install Ronaldo on jupyter docker, add automation test and include ex…

…ample use case (#575)

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

@@ -111,6 +111,13 @@ class NotebookRKernelSpec extends ClusterFixtureSpec {
       }
     }
 
+    "should have Ronaldo automatically installed" in { clusterFixture =>
+      withWebDriver { implicit driver =>
+        withNewNotebook(clusterFixture.cluster, RKernel) { notebookPage =>
+          notebookPage.executeCell(""""Ronaldo" %in% installed.packages()""") shouldBe Some("TRUE")
+        }
+      }
+    }
   }
 
 }

example-notebooks/RonaldoExample.ipynb

@@ -0,0 +1,61 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This notebook shows how the Ronaldo package can be use to get the service account key for the Leonardo user. The getServiceAccountKey function uses SAM to get the key for the service account associated with the user."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "key <- Ronaldo::getServiceAccountKey()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This key can be used to access resources associated with the Leonardo notebook user. In this example we can use the key to access bigquery data. The following command sets the service token which configures the bigquery library to access data that is available to the user."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "library(bigrquery)\n",
+    "set_service_token(key)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "3.4.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

jupyter-docker/Dockerfile

@@ -233,6 +233,7 @@ RUN R -e 'install.packages(c( \
     "bigrquery",  \
     "tidyverse"), \
     repos="http://cran.mtu.edu")' \
+ && R -e 'devtools::install_github("DataBiosphere/Ronaldo")' \
  && R -e 'devtools::install_github("IRkernel/IRkernel")' \
  && R -e 'IRkernel::installspec(user=FALSE)' \
  && chown -R $USER:users /home/jupyter-user/.local  \