From fabcdaf7a995d024d65d4fdcb4bfce6960ceb385 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 11 Oct 2023 14:26:46 -0400 Subject: [PATCH 01/19] original attempt at creating a leaner terra base docker image --- .gitignore | 3 +- terra-base/.python-version | 1 + terra-base/Dockerfile | 144 + terra-base/README.md | 91 + terra-base/custom/.eslintrc.js | 32 + terra-base/custom/README.md | 6 + terra-base/custom/edit-mode.js | 447 ++ terra-base/custom/extension_entry_jupyter.js | 7 + .../custom/extension_entry_jupyterlab.js | 7 + terra-base/custom/google_sign_in.js | 174 + terra-base/custom/jupyter_delocalize.py | 148 + .../custom/jupyter_localize_extension.py | 149 + terra-base/custom/package.json | 19 + terra-base/custom/safe-mode.js | 128 + terra-base/custom/test/README.md | 16 + .../custom/test/jupyter_delocalize_test.py | 448 ++ terra-base/custom/test/test-requirements.txt | 3 + terra-base/jupyter_notebook_config.py | 44 + terra-base/poetry.lock | 4119 +++++++++++++++++ terra-base/poetry.toml | 1 + terra-base/pyproject.toml | 33 + .../install_jupyter_contrib_nbextensions.sh | 11 + .../jupyter_install_combined_extension.sh | 14 + .../jupyter_install_lab_extension.sh | 29 + .../jupyter_install_notebook_extension.sh | 15 + .../jupyter_install_server_extension.sh | 12 + .../jupyter_pip_install_combined_extension.sh | 11 + .../jupyter_pip_install_notebook_extension.sh | 9 + .../jupyter_pip_install_server_extension.sh | 9 + terra-base/scripts/kernel/kernel_bootstrap.sh | 24 + terra-base/scripts/kernel/kernelspec.sh | 7 + .../scripts/kernel/python_kernelspec.tmpl | 12 + terra-base/scripts/run-jupyter.sh | 17 + 33 files changed, 6189 insertions(+), 1 deletion(-) create mode 100644 terra-base/.python-version create mode 100644 terra-base/Dockerfile create mode 100644 terra-base/README.md create mode 100644 terra-base/custom/.eslintrc.js create mode 100644 terra-base/custom/README.md create mode 100644 terra-base/custom/edit-mode.js create mode 100644 terra-base/custom/extension_entry_jupyter.js create mode 100644 terra-base/custom/extension_entry_jupyterlab.js create mode 100644 terra-base/custom/google_sign_in.js create mode 100644 terra-base/custom/jupyter_delocalize.py create mode 100644 terra-base/custom/jupyter_localize_extension.py create mode 100644 terra-base/custom/package.json create mode 100644 terra-base/custom/safe-mode.js create mode 100644 terra-base/custom/test/README.md create mode 100644 terra-base/custom/test/jupyter_delocalize_test.py create mode 100644 terra-base/custom/test/test-requirements.txt create mode 100755 terra-base/jupyter_notebook_config.py create mode 100644 terra-base/poetry.lock create mode 100644 terra-base/poetry.toml create mode 100644 terra-base/pyproject.toml create mode 100644 terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh create mode 100644 terra-base/scripts/extension/jupyter_install_combined_extension.sh create mode 100644 terra-base/scripts/extension/jupyter_install_lab_extension.sh create mode 100644 terra-base/scripts/extension/jupyter_install_notebook_extension.sh create mode 100644 terra-base/scripts/extension/jupyter_install_server_extension.sh create mode 100644 terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh create mode 100644 terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh create mode 100644 terra-base/scripts/extension/jupyter_pip_install_server_extension.sh create mode 100644 terra-base/scripts/kernel/kernel_bootstrap.sh create mode 100644 terra-base/scripts/kernel/kernelspec.sh create mode 100644 terra-base/scripts/kernel/python_kernelspec.tmpl create mode 100644 terra-base/scripts/run-jupyter.sh diff --git a/.gitignore b/.gitignore index c7b1ac97..79219772 100644 --- a/.gitignore +++ b/.gitignore @@ -17,4 +17,5 @@ package-lock.json .python_history .keras/ .ammonite/ -.metals/ \ No newline at end of file +.metals/ +.venv/ \ No newline at end of file diff --git a/terra-base/.python-version b/terra-base/.python-version new file mode 100644 index 00000000..c8cfe395 --- /dev/null +++ b/terra-base/.python-version @@ -0,0 +1 @@ +3.10 diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile new file mode 100644 index 00000000..4f0c8cf6 --- /dev/null +++ b/terra-base/Dockerfile @@ -0,0 +1,144 @@ +# Smallest image with ubuntu jammy, CUDA and NVDIA drivers installed - 80 mb +FROM --platform=linux/amd64 nvidia/cuda:12.2.0-base-ubuntu22.04 + +####################### +# Environment Variables +####################### +ENV DEBIAN_FRONTEND noninteractive +ENV LC_ALL en_US.UTF-8 +ENV USER jupyter +ENV HOME /home/$USER +# Ensure this matches c.NotebookApp.port in jupyter_notebook_config.py +ENV JUPYTER_PORT 8000 +ENV JUPYTER_HOME /etc/jupyter +ENV JUPYTER_KERNELSPEC_DIR /usr/local/share/jupyter +# The welder uid is consistent with the Welder docker definition here: +# https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala +# Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added +# files display nicer when viewed in a terminal. +ENV WELDER_USER welder-user +ENV WELDER_UID 1001 +# When using PIP_USER=true packages are installed into Python site.USER_BASE, which is '/home/jupyter' for this system. +# Append '/home/jupyter/.local/bin' to PATH +# pip docs: https://pip.pypa.io/en/stable/reference/pip_install/#cmdoption-user +ENV PATH "${PATH}:${HOME}/.local/bin:${HOME}/packages/bin:${POETRY_DIR}/bin" +# We need node >18 for jupyter to work +ENV NODE_MAJOR 20 + +####################### +# Users Setup +####################### +RUN useradd -m -s /bin/bash $USER +RUN usermod -g users $USER +RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER + +####################### +# Prerequisites +####################### +RUN apt-get update && apt-get install -yq --no-install-recommends \ + sudo \ + ca-certificates \ + curl \ + # gnupg requirement + gnupg \ + dirmngr \ + # useful utilities for debugging within the docker + nano \ + procps \ + lsb-release \ + # python requirements + checkinstall \ + build-essential \ + zlib1g-dev \ + # pip requirements + libssl-dev \ + libbz2-dev \ + libreadline-dev \ + libsqlite3-dev \ + libexempi8 \ + libnode-dev \ + llvm \ + libncurses5-dev \ + libncursesw5-dev \ + tk-dev \ + libffi-dev \ + liblzma-dev \ + python3-openssl \ + # install script requirements + locales \ + # for ssh-agent and ssh-add + keychain \ + # extras \ + wget \ + bzip2 \ + # git + git \ + # Uncomment en_US.UTF-8 for inclusion in generation + && sed -i 's/^# *\(en_US.UTF-8\)/\1/' /etc/locale.gen \ + # Generate locale + && locale-gen \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - +RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key add - + +# Install Node >18 +RUN apt-get update && apt-get install -yq --no-install-recommends +RUN sudo mkdir -p /etc/apt/keyrings +RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | sudo gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg + +RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | sudo tee /etc/apt/sources.list.d/nodesource.list +RUN sudo dpkg --remove --force-remove-reinstreq libnode-dev +RUN sudo apt-get update && apt-get install -f -yq nodejs + +######################################## +# Manage python dependencies with poetry +######################################## +# Install Python 3.10 and add to python path +RUN apt-get update && apt-get install -y python3.10 python3-pip +RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.10 1 \ + && update-alternatives --set python /usr/bin/python3.10 + +# Install Poetry +RUN curl -sSL https://install.python-poetry.org | python3 + +# Prevent poetry from creating a virtual environment (we want to install on the docker system python) +RUN poetry config virtualenvs.create false + +# Install python dependencies with poetry +COPY poetry.lock . +COPY pyproject.toml . +RUN poetry install --no-root --no-cache --no-interaction + +# ####################### +# # Utilities +# ####################### +COPY scripts $JUPYTER_HOME/scripts +COPY custom $JUPYTER_HOME/custom +COPY jupyter_notebook_config.py $JUPYTER_HOME + +# copy workspace_cromwell.py script and make it runnable by all users +RUN curl -o /usr/local/bin/workspace_cromwell.py https://raw.githubusercontent.com/broadinstitute/cromwhelm/1ceedf89587cffd355f37401b179001f029f77ed/scripts/workspace_cromwell.py \ + && chmod +x /usr/local/bin/workspace_cromwell.py + +RUN chown -R $USER:users $JUPYTER_KERNELSPEC_DIR \ + && find $JUPYTER_HOME/scripts -name '*.sh' -type f | xargs chmod +x \ + # You can get kernel directory by running `jupyter kernelspec list` + && $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel $JUPYTER_KERNELSPEC_DIR/kernels + +# Make sure that the jupyter user will have access to the jupyter path in the worksing directory +EXPOSE $JUPYTER_PORT +WORKDIR $HOME +RUN sudo chown -R $USER:users $HOME/.local/share + +# make pip install to a user directory, instead of a system directory which requires root. +# this is useful so `pip install` commands can be run in the context of a notebook. +ENV PIP_USER true +USER $USER + +# Note: this entrypoint is provided for running Jupyter independently of Leonardo. +# When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable +# additional setup inside the container before execution. Jupyter execution occurs when the +# init-actions.sh script uses 'docker exec' to call run-jupyter.sh. +ENTRYPOINT ["jupyter", "notebook"] \ No newline at end of file diff --git a/terra-base/README.md b/terra-base/README.md new file mode 100644 index 00000000..02fdd651 --- /dev/null +++ b/terra-base/README.md @@ -0,0 +1,91 @@ +# terra-base image + +This repo contains the terra-base image that is compatible with the +notebook service in [Terra]("https://app.terra.bio/") called Leonardo. +The goal is to provide a lean, GPU-enabled base image that can be use for both Terra-suported, and custome image builds. +[See design doc]("https://broadworkbench.atlassian.net/wiki/spaces/IA/pages/2842460165/2023-08-28+Terra+Docker+Refactoring+POC#Provide-a-leaner-set-of-terra-docker-images") + +## Image contents + +`terra-base` extends an cuda 12.2.0 and Ubuntu 22.04 base image with the minimum +requirements necessary to set up Jupyter and provide compatibility with Leonardo and GPU machines. + +- OS prerequisites +- Python 3.10 +- Anaconda +- Jupyter +- Leonardo customizations/extensions +- Terra python client library ([FISS](https://github.com/broadinstitute/fiss)) +- Terra notebook utils +- Full list of python packages is available [here](pyproject.toml) + +To see the complete contents of this image please see the [Dockerfile](./Dockerfile). + +## Contributing + +### Installing python 3.10 + +All terra-docker images are on Python 3.10, so make sure to have it installed on your +local machine, for mac users doing this via `pyenv` is the recommended way of doing it: + +```bash +$> brew install pyenv +$> pyenv install 3.10.0 +``` + +### Installing poetry + +All python package dependencies are managed by [poetry]("https://python-poetry.org/docs/"), +which allows for cross-platforms, deterministic python environments builds. + +You can install poetry via brew or curl commands (NEVER USE PIP!): + +```bash +# Via brew +$> brew install poetry +# Via curl +$> curl -sSL https://install.python-poetry.org | python3 - +``` + +### Managing python packages + +**Attention mac m1 users!** + +Make sure to do the following before installing any python packages: + +```bash +$> brew install libomp +$> brew install llvm +``` + +For compilers to find libomp and llvm you may need to set either in the terminal directly +or in your bash/zsh profile file: + +```bash +$> export LDFLAGS="-L/opt/homebrew/opt/libomp/lib -L/opt/homebrew/opt/llvm/lib" +$> export CPPFLAGS="-I/opt/homebrew/opt/libomp/include -I/opt/homebrew/opt/llvmp/include" +``` + +From inside the `terra-base` directory, run the following command to install +the python 3.10 environment with the relevant packages: + +```bash +$> poetry install +``` + +If you need to update an existing python dependencies, then modify the `pyproject.toml` +file (**it is strongly recommended to never pin an exact version, but floor/ceiling it instead**) +and then update the environment by running the following: + +```bash +$> poetry update +``` + +If you need to add a new dependency, **do not modify the pyproject.toml directly** and do this instead: + +```bash +$> poetry add +$> poetry update +``` + +The `poetry update` step will generate a new `poetry.lock` file that will be use in the docker image build. \ No newline at end of file diff --git a/terra-base/custom/.eslintrc.js b/terra-base/custom/.eslintrc.js new file mode 100644 index 00000000..a1781ad1 --- /dev/null +++ b/terra-base/custom/.eslintrc.js @@ -0,0 +1,32 @@ +module.exports = { + 'env': { + 'browser': true, + 'es6': true, + }, + 'extends': [ + 'google', + ], + 'globals': { + 'Atomics': 'readonly', + 'SharedArrayBuffer': 'readonly', + }, + 'parserOptions': { + 'ecmaVersion': 2018, + 'sourceType': 'module', + }, + 'rules': { + 'comma-dangle': ['error', 'never'], + //80 is the standard, but this required the least refactoring. + 'max-len': ['error', { 'code': 150 }], + //TODO: remove the following rules and fix the offenses + 'require-jsdoc': ['error', { + 'require': { + 'FunctionDeclaration': false, + 'MethodDefinition': false, + 'ClassDeclaration': false, + 'ArrowFunctionExpression': false, + 'FunctionExpression': false + } + }] + }, +}; \ No newline at end of file diff --git a/terra-base/custom/README.md b/terra-base/custom/README.md new file mode 100644 index 00000000..54a6e25e --- /dev/null +++ b/terra-base/custom/README.md @@ -0,0 +1,6 @@ +#Before you merge, lint the files with eslint. + +# `brew install eslint` +# `brew install npm` +# `npm i` +# `eslint --fix *.js` diff --git a/terra-base/custom/edit-mode.js b/terra-base/custom/edit-mode.js new file mode 100644 index 00000000..3670fb1f --- /dev/null +++ b/terra-base/custom/edit-mode.js @@ -0,0 +1,447 @@ +define(() => { + // define default values for config parameters + const params = { + googleProject: '', + clusterName: '', + welderEnabled: 'false' + }; + + // update params with any specified in the server's config file + function updateParams() { + const config = Jupyter.notebook.config; + for (const key in params) { + if (config.data.hasOwnProperty(key)) { + params[key] = config.data[key]; + } + } + + // generate URLs based on params + const leoUrl = ''; // we are choosing to use a relative path here + const welderUrl = leoUrl + `/proxy/${params.googleProject}/${params.clusterName}/welder`; + + // URLS for local testing + // let leoUrl = 'http://localhost:8080' //for testing against local server + // let welderUrl = leoUrl + // params.jupyterServerApi = '/api/contents/' + // params.jupyterFsHref = '/notebooks/' + + params.jupyterServerApi = leoUrl + `/notebooks/${params.googleProject}/${params.clusterName}` + '/api/contents/'; + params.jupyterFsHref = leoUrl + `/notebooks/${params.googleProject}/${params.clusterName}/notebooks/`; + params.localizeUrl = welderUrl + '/objects'; + params.checkMetaUrl = welderUrl + '/objects/metadata'; + params.lockUrl = welderUrl + '/objects/lock'; + } + + let modalOpen = false; + // this needs to be available so the loop can be cancelled where needed + let syncMaintainer; + let shouldExit = false; + + const syncIssueButtons = (res) => { + return { + 'Make a Copy': { + 'click': () => notebookSaveAs(), + 'class': 'btn-primary', + 'id': 'modal-copy-1' + }, + 'Reload the workspace version and discard your changes': { + 'click': () => updateLocalCopyWithRemote(res), + 'id': 'modal-reload' + } + }; + }; + + const lockIssueButtons = (res) => { + return { + 'Run in Playground Mode': { + 'click': () => openPlaygroundMode(res), + 'class': 'btn-primary', + 'id': 'modal-playground' + }, + 'Make a Copy': { + 'click': () => notebookSaveAs(), + 'id': 'modal-copy-2' + } + }; + }; + + const noRemoteFileButtons = { + 'Continue working': { + 'click': () => {}, + 'class': 'btn-primary' + } + }; + + const modeBannerId = 'notification_mode'; + const lockConflictTitle = 'File is in use'; + const syncIssueTitle = 'File versions out of sync'; + const syncIssueBody = 'Your version of this file does not match the version in the workspace. What would you like to do?'; + const syncIssueNotFoundBody = 'This file was either deleted from or was never saved to the workspace.'; + const lastLockedTimer = 60000; + + const headers = { + 'Content-Type': 'application/json', + 'Access-Control-Allow-Headers': '*' + }; + + const basePayload = { + mode: 'no-cors', + headers: headers + }; + + function init() { + console.info('edit mode plugin initialized'); + + if (!Jupyter.notebook) { + return; // exit, they are in list view + } + + updateParams(); + + if (!(params.welderEnabled == 'true')) { + console.info('welder is not enabled'); + return; + } + + checkMeta(); + + const initialSyncDelay = 27000; + // we want subsequent checkMeta + lock calls to be off-cycle of autosave + setTimeout(() => initSyncMaintainer(), initialSyncDelay); + } + + function initSyncMaintainer() { + syncMaintainer = setInterval(() => { + checkMeta(); + }, lastLockedTimer); + + window.onbeforeunload(function() { + clearInterval(syncMaintainer); + }); + } + + function checkMeta() { + const localPath = { + localPath: Jupyter.notebook.notebook_path + }; + + console.info('calling /objects/metadata/ with payload: ', JSON.stringify(localPath)); + + const payload = { + ...basePayload, + body: JSON.stringify(localPath), + method: 'POST' + }; + + return fetch(params.checkMetaUrl, payload) + .then((res) => { + processInitialCheckMeta(res); + return res.json(); + }) + .then((res) => { + handleMetaSuccess(res); + return res; + }) + .catch((err) => { + handleMetaFailure(err); + }); + } + + function renderFileNotTrackedBanner() { + removeElementById(modeBannerId); + + const toolTipText = '

Your changes are not being saved to the workspace.

'; + + $('#notification_area').append( + $('
').attr({ + 'id': 'notification_not_saving', + 'class': 'btn-warning btn btn-xs navbar-btn', + 'data-toggle': 'tooltip', + 'data-html': 'true', + 'title': toolTipText + }) + .tooltip({ + 'content': function() { + return $(this).prop('title'); + }, + 'placement': 'bottom' + }) + .append( + $('').html('Remote Save Disabled') + .append(' ') + ) + ); + } + + function processInitialCheckMeta(res) { + if (!res.ok) { + if (res.status == 412) { + console.warn('detected 412 from /objects/metadata. stopping loop'); + renderFileNotTrackedBanner(); + shouldExit = true; + clearInterval(syncMaintainer); + } + + throw Error(res.statusText); + } + } + + function handleMetaSuccess(res) { + toggleMetaFailureBanner(false); // sets banner for meta status + + const isEditMode = res.syncMode == 'EDIT'; + + if (isEditMode) { + handleCheckMetaResp(res); // displays modal if theres an issue in the payload + getLock(res); // gets lock if in edit mode + } + renderModeBanner(isEditMode); // sets edit/safe mode banner + } + + function handleMetaFailure(err) { + console.error(err); + if (!shouldExit) { + removeElementById(modeBannerId); + toggleMetaFailureBanner(true); + } + } + + // this function assumes any status not included in these lists represents a notebook out of sync + // this is done to defend against future fields being added being auto-categorized as failures + function handleCheckMetaResp(res) { + const healthySyncStatuses = ['LIVE']; + // below is included for reference, but commented out so it does not cause errors with linting + // const outOfSyncStatuses = ['DESYNCHRONIZED', 'REMOTE_CHANGED']; + const notFoundStatus = ['REMOTE_NOT_FOUND']; + const saveNeededStatus = ['LOCAL_CHANGED']; + + if (healthySyncStatuses.includes(res.syncStatus)) { + console.info('healthy sync status detected: ', res.syncStatus); + } else if (notFoundStatus.includes(res.syncStatus)) { + promptUserWithModal(syncIssueTitle, noRemoteFileButtons, syncIssueNotFoundBody); + } else if (saveNeededStatus.includes(res.syncStatus)) { + console.info('detected that we have changes that have not been delocalized.'); + // It is possible saving is the right call here (aka $("#save-notbook > button").click()), but we already do that on a periodic tick + // adding it here could possibly cause confusion + } else { + promptUserWithModal(syncIssueTitle, syncIssueButtons(res), syncIssueBody); + } + } + + function getLock(metaRes) { + const payload = { + ...basePayload, + method: 'POST', + body: JSON.stringify({localPath: Jupyter.notebook.notebook_path}) + }; + + fetch(params.lockUrl, payload) + .then((res) => { + handleLockStatus(res, metaRes); + }) + .catch((err) => { + console.error(err); + }); + } + + function toggleMetaFailureBanner(shouldShow) { + const bannerId = 'notification_metaFailure'; + const bannerText = 'Failed to check notebook status, changes may not be saved to workspace. Retrying...'; + + removeElementById(bannerId); + + if (shouldShow) { + const bannerStyling = 'btn btn-xs navbar-btn btn-danger'; + + $('#notification_area').append( + $('
').attr({ + 'id': bannerId, + 'class': bannerStyling + }) + .append($('').html(' ' + bannerText)) + ); + } + } + + const lockConflictBody = `

This file is currently being edited by another user. ` + + `Please allow 2-3 minutes after this user has closed the file for it to become available for editing.

` + + `

You can make a copy, or run it in Playground Mode to explore and execute its contents without saving any changes.`; + + function handleLockStatus(res, metaRes) { + if (!res.ok) { + const status = res.status; + const errorText = res.statusText; + + if (status == 409) { + res.json().then((res) => { + promptUserWithModal(lockConflictTitle, lockIssueButtons(metaRes), lockConflictBody); + }); + } + // for the lock endpoint, we consider all non 'ok' statuses an error + throw new Error(errorText); + } + } + + + function promptUserWithModal(title, buttons, htmlBody) { + if (modalOpen) return; + + modalOpen = true; + + // we need to require here because otherwise we haven't checked if the module is loaded + // (i.e. if we are in terminal view) + const dialog = require('base/js/dialog'); + + dialog.modal({ + body: $('

').html(htmlBody), + title: title, + buttons: buttons, + notebook: Jupyter.notebook, + keyboard_manager: Jupyter.notebook.keyboard_manager + }) + .on('hidden.bs.modal', () => modalOpen = false) + .attr('id', 'leoUserModal') + .find('.close').remove(); // TODO: test going back + } + + async function openPlaygroundMode(metaRes) { + const originalNotebookName = Jupyter.notebook.notebook_name; + + const safeModeDir = metaRes.storageLink.localSafeModeBaseDirectory; + + if (Jupyter.notebook.notebook_path.includes(safeModeDir)) { + console.warn('Attempted to navigate to enter safe mode while already in safe mode. Exitting.'); + return; // we're here already + } + + // create a new file with the contents + const postPayload = { + ...basePayload, + method: 'POST', + body: JSON.stringify({ + copy_from: Jupyter.notebook.notebook_path + }) + }; + + const patchPayload = { + headers: headers, + method: 'PATCH', + body: JSON.stringify({ + path: safeModeDir + '/' + originalNotebookName + }) + }; + + fetch(params.jupyterServerApi + safeModeDir, postPayload) + .then((res) => handleJupyterServerResponse(res)) + .then((res) => { + // then we rename the file, as POST does not allow us to specify the file name + fetch(params.jupyterServerApi + res.path, patchPayload) + .then((res) => { + // navigate to new file + window.location.href = params.jupyterFsHref + safeModeDir + '/' + originalNotebookName; + }); + }); + } + + function notebookSaveAs() { + // we need to require here because otherwise we haven't checked if the module is loaded + // (i.e. if we are in terminal view) + const utils = require('base/js/utils'); + // guarantees a path in [0] and file name in [1]. [0] is "" if just a file is passed + const originalPathSplit = utils.url_path_split(Jupyter.notebook.notebook_path); + const newNotebookPath = originalPathSplit[0]; + + // create a new file with the contents + const payload = { + ...basePayload, + method: 'POST', + body: JSON.stringify({ + copy_from: Jupyter.notebook.notebook_path + }) + }; + + fetch(params.jupyterServerApi + newNotebookPath, payload) + .then((res) => handleJupyterServerResponse(res)) + .then((res) => { + // navigate to new file. we rely on the jupyter post api to supply the name of the file we have created as it ensures it does not exist + // POST also does not allow for the specification of a file name + window.location.href = params.jupyterFsHref + res.path; + }); + } + + function handleJupyterServerResponse(res) { + if (!res.ok) { + throw new Error('failed to perform requested action, the jupyter server is unavailable'); + } + return res.json(); + } + + function removeElementById(id) { + if (!$('#' + id).length == 0) { + $('#' + id).remove(); + } + } + + // shows the user whether they are in playground mode or edit mode + function renderModeBanner(isEditMode) { + removeElementById(modeBannerId); // we always remove the banner because we re-render each loop + + let bannerText; + let toolTipText; + let bannerStyling; + + const baseStyling = 'btn btn-xs navbar-btn'; + + if (isEditMode) { + bannerText = 'Edit Mode'; + toolTipText = '

You have locked this file for editing and your changes are being automatically saved to the workspace.

'; + bannerStyling = 'notification_widget ' + baseStyling; + } else { + bannerText = 'Playground Mode (Edits not saved)'; + toolTipText = '

Playground mode allows you to explore, change, and run the notebook, but changes are not saved to the workspace.

