Integrate with hosted-app-utils

Strip down this repo and allow the hosted-app-utils `package` script to
auto-generate the package.

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "hosted-app-utils"]
+	path = hosted-app-utils
+	url = git@gitlab.com:signalytic/client-external/hosted-app-utils.git

README.md

@@ -2,12 +2,23 @@
 
 Packaging and installation tools for Streamline's "Streamline EMR" application.
 
-## Building
+## Setup
-1. ensure you have docker access to this project's container registry on GitLab
+1. login to the gitlab docker registry: `docker login registry.gitlab.com`
-2. run `package.sh` to generate a new application package
+2. update submodules: `git submodule update --init`
-3. package will be stored to `build-packages/`
 
-Several defaults can be overridden with command line options or by setting appropriate environment variables. A help prompt can be accessed using `package.sh -h`. For example, `package.sh -t latest -p linux/arm64` will build only the `linux/arm64` platform and use the `latest` tag instead of the current repo version.
+## Building
+To build, simply run `./package` to generate a new application package.
+
+The `package` script will assign a few variables by default, specifically:
+```
+CONFIG=${CONFIG:-${LOCATION}/config.json}
+COMPOSE=${COMPOSE:-${LOCATION}/docker-compose.yml}
+BUILD_DIR=${BUILD_DIR:-${LOCATION}/build-packages}
+```
+
+If necessary, each of these may be overridden by running with `VAR=VALUE ./package`.
+
+The `hosted-app-utils` project provides additional customization via command line arguments. This can be used to modify the package name, skip packaging of images, build for only one platform and more. For a list of options, run `./package -h`.
 
 ## Installing
 1. extract the generated archive file in a temporary folder on the target system

config.json

@@ -0,0 +1,17 @@
+{
+  "name": "streamline-emr",
+  "org": "streamline",
+  "version": "0.1",
+  "platforms": [
+    "linux/arm64",
+    "linux/amd64"
+  ],
+  "images": {
+    "linux/arm64": {
+      "registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/arm64:latest": "streamline-emr:latest"
+    },
+    "linux/amd64": {
+      "registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/amd64:latest": "streamline-emr:latest"
+    }
+  }
+}

docker-compose.yml

@@ -4,7 +4,7 @@ services:
     image: ${APP_IMAGE:-streamline-emr:latest}
     container_name: ${APP_CONTAINER:-streamline-emr}
     volumes:
-        - "${DATA_DIR:-/var/signalytic/clientapps/streamline/streamline-emr/data}:/var/lib/mysql"
+        - "${DATA_DIR:-./data}:/var/lib/mysql"
     ports:
       - "${APP_PORT:-3000}:80"
     dns: 0.0.0.0

images.csv

@@ -1,2 +0,0 @@
-linux/arm64,streamline-emr,registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/arm64
-linux/amd64,streamline-emr,registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/amd64

install.sh

@@ -1,55 +0,0 @@
-#!/bin/bash
-#
-# Copyright (C) Wendepunkt Medical Innovations, Inc - All Rights Reserved.
-# Unauthorized copying of this file, via any medium is strictly prohibited.
-# Proprietary and confidential
-#
-# For information: dev@signalytic.ca
-#
-
-#
-# Install the Streamline "Streamline EMR" application and services
-#
-# The caller of this script must check the exit value and possibly do a 
-# roll-back if it is non-zero. If the exit value is non-zero services have not
-# been restarted.
-
-LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-
-if [ "$EUID" -ne 0 ]
-  then echo "Please run as root"
-  exit 1
-fi
-
-
-# stop any running systemd service if not running in a docker environment
-if [ -f /.dockerenv ]; then
-  echo "Docker environment detected - skipping systemd installation"
-else
-  echo "stopping system service"
-  systemctl stop streamline-emr
-fi
-
-set -e
-
-# copy root files
-echo "importing root files"
-cp -rfv $LOCATION/root/* /
-
-# import docker images
-for f in $(find $LOCATION/images -name "*.img" 2>/dev/null);do
-  echo "importing docker image: $f"
-  docker load -i $f
-done
-for f in $(find $LOCATION/images -name "*.img.xz" 2>/dev/null);do
-  echo "importing docker image: $f"
-  xz -d -c $f | docker load
-done
-
-# install systemd service unless running in a docker environment
-if [ ! -f /.dockerenv ]; then
-  echo "installing system service"
-  systemctl daemon-reload
-  systemctl enable streamline-emr
-  systemctl start streamline-emr
-fi

