Docker shiny v 1.0.0

README.md

@@ -68,6 +68,8 @@ GH_TOKEN=your_github_pat
 RSTUDIO_PORT=
 # Password to access the Rstudio server
 RSTUDIO_PASSWD=
+# Port in which you want shiny server to be deployed (for running the app)
+SHINY_PORT=
 ```
 
 Finally, in a terminal located in the folder `docker` of this repository, run:

docker/Dockerfile.shiny

@@ -0,0 +1,93 @@
+#############################
+#       SHINY-SERVER        #
+#     VOLUME DOCKERFILE     #
+#############################
+# Set up the shiny server   #
+# for using deepVATS App    #
+#############################
+FROM misantamaria/dvats-rstudio:rocker-ml4.2
+SHELL [ "/bin/bash", "--login", "-c" ]
+
+# Add r-studio server user
+ARG USER=user \
+    UID=1000 \
+    GID=1000
+
+ENV USER=$USER \
+    UID=$UID \
+    GID=$GID
+
+# Paths
+ENV HOME=/home/$USER \
+    ENV_PREFIX=$HOME/env \
+    APP=$HOME/app
+
+# Ensure files and packages
+COPY --chown=app:app docker/entrypoint-rstudio.sh /usr/local/bin
+COPY --chown=app:app r_shiny_app $APP
+
+# Create groups and users
+RUN addgroup --gid $GID $USER \
+    && addgroup --system app \
+    && addgroup --system shared \
+    && adduser --disabled-password \
+       --gecos "Non-root user" \
+       --uid $UID \
+       --gid $GID \
+       --home $HOME \
+       $USER \
+    && adduser --system --ingroup app app \
+    && usermod -aG shared $USER \
+    && usermod -aG shared app
+
+# Agregar usuarios al grupo sudo después de crearlos
+RUN adduser $USER sudo \
+    && usermod -aG sudo app \
+    && echo $USER "ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER \
+    && echo "app ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/app \
+    && chmod 0440 /etc/sudoers.d/$USER \
+    && chmod 0440 /etc/sudoers.d/app
+
+ARG LOG_DIR=/var/log/shiny-server
+ENV LOG_DIR=${LOG_DIR} \
+    LOG_FILE=${LOG_DIR}/app.logs
+COPY --chown=app:app srv/shinylog $LOG_DIR
+
+# Fix ownership and permissions for the home directory
+RUN chown -R $USER:$USER $HOME \
+    && chmod -R 775 $HOME \
+    && chown -R app:app $HOME \
+    && chmod -R 775 $HOME
+
+# Ensure the log directory and file exist with correct permissions
+RUN mkdir -p $LOG_DIR \
+    && touch $LOG_FILE \
+    && chown -R app:app $LOG_DIR \
+    && chmod -R 775 $LOG_DIR
+
+RUN R -e "install.packages('semantic.dashboard', repos='http://cran.r-project.org')"\
+    && R -e "install.packages('randomcoloR', repos='http://cran.r-project.org')"
+
+### Run server
+ARG SHINY_PORT
+ENV SHINY_PORT=${SHINY_PORT}
+
+RUN chown -R app:app $APP
+RUN chown -R app:app $LOG_DIR
+RUN touch $LOG_FILE
+RUN chown -R app:app $LOG_DIR
+
+RUN [ -f ${LOG_DIR} ] && echo "${LOG_DIR} is a file" || echo "${LOG_DIR} is a directory"
+
+#RUN ls -la $LOG_DIR && sleep 3
+ARG SHINY_PORT
+ENV SHINY_PORT=$SHINY_PORT
+EXPOSE ${SHINY_PORT}
+EXPOSE 3838
+
+COPY  --chown=app:app docker/entrypoint-shiny.sh /usr/local/bin/entrypoint-shiny.sh
+RUN chmod u+x /usr/local/bin/entrypoint-shiny.sh 
+USER app
+RUN touch $LOG_FILE
+RUN ls -la $LOG_DIR && sleep 3
+CMD ["/usr/local/bin/entrypoint-shiny.sh"]

docker/docker-compose.yml

@@ -27,6 +27,7 @@ services:
       - ${LOCAL_DATA_PATH}:/home/${USER_NAME}/data/
       - conda-env:/usr/local/share/miniconda3/envs/env
       - miniconda:/usr/local/share/miniconda3
+      - lib:/usr/local/share/lib
     init: true
     stdin_open: true
     tty: true
@@ -44,8 +45,10 @@ services:
           dockerfile: docker/Dockerfile.rstudio
           args:
               - WANDB_API_KEY=${WANDB_API_KEY} #
-              - RETICULATE_PYTHON_ENV=/home/env
-              - RETICULATE_MINICONDA_PATH=/home/miniconda3
+              #- RETICULATE_PYTHON_ENV=/home/env
+              #- RETICULATE_MINICONDA_PATH=/home/miniconda3
+              - RETICULATE_PYTHON_ENV=/usr/local/share/miniconda3/envs/env
+              - RETICULATE_MINICONDA_PATH=/usr/local/share/miniconda3
               - USER=${USER_NAME} #* 
               - UID=${USER_ID} #*
               - GID=${GROUP_ID} #*
@@ -61,9 +64,7 @@ services:
           - GROUPID=${GROUP_ID} #*
