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Merge branch 'seek-1.16' into fairdomhub
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@stuzart
stuzart committed Nov 20, 2024
2 parents fc93be7 + 16c1ca0 commit c95ab2c
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Showing 515 changed files with 18,545 additions and 3,539 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/ansible-install.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
continue-on-error: true
strategy:
matrix:
os: [ubuntu-20.04,ubuntu-22.04]
os: [ubuntu-20.04,ubuntu-22.04,ubuntu-24.04]

services:
mysql:
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2 changes: 0 additions & 2 deletions .github/workflows/tests.yml
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Expand Up @@ -53,8 +53,6 @@ jobs:
- rake db:migrate
- rake seek:upgrade
include:
- database: postgres
suite: rails test test/unit
- database: sqlite3
suite: rails test test/unit
steps:
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3 changes: 3 additions & 0 deletions .rubocop.yml
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Expand Up @@ -9,3 +9,6 @@ Layout/LineLength:
# Don't enforce frozen string literals
Style/FrozenStringLiteralComment:
Enabled: false

Style/HashSyntax:
EnforcedShorthandSyntax: never
2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -2,7 +2,7 @@ FROM ruby:3.1-slim-bullseye

LABEL maintainer="Stuart Owen <orcid.org/0000-0003-2130-0865>, Finn Bacall"
ARG SOURCE_COMMIT
ENV APP_DIR /seek
ENV APP_DIR=/seek
ENV RAILS_ENV=production

