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Merge branch 'master' of github.com:ELIXIR-Belgium/seek into experime…
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…nt_template_make_over
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Kevin De Pelseneer committed Oct 9, 2023
2 parents 80536ae + 96c8da3 commit 57a161b
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -66,6 +66,7 @@ public/javascripts/i18n.js
public/javascripts/translations.js
public/stylesheets/*_cached.css
public/system/
public/sitemaps/*

public/assets/
public/assets_dev/
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5 changes: 5 additions & 0 deletions Gemfile
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Expand Up @@ -109,6 +109,7 @@ gem 'ransack'

gem 'terser', '~> 1.1', '>= 1.1.1'


# Rails 4 upgrade
gem 'activerecord-session_store'
gem 'rails-observers'
Expand Down Expand Up @@ -177,6 +178,8 @@ group :development do

gem 'web-console', '>= 4.1.0'
gem 'rack-mini-profiler', '~> 2.0'
gem "flamegraph", "~> 0.9.5"
gem "stackprof", "~> 0.2.25"
gem 'listen', '~> 3.3'
end

Expand All @@ -202,3 +205,5 @@ group :test, :development do
gem 'teaspoon'
gem 'teaspoon-mocha'
end

gem "sitemap_generator", "~> 6.3"
137 changes: 73 additions & 64 deletions Gemfile.lock
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Expand Up @@ -51,40 +51,40 @@ GEM
remote: https://rubygems.org/
specs:
RedCloth (4.3.2)
actioncable (6.1.7.3)
actionpack (= 6.1.7.3)
activesupport (= 6.1.7.3)
actioncable (6.1.7.6)
actionpack (= 6.1.7.6)
activesupport (= 6.1.7.6)
nio4r (~> 2.0)
websocket-driver (>= 0.6.1)
actionmailbox (6.1.7.3)
actionpack (= 6.1.7.3)
activejob (= 6.1.7.3)
activerecord (= 6.1.7.3)
activestorage (= 6.1.7.3)
activesupport (= 6.1.7.3)
actionmailbox (6.1.7.6)
actionpack (= 6.1.7.6)
activejob (= 6.1.7.6)
activerecord (= 6.1.7.6)
activestorage (= 6.1.7.6)
activesupport (= 6.1.7.6)
mail (>= 2.7.1)
actionmailer (6.1.7.3)
actionpack (= 6.1.7.3)
actionview (= 6.1.7.3)
activejob (= 6.1.7.3)
activesupport (= 6.1.7.3)
actionmailer (6.1.7.6)
actionpack (= 6.1.7.6)
actionview (= 6.1.7.6)
activejob (= 6.1.7.6)
activesupport (= 6.1.7.6)
mail (~> 2.5, >= 2.5.4)
rails-dom-testing (~> 2.0)
actionpack (6.1.7.3)
actionview (= 6.1.7.3)
activesupport (= 6.1.7.3)
actionpack (6.1.7.6)
actionview (= 6.1.7.6)
activesupport (= 6.1.7.6)
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 (6.1.7.3)
actionpack (= 6.1.7.3)
activerecord (= 6.1.7.3)
activestorage (= 6.1.7.3)
activesupport (= 6.1.7.3)
actiontext (6.1.7.6)
actionpack (= 6.1.7.6)
activerecord (= 6.1.7.6)
activestorage (= 6.1.7.6)
activesupport (= 6.1.7.6)
nokogiri (>= 1.8.5)
actionview (6.1.7.3)
activesupport (= 6.1.7.3)
actionview (6.1.7.6)
activesupport (= 6.1.7.6)
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 (6.1.7.3)
activesupport (= 6.1.7.3)
activejob (6.1.7.6)
activesupport (= 6.1.7.6)
globalid (>= 0.3.6)
activemodel (6.1.7.3)
activesupport (= 6.1.7.3)
activerecord (6.1.7.3)
activemodel (= 6.1.7.3)
activesupport (= 6.1.7.3)
activemodel (6.1.7.6)
activesupport (= 6.1.7.6)
activerecord (6.1.7.6)
activemodel (= 6.1.7.6)
activesupport (= 6.1.7.6)
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 (6.1.7.3)
actionpack (= 6.1.7.3)
activejob (= 6.1.7.3)
activerecord (= 6.1.7.3)
activesupport (= 6.1.7.3)
activestorage (6.1.7.6)
actionpack (= 6.1.7.6)
activejob (= 6.1.7.6)
activerecord (= 6.1.7.6)
activesupport (= 6.1.7.6)
marcel (~> 1.0)
mini_mime (>= 1.1.0)
activesupport (6.1.7.3)
activesupport (6.1.7.6)
