Render notebook via CLI (#48)

* Patch README after title duplication

* Use native RStudio env vars in .env

* Fix conda env sage-bionetworks and add docker-entrypoint.sh

* Update README

* Fix typo in docker-compose.yml

.env.example

@@ -1,9 +1,9 @@
 # RStudio
-RSTUDIO_USER=rstudio
-RSTUDIO_PASSWORD=yourpassword
-RSTUDIO_USERID=1000
-RSTUDIO_GROUPID=1000
-RSTUDIO_ROOT=FALSE
+USER=rstudio
+PASSWORD=yourpassword
+USERID=1000
+GROUPID=1000
+ROOT=FALSE
 
 # Synapse
 SYNAPSE_TOKEN=yourtoken

Dockerfile

@@ -15,6 +15,7 @@ RUN apt-get update -qq -y \
     && apt-get install --no-install-recommends -qq -y \
         bash-completion \
         curl \
+        gosu \
         libxml2-dev \
         zlib1g-dev \
         # Fix https://github.com/tschaffter/rstudio/issues/11 (1/2)
@@ -41,11 +42,11 @@ RUN apt-get update -qq -y \
 # Create conda environments
 COPY conda /tmp/conda
 RUN conda init bash \
-    && conda env create -f /tmp/conda/sage-bionetworks/environment.yaml \
+    && conda env create -f /tmp/conda/sage-bionetworks/environment.yml \
     && rm -fr /tmp/conda \
     # Fix libssl issue that affects conda env used with reticulate
     && cp /usr/lib/x86_64-linux-gnu/libssl.so.1.1 \
-        /opt/miniconda/envs/sage/lib/libssl.so.1.1 \
+        /opt/miniconda/envs/sage-bionetworks/lib/libssl.so.1.1 \
     && conda activate base || true \
     && echo "conda activate sage-bionetworks" >> ~/.bashrc
 
@@ -59,4 +60,11 @@ RUN install2.r --error renv \
 
 # Configure S6 init system
 RUN mv /etc/cont-init.d/userconf /etc/cont-init.d/10-rstudio-userconf
-COPY root /
+COPY root /
+
+WORKDIR /
+COPY docker-entrypoint.sh .
+RUN chmod +x docker-entrypoint.sh
+
+ENTRYPOINT ["/docker-entrypoint.sh"]
+CMD ["rstudio"]

README.md

@@ -128,24 +128,20 @@ $ id
 uid=1000(kelsey) gid=1000(kelsey) groups=1000(kelsey)
 ```
 
-In this example, we would set `RSTUDIO_USERID=1000` and `RSTUDIO_GROUPID=1000`.
+In this example, we would set `USERID=1000` and `GROUPID=1000`.
 
 ## Giving the user root permissions
 
 Set the environment variable `ROOT=TRUE` (default is `FALSE`).
 
 ## Accessing logs
 
-## Setting Synapse credentials
-
 ```console
 docker logs --follow rstudio
 ```
 
 ## Generating an HTML notebook
 
-## Generating an HTML notebook
-
 This Docker image provides the command `render` that generates an HTML or PDF
 notebook from an R notebook (*.Rmd*). Run the command below from the host to
 mount the directory `$(pwd)/notebooks` where the R notebook is and generate the
@@ -154,8 +150,9 @@ HTML notebook that will be saved to the same directory with the extension
 
 ```console
 docker run --rm \
+    --env-file .env \
     -v $(pwd)/notebooks:/data \
-    -e RENDER_INPUT="/data/example.Rmd" \
+    -e RENDER_INPUT="/data/examples/notebook.Rmd" \
     tschaffter/rstudio \
     render
 ```

docker-compose.yml

@@ -2,19 +2,15 @@ version: "3.8"
 
 services:
   rstudio:
-    image: tschaffter/rstudio:latest
+    image: tschaffter/rstudio:4.0.5
     build:
       context: .
       dockerfile: Dockerfile
     container_name: rstudio
-    environment:
-      - USER=${RSTUDIO_USER}
-      - PASSWORD=${RSTUDIO_PASSWORD}
-      - USERID=${RSTUDIO_USERID}
-      - GROUPID=${RSTUDIO_GROUPID}
-      - ROOT=${RSTUDIO_ROOT}
-      - SYNAPSE_TOKEN
+    env_file:
+      - .env
     volumes:
       - .:/home/rstudio/awesome-project:rw
     ports:
-      - "${HOST_PORT}:8787"
+      - "${HOST_PORT}:8787"
+    command: rstudio

docker-entrypoint.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+set -e
+
+if [ "$1" = 'rstudio' ]; then
+    # RStudio userconf.sh script runs RStudio as $USER
+    exec /init
+fi
+
+exec /init gosu $USER "$@"

root/etc/cont-init.d/20-create-rstudio-logfolder

@@ -1,4 +1,6 @@
 #!/bin/sh
+#
+# Enable logging for RStudio.
 
 mkdir -p /var/log/rstudio
 chown nobody:nogroup /var/log/rstudio

root/etc/cont-init.d/30-configure-user

@@ -1,4 +1,6 @@
 #!/usr/bin/with-contenv bash
+#
+# Prepare the user's environment.
 
 set -euo pipefail
 
@@ -11,6 +13,14 @@ BASHRC_FILENAME="/home/${USER}/.bashrc"
 # Change the shell of the user to bash
 usermod --shell /bin/bash ${USER}
 
+# Create ~/.bashrc
+if [[ ! -f ${BASHRC_FILENAME} ]]; then
+    echo "export PATH=${PATH}" > ${BASHRC_FILENAME}
+
+    chown "${USER}:${USER}" ${BASHRC_FILENAME}
+    chmod 644 ${BASHRC_FILENAME}
+fi
+
 # Create Synapse Python client configuration file
 if [[ ! -z ${SYNAPSE_TOKEN} ]]; then
     if [ ! -f ${SYNAPSE_CONFIG_FILENAME} ]; then
@@ -23,23 +33,6 @@ if [[ ! -z ${SYNAPSE_TOKEN} ]]; then
     fi
 fi
 
-# Create ~/.bashrc
-if [[ ! -f ${BASHRC_FILENAME} ]]; then
-    echo "export PATH=${PATH}" > ${BASHRC_FILENAME}
-
-    chown "${USER}:${USER}" ${BASHRC_FILENAME}
-    chmod 644 ${BASHRC_FILENAME}
-fi
-
 # Fix sudo: setrlimit(RLIMIT_CORE): Operation not permitted
 # https://github.com/sudo-project/sudo/issues/42#issuecomment-659253293
 echo "Set disable_coredump false" >> /etc/sudo.conf
-
-# Configure shell to use `conda activate`
-# TODO
-
-# sudo -u rstudio bash <<EOF
-# conda --version
-# conda config --set auto_activate_base false
-# conda init bash
-# EOF