.aspell.en.pws

+personal_ws-1.1 en 0 utf-8
+Affero
+AGPL
+alice
+Alper
+Backend
+backend
+backends
+Biomedicine
+Christophe
+DAISY’s
+DAta
+Dataset
+dataset
+Dataset’s
+dataset’s
+datasets
+Datasets
+datatypes
+Ded
+DOI
+du
+GDPR
+GigaScience
+github
+giz
+Grouès
+howto
+Jacek
+Jarosz
+jekyll
+Kavita
+lcsb
+LCSB's
+LDAP
+Lebioda
+LuxPARK
+Menubar
+Pinar
+pre
+projects’s
+Rege
+Reinhard
+repo
+Sandrine
+Satagopam
+STDOUT
+Storages
+SYSCID
+SYstem
+TBC
+Trefois
+Université
+unlinked
+Venkata
+Vilem
+vip
+Yohan
+YYYY
+Quickstart

.gitignore

 _site
 .sass-cache
 .jekyll-metadata
+.jekyll-cache
+/Thumbs.db
+/.DS_Store
+/.idea

.gitlab-ci.yml

+# In case something goes horribly wrong, you can fall back to `image: ruby:latest`
+image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb:1.5
+
+build:
+  stage: build
+  before_script:
+  - gem install bundler -v2.0.2
+  - bundle install && bundle update jekyll-theme-lcsb-default && bundle update jekyll-theme-lcsb-frozen-components
+  script:
+  - 'echo "baseurl: /$CI_PROJECT_NAME" >> _config_ci.yml'
+  - 'echo "url: https://$CI_PROJECT_NAMESPACE.$CI_PAGES_DOMAIN" >> _config_ci.yml'
+  - bundle exec jekyll build -d test --config "_config.yml,_config_ci.yml"
+  - 'echo $CI_COMMIT_SHA > test/version'
+  artifacts:
+    expire_in: 3 days
+    paths:
+    - test
+  variables:
+    JEKYLL_ENV: production
+
+
+test_spell_check:
+  image: debian
+  stage: test
+  dependencies:
+     - build
+  script:
+  - apt-get update
+  - apt-get install -y aspell aspell-en
+  - ./test_spell_check.sh
+  except:
+  - master
+
+
+pages:
+  stage: deploy
+  only:
+  - master
+  script:
+  - mv test public
+  - echo "Your website is available at $CI_PAGES_URL"
+  artifacts:
+    expire_in: 1 week
+    paths:
+    - public

Gemfile

 source "https://rubygems.org"
-ruby 2.5
+
 
 # Hello! This is where you manage which Jekyll version is used to run.
 # When you want to use a different version, change it below, save the
@@ -7,15 +7,12 @@ ruby 2.5
 #
 #     bundle exec jekyll serve
 #
-# This will help ensure the proper Jekyll version is running.
-# Happy Jekylling!
-gem "jekyll", "~> 3.7.3"
-gem "bundler", "~> 1.16.1"
 
-# This is the default theme for new Jekyll sites. You may change this to anything you like.
-gem "minima", "~> 2.0"
-gem 'jekyll-theme-primer', '~> 0.5.2'
-gem 'jekyll-theme-lcsb-default', :git => "ssh://git@git-r3lab-server.uni.lu:8022/core-services/jekyll-theme-lcsb-default.git", :branch => "master"
+gem "jekyll", "~> 4.0"
+gem "bundler", "> 2.0"
+
+gem "minima", "~> 2.5"
+gem 'jekyll-theme-lcsb-default', '~> 0.3'
 
 # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
 # uncomment the line below. To upgrade, run `bundle update github-pages`.
@@ -23,12 +20,21 @@ gem 'jekyll-theme-lcsb-default', :git => "ssh://git@git-r3lab-server.uni.lu:8022
 
 # If you have any plugins, put them here!
 group :jekyll_plugins do
-  gem "jekyll-feed", "~> 0.6"
+ gem "jekyll-paginate-v2", 
+     "~> 3"
+
+ gem "jekyll-feed", 
+     "~> 0.6"
+
+ gem 'jekyll-theme-lcsb-frozen-components', 
+     '~> 0.0.1', 
+     :git => "https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-frozen-components.git", 
+     :branch => "master"
+
 end
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
 gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
 
 # Performance-booster for watching directories on Windows
-gem "wdm", "~> 0.1.0" if Gem.win_platform?
-
+gem "wdm", "~> 0.1.1" if Gem.win_platform?

