ERROR: operator does not exist: jsonb = bytea

[martinchapman]

Description

Hard to rule out a quirk of my setup as the source of this, but on the off chance this is a wider issue thought it worth flagging that I'm currently receiving ERROR: operator does not exist: jsonb = bytea from the Spring container on a fresh clone. I understand this issue was identified and fixed as a part of #568 (#568 (comment)), but for some reason it seems to persist for me.

Expected Behavior

Able to successfully view any example workflows after executing the steps in Recommended - Running with Docker.

Actual Behavior

Unable to view any example workflows.

Possible Fix

Behaviour is as expected if reverting the changes in 26843b2.

Fixes attempted with latest commit:

• Later Postgres image versions
• Reverting all (relevant) package version updates since 26843b2
• Pruning Docker system

Steps to Reproduce

1. git clone git@github.com:common-workflow-language/cwlviewer.git
2. cd cwlviewer
3. Optional (issue persists with or without): Switch from Spring image to local build in docker-compose.yml.
4. docker compose up
5. Visit http://localhost:8080/
6. Select 'compile' from 'Don't know what to view?'
7. Select 'Parse Workflow'

Context

Originally occurred after syncing a fork of CWL Viewer.

Your Environment

• Version used: main
• Environment name and version (e.g. Chrome 39, Java 17): Chrome 131.0.6778.70. Docker 27.1.1. Arch (256.8-1-arch) via WSL2 (5.15.167.4-microsoft-standard-WSL2)

[kinow]

Exception logged:

  Hint: No operator matches the given name and argument types. You might need to add explicit type casts.
  Position: 270
2024-11-17 21:27:31,986 ERROR [http-nio-8080-exec-2] o.a.j.l.DirectJDKLog: Servlet.service() for servlet [dispatcherServlet] in context with path [] threw exception [Request processing failed: org.springframework.dao.InvalidDataAccessResourceUsageException: JDBC exception executing SQL [select w1_0.id,w1_0.cwltool_version,w1_0.doc,w1_0.docker_link,w1_0.inputs,w1_0.label,w1_0.last_commit,w1_0.license_link,w1_0.outputs,w1_0.retrieved_from,w1_0.retrieved_on,w1_0.ro_bundle_path,w1_0.steps,w1_0.visualisation_dot from workflow w1_0 where w1_0.retrieved_from=?] [ERROR: operator does not exist: jsonb = bytea
  Hint: No operator matches the given name and argument types. You might need to add explicit type casts.
  Position: 270] [n/a]; SQL [n/a]] with root cause
org.postgresql.util.PSQLException: ERROR: operator does not exist: jsonb = bytea
  Hint: No operator matches the given name and argument types. You might need to add explicit type casts.
  Position: 270
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2713)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2401)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:368)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:498)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:415)
	at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:190)
	at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:134)
	at com.zaxxer.hikari.pool.ProxyPreparedStatement.executeQuery(ProxyPreparedStatement.java:52)
	at com.zaxxer.hikari.pool.HikariProxyPreparedStatement.executeQuery(HikariProxyPreparedStatement.java)
	at org.hibernate.sql.results.jdbc.internal.DeferredResultSetAccess.executeQuery(DeferredResultSetAccess.java:239)
	at org.hibernate.sql.results.jdbc.internal.DeferredResultSetAccess.getResultSet(DeferredResultSetAccess.java:163)
	at org.hibernate.sql.results.jdbc.internal.JdbcValuesResultSetImpl.advanceNext(JdbcValuesResultSetImpl.java:254)
	at org.hibernate.sql.results.jdbc.internal.JdbcValuesResultSetImpl.processNext(JdbcValuesResultSetImpl.java:134)
	at org.hibernate.sql.results.jdbc.internal.AbstractJdbcValues.next(AbstractJdbcValues.java:19)
	at org.hibernate.sql.results.internal.RowProcessingStateStandardImpl.next(RowProcessingStateStandardImpl.java:66)
	at org.hibernate.sql.results.spi.ListResultsConsumer.consume(ListResultsConsumer.java:198)
	at org.hibernate.sql.results.spi.ListResultsConsumer.consume(ListResultsConsumer.java:33)
	at org.hibernate.sql.exec.internal.JdbcSelectExecutorStandardImpl.doExecuteQuery(JdbcSelectExecutorStandardImpl.java:361)
	at org.hibernate.sql.exec.internal.JdbcSelectExecutorStandardImpl.executeQuery(JdbcSelectExecutorStandardImpl.java:168)
	at org.hibernate.sql.exec.internal.JdbcSelectExecutorStandardImpl.list(JdbcSelectExecutorStandardImpl.java:93)
	at org.hibernate.sql.exec.spi.JdbcSelectExecutor.list(JdbcSelectExecutor.java:31)
	at org.hibernate.query.sqm.internal.ConcreteSqmSelectQueryPlan.lambda$new$0(ConcreteSqmSelectQueryPlan.java:110)
	at org.hibernate.query.sqm.internal.ConcreteSqmSelectQueryPlan.withCacheableSqmInterpretation(ConcreteSqmSelectQueryPlan.java:303)
	at org.hibernate.query.sqm.internal.ConcreteSqmSelectQueryPlan.performList(ConcreteSqmSelectQueryPlan.java:244)
	at org.hibernate.query.sqm.internal.QuerySqmImpl.doList(QuerySqmImpl.java:518)
	at org.hibernate.query.spi.AbstractSelectionQuery.list(AbstractSelectionQuery.java:367)
	at org.hibernate.query.spi.AbstractSelectionQuery.getSingleResult(AbstractSelectionQuery.java:473)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.springframework.orm.jpa.SharedEntityManagerCreator$DeferredQueryInvocationHandler.invoke(SharedEntityManagerCreator.java:405)
	at jdk.proxy2/jdk.proxy2.$Proxy143.getSingleResult(Unknown Source)
	at org.springframework.data.jpa.repository.query.JpaQueryExecution$SingleEntityExecution.doExecute(JpaQueryExecution.java:223)
	at org.springframework.data.jpa.repository.query.JpaQueryExecution.execute(JpaQueryExecution.java:92)
	at org.springframework.data.jpa.repository.query.AbstractJpaQuery.doExecute(AbstractJpaQuery.java:148)
	at org.springframework.data.jpa.repository.query.AbstractJpaQuery.execute(AbstractJpaQuery.java:136)
	at org.springframework.data.repository.core.support.RepositoryMethodInvoker.doInvoke(RepositoryMethodInvoker.java:136)
	at org.springframework.data.repository.core.support.RepositoryMethodInvoker.invoke(RepositoryMethodInvoker.java:120)
	at org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.doInvoke(QueryExecutorMethodInterceptor.java:164)
	at org.springframework.data.repository.core.support.QueryExecutorMethodInterceptor.invoke(QueryExecutorMethodInterceptor.java:143)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:391)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:137)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.data.jpa.repository.support.CrudMethodMetadataPostProcessor$CrudMethodMetadataPopulatingMethodInterceptor.invoke(CrudMethodMetadataPostProcessor.java:135)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:97)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:244)
	at jdk.proxy2/jdk.proxy2.$Proxy138.findByRetrievedFrom(Unknown Source)
	at org.commonwl.view.workflow.WorkflowService.getWorkflow(WorkflowService.java:167)
	at org.commonwl.view.workflow.WorkflowController.createWorkflow(WorkflowController.java:140)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
	at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150)
	at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:118)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:884)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:797)
	at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1081)
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:974)
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1011)
	at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:914)
	at jakarta.servlet.http.HttpServlet.service(HttpServlet.java:590)
	at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:885)
	at jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:205)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)
	at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)
	at org.springframework.web.filter.FormContentFilter.doFilterInternal(FormContentFilter.java:93)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)
	at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:167)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:482)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:115)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:341)
	at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:391)
	at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)
	at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:894)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1740)
	at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)
	at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
	at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.base/java.lang.Thread.run(Thread.java:840)

[kinow]

Linking issue in hypersistence utils repo: vladmihalcea/hypersistence-utils#589

[kinow]

Another similar issue, vladmihalcea/hypersistence-utils#731

[kinow]

Issue fixed locally, still need to

• check if tests are passing
• review logs for warns/errors
• separate commits into separate PRs to minimize change here

[kinow]

(Found one more warning, about postgres version when running tests, but no more bandwidth to work on the viewer's code, maybe will fix it over next days, but at least this bug should be done 🤞 )