'; + bannerStyling = 'btn-warning ' + baseStyling; + } + + $('#notification_area').append( + $('
').attr({ + 'id': modeBannerId, + 'class': bannerStyling, + 'data-toggle': 'tooltip', + 'data-html': 'true', + 'title': toolTipText + }) + .tooltip({ + 'content': function() { + return $(this).prop('title'); + }, + 'placement': 'bottom' + }) + .append( + $('').html(bannerText) + .append(' ') + ) + ); + } + + async function updateLocalCopyWithRemote(meta) { + const entries = { + action: 'localize', + entries: [{ + sourceUri: meta.storageLink.cloudStorageDirectory + '/' + Jupyter.notebook.notebook_name, + localDestinationPath: Jupyter.notebook.notebook_path + }] + }; + + const payload = { + ...basePayload, + method: 'POST', + body: JSON.stringify(entries) + }; + + await fetch(params.localizeUrl, payload); + + location.reload(true); + } + + init(); +}); diff --git a/terra-base/custom/extension_entry_jupyter.js b/terra-base/custom/extension_entry_jupyter.js new file mode 100644 index 00000000..0515b726 --- /dev/null +++ b/terra-base/custom/extension_entry_jupyter.js @@ -0,0 +1,7 @@ +define([ + 'base/js/events' +], function(events) { + require(['custom/google_sign_in']); + require(['custom/edit-mode']); + require(['custom/safe-mode']); +}); diff --git a/terra-base/custom/extension_entry_jupyterlab.js b/terra-base/custom/extension_entry_jupyterlab.js new file mode 100644 index 00000000..333ccad9 --- /dev/null +++ b/terra-base/custom/extension_entry_jupyterlab.js @@ -0,0 +1,7 @@ +module.exports = [{ + id: 'google_plugin_jupyterlab', + autoStart: true, + activate: function(app) { + require('/home/jupyter/.jupyter/custom/google_sign_in'); + } +}]; diff --git a/terra-base/custom/google_sign_in.js b/terra-base/custom/google_sign_in.js new file mode 100644 index 00000000..c63e58bf --- /dev/null +++ b/terra-base/custom/google_sign_in.js @@ -0,0 +1,174 @@ +/* + * This library is designed to run as a Jupyter/JupyterLab extension to refresh the user's + * Google credentials while using a notebook. This flow is described in more detail here: + * https://github.com/DataBiosphere/leonardo/wiki/Connecting-to-a-Leo-Notebook#token-refresh + * + * Note since this runs inside both Jupyter and JupyterLab, it should not use any + * libraries/functionality that exists in one but not the other. Examples: node, requireJS. + */ + + +// define default values for config parameters +const params = { + loginHint: '', + googleClientId: '', + googleProject: '', + clusterName: '' +}; + +// update params with any specified in the server's config file, +// or retrieve that info from the url if we cannot access it (as is the case in terminal view) +function updateParams() { + if (!Jupyter.notebook || !Jupyter.notebook.config || !Jupyter.notebook.config.data) { + console.warn('Unable to read notebook config. This is expected in terminal view, but not elsewhere. Attempting to read fallback config.'); + readFallbackConfig(); + } else { + readNotebookConfig(Jupyter.notebook.config.data); + } +} + +function readNotebookConfig(config) { + for (const key in params) { + if (config.hasOwnProperty(key)) { + params[key] = config[key]; + } + } +} + +// here we attempt to parse the url for the googleProject and the clusterName +function readFallbackConfig() { + const url = window.location.href; + const initialSearch = 'proxy/'; + + const projectSubstringStartLocation = url.search(initialSearch) + initialSearch.length; + const projectSubstring = url.substring(projectSubstringStartLocation, url.length); + const projectEndLocation = projectSubstring.search('/'); + const googleProject = projectSubstring.substring(0, projectEndLocation); + + // we add 1 for the slash between project and cluster + const clusterSubstring = projectSubstring.substring(projectEndLocation + 1, projectSubstring.length); + const clusterEndLocation = clusterSubstring.search('/'); + const clusterName = clusterSubstring.substring(0, clusterEndLocation); + + console.info(`Attempted to parse the url for a fallback configuration. + Found googleProject: '${googleProject}' and clusterName '${clusterName}'`); + + params.googleProject = googleProject; + params.clusterName = clusterName; + + fallbackReadNotebookConfig(googleProject, clusterName); +} + +function fallbackReadNotebookConfig(googleProject, clusterName) { + const url = `/proxy/${googleProject}/${clusterName}/jupyter/api/config/notebook`; + xhttpGet(url, (res) => { + readNotebookConfig(res); + }); +} + +function receive(event) { + if (event.data.type == 'bootstrap-auth.response') { + if (event.source !== window.opener) { + return; + } + params.googleClientId = event.data.body.googleClientId; + } else if (event.data.type == 'bootstrap-auth.request') { + if (event.origin !== window.origin) { + return; + } + if (!params.googleClientId) { + return; + } + event.source.postMessage({ + 'type': 'bootstrap-auth.response', + 'body': { + 'googleClientId': params.googleClientId + } + }, event.origin); + } +} + +// https://developer.mozilla.org/en-US/docs/Web/API/XMLHttpRequest/response +function xhttpGet(url, callback) { + const xhr = new XMLHttpRequest(); + + xhr.onreadystatechange = function() { + if (xhr.readyState === 4 && xhr.status == 200) { + const jsonResp = JSON.parse(xhr.responseText); + callback(jsonResp); + } + }; + + xhr.open('GET', url, true); + xhr.send(''); +} + +function startTimer() { + loadGapi('auth2', function() { + function doAuth() { + if (params.googleClientId) { + gapi.auth2.authorize({ + 'client_id': params.googleClientId, + 'scope': 'openid profile email', + 'login_hint': params.loginHint, + 'prompt': 'none' + }, function(result) { + if (result.error) { + console.error('Error occurred authorizing with Google: ' + result.error); + return; + } + setCookie(result.access_token, result.expires_in); + }); + } + } + + // refresh token every 3 minutes + console.log('Starting token refresh timer'); + setInterval(doAuth, 180000); + }); + + function statusCheck() { + const url = `/proxy/${params.googleProject}/${params.clusterName}/jupyter/api/status`; + // logging the statusCheck can be noisy, and it will tell us in the console if it fails + xhttpGet(url, () => {}); + } + + setInterval(statusCheck, 60000); +} + +// Note: this should match +// https://github.com/DataBiosphere/leonardo/blob/develop/http/src/main/scala/org/broadinstitute/dsde/workbench/leonardo/util/CookieHelper.scala +function setCookie(token, expiresIn) { + document.cookie = 'LeoToken=' + token + '; Max-Age=' + expiresIn + '; Path=/; Secure; SameSite=None'; +} + +function loadGapi(googleLib, continuation) { + console.log('Loading Google APIs'); + // Get the gapi script from Google. + const gapiScript = document.createElement('script'); + gapiScript.src = 'https://apis.google.com/js/api.js'; + gapiScript.type = 'text/javascript'; + gapiScript.async = true; + + // Load requested API scripts onto the page. + gapiScript.onload = function() { + console.log('Loading Google library \'' + googleLib + '\''); + gapi.load(googleLib, continuation); + }; + gapiScript.onerror = function() { + console.error('Unable to load Google APIs'); + }; + document.head.appendChild(gapiScript); +} + +function init() { + console.log('Starting google_sign_in extension'); + updateParams(); + startTimer(); + window.addEventListener('message', receive); + if (!params.googleClientId && window.opener) { + window.opener.postMessage({'type': 'bootstrap-auth.request'}, '*'); + } +} + +init(); diff --git a/terra-base/custom/jupyter_delocalize.py b/terra-base/custom/jupyter_delocalize.py new file mode 100644 index 00000000..e0e77bc9 --- /dev/null +++ b/terra-base/custom/jupyter_delocalize.py @@ -0,0 +1,148 @@ +from datetime import timedelta +import json +import os +import requests +import tornado +from notebook.services.contents.largefilemanager import LargeFileManager + +METADATA_TTL = timedelta(minutes=5) + +class WelderContentsManager(LargeFileManager): + """ + A contents manager which integrates with the Leo Welder service. + + Blocking Welder API calls are made before files are persisted. After a + successful call to Welder, files are persisted to the local Jupyter file + system as usual. + """ + + def __init__(self, *args, **kwargs): + # This log line shouldn't be necessary, but Jupyter's built-in logging is + # lacking and its configuration can be complex. Having this in the server + # logs is useful for confirming which ContentsManager is in use. + self.log.info('initializing WelderContentsManager') + self.welder_base_url = 'http://welder:8080' + super(WelderContentsManager, self).__init__(*args, **kwargs) + + def _extract_welder_error(self, resp): + try: + return json.dumps(resp.json()) + except: + return resp.reason or 'unknown Welder error' + + def _is_nonempty_dir(self, path): + os_path = self._get_os_path(path) + return os.path.isdir(os_path) and len(os.listdir(os_path)) > 0 + + + def _check_welder_edit_mode(self, path): + resp = requests.post(self.welder_base_url + '/objects/metadata', data=json.dumps({ + # Sometimes the Jupyter UI provided "path" contains a leading /, sometimes + # not; strip for Welder. + 'localPath': path.lstrip('/') + })) + if resp.status_code == 412: + return False + + if not resp.ok: + raise IOError("checkMetadata failed: '{}'".format(self._extract_welder_error(resp))) + + return resp.json().get("syncMode") == "EDIT" + + + def _post_welder(self, action, path): + # Ignore storage link failure, throw other errors. + resp = requests.post(self.welder_base_url + '/objects', data=json.dumps({ + 'action': action, + # Sometimes the Jupyter UI provided "path" contains a leading /, sometimes + # not; strip for Welder. + 'localPath': path.lstrip('/') + })) + if not resp.ok: + error_json = {} + try: + error_json = resp.json() + except: + pass + + # See https://github.com/DataBiosphere/welder/blob/cd39caba30989e9f2b1c76986abccf22d8e8a1c5/server/src/main/resources/api-docs.yaml#L197 + ignore_codes = set([ + 1, # Storage Link not found; expected for unmanaged files. + 2, 3 # Delocalize/delete safe mode file; expected in safe mode directories. + ]) + if resp.status_code == 412 and error_json.get('errorCode', -1) in ignore_codes: + return + + raise IOError("welder action '{}' failed: '{}'".format(action, self._extract_welder_error(resp))) + + def save(self, model, path=''): + # Don't intefere with intermediate chunks during multipart upload: + # https://jupyter-notebook.readthedocs.io/en/stable/extending/contents.html#chunked-saving + if model.get("chunk", -1) >= 0: + return super(WelderContentsManager, self).save(model, path) + + # Capture the pre-save file so we can revert if Welder fails. + orig_model = None + try: + orig_model = self.get(path) + except tornado.web.HTTPError as err: + if err.status_code != 404: + self.log.warn('failed to get file "{}", cannot revert: {}'.format(path, err.log_message)) + + # Welder reads the file from local disk, so we need to write the updated file + # before calling Welder. + # TODO(calbach): Consider changing the safeDelocalize API to support either + # direct passing of contents, or passing a file via a temporary transfer file. + ret = super(WelderContentsManager, self).save(model, path) + if not path or model['type'] == 'directory': + return ret + + try: + self._post_welder('safeDelocalize', path) + except IOError as werr: + self.log.warn("welder save failed, attempting to revert local file: " + str(werr)) + try: + if orig_model: + super(WelderContentsManager, self).save(orig_model, path) + else: + super(WelderContentsManager, self).delete_file(path) + except Exception as rerr: + self.log.error("failed to revert after Welder error, local disk is in an inconsistent state: " + str(rerr)) + raise werr + return ret + + def rename_file(self, old_path, new_path): + from_edit_mode = self._check_welder_edit_mode(old_path) + to_edit_mode = self._check_welder_edit_mode(new_path) + if not from_edit_mode and not to_edit_mode: + # If we're not touching any edit mode files, just do a normal move. + return super(WelderContentsManager, self).rename_file(old_path, new_path) + + if self._is_nonempty_dir(old_path): + raise NotImplementedError("renaming of non-empty edit mode directories is not supported") + + # These methods already properly handle edit mode semantics. + self.save(self.get(old_path), new_path) + try: + self.delete_file(old_path, from_edit_mode) + except Exception as err: + self.log.error("failed to delete old file during two-phase rename, " + + "attempting to revert save from the first phase: " + str(err)) + try: + self.delete_file(new_path, to_edit_mode) + except Exception as rerr: + self.log.error("failed to revert first phase of rename via delete, " + + "extra file will remain on disk and/or GCS: " + str(rerr)) + raise rerr + raise err + + def delete_file(self, path, edit_mode=None): + if edit_mode is None: + edit_mode = self._check_welder_edit_mode(path) + + if edit_mode: + if self._is_nonempty_dir(path): + raise NotImplementedError("deletion of non-empty edit mode directories is not supported") + self._post_welder('delete', path) + + super(WelderContentsManager, self).delete_file(path) diff --git a/terra-base/custom/jupyter_localize_extension.py b/terra-base/custom/jupyter_localize_extension.py new file mode 100644 index 00000000..bd7221ee --- /dev/null +++ b/terra-base/custom/jupyter_localize_extension.py @@ -0,0 +1,149 @@ +import distutils.util +import subprocess +import os +import sys +import tornado +from tornado import gen +from tornado.web import HTTPError +from notebook.base.handlers import IPythonHandler +from notebook.utils import url_path_join +from datauri import DataURI + +class LocalizeHandler(IPythonHandler): + def _sanitize(self, pathstr): + """Sanitizes paths. Handles local paths, gs: URIs, and data: URIs.""" + # return gs or data uris as is + if pathstr.startswith("gs:") or pathstr.startswith("data:"): + return pathstr + # expand user directories and make intermediate directories + else: + expanded = os.path.expanduser(pathstr) + try: + os.makedirs(os.path.dirname(expanded)) + except OSError: #thrown if dirs already exist + pass + return expanded + + def _localize_gcs_uri(self, locout, source, dest): + """Localizes an entry where either the source or destination is a gs: path. + Simply invokes gsutil in a subprocess.""" + + # Use a sequence of arguments with Shell=False. The subprocess module takes care + # of quoting/escaping arguments. See: + # https://docs.python.org/2/library/subprocess.html#subprocess.call + # https://docs.python.org/2/library/subprocess.html#frequently-used-arguments + cmd = ['gsutil', '-m', '-q', 'cp', '-R', '-c', '-e', source, dest] + locout.write(' '.join(cmd) + '\n') + result = subprocess.call(cmd, stderr=locout) + return result == 0 + + def check_gcs_object_status(self, locout, source): + if source.startswith("gs:"): + source_check = ['gsutil', '-m', '-q', 'ls', source] + locout.write(' '.join(source_check) + '\n') + source_status = subprocess.call(source_check, stderr=locout) + else: + source_status = 0 + return source_status == 0 + + def _localize_data_uri(self, locout, source, dest): + """Localizes an entry where the source is a data: URI""" + try: + uri = DataURI(source) + except ValueError: + locout.write('Could not parse "{}" as a data URI: {}\n'.format(source, str(e))) + return False + + try: + with open(dest, 'w+', buffering=1) as destout: + try: + uri_data = uri.data.decode() + except AttributeError: + uri_data = uri.data + destout.write(uri_data) + locout.write('{}: wrote {} bytes\n'.format(dest, len(uri_data))) + except IOError as e: + locout.write('{}: I/O error({0}): {1}\n'.format(dest, e.errno, e.strerror)) + return False + except: + locout.write('{}: unexpected error: {}\n'.format(sys.exc_info()[0])) + return False + + return True + + @gen.coroutine + def localize(self, pathdict): + """Treats the given dict as a string/string map and localizes each entry one by one. + Returns a list of any failed entries.""" + failures = [] + #This gets dropped inside the user's notebook working directory + with open("localization.log", 'a', buffering=1) as locout: + for key in pathdict: + #NOTE: keys are destinations, values are sources + source = self._sanitize(pathdict[key]) + dest = self._sanitize(key) + + if source.startswith('gs:') or dest.startswith('gs:'): + status = self.check_gcs_object_status(locout, source) + if status: + success = self._localize_gcs_uri(locout, source, dest) + else: + locout.write('Could not validate source or destination: {} -> {}.\n'.format(source, dest)) + success = False + elif source.startswith('data:'): + success = self._localize_data_uri(locout, source, dest) + else: + locout.write('Unhandled localization entry: {} -> {}. Required gs: or data: URIs.\n'.format(source, dest)) + success = False + + if not success: + failures.append((dest, source)) + + return failures + + def post(self): + try: + pathdict = tornado.escape.json_decode(self.request.body) + except ValueError: + raise HTTPError(400, "Body must be JSON object of type string/string") + + if type(pathdict) is not dict: + raise HTTPError(400, "Body must be JSON object of type string/string") + + if not all(map(lambda v: type(v) is str, pathdict.values())): + raise HTTPError(400, "Body must be JSON object of type string/string") + + try: + raw = self.get_query_argument('async', 'false') + isAsync = distutils.util.strtobool(raw) + except ValueError: + raise HTTPError(400, "Could not parse isAsync parameter as a boolean: '{}'".format(raw)) + + if isAsync: + #complete the request HERE, without waiting for the localize to run + self.set_status(200) + self.finish() + + #fire and forget the actual work -- it'll log to a file in the user's homedir + tornado.ioloop.IOLoop.current().spawn_callback(self.localize, pathdict) + + else: + #run localize synchronous to the HTTP request + #run_sync() doesn't take arguments, so we must wrap the call in a lambda. + failures = tornado.ioloop.IOLoop().run_sync(lambda: self.localize(pathdict)) + + #complete the request only after localize completes + if failures: + raise HTTPError(500, "Error occurred localizing the following {} entries: {}. See localization.log for details.".format( + len(failures), str(failures))) + else: + self.set_status(200) + self.finish() + +def load_jupyter_server_extension(nb_server_app): + """Entrypoint for the Jupyter extension.""" + web_app = nb_server_app.web_app + host_pattern = '.*$' + route_pattern = url_path_join(web_app.settings['base_url'], '/api/localize') + web_app.add_handlers(host_pattern, [(route_pattern, LocalizeHandler)]) + nb_server_app.log.info('initialized jupyter_localize_extension') diff --git a/terra-base/custom/package.json b/terra-base/custom/package.json new file mode 100644 index 00000000..1c1a6692 --- /dev/null +++ b/terra-base/custom/package.json @@ -0,0 +1,19 @@ +{ + "name": "jupyter-nbextension", + "version": "1.0.0", + "description": "Used exclusively for linting the nbextension files. See the README for instructions.", + "main": "edit-mode.js", + "directories": { + "test": "test" + }, + "dependencies": {}, + "devDependencies": { + "eslint": "^6.1.0", + "eslint-config-google": "^0.13.0" + }, + "scripts": { + "test": "echo \"Error: no test specified\" && exit 1" + }, + "author": "", + "license": "ISC" +} diff --git a/terra-base/custom/safe-mode.js b/terra-base/custom/safe-mode.js new file mode 100644 index 00000000..6adda657 --- /dev/null +++ b/terra-base/custom/safe-mode.js @@ -0,0 +1,128 @@ +// Adapted from the All of Us Researcher Workbench "Playground Mode" +// https://github.com/all-of-us/workbench/blob/master/api/cluster-resources/playground-extension.js + +// In "Safe Mode", changes are not saved back to GCS. This extension makes +// minor UI tweaks to differentiate this mode from normal Jupyter usage, and +// also removes/hides controls relating to persistence. Technically +// this does not stop autosave from continuing to happen in the background, but +// the intended use of this plugin is in a separate space from normal operation +// which does not support localization features. + +// const namespace = require('base/js/namespace') + +define(() => { + // define default values for config parameters + const params = { + googleProject: '', + clusterName: '', + welderEnabled: 'false' + }; + + // update params with any specified in the server's config file + function updateParams() { + const config = Jupyter.notebook.config; + for (const key in params) { + if (config.data.hasOwnProperty(key)) { + params[key] = config.data[key]; + } + } + + // generate URLs based on params + const welderUrl = `/proxy/${params.googleProject}/${params.clusterName}/welder`; + params.checkMetaUrl = welderUrl + '/objects/metadata'; + } + + const headers = { + 'Content-Type': 'application/json', + 'Access-Control-Allow-Headers': '*' + }; + + const basePayload = { + mode: 'no-cors', + headers: headers + }; + + function load() { + console.info('safe mode plugin initialized'); + + if (!Jupyter.notebook) { + return; // exit, they are in list view + } + + updateParams(); + + if (!(params.welderEnabled == 'true')) { + console.info('welder is not enabled'); + return; + } + + checkMetaLoop(); + } + + function checkMetaLoop() { + triggerUIToggle(); + + const interval = setInterval(() => { + triggerUIToggle(); + }, 60000); + + window.onbeforeunload(() => { + clearInterval(interval); + }); + } + + async function triggerUIToggle() { + checkMeta() + .then((res) => { + if (res.syncMode == 'EDIT') { + toggleUIControls(false); + } else { + // there is an icon in the jupyter UI that has a tool tip that says 'edit mode'. + // this shows up whenever a user types, so we change the tool-tip to avoid confusion + $('#modal_indicator').tooltip({'content': 'Adding code'}); + toggleUIControls(true); + } + }) + .catch((err) => { + console.error(err); + toggleUIControls(false); // we always assume safe mode if the check meta call fails + }); + } + + function checkMeta() { + const payload = { + ...basePayload, + body: JSON.stringify({localPath: Jupyter.notebook.notebook_path}), + method: 'POST' + }; + + return fetch(params.checkMetaUrl, payload) + .then((res) => { + if (!res.ok) { + throw Error('check metadata call failed due to status code'); + } + return res.json(); + }); + } + + function toggleUIControls(shouldHide) { + // these are the jquery selectors for the elements we will toggle + // "notbook" is an intentional typo to match the Jupyter UI HTML. + const selectorsToHide = ['#save-notbook', '#new_notebook', + '#open_notebook', '#copy_notebook', '#save_notebook_as', + '#save_checkpoint', '#restore_checkpoint', '.checkpoint_status', + '.autosave_status', '#notification_notebook', '#file_menu > li.divider:eq(0)', + '#file_menu > li.divider:eq(2)' + ]; + + selectorsToHide.forEach((selector) => { + if (shouldHide) { + $(selector).hide(); + } else { + $(selector).show(); + } + }); + } + + load(); +}); diff --git a/terra-base/custom/test/README.md b/terra-base/custom/test/README.md new file mode 100644 index 00000000..985b09cf --- /dev/null +++ b/terra-base/custom/test/README.md @@ -0,0 +1,16 @@ +## Python testing + +TODO: Integrate this into automated testing processes. + +- Initialize and activate a virtualenv +- Install requirements: + + ``` + jupyter-server$ pip3 install -r test-requirements.txt + ``` +- Run the tests: + + ``` + jupyter-server$ PYTHONPATH=$PYTHONPATH:. python3 -m nose + ``` + diff --git a/terra-base/custom/test/jupyter_delocalize_test.py b/terra-base/custom/test/jupyter_delocalize_test.py new file mode 100644 index 00000000..377a0274 --- /dev/null +++ b/terra-base/custom/test/jupyter_delocalize_test.py @@ -0,0 +1,448 @@ +import copy +import datetime +import json +import os +import requests_mock +import shutil +import tempfile +import unittest +from datetime import timedelta +from nbformat.v4 import new_notebook +from tornado.testing import AsyncTestCase, gen_test +from unittest.mock import patch + +# Import this first; see https://github.com/jupyter/notebook/issues/2798 +import notebook.transutils +import jupyter_delocalize + +class TestDelocalizingContentsManager(AsyncTestCase): + """DelocalizingContentsManager tests""" + + def setUp(self): + super(TestDelocalizingContentsManager, self).setUp() + self.orig_ttl = jupyter_delocalize.METADATA_TTL + jupyter_delocalize.METADATA_TTL = timedelta() + self.manager = jupyter_delocalize.DelocalizingContentsManager( + root_dir=tempfile.mkdtemp(), + delete_to_trash=False + ) + # Replaces gsutil with normal file commands. + self.manager.file_cmd = [] + self.manager.new(model={'type': 'directory'}, path='dir') + self.out_dir = tempfile.mkdtemp() + + def tearDown(self): + jupyter_delocalize.METADATA_TTL = self.orig_ttl + shutil.rmtree(self.manager.root_dir) + shutil.rmtree(self.out_dir) + super(TestDelocalizingContentsManager, self).tearDown() + + def _await_tornado(self): + # We spawn the delocalize processes in a Tornado callback, which executes + # asynchronously. + self.io_loop.add_callback(self.stop) + self.wait() + + def _save_new_notebook(self, path): + content = new_notebook() + self.manager.save({ + 'type': 'notebook', + 'content': content, + 'format': 'text' + }, path=path) + self._await_tornado() + return content.dict() + + def _save_delocalize_config(self, dir_path, config=None): + if not config: + config = { + 'destination': self.out_dir + } + self.manager.save({ + 'type': 'file', + 'content': json.dumps(config), + 'format': 'text' + }, path=dir_path + '/.delocalize.json') + self._await_tornado() + + def _rename_file(self, from_path, to_path): + self.manager.rename_file(from_path, to_path) + self._await_tornado() + + def _delete_file(self, path): + self.manager.delete_file(path) + self._await_tornado() + + def test_save_normal(self): + want = self._save_new_notebook('dir/foo.ipynb') + self.assertEqual(os.listdir(self.out_dir), []) + with open(self.manager.root_dir + '/dir/foo.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + def test_save_delocalize(self): + self._save_delocalize_config('dir') + want = self._save_new_notebook('dir/foo.ipynb') + + with open(self.out_dir + '/foo.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + with open(self.manager.root_dir + '/dir/foo.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + def test_save_delocalize_other_dirs(self): + self.manager.new(model={'type': 'directory'}, path='dirA') + self.manager.new(model={'type': 'directory'}, path='dir/dirB') + self._save_delocalize_config('dir') + + self._save_new_notebook('foo.ipynb') + self._save_new_notebook('dirA/fizz.ipynb') + self._save_new_notebook('dir/dirB/bar.ipynb') + self.assertEqual(os.listdir(self.out_dir), []) + + def test_save_delocalize_with_pattern(self): + self._save_delocalize_config('.', config={ + 'destination': self.out_dir, + 'pattern': '.*\.ipynb$' + }) + + self._save_new_notebook('foo.ipynb') + self._save_new_notebook('falco.jpg') + self._save_new_notebook('lombardi.pdf') + self.assertEqual(os.listdir(self.out_dir), ['foo.ipynb']) + + def test_rename_normal(self): + want = self._save_new_notebook('dir/foo.ipynb') + self._rename_file('dir/foo.ipynb', 'dir/bar.ipynb') + + self.assertFalse(os.path.isfile(self.manager.root_dir + '/dir/foo.ipynb')) + with open(self.manager.root_dir + '/dir/bar.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + def test_rename_delocalize(self): + self._save_delocalize_config('dir') + want = self._save_new_notebook('dir/foo.ipynb') + self._rename_file('dir/foo.ipynb', 'dir/bar.ipynb') + + self.assertFalse(os.path.isfile(self.out_dir + '/foo.ipynb')) + self.assertFalse(os.path.isfile(self.manager.root_dir + '/foo.ipynb')) + with open(self.out_dir + '/bar.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + with open(self.manager.root_dir + '/dir/bar.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + def test_rename_delocalize_with_pattern(self): + self._save_delocalize_config('dir', config={ + 'destination': self.out_dir, + 'pattern': 'foo' + }) + want = self._save_new_notebook('dir/foo.ipynb') + self._rename_file('dir/foo.ipynb', 'dir/bar.ipynb') + + # The delocalization behavior for foo.ipynb in this case is unspecified; + # currently it won't delete the file, but would be better if it did. + self.assertFalse(os.path.isfile(self.out_dir + '/bar.ipynb')) + self.assertFalse(os.path.isfile(self.manager.root_dir + '/foo.ipynb')) + with open(self.manager.root_dir + '/dir/bar.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + def test_delete_normal(self): + self._save_new_notebook('foo.ipynb') + self._delete_file('foo.ipynb') + + self.assertFalse(os.path.isfile(self.manager.root_dir + '/foo.ipynb')) + + def test_delete_delocalize(self): + self._save_delocalize_config('.') + self._save_new_notebook('foo.ipynb') + self._delete_file('foo.ipynb') + + self.assertFalse(os.path.isfile(self.out_dir + '/foo.ipynb')) + self.assertFalse(os.path.isfile(self.manager.root_dir + '/foo.ipynb')) + + def test_delete_delocalize_with_pattern(self): + self._save_delocalize_config('.') + self._save_new_notebook('foo.ipynb') + + self._save_delocalize_config('.', config={ + 'destination': self.out_dir, + 'pattern': 'doesnt match' + }) + self._delete_file('foo.ipynb') + + self.assertTrue(os.path.isfile(self.out_dir + '/foo.ipynb')) + self.assertFalse(os.path.isfile(self.manager.root_dir + '/foo.ipynb')) + + def test_metadata_cache(self): + jupyter_delocalize.METADATA_TTL = timedelta(minutes=5) + # Stub out and advance time manually. + now = datetime.datetime(2018, 3, 20) + self.manager._now = lambda: now + self._save_new_notebook('foo.ipynb') + self.assertEqual(os.listdir(self.out_dir), []) + + # A "not-found" should be cached, only 1 minute passed + now += timedelta(minutes=1) + self._save_delocalize_config('.') + self._save_new_notebook('foo.ipynb') + self.assertEqual(os.listdir(self.out_dir), []) + + # Cache TTL expired, will check again for delocalization config. + now += timedelta(minutes=20) + self._save_new_notebook('foo.ipynb') + self.assertEqual(os.listdir(self.out_dir), ['foo.ipynb']) + +class TestWelderContentsManager(AsyncTestCase): + """WelderContentsManager tests""" + + def setUp(self): + super(TestWelderContentsManager, self).setUp() + self.manager = jupyter_delocalize.WelderContentsManager( + root_dir=tempfile.mkdtemp(), + delete_to_trash=False + ) + self.manager.new(model={'type': 'directory'}, path='dir') + + def tearDown(self): + shutil.rmtree(self.manager.root_dir) + super(TestWelderContentsManager, self).tearDown() + + def _save_new_notebook(self, path): + content = new_notebook() + self.manager.save({ + 'type': 'notebook', + 'content': content, + 'format': 'text' + }, path=path) + return content.dict() + + def _save_new_dir(self, path): + self.manager.save({ + 'type': 'directory', + 'content': '[]', + 'format': 'json' + }, path=path) + + @requests_mock.mock() + def test_save(self, mock_request): + mock_request.post(self.manager.welder_base_url + '/objects') + want = self._save_new_notebook('dir/foo.ipynb') + with open(self.manager.root_dir + '/dir/foo.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + @requests_mock.mock() + def test_save_dir(self, mock_request): + self._save_new_dir('dir/foo') + self.assertTrue(os.path.isdir(self.manager.root_dir + '/dir/foo')) + + @requests_mock.mock() + def test_save_scratch_file(self, mock_request): + mock_request.post(self.manager.welder_base_url + '/objects', status_code=412, json={ + 'errorCode': 1 + }) + want = self._save_new_notebook('dir/foo.ipynb') + with open(self.manager.root_dir + '/dir/foo.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + @requests_mock.mock() + def test_save_new_file_reverts_on_fail(self, mock_request): + mock_request.post(self.manager.welder_base_url + '/objects', status_code=412, json={ + 'errorCode': 4 + }) + try: + self._save_new_notebook('dir/foo.ipynb') + self.fail('expected error on save') + except IOError: + pass + self.assertFalse(os.path.isfile(self.manager.root_dir + '/dir/foo.ipynb')) + + @requests_mock.mock() + def test_save_reverts_on_fail(self, mock_request): + mock_request.post(self.manager.welder_base_url + '/objects') + content = new_notebook() + self.manager.save({ + 'type': 'notebook', + 'content': content, + 'format': 'text' + }, path='dir/foo.ipynb') + + mock_request.post(self.manager.welder_base_url + '/objects', status_code=412) + updated_content = copy.deepcopy(content) + updated_content['cells'] = [{ + 'cell_type': 'markdown', + 'metadata': {}, + 'source': ['XD'], + }] + try: + self.manager.save({ + 'type': 'notebook', + 'content': updated_content, + 'format': 'text' + }, path='dir/foo.ipynb') + self.fail('expected error on save') + except IOError: + pass + with open(self.manager.root_dir + '/dir/foo.ipynb', 'r') as got: + self.assertEqual(json.load(got)['cells'], content.dict()['cells']) + + def mock_edit_mode_meta(self, mock_request, edit_mode=True): + if not edit_mode: + mock_request.post(self.manager.welder_base_url + '/objects/metadata', status_code=412) + else: + mock_request.post(self.manager.welder_base_url + '/objects/metadata', json={ + 'syncMode': 'EDIT' + }) + + @requests_mock.mock() + def test_delete(self, mock_request): + self.mock_edit_mode_meta(mock_request) + mock_request.post(self.manager.welder_base_url + '/objects') + self._save_new_notebook('dir/foo.ipynb') + + self.manager.delete_file('dir/foo.ipynb') + self.assertFalse(os.path.isfile(self.manager.root_dir + '/dir/foo.ipynb')) + + @requests_mock.mock() + def test_delete_empty_dir(self, mock_request): + self.mock_edit_mode_meta(mock_request) + mock_request.post(self.manager.welder_base_url + '/objects') + self._save_new_dir('dir/foo') + + self.manager.delete_file('dir/foo') + self.assertFalse(os.path.isdir(self.manager.root_dir + '/dir/foo')) + + @requests_mock.mock() + def test_delete_dir_with_notebook(self, mock_request): + self.mock_edit_mode_meta(mock_request) + mock_request.post(self.manager.welder_base_url + '/objects') + self._save_new_dir('dir/foo') + self._save_new_notebook('dir/foo/nb.ipynb') + + try: + self.manager.delete_file('dir/foo') + self.fail('expected error on non-empty edit mode directory deletion') + except NotImplementedError: + pass + self.assertTrue(os.path.isdir(self.manager.root_dir + '/dir/foo')) + + @requests_mock.mock() + def test_delete_scratch_file(self, mock_request): + self.mock_edit_mode_meta(mock_request, edit_mode=False) + mock_request.post(self.manager.welder_base_url + '/objects') + self._save_new_notebook('dir/foo.ipynb') + + self.manager.delete_file('dir/foo.ipynb') + self.assertFalse(os.path.isfile(self.manager.root_dir + '/dir/foo.ipynb')) + + @requests_mock.mock() + def test_delete_scratch_dir(self, mock_request): + self.mock_edit_mode_meta(mock_request, edit_mode=False) + self._save_new_dir('dir/foo') + + self.manager.delete_file('dir/foo') + self.assertFalse(os.path.isdir(self.manager.root_dir + '/dir/foo')) + + @requests_mock.mock() + def test_delete_local_file_survives_welder_error(self, mock_request): + self.mock_edit_mode_meta(mock_request) + mock_request.post(self.manager.welder_base_url + '/objects') + self._save_new_notebook('dir/foo.ipynb') + + mock_request.post(self.manager.welder_base_url + '/objects', status_code=412, json={ + 'errorCode': 4 + }) + try: + self.manager.delete_file('dir/foo.ipynb') + self.fail('expected error on delete') + except IOError: + pass + self.assertTrue(os.path.isfile(self.manager.root_dir + '/dir/foo.ipynb')) + + @requests_mock.mock() + def test_rename(self, mock_request): + post_mock = mock_request.post(self.manager.welder_base_url + '/objects') + self.mock_edit_mode_meta(mock_request) + want = self._save_new_notebook('dir/foo.ipynb') + + # Creating the initial notebook above results in a Welder post. + posts_before_rename = post_mock.call_count + self.manager.rename('dir/foo.ipynb', 'dir/bar.ipynb') + self.assertFalse(os.path.isfile(self.manager.root_dir + '/dir/foo.ipynb')) + with open(self.manager.root_dir + '/dir/bar.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + self.assertEqual(post_mock.call_count - posts_before_rename, 2) + + @requests_mock.mock() + def test_rename_empty_dir(self, mock_request): + self.mock_edit_mode_meta(mock_request) + mock_request.post(self.manager.welder_base_url + '/objects') + self._save_new_dir('dir/foo') + + self.manager.rename('dir/foo', 'dir/bar') + self.assertFalse(os.path.isdir(self.manager.root_dir + '/dir/foo')) + self.assertTrue(os.path.isdir(self.manager.root_dir + '/dir/bar')) + + @requests_mock.mock() + def test_rename_dir_with_notebook(self, mock_request): + post_mock = mock_request.post(self.manager.welder_base_url + '/objects') + self.mock_edit_mode_meta(mock_request) + self._save_new_dir('dir/foo') + self._save_new_notebook('dir/foo/nb.ipynb') + + try: + self.manager.rename('dir/foo', 'dir/bar') + self.fail('expected error on non-empty edit mode rename') + except: + pass + self.assertTrue(os.path.isdir(self.manager.root_dir + '/dir/foo')) + self.assertFalse(os.path.isdir(self.manager.root_dir + '/dir/bar')) + + @requests_mock.mock() + def test_rename_scratch_file(self, mock_request): + post_mock = mock_request.post(self.manager.welder_base_url + '/objects') + self.mock_edit_mode_meta(mock_request, edit_mode=False) + want = self._save_new_notebook('dir/foo.ipynb') + + # Creating the initial notebook above results in a Welder post. + posts_before_rename = post_mock.call_count + self.manager.rename('dir/foo.ipynb', 'dir/bar.ipynb') + self.assertFalse(os.path.isfile(self.manager.root_dir + '/dir/foo.ipynb')) + with open(self.manager.root_dir + '/dir/bar.