Study Import in cBioPortal with redis and keycloak

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Leila Kamkar

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11:23 AM (8 hours ago) 11:23 AM

to cBioPortal for Cancer Genomics Discussion Group

Dear cBioPortal Team,

I have configured cBioPortal to use Redis for caching (versions: cbioportal/cbioportal:6.4.1, cbioportal/session-service:0.6.4, MongoDB:4.2, MySQL:8.0, Redis:7.4.2).

However, when I attempt to import a study, I encounter the following error while creating the portal_info_folder. The portal is deployed behind Keycloak for authentication.

I would greatly appreciate your guidance on resolving this issue.

Thank you in advance for your support.

Kind regards,
Leila Kamkar

Error message:

root@f4505484fbff:/core/scripts# ./dumpPortalInfo.pl /cbioportal/my_portal_info_folder

ABORTED!

org.springframework.beans.factory.BeanDefinitionStoreException: Failed to read candidate component class: URL [jar:file:/core/core-1.0.11.jar!/org/cbioportal/legacy/persistence/config/RedisConfig.class]

at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.scanCandidateComponents(ClassPathScanningCandidateComponentProvider.java:510)

at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.findCandidateComponents(ClassPathScanningCandidateComponentProvider.java:351)

at org.springframework.context.annotation.ClassPathBeanDefinitionScanner.doScan(ClassPathBeanDefinitionScanner.java:277)

at org.springframework.context.annotation.ComponentScanBeanDefinitionParser.parse(ComponentScanBeanDefinitionParser.java:91)

at org.springframework.beans.factory.xml.NamespaceHandlerSupport.parse(NamespaceHandlerSupport.java:74)

at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1391)

at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1371)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.parseBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:179)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.doRegisterBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:150)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.parseDefaultElement(DefaultBeanDefinitionDocumentReader.java:201)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.parseBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:176)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.doRegisterBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:150)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.registerBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:96)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.registerBeanDefinitions(XmlBeanDefinitionReader.java:520)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:400)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:347)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:319)

at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:184)

at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:220)

at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:191)

at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:253)

at org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:130)

at org.springframework.context.support.AbstractXmlApplicationContext.loadBeanDefinitions(AbstractXmlApplicationContext.java:95)

at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:131)

at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:716)

at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:598)

at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:144)

at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:85)

at org.mskcc.cbio.portal.util.SpringUtil.initDataSource(SpringUtil.java:62)

at org.mskcc.cbio.portal.scripts.DumpPortalInfo.run(DumpPortalInfo.java:123)

at org.mskcc.cbio.portal.scripts.ConsoleRunnable.runInConsole(ConsoleRunnable.java:145)

at org.mskcc.cbio.portal.scripts.DumpPortalInfo.main(DumpPortalInfo.java:192)

Caused by: java.lang.IllegalStateException: Error processing condition on org.cbioportal.legacy.persistence.config.RedisConfig

at org.springframework.boot.autoconfigure.condition.SpringBootCondition.matches(SpringBootCondition.java:60)

at org.springframework.context.annotation.ConditionEvaluator.shouldSkip(ConditionEvaluator.java:99)

at org.springframework.context.annotation.ConditionEvaluator.shouldSkip(ConditionEvaluator.java:88)

at org.springframework.context.annotation.ConditionEvaluator.shouldSkip(ConditionEvaluator.java:71)

at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.isConditionMatch(ClassPathScanningCandidateComponentProvider.java:564)

at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.isCandidateComponent(ClassPathScanningCandidateComponentProvider.java:547)

at org.springframework.context.annotation.ClassPathScanningCandidateComponentProvider.scanCandidateComponents(ClassPathScanningCandidateComponentProvider.java:471)

... 31 more

Caused by: org.springframework.beans.factory.BeanExpressionException: Expression parsing failed

at org.springframework.context.expression.StandardBeanExpressionResolver.evaluate(StandardBeanExpressionResolver.java:185)

at org.springframework.boot.autoconfigure.condition.OnExpressionCondition.evaluateExpression(OnExpressionCondition.java:60)

at org.springframework.boot.autoconfigure.condition.OnExpressionCondition.getMatchOutcome(OnExpressionCondition.java:48)

at org.springframework.boot.autoconfigure.condition.SpringBootCondition.matches(SpringBootCondition.java:47)

... 37 more

Caused by: org.springframework.expression.spel.SpelEvaluationException: EL1008E: Property or field 'environment' cannot be found on object of type 'org.springframework.beans.factory.config.BeanExpressionContext' - maybe not public or not valid?

at org.springframework.expression.spel.ast.PropertyOrFieldReference.readProperty(PropertyOrFieldReference.java:229)

at org.springframework.expression.spel.ast.PropertyOrFieldReference.getValueInternal(PropertyOrFieldReference.java:112)

at org.springframework.expression.spel.ast.PropertyOrFieldReference.getValueInternal(PropertyOrFieldReference.java:100)

at org.springframework.expression.spel.ast.CompoundExpression.getValueRef(CompoundExpression.java:60)

at org.springframework.expression.spel.ast.CompoundExpression.getValueInternal(CompoundExpression.java:96)

at org.springframework.expression.spel.ast.OpEQ.getValueInternal(OpEQ.java:42)

at org.springframework.expression.spel.ast.OpEQ.getValueInternal(OpEQ.java:32)

at org.springframework.expression.spel.ast.SpelNodeImpl.getValue(SpelNodeImpl.java:203)

at org.springframework.expression.spel.ast.OpOr.getBooleanValue(OpOr.java:57)

at org.springframework.expression.spel.ast.OpOr.getValueInternal(OpOr.java:48)

at org.springframework.expression.spel.ast.OpOr.getValueInternal(OpOr.java:38)

at org.springframework.expression.spel.ast.SpelNodeImpl.getValue(SpelNodeImpl.java:116)

at org.springframework.expression.spel.standard.SpelExpression.getValue(SpelExpression.java:273)

at org.springframework.context.expression.StandardBeanExpressionResolver.evaluate(StandardBeanExpressionResolver.java:182)