Merge branch 'develop' into 'master'

[release] Regular merge of develop

See merge request R3/howto-cards!277

.ci/generateIndex.py

@@ -28,6 +28,7 @@ def build_section_start(title, shortcut):
     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}">\n\t\t<h3>{title}</h3>\n\t\t<ul>\n'
 

.gitlab-ci.yml

-# In case something goes horribly wrong, you can fall back to `image: ruby:2.5`
-image: $CI_REGISTRY/r3/docker/jekyll-lcsb:1.6
-
 stages:
   - prepare
   - save
   - build
   - generate
   - deploy
+  - trigger
+
+variables:
+    GIT_STRATEGY: clone
+    DOCKER_DRIVER: overlay2
+    DOCKER_TLS_CERTDIR: ""
 
 # prepare
 # ------------------------------------------------------------------------------------
@@ -65,6 +68,7 @@ save:commitIndex:
 # ------------------------------------------------------------------------------------
 
 build:pages:
+  image: $CI_REGISTRY/r3/docker/jekyll-lcsb:1.8
   stage: build
   variables:
     JEKYLL_ENV: production
@@ -119,7 +123,8 @@ pages:
   image: alpine:3.11.3
   stage: deploy
   rules:
-    - if: '$CI_MERGE_REQUEST_ID && $CI_PROJECT_NAMESPACE != "R3" && $CI_PROJECT_NAMESPACE != "R3-core"'
+    - if: '$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:
     - mv processed_build public
   artifacts:
@@ -147,3 +152,15 @@ deploy:vm:
     - scp -P $SSHPORT -r processed_build/* $SSHCONNECT:~/$CI_COMMIT_REF_NAME/sources/public/$CI_JOB_ID
     - ssh -p $SSHPORT $SSHCONNECT "cd ~/$CI_COMMIT_REF_NAME/public && ln -fs ../sources/public/$CI_JOB_ID/* . && cd ~/$CI_COMMIT_REF_NAME/sources/public/ && find . -type d -not -newermt '-1 minutes' -exec rm -rf {} +;"
 
+# Trigger pipelines in internal repo
+# ------------------------------------------------------------------------------------
+
+trigger:
+  stage: trigger
+  image: curlimages/curl
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master" || $CI_COMMIT_BRANCH == "develop"'
+  tags:
+    - privileged
+  script:
+    - curl --silent --output /dev/null -X POST -F token=$INTERNAL_TRIGGER_TOKEN -F ref=$CI_COMMIT_BRANCH $INTERNAL_REPO
\ No newline at end of file

Gemfile

@@ -32,7 +32,7 @@ group :jekyll_plugins do
 
  gem 'jekyll-theme-lcsb-frozen-components',
      '~> 0.0.2',
-     :git => "https://git-r3lab.uni.lu/core-services/jekyll-theme-lcsb-frozen-components.git",
+     :git => "https://gitlab.lcsb.uni.lu/core-services/jekyll-theme-lcsb-frozen-components.git",
      :tag => "0.0.2"
 
  gem 'jekyll-redirect-from',

cards.md

@@ -89,8 +89,10 @@ order: -1
 			<li><a href="external/lab/book-lab-equipment">How to book a Lab Equipment in Quarks</a></li>
 			<li><a href="external/lab/dishwasher-utilization-and-maintenance">Dishwasher utilization and maintenance</a></li>
 			<li><a href="external/lab/handwashing">Handwashing</a></li>
+			<li><a href="external/lab/lab-coats">Lab coats</a></li>
 			<li><a href="external/lab/maintenance_of_cold_traps">Maintenance of cold traps  </a></li>
 			<li><a href="external/lab/personal-alert-safety-system">Personal alert safety system (PASS)</a></li>
+			<li><a href="external/lab/quarks-chemical-platform">Quarks - Chemical platform</a></li>
 			<li><a href="external/lab/utilization-of-balances">Utilization of balances</a></li>
 			<li><a href="external/lab/utilization-of-pH-meter">Utilization of pH meter</a></li>
 

