docker-compose should be replaced with docker compose #105
Description
Hi,
I tried running the docker setup on a MacBook (Apple M2 Pro).
10.2
The 10.2 version failed with:
docker compose up
WARN[0000] /Users/sdrwacker/workspace/molgenis-docker/molgenis/10.2/docker-compose.yml: the attribute `version` is obsolete, it will be ignored, please remove it to avoid potential confusion
[+] Running 0/2
⠦ molgenis Pulling 1.6s
⠦ frontend Pulling 1.6s
no matching manifest for linux/arm64/v8 in the manifest list entries
10.1
I noticed that the readme still uses docker-compose which is quite outdated. I think, it should be replaced with docker compose.
With neither command I was able to run the setup (10.1)
docker compose up
...
molgenis-1 | Caused by: org.springframework.jdbc.CannotGetJdbcConnectionException: Failed to obtain JDBC Connection; nested exception is org.postgresql.util.PSQLException: FATAL: no pg_hba.conf entry for host "172.18.0.5", user "molgenis", database "molgenis", SSL off
...
molgenis-1 | 30-Jun-2025 12:27:26.558 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [schedulerFactoryBean_Worker-10] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
molgenis-1 | java.base@17/java.lang.Object.wait(Native Method)
molgenis-1 | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
molgenis-1 | 30-Jun-2025 12:27:26.569 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/ROOT] has finished in [17,887] ms
molgenis-1 | 30-Jun-2025 12:27:26.572 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
molgenis-1 | 30-Jun-2025 12:27:26.583 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [17971] milliseconds
molgenis-1 | 30-Jun-2025 12:27:26.811 INFO [schedulerFactoryBean_Worker-5] org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading Illegal access: this web application instance has been stopped already. Could not load [ch.qos.logback.core.status.WarnStatus]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
molgenis-1 | java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [ch.qos.logback.core.status.WarnStatus]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1427)
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1415)
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1254)
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1215)
molgenis-1 | at ch.qos.logback.classic.LoggerContext.noAppenderDefinedWarning(LoggerContext.java:186)
molgenis-1 | at ch.qos.logback.classic.Logger.callAppenders(Logger.java:264)
molgenis-1 | at ch.qos.logback.classic.Logger.buildLoggingEventAndAppend(Logger.java:421)
molgenis-1 | at ch.qos.logback.classic.Logger.filterAndLog_0_Or3Plus(Logger.java:383)
molgenis-1 | at ch.qos.logback.classic.Logger.debug(Logger.java:482)
molgenis-1 | at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:612)
molgenis-1 | Exception in thread "schedulerFactoryBean_Worker-5" java.lang.NoClassDefFoundError: ch/qos/logback/core/status/WarnStatus
molgenis-1 | at ch.qos.logback.classic.LoggerContext.noAppenderDefinedWarning(LoggerContext.java:186)
molgenis-1 | at ch.qos.logback.classic.Logger.callAppenders(Logger.java:264)
molgenis-1 | at ch.qos.logback.classic.Logger.buildLoggingEventAndAppend(Logger.java:421)
molgenis-1 | at ch.qos.logback.classic.Logger.filterAndLog_0_Or3Plus(Logger.java:383)
molgenis-1 | at ch.qos.logback.classic.Logger.debug(Logger.java:482)
molgenis-1 | at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:612)
molgenis-1 | Caused by: java.lang.ClassNotFoundException: Illegal access: this web application instance has been stopped already. Could not load [ch.qos.logback.core.status.WarnStatus]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1417)
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1254)
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1215)
molgenis-1 | ... 6 more
molgenis-1 | Caused by: java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [ch.qos.logback.core.status.WarnStatus]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1427)
molgenis-1 | at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1415)
molgenis-1 | ... 8 more
and on localhost:80 I see
10.0
This version worked.
But I was not able to upload the simple data example:
simple_data_example_v20180912.xlsx
Import failed; No packages exist that allow for adding entity types and packages. (DS07)