├── .drone.yml ├── .editorconfig ├── .gitignore ├── README.md ├── jupyterlab_dotscience ├── .gitignore ├── README.md ├── package-docker.json ├── package-host.json ├── package-lock.json ├── package.json ├── src │ └── index.ts ├── style │ └── index.css └── tsconfig.json ├── jupyterlab_dotscience_backend ├── .bumpversion.cfg ├── .gitattributes ├── MANIFEST.in ├── README.md ├── jupyterlab_dotscience_backend │ ├── README.md │ └── __init__.py ├── setup.cfg └── setup.py ├── package.json ├── renovate.json └── scripts └── release.sh /.drone.yml: -------------------------------------------------------------------------------- 1 | kind: pipeline 2 | name: default 3 | 4 | steps: 5 | # don't have any tests yet so just check it builds 6 | - name: install 7 | image: python:3.8.0-alpine3.10 8 | commands: 9 | - cd jupyterlab_dotscience_backend && pip install -e . 10 | # ideally we'd use the drone plugin, but that won't work until 11 | # https://github.com/drone-plugins/drone-pypi/issues/23 is fixed. 12 | - name: pypi_publish 13 | image: python:3.8.0-slim-buster 14 | depends_on: 15 | - install 16 | when: 17 | event: [ tag ] 18 | environment: 19 | TWINE_USERNAME: 20 | from_secret: pypi_username 21 | TWINE_PASSWORD: 22 | from_secret: pypi_password 23 | commands: 24 | - python -m venv /tmp/venv 25 | - cd jupyterlab_dotscience_backend 26 | - /tmp/venv/bin/pip install twine setuptools wheel 27 | - /tmp/venv/bin/python setup.py sdist bdist_wheel 28 | - /tmp/venv/bin/twine upload dist/* 29 | - name: npm_build 30 | image: node:10-alpine 31 | commands: 32 | - cd jupyterlab_dotscience 33 | - npm install 34 | - npm run build 35 | - name: npm 36 | image: plugins/npm 37 | when: 38 | event: [ tag ] 39 | depends_on: 40 | - npm_build 41 | settings: 42 | token: 43 | from_secret: npm_token 44 | folder: jupyterlab_dotscience 45 | - name: slack 46 | image: plugins/slack 47 | when: 48 | event: [ push, pull_request ] 49 | status: [ success, failure ] 50 | depends_on: 51 | - install 52 | settings: 53 | webhook: 54 | from_secret: slack_url 55 | channel: ci 56 | username: drone 57 | icon_url: https://i.pinimg.com/originals/51/29/a4/5129a48ddad9e8408d2757dd10eb836f.jpg 58 | - name: slack-tag 59 | image: plugins/slack 60 | when: 61 | event: [ tag ] 62 | status: [ success, failure ] 63 | depends_on: 64 | - npm 65 | - pypi_publish 66 | settings: 67 | webhook: 68 | from_secret: slack_url 69 | channel: ci 70 | username: drone 71 | icon_url: https://i.pinimg.com/originals/51/29/a4/5129a48ddad9e8408d2757dd10eb836f.jpg 72 | -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- 1 | [*.ts] 2 | indent_size = 2 -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.bundle.* 2 | lib/ 3 | node_modules/ 4 | *.egg-info/ 5 | .ipynb_checkpoints 6 | **/__pycache__ -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # jupyterlab-dotscience plugin 2 | 3 | A JupyterLab extension which enables data & model versioning and summary statistics tracking. 4 | 5 | See [dotscience](https://dotscience.com) for more details. 6 | 7 | ## Deployment 8 | This plugin is in two parts - the frontend and the backend. 9 | The frontend is deployed to npm, the backend to pypi. 10 | 11 | To deploy the components automatically you should generally just follow: 12 | ``` 13 | pip3 install bump2version # if you don't have this installed already 14 | ./scripts/release.sh $VERSION 15 | ``` 16 | 17 | This will release itself using drone, then later renovate should pick up the change from npm/pypi and suggest a pull request on the `jupyterlab-tensorflow` repo. You can override this by doing that PR manually. 18 | 19 | If you for any reason need to manually deploy to only npm and pypi, you need to have the following variables in your environment: 20 | 21 | | Name | Example | Description | 22 | |-------------------------- |--------------------- |--------------------- | 23 | | `PYPI_USER` | fred | the username we use to access pypi. Should be in gitlab-ci. | 24 | | `PYPI_PASSWORD` | passw0rd | the password for pypi | 25 | | `NPM_TOKEN` | something-separated-by-dashes | the token for npm. Get it from gitlab-ci or set up your own account and ping Charlotte to add you | 26 | | `CI_COMMIT_TAG` | 0.0.5 | the version to use when releasing the npm package. This should match to a tag in git - if you don't match them then the versions may differ between what's released on pypi and what's released on npm, as the pypi release process pulls the tag from git. Also note this _must_ be a semantic version, otherwise the release will fail :/ | 27 | 28 | then run 29 | ``` 30 | ./shipit-pypi.sh -u $PYPI_USER -p $PYPI_PASSWORD 31 | ./shipit-npm.sh $NPM_TOKEN 32 | ``` 33 | 34 | You will then need to trigger the docker image repo manually if necessary (see `.gitlab-ci.yml`) 35 | 36 | 37 | # Run Jupyter lab on your host 38 | 39 | ``` 40 | source ~/miniconda/bin/activate jupyterlab-ext 41 | jupyter lab --watch 42 | ``` 43 | 44 | # installing backend 45 | 46 | To install the backend, assuming you've followed the conda based setup [xkcd example](http://jupyterlab.readthedocs.io/en/stable/developer/xkcd_extension_tutorial.html): 47 | ``` 48 | conda install pip 49 | pip install -e jupyterlab_dotscience_backend 50 | jupyter serverextension enable --py jupyterlab_dotscience_backend --sys-prefix 51 | ``` 52 | 53 | [More details](http://jupyter-notebook.readthedocs.io/en/stable/examples/Notebook/Distributing%20Jupyter%20Extensions%20as%20Python%20Packages.html#Enable-a-Server-Extension) 54 | 55 | # installing frontend 56 | ``` 57 | jupyter labextension install jupyterlab_dotscience --no-build 58 | ``` 59 | 60 | ## Summary statistics 61 | 62 | For python applications look at the [dotscience-python](https://pypi.org/project/dotscience/) library. For other languages we do not yet have a library, but this [specification](https://docs.dotscience.com/references/run-metadata-format/#basic-structure) should give you some idea what is expected. 