Fix TAXONLABEL.linked column type mismatch causing nexus file upload failure

[Copilot]

Nexus file uploads fail with SQLGrammarException because TAXONLABEL.linked column is smallint in the database but the Java entity expects boolean. PostgreSQL rejects the type mismatch on insert.

Changes

• Database migration (patches/0010_fix-taxonlabel-linked-column-type.sql): Converts linked column from smallint to boolean

  ALTER TABLE taxonlabel
      ALTER COLUMN linked TYPE boolean
      USING (linked <> 0);

• Updated init_db_uptodate.pg: Added missing patch includes (0008, 0009) and new patch (0010)

Applying to existing databases

psql -d treebase -f patches/0010_fix-taxonlabel-linked-column-type.sql

Original prompt

When I do a nexus file upload, the parsing works but the insert of the resulting data files:

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(MonitoringFil...

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