trigger build

This commit is contained in:
Jörn Guy Süß 2025-07-16 13:50:20 +10:00
parent ea402ceaa9
commit 1d9a263d23
14 changed files with 7419 additions and 339 deletions

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@ -1,26 +0,0 @@
Docker Commands.MD
<HAPI-server.>
to pull and clone:
git clone https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git hapi-fhir-jpaserver
to build:
mvn clean package -DskipTests=true -Pboot
to run:
java -jar target/ROOT.war
<rest-of-the-app:>
docker-compose build --no-cache
docker-compose up -d
<useful-stuff:>
cp <CONTAINERID>:/app/PATH/Filename.ext . - . copies to the root folder you ran it from
docker exec -it <CONTAINERID> bash - to get a bash - session in the container -

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FROM flare.lite
# Ensure /tmp, /app/static/uploads, and /app/logs are writable
RUN mkdir -p /tmp /app/h2-data /app/static/uploads /app/logs && chmod 777 /tmp /app/h2-data /app/static/uploads /app/logs
# Copy pre-built HAPI WAR and configuration
COPY hapi-fhir-jpaserver/target/ROOT.war /usr/local/tomcat/webapps/
COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/conf/
COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application.yaml
COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/webapps/app/config/application.yaml
COPY hapi-fhir-jpaserver/custom/ /usr/local/tomcat/webapps/custom/

25
Run.bat
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REM --- Step 1: Start Docker containers ---
echo ===> Starting Docker containers (Step 7)...
docker-compose up -d
if errorlevel 1 (
echo ERROR: Docker Compose up failed. Check Docker installation and container configurations. ErrorLevel: %errorlevel%
goto :error
)
echo Docker containers started successfully. ErrorLevel: %errorlevel%
echo.
echo ====================================
echo Script finished successfully!
echo ====================================
goto :eof
:error
echo ------------------------------------
echo An error occurred. Script aborted.
echo ------------------------------------
pause
exit /b 1
:eof
echo Script execution finished.
pause

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@ -34,7 +34,7 @@ podAnnotations: {}
# runAsUser: 65532
# seccompProfile:
# type: RuntimeDefault
#
# securityContext:
# allowPrivilegeEscalation: false
# capabilities:

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services:
fhirflare:
image: ghcr.io/jgsuess/fhirflare-ig-toolkit:latest
ports:
- "5000:5000"
volumes:
- ./instance:/app/instance
- ./static/uploads:/app/static/uploads
- ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
- ./logs:/app/logs
environment:
- FLASK_APP=app.py
- FLASK_ENV=development
- NODE_PATH=/usr/lib/node_modules
- APP_MODE=lite
- APP_BASE_URL=http://localhost:5000
- HAPI_FHIR_URL=http://fhir:8080/fhir
command: supervisord -c /etc/supervisord.conf
fhir:
container_name: hapi
image: "hapiproject/hapi:v8.2.0-1"
ports:
- "8080:8080"
configs:
- source: hapi
target: /app/config/application.yaml
depends_on:
- db
db:
image: "postgres:17.2-bookworm"
restart: always
environment:
POSTGRES_PASSWORD: admin
POSTGRES_USER: admin
POSTGRES_DB: hapi
volumes:
- ./hapi.postgress.data:/var/lib/postgresql/data
configs:
hapi:
file: ./application.yaml

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* Serving Flask app 'app'
* Debug mode: off
* Serving Flask app 'app'
* Debug mode: off
* Serving Flask app 'app'
* Debug mode: off
* Serving Flask app 'app'
* Debug mode: off