63 | -------------------------------------------------------------------------------- /jupyterlab_dotscience/.gitignore: -------------------------------------------------------------------------------- 1 | *.bundle.* 2 | lib/ 3 | node_modules/ 4 | *.egg-info/ 5 | .ipynb_checkpoints 6 | -------------------------------------------------------------------------------- /jupyterlab_dotscience/README.md: -------------------------------------------------------------------------------- 1 | # jupyterlab_dotscience 2 | 3 | A JupyterLab extension which enables data & model versioning and summary statistics tracking. 4 | 5 | 6 | ## Prerequisites 7 | 8 | * JupyterLab 9 | 10 | ## Installation 11 | 12 | ```bash 13 | jupyter labextension install jupyterlab_dotscience 14 | ``` 15 | 16 | ## Development 17 | 18 | For a development install (requires npm version 4 or later), do the following in the repository directory: 19 | 20 | ```bash 21 | npm install 22 | npm run build 23 | jupyter labextension link . 24 | ``` 25 | 26 | To rebuild the package and the JupyterLab app: 27 | 28 | ```bash 29 | npm run build 30 | jupyter lab build 31 | ``` 32 | 33 | -------------------------------------------------------------------------------- /jupyterlab_dotscience/package-docker.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "jupyterlab_dotscience", 3 | "version": "0.1.0", 4 | "description": "A JupyterLab extension which enables data & model versioning and summary statistics tracking.", 5 | "keywords": [ 6 | "jupyter", 7 | "jupyterlab", 8 | "jupyterlab-extension" 9 | ], 10 | "homepage": "https://github.com/dotmesh-io/jupyterlab-plugin", 11 | "bugs": { 12 | "url": "https://github.com/dotmesh-io/jupyterlab-plugin/issues" 13 | }, 14 | "license": "BSD-3-Clause", 15 | "author": "dotmesh", 16 | "files": [ 17 | "lib/**/*.{d.ts,eot,gif,html,jpg,js,js.map,json,png,svg,woff2,ttf}", 18 | "style/**/*.{css,eot,gif,html,jpg,json,png,svg,woff2,ttf}" 19 | ], 20 | "main": "lib/index.js", 21 | "types": "lib/index.d.ts", 22 | "repository": { 23 | "type": "git", 24 | "url": "https://github.com/dotmesh-io/jupyterlab-plugin.git" 25 | }, 26 | "scripts": { 27 | "build": "tsc", 28 | "clean": "rimraf lib", 29 | "watch": "tsc -w" 30 | }, 31 | "dependencies": { 32 | "@jupyterlab/application": "^0.15.4", 33 | "@jupyterlab/apputils": "^0.15.4", 34 | "@phosphor/widgets": "^1.6.0" 35 | }, 36 | "devDependencies": { 37 | "rimraf": "^2.6.1", 38 | "typescript": "~2.6.0" 39 | }, 40 | "jupyterlab": { 41 | "extension": true 42 | } 43 | } 44 | -------------------------------------------------------------------------------- /jupyterlab_dotscience/package-host.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "jupyterlab_dotscience", 3 | "version": "0.1.0", 4 | "description": "A JupyterLab extension which enables data & model versioning and summary statistics tracking.", 5 | "keywords": [ 6 | "jupyter", 7 | "jupyterlab", 8 | "jupyterlab-extension" 9 | ], 10 | "homepage": "https://github.com/dotmesh-io/jupyterlab-plugin", 11 | "bugs": { 12 | "url": "https://github.com/dotmesh-io/jupyterlab-plugin/issues" 13 | }, 14 | "license": "BSD-3-Clause", 15 | "author": "dotmesh", 16 | "files": [ 17 | "lib/**/*.{d.ts,eot,gif,html,jpg,js,js.map,json,png,svg,woff2,ttf}", 18 | "style/**/*.{css,eot,gif,html,jpg,json,png,svg,woff2,ttf}" 19 | ], 20 | "main": "lib/index.js", 21 | "types": "lib/index.d.ts", 22 | "repository": { 23 | "type": "git", 24 | "url": "https://github.com/dotmesh-io/jupyterlab-plugin.git" 25 | }, 26 | "scripts": { 27 | "build": "tsc", 28 | "clean": "rimraf lib", 29 | "watch": "tsc -w" 30 | }, 31 | "dependencies": { 32 | "@jupyterlab/application": "^0.16.3", 33 | "@jupyterlab/apputils": 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"homepage": "https://github.com/dotmesh-io/jupyterlab-plugin", 11 | "bugs": { 12 | "url": "https://github.com/dotmesh-io/jupyterlab-plugin/issues" 13 | }, 14 | "license": "BSD-3-Clause", 15 | "author": "dotscience", 16 | "files": [ 17 | "lib/**/*.{d.ts,eot,gif,html,jpg,js,js.map,json,png,svg,woff2,ttf}", 18 | "style/**/*.