# need to set the locale, otherwise some gems file to install
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156 changes: 77 additions & 79 deletions Gemfile.lock
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Expand Up @@ -51,40 +51,40 @@ GEM
remote: https://rubygems.org/
specs:
RedCloth (4.3.3)
actioncable (6.1.7.8)
actionpack (= 6.1.7.8)
activesupport (= 6.1.7.8)
actioncable (6.1.7.10)
actionpack (= 6.1.7.10)
activesupport (= 6.1.7.10)
nio4r (~> 2.0)
websocket-driver (>= 0.6.1)
actionmailbox (6.1.7.8)
actionpack (= 6.1.7.8)
activejob (= 6.1.7.8)
activerecord (= 6.1.7.8)
activestorage (= 6.1.7.8)
activesupport (= 6.1.7.8)
actionmailbox (6.1.7.10)
actionpack (= 6.1.7.10)
activejob (= 6.1.7.10)
activerecord (= 6.1.7.10)
activestorage (= 6.1.7.10)
activesupport (= 6.1.7.10)
mail (>= 2.7.1)
actionmailer (6.1.7.8)
actionpack (= 6.1.7.8)
actionview (= 6.1.7.8)
activejob (= 6.1.7.8)
activesupport (= 6.1.7.8)
actionmailer (6.1.7.10)
actionpack (= 6.1.7.10)
actionview (= 6.1.7.10)
activejob (= 6.1.7.10)
activesupport (= 6.1.7.10)
mail (~> 2.5, >= 2.5.4)
rails-dom-testing (~> 2.0)
actionpack (6.1.7.8)
actionview (= 6.1.7.8)
activesupport (= 6.1.7.8)
actionpack (6.1.7.10)
actionview (= 6.1.7.10)
activesupport (= 6.1.7.10)
rack (~> 2.0, >= 2.0.9)
rack-test (>= 0.6.3)
rails-dom-testing (~> 2.0)
rails-html-sanitizer (~> 1.0, >= 1.2.0)
actiontext (6.1.7.8)
actionpack (= 6.1.7.8)
activerecord (= 6.1.7.8)
activestorage (= 6.1.7.8)
activesupport (= 6.1.7.8)
actiontext (6.1.7.10)
actionpack (= 6.1.7.10)
activerecord (= 6.1.7.10)
activestorage (= 6.1.7.10)
activesupport (= 6.1.7.10)
nokogiri (>= 1.8.5)
actionview (6.1.7.8)
activesupport (= 6.1.7.8)
actionview (6.1.7.10)
activesupport (= 6.1.7.10)
builder (~> 3.1)
erubi (~> 1.4)
rails-dom-testing (~> 2.0)
Expand All @@ -94,14 +94,14 @@ GEM
activemodel (>= 4.1, < 7.1)
case_transform (>= 0.2)
jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
activejob (6.1.7.8)
activesupport (= 6.1.7.8)
activejob (6.1.7.10)
activesupport (= 6.1.7.10)
globalid (>= 0.3.6)
activemodel (6.1.7.8)
activesupport (= 6.1.7.8)
activerecord (6.1.7.8)
activemodel (= 6.1.7.8)
activesupport (= 6.1.7.8)
activemodel (6.1.7.10)
activesupport (= 6.1.7.10)
activerecord (6.1.7.10)
activemodel (= 6.1.7.10)
activesupport (= 6.1.7.10)
activerecord-import (1.3.0)
activerecord (>= 4.2)
activerecord-session_store (2.0.0)
Expand All @@ -110,14 +110,14 @@ GEM
multi_json (~> 1.11, >= 1.11.2)
rack (>= 2.0.8, < 3)
railties (>= 5.2.4.1)
activestorage (6.1.7.8)
actionpack (= 6.1.7.8)
activejob (= 6.1.7.8)
activerecord (= 6.1.7.8)
activesupport (= 6.1.7.8)
activestorage (6.1.7.10)
actionpack (= 6.1.7.10)
activejob (= 6.1.7.10)
activerecord (= 6.1.7.10)
activesupport (= 6.1.7.10)
marcel (~> 1.0)
mini_mime (>= 1.1.0)
activesupport (6.1.7.8)
activesupport (6.1.7.10)
concurrent-ruby (~> 1.0, >= 1.0.2)
i18n (>= 1.6, < 2)
minitest (>= 5.1)
Expand Down Expand Up @@ -165,7 +165,7 @@ GEM
bootstrap-sass (3.4.1)
autoprefixer-rails (>= 5.2.1)
sassc (>= 2.0.0)
builder (3.2.4)
builder (3.3.0)
case_transform (0.2)
activesupport
caxlsx (4.0.0)
Expand Down Expand Up @@ -198,7 +198,7 @@ GEM
execjs
coffee-script-source (1.12.2)
commonmarker (0.23.10)
concurrent-ruby (1.3.1)
concurrent-ruby (1.3.4)
connection_pool (2.3.0)
countries (5.2.0)
unaccent (~> 0.3)
Expand Down Expand Up @@ -241,7 +241,7 @@ GEM
encryptor (3.0.0)
equivalent-xml (0.6.0)
nokogiri (>= 1.4.3)
erubi (1.12.0)
erubi (1.13.0)
erubis (2.7.0)
exception_notification (4.5.0)
actionmailer (>= 5.2, < 8)
Expand Down Expand Up @@ -322,7 +322,7 @@ GEM
httpclient (2.8.3)
httpi (1.1.1)
rack
i18n (1.14.5)
i18n (1.14.6)
concurrent-ruby (~> 1.0)
i18n-js (3.9.0)
i18n (>= 0.6.6)
Expand All @@ -337,7 +337,7 @@ GEM
rails-dom-testing (>= 1, < 3)
railties (>= 4.2.0)
thor (>= 0.14, < 2.0)
jquery-ui-rails (6.0.1)
jquery-ui-rails (7.0.0)
railties (>= 3.2.16)
json (2.3.1)
json-canonicalization (0.3.0)
Expand Down Expand Up @@ -415,7 +415,7 @@ GEM
activesupport (>= 4)
railties (>= 4)
request_store (~> 1.0)
loofah (2.21.3)
loofah (2.23.1)
crass (~> 1.0.2)
nokogiri (>= 1.12.0)
macaddr (1.7.2)
Expand All @@ -429,7 +429,7 @@ GEM
net-imap
net-pop
net-smtp
marcel (1.0.2)
marcel (1.0.4)
