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Commit 3a54bff5 authored by romuald dubourg's avatar romuald dubourg
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target/
!.mvn/wrapper/maven-wrapper.jar
!**/src/main/**/target/
!**/src/test/**/target/
### IntelliJ IDEA ###
.idea/modules.xml
.idea/jarRepositories.xml
.idea/compiler.xml
.idea/libraries/
*.iws
*.iml
*.ipr
### Eclipse ###
.apt_generated
.classpath
.factorypath
.project
.settings
.springBeans
.sts4-cache
### NetBeans ###
/nbproject/private/
/nbbuild/
/dist/
/nbdist/
/.nb-gradle/
build/
!**/src/main/**/build/
!**/src/test/**/build/
### VS Code ###
.vscode/
### Mac OS ###
.DS_Store
\ No newline at end of file
# Define templates
include:
- project: ${GITLAB_CI_TEMPLATES_PATH}
file: ${GITLAB_CI_TEMPLATES_FILE}
ref: '1.0.3'
# Define stages
stages:
- build
- predeploy
- deploy
- test
- publish
- release
- upgrade
- clean
# Define global variables
variables:
P_NAME: "pdqm-fhir-simulators"
P_APP_TYPE: "java"
P_CODE_SRC_PATH: "."
P_MAVEN_IMAGE_TAG: "3.8.1-openjdk-17-slim"
SERVICE_PATH: "${CI_PROJECT_NAME}-service"
# Define jobs
compile/unit-test:
stage: build
extends:
- .buildJavaMavenTest
package:
stage: build
extends:
- .buildJavaMavenPackage
needs:
- job: compile/unit-test
artifacts: true
static-analysis:
stage: test
extends:
- .testJavaMavenSonarAnalysis
needs:
- job: compile/unit-test
artifacts: true
install-cache-repo:
stage: publish
extends:
- .publishJavaMavenInstall
needs:
- job: package
artifacts: true
release/code:
stage: release
extends:
- .releaseCodeForQuarkus
# MHD FHIR simulators # mhd-fhir-simulator
This project is composed of two subprojects:
- mhd-fhir-server-simulator
- mhd-fhir-client-simulator
## mhd-fhir-server-simulator
This project uses Quarkus, the Supersonic Subatomic Java Framework.
MHD manage two kinds of resources : `Document` and `DocumentReference.
This project handles two kinds of requests:
## Getting started - `GET /Document/{id}` : Get a document by id.
- `GET/POST /Document?` : Search for patients.
To make it easy for you to get started with GitLab, here's a list of recommended next steps. THe app has one servlet:
- `CH` : The CH servlet is used to simulate the CH FHIR server.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Add your files ## mhd-fhir-client-simulator
To be defined.
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files \ No newline at end of file
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
```
cd existing_repo
git remote add origin https://gitlab.inria.fr/gazelle/public/simulation/mhd-fhir-simulators.git
git branch -M main
git push -uf origin main
```
## Integrate with your tools
- [ ] [Set up project integrations](https://gitlab.inria.fr/gazelle/public/simulation/mhd-fhir-simulators/-/settings/integrations)
## Collaborate with your team
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
## Test and Deploy
Use the built-in continuous integration in GitLab.
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
Choose a self-explaining name for your project.
## Description
Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
## Badges
On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
## Visuals
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
## Installation
Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
## Usage
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
## Authors and acknowledgment
Show your appreciation to those who have contributed to the project.
## License
For open source projects, say how it is licensed.
## Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
target/
!.mvn/wrapper/maven-wrapper.jar
!**/src/main/**/target/
!**/src/test/**/target/
### IntelliJ IDEA ###
.idea/modules.xml
.idea/jarRepositories.xml
.idea/compiler.xml
.idea/libraries/
*.iws
*.iml
*.ipr
### Eclipse ###
.apt_generated
.classpath
.factorypath
.project
.settings
.springBeans
.sts4-cache
### NetBeans ###
/nbproject/private/
/nbbuild/
/dist/
/nbdist/
/.nb-gradle/
build/
!**/src/main/**/build/
!**/src/test/**/build/
### VS Code ###
.vscode/
### Mac OS ###
.DS_Store
\ No newline at end of file
# pdqm-fhir-server-simulator
This project uses Quarkus, the Supersonic Subatomic Java Framework.
If you want to learn more about Quarkus, please visit its website: https://quarkus.io/ .
## Running the application in dev mode
You can run your application in dev mode that enables live coding using:
```shell script
./mvnw compile quarkus:dev
```
> **_NOTE:_** Quarkus now ships with a Dev UI, which is available in dev mode only at http://localhost:8080/q/dev/.
## Packaging and running the application
The application can be packaged using:
```shell script
./mvnw package
```
It produces the `quarkus-run.jar` file in the `target/quarkus-app/` directory.
Be aware that it’s not an _über-jar_ as the dependencies are copied into the `target/quarkus-app/lib/` directory.
The application is now runnable using `java -jar target/quarkus-app/quarkus-run.jar`.
If you want to build an _über-jar_, execute the following command:
```shell script
./mvnw package -Dquarkus.package.type=uber-jar
```
The application, packaged as an _über-jar_, is now runnable using `java -jar target/*-runner.jar`.
## Creating a native executable
You can create a native executable using:
```shell script
./mvnw package -Dnative
```
Or, if you don't have GraalVM installed, you can run the native executable build in a container using:
```shell script
./mvnw package -Dnative -Dquarkus.native.container-build=true
```
You can then execute your native executable with: `./target/pdqm-fhir-server-simulator-1.0.0-SNAPSHOT-runner`
If you want to learn more about building native executables, please consult https://quarkus.io/guides/maven-tooling.
## Provided Code
### RESTEasy Reactive
Easily start your Reactive RESTful Web Services
[Related guide section...](https://quarkus.io/guides/getting-started-reactive#reactive-jax-rs-resources)
## Building the Docker image
```shell script
cd pdqm-fhir-server-simulator
docker build -f src/main/docker/Dockerfile.jvm -t rg.fr-par.scw.cloud/gazelle-snapshot/app/pdqm-fhir-simulators:1.0.0-SNAPSHOT .
```
## Running the Docker image
Checkout the industrialization project to see how to run the docker image.