concurrent-ruby (~> 1.0, >= 1.0.2)
i18n (>= 1.6, < 2)
minitest (>= 5.1)
Expand Down Expand Up @@ -286,15 +286,16 @@ GEM
loofah (>= 2.3.1)
sax-machine (>= 1.0)
ffi (1.15.5)
flamegraph (0.9.5)
fssm (0.2.10)
gem-licenses (0.2.2)
gitlab_omniauth-ldap (2.2.0)
net-ldap (~> 0.16)
omniauth (>= 1.3, < 3)
pyu-ruby-sasl (>= 0.0.3.3, < 0.1)
rubyntlm (~> 0.5)
globalid (1.1.0)
activesupport (>= 5.0)
globalid (1.2.1)
activesupport (>= 6.1)
google-analytics-rails (1.1.1)
gyoku (0.4.6)
builder (>= 2.1.2)
Expand Down Expand Up @@ -458,8 +459,9 @@ GEM
mimemagic (0.3.10)
nokogiri (~> 1)
rake
mini_mime (1.1.2)
minitest (5.18.0)
mini_mime (1.1.5)
mini_portile2 (2.8.4)
minitest (5.20.0)
minitest-reporters (1.5.0)
ansi
builder
Expand All @@ -478,7 +480,7 @@ GEM
net-http-digest_auth (1.4.1)
net-http-persistent (4.0.1)
connection_pool (~> 2.2)
net-imap (0.3.4)
net-imap (0.3.7)
date
net-protocol
net-ldap (0.17.1)
Expand All @@ -491,6 +493,7 @@ GEM
netrc (0.11.0)
nio4r (2.5.9)
nokogiri (1.14.5)
mini_portile2 (~> 2.8.0)
racc (~> 1.4)
nori (1.1.5)
oauth2 (2.0.9)
Expand Down Expand Up @@ -563,7 +566,7 @@ GEM
nio4r (~> 2.0)
pyu-ruby-sasl (0.0.3.3)
racc (1.7.1)
rack (2.2.7)
rack (2.2.8)
rack-attack (6.6.0)
rack (>= 1.0, < 3)
rack-cors (1.1.1)
Expand All @@ -580,26 +583,26 @@ GEM
rack
rack-test (2.1.0)
rack (>= 1.3)
rails (6.1.7.3)
actioncable (= 6.1.7.3)
actionmailbox (= 6.1.7.3)
actionmailer (= 6.1.7.3)
actionpack (= 6.1.7.3)
actiontext (= 6.1.7.3)
actionview (= 6.1.7.3)
activejob (= 6.1.7.3)
activemodel (= 6.1.7.3)
activerecord (= 6.1.7.3)
activestorage (= 6.1.7.3)
activesupport (= 6.1.7.3)
rails (6.1.7.6)
actioncable (= 6.1.7.6)
actionmailbox (= 6.1.7.6)
actionmailer (= 6.1.7.6)
actionpack (= 6.1.7.6)
actiontext (= 6.1.7.6)
actionview (= 6.1.7.6)
activejob (= 6.1.7.6)
activemodel (= 6.1.7.6)
activerecord (= 6.1.7.6)
activestorage (= 6.1.7.6)
activesupport (= 6.1.7.6)
bundler (>= 1.15.0)
railties (= 6.1.7.3)
railties (= 6.1.7.6)
sprockets-rails (>= 2.0.0)
rails-controller-testing (1.0.5)
actionpack (>= 5.0.1.rc1)
actionview (>= 5.0.1.rc1)
activesupport (>= 5.0.1.rc1)
rails-dom-testing (2.1.1)
rails-dom-testing (2.2.0)
activesupport (>= 5.0.0)
minitest
nokogiri (>= 1.6)
Expand All @@ -621,9 +624,9 @@ GEM
json
require_all (~> 3.0)
ruby-progressbar
railties (6.1.7.3)
actionpack (= 6.1.7.3)
activesupport (= 6.1.7.3)
railties (6.1.7.6)
actionpack (= 6.1.7.6)
activesupport (= 6.1.7.6)
method_source
rake (>= 12.2)
thor (~> 1.0)
Expand Down Expand Up @@ -828,6 +831,8 @@ GEM
simplecov_json_formatter (~> 0.1)
simplecov-html (0.12.3)
simplecov_json_formatter (0.1.3)
sitemap_generator (6.3.0)
builder (~> 3.0)
slop (3.6.0)
snaky_hash (2.0.0)
hashie
Expand All @@ -844,14 +849,15 @@ GEM
sparql-client (3.2.0)
net-http-persistent (~> 4.0, >= 4.0.1)
rdf (~> 3.2)
sprockets (4.2.0)
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 (>= 3.0.0)
sqlite3 (1.4.2)
stackprof (0.2.25)
stringio (3.0.1)
sunspot (2.6.0)
pr_geohash (~> 1.0)
Expand Down Expand Up @@ -882,7 +888,7 @@ GEM
tilt (2.0.10)
time (0.2.2)
date
timeout (0.3.2)
timeout (0.4.0)
tzinfo (2.0.6)
concurrent-ruby (~> 1.0)
ucf (2.0.2)
Expand Down Expand Up @@ -930,7 +936,7 @@ GEM
hashdiff (>= 0.4.0, < 2.0.0)
webrick (1.7.0)
webrobots (0.1.2)
websocket-driver (0.7.5)
websocket-driver (0.7.6)
websocket-extensions (>= 0.1.0)
websocket-extensions (0.1.5)
whenever (1.0.0)
Expand All @@ -943,7 +949,7 @@ GEM
rake (>= 0.8.7)
yard (0.9.27)
webrick (~> 1.7.0)
zeitwerk (2.6.8)
zeitwerk (2.6.11)
zip-container (4.0.2)
rubyzip (~> 2.0.0)