package

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+CONFIG=${CONFIG:-${LOCATION}/config.json}
+COMPOSE=${COMPOSE:-${LOCATION}/docker-compose.yml}
+BUILD_DIR=${BUILD_DIR:-${LOCATION}/build-packages}
+
+${LOCATION}/hosted-app-utils/package ${CONFIG} ${COMPOSE} output=${BUILD_DIR} $@

package.sh

@@ -1,206 +0,0 @@
-#!/bin/bash
-
-#
-# Copyright (C) Wendepunkt Medical Innovations, Inc - All Rights Reserved.
-# Unauthorized copying of this file, via any medium is strictly prohibited.
-# Proprietary and confidential
-#
-# For information: dev@signalytic.ca
-#
-
-# basic path info
-LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-PROJECT_ROOT="$(realpath $LOCATION)"
-
-# determine version name from git
-# use ci tag name if available (e.g. "v1.2")
-if [ $CI_COMMIT_TAG ]; then
-  VERSION_NAME="$CI_COMMIT_TAG"
-# otherwise if ci, use BRANCH-COMMIT
-elif [ $CI_COMMIT_BRANCH ]; then
-  VERSION_NAME="$CI_COMMIT_REF_SLUG-$CI_COMMIT_SHORT_SHA"
-# if not ci, try to use git
-elif command -v git &> /dev/null; then
-  VERSION_NAME=$(git describe --always --tags --abbrev=7 --dirty)
-# fallback
-else
-  VERSION_NAME="latest"
-fi
-
-# configurable options (override with env vars as needed)
-PACKAGE_NAME=${PACKAGE_NAME-"streamline-emr"}
-OUTPUT_DIR=${OUTPUT_DIR-"$PROJECT_ROOT/build-packages"}
-PACKAGE_IMAGES=${PACKAGE_IMAGES:-1}
-COMPRESS_IMAGES=${COMPRESS_IMAGES:-1}
-IMAGE_TAG=${IMAGE_TAG:-${VERSION_NAME}}
-IMAGES_LIST=${IMAGES_LIST:-${PROJECT_ROOT}/images.csv}
-
-
-function print_usage {
-  echo "Streamline EMR packaging utility"
-  echo
-  echo "Usage: package.sh [ OPTIONS ]"
-  echo
-  echo "Options:"
-  echo "  -h                 Print this help prompt and exit"
-  echo "  -p PLATFORM        Specify a docker platform to target, may be passed multiple"
-  echo "                     times. If none specified, all platforms built. Supported"
-  echo "                     platforms: 'linux/amd64', 'linux/arm64'"
-  echo "  -t IMAGE_TAG       Specify an image tag. It not specified, the tag will be"
-  echo "                     inferred from the current git version ('${IMAGE_TAG}')"
-  echo "  -n PACKAGE_NAME    Specify the package base name. Default: ${PACKAGE_NAME}"
-  echo "  -o OUTPUT_DIR      Specify a directory to save packages. Default: ${OUTPUT_DIR}"
-  echo "  -l IMAGES_LIST     Specify a file containing a list of images. Default: ${IMAGES_LIST}"
-  echo "  -I                 Do not package images"
-  echo "  -C                 Do not compress images"
-  echo
-}
-
-# collect user args
-PLATFORMS=()
-while getopts ":p:t:n:o:l:ICh" options; do
-  case "${options}" in
-    p)
-      PLATFORMS+=(${OPTARG})
-      ;;
-    t)
-      IMAGE_TAG=${OPTARG}
-      ;;
-    n)
-      PACKAGE_NAME=${OPTARG}
-      ;;
-    o)
-      OUTPUT_DIR=${OPTARG}
-      ;;
-    l)
-      IMAGES_LIST=${OPTARG}
-      ;;
-    I)
-      PACKAGE_IMAGES=0
-      ;;
-    C)
-      COMPRESS_IMAGES=0
-      ;;
-    h)
-      print_usage
-      exit 0
-      ;;
-    *)
-      print_usage
-      exit 1
-      ;;
-  esac
-done
-shift $((OPTIND -1))
-
-# set defaults
-if [ ${#PLATFORMS} -eq 0 ]; then
-  PLATFORMS=("linux/amd64" "linux/arm64")
-fi
-
-echo "packaging $PACKAGE_NAME"
-echo "  output dir: $OUTPUT_DIR"
-echo "  package images: $PACKAGE_IMAGES"
