mirror of
https://gitlab.com/signalytic/client-external/streamline/streamline-emr.git
synced 2026-09-11 10:41:32 +00:00
Integrate with hosted-app-utils
Strip down this repo and allow the hosted-app-utils `package` script to auto-generate the package.
This commit is contained in:
@@ -0,0 +1,3 @@
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[submodule "hosted-app-utils"]
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path = hosted-app-utils
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url = git@gitlab.com:signalytic/client-external/hosted-app-utils.git
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@@ -2,12 +2,23 @@
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Packaging and installation tools for Streamline's "Streamline EMR" application.
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## Building
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1. ensure you have docker access to this project's container registry on GitLab
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2. run `package.sh` to generate a new application package
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3. package will be stored to `build-packages/`
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## Setup
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1. login to the gitlab docker registry: `docker login registry.gitlab.com`
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2. update submodules: `git submodule update --init`
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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.
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## Building
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To build, simply run `./package` to generate a new application package.
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The `package` script will assign a few variables by default, specifically:
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```
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CONFIG=${CONFIG:-${LOCATION}/config.json}
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COMPOSE=${COMPOSE:-${LOCATION}/docker-compose.yml}
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BUILD_DIR=${BUILD_DIR:-${LOCATION}/build-packages}
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```
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If necessary, each of these may be overridden by running with `VAR=VALUE ./package`.
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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`.
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## Installing
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1. extract the generated archive file in a temporary folder on the target system
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+17
@@ -0,0 +1,17 @@
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{
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"name": "streamline-emr",
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"org": "streamline",
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"version": "0.1",
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"platforms": [
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"linux/arm64",
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"linux/amd64"
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],
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"images": {
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"linux/arm64": {
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"registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/arm64:latest": "streamline-emr:latest"
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},
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"linux/amd64": {
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"registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/amd64:latest": "streamline-emr:latest"
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}
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}
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}
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+1
-1
@@ -4,7 +4,7 @@ services:
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image: ${APP_IMAGE:-streamline-emr:latest}
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container_name: ${APP_CONTAINER:-streamline-emr}
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volumes:
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- "${DATA_DIR:-/var/signalytic/clientapps/streamline/streamline-emr/data}:/var/lib/mysql"
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- "${DATA_DIR:-./data}:/var/lib/mysql"
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ports:
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- "${APP_PORT:-3000}:80"
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dns: 0.0.0.0
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Submodule
+1
Submodule hosted-app-utils added at 6f1a9493c1
@@ -1,2 +0,0 @@
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linux/arm64,streamline-emr,registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/arm64
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linux/amd64,streamline-emr,registry.gitlab.com/signalytic/client-external/streamline/streamline-emr/streamline-emr/amd64
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|
-55
@@ -1,55 +0,0 @@
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#!/bin/bash
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#
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# Copyright (C) Wendepunkt Medical Innovations, Inc - All Rights Reserved.
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# Unauthorized copying of this file, via any medium is strictly prohibited.
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# Proprietary and confidential
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#
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# For information: dev@signalytic.ca
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#
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#
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# Install the Streamline "Streamline EMR" application and services
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#
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# The caller of this script must check the exit value and possibly do a
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# roll-back if it is non-zero. If the exit value is non-zero services have not
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# been restarted.
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LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
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if [ "$EUID" -ne 0 ]
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then echo "Please run as root"
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exit 1
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fi
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# stop any running systemd service if not running in a docker environment
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if [ -f /.dockerenv ]; then
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echo "Docker environment detected - skipping systemd installation"
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else
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echo "stopping system service"
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systemctl stop streamline-emr
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fi
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set -e
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# copy root files
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echo "importing root files"
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cp -rfv $LOCATION/root/* /
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# import docker images
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for f in $(find $LOCATION/images -name "*.img" 2>/dev/null);do
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echo "importing docker image: $f"
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docker load -i $f
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done
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for f in $(find $LOCATION/images -name "*.img.xz" 2>/dev/null);do
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echo "importing docker image: $f"
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xz -d -c $f | docker load
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done
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# install systemd service unless running in a docker environment
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if [ ! -f /.dockerenv ]; then
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echo "installing system service"
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systemctl daemon-reload
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systemctl enable streamline-emr
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systemctl start streamline-emr
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fi
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@@ -0,0 +1,9 @@
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#!/bin/bash
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LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
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CONFIG=${CONFIG:-${LOCATION}/config.json}
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COMPOSE=${COMPOSE:-${LOCATION}/docker-compose.yml}
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BUILD_DIR=${BUILD_DIR:-${LOCATION}/build-packages}
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${LOCATION}/hosted-app-utils/package ${CONFIG} ${COMPOSE} output=${BUILD_DIR} $@
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-206
@@ -1,206 +0,0 @@
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#!/bin/bash
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#
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# Copyright (C) Wendepunkt Medical Innovations, Inc - All Rights Reserved.