external/access/lums-passwords/lums-passwords.md

@@ -9,7 +9,7 @@ redirect_from:
 # LUMS account
 
 In addition to the standard university account, LCSB researchers and external collaborators are provided with the LUMS (LCSB User Management System) account.
-This serves for internal authentication for resources provided by the LCSB, e.g. LCSB hosted [GitLab](https://git-r3lab.uni.lu), LCSB [OwnCloud](https://owncloud.lcsb.uni.lu) storage or access to virtual machines.
+This serves for internal authentication for resources provided by the LCSB, e.g. LCSB hosted [GitLab](https://gitlab.lcsb.uni.lu), LCSB [OwnCloud](https://owncloud.lcsb.uni.lu) storage or access to virtual machines.
 
 ## Requesting LUMS account
 

external/contribute/install-git/install-git.md

@@ -13,8 +13,8 @@ Several git clients are presented [here](https://howto.lcsb.uni.lu/?contribute:g
 
 For most of the git clients, `git` is actually required to be installed on the system. You can find installers for Windows, MacOS and Linux on the [Git webpage](https://git-scm.com/downloads).
 
-If you are using Visual Studio Code, and if you want to contribute to a repository hosted on the [LCSB Gitlab](https://git-r3lab.uni.lu), you will need to verify the host key first before you are able to clone or push to a repository. For this, open a terminal (on Linux or macOS) or Git Bash (on Windows), and type:
+If you are using Visual Studio Code, and if you want to contribute to a repository hosted on the [LCSB Gitlab](https://gitlab.lcsb.uni.lu), you will need to verify the host key first before you are able to clone or push to a repository. For this, open a terminal (on Linux or macOS) or Git Bash (on Windows), and type:
 ```bash
-ssh git@git-r3lab-server.uni.lu -p8022
+ssh git@gitlab.lcsb.uni.lu -p8022
 ```
 Then, press Enter and type `yes`. This will add the git-r3lab server to the known hosts on your system.
\ No newline at end of file

external/contribute/vscode/vscode.md

@@ -75,14 +75,14 @@ If you need more details on how to do this, refer to the [corresponding howto-ca
 
     <img src="img/visual-code_img_13.png">
 
-## Step 6: Push to git-r3lab
+## Step 6: Push to the LCSB Gitlab server
 
 - When you push your procedure for the first time click on the cloud icon:
 
     <img src="img/visual-code_img_15.png">
 
 - Choose origin/"your gitlab user name"
-- Open git-r3lab: https://git-r3lab.uni.lu/
+- Open Gitlab: https://gitlab.lcsb.uni.lu/
 
     <img src="img/visual-code_img_16.png">
 

external/general/remote-working/remote-working.md

@@ -70,7 +70,7 @@ directly with your collaborators by following [these instructions](https://howto
 
 ## Development of code
 
-Use the [LCSB R3 Gitlab](https://git-r3lab.uni.lu) to develop and share code.
+Use the [LCSB R3 Gitlab](https://gitlab.lcsb.uni.lu) to develop and share code.
 
 ## Forwarding phone calls
 

external/integrity/naming/file_naming.md

@@ -238,4 +238,4 @@ The **consistency** is much more important than your preferred naming.
 
 * Jenny Brian's [slides](https://speakerdeck.com/jennybc/how-to-name-files) on "Naming things" from Reproducible Science Workshop, Duke, 2015
 * Semantic versioning - [semverdoc.org](https://semverdoc.org/)
-* LCSB *IT101* training [presentation](https://git-r3lab.uni.lu/R3/howto-cardsrds/uploads/738930b9a533a2f308cc62c431d9246f/it101.html)
+* LCSB *IT101* training [presentation](https://courses.lcsb.uni.lu/)

external/lab/book-lab-equipment/book-lab-equipment.md

@@ -11,23 +11,23 @@ redirect_from:
 
 To help the lab users to plan their work and to ensure that a lab equipment will be free to use, the Quarks software provides a booking tool. This booking tool is also used by the support team to indicate the maintenance periods, or if an equipment is not available due to a failure or a breakdown.
 
