Merge branch 'master' into chore/get-stata-license-from-sidecar

.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"

.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:

.github/workflows/build_jupyter_covid19_image.yml

@@ -0,0 +1,22 @@
+name: Build and Push jupyter-covid19
+
+on:
+  push:
+    paths:
+    - jupyter-covid19/**
+    - .github/workflows/build_jupyter_covid19_image.yml
+
+jobs:
+  jupyter-covid19:
+    name: Build and Push jupyter-covid19
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      DOCKERFILE_LOCATION: "./jupyter-covid19/Dockerfile"
+      DOCKERFILE_BUILD_CONTEXT: "./jupyter-covid19"
+      OVERRIDE_REPO_NAME: "jupyter-notebook"
+      OVERRIDE_TAG_NAME: "covid19-$(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 }}

.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:

.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 }}

.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:

.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"

jupyter-covid19/Dockerfile

@@ -1,100 +1,106 @@
-FROM quay.io/cdis/jupyter-notebook:1.1.0
+FROM quay.io/cdis/jupyter-notebook:restricted-download-1.3.1
 
 USER $NB_USER
 WORKDIR /home/$NB_USER
 ARG COVID_TOOLS_BRANCH=master
 
 # copy welcome splash page
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/welcome.html /home/$NB_USER/
+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
 
 # copy readme and notebooks requirements
 RUN mkdir /home/$NB_USER/covid19-notebook
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/readme.md /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/readme.md /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/readme.md
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/requirements.txt /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/requirements.txt /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/requirements.txt
 
 # copy premade notebooks
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/jhu-summary-overview/COVID-19-JHU_data_analysis.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/jhu-summary-overview/COVID-19-JHU_data_analysis.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/COVID-19-JHU_data_analysis.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/kaggle-demographics/kaggle_data_analysis.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/kaggle-demographics/kaggle_data_analysis.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/kaggle_data_analysis.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/covid19_seir.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/covid19_seir.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/covid19_seir.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/seir_diagram.png /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/chicago-seir-forecast/seir_diagram.png /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/seir_diagram.png
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ctp_testing/CTP_testing.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ctp_testing/CTP_testing.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/CTP_testing.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/TCGA_COAD_COVID.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/TCGA_COAD_COVID.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/TCGA_COAD_COVID.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/nCoV-2019_data_analysis.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/nCoV-2019_data_analysis.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/nCoV-2019_data_analysis.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/SSR/SSR_notebook.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/SSR/SSR_notebook.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/SSR_notebook.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/DarkCovidNet_binary_classes.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/DarkCovidNet_binary_classes.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/DarkCovidNet_binary_classes.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/CNN_XRAY_CF.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/CNN_XRAY_CF.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/CNN_XRAY_CF.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/google_mobility.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/google_mobility.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/google_mobility.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/PFB_example.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/IL_tab_charts.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/IL_tab_charts.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/IL_tab_charts.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_gui.png /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_gui.png /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_7D4F_gui.png
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_view.html /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_7D4F_view.html /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_7D4F_view.html
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_A_view.html /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_A_view.html /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_A_view.html
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_B_view.html /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_B_view.html /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_B_view.html
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_demo_view.html /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/3D_Protein_Vis/3D_Protein_Vis_demo_view.html /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/3D_Protein_Vis_demo_view.html
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ICU_prediction/Percentage_ICU_prediction.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/ICU_prediction/Percentage_ICU_prediction.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/Percentage_ICU_prediction.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir.ipynb /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir.ipynb /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/extended-seir.ipynb
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_diagram.png /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_diagram.png /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/extended-seir_diagram.png
 
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_parameters.png /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/extended-seir/extended-seir_parameters.png /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/extended-seir_parameters.png
 
 # small pfb file
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.avro /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/pypfb/PFB_example.avro /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/PFB_example.avro
 
 # peregrine helper script required by the X-ray notebooks
-ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/peregrine.py /home/$NB_USER/covid19-notebook/
+ADD --chown=$NB_USER:users https://raw.githubusercontent.com/uc-cdis/covid19-tools/$COVID_TOOLS_BRANCH/covid19-notebooks/X-ray/peregrine.py /home/$NB_USER/covid19-notebook/
 RUN touch /home/$NB_USER/covid19-notebook/peregrine.py
 
