.ci/add-timestamp-to-howtocard.sh

+#!/bin/sh
+
+# change this with environment
+DEFAULT_NOT_SOURCE_REGEX="/\\/assets\\//"
+NOT_SOURCE_REGEX="${NOT_SOURCE_REGEX:-$DEFAULT_NOT_SOURCE_REGEX}"
+TIMESTAMP_SUFFIX="${SUFFIX:-.timestamp}"
+LOGFILE="${LOGFILE:-/dev/null}"
+
+[ -z "$1" ] && echo "$0: no inputs specified?" >/dev/stderr
+
+while [ -n "$1" ]
+do
+	echo "sourcing directory '$1' ..." >> "$LOGFILE"
+	find "$1" -type f -name '*.md' | grep -v "$NOT_SOURCE_REGEX" | while read file ; do
+		fn=`basename "$file"`
+		dir=`dirname "$file"`
+		tsfn="$fn.timestamp"
+		(
+			echo "making timestamp in '$dir' for file '$fn' ..." >> "$LOGFILE"
+			cd "$dir"
+			if [ -f "$tsfn" ]
+			then echo "... but it already exists; skipping!" >> "$LOGFILE"
+			else
+				TIMESTAMP=`git log -n 1 --pretty=format:%cs -- "$fn"`
+				mv "$fn" "$fn.temporary"
+				head -n1 "$fn.temporary" > "$fn"
+				echo "timestamp: \"$TIMESTAMP\"" >> "$fn"
+				tail -n+2 "$fn.temporary" >> "$fn"
+				rm -f "$fn.temporary"
+			fi
+		)
+	done
+	shift
+done

.ci/generateIndex.py

-import os, re
-from os import path
-from natsort import natsorted
-from pathlib import Path
+from generator import core, save
 
-def line_prepender(filename, line):
-    with open(filename, 'r+') as f:
-        content = f.read()
-        f.seek(0, 0)
-        f.write(line.rstrip('\r\n') + '\n' + content)
+# walk through the folders with all the cards
+ind, wl = core.core(["external"])
 
