Merge remote-tracking branch 'origin/master' into michal/6437

* origin/master:
  removing error message from stdout in test + test refactoring (#6480)
  #6479 add readme to find start of documentation
  #6479 - fixed doc file names to match camel case (#6488)
  #6429 Added jupyterlab and jupyterhub. (#6472)
  Spot/6483 (#6485)
  #6410 implement %%javascript magic for rendering the `application/javascript` mime (#6482)

# Conflicts:
#	docker/setup.sh

beakerx/jslab/src/javascriptRendererExtension.ts

@@ -0,0 +1,62 @@
+/*
+ *  Copyright 2017 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+import { IRenderMime } from '@jupyterlab/rendermime-interfaces';
+import { RenderedJavaScript } from '@jupyterlab/rendermime';
+
+export const TEXT_JAVASCRIPT_MIMETYPE = 'text/javascript';
+export const APPLICATION_JAVASCRIPT_MIMETYPE = 'application/javascript';
+
+export class BeakerxRenderedJavascript extends RenderedJavaScript {
+  render(model: IRenderMime.IMimeModel): Promise<void> {
+    const evalInContext = function (str) { return eval(str); }.bind(this);
+
+    try {
+      evalInContext(String(model.data[this.mimeType]));
+
+      return Promise.resolve(undefined);
+    } catch (err) {
+      console.error(err);
+
+      const pre = document.createElement('pre');
+
+      pre.classList.add('js-error');
+      pre.innerHTML = `${String(err.message)}<br>See your browser Javascript console for more details.`;
+      this.node.appendChild(pre);
+
+      return Promise.resolve(undefined);
+    }
+  }
+}
+
+/**
+ * A mime renderer factory for text/javascript data.
+ */
+export
+const rendererFactory: IRenderMime.IRendererFactory = {
+  safe: true,
+  mimeTypes: [TEXT_JAVASCRIPT_MIMETYPE, APPLICATION_JAVASCRIPT_MIMETYPE],
+  createRenderer: options => new BeakerxRenderedJavascript(options)
+};
+
+const extension: IRenderMime.IExtension = {
+  id: 'beakerx.javascript:factory',
+  rendererFactory,
+  rank: 0,
+  dataType: 'string'
+};
+
+export default extension;

doc/README.md

@@ -0,0 +1,19 @@
+<!--
+    Copyright 2017 TWO SIGMA OPEN SOURCE, LLC
+
+    Licensed under the Apache License, Version 2.0 (the "License");
+    you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+           http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing, software
+    distributed under the License is distributed on an "AS IS" BASIS,
+    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+    See the License for the specific language governing permissions and
+    limitations under the License.
+-->
+
+# Documentation
+
+[Start Here](../StartHere.ipynb)

docker/setup.sh

@@ -16,6 +16,8 @@
 source activate beakerx
 (cd beakerx; pip install -e . --verbose)
 beakerx-install
+jupyter labextension install @jupyter-widgets/jupyterlab-manager
+(cd js/lab; jupyter labextension install .)
 
 rm -r /home/beakerx/beakerx/js/node_modules
 rm -r /home/beakerx/beakerx/js/dist

js/lab/.gitignore

@@ -1,2 +1,3 @@
 /lib
+/dist
 node_modules/

js/lab/package.json

@@ -3,7 +3,7 @@
   "version": "0.9.1",
   "description": "BeakerX: Beaker Extensions for JupyterLab",
   "author": "Two Sigma Open Source, LLC",
-  "main": "index.js",
+  "main": "dist/index.js",
   "license": "Apache-2.0",
   "repository": {
     "type": "git",
@@ -15,9 +15,35 @@
     "jupyterlab extension"
   ],
   "scripts": {
+    "build": "npm run build:src",
+    "build:src": "tsc --project src",
+    "prepublish": "npm run build:src",
     "test": "echo \"Error: no test specified\" && exit 1"
   },
+  "devDependencies": {
+    "@jupyter-widgets/base": "^1.1.5",
+    "@jupyter-widgets/controls": "^1.1.2",
+    "@jupyter-widgets/output": "^1.0.10",
+    "@jupyterlab/application": "^0.13.0",
+    "@jupyterlab/coreutils": "^0.13.0",
+    "@jupyterlab/docregistry": "^0.13.0",
+    "@jupyterlab/notebook": "^0.13.0",
+    "@jupyterlab/outputarea": "^0.13.1",
+    "@jupyterlab/rendermime": "^0.13.0",
+    "@jupyterlab/rendermime-interfaces": "^0.4.2",
+    "@jupyterlab/services": "^0.52.0",
+    "@types/node": "^8.0.56",
+    "typescript": "~2.6.2"
+  },
   "jupyterlab": {
-    "extension": true
+    "extension": "dist/index.js",
+    "mimeExtension": "dist/javascriptRendererExtension.js"
+  },
+  "files": [
+    "dist/*.js",
+    "lib/*.js"
+  ],
+  "dependencies": {
+    "beakerx": "^0.9.1"
   }
 }