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# Unauthorized copying of this file, via any medium is strictly prohibited.
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# Proprietary and confidential
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#
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# For information: dev@signalytic.ca
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#
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# basic path info
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LOCATION="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
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PROJECT_ROOT="$(realpath $LOCATION)"
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# determine version name from git
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# use ci tag name if available (e.g. "v1.2")
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if [ $CI_COMMIT_TAG ]; then
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VERSION_NAME="$CI_COMMIT_TAG"
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# otherwise if ci, use BRANCH-COMMIT
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elif [ $CI_COMMIT_BRANCH ]; then
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VERSION_NAME="$CI_COMMIT_REF_SLUG-$CI_COMMIT_SHORT_SHA"
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# if not ci, try to use git
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elif command -v git &> /dev/null; then
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VERSION_NAME=$(git describe --always --tags --abbrev=7 --dirty)
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# fallback
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else
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VERSION_NAME="latest"
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fi
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# configurable options (override with env vars as needed)
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PACKAGE_NAME=${PACKAGE_NAME-"streamline-emr"}
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OUTPUT_DIR=${OUTPUT_DIR-"$PROJECT_ROOT/build-packages"}
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PACKAGE_IMAGES=${PACKAGE_IMAGES:-1}
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COMPRESS_IMAGES=${COMPRESS_IMAGES:-1}
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IMAGE_TAG=${IMAGE_TAG:-${VERSION_NAME}}
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IMAGES_LIST=${IMAGES_LIST:-${PROJECT_ROOT}/images.csv}
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function print_usage {
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echo "Streamline EMR packaging utility"
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echo
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echo "Usage: package.sh [ OPTIONS ]"
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echo
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echo "Options:"
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echo " -h Print this help prompt and exit"
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echo " -p PLATFORM Specify a docker platform to target, may be passed multiple"
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echo " times. If none specified, all platforms built. Supported"
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echo " platforms: 'linux/amd64', 'linux/arm64'"
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echo " -t IMAGE_TAG Specify an image tag. It not specified, the tag will be"
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echo " inferred from the current git version ('${IMAGE_TAG}')"
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echo " -n PACKAGE_NAME Specify the package base name. Default: ${PACKAGE_NAME}"
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echo " -o OUTPUT_DIR Specify a directory to save packages. Default: ${OUTPUT_DIR}"
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echo " -l IMAGES_LIST Specify a file containing a list of images. Default: ${IMAGES_LIST}"
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echo " -I Do not package images"
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echo " -C Do not compress images"
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echo
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}
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# collect user args
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PLATFORMS=()
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while getopts ":p:t:n:o:l:ICh" options; do
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case "${options}" in
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p)
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PLATFORMS+=(${OPTARG})
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;;
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t)
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IMAGE_TAG=${OPTARG}
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;;
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n)
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PACKAGE_NAME=${OPTARG}
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;;
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o)
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OUTPUT_DIR=${OPTARG}
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;;
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l)
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IMAGES_LIST=${OPTARG}
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;;
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I)
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PACKAGE_IMAGES=0
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;;
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C)
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COMPRESS_IMAGES=0
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;;
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h)
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print_usage
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exit 0
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;;
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*)
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print_usage
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exit 1
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;;
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esac
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done
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shift $((OPTIND -1))
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# set defaults
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if [ ${#PLATFORMS} -eq 0 ]; then
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PLATFORMS=("linux/amd64" "linux/arm64")
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fi
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echo "packaging $PACKAGE_NAME"
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echo " output dir: $OUTPUT_DIR"
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echo " package images: $PACKAGE_IMAGES"
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echo " compress images: $COMPRESS_IMAGES"