-def build_link(title, href):
-
-    # strip the number of the title
-    if ('handbook' in href):
-        title = re.sub('[0-9.]', '', title).strip()
-
-    # add relative url
-    href = "{{ '" + href + "' | relative_url }}"
-
-    return f'\t\t\t<li><a href="{href}">{title}</a></li>\n'
-
-def build_section_start(title, shortcut):
-
-    title = title.replace("Gdpr", "GDPR")
-    title = title.replace("Handbook additional", "PI/Supervisor specifics")
-    title = title.replace("Handbook annexes", "Annexes")
-    title = title.replace("Covid 19", "COVID-19")
-    title = title.replace("Ppc", "PPC")
-
-    return f'\n\t<div class="index-box noborderbox" id="{shortcut}-card">\n\t\t<h3>{title}</h3>\n\t\t<ul>\n'
-
-def build_section_end():
-    return "\t\t</ul>\n\t</div>"
-
-def remove_header(localroot, root, filename, n=5):
-    nfirstlines = []
-
-    #cwd = os.getcwd()
-
-    os.chdir(localroot)
-    #print("Local root folder:" + os.getcwd())
-
-    os.chdir(root)
-    #print("Local folder:" + os.getcwd())
-
-    # count the number of lines
-    count = 0
-    headerCheck = False
-    with open(filename, 'r') as f:
-        for line in f:
-            count += 1
-
-            # check if the header is actually a header
-            if (count == 0 or count == n) and line[0:3] == "---":
-                headerCheck = True
-
-    # remove the header
-    if count > n and headerCheck:
-        with open(filename) as f, open("tmp"+filename, "w") as out:
-            for _ in range(n):
-                nfirstlines.append(next(f))
-            for line in f:
-                out.write(line)
-
-        os.remove(filename)
-        os.rename("tmp"+filename, filename)
-        print(" - Old header removed.")
-
-    # change back to the local root
-    os.chdir(localroot)
-    #print("exit folder:" + os.getcwd())
-
-# loop through the entire internal tree
-localroot = os.getcwd()
-
-
-# generate the index properly speaking
-cardDirs = ["internal", "external", "policies"]
-sections = []
-
-# determine first the directories
-for direct in cardDirs:
-    if path.isdir(direct):
-        dirs = os.listdir(direct)
-        dirs = natsorted(dirs)
-
-        for d in dirs:
-            if d[0] != ".":
-                sections.append(d)
-
-sections = list(set(sections))
-sections = natsorted(sections)
-
-# Index contains the generated content, init it with an empty container
-index = ''
-index += '\n<div class="index-box-container">\n'
-whiteList = ''
-
-localIndexArr = [[]] * len(sections)
-for folder in cardDirs:
-
-    # check if folder exists
-    if path.isdir(folder):
-        dirs = os.listdir(folder)
-        dirs = natsorted(dirs)
-
-        for d in dirs:
-            if d[0] != ".":
-                # set the header of the section
-                #index += "\n### " + d.replace("-", " ").capitalize() + "\n"
-
-
-                # get the index of the section
-                indexS = sections.index(d)
-
-                #print(indexS)
-                if len(localIndexArr[indexS]) == 0:
-                    localIndexArr[indexS] = ["\n"]
-
-                # walk through the folders with all the cards
-                for root, dirs, files in os.walk(folder+"/"+d):
-                    for file in files:
-                        if file.endswith(".md"):
-                            fileName = os.path.join(root, file)
-
-                            # ignore subsections (.md files that start with _)
-                            if file[0] != "_":
-                                print(" > Generating header for: " + fileName)
-
-                                # remove the previous header
-                                remove_header(localroot, root, file, 8)
-
-                                # generate a permalink
-                                permalink = "/" + root + "/"
-
-                                # generate the shortcut
-                                shortcut = re.sub(folder, '', root)
-
-                                # remove the first /
-                                shortcut = shortcut[1:]
-
-                                # replace the / with a :
-                                shortcut = re.sub('/', ':', shortcut)
-
-                                # define the header for each card
-                                header = "---\n"
-                                header += "layout: page\n"
-                                header += "permalink: " + permalink + "\n"
-                                header += "shortcut: " + shortcut + "\n"
-                                header += "redirect_from:\n"
-                                header += "  - /cards/" + shortcut + "\n"
-                                header += "  - /" + folder + "/cards/" + shortcut + "\n"
-                                header += "---"
-
-                                # add autogenerated links to whitelist
-                                whiteList += permalink + "\n"
-                                whiteList += "/?" + shortcut + "\n"
-                                whiteList += "/cards/" +shortcut + "\n"
-                                whiteList += "/" + folder + "/cards/" + shortcut + "\n"
-
-                                # add the header properly speaking
-                                line_prepender(fileName, header)
-
-                                # open file and get the title after the header
-                                count = 0
-                                title = ""
-                                bp = 9
-                                with open(fileName, 'r') as f:
-                                    for line in f:
-                                        count += 1
-                                        if count == bp:
-                                            if len(line) > 2:
-                                                title = line
-                                                break
-                                            else:
-                                                bp += 1
-
-                                # remove first and last chars
-                                title = title.rstrip("\n\r")
-                                title = title[2:]
-
-                                localIndexArr[indexS].append(build_link(title, root))
-
-                                # output
-                                print(" + New header added.")
-                                print("-----------------------")
-
-                # join all subcategories to the index
-                localIndexArr[indexS] = natsorted(localIndexArr[indexS])
-
-print(localIndexArr)
-
-# determine the index
-k = 0
-for s in sections:
-    index += build_section_start(s.replace("-", " ").capitalize(), s)
-    index += ''.join(localIndexArr[k])
-    index += build_section_end()
-    k += 1
-
-# close the container
-index += "\n</div>"
-
-## add link to return to main index
-index += """<br><center><a href="{{ '/' | relative_url }}">go back</a></center>"""
-index += """<br><center><a href="{{ '/cards' | relative_url }}">Overview of all HowTo cards</a></center>"""
-
-# output the index
-#print(index)
-# Read in the file
-indexFile = "cards.md"
-filedata = ""
-with open(indexFile, 'r') as file :
-    for line in file:
-        filedata += line
-
-        # stop reading once the index place holder has been reached
-        if re.search("<!-- index -->", line):
-            filedata += "[[ index ]]"
-            break
-
-# Replace the target string
-filedata = filedata.replace('[[ index ]]', index)
-
-# Write the file out again
-with open(indexFile, 'w') as file:
-  file.write(filedata)
-
-print("\n > New index generated and saved in " + indexFile)
-
-# write link whitelist out
-whiteListFile = ".ci/whitelist.txt"
-if Path(whiteListFile).exists():
-    with open(whiteListFile, 'r') as file :
-        for line in file:
-            whiteList += line
-
-with open(whiteListFile, 'w') as file:
-    file.write(whiteList)
+save.save_index(ind, "cards.md")
+save.save_whitelist(wl, ".ci/whitelist.txt")

