Opal and the old rserve (pre Rock)

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Tom Bishop

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Jul 11, 2023, 2:49:52 PM7/11/23

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Hi,

We have a collaborator who we have been unable to persuade to move to a containerised deployment and is in fact not even running Rock.

Since upgrading to Opal 4.6.1, we have not been able to work with DataSHIELD because of a problem with rserve. The error is:

2023-07-07 14:56:59,543 [main] ERROR org.obiba.opal.r.service.RResourceProvidersService - Resource packages discovery failed for R servers cluster: default
org.apache.shiro.UnavailableSecurityManagerException: No SecurityManager accessible to the calling code, either bound to the org.apache.shiro.util.ThreadContext or as a vm static singleton.  This is an invalid application configuration.

We also see:

2023-07-07 06:56:50,183 [pool-13-thread-1] ERROR org.obiba.opal.r.rserve.RserveService - Error when reading installed packages

In the Administration-R UI it says that rserve is alive and it has a green status.

Is there anything simple we can try, or will I need to more strongly insist that they move to Docker?

Thanks,

Tom

Ramin H.A.

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Jul 11, 2023, 3:29:23 PM7/11/23

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Hi Tom,

Just a quick note, the collaborator can install Rock as a service (deb/rpm) w/out using a Docker image. The transition is simple:

stop Opal
stop the RServer
remove/comment out any reference to the RServer in Opal configuration file opal-config.properties
start Opal and Rock
add Rock server address via Opal `Administration / Apps` section as in Opal Demo

More information:

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Tom Bishop

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Jul 12, 2023, 5:53:59 AM7/12/23

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Thanks Ramin - we will give this a go as a compromise between a full rebuild of their deployment and fixing what they have already. Hopefully it will go smoothly....

From: obiba...@googlegroups.com <obiba...@googlegroups.com> on behalf of Ramin H.A. <rha...@maelstrom-research.org>
Sent: Tuesday, July 11, 2023 8:28 PM
To: obiba...@googlegroups.com <obiba...@googlegroups.com>
Subject: Re: [OBiBa] Opal and the old rserve (pre Rock)

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Yannick Marcon

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Jul 12, 2023, 6:07:20 AM7/12/23

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Hi,

If it is an R failure, changing for Rock will not help. What is the stack trace you get after the message "Error when reading installed packages"?

Regqrds

Yannick

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Tom Bishop

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Jul 12, 2023, 6:08:48 AM7/12/23

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Hi Yannick,

We have this:

2023-07-07 06:56:50,183 [pool-13-thread-1] ERROR org.obiba.opal.r.rserve.RserveService - Error when reading installed packages
java.lang.NullPointerException: null
	at org.obiba.opal.r.service.AbstractRServerSession.setBusy(AbstractRServerSession.java:262)
	at org.obiba.opal.r.rserve.RserveSession.execute(RserveSession.java:67)
	at org.obiba.opal.r.rserve.RserveService.execute(RserveService.java:113)
	at org.obiba.opal.r.rserve.RserveService.getInstalledPackages(RserveService.java:322)
	at org.obiba.opal.r.rserve.RserveService.getInstalledPackagesDtos(RserveService.java:197)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
2023-07-07 06:58:44,222 [qtp1894861020-152] INFO  org.obiba.opal.fs.OpalFileSystem - Setting up Opal filesystem rooted at 'file:///var/lib/opal/fs'
2023-07-07 06:58:44,240 [qtp1894861020-152] INFO  org.apache.commons.vfs2.impl.StandardFileSystemManager - Using "/tmp/vfs_cache" as temporary files store.
2023-07-07 06:58:55,377 [qtp1894861020-33] WARN  org.jboss.resteasy.resteasy_jaxrs.i18n - RESTEASY002142: Multiple resource methods match request "GET

Thanks

Tom

From: obiba...@googlegroups.com <obiba...@googlegroups.com> on behalf of Yannick Marcon <yannick...@obiba.org>
Sent: Wednesday, July 12, 2023 11:07 AM

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Yannick Marcon

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Jul 12, 2023, 6:41:37 AM7/12/23

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Ah let me check the code before upgrading anything.

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Yannick Marcon

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Jul 12, 2023, 8:31:23 AM7/12/23

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Please try with opal 4.6.2.

