Merge pull request #68 from dominikl/jupyter_docker

Jupyter docker

.Rbuildignore

@@ -17,3 +17,4 @@
 ^inst$
 ^java$
 ^CHANGELOG.md$
+^jupyter$

README.md

@@ -46,6 +46,12 @@ Alternatively: In R console run `install.packages("https://github.com/ome/rOMERO
 
 See [Tips for Unix users](#tips-for-unix-users) section if you are running into difficulties.
 
+### Docker / Jupyter
+
+With [Docker](https://www.docker.com/) and [Jupyter](https://jupyter.org/) there is a quick and easy way to
+get an R OMERO enviroment set up and running in your browser. Ideal to quickly try out some snippets. Go to
+(jupyter)[jupyter] directory and see the instructions there.
+
 ## Usage
 
 * Like any other R package load the package ```library(romero.gateway)```

jupyter/Dockerfile

@@ -0,0 +1,36 @@
+FROM imagedata/jupyter-docker:0.9.0
+MAINTAINER ome-devel@lists.openmicroscopy.org.uk
+
+# The branch to build the romero.gateway from
+ARG ROMERO_VERSION=
+ARG ROMERO_BRANCH_USER=ome
+ARG ROMERO_BRANCH=master
+ARG INSTALL_SCRIPT_URL=https://raw.githubusercontent.com/ome/rOMERO-gateway/master/install.R
+
+# R-kernel and R-OMERO prerequisites
+ADD environment-r-omero.yml .setup/
+RUN conda env update -n r-omero -q -f .setup/environment-r-omero.yml && \
+    /opt/conda/envs/r-omero/bin/Rscript -e "IRkernel::installspec(displayname='OMERO R')"
+
+USER root
+RUN mkdir /opt/romero /opt/omero && \
+    fix-permissions /opt/romero /opt/omero
+# R requires these two packages at runtime
+RUN apt-get install -y -q \
+    libxrender1 \
+    libsm6
+USER $NB_UID
+
+# build/install rOMERO
+ENV _JAVA_OPTIONS="-Xss2560k -Xmx2g"
+RUN cd /opt/romero && \
+    curl -sf $INSTALL_SCRIPT_URL --output install.R
+RUN if [ -z ${ROMERO_VERSION} ]; then \
+    bash -c "source activate r-omero && Rscript /opt/romero/install.R --user=$ROMERO_BRANCH_USER --branch=$ROMERO_BRANCH --quiet"; else \
+    bash -c "source activate r-omero && Rscript /opt/romero/install.R --version=$ROMERO_VERSION --quiet"; fi
+
+ENV OMERO_LIBS_DOWNLOAD=TRUE
+RUN bash -c "source activate r-omero && echo \"library('romero.gateway')\" | R --no-save"
+
+COPY --chown=1000:100 Get_Started.ipynb notebooks/
+

jupyter/Get_Started.ipynb

@@ -0,0 +1,82 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Load library and connect to an OMERO server"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "library(romero.gateway)\n",
+    "library(EBImage) # for displaying an image (also useful for image analysis!)\n",
+    "\n",
+    "# Connect to server\n",
+    "server <- OMEROServer(host = 'SERVER_NAME', username='USER_NAME', password='PASSWORD', port= as.integer(4064))\n",
+    "server <- connect(server)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Perform some tasks"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load an image\n",
+    "imageId <- IMAGE_ID # Replace with an actual image id\n",
+    "image <- loadObject(server, \"ImageData\", imageId)\n",
+    "pixels <- getPixelValues(image, 1, 1, 1)\n",
+    "\n",
+    "# Use EBImage to display it\n",
+    "ebimage <- EBImage::Image(data = pixels, colormode = 'Grayscale')\n",
+    "ebimage <- normalize(ebimage)\n",
+    "EBImage::display(ebimage)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Disconnect again"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "disconnect(server)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "OMERO R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "3.5.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

jupyter/README.md

@@ -0,0 +1,28 @@
+Jupyter server
+==============
+
+Spin up a Jupyter server with Docker:
+
+CD into this directory and run:
+```
+docker build -t romero .
+
+```
+(this will build the romero.gateway from the current ome/master branch)
+
+Run the docker image:
+```
+docker run -it -p 8888:8888 romero
+```
+
+Go to the respective URL in your browser and open the `Get_Started` notebook in `notebooks`,
+or create a new 'OMERO R' notebook from scratch!
+
+Notes:
+- If you want to build a specific version or branch use:
+  ```
+  docker build --build-arg ROMERO_VERSION=0.4.5 .
+  docker build --build-arg ROMERO_BRANCH_USER=ome --build-arg ROMERO_BRANCH=master .
+  ```
+- The Dockerfile uses the  [install.R](../install.R) script from the master branch.
+  You can specify a different script with the `INSTALL_SCRIPT_URL` parameter.

jupyter/environment-r-omero.yml

@@ -0,0 +1,25 @@
+# Install some common, useful R packages. These are
+# not all strictly necessary for romero.gateway.
+channels:
+- bioconda
+- conda-forge
+- defaults
+dependencies:
+- bioconductor-ebimage
+- openjdk=8.0.*
+- r-assertthat
+- r-base=3.5.*
+- r-devtools
+- r-git2r
+- r-httr
+- r-irdisplay
+- r-irkernel
+- r-jpeg
+- r-repr
+- r-rjava
+- r-roxygen2
+- r-testthat
+- r-tidyverse
+- r-xml2
+- r-getpass
+prefix: /opt/conda/envs/r-omero