generator @ 53a922a1

+Subproject commit 53a922a13c4e8916c97599b5242493a47ea0a2e2

.ci/whitelist.txt

@@ -10,10 +10,10 @@ media/7zip-encryption-windows.mp4?width=400
 media/Get_MD5_checksum_windows.mp4
 https://intranet.uni.lux
 https://intranet.uni.lux/the_university/lcsb/lscb_internal/
-https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Godparent%20Checklist%20-%20newcomers.pdf
-https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20Before%20Arriving%20in%20Luxembourg.pdf
-https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20upon%20Arrival%20in%20Luxembourg.pdf
-https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx
-https://intranet.uni.lux/the_university/sc/Lists/Policies%20%20Procedures/DispForm.aspx?ID=9
-https://intranet.uni.lux/the_university/siu/Documents/Dropit%20client%20-%20configuration%20guide.pdf#search=dropit
-https://intranet.uni.lux/the_university/siu/Pages/siu-guides.aspx
+https://uniluxembourg.sharepoint.com/sites/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Godparent%20Checklist%20-%20newcomers.pdf
+https://uniluxembourg.sharepoint.com/sites/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20Before%20Arriving%20in%20Luxembourg.pdf
+https://uniluxembourg.sharepoint.com/sites/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20upon%20Arrival%20in%20Luxembourg.pdf
+https://uniluxembourg.sharepoint.com/sites/lcsb/lscb_internal/SitePages/default.aspx
+https://uniluxembourg.sharepoint.com/sites/sc/Lists/Policies%20%20Procedures/DispForm.aspx?ID=9
+https://uniluxembourg.sharepoint.com/sites/siu/Documents%20partages/Dropit%20client%20-%20configuration%20guide.pdf#search=dropit
+https://uniluxembourg.sharepoint.com/sites/siu/SitePages/siu-guides.aspx
\ No newline at end of file

.gitattributes

-*.png filter=lfs diff=lfs merge=lfs -text
-*.jpg filter=lfs diff=lfs merge=lfs -text
-*.jpeg filter=lfs diff=lfs merge=lfs -text
-*.mp4 filter=lfs diff=lfs merge=lfs -text

.gitlab-ci.yml

@@ -11,8 +11,10 @@ stages:
 
 variables:
     GIT_STRATEGY: clone
+    GIT_DEPTH: 0
     DOCKER_DRIVER: overlay2
     DOCKER_TLS_CERTDIR: ""
+    GIT_SUBMODULE_STRATEGY: recursive
 
 # prepare
 # ------------------------------------------------------------------------------------
@@ -24,7 +26,7 @@ prepare:index:
     - if: $CI_COMMIT_REF_NAME
     - if: '$CI_PIPELINE_SOURCE == "merge_request_event" && $CI_COMMIT_MESSAGE !~ /tmpBranch/ && $CI_COMMIT_MESSAGE !~ /Update index/'
   before_script:
-    - pip install natsort
+    - pip install -r .ci/generator/requirements.txt
   script:
     - python .ci/generateIndex.py
     - mkdir .tmp
@@ -72,11 +74,11 @@ save:commitIndex:
 # ------------------------------------------------------------------------------------
 
 build:pages:
-  image: $CI_REGISTRY/r3/docker/jekyll-lcsb:1.8
+  image: $CI_REGISTRY/r3/docker/jekyll-lcsb
   stage: build
   variables:
     JEKYLL_ENV: production
-    BUNDLER_VERSION: 2.0.2
+    BUNDLER_VERSION: 2.1.4
   artifacts:
     expire_in: 1 day
     paths:
@@ -89,6 +91,8 @@ build:pages:
     - apt-get install -y -qq git-lfs
     - gem install bundler:$BUNDLER_VERSION && bundle install
   script:
+    # copy the index
+    - cp .tmp/cards.md .
     # Generate the configuration for forks (will use Gitlab Pages on personal namespaces)
     - |
       if [ $CI_MERGE_REQUEST_ID ]; then
@@ -105,6 +109,7 @@ build:pages:
     - |
       echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"
     # Run Jekyll with custom configuration
+    - LOGFILE=/dev/stdout .ci/add-timestamp-to-howtocard.sh external
     - bundle exec jekyll build -d build --config "_config.yml,.ci/_config_$CI_COMMIT_REF_NAME.yml"
 
