Merge/security hardening to main - #33

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prmunday wants to merge 330 commits into

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merge/security-hardening-to-main

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Commits on Nov 27, 2024

Enabling user to select motif lenght for class I
prmunday
committed
a943b06

Commits on Dec 2, 2024

Pepscanner fix : replace quotes if present in column names
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fad4b31
Pepscaner : Sort proteins by peptide count
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30121bd

Commits on Jan 16, 2025

Update species name
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committed
92ad7ad

Commits on Jan 23, 2025

Update h2 allele names
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e41d812
py script to fix depenencies issue
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ba85620
Initial docker file setup
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efcc873
clean up
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35d7573
Merge branch 'develop' of https://github.com/prmunday/Immunolyser into develop
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0567410

Commits on Jan 29, 2025

main gibbs setting update
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ccf8b99
gibbs bug fix and reverse last change
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committed
ba443f5
bug fix
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685c59e
gubbs update
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7ea4ef2
updated gibss running when ran individually
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f0f028a
bug fix from last commit
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4661642

Commits on Feb 4, 2025

gibbs py reverse
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3f7ee6d
dynamic set CELERY_BROKER_URL based on env
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29ba2f7
docker git repo update : temp
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d6287b6
Initial set up to run celery in docker
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47952d2
docker mount fix
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8562377
adding python 2 in repo
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4b146d9
remove python2 and type might not be copmatible
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759825b
seq2logo gs fix
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f9d2bb6
updated docker file to load data files into host folder
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c8e0c65
updated gibbs cluster script to use project root to determine seq2logo path
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817201c
added logging in utils method
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75c6f89
pass logger in utls method
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fbbf5b1
util method update
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4a30297
testing docker file update
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1325249
added option to check no prefix is created
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3f6fed1
reverse last change
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d3509b4
pushing latest yml file
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aea3a02
uodate docker file to install binder tools
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3a597c6
man command for netmhcpab
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f8beea4
use full path for the predictors
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6866601
path updates to use full path
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75f5705
docker file fixes to run binders
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47629e9
netmhcpan path update
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2e3b194
mkdir tmp for netmhc pan
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7e9cfd1
docker file update
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ff4d8b4

Commits on Feb 9, 2025

Input file exmaple update
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8404865

Commits on Feb 12, 2025

Use presentation_percentile for MHCflurry
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d222c8c
Update celery status from Pending to Progressing
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e9e3d87
update Progressing to Processing
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6edaf2d

Commits on Feb 20, 2025

update gibbs class 1 and 2 args.. feed all mers for gibbs
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5f27164
remove function to generate gibbs cluster by click
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c57d64e

Commits on Feb 25, 2025

Report text updated based on updated gibbs updated logic.
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488c4e8
Creation of folders to store majority voted binders
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91bafee

Commits on Feb 27, 2025

Revert seqlgog message about input peptides
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4b3b1a3
Run Seq2Logo conditionally
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ad76a57
Conditionally running Seq2logo
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35d5852
Analytics text update
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0a34086
Hide Seq2Logo for class2 if no alleles are selected
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95068dd

Commits on Feb 28, 2025

method not ready
prmunday
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75633d0
bug fix for Gibbs motif length
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9fe3137
gibbs fix for docker
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f695abe

Commits on Mar 1, 2025

Clearn pepscnaner input files based on Accession column
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committed
73a21b9

Commits on Mar 2, 2025

Functionality to majority voted binder as csv files
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eb95fb8
Generation of majority voted binder
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42c29f6
Merge branch 'upgrade/download-majority-voted-binders' into develop
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93dc71d
Bug fix
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e128a06
Bug fix
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d78bbfe

Commits on Mar 6, 2025

Run HLA-clust
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70e5ce4
Show HLA clust resutls in front end
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cb37377
Update hla-clust
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d233767

Commits on Mar 12, 2025

Upated code to run hla clust
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b2e91c8

Commits on Mar 13, 2025

Gibbs update to cluster 1-6
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8c3d9bf
Fix to run HLAClust
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e797db2

Commits on Mar 19, 2025

Update Dockerfile
prmunday
authored
cd5bcb0

Commits on Apr 4, 2025

run MHC tp without n_clusters arg
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81e42c9
description of MHC-TP
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30122fa

Commits on Apr 21, 2025

Update gibbs output with MHC-TP output
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452c1ca

