Migrating Sonarqube - Database Upgrade Error

Parasappa_Yaragal · February 27, 2022, 2:50pm

Hi,

Version: sonarqube:9.3.0-community
Trying to restore Database from Version: sonarqube:8.5.1-community** to **Version: sonarqube:9.3.0-community`

Currently we are running charts/charts/sonarqube at master · Oteemo/charts · GitHub helm chart with app version `Version: sonarqube:8.5.1-community.

Now we would like to use official [helm chart](https://github.com/SonarSource/helm-chart-sonarqube/tree/master/charts/sonarqube) from SonarQube.

I have followed below steps to backup and restore data from `Version: sonarqube:8.5.1-community.

Steps:

Connect to sonarqube-postgres-0 pod in source
Dump all data from source postgres
pg_dumpall -U postgres --column-inserts -f /tmp/dbAll.sql
Copy /tmp/dbAll.sql from source container to local machine
kubectl cp sonarqube-postgresql-0:/tmp/dbAll.sql ./dbAll.sql
Copy ./dbAll.sql to /tmp/dbAll.sql of destination sonarqube-postgres-0 container
kubectl cp ./dbAll.sql sonarqube-postgresql-0:/tmp/dbAll.sql
In destination sonarqube-postgres-0 pod

psql -U postgres
postgres=# UPDATE pg_database SET datallowconn = 'false' WHERE datname = 'sonarDB';
postgres=# SELECT pg_terminate_backend(pid) FROM pg_stat_activity WHERE datname = 'sonarDB';
postgres=# DROP DATABASE "sonarDB";

7.Connnect to pod sonarqube-postgres-0 and restore from the backup
psql -U postgres < /tmp/dbAll.sql

8.After restore, revert back the datallowconn status disabled in step 6

psql -U postgres
postgres=# UPDATE pg_database SET datallowconn = 'true' WHERE datname = 'sonarDB';

When i visit https:///setup got below error.

Screen Shot 2022-02-27 at 7.30.02 PM3360×1706 188 KB

sonarqube-sonarqube-0 pod logs showing Cannot connect to Database.

