = false -python-versions = ">=3.8" +python-versions = ">=3.7" files = [ - {file = "azure-core-1.30.2.tar.gz", hash = "sha256:a14dc210efcd608821aa472d9fb8e8d035d29b68993819147bc290a8ac224472"}, - {file = "azure_core-1.30.2-py3-none-any.whl", hash = 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insertions(+), 712 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9e8fde43d..a4f9e5464 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[package]] name = "alembic" -version = "1.12.1" +version = "1.13.2" description = "A database migration tool for SQLAlchemy." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "alembic-1.12.1-py3-none-any.whl", hash = "sha256:47d52e3dfb03666ed945becb723d6482e52190917fdb47071440cfdba05d92cb"}, - {file = "alembic-1.12.1.tar.gz", hash = "sha256:bca5877e9678b454706347bc10b97cb7d67f300320fa5c3a94423e8266e2823f"}, + {file = "alembic-1.13.2-py3-none-any.whl", hash = "sha256:6b8733129a6224a9a711e17c99b08462dbf7cc9670ba8f2e2ae9af860ceb1953"}, + {file = "alembic-1.13.2.tar.gz", hash = "sha256:1ff0ae32975f4fd96028c39ed9bb3c867fe3af956bd7bb37343b54c9fe7445ef"}, ] [package.dependencies] @@ -28,7 +28,7 @@ SQLAlchemy = ">=1.3.0" typing-extensions = ">=4" [package.extras] -tz = 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9883f051c2a5c7b01b4c3a1059b25032adb443e3 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 6 Sep 2024 09:52:18 -0600 Subject: [PATCH 3/9] updating the command --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 51d8a8ba6..ed075b26d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -83,4 +83,4 @@ ENV PYTHONUNBUFFERED=1 \ PYTHONIOENCODING=UTF-8 -CMD ["/fence/dockerrun.bash"] +CMD ["/bin/bash", "-c", "/fence/dockerrun.bash"] From 0238816ec58deb952b5e3b56d12b591aaea47949 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Wed, 16 Oct 2024 14:55:25 -0600 Subject: [PATCH 4/9] updating poetry lock --- poetry.lock | 802 +++++++++++++++++++++++++++------------------------- 1 file changed, 418 insertions(+), 384 deletions(-) diff --git a/poetry.lock b/poetry.lock index 64d874af5..6ec7abcbf 100644 --- a/poetry.lock +++ b/poetry.lock @@ 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[[package]] @@ -2287,13 +2321,13 @@ pyasn1 = ">=0.1.3" [[package]] name = "s3transfer" -version = "0.10.2" +version = "0.10.3" description = "An Amazon S3 Transfer Manager" optional = false python-versions = ">=3.8" files = [ - {file = "s3transfer-0.10.2-py3-none-any.whl", hash = "sha256:eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69"}, - {file = "s3transfer-0.10.2.tar.gz", hash = "sha256:0711534e9356d3cc692fdde846b4a1e4b0cb6519971860796e6bc4c7aea00ef6"}, + {file = "s3transfer-0.10.3-py3-none-any.whl", hash = "sha256:263ed587a5803c6c708d3ce44dc4dfedaab4c1a32e8329bab818933d79ddcf5d"}, + {file = "s3transfer-0.10.3.tar.gz", hash = "sha256:4f50ed74ab84d474ce614475e0b8d5047ff080810aac5d01ea25231cfc944b0c"}, ] [package.dependencies] @@ -2409,13 +2443,13 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "urllib3" -version = "2.2.2" +version = "2.2.3" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" files = [ - {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, - {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, + {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"}, + {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"}, ] [package.extras] @@ -2553,24 +2587,24 @@ email = ["email-validator"] [[package]] name = "xmltodict" -version = "0.13.0" +version = "0.14.2" description = "Makes working with XML feel like you are working with JSON" optional = false -python-versions = ">=3.4" +python-versions = ">=3.6" files = [ - {file = "xmltodict-0.13.0-py2.py3-none-any.whl", hash = "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"}, - {file = "xmltodict-0.13.0.tar.gz", hash = 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`user.yaml` file is one way to get authorization information into Gen3. It is ingested via [Fence's `usersync` script](usersync.md). The format of this file is tightly coupled with the notions of resource, role and policy as defined by Gen3's policy engine, [Arborist](https://github.com/uc-cdis/arborist#arborist). -For Gen3 Data Commons that do not use Arborist or that use the Google Data Access method of [Google Service Account Registration](https://github.com/uc-cdis/fence/blob/master/docs/google_architecture.md#google-account-linking-and-service-account-registration), refer to the [Deprecated format](#deprecated-format) section. +For Gen3 Data Commons that do not use Arborist or that use the Google Data Access method of [Google Service Account Registration](https://github.com/uc-cdis/fence/blob/master/docs/additional_documentation/google_architecture.md#google-account-linking-and-service-account-registration), refer to the [Deprecated format](#deprecated-format) section. In a fully deployed Gen3 Commons using [Cloud Automation](https://github.com/uc-cdis/cloud-automation), the `user.yaml` file is usually hosted in S3 and configured via the `global.useryaml_s3path` setting of the Gen3 Data Commons manifest: ``` From 0fe5859071cabece31b2c836c237d6cfef213d44 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Thu, 17 Oct 2024 10:10:12 -0600 Subject: [PATCH 6/9] fixing deadlinks --- docs/additional_documentation/fence_create.md | 2 +- docs/additional_documentation/setup.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/additional_documentation/fence_create.md b/docs/additional_documentation/fence_create.md index 398544f98..db2b735f3 100644 --- a/docs/additional_documentation/fence_create.md +++ b/docs/additional_documentation/fence_create.md @@ -53,7 +53,7 @@ curl --request POST https://FENCE_URL/oauth2/token?grant_type=client_credentials The optional `--expires-in` parameter allows specifying the number of *days* until this client expires. The recommendation is to rotate credentials with the `client_credentials` grant at least once a year (see [Rotate client credentials](#rotate-client-credentials) section). -NOTE: In Gen3, you can grant specific access to a client the same way you would to a user. See the [user.yaml guide](https://github.com/uc-cdis/fence/blob/master/docs/user.yaml_guide.md) for more details. +NOTE: In Gen3, you can grant specific access to a client the same way you would to a user. See the [user.yaml guide](https://github.com/uc-cdis/fence/blob/master/docs/additional_documentation/user.yaml_guide.md) for more details. NOTE: Client credentials tokens are not linked to a user (the claims contain no `sub` or `context.user.name` like other tokens). Some Gen3 endpoints that assume the token is linked to a user, or whose logic require there being a user, do not support them. For an example of how to adapt an endpoint to support client credentials tokens, see [here](https://github.com/uc-cdis/requestor/commit/a5078fae27fa258ac78045cf2bb89cb2104f53cf). For an example of how to explicitly reject client credentials tokens, see [here](https://github.com/uc-cdis/requestor/commit/0f4974c25343d2185c7cdb48dcdeb58f97800672). diff --git a/docs/additional_documentation/setup.md b/docs/additional_documentation/setup.md index 5dcafc37b..0997e7448 100644 --- a/docs/additional_documentation/setup.md +++ b/docs/additional_documentation/setup.md @@ -154,4 +154,4 @@ saved by the OAuth client to use with ## Quickstart with