Tom Bishop

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Jul 12, 2023, 8:36:29 AM7/12/23

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Thanks Yannick we will give it a try

From: obiba...@googlegroups.com <obiba...@googlegroups.com> on behalf of Yannick Marcon <yannick...@obiba.org>

Sent: Wednesday, July 12, 2023 1:31 PM

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Tom Bishop

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Jul 12, 2023, 9:10:36 AM7/12/23

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Well, we don't see the error in the log anymore - thank you! - , but unfortunately we still cannot start a DataSHIELD session. The Opal log is copied below. From R, when assigning data we just get stuck on this forever:

As far as I can see there weren't errors in other logs (e.g. RServe.log), which is why I focused on Opal where we saw the R related error.

2023-07-12 12:39:52,523 [main] INFO org.obiba.opal.server.OpalServer - Starting Opal server!

2023-07-12 12:39:52,526 [main] INFO org.obiba.opal.server.OpalServer - Upgrading Opal...

2023-07-12 12:39:53,254 [main] INFO org.objectweb.jotm - CAROL initialization

2023-07-12 12:39:53,263 [main] INFO org.objectweb.jotm - JOTM started with a local transaction factory

2023-07-12 12:39:54,146 [main] INFO org.hibernate.validator.internal.util.Version - HV000001: Hibernate Validator 6.2.4.Final

2023-07-12 12:39:54,414 [main] INFO org.obiba.opal.core.service.LocalOrientDbServerFactory - Start OrientDB server (plocal:/var/lib/opal/data/orientdb/opal-config)

2023-07-12 12:39:54,728 [main] INFO com.orientechnologies.orient.server.config.OServerConfigurationLoaderXml - Loading configuration from input stream

2023-07-12 12:40:00,594 [main] INFO hsqldb.db.HSQLDB6899FD123C.ENGINE - checkpointClose start

2023-07-12 12:40:00,595 [main] INFO hsqldb.db.HSQLDB6899FD123C.ENGINE - checkpointClose synched

2023-07-12 12:40:00,605 [main] INFO hsqldb.db.HSQLDB6899FD123C.ENGINE - checkpointClose script done

2023-07-12 12:40:00,613 [main] INFO hsqldb.db.HSQLDB6899FD123C.ENGINE - checkpointClose end

2023-07-12 12:40:00,660 [main] INFO hsqldb.db.HSQLDB6899FD123C.ENGINE - Database closed

2023-07-12 12:40:00,847 [main] INFO org.obiba.runtime.upgrade.support.DefaultUpgradeManager - Setting version to : 4.6.2

2023-07-12 12:40:00,869 [main] INFO org.obiba.opal.core.service.LocalOrientDbServerFactory - Stop OrientDB server (plocal:/var/lib/opal/data/orientdb/opal-config)

2023-07-12 12:40:01,138 [main] INFO org.objectweb.jotm - stop JOTM

2023-07-12 12:40:01,143 [main] INFO org.obiba.opal.server.OpalServer - Upgrade successful.

2023-07-12 12:40:01,143 [main] INFO org.obiba.opal.server.OpalServer - Starting Opal...

2023-07-12 12:40:01,172 [main] INFO org.eclipse.jetty.util.log - Logging initialized @9401ms to org.eclipse.jetty.util.log.Slf4jLog

2023-07-12 12:40:01,232 [main] INFO org.obiba.opal.server.httpd.OpalJettyServer - Creating a file handler for the following URL : file:///usr/share/opal-server-4.6.2//webapp

2023-07-12 12:40:01,273 [main] INFO org.obiba.opal.server.httpd.OpalJettyServer - Creating a file handler for the following URL : file:///var/lib/opal/extensions/webapp/

2023-07-12 12:40:01,320 [main] INFO org.obiba.opal.server.httpd.OpalJettyServer - Starting Opal HTTP/s Server on ports 8080/8443

2023-07-12 12:40:01,324 [main] INFO org.eclipse.jetty.server.Server - jetty-9.4.51.v20230217; built: 2023-02-17T08:19:37.309Z; git: b45c405e4544384de066f814ed42ae3dceacdd49; jvm 1.8.0_201-b09

2023-07-12 12:40:01,344 [main] INFO org.eclipse.jetty.server.handler.ContextHandler - Started o.e.j.s.h.ContextHandler@1002d192{/,null,AVAILABLE}

2023-07-12 12:40:01,344 [main] INFO org.eclipse.jetty.server.handler.ContextHandler - Started o.e.j.s.h.ContextHandler@9281d19{/,null,AVAILABLE}

2023-07-12 12:40:01,349 [main] INFO org.eclipse.jetty.server.session - DefaultSessionIdManager workerName=node0