#!/bin/sh
# ----------------------------------------------------------------------------
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
# ----------------------------------------------------------------------------
# ----------------------------------------------------------------------------
# Apache Maven Wrapper startup batch script, version 3.2.0
#
# Required ENV vars:
# ------------------
# JAVA_HOME - location of a JDK home dir
#
# Optional ENV vars
# -----------------
# MAVEN_OPTS - parameters passed to the Java VM when running Maven
# e.g. to debug Maven itself, use
# set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
# MAVEN_SKIP_RC - flag to disable loading of mavenrc files
# ----------------------------------------------------------------------------
if [ -z "$MAVEN_SKIP_RC" ] ; then
if [ -f /usr/local/etc/mavenrc ] ; then
. /usr/local/etc/mavenrc
fi
if [ -f /etc/mavenrc ] ; then
. /etc/mavenrc
fi
if [ -f "$HOME/.mavenrc" ] ; then
. "$HOME/.mavenrc"
fi
fi
# OS specific support. $var _must_ be set to either true or false.
cygwin=false;
darwin=false;
mingw=false
case "$(uname)" in
CYGWIN*) cygwin=true ;;
MINGW*) mingw=true;;
Darwin*) darwin=true
# Use /usr/libexec/java_home if available, otherwise fall back to /Library/Java/Home
# See https://developer.apple.com/library/mac/qa/qa1170/_index.html
if [ -z "$JAVA_HOME" ]; then
if [ -x "/usr/libexec/java_home" ]; then
JAVA_HOME="$(/usr/libexec/java_home)"; export JAVA_HOME
else
JAVA_HOME="/Library/Java/Home"; export JAVA_HOME
fi
fi
;;
esac
if [ -z "$JAVA_HOME" ] ; then
if [ -r /etc/gentoo-release ] ; then
JAVA_HOME=$(java-config --jre-home)
fi
fi
# For Cygwin, ensure paths are in UNIX format before anything is touched
if $cygwin ; then
[ -n "$JAVA_HOME" ] &&
JAVA_HOME=$(cygpath --unix "$JAVA_HOME")
[ -n "$CLASSPATH" ] &&
CLASSPATH=$(cygpath --path --unix "$CLASSPATH")
fi
# For Mingw, ensure paths are in UNIX format before anything is touched
if $mingw ; then
[ -n "$JAVA_HOME" ] && [ -d "$JAVA_HOME" ] &&
JAVA_HOME="$(cd "$JAVA_HOME" || (echo "cannot cd into $JAVA_HOME."; exit 1); pwd)"
fi
if [ -z "$JAVA_HOME" ]; then
javaExecutable="$(which javac)"
if [ -n "$javaExecutable" ] && ! [ "$(expr "\"$javaExecutable\"" : '\([^ ]*\)')" = "no" ]; then
# readlink(1) is not available as standard on Solaris 10.
readLink=$(which readlink)
if [ ! "$(expr "$readLink" : '\([^ ]*\)')" = "no" ]; then
if $darwin ; then
javaHome="$(dirname "\"$javaExecutable\"")"
javaExecutable="$(cd "\"$javaHome\"" && pwd -P)/javac"
else
javaExecutable="$(readlink -f "\"$javaExecutable\"")"
fi
javaHome="$(dirname "\"$javaExecutable\"")"
javaHome=$(expr "$javaHome" : '\(.*\)/bin')
JAVA_HOME="$javaHome"
export JAVA_HOME
fi
fi
fi
if [ -z "$JAVACMD" ] ; then
if [ -n "$JAVA_HOME" ] ; then
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
# IBM's JDK on AIX uses strange locations for the executables
JAVACMD="$JAVA_HOME/jre/sh/java"
else
JAVACMD="$JAVA_HOME/bin/java"
fi
else
JAVACMD="$(\unset -f command 2>/dev/null; \command -v java)"
fi
fi
if [ ! -x "$JAVACMD" ] ; then
echo "Error: JAVA_HOME is not defined correctly." >&2
echo " We cannot execute $JAVACMD" >&2
exit 1
fi
if [ -z "$JAVA_HOME" ] ; then
echo "Warning: JAVA_HOME environment variable is not set."
fi
# traverses directory structure from process work directory to filesystem root
# first directory with .mvn subdirectory is considered project base directory
find_maven_basedir() {
if [ -z "$1" ]
then
echo "Path not specified to find_maven_basedir"
return 1
fi
basedir="$1"
wdir="$1"
while [ "$wdir" != '/' ] ; do
if [ -d "$wdir"/.mvn ] ; then
basedir=$wdir
break
fi
# workaround for JBEAP-8937 (on Solaris 10/Sparc)
if [ -d "${wdir}" ]; then
wdir=$(cd "$wdir/.." || exit 1; pwd)
fi
# end of workaround
done
printf '%s' "$(cd "$basedir" || exit 1; pwd)"
}
# concatenates all lines of a file
concat_lines() {
if [ -f "$1" ]; then
# Remove \r in case we run on Windows within Git Bash
# and check out the repository with auto CRLF management
# enabled. Otherwise, we may read lines that are delimited with
# \r\n and produce $'-Xarg\r' rather than -Xarg due to word
# splitting rules.
tr -s '\r\n' ' ' < "$1"
fi
}
log() {
if [ "$MVNW_VERBOSE" = true ]; then
printf '%s\n' "$1"
fi
}
BASE_DIR=$(find_maven_basedir "$(dirname "$0")")
if [ -z "$BASE_DIR" ]; then
exit 1;
fi
MAVEN_PROJECTBASEDIR=${MAVEN_BASEDIR:-"$BASE_DIR"}; export MAVEN_PROJECTBASEDIR
log "$MAVEN_PROJECTBASEDIR"
##########################################################################################
# Extension to allow automatically downloading the maven-wrapper.jar from Maven-central
# This allows using the maven wrapper in projects that prohibit checking in binary data.
##########################################################################################
wrapperJarPath="$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar"
if [ -r "$wrapperJarPath" ]; then
log "Found $wrapperJarPath"
else
log "Couldn't find $wrapperJarPath, downloading it ..."
if [ -n "$MVNW_REPOURL" ]; then
wrapperUrl="$MVNW_REPOURL/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar"
else
wrapperUrl="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar"
fi
while IFS="=" read -r key value; do
# Remove '\r' from value to allow usage on windows as IFS does not consider '\r' as a separator ( considers space, tab, new line ('\n'), and custom '=' )
safeValue=$(echo "$value" | tr -d '\r')
case "$key" in (wrapperUrl) wrapperUrl="$safeValue"; break ;;
esac
done < "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.properties"
log "Downloading from: $wrapperUrl"
if $cygwin; then
wrapperJarPath=$(cygpath --path --windows "$wrapperJarPath")
fi
if command -v wget > /dev/null; then
log "Found wget ... using wget"
[ "$MVNW_VERBOSE" = true ] && QUIET="" || QUIET="--quiet"
if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then
wget $QUIET "$wrapperUrl" -O "$wrapperJarPath" || rm -f "$wrapperJarPath"
else
wget $QUIET --http-user="$MVNW_USERNAME" --http-password="$MVNW_PASSWORD" "$wrapperUrl" -O "$wrapperJarPath" || rm -f "$wrapperJarPath"
fi
elif command -v curl > /dev/null; then
log "Found curl ... using curl"
[ "$MVNW_VERBOSE" = true ] && QUIET="" || QUIET="--silent"
if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then
curl $QUIET -o "$wrapperJarPath" "$wrapperUrl" -f -L || rm -f "$wrapperJarPath"
else
curl $QUIET --user "$MVNW_USERNAME:$MVNW_PASSWORD" -o "$wrapperJarPath" "$wrapperUrl" -f -L || rm -f "$wrapperJarPath"
fi
else
log "Falling back to using Java to download"
javaSource="$MAVEN_PROJECTBASEDIR/.mvn/wrapper/MavenWrapperDownloader.java"
javaClass="$MAVEN_PROJECTBASEDIR/.mvn/wrapper/MavenWrapperDownloader.class"
# For Cygwin, switch paths to Windows format before running javac
if $cygwin; then
javaSource=$(cygpath --path --windows "$javaSource")
javaClass=$(cygpath --path --windows "$javaClass")
fi
if [ -e "$javaSource" ]; then
if [ ! -e "$javaClass" ]; then
log " - Compiling MavenWrapperDownloader.java ..."