Expand Down Expand Up @@ -990,6 +996,7 @@ DEPENDENCIES
exception_notification
factory_bot (~> 6.2.1)
feedjira
flamegraph (~> 0.9.5)
fleximage!
fssm
gem-licenses
Expand Down Expand Up @@ -1073,8 +1080,10 @@ DEPENDENCIES
seedbank
simple-spreadsheet-extractor (~> 0.18.0)
simplecov
sitemap_generator (~> 6.3)
sprockets-rails
sqlite3 (~> 1.4)
stackprof (~> 0.2.25)
stringio (= 3.0.1)
sunspot_matchers
sunspot_rails
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3 changes: 2 additions & 1 deletion app/assets/javascripts/application.js
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Expand Up @@ -56,7 +56,7 @@
//= require calendar
//= require inplace
//= require strain
//= require checkbox
//= require batch_asset_selection
//= require cytoscape.js-2.5.0/cytoscape
//= require cytoscape_isa_graph
//= require bives
Expand All @@ -75,3 +75,4 @@
//= require git
//= require jquery.splitter/jquery.splitter.min
//= require select2.full.min
//= require licenses
2 changes: 2 additions & 0 deletions app/assets/javascripts/application_shared.js.erb
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Expand Up @@ -399,6 +399,8 @@ $j(document).ready(function () {
$j('#sidebar-toggle').click(Sidebar.toggle);
$j('#sidebar-close').click(Sidebar.toggle);
$j(document).on('click', '.sidebar-backdrop', Sidebar.toggle);

Licenses.init();
});

var URL_ROOT = '<%= Rails.application.config.relative_url_root %>';
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