2023-07-12 12:40:01,349 [main] INFO org.eclipse.jetty.server.session - No SessionScavenger set, using defaults

2023-07-12 12:40:01,351 [main] INFO org.eclipse.jetty.server.session - node0 Scavenging every 660000ms

2023-07-12 12:40:01,354 [main] WARN org.eclipse.jetty.security.SecurityHandler - Servlet...@o.e.j.s.ServletContextHandler@19d53ab4{/,null,STARTING} has uncovered http methods for path: /

2023-07-12 12:40:01,467 [main] INFO org.eclipse.jetty.server.handler.ContextHandler.ROOT - Initializing Spring root WebApplicationContext

2023-07-12 12:40:01,467 [main] INFO org.springframework.web.context.ContextLoader - Root WebApplicationContext: initialization started

2023-07-12 12:40:02,573 [main] INFO org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - Bean 'eventBusConfiguration' of type [org.obiba.opal.core.runtime.EventBusConfiguration$$EnhancerBySpringCGLIB$$4f1631ea] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2023-07-12 12:40:02,664 [main] INFO org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker - Bean 'eventBus' of type [com.google.common.eventbus.EventBus] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)

2023-07-12 12:40:02,766 [main] INFO org.obiba.opal.core.service.LocalOrientDbServerFactory - Start OrientDB server (plocal:/var/lib/opal/data/orientdb/opal-config)

2023-07-12 12:40:04,988 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean subjectAclServiceImpl (org.obiba.opal.core.service.security.SubjectAclServiceImpl) containing method onSubjectProfileDeleted to EventBus

2023-07-12 12:40:05,168 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean subjectProfileServiceImpl (org.obiba.opal.core.service.SubjectProfileServiceImpl) containing method onSubjectCredentialsDeleted to EventBus

2023-07-12 12:40:05,472 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean spatialRealm (org.obiba.opal.core.service.security.realm.SpatialRealm) containing method onSubjectAclChangedEvent to EventBus

2023-07-12 12:40:05,490 [main] WARN org.apache.shiro.realm.text.IniRealm - Users or Roles are already populated. Configured Ini instance will be ignored.

2023-07-12 12:40:05,490 [main] WARN org.apache.shiro.realm.text.IniRealm - Users or Roles are already populated. resourcePath 'classpath:shiro.ini' will be ignored.

2023-07-12 12:40:05,618 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean subjectTokenServiceImpl (org.obiba.opal.core.service.SubjectTokenServiceImpl) containing method onSubjectProfileDeleted to EventBus

2023-07-12 12:40:05,961 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.shiro.realm.CookieAuthenticatingRealm.authorizationCache' does not yet exist. Creating now.

2023-07-12 12:40:05,973 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.shiro.realm.CookieAuthenticatingRealm.authorizationCache]

2023-07-12 12:40:05,975 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.shiro.realm.HttpHeaderAuthenticatingRealm.authorizationCache.1' does not yet exist. Creating now.

2023-07-12 12:40:05,980 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.shiro.realm.HttpHeaderAuthenticatingRealm.authorizationCache.1]

2023-07-12 12:40:05,980 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.shiro.realm.SudoRealm.authorizationCache.2' does not yet exist. Creating now.

2023-07-12 12:40:05,985 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.shiro.realm.SudoRealm.authorizationCache.2]

2023-07-12 12:40:05,985 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.opal.core.service.security.realm.BackgroundJobRealm.authorizationCache.3' does not yet exist. Creating now.

2023-07-12 12:40:05,989 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.opal.core.service.security.realm.BackgroundJobRealm.authorizationCache.3]

2023-07-12 12:40:05,990 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.opal.core.service.security.realm.OpalApplicationRealm.authorizationCache.4' does not yet exist. Creating now.

2023-07-12 12:40:05,994 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.opal.core.service.security.realm.OpalApplicationRealm.authorizationCache.4]

2023-07-12 12:40:05,995 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.opal.core.service.security.realm.OpalTokenRealm.authorizationCache.7' does not yet exist. Creating now.

2023-07-12 12:40:05,999 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.opal.core.service.security.realm.OpalTokenRealm.authorizationCache.7]

2023-07-12 12:40:06,000 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.opal.core.service.security.realm.SpatialRealm.authorizationCache.5' does not yet exist. Creating now.

2023-07-12 12:40:06,004 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.opal.core.service.security.realm.SpatialRealm.authorizationCache.5]

2023-07-12 12:40:06,004 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.opal.core.service.security.realm.SpatialRealm.authorizationCache.5_role' does not yet exist. Creating now.