Gemfile.lock

 GIT
-  remote: ssh://git@git-r3lab-server.uni.lu:8022/core-services/jekyll-theme-lcsb-default.git
-  revision: 852e566edd26ac75be4bec07cd26dc44e0c6d4fe
+  remote: https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-frozen-components.git
+  revision: 068c2c0edc8ae3b462008bfd9882fa2c36909c2b
   branch: master
   specs:
-    jekyll-theme-lcsb-default (0.1.0)
-      jekyll (~> 3.7)
-      jekyll-seo-tag (~> 2.1)
+    jekyll-theme-lcsb-frozen-components (0.0.2)
+      jekyll (> 3.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.5.2)
-      public_suffix (>= 2.0.2, < 4.0)
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
     colorator (1.1.0)
-    concurrent-ruby (1.0.5)
+    concurrent-ruby (1.1.6)
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
-    eventmachine (1.2.5)
-    faraday (0.14.0)
-      multipart-post (>= 1.2, < 3)
-    ffi (1.9.23)
+    eventmachine (1.2.7)
+    ffi (1.12.2)
     forwardable-extended (2.6.0)
     http_parser.rb (0.6.0)
-    i18n (0.9.5)
+    i18n (1.8.2)
       concurrent-ruby (~> 1.0)
-    jekyll (3.7.3)
+    jekyll (4.0.0)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
-      i18n (~> 0.7)
-      jekyll-sass-converter (~> 1.0)
+      i18n (>= 0.9.5, < 2)
+      jekyll-sass-converter (~> 2.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 1.14)
+      kramdown (~> 2.1)
+      kramdown-parser-gfm (~> 1.0)
       liquid (~> 4.0)
       mercenary (~> 0.3.3)
       pathutil (~> 0.9)
-      rouge (>= 1.7, < 4)
+      rouge (~> 3.0)
       safe_yaml (~> 1.0)
-    jekyll-feed (0.9.3)
-      jekyll (~> 3.3)
-    jekyll-github-metadata (2.9.4)
-      jekyll (~> 3.1)
-      octokit (~> 4.0, != 4.4.0)
-    jekyll-sass-converter (1.5.2)
-      sass (~> 3.4)
-    jekyll-seo-tag (2.4.0)
-      jekyll (~> 3.3)
-    jekyll-theme-primer (0.5.2)
-      jekyll (~> 3.5)
-      jekyll-github-metadata (~> 2.9)
-      jekyll-seo-tag (~> 2.2)
-    jekyll-watch (2.0.0)
+      terminal-table (~> 1.8)
+    jekyll-feed (0.13.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-paginate-v2 (3.0.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-sass-converter (2.1.0)
+      sassc (> 2.0.1, < 3.0)
+    jekyll-seo-tag (2.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-theme-lcsb-default (0.3.17)
+      jekyll (~> 4.0)
+      jekyll-seo-tag (~> 2.5)
+    jekyll-watch (2.2.1)
       listen (~> 3.0)
-    kramdown (1.16.2)
-    liquid (4.0.0)
-    listen (3.1.5)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-      ruby_dep (~> 1.2)
+    kramdown (2.1.0)
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.3)
+    listen (3.2.1)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
-    minima (2.4.0)
-      jekyll (~> 3.5)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    multipart-post (2.0.0)
-    octokit (4.8.0)
-      sawyer (~> 0.8.0, >= 0.5.3)
-    pathutil (0.16.1)
+    pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (3.0.2)
+    public_suffix (4.0.4)
     rb-fsevent (0.10.3)
-    rb-inotify (0.9.10)
-      ffi (>= 0.5.0, < 2)
-    rouge (3.1.1)
-    ruby_dep (1.5.0)
-    safe_yaml (1.0.4)
-    sass (3.5.5)
-      sass-listen (~> 4.0.0)
-    sass-listen (4.0.0)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-    sawyer (0.8.1)
-      addressable (>= 2.3.5, < 2.6)
-      faraday (~> 0.8, < 1.0)
+    rb-inotify (0.10.1)
+      ffi (~> 1.0)
+    rouge (3.17.0)
+    safe_yaml (1.0.5)
+    sassc (2.2.1)
+      ffi (~> 1.9)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    unicode-display_width (1.7.0)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.16.1)
-  jekyll (~> 3.7.3)
+  bundler (> 2.0)
+  jekyll (~> 4.0)
   jekyll-feed (~> 0.6)
-  jekyll-theme-lcsb-default!
-  jekyll-theme-primer (~> 0.5.2)
-  minima (~> 2.0)
+  jekyll-paginate-v2 (~> 3)
+  jekyll-theme-lcsb-default (~> 0.3)
+  jekyll-theme-lcsb-frozen-components (~> 0.0.1)!
+  minima (~> 2.5)
   tzinfo-data
 