("$JAVA_HOME/bin/javac" "$javaSource")
fi
if [ -e "$javaClass" ]; then
log " - Running MavenWrapperDownloader.java ..."
("$JAVA_HOME/bin/java" -cp .mvn/wrapper MavenWrapperDownloader "$wrapperUrl" "$wrapperJarPath") || rm -f "$wrapperJarPath"
fi
fi
fi
fi
##########################################################################################
# End of extension
##########################################################################################
# If specified, validate the SHA-256 sum of the Maven wrapper jar file
wrapperSha256Sum=""
while IFS="=" read -r key value; do
case "$key" in (wrapperSha256Sum) wrapperSha256Sum=$value; break ;;
esac
done < "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.properties"
if [ -n "$wrapperSha256Sum" ]; then
wrapperSha256Result=false
if command -v sha256sum > /dev/null; then
if echo "$wrapperSha256Sum $wrapperJarPath" | sha256sum -c > /dev/null 2>&1; then
wrapperSha256Result=true
fi
elif command -v shasum > /dev/null; then
if echo "$wrapperSha256Sum $wrapperJarPath" | shasum -a 256 -c > /dev/null 2>&1; then
wrapperSha256Result=true
fi
else
echo "Checksum validation was requested but neither 'sha256sum' or 'shasum' are available."
echo "Please install either command, or disable validation by removing 'wrapperSha256Sum' from your maven-wrapper.properties."
exit 1
fi
if [ $wrapperSha256Result = false ]; then
echo "Error: Failed to validate Maven wrapper SHA-256, your Maven wrapper might be compromised." >&2
echo "Investigate or delete $wrapperJarPath to attempt a clean download." >&2
echo "If you updated your Maven version, you need to update the specified wrapperSha256Sum property." >&2
exit 1
fi
fi
MAVEN_OPTS="$(concat_lines "$MAVEN_PROJECTBASEDIR/.mvn/jvm.config") $MAVEN_OPTS"
# For Cygwin, switch paths to Windows format before running java
if $cygwin; then
[ -n "$JAVA_HOME" ] &&
JAVA_HOME=$(cygpath --path --windows "$JAVA_HOME")
[ -n "$CLASSPATH" ] &&
CLASSPATH=$(cygpath --path --windows "$CLASSPATH")
[ -n "$MAVEN_PROJECTBASEDIR" ] &&
MAVEN_PROJECTBASEDIR=$(cygpath --path --windows "$MAVEN_PROJECTBASEDIR")
fi
# Provide a "standardized" way to retrieve the CLI args that will
# work with both Windows and non-Windows executions.
MAVEN_CMD_LINE_ARGS="$MAVEN_CONFIG $*"
export MAVEN_CMD_LINE_ARGS
WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
# shellcheck disable=SC2086 # safe args
exec "$JAVACMD" \
$MAVEN_OPTS \
$MAVEN_DEBUG_OPTS \
-classpath "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" \
"-Dmaven.multiModuleProjectDirectory=${MAVEN_PROJECTBASEDIR}" \
${WRAPPER_LAUNCHER} $MAVEN_CONFIG "$@"
@REM ----------------------------------------------------------------------------
@REM Licensed to the Apache Software Foundation (ASF) under one
@REM or more contributor license agreements. See the NOTICE file
@REM distributed with this work for additional information
@REM regarding copyright ownership. The ASF licenses this file
@REM to you under the Apache License, Version 2.0 (the
@REM "License"); you may not use this file except in compliance
@REM with the License. You may obtain a copy of the License at
@REM
@REM http://www.apache.org/licenses/LICENSE-2.0
@REM
@REM Unless required by applicable law or agreed to in writing,
@REM software distributed under the License is distributed on an
@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
@REM KIND, either express or implied. See the License for the
@REM specific language governing permissions and limitations
@REM under the License.
@REM ----------------------------------------------------------------------------
@REM ----------------------------------------------------------------------------
@REM Apache Maven Wrapper startup batch script, version 3.2.0
@REM
@REM Required ENV vars:
@REM JAVA_HOME - location of a JDK home dir
@REM
@REM Optional ENV vars
@REM MAVEN_BATCH_ECHO - set to 'on' to enable the echoing of the batch commands
@REM MAVEN_BATCH_PAUSE - set to 'on' to wait for a keystroke before ending
@REM MAVEN_OPTS - parameters passed to the Java VM when running Maven
@REM e.g. to debug Maven itself, use
@REM set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
@REM MAVEN_SKIP_RC - flag to disable loading of mavenrc files
@REM ----------------------------------------------------------------------------
@REM Begin all REM lines with '@' in case MAVEN_BATCH_ECHO is 'on'
@echo off
@REM set title of command window
title %0
@REM enable echoing by setting MAVEN_BATCH_ECHO to 'on'
@if "%MAVEN_BATCH_ECHO%" == "on" echo %MAVEN_BATCH_ECHO%
@REM set %HOME% to equivalent of $HOME
if "%HOME%" == "" (set "HOME=%HOMEDRIVE%%HOMEPATH%")
@REM Execute a user defined script before this one
if not "%MAVEN_SKIP_RC%" == "" goto skipRcPre
@REM check for pre script, once with legacy .bat ending and once with .cmd ending
if exist "%USERPROFILE%\mavenrc_pre.bat" call "%USERPROFILE%\mavenrc_pre.bat" %*
if exist "%USERPROFILE%\mavenrc_pre.cmd" call "%USERPROFILE%\mavenrc_pre.cmd" %*
:skipRcPre
@setlocal
set ERROR_CODE=0
@REM To isolate internal variables from possible post scripts, we use another setlocal
@setlocal
@REM ==== START VALIDATION ====
if not "%JAVA_HOME%" == "" goto OkJHome
echo.
echo Error: JAVA_HOME not found in your environment. >&2
echo Please set the JAVA_HOME variable in your environment to match the >&2
echo location of your Java installation. >&2
echo.
goto error
:OkJHome
if exist "%JAVA_HOME%\bin\java.exe" goto init
echo.
echo Error: JAVA_HOME is set to an invalid directory. >&2
echo JAVA_HOME = "%JAVA_HOME%" >&2
echo Please set the JAVA_HOME variable in your environment to match the >&2
echo location of your Java installation. >&2
echo.
goto error
@REM ==== END VALIDATION ====
:init
@REM Find the project base dir, i.e. the directory that contains the folder ".mvn".