2023-07-12 12:40:06,008 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.opal.core.service.security.realm.SpatialRealm.authorizationCache.5_role]

2023-07-12 12:40:06,008 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Cache with name 'org.obiba.shiro.realm.ObibaRealm.authorizationCache.9' does not yet exist. Creating now.

2023-07-12 12:40:06,012 [main] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Added EhCache named [org.obiba.shiro.realm.ObibaRealm.authorizationCache.9]

2023-07-12 12:40:06,097 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean RServerManagerService (org.obiba.opal.r.service.RServerManagerService) containing method onAppUnregistered to EventBus

2023-07-12 12:40:06,108 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean opalRSessionManager (org.obiba.opal.r.service.OpalRSessionManager) containing method onRServiceStopped to EventBus

2023-07-12 12:40:06,357 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean defaultDatabaseRegistry (com.sun.proxy.$Proxy39) containing method onDatasourceDeleted to EventBus

2023-07-12 12:40:06,364 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean RSQLService (org.obiba.opal.r.service.RSQLService) containing method onRServiceStarted to EventBus

2023-07-12 12:40:06,402 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean RResourceProvidersService (org.obiba.opal.r.service.RResourceProvidersService) containing method onRServiceInitialized to EventBus

2023-07-12 12:40:06,424 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean opalSearchService (org.obiba.opal.search.service.OpalSearchService) containing method onValueTableRenamed to EventBus

2023-07-12 12:40:06,469 [main] INFO org.apache.sshd.common.util.SecurityUtils - Trying to register BouncyCastle as a JCE provider

2023-07-12 12:40:06,659 [main] INFO org.apache.sshd.common.util.SecurityUtils - Registration succeeded

2023-07-12 12:40:06,842 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean resourceReferenceServiceImpl (org.obiba.opal.core.service.ResourceReferenceServiceImpl) containing method onProjectDeleted to EventBus

2023-07-12 12:40:07,009 [Datasource Loader 1] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource Loader 1: started

2023-07-12 12:40:07,010 [Datasource Loader 3] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource Loader 3: started

2023-07-12 12:40:07,009 [Datasource Loader 2] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource Loader 2: started

2023-07-12 12:40:07,110 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean projectsServiceImpl (com.sun.proxy.$Proxy83) containing method onValueTableDeleted to EventBus

2023-07-12 12:40:07,119 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-memory-5.5.4.jar

2023-07-12 12:40:07,120 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-sandbox-5.5.4.jar

2023-07-12 12:40:07,121 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/t-digest-3.0.jar

2023-07-12 12:40:07,121 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-suggest-5.5.4.jar

2023-07-12 12:40:07,121 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/jsr166e-1.1.0.jar

2023-07-12 12:40:07,121 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-backward-codecs-5.5.4.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/compress-lzf-1.0.2.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/opal-search-es-1.0.0.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-spatial-5.5.4.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/jackson-dataformat-yaml-2.8.1.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/securesm-1.0.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-spatial3d-5.5.4.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-analyzers-common-5.5.4.jar

2023-07-12 12:40:07,122 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/jackson-dataformat-smile-2.8.1.jar

2023-07-12 12:40:07,123 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-join-5.5.4.jar

2023-07-12 12:40:07,123 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-queryparser-5.5.4.jar

2023-07-12 12:40:07,124 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-misc-5.5.4.jar

2023-07-12 12:40:07,124 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/jackson-dataformat-cbor-2.8.1.jar

2023-07-12 12:40:07,126 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-grouping-5.5.4.jar

2023-07-12 12:40:07,126 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-core-5.5.4.jar

2023-07-12 12:40:07,126 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/hppc-0.7.1.jar

2023-07-12 12:40:07,126 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-highlighter-5.5.4.jar

2023-07-12 12:40:07,126 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/lucene-queries-5.5.4.jar

2023-07-12 12:40:07,126 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/netty-3.10.6.Final.jar

2023-07-12 12:40:07,126 [main] INFO org.obiba.plugins.PluginResources - Adding library file to classpath: /var/lib/opal/plugins/opal-search-es-1.0.0/lib/elasticsearch-2.4.5.jar

2023-07-12 12:40:11,147 [main] INFO org.elasticsearch.node - [Harold "Happy" Hogan] version[2.4.5], pid[27480], build[c849dd1/2017-04-24T16:18:17Z]

2023-07-12 12:40:11,148 [main] INFO org.elasticsearch.node - [Harold "Happy" Hogan] initializing ...