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + + self.assertEqual(post_mock.call_count - posts_before_rename, 0) + + @requests_mock.mock() + def test_rename_scratch_dir(self, mock_request): + self.mock_edit_mode_meta(mock_request, edit_mode=False) + self._save_new_dir('dir/foo') + + self.manager.rename('dir/foo', 'dir/bar') + self.assertFalse(os.path.isdir(self.manager.root_dir + '/dir/foo')) + self.assertTrue(os.path.isdir(self.manager.root_dir + '/dir/bar')) + + def _delete_req_matcher(self, path): + def m(req): + return req.json()['action'] == 'delete' and req.json()['localPath'] == path + return m + + @requests_mock.mock() + def test_rename_cleanup_on_delete_fail(self, mock_request): + mock_request.post(self.manager.welder_base_url + '/objects') + mock_request.post(self.manager.welder_base_url + '/objects', additional_matcher=self._delete_req_matcher('dir/foo.ipynb'), status_code=500) + mock_request.post(self.manager.welder_base_url + '/objects', additional_matcher=self._delete_req_matcher('dir/bar.ipynb')) + self.mock_edit_mode_meta(mock_request) + want = self._save_new_notebook('dir/foo.ipynb') + + # Creating the initial notebook above results in a Welder post. + try: + self.manager.rename('dir/foo.ipynb', 'dir/bar.ipynb') + self.fail('expected rename exception') + except IOError: + pass + + self.assertFalse(os.path.isfile(self.manager.root_dir + '/dir/bar.ipynb')) + with open(self.manager.root_dir + '/dir/foo.ipynb', 'r') as got: + self.assertEqual(json.load(got), want) + +if __name__ == '__main__': + unittest.main() diff --git a/terra-base/custom/test/test-requirements.txt b/terra-base/custom/test/test-requirements.txt new file mode 100644 index 00000000..e7c6ae7e --- /dev/null +++ b/terra-base/custom/test/test-requirements.txt @@ -0,0 +1,3 @@ +jupyter==1.0.0 +nose==1.3.7 +requests-mock==1.6.0 diff --git a/terra-base/jupyter_notebook_config.py b/terra-base/jupyter_notebook_config.py new file mode 100755 index 00000000..c9f94268 --- /dev/null +++ b/terra-base/jupyter_notebook_config.py @@ -0,0 +1,44 @@ +# adapted from https://github.com/jupyter/docker-stacks/blob/master/base-notebook/jupyter_notebook_config.py +# Note: this file also lives in the Leonardo repo here: +# https://github.com/DataBiosphere/leonardo/blob/develop/http/src/main/resources/jupyter/jupyter_notebook_config.py +# If you change this please keep the other version consistent as well. + +import os + +c = get_config() + +if os.environ.get('JUPYTER_DEBUG_LOGGING') == 'true': + c.Application.log_level = 'DEBUG' + +c.NotebookApp.ip = '0.0.0.0' +c.NotebookApp.port = 8000 +c.NotebookApp.open_browser = False + +c.NotebookApp.token = '' +c.NotebookApp.disable_check_xsrf = True #see https://github.com/nteract/hydrogen/issues/922 +c.NotebookApp.allow_origin = '*' + +c.NotebookApp.terminado_settings={'shell_command': ['bash']} + +if 'GOOGLE_PROJECT' in os.environ and 'CLUSTER_NAME' in os.environ: + fragment = '/' + os.environ['GOOGLE_PROJECT'] + '/' + os.environ['CLUSTER_NAME'] + '/' +else: + fragment = '/' + +c.NotebookApp.base_url = '/notebooks' + fragment + +# This is also specified in run-jupyter.sh +c.NotebookApp.nbserver_extensions = { + 'jupyter_localize_extension': True +} + +c.NotebookApp.kernel_manager_class = 'notebook.services.kernels.kernelmanager.AsyncMappingKernelManager' + +mgr_class = 'DelocalizingContentsManager' +if os.environ.get('WELDER_ENABLED') == 'true': + mgr_class = 'WelderContentsManager' +c.NotebookApp.contents_manager_class = 'jupyter_delocalize.' + mgr_class + +c.NotebookApp.tornado_settings = { + 'static_url_prefix':'/notebooks' + fragment + 'static/' +} diff --git a/terra-base/poetry.lock b/terra-base/poetry.lock new file mode 100644 index 00000000..fa43dc77 --- /dev/null +++ b/terra-base/poetry.lock @@ -0,0 +1,4119 @@ +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. + 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"terra-base-env" +version = "0.1.0" +description = "" +authors = ["LizBaldo "] +readme = "README.md" + +[tool.poetry.dependencies] +python = "^3.10" +anaconda = "^0.0.1.1" +notebook = "^7.0.4" +cookiecutter = "^2.3.0" +tornado = "^6.3.3" +python-datauri = "^2.1.0" +jupyter-contrib-nbextensions = "^0.7.0" +jupyter-nbextensions-configurator = "^0.6.3" +markupsafe = "^2.1.3" +nbconvert = "^7.8.0" +nbclassic = "^1.0.0" +requests = "^2.31.0" +firecloud = "^0.16.35" +crcmod = "^1.7" +cromshell = "^2.0.0" +google-crc32c = "^1.5.0" +terra-notebook-utils = "^0.13.0" + + +[tool.poetry.dev-dependencies] +pytest = "*" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" \ No newline at end of file diff --git a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh new file mode 100644 index 00000000..378f4575 --- /dev/null +++ b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash + +set -e +# installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions +# also installs the jupyter_nbextensions_configurator https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator +sudo -E -u jupyter /opt/conda/bin/jupyter nbextensions_configurator enable --user +sudo -E -u jupyter /opt/conda/bin/jupyter contrib nbextension install --user +sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable toc2/main +sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable codefolding/main +sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable collapsible_headings/main + diff --git a/terra-base/scripts/extension/jupyter_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_install_combined_extension.sh new file mode 100644 index 00000000..396a3fea --- /dev/null +++ b/terra-base/scripts/extension/jupyter_install_combined_extension.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` + mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter /opt/conda/bin/jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --user + sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} +fi diff --git a/terra-base/scripts/extension/jupyter_install_lab_extension.sh b/terra-base/scripts/extension/jupyter_install_lab_extension.sh new file mode 100644 index 00000000..0c3c4eaf --- /dev/null +++ b/terra-base/scripts/extension/jupyter_install_lab_extension.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +set -e + + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + if [[ ${JUPYTER_EXTENSION} == *'.js' ]]; then + # use jupyterlab extension template to create an extension using the specified JS file + # see https://github.com/jupyterlab/extension-cookiecutter-js + JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` + cookiecutter --no-input https://github.com/jupyterlab/extension-cookiecutter-js extension_name=${JUPYTER_EXTENSION_NAME} + cp -f ${JUPYTER_EXTENSION} ${JUPYTER_EXTENSION_NAME}/lib/plugin.js + cd ${JUPYTER_EXTENSION_NAME} + jlpm + jupyter labextension install . + elif [[ ${JUPYTER_EXTENSION} == *'.ts' ]]; then + # same as above but in typescript, see https://github.com/jupyterlab/extension-cookiecutter-ts + JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` + cookiecutter --no-input https://github.com/jupyterlab/extension-cookiecutter-ts extension_name=${JUPYTER_EXTENSION_NAME} + cp -f ${JUPYTER_EXTENSION} ${JUPYTER_EXTENSION_NAME}/src/index.ts + cd ${JUPYTER_EXTENSION_NAME} + jlpm + jupyter labextension install . + else + jupyter labextension install $JUPYTER_EXTENSION + fi +fi + diff --git a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh new file mode 100644 index 00000000..ef038e2a --- /dev/null +++ b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh @@ -0,0 +1,15 @@ +#!/bin/bash +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` + mkdir -p ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + if [[ ${JUPYTER_EXTENSION} == *'.tar.gz' ]]; then + tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + else + mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js + fi + sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user + sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main +fi diff --git a/terra-base/scripts/extension/jupyter_install_server_extension.sh b/terra-base/scripts/extension/jupyter_install_server_extension.sh new file mode 100644 index 00000000..88816bb9 --- /dev/null +++ b/terra-base/scripts/extension/jupyter_install_server_extension.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` + mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} +fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh new file mode 100644 index 00000000..1054d99f --- /dev/null +++ b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + pip3 install ${JUPYTER_EXTENSION} + sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION} + sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION} --user + sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION} +fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh new file mode 100644 index 00000000..5ad45c9a --- /dev/null +++ b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh @@ -0,0 +1,9 @@ +#!/bin/bash +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + pip3 install ${JUPYTER_EXTENSION} + sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION} --user + sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION} +fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh new file mode 100644 index 00000000..c643d9f2 --- /dev/null +++ b/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh @@ -0,0 +1,9 @@ +#!/bin/bash + +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + pip3 install ${JUPYTER_EXTENSION} + sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION} +fi diff --git a/terra-base/scripts/kernel/kernel_bootstrap.sh b/terra-base/scripts/kernel/kernel_bootstrap.sh new file mode 100644 index 00000000..d4811a94 --- /dev/null +++ b/terra-base/scripts/kernel/kernel_bootstrap.sh @@ -0,0 +1,24 @@ +#!/usr/bin/env bash + +# This script runs at kernel startup time and sets environment variables for the +# workspace name and workspace bucket. +# +# Note: this script is highly dependent on a convention used by Terra and AllOfUs +# applications to place notebooks in the following directory structure: +# +# /home/jupyter///notebook.ipynb +# +# It exploits the fact that the CWD of a launching notebook is named after the workspace. +# If notebooks are ever launched from other directories, this script will break. + +PWD="$(pwd)" +# The workspace name is simply the CWD of the running notebook. +export WORKSPACE_NAME=`basename "$(dirname "$PWD")"` + +# Parse the .delocalize.json file (if it exists) in the workspace directory to obtain the workspace bucket. +DELOCALIZE_FILE="$PWD/.delocalize.json" +if [ -f "$DELOCALIZE_FILE" ]; then + export WORKSPACE_BUCKET="$(dirname "$(cat "$DELOCALIZE_FILE" | jq -r '.destination')")" +fi + +exec "$@" \ No newline at end of file diff --git a/terra-base/scripts/kernel/kernelspec.sh b/terra-base/scripts/kernel/kernelspec.sh new file mode 100644 index 00000000..59f1cc6f --- /dev/null +++ b/terra-base/scripts/kernel/kernelspec.sh @@ -0,0 +1,7 @@ +#!/usr/bin/env bash + +TMP_KERNELSPEC_DIR=$1 +KERNELSPEC_HOME=$2 + +# Replace the contents of the Python kernel scripts +sed -e 's/${PY_VERSION}/3/g' -e 's|${JUPYTER_HOME}|'${JUPYTER_HOME}'|g' ${TMP_KERNELSPEC_DIR}/python_kernelspec.tmpl > ${KERNELSPEC_HOME}/python3/kernel.json diff --git a/terra-base/scripts/kernel/python_kernelspec.tmpl b/terra-base/scripts/kernel/python_kernelspec.tmpl new file mode 100644 index 00000000..a2b0b66a --- /dev/null +++ b/terra-base/scripts/kernel/python_kernelspec.tmpl @@ -0,0 +1,12 @@ +{ + "language": "python", + "display_name": "Python ${PY_VERSION}", + "argv": [ + "${JUPYTER_HOME}/scripts/kernel/kernel_bootstrap.sh", + "python${PY_VERSION}", + "-m", + "ipykernel_launcher", + "-f", + "{connection_file}" + ] +} diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh new file mode 100644 index 00000000..2d527695 --- /dev/null +++ b/terra-base/scripts/run-jupyter.sh @@ -0,0 +1,17 @@ +#!/usr/bin/env bash + +set -e + +# Change the default umask to support R/W access to the shared volume with welder +umask 002 + +# TODO: change default to ${HOME}/notebooks once welder is rolled out to all clusters +NOTEBOOKS_DIR=${1:-${HOME}} + +# Forces python 3 +JUPYTER_BASE="/opt/conda/bin/python3 /opt/conda/bin/jupyter-notebook" +JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" + +echo $JUPYTER_CMD + +eval $JUPYTER_CMD From 82c8ec9434e9b7533447cd3df31950b21c2cfc86 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 12 Oct 2023 12:54:13 -0400 Subject: [PATCH 02/19] remove opt/conda jupyter path --- .../extension/install_jupyter_contrib_nbextensions.sh | 10 +++++----- .../extension/jupyter_install_combined_extension.sh | 6 +++--- .../extension/jupyter_install_notebook_extension.sh | 4 ++-- .../jupyter_pip_install_notebook_extension.sh | 4 ++-- terra-base/scripts/run-jupyter.sh | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-) diff --git a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh index 378f4575..59492924 100644 --- a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh +++ b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh @@ -3,9 +3,9 @@ set -e # installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions # also installs the jupyter_nbextensions_configurator https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator -sudo -E -u jupyter /opt/conda/bin/jupyter nbextensions_configurator enable --user -sudo -E -u jupyter /opt/conda/bin/jupyter contrib nbextension install --user -sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable toc2/main -sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable codefolding/main -sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable collapsible_headings/main +sudo -E -u jupyter jupyter nbextensions_configurator enable --user +sudo -E -u jupyter jupyter contrib nbextension install --user +sudo -E -u jupyter jupyter nbextension enable toc2/main +sudo -E -u jupyter jupyter nbextension enable codefolding/main +sudo -E -u jupyter jupyter nbextension enable collapsible_headings/main diff --git a/terra-base/scripts/extension/jupyter_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_install_combined_extension.sh index 396a3fea..2d82b796 100644 --- a/terra-base/scripts/extension/jupyter_install_combined_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_combined_extension.sh @@ -8,7 +8,7 @@ if [ -n "$1" ]; then mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter /opt/conda/bin/jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --user - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --user + sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} fi diff --git a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh index ef038e2a..85b8f30f 100644 --- a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh @@ -10,6 +10,6 @@ if [ -n "$1" ]; then else mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js fi - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main + sudo -E -u jupyter jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user + sudo -E -u jupyter jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh index 5ad45c9a..1b7020bb 100644 --- a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh +++ b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh @@ -4,6 +4,6 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension install --py ${JUPYTER_EXTENSION} --user - sudo -E -u jupyter /opt/conda/bin/jupyter nbextension enable --py ${JUPYTER_EXTENSION} + sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION} --user + sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION} fi diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh index 2d527695..4584d548 100644 --- a/terra-base/scripts/run-jupyter.sh +++ b/terra-base/scripts/run-jupyter.sh @@ -9,7 +9,7 @@ umask 002 NOTEBOOKS_DIR=${1:-${HOME}} # Forces python 3 -JUPYTER_BASE="/opt/conda/bin/python3 /opt/conda/bin/jupyter-notebook" +JUPYTER_BASE="python3 jupyter-notebook" JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From d5dc18a8c40712c26a9dd3ff5372395ffd1b423c Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 12 Oct 2023 14:59:43 -0400 Subject: [PATCH 03/19] use nbclassic instead of notebook to maintain backward compatibility with nbextensions --- terra-base/Dockerfile | 2 +- .../extension/install_jupyter_contrib_nbextensions.sh | 10 +++++----- .../extension/jupyter_install_combined_extension.sh | 6 +++--- .../extension/jupyter_install_notebook_extension.sh | 4 ++-- .../extension/jupyter_install_server_extension.sh | 2 +- .../jupyter_pip_install_combined_extension.sh | 6 +++--- .../jupyter_pip_install_notebook_extension.sh | 4 ++-- .../extension/jupyter_pip_install_server_extension.sh | 2 +- terra-base/scripts/run-jupyter.sh | 2 +- 9 files changed, 19 insertions(+), 19 deletions(-) diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile index 4f0c8cf6..94fda863 100644 --- a/terra-base/Dockerfile +++ b/terra-base/Dockerfile @@ -141,4 +141,4 @@ USER $USER # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. Jupyter execution occurs when the # init-actions.sh script uses 'docker exec' to call run-jupyter.sh. -ENTRYPOINT ["jupyter", "notebook"] \ No newline at end of file +ENTRYPOINT ["jupyter", "nbclassic"] \ No newline at end of file diff --git a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh index 59492924..109ff880 100644 --- a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh +++ b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh @@ -3,9 +3,9 @@ set -e # installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions # also installs the jupyter_nbextensions_configurator https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator -sudo -E -u jupyter jupyter nbextensions_configurator enable --user -sudo -E -u jupyter jupyter contrib nbextension install --user -sudo -E -u jupyter jupyter nbextension enable toc2/main -sudo -E -u jupyter jupyter nbextension enable codefolding/main -sudo -E -u jupyter jupyter nbextension enable collapsible_headings/main +sudo -E -u jupyter nbextensions_configurator enable --user +sudo -E -u jupyter contrib nbextension install --user +sudo -E -u jupyter nbextension enable toc2/main +sudo -E -u jupyter nbextension enable codefolding/main +sudo -E -u jupyter nbextension enable collapsible_headings/main diff --git a/terra-base/scripts/extension/jupyter_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_install_combined_extension.sh index 2d82b796..ce596185 100644 --- a/terra-base/scripts/extension/jupyter_install_combined_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_combined_extension.sh @@ -8,7 +8,7 @@ if [ -n "$1" ]; then mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --user - sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --user + sudo -E -u jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} fi diff --git a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh index 85b8f30f..84a8d720 100644 --- a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh @@ -10,6 +10,6 @@ if [ -n "$1" ]; then else mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js fi - sudo -E -u jupyter jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user - sudo -E -u jupyter jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main + sudo -E -u jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user + sudo -E -u jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main fi diff --git a/terra-base/scripts/extension/jupyter_install_server_extension.sh b/terra-base/scripts/extension/jupyter_install_server_extension.sh index 88816bb9..d37688fa 100644 --- a/terra-base/scripts/extension/jupyter_install_server_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_server_extension.sh @@ -8,5 +8,5 @@ if [ -n "$1" ]; then mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} + sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh index 1054d99f..100cacba 100644 --- a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh +++ b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh @@ -5,7 +5,7 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION} - sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION} --user - sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION} + sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION} + sudo -E -u jupyter nbextension install --py ${JUPYTER_EXTENSION} --user + sudo -E -u jupyter nbextension enable --py ${JUPYTER_EXTENSION} fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh index 1b7020bb..11b49c4b 100644 --- a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh +++ b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh @@ -4,6 +4,6 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter jupyter nbextension install --py ${JUPYTER_EXTENSION} --user - sudo -E -u jupyter jupyter nbextension enable --py ${JUPYTER_EXTENSION} + sudo -E -u jupyter nbextension install --py ${JUPYTER_EXTENSION} --user + sudo -E -u jupyter nbextension enable --py ${JUPYTER_EXTENSION} fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh index c643d9f2..bd1fdd92 100644 --- a/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh +++ b/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh @@ -5,5 +5,5 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter jupyter serverextension enable --py ${JUPYTER_EXTENSION} + sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION} fi diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh index 4584d548..f28433d7 100644 --- a/terra-base/scripts/run-jupyter.sh +++ b/terra-base/scripts/run-jupyter.sh @@ -9,7 +9,7 @@ umask 002 NOTEBOOKS_DIR=${1:-${HOME}} # Forces python 3 -JUPYTER_BASE="python3 jupyter-notebook" +JUPYTER_BASE="python3 jupyter-nbclassic" JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 1efe5a53d47d5a40c722382d11aba91ac5f35f2d Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 12 Oct 2023 16:27:00 -0400 Subject: [PATCH 04/19] do not install notebook extensions anymore - should not be necessary with notebook 7+ --- terra-base/Dockerfile | 2 +- terra-base/poetry.lock | 1436 +++++++---------- terra-base/pyproject.toml | 3 - .../install_jupyter_contrib_nbextensions.sh | 11 - .../jupyter_install_combined_extension.sh | 2 - .../jupyter_install_notebook_extension.sh | 15 - .../jupyter_pip_install_combined_extension.sh | 2 - .../jupyter_pip_install_notebook_extension.sh | 9 - terra-base/scripts/run-jupyter.sh | 2 +- 9 files changed, 551 insertions(+), 931 deletions(-) delete mode 100644 terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh delete mode 100644 terra-base/scripts/extension/jupyter_install_notebook_extension.sh delete mode 100644 terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile index 94fda863..4f0c8cf6 100644 --- a/terra-base/Dockerfile +++ b/terra-base/Dockerfile @@ -141,4 +141,4 @@ USER $USER # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. 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= "^7.0.4" cookiecutter = "^2.3.0" tornado = "^6.3.3" python-datauri = "^2.1.0" -jupyter-contrib-nbextensions = "^0.7.0" -jupyter-nbextensions-configurator = "^0.6.3" markupsafe = "^2.1.3" nbconvert = "^7.8.0" -nbclassic = "^1.0.0" requests = "^2.31.0" firecloud = "^0.16.35" crcmod = "^1.7" diff --git a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh deleted file mode 100644 index 109ff880..00000000 --- a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env bash - -set -e -# installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions -# also installs the jupyter_nbextensions_configurator https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator -sudo -E -u jupyter nbextensions_configurator enable --user -sudo -E -u jupyter contrib nbextension install --user -sudo -E -u jupyter nbextension enable toc2/main -sudo -E -u jupyter nbextension enable codefolding/main -sudo -E -u jupyter nbextension enable collapsible_headings/main - diff --git a/terra-base/scripts/extension/jupyter_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_install_combined_extension.sh index ce596185..d37688fa 100644 --- a/terra-base/scripts/extension/jupyter_install_combined_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_combined_extension.sh @@ -9,6 +9,4 @@ if [ -n "$1" ]; then tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter nbextension install --py ${JUPYTER_EXTENSION_NAME} --user - sudo -E -u jupyter nbextension enable --py ${JUPYTER_EXTENSION_NAME} fi diff --git a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh deleted file mode 100644 index 84a8d720..00000000 --- a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` - mkdir -p ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - if [[ ${JUPYTER_EXTENSION} == *'.tar.gz' ]]; then - tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - else - mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js - fi - sudo -E -u jupyter nbextension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user - sudo -E -u jupyter nbextension enable ${JUPYTER_EXTENSION_NAME}/main -fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh index 100cacba..bd1fdd92 100644 --- a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh +++ b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh @@ -6,6 +6,4 @@ if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 pip3 install ${JUPYTER_EXTENSION} sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION} - sudo -E -u jupyter nbextension install --py ${JUPYTER_EXTENSION} --user - sudo -E -u jupyter nbextension enable --py ${JUPYTER_EXTENSION} fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh deleted file mode 100644 index 11b49c4b..00000000 --- a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter nbextension install --py ${JUPYTER_EXTENSION} --user - sudo -E -u jupyter nbextension enable --py ${JUPYTER_EXTENSION} -fi diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh index f28433d7..4584d548 100644 --- a/terra-base/scripts/run-jupyter.sh +++ b/terra-base/scripts/run-jupyter.sh @@ -9,7 +9,7 @@ umask 002 NOTEBOOKS_DIR=${1:-${HOME}} # Forces python 3 -JUPYTER_BASE="python3 jupyter-nbclassic" +JUPYTER_BASE="python3 jupyter-notebook" JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 6c42c840ee70f30779cba5b3ef840cb3f726733a Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 25 Oct 2023 11:23:04 -0400 Subject: [PATCH 05/19] better jupyter creation best practice, sudo permissions, and conda installation --- terra-base/Dockerfile | 88 ++++++++++++++++--------- terra-base/README.md | 1 + terra-base/custom/jupyter_delocalize.py | 2 +- terra-base/jupyter_notebook_config.py | 2 +- terra-base/poetry.lock | 13 +--- terra-base/pyproject.toml | 1 - terra-base/scripts/run-jupyter.sh | 3 +- 7 files changed, 63 insertions(+), 47 deletions(-) diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile index 4f0c8cf6..1d1e2eb6 100644 --- a/terra-base/Dockerfile +++ b/terra-base/Dockerfile @@ -6,32 +6,36 @@ FROM --platform=linux/amd64 nvidia/cuda:12.2.0-base-ubuntu22.04 ####################### ENV DEBIAN_FRONTEND noninteractive ENV LC_ALL en_US.UTF-8 -ENV USER jupyter -ENV HOME /home/$USER # Ensure this matches c.NotebookApp.port in jupyter_notebook_config.py ENV JUPYTER_PORT 8000 ENV JUPYTER_HOME /etc/jupyter ENV JUPYTER_KERNELSPEC_DIR /usr/local/share/jupyter -# The welder uid is consistent with the Welder docker definition here: -# https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala -# Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added -# files display nicer when viewed in a terminal. -ENV WELDER_USER welder-user -ENV WELDER_UID 1001 -# When using PIP_USER=true packages are installed into Python site.USER_BASE, which is '/home/jupyter' for this system. -# Append '/home/jupyter/.local/bin' to PATH -# pip docs: https://pip.pypa.io/en/stable/reference/pip_install/#cmdoption-user -ENV PATH "${PATH}:${HOME}/.local/bin:${HOME}/packages/bin:${POETRY_DIR}/bin" # We need node >18 for jupyter to work ENV NODE_MAJOR 20 ####################### # Users Setup ####################### -RUN useradd -m -s /bin/bash $USER -RUN usermod -g users $USER +# Create the jupyter user, add it to the `users` group and specify the home directory path +ENV USER jupyter +ENV USER_HOME /home/$USER +RUN useradd -m -s /bin/bash -d $USER_HOME -N -g users $USER +# Create the welder user +# The welder uid is consistent with the Welder docker definition here: +# https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala +# Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added +# files display nicer when viewed in a terminal. +ENV WELDER_USER welder-user +ENV WELDER_UID 1001 RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER +# We want to grant the jupyter user limited sudo permissions +# without password so they can install the necessary packages that they +# want to use on the docker container +RUN mkdir -p /etc/sudoers.d \ + && echo "$USER ALL=(ALL) NOPASSWD: /usr/bin/apt-get install *, /opt/conda install *, /opt/poetry install *" > /etc/sudoers.d/$USER \ + && chmod 0440 /etc/sudoers.d/$USER + ####################### # Prerequisites ####################### @@ -39,6 +43,7 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \ sudo \ ca-certificates \ curl \ + jq \ # gnupg requirement gnupg \ dirmngr \ @@ -80,28 +85,42 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \ && apt-get clean \ && rm -rf /var/lib/apt/lists/* -RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - -RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key add - +RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - +RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - -# Install Node >18 +# Install Node >18 (needed for jupyterlab) RUN apt-get update && apt-get install -yq --no-install-recommends -RUN sudo mkdir -p /etc/apt/keyrings -RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | sudo gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg +RUN mkdir -p /etc/apt/keyrings +RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg + +RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list +RUN dpkg --remove --force-remove-reinstreq libnode-dev +RUN apt-get update && apt-get install -f -yq nodejs -RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | sudo tee /etc/apt/sources.list.d/nodesource.list -RUN sudo dpkg --remove --force-remove-reinstreq libnode-dev -RUN sudo apt-get update && apt-get install -f -yq nodejs +############ +# Install R +############ +RUN apt-get update && apt-get install -y r-base -######################################## -# Manage python dependencies with poetry -######################################## +################ +# Install Python +################ # Install Python 3.10 and add to python path RUN apt-get update && apt-get install -y python3.10 python3-pip RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.10 1 \ && update-alternatives --set python /usr/bin/python3.10 +############################ +# Manage python dependencies +############################ +## POETRY is the prefered tool to create virtual environments and +## manage dependencies - Should be used by Terra devs # Install Poetry -RUN curl -sSL https://install.python-poetry.org | python3 +ENV POETRY_HOME /opt/poetry +RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME python3 +# Append '/home/jupyter/.local/bin' to PATH +# poetry docs: https://python-poetry.org/docs/ +ENV PATH "${PATH}:${POETRY_HOME}/bin" # Prevent poetry from creating a virtual environment (we want to install on the docker system python) RUN poetry config virtualenvs.create false @@ -109,7 +128,16 @@ RUN poetry config virtualenvs.create false # Install python dependencies with poetry COPY poetry.lock . COPY pyproject.toml . -RUN poetry install --no-root --no-cache --no-interaction +RUN poetry install --no-cache --no-interaction + +## CONDA should not be used by terra devs, but is a widely used tools +## to manage python environments in a runtime and we should provide it to users +ENV CONDA_HOME /opt/conda +RUN curl -so $HOME/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.1-0-Linux-x86_64.sh \ + && chmod +x $HOME/miniconda.sh \ + && $HOME/miniconda.sh -b -p $CONDA_HOME \ + && rm $HOME/miniconda.sh +ENV PATH "${PATH}:${CONDA_HOME}/bin" # ####################### # # Utilities @@ -117,6 +145,7 @@ RUN poetry install --no-root --no-cache --no-interaction COPY scripts $JUPYTER_HOME/scripts COPY custom $JUPYTER_HOME/custom COPY jupyter_notebook_config.py $JUPYTER_HOME +RUN chown -R $USER:users $JUPYTER_HOME # copy workspace_cromwell.py script and make it runnable by all users RUN curl -o /usr/local/bin/workspace_cromwell.py https://raw.githubusercontent.com/broadinstitute/cromwhelm/1ceedf89587cffd355f37401b179001f029f77ed/scripts/workspace_cromwell.py \ @@ -127,10 +156,9 @@ RUN chown -R $USER:users $JUPYTER_KERNELSPEC_DIR \ # You can get kernel directory by running `jupyter kernelspec list` && $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel $JUPYTER_KERNELSPEC_DIR/kernels -# Make sure that the jupyter user will have access to the jupyter path in the worksing directory +# Make sure that the jupyter user will have access to the jupyter path in the working directory EXPOSE $JUPYTER_PORT -WORKDIR $HOME -RUN sudo chown -R $USER:users $HOME/.local/share +WORKDIR $USER_HOME # make pip install to a user directory, instead of a system directory which requires root. # this is useful so `pip install` commands can be run in the context of a notebook. diff --git a/terra-base/README.md b/terra-base/README.md index 02fdd651..e0d597e6 100644 --- a/terra-base/README.md +++ b/terra-base/README.md @@ -12,6 +12,7 @@ requirements necessary to set up Jupyter and provide compatibility with Leonardo - OS prerequisites - Python 3.10 +- R 4.1.2 - Anaconda - Jupyter - Leonardo customizations/extensions diff --git a/terra-base/custom/jupyter_delocalize.py b/terra-base/custom/jupyter_delocalize.py index e0e77bc9..ded62c4d 100644 --- a/terra-base/custom/jupyter_delocalize.py +++ b/terra-base/custom/jupyter_delocalize.py @@ -3,7 +3,7 @@ import os import requests import tornado -from notebook.services.contents.largefilemanager import LargeFileManager +from jupyter_server.services.contents.largefilemanager import LargeFileManager METADATA_TTL = timedelta(minutes=5) diff --git a/terra-base/jupyter_notebook_config.py b/terra-base/jupyter_notebook_config.py index c9f94268..490ece52 100755 --- a/terra-base/jupyter_notebook_config.py +++ b/terra-base/jupyter_notebook_config.py @@ -32,7 +32,7 @@ 'jupyter_localize_extension': True } -c.NotebookApp.kernel_manager_class = 'notebook.services.kernels.kernelmanager.AsyncMappingKernelManager' +c.NotebookApp.kernel_manager_class = 'jupyter_server.services.kernels.kernelmanager.AsyncMappingKernelManager' mgr_class = 'DelocalizingContentsManager' if os.environ.get('WELDER_ENABLED') == 'true': diff --git a/terra-base/poetry.lock b/terra-base/poetry.lock index 8fbbf403..280e32f7 100644 --- a/terra-base/poetry.lock +++ b/terra-base/poetry.lock @@ -124,17 +124,6 @@ files = [ [package.dependencies] frozenlist = ">=1.1.0" -[[package]] -name = "anaconda" -version = "0.0.1.1" -description = "Please use the Anaconda installer." -category = "main" -optional = false -python-versions = "*" -files = [ - {file = "anaconda-0.0.1.1.tar.gz", hash = "sha256:2e26def2dc581e92783d62772d8bf8c8328c9cc10407dc51c94268ca41decf37"}, -] - [[package]] name = "anyio" version = "4.0.0" @@ -3778,4 +3767,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "8e761b8c0c8b14e41e9a89512b0b5e98219efa0bb1c8493bddfced33d20e90f3" +content-hash = "00881af73ba51e0dbaf45d0fd7d2058c56d84c9de282b1187d3e0db68837b0b8" diff --git a/terra-base/pyproject.toml b/terra-base/pyproject.toml index 13066412..2d8e4342 100644 --- a/terra-base/pyproject.toml +++ b/terra-base/pyproject.toml @@ -7,7 +7,6 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.10" -anaconda = "^0.0.1.1" notebook = "^7.0.4" cookiecutter = "^2.3.0" tornado = "^6.3.3" diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh index 4584d548..fe5478ad 100644 --- a/terra-base/scripts/run-jupyter.sh +++ b/terra-base/scripts/run-jupyter.sh @@ -8,8 +8,7 @@ umask 002 # TODO: change default to ${HOME}/notebooks once welder is rolled out to all clusters NOTEBOOKS_DIR=${1:-${HOME}} -# Forces python 3 -JUPYTER_BASE="python3 jupyter-notebook" +JUPYTER_BASE="jupyter-notebook" JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 9863460c391e5d9a4838de0d2fb824859838f6ce Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 26 Oct 2023 14:27:17 -0400 Subject: [PATCH 06/19] this seems to work well on my BEE so saving it --- terra-base/Dockerfile | 12 +++++++++--- terra-base/jupyter_notebook_config.py | 1 + terra-base/scripts/run-jupyter.sh | 1 + 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile index 1d1e2eb6..4e2ac3d2 100644 --- a/terra-base/Dockerfile +++ b/terra-base/Dockerfile @@ -33,7 +33,7 @@ RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER # without password so they can install the necessary packages that they # want to use on the docker container RUN mkdir -p /etc/sudoers.d \ - && echo "$USER ALL=(ALL) NOPASSWD: /usr/bin/apt-get install *, /opt/conda install *, /opt/poetry install *" > /etc/sudoers.d/$USER \ + && echo "$USER ALL=(ALL) NOPASSWD: /usr/bin/apt-get install *, conda install *, poetry install" > /etc/sudoers.d/$USER \ && chmod 0440 /etc/sudoers.d/$USER ####################### @@ -105,7 +105,10 @@ RUN apt-get update && apt-get install -y r-base ################ # Install Python ################ -# Install Python 3.10 and add to python path +# Install Python 3.10 and add to system python path +# Note that miniconda does come with it's own installation of python, +# but it is cleaner to do a proper system instalation here and set the +# path properly RUN apt-get update && apt-get install -y python3.10 python3-pip RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.10 1 \ && update-alternatives --set python /usr/bin/python3.10 @@ -130,6 +133,9 @@ COPY poetry.lock . COPY pyproject.toml . RUN poetry install --no-cache --no-interaction +################### +# Install Miniconda +################### ## CONDA should not be used by terra devs, but is a widely used tools ## to manage python environments in a runtime and we should provide it to users ENV CONDA_HOME /opt/conda @@ -169,4 +175,4 @@ USER $USER # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. Jupyter execution occurs when the # init-actions.sh script uses 'docker exec' to call run-jupyter.sh. -ENTRYPOINT ["jupyter", "notebook"] \ No newline at end of file +ENTRYPOINT ["/usr/local/bin/jupyter-notebook"] \ No newline at end of file diff --git a/terra-base/jupyter_notebook_config.py b/terra-base/jupyter_notebook_config.py index 490ece52..144fe7bf 100755 --- a/terra-base/jupyter_notebook_config.py +++ b/terra-base/jupyter_notebook_config.py @@ -13,6 +13,7 @@ c.NotebookApp.ip = '0.0.0.0' c.NotebookApp.port = 8000 c.NotebookApp.open_browser = False +c.NotebookApp.use_redirect_file = False c.NotebookApp.token = '' c.NotebookApp.disable_check_xsrf = True #see https://github.com/nteract/hydrogen/issues/922 diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh index fe5478ad..9f4e07a4 100644 --- a/terra-base/scripts/run-jupyter.sh +++ b/terra-base/scripts/run-jupyter.sh @@ -9,6 +9,7 @@ umask 002 NOTEBOOKS_DIR=${1:-${HOME}} JUPYTER_BASE="jupyter-notebook" +JUPYTER_BASE="/usr/bin/python /usr/local/bin/jupyter-notebook" JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 907590786c302d0c61e186c38205c22dc7ffda89 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Fri, 27 Oct 2023 13:45:24 -0400 Subject: [PATCH 07/19] latest backup --- terra-base/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile index 4e2ac3d2..7d98d124 100644 --- a/terra-base/Dockerfile +++ b/terra-base/Dockerfile @@ -33,7 +33,7 @@ RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER # without password so they can install the necessary packages that they # want to use on the docker container RUN mkdir -p /etc/sudoers.d \ - && echo "$USER ALL=(ALL) NOPASSWD: /usr/bin/apt-get install *, conda install *, poetry install" > /etc/sudoers.d/$USER \ + && echo "$USER ALL=(ALL) NOPASSWD: /usr/bin/apt-get install *, /opt/conda/bin/conda install *, /opt/poetry/bin/poetry install" > /etc/sudoers.d/$USER \ && chmod 0440 /etc/sudoers.d/$USER ####################### From 9a63654a97a0170d0f5daf283b9d1324437a78c4 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Tue, 31 Oct 2023 21:12:36 -0400 Subject: [PATCH 08/19] use nbclassic to stay backward compatible with js extensions --- terra-base/Dockerfile | 2 +- terra-base/custom/extension_entry_jupyter.js | 2 +- terra-base/poetry.lock | 239 +++++++++++++++++- terra-base/pyproject.toml | 2 + .../install_jupyter_contrib_nbextensions.sh | 15 ++ .../jupyter_install_combined_extension.sh | 2 +- .../jupyter_install_notebook_extension.sh | 15 ++ .../jupyter_install_server_extension.sh | 2 +- .../jupyter_pip_install_combined_extension.sh | 2 +- .../jupyter_pip_install_notebook_extension.sh | 9 + .../jupyter_pip_install_server_extension.sh | 2 +- terra-base/scripts/run-jupyter.sh | 3 +- 12 files changed, 286 insertions(+), 9 deletions(-) create mode 100644 terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh create mode 100644 terra-base/scripts/extension/jupyter_install_notebook_extension.sh create mode 100644 terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile index 7d98d124..9af6eef6 100644 --- a/terra-base/Dockerfile +++ b/terra-base/Dockerfile @@ -175,4 +175,4 @@ USER $USER # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. Jupyter execution occurs when the # init-actions.sh script uses 'docker exec' to call run-jupyter.sh. -ENTRYPOINT ["/usr/local/bin/jupyter-notebook"] \ No newline at end of file +ENTRYPOINT ["/usr/local/bin/jupyter-nbclassic"] \ No newline at end of file diff --git a/terra-base/custom/extension_entry_jupyter.js b/terra-base/custom/extension_entry_jupyter.js index 0515b726..9d07f2dd 100644 --- a/terra-base/custom/extension_entry_jupyter.js +++ b/terra-base/custom/extension_entry_jupyter.js @@ -4,4 +4,4 @@ define([ require(['custom/google_sign_in']); require(['custom/edit-mode']); require(['custom/safe-mode']); -}); +}); \ No newline at end of file diff --git a/terra-base/poetry.lock b/terra-base/poetry.lock index 280e32f7..5a1ed399 100644 --- a/terra-base/poetry.lock +++ b/terra-base/poetry.lock @@ -1577,6 +1577,18 @@ qtconsole = ["qtconsole"] test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] +[[package]] +name = "ipython-genutils" +version = "0.2.0" +description = "Vestigial utilities from IPython" +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "ipython_genutils-0.2.0-py2.py3-none-any.whl", hash = "sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8"}, + {file = "ipython_genutils-0.2.0.tar.gz", hash = "sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"}, +] + [[package]] name = "isoduration" version = "20.11.0" @@ -1755,6 +1767,53 @@ traitlets = ">=5.3" docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"] +[[package]] +name = "jupyter-contrib-core" +version = "0.4.2" +description = "Common utilities for jupyter-contrib projects." +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "jupyter_contrib_core-0.4.2.tar.gz", hash = "sha256:1887212f3ca9d4487d624c0705c20dfdf03d5a0b9ea2557d3aaeeb4c38bdcabb"}, +] + +[package.dependencies] +jupyter_core = "*" +notebook = ">=4.0" +setuptools = "*" +tornado = "*" +traitlets = "*" + +[package.extras] +testing-utils = ["mock", "nose"] + +[[package]] +name = "jupyter-contrib-nbextensions" +version = "0.7.0" +description = "A collection of Jupyter nbextensions." +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "jupyter_contrib_nbextensions-0.7.0.tar.gz", hash = "sha256:06e33f005885eb92f89cbe82711e921278201298d08ab0d886d1ba09e8c3e9ca"}, +] + +[package.dependencies] +ipython_genutils = "*" +jupyter_contrib_core = ">=0.3.3" +jupyter_core = "*" +jupyter_highlight_selected_word = ">=0.1.1" +jupyter_nbextensions_configurator = ">=0.4.0" +lxml = "*" +nbconvert = ">=6.0" +notebook = ">=6.0" +tornado = "*" +traitlets = ">=4.1" + +[package.extras] +test = ["mock", "nbformat", "nose", "pip", "requests"] + [[package]] name = "jupyter-core" version = "5.4.0" @@ -1802,6 +1861,18 @@ cli = ["click", "rich"] docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme", "sphinxcontrib-spelling"] test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "rich"] +[[package]] +name = "jupyter-highlight-selected-word" +version = "0.2.0" +description = "Jupyter notebook extension that enables highlighting every instance of the current word in the notebook." +category = "main" +optional = false +python-versions = "*" +files = [ + {file = "jupyter_highlight_selected_word-0.2.0-py2.py3-none-any.whl", hash = "sha256:9545dfa9cb057eebe3a5795604dcd3a5294ea18637e553f61a0b67c1b5903c58"}, + {file = "jupyter_highlight_selected_word-0.2.0.tar.gz", hash = "sha256:9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b"}, +] + 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"sha256:48628bd53a426c9eb9bc066a923acaa0878d1e86129fd5359aee99285f4eed9c"}, +] + +[package.extras] +cssselect = ["cssselect (>=0.7)"] +html5 = ["html5lib"] +htmlsoup = ["BeautifulSoup4"] +source = ["Cython (>=0.29.35)"] + [[package]] name = "markdown-it-py" version = "3.0.0" @@ -2213,6 +2414,42 @@ files = [ {file = "multidict-6.0.4.tar.gz", hash = "sha256:3666906492efb76453c0e7b97f2cf459b0682e7402c0489a95484965dbc1da49"}, ] +[[package]] +name = "nbclassic" +version = "1.0.0" +description = "Jupyter Notebook as a Jupyter Server extension." +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "nbclassic-1.0.0-py3-none-any.whl", hash = "sha256:f99e4769b4750076cd4235c044b61232110733322384a94a63791d2e7beacc66"}, + {file = "nbclassic-1.0.0.tar.gz", hash = "sha256:0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3"}, +] + +[package.dependencies] +argon2-cffi = "*" +ipykernel = "*" +ipython-genutils = "*" +jinja2 = "*" +jupyter-client = ">=6.1.1" +jupyter-core = ">=4.6.1" +jupyter-server = ">=1.8" +nbconvert = ">=5" +nbformat = "*" +nest-asyncio = ">=1.5" +notebook-shim = ">=0.2.3" +prometheus-client = "*" +pyzmq = ">=17" +Send2Trash = ">=1.8.0" +terminado = ">=0.8.3" +tornado = ">=6.1" +traitlets = ">=4.2.1" + +[package.extras] +docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] +json-logging = ["json-logging"] +test = ["coverage", "nbval", "pytest", "pytest-cov", "pytest-jupyter", "pytest-playwright", "pytest-tornasync", "requests", "requests-unixsocket", "testpath"] + [[package]] name = "nbclient" version = "0.8.0" @@ -3767,4 +4004,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "00881af73ba51e0dbaf45d0fd7d2058c56d84c9de282b1187d3e0db68837b0b8" +content-hash = "7ba5037a36b003bfbae87fe0582a205c6a6e77a6cac1cd889dff154e46871e62" diff --git a/terra-base/pyproject.toml b/terra-base/pyproject.toml index 2d8e4342..5cf51c0f 100644 --- a/terra-base/pyproject.toml +++ b/terra-base/pyproject.toml @@ -19,6 +19,8 @@ crcmod = "^1.7" cromshell = "^2.0.0" google-crc32c = "^1.5.0" terra-notebook-utils = "^0.13.0" +nbclassic = "^1.0.0" +jupyter-contrib-nbextensions = "^0.7.0" [tool.poetry.dev-dependencies] diff --git a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh new file mode 100644 index 00000000..47b2725f --- /dev/null +++ b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh @@ -0,0 +1,15 @@ +#!/usr/bin/env bash + +# installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions +# unfortunately this package is not compatible with new versions of notebooks +# or nbclassic, so this is a temporary hack to directly install the js extensions +# using NBclassic + +set -e +NBEXTENSION_HOME=/usr/local/lib/python3.10/dist-packages/jupyter_contrib_nbextensions/nbextensions +jupyter nbclassic-extension install ${NBEXTENSION_HOME}/toc2 --user +jupyter nbclassic-extension install ${NBEXTENSION_HOME}/codefolding --user +jupyter nbclassic-extension install ${NBEXTENSION_HOME}/collapsible_headings --user +jupyter nbclassic-extension enable toc2/main +jupyter nbclassic-extension enable codefolding/main +jupyter nbclassic-extension enable collapsible_headings/main diff --git a/terra-base/scripts/extension/jupyter_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_install_combined_extension.sh index d37688fa..7a2b3081 100644 --- a/terra-base/scripts/extension/jupyter_install_combined_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_combined_extension.sh @@ -8,5 +8,5 @@ if [ -n "$1" ]; then mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} + jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} fi diff --git a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh new file mode 100644 index 00000000..cf43eaa1 --- /dev/null +++ b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh @@ -0,0 +1,15 @@ +#!/bin/bash +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` + mkdir -p ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + if [[ ${JUPYTER_EXTENSION} == *'.tar.gz' ]]; then + tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} + else + mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js + fi + jupyter nbclassic-extension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user + jupyter nbclassic-extension enable ${JUPYTER_EXTENSION_NAME}/main +fi diff --git a/terra-base/scripts/extension/jupyter_install_server_extension.sh b/terra-base/scripts/extension/jupyter_install_server_extension.sh index d37688fa..7a2b3081 100644 --- a/terra-base/scripts/extension/jupyter_install_server_extension.sh +++ b/terra-base/scripts/extension/jupyter_install_server_extension.sh @@ -8,5 +8,5 @@ if [ -n "$1" ]; then mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} + jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh index bd1fdd92..8c4c5557 100644 --- a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh +++ b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh @@ -5,5 +5,5 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION} + jupyter serverextension enable --py ${JUPYTER_EXTENSION} fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh new file mode 100644 index 00000000..0215f14f --- /dev/null +++ b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh @@ -0,0 +1,9 @@ +#!/bin/bash +set -e + +if [ -n "$1" ]; then + JUPYTER_EXTENSION=$1 + pip3 install ${JUPYTER_EXTENSION} + jupyter nbclassic-extension install --py ${JUPYTER_EXTENSION} --user + jupyter nbclassic-extension enable --py ${JUPYTER_EXTENSION} +fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh index bd1fdd92..8c4c5557 100644 --- a/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh +++ b/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh @@ -5,5 +5,5 @@ set -e if [ -n "$1" ]; then JUPYTER_EXTENSION=$1 pip3 install ${JUPYTER_EXTENSION} - sudo -E -u jupyter serverextension enable --py ${JUPYTER_EXTENSION} + jupyter serverextension enable --py ${JUPYTER_EXTENSION} fi diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh index 9f4e07a4..88acd892 100644 --- a/terra-base/scripts/run-jupyter.sh +++ b/terra-base/scripts/run-jupyter.sh @@ -8,8 +8,7 @@ umask 002 # TODO: change default to ${HOME}/notebooks once welder is rolled out to all clusters NOTEBOOKS_DIR=${1:-${HOME}} -JUPYTER_BASE="jupyter-notebook" -JUPYTER_BASE="/usr/bin/python /usr/local/bin/jupyter-notebook" +JUPYTER_BASE="/usr/bin/python /usr/local/bin/jupyter-nbclassic" JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 0d4096e07d7662f89979086f29be5c5140620b09 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Tue, 9 Apr 2024 21:53:59 -0400 Subject: [PATCH 09/19] working image with jupyter in base and user virtual environment --- terra-base-jupyter/Dockerfile | 192 + {terra-base => terra-base-jupyter}/README.md | 0 terra-base-jupyter/conda-environment.yml | 11 + terra-base-jupyter/conda_init.txt | 14 + .../custom/.eslintrc.js | 0 .../custom/README.md | 0 .../custom/extension_entry_jupyterlab.js | 0 .../custom/google_sign_in.js | 0 .../custom/jupyter_delocalize.py | 2 +- .../custom/package.json | 0 .../custom/test/README.md | 0 .../custom/test/jupyter_delocalize_test.py | 0 .../custom/test/test-requirements.txt | 0 terra-base-jupyter/ipython_config.py | 1 + terra-base-jupyter/jupyter_server_config.py | 13 + terra-base-jupyter/poetry.lock | 2395 ++++++++++ .../poetry.toml | 0 terra-base-jupyter/pyproject.toml | 21 + terra-base-jupyter/run-jupyter.sh | 18 + terra-base/.python-version | 1 - terra-base/Dockerfile | 178 - terra-base/custom/edit-mode.js | 447 -- terra-base/custom/extension_entry_jupyter.js | 7 - .../custom/jupyter_localize_extension.py | 149 - terra-base/custom/safe-mode.js | 128 - terra-base/jupyter_notebook_config.py | 45 - terra-base/poetry.lock | 4007 ----------------- terra-base/pyproject.toml | 31 - .../install_jupyter_contrib_nbextensions.sh | 15 - .../jupyter_install_combined_extension.sh | 12 - .../jupyter_install_lab_extension.sh | 29 - .../jupyter_install_notebook_extension.sh | 15 - .../jupyter_install_server_extension.sh | 12 - .../jupyter_pip_install_combined_extension.sh | 9 - .../jupyter_pip_install_notebook_extension.sh | 9 - .../jupyter_pip_install_server_extension.sh | 9 - terra-base/scripts/kernel/kernel_bootstrap.sh | 24 - terra-base/scripts/kernel/kernelspec.sh | 7 - .../scripts/kernel/python_kernelspec.tmpl | 12 - terra-base/scripts/run-jupyter.sh | 16 - 40 files changed, 2666 insertions(+), 5163 deletions(-) create mode 100644 terra-base-jupyter/Dockerfile rename {terra-base => terra-base-jupyter}/README.md (100%) create mode 100644 terra-base-jupyter/conda-environment.yml create mode 100644 terra-base-jupyter/conda_init.txt rename {terra-base => terra-base-jupyter}/custom/.eslintrc.js (100%) rename {terra-base => terra-base-jupyter}/custom/README.md (100%) rename {terra-base => terra-base-jupyter}/custom/extension_entry_jupyterlab.js (100%) rename {terra-base => terra-base-jupyter}/custom/google_sign_in.js (100%) rename {terra-base => terra-base-jupyter}/custom/jupyter_delocalize.py (99%) rename {terra-base => terra-base-jupyter}/custom/package.json (100%) rename {terra-base => terra-base-jupyter}/custom/test/README.md (100%) rename {terra-base => terra-base-jupyter}/custom/test/jupyter_delocalize_test.py (100%) rename {terra-base => terra-base-jupyter}/custom/test/test-requirements.txt (100%) create mode 100644 terra-base-jupyter/ipython_config.py create mode 100644 terra-base-jupyter/jupyter_server_config.py create mode 100644 terra-base-jupyter/poetry.lock rename {terra-base => terra-base-jupyter}/poetry.toml (100%) create mode 100644 terra-base-jupyter/pyproject.toml create mode 100644 terra-base-jupyter/run-jupyter.sh delete mode 100644 terra-base/.python-version delete mode 100644 terra-base/Dockerfile delete mode 100644 terra-base/custom/edit-mode.js delete mode 100644 terra-base/custom/extension_entry_jupyter.js delete mode 100644 terra-base/custom/jupyter_localize_extension.py delete mode 100644 terra-base/custom/safe-mode.js delete mode 100755 terra-base/jupyter_notebook_config.py delete mode 100644 terra-base/poetry.lock delete mode 100644 terra-base/pyproject.toml delete mode 100644 terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh delete mode 100644 terra-base/scripts/extension/jupyter_install_combined_extension.sh delete mode 100644 terra-base/scripts/extension/jupyter_install_lab_extension.sh delete mode 100644 terra-base/scripts/extension/jupyter_install_notebook_extension.sh delete mode 100644 terra-base/scripts/extension/jupyter_install_server_extension.sh delete mode 100644 terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh delete mode 100644 terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh delete mode 100644 terra-base/scripts/extension/jupyter_pip_install_server_extension.sh delete mode 100644 terra-base/scripts/kernel/kernel_bootstrap.sh delete mode 100644 terra-base/scripts/kernel/kernelspec.sh delete mode 100644 terra-base/scripts/kernel/python_kernelspec.tmpl delete mode 100644 terra-base/scripts/run-jupyter.sh diff --git a/terra-base-jupyter/Dockerfile b/terra-base-jupyter/Dockerfile new file mode 100644 index 00000000..aca5ad56 --- /dev/null +++ b/terra-base-jupyter/Dockerfile @@ -0,0 +1,192 @@ +# Smallest image with ubuntu jammy, CUDA and NVDIA drivers installed - 80 mb +FROM --platform=linux/amd64 nvidia/cuda:12.2.0-base-ubuntu22.04 + +####################### +# Environment Variables +####################### +ENV DEBIAN_FRONTEND noninteractive +ENV LC_ALL en_US.UTF-8 + +# We need node >18 for jupyter to work +ENV NODE_MAJOR 20 + +############# +# Users Setup +############# +# Create the jupyter home directories where they will save their +# notebooks and install their conda environments +# Note that there is no jupyter user created, the intent is to run this docker +# container as root +ENV USER_HOME /home/jupyter +RUN mkdir $USER_HOME +# We want to store the user virtual environments in a directory +# that will be in the persistent disk +ENV CONDA_ENV_NAME terra-python3.10 +ENV CONDA_ENV_HOME $USER_HOME/.envs/$CONDA_ENV_NAME +RUN mkdir -p $CONDA_ENV_HOME + +# Create the welder user +# The welder uid is consistent with the Welder docker definition here: +# https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala +# Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added +# files display nicer when viewed in a terminal. +ENV WELDER_USER welder-user +ENV WELDER_UID 1001 +RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER + +############### +# Prerequisites +############### +RUN apt-get update && apt-get install -yq --no-install-recommends \ + sudo \ + ca-certificates \ + curl \ + jq \ + # gnupg requirement + gnupg \ + dirmngr \ + # useful utilities for debugging within the docker + nano \ + procps \ + lsb-release \ + # python requirements + checkinstall \ + build-essential \ + zlib1g-dev \ + # pip requirements + libssl-dev \ + libbz2-dev \ + libreadline-dev \ + libsqlite3-dev \ + libexempi8 \ + libnode-dev \ + llvm \ + libncurses5-dev \ + libncursesw5-dev \ + tk-dev \ + libffi-dev \ + liblzma-dev \ + python3-openssl \ + # install script requirements + locales \ + # for ssh-agent and ssh-add + keychain \ + # extras \ + wget \ + bzip2 \ + # git + git \ + # Uncomment en_US.UTF-8 for inclusion in generation + && sed -i 's/^# *\(en_US.UTF-8\)/\1/' /etc/locale.gen \ + # Generate locale + && locale-gen \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +# Install Node >18 (needed for jupyterlab) +RUN apt-get update && apt-get install -yq --no-install-recommends +RUN mkdir -p /etc/apt/keyrings +RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg + +RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list +RUN dpkg --remove --force-remove-reinstreq libnode-dev +RUN apt-get update && apt-get install -f -yq nodejs + +############################## +# Install Python via Miniconda +############################## +## Note: CONDA should not be used by terra devs, but is a widely used tools +## to manage python environments in a runtime and we should provide it to users +ENV CONDA_HOME /opt/conda +RUN curl -so $HOME/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.1-0-Linux-x86_64.sh \ + && chmod +x $HOME/miniconda.sh \ + && $HOME/miniconda.sh -b -p $CONDA_HOME \ + && rm $HOME/miniconda.sh +ENV PATH "${PATH}:${CONDA_HOME}/bin" + +ENV BASE_PYTHON_PATH /opt/conda/bin/python +ENV PYTHONDONTWRITEBYTECODE=true + +################################################ +# Install Jupyter in the base python environment +################################################ +## POETRY is the prefered tool to create virtual environments and +## manage dependencies - Should be used by Terra devs - poetry docs: https://python-poetry.org/docs/ +ENV POETRY_HOME /opt/poetry +# Append POETRY_HOME to PATH +ENV PATH "${PATH}:${POETRY_HOME}/bin" +COPY poetry.lock . +COPY pyproject.toml . + +# Install Poetry, set up the base environment for jupyter to run and then cleanup / uninstall poetry +RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE_PYTHON_PATH \ + # Prevent poetry from creating a virtual environment (we want to install on the docker system python) + && poetry config virtualenvs.create false \ + # Install python dependencies with poetry + && poetry install --no-dev --no-cache --no-interaction \ + # Cleanup + && rm poetry.lock && rm pyproject.toml \ + && curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE_PYTHON_PATH - --uninstall + +# Remove the base environment from the list of available kernels so it is hidden from the user +# Note that this needs to be done with setting the c.KernelSpecManager.ensure_native_kernel flag +# to False in 'jupyter_server_config.py' +RUN jupyter kernelspec remove python3 -y + +####################################################### +# Create a CONDA virtual environment for user isolation +####################################################### +# Create a new conda environment for the user, activate it, and add it to the list of python kernels +# This step is a bit slow to build, but worth it to provide the user with an isolated environment +COPY conda-environment.yml . +RUN conda env create -f conda-environment.yml --prefix=$CONDA_ENV_HOME\ + # Remove packages tarballs and python bytecode files from the image + && conda clean -afy \ + && find $CONDA_ENV_HOME -follow -type f -name '*.pyc' -delete \ + && rm conda-environment.yml +# Add the user conda environment as a jupyter kernel - this should be the default now +# This commands activates the conda environment and then calls ipykernel from within +# to install it as a kernel under the same name +RUN conda run -p ${CONDA_ENV_HOME} python -m ipykernel install --user --name=$CONDA_ENV_NAME + +# Automagically activate the user conda environment when opening the jupyter terminal +COPY conda_init.txt . +RUN cat conda_init.txt >> ~/.bashrc && \ + printf "\nconda activate ${CONDA_ENV_HOME}" >> ~/.bashrc && \ + conda config --set env_prompt '({name})' && \ + echo "auto_activate_base: false" >> ~/.condarc && \ + rm conda_init.txt + +# ################################## +# # Terra-specific Jupyter Utilities +# ################################## +# Ensure this matches c.ServerApp.port in 'jupyter_server_config.py' +ENV JUPYTER_PORT 8888 +EXPOSE $JUPYTER_PORT +ENV JUPYTER_HOME /etc/jupyter + +# Install the custom extensions to enable welder for file syncing +COPY custom $JUPYTER_HOME/custom +ENV PYTHON_LIBRARIES_PATH $CONDA_HOME/lib/python3.10/site-packages +COPY custom/jupyter_delocalize.py $PYTHON_LIBRARIES_PATH +COPY jupyter_server_config.py $JUPYTER_HOME + +# Disable the use of system shell commands in the notebook to avoid users +# interacting with our base python via the notebook +ENV IPYTHON_HOME /etc/ipython/ +COPY ipython_config.py $IPYTHON_HOME + +# Set up the working directory to be /home/jupyter, and make sure the +# shell is bash, like the jupyter terminal (just nicer to work with than sh) +WORKDIR $USER_HOME +ENV SHELL /usr/bin/bash +SHELL ["/usr/bin/bash", "-c"] +RUN source ~/.bashrc + +# Copy the script that the service deploying to Terra (e.g. leonardo) will use for docker exec +COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh +# Note: this entrypoint is provided for running Jupyter independently of Leonardo. +# When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable +# additional setup inside the container before execution. Jupyter execution occurs when the +# init-actions.sh script uses 'docker exec' to call run-jupyter.sh. +ENTRYPOINT ["/opt/conda/bin/jupyter", "lab"] \ No newline at end of file diff --git a/terra-base/README.md b/terra-base-jupyter/README.md similarity index 100% rename from terra-base/README.md rename to terra-base-jupyter/README.md diff --git a/terra-base-jupyter/conda-environment.yml b/terra-base-jupyter/conda-environment.yml new file mode 100644 index 00000000..d43aee93 --- /dev/null +++ b/terra-base-jupyter/conda-environment.yml @@ -0,0 +1,11 @@ +name: terra-base +channels: + - defaults +dependencies: + - pip=23.1.2 + - python=3.10.12 + - pip: + - bgzip==0.3.5 + - firecloud==0.16.37 + - ipykernel==6.29.4 + - terra-notebook-utils==0.13.0 \ No newline at end of file diff --git a/terra-base-jupyter/conda_init.txt b/terra-base-jupyter/conda_init.txt new file mode 100644 index 00000000..36711f02 --- /dev/null +++ b/terra-base-jupyter/conda_init.txt @@ -0,0 +1,14 @@ +# >>> conda initialize >>> +# !! Contents within this block are managed by 'conda init' !! +__conda_setup="$('/opt/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" +if [ $? -eq 0 ]; then +eval "$__conda_setup" +else +if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then +. "/opt/conda/etc/profile.d/conda.sh" +else +export PATH="/opt/conda/bin:$PATH" +fi +fi +unset __conda_setup +# <<< conda initialize <<< diff --git a/terra-base/custom/.eslintrc.js b/terra-base-jupyter/custom/.eslintrc.js similarity index 100% rename from terra-base/custom/.eslintrc.js rename to terra-base-jupyter/custom/.eslintrc.js diff --git a/terra-base/custom/README.md b/terra-base-jupyter/custom/README.md similarity index 100% rename from terra-base/custom/README.md rename to terra-base-jupyter/custom/README.md diff --git a/terra-base/custom/extension_entry_jupyterlab.js b/terra-base-jupyter/custom/extension_entry_jupyterlab.js similarity index 100% rename from terra-base/custom/extension_entry_jupyterlab.js rename to terra-base-jupyter/custom/extension_entry_jupyterlab.js diff --git a/terra-base/custom/google_sign_in.js b/terra-base-jupyter/custom/google_sign_in.js similarity index 100% rename from terra-base/custom/google_sign_in.js rename to terra-base-jupyter/custom/google_sign_in.js diff --git a/terra-base/custom/jupyter_delocalize.py b/terra-base-jupyter/custom/jupyter_delocalize.py similarity index 99% rename from terra-base/custom/jupyter_delocalize.py rename to terra-base-jupyter/custom/jupyter_delocalize.py index ded62c4d..7537e17a 100644 --- a/terra-base/custom/jupyter_delocalize.py +++ b/terra-base-jupyter/custom/jupyter_delocalize.py @@ -21,7 +21,7 @@ def __init__(self, *args, **kwargs): # lacking and its configuration can be complex. Having this in the server # logs is useful for confirming which ContentsManager is in use. self.log.info('initializing WelderContentsManager') - self.welder_base_url = 'http://welder:8080' + self.welder_base_url = 'http://127.0.0.1:8081' super(WelderContentsManager, self).__init__(*args, **kwargs) def _extract_welder_error(self, resp): diff --git a/terra-base/custom/package.json b/terra-base-jupyter/custom/package.json similarity index 100% rename from terra-base/custom/package.json rename to terra-base-jupyter/custom/package.json diff --git a/terra-base/custom/test/README.md b/terra-base-jupyter/custom/test/README.md similarity index 100% rename from terra-base/custom/test/README.md rename to terra-base-jupyter/custom/test/README.md diff --git a/terra-base/custom/test/jupyter_delocalize_test.py b/terra-base-jupyter/custom/test/jupyter_delocalize_test.py similarity index 100% rename from terra-base/custom/test/jupyter_delocalize_test.py rename to terra-base-jupyter/custom/test/jupyter_delocalize_test.py diff --git a/terra-base/custom/test/test-requirements.txt b/terra-base-jupyter/custom/test/test-requirements.txt similarity index 100% rename from terra-base/custom/test/test-requirements.txt rename to terra-base-jupyter/custom/test/test-requirements.txt diff --git a/terra-base-jupyter/ipython_config.py b/terra-base-jupyter/ipython_config.py new file mode 100644 index 00000000..275d1916 --- /dev/null +++ b/terra-base-jupyter/ipython_config.py @@ -0,0 +1 @@ +#c.InteractiveShellApp.exec_lines = ['get_ipython().system = lambda *args: print("Use of the ! operator is disabled, please use the % operator in the notebook cell, or do the operation in the terminal instead.")'] diff --git a/terra-base-jupyter/jupyter_server_config.py b/terra-base-jupyter/jupyter_server_config.py new file mode 100644 index 00000000..2d93b40c --- /dev/null +++ b/terra-base-jupyter/jupyter_server_config.py @@ -0,0 +1,13 @@ +from jupyter_delocalize import 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["poetry-core"] +build-backend = "poetry.core.masonry.api" \ No newline at end of file diff --git a/terra-base-jupyter/run-jupyter.sh b/terra-base-jupyter/run-jupyter.sh new file mode 100644 index 00000000..99572082 --- /dev/null +++ b/terra-base-jupyter/run-jupyter.sh @@ -0,0 +1,18 @@ +#!/usr/bin/env bash + +set -e + +# Change the default umask to support R/W access to the shared volume with welder +umask 002 + +# TODO: change default to ${HOME}/notebooks once welder is rolled out to all clusters +SERVER_APP_BASE_URL=${1:-${HOME}} +SERVER_APP_WEBSOCKET_URL=${2:-${HOME}} +NOTEBOOKS_DIR=${3:-${HOME}} + +JUPYTER_BASE="/opt/conda/bin/python /opt/conda/bin/jupyter server" +JUPYTER_CMD="$JUPYTER_BASE --ServerApp.base_url=${SERVER_APP_BASE_URL} --ServerApp.websocket_url=${SERVER_APP_WEBSOCKET_URL} --autoreload --notebook-dir=${NOTEBOOKS_DIR}&> ${NOTEBOOKS_DIR}/jupyter.log" + +echo $JUPYTER_CMD + +eval $JUPYTER_CMD diff --git a/terra-base/.python-version b/terra-base/.python-version deleted file mode 100644 index c8cfe395..00000000 --- a/terra-base/.python-version +++ /dev/null @@ -1 +0,0 @@ -3.10 diff --git a/terra-base/Dockerfile b/terra-base/Dockerfile deleted file mode 100644 index 9af6eef6..00000000 --- a/terra-base/Dockerfile +++ /dev/null @@ -1,178 +0,0 @@ -# Smallest image with ubuntu jammy, CUDA and NVDIA drivers installed - 80 mb -FROM --platform=linux/amd64 nvidia/cuda:12.2.0-base-ubuntu22.04 - -####################### -# Environment Variables -####################### -ENV DEBIAN_FRONTEND noninteractive -ENV LC_ALL en_US.UTF-8 -# Ensure this matches c.NotebookApp.port in jupyter_notebook_config.py -ENV JUPYTER_PORT 8000 -ENV JUPYTER_HOME /etc/jupyter -ENV JUPYTER_KERNELSPEC_DIR /usr/local/share/jupyter -# We need node >18 for jupyter to work -ENV NODE_MAJOR 20 - -####################### -# Users Setup -####################### -# Create the jupyter user, add it to the `users` group and specify the home directory path -ENV USER jupyter -ENV USER_HOME /home/$USER -RUN useradd -m -s /bin/bash -d $USER_HOME -N -g users $USER -# Create the welder user -# The welder uid is consistent with the Welder docker definition here: -# https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala -# Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added -# files display nicer when viewed in a terminal. -ENV WELDER_USER welder-user -ENV WELDER_UID 1001 -RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER - -# We want to grant the jupyter user limited sudo permissions -# without password so they can install the necessary packages that they -# want to use on the docker container -RUN mkdir -p /etc/sudoers.d \ - && echo "$USER ALL=(ALL) NOPASSWD: /usr/bin/apt-get install *, /opt/conda/bin/conda install *, /opt/poetry/bin/poetry install" > /etc/sudoers.d/$USER \ - && chmod 0440 /etc/sudoers.d/$USER - -####################### -# Prerequisites -####################### -RUN apt-get update && apt-get install -yq --no-install-recommends \ - sudo \ - ca-certificates \ - curl \ - jq \ - # gnupg requirement - gnupg \ - dirmngr \ - # useful utilities for debugging within the docker - nano \ - procps \ - lsb-release \ - # python requirements - checkinstall \ - build-essential \ - zlib1g-dev \ - # pip requirements - libssl-dev \ - libbz2-dev \ - libreadline-dev \ - libsqlite3-dev \ - libexempi8 \ - libnode-dev \ - llvm \ - libncurses5-dev \ - libncursesw5-dev \ - tk-dev \ - libffi-dev \ - liblzma-dev \ - python3-openssl \ - # install script requirements - locales \ - # for ssh-agent and ssh-add - keychain \ - # extras \ - wget \ - bzip2 \ - # git - git \ - # Uncomment en_US.UTF-8 for inclusion in generation - && sed -i 's/^# *\(en_US.UTF-8\)/\1/' /etc/locale.gen \ - # Generate locale - && locale-gen \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* - -RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - -RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - - -# Install Node >18 (needed for jupyterlab) -RUN apt-get update && apt-get install -yq --no-install-recommends -RUN mkdir -p /etc/apt/keyrings -RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg - -RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list -RUN dpkg --remove --force-remove-reinstreq libnode-dev -RUN apt-get update && apt-get install -f -yq nodejs - -############ -# Install R -############ -RUN apt-get update && apt-get install -y r-base - -################ -# Install Python -################ -# Install Python 3.10 and add to system python path -# Note that miniconda does come with it's own installation of python, -# but it is cleaner to do a proper system instalation here and set the -# path properly -RUN apt-get update && apt-get install -y python3.10 python3-pip -RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.10 1 \ - && update-alternatives --set python /usr/bin/python3.10 - -############################ -# Manage python dependencies -############################ -## POETRY is the prefered tool to create virtual environments and -## manage dependencies - Should be used by Terra devs -# Install Poetry -ENV POETRY_HOME /opt/poetry -RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME python3 -# Append '/home/jupyter/.local/bin' to PATH -# poetry docs: https://python-poetry.org/docs/ -ENV PATH "${PATH}:${POETRY_HOME}/bin" - -# Prevent poetry from creating a virtual environment (we want to install on the docker system python) -RUN poetry config virtualenvs.create false - -# Install python dependencies with poetry -COPY poetry.lock . -COPY pyproject.toml . -RUN poetry install --no-cache --no-interaction - -################### -# Install Miniconda -################### -## CONDA should not be used by terra devs, but is a widely used tools -## to manage python environments in a runtime and we should provide it to users -ENV CONDA_HOME /opt/conda -RUN curl -so $HOME/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.1-0-Linux-x86_64.sh \ - && chmod +x $HOME/miniconda.sh \ - && $HOME/miniconda.sh -b -p $CONDA_HOME \ - && rm $HOME/miniconda.sh -ENV PATH "${PATH}:${CONDA_HOME}/bin" - -# ####################### -# # Utilities -# ####################### -COPY scripts $JUPYTER_HOME/scripts -COPY custom $JUPYTER_HOME/custom -COPY jupyter_notebook_config.py $JUPYTER_HOME -RUN chown -R $USER:users $JUPYTER_HOME - -# copy workspace_cromwell.py script and make it runnable by all users -RUN curl -o /usr/local/bin/workspace_cromwell.py https://raw.githubusercontent.com/broadinstitute/cromwhelm/1ceedf89587cffd355f37401b179001f029f77ed/scripts/workspace_cromwell.py \ - && chmod +x /usr/local/bin/workspace_cromwell.py - -RUN chown -R $USER:users $JUPYTER_KERNELSPEC_DIR \ - && find $JUPYTER_HOME/scripts -name '*.sh' -type f | xargs chmod +x \ - # You can get kernel directory by running `jupyter kernelspec list` - && $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel $JUPYTER_KERNELSPEC_DIR/kernels - -# Make sure that the jupyter user will have access to the jupyter path in the working directory -EXPOSE $JUPYTER_PORT -WORKDIR $USER_HOME - -# make pip install to a user directory, instead of a system directory which requires root. -# this is useful so `pip install` commands can be run in the context of a notebook. -ENV PIP_USER true -USER $USER - -# Note: this entrypoint is provided for running Jupyter independently of Leonardo. -# When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable -# additional setup inside the container before execution. Jupyter execution occurs when the -# init-actions.sh script uses 'docker exec' to call run-jupyter.sh. -ENTRYPOINT ["/usr/local/bin/jupyter-nbclassic"] \ No newline at end of file diff --git a/terra-base/custom/edit-mode.js b/terra-base/custom/edit-mode.js deleted file mode 100644 index 3670fb1f..00000000 --- a/terra-base/custom/edit-mode.js +++ /dev/null @@ -1,447 +0,0 @@ -define(() => { - // define default values for config parameters - const params = { - googleProject: '', - clusterName: '', - welderEnabled: 'false' - }; - - // update params with any specified in the server's config file - function updateParams() { - const config = Jupyter.notebook.config; - for (const key in params) { - if (config.data.hasOwnProperty(key)) { - params[key] = config.data[key]; - } - } - - // generate URLs based on params - const leoUrl = ''; // we are choosing to use a relative path here - const welderUrl = leoUrl + `/proxy/${params.googleProject}/${params.clusterName}/welder`; - - // URLS for local testing - // let leoUrl = 'http://localhost:8080' //for testing against local server - // let welderUrl = leoUrl - // params.jupyterServerApi = '/api/contents/' - // params.jupyterFsHref = '/notebooks/' - - params.jupyterServerApi = leoUrl + `/notebooks/${params.googleProject}/${params.clusterName}` + '/api/contents/'; - params.jupyterFsHref = leoUrl + `/notebooks/${params.googleProject}/${params.clusterName}/notebooks/`; - params.localizeUrl = welderUrl + '/objects'; - params.checkMetaUrl = welderUrl + '/objects/metadata'; - params.lockUrl = welderUrl + '/objects/lock'; - } - - let modalOpen = false; - // this needs to be available so the loop can be cancelled where needed - let syncMaintainer; - let shouldExit = false; - - const syncIssueButtons = (res) => { - return { - 'Make a Copy': { - 'click': () => notebookSaveAs(), - 'class': 'btn-primary', - 'id': 'modal-copy-1' - }, - 'Reload the workspace version and discard your changes': { - 'click': () => updateLocalCopyWithRemote(res), - 'id': 'modal-reload' - } - }; - }; - - const lockIssueButtons = (res) => { - return { - 'Run in Playground Mode': { - 'click': () => openPlaygroundMode(res), - 'class': 'btn-primary', - 'id': 'modal-playground' - }, - 'Make a Copy': { - 'click': () => notebookSaveAs(), - 'id': 'modal-copy-2' - } - }; - }; - - const noRemoteFileButtons = { - 'Continue working': { - 'click': () => {}, - 'class': 'btn-primary' - } - }; - - const modeBannerId = 'notification_mode'; - const lockConflictTitle = 'File is in use'; - const syncIssueTitle = 'File versions out of sync'; - const syncIssueBody = 'Your version of this file does not match the version in the workspace. What would you like to do?'; - const syncIssueNotFoundBody = 'This file was either deleted from or was never saved to the workspace.'; - const lastLockedTimer = 60000; - - const headers = { - 'Content-Type': 'application/json', - 'Access-Control-Allow-Headers': '*' - }; - - const basePayload = { - mode: 'no-cors', - headers: headers - }; - - function init() { - console.info('edit mode plugin initialized'); - - if (!Jupyter.notebook) { - return; // exit, they are in list view - } - - updateParams(); - - if (!(params.welderEnabled == 'true')) { - console.info('welder is not enabled'); - return; - } - - checkMeta(); - - const initialSyncDelay = 27000; - // we want subsequent checkMeta + lock calls to be off-cycle of autosave - setTimeout(() => initSyncMaintainer(), initialSyncDelay); - } - - function initSyncMaintainer() { - syncMaintainer = setInterval(() => { - checkMeta(); - }, lastLockedTimer); - - window.onbeforeunload(function() { - clearInterval(syncMaintainer); - }); - } - - function checkMeta() { - const localPath = { - localPath: Jupyter.notebook.notebook_path - }; - - console.info('calling /objects/metadata/ with payload: ', JSON.stringify(localPath)); - - const payload = { - ...basePayload, - body: JSON.stringify(localPath), - method: 'POST' - }; - - return fetch(params.checkMetaUrl, payload) - .then((res) => { - processInitialCheckMeta(res); - return res.json(); - }) - .then((res) => { - handleMetaSuccess(res); - return res; - }) - .catch((err) => { - handleMetaFailure(err); - }); - } - - function renderFileNotTrackedBanner() { - removeElementById(modeBannerId); - - const toolTipText = '