@REM Fallback to current working directory if not found.
set MAVEN_PROJECTBASEDIR=%MAVEN_BASEDIR%
IF NOT "%MAVEN_PROJECTBASEDIR%"=="" goto endDetectBaseDir
set EXEC_DIR=%CD%
set WDIR=%EXEC_DIR%
:findBaseDir
IF EXIST "%WDIR%"\.mvn goto baseDirFound
cd ..
IF "%WDIR%"=="%CD%" goto baseDirNotFound
set WDIR=%CD%
goto findBaseDir
:baseDirFound
set MAVEN_PROJECTBASEDIR=%WDIR%
cd "%EXEC_DIR%"
goto endDetectBaseDir
:baseDirNotFound
set MAVEN_PROJECTBASEDIR=%EXEC_DIR%
cd "%EXEC_DIR%"
:endDetectBaseDir
IF NOT EXIST "%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config" goto endReadAdditionalConfig
@setlocal EnableExtensions EnableDelayedExpansion
for /F "usebackq delims=" %%a in ("%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config") do set JVM_CONFIG_MAVEN_PROPS=!JVM_CONFIG_MAVEN_PROPS! %%a
@endlocal & set JVM_CONFIG_MAVEN_PROPS=%JVM_CONFIG_MAVEN_PROPS%
:endReadAdditionalConfig
SET MAVEN_JAVA_EXE="%JAVA_HOME%\bin\java.exe"
set WRAPPER_JAR="%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.jar"
set WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
set WRAPPER_URL="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar"
FOR /F "usebackq tokens=1,2 delims==" %%A IN ("%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties") DO (
IF "%%A"=="wrapperUrl" SET WRAPPER_URL=%%B
)
@REM Extension to allow automatically downloading the maven-wrapper.jar from Maven-central
@REM This allows using the maven wrapper in projects that prohibit checking in binary data.
if exist %WRAPPER_JAR% (
if "%MVNW_VERBOSE%" == "true" (
echo Found %WRAPPER_JAR%
)
) else (
if not "%MVNW_REPOURL%" == "" (
SET WRAPPER_URL="%MVNW_REPOURL%/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar"
)
if "%MVNW_VERBOSE%" == "true" (
echo Couldn't find %WRAPPER_JAR%, downloading it ...
echo Downloading from: %WRAPPER_URL%
)
powershell -Command "&{"^
"$webclient = new-object System.Net.WebClient;"^
"if (-not ([string]::IsNullOrEmpty('%MVNW_USERNAME%') -and [string]::IsNullOrEmpty('%MVNW_PASSWORD%'))) {"^
"$webclient.Credentials = new-object System.Net.NetworkCredential('%MVNW_USERNAME%', '%MVNW_PASSWORD%');"^
"}"^
"[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12; $webclient.DownloadFile('%WRAPPER_URL%', '%WRAPPER_JAR%')"^
"}"
if "%MVNW_VERBOSE%" == "true" (
echo Finished downloading %WRAPPER_JAR%
)
)
@REM End of extension
@REM If specified, validate the SHA-256 sum of the Maven wrapper jar file
SET WRAPPER_SHA_256_SUM=""
FOR /F "usebackq tokens=1,2 delims==" %%A IN ("%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties") DO (
IF "%%A"=="wrapperSha256Sum" SET WRAPPER_SHA_256_SUM=%%B
)
IF NOT %WRAPPER_SHA_256_SUM%=="" (
powershell -Command "&{"^
"$hash = (Get-FileHash \"%WRAPPER_JAR%\" -Algorithm SHA256).Hash.ToLower();"^
"If('%WRAPPER_SHA_256_SUM%' -ne $hash){"^
" Write-Output 'Error: Failed to validate Maven wrapper SHA-256, your Maven wrapper might be compromised.';"^
" Write-Output 'Investigate or delete %WRAPPER_JAR% to attempt a clean download.';"^
" Write-Output 'If you updated your Maven version, you need to update the specified wrapperSha256Sum property.';"^
" exit 1;"^
"}"^
"}"
if ERRORLEVEL 1 goto error
)
@REM Provide a "standardized" way to retrieve the CLI args that will
@REM work with both Windows and non-Windows executions.
set MAVEN_CMD_LINE_ARGS=%*
%MAVEN_JAVA_EXE% ^
%JVM_CONFIG_MAVEN_PROPS% ^
%MAVEN_OPTS% ^
%MAVEN_DEBUG_OPTS% ^
-classpath %WRAPPER_JAR% ^
"-Dmaven.multiModuleProjectDirectory=%MAVEN_PROJECTBASEDIR%" ^
%WRAPPER_LAUNCHER% %MAVEN_CONFIG% %*
if ERRORLEVEL 1 goto error
goto end
:error
set ERROR_CODE=1
:end
@endlocal & set ERROR_CODE=%ERROR_CODE%
if not "%MAVEN_SKIP_RC%"=="" goto skipRcPost
@REM check for post script, once with legacy .bat ending and once with .cmd ending
if exist "%USERPROFILE%\mavenrc_post.bat" call "%USERPROFILE%\mavenrc_post.bat"
if exist "%USERPROFILE%\mavenrc_post.cmd" call "%USERPROFILE%\mavenrc_post.cmd"
:skipRcPost
@REM pause the script if MAVEN_BATCH_PAUSE is set to 'on'
if "%MAVEN_BATCH_PAUSE%"=="on" pause
if "%MAVEN_TERMINATE_CMD%"=="on" exit %ERROR_CODE%
cmd /C exit /B %ERROR_CODE%
<?xml version="1.0"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd"
xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<modelVersion>4.0.0</modelVersion>
<groupId>gazelle.ihe.net</groupId>
<artifactId>mhd-fhir-server-simulator</artifactId>
<version>1.0.0-SNAPSHOT</version>
<properties>
<compiler-plugin.version>3.12.1</compiler-plugin.version>
<maven.compiler.release>17</maven.compiler.release>
<mockito.version>5.11.0</mockito.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
<quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
<quarkus.platform.version>3.8.2</quarkus.platform.version>
<skipITs>true</skipITs>
<surefire-plugin.version>3.2.5</surefire-plugin.version>
<hapifhir_version>7.0.2</hapifhir_version>
<app.patient.registry.version>2.2.1-SNAPSHOT</app.patient.registry.version>
<thymeleaf.version>3.1.2.RELEASE</thymeleaf.version>
<jakarta.version>6.0.0</jakarta.version>
<jacoco-maven-plugin.version>0.8.10</jacoco-maven-plugin.version>
</properties>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>${quarkus.platform.group-id}</groupId>
<artifactId>${quarkus.platform.artifact-id}</artifactId>
<version>${quarkus.platform.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-arc</artifactId>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-resteasy-reactive</artifactId>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-junit5</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.quarkus</groupId>
<artifactId>quarkus-undertow</artifactId>
</dependency>
<dependency>
<groupId>io.rest-assured</groupId>
<artifactId>rest-assured</artifactId>
<scope>test</scope>
</dependency>
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${hapifhir_version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${hapifhir_version}</version>
</dependency>
<!-- At least one "structures" JAR must also be included -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>${hapifhir_version}</version>
</dependency>
<!-- Used for validation -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>${hapifhir_version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-caching-caffeine</artifactId>
<version>${hapifhir_version}</version> <!-- replace with your HAPI FHIR version -->
</dependency>
<dependency>
<groupId>org.fhir</groupId>
<artifactId>ucum</artifactId>
<version>1.0.8</version>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>jakarta.servlet</groupId>
<artifactId>jakarta.servlet-api</artifactId>
<version>${jakarta.version}</version>
</dependency>
<!--
If you are using HAPI narrative generation, you will need to include Thymeleaf
as well. Otherwise the following can be omitted.