2023-07-12 12:40:11,154 [main] INFO org.elasticsearch.plugins - [Harold "Happy" Hogan] modules [], plugins [], sites []

2023-07-12 12:40:11,183 [main] INFO org.elasticsearch.env - [Harold "Happy" Hogan] using [1] data paths, mounts [[/ (/dev/vda1)]], net usable_space [70.2gb], net total_space [77.3gb], spins? [possibly], types [ext4]

2023-07-12 12:40:11,183 [main] INFO org.elasticsearch.env - [Harold "Happy" Hogan] heap size [4gb], compressed ordinary object pointers [true]

2023-07-12 12:40:11,184 [main] WARN org.elasticsearch.env - [Harold "Happy" Hogan] max file descriptors [16384] for elasticsearch process likely too low, consider increasing to at least [65536]

2023-07-12 12:40:13,647 [main] INFO org.elasticsearch.node - [Harold "Happy" Hogan] initialized

2023-07-12 12:40:13,647 [main] INFO org.elasticsearch.node - [Harold "Happy" Hogan] starting ...

2023-07-12 12:40:13,751 [main] INFO org.elasticsearch.transport - [Harold "Happy" Hogan] publish_address {127.0.0.1:9300}, bound_addresses {[::1]:9300}, {127.0.0.1:9300}

2023-07-12 12:40:13,757 [main] INFO org.elasticsearch.discovery - [Harold "Happy" Hogan] opal/6iTw62swRWSrOOVozjX-BA

2023-07-12 12:40:16,865 [elasticsearch[Harold "Happy" Hogan][clusterService#updateTask][T#1]] INFO org.elasticsearch.cluster.service - [Harold "Happy" Hogan] new_master {Harold "Happy" Hogan}{6iTw62swRWSrOOVozjX-BA}{127.0.0.1}{127.0.0.1:9300}, reason: zen-disco-join(elected_as_master, [0] joins received)

2023-07-12 12:40:16,877 [main] INFO org.elasticsearch.node - [Harold "Happy" Hogan] started

2023-07-12 12:40:16,878 [main] INFO org.obiba.opal.server.sshd.OpalSshServer - Starting Opal SSH Server on port 8022

2023-07-12 12:40:16,986 [elasticsearch[Harold "Happy" Hogan][clusterService#updateTask][T#1]] INFO org.elasticsearch.gateway - [Harold "Happy" Hogan] recovered [2] indices into cluster_state

2023-07-12 12:40:17,025 [transactional-thread-org.obiba.opal.core.runtime.DefaultOpalRuntime$$Lambda$261/1736382819] INFO org.obiba.opal.core.service.ProjectsState - Project test to state LOADING

2023-07-12 12:40:17,025 [transactional-thread-org.obiba.opal.core.runtime.DefaultOpalRuntime$$Lambda$261/1736382819] INFO org.obiba.opal.core.service.ProjectsState - Project fish to state LOADING

2023-07-12 12:40:17,025 [transactional-thread-org.obiba.opal.core.runtime.DefaultOpalRuntime$$Lambda$261/1736382819] INFO org.obiba.opal.core.service.ProjectsState - Project Meat to state LOADING

2023-07-12 12:40:17,025 [transactional-thread-org.obiba.opal.core.runtime.DefaultOpalRuntime$$Lambda$261/1736382819] INFO org.obiba.opal.core.service.ProjectsState - Project legumes to state LOADING

2023-07-12 12:40:17,034 [Datasource Loader 1] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource Loader 1: loading datasource of project test

2023-07-12 12:40:17,034 [Datasource Loader 2] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource Loader 2: loading datasource of project Meat

2023-07-12 12:40:17,034 [Datasource Loader 3] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource Loader 3: loading datasource of project fish

2023-07-12 12:40:17,057 [Datasource Loader 1] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load start: test

2023-07-12 12:40:17,057 [Datasource Loader 2] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load start: Meat

2023-07-12 12:40:17,057 [Datasource Loader 3] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load start: fish

2023-07-12 12:40:17,063 [Datasource Loader 2] INFO org.obiba.opal.core.service.DefaultDatabaseRegistry - Building DataSource opal_data

2023-07-12 12:40:17,670 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean appsServiceImpl (org.obiba.opal.core.service.AppsServiceImpl) containing method onAppRejected to EventBus