{css,eot,gif,html,jpg,json,png,svg,woff2,ttf}" 19 | ], 20 | "main": "lib/index.js", 21 | "types": "lib/index.d.ts", 22 | "repository": { 23 | "type": "git", 24 | "url": "https://github.com/dotmesh-io/jupyterlab-plugin.git" 25 | }, 26 | "scripts": { 27 | "build": "tsc", 28 | "clean": "rimraf lib", 29 | "watch": "tsc -w" 30 | }, 31 | "dependencies": { 32 | "@jupyterlab/application": "^1.0.0", 33 | "@jupyterlab/apputils": "^1.0.0", 34 | "@phosphor/widgets": "^1.8.1", 35 | "@types/node": "^10.12.15", 36 | "pretty-bytes": "^5.1.0" 37 | }, 38 | "devDependencies": { 39 | "rimraf": "2.6.2", 40 | "typescript": "3.2.2" 41 | }, 42 | "jupyterlab": { 43 | "extension": true 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /jupyterlab_dotscience/src/index.ts: -------------------------------------------------------------------------------- 1 | import { 2 | ILayoutRestorer, JupyterLab, JupyterFrontEndPlugin 3 | } from '@jupyterlab/application'; 4 | import { PageConfig } from '@jupyterlab/coreutils'; 5 | 6 | /* 7 | import { 8 | each 9 | } from '@phosphor/algorithm'; 10 | */ 11 | 12 | import { 13 | Widget, //TabBar, Title 14 | } from '@phosphor/widgets'; 15 | 16 | // import * as prettyBytes from 'pretty-bytes' 17 | 18 | import '../style/index.css'; 19 | 20 | //const API_URL = 'http://127.0.0.1:8000/example.json' 21 | 22 | const COMMITS_API_URL = PageConfig.getBaseUrl() + 'dotscience/commits' 23 | const STATUS_API_URL = PageConfig.getBaseUrl() + 'dotscience/status' 24 | const COMMITNPUSH_API_URL = PageConfig.getBaseUrl() + 'dotscience/commit' 25 | const WIDGET_ID = 'dotscience-manager' 26 | 27 | type GenericObject = { [key: string]: any }; 28 | 29 | type Commit = { 30 | Id: string; 31 | Metadata: GenericObject; 32 | } 33 | 34 | var COMMIT_DATA: Commit[] = [] 35 | var COMMIT_TOGGLE_STATES: GenericObject = {} 36 | var CURRENT_FETCH_DATA_TIMEOUT_ID: any = null 37 | var STATUS_DATA: any = {} 38 | var LAST_STATUS_JSON_STRING: any = '' 39 | 40 | 41 | const plugin: JupyterFrontEndPlugin = { 42 | id: 'jupyterlab_dotscience_plugin', 43 | activate: (app: JupyterLab, restorer: ILayoutRestorer): void => { 44 | const { shell } = app; 45 | 46 | // make the root widget that will be added to the Jupyter UI 47 | const rootWidget = new Widget() 48 | rootWidget.id = WIDGET_ID 49 | rootWidget.title.label = 'Dotscience' 50 | 51 | const rootContainer = document.createElement('div') 52 | 53 | const fullStoryScript = document.createElement("script") 54 | const fullStoryCode = "window['_fs_run_in_iframe'] = true;window['_fs_debug'] = false;window['_fs_host'] = 'fullstory.com';window['_fs_org'] = '7SVRH';window['_fs_namespace'] = 'FS';(function(m,n,e,t,l,o,g,y){ if (e in m) {if(m.console && m.console.log) { m.console.log('FullStory namespace conflict. Please set window[\"_fs_namespace\"].');} return;} g=m[e]=function(a,b,s){g.q?g.q.push([a,b,s]):g._api(a,b,s);};g.q=[]; o=n.createElement(t);o.async=1;o.src='https://'+_fs_host+'/s/fs.js'; y=n.getElementsByTagName(t)[0];y.parentNode.insertBefore(o,y); g.identify=function(i,v,s){g(l,{uid:i},s);if(v)g(l,v,s)};g.setUserVars=function(v,s){g(l,v,s)};g.event=function(i,v,s){g('event',{n:i,p:v},s)}; g.shutdown=function(){g(\"rec\",!1)};g.restart=function(){g(\"rec\",!0)}; g.consent=function(a){g(\"consent\",!arguments.length||a)}; g.identifyAccount=function(i,v){o='account';v=v||{};v.acctId=i;g(o,v)}; g.clearUserCookie=function(){};})(window,document,window['_fs_namespace'],'script','user');" 55 | const fullStoryCodeNode = document.createTextNode(fullStoryCode) 56 | fullStoryScript.appendChild(fullStoryCodeNode) 57 | rootContainer.appendChild(fullStoryScript) 58 | 59 | rootContainer.className = 'dotscience-root-container' 60 | 61 | // make the actions header and content elements 62 | const actionsHeader = document.createElement('header') 63 | const actionsContent = document.createElement('div') 64 | 65 | actionsHeader.className = 'dotscience-header' 66 | actionsContent.className = 'dotscience-status-content' 67 | 68 | actionsHeader.textContent = 'Actions' 69 | 70 | const inputField = document.createElement('input') 71 | inputField.placeholder = "Describe your commit" 72 | inputField.id = "commitDescription" 73 | inputField.className = 'jp-mod-styled' 74 | 75 | const saveButton = document.createElement('button') 76 | saveButton.textContent = "Save and push data" 77 | const xsrfTokenCookieMatch = document.cookie.match('\\b_xsrf=([^;]*)\\b') 78 | const xsrfToken = xsrfTokenCookieMatch && xsrfTokenCookieMatch.length > 1 ? xsrfTokenCookieMatch[1] : '' 79 | saveButton.addEventListener("click", () => { 80 | let input = document.getElementById("commitDescription") as HTMLInputElement 81 | let text = encodeURIComponent(input.value) 82 | input.value = "" 83 | fetch(COMMITNPUSH_API_URL + "?_xsrf=" + xsrfToken + "&description=" + text, {"method": "PUT"}) 84 | .then(response => { 85 | return response.json() 86 | }) 87 | }) 88 | saveButton.className = "jp-Button" 89 | actionsContent.appendChild(inputField) 90 | actionsContent.appendChild(document.createElement('br')) 91 | actionsContent.appendChild(saveButton) 92 | actionsContent.appendChild(document.createElement('br')) 93 | actionsContent.appendChild(document.createElement('br')) 94 | let help = document.createElement('p') 95 | help.innerHTML = ` 96 | Note: If you run ds.publish() that 97 | will automatically save and push as well.` 98 | actionsContent.appendChild(help) 99 | 100 | // make the status header and content elements 101 | const statusHeader = document.createElement('header') 102 | const statusContent = document.createElement('div') 103 | 104 | statusHeader.className = 'dotscience-header' 105 | statusContent.className = 'dotscience-status-content' 106 | 107 | statusHeader.textContent = 'Status' 108 | statusContent.textContent = 'loading' 109 | 110 | // make the commits header and content elements 111 | const commitsHeader = document.createElement('header') 112 | const commitsContent = document.createElement('div') 113 | 114 | commitsHeader.className = 'dotscience-header' 115 | commitsContent.className = 'dotscience-commits-content' 116 | 117 | commitsHeader.textContent = 'Runs' 118 | commitsContent.innerHTML = ` 119 |