- - [1. How to look for an instrument](#1-how-to-look-for-an-instrument)
- - [2. How to know if an instrument is bookable](#2-how-to-know-if-an-instrument-is-bookable)
- - [3. How to add an equipment to your Favorites list](#3-how-to-add-an-equipment-to-your-favorites-list)
- - [4. How to book an instrument](#4-how-to-book-an-instrument)
- - [5. How to edit or cancel a booking](#5-how-to-edit-or-cancel-a-booking)
- - [6. How to book a lab (location)](#6-how-to-book-a-lab-(location))
- - [7. How to access the booking history](#7-how-to-access-the-booking-history)
- - [8. How to request booking configuration change or report an issue with Quarks?](#8-how-to-request-booking-configuration-change-or-report-an-issue-with-Quarks?)
+ - [How to look for an instrument](#how-to-look-for-an-instrument)
+ - [How to know if an instrument is bookable](#how-to-know-if-an-instrument-is-bookable)
+ - [How to add an equipment to your Favorites list](#how-to-add-an-equipment-to-your-favorites-list)
+ - [How to book an instrument](#how-to-book-an-instrument)
+ - [How to edit or cancel a booking](#how-to-edit-or-cancel-a-booking)
+ - [How to book a lab (location)](#how-to-book-a-lab-(location))
+ - [How to access the booking history](#how-to-access-the-booking-history)
+ - [How to request booking configuration change or report an issue with Quarks?](#how-to-request-booking-configuration-change-or-report-an-issue-with-Quarks?)
 
-## 1. How to look for an instrument
+## How to look for an instrument
 
 In your Quarks account, go on the _Equipment_ platform. In the _Equipment_ section, you have a search tool to help you find an equipment among all the LCSB equipment. You can search by internal reference number (e.g. LCSB01685), model, manufacturer or serial number in the “quick search” field.
 If you want to add more search criteria, you can do so in the drop down list “Add a filter”.
 
 ![1](img/1.png)
 
-## 2. How to know if an instrument is bookable
+## How to know if an instrument is bookable
 
 You can easily know if the instrument you are looking for is bookable or not thanks to the calendar symbol in the “Actions” column.
 
@@ -39,7 +39,7 @@ You can also see if the instrument is bookable or not on the side panel that wil
 
 A bookable instrument will have a calendar icon available. Typically, only specific equipment or equipment that is usually used for long experiments is bookable.
 
-## 3. How to add an equipment to your Favorites list
+## How to add an equipment to your Favorites list
 
 In the “Actions” tools, you have the option to add an instrument in your favorite list by clicking on the heart.
 
@@ -63,7 +63,7 @@ You can directly see for which instrument you have the notifications activated b
 
 ![9](img/9.png)
 
-## 4. How to book an instrument
+## How to book an instrument
 
 You have three ways to create a new booking.
 1.	You can book your instrument by clicking on its name, you will have in the right window a reservation section.
@@ -113,7 +113,7 @@ You have three ways to create a new booking.
 
     ![22](img/22.png)
 
-## 5. How to edit or cancel a booking
+## How to edit or cancel a booking
 
 You can edit a booking by clicking on the time period. The right window will be displayed.
 
@@ -131,21 +131,21 @@ You can also edit or cancel your booking in the “Reservations” – “ Reser
 
 ![27](img/27.png)
 
-## 6. How to access the booking a lab (location)
+## How to access the booking a lab (location)
 
 In some cases the equipment reservation is organized via lab booking. If you want to reserve a lab please select under Reservations “Locations” instead of “Equipment” as Type. The further way of proceeding is similar to described above for Equipment reservations.
 
