Sudo-JHare/FHIRFLARE-IG-Toolkit
Sudo-JHare/FHIRFLARE-IG-Toolkit
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This commit is contained in:
Joshua Hare 2025-04-22 11:22:10 +10:00
parent 38c663e4f1
commit 7598e6d779
5 changed files with 205 additions and 1 deletions
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2
Starting
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@ -1 +1 @@
=== Docker build (Step 6)...
=== Docker containers (Step 7)...

2
logs/flask.log
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@ -4,3 +4,5 @@
* Debug mode: off
* Serving Flask app 'app'
* Debug mode: off
* Serving Flask app 'app'
* Debug mode: off

22
logs/flask_err.log
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@ -287,3 +287,25 @@ INFO:werkzeug:172.18.0.1 - - [22/Apr/2025 00:12:44] "GET /about HTTP/1.1" 200 -
INFO:werkzeug:172.18.0.1 - - [22/Apr/2025 00:12:44] "GET /static/FHIRFLARE.png HTTP/1.1" 304 -
INFO:werkzeug:172.18.0.1 - - [22/Apr/2025 00:13:32] "GET / HTTP/1.1" 200 -
INFO:werkzeug:172.18.0.1 - - [22/Apr/2025 00:13:32] "GET /static/FHIRFLARE.png HTTP/1.1" 304 -
INFO:__main__:Application running in mode: lite
DEBUG:__main__:Instance path configuration: /app/instance
DEBUG:__main__:Database URI: sqlite:////app/instance/fhir_ig.db
DEBUG:__main__:Packages path: /app/instance/fhir_packages
DEBUG:__main__:Flask instance folder path: /app/instance
DEBUG:__main__:Directories created/verified: Instance: /app/instance, Packages: /app/instance/fhir_packages
DEBUG:__main__:Attempting to create database tables for URI: sqlite:////app/instance/fhir_ig.db
INFO:__main__:Database tables created successfully (if they didn't exist).
DEBUG:__main__:Instance path configuration: /app/instance
DEBUG:__main__:Database URI: sqlite:////app/instance/fhir_ig.db
DEBUG:__main__:Packages path: /app/instance/fhir_packages
DEBUG:__main__:Flask instance folder path: /app/instance
DEBUG:__main__:Directories created/verified: Instance: /app/instance, Packages: /app/instance/fhir_packages
DEBUG:__main__:Attempting to create database tables for URI: sqlite:////app/instance/fhir_ig.db
INFO:__main__:Database tables created successfully (if they didn't exist).
INFO:werkzeug:WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead.
* Running on all addresses (0.0.0.0)
* Running on http://127.0.0.1:5000
* Running on http://172.18.0.2:5000
INFO:werkzeug:Press CTRL+C to quit
INFO:werkzeug:172.18.0.1 - - [22/Apr/2025 00:28:51] "GET / HTTP/1.1" 200 -
INFO:werkzeug:172.18.0.1 - - [22/Apr/2025 00:28:52] "GET /static/FHIRFLARE.png HTTP/1.1" 304 -

10
logs/supervisord.log
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@ -28,3 +28,13 @@
2025-04-22 00:25:04,493 INFO waiting for flask, tomcat to die
2025-04-22 00:25:05,830 WARN stopped: tomcat (exit status 143)
2025-04-22 00:25:06,852 WARN stopped: flask (terminated by SIGTERM)
2025-04-22 00:27:24,713 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.
2025-04-22 00:27:24,719 INFO supervisord started with pid 1
2025-04-22 00:27:25,731 INFO spawned: 'flask' with pid 7
2025-04-22 00:27:25,736 INFO spawned: 'tomcat' with pid 8
2025-04-22 00:27:36,540 INFO success: flask entered RUNNING state, process has stayed up for > than 10 seconds (startsecs)
2025-04-22 00:27:56,565 INFO success: tomcat entered RUNNING state, process has stayed up for > than 30 seconds (startsecs)
2025-04-22 00:54:33,995 WARN received SIGTERM indicating exit request
2025-04-22 00:54:34,047 INFO waiting for flask, tomcat to die
2025-04-22 00:54:34,740 WARN stopped: tomcat (exit status 143)
2025-04-22 00:54:35,770 WARN stopped: flask (terminated by SIGTERM)