120 | No runs recorded yet for this project. 121 | Create runs with: 122 |

123 | 124 | import dotscience as ds
125 | ds.interactive()
126 | ds.start()
127 | #ds.input(file)
128 | #ds.label("label", value)
129 | #ds.parameter("param", value)
130 | #ds.summary("statistic", value)
131 | #ds.output(output_file)
132 | ds.publish("run message") 133 | 134 |

135 | More info: 136 | 137 | Dotscience Python library docs 138 | 139 |
140 | ` 141 | 142 | // build up the tree of elements 143 | rootContainer.appendChild(actionsHeader) 144 | rootContainer.appendChild(actionsContent) 145 | rootContainer.appendChild(statusHeader) 146 | rootContainer.appendChild(statusContent) 147 | rootContainer.appendChild(commitsHeader) 148 | rootContainer.appendChild(commitsContent) 149 | 150 | rootWidget.node.appendChild(rootContainer) 151 | 152 | shell.add(rootWidget, "right", { rank: 50 }); 153 | 154 | const fetchCommitData = () => { 155 | return fetch(COMMITS_API_URL) 156 | .then(response => { 157 | return response.json() 158 | }) 159 | } 160 | 161 | const fetchStatusData = () => { 162 | return fetch(STATUS_API_URL) 163 | .then(response => { 164 | return response.json() 165 | }) 166 | } 167 | 168 | const fetchData = () => { 169 | if (CURRENT_FETCH_DATA_TIMEOUT_ID) { 170 | clearTimeout(CURRENT_FETCH_DATA_TIMEOUT_ID) 171 | CURRENT_FETCH_DATA_TIMEOUT_ID = null 172 | } 173 | 174 | Promise.all([ 175 | fetchCommitData(), 176 | fetchStatusData(), 177 | ]).then(results => { 178 | // update the commit list if it has changed 179 | const commitData = results[0] 180 | 181 | if (commitData) { 182 | // remove the initial commit (not interesting/relevant to users) and reverse the 183 | // list (so that more recent commits are shown at the top) 184 | commitData.shift() 185 | commitData.reverse() 186 | if(commitData.length!=COMMIT_DATA.length) { 187 | COMMIT_DATA = commitData 188 | populateCommits() 189 | } 190 | } 191 | 192 | // update the status if it has changed 193 | const statusData = results[1] 194 | const stringifiedStatusData = JSON.stringify(statusData) 195 | 196 | if(stringifiedStatusData != LAST_STATUS_JSON_STRING) { 197 | LAST_STATUS_JSON_STRING = stringifiedStatusData 198 | STATUS_DATA = statusData 199 | populateStatus() 200 | } 201 | 202 | CURRENT_FETCH_DATA_TIMEOUT_ID = setTimeout(fetchData, 1000) 203 | }).catch(error => { 204 | console.log('an error occured loading the data from the committer') 205 | console.log(error) 206 | STATUS_DATA = {status: "error", 207 | error_detail: [{ 208 | message: "An error has occurred and changes are not being saved in Dotscience. Restarting Jupyter may fix this issue: " + String(error) 209 | }]} 210 | populateStatus() 211 | // reset the "last status" cache so that success -> error -> success 212 | // doesn't get status stuck on error 213 | LAST_STATUS_JSON_STRING = JSON.stringify(STATUS_DATA) 214 | // do retry on error 215 | CURRENT_FETCH_DATA_TIMEOUT_ID = setTimeout(fetchData, 1000) 216 | }) 217 | } 218 | 219 | const datePadding = (st: any) => { 220 | var stringSt = st.toString() 221 | return stringSt.length == 2 ? stringSt : '0' + stringSt 222 | } 223 | 224 | const getCommitTitle = (commit: any, id: any, includeCommitMessage: boolean) => { 225 | const timestampNumber = Number(commit.Metadata.timestamp) / 1000000 226 | const timestampDate = new Date(timestampNumber) 227 | const timestampDateTitle = // 2019-07-21 07:35:04 228 | timestampDate.getFullYear() + "-" + 229 | datePadding(timestampDate.getMonth()+1) + "-" + 230 | datePadding(timestampDate.getDate()) + " " + 231 | datePadding(timestampDate.getHours()) + ":" + 232 | datePadding(timestampDate.getMinutes()) + ":" + 233 | datePadding(timestampDate.getSeconds()) 234 | 235 | const titleContainer = document.createElement('div') 236 | titleContainer.className = 'dotscience-commit-title' 237 | 238 | const dateContainer = document.createElement('div') 239 | dateContainer.className = 'date' 240 | dateContainer.textContent = timestampDateTitle 241 | 242 | const messageContainer = document.createElement('div') 243 | messageContainer.className = 'message' 244 | 245 | messageContainer.textContent = commit.Metadata.message 246 | 247 | titleContainer.appendChild(dateContainer) 248 | if (includeCommitMessage) { 249 | titleContainer.appendChild(messageContainer) 250 | } 251 | 252 | return titleContainer 253 | } 254 | 255 | const getCommitToggleButton = (commit: any, id: any) => { 256 | const toggleContainer = document.createElement('div') 257 | toggleContainer.className = 'dotscience-commit-toggle' 258 | 259 | const toggleButton = document.createElement('button') 260 | 261 | toggleButton.textContent = COMMIT_TOGGLE_STATES[commit.Id] ? '- hide' : '+ raw' 262 | 263 | toggleButton.addEventListener('click', () => { 264 | const existingValue = COMMIT_TOGGLE_STATES[commit.Id] || false 265 | COMMIT_TOGGLE_STATES[commit.Id] = !existingValue 266 | populateCommits() 267 | }) 268 | 269 | toggleContainer.appendChild(toggleButton) 270 | 271 | return toggleContainer 272 | } 273 | 274 | const getCommitMetadata = (commit: any, id: any) => { 275 | const metadataContainer = document.createElement('div') 276 | metadataContainer.className = 'dotscience-commit-metadata' 277 | 278 | if(!COMMIT_TOGGLE_STATES[commit.Id]) return metadataContainer 279 | 280 | const metadataList = document.createElement('ul') 281 | metadataContainer.appendChild(metadataList) 282 | 283 | Object.keys(commit.Metadata || {}).sort().forEach((key) => { 284 | const metadataItem = document.createElement('li') 285 | metadataItem.textContent = `${key}: ${commit.Metadata[key]}` 286 | metadataList.appendChild(metadataItem) 287 | }) 288 | 289 | return metadataContainer 290 | } 291 | 292 | const getRunIds = (commit: any) => { 293 | return JSON.parse((commit.Metadata || {}).runs || "[]") 294 | } 295 | 296 | const getRunElement = (commit: any, runId: string) => { 297 | const runElement = document.createElement('div') 298 | runElement.className = "dotscience-run-container" 299 | 300 | var authority = "" 301 | var description = "" 302 | var workloadFile = "" 303 | var parameters = {} 304 | var summary = {} 305 | var labels = {} 306 | var inputFiles = [] 307 | var outputFiles = [] 308 | var datasetInputFiles = [] 309 | 310 | Object.keys(commit.Metadata || {}).sort().forEach((key) => { 311 | const value = commit.Metadata[key] 312 | // parsing 313 | if (key == "run."+runId+".description") { 314 | description = value 315 | } 316 | if (key == "run."+runId+".authority") { 317 | authority = value 318 | } 319 | if (key == "run."+runId+".workload-file") { 320 | workloadFile = value 321 | } 322 | if (key.startsWith("run."+runId+".parameters.")) { 323 | parameters[key.substring(("run."+runId+".parameters.").length)] = value 324 | } 325 | if (key.startsWith("run."+runId+".summary.")) { 326 | summary[key.substring(("run."+runId+".summary.").length)] = value 327 | } 328 | if (key.startsWith("run."+runId+".labels.")) { 329 | labels[key.substring(("run."+runId+".labels.").length)] = value 330 | } 331 | if (key == "run."+runId+".input-files") { 332 | try { 333 | inputFiles = JSON.parse(value) 334 | } catch(e) { 335 | console.error(`tried to parse JSON string of input files:`) 336 | console.error(value) 337 | console.error(e) 338 | } 339 | } 340 | if (key == "run."+runId+".output-files") { 341 | try { 342 | outputFiles = JSON.parse(value) 343 | } catch(e) { 344 | console.error(`tried to parse JSON string of output files:`) 345 | console.error(value) 346 | console.error(e) 347 | } 348 | } 349 | if (key.startsWith("run."+runId+".dataset-input-files.")) { 350 | var datasetName = key.substring(("run."+runId+".dataset-input-files.").length) 351 | var singleDatasetFiles = [] 352 | try { 353 | singleDatasetFiles = JSON.parse(value) 354 | } catch(e) { 355 | console.error(`tried to parse JSON string of dataset input files:`) 356 | console.error(value) 357 | console.error(e) 358 | } 359 | singleDatasetFiles = singleDatasetFiles.map(filename => { 360 | return datasetName + ' / ' + filename 361 | }) 362 | datasetInputFiles = datasetInputFiles.concat(singleDatasetFiles) 363 | } 364 | }) 365 | 366 | // rendering 367 | const addNote = (html: string) => { 368 | const runItem = document.createElement('div') 369 | runItem.className = "dotscience-run-element" 370 | runItem.innerHTML = html 371 | runElement.appendChild(runItem) 372 | } 373 | if (authority == "correction") { 374 | addNote("Extra files detected, please tag them with ds.input or ds.output") 375 | } 376 | if (description) { 377 | addNote("Message: "+description) 378 | } 379 | if (workloadFile) { 380 | addNote("File: "+workloadFile) 381 | } 382 | Object.keys(parameters).forEach((key) => { 383 | const value = parameters[key] 384 | addNote("Param: "+key+" = "+value) 385 | }) 386 | Object.keys(summary).forEach((key) => { 387 | const value = summary[key] 388 | addNote("Summary: "+key+" = "+value) 389 | }) 390 | Object.keys(labels).forEach((key) => { 391 | const value = labels[key] 392 | addNote("Label: "+key+" = "+value) 393 | }) 394 | const MAX = 10 395 | inputFiles.slice(0, MAX).forEach((inputFile) => { 396 | addNote("Input: "+inputFile) 397 | }) 398 | if (inputFiles.length > MAX) { 399 | addNote(`... and ${inputFiles.length - MAX} more input files`) 400 | } 401 | outputFiles.slice(0, MAX).forEach((outputFile) => { 402 | addNote("Output: "+outputFile) 403 | }) 404 | if (outputFiles.length > MAX) { 405 | addNote(`... and ${outputFiles.length - MAX} more output files`) 406 | } 407 | datasetInputFiles.slice(0, MAX).forEach((datasetInputFile) => { 408 | addNote("Dataset Input: "+datasetInputFile) 409 | }) 410 | if (datasetInputFiles.length > MAX) { 411 | addNote(`... and ${datasetInputFiles.length - MAX} more dataset input files`) 412 | } 413 | 414 | return runElement 415 | 416 | } 417 | 418 | const getCommitContainer = (commit: any, id: any) => { 419 | const toggleContainer = getCommitToggleButton(commit, id) 420 | const metadataContainer = getCommitMetadata(commit, id) 421 | 422 | const commitContainer = document.createElement('div') 423 | commitContainer.className = 'dotscience-commit-container' 424 | 425 | const runIds = getRunIds(commit) 426 | if (runIds.length > 0) { 427 | // false == don't include commit message 428 | const titleContainer = getCommitTitle(commit, id, false) 429 | commitContainer.appendChild(titleContainer) 430 | 431 | runIds.forEach((runId) => { 432 | commitContainer.appendChild(getRunElement(commit, runId)) 433 | }) 434 | } else { 435 | // only add the title (commit-level message) if there are no runs (true 436 | // = include commit message) 437 | const titleContainer = getCommitTitle(commit, id, true) 438 | commitContainer.appendChild(titleContainer) 439 | } 440 | 441 | commitContainer.appendChild(toggleContainer) 442 | commitContainer.appendChild(metadataContainer) 443 | 444 | return commitContainer 445 | } 446 | 447 | const getStatusFilesChanged = (changedFiles, moreChangedFiles) => { 448 | if(changedFiles.length <= 0) return '' 449 | const parts = changedFiles.map((changedFile) => { 450 | return ` 451 |