js/lab/index.js → js/lab/src/index.ts

@@ -14,18 +14,25 @@
  *  limitations under the License.
  */
 
-var beakerx = require('./lib/index.js');
-var base = require('@jupyter-widgets/base');
+declare function require(moduleName: string): any;
 
-module.exports = {
+import { IJupyterWidgetRegistry } from '@jupyter-widgets/base';
+import BeakerxExtension from './plugin';
+import { JupyterLab } from '@jupyterlab/application';
+
+const beakerx = require('../lib/index.js');
+
+export default {
   id: 'beakerx',
-  requires: [base.IJupyterWidgetRegistry],
-  activate: function(app, widgets) {
+  requires: [IJupyterWidgetRegistry],
+  activate: (app: JupyterLab, widgets: IJupyterWidgetRegistry ) => {
     widgets.registerWidget({
       name: 'beakerx',
       version: beakerx.version,
       exports: beakerx
     });
+
+    app.docRegistry.addWidgetExtension('Notebook', new BeakerxExtension());
   },
   autoStart: true
 };

js/lab/src/javascriptRendererExtension.ts

@@ -0,0 +1,56 @@
+/*
+ *  Copyright 2017 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+import { IRenderMime } from '@jupyterlab/rendermime-interfaces';
+import { RenderedJavaScript } from '@jupyterlab/rendermime'
+
+export const TEXT_JAVASCRIPT_MIMETYPE = 'text/javascript';
+export const APPLICATION_JAVASCRIPT_MIMETYPE = 'application/javascript';
+
+export class BeakerxRenderedJavascript extends RenderedJavaScript {
+  render(model: IRenderMime.IMimeModel): Promise<void> {
+    const evalInContext = function(code: string) {
+      return eval(code);
+    }.bind(this);
+
+    try {
+      evalInContext(String(model.data[this.mimeType]));
+    } catch (e) {
+      this.node.innerHTML = `<pre>${String(e.message)} - please check console</pre>`;
+    }
+
+    return Promise.resolve(undefined);
+  }
+}
+
+/**
+ * A mime renderer factory for text/javascript data.
+ */
+export
+const rendererFactory: IRenderMime.IRendererFactory = {
+  safe: true,
+  mimeTypes: [TEXT_JAVASCRIPT_MIMETYPE, APPLICATION_JAVASCRIPT_MIMETYPE],
+  createRenderer: options => new BeakerxRenderedJavascript(options)
+};
+
+const extension: IRenderMime.IExtension = {
+  id: 'beakerx.javascript:factory',
+  rendererFactory,
+  rank: 0,
+  dataType: 'string'
+};
+
+export default extension;