Commits on Apr 24, 2025

Integrate MHC-TP results into GibbCluster results
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85796f6

Commits on May 2, 2025

temporary progress to remote
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013216f
Run protpetigram from the form submission, pending UI
prmunday
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54cae88
updated demo page for pepscanner
prmunday
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70950f4
pepscanner update pending bug of accession selectioin
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77e6ec3
Final integration ProtPeptigram
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aea14e9
added protpeptigram in pip list
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f82ae05
Run protpeptigram one by one
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ef0e72b

Commits on May 3, 2025

pepsacnner metadata table css adjust
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f999c23
Option to export data used to generate graphs
prmunday
committed
5796a0d

Commits on May 14, 2025

rearrange pepscanner
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351592f

Commits on May 15, 2025

pepsanner update
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319ce83

Commits on May 18, 2025

added email functionality
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e008046

Commits on May 26, 2025

updated text
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f58829f

Commits on May 27, 2025

UI update
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51f870b

Commits on May 28, 2025

initialiser page ui update
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0cd3715

Commits on Jun 2, 2025

add job resitry
prmunday
committed
a9cf42b

Commits on Jun 5, 2025

Ability to download peptides from overlap
prmunday
committed
b77427b
update text ui
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2580f09

Commits on Jun 8, 2025

Create README.md
prmunday
authored
ef62591
test readme update
prmunday
committed
e9abf4a

Commits on Jun 12, 2025

generate gibbs update. test on remote server
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bb96d19
slick css update
prmunday
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35ca763
fix xhr of setupPeptideOverlapUpsetPlot
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54f583d
bug fix js
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18592ee
bug fix js
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c4cb0c7
remote debuggin
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cd82261
remote debug js
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f833c6d
remote debug js
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4db13c6
remote js debug
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ecbb04d
slcik update
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5097810
slcick upadte
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4fb70fb
test slcik
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adac42f

Commits on Jun 15, 2025

Binding motif click on upset
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464a5d3

Commits on Jun 19, 2025

UI update
prmunday
committed
7d1d2ab

Commits on Jun 24, 2025

UI update. feedback from Natham
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committed
2008a98
ui update
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committed
347f350

Commits on Jun 25, 2025

ability to download seq2logo input peptides
prmunday
committed
8c90ed1

Commits on Jun 26, 2025

seq2logo peptide download fix and completed
prmunday
committed
bb0f8c0
enabling core download method for giibs
prmunday
committed
bdb34c7
Protpeptigram update
prmunday
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7b87836
protpeptigram fix
prmunday
committed
c46ce1e

Commits on Jul 1, 2025

MHC-TP ui update
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committed
4beb947
ui fix
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03ec8cd
ui fix
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8beb7c9
ui fix
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4850fee
ui
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committed
bc80f5e

Commits on Jul 2, 2025

revert gibb scroll bar ui update
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committed
4060218

Commits on Jul 8, 2025

pepscanner fix
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committed
470d3d5

Commits on Jul 10, 2025

fix pepscanner image
prmunday
committed
c37a6c8

Commits on Jul 11, 2025

Update README.md
prmunday
authored
af4342e

Commits on Jul 16, 2025

add traceback to hadnle no peptides after contan clean opetation
prmunday
committed
c9ac734
fix exception handling
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committed
d1b52d2

Commits on Jul 30, 2025

hiding help page until updated
prmunday
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406dc55

Commits on Aug 21, 2025

Overlap plot selection option
prmunday
committed
b2ac25f
update text
prmunday
committed
608822e

Commits on Aug 25, 2025

binding prediction adjust and issue fix
prmunday
committed
445b300
remove extra space
prmunday
committed
5ddb583

Commits on Sep 9, 2025

Option to search a smaller database for mhc-tp
prmunday
committed
0a77a6e

Commits on Sep 16, 2025

have all peptide in binding results
prmunday
committed
07cc37b
hla arg fix for mhc-tp
prmunday
committed
188a475

Commits on Sep 18, 2025

update utils to run mhc-tp and update top 40 allele file per hla type
prmunday
committed
e71d4c4
update to config netmhcpan 4.2
prmunday
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517d2e5

Commits on Sep 20, 2025

updates for netmhcpan integration
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2cef177
change
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eb70afd

Commits on Sep 21, 2025

initaliser page udpates
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21ed339
added logs
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3739e0f
pepscanner message update
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f683388
tyring out upset update for violin plot
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f1281b5