2023-07-12 12:40:17,672 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean rockServerDiscoveryService (org.obiba.opal.r.rock.RockServerDiscoveryService) containing method onAppUnregistered to EventBus

2023-07-12 12:40:18,368 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean RActivityService (org.obiba.opal.r.service.RActivityService) containing method onRServerSessionStarted to EventBus

2023-07-12 12:40:18,477 [elasticsearch[Harold "Happy" Hogan][clusterService#updateTask][T#1]] INFO org.elasticsearch.cluster.routing.allocation - [Harold "Happy" Hogan] Cluster health status changed from [RED] to [YELLOW] (reason: [shards started [[opal-variables][3], [opal-variables][3]] ...]).

2023-07-12 12:40:18,699 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean indexManagerConfigurationService (org.obiba.opal.search.IndexManagerConfigurationService) containing method onValueTableRenamed to EventBus

2023-07-12 12:40:18,718 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean indexSynchronizationManager (org.obiba.opal.search.IndexSynchronizationManager$$EnhancerBySpringCGLIB$$f0d283b0) containing method onSynchronizeIndex to EventBus

2023-07-12 12:40:18,818 [Datasource Loader 1] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load end: test (JdbcDatasourceFactory)

2023-07-12 12:40:18,820 [Datasource Loader 1] INFO org.obiba.opal.core.service.ProjectsState - Project test to state READY

2023-07-12 12:40:18,820 [Datasource Loader 1] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource Loader 1: loading datasource of project legumes

2023-07-12 12:40:18,820 [Datasource Loader 1] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load start: legumes

2023-07-12 12:40:18,863 [main] INFO org.quartz.impl.StdSchedulerFactory - Using default implementation for ThreadExecutor

2023-07-12 12:40:18,935 [main] INFO org.quartz.core.SchedulerSignalerImpl - Initialized Scheduler Signaller of type: class org.quartz.core.SchedulerSignalerImpl

2023-07-12 12:40:18,935 [main] INFO org.quartz.core.QuartzScheduler - Quartz Scheduler v.2.3.2 created.

2023-07-12 12:40:18,944 [Datasource Loader 3] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load end: fish (JdbcDatasourceFactory)

2023-07-12 12:40:18,944 [Datasource Loader 2] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load end: Meat (JdbcDatasourceFactory)

2023-07-12 12:40:18,946 [Datasource Loader 3] INFO org.obiba.opal.core.service.ProjectsState - Project fish to state READY

2023-07-12 12:40:18,948 [main] INFO org.springframework.scheduling.quartz.LocalDataSourceJobStore - JobStoreCMT initialized.

2023-07-12 12:40:18,949 [main] INFO org.quartz.core.QuartzScheduler - Scheduler meta-data: Quartz Scheduler (v2.3.2) 'Opal Scheduler' with instanceId 'NON_CLUSTERED'

Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.

NOT STARTED.

Currently in standby mode.

Number of jobs executed: 0

Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 10 threads.

Using job-store 'org.springframework.scheduling.quartz.LocalDataSourceJobStore' - which supports persistence. and is not clustered.

2023-07-12 12:40:18,949 [main] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler 'Opal Scheduler' initialized from an externally provided properties instance.

2023-07-12 12:40:18,949 [main] INFO org.quartz.impl.StdSchedulerFactory - Quartz scheduler version: 2.3.2

2023-07-12 12:40:18,949 [main] INFO org.quartz.core.QuartzScheduler - JobFactory set to: org.springframework.scheduling.quartz.SpringBeanJobFactory@268206aa

2023-07-12 12:40:18,949 [Datasource Loader 2] INFO org.obiba.opal.core.service.ProjectsState - Project Meat to state READY

2023-07-12 12:40:19,067 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean opalCallbackFilter (org.obiba.opal.server.httpd.OpalCallbackFilter) containing method onOpalGeneralConfigUpdated to EventBus

2023-07-12 12:40:19,077 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean opalLoginFilter (org.obiba.opal.server.httpd.OpalLoginFilter) containing method onOpalGeneralConfigUpdated to EventBus

2023-07-12 12:40:19,162 [Datasource Loader 1] INFO org.obiba.opal.core.service.DatasourceLoaderServiceImpl - Datasource load end: legumes (JdbcDatasourceFactory)

2023-07-12 12:40:19,163 [Datasource Loader 1] INFO org.obiba.opal.core.service.ProjectsState - Project legumes to state READY

