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Commit 2703086d authored by Laurent Heirendt's avatar Laurent Heirendt ✈
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Merge branch 'develop' into 'master' 

[release] Regular merge of develop

See merge request !305
parents 703e2132 0fe8cc11
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.ci/generateIndex.py
View file @ 2703086d
import os, re
from os import path
from natsort import natsorted
from pathlib import Path
def line_prepender(filename, line):
with open(filename, 'r+') as f:
......@@ -33,7 +34,7 @@ def build_section_start(title, shortcut):
title = title.replace("Covid 19", "COVID-19")
title = title.replace("Ppc", "PPC")
return f'\n\t<div class="index-box noborderbox" id="{shortcut}">\n\t\t<h3>{title}</h3>\n\t\t<ul>\n'
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>"
......@@ -100,6 +101,7 @@ 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:
......@@ -157,6 +159,12 @@ for folder in cardDirs:
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)
......@@ -197,7 +205,7 @@ for s in sections:
index += build_section_end()
k += 1
# Close the container
# close the container
index += "\n</div>"
## add link to return to main index
......@@ -226,3 +234,13 @@ 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)
.ci/whitelist.txt 0 → 100644
View file @ 2703086d
/privacy-policy
/search
https://www.dev47apps.com/
https://www.dev47apps.com/droidcam/connect/
https://cerbere.uni.lu/
http://iptel.uni.lux/
javascript:%20showBanner();
javascript:showBanner();
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
\ No newline at end of file
.gitignore
View file @ 2703086d
......@@ -42,4 +42,6 @@ handbook/
internal/handbook
internal/handbook-additional
internal/handbook-annexes
!internal/covid-19/exit-strategy/*.pdf
\ No newline at end of file
!internal/covid-19/exit-strategy/*.pdf
checkFolder
.cache/
.gitlab-ci.yml
View file @ 2703086d
stages:
- prepare
- save
- build
- check
- generate
- deploy
- trigger
......@@ -26,6 +29,7 @@ prepare:index:
- python .ci/generateIndex.py
- mkdir .tmp
- cp cards.md .tmp/.
- cp .ci/whitelist.txt .tmp/.
artifacts:
expire_in: 1 day
paths:
......@@ -77,27 +81,49 @@ build:pages:
expire_in: 1 day
paths:
- build
- .tmp
rules:
- if: $CI_COMMIT_REF_NAME
- if: $CI_MERGE_REQUEST_ID
before_script:
- apt-get -qq update
- apt-get install -y -qq git-lfs
- gem install bundler:$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'
- |
if [ $CI_MERGE_REQUEST_ID ]; then
export CI_COMMIT_REF_NAME="develop";
else
echo "url: https://$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
fi
# Display, which configuration is used
- 'echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"'
- |
echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"
# Run Jekyll with custom configuration
- bundle exec jekyll build -d build --config "_config.yml,.ci/_config_$CI_COMMIT_REF_NAME.yml"
# check
# ------------------------------------------------------------------------------------
check:links:
stage: check
image: $CI_REGISTRY/r3/apps/tailorbird/linkchecker
rules:
- if: $CI_COMMIT_REF_NAME
- if: $CI_MERGE_REQUEST_ID
allow_failure: true
before_script:
- cp .tmp/whitelist.txt build/.
- cp -r build /check
- cd /
script:
- python link_check.py
# generate
# ------------------------------------------------------------------------------------
......@@ -163,4 +189,4 @@ trigger:
tags:
- privileged
script:
- curl --silent --output /dev/null -X POST -F token=$INTERNAL_TRIGGER_TOKEN -F ref=$CI_COMMIT_BRANCH $INTERNAL_REPO
\ No newline at end of file
- curl --silent --output /dev/null -X POST -F token=$INTERNAL_TRIGGER_TOKEN -F ref=$CI_COMMIT_BRANCH $INTERNAL_REPO
_config.yml
View file @ 2703086d
......@@ -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: "/" # 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/
baseurl: "/howto-cards" # the subpath of your site, e.g. /gitlab-repository-name
url: "https://howto.lcsb.uni.lu" # 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
......