 ![29](img/29.png)
 
 
-## 7. How to access the booking history
+## How to access the booking history
 
 You can have an overview of all the bookings in the “Reservations” – “Reservations” section. You can filter them by date, type (Location or Equipment), name (Bookable item) and person who have made the booking (Reserved by).
 
 ![28](img/28.png)
 
 
-## 8. How to request booking configuration change or report an issue with Quarks?
+## How to request booking configuration change or report an issue with Quarks?
 
 If you wish to make one equipment bookable or make it 24 hours bookable [please send a ticket](https://service.uni.lu/sp?id=sc_cat_item_lsmc&sys_id=1dac368d54be72000a5374545c1c6a62&business_service_id=014ebe3ddb6a14148bcbf9b41d96195e&action_id=ec38cb7ddbaa14148bcbf9b41d9619a3). 
 

external/lab/dishwasher-utilization-and-maintenance/dishwasher-utilization-and-maintenance.md

@@ -11,7 +11,7 @@ redirect_from:
 
 Utilization of the Miele dishwashers on the 5th floor of BT1 and on the 1st floor of BT2.
 
-## 1. Description
+## Description
 
 <div align="center">
 <img src="img/dishwasher_img_1.jpg" height="400">
@@ -43,9 +43,9 @@ Utilization of the Miele dishwashers on the 5th floor of BT1 and on the 1st floo
 8. OK button
 9. Selection button: down
 
-## 2. Utilization
+## Utilization
 
-### **1. Loading the dishwasher**
+### **Loading the dishwasher**
 
 1. Ensure that no acid or solvent residues, especially hydrochloric acid or chlorides, get inside the machine
 2. Empty all glassware before loading into the machine
@@ -55,7 +55,7 @@ Utilization of the Miele dishwashers on the 5th floor of BT1 and on the 1st floo
 6. Load your items on the tray
 7. Close the door
 
-### **2. Selecting a program and running the dishwasher**
+### **Selecting a program and running the dishwasher**
 
 1. Click on <img src="img/dishwasher_img_3.jpg"> to switch on the instrument
 2. Select the “Chemistry Bio” program using the up and down arrows
@@ -66,7 +66,7 @@ Utilization of the Miele dishwashers on the 5th floor of BT1 and on the 1st floo
 
 3. Click on <img src="img/dishwasher_img_5.jpg">  to start the program
 
-### **3. Cancel a program during run**
+### **Cancel a program during run**
 
 1. To cancel the program, click on <img src="img/dishwasher_img_6.jpg">
 2. The program is then interrupted
@@ -76,15 +76,15 @@ Utilization of the Miele dishwashers on the 5th floor of BT1 and on the 1st floo
 6. The following message appears on the display: “Program cancelled. Water drainage”
 7. After the water has drained away, the program list returns to the display
 
-### **4. Unloading**
+### **Unloading**
 
 1. When the program is finished, the message “End of program” is displayed on the screen
 2. Click on <img src="img/dishwasher_img_8.jpg"> to open the door
 3. Unload the tray and store the items in the cupboards
 
-## 3. Maintenance
+## Maintenance
 
-### **1. Reactivation**
+### **Reactivation**
 1. This section is available in the dishwasher room
 2. If the display shows “Reactivation”, salt needs to be added to the dishwasher **directly when the message appears! Do not run a cycle when reactivation is needed!**
 3. Material needed: salt and container
@@ -134,9 +134,9 @@ Utilization of the Miele dishwashers on the 5th floor of BT1 and on the 1st floo
 
 * BT2: some boxes are available in the cupboard above the sink and the main stocks are in the -2 stock room
 
-### **2. Routine checks**
+### **Routine checks**
 
-#### 1. The filters in the base of the wash cabinet
+#### The filters in the base of the wash cabinet
 
