Merge branch 'develop' into 'master'

Develop

See merge request !129

.ci/_config_develop.yml

+url: "https://howto-latest.lcsb.uni.lu"
+baseurl: "/"

.ci/_config_master.yml

+url: "https://howto.lcsb.uni.lu"
+baseurl: "/"

.ci/_config_old.yml

+url: "https://r3.pages.uni.lu"

.ci/build_indices_new.sh

+#!/bin/bash
+
+# Install lunr to build the index
+npm install lunr@$LUNR_VERSION
+
+# Go to the directory containing the built website...
+cd $DIRECTORY
+
+echo "Generating the index..."    
+
+# Pipe documents.js file (which should be generated by Jekyll after building the website) through build script
+cat documents.js | node build_index.js > index.js
+
+# Show the results (should not be empty)
+echo "...should be completed. First 50 characters of the index: "
+cat index.js | head -c50
+echo ""
+
+rm documents.js build_index.js

.ci/deploy.sh

@@ -16,9 +16,12 @@ for branch in $(git for-each-ref --format='%(refname:strip=3)' refs/remotes); do
     git reset --hard $branch
     git pull
 
+    # Generate the config dynamically
+    echo 'url: "https://r3.pages.uni.lu"' > _config_url.yml
+
     # build the website
     bundle install
-    bundle exec jekyll build --baseurl="howto-cards/$artefact" -d "build/$artefact"
+    bundle exec jekyll build --config "_config.yml,_config_url.yml" --baseurl="howto-cards/$artefact" -d "build/$artefact"
 
     if [[ $branch == "master" ]]; then
         # set the 404

.gitlab-ci.yml

@@ -6,6 +6,16 @@ stages:
   - generate_index
   - deploy
 
+# !!!!!!!      README      !!!!!
+# We are in the transition period - and the website is deployed two times - to gitlab pages and to a separate VM
+# In order to migrate to a new deployment:
+#  1) remove "Old deployment" section - build_pages, generate the search index and pages tasks
+#  2) rename "new pages" to "pages" in the new deployment section, and "new_public" to "public"; you might also rename directories (skip "new" part)
+#  3) remove ".ci/deploy.sh", ".ci/build_indices.sh"
+
+
+# Old deployment =================================================================
+
 build_pages:
   stage: build
   before_script:
@@ -48,3 +58,80 @@ pages:
     expire_in: 1 week
     paths:
       - public
+
+
+# New deployment ==================================================================
+
+build pages for VM deployment:
+  stage: build
+  variables:
+    JEKYLL_ENV: production
+    BUNDLER_VERSION: 2.0.2
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - new_build
+  before_script:
+    - gem install bundler:$BUNDLER_VERSION && bundle install  
+  script:
+    # Generate the configuration for forks (will use Gitlab Pages on personal namespaces)
+    - 'echo "url: https://$CI_PROJECT_NAMESPACE.$CI_PAGES_DOMAIN" >> .ci/_config_gitlab_pages.yml'
+    - 'echo "baseurl: /$CI_PROJECT_NAME" >> .ci/_config_gitlab_pages.yml'
+
+    # If there is no config for the current branch, use the one for Gitlab Pages
+    - 'if [ ! -f ".ci/_config_$CI_COMMIT_REF_NAME.yml" ]; then mv .ci/_config_gitlab_pages.yml .ci/_config_$CI_COMMIT_REF_NAME.yml; fi'
+
+    # Display, which configuration is used
+    - 'echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"'
+
+    # Run Jekyll with custom configuration
+    - bundle exec jekyll build -d new_build --config "_config.yml,.ci/_config_$CI_COMMIT_REF_NAME.yml"
+
+
+generate the search index for VM deployment:
+  stage: generate_index
+  image: node:13.8.0-slim
+  variables:
+    LUNR_VERSION: 2.3.8
+    DIRECTORY: new_build
+  script:
+    - bash .ci/build_indices_new.sh
+    - mv new_build new_processed_build
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - new_processed_build
+
+# Deploy to Gitlab Pages - to be run only by forks; change to pages once it's ready
+new pages:
+  image: alpine:3.11.3
+  stage: deploy
+  rules:
+    - if: '$CI_PROJECT_NAMESPACE != "R3" && $CI_PROJECT_NAMESPACE != "R3-core"'
+  script:
+    - mv new_processed_build new_public
+  artifacts:
+    expire_in: 1 week
+    paths:
+      - new_public
+
+## Deploys the website to a separate VM
+deploy to production:
+  stage: deploy
+  image: alpine:3.1
+  before_script:
+    - 'which ssh-agent || ( apk add --update openssh )'
+    - eval $(ssh-agent -s)
+    - echo "$B64SSHPRIVKEY" | base64 -d | tr -d '\r' | ssh-add - > /dev/null
+    - mkdir -p ~/.ssh && chmod 700 ~/.ssh
+    - 'echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config'
+    - echo "$KNOWNHOSTS" > ~/.ssh/known_hosts
+    - chmod 644 ~/.ssh/known_hosts
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "develop" && $CI_PROJECT_PATH == "R3/howto-cards"'
+    - if: '$CI_COMMIT_BRANCH == "master" && $CI_PROJECT_PATH == "R3/howto-cards"'
+  script:
+    - ssh -p $SSHPORT $SSHCONNECT "mkdir -p ~/$CI_COMMIT_BRANCH/sources/public/$CI_JOB_ID ~/$CI_COMMIT_BRANCH/public"
+    - scp -P $SSHPORT -r new_processed_build/* $SSHCONNECT:~/$CI_COMMIT_BRANCH/sources/public/$CI_JOB_ID
+    - ssh -p $SSHPORT $SSHCONNECT "cd ~/$CI_COMMIT_BRANCH/public && ln -fs ../sources/public/$CI_JOB_ID/* . && cd ~/$CI_COMMIT_BRANCH/sources/public/ && find . -type d -not -newermt '-1 minutes' -exec rm -rf {} +;"
+

