diff --git a/.github/workflows/build_and_push_python_image.yml b/.github/workflows/build_and_push_python_image.yml index 9fd8b8b4..e965638d 100644 --- a/.github/workflows/build_and_push_python_image.yml +++ b/.github/workflows/build_and_push_python_image.yml @@ -1,14 +1,14 @@ -name: Build Python Images and Push to Quay and ECR +name: Build and Push python3.9-data-science on: push: paths: - - python3.9-data-science/Dockerfile + - python3.9-data-science/** - .github/workflows/build_and_push_python_image.yml jobs: python_3-9: - name: Python 3.9 Build and Push + name: Build and Push python3.9-data-science uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./python3.9-data-science/Dockerfile" diff --git a/.github/workflows/build_azlinux_jupyter_scipy_image.yml b/.github/workflows/build_azlinux_jupyter_scipy_image.yml index ac934e81..59144ab3 100644 --- a/.github/workflows/build_azlinux_jupyter_scipy_image.yml +++ b/.github/workflows/build_azlinux_jupyter_scipy_image.yml @@ -3,7 +3,7 @@ name: Build and push AmazonLinux jupyter-scipy on: push: paths: - - azlinux-jupyter-scipy/Dockerfile + - azlinux-jupyter-scipy/** - .github/workflows/build_azlinux_jupyter_scipy_image.yml jobs: diff --git a/.github/workflows/build_jupyter_nextflow_image.yml b/.github/workflows/build_jupyter_nextflow_image.yml index abf56048..7d4993c6 100644 --- a/.github/workflows/build_jupyter_nextflow_image.yml +++ b/.github/workflows/build_jupyter_nextflow_image.yml @@ -3,7 +3,7 @@ name: Build and Push Jupyter-Nextflow image on: push: paths: - - jupyter-nextflow + - jupyter-nextflow/** - .github/workflows/build_jupyter_nextflow_image.yml jobs: diff --git a/.github/workflows/build_jupyter_restricted_download_image.yml b/.github/workflows/build_jupyter_restricted_download_image.yml new file mode 100644 index 00000000..d28b2bfa --- /dev/null +++ b/.github/workflows/build_jupyter_restricted_download_image.yml @@ -0,0 +1,22 @@ +name: Build and Push jupyter-restricted-download + +on: + push: + paths: + - jupyter-restricted-download/** + - .github/workflows/build_jupyter_restricted_download_image.yml + +jobs: + jupyter-restricted-download: + name: Build and Push jupyter-restricted-download + uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master + with: + DOCKERFILE_LOCATION: "./jupyter-restricted-download/Dockerfile" + DOCKERFILE_BUILD_CONTEXT: "./jupyter-restricted-download" + OVERRIDE_REPO_NAME: "jupyter-notebook" + OVERRIDE_TAG_NAME: "restricted-download-$(echo ${GITHUB_REF#refs/*/} | tr / _)" + 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 }} diff --git a/.github/workflows/build_vadc_notebook_image.yml b/.github/workflows/build_vadc_notebook_image.yml index b12f4367..da7c92f6 100644 --- a/.github/workflows/build_vadc_notebook_image.yml +++ b/.github/workflows/build_vadc_notebook_image.yml @@ -4,6 +4,7 @@ on: push: paths: - jupyter-vadc/** + - .github/workflows/build_vadc_notebook_image.yml jobs: push-image: diff --git a/.github/workflows/build_vlmd_submission_python_image.yml b/.github/workflows/build_vlmd_submission_python_image.yml index 1d2406ce..cccc08a3 100644 --- a/.github/workflows/build_vlmd_submission_python_image.yml +++ b/.github/workflows/build_vlmd_submission_python_image.yml @@ -1,4 +1,4 @@ -name: Build Python Image and Push to Quay and ECR +name: Build VLMD Image on: push: @@ -8,7 +8,7 @@ on: jobs: ci: - name: Build Image and Push to Quay + name: Build VLMD Image uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: DOCKERFILE_LOCATION: "./vlmd-submission-tools/Dockerfile" diff --git a/jupyter-restricted-download/.env b/jupyter-restricted-download/.env new file mode 100644 index 00000000..a73747cf --- /dev/null +++ b/jupyter-restricted-download/.env @@ -0,0 +1,3 @@ +SERVICE_PORT=9880 +USER_VOLUME=./user-volume +DATA_VOLUME=./data-volume diff --git a/jupyter-restricted-download/Dockerfile b/jupyter-restricted-download/Dockerfile new file mode 100644 index 00000000..259eb219 --- /dev/null +++ b/jupyter-restricted-download/Dockerfile @@ -0,0 +1,95 @@ +ARG ROOT_CONTAINER=quay.io/cdis/ubuntu:focal + +FROM $ROOT_CONTAINER + +LABEL maintainer="Jupyter Project " + +# Fix DL4006 +SHELL ["/bin/bash", "-o", "pipefail", "-c"] + +USER root + +# Install all OS dependencies for the notebook server that starts but lacks all +# features (e.g., download as all possible file formats) +ENV DEBIAN_FRONTEND noninteractive +RUN apt-get update --yes && \ + apt-get install --yes --no-install-recommends \ + python3.9 \ + python3-pip \ + tini \ + wget \ + git \ + curl \ + ca-certificates \ + sudo \ + locales \ + fonts-liberation \ + vim \ + run-one && \ + apt-get clean && rm -rf /var/lib/apt/lists/* && \ + echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \ + locale-gen + +# Set Python 3.9 as the default Python version +RUN ln -s /usr/bin/python3.9 /usr/bin/python + +# Add the Python 3.9 executable path to the PATH environment variable +ENV PATH="/usr/bin/python3.9:$PATH" + +# Upgrade pip to ensure it's associated with Python 3.9.5 +RUN python3.9 -m pip install --upgrade pip + +# Remove /usr/bin/pip3 if it exists +RUN rm -f /usr/bin/pip3 + +# Create a symbolic link from pip3 to pip +RUN ln -s /usr/bin/pip /usr/bin/pip3 + +RUN pip install JPype1 jupyter + +RUN jupyter notebook --generate-config + +# this is where we disable downloads +RUN jupyter labextension disable @jupyterlab/docmanager-extension:download \ + && jupyter labextension disable @jupyterlab/filebrowser-extension:download + +RUN pip install pandas numpy seaborn scipy matplotlib pyNetLogo SALib boto3 awscli --upgrade + +# RUN pip install PyYAML==5.3.1 --upgrade +RUN pip install gen3==4.18.0 --upgrade + +RUN pip install jupyter --upgrade + +RUN pip uninstall nbconvert --yes +# Create a non-root user for Jupyter without copying /bin or /bin/bash +ARG NB_USER=jupyter +ARG NB_UID=1000 +RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER +RUN chown -R $NB_USER:users /home/$NB_USER +RUN chmod -R u+rwx /home/$NB_USER + +# Expose port 8888 for JupyterLab +EXPOSE 8888 + +ARG COVID_TOOLS_BRANCH=master +ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/welcome.html /home/$NB_USER/ +RUN touch /home/$NB_USER/welcome.html + +# Add local files as late as possible to avoid cache busting +COPY start.sh /usr/local/bin/ +COPY start-notebook.sh /usr/local/bin/ +COPY start-singleuser.sh /usr/local/bin/ +RUN chmod +x /usr/local/bin/*.sh + +COPY resources/custom.js /home/$NB_USER/.jupyter/custom/ +COPY resources/jupyter_notebook_config.py /home/$NB_USER/.jupyter/tmp.py +RUN cat /home/$NB_USER/.jupyter/tmp.py >> /home/$NB_USER/.jupyter/jupyter_notebook_config.py && rm /home/$NB_USER/.jupyter/tmp.py + +# Putting this all the way down here, to make sure its the last thing done +# The image can't function with jsonschema version 3.20.0, which some dependency installs +RUN pip install jsonschema==4.20.0 + +# Set the default command to start JupyterLab +USER $NB_USER +WORKDIR /home/$NB_USER +ENTRYPOINT ["jupyter", "lab", "--allow-root", "--ip=0.0.0.0", "--port=8888", "--no-browser"] diff --git a/jupyter-restricted-download/README.md b/jupyter-restricted-download/README.md new file mode 100644 index 00000000..f0d810ea --- /dev/null +++ b/jupyter-restricted-download/README.md @@ -0,0 +1,3 @@ +# jupyter-restricted-download + +A "restricted" build of `jupyter-slim`. Basically