.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 root_handbook(href):
-    # remove sym link reference in href
-    if ('handbook-additional' in href):
-        href = href.replace('handbook-additional', 'handbook').strip()
-    elif ('handbook-annexes' in href):
-        href = href.replace('handbook-annexes', 'handbook').strip()
-
-    return href
-
-def root_lab(href):
-    # remove sym link reference in href
-    if ('lab-software' in href):
-        href = href.replace('lab-software', 'lab').strip()
-    elif ('lab-equipment' in href):
-        href = href.replace('lab-equipment', 'lab').strip()
-    elif ('lab-hsa' in href):
-        href = href.replace('lab-hsa', 'lab').strip()
-
-    return href
-
-def build_section_start(title, shortcut):
-
-    title = title.replace("Gdpr", "GDPR")
-    title = title.replace("Handbook additional", "Handbook: PI/Supervisor specifics")
-    title = title.replace("Handbook annexes", "Handbook: Annexes")
-    title = title.replace("Covid 19", "COVID-19")
-    title = title.replace("Ppc", "PPC")
-    title = title.replace("Lab software", "Lab: Software")
-    title = title.replace("Lab equipment", "Lab: Equipment")
-    title = title.replace("Lab hsa", "Lab: Health & Safety, Access")
-
-    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 save_tag(localroot, root, filename, tag):
-    return_tag = ""
-    os.chdir(root)
-
-    length_tag = len(tag)
-
-    with open(filename, 'r') as f:
-        for line in f:
-            # check for the start of the section
-            if line[0:length_tag+1] == tag + ":":
-                return_tag = line[length_tag+2:]
-                break
-
-    # change back to the local root
-    os.chdir(localroot)
-
-    return return_tag.rstrip()
-
-def get_ignore():
-    return ["404.html",
-            "Gemfile",
-            "Gemfile.lock",
-            "README.md",
-            "_config.yml",
-            "_site",
-            "assets",
-            "help.md",
-            "index.md",
-            "pagination.md"
-            ]
-
-def save_legacy_from(localroot, root, filename):
-    legacy_from = []
-    os.chdir(root)
-
-    count = 0
-    legacy_from_flag = False
-    with open(filename, 'r') as f:
-        for line in f:
-            count += 1
-            # check for the start of the section
-            if line[0:12] == "legacy_from:":
-                legacy_from_flag = True
-
-            # append lines from the legacy section
-            if legacy_from_flag:
-                legacy_from.append(line)
-
-            # check for the end of the header
-            if legacy_from_flag and line[0:3] == "---":
-               legacy_from_flag = False
-               break
-
-    # change back to the local root
-    os.chdir(localroot)
-
-    return legacy_from
-
-def remove_header(localroot, root, filename):
-    nfirstlines = []
-
-    os.chdir(root)
-
-    # count the number of lines
-    count = 0
-    n = 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 > 1 and line[0:3] == "---":
-                headerCheck = True
-                n = count
-
-    # remove the header
-    if 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)
-
-    return n
-
-def generate_header(folder, permalink, shortcut, order, legacy_from, title, description):
-    header = "---\n"
-
-    if len(order) > 0:
-        header += "card_order: " + str(order) + "\n"
-
-    header += "layout: page\n"
-    header += "permalink: " + permalink + "\n"
-    header += "shortcut: " + root_handbook(shortcut) + "\n"
-    header += "redirect_from:\n"
-    header += "  - /cards/" + shortcut + "\n"
-    header += "  - /" + folder + "/cards/" + shortcut + "\n"
-    # special case of handbook
-    if "handbook-annexes" in permalink or "handbook-additional" in permalink:
-        header += "  - /cards/" + root_handbook(shortcut) + "\n"
-        header += "  - /" + folder + "/cards/" + root_handbook(shortcut) + "\n"
-    # separate lab section
-    if "lab-software" in permalink or "lab-equipment" in permalink or "lab-hsa" in permalink:
-        header += "  - /cards/" + root_lab(shortcut) + "\n"
-        header += "  - /" + folder + "/cards/" + root_lab(shortcut) + "\n"
-
-    # add the title and description
-    if len(title) > 0:
-        header += "title: " + title + "\n"
-    if len(description) > 0:
-        header += "description: " + description + "\n"
-
-    # include the legacy section
-    if len(legacy_from) > 0:
-        for item in legacy_from:
-            header += str(item)
-    else:
-        header += "---"
-
-    return header
-
-def generate_whitelist_entry(folder, permalink, shortcut):