 1.	The filters of the cabinets need to be checked and cleaned regularly
 2.	To clean the coarse filter, press the two lugs together, remove and clean the coarse filter

external/lab/lab-coats/lab-coats.md

+---
+layout: page
+permalink: /external/lab/lab-coats/
+shortcut: lab:lab-coats
+redirect_from:
+  - /cards/lab:lab-coats
+  - /external/cards/lab:lab-coats
+---
+
+# Lab coats
+
+Which lab coat should I wear? Where do I get a new lab coat and where do I dispose a dirty one?
+
+
+## Wear the right lab coat in the right area
+
+<div align="center">
+<img src="img/1.png">
+</div>
+
+### Lab coat mandatory
+
+<div align="center">
+<img src="img/2.png">
+</div>
+
+
+- All BSL1 and BSL2 laboratories
+- Storage Rooms : Chemical Storage/ cryostorage/LCSB stock For all users, visitors, technicians. 
+
+### Lab coat forbidden
+
+<div align="center">
+<img src="img/3.png">
+</div>
+
+- Offices and open offices
+- Kitchen, Coffee Points (red flooring)
+- Toilets
+
+### Lab coat allowed
+
+<div align="center">
+<img src="img/4.png">
+</div>
+
+- Lift 
+- Staircases 
+- Corridor to the stairs/lift
+- Corridor to the support team zone BT2 1st floor (trolleys/ fridges) __BUT not the support team offices__
+
+## Where can i find a new clean lab coat?
+
+### BT1
+
+Clean lab coats are stored in the cupboard behind the Support Biotech Team desk, on the 2nd floor. They are sorted by Biosafety Level (BSL1 and BSL2) and sizes. For the larger sizes, you can find them with extra lengths on the sleeves (+15cm).
+
+### BT2
+
+Clean lab coats are stored in the cupboards of the MUF room, on the 1st floor, close to the Support Biotech Team offices. They are sorted by Biosafety Level (BSL1 and BSL2) and sizes. For the larger sizes, you can find them with extra lengths on the sleeves (+15cm).
+
+In addition to the lab coat, it is strongly recommended to __wear safety goggles__ to protect your eyes. You can find some in the lab coat cupboards or in the common stocks (2nd floor for BT1, -2 floor for BT2).
+
+<div align="center">
+<img src="img/5.png">
+</div>
+
+<div align="center">
+<img src="img/6.png">
+</div>
+
+## What should I do whith my dirty lab coat?
+
+Please put your lab coat in the white plastic box close to the vending machine on the ground floor in BT1 or BT2. Someone from the Support Biotech Team will take care to send the lab coats for cleaning.
+
+## Badges
+To identify your lab coat as yours, do not forget to pin your badge on it. 
+
+## Help needed?
+
+If you need a new badge, or if you have any question regarding lab coats, goggles or other PPE, [please send a ticket](https://service.uni.lu/sp?id=sc_cat_item_lsmc&sys_id=1dac368d54be72000a5374545c1c6a62&business_service_id=2d0be5b3db500f40b0b4f9851d9619ac&action_id=689b61f3db500f40b0b4f9851d9619f8).
+

external/lab/personal-alert-safety-system/personal-alert-safety-system.md

@@ -17,7 +17,7 @@ The call can be triggered voluntarily or automatically, in the event of a fall f
 The lone worker should pick up and register the utilization of the PASS in the logbook.
 After use, they should ensure the device is correctly plugged to charge the battery.
 
-## 1. Overview
+## Overview
 
 1.	The phones detect if the user is:
 
@@ -37,17 +37,17 @@ If this pre-alarm is not reset, the PASS calls the emergency number 5555.
 
 5.	It is forbidden to perform dangerous experiments during the night and weekends (including work with Piranha solution, highly corrosive or explosive compounds).
 