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2025-07-15 02:43:35,572 CRIT Supervisor is running as root. Privileges were not dropped because no user is specified in the config file. If you intend to run as root, you can set user=root in the config file to avoid this message.
2025-07-15 02:43:35,575 INFO supervisord started with pid 1
2025-07-15 02:43:36,577 INFO spawned: 'flask' with pid 7
2025-07-15 02:43:36,578 INFO spawned: 'tomcat' with pid 8
2025-07-15 02:43:46,682 INFO success: flask entered RUNNING state, process has stayed up for > than 10 seconds (startsecs)
2025-07-15 02:44:07,102 INFO success: tomcat entered RUNNING state, process has stayed up for > than 30 seconds (startsecs)
2025-07-15 03:33:26,668 WARN received SIGTERM indicating exit request
2025-07-15 03:33:26,676 INFO waiting for flask, tomcat to die
2025-07-15 03:33:26,787 WARN stopped: tomcat (exit status 143)
2025-07-15 03:33:26,798 WARN stopped: flask (terminated by SIGTERM)
2025-07-15 03:35:53,949 CRIT Supervisor is running as root. Privileges were not dropped because no user is specified in the config file. If you intend to run as root, you can set user=root in the config file to avoid this message.
2025-07-15 03:35:53,950 INFO supervisord started with pid 1
2025-07-15 03:35:54,952 INFO spawned: 'flask' with pid 7
2025-07-15 03:35:54,954 INFO spawned: 'tomcat' with pid 8
2025-07-15 03:36:05,793 INFO success: flask entered RUNNING state, process has stayed up for > than 10 seconds (startsecs)
2025-07-15 03:36:25,546 INFO success: tomcat entered RUNNING state, process has stayed up for > than 30 seconds (startsecs)
2025-07-15 03:36:32,553 WARN received SIGTERM indicating exit request
2025-07-15 03:36:32,555 INFO waiting for flask, tomcat to die
2025-07-15 03:36:32,608 WARN stopped: tomcat (exit status 143)
2025-07-15 03:36:32,615 WARN stopped: flask (terminated by SIGTERM)
2025-07-15 03:36:48,443 CRIT Supervisor is running as root. Privileges were not dropped because no user is specified in the config file. If you intend to run as root, you can set user=root in the config file to avoid this message.
2025-07-15 03:36:48,444 INFO supervisord started with pid 1
2025-07-15 03:36:49,446 INFO spawned: 'flask' with pid 7
2025-07-15 03:36:49,448 INFO spawned: 'tomcat' with pid 8
2025-07-15 03:37:00,401 INFO success: flask entered RUNNING state, process has stayed up for > than 10 seconds (startsecs)
2025-07-15 03:37:20,421 INFO success: tomcat entered RUNNING state, process has stayed up for > than 30 seconds (startsecs)
2025-07-15 03:41:24,314 WARN received SIGTERM indicating exit request
2025-07-15 03:41:24,314 INFO waiting for flask, tomcat to die
2025-07-15 03:41:24,355 WARN stopped: tomcat (exit status 143)
2025-07-15 03:41:24,371 WARN stopped: flask (terminated by SIGTERM)
2025-07-15 03:42:33,879 CRIT Supervisor is running as root. Privileges were not dropped because no user is specified in the config file. If you intend to run as root, you can set user=root in the config file to avoid this message.
2025-07-15 03:42:33,880 INFO supervisord started with pid 1
2025-07-15 03:42:34,883 INFO spawned: 'flask' with pid 7
2025-07-15 03:42:34,885 INFO spawned: 'tomcat' with pid 8
2025-07-15 03:42:44,901 INFO success: flask entered RUNNING state, process has stayed up for > than 10 seconds (startsecs)
2025-07-15 03:43:04,922 INFO success: tomcat entered RUNNING state, process has stayed up for > than 30 seconds (startsecs)
2025-07-15 04:54:10,136 WARN received SIGTERM indicating exit request
2025-07-15 04:54:10,146 INFO waiting for flask, tomcat to die
2025-07-15 04:54:10,310 WARN stopped: tomcat (exit status 143)
2025-07-15 04:54:10,320 WARN stopped: flask (terminated by SIGTERM)

