Issue 404: Install TOC extension by default (#721)

* install TOC extension and nbconfigurator by default

Author: vkumra-broad

automation/src/test/scala/org/broadinstitute/dsde/workbench/leonardo/NotebookInstallSpec.scala

@@ -17,7 +17,7 @@ class NotebookInstallSpec extends ClusterFixtureSpec {
               |bx.bitset.sys.copyright""".stripMargin
 
           notebookPage.executeCell("1+1") shouldBe Some("2")
-          notebookPage.executeCell(getPythonVersion) shouldBe Some("3.6.7")
+          notebookPage.executeCell(getPythonVersion) shouldBe Some("3.6.8")
           notebookPage.executeCell(getBxPython).get should include("Copyright (c)")
         }
       }
@@ -76,6 +76,20 @@ class NotebookInstallSpec extends ClusterFixtureSpec {
       }
     }
 
-  }
+    "should install Table of Content from jupyter_contrib_nbextensions" in { clusterFixture =>
+      withWebDriver { implicit driver =>
+        withNewNotebook(clusterFixture.cluster) { notebookPage =>
+          notebookPage.executeCell("! jupyter nbextension list").get should include("toc2/main  enabled")
+        }
+      }
+    }
 
+    "should install and enable nbextensions_configurator" in { clusterFixture =>
+      withWebDriver { implicit driver =>
+        withNewNotebook(clusterFixture.cluster) { notebookPage =>
+          notebookPage.executeCell("! jupyter serverextension list ").get should include("jupyter_nbextensions_configurator  enabled")
+        }
+      }
+    }
+  }
 }

docker/jupyter/Dockerfile

@@ -206,6 +206,8 @@ RUN apt-get update \
  && pip3 install matplotlib-venn==0.11.5 \
  # for jupyter_localize_extension
  && pip3 install python-datauri \
+ && pip3 install jupyter_contrib_nbextensions \
+ && pip3 install jupyter_nbextensions_configurator \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
 

docker/jupyter/scripts/extension/install_jupyter_contrib_nbextensions.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+set -e
+# installs jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensions
+# also installs the jupyter_nbextensions_configurator https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator
+sudo -E -u jupyter-user jupyter nbextensions_configurator enable --user
+sudo -E -u jupyter-user jupyter contrib nbextension install --user
+sudo -E -u jupyter-user jupyter nbextension enable toc2/main

src/main/resources/jupyter/init-actions.sh

@@ -247,6 +247,9 @@ if [[ "${ROLE}" == 'Master' ]]; then
       done
     fi
 
+
+    retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} ${JUPYTER_SCRIPTS}/extension/install_jupyter_contrib_nbextensions.sh
+
     # If a custom.js was specified, copy it into the jupyter docker container.
     if [ ! -z ${JUPYTER_CUSTOM_JS_URI} ] ; then
       log 'Installing Jupyter custom.js...'