-RUBY VERSION
-   ruby 2.5.0p0
-
 BUNDLED WITH
-   1.16.1
+   2.1.4

README.md

+# Daisy documentation
+
+## How to get started
+
+1. clone the repository
+
+2. install dependencies using bundler
+
+```bash
+bundle install --path vendor/bundle
+```
+
+1. run server locally
+
+```bash
+bundle exec jekyll server
+```
+

_config.yml

-# Welcome to Jekyll!
-#
-# This config file is meant for settings that affect your whole blog, values
-# which you are expected to set up once and rarely edit after that. If you find
-# yourself editing this file very often, consider using Jekyll's data files
-# feature for the data you need to update frequently.
-#
+# This config file is meant to be edited once, before the site is deployed.
+# After that, new edits are rarely needed.
+
+# Usually, you need only to change `title`, `email`, `description`, `baseurl`, `url` and `date`.
+# To see complete guide, please take a look into `readme.md` file.
+
 # For technical reasons, this file is *NOT* reloaded automatically when you use
 # 'bundle exec jekyll serve'. If you change this file, please restart the server process.
 
@@ -13,24 +12,54 @@
 # you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
 # You can create any custom variable you would like, and they will be accessible
 # in the templates via {{ site.myvariable }}.
-title: This is Trefex
-email: your-email@example.com
+title: DAta Information SYstem (DAISY)
+email: pinar.alper@uni.lu
 description: >- # this means to ignore newlines until "baseurl:"
-  Write an awesome description for your new site here. You can edit this
-  line in _config.yml. It will appear in your document head meta (for
-  Google search results) and in your feed.xml site description.
-baseurl: "" # the subpath of your site, e.g. /blog
-url: "" # the base hostname & protocol for your site, e.g. http://example.com
-twitter_username: jekyllrb
-github_username:  jekyll
-
-# Build settings
+  The user guide for the DAta Information SYstem (DAISY). It allows to manage your research data
+  in a GDPR-compliant manner and share the projects with your collaboration partners.
+
+
+# URL settings that will be used to access on your local machine
+# Note #1: by default you will need to use port 4000 (https://localhost:4000/website) to access the website in your browser running on your machine with `bundle exec jekyll serve`
+# Note #2: the configuration used in GitlabCI is generated in `.gitlab-ci.yml` file automatically for you, if you need to change that - do it there
+baseurl: "/website"
+url: "https://localhost"
+
+# Banner settings
+banner: default  # When you have custom images, change this setting's value to the name of the folder containing them
+logo: small  # Change to "big" (without quotas) in case of having broad logo
+date: "2018"
+
+# Social media icon settings
+twitter_username: uni_lu
+facebook_username: uni.lu
+linkedin_schoolname: university-of-luxembourg
+
+# Produces a cleaner folder structure when using categories
+permalink: /:year/:month/:title.html
+
+# Pagination Settings
+# pagination:
+#   enabled: true
+#   title: ':title - page :num of :max'
+#   per_page: 7
+#   permalink: '/page/:num/'
+#   limit: 0
+#   sort_field: 'date'
+#   sort_reverse: true
+#   trail:
+#     before: 2
+#     after: 2
+
+# Build settings (no need to touch these)
 markdown: kramdown
 theme: jekyll-theme-lcsb-default
 plugins:
   - jekyll-feed
+  - jekyll-paginate-v2
+  - jekyll-theme-lcsb-frozen-components
 
