Merge branch 'release/1.3.1'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: redcapcustodian
 Type: Package
 Title: System data cleaning for REDCap
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(
   person("Philip", "Chase",
         email = "[email protected]",

NEWS.md

@@ -3,6 +3,11 @@ All notable changes to the redcapcustodian package and its contained scripts wil
 This project adheres to [Semantic Versioning](http://semver.org/).
 
 
+## [1.3.1] - 2022-08-30
+### Added
+- Remove remants of the site concept (Philip Chase)
+
+
 ## [1.3.0] - 2022-08-29
 ### Added
 - Add get_bad_emails_from_individual_emails function (Kyle Chesney)

README.md

@@ -13,7 +13,7 @@ To build upon that foundation, this repository also provides a folder, [`study_t
 
 In such an automated environment, each ETL job in this system is an Rscript run via Docker. Each report is an RMarkdown file again run via Docker. The design assumes the Docker containers are hosted on a Linux host with API access to one or more REDCap systems, a mail server, a MySQL database, and, optionally, the REDCap database itself.
 
-For sites without container infrastructure, each image can be instantiated into a container via a cron job as documented in the files in [`examples/crons/`](examples/crons/). Each file in that folder runs a single job. To run a job, its cron script must be copied to the `/etc/cron.d/` folder on the Linux host. The `build.sh` script builds the containers and optionally deploys the environment files and cron scripts.
+For sites without container infrastructure, each image can be instantiated into a container via a cron job as documented in the files in [`examples/crons/`](examples/crons/). Each file in that folder runs a single job. To run a job, its cron script must be copied to the `/etc/cron.d/` folder on the Linux host. The `build.sh` script builds the redcapcustodian container upon which containers built by the study template would depend.
 
 
 # How to use this project

VERSION

@@ -1 +1 @@
-1.3.0
+1.3.1

build.sh

@@ -1,21 +1,13 @@
 #!/bin/sh
-# build.sh - a script to construct and optionally deploy a redcapcustodian
-#   container
-
-# This script requires a single parameter that names the host for which
-# the container will be built. The parameter can be either full or 
-# relative path to the host folder or the name of the host folder itself.
-# In the latter case, "./site/" will be prepended to the parameter 
-# given in an attempt to locate the host folder
+# build.sh - a script to construct a redcapcustodian Docker image
 
 # Parse options to the `build.sh` command
 while getopts ":hd" opt; do
   case ${opt} in
     h )
       echo "Usage:"
       echo "    build.sh -h                      Display this help message."
-      echo "    build.sh                         Build the redcapcustodian and rcc.site Docker images."
-      echo "    build.sh -d                      Build the images and deploy all configuration files"
+      echo "    build.sh                         Build the redcapcustodian Docker image"
       exit 0
       ;;
     d )
@@ -29,55 +21,6 @@ while getopts ":hd" opt; do
 done
 shift $((OPTIND -1))
 
-sitepath='./site'
-image_name=rcc.site
-
-if [ $deploy ]; then
-  echo Deploying redcapcustodian
-  TARGET_CRON_FOLDER=/etc/cron.d/
-  if [ -d $TARGET_CRON_FOLDER ]; then
-    echo Copying cron files
-    old_pwd=$(pwd)
-    cd $sitepath
-    find . -type d -iname cron -exec ls -d {} \; | \
-    xargs -i find {} -type f | sed "s/.\{2\}//;" | \
-    perl -n -e 'chop(); $src=$_; $target=$_; $target =~ s/\//-/g; $cmd = "cp $src /etc/cron.d/rcc-$target\n"; print $cmd; system($cmd);'
-    ls -ltr /etc/cron.d/rcc-*
-    cd $old_pwd
-  fi
-
-  # Deploy environment files
-  # Specify the target folder for environment files
-  ENV_FILES_FOLDER=/rcc
-  if [ -e $sitepath/.env ]; then
-    . $sitepath/.env
-  fi
-  # make the target folder for env files if it does not exist
-  if [ ! -d $ENV_FILES_FOLDER ]; then 
-    mkdir -p $ENV_FILES_FOLDER
-  fi
-
-  # Copy all of the env files from the site project to the config folder.  
-  if [ -e $sitepath/.env ]; then
-    cp $sitepath/.env $ENV_FILES_FOLDER
-  fi
-
-  # Deploy all env folders
-  old_pwd=$(pwd)
-  cd $sitepath
-  find . -type d -iname "env" | xargs -i mkdir -p ${ENV_FILES_FOLDER}/{} 
-  find . -type d -iname "env" | xargs -i rsync -arcv {}/ ${ENV_FILES_FOLDER}/{} 
-  cd $old_pwd
-
-fi
-
 shared_image=redcapcustodian
 echo "Building $shared_image image"
 docker build -t $shared_image . && docker tag $shared_image:latest $shared_image:`cat VERSION` && docker image ls $shared_image | head -n 5
-
-site_image=rcc.site
-echo "Building site-specific redcapcustodian image $site_image"
-old_pwd=$(pwd)
-cd site
-docker build -t $site_image . && docker tag $site_image:latest $site_image:`cat VERSION` && docker image ls $site_image | head -n 5
-cd $old_pwd