2022.02.27 13:21:42 ERROR web[AX87RidhiK28YnMSAACV][o.s.s.w.WebServiceEngine] Fail to process request http://<host>/api/system/db_migration_status
java.lang.IllegalStateException: Cannot connect to Database.
	at com.google.common.base.Preconditions.checkState(Preconditions.java:508)
	at org.sonar.server.platform.ws.DbMigrationStatusAction.handle(DbMigrationStatusAction.java:69)
	at org.sonar.server.ws.WebServiceEngine.execute(WebServiceEngine.java:111)
	at org.sonar.server.platform.web.WebServiceFilter.doFilter(WebServiceFilter.java:84)
	at org.sonar.server.platform.web.MasterServletFilter$GodFilterChain.doFilter(MasterServletFilter.java:139)
	at org.sonar.server.platform.web.SonarLintConnectionFilter.doFilter(SonarLintConnectionFilter.java:66)
	at org.sonar.server.platform.web.MasterServletFilter$GodFilterChain.doFilter(MasterServletFilter.java:139)
	at org.sonar.server.platform.web.MasterServletFilter.doFilter(MasterServletFilter.java:108)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:282)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:279)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/javax.security.auth.Subject.doAsPrivileged(Subject.java:550)
	at org.apache.catalina.security.SecurityUtil.execute(SecurityUtil.java:314)
	at org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:253)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:191)
	at org.apache.catalina.core.ApplicationFilterChain.access$000(ApplicationFilterChain.java:47)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:148)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:144)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:143)
	at org.sonar.server.platform.web.UserSessionFilter.doFilter(UserSessionFilter.java:81)
	at org.sonar.server.platform.web.UserSessionFilter.doFilter(UserSessionFilter.java:68)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:282)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:279)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/javax.security.auth.Subject.doAsPrivileged(Subject.java:550)
	at org.apache.catalina.security.SecurityUtil.execute(SecurityUtil.java:314)
	at org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:253)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:191)
	at org.apache.catalina.core.ApplicationFilterChain.access$000(ApplicationFilterChain.java:47)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:148)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:144)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:143)
	at org.sonar.server.platform.web.CacheControlFilter.doFilter(CacheControlFilter.java:76)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:282)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:279)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/javax.security.auth.Subject.doAsPrivileged(Subject.java:550)
	at org.apache.catalina.security.SecurityUtil.execute(SecurityUtil.java:314)
	at org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:253)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:191)
	at org.apache.catalina.core.ApplicationFilterChain.access$000(ApplicationFilterChain.java:47)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:148)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:144)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:143)
	at org.sonar.server.platform.web.SecurityServletFilter.doHttpFilter(SecurityServletFilter.java:75)
	at org.sonar.server.platform.web.SecurityServletFilter.doFilter(SecurityServletFilter.java:47)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:282)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:279)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/javax.security.auth.Subject.doAsPrivileged(Subject.java:550)
	at org.apache.catalina.security.SecurityUtil.execute(SecurityUtil.java:314)
	at org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:253)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:191)
	at org.apache.catalina.core.ApplicationFilterChain.access$000(ApplicationFilterChain.java:47)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:148)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:144)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:143)
	at org.sonar.server.platform.web.RedirectFilter.doFilter(RedirectFilter.java:57)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:282)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:279)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/javax.security.auth.Subject.doAsPrivileged(Subject.java:550)
	at org.apache.catalina.security.SecurityUtil.execute(SecurityUtil.java:314)
	at org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:253)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:191)
	at org.apache.catalina.core.ApplicationFilterChain.access$000(ApplicationFilterChain.java:47)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:148)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:144)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:143)
	at org.sonar.server.platform.web.RequestIdFilter.doFilter(RequestIdFilter.java:66)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:282)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:279)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/javax.security.auth.Subject.doAsPrivileged(Subject.java:550)
	at org.apache.catalina.security.SecurityUtil.execute(SecurityUtil.java:314)
	at org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:253)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:191)
	at org.apache.catalina.core.ApplicationFilterChain.access$000(ApplicationFilterChain.java:47)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:148)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:144)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:143)
	at org.sonar.server.platform.web.RootFilter.doFilter(RootFilter.java:62)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:282)
	at org.apache.catalina.security.SecurityUtil$1.run(SecurityUtil.java:279)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/javax.security.auth.Subject.doAsPrivileged(Subject.java:550)
	at org.apache.catalina.security.SecurityUtil.execute(SecurityUtil.java:314)
	at org.apache.catalina.security.SecurityUtil.doAsPrivilege(SecurityUtil.java:253)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:191)
	at org.apache.catalina.core.ApplicationFilterChain.access$000(ApplicationFilterChain.java:47)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:148)
	at org.apache.catalina.core.ApplicationFilterChain$1.run(ApplicationFilterChain.java:144)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:143)
	at org.apache.catalina.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:109)
	at jdk.internal.reflect.GeneratedMethodAccessor20.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

If i try to restart the sonarqube-sonarqube-0 container, it runs the initial database schema migration and fails with relationships are already exist. See attached log.