-->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
<version>3.1.2.RELEASE</version>
</dependency>
<!-- Used for CORS support -->
<dependency>
<groupId>org.ebaysf.web</groupId>
<artifactId>cors-filter</artifactId>
<version>1.0.1</version>
<exclusions>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.ihe.gazelle</groupId>
<artifactId>evs-client-api</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>net.ihe.gazelle</groupId>
<artifactId>fhir-server-simulator</artifactId>
<version>1.0.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
<exclusion>
<artifactId>xpp3</artifactId>
<groupId>org.ogce</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco-maven-plugin.version}</version>
<executions>
<execution>
<id>pre-unit-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>${surefire-plugin.version}</version>
<configuration>
<systemPropertyVariables>
<!--suppress UnresolvedMavenProperty -->
<skipTests>${skipTests}</skipTests>
</systemPropertyVariables>
</configuration>
<executions>
<execution>
<id>default-test</id>
<phase>test</phase>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>${quarkus.platform.group-id}</groupId>
<artifactId>quarkus-maven-plugin</artifactId>
<version>${quarkus.platform.version}</version>
<extensions>true</extensions>
<executions>
<execution>
<goals>
<goal>build</goal>
<goal>generate-code</goal>
<goal>generate-code-tests</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>${compiler-plugin.version}</version>
<configuration>
<compilerArgs>
<arg>-parameters</arg>
</compilerArgs>
</configuration>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>${surefire-plugin.version}</version>
<configuration>
<systemPropertyVariables>
<java.util.logging.manager>org.jboss.logmanager.LogManager</java.util.logging.manager>
<maven.home>${maven.home}</maven.home>
</systemPropertyVariables>
</configuration>
</plugin>
<plugin>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${surefire-plugin.version}</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
<configuration>
<systemPropertyVariables>
<native.image.path>${project.build.directory}/${project.build.finalName}-runner
</native.image.path>
<java.util.logging.manager>org.jboss.logmanager.LogManager</java.util.logging.manager>
<maven.home>${maven.home}</maven.home>
</systemPropertyVariables>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<releases>
<enabled>true</enabled>
<updatePolicy>never</updatePolicy>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
