Merge recent refactorings and bug fixes #420
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Replace EL expression `${errors.class.simpleName}` with scriptlet-based
type checking to avoid NumberFormatException in modern EL resolvers.
The issue occurred because when `errors` is a List, the EL resolver
tries to interpret `.class` as a list index access, attempting to parse
"class" as an integer, which fails with NumberFormatException.
Co-authored-by: rvosa <[email protected]>
…tion Fix NumberFormatException in messages.jsp type checking
…teWindow.headless=true before Mesquite.main() Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Fix NullPointerException in Mesquite headless initialization during nexus file upload
… copying Mesquite library files to Docker Co-authored-by: rvosa <[email protected]>
…tract common logic and use specific exception types Co-authored-by: rvosa <[email protected]>
Fix NullPointerException in Mesquite headless initialization during NEXUS file upload
…lint to boolean Co-authored-by: rvosa <[email protected]>
…nsert Fix TAXONLABEL.linked column type mismatch causing nexus file upload failure
…nal to 500 chars Co-authored-by: rvosa <[email protected]>
Increase CITATION column lengths to fix insert failures
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 <[email protected]>
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 <[email protected]>
…-again Fix TAXONLABEL.linked column type mismatch (smallint → boolean)
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
…ssue Add missing hibernate_sequence to database schema
…ment Co-authored-by: rvosa <[email protected]>
…sults Co-authored-by: rvosa <[email protected]>
…tches Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Fix Autocompleter is not defined error by making autocomplete.js self-contained
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Update image paths in styles.css
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
…place-prototypejs Replace Prototype.js with jQuery
Co-authored-by: rvosa <[email protected]>
Fix JavaScript MIME type in validator.jsp
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Co-authored-by: rvosa <[email protected]>
Remove unused raphael-min.js and jsphylosvg-min.js
Remove unused d3.phylogram.js
Remove unused newick.js file
Co-authored-by: rvosa <[email protected]>
Remove unused sha1.js
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