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15-Jul-2025 02:43:37.029 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/10.1.43
15-Jul-2025 02:43:37.034 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jul 1 2025 21:30:20 UTC
15-Jul-2025 02:43:37.034 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 10.1.43.0
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.11.0-29-generic
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/java/openjdk
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 17.0.15+6
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Eclipse Adoptium
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
15-Jul-2025 02:43:37.035 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
15-Jul-2025 02:43:37.049 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
15-Jul-2025 02:43:37.049 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dsun.io.useCanonCaches=false
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang.reflect=ALL-UNNAMED
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED
15-Jul-2025 02:43:37.050 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util=ALL-UNNAMED
15-Jul-2025 02:43:37.051 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
15-Jul-2025 02:43:37.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
15-Jul-2025 02:43:37.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat
15-Jul-2025 02:43:37.052 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat
15-Jul-2025 02:43:37.053 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
15-Jul-2025 02:43:37.059 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [2.0.9] using APR version [1.7.2].
15-Jul-2025 02:43:37.063 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 3.0.13 30 Jan 2024]
15-Jul-2025 02:43:37.283 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
15-Jul-2025 02:43:37.305 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [468] milliseconds
15-Jul-2025 02:43:37.354 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
15-Jul-2025 02:43:37.354 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/10.1.43]
15-Jul-2025 02:43:37.370 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
15-Jul-2025 02:43:37.382 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [77] milliseconds
15-Jul-2025 03:33:26.694 INFO [Thread-1] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:33:26.730 INFO [Thread-1] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
15-Jul-2025 03:33:26.735 INFO [Thread-1] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:33:26.748 INFO [Thread-1] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:35:55.373 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/10.1.43
15-Jul-2025 03:35:55.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jul 1 2025 21:30:20 UTC
15-Jul-2025 03:35:55.379 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 10.1.43.0
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.11.0-29-generic
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/java/openjdk
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 17.0.15+6
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Eclipse Adoptium
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
15-Jul-2025 03:35:55.380 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
15-Jul-2025 03:35:55.397 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
15-Jul-2025 03:35:55.397 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dsun.io.useCanonCaches=false
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang.reflect=ALL-UNNAMED
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util=ALL-UNNAMED
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
15-Jul-2025 03:35:55.398 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
15-Jul-2025 03:35:55.399 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat
15-Jul-2025 03:35:55.399 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat
15-Jul-2025 03:35:55.399 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
15-Jul-2025 03:35:55.402 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [2.0.9] using APR version [1.7.2].
15-Jul-2025 03:35:55.405 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 3.0.13 30 Jan 2024]
15-Jul-2025 03:35:55.684 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:35:55.723 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [531] milliseconds
15-Jul-2025 03:35:55.782 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
15-Jul-2025 03:35:55.782 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/10.1.43]
15-Jul-2025 03:35:55.804 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:35:55.819 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [96] milliseconds
15-Jul-2025 03:36:32.560 INFO [Thread-1] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:36:32.570 INFO [Thread-1] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
15-Jul-2025 03:36:32.571 INFO [Thread-1] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:36:32.575 INFO [Thread-1] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:36:49.853 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/10.1.43
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jul 1 2025 21:30:20 UTC
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 10.1.43.0
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.11.0-29-generic
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/java/openjdk
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 17.0.15+6
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Eclipse Adoptium
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
15-Jul-2025 03:36:49.857 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dsun.io.useCanonCaches=false
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED
15-Jul-2025 03:36:49.864 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang.reflect=ALL-UNNAMED
15-Jul-2025 03:36:49.865 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED
