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Release 2 #39

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@AndrewRadev AndrewRadev commented Dec 8, 2025

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@AndrewRadev
Fix issue with partial port declaration
e18b90d
@AndrewRadev
Add js-cookie plugin
39adb5e
@AndrewRadev
Save sidebar open/closed state in a cookie
8780912
@AndrewRadev
Remove note
b3852dc
@AndrewRadev
Move static directory to the root of the app
3f812c4
@AndrewRadev
Minor script fix
e1f9de2
@AndrewRadev
Script to export study design and data
d04b9f8
@AndrewRadev
Record changelog entries, clean up old files
2da8f9f
@AndrewRadev
Export study on publish and on update
3cb98a4
@AndrewRadev
Minor line spacing fix for text areas
110cc46
@AndrewRadev
Validate uniqueness of techniques
07d4e9b
@AndrewRadev
Minor modeling fixes
35383f0
@AndrewRadev
Security fixes for submissions
2d1768f
@AndrewRadev
Make sure we're copying the default params
1f21701
@AndrewRadev
Fix export page
ea867a8
@AndrewRadev
Fix compare links for experiments
4bdee3a
@AndrewRadev
Extract common js code
0fcd94b
@AndrewRadev
Better naming for step3 form
5defa7e
@AndrewRadev
Slight refactoring
9b175e6
@AndrewRadev
Experiment export form tests and fixes
f4ed26e
@AndrewRadev
Use /bin/bash to avoid some production issues
6d02577
@AndrewRadev
Add empty __init__.py files for documentation parser
79c6326
@AndrewRadev
Increase API documentation depth
72d205c
@AndrewRadev
Use study/project publicId as a primary key
0046ddf
@AndrewRadev
Initial Project, Study, Experiment JSON endpoints
a5d1737
@AndrewRadev
Handle non-public study/experiment
3f80998
@AndrewRadev
Add studies to project JSON
85209f8
@AndrewRadev
Fix missing community ID constraint for experiments
4881784
@AndrewRadev
Render more API fields
ac47a0b
@AndrewRadev
Revert "Fix missing community ID constraint for experiments"
1bdf529 
This reverts commit b5f3592.

Communities get recreated when a study gets rebuilt, which causes
problems with "orphaned" experiments. Seems like we have to allow
missing communities in this particular case.
@AndrewRadev
Rename Strains to StudyStrains, NCBId to ncbiId
d435db3
@AndrewRadev
Rename chebi_id to chebiId
4c21377
@AndrewRadev
Fix bug with label function
9c41474
@AndrewRadev
Prod server that can be reloaded
229d325
@AndrewRadev
Try to get server reloading to work
29c416a
@AndrewRadev
Try to encapsulate prod server reloading in a separate script
38b47d3
@AndrewRadev
Systemd documentation
b7a099f
@AndrewRadev
Fix modeling dropdown
0734763
@AndrewRadev
Fix development note
bc29f14
@AndrewRadev
First step for new search interface
446fd69
@AndrewRadev
Add link to new search
22ca449
@AndrewRadev
Minor title fix
e20f1b1
@AndrewRadev
Extract and test search object
78af0e3
@AndrewRadev
Rename Strains to StudyStrains, NCBId to ncbiId
c08fb14
@AndrewRadev
Revert change to isPublished
3455f1e
@AndrewRadev
Working strain search in model
8223fb2
@AndrewRadev
Search for metabolites in the model
942a660
@AndrewRadev
Rename chebi_id to chebiId
db8e996
@AndrewRadev
Strain and metabolite search UI
ed85f8e
@AndrewRadev
WIP strain and metabolite searches
2ed0ce0
@AndrewRadev
Fix study strain count on homepage
f80a778 
Multiple custom strains can be uploaded with different names, but the
same NCBI identifier.
@AndrewRadev
Implementation work on new search
b3a26e9
@AndrewRadev
Add icons to search
0b76010
@AndrewRadev
Apply search fixes, implement more highlighting
83e16ac
@AndrewRadev
Fix text filter tests
2f6105f
@AndrewRadev
Order search result by number of matched strains/metabolites
9888712
@AndrewRadev
Systemd documentation
111441b
@AndrewRadev
Add GPL3 license
cbcd5fc
@AndrewRadev
Deploy documentation from main branch
e145128
@AndrewRadev
Resolve leftover merge conflict
cf04f1a
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@AndrewRadev