-    wl_entry = permalink + "\n"
-    wl_entry += "/?" + shortcut + "\n"
-    wl_entry += "/cards/" + shortcut + "\n"
-    wl_entry += "/" + folder + "/cards/" + shortcut + "\n"
-    if "handbook-annexes" in permalink or "handbook-additional" in permalink:
-        wl_entry += "/cards/" + root_handbook(shortcut) + "\n"
-        wl_entry += "/" + folder + "/cards/" + root_handbook(shortcut) + "\n"
-    # separate lab section
-    if "lab-software" in permalink or "lab-equipment" in permalink or "lab-hsa" in permalink:
-        wl_entry += "/cards/" + root_lab(shortcut) + "\n"
-        wl_entry += "/" + folder + "/cards/" + root_lab(shortcut) + "\n"
-
-    return wl_entry
-
-# loop through the entire internal tree
-localroot = os.getcwd()
-
-# retrieve ignore list
-ignore = get_ignore()
-
-# 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] != "." and d not in ignore:
-                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 = {k: [] for k in range(len(sections))}
-orderArr = {k: [] for k in range(len(sections))}
-
-for folder in cardDirs:
-    # FolderFlag gets set to true at the first iteration
-    folderFlag = True
-
-    # check if folder exists
-    if path.isdir(folder) and folder not in ignore:
-        dirs = os.listdir(folder)
-        dirs = natsorted(dirs)
-
-        for d in dirs:
-            if d[0] != "." and d not in ignore:
-                # set the header of the section
-                #index += "\n### " + d.replace("-", " ").capitalize() + "\n"
-
-                # get the index of the section
-                indexS = sections.index(d)
-                maxOrder = 0
-
-                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)
-
-                                # save order and legacy section
-                                order = save_tag(localroot, root, file, "card_order")
-                                legacy_from = save_legacy_from(localroot, root, file)
-                                title = save_tag(localroot, root, file, "title")
-                                description = save_tag(localroot, root, file, "description")
-
-                                # remove the previous header
-                                n = remove_header(localroot, root, file)
-
-                                # 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)
-
-                                if len(order) > 0:
-                                     # find the maximum of existing orders
-                                    if folderFlag:
-                                        if len(orderArr[indexS]) > 0:
-                                            maxOrder = max(orderArr[indexS])
-                                        else:
-                                            maxOrder = 0
-                                        # after determining the max order, set the folder flag to False to avoid another entry into the same block of code
-                                        folderFlag = False
-
-                                    tmp = orderArr[indexS].copy()
-                                    tmp.append(maxOrder + int(order))
-                                    orderArr[indexS] = tmp
-                                else:
-                                    orderArr[indexS] = []
-
-                                # generate the header for each card
-                                header = generate_header(folder, permalink, shortcut, order, legacy_from, title, description)
-
-                                # add autogenerated links to whitelist
-                                whiteList += generate_whitelist_entry(folder, permalink, shortcut)
-
-                                # add the header properly speaking
-                                line_prepender(fileName, header)
-
-                                # open file and get the title after the header
-                                count = 0
-                                title = ""
-                                bp = n + 1
-
-                                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("-----------------------")
-
-
-# ordering of cards
-for d in sections:
-    indexS = sections.index(d)
-
-    # join all subcategories to the index
-    # if all subcategories have a predefined order
-    if len(orderArr[indexS]) == len(localIndexArr[indexS])-1 and len(orderArr[indexS]) > 0:
-        print("")
-        X = localIndexArr[indexS][1:]
-        Y = orderArr[indexS]
-        localIndexArr[indexS] = [x for _, x in sorted(zip(Y, X))]
-    # natural sorting otherwise
-    else:
-        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