 # check
@@ -171,7 +176,7 @@ deploy:vm:
     - echo "$KNOWNHOSTS" > ~/.ssh/known_hosts
     - chmod 644 ~/.ssh/known_hosts
   rules:
-    - if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "develop" && $CI_PROJECT_PATH == "R3/howto-cards"'
+    #- if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "develop" && $CI_PROJECT_PATH == "R3/howto-cards"'
     - if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "master" && $CI_PROJECT_PATH == "R3/howto-cards"'
   script:
     - ssh -p $SSHPORT $SSHCONNECT "mkdir -p ~/$CI_COMMIT_REF_NAME/sources/public/$CI_JOB_ID ~/$CI_COMMIT_REF_NAME/public"

.gitmodules

+[submodule ".ci/generator"]
+	path = .ci/generator
+	url = https://gitlab.lcsb.uni.lu/R3/apps/generator.git

Gemfile

@@ -12,7 +12,7 @@ gem "jekyll", "~> 4.0"
 gem "bundler", "> 2.0"
 
 gem "minima", "~> 2.5"
-gem 'jekyll-theme-lcsb-default', '~> 0.4.7'
+gem 'jekyll-theme-lcsb-default', '~> 0.5.0'
 
 # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
 # uncomment the line below. To upgrade, run `bundle update github-pages`.
@@ -46,3 +46,5 @@ gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
 gem "wdm", "~> 0.1.1" if Gem.win_platform?
 
 gem 'jekyll-spaceship', "~> 0.9"
+
+gem "webrick", "~> 1.7"

_includes/footer.html

@@ -10,6 +10,10 @@
 
           {% comment %}This is used to generate share URL for howto-pages{% endcomment %}
           <div class="footer-text-container">
+          {% if page.timestamp %}
+            <p>Last page modification: {{ page.timestamp }}</p>
+          {% endif %}
+
           {% if page.shortcut %}
               <p>
                   Share this page:
@@ -44,4 +48,4 @@
   </footer>
   {% if site.siteID > 0 %}
       {%- include gdpr-banner.html -%}
-  {% endif %}
+  {% endif %}
\ No newline at end of file

_includes/scripts-head.html

+<script src="{{ '/assets/vendor/js/jquery-3.6.0.min.js' | relative_url }}"></script>

_includes/scripts.html

-<script type="text/javascript" src="https://analytics.lcsb.uni.lu/lap/static/js/jquery.min.js"></script>
 <script type="text/javascript" src="{{ "assets/js/router.js" | relative_url }}"></script>
 <script type="text/javascript" src="{{ "assets/js/box_hider.js" | relative_url }}"></script>
 <script>

assets/css/landing.css

@@ -32,7 +32,7 @@
     align-content: flex-start;
     padding-right: 10px;
     border: solid 1px rgba(0,0,0,0);
-    border-right: solid 2px rgba(240, 240, 240, 0.7);    
+    border-right: solid 2px rgba(240, 240, 240, 0.7);
 }
 @media (max-width: 1080px) {
     .container > .left-inner-container {
@@ -241,19 +241,19 @@
     color: #ccc;
 }
 .right-inner-container.droppable > .card-pinned.card-grayed.card-pulsate {
-    animation-name: stretch; 
+    animation-name: stretch;
     animation-duration: 0.6s;
-    animation-direction: alternate; 
-    animation-iteration-count: infinite; 
-    animation-play-state: running; 
-}
-@keyframes stretch { 
-    0% { 
-        transform: scale(.90); 
-    } 
-    100% { 
-        transform: scale(1.1); 
-    } 
+    animation-direction: alternate;
+    animation-iteration-count: infinite;
+    animation-play-state: running;
+}
+@keyframes stretch {
+    0% {
+        transform: scale(.90);
+    }
+    100% {
+        transform: scale(1.1);
+    }
 }
 /* ==================================================== */
 /*    Search bar                                        */
@@ -305,15 +305,15 @@ div.search-bar {
     text-align: center;
     cursor: pointer;
 }
-@media (max-width: 1080px) { 
+@media (max-width: 1080px) {
     .indicator {
         top: 128px;
         right: 72px;
     }
 }
-@media (max-width: 650px) { 
+@media (max-width: 700px) {
     .indicator {
-        top: 50px;
+        top: 10px;
         right: 50px;
     }
 }
@@ -330,7 +330,7 @@ div.search-bar {
 /*    Tooltip                                           */
 /* ==================================================== */
 .tooltip .tooltip-text {
-    visibility: hidden;        
+    visibility: hidden;
     width: 400px;
     right: 120%;
     top: -43px;

