Update dockerfile for r4.4.1 with strategus library

- update dockerfile to base 4.4.1
- update docker for StrategusStudyRepoTemplate library

Author: Pongjirapat-N

Dockerfile

@@ -1,32 +1,32 @@
 # syntax=docker/dockerfile:1
-FROM rocker/rstudio:4.2.1
+FROM rocker/rstudio:4.4.1
 MAINTAINER Lee Evans <evans@ohdsi.org>
 
 # install OS dependencies including java and python 3
-RUN apt-get update && apt-get install -y openjdk-11-jdk liblzma-dev libbz2-dev libncurses5-dev curl python3-dev python3.venv \
+RUN apt-get update && apt-get install -y openjdk-11-jdk liblzma-dev libbz2-dev libncurses5-dev curl python3-dev python3.venv python3-pip cmake libfontconfig-dev libsodium-dev libxml2-dev\
 && R CMD javareconf \
 && rm -rf /var/lib/apt/lists/*
 
-# install utility R packages
-RUN install2.r \
-	openssl \
-	httr \
-	xml2 \
-	remotes \
-&& rm -rf /tmp/download_packages/ /tmp/*.rds
+COPY strategus_template/renv.lock /home/rstudio/renv.lock
+
+WORKDIR /home/rstudio/
 
 # install OHDSI HADES R packages from CRAN and GitHub, temporarily adding a GitHub Personal Access Token (PAT) to the Renviron file
-RUN --mount=type=secret,id=build_github_pat \
+RUN --mount=type=secret,id=github_build_pat \
 	cp /usr/local/lib/R/etc/Renviron /tmp/Renviron \
-        && echo "GITHUB_PAT=$(cat /run/secrets/build_github_pat)" >> /usr/local/lib/R/etc/Renviron \
-        && R -e "remotes::install_github(repo = 'OHDSI/Hades', upgrade = 'always')" \
-        && cp /tmp/Renviron /usr/local/lib/R/etc/Renviron
+        && echo "GITHUB_PAT=$(cat /run/secrets/github_build_pat)" >> /usr/local/lib/R/etc/Renviron \
+        && R -e "install.packages('renv')" \
+		&& R -e "renv::install('curl@5.2.3')" \
+        && R -e "renv::restore(clean = FALSE, prompt = FALSE)" \
+		&& R -e "renv::install('OHDSI/Eunomia')" \
+        && cp /tmp/Renviron /usr/local/lib/R/etc/Renviron \
+		&& rm -rf /tmp/download_packages/ /tmp/*.rds 
 
 # install useful R libraries to help RStudio users to create/use their own GitHub Personal Access Token
 RUN install2.r \
         usethis \
         gitcreds \
-&& rm -rf /tmp/download_packages/ /tmp/*.rds
+&& rm -rf /tmp/download_packages/ /tmp/*.rds /home/rstudio/renv.lock
 
 # create Python virtual environment used by the OHDSI PatientLevelPrediction R package
 ENV WORKON_HOME="/opt/.virtualenvs"
@@ -51,7 +51,8 @@ RUN install2.r \
 
 # install the jdbc drivers for database access using the OHDSI DatabaseConnector R package
 ENV DATABASECONNECTOR_JAR_FOLDER="/opt/hades/jdbc_drivers"
-RUN R -e "DatabaseConnector::downloadJdbcDrivers('all');"
+RUN mkdir /opt/hades/ \ 
+	&& R -e "DatabaseConnector::downloadJdbcDrivers('all');"
 
 # Install Rserve server and client
 RUN install2.r \
@@ -70,6 +71,17 @@ EXPOSE 6311
 # install supervisor process controller
 RUN apt-get update && apt-get install -y supervisor
 
+COPY strategus_template/StrategusStudyRepoTemplate-main.zip /tmp/StrategusStudyRepoTemplate-main.zip
+
+RUN echo "RENV_PATHS_CACHE=/root/.cache/R/renv/cache" >> /usr/local/lib/R/etc/Renviron.site \
+		&& unzip -o -d /home/ /tmp/StrategusStudyRepoTemplate-main.zip \
+		&& chmod -R a+rwx /home/StrategusStudyRepoTemplate-main \
+		&& chmod -R a+rwx /home/StrategusStudyRepoTemplate-main/StrategusStudyRepoTemplate.Rproj \
+		&& rm -r /home/StrategusStudyRepoTemplate-main/renv \
+		&& chmod a+rwx /root/ \
+		&& chmod -R a+rwx /root/.cache/R/renv/cache \
+		&& rm /tmp/StrategusStudyRepoTemplate-main.zip 
+		
 # start Rserve & RStudio using supervisor
 RUN echo "" >> /etc/supervisor/conf.d/supervisord.conf \
 	&& echo "[supervisord]" >> /etc/supervisor/conf.d/supervisord.conf \
@@ -82,6 +94,8 @@ RUN echo "" >> /etc/supervisor/conf.d/supervisord.conf \
 	&& echo "command=/init" >> /etc/supervisor/conf.d/supervisord.conf \
 	&& echo "" >> /etc/supervisor/conf.d/supervisord.conf \
 	&& echo "stdout_logfile=/var/log/supervisor/%(program_name)s.log" >> /etc/supervisor/conf.d/supervisord.conf \
-	&& echo "stderr_logfile=/var/log/supervisor/%(program_name)s.log" >> /etc/supervisor/conf.d/supervisord.conf
+	&& echo "stderr_logfile=/var/log/supervisor/%(program_name)s.log" >> /etc/supervisor/conf.d/supervisord.conf 
+
+WORKDIR /
 
 CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.conf"]