Increase CITATION column lengths to fix insert failures

[Copilot]

Citation inserts fail with DataIntegrityViolationException: value too long for type character varying(255) when keywords or journal names exceed 255 characters.

Changes

• Entity annotations: Updated @Column length for Keywords (255 → 1000) and Journal (255 → 500)
• Constants: Added CITATION_KEYWORDS_COLUMN_LENGTH and CITATION_JOURNAL_COLUMN_LENGTH to TBPersistable.java
• DB migration: Added patch 0011_increase-citation-column-lengths.sql for existing databases
• Schema: Updated TBASE2_POSTGRES_CREATION.sql for new installations

// Citation.java
@Column(name = "Keywords", length = TBPersistable.CITATION_KEYWORDS_COLUMN_LENGTH)
public String getKeywords() { ... }

// ArticleCitation.java  
@Column(name = "Journal", length = TBPersistable.CITATION_JOURNAL_COLUMN_LENGTH)
public String getJournal() { ... }

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• getahead.org
  • Triggering command: /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/tools/linux64/java/bin/java -jar /opt/hostedtoolcache/CodeQL/2.23.8/x64/codeql/xml/tools/xml-extractor.jar --fileList=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/working/files-to-index1801546077663301312.list --sourceArchiveDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/src --outputDir=/home/REDACTED/work/treebase/.codeql-scratch/dbs/java/trap/java (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

I try to insert a citation and this happens:

Data Access Failure
could not execute batch; SQL [insert into CITATION (VERSION, PMID, URL, ABSTRACT, CITATIONSTATUS_ID, Doi, Keywords, Pages, PublishYear, Published, Title, Issue, Journal, Volume, TYPE, CITATION_ID) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 'A', ?)]; nested exception is org.hibernate.exception.DataException: could not execute batch

org.springframework.dao.DataIntegrityViolationException: could not execute batch; SQL [insert into CITATION (VERSION, PMID, URL, ABSTRACT, CITATIONSTATUS_ID, Doi, Keywords, Pages, PublishYear, Published, Title, Issue, Journal, Volume, TYPE, CITATION_ID) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 'A', ?)]; nested exception is org.hibernate.exception.DataException: could not execute batch at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:216) at org.springframework.orm.hibernate5.HibernateTransactionManager.convertHibernateAccessException(HibernateTransactionManager.java:785) at org.springframework.orm.hibernate5.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:657) at org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:744) at org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:712) at org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:654) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:407) 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.$Proxy140.update(Unknown Source) at org.cipres.treebase.web.controllers.CitationFormController.onSubmit(CitationFormController.java:287) 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) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:142) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:176) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:145) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:92) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:389) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:142) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:142) at org.springframework.orm.hibernate5.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:156) at org.springframework.web.filter.OncePerR...

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