Your changes are not being saved to the workspace.

'; - - $('#notification_area').append( - $('
').attr({ - 'id': 'notification_not_saving', - 'class': 'btn-warning btn btn-xs navbar-btn', - 'data-toggle': 'tooltip', - 'data-html': 'true', - 'title': toolTipText - }) - .tooltip({ - 'content': function() { - return $(this).prop('title'); - }, - 'placement': 'bottom' - }) - .append( - $('').html('Remote Save Disabled') - .append(' ') - ) - ); - } - - function processInitialCheckMeta(res) { - if (!res.ok) { - if (res.status == 412) { - console.warn('detected 412 from /objects/metadata. stopping loop'); - renderFileNotTrackedBanner(); - shouldExit = true; - clearInterval(syncMaintainer); - } - - throw Error(res.statusText); - } - } - - function handleMetaSuccess(res) { - toggleMetaFailureBanner(false); // sets banner for meta status - - const isEditMode = res.syncMode == 'EDIT'; - - if (isEditMode) { - handleCheckMetaResp(res); // displays modal if theres an issue in the payload - getLock(res); // gets lock if in edit mode - } - renderModeBanner(isEditMode); // sets edit/safe mode banner - } - - function handleMetaFailure(err) { - console.error(err); - if (!shouldExit) { - removeElementById(modeBannerId); - toggleMetaFailureBanner(true); - } - } - - // this function assumes any status not included in these lists represents a notebook out of sync - // this is done to defend against future fields being added being auto-categorized as failures - function handleCheckMetaResp(res) { - const healthySyncStatuses = ['LIVE']; - // below is included for reference, but commented out so it does not cause errors with linting - // const outOfSyncStatuses = ['DESYNCHRONIZED', 'REMOTE_CHANGED']; - const notFoundStatus = ['REMOTE_NOT_FOUND']; - const saveNeededStatus = ['LOCAL_CHANGED']; - - if (healthySyncStatuses.includes(res.syncStatus)) { - console.info('healthy sync status detected: ', res.syncStatus); - } else if (notFoundStatus.includes(res.syncStatus)) { - promptUserWithModal(syncIssueTitle, noRemoteFileButtons, syncIssueNotFoundBody); - } else if (saveNeededStatus.includes(res.syncStatus)) { - console.info('detected that we have changes that have not been delocalized.'); - // It is possible saving is the right call here (aka $("#save-notbook > button").click()), but we already do that on a periodic tick - // adding it here could possibly cause confusion - } else { - promptUserWithModal(syncIssueTitle, syncIssueButtons(res), syncIssueBody); - } - } - - function getLock(metaRes) { - const payload = { - ...basePayload, - method: 'POST', - body: JSON.stringify({localPath: Jupyter.notebook.notebook_path}) - }; - - fetch(params.lockUrl, payload) - .then((res) => { - handleLockStatus(res, metaRes); - }) - .catch((err) => { - console.error(err); - }); - } - - function toggleMetaFailureBanner(shouldShow) { - const bannerId = 'notification_metaFailure'; - const bannerText = 'Failed to check notebook status, changes may not be saved to workspace. Retrying...'; - - removeElementById(bannerId); - - if (shouldShow) { - const bannerStyling = 'btn btn-xs navbar-btn btn-danger'; - - $('#notification_area').append( - $('
').attr({ - 'id': bannerId, - 'class': bannerStyling - }) - .append($('').html(' ' + bannerText)) - ); - } - } - - const lockConflictBody = `