<id>IHE</id>
<name>IHE Public Maven Repository Group</name>
<url>https://gazelle.ihe.net/nexus/content/groups/public/</url>
</repository>
</repositories>
<profiles>
<profile>
<id>native</id>
<activation>
<property>
<name>native</name>
</property>
</activation>
<properties>
<skipITs>false</skipITs>
<quarkus.package.type>native</quarkus.package.type>
</properties>
</profile>
</profiles>
</project>
####
# This Dockerfile is used in order to build a container that runs the Quarkus application in JVM mode
#
# Before building the container image run:
#
# ./mvnw package
#
# Then, build the image with:
#
# docker build -f src/main/docker/Dockerfile.jvm -t quarkus/gazelle-fhir-server-simulator-jvm .
#
# Then run the container using:
#
# docker run -i --rm -p 8080:8080 quarkus/gazelle-fhir-server-simulator-jvm
#
# If you want to include the debug port into your docker image
# you will have to expose the debug port (default 5005 being the default) like this : EXPOSE 8080 5005.
# Additionally you will have to set -e JAVA_DEBUG=true and -e JAVA_DEBUG_PORT=*:5005
# when running the container
#
# Then run the container using :
#
# docker run -i --rm -p 8080:8080 quarkus/gazelle-fhir-server-simulator-jvm
#
# This image uses the `run-java.sh` script to run the application.
# This scripts computes the command line to execute your Java application, and
# includes memory/GC tuning.
# You can configure the behavior using the following environment properties:
# - JAVA_OPTS: JVM options passed to the `java` command (example: "-verbose:class")
# - JAVA_OPTS_APPEND: User specified Java options to be appended to generated options
# in JAVA_OPTS (example: "-Dsome.property=foo")
# - JAVA_MAX_MEM_RATIO: Is used when no `-Xmx` option is given in JAVA_OPTS. This is
# used to calculate a default maximal heap memory based on a containers restriction.
# If used in a container without any memory constraints for the container then this
# option has no effect. If there is a memory constraint then `-Xmx` is set to a ratio
# of the container available memory as set here. The default is `50` which means 50%
# of the available memory is used as an upper boundary. You can skip this mechanism by
# setting this value to `0` in which case no `-Xmx` option is added.
# - JAVA_INITIAL_MEM_RATIO: Is used when no `-Xms` option is given in JAVA_OPTS. This
# is used to calculate a default initial heap memory based on the maximum heap memory.
# If used in a container without any memory constraints for the container then this
# option has no effect. If there is a memory constraint then `-Xms` is set to a ratio
# of the `-Xmx` memory as set here. The default is `25` which means 25% of the `-Xmx`
# is used as the initial heap size. You can skip this mechanism by setting this value
# to `0` in which case no `-Xms` option is added (example: "25")
# - JAVA_MAX_INITIAL_MEM: Is used when no `-Xms` option is given in JAVA_OPTS.
# This is used to calculate the maximum value of the initial heap memory. If used in
# a container without any memory constraints for the container then this option has
# no effect. If there is a memory constraint then `-Xms` is limited to the value set
# here. The default is 4096MB which means the calculated value of `-Xms` never will
# be greater than 4096MB. The value of this variable is expressed in MB (example: "4096")
# - JAVA_DIAGNOSTICS: Set this to get some diagnostics information to standard output
# when things are happening. This option, if set to true, will set
# `-XX:+UnlockDiagnosticVMOptions`. Disabled by default (example: "true").
# - JAVA_DEBUG: If set remote debugging will be switched on. Disabled by default (example:
# true").
# - JAVA_DEBUG_PORT: Port used for remote debugging. Defaults to 5005 (example: "8787").
# - CONTAINER_CORE_LIMIT: A calculated core limit as described in
# https://www.kernel.org/doc/Documentation/scheduler/sched-bwc.txt. (example: "2")
# - CONTAINER_MAX_MEMORY: Memory limit given to the container (example: "1024").
# - GC_MIN_HEAP_FREE_RATIO: Minimum percentage of heap free after GC to avoid expansion.
# (example: "20")
# - GC_MAX_HEAP_FREE_RATIO: Maximum percentage of heap free after GC to avoid shrinking.
# (example: "40")
# - GC_TIME_RATIO: Specifies the ratio of the time spent outside the garbage collection.
# (example: "4")
# - GC_ADAPTIVE_SIZE_POLICY_WEIGHT: The weighting given to the current GC time versus
# previous GC times. (example: "90")
# - GC_METASPACE_SIZE: The initial metaspace size. (example: "20")
# - GC_MAX_METASPACE_SIZE: The maximum metaspace size. (example: "100")
# - GC_CONTAINER_OPTIONS: Specify Java GC to use. The value of this variable should
# contain the necessary JRE command-line options to specify the required GC, which
# will override the default of `-XX:+UseParallelGC` (example: -XX:+UseG1GC).
# - HTTPS_PROXY: The location of the https proxy. (example: "myuser@127.0.0.1:8080")
# - HTTP_PROXY: The location of the http proxy. (example: "myuser@127.0.0.1:8080")
# - NO_PROXY: A comma separated lists of hosts, IP addresses or domains that can be
# accessed directly. (example: "foo.example.com,bar.example.com")
#
###
FROM registry.access.redhat.com/ubi8/openjdk-17:1.18
ENV LANGUAGE='en_US:en'
# We make four distinct layers so if there are application changes the library layers can be re-used
COPY --chown=185 target/quarkus-app/lib/ /deployments/lib/
COPY --chown=185 target/quarkus-app/*.jar /deployments/
COPY --chown=185 target/quarkus-app/app/ /deployments/app/
COPY --chown=185 target/quarkus-app/quarkus/ /deployments/quarkus/
EXPOSE 8080
USER 185
ENV JAVA_OPTS_APPEND="-Dquarkus.http.host=0.0.0.0 -Djava.util.logging.manager=org.jboss.logmanager.LogManager"
ENV JAVA_APP_JAR="/deployments/quarkus-run.jar"
ENTRYPOINT [ "/opt/jboss/container/java/run/run-java.sh" ]
