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Merged
rvosa merged 102 commits into from
Jan 27, 2026
Merged

Merge recent refactorings and bug fixes #420

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94483f1
Initial plan
Copilot Jan 13, 2026
b51f5be
Fix NumberFormatException when displaying errors/messages in JSP
Copilot Jan 13, 2026
4bf3c7b
Merge pull request #398 from TreeBASE/copilot/fix-number-format-excep…
rvosa Jan 13, 2026
8ff2f9e
Initial plan
Copilot Jan 13, 2026
bec7e06
Fix NullPointerException when uploading nexus files by setting Mesqui…
Copilot Jan 13, 2026
86ff5bb
Add MesquiteWindow import and use unqualified class name per code review
Copilot Jan 13, 2026
885590d
Merge pull request #400 from TreeBASE/copilot/fix-nullpointer-exception
rvosa Jan 13, 2026
b8d5674
Initial plan
Copilot Jan 13, 2026
5281ce0
Fix Mesquite headless initialization by adding exception handling and…
Copilot Jan 13, 2026
f69cd48
Refactor Mesquite initialization to address code review comments - ex…
Copilot Jan 13, 2026
dfce5b9
Merge pull request #401 from TreeBASE/copilot/fix-null-pointer-exception
rvosa Jan 13, 2026
d2add30
Initial plan
Copilot Jan 13, 2026
614f120
Add database migration to fix TAXONLABEL.linked column type from smal…
Copilot Jan 13, 2026
331f0cd
Merge pull request #402 from TreeBASE/copilot/fix-nexus-file-upload-i…
rvosa Jan 13, 2026
30d9b64
Initial plan
Copilot Jan 13, 2026
1518a87
Fix citation column length issue - increase Keywords to 1000 and Jour…
Copilot Jan 13, 2026
f4b18a1
Initial plan
Copilot Jan 13, 2026
2f52bbf
Merge pull request #403 from TreeBASE/copilot/fix-data-access-failure
rvosa Jan 13, 2026
1f2075e
Fix TAXONLABEL.linked column type from smallint to boolean
Copilot Jan 13, 2026
203c12b
Fix all ORM/database smallint→boolean type mismatches
Copilot Jan 13, 2026
0703486
Merge pull request #404 from TreeBASE/copilot/fix-data-access-failure…
rvosa Jan 13, 2026
0d720c2
Initial plan
Copilot Jan 13, 2026
d5b64d6
Add missing hibernate_sequence to database schema for file uploads
Copilot Jan 13, 2026
e5d0972
Add auto-migration for hibernate_sequence to fix existing databases
Copilot Jan 13, 2026
a53ee2c
Merge pull request #405 from TreeBASE/copilot/fix-nexus-file-upload-i…
rvosa Jan 14, 2026
c60296c
Initial plan
Copilot Jan 15, 2026
b6724b6
Add patch 0011 to init_db_uptodate.pg and create schema analysis docu…
Copilot Jan 15, 2026
95b66e1
Complete schema analysis: fix idempotent patches and document test re…
Copilot Jan 15, 2026
6e33937
Address code review: add schema qualification and NULL handling to pa…
Copilot Jan 15, 2026
f9f4c13
Fix Hibernate @Lob type mismatch causing MatrixRow data loading failure
Copilot Jan 15, 2026
aa2f710
Merge pull request #406 from TreeBASE/copilot/compare-hibernate-postg…
rvosa Jan 15, 2026
b55e6ac
Initial plan
Copilot Jan 16, 2026
867cd90
Remove legacy applet code and migrate to phylotree.js inline viewer
Copilot Jan 16, 2026
78d0923
Fix XSS vulnerabilities in tree viewer components
Copilot Jan 16, 2026
37c8564
Fix phylotree.js integration with local libraries
Copilot Jan 16, 2026
1951df2
Add shim for phylotree.js UMD bundle
rvosa Jan 18, 2026
00c79ed
Implement library wrapper for lodash and underscore
rvosa Jan 18, 2026
e200d41
Add cladogram support to phylotree.js tree viewer
Copilot Jan 18, 2026
4520ddd
Fix cladogram branch length conversion regex causing NaN errors
Copilot Jan 18, 2026
a22d930
Use phylotree.js tree traversal for cladogram handling
Copilot Jan 18, 2026
33f253b
Fix: Use string type for node.data.attribute in makeUltrametric
Copilot Jan 18, 2026
88960d3
Fix: Set root node attribute to "0" for phylotree.js compatibility
Copilot Jan 18, 2026
474585f
Fix: Manually append SVG to container after render()
Copilot Jan 18, 2026
33f0335
Simplify cladogram handling - use phylotree.js built-in support
Copilot Jan 18, 2026
0f03c35
Load phylotree.js stack BEFORE Prototype.js to fix Array pollution
Copilot Jan 23, 2026
2a8c892
Comment out unused menu toggle and script in adminMenu.jsp
rvosa Jan 27, 2026
aa4f992
Comment out unused Prototype.js scripts in adminTemplate.jsp
rvosa Jan 27, 2026
12651c8
Comment out unused Prototype.js and script.aculo.us scripts in defaul…
rvosa Jan 27, 2026
6606aa1
Comment out unused Prototype.js and script.aculo.us scripts in defaul…
rvosa Jan 27, 2026
3ba6ffd
Comment out center-aligned paragraph in footer.jsp for cleaner markup
rvosa Jan 27, 2026
99d22b0
Comment out unused Prototype.js script in mainTemplate.jsp for cleane…