-echo "  compress images: $COMPRESS_IMAGES"
-echo "  image tag: $IMAGE_TAG"
-echo "  image list: $IMAGES_LIST"
-echo "  platforms: ${PLATFORMS[@]}"
-
-# work from the project root
-pushd $PROJECT_ROOT > /dev/null
-
-# Exit on error:
-set -e
-trap 'echo "Error: Last command failed with exit code $?."' ERR
-
-# build for each relevant platform
-for platform in ${PLATFORMS[@]}; do
-  echo "preparing package for platform $platform"
-  if [ "$platform" == "linux/amd64" ];then
-    pkg_arch="x86_64"
-  elif [ "$platform" == "linux/arm64" ];then
-    pkg_arch="aarch64"
-  else
-    echo "unexpected platform '$platform'"
-    exit 1
-  fi
-  OUTPUT_NAME="$PACKAGE_NAME-$VERSION_NAME-${pkg_arch}"
-  OUTPUT_FILE="$OUTPUT_NAME.tar.bz2"
-  OUTPUT_PATH="$OUTPUT_DIR/$OUTPUT_FILE"
-
-  # create a new temp directory to stage files
-  for i in {1..9999};do
-    STAGING_DIR="tmp-staging-$i"
-    if [ ! -d $STAGING_DIR ]; then
-      break
-    fi
-  done
-  if [ -d $STAGING_DIR ]; then
-    echo "Failed to generate temp staging dir"
-    exit 1
-  fi
-
-  # add files
-  PACKAGE_ROOT=${STAGING_DIR}/${OUTPUT_NAME}
-  IMAGES_DIR=${PACKAGE_ROOT}/images
-  mkdir -p ${IMAGES_DIR}
-  cp ${PROJECT_ROOT}/install.sh ${PACKAGE_ROOT}/
-  cp -a ${PROJECT_ROOT}/root ${PACKAGE_ROOT}/
-  echo "${VERSION_NAME}" > ${PACKAGE_ROOT}/root/var/signalytic/clientapps/streamline/streamline-emr/version
-
-  if [ "${PACKAGE_IMAGES}" = 1 ]; then
-    # add images
-    # read image list from file (e.g. 'images-aarch64')
-    # images are listed as SAVED_TAG=SOURCE_IMAGE
-    for image in $(cat ${IMAGES_LIST});do
-      IFS=, read -r img_platform dest source <<< "${image}"
-      # package only if the platforms match
-      if [ "${img_platform}" = "${platform}" ]; then
-        echo "pulling image '${source}' (${platform})"
-        docker pull --platform ${platform} ${source}:${IMAGE_TAG}
-        # re-tag the image with a more generic name
-        echo "tagging image as '${dest}:latest'"
-        docker tag ${source}:${IMAGE_TAG} ${dest}:latest
-        # save the image to file
-        if [ "${COMPRESS_IMAGES}" = 1 ]; then
-          path="${IMAGES_DIR}/${dest}.img.xz"
-          echo "saving to '${path}'"
-          # if installed, use pv to show progress
-          if command -v pv &> /dev/null; then
-            docker save ${dest}:latest | xz -9 - -c | pv -t -r -b -N "saving compressed image..." > ${path}
-          else
-            docker save ${dest}:latest | xz -9 - -c > ${path}
-          fi
-        else
-          path="${IMAGES_DIR}/${dest}.img"
-          echo "saving to '${path}'"
-          # if installed, use pv to show progress
-          if command -v pv &> /dev/null; then
-            docker save ${dest}:latest | pv -t -r -b -N "saving raw image..." > ${path}
-          else
-            docker save -o ${path} ${dest}:latest
-          fi
-        fi
-      fi
-    done
-  else
-    echo "skipping image packaging as requested"
-  fi
-
-  # setup output directory and cleanup old files if necessary
-  mkdir -p $OUTPUT_DIR
-  rm -rf $OUTPUT_PATH
-
-  pushd $STAGING_DIR  > /dev/null
-  tar -cjf $OUTPUT_PATH ${OUTPUT_NAME}
-  popd > /dev/null
-
-  # cleanup staging files
-  rm -r $STAGING_DIR
-
-  echo "output: $OUTPUT_PATH"
-done  
-
-popd > /dev/null
-
-exit 0