15-Jul-2025 03:36:49.865 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util=ALL-UNNAMED
15-Jul-2025 03:36:49.865 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
15-Jul-2025 03:36:49.865 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
15-Jul-2025 03:36:49.865 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat
15-Jul-2025 03:36:49.865 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat
15-Jul-2025 03:36:49.865 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
15-Jul-2025 03:36:49.868 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [2.0.9] using APR version [1.7.2].
15-Jul-2025 03:36:49.872 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 3.0.13 30 Jan 2024]
15-Jul-2025 03:36:50.082 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:36:50.100 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [398] milliseconds
15-Jul-2025 03:36:50.141 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
15-Jul-2025 03:36:50.141 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/10.1.43]
15-Jul-2025 03:36:50.154 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:36:50.163 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [62] milliseconds
15-Jul-2025 03:41:24.321 INFO [Thread-1] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:41:24.328 INFO [Thread-1] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
15-Jul-2025 03:41:24.329 INFO [Thread-1] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:41:24.334 INFO [Thread-1] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:42:35.284 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/10.1.43
15-Jul-2025 03:42:35.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jul 1 2025 21:30:20 UTC
15-Jul-2025 03:42:35.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 10.1.43.0
15-Jul-2025 03:42:35.291 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
15-Jul-2025 03:42:35.292 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 6.11.0-29-generic
15-Jul-2025 03:42:35.292 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
15-Jul-2025 03:42:35.292 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/java/openjdk
15-Jul-2025 03:42:35.292 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 17.0.15+6
15-Jul-2025 03:42:35.292 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Eclipse Adoptium
15-Jul-2025 03:42:35.292 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
15-Jul-2025 03:42:35.292 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
15-Jul-2025 03:42:35.304 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
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15-Jul-2025 03:42:35.304 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
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15-Jul-2025 03:42:35.308 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [2.0.9] using APR version [1.7.2].
15-Jul-2025 03:42:35.311 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 3.0.13 30 Jan 2024]
15-Jul-2025 03:42:35.488 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
15-Jul-2025 03:42:35.511 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [361] milliseconds
15-Jul-2025 03:42:35.562 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
15-Jul-2025 03:42:35.562 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/10.1.43]
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@ -1,233 +0,0 @@
#!/bin/bash
# --- Configuration ---
REPO_URL="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
CLONE_DIR="hapi-fhir-jpaserver"
SOURCE_CONFIG_DIR="hapi-fhir-Setup" # Assuming this is relative to the script's parent
CONFIG_FILE="application.yaml"
# --- Define Paths ---
# Note: Adjust SOURCE_CONFIG_PATH if SOURCE_CONFIG_DIR is not a sibling directory
# This assumes the script is run from a directory, and hapi-fhir-setup is at the same level
SOURCE_CONFIG_PATH="../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
DEST_CONFIG_PATH="${CLONE_DIR}/target/classes/${CONFIG_FILE}"
APP_MODE=""
# --- Error Handling Function ---
handle_error() {
echo "------------------------------------"
echo "An error occurred: $1"
echo "Script aborted."
echo "------------------------------------"
# Removed 'read -p "Press Enter to exit..."' as it's not typical for non-interactive CI/CD
exit 1
}
# === Prompt for Installation Mode ===
get_mode_choice() {
echo "Select Installation Mode:"
echo "1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)"
echo "2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)"
while true; do
read -r -p "Enter your choice (1 or 2): " choice
case "$choice" in
1)
APP_MODE="standalone"
break
;;
2)
APP_MODE="lite"
break
;;
*)
echo "Invalid input. Please try again."
;;
esac
done
echo "Selected Mode: $APP_MODE"
echo
}
# Call the function to get mode choice
get_mode_choice
# === Conditionally Execute HAPI Setup ===
if [ "$APP_MODE" = "standalone" ]; then
echo "Running Standalone setup including HAPI FHIR..."
echo
# --- Step 0: Clean up previous clone (optional) ---
echo "Checking for existing directory: $CLONE_DIR"
if [ -d "$CLONE_DIR" ]; then
echo "Found existing directory, removing it..."
rm -rf "$CLONE_DIR"
if [ $? -ne 0 ]; then
handle_error "Failed to remove existing directory: $CLONE_DIR"
fi
echo "Existing directory removed."
else
echo "Directory does not exist, proceeding with clone."
fi
echo
# --- Step 1: Clone the HAPI FHIR server repository ---
echo "Cloning repository: $REPO_URL into $CLONE_DIR..."
git clone "$REPO_URL" "$CLONE_DIR"
if [ $? -ne 0 ]; then
handle_error "Failed to clone repository. Check Git installation and network connection."
fi
echo "Repository cloned successfully."
echo
# --- Step 2: Navigate into the cloned directory ---
echo "Changing directory to $CLONE_DIR..."
cd "$CLONE_DIR" || handle_error "Failed to change directory to $CLONE_DIR."
echo "Current directory: $(pwd)"
echo
# --- Step 3: Build the HAPI server using Maven ---
echo "===> Starting Maven build (Step 3)..."