Gemfile

@@ -27,6 +27,9 @@ group :jekyll_plugins do
  gem "jekyll-feed",
      "~> 0.6"
 
+ gem 'jekyll-email-protect',
+     "~> 1.1"
+
  gem 'jekyll-theme-lcsb-frozen-components',
      '~> 0.0.2',
      :git => "https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-frozen-components.git",

_config.yml

@@ -19,8 +19,8 @@ description: >- # this means to ignore newlines until "baseurl:"
   This page is an index for lab cards  that are intended to provide practical guidance  in  implementing Data Management, Data Protection and IT setup.
 
 # URL settings (the most difficult part, please refer to the guide)
-baseurl: "/howto-cards"  # the subpath of your site, e.g. /gitlab-repository-name
-url: "https://r3.pages.uni.lu"  # the base hostname & protocol for your site, e.g. http://gitlab-namespace-name.pages.uni.lu/
+baseurl: "/"  # the subpath of your site, e.g. /gitlab-repository-name
+url: "https://localhost"  # the base hostname & protocol for your site, e.g. http://gitlab-namespace-name.pages.uni.lu/
 
 # Banner settings
 banner: howto-card  # When you have custom images, change this setting's value to the name of the folder containing them
@@ -62,6 +62,8 @@ plugins:
 # The display logic itself is in the template
 share_url: https://howto.lcsb.uni.lu/?
 include_link_index: 4
+
+# These values are injected into cards
 defaults:
   -
     scope:

_plugins/hook_email_protect.rb

+Jekyll::Hooks.register([:pages, :posts, :documents], :pre_render) do |post|
+  # This will run every time the website is built
+
+  # Include a plugin (needs to be in gemfile)
+  include Jekyll::EmailProtect::EmailProtectionFilter
+
+  # Using a simpler version of email regexp
+  email_regexp = /mailto\:(?:[\'\"]*)(?:[\w+\-]\.?)+@[a-z\d\-]+(?:\.[a-z]+)*\.[a-z]+(?:[\'\"]*)/i
+
+  # Take post's content, and transform every occurence of the following regexp (an email)
+  post.content = post.content.gsub(email_regexp) {
+    # For every occurence, apply protection function:
+    |param| "mailto:" + Jekyll::EmailProtect::EmailProtectionFilter::encode_email(param[7..-1].delete("'").delete('"'))
+  }
+end

help.md

@@ -7,7 +7,4 @@ order: 3
 
 If you need help, please create a request for support by creating a ticket on [ServiceNow](https://service.uni.lu/) using the catalog item _LCSB/BioCore: Application Services_.
 
-If you don't have access to service now, please contact us using <span id="obf"><noscript><span style="unicode-bidi:bidi-override;direction:rtl;">ul.inu@snimdasys-bscl</span></noscript></span>.
-
-
-<script>document.getElementById("obf").innerHTML="<n uers=\"znvygb:ypfo-flfnqzvaf@hav.yh?fhowrpg=[ynoPneqf] Freivpr erdhrfg\" gnetrg=\"_oynax\">guvf rznvy</n>".replace(/[a-zA-Z]/g,function(c){return String.fromCharCode((c<="Z"?90:122)>=(c=c.charCodeAt(0)+13)?c:c-26);});document.body.appendChild(eo);</script>
\ No newline at end of file
+If you don’t have access to service now, please contact us using [this email](mailto:lcsb-sysadmins@uni.lu?subject=[How-to cards]%20Service%20request).
\ No newline at end of file