assets/js/box_hider.js
View file @ 2703086d
/**
/**
* This is used to hide the sections of the index page
* based on the URL fragment (a.k.a. "hash")
*/
window.boxHider = (function() {
function GetSelectedId() {
var boxId = window.location.hash;
var boxId = window.location.hash + '-card';
if (boxId.length > 0) {
return boxId.substring(1);
}
......@@ -24,10 +24,10 @@ window.boxHider = (function() {
function GetSelectedBoxElement(id) {
var allBoxesArray = GetAllBoxElementsArray();
var element = document.getElementById(id);
if (allBoxesArray.includes(element)) {
return element;
}
}
return false;
}
......@@ -61,7 +61,7 @@ window.boxHider = (function() {
var boxId = GetSelectedId();
if (boxId.length == 0) {
// If there is no hash in the URL, just show all the boxes
ShowAllBoxes();
ShowAllBoxes();
return;
}
// Otherwise, proceed to getting the corresponding div element
......
cards.md
View file @ 2703086d
......@@ -31,17 +31,25 @@ order: -1
<div class="index-box-container">
<div class="index-box noborderbox" id="access">
<div class="index-box noborderbox" id="access-card">
<h3>Access</h3>
<ul>
<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/wifiNetworkAccessGuests' | relative_url }}">WiFi network access for guests</a></li>
</ul>
</div>
<div class="index-box noborderbox" id="contribute">
<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">
<h3>Contribute</h3>
<ul>
<li><a href="{{ 'external/contribute/git-clients' | relative_url }}">Git clients</a></li>
......@@ -53,7 +61,7 @@ order: -1
</ul>
</div>
<div class="index-box noborderbox" id="exchange-channels">
<div class="index-box noborderbox" id="exchange-channels-card">
<h3>Exchange channels</h3>
<ul>
<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
......@@ -62,15 +70,20 @@ order: -1
</ul>
</div>
<div class="index-box noborderbox" id="general">
<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/getToLCSB' | relative_url }}">How to get to the Luxembourg Centre for Systems Biomedicine</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>
</ul>
</div>
<div class="index-box noborderbox" id="integrity">
<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>
......@@ -79,11 +92,12 @@ order: -1
<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>
</ul>
</div>
<div class="index-box noborderbox" id="lab">
<div class="index-box noborderbox" id="lab-card">
<h3>Lab</h3>
<ul>
<li><a href="{{ 'external/lab/book-lab-equipment' | relative_url }}">How to book a Lab Equipment in Quarks</a></li>
......@@ -92,10 +106,38 @@ order: -1
<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-chemical-platform' | relative_url }}">Quarks - Chemical platform</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>
</ul>
</div>
<div class="index-box noborderbox" id="on-offboarding-card">
<h3>On offboarding</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>
</ul>
</div>
<div class="index-box noborderbox" id="ppc-card">
<h3>PPC</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>
</ul>
</div>
<div class="index-box noborderbox" id="publication-card">
<h3>Publication</h3>
<ul>
<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><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/lums-passwords/lums-passwords.md
View file @ 2703086d
......@@ -31,7 +31,7 @@ In case you are not a member of the university, please ask your collaborator at
## (Re-)Activating LUMS account upon receiving credentials or after password reset
The password you will receive from the system administrators is temporary and **it will expire after one month**, so you have to reset it as soon as possible. It is usually sent as a link to [PrivateBin](https://howto.lcsb.uni.lu/?passwords). **This link is valid for one week and is deleted after you see it once**, thus you need to keep it open until you have followed these steps to reset your password:
The password you will receive from the system administrators is temporary and **it will expire after one month**, so you have to reset it as soon as possible. It is usually sent as a link to [PrivateBin]({{ '/?access:passwords' | relative_url }}). **This link is valid for one week and is deleted after you see it once**, thus you need to keep it open until you have followed these steps to reset your password:
1. Go to [lums.uni.lu](https://lums.uni.lu) and login with your LUMS username and the temporary password you received.<br>**NOTE:** If you experience any issues at this step, try to use *Chrome* browser for this procedure.<br/><img src="img/lums_login.png" height="200px"><br/>
Should the login look different from this, e.g. like a pop-up, click on **x** or **Cancel** to close it.