-## 2. Handling the device
+## Handling the device
 
-### 1. Description of the System
+### Description of the System
 
 <img src="img/pass_img-1.jpg">
 
-### 2. Quick user guide
+### Quick user guide
 
 <img src="img/pass_img-2.jpg">
 
-### 3. How to obtain the PASS
+### How to obtain the PASS
 
 1.	The PASS are stored by the guard stations in both BT1 and BT2.
 
@@ -65,7 +65,7 @@ If this pre-alarm is not reset, the PASS calls the emergency number 5555.
 
 3.	Fill in the logbook
 
-### 4. Switch on
+### Switch on
 
 1.	Press on the power button
 
@@ -76,13 +76,13 @@ The power button and SureSafe indicator light (green) will continue to flash whi
 
 4.	Once connected, the SureSafe indicator light will remain continuously on
 
-### 5. Fastening the emergency phone to the clothing
+### Fastening the emergency phone to the clothing
 
 5.	The PASS can be fastened to the clothes using the clip located in the back of the unit
 
 6.	Hold the PASS in a vertical position while fastening it
 
-### 6. Switch off
+### Switch off
 
 7.	 Press and hold the power button for approximately 3 seconds (until the device stops beeping).
 
@@ -90,15 +90,15 @@ The power button and SureSafe indicator light (green) will continue to flash whi
 
 The alarm, vibration motor and power button and SureSafe indicator light will turn off after the shutdown is complete.
 
-### 7. Return the PASS
+### Return the PASS
 
 9.	When you are done with the PASS, place it back on the charger, a red light will flash to indicate that the battery is charging.
 
 10.	Fill the logbook and close the box by placing your BT2 badge in front of the lock.
 
-## 3. Types of alerts
+## Types of alerts
 
-### 1. Emergency alert
+### Emergency alert
 
 1.	Pull the emergency latch. The device will instantly send an emergency message to the 5555.
 
@@ -111,7 +111,7 @@ The device will return to regular operation.
 
 5. <img src="img/pass_img-6.jpg"> silencing the alert will not cancel it: the 5555 will still intervene.
 
-### 2. Fall impact detected alert
+### Fall impact detected alert
 
 The device is constantly monitoring your motion or falls. If the device detects a fall impact, it will trigger the “pending alarm” mode.
 
@@ -135,7 +135,7 @@ If you do not require assistance, you have 30 seconds to cancel the alert by pre
 
     d. <img src="img/pass_img-6.jpg"> Silencing an alarm will not cancel the call, 5555 will still intervene.
 
-### 3. No-motion alert
+### No-motion alert
 
 The device is constantly monitoring your motion to detect a possible person down incident.
 If the device has not detected motion within 5 minutes, it will prompt you to acknowledge your safety, entering the alarm mode and triggering the low alarm pattern.
@@ -159,7 +159,7 @@ If you do not require assistance, you have 30 seconds to cancel the alert by pre
 
     d. <img src="img/pass_img-6.jpg"> Silencing an alarm will not cancel the call, 5555 will still intervene.
 
-### 4. Voice call alert
+### Voice call alert
 
 1.	When a phone call has been initiated by 5555, the device will trigger the “high alarm” pattern accompanied by a blue flashing of the LiveResponse light.
 
@@ -180,7 +180,7 @@ The device will trigger a long beep signifying the end of the call.
 
 9.	NOTE: during the call, the volume of the speaker can be switched to speaker and back to lower volume by pressing the acknowledge button once.
 
-### 5. Low battery notification
+### Low battery notification
 
 1.	If the battery level on the device drops below 20% capacity, the device will flash the charging light and beep once every 5 minutes.
 Once the device battery is depleted, it will automatically shut down.
@@ -188,7 +188,7 @@ Once the device battery is depleted, it will automatically shut down.
 2.	This is considered an unsafe log off.
 If the device is configured to require a periodic check-in, a low battery shutdown will not stop the timer and a missed check-in alter will be generated.
 
-## 4. Types of alarms
+## Types of alarms
 
 |Type|Beeper|Vibration|Visual indicator|
 |----|------|---------|----------------|