the same as `../jupyter-slim/`, but it prevents users from downloading anything from the jupyter lab diff --git a/jupyter-restricted-download/resources/custom.js b/jupyter-restricted-download/resources/custom.js new file mode 100644 index 00000000..2f6d4c13 --- /dev/null +++ b/jupyter-restricted-download/resources/custom.js @@ -0,0 +1,3 @@ +define(['base/js/namespace'], function(Jupyter){ + Jupyter._target = '_self'; +}) diff --git a/jupyter-restricted-download/resources/jupyter_notebook_config.py b/jupyter-restricted-download/resources/jupyter_notebook_config.py new file mode 100644 index 00000000..89d1b20c --- /dev/null +++ b/jupyter-restricted-download/resources/jupyter_notebook_config.py @@ -0,0 +1,3 @@ +c.NotebookApp.tornado_settings = { + "headers": {"Content-Security-Policy": "frame-ancestors 'self'"} +} diff --git a/jupyter-restricted-download/start-notebook.sh b/jupyter-restricted-download/start-notebook.sh new file mode 100644 index 00000000..d028cfd6 --- /dev/null +++ b/jupyter-restricted-download/start-notebook.sh @@ -0,0 +1,7 @@ +#!/bin/bash +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +set -e + +. /usr/local/bin/start.sh jupyter notebook --no-browser --port 8888 --ip=* --NotebookApp.token='' --NotebookApp.disable_check_xsrf=True $* diff --git a/jupyter-restricted-download/start-singleuser.sh b/jupyter-restricted-download/start-singleuser.sh new file mode 100644 index 00000000..09c1d695 --- /dev/null +++ b/jupyter-restricted-download/start-singleuser.sh @@ -0,0 +1,43 @@ +#!/bin/bash +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +set -e + +# set default ip to 0.0.0.0 +if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then + NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS" +fi + +# handle some deprecated environment variables +# from DockerSpawner < 0.8. +# These won't be passed from DockerSpawner 0.9, +# so avoid specifying --arg=empty-string +if [ ! -z "$NOTEBOOK_DIR" ]; then + NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS" +fi +if [ ! -z "$JPY_PORT" ]; then + NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS" +fi +if [ ! -z "$JPY_USER" ]; then + NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS" +fi +if [ ! -z "$JPY_COOKIE_NAME" ]; then + NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS" +fi +if [ ! -z "$JPY_BASE_URL" ]; then + NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS" +fi +if [ ! -z "$JPY_HUB_PREFIX" ]; then + NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS" +fi +if [ ! -z "$JPY_HUB_API_URL" ]; then + NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS" +fi +if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then + NOTEBOOK_BIN="jupyter labhub" +else + NOTEBOOK_BIN=jupyterhub-singleuser +fi + +. /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS $@ diff --git a/jupyter-restricted-download/start.sh b/jupyter-restricted-download/start.sh new file mode 100644 index 00000000..f3c3a67f --- /dev/null +++ b/jupyter-restricted-download/start.sh @@ -0,0 +1,25 @@ +#!/bin/bash +# Copyright (c) Jupyter Development Team. +# Distributed under the terms of the Modified BSD License. + +set -e + +# Handle special flags if we're root +if [ $UID == 0 ] ; then + # Change UID of NB_USER to NB_UID if it does not match + if [ "$NB_UID" != $(id -u $NB_USER) ] ; then + usermod -u $NB_UID $NB_USER + chown -R $NB_UID $CONDA_DIR . + fi + + # Enable sudo if requested + if [ ! -z "$GRANT_SUDO" ]; then + echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook #pragma: allowlist secret + fi + + # Exec the command as NB_USER + exec su $NB_USER -c "env PATH=$PATH $*" +else + # Exec the command + exec $* +fi