Improve docker build speed and caching

.env.sample

@@ -11,6 +11,7 @@ PREPROCESS_DB_USERNAME=             # username for the source database
 PREPROCESS_DB_PASSWORD=             # password for the source database
 PREPROCESS_DB_CDM_SCHEMA=           # Schema name in the database to connect the OMOP CDM to
 PREPROCESS_SUMMARISE_LEVEL=monthly  # Level to summarise record counts at (monthly or quarterly)
+PREPROCESS_BUILD_CORES=4            # Number of cores to use for make in docker build
 
 # Low-frequency replacement
 LOW_FREQUENCY_THRESHOLD=5

app/Dockerfile

@@ -13,7 +13,7 @@ RUN install2.r --error --skipinstalled renv remotes && \
 RUN R -e 'remotes::install_github("SAFEHR-data/omop-bundles")'
 
 # Install the app
-RUN R -e 'remotes::install_local(".", dependencies = TRUE)'
+RUN R -e 'devtools::install(".", dependencies = TRUE)'
 
 EXPOSE 3838
 CMD ["R", "-e", "options('shiny.port'=3838, shiny.host='0.0.0.0'); omopcat::run_app()" ]

docker-compose.yml

@@ -7,6 +7,7 @@ services:
         # Required for running on GAE
         HTTP_PROXY: ${HTTP_PROXY}
         HTTPS_PROXY: ${HTTPS_PROXY}
+        CORES: ${PREPROCESS_BUILD_CORES}
     image: omopcat_preprocessing:latest
     platform: linux/amd64
     environment:

preprocessing/Dockerfile

@@ -1,13 +1,18 @@
 FROM rocker/tidyverse:4.4.1
 
 WORKDIR /pkg
-ADD preprocessing .
 COPY preprocessing/renv.lock ./renv.lock
 
+# Speed up building by setting make with multiple cores from env
+ARG CORES
+ENV MAKE="make -j${CORES}"
+
 RUN install2.r --error --skipinstalled renv remotes && \
     R -e 'renv::restore()' && \
     rm -rf /tmp/downloaded_packages
 
+ADD preprocessing .
+
 RUN R -e 'remotes::install_local(path = ".", dependencies = TRUE)'
 
 CMD ["R", "-e", "omopcat.preprocessing::preprocess()"]

public.env.sample

@@ -11,7 +11,7 @@ PREPROCESS_DB_USERNAME=             # username for the source database
 PREPROCESS_DB_PASSWORD=             # password for the source database
 PREPROCESS_DB_CDM_SCHEMA=           # Schema name in the database to connect the OMOP CDM to
 PREPROCESS_SUMMARISE_LEVEL=quarterly  # Level to summarise record counts at (monthly or quarterly)
-
+PREPROCESS_BUILD_CORES=4            # Number of cores to use for make in docker build
 # Low-frequency replacement
 LOW_FREQUENCY_THRESHOLD=10
 LOW_FREQUENCY_REPLACEMENT=5