2022.02.27 13:58:38 INFO  web[][o.s.s.p.d.m.AutoDbMigration] Automatically perform DB migration on fresh install
2022.02.27 13:58:38 INFO  web[][DbMigrations] Executing DB migrations...
2022.02.27 13:58:38 INFO  web[][DbMigrations] #1 'Create initial schema'...
2022.02.27 13:58:39 ERROR web[][DbMigrations] #1 'Create initial schema': failure | time=96ms
2022.02.27 13:58:39 ERROR web[][DbMigrations] Executed DB migrations: failure | time=102ms
2022.02.27 13:58:39 ERROR web[][o.s.s.p.PlatformImpl] Web server startup failed
org.sonar.server.platform.db.migration.step.MigrationStepExecutionException: Execution of migration step #1 'Create initial schema' failed
	at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:79)
	at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:67)
	at com.google.common.collect.ImmutableList.forEach(ImmutableList.java:405)
	at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:52)
	at org.sonar.server.platform.db.migration.engine.MigrationEngineImpl.execute(MigrationEngineImpl.java:68)
	at org.sonar.server.platform.db.migration.AutoDbMigration.start(AutoDbMigration.java:40)
	at org.sonar.core.platform.StartableCloseableSafeLifecyleStrategy.start(StartableCloseableSafeLifecyleStrategy.java:40)
	at org.picocontainer.injectors.AbstractInjectionFactory$LifecycleAdapter.start(AbstractInjectionFactory.java:84)
	at org.picocontainer.behaviors.AbstractBehavior.start(AbstractBehavior.java:169)
	at org.picocontainer.behaviors.Stored$RealComponentLifecycle.start(Stored.java:132)
	at org.picocontainer.behaviors.Stored.start(Stored.java:110)
	at org.picocontainer.DefaultPicoContainer.potentiallyStartAdapter(DefaultPicoContainer.java:1016)
	at org.picocontainer.DefaultPicoContainer.startAdapters(DefaultPicoContainer.java:1009)
	at org.picocontainer.DefaultPicoContainer.start(DefaultPicoContainer.java:767)
	at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:136)
	at org.sonar.server.platform.platformlevel.PlatformLevel.start(PlatformLevel.java:90)
	at org.sonar.server.platform.PlatformImpl.start(PlatformImpl.java:213)
	at org.sonar.server.platform.PlatformImpl.startSafeModeContainer(PlatformImpl.java:205)
	at org.sonar.server.platform.PlatformImpl.doStart(PlatformImpl.java:105)
	at org.sonar.server.platform.PlatformImpl.doStart(PlatformImpl.java:96)
	at org.sonar.server.platform.web.PlatformServletContextListener.contextInitialized(PlatformServletContextListener.java:44)
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4763)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5232)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
	at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1427)
	at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1417)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.IllegalStateException: Fail to execute CREATE TABLE active_rule_parameters (uuid VARCHAR (40) NOT NULL,value VARCHAR (4000) NULL,rules_parameter_key VARCHAR (128) NULL,active_rule_uuid VARCHAR (40) NOT NULL,rules_parameter_uuid VARCHAR (40) NOT NULL, CONSTRAINT pk_active_rule_parameters PRIMARY KEY (uuid))
	at org.sonar.server.platform.db.migration.step.DdlChange$ContextImpl.execute(DdlChange.java:106)
	at org.sonar.server.platform.db.migration.step.DdlChange$ContextImpl.execute(DdlChange.java:86)
	at org.sonar.server.platform.db.migration.step.DdlChange$ContextImpl.execute(DdlChange.java:128)
	at org.sonar.server.platform.db.migration.version.v00.CreateInitialSchema.createActiveRuleParameters(CreateInitialSchema.java:171)
	at org.sonar.server.platform.db.migration.version.v00.CreateInitialSchema.execute(CreateInitialSchema.java:97)
	at org.sonar.server.platform.db.migration.step.DdlChange.execute(DdlChange.java:45)
	at org.sonar.server.platform.db.migration.step.MigrationStepsExecutorImpl.execute(MigrationStepsExecutorImpl.java:75)
	... 29 common frames omitted
Caused by: org.postgresql.util.PSQLException: ERROR: relation "active_rule_parameters" already exists
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2674)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2364)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:354)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:484)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:404)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:325)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:311)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:287)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:282)
	at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:193)
	at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:193)
	at org.sonar.server.platform.db.migration.step.DdlChange$ContextImpl.execute(DdlChange.java:91)
	... 35 common frames omitted
2022.02.27 13:58:39 INFO  web[][o.s.s.a.EmbeddedTomcat] HTTP connector enabled on port 9000
2022.02.27 13:58:39 INFO  web[][o.s.p.ProcessEntryPoint] Hard stopping process
2022.02.27 13:58:40 INFO  app[][o.s.a.SchedulerImpl] Process[web] is stopped
2022.02.27 13:58:40 WARN  app[][o.s.a.p.AbstractManagedProcess] Process exited with exit value [es]: 143
2022.02.27 13:58:40 INFO  app[][o.s.a.SchedulerImpl] Process[es] is stopped
2022.02.27 13:58:40 INFO  app[][o.s.a.SchedulerImpl] SonarQube is stopped

Not sure what mistake i am doing, any help would be appreciated.
Thanks

Carine_Bayon · February 28, 2022, 7:42am

Hi @Parasappa_Yaragal

I’m not as technical as my colleagues here, but just a thought while reading your post:
did you upgrade from 8.5 to 9.3 directly?
In that case, you missed a step, the good path should be 8.5 → 8.9 LTS → 9.3 as mentioned in our docs here
You can also find help here if needed.

Hope this will help you, and if not, then another colleague or user will answer your post here!

Carine

Parasappa_Yaragal · February 28, 2022, 11:43am

@Carine_Bayon Thank you. That really helped. Now able to restore and see all the projects & its data.

Parasappa

system · March 7, 2022, 11:43am

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Migrating Sonarqube - Database Upgrade Error

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