Upgrading sonarqube from 9.4.0 to 9.5.0 produces db migration errors

[taavit21]

Trying to upgrade from 9.4 to 9.5

ERROR LOG:

2022.06.15 14:36:36 WARN  web[][o.s.c.a.AnnotationConfigApplicationContext] Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jdk.internal.loader.ClassLoaders$
AppClassLoader@55054057-org.sonar.server.rule.RegisterRules': Initialization of bean failed; nested exception is org.apache.ibatis.exceptions.PersistenceException: \n### Error querying database.  Cause: org.postgresql.util.PSQLException: ERROR: mergejoin input data is out of ord
er\n### The error may exist in org.sonar.db.rule.RuleMapper\n### The error may involve defaultParameterMap\n### The error occurred while setting parameters\n### SQL: select             rds.content as "rds_content",     rds.uuid as "rds_uuid",     rds.kee as "rds_kee",     r.uuid
 as "r_uuid",            r.plugin_rule_key as "ruleKey",     r.plugin_name as "repositoryKey",     r.description_format as "descriptionFormat",     r.status,     r.name,     r.plugin_config_key as "configKey",     r.priority as "severity",     r.is_template as "isTemplate",
r.is_external as "isExternal",     r.is_ad_hoc as "isAdHoc",     r.language as "language",     r.template_uuid as "templateUuid",     r.def_remediation_function as "defRemediationFunction",     r.def_remediation_gap_mult as "defRemediationGapMultiplier",     r.def_remediation_ba
se_effort as "defRemediationBaseEffort",     r.gap_description as "gapDescription",     r.system_tags as "systemTagsField",     r.security_standards as "securityStandardsField",     r.rule_type as "type",     r.plugin_key as "pluginKey",     r.scope,     r.created_at as "created
At",     r.updated_at as "updatedAt",     r.note_data as "noteData",     r.note_user_uuid as "noteUserUuid",     r.note_created_at as "noteCreatedAt",     r.note_updated_at as "noteUpdatedAt",     r.remediation_function as "remediationFunction",     r.remediation_gap_mult as "re
mediationGapMultiplier",     r.remediation_base_effort as "remediationBaseEffort",     r.tags as "tagsField",     r.ad_hoc_name as "adHocName",     r.ad_hoc_description as "adHocDescription",     r.ad_hoc_severity as "adHocSeverity",     r.ad_hoc_type as "adHocType"
from       rules r           left outer join rule_desc_sections rds on       rds.rule_uuid = r.uuid\n### Cause: org.postgresql.util.PSQLException: ERROR: mergejoin input data is out of order
2022.06.15 14:36:36 ERROR web[][o.s.s.p.Platform] Background initialization failed. Stopping SonarQube
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'jdk.internal.loader.ClassLoaders$AppClassLoader@55054057-org.sonar.server.rule.RegisterRules': Initialization of bean failed; nested exception is org.apache.ibatis.exceptions.PersistenceExcep
tion:
### Error querying database.  Cause: org.postgresql.util.PSQLException: ERROR: mergejoin input data is out of order
### The error may exist in org.sonar.db.rule.RuleMapper
### The error may involve defaultParameterMap
### The error occurred while setting parameters
### SQL: select             rds.content as "rds_content",     rds.uuid as "rds_uuid",     rds.kee as "rds_kee",     r.uuid as "r_uuid",            r.plugin_rule_key as "ruleKey",     r.plugin_name as "repositoryKey",     r.description_format as "descriptionFormat",     r.status,
     r.name,     r.plugin_config_key as "configKey",     r.priority as "severity",     r.is_template as "isTemplate",     r.is_external as "isExternal",     r.is_ad_hoc as "isAdHoc",     r.language as "language",     r.template_uuid as "templateUuid",     r.def_remediation_funct
ion as "defRemediationFunction",     r.def_remediation_gap_mult as "defRemediationGapMultiplier",     r.def_remediation_base_effort as "defRemediationBaseEffort",     r.gap_description as "gapDescription",     r.system_tags as "systemTagsField",     r.security_standards as "secu
rityStandardsField",     r.rule_type as "type",     r.plugin_key as "pluginKey",     r.scope,     r.created_at as "createdAt",     r.updated_at as "updatedAt",     r.note_data as "noteData",     r.note_user_uuid as "noteUserUuid",     r.note_created_at as "noteCreatedAt",     r.
note_updated_at as "noteUpdatedAt",     r.remediation_function as "remediationFunction",     r.remediation_gap_mult as "remediationGapMultiplier",     r.remediation_base_effort as "remediationBaseEffort",     r.tags as "tagsField",     r.ad_hoc_name as "adHocName",     r.ad_hoc_
description as "adHocDescription",     r.ad_hoc_severity as "adHocSeverity",     r.ad_hoc_type as "adHocType"             from       rules r           left outer join rule_desc_sections rds on       rds.rule_uuid = r.uuid
### Cause: org.postgresql.util.PSQLException: ERROR: mergejoin input data is out of order
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:628)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:953)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583)
        at org.sonar.core.platform.SpringComponentContainer.startComponents(SpringComponentContainer.java:187)
        at org.sonar.server.platform.platformlevel.PlatformLevel.start(PlatformLevel.java:80)
        at org.sonar.server.platform.platformlevel.PlatformLevelStartup.access$001(PlatformLevelStartup.java:55)
        at org.sonar.server.platform.platformlevel.PlatformLevelStartup$1.doPrivileged(PlatformLevelStartup.java:127)
        at org.sonar.server.user.DoPrivileged.execute(DoPrivileged.java:45)
        at org.sonar.server.platform.platformlevel.PlatformLevelStartup.start(PlatformLevelStartup.java:124)
        at org.sonar.server.platform.PlatformImpl.executeStartupTasks(PlatformImpl.java:183)
        at org.sonar.server.platform.PlatformImpl$1.lambda$doRun$1(PlatformImpl.java:107)
        at org.sonar.server.platform.PlatformImpl$AutoStarterRunnable.runIfNotAborted(PlatformImpl.java:344)
        at org.sonar.server.platform.PlatformImpl$1.doRun(PlatformImpl.java:107)
        at org.sonar.server.platform.PlatformImpl$AutoStarterRunnable.run(PlatformImpl.java:328)
        at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: org.apache.ibatis.exceptions.PersistenceException:
### Error querying database.  Cause: org.postgresql.util.PSQLException: ERROR: mergejoin input data is out of order

[Colin]

Hey there.

Take a look here.

Failed to migrate database after migrate to 9.5

I saw that error during the migration (after accessing the /setup URL) from the 9.4 to the 9.5 version, and from now on, every time I tried to start SonarQube (docker start) it failed with the org.sonar.server.exceptions.BadRequestException: Rule with UUID AX2_I9xF-Xhu6cui6fS_ not found error. After digging more into this, I discovered that the the rules table was not behaving correctly (I couldn’t perform a simple select * from rules where uuid = ‘AX2_I9xF-Xhu6cui6fS_’ even though the row was …

[taavit21]

Thank you, that worked.