From f041116723595459c196e3299d5689995a4808ed Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>
Date: Tue, 29 Mar 2022 12:43:39 +0200
Subject: [PATCH] Added more compilation steps.

---
 03_setup_root_path.sh           | 11 +++++++++++
 04_copy_env.sh                  |  3 +++
 05_setup_rsession_parameters.sh | 13 +++++++++++++
 Dockerfile                      | 34 ++++++++++++++++++++++++++++++++-
 4 files changed, 60 insertions(+), 1 deletion(-)
 create mode 100644 03_setup_root_path.sh
 create mode 100644 04_copy_env.sh
 create mode 100644 05_setup_rsession_parameters.sh

diff --git a/03_setup_root_path.sh b/03_setup_root_path.sh
new file mode 100644
index 0000000..e282d68
--- /dev/null
+++ b/03_setup_root_path.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/with-contenv bash
+
+echo "root path: $WWW_ROOT_PATH"
+
+if [[ ! -z $WWW_ROOT_PATH ]]
+then
+        echo "Set www-root-path to $WWW_ROOT_PATH"
+        echo "www-root-path=$WWW_ROOT_PATH" >> /etc/rstudio/rserver.conf
+else
+        echo "Not setting www-root-path"
+fi
diff --git a/04_copy_env.sh b/04_copy_env.sh
new file mode 100644
index 0000000..b8e0984
--- /dev/null
+++ b/04_copy_env.sh
@@ -0,0 +1,3 @@
+#!/usr/bin/with-contenv bash
+
+printenv >> /home/$USER/.Renviron
diff --git a/05_setup_rsession_parameters.sh b/05_setup_rsession_parameters.sh
new file mode 100644
index 0000000..64423b6
--- /dev/null
+++ b/05_setup_rsession_parameters.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/with-contenv bash
+
+echo "session-timeout-minutes=360" >> /etc/rstudio/rsession.conf
+echo "session-disconnected-timeout-minutes=360" >> /etc/rstudio/rsession.conf
+echo "session-quit-child-processes-on-exit=0" >> /etc/rstudio/rsession.conf
+echo "session-default-working-dir=~" >> /etc/rstudio/rsession.conf
+echo "session-default-new-project-dir=~" >> /etc/rstudio/rsession.conf
+echo "session-save-action-default=yes" >> /etc/rstudio/rsession.conf
+echo "allow-shell=0" >> /etc/rstudio/rsession.conf
+echo "allow-terminal-websockets=1" >> /etc/rstudio/rsession.conf
+echo "limit-cpu-time-minutes=0" >> /etc/rstudio/rsession.conf
+echo "limit-file-upload-size-mb=0" >> /etc/rstudio/rsession.conf
+echo "limit-xfs-disk-quota=no" >> /etc/rstudio/rsession.conf
diff --git a/Dockerfile b/Dockerfile
index 37b9042..24e3f68 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,9 +11,41 @@ ENV DEFAULT_USER=rstudio
 ENV PANDOC_VERSION=default
 ENV PATH=/usr/lib/rstudio-server/bin:$PATH
 
+# Install OpenJDK
+RUN apt-get update && apt-get install -y openjdk-8-jdk-headless openjdk-8-jre-headless
+
+# Install a lot of R packages
+ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/install2r-packages.txt /tmp
+RUN for f in `cat /tmp/install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f ; done
+
+# Non CRAN repositories
+ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_non_cran_pkgs.txt /tmp
+RUN for l in `cat /tmp/r_non_cran_pkgs.txt` ; do \
+    pkg=`echo $l | cut -d : -f 1` ; \
+    mirror=`echo $l | cut -d : -f 2-` ; \
+    Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
+    -e "install.packages(pkgs='$pkg', repos=c('$mirror/'));" ; done
+
+# From github
+ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
+RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
+    Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
+    -e " require(devtools); devtools::install_github('$g')" ; done
+
 RUN /rocker_scripts/install_rstudio.sh
 RUN /rocker_scripts/install_pandoc.sh
 
+# This part comes from https://github.com/openanalytics/shinyproxy-rstudio-ide-demo/blob/master/Dockerfile
+RUN echo "www-frame-origin=disabled" >> /etc/rstudio/disable_auth_rserver.conf
+RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
+
+ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path.sh
+
+# By default RStudio does not give access to all enviornment variables defined in the container (e.g. using ShinyProxy).
+# Uncomment the next line, to change this behavior.
+ADD 04_copy_env.sh /etc/cont-init.d/04_copy_env.sh
+ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters.sh
+
 EXPOSE 8787
 
-CMD ["/init"]
\ No newline at end of file
+CMD ["/init"]