assets/js/box_hider.js

@@ -23,13 +23,17 @@ window.boxHider = (function() {
 
     function GetSelectedBoxElement(id) {
         var allBoxesArray = GetAllBoxElementsArray();
-        var element = document.getElementById(id);
+        // note: handbook and lab are actually grouped sections
+        if (id.startsWith('handbook') || id.startsWith('lab') || id.startsWith('qms') || id.startsWith('publication')) {
+            return true;
+        } else {
+            var element = document.getElementById(id);
 
-        if (allBoxesArray.includes(element)) {
-            return element;
+            if (allBoxesArray.includes(element)) {
+                return element;
+            }
+            return false;
         }
-
-        return false;
     }
 
     function HideElement(element) {
@@ -84,6 +88,30 @@ window.boxHider = (function() {
                     ShowElement(box);
                 }
             });
+        } else if (boxId.startsWith('lab')) {
+            allBoxes.map(function(box) {
+                if (!box.id.startsWith('lab')) {
+                    HideElement(box);
+                } else {
+                    ShowElement(box);
+                }
+            });
+        } else if (boxId.startsWith('qms')) {
+            allBoxes.map(function(box) {
+                if (!box.id.startsWith('qms')) {
+                    HideElement(box);
+                } else {
+                    ShowElement(box);
+                }
+            });
+        } else if (boxId.startsWith('publication')) {
+            allBoxes.map(function(box) {
+                if (!box.id.startsWith('publication')) {
+                    HideElement(box);
+                } else {
+                    ShowElement(box);
+                }
+            });
         } else {
             allBoxes.map(function(box) {
                 if (box != selectedBox) {

cards.md

@@ -37,16 +37,16 @@ order: -1
 			<li><a href="{{ 'external/access/harrenhal-access' | relative_url }}">HARRENHAL access</a></li>
 			<li><a href="{{ 'external/access/lums-passwords' | relative_url }}">LUMS account</a></li>
 			<li><a href="{{ 'external/access/passwords' | relative_url }}">Managing your passwords</a></li>
-			<li><a href="{{ 'external/access/vpn-cerbere-access' | relative_url }}">VPN/CERBERE connection</a></li>
+			<li><a href="{{ 'external/access/vpn-access' | relative_url }}">VPN connection</a></li>
+			<li><a href="{{ 'external/access/vpn-cerbere-access' | relative_url }}">Connect to Cerbere via VPN</a></li>
+			<li><a href="{{ 'external/access/vpn-mobile' | relative_url }}">VPN connection on your mobile phone</a></li>
 			<li><a href="{{ 'external/access/wifiNetworkAccessGuests' | relative_url }}">WiFi network access for guests</a></li>
-
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="backup-card">
 		<h3>Backup</h3>
 		<ul>
 			<li><a href="{{ 'external/backup/computer' | relative_url }}">Staff Computer</a></li>
-
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="contribute-card">
@@ -56,6 +56,9 @@ order: -1
 			<li><a href="{{ 'external/contribute/install-git' | relative_url }}">Installation of Git</a></li>
 			<li><a href="{{ 'external/contribute/markdown' | relative_url }}">Markdown</a></li>
 			<li><a href="{{ 'external/contribute/mirror-fork' | relative_url }}">Mirror fork automatically</a></li>
+			<li><a href="{{ 'external/contribute/review' | relative_url }}">Reviewing in Git</a></li>
+			<li><a href="{{ 'external/contribute/ssh-key-generation' | relative_url }}">Key-based Authentication on GitLab</a></li>
+			<li><a href="{{ 'external/contribute/supersede' | relative_url }}">Take over a stale merge request</a></li>
 			<li><a href="{{ 'external/contribute/vscode' | relative_url }}">Contribute using Visual Studio Code</a></li>
 			<li><a href="{{ 'external/contribute/web-ide' | relative_url }}">Contribute using Gitlab Web IDE</a></li>
 
