R repositories not browsable with a PostgreSQL database backend

post by Ralf_Schuchardt on Feb 14, 2025

Ralf Schuchardt

When I configure Nexus (CE, 3.77.1) with a PostgreSQL database, I cannot browse R repositories anymore. Instead an “Database error” is displayed, and the Nexus logfile has the following Exception logged:

2025-02-14 15:53:01,387+0100 ERROR [qtp1706962391-743]  admin org.sonatype.nexus.extdirect.internal.ExtDirectExceptionHandler - Failed to invoke action method: coreui_Browse.read, java-method: org.sonatype.nexus.coreui.BrowseComponent.read
org.sonatype.nexus.datastore.api.DataAccessException:
### Error querying database.  Cause: java.lang.NumberFormatException: For input string: "conan"
### Cause: java.lang.NumberFormatException: For input string: "conan"
    at org.sonatype.nexus.datastore.mybatis.DataAccessSqlSession.unwrapMyBatisException(DataAccessSqlSession.java:125)
    at org.sonatype.nexus.datastore.mybatis.DataAccessSqlSession.selectList(DataAccessSqlSession.java:76)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:142)
    at org.apache.ibatis.binding.MapperMethod.executeForMany(MapperMethod.java:147)
    at org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:80)
    at org.apache.ibatis.binding.MapperProxy$PlainMethodInvoker.invoke(MapperProxy.java:141)
    at org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:86)
    at jdk.proxy67/jdk.proxy67.$Proxy284.getByDisplayPath(Unknown Source)
    at org.sonatype.nexus.repository.content.browse.store.BrowseNodeStore.getByDisplayPath(BrowseNodeStore.getByDisplayPath.java:64)
    at org.sonatype.nexus.transaction.TransactionalWrapper.proceedWithTransaction(TransactionalWrapper.java:58)
    at org.sonatype.nexus.transaction.TransactionInterceptor.proceedWithTransaction(TransactionInterceptor.java:66)
    at org.sonatype.nexus.transaction.TransactionInterceptor.invoke(TransactionInterceptor.java:55)
    at org.sonatype.nexus.repository.content.browse.store.BrowseNodeManager.getByDisplayPath(BrowseNodeManager.java:67)
    at org.sonatype.nexus.repository.content.browse.BrowseFacetImpl.getByDisplayPath(BrowseFacetImpl.java:125)
    at org.sonatype.nexus.common.stateguard.MethodInvocationAction.run(MethodInvocationAction.java:39)
    at org.sonatype.nexus.common.stateguard.StateGuard$GuardImpl.run(StateGuard.java:298)
    at org.sonatype.nexus.common.stateguard.GuardedInterceptor.invoke(GuardedInterceptor.java:54)
    at org.sonatype.nexus.repository.content.browse.store.BrowseNodeQueryServiceImpl.lambda$selectByPath$3(BrowseNodeQueryServiceImpl.java:184)
    at java.base/java.util.Optional.map(Optional.java:260)
    at org.sonatype.nexus.repository.content.browse.store.BrowseNodeQueryServiceImpl.selectByPath(BrowseNodeQueryServiceImpl.java:184)
    at org.sonatype.nexus.repository.content.browse.store.BrowseNodeQueryServiceImpl.getByPath(BrowseNodeQueryServiceImpl.java:164)
    at org.sonatype.nexus.coreui.BrowseComponent.read(BrowseComponent.java:94)
    at com.palominolabs.metrics.guice.ExceptionMeteredInterceptor.invoke(ExceptionMeteredInterceptor.java:23)
    at com.palominolabs.metrics.guice.TimedInterceptor.invoke(TimedInterceptor.java:26)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at com.softwarementors.extjs.djn.router.dispatcher.DispatcherBase.invokeJavaMethod(DispatcherBase.java:142)
    at com.softwarementors.extjs.djn.router.dispatcher.DispatcherBase.invokeMethod(DispatcherBase.java:133)
    at org.sonatype.nexus.extdirect.internal.ExtDirectDispatcher.invokeMethod(ExtDirectDispatcher.java:82)
    at com.softwarementors.extjs.djn.router.dispatcher.DispatcherBase.dispatch(DispatcherBase.java:63)
    at com.softwarementors.extjs.djn.router.processor.standard.StandardRequestProcessorBase.dispatchStandardMethod(StandardRequestProcessorBase.java:73)
    at com.softwarementors.extjs.djn.router.processor.standard.json.JsonRequestProcessor.processIndividualRequest(JsonRequestProcessor.java:502)
    at com.softwarementors.extjs.djn.router.processor.standard.json.JsonRequestProcessor.processIndividualRequestsInThisThread(JsonRequestProcessor.java:150)
    at com.softwarementors.extjs.djn.router.processor.standard.json.JsonRequestProcessor.process(JsonRequestProcessor.java:133)
    at com.softwarementors.extjs.djn.router.RequestRouter.processJsonRequest(RequestRouter.java:83)
    at com.softwarementors.extjs.djn.servlet.DirectJNgineServlet.processRequest(DirectJNgineServlet.java:632)
    at com.softwarementors.extjs.djn.servlet.DirectJNgineServlet.doPost(DirectJNgineServlet.java:595)
    at org.sonatype.nexus.extdirect.internal.ExtDirectServlet.doPost(ExtDirectServlet.java:137)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
    at com.google.inject.servlet.ServletDefinition.doServiceImpl(ServletDefinition.java:293)
    at com.google.inject.servlet.ServletDefinition.doService(ServletDefinition.java:283)
    at com.google.inject.servlet.ServletDefinition.service(ServletDefinition.java:184)
    at com.google.inject.servlet.DynamicServletPipeline.service(DynamicServletPipeline.java:71)
    at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:85)
    at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
    at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
    at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
    at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
    at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
    at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilterChain.java:108)
    at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
    at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
    at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
    at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.class:154)
    at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
    at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilterChain.java:108)
    at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilterChain.java:137)
    at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154)
    at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
    at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilterChain.java:108)
    at org.apache.shiro.web.servlet.DoFilter(FilterChain.doFilter(FilterChain.jav://at (AbstractShiroFilter.executeChain(206) at org.sonatype.nexus.security.SecurityFilter.executeChain(SecurityFilter.java:96)
""