-# Exclude from processing.
+# Exclude from processing. (no need to touch these)
 # The following items will not be processed, by default. Create a custom list
 # to override the default setting.
 # exclude:

_posts/2018-03-12-welcome-to-jekyll.markdown

@@ -4,6 +4,7 @@ title:  "Welcome to Jekyll!"
 date:   2018-03-12 17:03:38 +0100
 categories: jekyll update
 ---
+
 You’ll find this post in your `_posts` directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different ways, but the most common way is to run `jekyll serve`, which launches a web server and auto-regenerates your site when a file is updated.
 
 To add new posts, simply add a file in the `_posts` directory that follows the convention `YYYY-MM-DD-name-of-post.ext` and includes the necessary front matter. Take a look at the source for this post to get an idea about how it works.

about.md

----
-layout: page
-title: About
-permalink: /about/
----
-
-This is the base Jekyll theme. You can find out more info about customizing your Jekyll theme, as well as basic Jekyll usage documentation at [jekyllrb.com](https://jekyllrb.com/)
-
-You can find the source code for Minima at GitHub:
-[jekyll][jekyll-organization] /
-[minima](https://github.com/jekyll/minima)
-
-You can find the source code for Jekyll at GitHub:
-[jekyll][jekyll-organization] /
-[jekyll](https://github.com/jekyll/jekyll)
-
-
-[jekyll-organization]: https://github.com/jekyll

assets/banners/readme

+Create a folder with your custom banners.
+Don't forget to change the settings to point to the newly created directory!
\ No newline at end of file

auditors.md

+---
+layout: page
+title: Auditor guide
+permalink: /auditors/
+order: 3
+---
+
+# DAISY user guide for the auditors
+
+<br>
+**Under construction** &#128296;

contact.md

+---
+layout: page
+title: Contact us
+permalink: /contact/
+order: 4
+---
+
+# Contact and credits
+
+For more details or information about DAISY application, contact us:
+
+ - Primary contact: [Pinar Alper](mailto:pinar.alper@uni.lu)
+ - Primary contact: [Regina Becker](mailto:regina.becker@uni.lu)
+
+ - Developer: [Valentin Grouès](mailto:valentin.groues@uni.lu)
+ - Developer: [Jacek Lebioda](mailto:jacek.lebioda@uni.lu)
+ - Developer [Yohan Jarosz](mailto:yohan.jarosz@uni.lu)
+ - Developer [Kavita Rege ](mailto:kavita.rege@uni.lu)
+
+ - Contributor: [Vilem Ded](mailto:vilem.ded@uni.lu)
+ - Contributor: [Sandrine Munoz](mailto:sandrine.munoz@uni.lu)
+ - Contributor: [Christophe Trefois](mailto:christophe.trefois@uni.lu)
+ - Contributor: [Venkata Satagopam](mailto:venkata.satagopam@uni.lu)
+ - Contributor: [Reinhard Schneider](mailto:reinhard.schneider@uni.lu)
+
+<br>
+In case of problems with this website please contact [LCSB data stewards](mailto:lcsb-datastewards@uni.lu).