root/etc/systemd/system/streamline-emr.service

@@ -1,16 +0,0 @@
-[Unit]
-Description=Run Streamline EMR
-Requires=docker.service
-After=docker.service
-
-[Service]
-Type=oneshot
-RemainAfterExit=yes
-User=root
-WorkingDirectory=/var/signalytic/clientapps/streamline/streamline-emr
-ExecStart=/var/signalytic/clientapps/streamline/streamline-emr/start
-ExecStop=/var/signalytic/clientapps/streamline/streamline-emr/stop
-TimeoutStartSec=0
-
-[Install]
-WantedBy=multi-user.target

root/var/signalytic/clientapps/streamline/streamline-emr/autoheal

@@ -1,40 +0,0 @@
-#!/bin/bash
-
-LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-
-INTERVAL=${INTERVAL:-60}
-
-# track pid with a file `autoheal.pid`. If a previous instance is still running, exit early.
-function cleanup() {
-  rm -f ${LOCATION}/autoheal.pid
-}
-trap cleanup EXIT
-kill -0 $(cat ${LOCATION}/autoheal.pid 2> /dev/null) 2> /dev/null && echo "autoheal script already running" && exit 1
-echo $$ > ${LOCATION}/autoheal.pid
-
-# exit on SIGINT
-trap exit INT
-
-# run at fixed interval, checking for and restarting any service marked as 'unhealthy'
-pushd $LOCATION > /dev/null
-  while [ 1 ]; do
-    # get current state (running or not) and status (healthy, unhealthy, etc)
-    app_state=$(docker compose ps --format '{{.State}}' streamline-emr)
-    app_status=$(docker compose ps --format '{{.Status}}' streamline-emr)
-
-    # check if app is running and healhty
-    if [ "${app_state}" = "running" ]; then
-      if [[ "${app_status}" = *\(unhealthy\) ]]; then
-        echo "Unhealthy service detected. Restarting 'streamline-emr'"
-        docker compose restart streamline-emr
-      fi
-    # app should be running - restart
-    else
-      echo "Container not running. Starting 'streamline-emr'"
-      docker compose up -d streamline-emr
-    fi
-
-    # wait a little while before checking again
-    sleep $INTERVAL
-  done
-popd > /dev/null