Helm You can now deploy individual services via Helm! -Please refer to the Helm quickstart guide HERE (https://github.com/uc-cdis/fence/blob/master/docs/quickstart_helm.md) +Please refer to the Helm quickstart guide HERE (https://github.com/uc-cdis/fence/blob/master/docs/additional_documentation/quickstart_helm.md) From 6708a844c6224b18ef7f5a6bb2c0bf56a4348763 Mon Sep 17 00:00:00 2001 From: EliseCastle23 <109446148+EliseCastle23@users.noreply.github.com> Date: Fri, 18 Oct 2024 13:36:24 -0600 Subject: [PATCH 7/9] fixing case --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index ed075b26d..49c248112 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ ARG AZLINUX_BASE_VERSION=master # Base stage with python-build-base -FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} as base +FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} AS base # Comment this in, and comment out the line above, if quay is down # FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base @@ -24,7 +24,7 @@ RUN groupadd -g 1000 gen3 && \ # Builder stage -FROM base as builder +FROM base AS builder USER gen3 From 2031c749a5fb29002048d4e1e1ee26e88c3deb41 Mon Sep 17 00:00:00 2001 From: Alexander VanTol Date: Fri, 1 Nov 2024 14:29:13 -0500 Subject: [PATCH 8/9] feat(docker): update to use new base image --- Dockerfile | 87 +++++++++----------------------- deployment/fence.conf | 19 ------- deployment/nginx/nginx.conf | 44 ---------------- deployment/wsgi/gunicorn.conf.py | 2 +- dockerrunshib.bash | 24 --------- keys/key/README.md | 1 - 6 files changed, 26 insertions(+), 151 deletions(-) delete mode 100644 deployment/fence.conf delete mode 100644 deployment/nginx/nginx.conf delete mode 100755 dockerrunshib.bash delete mode 100644 keys/key/README.md diff --git a/Dockerfile b/Dockerfile index 49c248112..a2762ecce 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,86 +1,49 @@ -ARG AZLINUX_BASE_VERSION=master +# To build: docker build -t fence:latest . +# To run interactive: +# docker run -v ~/.gen3/fence/fence-config.yaml:/var/www/fence/fence-config.yaml -v ./keys/:/fence/keys/ fence:latest +# To check running container do: docker exec -it CONTAINER bash -# Base stage with python-build-base -FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} AS base +ARG AZLINUX_BASE_VERSION=feat_python-nginx + +# ------ Base stage ------ +FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base # Comment this in, and comment out the line above, if quay is down -# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-nginx-al:${AZLINUX_BASE_VERSION} as base ENV appname=fence -ENV POETRY_NO_INTERACTION=1 \ - POETRY_VIRTUALENVS_IN_PROJECT=1 \ - POETRY_VIRTUALENVS_CREATE=1 WORKDIR /${appname} -# create gen3 user -# Create a group 'gen3' with GID 1000 and a user 'gen3' with UID 1000 -RUN groupadd -g 1000 gen3 && \ - useradd -m -s /bin/bash -u 1000 -g gen3 gen3 && \ - chown -R gen3:gen3 /$appname && \ - mkdir -p /var/www/$appname && \ - chown -R gen3:gen3 /var/www/$appname && \ - chown -R gen3:gen3 /venv - +RUN chown -R gen3:gen3 /${appname} -# Builder stage +# ------ Builder stage ------ FROM base AS builder -USER gen3 - - -RUN python -m venv /venv - - +# Install just the deps without the code as it's own step to avoid redoing this on code changes COPY poetry.lock pyproject.toml /${appname}/ +RUN poetry install -vv --only main --no-interaction -RUN pip install poetry && \ - poetry install -vv --only main --no-interaction - +# Move app files into working directory COPY --chown=gen3:gen3 . /$appname COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py -# Run poetry again so this app itself gets installed too -RUN poetry install --without