####
# This Dockerfile is used in order to build a container that runs the Quarkus application in JVM mode
#
# Before building the container image run:
#
# ./mvnw package -Dquarkus.package.type=legacy-jar
#
# Then, build the image with:
#
# docker build -f src/main/docker/Dockerfile.legacy-jar -t quarkus/gazelle-fhir-server-simulator-legacy-jar .
#
# Then run the container using:
#
# docker run -i --rm -p 8080:8080 quarkus/gazelle-fhir-server-simulator-legacy-jar
#
# If you want to include the debug port into your docker image
# you will have to expose the debug port (default 5005 being the default) like this : EXPOSE 8080 5005.
# Additionally you will have to set -e JAVA_DEBUG=true and -e JAVA_DEBUG_PORT=*:5005
# when running the container
#
# Then run the container using :
#
# docker run -i --rm -p 8080:8080 quarkus/gazelle-fhir-server-simulator-legacy-jar
#
# This image uses the `run-java.sh` script to run the application.
# This scripts computes the command line to execute your Java application, and
# includes memory/GC tuning.
# You can configure the behavior using the following environment properties:
# - JAVA_OPTS: JVM options passed to the `java` command (example: "-verbose:class")
# - JAVA_OPTS_APPEND: User specified Java options to be appended to generated options
# in JAVA_OPTS (example: "-Dsome.property=foo")
# - JAVA_MAX_MEM_RATIO: Is used when no `-Xmx` option is given in JAVA_OPTS. This is
# used to calculate a default maximal heap memory based on a containers restriction.
# If used in a container without any memory constraints for the container then this
# option has no effect. If there is a memory constraint then `-Xmx` is set to a ratio
# of the container available memory as set here. The default is `50` which means 50%
# of the available memory is used as an upper boundary. You can skip this mechanism by
# setting this value to `0` in which case no `-Xmx` option is added.
# - JAVA_INITIAL_MEM_RATIO: Is used when no `-Xms` option is given in JAVA_OPTS. This
# is used to calculate a default initial heap memory based on the maximum heap memory.
# If used in a container without any memory constraints for the container then this
# option has no effect. If there is a memory constraint then `-Xms` is set to a ratio
# of the `-Xmx` memory as set here. The default is `25` which means 25% of the `-Xmx`
# is used as the initial heap size. You can skip this mechanism by setting this value
# to `0` in which case no `-Xms` option is added (example: "25")
# - JAVA_MAX_INITIAL_MEM: Is used when no `-Xms` option is given in JAVA_OPTS.
# This is used to calculate the maximum value of the initial heap memory. If used in
# a container without any memory constraints for the container then this option has
# no effect. If there is a memory constraint then `-Xms` is limited to the value set
# here. The default is 4096MB which means the calculated value of `-Xms` never will
# be greater than 4096MB. The value of this variable is expressed in MB (example: "4096")
# - JAVA_DIAGNOSTICS: Set this to get some diagnostics information to standard output
# when things are happening. This option, if set to true, will set
# `-XX:+UnlockDiagnosticVMOptions`. Disabled by default (example: "true").
# - JAVA_DEBUG: If set remote debugging will be switched on. Disabled by default (example:
# true").
# - JAVA_DEBUG_PORT: Port used for remote debugging. Defaults to 5005 (example: "8787").
# - CONTAINER_CORE_LIMIT: A calculated core limit as described in
# https://www.kernel.org/doc/Documentation/scheduler/sched-bwc.txt. (example: "2")
# - CONTAINER_MAX_MEMORY: Memory limit given to the container (example: "1024").
# - GC_MIN_HEAP_FREE_RATIO: Minimum percentage of heap free after GC to avoid expansion.
# (example: "20")
# - GC_MAX_HEAP_FREE_RATIO: Maximum percentage of heap free after GC to avoid shrinking.
# (example: "40")
# - GC_TIME_RATIO: Specifies the ratio of the time spent outside the garbage collection.
# (example: "4")
# - GC_ADAPTIVE_SIZE_POLICY_WEIGHT: The weighting given to the current GC time versus
# previous GC times. (example: "90")
# - GC_METASPACE_SIZE: The initial metaspace size. (example: "20")
# - GC_MAX_METASPACE_SIZE: The maximum metaspace size. (example: "100")
# - GC_CONTAINER_OPTIONS: Specify Java GC to use. The value of this variable should
# contain the necessary JRE command-line options to specify the required GC, which
# will override the default of `-XX:+UseParallelGC` (example: -XX:+UseG1GC).
# - HTTPS_PROXY: The location of the https proxy. (example: "myuser@127.0.0.1:8080")
# - HTTP_PROXY: The location of the http proxy. (example: "myuser@127.0.0.1:8080")
# - NO_PROXY: A comma separated lists of hosts, IP addresses or domains that can be
# accessed directly. (example: "foo.example.com,bar.example.com")
#
###
FROM registry.access.redhat.com/ubi8/openjdk-17:1.18
ENV LANGUAGE='en_US:en'
COPY target/lib/* /deployments/lib/
COPY target/*-runner.jar /deployments/quarkus-run.jar
EXPOSE 8080
USER 185
ENV JAVA_OPTS_APPEND="-Dquarkus.http.host=0.0.0.0 -Djava.util.logging.manager=org.jboss.logmanager.LogManager"
ENV JAVA_APP_JAR="/deployments/quarkus-run.jar"
ENTRYPOINT [ "/opt/jboss/container/java/run/run-java.sh" ]
####
# This Dockerfile is used in order to build a container that runs the Quarkus application in native (no JVM) mode.
#
# Before building the container image run:
#
# ./mvnw package -Dnative
#
# Then, build the image with:
#
# docker build -f src/main/docker/Dockerfile.native -t quarkus/gazelle-fhir-server-simulator .
#
# Then run the container using:
#
# docker run -i --rm -p 8080:8080 quarkus/gazelle-fhir-server-simulator
#
###
FROM registry.access.redhat.com/ubi8/ubi-minimal:8.9
WORKDIR /work/
RUN chown 1001 /work \
&& chmod "g+rwX" /work \
&& chown 1001:root /work
COPY --chown=1001:root target/*-runner /work/application
EXPOSE 8080
USER 1001
ENTRYPOINT ["./application", "-Dquarkus.http.host=0.0.0.0"]
####
# This Dockerfile is used in order to build a container that runs the Quarkus application in native (no JVM) mode.
# It uses a micro base image, tuned for Quarkus native executables.
# It reduces the size of the resulting container image.
# Check https://quarkus.io/guides/quarkus-runtime-base-image for further information about this image.
#
# Before building the container image run:
#
# ./mvnw package -Dnative
#
# Then, build the image with:
#
# docker build -f src/main/docker/Dockerfile.native-micro -t quarkus/gazelle-fhir-server-simulator .
#
# Then run the container using:
#
# docker run -i --rm -p 8080:8080 quarkus/gazelle-fhir-server-simulator
#
###
FROM quay.io/quarkus/quarkus-micro-image:2.0
WORKDIR /work/
RUN chown 1001 /work \
&& chmod "g+rwX" /work \
&& chown 1001:root /work
COPY --chown=1001:root target/*-runner /work/application
EXPOSE 8080
USER 1001
ENTRYPOINT ["./application", "-Dquarkus.http.host=0.0.0.0"]
package net.ihe.gazelle.fhir.simulator.server.adapter.servlet;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import net.ihe.evsapi.client.domain.ValidationService;
import net.ihe.gazelle.fhir.simulator.server.interlay.loader.DocumentReferencesProviderServiceImpl;
import net.ihe.gazelle.fhir.simulator.server.interlay.loader.ListProviderServiceImpl;
import net.ihe.gazelle.fhir.simulator.server.interlay.provider.DocumentReferencesResourceProvider;
import net.ihe.gazelle.fhir.simulator.server.interlay.provider.ListResourceProvider;
import net.ihe.gazelle.interceptors.FhirValidatorInterceptor;
import net.ihe.gazelle.interceptors.HTTPValidatorInterceptor;
import net.ihe.gazelle.model.ValidationConfiguration;
import org.eclipse.microprofile.config.ConfigProvider;
import java.util.ArrayList;
import java.util.List;
/**
* This servlet is the actual FHIR server itself
*/
public class MDHRestfullServer extends RestfulServer {
private static final long serialVersionUID = 1L;
/**
* Constructor
*/
public MDHRestfullServer() {
super(FhirContext.forR4Cached()); // This is an R4 server
}
/**
* This method is called automatically when the
* servlet is initializing.
*/
@Override
public void initialize() {
/*
* Two resource providers are defined. Each one handles a specific
* type of resource.
*/
List<IResourceProvider> providers = new ArrayList<>();
providers.add(new DocumentReferencesResourceProvider(new DocumentReferencesProviderServiceImpl()));
providers.add(new ListResourceProvider(new ListProviderServiceImpl()));
setResourceProviders(providers);
/*
* Use a narrative generator. This is a completely optional step,
* but can be useful as it causes HAPI to generate narratives for
* resources which don't otherwise have one.
*/
INarrativeGenerator narrativeGen = new DefaultThymeleafNarrativeGenerator();
getFhirContext().setNarrativeGenerator(narrativeGen);
/*
* Use nice coloured HTML when a browser is used to request the content
*/
String evsEndpoint = ConfigProvider.getConfig().getValue("evs.endpoint", String.class);
if (Boolean.TRUE.equals(ConfigProvider.getConfig().getValue("activate.http.validator", Boolean.class))) {
String httpValidationName = ConfigProvider.getConfig().getValue("http.validation.name", String.class);
String httpValidationSchematronName = ConfigProvider.getConfig().getValue("http.validation.schematron.name", String.class);
registerInterceptor(new HTTPValidatorInterceptor(new ValidationConfiguration().setEvsEndpoint(evsEndpoint).setValidationService(new ValidationService().setValidator(httpValidationName).setName(httpValidationSchematronName))));