Caused by: java.lang.NumberFormatException: For input string: "conan"
    at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
    at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
    at java.base/java.lang.Double.parseDouble(Double.java:651)
    at org.apache.ibatis.ognl.OgnlOps.doubleValue(OgnlOps.java:222)
    at org.apache.ibatis.ognl.OgnlOps.compareWithConversion(OgnlOps.java:86)
    at org.apache.ibatis.ognl.OgnlOps.isEqual(OgnlOps.java:131)
    at org.apache.ibatis.ognl.OgnlOps.equal(OgnlOps.java:703)
    at org.apache.ibatis.ognl.ASTEq.getValueBody(ASTEq.java:36)
    at org.apache.ibatis.ognl.SimpleNode.evaluateGetValueBody(SimpleNode.java:165)
    at org.apache.ibatis.ognl.SimpleNode.getValue(SimpleNode.java:206)
    at org.apache.ibatis.ognl.Ognl.getValue(Ognl.java:408)
    at org.apache.ibatis.ognl.Ognl.getValue(Ognl.java:383)
    at org.apache.ibatis.scripting.xmltags.OgnlCache.getValue(OgnlCache.java:47)
    at org.apache.ibatis.scripting.xmltags.VarDeclSqlNode.apply(VarDeclSqlNode.java:33)
    at org.apache.ibatis.scripting.xmltags.MixedSqlNode.lambda$apply$0(MixedSqlNode.java:32)
    at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
    at org.apache.ibatis.scripting.xmltags.MixedSqlNode.apply(MixedSqlNode.java:32)
    at org.apache.ibatis.scripting.xmltags.DynamicSqlSource.getBoundSql(DynamicSqlSource.java:39)
    at org.apache.ibatis.mapping.MappedStatement.getBoundSql(MappedStatement.java:320)
    at org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:88)
    at org.sonatype.nexus.datastore.mybatis.EntityExecutor.query(EntityExecutor.java:106)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:154)
    at org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:147)
    ... 142 common frames omitted

I get this error with a new installation, or an upgraded installation after migrating H2 to PostgreSQL. When I stay on H2 it apparently works.

Has anybody the same issue and found a solution?

post by mpiggott on Feb 14, 2025

Matthew Piggott

If you can, turn on trace logging for com.sonatype.nexus.repository.r.datastore.internal.browse.RBrowseNodeDAO

and capture the output from the log. After triggering the error reset the logger to avoid logging a lot of noise.

If you could then include the query that triggers the error and file it at GitHub · Where software is built

post by Ralf_Schuchardt on Feb 14, 2025

Ralf Schuchardt

For anyone interested, I could solve this by modifying “BrowseNodeDAO.xml” to use an equals method instead of == when comparing “format” with the string “conan".