dev --no-interaction +# Do the install again incase the app itself needs install +RUN poetry install -vv --only main --no-interaction + +ENV PATH="$(poetry env info --path)/bin:$PATH" +# Setup version info RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \ && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py -# Final stage -FROM base - -COPY --from=builder /venv /venv -COPY --from=builder /$appname /$appname - # install tar -RUN yum install tar -y +# RUN yum install tar -y +# do we need to untar jwt-keys? -# install nginx -RUN yum install nginx -y - -RUN setcap 'cap_net_bind_service=+ep' /usr/sbin/nginx - -# chown nginx directories -RUN chown -R gen3:gen3 /var/log/nginx - -# pipe nginx logs to stdout and stderr -RUN ln -sf /dev/stdout /var/log/nginx/access.log && ln -sf /dev/stderr /var/log/nginx/error.log - -# create /var/lib/nginx/tmp/client_body to allow nginx to write to fence -RUN mkdir -p /var/lib/nginx/tmp/client_body -RUN chown -R gen3:gen3 /var/lib/nginx/ - -# copy nginx config -COPY ./deployment/nginx/nginx.conf /etc/nginx/nginx.conf - - -# Switch to non-root user 'gen3' for the serving process -USER gen3 - -RUN source /venv/bin/activate - -ENV PYTHONUNBUFFERED=1 \ -PYTHONIOENCODING=UTF-8 +# ------ Final stage ------ +FROM base +COPY --chown=gen3:gen3 --from=builder /$appname /$appname -CMD ["/bin/bash", "-c", "/fence/dockerrun.bash"] +CMD ["poetry", "run", "gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] diff --git a/deployment/fence.conf b/deployment/fence.conf deleted file mode 100644 index 03c5d6812..000000000 --- a/deployment/fence.conf +++ /dev/null @@ -1,19 +0,0 @@ - - WSGIDaemonProcess /fence processes=2 threads=4 python-path=/var/www/fence/:/fence/:/usr/bin/python - WSGIScriptAlias / /var/www/fence/wsgi.py - WSGIPassAuthorization On - - WSGIProcessGroup /fence - WSGIApplicationGroup %{GLOBAL} - Options +ExecCGI - Order deny,allow - Allow from all - - ErrorLog ${APACHE_LOG_DIR}/error.log - LogLevel info - LogFormat "%{X-Forwarded-For}i %l %{X-UserId}i %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-agent}i\"" aws - LogFormat "{\"gen3log\": \"apache2\", \"date_access\": \"%t\", \"user_id\": \"%{X-UserId}i\", \"request_id\": \"%{X-ReqId}i\", \"session_id\": \"%{X-SessionId}i\", \"visitor_id\": \"%{X-VisitorId}i\", \"network_client_ip\": \"%{X-Forwarded-For}i\", \"network_bytes_write\": \"%b\", \"http_response_time\": \"%T\", \"http_status_code\": \"%>s\", \"http_request\": \"%U\", \"http_verb\": \"%m\", \"http_referer\": \"%{Referer}i\", \"http_useragent\": \"%{User-agent}i\", \"message\": \"%r\"}" json - SetEnvIf X-Forwarded-For "^..*" forwarded - #CustomLog ${APACHE_LOG_DIR}/access.log combined env=!forwarded - CustomLog ${APACHE_LOG_DIR}/access.log json - diff --git a/deployment/nginx/nginx.conf b/deployment/nginx/nginx.conf deleted file mode 100644 index c64485a90..000000000 --- a/deployment/nginx/nginx.conf +++ /dev/null @@ -1,44 +0,0 @@ -user gen3; -worker_processes auto; -error_log /var/log/nginx/error.log notice; -pid /var/lib/nginx/nginx.pid; - -# Load dynamic modules. See /usr/share/doc/nginx/README.dynamic. -include /usr/share/nginx/modules/*.conf; - -events { - worker_connections 1024; -} - -http { - log_format main '$remote_addr - $remote_user [$time_local] "$request" ' - '$status $body_bytes_sent "$http_referer" ' - '"$http_user_agent" "$http_x_forwarded_for"'; - - access_log /var/log/nginx/access.log main; - - sendfile on; - tcp_nopush on; - keepalive_timeout 65; - types_hash_max_size 4096; - - include /etc/nginx/mime.types; - default_type application/octet-stream; - - # Load modular configuration files from the /etc/nginx/conf.d directory. - # See