mvn clean package -DskipTests=true -Pboot
if [ $? -ne 0 ]; then
echo "ERROR: Maven build failed."
cd ..
handle_error "Maven build process resulted in an error."
fi
echo "Maven build completed successfully."
echo
# --- Step 4: Copy the configuration file ---
echo "===> Starting file copy (Step 4)..."
echo "Copying configuration file..."
# Corrected SOURCE_CONFIG_PATH to be relative to the new current directory ($CLONE_DIR)
# This assumes the original script's SOURCE_CONFIG_PATH was relative to its execution location
# If SOURCE_CONFIG_DIR is ../hapi-fhir-setup relative to script's original location:
# Then from within CLONE_DIR, it becomes ../../hapi-fhir-setup
# We defined SOURCE_CONFIG_PATH earlier relative to the script start.
# So, when inside CLONE_DIR, the path from original script location should be used.
# The original script had: set SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%
# And then: xcopy "%SOURCE_CONFIG_PATH%" "target\classes\"
# This implies SOURCE_CONFIG_PATH is relative to the original script's location, not the $CLONE_DIR
# Therefore, we need to construct the correct relative path from *within* $CLONE_DIR back to the source.
# Assuming the script is in dir X, and SOURCE_CONFIG_DIR is ../hapi-fhir-setup from X.
# So, hapi-fhir-setup is a sibling of X's parent.
# If CLONE_DIR is also in X, then from within CLONE_DIR, the path is ../ + original SOURCE_CONFIG_PATH
# For simplicity and robustness, let's use an absolute path or a more clearly defined relative path from the start.
# The original `SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%` implies
# that `hapi-fhir-setup` is a sibling of the directory where the script *is being run from*.
# Let's assume the script is run from the root of FHIRFLARE-IG-Toolkit.
# And hapi-fhir-setup is also in the root, next to this script.
# Then SOURCE_CONFIG_PATH would be ./hapi-fhir-setup/target/classes/application.yaml
# And from within ./hapi-fhir-jpaserver/, the path would be ../hapi-fhir-setup/target/classes/application.yaml
# The original batch file sets SOURCE_CONFIG_PATH as "..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%"
# And COPIES it to "target\classes\" *while inside CLONE_DIR*.
# This means the source path is relative to where the *cd %CLONE_DIR%* happened from.
# Let's make it relative to the script's initial execution directory.
INITIAL_SCRIPT_DIR=$(pwd)
ABSOLUTE_SOURCE_CONFIG_PATH="${INITIAL_SCRIPT_DIR}/../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}" # This matches the ..\ logic
echo "Source: $ABSOLUTE_SOURCE_CONFIG_PATH"
echo "Destination: target/classes/$CONFIG_FILE"
if [ ! -f "$ABSOLUTE_SOURCE_CONFIG_PATH" ]; then
echo "WARNING: Source configuration file not found at $ABSOLUTE_SOURCE_CONFIG_PATH."
echo "The script will continue, but the server might use default configuration."
else
cp "$ABSOLUTE_SOURCE_CONFIG_PATH" "target/classes/"
if [ $? -ne 0 ]; then
echo "WARNING: Failed to copy configuration file. Check if the source file exists and permissions."
echo "The script will continue, but the server might use default configuration."
else
echo "Configuration file copied successfully."
fi
fi
echo
# --- Step 5: Navigate back to the parent directory ---
echo "===> Changing directory back (Step 5)..."
cd .. || handle_error "Failed to change back to the parent directory."
echo "Current directory: $(pwd)"
echo
else # APP_MODE is "lite"
echo "Running Lite setup, skipping HAPI FHIR build..."
# Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen
if [ -d "$CLONE_DIR" ]; then
echo "Found existing HAPI directory ($CLONE_DIR) in Lite mode. Removing it..."
rm -rf "$CLONE_DIR"
fi
# Create empty target directories expected by Dockerfile COPY, even if not used
mkdir -p "${CLONE_DIR}/target/classes"
mkdir -p "${CLONE_DIR}/custom" # This was in the original batch, ensure it's here
# Create a placeholder empty WAR file and application.yaml to satisfy Dockerfile COPY
touch "${CLONE_DIR}/target/ROOT.war"
touch "${CLONE_DIR}/target/classes/application.yaml"
echo "Placeholder files and directories created for Lite mode build in $CLONE_DIR."
echo
fi
# === Modify docker-compose.yml to set APP_MODE ===
echo "Updating docker-compose.yml with APP_MODE=$APP_MODE..."
DOCKER_COMPOSE_TMP="docker-compose.yml.tmp"
DOCKER_COMPOSE_ORIG="docker-compose.yml"
cat << EOF > "$DOCKER_COMPOSE_TMP"
version: '3.8'
services:
fhirflare:
build:
context: .
dockerfile: Dockerfile
ports:
- "5000:5000"
- "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
volumes:
- ./instance:/app/instance
- ./static/uploads:/app/static/uploads
- ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
- ./logs:/app/logs
environment:
- FLASK_APP=app.py
- FLASK_ENV=development
- NODE_PATH=/usr/lib/node_modules
- APP_MODE=${APP_MODE}
- APP_BASE_URL=http://localhost:5000
- HAPI_FHIR_URL=http://localhost:8080/fhir
command: supervisord -c /etc/supervisord.conf
EOF
if [ ! -f "$DOCKER_COMPOSE_TMP" ]; then
handle_error "Failed to create temporary docker-compose file ($DOCKER_COMPOSE_TMP)."
fi
# Replace the original docker-compose.yml
mv "$DOCKER_COMPOSE_TMP" "$DOCKER_COMPOSE_ORIG"
echo "docker-compose.yml updated successfully."
echo
# --- Step 6: Build Docker images ---
echo "===> Starting Docker build (Step 6)..."
docker-compose build --no-cache
if [ $? -ne 0 ]; then
handle_error "Docker Compose build failed. Check Docker installation and docker-compose.yml file."
fi
echo "Docker images built successfully."
echo
# --- Step 7: Start Docker containers ---
echo "===> Starting Docker containers (Step 7)..."
docker-compose up -d
if [ $? -ne 0 ]; then
handle_error "Docker Compose up failed. Check Docker installation and container configurations."
fi
echo "Docker containers started successfully."
echo
echo "===================================="
echo "Script finished successfully! (Mode: $APP_MODE)"
echo "===================================="
exit 0