matrix (0.4.2)
mechanize (2.8.5)
addressable (~> 2.8)
Expand All @@ -452,7 +452,7 @@ GEM
fastimage (~> 2.2)
nesty (~> 1.0)
nokogiri (~> 1.11)
method_source (1.0.0)
method_source (1.1.0)
mime-types (3.4.1)
mime-types-data (~> 3.2015)
mime-types-data (3.2022.0105)
Expand All @@ -461,7 +461,7 @@ GEM
rake
mini_mime (1.1.5)
mini_portile2 (2.8.7)
minitest (5.20.0)
minitest (5.25.1)
minitest-reporters (1.5.0)
ansi
builder
Expand All @@ -480,19 +480,19 @@ GEM
net-http-digest_auth (1.4.1)
net-http-persistent (4.0.1)
connection_pool (~> 2.2)
net-imap (0.4.10)
net-imap (0.5.0)
date
net-protocol
net-ldap (0.17.1)
net-pop (0.1.2)
net-protocol
net-protocol (0.2.2)
timeout
net-smtp (0.4.0.1)
net-smtp (0.5.0)
net-protocol
netrc (0.11.0)
nio4r (2.7.0)
nokogiri (1.16.5)
nio4r (2.7.4)
nokogiri (1.16.7)
mini_portile2 (~> 2.8.2)
racc (~> 1.4)
nori (1.1.5)
Expand Down Expand Up @@ -563,11 +563,11 @@ GEM
psych (5.1.0)
stringio
public_suffix (5.0.0)
puma (5.6.8)
puma (5.6.9)
nio4r (~> 2.0)
pyu-ruby-sasl (0.0.3.3)
racc (1.8.0)
rack (2.2.9)
racc (1.8.1)
rack (2.2.10)
rack-attack (6.6.0)
rack (>= 1.0, < 3)
rack-cors (1.1.1)
Expand All @@ -584,20 +584,20 @@ GEM
rack
rack-test (2.1.0)
rack (>= 1.3)
rails (6.1.7.8)
actioncable (= 6.1.7.8)
actionmailbox (= 6.1.7.8)
actionmailer (= 6.1.7.8)
actionpack (= 6.1.7.8)
actiontext (= 6.1.7.8)
actionview (= 6.1.7.8)
activejob (= 6.1.7.8)
activemodel (= 6.1.7.8)
activerecord (= 6.1.7.8)
activestorage (= 6.1.7.8)
activesupport (= 6.1.7.8)
rails (6.1.7.10)
actioncable (= 6.1.7.10)
actionmailbox (= 6.1.7.10)
actionmailer (= 6.1.7.10)
actionpack (= 6.1.7.10)
actiontext (= 6.1.7.10)
actionview (= 6.1.7.10)
activejob (= 6.1.7.10)
activemodel (= 6.1.7.10)
activerecord (= 6.1.7.10)
activestorage (= 6.1.7.10)
activesupport (= 6.1.7.10)
bundler (>= 1.15.0)
railties (= 6.1.7.8)
railties (= 6.1.7.10)
sprockets-rails (>= 2.0.0)
rails-controller-testing (1.0.5)
actionpack (>= 5.0.1.rc1)
Expand Down Expand Up @@ -625,15 +625,15 @@ GEM
json
require_all (~> 3.0)
ruby-progressbar
railties (6.1.7.8)
actionpack (= 6.1.7.8)
activesupport (= 6.1.7.8)
railties (6.1.7.10)
actionpack (= 6.1.7.10)
activesupport (= 6.1.7.10)
method_source
rake (>= 12.2)
thor (~> 1.0)
rainbow (3.1.1)
raindrops (0.20.0)
rake (13.1.0)
rake (13.2.1)
ransack (2.5.0)
activerecord (>= 5.2.4)
activesupport (>= 5.2.4)
Expand Down Expand Up @@ -728,8 +728,7 @@ GEM
netrc (~> 0.8)
reverse_markdown (2.1.1)
nokogiri
rexml (3.2.8)
strscan (>= 3.0.9)
rexml (3.3.9)
rfc-822 (0.4.1)
rmagick (5.3.0)
pkg-config (~> 1.4)
Expand Down Expand Up @@ -855,14 +854,13 @@ GEM
sprockets (4.2.1)
concurrent-ruby (~> 1.0)
rack (>= 2.2.4, < 4)
sprockets-rails (3.4.2)
actionpack (>= 5.2)
activesupport (>= 5.2)
sprockets-rails (3.5.2)
actionpack (>= 6.1)
activesupport (>= 6.1)
sprockets (>= 3.0.0)
sqlite3 (1.4.2)
stackprof (0.2.25)
stringio (3.0.1.1)
strscan (3.1.0)
sunspot (2.6.0)
pr_geohash (~> 1.0)
rsolr (>= 1.1.1, < 3)
Expand All @@ -888,7 +886,7 @@ GEM
terser (1.1.8)
execjs (>= 0.3.0, < 3)
test-prof (1.0.7)
thor (1.3.1)
thor (1.3.2)
tilt (2.0.10)
time (0.2.2)
date
Expand Down Expand Up @@ -938,7 +936,7 @@ GEM
addressable (>= 2.3.6)
crack (>= 0.3.2)
hashdiff (>= 0.4.0, < 2.0.0)
webrick (1.8.1)
webrick (1.8.2)
webrobots (0.1.2)
websocket-driver (0.7.6)
websocket-extensions (>= 0.1.0)
Expand All @@ -952,7 +950,7 @@ GEM
rails (>= 3.0)
rake (>= 0.8.7)
yard (0.9.36)
zeitwerk (2.6.15)
zeitwerk (2.6.18)
zip-container (4.0.2)
rubyzip (~> 2.0.0)

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7 changes: 7 additions & 0 deletions app/assets/javascripts/application.js
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Expand Up @@ -50,6 +50,7 @@
//= require DataTables-1.11.3/buttons.html5
//= require DataTables-1.11.3/autoFill.bootstrap
//= require samples
//= require datafiles
//= require jstree
//= require clipboard
//= require openbis
Expand Down Expand Up @@ -77,3 +78,9 @@
//= require select2.full.min
//= require licenses
//= require svg-pan-zoom-3.6.1/svg-pan-zoom.min
//= require copasi/copasi
//= require copasi/copasijs
//= require copasi/copasi_simulation
//= require plotly-2.27.0.min
//= require extended_metadata_type

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