From 1a96c8fd7a00c0bb68f2ab04b1408d87c6c8db05 Mon Sep 17 00:00:00 2001 From: Pauline <4224001+paulineribeyre@users.noreply.github.com> Date: Fri, 19 Jan 2024 14:54:11 +0100 Subject: [PATCH] rename to 'restricted' + remove jupyter-covid19 changes for now --- .github/workflows/build_and_push_python_image.yml | 6 +++--- .../workflows/build_azlinux_jupyter_scipy_image.yml | 2 +- .github/workflows/build_jupyter_nextflow_image.yml | 2 +- ...ml => build_jupyter_restricted_download_image.yml} | 11 +++++------ .github/workflows/build_vadc_notebook_image.yml | 1 + .../workflows/build_vlmd_submission_python_image.yml | 4 ++-- jupyter-covid19/Dockerfile | 7 +++---- .../.env | 0 .../Dockerfile | 1 + .../README.md | 2 +- .../resources/custom.js | 0 .../resources/jupyter_notebook_config.py | 0 .../start-notebook.sh | 0 .../start-singleuser.sh | 0 .../start.sh | 0 15 files changed, 18 insertions(+), 18 deletions(-) rename .github/workflows/{build_jupyter_covid19_restricted_download.yml => build_jupyter_restricted_download_image.yml} (72%) rename {jupyter-restrict-download => jupyter-restricted-download}/.env (100%) rename {jupyter-restrict-download => jupyter-restricted-download}/Dockerfile (98%) rename {jupyter-restrict-download => jupyter-restricted-download}/README.md (51%) rename {jupyter-restrict-download => jupyter-restricted-download}/resources/custom.js (100%) rename {jupyter-restrict-download => jupyter-restricted-download}/resources/jupyter_notebook_config.py (100%) rename {jupyter-restrict-download => jupyter-restricted-download}/start-notebook.sh (100%) rename {jupyter-restrict-download => jupyter-restricted-download}/start-singleuser.sh (100%) rename {jupyter-restrict-download => jupyter-restricted-download}/start.sh (100%) 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_covid19_restricted_download.yml b/.github/workflows/build_jupyter_restricted_download_image.yml similarity index 72% rename from .github/workflows/build_jupyter_covid19_restricted_download.yml rename to .github/workflows/build_jupyter_restricted_download_image.yml index ec6eb2e1..d28b2bfa 100644 --- a/.github/workflows/build_jupyter_covid19_restricted_download.yml +++ b/.github/workflows/build_jupyter_restricted_download_image.yml @@ -1,21 +1,20 @@ -name: Build and push PRC images +name: Build and Push jupyter-restricted-download on: push: paths: - - jupyter-restricted-download/Dockerfile - - .github/workflows/build_jupyter_restricted_download.yml + - jupyter-restricted-download/** + - .github/workflows/build_jupyter_restricted_download_image.yml jobs: - jupyter-covid19-restricted-download: + 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-covid19" + OVERRIDE_REPO_NAME: "jupyter-notebook" OVERRIDE_TAG_NAME: "restricted-download-$(echo ${GITHUB_REF#refs/*/} | tr / _)" - USE_QUAY_ONLY: true secrets: ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }} 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-covid19/Dockerfile b/jupyter-covid19/Dockerfile index f6acee03..d4d514b9 100644 --- a/jupyter-covid19/Dockerfile +++ b/jupyter-covid19/Dockerfile @@ -1,4 +1,4 @@ -FROM quay.io/cdis/jupyter-restrict-download:1.1.0 +FROM quay.io/cdis/jupyter-notebook:1.1.0 USER $NB_USER WORKDIR /home/$NB_USER @@ -96,6 +96,5 @@ ADD --chown=jovyan:users https://raw.githubusercontent.com/uc-cdis/covid19-tools RUN touch /home/$NB_USER/covid19-notebook/peregrine.py # premade notebooks dependencies -# RUN pip install --upgrade 'pip<20.3' # pip 20.3 causes dependency resolution issues -COPY requirements.txt /home/$NB_USER/covid19-notebook/requirements.txt -RUN pip install -r /home/$NB_USER/covid19-notebook/requirements.txt --upgrade +RUN pip install --upgrade 'pip<20.3' # pip 20.3 causes dependency resolution issues +RUN pip install -r /home/$NB_USER/covid19-notebook/requirements.txt diff --git a/jupyter-restrict-download/.env b/jupyter-restricted-download/.env similarity index 100% rename from jupyter-restrict-download/.env rename to jupyter-restricted-download/.env diff --git a/jupyter-restrict-download/Dockerfile b/jupyter-restricted-download/Dockerfile similarity index 98% rename from jupyter-restrict-download/Dockerfile rename to jupyter-restricted-download/Dockerfile index b8429e1e..877c98fa 100644 --- a/jupyter-restrict-download/Dockerfile +++ b/jupyter-restricted-download/Dockerfile @@ -49,6 +49,7 @@ 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 diff --git a/jupyter-restrict-download/README.md b/jupyter-restricted-download/README.md similarity index 51% rename from jupyter-restrict-download/README.md rename to jupyter-restricted-download/README.md index ca3a367a..f0d810ea 100644 --- a/jupyter-restrict-download/README.md +++ b/jupyter-restricted-download/README.md @@ -1,3 +1,3 @@ # jupyter-restricted-download -A "restricted" build of `jupyter-slim`. Basically the same as `../jupyter-slim/`, but it restricts user to download anything from the jupyter lab +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-restrict-download/resources/custom.js b/jupyter-restricted-download/resources/custom.js similarity index 100% rename from jupyter-restrict-download/resources/custom.js rename to jupyter-restricted-download/resources/custom.js diff --git a/jupyter-restrict-download/resources/jupyter_notebook_config.py b/jupyter-restricted-download/resources/jupyter_notebook_config.py similarity index 100% rename from jupyter-restrict-download/resources/jupyter_notebook_config.py rename to jupyter-restricted-download/resources/jupyter_notebook_config.py diff --git a/jupyter-restrict-download/start-notebook.sh b/jupyter-restricted-download/start-notebook.sh similarity index 100% rename from jupyter-restrict-download/start-notebook.sh rename to jupyter-restricted-download/start-notebook.sh diff --git a/jupyter-restrict-download/start-singleuser.sh b/jupyter-restricted-download/start-singleuser.sh similarity index 100% rename from jupyter-restrict-download/start-singleuser.sh rename to jupyter-restricted-download/start-singleuser.sh diff --git a/jupyter-restrict-download/start.sh b/jupyter-restricted-download/start.sh similarity index 100% rename from jupyter-restrict-download/start.sh rename to jupyter-restricted-download/start.sh