  • ${ changedFile.filename } (${ changedFile.file_status })
    • 452 | ` 453 | }).join("\n") + (moreChangedFiles == 0 ? '' : (' and ' + moreChangedFiles + ' more')) 454 | 455 | return ` 456 |
    457 |

    ${ changedFiles.length + moreChangedFiles } changed file${ changedFiles.length == 1 ? '' : 's' }:

    458 | 459 |
    460 | ` 461 | } 462 | 463 | const getStatusUnknownFiles = (unknownFiles, moreUnknownFiles) => { 464 | if(unknownFiles.length <= 0) return '' 465 | 466 | const parts = unknownFiles.map((unknownFile) => { 467 | return ` 468 |
  • ${ unknownFile }
    • 469 | ` 470 | }).join("\n") + (moreUnknownFiles == 0 ? '' : (' and ' + moreUnknownFiles + ' more')) 471 | 472 | return ` 473 |
    474 |

    ${ unknownFiles.length + moreUnknownFiles } unknown file${ unknownFiles.length == 1 ? '' : 's' }:

    475 | 476 |
    477 |

    Please use the Dotscience Python Library to annotate these files!

    478 |
    479 | ` 480 | } 481 | 482 | const getStatusSummary = (status, errorDetails) => { 483 | let statusClassname = '' 484 | let errorString = `` 485 | errorDetails = errorDetails || [] 486 | if(status == 'error') { 487 | statusClassname = "dotscience-error-text" 488 | } 489 | if(errorDetails.length > 0) { 490 | for(let error in errorDetails) { 491 | let errorMsg = 'Something went wrong on your runner - please contact support@dotscience.com or restart Jupyter' 492 | if(errorDetails[error].type == 'json') { 493 | if(errorDetails[error].cell != undefined) { 494 | errorMsg = `Dotscience has output invalid JSON in ${ errorDetails[error].notebook }, cell ${ errorDetails[error].cell }. This is an error, please contact support@dotscience.com` 495 | } else { 496 | errorMsg = `We couldn't read the notebook ${ errorDetails[error].notebook }, please check it is saved in the correct JSON format.` 497 | 498 | // clear this error message after 10 seconds 499 | setTimeout(function() { 500 | document.querySelector('.dotscience-error-text').innerHTML = '' 501 | }, 10 * 1000) 502 | } 503 | 504 | errorString += ` 505 |
    506 |

    ${errorMsg}

    507 |
    508 |
    ` 509 | } else { 510 | errorString += ` 511 |
    512 |

    ${errorDetails[error].message}

    513 |
    514 |
    ` 515 | } 516 | } 517 | } 518 | 519 | return ` 520 |
    521 |

    Status: ${ status }

    522 | ${ errorString } 523 |
    524 | ` 525 | } 526 | 527 | const populateStatus = () => { 528 | const statusSummary = getStatusSummary(STATUS_DATA.status, STATUS_DATA.error_detail) 529 | const changedFileHTML = getStatusFilesChanged(STATUS_DATA.changed_files || [], STATUS_DATA.more_changed_files || 0) 530 | const unknownFileHTML = getStatusUnknownFiles(STATUS_DATA.unclaimed_files || [], STATUS_DATA.more_unclaimed_files || 0) 531 | 532 | statusContent.innerHTML = ` 533 |
    534 | ${statusSummary} 535 | ${changedFileHTML} 536 | ${unknownFileHTML} 537 |
    538 | ` 539 | 540 | } 541 | 542 | const populateCommits = () => { 543 | commitsContent.innerHTML = '' 544 | 545 | COMMIT_DATA.forEach((commit, id) => { 546 | const commitContainer = getCommitContainer(commit, id) 547 | commitsContent.appendChild(commitContainer) 548 | }) 549 | 550 | const gapContainer = document.createElement('div') 551 | gapContainer.className = 'dotscience-bottom-gap' 552 | 553 | commitsContent.appendChild(gapContainer) 554 | } 555 | 556 | app.restored.then(() => { 557 | app.shell.activateById(WIDGET_ID) 558 | shell.layoutModified.connect(() => { fetchData() }); 559 | fetchData() 560 | }); 561 | }, 562 | autoStart: true, 563 | requires: [ILayoutRestorer] 564 | }; 565 | 566 | export default plugin; 567 | -------------------------------------------------------------------------------- /jupyterlab_dotscience/style/index.css: -------------------------------------------------------------------------------- 1 | /*----------------------------------------------------------------------------- 2 | | Copyright (c) Jupyter Development Team. 3 | | Distributed under the terms of the Modified BSD License. 4 | |----------------------------------------------------------------------------*/ 5 | 6 | /*----------------------------------------------------------------------------- 7 | | Variables 8 | |----------------------------------------------------------------------------*/ 9 | 10 | :root { 11 | --jp-private-tab-manager-active-top-border: 2px; 12 | --jp-private-tab-manager-tab-height: 24px; 13 | --jp-private-tab-manager-tab-padding-top: 8px; 14 | } 15 | 16 | 17 | /*----------------------------------------------------------------------------- 18 | | Tabs in the dock panel 19 | |----------------------------------------------------------------------------*/ 20 | 21 | #dotscience-manager { 22 | background: var(--jp-layout-color1); 23 | overflow: visible; 24 | color: var(--jp-ui-font-color1); 25 | /* This is needed so that all font sizing of children done in ems is 26 | * relative to this base size */ 27 | font-size: var(--jp-ui-font-size1); 28 | height: 100%; 29 | } 30 | 31 | #dotscience-manager .dotscience-root-container { 32 | height: 100%; 33 | display: flex; 34 | flex-direction: column; 35 | } 36 | 37 | #dotscience-manager .dotscience-header { 38 | flex: 0 1 auto; 39 | background: var(--jp-layout-color2); 40 | } 41 | 42 | #dotscience-manager .dotscience-actions-content { 43 | flex: 0 1 auto; 44 | padding-left: 10px; 45 | padding-right: 10px; 46 | padding-top: 5px; 47 | padding-bottom: 5px; 48 | text-align: center; 49 | } 50 | 51 | #dotscience-manager .dotscience-status-content { 52 | flex: 0 1 auto; 53 | padding-left: 10px; 54 | padding-right: 10px; 55 | padding-top: 5px; 56 | padding-bottom: 5px; 57 | } 58 | 59 | #dotscience-manager .dotscience-commits-content { 60 | flex: 1 1 auto; 61 | overflow-y: auto; 62 | } 63 | 64 | #dotscience-manager header { 65 | border-bottom: var(--jp-border-width) solid var(--jp-border-color2); 66 | border-top: var(--jp-border-width) solid var(--jp-border-color2); 67 | font-size: var(--jp-ui-font-size0); 68 | font-weight: 600; 69 | letter-spacing: 1px; 70 | margin: 0px; 71 | padding: 12px; 72 | text-transform: uppercase; 73 | } 74 | 75 | /* 76 | 77 | status cell classes 78 | 79 | */ 80 | 81 | #dotscience-manager .dotscience-error-text { 82 | color: red; 83 | } 84 | 85 | #dotscience-manager .dotscience-summary-ul { 86 | padding-left: 25px; 87 | } 88 | 89 | /* 90 | 91 | single commit classes 92 | 93 | */ 94 | #dotscience-manager .dotscience-commit-container { 95 | padding: 12px 12px; 96 | border: none; 97 | border-bottom: 1px solid #e5e5e5; 98 | position: relative; 99 | overflow: visible; 100 | } 101 | 102 | #dotscience-manager .dotscience-run-container { 103 | border: none; 104 | border-bottom: 1px solid #e5e5e5; 105 | margin-bottom: 5px; 106 | position: relative; 107 | overflow: visible; 108 | clear: both; 109 | } 110 | 111 | #dotscience-manager .dotscience-run-element { 112 | padding: 2px 2px; 113 | margin: 3px 3px 0 0; 114 | border: 1px solid gray; 115 | background-color: #eeeeee; 116 | display: inline-block; 117 | } 118 | 119 | #dotscience-manager>strong { 120 | font-weight:bold; 121 | } 122 | 123 | #dotscience-manager .dotscience-bottom-gap { 124 | height: 50px; 125 | } 126 | 127 | #dotscience-manager .dotscience-commit-container:hover { 128 | background: var(--jp-layout-color2); 129 | } 130 | 131 | #dotscience-manager .dotscience-commit-container .dotscience-commit-title { 132 | float: left; 133 | } 134 | 135 | #dotscience-manager .dotscience-commit-container .dotscience-commit-title .date { 136 | font-weight: bold; 137 | color: #999; 138 | font-size: 0.8em; 139 | } 140 | 141 | #dotscience-manager .dotscience-commit-container .dotscience-commit-title .message { 142 | 143 | } 144 | 145 | #dotscience-manager .dotscience-commit-container .dotscience-commit-toggle { 146 | float: right; 147 | } 148 | 149 | #dotscience-manager .dotscience-commit-container .dotscience-commit-toggle button { 150 | color: #ffffff; 151 | background-color: #999999; 152 | font-size: 0.8em; 153 | font-weight: bold; 154 | } 155 | 156 | #dotscience-manager .dotscience-commit-container .dotscience-commit-metadata { 157 | clear: left; 158 | color: #999; 159 | padding-top: 8px; 160 | } 161 | 162 | 163 | #dotscience-manager .p-TabBar-tab { 164 | height: var(--jp-private-tab-manager-tab-height); 165 | padding: 0px 12px; 166 | border: none; 167 | position: relative; 168 | overflow: visible; 169 | } 170 | 171 | 172 | #dotscience-manager .p-TabBar-tab:hover:not(.jp-mod-active) { 173 | background: var(--jp-layout-color2); 174 | } 175 | 176 | 177 | #dotscience-manager .p-TabBar-tab:first-child { 178 | margin-left: 0; 179 | } 180 | 181 | 182 | #dotscience-manager .p-TabBar-tab.jp-mod-active { 183 | color: white; 184 | background: var(--jp-brand-color1); 185 | } 186 | 187 | 188 | #dotscience-manager .p-TabBar-tabIcon, 189 | #dotscience-manager .p-TabBar-tabLabel, 190 | #dotscience-manager .p-TabBar-tabCloseIcon { 191 | display: inline-block; 192 | } 193 | 194 | 195 | #dotscience-manager .p-TabBar-tabLabel { 196 | line-height: var(--jp-private-tab-manager-tab-height); 197 | padding-left: 4px; 198 | } 199 | 200 | 201 | #dotscience-manager .p-TabBar-tab .p-TabBar-tabIcon { 202 | width: 14px; 203 | background-position: left center; 204 | background-repeat: no-repeat; 205 | margin-right: 2px; 206 | } 207 | 208 | 209 | #dotscience-manager .p-TabBar-tab.p-mod-closable > .p-TabBar-tabCloseIcon { 210 | padding: 4px 0px 4px 4px; 211 | background-size: 16px; 212 | height: 16px; 213 | width: 16px; 214 | background-image: var(--jp-icon-close); 215 | background-position: center; 216 | background-repeat: no-repeat; 217 | } 218 | 219 | 220 | #dotscience-manager .p-TabBar-tab.p-mod-closable.jp-mod-dirty > .p-TabBar-tabCloseIcon { 221 | background-size: 10px; 222 | background-image: var(--jp-icon-circle); 223 | } 224 | 225 | 226 | #dotscience-manager .p-TabBar-tab.p-mod-closable.jp-mod-dirty.jp-mod-active > .p-TabBar-tabCloseIcon { 227 | background-size: 10px; 228 | background-image: var(--jp-icon-inverse-circle); 229 | } 230 | 231 | 232 | #dotscience-manager .p-TabBar-tab.p-mod-closable.jp-mod-active > .p-TabBar-tabCloseIcon { 233 | background-image: var(--jp-icon-inverse-close); 234 | } 235 | 236 | #dotscience-manager .p-TabBar-tab.p-mod-closable > .p-TabBar-tabCloseIcon:hover { 237 | background-size: 16px; 238 | background-image: var(--jp-icon-close-circle); 239 | } 240 | 241 | #dotscience-manager .p-TabBar-tab.p-mod-closable.jp-mod-active > .p-TabBar-tabCloseIcon:hover { 242 | background-size: 16px; 243 | background-image: var(--jp-icon-inverse-close-circle); 244 | } 245 | -------------------------------------------------------------------------------- /jupyterlab_dotscience/tsconfig.json: -------------------------------------------------------------------------------- 1 | { 2 | "compilerOptions": { 3 | "declaration": true, 4 | "noImplicitAny": false, 5 | "noEmitOnError": true, 6 | "noUnusedLocals": true, 7 | "allowSyntheticDefaultImports": true, 8 | "module": "commonjs", 9 | "moduleResolution": "node", 10 | "target": "ES5", 11 | "outDir": "./lib", 12 | "lib": ["ES5", "ES2015.Promise", "DOM", "es2015", "es2015.iterable"], 13 | "types": [] 14 | }, 15 | "include": ["src/*"] 16 | } 17 | -------------------------------------------------------------------------------- /jupyterlab_dotscience_backend/.bumpversion.cfg: -------------------------------------------------------------------------------- 1 | [bumpversion] 2 | current_version = 0.2.30 3 | commit = False 4 | tag = False 5 | tag_name = {new_version} 6 | 7 | [bumpversion:file:jupyterlab_dotscience_backend/__init__.py] 8 | 9 | [bumpversion:file:setup.py] 10 | 11 | -------------------------------------------------------------------------------- /jupyterlab_dotscience_backend/.gitattributes: -------------------------------------------------------------------------------- 1 | jupyterlab_dotscience_backend/_version.py export-subst 2 | -------------------------------------------------------------------------------- /jupyterlab_dotscience_backend/MANIFEST.in: -------------------------------------------------------------------------------- 1 | include jupyterlab_dotscience_backend -------------------------------------------------------------------------------- /jupyterlab_dotscience_backend/README.md: -------------------------------------------------------------------------------- 1 | # jupyterlab-dotscience plugin 2 | 3 | A JupyterLab extension which enables data & model versioning and summary statistics tracking. 4 | 5 | See [dotscience](https://github.com/dotmesh-io/dotscience) for more details. 6 | -------------------------------------------------------------------------------- /jupyterlab_dotscience_backend/jupyterlab_dotscience_backend/README.md: -------------------------------------------------------------------------------- 1 | XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 | 3 | newer versions of this code are now being maintained in github.com/dotmesh-io/jupyterlab-tensorflow/argh 4 | 5 | XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6 | -------------------------------------------------------------------------------- /jupyterlab_dotscience_backend/jupyterlab_dotscience_backend/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | JupyterLab dotscience: proxy through to local dotscience instance 3 | """ 4 | 5 | from notebook.utils import url_path_join 6 | 7 | __version__ = '0.2.30' 8 | 9 | import os, json 10 | from tornado import web 11 | from notebook.base.handlers import APIHandler 12 | import requests 13 | 14 | # TODO pip3 install datadots-api==0.1.2 15 | from dotmesh.client import DotmeshClient, DotName 16 | 17 | import logging 18 | logging.getLogger('jsonrpcclient.client.request').setLevel(logging.ERROR) 19 | logging.getLogger('jsonrpcclient.client.response').setLevel(logging.ERROR) 20 | 21 | # XXX is this right??? 22 | path_regex = r'(?P(?:(?:/[^/]+)+|/?))' 23 | 24 | import socket, struct 25 | def get_default_gateway_linux(): 26 | """Read the default gateway directly from /proc.""" 27 | with open("/proc/net/route") as fh: 28 | for line in fh: 29 | fields = line.strip().split() 30 | if fields[1] != '00000000' or not int(fields[3], 16) & 2: 31 | continue 32 | 33 | return socket.inet_ntoa(struct.pack("=0.2.4'], 17 | classifiers=( 18 | "Programming Language :: Python :: 3", 19 | "License :: OSI Approved :: MIT License", 20 | "Operating System :: OS Independent", 21 | ), 22 | ) 23 | -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "@dotscience/jupyterlab-plugin", 3 | "version": "0.0.2", 4 | "description": "jupyterlab plugin for using dotscience", 5 | "main": "index.js", 6 | "scripts": { 7 | "test": "echo \"Error: no test specified\" && exit 1" 8 | }, 9 | "repository": { 10 | "type": "git", 11 | "url": "git+https://github.com/dotmesh-io/jupyterlab-plugin.git" 12 | }, 13 | "author": "", 14 | "license": "ISC", 15 | "bugs": { 16 | "url": "https://github.com/dotmesh-io/jupyterlab-plugin/issues" 17 | }, 18 | "homepage": "https://github.com/dotmesh-io/jupyterlab-plugin#readme" 19 | } 20 | -------------------------------------------------------------------------------- /renovate.json: -------------------------------------------------------------------------------- 1 | { 2 | "extends": ["github>dotmesh-io/renovate-config"] 3 | } 4 | -------------------------------------------------------------------------------- /scripts/release.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -euo pipefail 3 | VERSION=$1 4 | cd jupyterlab_dotscience_backend && bump2version --new-version $VERSION patch 5 | cd ../jupyterlab_dotscience && npm --no-git-tag-version version $VERSION 6 | git commit -am "Bump to version ${VERSION}" && git tag $VERSION 7 | git push && git push --tags 8 | --------------------------------------------------------------------------------