http://nginx.org/en/docs/ngx_core_module.html#include - # for more information. - include /etc/nginx/conf.d/*.conf; - - server { - - listen 80; - server_name localhost; - - location / { - proxy_pass http://127.0.0.1:8000; - proxy_set_header Host $host; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - } - } -} diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py index 1eaa94a1e..64092ba3d 100644 --- a/deployment/wsgi/gunicorn.conf.py +++ b/deployment/wsgi/gunicorn.conf.py @@ -1,6 +1,6 @@ wsgi_app = "deployment.wsgi.wsgi:application" bind = "0.0.0.0:8000" -workers = 4 +workers = 1 preload_app = True user = "gen3" group = "gen3" diff --git a/dockerrunshib.bash b/dockerrunshib.bash deleted file mode 100755 index 1ad35e65b..000000000 --- a/dockerrunshib.bash +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# -# Update certificate authority index - -# environment may have mounted more authorities -# -update-ca-certificates -# -# Kubernetes may mount jwt-keys as a tar ball -# -if [ -f /fence/jwt-keys.tar ]; then - ( - cd /fence - tar xvf jwt-keys.tar - if [ -d jwt-keys ]; then - mkdir -p keys - mv jwt-keys/* keys/ - fi - ) -fi -service shibd start -sed -i "s/ServerName SERVERNAME/ServerName https:\/\/$HOSTNAME/g" /etc/apache2/sites-available/fence.conf -rm -rf /var/run/apache2/apache2.pid -/usr/sbin/apache2ctl -D FOREGROUND diff --git a/keys/key/README.md b/keys/key/README.md deleted file mode 100644 index cdfd6f26e..000000000 --- a/keys/key/README.md +++ /dev/null @@ -1 +0,0 @@ -# Need this folder for permission reasons inside the container From cc0e908465826365c88edac030cc8d33afcb1922 Mon Sep 17 00:00:00 2001 From: Alexander VanTol Date: Fri, 8 Nov 2024 11:02:36 -0600 Subject: [PATCH 9/9] feat(mcrypt): add wip work to have 2 images --- .github/workflows/ci.yaml | 25 +++++++++++++++++++++---- DockerfileMcrypt | 1 + 2 files changed, 22 insertions(+), 4 deletions(-) create mode 100644 DockerfileMcrypt diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 9d7ab6592..96b8db5d5 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -10,7 +10,7 @@ jobs: Security: name: Security Pipeline uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master - secrets: inherit + secrets: inherit # pragma: allowlist secret UnitTest: name: Python Unit Test with Postgres @@ -19,13 +19,30 @@ jobs: python-version: '3.9' test-script: 'tests/ci_commands_script.sh' run-coveralls: true - ci: + + BuildImageAndPush: + name: Build Image and Push + needs: Security + # https://github.com/uc-cdis/.github/blob/master/.github/workflows/image_build_push.yaml + uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master + secrets: + ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} + ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} + QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} + QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} + + # I did not test that this works + BuildMcryptImageAndPush: name: Build Image and Push - # TODO Uncomment after PXP-9212 - # needs: Security + needs: Security + # https://github.com/uc-cdis/.github/blob/master/.github/workflows/image_build_push.yaml uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master secrets: ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }} QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }} + # we can either use the repo name or +# OVERRIDE_REPO_NAME: fenceMcrypt + OVERRIDE_TAG_NAME: "mcrypt_$(echo ${GITHUB_REF#refs/*/} | tr / _)" + DOCKERFILE_LOCATION: "./DockerfileMcrypt" diff --git a/DockerfileMcrypt b/DockerfileMcrypt new file mode 100644 index 000000000..383c07bbf --- /dev/null +++ b/DockerfileMcrypt @@ -0,0 +1 @@ +# old Dockerfile