@@ -65,7 +68,10 @@ order: -1
 		<h3>Exchange channels</h3>
 		<ul>
 			<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
+			<li><a href="{{ 'external/exchange-channels/atlas-hpc' | relative_url }}">Data transfer between Atlas and UL HPC Clusters</a></li>
 			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
+			<li><a href="{{ 'external/exchange-channels/cryptomator' | relative_url }}">Cryptomator</a></li>
+			<li><a href="{{ 'external/exchange-channels/lft' | relative_url }}">LCSB file transfer (LFT) Quick Guide</a></li>
 			<li><a href="{{ 'external/exchange-channels/owncloud' | relative_url }}">Owncloud</a></li>
 
 		</ul>
@@ -73,71 +79,105 @@ order: -1
 	<div class="index-box noborderbox" id="general-card">
 		<h3>General</h3>
 		<ul>
-			<li><a href="{{ 'external/general/BelvalCampusMap' | relative_url }}">Belval Campus Map</a></li>
-			<li><a href="{{ 'external/general/attend-webex' | relative_url }}">Attend the LCSB Team Meeting online (webex)</a></li>
+			<li><a href="{{ 'external/general/usefulLinks' | relative_url }}">Useful links for living in Luxembourg</a></li>
 			<li><a href="{{ 'external/general/getToLCSB' | relative_url }}">How to get to the Luxembourg Centre for Systems Biomedicine</a></li>
+			<li><a href="{{ 'external/general/BelvalCampusMap' | relative_url }}">Belval Campus Map</a></li>
 			<li><a href="{{ 'external/general/glossary' | relative_url }}">Glossary</a></li>
 			<li><a href="{{ 'external/general/links' | relative_url }}">Important websites</a></li>
 			<li><a href="{{ 'external/general/remote-working' | relative_url }}">Work remotely</a></li>
-			<li><a href="{{ 'external/general/usefulLinks' | relative_url }}">Useful links for living in Luxemburg</a></li>
-
+			<li><a href="{{ 'external/general/attend-webex' | relative_url }}">Attend the LCSB Team Meeting online (webex)</a></li>
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="integrity-card">
 		<h3>Integrity</h3>
 		<ul>
 			<li><a href="{{ 'external/integrity/checksum' | relative_url }}">Ensuring Integrity of Data Files with Checksums</a></li>
-			<li><a href="{{ 'external/integrity/encryption/cloud' | relative_url }}">Data upload to cloud</a></li>
+			<li><a href="{{ 'external/integrity/dmp' | relative_url }}">Data Management Plan</a></li>
 			<li><a href="{{ 'external/integrity/encryption/disk' | relative_url }}">Encrypting the Startup Disk for Your Laptop/Desktop</a></li>
 			<li><a href="{{ 'external/integrity/encryption/file' | relative_url }}">Encrypting Files and Folders</a></li>
 			<li><a href="{{ 'external/integrity/naming' | relative_url }}">Naming files</a></li>
 			<li><a href="{{ 'external/integrity/organization' | relative_url }}">Organization</a></li>
 			<li><a href="{{ 'external/integrity/sanitisation' | relative_url }}">Sanitising Data Files</a></li>
 			<li><a href="{{ 'external/integrity/spreadsheets' | relative_url }}">Working with spreadsheets</a></li>
+			<li><a href="{{ 'external/integrity/transfer/owncloud-privatebin' | relative_url }}">Transfer of Human Data with OwnCloud</a></li>
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="lab-card">
-		<h3>Lab</h3>
+	<div class="index-box noborderbox" id="lab-equipment-card">
+		<h3>Lab: Equipment</h3>
 		<ul>
-			<li><a href="{{ 'external/lab/book-lab-equipment' | relative_url }}">How to book a Lab Equipment in Quarks</a></li>
-			<li><a href="{{ 'external/lab/dishwasher-utilization-and-maintenance' | relative_url }}">Dishwasher utilization and maintenance</a></li>
-			<li><a href="{{ 'external/lab/handwashing' | relative_url }}">Handwashing</a></li>
-			<li><a href="{{ 'external/lab/lab-coats' | relative_url }}">Lab coats</a></li>
-			<li><a href="{{ 'external/lab/maintenance_of_cold_traps' | relative_url }}">Maintenance of cold traps  </a></li>
-			<li><a href="{{ 'external/lab/personal-alert-safety-system' | relative_url }}">Personal alert safety system (PASS)</a></li>
-			<li><a href="{{ 'external/lab/quarks-general' | relative_url }}">Quarks - General information</a></li>
-			<li><a href="{{ 'external/lab/utilization-of-balances' | relative_url }}">Utilization of balances</a></li>
-			<li><a href="{{ 'external/lab/utilization-of-pH-meter' | relative_url }}">Utilization of pH meter</a></li>
+			<li><a href="{{ 'external/lab-equipment/autoclaves' | relative_url }}">Autoclaves: utilization</a></li>