           - PASSWORD=${RSTUDIO_PASSWD} #*
           - ROOT=FALSE
-          - CUDA_VISIBLE_DEVICES=0,1,2
-          #- CUDA_VISIBLE_DEVICES=1
-            #          - CUDA_VISIBLE_DEVICES=${CUDA_VISIBLE_DEVICES}
+          - CUDA_VISIBLE_DEVICES=${CUDA_VISIBLE_DEVICES}
           - GH_TOKEN=${GH_TOKEN} #*
           # TODO (28/03/2023): I don't know why it is not working without this
           - ENV_VARS=WANDB_ENTITY,WANDB_API_KEY,WANDB_PROJECT,USER,USERID,GROUPID,PASSWORD,ROOT,CUDA_VISIBLE_DEVICES
@@ -72,7 +73,8 @@ services:
          - ${LOCAL_DATA_PATH}:/home/${USER_NAME}/data/ 
          - ../dvats:/home/${USER_NAME}/dvats
          - conda-env:/usr/local/share/miniconda3/envs/env
-         - miniconda:/home/user/local/share/miniconda3 
+         - miniconda:/usr/local/share/miniconda3 
+         - lib:/usr/local/share/lib
       deploy:
         resources:
           #limits:
@@ -82,7 +84,51 @@ services:
               - driver: nvidia
                 count: all
                 capabilities: [gpu]
-
+  shiny-server:
+    build:
+      context: ../
+      dockerfile: docker/Dockerfile.shiny
+      args:
+        - WANDB_API_KEY=${WANDB_API_KEY}
+        - RETICULATE_PYTHON_ENV=/usr/local/share/miniconda3/envs/env
+        - RETICULATE_MINICONDA_PATH=/usr/local/share/miniconda3
+        - USER=${USER_NAME} #* 
+        - UID=${USER_ID} #*
+        - GID=${GROUP_ID} #*
+        - SHINY_PORT=${SHINY_PORT}
+    image: dvats-shiny:${USER_NAME}
+    ports:
+        - "${SHINY_PORT}:3838" #*
+    expose:
+        - "8888"
+    environment:
+      - WANDB_ENTITY=${WANDB_ENTITY}
+      - WANDB_API_KEY=${WANDB_API_KEY}
+      - WANDB_PROJECT=${WANDB_PROJECT}
+      - USER=${USER_NAME} #* 
+      - USERID=${USER_ID} #*
+      - GROUPID=${GROUP_ID} #*
+      - PASSWORD=${SHINY_PASSWD} #*
+      - ROOT=FALSE
+      - CUDA_VISIBLE_DEVICES=${CUDA_VISIBLE_DEVICES}
+      - GH_TOKEN=${GH_TOKEN} #*
+      # TODO (28/03/2023): I don't know why it is not working without this
+      - ENV_VARS=WANDB_ENTITY,WANDB_API_KEY,WANDB_PROJECT,USER,USERID,GROUPID,PASSWORD,ROOT,CUDA_VISIBLE_DEVICES
+    volumes:
+      - ../r_shiny_app:/home/${USER_NAME}/app 
+      - ${LOCAL_DATA_PATH}:/home/${USER_NAME}/data/ 
+      - ../dvats:/home/${USER_NAME}/dvats
+      - conda-env:/usr/local/share/miniconda3/envs/env
+      - miniconda:/usr/local/share/miniconda3 
+      - lib:/usr/local/share/lib
+      - ../srv/shinylog:/var/log/shiny-server
+    deploy:
+      resources:
+        reservations:
+          devices:
+            - driver: nvidia
+              count: all
+              capabilities: [gpu]
 volumes:
   conda-env:
   miniconda:

docker/entrypoint-shiny.sh

@@ -0,0 +1,38 @@
+#!/bin/bash --login
+set -e
+
+[ -f ${LOG_DIR} ] && echo "${LOG_DIR} is a file" || echo "${LOG_DIR} is a directory"
+[ -f ${LOG_FILE} ] && echo "${LOG_FILE} is a file" || echo "${LOG_FILE} is a directory"
+
+echo ". ${HOME}/miniconda3/etc/profile.d/conda.sh" >> ${HOME}/.bashrc
+# Make bash automatically activate the conda environment
+echo "conda activate ${ENV_PREFIX}" >> ${HOME}/.bashrc
+
+#... added for fixing fails when rebuilding docker ...#
+### Ensuring to activate the correct conda
+source /usr/local/share/miniconda3/etc/profile.d/conda.sh
+conda activate /usr/local/share/miniconda3/envs/env
+
+# Define an array of environment variable names from the ENV_VARS Compose variable
+IFS=',' read -ra ENV_VAR_NAMES <<< "$ENV_VARS"
+
+echo "ENV_VAR_NAMES=${ENV_VAR_NAMES[@]}"
+
+# Loop through the array of environment variable names and set the variables
+for ENV_VAR_NAME in "${ENV_VAR_NAMES[@]}"; do
+  ENV_VAR_VALUE="${!ENV_VAR_NAME:-default}"
+  echo "$ENV_VAR_NAME=$ENV_VAR_VALUE" >> ${HOME}/.Renviron
+done
+
+ulimit -s 16384
+echo $LOG_FILE
+#sudo chown app:app "$LOG_FILE"
+sudo chown -R $UID:shared "$LOG_DIR"
+sudo chmod -R 775 /var/log/shiny-server
+
+ls -la $LOG_DIR
+
+echo "DEBUG: Writing to ${LOG_FILE}" >> ${LOG_FILE}
+exec >> $LOG_FILE 2>&1
+
+R --quiet -e "shiny::runApp('${APP}', host='0.0.0.0', port=3838)"