}
if (Boolean.TRUE.equals(ConfigProvider.getConfig().getValue("activate.fhir.validator", Boolean.class))) {
String fhirValidationName = ConfigProvider.getConfig().getValue("fhir.validation.name", String.class);
String fhirValidationSchematronName = ConfigProvider.getConfig().getValue("fhir.validation.schematron.name", String.class);
registerInterceptor(new FhirValidatorInterceptor(new ValidationConfiguration().setEvsEndpoint(evsEndpoint).setValidationService(new ValidationService().setValidator(fhirValidationName).setName(fhirValidationSchematronName))));
}
}
}
package net.ihe.gazelle.fhir.simulator.server.interlay.loader;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.DocumentReference;
import java.util.List;
public interface DocumentReferencesProviderService {
DocumentReference getDocumentReference(String id);
List<DocumentReference> searchDocumentReferences(RequestDetails parameters);
Bundle createBundleResource(Bundle bundleDocument);
}
\ No newline at end of file
package net.ihe.gazelle.fhir.simulator.server.interlay.loader;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.gclient.IQuery;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import jakarta.enterprise.context.ApplicationScoped;
import org.eclipse.microprofile.config.ConfigProvider;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.DocumentReference;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@ApplicationScoped
public class DocumentReferencesProviderServiceImpl implements DocumentReferencesProviderService {
private final IGenericClient client;
public DocumentReferencesProviderServiceImpl() {
FhirContext ctx = FhirContext.forR4(); // or the appropriate version
String serverBase = ConfigProvider.getConfig().getValue("nist.fhir.toolkit.endpoint", String.class);
client = ctx.newRestfulGenericClient(serverBase);
}
@Override
public DocumentReference getDocumentReference(String id) {
// Use the FHIR client to send a request to the other server
return client.read()
.resource(DocumentReference.class)
.withId(id)
.execute();
}
@Override
public List<DocumentReference> searchDocumentReferences(RequestDetails request) {
Map<String, String[]> parameterMap = request.getParameters();
Map<String, String> singleValueMap = new HashMap<>();
for (Map.Entry<String, String[]> entry : parameterMap.entrySet()) {
singleValueMap.put(entry.getKey(), entry.getValue()[0]);
}
// Use the FHIR client to send a request to the other server
IQuery<IBaseBundle> query = client.search().forResource(DocumentReference.class);
for (Map.Entry<String, String> entry : singleValueMap.entrySet()) {
String key = entry.getKey();
String value = entry.getValue();
query = query.where(new StringClientParam(key).matches().value(value));
}
return query.returnBundle(org.hl7.fhir.r4.model.Bundle.class)
.execute()
.getEntry()
.stream()
.map(e -> (DocumentReference) e.getResource())
.toList();
}
@Override
public Bundle createBundleResource(Bundle bundleDocument) {
// Use the FHIR client to send a request to the other server
return client.transaction()
.withBundle(bundleDocument)
.execute();
}
}
package net.ihe.gazelle.fhir.simulator.server.interlay.loader;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.ListResource;
import java.util.List;
public interface ListProviderService {
List<ListResource> searchListResource(RequestDetails parameters);
}
\ No newline at end of file
package net.ihe.gazelle.fhir.simulator.server.interlay.loader;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.gclient.IQuery;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import jakarta.enterprise.context.ApplicationScoped;
import org.eclipse.microprofile.config.ConfigProvider;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.r4.model.ListResource;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@ApplicationScoped
public class ListProviderServiceImpl implements ListProviderService {
private final IGenericClient client;
public ListProviderServiceImpl() {
FhirContext ctx = FhirContext.forR4(); // or the appropriate version
String serverBase = ConfigProvider.getConfig().getValue("nist.fhir.toolkit.endpoint", String.class);
client = ctx.newRestfulGenericClient(serverBase);
}
@Override
public List<ListResource> searchListResource(RequestDetails request) {
Map<String, String[]> parameterMap = request.getParameters();
Map<String, String> singleValueMap = new HashMap<>();
for (Map.Entry<String, String[]> entry : parameterMap.entrySet()) {
singleValueMap.put(entry.getKey(), entry.getValue()[0]);
}
// Use the FHIR client to send a request to the other server
IQuery<IBaseBundle> query = client.search().forResource(ListResource.class);
for (Map.Entry<String, String> entry : singleValueMap.entrySet()) {
String key = entry.getKey();
String value = entry.getValue();
query = query.where(new StringClientParam(key).matches().value(value));
}
return query.returnBundle(org.hl7.fhir.r4.model.Bundle.class)
.execute()
.getEntry()
.stream()
.map(e -> (ListResource) e.getResource())
.toList();
}
}
package net.ihe.gazelle.fhir.simulator.server.interlay.provider;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.BundleProviders;
import ca.uhn.fhir.rest.server.IResourceProvider;
import jakarta.inject.Inject;
import jakarta.servlet.http.HttpServletRequest;
import net.ihe.gazelle.fhir.simulator.server.interlay.loader.DocumentReferencesProviderService;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import java.net.http.HttpRequest;
import java.util.ArrayList;
import java.util.List;
/**
* This is a resource provider that retrieves Patient resources from a PatientResourceProviderService.
*/
public class DocumentReferencesResourceProvider implements IResourceProvider {
protected final DocumentReferencesProviderService documentReferencesProviderService;
@Inject
public DocumentReferencesResourceProvider(DocumentReferencesProviderService patientResourceProviderService) {
this.documentReferencesProviderService = patientResourceProviderService;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return DocumentReference.class;
}
//IT-68
@Read
public DocumentReference readDocumentReference( @IdParam IIdType theId) {
return documentReferencesProviderService.getDocumentReference(theId.getValue());
}
//IT-67
@Search()
public List<DocumentReference> findDocumentReference(
@OptionalParam(name = DocumentReference.SP_PATIENT) TokenParam thePatient,
@OptionalParam(name = DocumentReference.SP_DATE) DateParam date,
@OptionalParam(name = DocumentReference.SP_AUTHOR) StringParam author,
@OptionalParam(name = DocumentReference.SP_STATUS) StringParam status,
@OptionalParam(name = DocumentReference.SP_CATEGORY) StringParam category,
@OptionalParam(name = DocumentReference.SP_TYPE) StringParam type,
@OptionalParam(name = DocumentReference.SP_SETTING) StringParam setting,
@OptionalParam(name = DocumentReference.SP_PERIOD) DateParam period,
@OptionalParam(name = DocumentReference.SP_FACILITY) StringParam facilty,
@OptionalParam(name = DocumentReference.SP_EVENT) StringParam event,
@OptionalParam(name = DocumentReference.SP_SECURITY_LABEL) StringParam securityLabel,
@OptionalParam(name = DocumentReference.SP_FORMAT) StringParam format,
@OptionalParam(name = DocumentReference.SP_RELATED) StringParam related, RequestDetails requestDetails) {
return documentReferencesProviderService.searchDocumentReferences(requestDetails);
}
//IT-65
@Transaction()
public Bundle createDocumentReference(@TransactionParam Bundle bundle) {
return documentReferencesProviderService.createBundleResource(bundle);
}
}
package net.ihe.gazelle.fhir.simulator.server.interlay.provider;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.OptionalParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.IResourceProvider;
import jakarta.inject.Inject;
import net.ihe.gazelle.fhir.simulator.server.interlay.loader.ListProviderService;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.ListResource;
import java.util.List;
/**
* This is a resource provider that retrieves Patient resources from a PatientResourceProviderService.
*/
public class ListResourceProvider implements IResourceProvider {
protected final ListProviderService listProviderService;
@Inject
public ListResourceProvider(ListProviderService listProviderService) {
this.listProviderService = listProviderService;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return ListResource.class;
}
//IT-66
@Search()
public List<ListResource> findListResource(@OptionalParam(name = ListResource.SP_CODE) TokenParam code,
@OptionalParam(name = ListResource.SP_DATE) DateParam date,
@OptionalParam(name = ListResource.SP_PATIENT) TokenParam patient,
@OptionalParam(name = ListResource.SP_SOURCE) TokenParam source,
@OptionalParam(name = ListResource.SP_STATUS) String status,
@OptionalParam(name = ListResource.SP_SUBJECT) TokenParam subject,
@OptionalParam(name = "designationType") String designationType,
RequestDetails requestDetails
) {
return listProviderService.searchListResource(requestDetails);
}
}
<web-app>
<servlet>
<servlet-name>MHDServlet</servlet-name>
<servlet-class>net.ihe.gazelle.fhir.simulator.server.adapter.servlet.MDHRestfullServer</servlet-class>
</servlet>
<servlet-mapping>
<servlet-name>MHDServlet</servlet-name>
<url-pattern>/MHD/fhir/*</url-pattern>
</servlet-mapping>
</web-app>
\ No newline at end of file
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