+			<li><a href="{{ 'external/lab-equipment/balances' | relative_url }}">Balances: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/biosafety-cabinets' | relative_url }}">Biosafety Cabinets: good practices</a></li>
+			<li><a href="{{ 'external/lab-equipment/cold-traps' | relative_url }}">Cold traps: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/cryostorage' | relative_url }}">Cryostorage: utilization</a></li>
+			<li><a href="{{ 'external/lab-equipment/dishwasher-utilization-and-maintenance' | relative_url }}">Dishwasher: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/electric-car' | relative_url }}">Electric Car</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers' | relative_url }}">-20°C Freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers-80' | relative_url }}">-80°C freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers-150' | relative_url }}">-150°C freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/fridges' | relative_url }}">Fridges: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/hoods' | relative_url }}">Hoods: Laminar Flow - Fume Hood - Biosafety Cabinet</a></li>
+			<li><a href="{{ 'external/lab-equipment/incubators' | relative_url }}">Incubators: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/lightcycler' | relative_url }}">LightCycler: leave the virtual instrument mode</a></li>
+			<li><a href="{{ 'external/lab-equipment/pH-meter' | relative_url }}">pH meter: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/power-consumption' | relative_url }}">Power consumption of the equipment</a></li>
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="on-offboarding-card">
-		<h3>On offboarding</h3>
+	<div class="index-box noborderbox" id="lab-good-practice-card">
+		<h3>Lab: Good Practice</h3>
 		<ul>
-			<li><a href="{{ 'external/on-offboarding/checklistArrival' | relative_url }}">Checklist upon arrival in Luxemburg</a></li>
-			<li><a href="{{ 'external/on-offboarding/checklistBeforeArriving' | relative_url }}">Newcomer Checklist before Arriving in Luxembourg</a></li>
-			<li><a href="{{ 'external/on-offboarding/checklistGetStarted' | relative_url }}">Newcomer's checklist</a></li>
-			<li><a href="{{ 'external/on-offboarding/checklistGodparent' | relative_url }}">Checklist for godparents</a></li>
-			<li><a href="{{ 'external/on-offboarding/godparent' | relative_url }}">Godparents for Newcomers</a></li>
-			<li><a href="{{ 'external/on-offboarding/onboarding' | relative_url }}">Onboarding new members at the LCSB</a></li>
+			<li><a href="{{ 'external/lab-good-practice/mycoplasma' | relative_url }}">Mycoplasma contamination check</a></li>
+
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="lab-hsa-card">
+		<h3>Lab: Health & Safety, Access</h3>
+		<ul>
+			<li><a href="{{ 'external/lab-hsa/diphoterine' | relative_url }}">Diphoterine: utilization</a></li>
+			<li><a href="{{ 'external/lab-hsa/handwashing' | relative_url }}">Handwashing</a></li>
+			<li><a href="{{ 'external/lab-hsa/lab-coats' | relative_url }}">Lab coats</a></li>
+			<li><a href="{{ 'external/lab-hsa/personal-alert-safety-system' | relative_url }}">Personal alert safety system (PASS)</a></li>
+			<li><a href="{{ 'external/lab-hsa/pictograms' | relative_url }}">Pictograms</a></li>
+			<li><a href="{{ 'external/lab-hsa/ppe' | relative_url }}">Personal Protective Equipment (PPE)</a></li>
+			<li><a href="{{ 'external/lab-hsa/shipment' | relative_url }}">Shipment of biological or chemical samples with carrier</a></li>
+			<li><a href="{{ 'external/lab-hsa/spill' | relative_url }}">Spill in a laboratory</a></li>
+			<li><a href="{{ 'external/lab-hsa/spill-bsc' | relative_url }}">Spill in a Biosafety Cabinet</a></li>
+			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Waste Management: Chemical and Biological waste</a></li>
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="ppc-card">
-		<h3>PPC</h3>
+	<div class="index-box noborderbox" id="lab-quarks-card">
+		<h3>Lab: Quarks</h3>
 		<ul>
-			<li><a href="{{ 'external/ppc/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
-			<li><a href="{{ 'external/ppc/publish-repo' | relative_url }}">Publish a repository</a></li>
+			<li><a href="{{ 'external/lab-quarks/book-lab-equipment' | relative_url }}">Booking of a Lab Equipment</a></li>
+			<li><a href="{{ 'external/lab-quarks/general' | relative_url }}">General information on Quarks</a></li>
 