2023-07-12 12:40:19,297 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean opalAnalysisServiceImpl (org.obiba.opal.core.service.OpalAnalysisServiceImpl) containing method onDatasourceDeleted to EventBus

2023-07-12 12:40:19,468 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean projectPermissionsUpdateListener (org.obiba.opal.core.service.ProjectPermissionsUpdateListener) containing method onDatasourceDeleted to EventBus

2023-07-12 12:40:19,678 [main] INFO org.obiba.opal.core.runtime.EventBusConfiguration$EventBusSubscriberPostProcessor - Register bean VCFSamplesMappingServiceImpl (org.obiba.opal.core.service.VCFSamplesMappingServiceImpl) containing method onValueTableRenamed to EventBus

2023-07-12 12:40:19,710 [main] INFO org.obiba.opal.core.service.QuartzTablesCreator - Don't Quartz tables as they already exist

2023-07-12 12:40:20,080 [main] INFO org.springframework.scheduling.quartz.SchedulerFactoryBean - Starting Quartz Scheduler now

2023-07-12 12:40:20,102 [main] INFO org.springframework.scheduling.quartz.LocalDataSourceJobStore - Freed 0 triggers from 'acquired' / 'blocked' state.

2023-07-12 12:40:20,105 [main] INFO org.springframework.scheduling.quartz.LocalDataSourceJobStore - Recovering 0 jobs that were in-progress at the time of the last shut-down.

2023-07-12 12:40:20,105 [main] INFO org.springframework.scheduling.quartz.LocalDataSourceJobStore - Recovery complete.

2023-07-12 12:40:20,106 [main] INFO org.springframework.scheduling.quartz.LocalDataSourceJobStore - Removed 0 'complete' triggers.

2023-07-12 12:40:20,106 [main] INFO org.springframework.scheduling.quartz.LocalDataSourceJobStore - Removed 0 stale fired job entries.

2023-07-12 12:40:20,111 [main] INFO org.quartz.core.QuartzScheduler - Scheduler Opal Scheduler_$_NON_CLUSTERED started.

2023-07-12 12:40:20,359 [main] INFO org.springframework.scheduling.annotation.ScheduledAnnotationBeanPostProcessor - No TaskScheduler/ScheduledExecutorService bean found for scheduled processing

2023-07-12 12:40:20,374 [main] INFO org.springframework.web.context.ContextLoader - Root WebApplicationContext initialized in 18906 ms

2023-07-12 12:40:20,374 [main] INFO org.eclipse.jetty.server.handler.ContextHandler.ROOT - Initializing Shiro environment

2023-07-12 12:40:20,374 [main] INFO org.apache.shiro.web.env.EnvironmentLoader - Starting Shiro environment initialization.

2023-07-12 12:40:20,378 [main] INFO org.apache.shiro.web.env.EnvironmentLoader - Shiro environment initialized in 4 ms.

2023-07-12 12:40:20,392 [main] INFO org.eclipse.jetty.server.handler.ContextHandler - Started o.e.j.s.ServletContextHandler@19d53ab4{/,null,AVAILABLE}

2023-07-12 12:40:20,409 [main] INFO org.eclipse.jetty.server.AbstractConnector - Started ServerConnector@dada335{HTTP/1.1, (http/1.1)}{0.0.0.0:8080}

2023-07-12 12:40:20,503 [main] INFO org.eclipse.jetty.server.AbstractConnector - Started ServerConnector@693f2213{SSL, (ssl, http/1.1)}{0.0.0.0:8443}

2023-07-12 12:40:20,503 [main] INFO org.eclipse.jetty.server.Server - Started @28732ms

2023-07-12 12:40:20,503 [main] INFO org.obiba.opal.server.OpalServer - Opal Server successfully started.

2023-07-12 12:40:20,508 [main] INFO org.obiba.opal.r.service.RResourceProvidersService - Opal started, R services to be finalized...

2023-07-12 12:40:20,508 [main] INFO org.obiba.opal.core.service.ProjectsServiceImpl - Resource providers ready, scanning for views to initialise...

2023-07-12 12:43:12,033 [qtp1894861020-35] INFO org.apache.shiro.session.mgt.AbstractValidatingSessionManager - Enabling session validation scheduler...