This file is currently being edited by another user. ` + - `Please allow 2-3 minutes after this user has closed the file for it to become available for editing.

` + - `

You can make a copy, or run it in Playground Mode to explore and execute its contents without saving any changes.`; - - function handleLockStatus(res, metaRes) { - if (!res.ok) { - const status = res.status; - const errorText = res.statusText; - - if (status == 409) { - res.json().then((res) => { - promptUserWithModal(lockConflictTitle, lockIssueButtons(metaRes), lockConflictBody); - }); - } - // for the lock endpoint, we consider all non 'ok' statuses an error - throw new Error(errorText); - } - } - - - function promptUserWithModal(title, buttons, htmlBody) { - if (modalOpen) return; - - modalOpen = true; - - // we need to require here because otherwise we haven't checked if the module is loaded - // (i.e. if we are in terminal view) - const dialog = require('base/js/dialog'); - - dialog.modal({ - body: $('

').html(htmlBody), - title: title, - buttons: buttons, - notebook: Jupyter.notebook, - keyboard_manager: Jupyter.notebook.keyboard_manager - }) - .on('hidden.bs.modal', () => modalOpen = false) - .attr('id', 'leoUserModal') - .find('.close').remove(); // TODO: test going back - } - - async function openPlaygroundMode(metaRes) { - const originalNotebookName = Jupyter.notebook.notebook_name; - - const safeModeDir = metaRes.storageLink.localSafeModeBaseDirectory; - - if (Jupyter.notebook.notebook_path.includes(safeModeDir)) { - console.warn('Attempted to navigate to enter safe mode while already in safe mode. Exitting.'); - return; // we're here already - } - - // create a new file with the contents - const postPayload = { - ...basePayload, - method: 'POST', - body: JSON.stringify({ - copy_from: Jupyter.notebook.notebook_path - }) - }; - - const patchPayload = { - headers: headers, - method: 'PATCH', - body: JSON.stringify({ - path: safeModeDir + '/' + originalNotebookName - }) - }; - - fetch(params.jupyterServerApi + safeModeDir, postPayload) - .then((res) => handleJupyterServerResponse(res)) - .then((res) => { - // then we rename the file, as POST does not allow us to specify the file name - fetch(params.jupyterServerApi + res.path, patchPayload) - .then((res) => { - // navigate to new file - window.location.href = params.jupyterFsHref + safeModeDir + '/' + originalNotebookName; - }); - }); - } - - function notebookSaveAs() { - // we need to require here because otherwise we haven't checked if the module is loaded - // (i.e. if we are in terminal view) - const utils = require('base/js/utils'); - // guarantees a path in [0] and file name in [1]. [0] is "" if just a file is passed - const originalPathSplit = utils.url_path_split(Jupyter.notebook.notebook_path); - const newNotebookPath = originalPathSplit[0]; - - // create a new file with the contents - const payload = { - ...basePayload, - method: 'POST', - body: JSON.stringify({ - copy_from: Jupyter.notebook.notebook_path - }) - }; - - fetch(params.jupyterServerApi + newNotebookPath, payload) - .then((res) => handleJupyterServerResponse(res)) - .then((res) => { - // navigate to new file. we rely on the jupyter post api to supply the name of the file we have created as it ensures it does not exist - // POST also does not allow for the specification of a file name - window.location.href = params.jupyterFsHref + res.path; - }); - } - - function handleJupyterServerResponse(res) { - if (!res.ok) { - throw new Error('failed to perform requested action, the jupyter server is unavailable'); - } - return res.json(); - } - - function removeElementById(id) { - if (!$('#' + id).length == 0) { - $('#' + id).remove(); - } - } - - // shows the user whether they are in playground mode or edit mode - function renderModeBanner(isEditMode) { - removeElementById(modeBannerId); // we always remove the banner because we re-render each loop - - let bannerText; - let toolTipText; - let bannerStyling; - - const baseStyling = 'btn btn-xs navbar-btn'; - - if (isEditMode) { - bannerText = 'Edit Mode'; - toolTipText = '

You have locked this file for editing and your changes are being automatically saved to the workspace.

'; - bannerStyling = 'notification_widget ' + baseStyling; - } else { - bannerText = 'Playground Mode (Edits not saved)'; - toolTipText = '

Playground mode allows you to explore, change, and run the notebook, but changes are not saved to the workspace.