js/lab/src/plugin.ts

@@ -0,0 +1,143 @@
+/*
+ *  Copyright 2017 TWO SIGMA OPEN SOURCE, LLC
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+import { JSONArray } from '@phosphor/coreutils';
+import { Widget } from '@phosphor/widgets';
+import { DisposableDelegate } from '@phosphor/disposable';
+import { DocumentRegistry } from '@jupyterlab/docregistry';
+import { INotebookModel, NotebookPanel, Notebook } from '@jupyterlab/notebook';
+import { Cell, CodeCell, CodeCellModel } from '@jupyterlab/cells';
+import { showDialog, Dialog } from '@jupyterlab/apputils';
+import { Kernel } from '@jupyterlab/services';
+
+interface msgData {
+  name?: string,
+  value?: any
+}
+
+declare global {
+  interface Window {
+    beakerx: any,
+    require: Function
+  }
+}
+
+function displayHTML(widget: Widget, html: string): void {
+  if (!widget.node || !html) {
+    return;
+  }
+
+  const childElement = document.createElement('pre');
+
+  childElement.classList.add('jp-RenderedHTML');
+  childElement.innerHTML = html;
+  widget.node.appendChild(childElement);
+}
+
+function registerGlobal(): void {
+  window.beakerx = window.beakerx || {};
+  window.beakerx.displayHTML = displayHTML;
+}
+
+function sendJupyterCodeCells(
+  kernelInstance: Kernel.IKernelConnection,
+  notebook: Notebook,
+  comm: Kernel.IComm,
+  filter: string
+): void {
+  const codeCells = <JSONArray>getCodeCellsByTag(notebook, filter).map(
+    (cell: CodeCell): object => cell.model.toJSON()
+  );
+
+  comm.send({ code_cells: codeCells });
+}
+
+function getCodeCellsByTag(notebook: Notebook, tag: string): Cell[] {
+  let cells = notebook.widgets || [];
+
+  return cells.filter(function(cell) {
+    const tags: any = cell.model.metadata.get('tags');
+
+    return (
+      cell.model instanceof CodeCellModel &&
+      tags && tags.length && tags.includes(tag)
+    );
+  });
+}
+
+function registerCommTargets(panel: NotebookPanel, context: DocumentRegistry.IContext<INotebookModel>) {
+  const session = context.session;
+  const kernelInstance = session.kernel;
+  const notebook = panel.notebook;
+
+  kernelInstance.registerCommTarget('beaker.getcodecells', function(comm, msg) {
+    const data: msgData = <object>msg.content.data;
+
+    comm.onMsg = function(msg) {
+      if(data.name == "CodeCells") {
+        sendJupyterCodeCells(kernelInstance, notebook, comm, JSON.parse(data.value));
+      }
+
+      window.beakerx[data.name] = JSON.parse(data.value);
+    };
+  });
+
+  kernelInstance.registerCommTarget('beaker.autotranslation', function(comm, msg) {
+    comm.onMsg = function(msg) {
+      const data: msgData = <object>msg.content.data;
+
+      window.beakerx[data.name] = JSON.parse(data.value);
+    };
+  });
+
+  kernelInstance.registerCommTarget('beaker.tag.run', function(comm, msg) {
+    comm.onMsg = function(msg) {
+      const data: { state?: any } = <object>msg.content.data;
+
+      if(!data.state || !data.state.runByTag) {
+        return;
+      }
+
+      const matchedCells = getCodeCellsByTag(notebook, data.state.runByTag);
+
+      if (matchedCells.length === 0) {
+        showDialog({
+          title: 'No cell with the tag !',
+          body: 'Tag: ' + data.state.runByTag,
+          buttons: [ Dialog.okButton({ label: 'OK' }) ]
+        });
+      } else {
+        matchedCells.forEach((cell) => {
+          cell instanceof CodeCell && CodeCell.execute(cell, session);
+        });
+      }
+    };
+  });
+}
+
+class BeakerxExtension implements DocumentRegistry.WidgetExtension {
+  createNew(panel: NotebookPanel, context: DocumentRegistry.IContext<INotebookModel>) {
+    registerGlobal();
+
+    Promise.all([panel.ready, context.ready]).then(function() {
+      registerCommTargets(panel, context);
+    });
+
+    return new DisposableDelegate(() => { });
+  }
+}
+
+export default BeakerxExtension;

js/lab/src/tsconfig.json

@@ -0,0 +1,14 @@
+{
+  "compilerOptions": {
+    "allowJs": true,
+    "noImplicitAny": true,
+    "noEmitOnError": true,
+    "noUnusedLocals": true,
+    "lib": ["dom", "es5", "es2015.promise"],
+    "types": ["node"],
+    "module": "commonjs",
+    "moduleResolution": "node",
+    "target": "ES5",
+    "outDir": "../dist"
+  }
+}