root/var/signalytic/clientapps/streamline/streamline-emr/monitor

@@ -1,43 +0,0 @@
-#!/bin/bash
-
-LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-
-SYSTEMLOG=${SYSTEMLOG:-1}
-if ! command -v bgsystemlog &> /dev/null; then
-  SYSTEMLOG=0
-fi
-
-# get container info
-APP_CONTAINER=${APP_CONTAINER:-streamline-emr}
-if grep -q "^APP_CONTAINER=" ${LOCATION}/.env > /dev/null 2>&1; then
-  APP_CONTAINER=$(sed -n 's/APP_CONTAINER=//p' ${LOCATION}/.env)
-fi
-
-pushd $LOCATION > /dev/null
-  # get process status for each service
-  echo "checking streamline-emr service status"
-  for service in $(docker compose ps --services); do
-    status=$(docker compose ps --format '{"name":"{{.Names}}","created":"{{.CreatedAt}}","elapsed":"{{.RunningFor}}","state":"{{.State}}","status":"{{.Status}}"}' ${service})
-    if [ "${status}" ]; then
-      echo $status
-      if [ "$SYSTEMLOG" -eq 1 ]; then
-        bgsystemlog -j streamline_emr_status -m ${status}
-      fi
-    else
-      echo "no status results found for service ${service}"
-    fi
-  done
-  # get resource usage
-  echo "checking streamline-emr resource usage"
-  status=$(docker stats --no-stream --format '{"name":"{{.Name}}","cpu_p":"{{.CPUPerc}}","mem_p":"{{.MemPerc}}","mem_u":"{{.MemUsage}}","net_io":"{{.NetIO}}","block_io":"{{.BlockIO}}"}' ${APP_CONTAINER})
-  if [ "${status}" ]; then
-    echo $status
-    if [ "$SYSTEMLOG" -eq 1 ]; then
-      bgsystemlog -j streamline_emr_usage -m ${status}
-    fi
-  else
-    echo "no usage results found for container ${APP_CONTAINER}"
-  fi
-popd > /dev/null
-
-echo "done."

root/var/signalytic/clientapps/streamline/streamline-emr/start

@@ -1,25 +0,0 @@
-#!/bin/bash
-
-LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-
-VERSION_FILE=${LOCATION}/version
-version=$(head -n 1 ${VERSION_FILE} 2>/dev/null)
-if [ $? -ne 0 ];then
-  version="unknown version"
-fi
-echo "Starting Streamline EMR: $version"
-
-# work from the install root
-pushd $LOCATION > /dev/null
-  # make sure we're always working from a clean state
-  ./stop
-
-  # start the application
-  echo "starting services"
-  docker compose up -d
-
-  # start autoheal to restart unhealthy containers
-  ./autoheal &
-popd > /dev/null
-
-echo "done."

root/var/signalytic/clientapps/streamline/streamline-emr/stop

@@ -1,12 +0,0 @@
-#!/bin/bash
-
-LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-
-echo "stopping streamline emr"
-pushd $LOCATION > /dev/null
-  if [ -f autoheal.pid ];then
-    kill $(cat autoheal.pid)
-  fi
-  docker compose down
-popd > /dev/null
-echo "done."

root/var/signalytic/clientapps/streamline/streamline-emr/template.app.conf

@@ -1,28 +0,0 @@
-{
-  "name": "Streamline EMR",
-  "dbsync": {
-    "database": {
-      "type": "mysql",
-      "version": "8.0.23",
-      "name": "main",
-      "username": "",
-      "password": "",
-      "db_path": "/var/lib/mysql",
-      "logs_path": "/var/lib/mysql/logs",
-      "log_pattern": "binlog.[0-9]*"
-    },
-    "blockgraph": {
-      "district": "",
-      "name": "",
-      "username": "",
-      "password": ""
-    },
-    "instances": {
-      "streamline-emr": {
-        "source": "streamline-emr",
-        "node": "",
-        "location": "_default"
-      }
-    }
-  }
-}

root/var/signalytic/clientapps/streamline/streamline-emr/template.env

@@ -1,5 +0,0 @@
-COMPOSE_PROJECT_NAME=streamline-emr
-DATA_DIR=/var/signalytic/clientapps/streamline/streamline-emr/data
-APP_IMAGE=streamline-emr:latest
-APP_CONTAINER=streamline-emr
-APP_PORT=3000