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echo " image tag: $IMAGE_TAG"
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echo " image list: $IMAGES_LIST"
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echo " platforms: ${PLATFORMS[@]}"
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# work from the project root
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pushd $PROJECT_ROOT > /dev/null
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# Exit on error:
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set -e
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trap 'echo "Error: Last command failed with exit code $?."' ERR
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# build for each relevant platform
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for platform in ${PLATFORMS[@]}; do
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echo "preparing package for platform $platform"
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if [ "$platform" == "linux/amd64" ];then
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pkg_arch="x86_64"
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elif [ "$platform" == "linux/arm64" ];then
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pkg_arch="aarch64"
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else
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echo "unexpected platform '$platform'"
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exit 1
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fi
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OUTPUT_NAME="$PACKAGE_NAME-$VERSION_NAME-${pkg_arch}"
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OUTPUT_FILE="$OUTPUT_NAME.tar.bz2"
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OUTPUT_PATH="$OUTPUT_DIR/$OUTPUT_FILE"
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# create a new temp directory to stage files
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for i in {1..9999};do
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STAGING_DIR="tmp-staging-$i"
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if [ ! -d $STAGING_DIR ]; then
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break
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fi
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done
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if [ -d $STAGING_DIR ]; then
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echo "Failed to generate temp staging dir"
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exit 1
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fi
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# add files
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PACKAGE_ROOT=${STAGING_DIR}/${OUTPUT_NAME}
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IMAGES_DIR=${PACKAGE_ROOT}/images
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mkdir -p ${IMAGES_DIR}
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cp ${PROJECT_ROOT}/install.sh ${PACKAGE_ROOT}/
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cp -a ${PROJECT_ROOT}/root ${PACKAGE_ROOT}/
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echo "${VERSION_NAME}" > ${PACKAGE_ROOT}/root/var/signalytic/clientapps/streamline/streamline-emr/version
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if [ "${PACKAGE_IMAGES}" = 1 ]; then
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# add images
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# read image list from file (e.g. 'images-aarch64')
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# images are listed as SAVED_TAG=SOURCE_IMAGE
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for image in $(cat ${IMAGES_LIST});do
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IFS=, read -r img_platform dest source <<< "${image}"
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# package only if the platforms match
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if [ "${img_platform}" = "${platform}" ]; then
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echo "pulling image '${source}' (${platform})"
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docker pull --platform ${platform} ${source}:${IMAGE_TAG}
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# re-tag the image with a more generic name
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echo "tagging image as '${dest}:latest'"
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docker tag ${source}:${IMAGE_TAG} ${dest}:latest
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# save the image to file
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if [ "${COMPRESS_IMAGES}" = 1 ]; then
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path="${IMAGES_DIR}/${dest}.img.xz"
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||||
echo "saving to '${path}'"
|
||||
# if installed, use pv to show progress
|
||||
if command -v pv &> /dev/null; then
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docker save ${dest}:latest | xz -9 - -c | pv -t -r -b -N "saving compressed image..." > ${path}
|
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else
|
||||
docker save ${dest}:latest | xz -9 - -c > ${path}
|
||||
fi
|
||||
else
|
||||
path="${IMAGES_DIR}/${dest}.img"
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||||
echo "saving to '${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: $OUTPUT_PATH"
|
||||
done
|
||||
|
||||
popd > /dev/null
|
||||
|
||||
exit 0
|
||||
@@ -1,16 +0,0 @@
|
||||
[Unit]
|
||||
Description=Run Streamline EMR
|
||||
Requires=docker.service
|
||||
After=docker.service
|
||||
|
||||
[Service]
|
||||
Type=oneshot
|
||||
RemainAfterExit=yes
|
||||
User=root
|
||||
WorkingDirectory=/var/signalytic/clientapps/streamline/streamline-emr
|
||||
ExecStart=/var/signalytic/clientapps/streamline/streamline-emr/start
|
||||
ExecStop=/var/signalytic/clientapps/streamline/streamline-emr/stop
|
||||
TimeoutStartSec=0
|
||||
|
||||
[Install]
|
||||
WantedBy=multi-user.target
|
||||
@@ -1,40 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
LOCATION="$( 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 $INTERVAL
|
||||
done
|
||||
popd > /dev/null
|
||||
@@ -1,43 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
LOCATION="$( 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 ${APP_CONTAINER}"
|
||||
fi
|
||||
popd > /dev/null
|
||||
|
||||
echo "done."
|
||||
@@ -1,25 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
LOCATION="$( 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 $LOCATION > /dev/null
|
||||
# make sure we're always working from a clean state
|
||||
./stop
|
||||
|
||||
# start the application
|
||||
echo "starting services"
|
||||
docker compose up -d
|
||||
|
||||
# start autoheal to restart unhealthy containers
|
||||
./autoheal &
|
||||
popd > /dev/null
|
||||
|
||||
echo "done."
|
||||
@@ -1,12 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
LOCATION="$( 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."
|
||||
@@ -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"
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -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
|
||||
Reference in New Issue
Block a user