 # premade notebooks dependencies
-RUN pip install --upgrade 'pip<20.3' # pip 20.3 causes dependency resolution issues
-RUN pip install -r /home/$NB_USER/covid19-notebook/requirements.txt
+RUN pip install -U -r /home/$NB_USER/covid19-notebook/requirements.txt
+
+# The image can't function (see error below) with `jsonschema` version 3.2.0. Some dependencies are
+# preventing `jsonschema` from being upgraded to a more recent version. Updating it here as a quick fix.
+#   File "/usr/local/lib/python3.9/dist-packages/jupyter_events/validators.py", line 44, in <module>
+#     JUPYTER_EVENTS_SCHEMA_VALIDATOR = Draft7Validator(
+# TypeError: __init__() got an unexpected keyword argument 'registry'
+RUN pip install jsonschema==4.20.0 --upgrade

jupyter-restricted-download/.env

@@ -0,0 +1,3 @@
+SERVICE_PORT=9880
+USER_VOLUME=./user-volume
+DATA_VOLUME=./data-volume

jupyter-restricted-download/Dockerfile

@@ -0,0 +1,104 @@
+ARG ROOT_CONTAINER=quay.io/cdis/ubuntu:focal
+
+FROM $ROOT_CONTAINER
+
+LABEL maintainer="Jupyter Project <[email protected]>"
+
+# Fix DL4006
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+USER root
+
+# Install all OS dependencies for the notebook server that starts but lacks all
+# features (e.g., download as all possible file formats)
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update --yes && \
+    apt-get install --yes --no-install-recommends \
+    python3.9 \
+    python3-pip \
+    tini \
+    wget \
+    git \
+    curl \
+    ca-certificates \
+    sudo \
+    locales \
+    fonts-liberation \
+    vim \
+    run-one && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* && \
+    echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+# Set Python 3.9 as the default Python version
+RUN ln -s /usr/bin/python3.9 /usr/bin/python
+
+# Add the Python 3.9 executable path to the PATH environment variable
+ENV PATH="/usr/bin/python3.9:$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
+
+# step 1 to 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 gen3==4.18.0 --upgrade
+RUN pip install jupyter --upgrade
+# step 2 to disable downloads:
+RUN pip uninstall nbconvert --yes
+
+# Create a non-root user for Jupyter without copying /bin or /bin/bash
+ARG NB_USER=jovyan
+ARG NB_UID=1000
+ARG NB_GID=100
+RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
+    chown -R $NB_USER:users /home/$NB_USER && \
+    chmod -R u+rwx /home/$NB_USER && \
+    mkdir -p /home/$NB_USER/pd
+
+# Configure environment
+ENV CONDA_DIR=/opt/conda \
+    PATH=/usr/local/bin:$PATH \
+    SHELL=/bin/bash \
+    NB_USER=${NB_USER} \
+    NB_UID=${NB_UID} \
+    NB_GID=${NB_GID} \
+    HOME=/home/$NB_USER \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    LANGUAGE=en_US.UTF-8
+
+# Expose port 8888 for JupyterLab
+EXPOSE 8888
+
+# Add local files as late as possible to avoid cache busting
+RUN wget https://raw.githubusercontent.com/jupyter/docker-stacks/7e1a19a8427f99652c75d1d4fda3df780721b574/images/docker-stacks-foundation/fix-permissions
+RUN mv fix-permissions /usr/local/bin/fix-permissions.sh
+COPY start.sh /usr/local/bin/
+COPY start-notebook.sh /usr/local/bin/
+COPY start-singleuser.sh /usr/local/bin/
+RUN chmod +x /usr/local/bin/*.sh
+
+COPY resources/custom.js /home/$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
+
+RUN fix-permissions.sh "/home/${NB_USER}"
+
+USER $NB_USER
+
+# Set the default command to start JupyterLab
+WORKDIR /home/$NB_USER
+ENTRYPOINT ["jupyter", "lab", "--allow-root", "--ip=0.0.0.0", "--port=8888", "--no-browser"]

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

jupyter-restricted-download/resources/custom.js

@@ -0,0 +1,3 @@
+define(['base/js/namespace'], function(Jupyter){
+    Jupyter._target = '_self';
+})