170
logs/tomcat_err.log
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@ -508,3 +508,173 @@
22-Apr-2025 00:25:04.547 INFO [Thread-1] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Apr-2025 00:25:04.657 INFO [Thread-1] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Apr-2025 00:25:04.685 INFO [Thread-1] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]
22-Apr-2025 00:27:26.457 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/10.1.40
22-Apr-2025 00:27:26.467 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Apr 1 2025 17:20:53 UTC
22-Apr-2025 00:27:26.467 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 10.1.40.0
22-Apr-2025 00:27:26.467 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
22-Apr-2025 00:27:26.467 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 5.15.167.4-microsoft-standard-WSL2
22-Apr-2025 00:27:26.467 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
22-Apr-2025 00:27:26.468 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/java/openjdk
22-Apr-2025 00:27:26.468 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 17.0.14+7
22-Apr-2025 00:27:26.468 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Eclipse Adoptium
22-Apr-2025 00:27:26.468 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
22-Apr-2025 00:27:26.468 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dsun.io.useCanonCaches=false
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED
22-Apr-2025 00:27:26.492 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang.reflect=ALL-UNNAMED
22-Apr-2025 00:27:26.493 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED
22-Apr-2025 00:27:26.493 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util=ALL-UNNAMED
22-Apr-2025 00:27:26.493 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
22-Apr-2025 00:27:26.493 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
22-Apr-2025 00:27:26.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat
22-Apr-2025 00:27:26.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat
22-Apr-2025 00:27:26.494 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
22-Apr-2025 00:27:26.501 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [2.0.8] using APR version [1.7.2].
22-Apr-2025 00:27:26.505 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 3.0.13 30 Jan 2024]
22-Apr-2025 00:27:26.893 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
22-Apr-2025 00:27:26.937 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [790] milliseconds
22-Apr-2025 00:27:27.009 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
22-Apr-2025 00:27:27.009 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/10.1.40]
22-Apr-2025 00:27:27.033 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/usr/local/tomcat/webapps/ROOT.war]
22-Apr-2025 00:27:27.058 SEVERE [main] org.apache.catalina.startup.ContextConfig.beforeStart Exception fixing docBase for context []
java.util.zip.ZipException: zip END header not found
at java.base/java.util.zip.ZipFile$Source.findEND(ZipFile.java:1637)
at java.base/java.util.zip.ZipFile$Source.initCEN(ZipFile.java:1645)
at java.base/java.util.zip.ZipFile$Source.<init>(ZipFile.java:1483)
at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1445)
at java.base/java.util.zip.ZipFile$CleanableResource.<init>(ZipFile.java:717)
at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:251)
at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:180)
at java.base/java.util.jar.JarFile.<init>(JarFile.java:346)
at java.base/sun.net.www.protocol.jar.URLJarFile.<init>(URLJarFile.java:103)
at java.base/sun.net.www.protocol.jar.URLJarFile.getJarFile(URLJarFile.java:72)
at java.base/sun.net.www.protocol.jar.JarFileFactory.get(JarFileFactory.java:168)
at java.base/sun.net.www.protocol.jar.JarURLConnection.connect(JarURLConnection.java:131)
at java.base/sun.net.www.protocol.jar.JarURLConnection.getJarFile(JarURLConnection.java:92)
at org.apache.catalina.startup.ExpandWar.expand(ExpandWar.java:123)
at org.apache.catalina.startup.ContextConfig.fixDocBase(ContextConfig.java:812)
at org.apache.catalina.startup.ContextConfig.beforeStart(ContextConfig.java:948)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:292)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:109)
at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:389)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:163)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:599)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:571)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:654)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:964)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1902)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:123)
at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:769)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:420)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1620)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:303)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:109)
at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:389)
at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:336)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:776)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:772)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1203)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1193)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:145)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:749)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:203)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:412)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:870)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.startup.Catalina.start(Catalina.java:761)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:345)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:476)
22-Apr-2025 00:27:27.096 SEVERE [main] org.apache.catalina.startup.HostConfig.deployWAR Error deploying web application archive [/usr/local/tomcat/webapps/ROOT.war]
java.lang.IllegalStateException: Error starting child
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:602)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:571)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:654)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:964)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1902)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:123)
at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:769)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:420)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1620)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:303)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:109)
at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:389)
at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:336)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:776)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:772)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1203)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1193)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:145)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:749)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:203)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:412)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:870)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.startup.Catalina.start(Catalina.java:761)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:345)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:476)
Caused by: org.apache.catalina.LifecycleException: Failed to initialize component [org.apache.catalina.webresources.WarResourceSet@4b520ea8]
at org.apache.catalina.util.LifecycleBase.handleSubClassException(LifecycleBase.java:406)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:125)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:155)
at org.apache.catalina.webresources.StandardRoot.startInternal(StandardRoot.java:723)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.StandardContext.resourcesStart(StandardContext.java:4159)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4281)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:164)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:599)
... 37 more
Caused by: java.lang.IllegalArgumentException: java.util.zip.ZipException: zip END header not found
at org.apache.catalina.webresources.AbstractSingleArchiveResourceSet.initInternal(AbstractSingleArchiveResourceSet.java:141)
at org.apache.catalina.util.LifecycleBase.init(LifecycleBase.java:122)
... 44 more
Caused by: java.util.zip.ZipException: zip END header not found
at java.base/java.util.zip.ZipFile$Source.findEND(ZipFile.java:1637)
at java.base/java.util.zip.ZipFile$Source.initCEN(ZipFile.java:1645)
at java.base/java.util.zip.ZipFile$Source.<init>(ZipFile.java:1483)
at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1445)
at java.base/java.util.zip.ZipFile$CleanableResource.<init>(ZipFile.java:717)
at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:251)
at java.base/java.util.zip.ZipFile.<init>(ZipFile.java:180)
at java.base/java.util.jar.JarFile.<init>(JarFile.java:346)
at org.apache.catalina.webresources.AbstractSingleArchiveResourceSet.initInternal(AbstractSingleArchiveResourceSet.java:138)
... 45 more
22-Apr-2025 00:27:27.100 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/tomcat/webapps/ROOT.war] has finished in [67] ms
22-Apr-2025 00:27:27.101 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/custom]
22-Apr-2025 00:27:27.481 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/custom] has finished in [379] ms
22-Apr-2025 00:27:27.482 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/app]
22-Apr-2025 00:27:27.504 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/app] has finished in [22] ms
22-Apr-2025 00:27:27.510 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
22-Apr-2025 00:27:27.530 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [593] milliseconds
22-Apr-2025 00:54:34.132 INFO [Thread-1] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8080"]
22-Apr-2025 00:54:34.299 INFO [Thread-1] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
22-Apr-2025 00:54:34.497 INFO [Thread-1] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8080"]
22-Apr-2025 00:54:34.519 INFO [Thread-1] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8080"]