rvosa Jan 27, 2026
b93d9e4
Comment out unused script and menu link in searchMenuRight.jsp for cl…
rvosa Jan 27, 2026
e2b6904
Comment out unused script and menu link in searchSummaryMenuRight.jsp…
rvosa Jan 27, 2026
9b139ea
Comment out unused Mendeley link and image in sidebarLeft.jsp for cle…
rvosa Jan 27, 2026
7b4f8a7
Comment out unused menu and script elements in submissionMenu.jsp for…
rvosa Jan 27, 2026
b1124ec
Refactor treeViewer.jsp for cleaner markup and improved structure
rvosa Jan 27, 2026
e949d89
Merge pull request #408 from TreeBASE/copilot/update-tree-viewing-sol…
rvosa Jan 27, 2026
5022a13
Removing deprecated JS libraries
rvosa Jan 27, 2026
3b38c4f
Comment out unused menu toggle functionality and associated script in…
rvosa Jan 27, 2026
cfc7e6f
Comment out unused prototype and script.aculo.us libraries in adminTe…
rvosa Jan 27, 2026
a7cd427
Remove unused prototype and script.aculo.us libraries in defaultSearc…
rvosa Jan 27, 2026
f29ed13
Remove unused prototype and script.aculo.us libraries in defaultTempl…
rvosa Jan 27, 2026
525b30e
Remove unused logo and validation links in footer.jsp for cleaner markup
rvosa Jan 27, 2026
50461e8
Comment out unused prototype library in mainTemplate.jsp for cleaner …
rvosa Jan 27, 2026
95c5463
Remove unused JavaScript and commented-out code in searchMenuRight.js…
rvosa Jan 27, 2026
49ca491
Remove unused JavaScript and commented-out code in searchSummaryMenuR…
rvosa Jan 27, 2026
4f764c5
Remove commented-out links in sidebarLeft.jsp for cleaner markup
rvosa Jan 27, 2026
ce3ee45
Remove commented-out code and unused script in submissionMenu.jsp for…
rvosa Jan 27, 2026
0f287e1
Initial plan
Copilot Jan 27, 2026
cd87c69
Remove unused PhyloWidget JAR files from test folder
Copilot Jan 27, 2026
99860da
Merge pull request #410 from TreeBASE/copilot/remove-phylowidget-refe…
rvosa Jan 27, 2026
f9d0e9a
Initial plan
Copilot Jan 27, 2026
f5060d7
Fix Autocompleter is not defined error by making autocomplete.js self…
Copilot Jan 27, 2026
ed29977
Address code review feedback: fix onclick loop and add IE compatibility
Copilot Jan 27, 2026
4ba46b4
Merge pull request #411 from TreeBASE/copilot/fix-autocomplete-js-error
rvosa Jan 27, 2026
550bd0b
Initial plan
Copilot Jan 27, 2026
3b9d4a2
Replace Prototype.js with native DOM APIs
Copilot Jan 27, 2026
6517a08
Replace Prototype.js with jQuery
Copilot Jan 27, 2026
184ee75
Remove empty jquery.min.js (using CDN instead)
Copilot Jan 27, 2026
6a20de3
Address code review feedback: use jQuery prop() and attribute selectors
Copilot Jan 27, 2026
8b935c0
Update image paths in styles.css for consistency and improved resourc…
rvosa Jan 27, 2026
16c5a6c
Merge pull request #413 from TreeBASE/master
rvosa Jan 27, 2026
a2edee3
Use local jQuery file instead of CDN
Copilot Jan 27, 2026
2a3384d
Fix jQuery AJAX dataType to prevent auto script execution
Copilot Jan 27, 2026
73aaf9b
Add DWR error handlers to prevent autocomplete alerts on empty database
Copilot Jan 27, 2026
f38c89d
Merge pull request #412 from TreeBASE/copilot/refactor-js-codebase-re…
rvosa Jan 27, 2026
0085955
Initial plan
Copilot Jan 27, 2026
5a71e0c
Fix JavaScript MIME type from javascript/x-javascript to text/javascript
Copilot Jan 27, 2026
767b9f7
Merge pull request #414 from TreeBASE/copilot/fix-mime-type-error
rvosa Jan 27, 2026
bf5f103
Initial plan
Copilot Jan 27, 2026
1b95cde
Initial plan
Copilot Jan 27, 2026
ff873fe
Remove unused raphael-min.js and jsphylosvg-min.js files
Copilot Jan 27, 2026
6b0f584
Initial plan
Copilot Jan 27, 2026
a082971
Remove unused d3.phylogram.js file and update documentation
Copilot Jan 27, 2026
c58eec2
Remove unused newick.js file and update documentation
Copilot Jan 27, 2026
d9eee65
Merge pull request #416 from TreeBASE/copilot/remove-raphael-min-js
rvosa Jan 27, 2026
b5c3271
Merge pull request #417 from TreeBASE/copilot/remove-d3-phylogram-js
rvosa Jan 27, 2026
886668e
Merge branch 'master' into copilot/check-newick-js-usage
rvosa Jan 27, 2026
dbe0e22
Merge pull request #418 from TreeBASE/copilot/check-newick-js-usage
rvosa Jan 27, 2026
bf5228e
Initial plan
Copilot Jan 27, 2026
0ea6c81
Remove unused sha1.js file
Copilot Jan 27, 2026
fe65e6a
Merge pull request #419 from TreeBASE/copilot/check-sha1-js-usage
rvosa Jan 27, 2026
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Initial plan
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Copilot committed Jan 27, 2026
commit 550bd0b9ce1781507b2aa937f7156875ffb42235

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