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..9af6eef6 --- /dev/null +++ b/terra-base/Dockerfile @@ -0,0 +1,178 @@ +# 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 $USER + +# Note: this entrypoint is provided for running Jupyter independently of Leonardo. +# When Leonardo deploys this image onto a cluster, the entrypoint is overwritten to enable +# additional setup inside the container before execution. Jupyter execution occurs when the +# init-actions.sh script uses 'docker exec' to call run-jupyter.sh. +ENTRYPOINT ["/usr/local/bin/jupyter-nbclassic"] \ No newline at end of file diff --git a/terra-base/README.md b/terra-base/README.md new file mode 100644 index 00000000..e0d597e6 --- /dev/null +++ b/terra-base/README.md @@ -0,0 +1,92 @@ +# terra-base image + +This repo contains the terra-base image that is compatible with the +notebook service in [Terra]("https://app.terra.bio/") called Leonardo. +The goal is to provide a lean, GPU-enabled base image that can be use for both Terra-suported, and custome image builds. +[See design doc]("https://broadworkbench.atlassian.net/wiki/spaces/IA/pages/2842460165/2023-08-28+Terra+Docker+Refactoring+POC#Provide-a-leaner-set-of-terra-docker-images") + +## Image contents + +`terra-base` extends an cuda 12.2.0 and Ubuntu 22.04 base image with the minimum +requirements necessary to set up Jupyter and provide compatibility with Leonardo and GPU machines. + +- OS prerequisites +- Python 3.10 +- R 4.1.2 +- Anaconda +- Jupyter +- Leonardo customizations/extensions +- Terra python client library ([FISS](https://github.com/broadinstitute/fiss)) +- Terra notebook utils +- Full list of python packages is available [here](pyproject.toml) + +To see the complete contents of this image please see the [Dockerfile](./Dockerfile). + +## Contributing + +### Installing python 3.10 + +All terra-docker images are on Python 3.10, so make sure to have it installed on your +local machine, for mac users doing this via `pyenv` is the recommended way of doing it: + +```bash +$> 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..9d07f2dd --- /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']); +}); \ No newline at end of file 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..ded62c4d --- /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 jupyter_server.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..144fe7bf --- /dev/null +++ b/terra-base/jupyter_notebook_config.py @@ -0,0 +1,45 @@ +# 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']} + 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+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 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 new file mode 100644 index 00000000..7a2b3081 --- /dev/null +++ b/terra-base/scripts/extension/jupyter_install_combined_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} + 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 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..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 new file mode 100644 index 00000000..7a2b3081 --- /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} + 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..8c4c5557 --- /dev/null +++ b/terra-base/scripts/extension/jupyter_pip_install_combined_extension.sh @@ -0,0 +1,9 @@ +#!/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 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 new file mode 100644 index 00000000..8c4c5557 --- /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} + 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..88acd892 --- /dev/null +++ b/terra-base/scripts/run-jupyter.sh @@ -0,0 +1,16 @@ +#!/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