.gitattributes

-*.PNG filter=lfs diff=lfs merge=lfs -text
-*.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: $CI_REGISTRY/r3/docker/jekyll-lcsb
   stage: build
   variables:
     JEKYLL_ENV: production
-    BUNDLER_VERSION: 2.0.2
+    BUNDLER_VERSION: 2.1.4
   artifacts:
     expire_in: 1 day
     paths:
@@ -107,6 +109,7 @@ build:pages:
     - |
       echo "Configuration: " && cat ".ci/_config_$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
@@ -173,7 +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`.

_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 %}
\ No newline at end of file
+  {% endif %}

assets/js/box_hider.js

@@ -24,7 +24,7 @@ window.boxHider = (function() {
     function GetSelectedBoxElement(id) {
         var allBoxesArray = GetAllBoxElementsArray();
         // note: handbook and lab are actually grouped sections
-        if (id.startsWith('handbook') || id.startsWith('lab')) {
+        if (id.startsWith('handbook') || id.startsWith('lab') || id.startsWith('qms') || id.startsWith('publication')) {
             return true;
         } else {
             var element = document.getElementById(id);
@@ -96,6 +96,22 @@ window.boxHider = (function() {
                     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

@@ -37,7 +37,9 @@ 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>
@@ -54,6 +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>
 
@@ -62,9 +67,13 @@ order: -1
 	<div class="index-box noborderbox" id="exchange-channels-card">
 		<h3>Exchange channels</h3>
 		<ul>
-			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
 			<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>
 	</div>
 	<div class="index-box noborderbox" id="general-card">
@@ -83,48 +92,67 @@ order: -1
 		<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-equipment-card">
 		<h3>Lab: Equipment</h3>
 		<ul>
-			<li><a href="{{ 'external/lab-equipment/cryostorage' | relative_url }}">Utilization of the cryostorage</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/hoods' | relative_url }}">Laminar Flow - Fume Hood - Biosafety Cabinet: what are the differences and when to use them?</a></li>
-			<li><a href="{{ 'external/lab-equipment/maintenance-of-fridges' | relative_url }}">Maintenance of fridges and freezers</a></li>
-			<li><a href="{{ 'external/lab-equipment/maintenance_of_cold_traps' | relative_url }}">Maintenance of cold traps  </a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-autoclaves' | relative_url }}">Utilization of autoclaves</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-balances' | relative_url }}">Utilization of balances</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-bsc' | relative_url }}">Utilization of Biosafety Cabinets (BSC)</a></li>
-			<li><a href="{{ 'external/lab-equipment/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="lab-good-practice-card">
+		<h3>Lab: Good Practice</h3>
+		<ul>
+			<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/shipment' | relative_url }}">Shipment of a biological or chemical sample</a></li>
-			<li><a href="{{ 'external/lab-hsa/spill-bsc' | relative_url }}">How to deal with a spill in a BSC</a></li>
-			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Chemical and Biological Waste Management</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="lab-software-card">
-		<h3>Lab: Software</h3>
+	<div class="index-box noborderbox" id="lab-quarks-card">
+		<h3>Lab: Quarks</h3>
 		<ul>
-			<li><a href="{{ 'external/lab-software/book-lab-equipment' | relative_url }}">How to book a Lab Equipment in Quarks</a></li>
-			<li><a href="{{ 'external/lab-software/quarks-general' | relative_url }}">Quarks - General information</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>
@@ -139,10 +167,17 @@ order: -1
 	<div class="index-box noborderbox" id="publication-card">
 		<h3>Publication</h3>
 		<ul>
-			<li><a href="{{ 'external/publication/publish-repo' | relative_url }}">Publish a repository</a></li>
-			<li><a href="{{ 'external/publication/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
-			<li><a href="{{ 'external/publication/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
+			<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>
 		</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

@@ -6,8 +6,8 @@ shortcut: access:harrenhal-access
 redirect_from:
   - /cards/access:harrenhal-access
   - /external/cards/access:harrenhal-access
-title: HARRENHAL access
-description: This is the howto card that describes the access procedure to the HARRENHAL system
+  - /access/harrenhal-access
+  - /external/external/access/harrenhal-access/
 ---
 # HARRENHAL access