Fix TAXONLABEL.linked column type mismatch (smallint → boolean) #404
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The TBASE2_POSTGRES_CREATION.sql file defined the linked column as smallint, but the Java TaxonLabel entity uses a boolean field mapped to this column. This caused a type mismatch error when Hibernate tried to insert boolean values into the smallint column. This fix changes the column type to boolean in the schema creation script, matching the type expected by the Hibernate entity mapping and the existing snapshot schema. Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
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[WIP] Fix data access failure during nexus file upload
Fix TAXONLABEL.linked column type mismatch (smallint → boolean)
Jan 13, 2026
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@copilot do a comprehensive check to see if there are other similar cases, where the database schema has a smallint but the ORM layer has a boolean. Report and fix all such impedance mismatches. |
Comprehensive fix for all columns where the database schema defines smallint but the Java entity expects boolean type: - analysis.validated (Analysis.java) - analyzeddata.input (AnalyzedData.java) - geneticcode.predefined (GeneticCode.java) - matrix.aligned (DiscreteMatrix.java) - matrix.diagonal (DistanceMatrix.java) - matrix.casesensitive (StandardMatrix.java) - matrixelement.andlogic (CompoundMatrixElement.java) - matrixelement.gap (for consistency) - phylotree.bigtree (PhyloTree.java) - phylotree.rootedtree (PhyloTree.java) - statechangeset.reversible (StateChangeSet.java) - taxonlabelset.taxa (TaxonLabelSet.java) submission.test is correctly left as smallint since it maps to Integer. Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
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Completed comprehensive check. Found and fixed 12 additional columns in
The only Fixed in commit 203c12b. |
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Original prompt
I try to upload a nexus file through Mesquite, and this happens (in the web UI):
Data Access Failure
could not execute batch; SQL [insert into TAXONLABEL (VERSION, LINKED, STUDY_ID, TaxonLabel, TAXONVARIANT_ID, TAXONLABEL_ID) values (?, ?, ?, ?, ?, ?)]; nested exception is org.hibernate.exception.SQLGrammarException: could not execute batch
org.springframework.dao.InvalidDataAccessResourceUsageException: could not execute batch; SQL [insert into TAXONLABEL (VERSION, LINKED, STUDY_ID, TaxonLabel, TAXONVARIANT_ID, TAXONLABEL_ID) values (?, ?, ?, ?, ?, ?)]; nested exception is org.hibernate.exception.SQLGrammarException: could not execute batch at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:195) at org.springframework.orm.hibernate5.HibernateTemplate.doExecute(HibernateTemplate.java:374) at org.springframework.orm.hibernate5.HibernateTemplate.executeWithNativeSession(HibernateTemplate.java:334) at org.springframework.orm.hibernate5.HibernateTemplate.flush(HibernateTemplate.java:786) at org.cipres.treebase.dao.AbstractDAO.flush(AbstractDAO.java:164) 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.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:234) at jdk.proxy3/jdk.proxy3.$Proxy125.flush(Unknown Source) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:691) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:604) 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.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:241) at jdk.proxy3/jdk.proxy3.$Proxy141.addNexusFilesJDBC(Unknown Source) at org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:219) at org.cipres.treebase.web.compat.CancellableFormController.processFormSubmission(CancellableFormController.java:209) at org.cipres.treebase.web.compat.CancellableFormController.handleRequestInternal(CancellableFormController.java:112) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:177) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:51) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1072) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:965) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:909) at javax.servlet.http.HttpServlet.service(HttpServlet.java:555) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883) at javax.servlet.http.HttpServlet.service(HttpServlet.java:623) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:197) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:142) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:142) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:239) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:215)...
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