 		</ul>
 	</div>
+	<div class="index-box noborderbox" id="on-offboarding-card">
+		<h3>On offboarding</h3>
+		<ul>
+			<li><a href="{{ 'external/on-offboarding/checklistBeforeArriving' | relative_url }}">Newcomer Checklist before Arriving in Luxembourg</a></li>
+			<li><a href="{{ 'external/on-offboarding/checklistArrival' | relative_url }}">Checklist upon arrival in Luxembourg</a></li>
+			<li><a href="{{ 'external/on-offboarding/onboarding' | relative_url }}">Onboarding new members at the LCSB</a></li>
+		</ul>
+	</div>
 	<div class="index-box noborderbox" id="publication-card">
 		<h3>Publication</h3>
 		<ul>
+			<li><a href="{{ 'external/publication/orcid' | relative_url }}">Obtain an ORCID</a></li>
+			<li><a href="{{ 'external/publication/phdThesisTemplate' | relative_url }}">LaTeX template for a doctoral thesis at University of Luxembourg</a></li>
 			<li><a href="{{ 'external/publication/10WaysImproveEnglish' | relative_url }}">10 ways to improve your English</a></li>
-			<li><a href="{{ 'external/publication/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
-
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="publication-code-card">
+		<h3>Publication: Publishing code and programs</h3>
+		<ul>
+			<li><a href="{{ 'external/publication-code/publish-repo' | relative_url }}">Publish a repository</a></li>
+			<li><a href="{{ 'external/publication-code/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
+			<li><a href="{{ 'external/publication-code/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
 		</ul>
 	</div>
 </div><br><center><a href="{{ '/' | relative_url }}">go back</a></center><br><center><a href="{{ '/cards' | relative_url }}">Overview of all HowTo cards</a></center>
\ No newline at end of file

external/access/harrenhal-access/harrenhal-access.md

 ---
+card_order: 100
 layout: page
 permalink: /external/access/harrenhal-access/
 shortcut: access:harrenhal-access
 redirect_from:
   - /cards/access:harrenhal-access
   - /external/cards/access:harrenhal-access
+  - /access/harrenhal-access
+  - /external/external/access/harrenhal-access/
 ---
 # HARRENHAL access
 
@@ -24,15 +27,7 @@ Launch your favorite web browser and go to [HARRENHAL](https://harrenhal.uni.lu)
 
    <img src="img/login_01.png" height="450px"><br/>
 
-2. Reset your temporary password
-
-   * New Password - New password that you want to use.
-   * Confirm New Password - Confirm the new password.
-   * Click **Continue**
-
-   <img src="img/login_02.png" height="300px"><br/>
-
-3. Configure the two-factor authentication.
+2. Configure the two-factor authentication.
 
    * Scan the QR code with your favorite two-factor authentication app. Or click **show** to display the TOTP key.
    * Enter the 6-digit authentication code provided by your two-factor authentication app.
@@ -70,14 +65,3 @@ Once you successfully complete the password reset and the two-factor authenticat
 2. Access to a VM in the list by clicking on it.
 
    <img src="img/server_01.png" height="500px"><br/>
-
-## How to change your password ?
-
-Go to your account menu and click **Settings**
-
-   * Current Password - Current password you want to change.
-   * New Password - New password you want to use.
-   * Confirm New Password - Same new password.
-   * Click **Update Password**
-
-   <img src="img/change_password_01.png" height="200px"><br/>