2023-07-12 12:43:12,037 [qtp1894861020-35] INFO org.apache.shiro.cache.ehcache.EhCacheManager - Using existing EHCache named [shiro-activeSessionCache]

2023-07-12 12:43:12,201 [qtp1894861020-35] INFO org.obiba.opal.fs.OpalFileSystem - Setting up Opal filesystem rooted at 'file:///var/lib/opal/fs'

2023-07-12 12:43:12,218 [qtp1894861020-35] INFO org.apache.commons.vfs2.impl.StandardFileSystemManager - Using "/tmp/vfs_cache" as temporary files store.

2023-07-12 12:43:12,841 [qtp1894861020-35] INFO org.obiba.opal.web.datashield.DatashieldSessionsResourceImpl - datashield.seed = 205042048

2023-07-12 12:44:40,264 [qtp1894861020-32] INFO org.obiba.opal.web.datashield.DatashieldSessionsResourceImpl - datashield.seed = 205042048

2023-07-12 12:45:27,314 [qtp1894861020-33] INFO org.obiba.opal.web.datashield.DatashieldSessionsResourceImpl - datashield.seed = 205042048

2023-07-12 12:48:12,038 [SessionValidationThread-1] INFO org.apache.shiro.session.mgt.AbstractValidatingSessionManager - Validating all active sessions...

2023-07-12 12:48:12,040 [SessionValidationThread-1] INFO org.apache.shiro.session.mgt.AbstractValidatingSessionManager - Finished session validation. No sessions were stopped.

2023-07-12 12:53:12,034 [SessionValidationThread-1] INFO org.apache.shiro.session.mgt.AbstractValidatingSessionManager - Validating all active sessions...

2023-07-12 12:53:12,035 [SessionValidationThread-1] INFO org.apache.shiro.session.mgt.AbstractValidatingSessionManager - Finished session validation. No sessions were stopped.

From: 'Tom Bishop' via obiba-users <obiba...@googlegroups.com>
Sent: Wednesday, July 12, 2023 1:36 PM

To view this discussion on the web visit https://groups.google.com/d/msgid/obiba-users/LO4P265MB3792D9783EF103D8A2015288B936A%40LO4P265MB3792.GBRP265.PROD.OUTLOOK.COM.

Yannick Marcon

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Jul 12, 2023, 9:38:13 AM7/12/23

to obiba...@googlegroups.com

I am pretty sure it is due to an outdated R package. I had modify some assignment R code to make it work properly with most recent environment.

https://github.com/obiba/opal/commit/faee0c8f0697172eaa5fe145ad626daeca5a9ee8

To view this discussion on the web visit https://groups.google.com/d/msgid/obiba-users/LO4P265MB3792C552D06D68615FA989B7B936A%40LO4P265MB3792.GBRP265.PROD.OUTLOOK.COM.

Tom Bishop

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Jul 12, 2023, 9:47:03 AM7/12/23

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Ok. Does this mean that I should ask them to update R packages through the "Update all packages..." button in Administration->R?

I know that this might not solve it because some updates might fail - but we could see this if they send the log?

Tom

From: obiba...@googlegroups.com <obiba...@googlegroups.com> on behalf of Yannick Marcon <yannick...@obiba.org>

Sent: Wednesday, July 12, 2023 2:37 PM

To view this discussion on the web visit https://groups.google.com/d/msgid/obiba-users/CAGrE6otcqZSa4xoPA3KYw_wT_OhGiy_CRjMn17TmAtVUOHcyUg%40mail.gmail.com.

Yannick Marcon

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Jul 12, 2023, 9:54:30 AM7/12/23

to obiba...@googlegroups.com

You can try this, but I am not sure it is simpler than using a docker image of rock. By the way, the "update all.." is now a background task, which is better in terms of user experience.

Yannick

To view this discussion on the web visit https://groups.google.com/d/msgid/obiba-users/LO4P265MB3792ECF0EA91F7749C5BCF07B936A%40LO4P265MB3792.GBRP265.PROD.OUTLOOK.COM.

Tom Bishop

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Jul 13, 2023, 1:55:50 PM7/13/23

to obiba...@googlegroups.com

We have updated everything in R, and the logs look clean of errors (attached), but it still hangs in the same place.

I guess I will have to go down the Docker route?

Tom

From: obiba...@googlegroups.com <obiba...@googlegroups.com> on behalf of Yannick Marcon <yannick...@obiba.org>

Sent: Wednesday, July 12, 2023 2:54 PM

To view this discussion on the web visit https://groups.google.com/d/msgid/obiba-users/CAGrE6osDzZQ1zbfsZH4Le8zhcuXf-Vim3QbE3hnS4yONdx1Fzw%40mail.gmail.com.

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