[WIP] Fix data access failure when uploading nexus file

[Copilot]

• Analyze the root cause of the "Bad value for type long" error
• Identify that the fix has already been applied in PR Fix Hibernate ORM vs SQL schema discrepancies and document analysis #406 (merged to master)
  • Root cause: @Lob annotation on MatrixRow.symbolString caused Hibernate to use OID-based CLOB handling, but data was inserted via direct JDBC using setString()
  • Solution: Replaced @Lob with @Column(columnDefinition = "text") in MatrixRow.java and PhyloTree.java
• Confirm this branch is based on master which already includes the fix
• Improve error page display and logging to address "how can I see the rest of the log"
  • Enhanced dataAccessFailure.jsp with:
    • Collapsible details section for stack trace
    • Proper HTML escaping for safe display
    • Server-side logging via SLF4J for administrator review
    • User-friendly messaging
    • Try-with-resources for proper resource cleanup
  • Enhanced uncaughtException.jsp with:
    • Same improvements as dataAccessFailure.jsp
    • Removed cookie display (security improvement)
    • Better root cause extraction
    • Single logger instance (code review fix)
    • Try-with-resources for proper resource cleanup
• Verify compilation and tests pass
• Code review feedback addressed
• CodeQL security check passed

Original prompt

I try to upload a nexus file but this happens:

Data Access Failure
could not load an entity: [org.cipres.treebase.domain.matrix.MatrixRow#37]; SQL [select matrixrow0_.MATRIXROW_ID as matrixro1_45_1_, matrixrow0_.VERSION as version2_45_1_, matrixrow0_.MATRIX_ID as matrix_i4_45_1_, matrixrow0_.SymbolString as symbolst3_45_1_, matrixrow0_.TAXONLABEL_ID as taxonlab5_45_1_, segments1_.MATRIXROW_ID as matrixr20_54_3_, segments1_.ROWSEGMENT_ID as rowsegme1_54_3_, segments1_.ROWSEGMENT_ID as rowsegme1_54_0_, segments1_.VERSION as version2_54_0_, segments1_.EndIndex as endindex3_54_0_, segments1_.MATRIXROW_ID as matrixr20_54_0_, segments1_.CatalogNum as catalogn4_54_0_, segments1_.CollectionCode as collecti5_54_0_, segments1_.Collector as collecto6_54_0_, segments1_.Country as country7_54_0_, segments1_.Elevation as elevatio8_54_0_, segments1_.GenBAccession as genbacce9_54_0_, segments1_.InstAcronym as instacr10_54_0_, segments1_.Latitude as latitud11_54_0_, segments1_.Locality as localit12_54_0_, segments1_.Longitude as longitu13_54_0_, segments1_.Notes as notes14_54_0_, segments1_.OtherAccession as otherac15_54_0_, segments1_.SampleDate as sampled16_54_0_, segments1_.State as state17_54_0_, segments1_.StartIndex as startin18_54_0_, segments1_.TAXONLABEL_ID as taxonla21_54_0_, segments1_.Title as title19_54_0_ from MATRIXROW matrixrow0_ left outer join ROWSEGMENT segments1_ on matrixrow0_.MATRIXROW_ID=segments1_.MATRIXROW_ID where matrixrow0_.MATRIXROW_ID=?]; nested exception is org.hibernate.exception.DataException: could not load an entity: [org.cipres.treebase.domain.matrix.MatrixRow#37]

org.springframework.dao.DataIntegrityViolationException: could not load an entity: [org.cipres.treebase.domain.matrix.MatrixRow#37]; SQL [select matrixrow0_.MATRIXROW_ID as matrixro1_45_1_, matrixrow0_.VERSION as version2_45_1_, matrixrow0_.MATRIX_ID as matrix_i4_45_1_, matrixrow0_.SymbolString as symbolst3_45_1_, matrixrow0_.TAXONLABEL_ID as taxonlab5_45_1_, segments1_.MATRIXROW_ID as matrixr20_54_3_, segments1_.ROWSEGMENT_ID as rowsegme1_54_3_, segments1_.ROWSEGMENT_ID as rowsegme1_54_0_, segments1_.VERSION as version2_54_0_, segments1_.EndIndex as endindex3_54_0_, segments1_.MATRIXROW_ID as matrixr20_54_0_, segments1_.CatalogNum as catalogn4_54_0_, segments1_.CollectionCode as collecti5_54_0_, segments1_.Collector as collecto6_54_0_, segments1_.Country as country7_54_0_, segments1_.Elevation as elevatio8_54_0_, segments1_.GenBAccession as genbacce9_54_0_, segments1_.InstAcronym as instacr10_54_0_, segments1_.Latitude as latitud11_54_0_, segments1_.Locality as localit12_54_0_, segments1_.Longitude as longitu13_54_0_, segments1_.Notes as notes14_54_0_, segments1_.OtherAccession as otherac15_54_0_, segments1_.SampleDate as sampled16_54_0_, segments1_.State as state17_54_0_, segments1_.StartIndex as startin18_54_0_, segments1_.TAXONLABEL_ID as taxonla21_54_0_, segments1_.Title as title19_54_0_ from MATRIXROW matrixrow0_ left outer join ROWSEGMENT segments1_ on matrixrow0_.MATRIXROW_ID=segments1_.MATRIXROW_ID where matrixrow0_.MATRIXROW_ID=?]; nested exception is org.hibernate.exception.DataException: could not load an entity: [org.cipres.treebase.domain.matrix.MatrixRow#37] at org.springframework.orm.hibernate5.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:216) 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.refresh(HibernateTemplate.java:542) at org.springframework.orm.hibernate5.HibernateTemplate.refresh(HibernateTemplate.java:537) at org.cipres.treebase.dao.AbstractDAO.refresh(AbstractDAO.java:41) 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.$Proxy115.refresh(Unknown Source) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:637) 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.ReflectiveMethodI...

</details>



<!-- START COPILOT CODING AGENT TIPS -->
---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our [2 minute survey](https://gh.io/copilot-coding-agent-survey).