'; - bannerStyling = 'btn-warning ' + baseStyling; - } - - $('#notification_area').append( - $('
').attr({ - 'id': modeBannerId, - 'class': bannerStyling, - 'data-toggle': 'tooltip', - 'data-html': 'true', - 'title': toolTipText - }) - .tooltip({ - 'content': function() { - return $(this).prop('title'); - }, - 'placement': 'bottom' - }) - .append( - $('').html(bannerText) - .append(' ') - ) - ); - } - - async function updateLocalCopyWithRemote(meta) { - const entries = { - action: 'localize', - entries: [{ - sourceUri: meta.storageLink.cloudStorageDirectory + '/' + Jupyter.notebook.notebook_name, - localDestinationPath: Jupyter.notebook.notebook_path - }] - }; - - const payload = { - ...basePayload, - method: 'POST', - body: JSON.stringify(entries) - }; - - await fetch(params.localizeUrl, payload); - - location.reload(true); - } - - init(); -}); diff --git a/terra-base/custom/extension_entry_jupyter.js b/terra-base/custom/extension_entry_jupyter.js deleted file mode 100644 index 9d07f2dd..00000000 --- a/terra-base/custom/extension_entry_jupyter.js +++ /dev/null @@ -1,7 +0,0 @@ -define([ - 'base/js/events' -], function(events) { - require(['custom/google_sign_in']); - require(['custom/edit-mode']); - require(['custom/safe-mode']); -}); \ No newline at end of file diff --git a/terra-base/custom/jupyter_localize_extension.py b/terra-base/custom/jupyter_localize_extension.py deleted file mode 100644 index bd7221ee..00000000 --- a/terra-base/custom/jupyter_localize_extension.py +++ /dev/null @@ -1,149 +0,0 @@ -import distutils.util -import subprocess -import os -import sys -import tornado -from tornado import gen -from tornado.web import HTTPError -from notebook.base.handlers import IPythonHandler -from notebook.utils import url_path_join -from datauri import DataURI - -class LocalizeHandler(IPythonHandler): - def _sanitize(self, pathstr): - """Sanitizes paths. Handles local paths, gs: URIs, and data: URIs.""" - # return gs or data uris as is - if pathstr.startswith("gs:") or pathstr.startswith("data:"): - return pathstr - # expand user directories and make intermediate directories - else: - expanded = os.path.expanduser(pathstr) - try: - os.makedirs(os.path.dirname(expanded)) - except OSError: #thrown if dirs already exist - pass - return expanded - - def _localize_gcs_uri(self, locout, source, dest): - """Localizes an entry where either the source or destination is a gs: path. - Simply invokes gsutil in a subprocess.""" - - # Use a sequence of arguments with Shell=False. The subprocess module takes care - # of quoting/escaping arguments. See: - # https://docs.python.org/2/library/subprocess.html#subprocess.call - # https://docs.python.org/2/library/subprocess.html#frequently-used-arguments - cmd = ['gsutil', '-m', '-q', 'cp', '-R', '-c', '-e', source, dest] - locout.write(' '.join(cmd) + '\n') - result = subprocess.call(cmd, stderr=locout) - return result == 0 - - def check_gcs_object_status(self, locout, source): - if source.startswith("gs:"): - source_check = ['gsutil', '-m', '-q', 'ls', source] - locout.write(' '.join(source_check) + '\n') - source_status = subprocess.call(source_check, stderr=locout) - else: - source_status = 0 - return source_status == 0 - - def _localize_data_uri(self, locout, source, dest): - """Localizes an entry where the source is a data: URI""" - try: - uri = DataURI(source) - except ValueError: - locout.write('Could not parse "{}" as a data URI: {}\n'.format(source, str(e))) - return False - - try: - with open(dest, 'w+', buffering=1) as destout: - try: - uri_data = uri.data.decode() - except AttributeError: - uri_data = uri.data - destout.write(uri_data) - locout.write('{}: wrote {} bytes\n'.format(dest, len(uri_data))) - except IOError as e: - locout.write('{}: I/O error({0}): {1}\n'.format(dest, e.errno, e.strerror)) - return False - except: - locout.write('{}: unexpected error: {}\n'.format(sys.exc_info()[0])) - return False - - return True - - @gen.coroutine - def localize(self, pathdict): - """Treats the given dict as a string/string map and localizes each entry one by one. - Returns a list of any failed entries.""" - failures = [] - #This gets dropped inside the user's notebook working directory - with open("localization.log", 'a', buffering=1) as locout: - for key in pathdict: - #NOTE: keys are destinations, values are sources - source = self._sanitize(pathdict[key]) - dest = self._sanitize(key) - - if source.startswith('gs:') or dest.startswith('gs:'): - status = self.check_gcs_object_status(locout, source) - if status: - success = self._localize_gcs_uri(locout, source, dest) - else: - locout.write('Could not validate source or destination: {} -> {}.\n'.format(source, dest)) - success = False - elif source.startswith('data:'): - success = self._localize_data_uri(locout, source, dest) - else: - locout.write('Unhandled localization entry: {} -> {}. Required gs: or data: URIs.\n'.format(source, dest)) - success = False - - if not success: - failures.append((dest, source)) - - return failures - - def post(self): - try: - pathdict = tornado.escape.json_decode(self.request.body) - except ValueError: - raise HTTPError(400, "Body must be JSON object of type string/string") - - if type(pathdict) is not dict: - raise HTTPError(400, "Body must be JSON object of type string/string") - - if not all(map(lambda v: type(v) is str, pathdict.values())): - raise HTTPError(400, "Body must be JSON object of type string/string") - - try: - raw = self.get_query_argument('async', 'false') - isAsync = distutils.util.strtobool(raw) - except ValueError: - raise HTTPError(400, "Could not parse isAsync parameter as a boolean: '{}'".format(raw)) - - if isAsync: - #complete the request HERE, without waiting for the localize to run - self.set_status(200) - self.finish() - - #fire and forget the actual work -- it'll log to a file in the user's homedir - tornado.ioloop.IOLoop.current().spawn_callback(self.localize, pathdict) - - else: - #run localize synchronous to the HTTP request - #run_sync() doesn't take arguments, so we must wrap the call in a lambda. - failures = tornado.ioloop.IOLoop().run_sync(lambda: self.localize(pathdict)) - - #complete the request only after localize completes - if failures: - raise HTTPError(500, "Error occurred localizing the following {} entries: {}. See localization.log for details.".format( - len(failures), str(failures))) - else: - self.set_status(200) - self.finish() - -def load_jupyter_server_extension(nb_server_app): - """Entrypoint for the Jupyter extension.""" - web_app = nb_server_app.web_app - host_pattern = '.*$' - route_pattern = url_path_join(web_app.settings['base_url'], '/api/localize') - web_app.add_handlers(host_pattern, [(route_pattern, LocalizeHandler)]) - nb_server_app.log.info('initialized jupyter_localize_extension') diff --git a/terra-base/custom/safe-mode.js b/terra-base/custom/safe-mode.js deleted file mode 100644 index 6adda657..00000000 --- a/terra-base/custom/safe-mode.js +++ /dev/null @@ -1,128 +0,0 @@ -// Adapted from the All of Us Researcher Workbench "Playground Mode" -// https://github.com/all-of-us/workbench/blob/master/api/cluster-resources/playground-extension.js - -// In "Safe Mode", changes are not saved back to GCS. This extension makes -// minor UI tweaks to differentiate this mode from normal Jupyter usage, and -// also removes/hides controls relating to persistence. Technically -// this does not stop autosave from continuing to happen in the background, but -// the intended use of this plugin is in a separate space from normal operation -// which does not support localization features. - -// const namespace = require('base/js/namespace') - -define(() => { - // define default values for config parameters - const params = { - googleProject: '', - clusterName: '', - welderEnabled: 'false' - }; - - // update params with any specified in the server's config file - function updateParams() { - const config = Jupyter.notebook.config; - for (const key in params) { - if (config.data.hasOwnProperty(key)) { - params[key] = config.data[key]; - } - } - - // generate URLs based on params - const welderUrl = `/proxy/${params.googleProject}/${params.clusterName}/welder`; - params.checkMetaUrl = welderUrl + '/objects/metadata'; - } - - const headers = { - 'Content-Type': 'application/json', - 'Access-Control-Allow-Headers': '*' - }; - - const basePayload = { - mode: 'no-cors', - headers: headers - }; - - function load() { - console.info('safe mode plugin initialized'); - - if (!Jupyter.notebook) { - return; // exit, they are in list view - } - - updateParams(); - - if (!(params.welderEnabled == 'true')) { - console.info('welder is not enabled'); - return; - } - - checkMetaLoop(); - } - - function checkMetaLoop() { - triggerUIToggle(); - - const interval = setInterval(() => { - triggerUIToggle(); - }, 60000); - - window.onbeforeunload(() => { - clearInterval(interval); - }); - } - - async function triggerUIToggle() { - checkMeta() - .then((res) => { - if (res.syncMode == 'EDIT') { - toggleUIControls(false); - } else { - // there is an icon in the jupyter UI that has a tool tip that says 'edit mode'. - // this shows up whenever a user types, so we change the tool-tip to avoid confusion - $('#modal_indicator').tooltip({'content': 'Adding code'}); - toggleUIControls(true); - } - }) - .catch((err) => { - console.error(err); - toggleUIControls(false); // we always assume safe mode if the check meta call fails - }); - } - - function checkMeta() { - const payload = { - ...basePayload, - body: JSON.stringify({localPath: Jupyter.notebook.notebook_path}), - method: 'POST' - }; - - return fetch(params.checkMetaUrl, payload) - .then((res) => { - if (!res.ok) { - throw Error('check metadata call failed due to status code'); - } - return res.json(); - }); - } - - function toggleUIControls(shouldHide) { - // these are the jquery selectors for the elements we will toggle - // "notbook" is an intentional typo to match the Jupyter UI HTML. - const selectorsToHide = ['#save-notbook', '#new_notebook', - '#open_notebook', '#copy_notebook', '#save_notebook_as', - '#save_checkpoint', '#restore_checkpoint', '.checkpoint_status', - '.autosave_status', '#notification_notebook', '#file_menu > li.divider:eq(0)', - '#file_menu > li.divider:eq(2)' - ]; - - selectorsToHide.forEach((selector) => { - if (shouldHide) { - $(selector).hide(); - } else { - $(selector).show(); - } - }); - } - - load(); -}); diff --git a/terra-base/jupyter_notebook_config.py b/terra-base/jupyter_notebook_config.py deleted file mode 100755 index 144fe7bf..00000000 --- a/terra-base/jupyter_notebook_config.py +++ /dev/null @@ -1,45 +0,0 @@ -# adapted from https://github.com/jupyter/docker-stacks/blob/master/base-notebook/jupyter_notebook_config.py -# Note: this file also lives in the Leonardo repo here: -# https://github.com/DataBiosphere/leonardo/blob/develop/http/src/main/resources/jupyter/jupyter_notebook_config.py -# If you change this please keep the other version consistent as well. - -import os - -c = get_config() - -if os.environ.get('JUPYTER_DEBUG_LOGGING') == 'true': - c.Application.log_level = 'DEBUG' - -c.NotebookApp.ip = '0.0.0.0' -c.NotebookApp.port = 8000 -c.NotebookApp.open_browser = False -c.NotebookApp.use_redirect_file = False - -c.NotebookApp.token = '' -c.NotebookApp.disable_check_xsrf = True #see https://github.com/nteract/hydrogen/issues/922 -c.NotebookApp.allow_origin = '*' - -c.NotebookApp.terminado_settings={'shell_command': ['bash']} - -if 'GOOGLE_PROJECT' in os.environ and 'CLUSTER_NAME' in os.environ: - fragment = '/' + os.environ['GOOGLE_PROJECT'] + '/' + os.environ['CLUSTER_NAME'] + '/' -else: - fragment = '/' - -c.NotebookApp.base_url = '/notebooks' + fragment - -# This is also specified in run-jupyter.sh -c.NotebookApp.nbserver_extensions = { - 'jupyter_localize_extension': True -} - -c.NotebookApp.kernel_manager_class = 'jupyter_server.services.kernels.kernelmanager.AsyncMappingKernelManager' - -mgr_class = 'DelocalizingContentsManager' -if os.environ.get('WELDER_ENABLED') == 'true': - 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-[tool.poetry.dependencies] -python = "^3.10" -notebook = "^7.0.4" -cookiecutter = "^2.3.0" -tornado = "^6.3.3" -python-datauri = "^2.1.0" -markupsafe = "^2.1.3" -nbconvert = "^7.8.0" -requests = "^2.31.0" -firecloud = "^0.16.35" -crcmod = "^1.7" -cromshell = "^2.0.0" -google-crc32c = "^1.5.0" -terra-notebook-utils = "^0.13.0" -nbclassic = "^1.0.0" -jupyter-contrib-nbextensions = "^0.7.0" - - -[tool.poetry.dev-dependencies] -pytest = "*" - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" \ No newline at end of file diff --git a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh b/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh deleted file mode 100644 index 47b2725f..00000000 --- a/terra-base/scripts/extension/install_jupyter_contrib_nbextensions.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env bash - -# installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions -# unfortunately this package is not compatible with new versions of notebooks -# or nbclassic, so this is a temporary hack to directly install the js extensions -# using NBclassic - -set -e -NBEXTENSION_HOME=/usr/local/lib/python3.10/dist-packages/jupyter_contrib_nbextensions/nbextensions -jupyter nbclassic-extension install ${NBEXTENSION_HOME}/toc2 --user -jupyter nbclassic-extension install ${NBEXTENSION_HOME}/codefolding --user -jupyter nbclassic-extension install ${NBEXTENSION_HOME}/collapsible_headings --user -jupyter nbclassic-extension enable toc2/main -jupyter nbclassic-extension enable codefolding/main -jupyter nbclassic-extension enable collapsible_headings/main diff --git a/terra-base/scripts/extension/jupyter_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_install_combined_extension.sh deleted file mode 100644 index 7a2b3081..00000000 --- a/terra-base/scripts/extension/jupyter_install_combined_extension.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash - -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` - mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} -fi diff --git a/terra-base/scripts/extension/jupyter_install_lab_extension.sh b/terra-base/scripts/extension/jupyter_install_lab_extension.sh deleted file mode 100644 index 0c3c4eaf..00000000 --- a/terra-base/scripts/extension/jupyter_install_lab_extension.sh +++ /dev/null @@ -1,29 +0,0 @@ -#!/bin/bash - -set -e - - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - if [[ ${JUPYTER_EXTENSION} == *'.js' ]]; then - # use jupyterlab extension template to create an extension using the specified JS file - # see https://github.com/jupyterlab/extension-cookiecutter-js - JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` - cookiecutter --no-input https://github.com/jupyterlab/extension-cookiecutter-js extension_name=${JUPYTER_EXTENSION_NAME} - cp -f ${JUPYTER_EXTENSION} ${JUPYTER_EXTENSION_NAME}/lib/plugin.js - cd ${JUPYTER_EXTENSION_NAME} - jlpm - jupyter labextension install . - elif [[ ${JUPYTER_EXTENSION} == *'.ts' ]]; then - # same as above but in typescript, see https://github.com/jupyterlab/extension-cookiecutter-ts - JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` - cookiecutter --no-input https://github.com/jupyterlab/extension-cookiecutter-ts extension_name=${JUPYTER_EXTENSION_NAME} - cp -f ${JUPYTER_EXTENSION} ${JUPYTER_EXTENSION_NAME}/src/index.ts - cd ${JUPYTER_EXTENSION_NAME} - jlpm - jupyter labextension install . - else - jupyter labextension install $JUPYTER_EXTENSION - fi -fi - diff --git a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_install_notebook_extension.sh deleted file mode 100644 index cf43eaa1..00000000 --- a/terra-base/scripts/extension/jupyter_install_notebook_extension.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` - mkdir -p ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - if [[ ${JUPYTER_EXTENSION} == *'.tar.gz' ]]; then - tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - else - mv ${JUPYTER_EXTENSION} ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/main.js - fi - jupyter nbclassic-extension install ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME}/ --user - jupyter nbclassic-extension enable ${JUPYTER_EXTENSION_NAME}/main -fi diff --git a/terra-base/scripts/extension/jupyter_install_server_extension.sh b/terra-base/scripts/extension/jupyter_install_server_extension.sh deleted file mode 100644 index 7a2b3081..00000000 --- a/terra-base/scripts/extension/jupyter_install_server_extension.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash - -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - JUPYTER_EXTENSION_NAME=`basename ${JUPYTER_EXTENSION%%.*}` - mkdir ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - tar -xzf ${JUPYTER_EXTENSION} -C${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - pip3 install -e ${JUPYTER_HOME}/${JUPYTER_EXTENSION_NAME} - jupyter serverextension enable --py ${JUPYTER_EXTENSION_NAME} -fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh deleted file mode 100644 index 8c4c5557..00000000 --- a/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - pip3 install ${JUPYTER_EXTENSION} - jupyter serverextension enable --py ${JUPYTER_EXTENSION} -fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh deleted file mode 100644 index 0215f14f..00000000 --- a/terra-base/scripts/extension/jupyter_pip_install_notebook_extension.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - pip3 install ${JUPYTER_EXTENSION} - jupyter nbclassic-extension install --py ${JUPYTER_EXTENSION} --user - jupyter nbclassic-extension enable --py ${JUPYTER_EXTENSION} -fi diff --git a/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh b/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh deleted file mode 100644 index 8c4c5557..00000000 --- a/terra-base/scripts/extension/jupyter_pip_install_server_extension.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -set -e - -if [ -n "$1" ]; then - JUPYTER_EXTENSION=$1 - pip3 install ${JUPYTER_EXTENSION} - jupyter serverextension enable --py ${JUPYTER_EXTENSION} -fi diff --git a/terra-base/scripts/kernel/kernel_bootstrap.sh b/terra-base/scripts/kernel/kernel_bootstrap.sh deleted file mode 100644 index d4811a94..00000000 --- a/terra-base/scripts/kernel/kernel_bootstrap.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env bash - -# This script runs at kernel startup time and sets environment variables for the -# workspace name and workspace bucket. -# -# Note: this script is highly dependent on a convention used by Terra and AllOfUs -# applications to place notebooks in the following directory structure: -# -# /home/jupyter///notebook.ipynb -# -# It exploits the fact that the CWD of a launching notebook is named after the workspace. -# If notebooks are ever launched from other directories, this script will break. - -PWD="$(pwd)" -# The workspace name is simply the CWD of the running notebook. -export WORKSPACE_NAME=`basename "$(dirname "$PWD")"` - -# Parse the .delocalize.json file (if it exists) in the workspace directory to obtain the workspace bucket. -DELOCALIZE_FILE="$PWD/.delocalize.json" -if [ -f "$DELOCALIZE_FILE" ]; then - export WORKSPACE_BUCKET="$(dirname "$(cat "$DELOCALIZE_FILE" | jq -r '.destination')")" -fi - -exec "$@" \ No newline at end of file diff --git a/terra-base/scripts/kernel/kernelspec.sh b/terra-base/scripts/kernel/kernelspec.sh deleted file mode 100644 index 59f1cc6f..00000000 --- a/terra-base/scripts/kernel/kernelspec.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/usr/bin/env bash - -TMP_KERNELSPEC_DIR=$1 -KERNELSPEC_HOME=$2 - -# Replace the contents of the Python kernel scripts -sed -e 's/${PY_VERSION}/3/g' -e 's|${JUPYTER_HOME}|'${JUPYTER_HOME}'|g' ${TMP_KERNELSPEC_DIR}/python_kernelspec.tmpl > ${KERNELSPEC_HOME}/python3/kernel.json diff --git a/terra-base/scripts/kernel/python_kernelspec.tmpl b/terra-base/scripts/kernel/python_kernelspec.tmpl deleted file mode 100644 index a2b0b66a..00000000 --- a/terra-base/scripts/kernel/python_kernelspec.tmpl +++ /dev/null @@ -1,12 +0,0 @@ -{ - "language": "python", - "display_name": "Python ${PY_VERSION}", - "argv": [ - "${JUPYTER_HOME}/scripts/kernel/kernel_bootstrap.sh", - "python${PY_VERSION}", - "-m", - "ipykernel_launcher", - "-f", - "{connection_file}" - ] -} diff --git a/terra-base/scripts/run-jupyter.sh b/terra-base/scripts/run-jupyter.sh deleted file mode 100644 index 88acd892..00000000 --- a/terra-base/scripts/run-jupyter.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env bash - -set -e - -# Change the default umask to support R/W access to the shared volume with welder -umask 002 - -# TODO: change default to ${HOME}/notebooks once welder is rolled out to all clusters -NOTEBOOKS_DIR=${1:-${HOME}} - -JUPYTER_BASE="/usr/bin/python /usr/local/bin/jupyter-nbclassic" -JUPYTER_CMD="$JUPYTER_BASE --NotebookApp.nbserver_extensions=\"{'jupyter_localize_extension':True}\" &> ${NOTEBOOKS_DIR}/jupyter.log" - -echo $JUPYTER_CMD - -eval $JUPYTER_CMD From b3b1a286bc06ade88c581bb493481ec0ef8c9c8a Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 10 Apr 2024 15:22:19 -0400 Subject: [PATCH 10/19] isolating jupyter env instead of user venv --- terra-base-jupyter/Dockerfile | 122 ++++++------ terra-base-jupyter/ipython_config.py | 1 - terra-base-jupyter/jupyter_server_config.py | 4 +- terra-base-jupyter/poetry.lock | 200 +++----------------- terra-base-jupyter/pyproject.toml | 2 - terra-base-jupyter/run-jupyter.sh | 2 +- 6 files changed, 95 insertions(+), 236 deletions(-) delete mode 100644 terra-base-jupyter/ipython_config.py diff --git a/terra-base-jupyter/Dockerfile b/terra-base-jupyter/Dockerfile index aca5ad56..35c6407c 100644 --- a/terra-base-jupyter/Dockerfile +++ b/terra-base-jupyter/Dockerfile @@ -1,6 +1,10 @@ # Smallest image with ubuntu jammy, CUDA and NVDIA drivers installed - 80 mb FROM --platform=linux/amd64 nvidia/cuda:12.2.0-base-ubuntu22.04 +# Use bash as the shell, like the jupyter terminal (just nicer to work with than sh) +ENV SHELL /usr/bin/bash +SHELL ["/usr/bin/bash", "-c"] + ####################### # Environment Variables ####################### @@ -19,11 +23,10 @@ ENV NODE_MAJOR 20 # container as root ENV USER_HOME /home/jupyter RUN mkdir $USER_HOME -# We want to store the user virtual environments in a directory +# We want to store the user conda environments in a directory # that will be in the persistent disk -ENV CONDA_ENV_NAME terra-python3.10 +ENV CONDA_ENV_NAME base-python3.10 ENV CONDA_ENV_HOME $USER_HOME/.envs/$CONDA_ENV_NAME -RUN mkdir -p $CONDA_ENV_HOME # Create the welder user # The welder uid is consistent with the Welder docker definition here: @@ -92,96 +95,95 @@ RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesourc RUN dpkg --remove --force-remove-reinstreq libnode-dev RUN apt-get update && apt-get install -f -yq nodejs -############################## -# Install Python via Miniconda -############################## -## Note: CONDA should not be used by terra devs, but is a widely used tools -## to manage python environments in a runtime and we should provide it to users -ENV CONDA_HOME /opt/conda +##################################### +# Install Python 3.10 via Miniconda +##################################### +## Note: CONDA should NOT be used by terra devs to manage dependencies (see the use of poetry below instead), +## but is a widely used tool to manage python environments in a runtime and we should provide it to users RUN curl -so $HOME/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.1-0-Linux-x86_64.sh \ && chmod +x $HOME/miniconda.sh \ - && $HOME/miniconda.sh -b -p $CONDA_HOME \ + && $HOME/miniconda.sh -b -p $CONDA_ENV_HOME \ && rm $HOME/miniconda.sh -ENV PATH "${PATH}:${CONDA_HOME}/bin" +ENV PATH "${PATH}:${CONDA_ENV_HOME}/bin" -ENV BASE_PYTHON_PATH /opt/conda/bin/python +ENV BASE_PYTHON_PATH $CONDA_ENV_HOME/bin/python ENV PYTHONDONTWRITEBYTECODE=true -################################################ -# Install Jupyter in the base python environment -################################################ -## POETRY is the prefered tool to create virtual environments and -## manage dependencies - Should be used by Terra devs - poetry docs: https://python-poetry.org/docs/ -ENV POETRY_HOME /opt/poetry -# Append POETRY_HOME to PATH -ENV PATH "${PATH}:${POETRY_HOME}/bin" -COPY poetry.lock . -COPY pyproject.toml . - -# Install Poetry, set up the base environment for jupyter to run and then cleanup / uninstall poetry -RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE_PYTHON_PATH \ - # Prevent poetry from creating a virtual environment (we want to install on the docker system python) - && poetry config virtualenvs.create false \ - # Install python dependencies with poetry - && poetry install --no-dev --no-cache --no-interaction \ - # Cleanup - && rm poetry.lock && rm pyproject.toml \ - && curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE_PYTHON_PATH - --uninstall - -# Remove the base environment from the list of available kernels so it is hidden from the user -# Note that this needs to be done with setting the c.KernelSpecManager.ensure_native_kernel flag -# to False in 'jupyter_server_config.py' -RUN jupyter kernelspec remove python3 -y - -####################################################### -# Create a CONDA virtual environment for user isolation -####################################################### -# Create a new conda environment for the user, activate it, and add it to the list of python kernels -# This step is a bit slow to build, but worth it to provide the user with an isolated environment +################################################### +# Set up the user to use the conda base environment +################################################### +## The user should have full access to the conda base environment, and can use it directly, or +## create new conda environments on top of it. The important part is that jupyter IS NOT installed +## in the base environment to provide isolation between the user environment, and the jupyter server +## to avoid cross-contamination COPY conda-environment.yml . -RUN conda env create -f conda-environment.yml --prefix=$CONDA_ENV_HOME\ +RUN conda env update --prefix $CONDA_ENV_HOME --file conda-environment.yml --prune\ # Remove packages tarballs and python bytecode files from the image && conda clean -afy \ && find $CONDA_ENV_HOME -follow -type f -name '*.pyc' -delete \ && rm conda-environment.yml -# Add the user conda environment as a jupyter kernel - this should be the default now + +# Add the user base conda environment as a jupyter kernel - this should be the default now # This commands activates the conda environment and then calls ipykernel from within # to install it as a kernel under the same name RUN conda run -p ${CONDA_ENV_HOME} python -m ipykernel install --user --name=$CONDA_ENV_NAME -# Automagically activate the user conda environment when opening the jupyter terminal +# Prep the jupyter terminal to conda init and make sure the base conda environment is +# activated and the name is displayed in the terminal prompt COPY conda_init.txt . RUN cat conda_init.txt >> ~/.bashrc && \ printf "\nconda activate ${CONDA_ENV_HOME}" >> ~/.bashrc && \ conda config --set env_prompt '({name})' && \ - echo "auto_activate_base: false" >> ~/.condarc && \ + source ~/.bashrc && \ rm conda_init.txt +#################################################### +# Install Jupyter in an isolated virtual environment +#################################################### +## Virtualenv and POETRY are the prefered tool to create virtual environments and +## manage dependencies for Terra Devs - poetry docs: https://python-poetry.org/docs/ +ENV POETRY_HOME /opt/poetry +# Append POETRY_HOME to PATH +ENV PATH "${PATH}:${POETRY_HOME}/bin" +COPY poetry.lock . +COPY pyproject.toml . + +ENV JUPYTER_VIRTUAL_ENV=/usr/jupytervenv +# Add jupyter virtual environmemt to PATH +ENV PATH="$JUPYTER_VIRTUAL_ENV/bin:$PATH" + +# Install Poetry, set up the virtual environment for jupyter to run and then cleanup / uninstall poetry +RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE_PYTHON_PATH \ + # Create a virtual environment and activate it for poetry to use + && $BASE_PYTHON_PATH -m venv $JUPYTER_VIRTUAL_ENV \ + && source activate $JUPYTER_VIRTUAL_ENV \ + # Install python dependencies with poetry + && poetry install --no-interaction --no-ansi --no-dev --no-cache \ + # Cleanup + && rm poetry.lock && rm pyproject.toml \ + && curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE_PYTHON_PATH - --uninstall + # ################################## # # Terra-specific Jupyter Utilities # ################################## # Ensure this matches c.ServerApp.port in 'jupyter_server_config.py' ENV JUPYTER_PORT 8888 EXPOSE $JUPYTER_PORT -ENV JUPYTER_HOME /etc/jupyter +ENV JUPYTER_HOME $JUPYTER_VIRTUAL_ENV/etc/jupyter # Install the custom extensions to enable welder for file syncing +# This can be done for system python packages so that they are always found COPY custom $JUPYTER_HOME/custom -ENV PYTHON_LIBRARIES_PATH $CONDA_HOME/lib/python3.10/site-packages -COPY custom/jupyter_delocalize.py $PYTHON_LIBRARIES_PATH +COPY custom/jupyter_delocalize.py $JUPYTER_VIRTUAL_ENV/lib/python3.10/site-packages COPY jupyter_server_config.py $JUPYTER_HOME -# Disable the use of system shell commands in the notebook to avoid users -# interacting with our base python via the notebook -ENV IPYTHON_HOME /etc/ipython/ -COPY ipython_config.py $IPYTHON_HOME +# Remove the jupyter environment from the list of available kernels so it is hidden from the user +# Note that this needs to be done with setting the c.KernelSpecManager.ensure_native_kernel flag +# to False in 'jupyter_server_config.py' +RUN jupyter kernelspec remove python3 -y -# Set up the working directory to be /home/jupyter, and make sure the -# shell is bash, like the jupyter terminal (just nicer to work with than sh) +# Set up the working directory to be /home/jupyter WORKDIR $USER_HOME -ENV SHELL /usr/bin/bash -SHELL ["/usr/bin/bash", "-c"] -RUN source ~/.bashrc # Copy the script that the service deploying to Terra (e.g. leonardo) will use for docker exec COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh @@ -189,4 +191,4 @@ COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. Jupyter execution occurs when the # init-actions.sh script uses 'docker exec' to call run-jupyter.sh. -ENTRYPOINT ["/opt/conda/bin/jupyter", "lab"] \ No newline at end of file +ENTRYPOINT ["/usr/jupytervenv/bin/jupyter", "lab"] \ No newline at end of file diff --git a/terra-base-jupyter/ipython_config.py b/terra-base-jupyter/ipython_config.py deleted file mode 100644 index 275d1916..00000000 --- a/terra-base-jupyter/ipython_config.py +++ /dev/null @@ -1 +0,0 @@ -#c.InteractiveShellApp.exec_lines = ['get_ipython().system = lambda *args: print("Use of the ! operator is disabled, please use the % operator in the notebook cell, or do the operation in the terminal instead.")'] diff --git a/terra-base-jupyter/jupyter_server_config.py b/terra-base-jupyter/jupyter_server_config.py index 2d93b40c..40c8f355 100644 --- a/terra-base-jupyter/jupyter_server_config.py +++ b/terra-base-jupyter/jupyter_server_config.py @@ -8,6 +8,6 @@ c.ServerApp.ip='' c.ServerApp.allow_origin="*" c.ServerApp.disable_check_xsrf=True # to prevent 'xsrf missing from POST' error https://broadworkbench.atlassian.net/browse/IA-4284 -c.KernelSpecManager.ensure_native_kernel = False # Hide the default python3 kernel that jupyter is running in to isolate from the user c.ServerApp.terminado_settings = {'shell_command': ['/usr/bin/bash']} -c.ServerApp.contents_manager_class=WelderContentsManager \ No newline at end of file +c.KernelSpecManager.ensure_native_kernel = False # Hide the default python3 kernel that jupyter is running in to isolate from the user +#c.ServerApp.contents_manager_class=WelderContentsManager \ No newline at end of file diff --git a/terra-base-jupyter/poetry.lock b/terra-base-jupyter/poetry.lock index 40d68e97..a7ed22fa 100644 --- a/terra-base-jupyter/poetry.lock +++ b/terra-base-jupyter/poetry.lock @@ -195,20 +195,6 @@ charset-normalizer = ["charset-normalizer"] html5lib = ["html5lib"] lxml = ["lxml"] -[[package]] -name = "binaryornot" -version = "0.4.4" -description = "Ultra-lightweight pure Python package to check if a file is binary or text." -optional = false -python-versions = "*" -files = [ - {file = "binaryornot-0.4.4-py2.py3-none-any.whl", hash = "sha256:b8b71173c917bddcd2c16070412e369c3ed7f0528926f70cac18a6c97fd563e4"}, - {file = "binaryornot-0.4.4.tar.gz", hash = "sha256:359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061"}, -] - -[package.dependencies] -chardet = ">=3.0.2" - [[package]] name = "bleach" version = "6.1.0" @@ -302,17 +288,6 @@ files = [ [package.dependencies] pycparser = "*" -[[package]] -name = "chardet" -version = "5.2.0" -description = "Universal encoding detector for Python 3" -optional = false -python-versions = ">=3.7" -files = [ - {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, - {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, -] - [[package]] name = "charset-normalizer" version = "3.3.2" @@ -412,20 +387,6 @@ files = [ {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = "sha256:3e4d1f6587322d2788836a99c69062fbb091331ec940e02d12d179c1d53e25fc"}, ] -[[package]] -name = "click" -version = "8.1.7" -description = "Composable command line interface toolkit" -optional = false -python-versions = ">=3.7" -files = [ - {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, - {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, -] - -[package.dependencies] -colorama = {version = "*", markers = "platform_system == \"Windows\""} - [[package]] name = "colorama" version = "0.4.6" @@ -454,27 +415,6 @@ traitlets = ">=4" [package.extras] test = ["pytest"] -[[package]] -name = "cookiecutter" -version = "2.6.0" -description = "A command-line utility that creates projects from project templates, e.g. creating a Python package project from a Python package project template." -optional = false -python-versions = ">=3.7" -files = [ - {file = "cookiecutter-2.6.0-py3-none-any.whl", hash = "sha256:a54a8e37995e4ed963b3e82831072d1ad4b005af736bb17b99c2cbd9d41b6e2d"}, - {file = "cookiecutter-2.6.0.tar.gz", hash = "sha256:db21f8169ea4f4fdc2408d48ca44859349de2647fbe494a9d6c3edfc0542c21c"}, -] - -[package.dependencies] -arrow = "*" -binaryornot = ">=0.4.4" -click = ">=7.0,<9.0.0" -Jinja2 = ">=2.7,<4.0.0" -python-slugify = ">=4.0.0" -pyyaml = ">=5.3.1" -requests = ">=2.23.0" -rich = "*" - [[package]] name = "debugpy" version = "1.8.1" @@ -979,13 +919,13 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p [[package]] name = "jupyter-lsp" -version = "2.2.4" +version = "2.2.5" description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" optional = false python-versions = ">=3.8" files = [ - {file = "jupyter-lsp-2.2.4.tar.gz", hash = "sha256:5e50033149344065348e688608f3c6d654ef06d9856b67655bd7b6bac9ee2d59"}, - {file = "jupyter_lsp-2.2.4-py3-none-any.whl", hash = "sha256:da61cb63a16b6dff5eac55c2699cc36eac975645adee02c41bdfc03bf4802e77"}, + {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"}, + {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"}, ] [package.dependencies] @@ -1048,19 +988,19 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (> [[package]] name = "jupyterlab" -version = "4.1.5" +version = "4.1.6" description = "JupyterLab computational environment" optional = false python-versions = ">=3.8" files = [ - {file = "jupyterlab-4.1.5-py3-none-any.whl", hash = "sha256:3bc843382a25e1ab7bc31d9e39295a9f0463626692b7995597709c0ab236ab2c"}, - {file = "jupyterlab-4.1.5.tar.gz", hash = "sha256:c9ad75290cb10bfaff3624bf3fbb852319b4cce4c456613f8ebbaa98d03524db"}, + {file = "jupyterlab-4.1.6-py3-none-any.whl", hash = "sha256:cf3e862bc10dbf4331e4eb37438634f813c238cfc62c71c640b3b3b2caa089a8"}, + {file = "jupyterlab-4.1.6.tar.gz", hash = "sha256:7935f36ba26eb615183a4f5c2bbca5791b5108ce2a00b5505f8cfd100d53648e"}, ] [package.dependencies] async-lru = ">=1.0.0" httpx = ">=0.25.0" -ipykernel = "*" +ipykernel = ">=6.5.0" jinja2 = ">=3.0.3" jupyter-core = "*" jupyter-lsp = ">=2.0.0" @@ -1068,7 +1008,7 @@ jupyter-server = ">=2.4.0,<3" jupyterlab-server = ">=2.19.0,<3" notebook-shim = ">=0.2" packaging = "*" -tomli = {version = "*", markers = "python_version < \"3.11\""} +tomli = {version = ">=1.2.2", markers = "python_version < \"3.11\""} tornado = ">=6.2.0" traitlets = "*" @@ -1077,6 +1017,7 @@ dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<7.3.0)", "sphinx-copybutton"] docs-screenshots = ["altair (==5.2.0)", "ipython (==8.16.1)", "ipywidgets (==8.1.1)", "jupyterlab-geojson (==3.4.0)", "jupyterlab-language-pack-zh-cn (==4.0.post6)", "matplotlib (==3.8.2)", "nbconvert (>=7.0.0)", "pandas (==2.2.0)", "scipy (==1.12.0)", "vega-datasets (==0.9.0)"] test = ["coverage", "pytest (>=7.0)", "pytest-check-links (>=0.7)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter (>=0.5.3)", "pytest-timeout", "pytest-tornasync", "requests", "requests-cache", "virtualenv"] +upgrade-extension = ["copier (>=8.0,<9.0)", "jinja2-time (<0.3)", "pydantic (<2.0)", "pyyaml-include (<2.0)", "tomli-w (<2.0)"] [[package]] name = "jupyterlab-pygments" @@ -1091,13 +1032,13 @@ files = [ [[package]] name = "jupyterlab-server" -version = "2.25.4" +version = "2.26.0" description = "A set of server components for JupyterLab and JupyterLab like applications." optional = false python-versions = ">=3.8" files = [ - {file = "jupyterlab_server-2.25.4-py3-none-any.whl", hash = "sha256:eb645ecc8f9b24bac5decc7803b6d5363250e16ec5af814e516bc2c54dd88081"}, - {file = "jupyterlab_server-2.25.4.tar.gz", hash = "sha256:2098198e1e82e0db982440f9b5136175d73bea2cd42a6480aa6fd502cb23c4f9"}, + {file = "jupyterlab_server-2.26.0-py3-none-any.whl", hash = "sha256:54622cbd330526a385ee0c1fdccdff3a1e7219bf3e864a335284a1270a1973df"}, + {file = "jupyterlab_server-2.26.0.tar.gz", hash = "sha256:9b3ba91cf2837f7f124fca36d63f3ca80ace2bed4898a63dd47e6598c1ab006f"}, ] [package.dependencies] @@ -1125,30 +1066,6 @@ files = [ {file = "jupyterlab_widgets-3.0.10.tar.gz", hash = "sha256:04f2ac04976727e4f9d0fa91cdc2f1ab860f965e504c29dbd6a65c882c9d04c0"}, ] -[[package]] -name = "markdown-it-py" -version = "3.0.0" -description = "Python port of markdown-it. Markdown parsing, done right!" -optional = false -python-versions = ">=3.8" -files = [ - {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"}, - {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"}, -] - -[package.dependencies] -mdurl = ">=0.1,<1.0" - -[package.extras] -benchmarking = ["psutil", "pytest", "pytest-benchmark"] -code-style = ["pre-commit (>=3.0,<4.0)"] -compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"] -linkify = ["linkify-it-py (>=1,<3)"] -plugins = ["mdit-py-plugins"] -profiling = ["gprof2dot"] -rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"] -testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] - [[package]] name = "markupsafe" version = "2.1.5" @@ -1232,17 +1149,6 @@ files = [ [package.dependencies] traitlets = "*" -[[package]] -name = "mdurl" -version = "0.1.2" -description = "Markdown URL utilities" -optional = false -python-versions = ">=3.7" -files = [ - {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"}, - {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"}, -] - [[package]] name = "mistune" version = "3.0.2" @@ -1315,19 +1221,19 @@ webpdf = ["playwright"] [[package]] name = "nbformat" -version = "5.10.3" +version = "5.10.4" description = "The Jupyter Notebook format" optional = false python-versions = ">=3.8" files = [ - {file = "nbformat-5.10.3-py3-none-any.whl", hash = "sha256:d9476ca28676799af85385f409b49d95e199951477a159a576ef2a675151e5e8"}, - {file = "nbformat-5.10.3.tar.gz", hash = "sha256:60ed5e910ef7c6264b87d644f276b1b49e24011930deef54605188ddeb211685"}, + {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"}, + {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"}, ] [package.dependencies] -fastjsonschema = "*" +fastjsonschema = ">=2.15" jsonschema = ">=2.6" -jupyter-core = "*" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" traitlets = ">=5.1" [package.extras] @@ -1432,18 +1338,18 @@ files = [ [[package]] name = "parso" -version = "0.8.3" +version = "0.8.4" description = "A Python Parser" optional = false python-versions = ">=3.6" files = [ - {file = "parso-0.8.3-py2.py3-none-any.whl", hash = "sha256:c001d4636cd3aecdaf33cbb40aebb59b094be2a74c556778ef5576c175e19e75"}, - {file = "parso-0.8.3.tar.gz", hash = "sha256:8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0"}, + {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"}, + {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"}, ] [package.extras] -qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] -testing = ["docopt", "pytest (<6.0.0)"] +qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] +testing = ["docopt", "pytest"] [[package]] name = "pexpect" @@ -1643,23 +1549,6 @@ files = [ {file = "python_json_logger-2.0.7-py3-none-any.whl", hash = "sha256:f380b826a991ebbe3de4d897aeec42760035ac760345e57b812938dc8b35e2bd"}, ] -[[package]] -name = "python-slugify" -version = "8.0.4" -description = "A Python slugify application that also handles Unicode" -optional = false -python-versions = ">=3.7" -files = [ - {file = "python-slugify-8.0.4.tar.gz", hash = "sha256:59202371d1d05b54a9e7720c5e038f928f45daaffe41dd10822f3907b937c856"}, - {file = "python_slugify-8.0.4-py2.py3-none-any.whl", hash = "sha256:276540b79961052b66b7d116620b36518847f52d5fd9e3a70164fc8c50faa6b8"}, -] - -[package.dependencies] -text-unidecode = ">=1.3" - -[package.extras] -unidecode = ["Unidecode (>=1.1.1)"] - [[package]] name = "pywin32" version = "306" @@ -1982,24 +1871,6 @@ files = [ {file = "rfc3986_validator-0.1.1.tar.gz", hash = "sha256:3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055"}, ] -[[package]] -name = "rich" -version = "13.7.1" -description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal" -optional = false -python-versions = ">=3.7.0" -files = [ - {file = "rich-13.7.1-py3-none-any.whl", hash = "sha256:4edbae314f59eb482f54e9e30bf00d33350aaa94f4bfcd4e9e3110e64d0d7222"}, - {file = "rich-13.7.1.tar.gz", hash = "sha256:9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432"}, -] - -[package.dependencies] -markdown-it-py = ">=2.2.0" -pygments = ">=2.13.0,<3.0.0" - -[package.extras] -jupyter = ["ipywidgets (>=7.5.1,<9)"] - [[package]] name = "rpds-py" version = "0.18.0" @@ -2110,13 +1981,13 @@ files = [ [[package]] name = "send2trash" -version = "1.8.2" +version = "1.8.3" description = "Send file to trash natively under Mac OS X, Windows and Linux" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ - {file = "Send2Trash-1.8.2-py3-none-any.whl", hash = "sha256:a384719d99c07ce1eefd6905d2decb6f8b7ed054025bb0e618919f945de4f679"}, - {file = "Send2Trash-1.8.2.tar.gz", hash = "sha256:c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312"}, + {file = "Send2Trash-1.8.3-py3-none-any.whl", hash = "sha256:0c31227e0bd08961c7665474a3d1ef7193929fedda4233843689baa056be46c9"}, + {file = "Send2Trash-1.8.3.tar.gz", hash = "sha256:b18e7a3966d99871aefeb00cfbcfdced55ce4871194810fc71f4aa484b953abf"}, ] [package.extras] @@ -2197,17 +2068,6 @@ docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"] typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"] -[[package]] -name = "text-unidecode" -version = "1.3" -description = "The most basic Text::Unidecode port" -optional = false -python-versions = "*" -files = [ - {file = "text-unidecode-1.3.tar.gz", hash = "sha256:bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93"}, - {file = "text_unidecode-1.3-py2.py3-none-any.whl", hash = "sha256:1311f10e8b895935241623731c2ba64f4c455287888b18189350b67134a822e8"}, -] - [[package]] name = "tinycss2" version = "1.2.1" @@ -2285,13 +2145,13 @@ files = [ [[package]] name = "typing-extensions" -version = "4.10.0" +version = "4.11.0" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"}, - {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"}, + {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, + {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, ] [[package]] @@ -2392,4 +2252,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "ecaa0b6d647a2cfadd530ed56ba7c6a3121a0c43680823e3a5a3ca82ad046a64" +content-hash = "e1125d0bc01be8714f78e07fcf4d4b97dfcf0d591d1bead1c1f8756333ecfaa9" diff --git a/terra-base-jupyter/pyproject.toml b/terra-base-jupyter/pyproject.toml index d7ec13d1..2f637259 100644 --- a/terra-base-jupyter/pyproject.toml +++ b/terra-base-jupyter/pyproject.toml @@ -8,8 +8,6 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.10" jupyter = "^1.0.0" -cookiecutter = "^2.6.0" -ipykernel = "^6.29.4" [tool.poetry.dev-dependencies] pytest = "*" diff --git a/terra-base-jupyter/run-jupyter.sh b/terra-base-jupyter/run-jupyter.sh index 99572082..7db40192 100644 --- a/terra-base-jupyter/run-jupyter.sh +++ b/terra-base-jupyter/run-jupyter.sh @@ -10,7 +10,7 @@ SERVER_APP_BASE_URL=${1:-${HOME}} SERVER_APP_WEBSOCKET_URL=${2:-${HOME}} NOTEBOOKS_DIR=${3:-${HOME}} -JUPYTER_BASE="/opt/conda/bin/python /opt/conda/bin/jupyter server" +JUPYTER_BASE="/usr/jupytervenv/bin/python /usr/jupytervenv/bin/jupyter server" JUPYTER_CMD="$JUPYTER_BASE --ServerApp.base_url=${SERVER_APP_BASE_URL} --ServerApp.websocket_url=${SERVER_APP_WEBSOCKET_URL} --autoreload --notebook-dir=${NOTEBOOKS_DIR}&> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 3a2ff3f26ffb5d36e4098c046a3885f03f25fcd1 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 11 Apr 2024 10:43:37 -0400 Subject: [PATCH 11/19] fixing conda env name display in jupyter terminal --- terra-base-jupyter/Dockerfile | 6 ++++-- terra-base-jupyter/conda_init.txt | 8 ++++---- terra-base-jupyter/jupyter_server_config.py | 2 +- 3 files changed, 9 insertions(+), 7 deletions(-) diff --git a/terra-base-jupyter/Dockerfile b/terra-base-jupyter/Dockerfile index 35c6407c..db87d779 100644 --- a/terra-base-jupyter/Dockerfile +++ b/terra-base-jupyter/Dockerfile @@ -25,6 +25,8 @@ ENV USER_HOME /home/jupyter RUN mkdir $USER_HOME # We want to store the user conda environments in a directory # that will be in the persistent disk +# Note: If you change the Conda home location, please update +# conda_init.txt accordingly ENV CONDA_ENV_NAME base-python3.10 ENV CONDA_ENV_HOME $USER_HOME/.envs/$CONDA_ENV_NAME @@ -172,7 +174,6 @@ EXPOSE $JUPYTER_PORT ENV JUPYTER_HOME $JUPYTER_VIRTUAL_ENV/etc/jupyter # Install the custom extensions to enable welder for file syncing -# This can be done for system python packages so that they are always found COPY custom $JUPYTER_HOME/custom COPY custom/jupyter_delocalize.py $JUPYTER_VIRTUAL_ENV/lib/python3.10/site-packages COPY jupyter_server_config.py $JUPYTER_HOME @@ -182,11 +183,12 @@ COPY jupyter_server_config.py $JUPYTER_HOME # to False in 'jupyter_server_config.py' RUN jupyter kernelspec remove python3 -y -# Set up the working directory to be /home/jupyter +# Set up the working directory WORKDIR $USER_HOME # Copy the script that the service deploying to Terra (e.g. leonardo) will use for docker exec COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh + # Note: this entrypoint is provided for running Jupyter independently of Leonardo. # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. Jupyter execution occurs when the diff --git a/terra-base-jupyter/conda_init.txt b/terra-base-jupyter/conda_init.txt index 36711f02..2805c5a2 100644 --- a/terra-base-jupyter/conda_init.txt +++ b/terra-base-jupyter/conda_init.txt @@ -1,13 +1,13 @@ # >>> conda initialize >>> # !! Contents within this block are managed by 'conda init' !! -__conda_setup="$('/opt/conda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" +__conda_setup="$('/home/jupyter/.envs/base-python3.10/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else -if [ -f "/opt/conda/etc/profile.d/conda.sh" ]; then -. "/opt/conda/etc/profile.d/conda.sh" +if [ -f "/home/jupyter/.envs/base-python3.10/etc/profile.d/conda.sh" ]; then +. "/home/jupyter/.envs/base-python3.10/etc/profile.d/conda.sh" else -export PATH="/opt/conda/bin:$PATH" +export PATH="/home/jupyter/.envs/base-python3.10/bin:$PATH" fi fi unset __conda_setup diff --git a/terra-base-jupyter/jupyter_server_config.py b/terra-base-jupyter/jupyter_server_config.py index 40c8f355..eef9e8bd 100644 --- a/terra-base-jupyter/jupyter_server_config.py +++ b/terra-base-jupyter/jupyter_server_config.py @@ -10,4 +10,4 @@ c.ServerApp.disable_check_xsrf=True # to prevent 'xsrf missing from POST' error https://broadworkbench.atlassian.net/browse/IA-4284 c.ServerApp.terminado_settings = {'shell_command': ['/usr/bin/bash']} c.KernelSpecManager.ensure_native_kernel = False # Hide the default python3 kernel that jupyter is running in to isolate from the user -#c.ServerApp.contents_manager_class=WelderContentsManager \ No newline at end of file +c.ServerApp.contents_manager_class=WelderContentsManager \ No newline at end of file From 2f7f7b4088aca7289b4a4797e88366004f47e3df Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 11 Apr 2024 17:13:06 -0400 Subject: [PATCH 12/19] adding smoke test, updating gha versions, and adding a readme --- .github/workflows/nodejs.yml | 2 +- .github/workflows/publish.yml | 4 +- .github/workflows/test-terra-base-jupyter.yml | 89 +++++++++++++++++++ .github/workflows/test-terra-jupyter-aou.yml | 4 +- .github/workflows/test-terra-jupyter-base.yml | 4 +- .../test-terra-jupyter-bioconductor.yml | 4 +- .github/workflows/test-terra-jupyter-gatk.yml | 4 +- .github/workflows/test-terra-jupyter-hail.yml | 4 +- .../workflows/test-terra-jupyter-python.yml | 4 +- terra-base-jupyter/README.md | 29 +++--- terra-base-jupyter/tests/smoke_test.py | 19 ++++ 11 files changed, 137 insertions(+), 30 deletions(-) create mode 100644 .github/workflows/test-terra-base-jupyter.yml create mode 100644 terra-base-jupyter/tests/smoke_test.py diff --git a/.github/workflows/nodejs.yml b/.github/workflows/nodejs.yml index 4fb37f18..35e733aa 100644 --- a/.github/workflows/nodejs.yml +++ b/.github/workflows/nodejs.yml @@ -13,7 +13,7 @@ jobs: node_version: [8, 10, 12] steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 - name: Use Node.js ${{ matrix.node-version }} uses: actions/setup-node@v1 with: diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index cb569f9f..8620507d 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -26,7 +26,7 @@ jobs: runs-on: self-hosted steps: - name: Checkout current code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: ${{ github.event.inputs.branch }} @@ -36,7 +36,7 @@ jobs: python-version: '3.10' - id: auth - uses: google-github-actions/auth@v1 + uses: google-github-actions/auth@v2 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-base-jupyter.yml b/.github/workflows/test-terra-base-jupyter.yml new file mode 100644 index 00000000..880d59e6 --- /dev/null +++ b/.github/workflows/test-terra-base-jupyter.yml @@ -0,0 +1,89 @@ +name: Test terra-base-jupyter +# Perform smoke tests on the terra-base-jupyter Docker image to have some amount of confidence that +# Python package versions are compatible. +# +# To configure the minimal auth needed for these tests to be able to read public data from Google Cloud Platform: +# Step 1: Create a service account per these instructions: +# https://github.com/google-github-actions/setup-gcloud/blob/master/setup-gcloud/README.md +# Step 2: Give the service account the following permissions within the project: BigQuery User +# Step 3: Store its key and project id as GitHub repository secrets TD_GCP_SA_KEY and GCP_PROJECT_ID. +# https://docs.github.com/en/free-pro-team@latest/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository + +on: + pull_request: + branches: [ master ] + paths: + - 'terra-base-jupyter/**' + - '.github/workflows/test-terra-base-jupyter.yml' + + push: + # Note: GitHub secrets are not passed to pull requests from forks. For community contributions from + # regular contributors, its a good idea for the contributor to configure the GitHub actions to run correctly + # in their fork as described above. + # + # For occasional contributors, the dev team will merge the PR fork branch to a branch in upstream named + # test-community-contribution- to run all the GitHub Action smoke tests. + branches: [ 'test-community-contribution*' ] + paths: + - 'terra-base-jupyter/**' + - '.github/workflows/test-terra-base-jupyter.yml' + + workflow_dispatch: + # Allows manually triggering of workflow on a selected branch via the GitHub Actions tab. + # GitHub blog demo: https://github.blog/changelog/2020-07-06-github-actions-manual-triggers-with-workflow_dispatch/. + +env: + GOOGLE_PROJECT: ${{ secrets.GCP_PROJECT_ID }} + +jobs: + + test_docker_image: + runs-on: self-hosted + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.10' + + - name: Free up some disk space + run: sudo rm -rf /usr/share/dotnet + + - id: auth + uses: google-github-actions/auth@v2 + with: + credentials_json: ${{ secrets.TD_GCP_SA_KEY }} + create_credentials_file: true + + - name: Set up Cloud SDK + uses: google-github-actions/setup-gcloud@v0.3.0 + with: + project_id: ${{ secrets.GCP_PROJECT_ID }} + + - name: Build Docker image and base images too, if needed + run: | + gcloud auth configure-docker + ./build_smoke_test_image.sh terra-base-jupyter + + - name: Upload workflow artifacts + uses: actions/upload-artifact@v2 + with: + name: notebook-execution-results + path: terra-base-jupyter/tests/*.html + retention-days: 30 + + - name: Test Python code with pytest + run: | + chmod a+r "${{ steps.auth.outputs.credentials_file_path }}" + docker run \ + --env GOOGLE_PROJECT \ + --volume "${{ steps.auth.outputs.credentials_file_path }}":/tmp/credentials.json:ro \ + --env GOOGLE_APPLICATION_CREDENTIALS="/tmp/credentials.json" \ + --volume $GITHUB_WORKSPACE/terra-base-jupyter/tests:/tests \ + --workdir=/tests \ + --entrypoint="" \ + terra-base-jupyter:smoke-test \ + /bin/sh -c "pip3 install pytest; pytest" diff --git a/.github/workflows/test-terra-jupyter-aou.yml b/.github/workflows/test-terra-jupyter-aou.yml index dd38e95e..278528cb 100644 --- a/.github/workflows/test-terra-jupyter-aou.yml +++ b/.github/workflows/test-terra-jupyter-aou.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v1 + uses: google-github-actions/auth@v2 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-base.yml b/.github/workflows/test-terra-jupyter-base.yml index 710c8cc6..e01850b0 100644 --- a/.github/workflows/test-terra-jupyter-base.yml +++ b/.github/workflows/test-terra-jupyter-base.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v1 + uses: google-github-actions/auth@v2 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-bioconductor.yml b/.github/workflows/test-terra-jupyter-bioconductor.yml index 8863d834..a161d0d5 100644 --- a/.github/workflows/test-terra-jupyter-bioconductor.yml +++ b/.github/workflows/test-terra-jupyter-bioconductor.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v2 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v1 + uses: google-github-actions/auth@v2 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-gatk.yml b/.github/workflows/test-terra-jupyter-gatk.yml index aa911c8e..d6f1e21c 100644 --- a/.github/workflows/test-terra-jupyter-gatk.yml +++ b/.github/workflows/test-terra-jupyter-gatk.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v1 + uses: google-github-actions/auth@v2 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-hail.yml b/.github/workflows/test-terra-jupyter-hail.yml index 20170074..2d427a14 100644 --- a/.github/workflows/test-terra-jupyter-hail.yml +++ b/.github/workflows/test-terra-jupyter-hail.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v1 + uses: google-github-actions/auth@v2 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-python.yml b/.github/workflows/test-terra-jupyter-python.yml index 1049957b..005df224 100644 --- a/.github/workflows/test-terra-jupyter-python.yml +++ b/.github/workflows/test-terra-jupyter-python.yml @@ -44,7 +44,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v4 @@ -55,7 +55,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v1 + uses: google-github-actions/auth@v2 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/terra-base-jupyter/README.md b/terra-base-jupyter/README.md index e0d597e6..a7c59433 100644 --- a/terra-base-jupyter/README.md +++ b/terra-base-jupyter/README.md @@ -1,24 +1,23 @@ -# terra-base image +# terra-base-jupyter image -This repo contains the terra-base image that is compatible with the -notebook service in [Terra]("https://app.terra.bio/") called Leonardo. -The goal is to provide a lean, GPU-enabled base image that can be use for both Terra-suported, and custome image builds. -[See design doc]("https://broadworkbench.atlassian.net/wiki/spaces/IA/pages/2842460165/2023-08-28+Terra+Docker+Refactoring+POC#Provide-a-leaner-set-of-terra-docker-images") +This repo contains the terra-base-jupyter image that is compatible with the +jupyter notebook service in [Terra]("https://app.terra.bio/") called Leonardo. +The goal is to provide a lean, GPU-enabled base image that can be use for both Terra-suported, and custom image builds. + +The goal is to provide the user with a base conda environment where they can install any +package they need, while keeping the jupyter server itself in an isolated virtual environment +that DSP devs control using poetry as the dependency manager ## Image contents -`terra-base` extends an cuda 12.2.0 and Ubuntu 22.04 base image with the minimum +`terra-base-jupyter` extends an cuda 12.2.0 and Ubuntu 22.04 base image with the minimum requirements necessary to set up Jupyter and provide compatibility with Leonardo and GPU machines. - OS prerequisites -- Python 3.10 -- R 4.1.2 -- Anaconda -- Jupyter -- Leonardo customizations/extensions -- Terra python client library ([FISS](https://github.com/broadinstitute/fiss)) -- Terra notebook utils -- Full list of python packages is available [here](pyproject.toml) +- Miniconda with python 3.10 +- Two python virtual environments based on miniconda python +-- The user base Conda environment, full list of python packages is available [here](conda-environment.yml) +-- The jupyter virtual environment managed separately by poetry, full list of python packages is available [here](pyproject.toml) that contains the terra-specific configurations (e.g. WelderContentManager) To see the complete contents of this image please see the [Dockerfile](./Dockerfile). @@ -67,7 +66,7 @@ $> export LDFLAGS="-L/opt/homebrew/opt/libomp/lib -L/opt/homebrew/opt/llvm/lib" $> export CPPFLAGS="-I/opt/homebrew/opt/libomp/include -I/opt/homebrew/opt/llvmp/include" ``` -From inside the `terra-base` directory, run the following command to install +From inside the `terra-base-jupyter` directory, run the following command to install the python 3.10 environment with the relevant packages: ```bash diff --git a/terra-base-jupyter/tests/smoke_test.py b/terra-base-jupyter/tests/smoke_test.py new file mode 100644 index 00000000..956a7ae7 --- /dev/null +++ b/terra-base-jupyter/tests/smoke_test.py @@ -0,0 +1,19 @@ +"""Brief smoke tests for terra-base-jupyter. + +Minimal tests simply import packages and run 'hello world' code to determine whether any exceptions +are thrown. + +TODO(all): Add additional tests and/or tests with particular assertions, as we encounter Python package version +incompatibilities not currently detected by these tests. +""" + +import os +import pytest +import subprocess + +def test_firecloud(): + import firecloud + +def test_terra_notebook_utils(): + os.system("gcloud auth application-default login") + import terra_notebook_utils \ No newline at end of file From cfd2af262fe8096a0550ebd14e56778bbc811123 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Tue, 16 Apr 2024 17:44:51 -0400 Subject: [PATCH 13/19] try not running as root but granting sudo priviledges to jupyter user --- terra-base-jupyter/Dockerfile | 67 ++++++++++++++++++----------------- terra-base-jupyter/README.md | 7 ++++ 2 files changed, 42 insertions(+), 32 deletions(-) diff --git a/terra-base-jupyter/Dockerfile b/terra-base-jupyter/Dockerfile index db87d779..2d9f3605 100644 --- a/terra-base-jupyter/Dockerfile +++ b/terra-base-jupyter/Dockerfile @@ -14,31 +14,6 @@ ENV LC_ALL en_US.UTF-8 # We need node >18 for jupyter to work ENV NODE_MAJOR 20 -############# -# Users Setup -############# -# Create the jupyter home directories where they will save their -# notebooks and install their conda environments -# Note that there is no jupyter user created, the intent is to run this docker -# container as root -ENV USER_HOME /home/jupyter -RUN mkdir $USER_HOME -# We want to store the user conda environments in a directory -# that will be in the persistent disk -# Note: If you change the Conda home location, please update -# conda_init.txt accordingly -ENV CONDA_ENV_NAME base-python3.10 -ENV CONDA_ENV_HOME $USER_HOME/.envs/$CONDA_ENV_NAME - -# Create the welder user -# The welder uid is consistent with the Welder docker definition here: -# https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala -# Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added -# files display nicer when viewed in a terminal. -ENV WELDER_USER welder-user -ENV WELDER_UID 1001 -RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER - ############### # Prerequisites ############### @@ -97,11 +72,38 @@ RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesourc RUN dpkg --remove --force-remove-reinstreq libnode-dev RUN apt-get update && apt-get install -f -yq nodejs +############# +# Users Setup +############# +# Create the welder user +# The welder uid is consistent with the Welder docker definition here: +# https://github.com/DataBiosphere/welder/blob/master/project/Settings.scala +# Adding welder-user to the Jupyter container isn't strictly required, but it makes welder-added +# files display nicer when viewed in a terminal. +ENV WELDER_USER welder-user +ENV WELDER_UID 1001 +RUN useradd -m -N -u $WELDER_UID $WELDER_USER + +# Create the jupyter user +ENV USER jupyter +ENV USER_HOME /home/$USER +RUN useradd -m -d $USER_HOME -N -g users $USER +# We want to grant the jupyter user sudo permissions +# without password so they can install the necessary packages that they +# want to use on the docker container +RUN echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER \ + && chmod 0440 /etc/sudoers.d/$USER + ##################################### # Install Python 3.10 via Miniconda ##################################### ## Note: CONDA should NOT be used by terra devs to manage dependencies (see the use of poetry below instead), ## but is a widely used tool to manage python environments in a runtime and we should provide it to users +## We want to store the user conda environments in a directory +## that will be in the persistent disk +## Attention: If you change the Conda home location, please update conda_init.txt accordingly +ENV CONDA_ENV_NAME base-python3.10 +ENV CONDA_ENV_HOME $USER_HOME/.envs/$CONDA_ENV_NAME RUN curl -so $HOME/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.1-0-Linux-x86_64.sh \ && chmod +x $HOME/miniconda.sh \ && $HOME/miniconda.sh -b -p $CONDA_ENV_HOME \ @@ -128,15 +130,15 @@ RUN conda env update --prefix $CONDA_ENV_HOME --file conda-environment.yml --pru # Add the user base conda environment as a jupyter kernel - this should be the default now # This commands activates the conda environment and then calls ipykernel from within # to install it as a kernel under the same name -RUN conda run -p ${CONDA_ENV_HOME} python -m ipykernel install --user --name=$CONDA_ENV_NAME +RUN conda run -p ${CONDA_ENV_HOME} python -m ipykernel install --name=$CONDA_ENV_NAME # Prep the jupyter terminal to conda init and make sure the base conda environment is # activated and the name is displayed in the terminal prompt COPY conda_init.txt . -RUN cat conda_init.txt >> ~/.bashrc && \ - printf "\nconda activate ${CONDA_ENV_HOME}" >> ~/.bashrc && \ +RUN cat conda_init.txt >> $USER_HOME/.bashrc && \ + printf "\nconda activate ${CONDA_ENV_HOME}" >> $USER_HOME/.bashrc && \ conda config --set env_prompt '({name})' && \ - source ~/.bashrc && \ + source $USER_HOME/.bashrc && \ rm conda_init.txt #################################################### @@ -183,12 +185,13 @@ COPY jupyter_server_config.py $JUPYTER_HOME # to False in 'jupyter_server_config.py' RUN jupyter kernelspec remove python3 -y -# Set up the working directory -WORKDIR $USER_HOME - # Copy the script that the service deploying to Terra (e.g. leonardo) will use for docker exec COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh +# Set up the user and working directory +USER $USER +WORKDIR $USER_HOME + # Note: this entrypoint is provided for running Jupyter independently of Leonardo. # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable # additional setup inside the container before execution. Jupyter execution occurs when the diff --git a/terra-base-jupyter/README.md b/terra-base-jupyter/README.md index a7c59433..cc1942d7 100644 --- a/terra-base-jupyter/README.md +++ b/terra-base-jupyter/README.md @@ -21,6 +21,13 @@ requirements necessary to set up Jupyter and provide compatibility with Leonardo To see the complete contents of this image please see the [Dockerfile](./Dockerfile). +Note that you can build the image locally and run it by using the following commands from within this directory: + +```bash +$> docker build . -t test-base-jupyter +$> docker run --rm -it -p 8888:8888 test-base-jupyter /home/jupyter/ /usr/jupytervenv/bin/jupyter lab --ip 0.0.0.0 --no-browser --allow-root +``` + ## Contributing ### Installing python 3.10 From 7c1da789988b4d1f10797a85df504ee049496f97 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 18 Apr 2024 16:52:55 -0400 Subject: [PATCH 14/19] addressing dockerfile comments --- terra-base-jupyter/Dockerfile | 73 +++++++++---------- terra-base-jupyter/README.md | 2 +- .../custom/test/test-requirements.txt | 3 - 3 files changed, 36 insertions(+), 42 deletions(-) delete mode 100644 terra-base-jupyter/custom/test/test-requirements.txt diff --git a/terra-base-jupyter/Dockerfile b/terra-base-jupyter/Dockerfile index 2d9f3605..3e7b0141 100644 --- a/terra-base-jupyter/Dockerfile +++ b/terra-base-jupyter/Dockerfile @@ -14,45 +14,36 @@ ENV LC_ALL en_US.UTF-8 # We need node >18 for jupyter to work ENV NODE_MAJOR 20 +# Set the python version and corresponding conda installer +ENV PYTHON_VERSION 3.10 +ENV CONDA_INSTALLER https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.1-0-Linux-x86_64.sh + ############### # Prerequisites ############### RUN apt-get update && apt-get install -yq --no-install-recommends \ + # basic necessities sudo \ ca-certificates \ curl \ jq \ + tree \ # gnupg requirement gnupg \ dirmngr \ - # useful utilities for debugging within the docker + # useful utilities for debugging within docker itself nano \ + less \ procps \ lsb-release \ - # python requirements - checkinstall \ + # gcc compiler build-essential \ - zlib1g-dev \ - # pip requirements - libssl-dev \ - libbz2-dev \ - libreadline-dev \ - libsqlite3-dev \ - libexempi8 \ - libnode-dev \ - llvm \ - libncurses5-dev \ - libncursesw5-dev \ - tk-dev \ - libffi-dev \ - liblzma-dev \ - python3-openssl \ - # install script requirements locales \ # for ssh-agent and ssh-add keychain \ # extras \ wget \ + aria2 \ bzip2 \ # git git \ @@ -69,7 +60,6 @@ RUN mkdir -p /etc/apt/keyrings RUN curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg RUN echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_MAJOR.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list -RUN dpkg --remove --force-remove-reinstreq libnode-dev RUN apt-get update && apt-get install -f -yq nodejs ############# @@ -95,22 +85,27 @@ RUN echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER \ && chmod 0440 /etc/sudoers.d/$USER ##################################### -# Install Python 3.10 via Miniconda +# Install Python via Miniconda ##################################### ## Note: CONDA should NOT be used by terra devs to manage dependencies (see the use of poetry below instead), ## but is a widely used tool to manage python environments in a runtime and we should provide it to users ## We want to store the user conda environments in a directory ## that will be in the persistent disk ## Attention: If you change the Conda home location, please update conda_init.txt accordingly -ENV CONDA_ENV_NAME base-python3.10 +ENV CONDA_ENV_NAME base-python${PYTHON_VERSION} ENV CONDA_ENV_HOME $USER_HOME/.envs/$CONDA_ENV_NAME -RUN curl -so $HOME/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.1-0-Linux-x86_64.sh \ - && chmod +x $HOME/miniconda.sh \ - && $HOME/miniconda.sh -b -p $CONDA_ENV_HOME \ - && rm $HOME/miniconda.sh +RUN curl -so $USER_HOME/miniconda.sh ${CONDA_INSTALLER} \ + && chmod +x $USER_HOME/miniconda.sh \ + && $USER_HOME/miniconda.sh -b -p $CONDA_ENV_HOME \ + # Make sure the USER is the owner of the folder where + # the base python is installed, and subsequent conda environments + && chown -R $USER:users $USER_HOME \ + && rm $USER_HOME/miniconda.sh ENV PATH "${PATH}:${CONDA_ENV_HOME}/bin" +# Set up the path to the user python ENV BASE_PYTHON_PATH $CONDA_ENV_HOME/bin/python +# Tell condo to NOT write bite code (aka these.pyc files) ENV PYTHONDONTWRITEBYTECODE=true ################################################### @@ -121,10 +116,10 @@ ENV PYTHONDONTWRITEBYTECODE=true ## in the base environment to provide isolation between the user environment, and the jupyter server ## to avoid cross-contamination COPY conda-environment.yml . -RUN conda env update --prefix $CONDA_ENV_HOME --file conda-environment.yml --prune\ +RUN conda env update --prefix $CONDA_ENV_HOME --file conda-environment.yml --prune \ # Remove packages tarballs and python bytecode files from the image && conda clean -afy \ - && find $CONDA_ENV_HOME -follow -type f -name '*.pyc' -delete \ + # && find $CONDA_ENV_HOME -follow -type f -name '*.pyc' -delete \ && rm conda-environment.yml # Add the user base conda environment as a jupyter kernel - this should be the default now @@ -152,15 +147,18 @@ ENV PATH "${PATH}:${POETRY_HOME}/bin" COPY poetry.lock . COPY pyproject.toml . -ENV JUPYTER_VIRTUAL_ENV=/usr/jupytervenv -# Add jupyter virtual environmemt to PATH -ENV PATH="$JUPYTER_VIRTUAL_ENV/bin:$PATH" +ENV JUPYTER_HOME /usr/jupytervenv +# Add jupyter virtual environmemt to PATH, +# but make sure to add it at the end so that the +# Conda base python takes precedence +# (aka the ! operator in iPython shells should NOT access the jupyter virtualenvironment) +ENV PATH "${PATH}:${JUPYTER_HOME}/bin" # Install Poetry, set up the virtual environment for jupyter to run and then cleanup / uninstall poetry RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE_PYTHON_PATH \ # Create a virtual environment and activate it for poetry to use - && $BASE_PYTHON_PATH -m venv $JUPYTER_VIRTUAL_ENV \ - && source activate $JUPYTER_VIRTUAL_ENV \ + && $BASE_PYTHON_PATH -m venv $JUPYTER_HOME \ + && source $JUPYTER_HOME/bin/activate \ # Install python dependencies with poetry && poetry install --no-interaction --no-ansi --no-dev --no-cache \ # Cleanup @@ -173,17 +171,16 @@ RUN curl -sSL https://install.python-poetry.org | POETRY_HOME=$POETRY_HOME $BASE # Ensure this matches c.ServerApp.port in 'jupyter_server_config.py' ENV JUPYTER_PORT 8888 EXPOSE $JUPYTER_PORT -ENV JUPYTER_HOME $JUPYTER_VIRTUAL_ENV/etc/jupyter # Install the custom extensions to enable welder for file syncing -COPY custom $JUPYTER_HOME/custom -COPY custom/jupyter_delocalize.py $JUPYTER_VIRTUAL_ENV/lib/python3.10/site-packages -COPY jupyter_server_config.py $JUPYTER_HOME +COPY custom $JUPYTER_HOME/etc/jupyter/custom +COPY custom/jupyter_delocalize.py $JUPYTER_HOME/lib/python${PYTHON_VERSION}/site-packages +COPY jupyter_server_config.py $JUPYTER_HOME/etc/jupyter # Remove the jupyter environment from the list of available kernels so it is hidden from the user # Note that this needs to be done with setting the c.KernelSpecManager.ensure_native_kernel flag # to False in 'jupyter_server_config.py' -RUN jupyter kernelspec remove python3 -y +RUN $JUPYTER_HOME/bin/jupyter kernelspec remove python3 -y # Copy the script that the service deploying to Terra (e.g. leonardo) will use for docker exec COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh diff --git a/terra-base-jupyter/README.md b/terra-base-jupyter/README.md index cc1942d7..1a3f9da2 100644 --- a/terra-base-jupyter/README.md +++ b/terra-base-jupyter/README.md @@ -2,7 +2,7 @@ This repo contains the terra-base-jupyter image that is compatible with the jupyter notebook service in [Terra]("https://app.terra.bio/") called Leonardo. -The goal is to provide a lean, GPU-enabled base image that can be use for both Terra-suported, and custom image builds. +The goal is to provide a lean GPU-enabled base image that can be use for both Terra-suported and custom image builds. The goal is to provide the user with a base conda environment where they can install any package they need, while keeping the jupyter server itself in an isolated virtual environment diff --git a/terra-base-jupyter/custom/test/test-requirements.txt b/terra-base-jupyter/custom/test/test-requirements.txt deleted file mode 100644 index e7c6ae7e..00000000 --- a/terra-base-jupyter/custom/test/test-requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -jupyter==1.0.0 -nose==1.3.7 -requests-mock==1.6.0 From a72f84ecd57269e26d784b114441ec56b40a77fe Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 24 Apr 2024 09:54:13 -0400 Subject: [PATCH 15/19] change jupyter-user uid and make run-jupyter.sh executable --- terra-base-jupyter/Dockerfile | 34 ++++++++++++++++--------------- terra-base-jupyter/README.md | 2 +- terra-base-jupyter/conda_init.txt | 8 ++++---- terra-base-jupyter/run-jupyter.sh | 2 +- 4 files changed, 24 insertions(+), 22 deletions(-) diff --git a/terra-base-jupyter/Dockerfile b/terra-base-jupyter/Dockerfile index 3e7b0141..6370d526 100644 --- a/terra-base-jupyter/Dockerfile +++ b/terra-base-jupyter/Dockerfile @@ -75,14 +75,15 @@ ENV WELDER_UID 1001 RUN useradd -m -N -u $WELDER_UID $WELDER_USER # Create the jupyter user -ENV USER jupyter -ENV USER_HOME /home/$USER -RUN useradd -m -d $USER_HOME -N -g users $USER +ENV JUPYTER_USER jupyter-user +ENV JUPYTER_UID 1002 +ENV JUPYTER_USER_HOME /home/$JUPYTER_USER +RUN useradd -m -d $JUPYTER_USER_HOME -N -u $JUPYTER_UID -g users $JUPYTER_USER # We want to grant the jupyter user sudo permissions # without password so they can install the necessary packages that they # want to use on the docker container -RUN echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER \ - && chmod 0440 /etc/sudoers.d/$USER +RUN echo "$JUPYTER_USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$JUPYTER_USER \ + && chmod 0440 /etc/sudoers.d/$JUPYTER_USER ##################################### # Install Python via Miniconda @@ -93,14 +94,14 @@ RUN echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER \ ## that will be in the persistent disk ## Attention: If you change the Conda home location, please update conda_init.txt accordingly ENV CONDA_ENV_NAME base-python${PYTHON_VERSION} -ENV CONDA_ENV_HOME $USER_HOME/.envs/$CONDA_ENV_NAME -RUN curl -so $USER_HOME/miniconda.sh ${CONDA_INSTALLER} \ - && chmod +x $USER_HOME/miniconda.sh \ - && $USER_HOME/miniconda.sh -b -p $CONDA_ENV_HOME \ +ENV CONDA_ENV_HOME $JUPYTER_USER_HOME/.envs/$CONDA_ENV_NAME +RUN curl -so $JUPYTER_USER_HOME/miniconda.sh ${CONDA_INSTALLER} \ + && chmod +x $JUPYTER_USER_HOME/miniconda.sh \ + && $JUPYTER_USER_HOME/miniconda.sh -b -p $CONDA_ENV_HOME \ # Make sure the USER is the owner of the folder where # the base python is installed, and subsequent conda environments - && chown -R $USER:users $USER_HOME \ - && rm $USER_HOME/miniconda.sh + && chown -R $USER:users $JUPYTER_USER_HOME \ + && rm $JUPYTER_USER_HOME/miniconda.sh ENV PATH "${PATH}:${CONDA_ENV_HOME}/bin" # Set up the path to the user python @@ -130,10 +131,10 @@ RUN conda run -p ${CONDA_ENV_HOME} python -m ipykernel install --name=$CONDA_ENV # Prep the jupyter terminal to conda init and make sure the base conda environment is # activated and the name is displayed in the terminal prompt COPY conda_init.txt . -RUN cat conda_init.txt >> $USER_HOME/.bashrc && \ - printf "\nconda activate ${CONDA_ENV_HOME}" >> $USER_HOME/.bashrc && \ +RUN cat conda_init.txt >> $JUPYTER_USER_HOME/.bashrc && \ + printf "\nconda activate ${CONDA_ENV_HOME}" >> $JUPYTER_USER_HOME/.bashrc && \ conda config --set env_prompt '({name})' && \ - source $USER_HOME/.bashrc && \ + source $JUPYTER_USER_HOME/.bashrc && \ rm conda_init.txt #################################################### @@ -184,10 +185,11 @@ RUN $JUPYTER_HOME/bin/jupyter kernelspec remove python3 -y # Copy the script that the service deploying to Terra (e.g. leonardo) will use for docker exec COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh +RUN chmod +x $JUPYTER_HOME/run-jupyter.sh # Set up the user and working directory -USER $USER -WORKDIR $USER_HOME +USER $JUPYTER_USER +WORKDIR $JUPYTER_USER_HOME # Note: this entrypoint is provided for running Jupyter independently of Leonardo. # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable diff --git a/terra-base-jupyter/README.md b/terra-base-jupyter/README.md index 1a3f9da2..f04f1a94 100644 --- a/terra-base-jupyter/README.md +++ b/terra-base-jupyter/README.md @@ -25,7 +25,7 @@ Note that you can build the image locally and run it by using the following comm ```bash $> docker build . -t test-base-jupyter -$> docker run --rm -it -p 8888:8888 test-base-jupyter /home/jupyter/ /usr/jupytervenv/bin/jupyter lab --ip 0.0.0.0 --no-browser --allow-root +$> docker run --rm -it -p 8888:8888 test-base-jupyter /home/jupyter-user/ /usr/jupytervenv/bin/jupyter lab --ip 0.0.0.0 --no-browser --allow-root ``` ## Contributing diff --git a/terra-base-jupyter/conda_init.txt b/terra-base-jupyter/conda_init.txt index 2805c5a2..d379d640 100644 --- a/terra-base-jupyter/conda_init.txt +++ b/terra-base-jupyter/conda_init.txt @@ -1,13 +1,13 @@ # >>> conda initialize >>> # !! Contents within this block are managed by 'conda init' !! -__conda_setup="$('/home/jupyter/.envs/base-python3.10/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" +__conda_setup="$('/home/jupyter-user/.envs/base-python3.10/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else -if [ -f "/home/jupyter/.envs/base-python3.10/etc/profile.d/conda.sh" ]; then -. "/home/jupyter/.envs/base-python3.10/etc/profile.d/conda.sh" +if [ -f "/home/jupyter-user/.envs/base-python3.10/etc/profile.d/conda.sh" ]; then +. "/home/jupyter-user/.envs/base-python3.10/etc/profile.d/conda.sh" else -export PATH="/home/jupyter/.envs/base-python3.10/bin:$PATH" +export PATH="/home/jupyter-user/.envs/base-python3.10/bin:$PATH" fi fi unset __conda_setup diff --git a/terra-base-jupyter/run-jupyter.sh b/terra-base-jupyter/run-jupyter.sh index 7db40192..8c117c32 100644 --- a/terra-base-jupyter/run-jupyter.sh +++ b/terra-base-jupyter/run-jupyter.sh @@ -11,7 +11,7 @@ SERVER_APP_WEBSOCKET_URL=${2:-${HOME}} NOTEBOOKS_DIR=${3:-${HOME}} JUPYTER_BASE="/usr/jupytervenv/bin/python /usr/jupytervenv/bin/jupyter server" -JUPYTER_CMD="$JUPYTER_BASE --ServerApp.base_url=${SERVER_APP_BASE_URL} --ServerApp.websocket_url=${SERVER_APP_WEBSOCKET_URL} --autoreload --notebook-dir=${NOTEBOOKS_DIR}&> ${NOTEBOOKS_DIR}/jupyter.log" +JUPYTER_CMD="$JUPYTER_BASE --ServerApp.base_url=${SERVER_APP_BASE_URL} --ServerApp.websocket_url=${SERVER_APP_WEBSOCKET_URL} --autoreload&> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 2be78da4b801f88d55af09c2c438407b40576e13 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Thu, 2 May 2024 14:16:50 -0400 Subject: [PATCH 16/19] specify notebook dir and change ownership to jupyter user --- terra-base-jupyter/Dockerfile | 14 +++++++------- terra-base-jupyter/run-jupyter.sh | 3 +-- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/terra-base-jupyter/Dockerfile b/terra-base-jupyter/Dockerfile index 6370d526..4900a091 100644 --- a/terra-base-jupyter/Dockerfile +++ b/terra-base-jupyter/Dockerfile @@ -77,6 +77,7 @@ RUN useradd -m -N -u $WELDER_UID $WELDER_USER # Create the jupyter user ENV JUPYTER_USER jupyter-user ENV JUPYTER_UID 1002 +# Create the jupyter user home ENV JUPYTER_USER_HOME /home/$JUPYTER_USER RUN useradd -m -d $JUPYTER_USER_HOME -N -u $JUPYTER_UID -g users $JUPYTER_USER # We want to grant the jupyter user sudo permissions @@ -98,9 +99,6 @@ ENV CONDA_ENV_HOME $JUPYTER_USER_HOME/.envs/$CONDA_ENV_NAME RUN curl -so $JUPYTER_USER_HOME/miniconda.sh ${CONDA_INSTALLER} \ && chmod +x $JUPYTER_USER_HOME/miniconda.sh \ && $JUPYTER_USER_HOME/miniconda.sh -b -p $CONDA_ENV_HOME \ - # Make sure the USER is the owner of the folder where - # the base python is installed, and subsequent conda environments - && chown -R $USER:users $JUPYTER_USER_HOME \ && rm $JUPYTER_USER_HOME/miniconda.sh ENV PATH "${PATH}:${CONDA_ENV_HOME}/bin" @@ -120,8 +118,10 @@ COPY conda-environment.yml . RUN conda env update --prefix $CONDA_ENV_HOME --file conda-environment.yml --prune \ # Remove packages tarballs and python bytecode files from the image && conda clean -afy \ - # && find $CONDA_ENV_HOME -follow -type f -name '*.pyc' -delete \ - && rm conda-environment.yml + && rm conda-environment.yml \ + # Make sure the JUPYTER_USER is the owner of the folder where + # the base conda is installed + && chown -R $JUPYTER_USER:users $JUPYTER_USER_HOME # Add the user base conda environment as a jupyter kernel - this should be the default now # This commands activates the conda environment and then calls ipykernel from within @@ -187,9 +187,9 @@ RUN $JUPYTER_HOME/bin/jupyter kernelspec remove python3 -y COPY run-jupyter.sh $JUPYTER_HOME/run-jupyter.sh RUN chmod +x $JUPYTER_HOME/run-jupyter.sh -# Set up the user and working directory +# Set up the user and working directory, which is where the persistent disk will be mounted USER $JUPYTER_USER -WORKDIR $JUPYTER_USER_HOME +WORKDIR $JUPYTER_USER_HOME/persistent_disk # Note: this entrypoint is provided for running Jupyter independently of Leonardo. # When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable diff --git a/terra-base-jupyter/run-jupyter.sh b/terra-base-jupyter/run-jupyter.sh index 8c117c32..f0259314 100644 --- a/terra-base-jupyter/run-jupyter.sh +++ b/terra-base-jupyter/run-jupyter.sh @@ -5,13 +5,12 @@ set -e # Change the default umask to support R/W access to the shared volume with welder umask 002 -# TODO: change default to ${HOME}/notebooks once welder is rolled out to all clusters SERVER_APP_BASE_URL=${1:-${HOME}} SERVER_APP_WEBSOCKET_URL=${2:-${HOME}} NOTEBOOKS_DIR=${3:-${HOME}} JUPYTER_BASE="/usr/jupytervenv/bin/python /usr/jupytervenv/bin/jupyter server" -JUPYTER_CMD="$JUPYTER_BASE --ServerApp.base_url=${SERVER_APP_BASE_URL} --ServerApp.websocket_url=${SERVER_APP_WEBSOCKET_URL} --autoreload&> ${NOTEBOOKS_DIR}/jupyter.log" +JUPYTER_CMD="$JUPYTER_BASE --ServerApp.base_url=${SERVER_APP_BASE_URL} --ServerApp.websocket_url=${SERVER_APP_WEBSOCKET_URL} --ServerApp.root_dir=${NOTEBOOKS_DIR} --autoreload&> ${NOTEBOOKS_DIR}/jupyter.log" echo $JUPYTER_CMD From 333085b0e964f81c884e7568f72c2eb32c6ba4c7 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 29 May 2024 10:50:29 -0400 Subject: [PATCH 17/19] only focus on changes for the new image --- .github/workflows/nodejs.yml | 2 +- .github/workflows/publish.yml | 2 +- .github/workflows/test-terra-jupyter-aou.yml | 4 ++-- .github/workflows/test-terra-jupyter-bioconductor.yml | 4 ++-- .github/workflows/test-terra-jupyter-gatk.yml | 4 ++-- .github/workflows/test-terra-jupyter-hail.yml | 4 ++-- .github/workflows/test-terra-jupyter-python.yml | 4 ++-- 7 files changed, 12 insertions(+), 12 deletions(-) diff --git a/.github/workflows/nodejs.yml b/.github/workflows/nodejs.yml index 35e733aa..4fb37f18 100644 --- a/.github/workflows/nodejs.yml +++ b/.github/workflows/nodejs.yml @@ -13,7 +13,7 @@ jobs: node_version: [8, 10, 12] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v1 - name: Use Node.js ${{ matrix.node-version }} uses: actions/setup-node@v1 with: diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 8620507d..fd2b12dd 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -26,7 +26,7 @@ jobs: runs-on: self-hosted steps: - name: Checkout current code - uses: actions/checkout@v4 + uses: actions/checkout@v3 with: ref: ${{ github.event.inputs.branch }} diff --git a/.github/workflows/test-terra-jupyter-aou.yml b/.github/workflows/test-terra-jupyter-aou.yml index 278528cb..dd38e95e 100644 --- a/.github/workflows/test-terra-jupyter-aou.yml +++ b/.github/workflows/test-terra-jupyter-aou.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v2 + uses: google-github-actions/auth@v1 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-bioconductor.yml b/.github/workflows/test-terra-jupyter-bioconductor.yml index a161d0d5..8863d834 100644 --- a/.github/workflows/test-terra-jupyter-bioconductor.yml +++ b/.github/workflows/test-terra-jupyter-bioconductor.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v2 - name: Set up Python uses: actions/setup-python@v2 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v2 + uses: google-github-actions/auth@v1 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-gatk.yml b/.github/workflows/test-terra-jupyter-gatk.yml index d6f1e21c..aa911c8e 100644 --- a/.github/workflows/test-terra-jupyter-gatk.yml +++ b/.github/workflows/test-terra-jupyter-gatk.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v2 + uses: google-github-actions/auth@v1 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-hail.yml b/.github/workflows/test-terra-jupyter-hail.yml index 2d427a14..20170074 100644 --- a/.github/workflows/test-terra-jupyter-hail.yml +++ b/.github/workflows/test-terra-jupyter-hail.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v2 + uses: google-github-actions/auth@v1 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-python.yml b/.github/workflows/test-terra-jupyter-python.yml index 005df224..1049957b 100644 --- a/.github/workflows/test-terra-jupyter-python.yml +++ b/.github/workflows/test-terra-jupyter-python.yml @@ -44,7 +44,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v4 @@ -55,7 +55,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v2 + uses: google-github-actions/auth@v1 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true From 4f6da7d48c5e9d85cc37f5597ccfdcf605574b2a Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 29 May 2024 10:52:07 -0400 Subject: [PATCH 18/19] more cleanup --- .github/workflows/publish.yml | 2 +- .github/workflows/test-terra-jupyter-base.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index fd2b12dd..cb569f9f 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -36,7 +36,7 @@ jobs: python-version: '3.10' - id: auth - uses: google-github-actions/auth@v2 + uses: google-github-actions/auth@v1 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true diff --git a/.github/workflows/test-terra-jupyter-base.yml b/.github/workflows/test-terra-jupyter-base.yml index e01850b0..710c8cc6 100644 --- a/.github/workflows/test-terra-jupyter-base.yml +++ b/.github/workflows/test-terra-jupyter-base.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v4 @@ -53,7 +53,7 @@ jobs: run: sudo rm -rf /usr/share/dotnet - id: auth - uses: google-github-actions/auth@v2 + uses: google-github-actions/auth@v1 with: credentials_json: ${{ secrets.TD_GCP_SA_KEY }} create_credentials_file: true From ae65b9846e183718d6e6880d3249b43544ad53e4 Mon Sep 17 00:00:00 2001 From: LizBaldo Date: Wed, 29 May 2024 11:21:48 -0400 Subject: [PATCH 19/19] try to ignore the platform flag when looking for base images --- build_smoke_test_image.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build_smoke_test_image.sh b/build_smoke_test_image.sh index aacf44f9..6e0dfe87 100755 --- a/build_smoke_test_image.sh +++ b/build_smoke_test_image.sh @@ -15,7 +15,7 @@ set -o xtrace build_smoke_test_image() { local IMAGE_TYPE=$1 pushd ${IMAGE_TYPE} - local BASE_IMAGES=$( egrep '^FROM (\S+)' Dockerfile |tr -s ' ' | cut -d ' ' -f 2 ) + local BASE_IMAGES=$( egrep '^FROM (\S+)' Dockerfile | sed 's/--platform.*//' |tr -s ' ' | cut -d ' ' -f 2 ) local BASE_IMAGE for BASE_IMAGE in ${BASE_IMAGES}; do