......@@ -43,7 +43,7 @@ The password you will receive from the system administrators is temporary and **
5. Enter a new password of your choice in the field **"New Password"** and repeat the same password in the field **"Verify Password"**. This is the actual password you need to use from now on, so make sure to remember it.
6. Click on **"Reset Password and Login"**.
It is a good practice to use a password manager which will not only help you to keep track of your passwords so you will never forget it, but it will also help you to generate passwords which are very safe (see [HowTo card](https://howto.lcsb.uni.lu/?passwords) on password management for more detail).
It is a good practice to use a password manager which will not only help you to keep track of your passwords so you will never forget it, but it will also help you to generate passwords which are very safe (see [HowTo card]({{ '/?access:passwords' | relative_url }}) on password management for more detail).
## Changing password for LUMS accounts
If you want to change your password for the LUMS account, you can:
......
external/access/wifiNetworkAccessGuests/wifiNetworkAccessGuests.md 0 → 100644
View file @ 2703086d
---
layout: page
permalink: /external/access/wifiNetworkAccessGuests/
shortcut: access:wifiNetworkAccessGuests
redirect_from:
- /cards/access:wifiNetworkAccessGuests
- /external/cards/access:wifiNetworkAccessGuests
---
# WiFi network access for guests
- Each UL staff member can provide wireless network access for her/his visitors by creating an account on the [Guest Sponsor Portal](https://sponsor.uni.lux:8443/sponsorportal/PortalSetup.action?portal=06f49c40-ad3a-11e4-ba4b-0050568059d7)
- In order to create the guest account, you must log in with your normal UL username and password
- Please also refer to the [process for visitor rules](https://howto.lcsb.uni.lu/?hr:visitorsRules)
- Such a visitor account has a lifetime of maximum 5 days. If you need accounts for people staying longer, please open a [ticket via the SIU helpdesk](https://service.uni.lu/sp)
- Guests will only have access to the internet and public services but not to internal resources
Other documentations on how to use the SIU systems can be found on the [UL intranet (section SIU-SIU-Guides-Wireless Network)](https://intranet.uni.lux/the_university/siu/Pages/siu-guides.aspx).
For any questions please open a [ticket via the SIU helpdesk](https://service.uni.lu/sp).
<!--Process owner: Julia Kessler-->
external/backup/computer/computer.md 0 → 100644
View file @ 2703086d
---
layout: page
permalink: /external/backup/computer/
shortcut: backup:computer
redirect_from:
- /cards/backup:computer
- /external/cards/backup:computer
---
# Staff Computer
## Backup to External Disk
### macOS
macOS platform comes with Time Machine, a very easy to use backup feature. Time Machine backups can be set up as follows:
1. Connect an external disk to your computer.
2. Using Finder open up **/Applications/System Preferences** and Select **Time Machine**. <br/> ![Alt](img/mac_tm_1.png "Title")
3. From the **Time Machine** main screen click **Select Backup Disk** &nbsp; ![Alt](img/mac_tm_2.png "Title")
4. From the list select your external disk. It is also recommended that you select the option to **encrypt backups**. <br/> ![Alt](img/mac_tm_3.png "Title")
5. If you opt for encryption you will be asked for an encryption password. You will need this password whenever you re-connect the disk to your computer or whenever you restart your Mac. You should keep this password safe using [Password Management software]({{ 'external/access/passwords' | relative_url }}). <br/> ![Alt](img/mac_tm_4.png "Title")
6. Time Machine requires an apple-specific disk format to work. Your external disk may not be in this format (e.g. may be in exFAT format which is accessible both by Windows and Mac). In such a case Time Machine will prompt you to approve the erasure and re-formatting of your external disk (see below). If you do not want to re-format, you may [create a disk image]({{ 'external/integrity/encryption/file' | relative_url }}) on your external disk and then point Time Machine to this image. <br/> ![Alt](img/mac_tm_5.png "Title")
7. After you select a backup disk, provide password and confirm disk format (if applicable), Time Machine will automatically start the backup process in the background. You may continue to work. You will receive a notification, when the first backup is complete. <br/> ![Alt](img/mac_tm_6.png "Title")
8. If you want to initiate another backup manually, click the Time Machine logo in your menu bar and select **Back Up Now**. It is recommended that you enable the automatic backup feature of Time Machine. To do so, go to **/Applications/System Preferences/Time Machine** and select the option **Back Up Automatically**. <br/> ![Alt](img/mac_tm_7.png "Title")
Official instructions for restoring your Mac using a Time Machine backup can be found [here](https://support.apple.com/en-us/HT201250)
### Windows
Windows's offerings for backup has different names in different versions.
* _Microsoft Backup and Restore_, which is available in [Windows 7](http://windows.microsoft.com/en-US/windows7/Back-up-your-files) and [Windows 10](https://support.microsoft.com/en-us/help/17143/windows-10-back-up-your-files), allows backup of your entire system or selected folders/files on your computer.
* _File History_, which is is available in [Windows 8 and 10](http://windows.microsoft.com/en-us/windows-8/set-drive-file-history), provides an easy to use option with which you can backup select files/folders. _File History_ runs periodically, tracks versions of your files, and allows you to go back older versions.
Before creating a backup, make sure that your backup drive is encrypted as a safety measure in case of disk loss or theft (see [howto page on disk encryption]({{ 'external/integrity/encryption/disk' | relative_url }})).
The steps to switch **File History** on your computer is as follows:
1. Connect an external disk to your computer.
2. From the **Start** menu select **Settings/Update & Security/Backup**. <br/> ![Alt](img/win_fh_1.png "Title")
3. Click the "+" next to Add a drive. You'll see a prompt to choose an external drive, choose the disk you have connected.
4. File History has now started archiving your data. An on/off slider will now appear under a new heading called **Automatically back up my files.** <br/> ![Alt](img/win_fh_2.png "Title")
5. By default, Windows 10's File History will back-up all the folders in the **User** folder. And it will run the backup on an hourly schedule. To change any of those settings click on More options under the on/off slider (see below). <br/> ![Alt](img/win_fh_2_2.png "Title")
6. In the **Backup Options** dialog, under the **Back up these folders.** you can remove existing folders and add new ones. **Important Note:** Make sure that any application that read/write your data files/folder are closed, when you're making this _File History_ configuration. <br/>
<img src="img/win_fh_3.png" height="200em"/>
The instructions for restoring your files from **File History** can be found [here](https://it.nmu.edu/docs/backup-using-windows-file-history)
## Backup to dropit.uni.lu
The University of Luxembourg's cloud service [DropIt](https://dropit.uni.lu/) provides all staff with 100GB of storage.
To use this service, first, visit [dropit.uni.lu](https://dropit.uni.lu/). You should be able to login with your university credentials. In case of login problems, request IT support using [ServiceNow](https://service.uni.lu/).
Second, in order to create backups of your computer on DropIt cloud, you need to install a client application. The University IT Guideline [here](https://intranet.uni.lux/the_university/siu/Documents/Dropit%20client%20-%20configuration%20guide.pdf#search=dropit) provides the details on how to install this client application for macOS, Windows and Linux platforms, and also, how to configure the backup process on your computer.
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