Commits on Sep 22, 2025

violine plot wokring
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037ee4c
identation
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6e823b7

Commits on Sep 23, 2025

single sample name post fix
prmunday
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4594e8c
finalise violin plot
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e9b510b

Commits on Sep 24, 2025

ignore local setup files
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df3f325
sample validation message update
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4cf7255

Commits on Sep 25, 2025

download core as text
prmunday
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4394140
MHC-TP description update
prmunday
committed
903cc7f
update majorityvoting
prmunday
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cdf4770
overlap upset fixed
prmunday
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6b24893
ignote test ipynb
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b016c2e
lower mhc-tp threshhold
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b214f96
lower mhc-tp threshold
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a797bd5

Commits on Sep 26, 2025

Updated majority voted downloadable files
prmunday
committed
a234d31
majority voting html update
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afeee82
majority voted output file update
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committed
ca3bebd

Commits on Sep 28, 2025

updates tools for docker purpose
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dc9f09b
try mhc-tp
prmunday
committed
cda65a9
docker update
prmunday
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7f5a4d3
MHC-TP dir name update
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4693995
reverse mhc-tp name
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fd60f21

Commits on Sep 29, 2025

undo error bars
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1094280
seq2logo div available always
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d84eb4c
control file fix
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committed
b7c83c4

Commits on Sep 30, 2025

Commits on Oct 1, 2025

update base page
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2791580
analytics page update
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76799ec
not show overlap upset for class 2
prmunday
committed
48703e7

Commits on Oct 2, 2025

use cors to generate upset plot for binder netmhc2pan
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82d04eb
ability to name the job
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1aa258f
send back email with job name in it
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56d8177
bug
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2cd4ec6

Commits on Oct 4, 2025

update pepscanner text
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5f226b7
add border to analytics section
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409fd0b
updated text alignment
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8ab352b

Commits on Oct 5, 2025

url update
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committed
9bb30ee

Commits on Oct 6, 2025

addition of banner
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committed
bbdcd0e
identation fix
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11f0093
banner update
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80a52d5

Commits on Oct 7, 2025

banner update
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2767a92
Stop tracking static/images symlink
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ea35212

Commits on Oct 8, 2025

manuscript accepted
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1905618
index page update
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12d7e67
text update
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bd16152

Commits on Oct 10, 2025

typo fix
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96375e8

Commits on Oct 12, 2025

update pepscanner
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committed
5789999

Commits on Oct 14, 2025

walkthruogh video
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65b8040

Commits on Oct 22, 2025

geo ip addtion
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ae7d72a
privacy note added
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634a17b
add ref for netmhc2pan 4.3
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6f2aa4b
privacy staement update
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8f78419

Commits on Oct 24, 2025

add doi link
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486fd14

Commits on Oct 29, 2025

flag to notify invalid amino acids
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49b7e49

Commits on Nov 4, 2025

dcoker local version fix
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32e3300
entrypoint update
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2fb4992

Commits on Nov 5, 2025

move sqlite file outside proj dir
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committed
dc61d5f

Commits on Nov 11, 2025

error bar fix
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committed
f1f92e7

Commits on Nov 25, 2025

update docker file
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b461475
isntall sqlite3
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f6100c0
docker setup update
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committed
b36fad2
mhc-tp name temp fix
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committed
7d3c7a5

Commits on Dec 8, 2025

Fix open redirect + input validation across Flask routes
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committed
4987082

Commits on Feb 3, 2026

hide banner
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committed
0f17d40

Commits on Apr 9, 2026

heatmap fix
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committed
2d12375

Commits on May 2, 2026

Fix job queue jams and duplicate email notifications
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committed
6333287
Update Dockerfile: fix COPY paths and bump tool versions
prmunday
committed
20233bb
Add versioning, release notes banner, and What's New section
prmunday
committed
4455491
Improve email notifications and update site logo
prmunday
committed
435f842
Fix path traversal in /api/generateGibbs endpoint
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committed
5cc72aa
Hide Generic Analysis tab unless viewing a job; fix /analytics redirect
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committed
b57d77a

Commits on May 3, 2026

Commits on May 13, 2026

Security hardening: fix path traversal, debug mode, secret key, headers
prmunday
committed
fa7a961

Commits on May 14, 2026

Commits on May 15, 2026

Commits on May 17, 2026

Commits on May 18, 2026

Commits on May 19, 2026