Minimize requirements for modelServr

Ensure we can install dependencies as part of modelServR install
Optimize the worker docker image to minimal size required

Dockerfile.worker

@@ -1,4 +1,4 @@
-FROM rocker/r-base:3.5.3
+FROM rocker/r-base
 LABEL description="Environment to execut model queries against"
 LABEL authors="ccollins@idmod.org"
 
@@ -6,31 +6,26 @@ LABEL authors="ccollins@idmod.org"
 ENV DEBIAN_FRONTEND=noninteractive
 ENV DEBCONF_NONINTERACTIVE_SEEN=true
 
-
-# install packages required and then cleanup
 RUN apt-get update && apt-get install -y \
     # required by devtools and ggmap
-    libssl-dev libcurl4-gnutls-dev \
-    # required by sf
-    libudunits2-dev libgdal-dev \
-    # required by INLA or a dependency of INLA
-    libxml2-dev libx11-dev texlive-binaries libglu1-mesa-dev libfreetype6-dev \
-    # required by geojsonio or a dependency of geojsonio
-    libgdal-dev libgeos-c1v5 libproj-dev libv8-dev libjq-dev libprotobuf-dev protobuf-compiler \
-    # Git for development tools
-    git-core git libgit2-dev && \
-    # cleanup apt cache to reduce final image size
-    rm -rf /var/lib/apt/lists/*
-
+    libssl-dev libcurl4-gnutls-dev
 
 # Set default make to parallel build
 ENV MAKE="make -j8"
+RUN Rscript -e "install.packages(c('devtools'))" \
+    && rm -rf /tmp/*
+ARG MODEL_SERVR_VERSION=0.0.0.9000
+RUn mkdir -p /worker
 # ADD our model file
-ADD modelServR.tar.gz /tmp
-RUN Rscript -e "install.packages("/tmp/modelServR.tar.gz", repos = NULL, type="source")"
+COPY modelServR/modelServR_${MODEL_SERVR_VERSION}.tar.gz /worker/modelServR.tar.gz
+WORKDIR /worker
+RUN cd /worker && \
+    Rscript -e 'untar("modelServR.tar.gz", exdir="/tmp")' && \
+    Rscript -e 'devtools::install("/tmp/modelServR", dependencies=TRUE)' && \
+    rm -rf /tmp/* /worker/*.tar.gz
 
 # Our Organization(as others do) map Active Directory to LDAP for linux
-# These means when mapping in our userids
+# These means when mapping in our us
 # docker -e USERID=$UID....
 # which remaps the rstudio UID,
 # the user ids can be large. To suppor that we need to update login.defs

Makefile

@@ -1,4 +1,4 @@
-BUILD_CONTAINER_NAME ?= idm-docker-staging.packages.idmod.org/sfim_build_env:latest
+BUILD_CONTAINER_NAME ?= idm-docker-staging.packages.idmod.org/sfim-build-env:latest
 DEPLOY_SERVER ?= 40.112.165.255
 DEPOLY_USERNAME ?= useradmin
 
@@ -22,8 +22,11 @@ build-r-package: pull-r-env ## Build the r package as tar ball
 	# We have to run this with the build user's ids
 	# otherwise we end up with files we cannot modify
 	docker run -u $(shell id -u):$(shell id -g) \
-		-v $(PWD)/predictModelTestPkg:/app -w /app $(BUILD_CONTAINER_NAME) \
-		R CMD build .
+		-v $(PWD)/:/app \
+		-w /app $(BUILD_CONTAINER_NAME) \
+		bash -c "cd dbViewR && R CMD build . && \
+				cd ../incidenceMapR && R CMD build . && \
+				cd ../modelServR && R CMD build ."
 
 build-api: build-r-package get_version ## Builds the api
 	-mkdir -p api_service/models

docker-compose.production.yml

@@ -16,7 +16,7 @@ services:
       build:
         context: api_service
         dockerfile: Dockerfile
-      image: idm-docker-production.packages.idmod.org/sfim:${version:-latest}
+      image: idm-docker-production.packages.idmod.org/sfim-api:${version:-latest}
       volumes:
       - "/model_store:/model_store"
       environment:

modelServR/DESCRIPTION

@@ -11,3 +11,7 @@ License: What license it uses
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
+Imports:
+    digest,
+    jsonlite,
+    logging

modelServR/NAMESPACE

@@ -2,11 +2,5 @@
 
 export(returnModel)
 export(saveModel)
-import(dbViewR)
 import(digest)
-import(jsonlite)
-import(magrittr)
-importFrom(RCurl,getURL)
-importFrom(dplyr,group_by_at)
-importFrom(jsonlite,toJSON)
-importFrom(tidyr,nest)
+import(jsonlite)