Merge branch 'develop' into 'master'

Regular merge of develop

See merge request !15

.gitlab-ci.yml

@@ -15,5 +15,6 @@ pages:
     - bash .ci/deploy.sh
 
   artifacts:
+    expire_in: 1 week
     paths:
       - public

Gemfile

@@ -25,6 +25,7 @@ gem 'jekyll-theme-lcsb-default', '~> 0.2.18', :git => "https://git-r3lab.uni.lu/
 group :jekyll_plugins do
  gem "jekyll-paginate-v2", "~> 1.7"
  gem "jekyll-feed", "~> 0.6"
+ gem "jekyll-email-protect"
 end
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem

_plugins/hook_mailto_email_protector.rb

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

external/exchange-channels/duma.md

-# Data Upload Manager - DUMA  Quick Guide
+# AsperaWEB Quick Guide
 
-{{TOC}}
+{:toc}
 
 ## Overview
-DUMA is an IBM Aspera  deployment at the LCSB-University of Luxembourg. DUMA supports end-to-end encrypted data transfer and can handle high data volumes e.g. several tera bytes.
+AsperaWEB is an IBM Aspera deployment at the LCSB-University of Luxembourg. AsperaWEB supports end-to-end encrypted data transfer and can handle high data volumes e.g. several tera bytes.
 
-## Obtaining a DUMA access link
+## Obtaining a AsperaWEB access link
 
-You need an **access link** to use DUMA. An access link is a temporary, password-protected space, much like a drop box, on LCSB's DUMA server. In order to obtain an access link, you should contact your research collaborator at the LCSB-University of Luxembourg. Once created, you will receive your **access link** and associated **password** (link) by e-mail.
+You need an **access link** to use AsperaWEB. An access link is a temporary, password-protected space, much like a drop box, on LCSB's AsperaWEB server. In order to obtain an access link, you should contact your research collaborator at the LCSB-University of Luxembourg. Once created, you will receive your **access link** and associated **password** (link) by e-mail.
 
-**IMPORTANT NOTE: Whenever the LCSB shares a password for a DUMA endpoint (collaborator), the password be reachable via a link, which will expire. Therefore you should make a record of your password once you view it.**
+> **IMPORTANT NOTE: Whenever the LCSB shares a password for a AsperaWEB endpoint (collaborator), the password is transmitted via a link which will expire. Therefore you should make a record of your password once you view it.**
 
 An access link can be reached via standard web browsers. Data can be transferred to/from an access link in two ways:
 
-* Through the web browser by visiting the link, which is our recommended way of data transfer, described in this [section of the guide](#DUMA_WEB)
-* Through the use of a command line tool. If your data sits in an environment, where you can not launch a web browser, then you may use use a command line client tool to reach an access link. This process is described in this [section of this guide](#DUMA_CLI).  
+* Through the web browser by visiting the link, which is our recommended way of data transfer, described in this [section of the guide](#ASPERAWEB_WEB)
+* Through the use of a command line tool. If your data sits in an environment, where you can not launch a web browser, then you may use use a command line client tool to reach an access link. This process is described in this [section of this guide](#ASPERAWEB_CLI).  
 
-The use of DUMA is mediated by LCSB's data stewards. If you require assistance in using DUMA, you should send an email to [LCSB admin team](lcsb-sysadmins@uni.lu).
+The use of DUMA is mediated by LCSB's data stewards. If you require assistance in using DUMA, you should send an email to [LCSB admin team](mailto:lcsb-sysadmins@uni.lu).
 
-<a name="DUMA_WEB"></a>
-## Accessing DUMA via Web Interface
+<a name="ASPERAWEB_WEB"></a>
+## Accessing AsperaWEB via Web Interface
 
-In the following steps we provide instructions on how to use DUMA web interface.
+In the following steps we provide instructions on how to use AsperaWEB web interface.
 
 1. Once you receive your **access link** and **password** from the LCSB, visit the link using a standard web browser. Firefox 66.x (or higher) recommended, but others should also work. You will be prompted for your password (see below).<br/>
  ![Alt](duma_1.png "Title")
 
-2. When you visit a DUMA access link for the very first time, you will be prompted to install **IBM Aspera Connect** client.
-      * click **Download** or **Download latest version** links (see below). <br/>![Alt](duma_2.png "Title")
+2. When you visit a AsperaWEB access link for the very first time, you will be prompted to install or update **IBM Aspera Connect** client.
+	* click **Download** or **Download the App** buttons (see below). <br/>![Alt](duma_2.png "Title")
 
+	* wait for the download to finish, the prompt should go to step 3. <br/>![Alt](duma_3.png "Title")
 
+	* open the installer just downloaded and start the installer. <br/>![Alt](duma_4.png "Title")
+	
+	* close the installer, the Aspera Connect should try to open - *depending on your Operating System you may be asked if you are sure to open it* -
 
-      * Your browser will download the client installer.
+	* the prompt should disapears
 
-        ![Alt](duma_3.png "Title")
 
-
-      * Run the installer till you receive the completion message.
-
-        ![Alt](duma_4.png "Title")
-
-
-      * Once **IBM Aspera Connect** client is installed, refresh the **access link**. You will be prompted whether you want to open **IBM Aspera Launcher**, click **Open**.
-
-         ![Alt](duma_5.png "Title")
-
-
-3. The **access link** page will display a **File Browser** section. Depending on the settings per access link, users can create or delete folders in the File Browser and upload or download data.<br/>
+3. The **access link** page will display a **File Browser** section. Depending on the settings per access link, users can create or delete folders in the File Browser and upload and/or download data.<br/>
   ![Alt](duma_6.png "Title")
 
 
-
-4. Clicking **Upload** or **Download** will launch the **IBM Aspera Connect** client on your computer. You first will be asked whether you allow the client to connect to aspera.lcsb.uni.lu. Choose **Allow**. <br/>
-  ![Alt](duma_7.png "Title")
+4. Clicking **Upload** or **Download** will launch the **IBM Aspera Connect** client on your computer. You first will be asked whether you allow the client to connect to aspera.lcsb.uni.lu. Choose **Allow**.
 
 
 
@@ -63,63 +53,21 @@ In the following steps we provide instructions on how to use DUMA web interface.
 
 6. All data are encrypted on server side and they stay encrypted also upon download. For decryption, you have to navigate into your **IBM Aspera Connect** window and click "**Unlock encrypted files**". <br/>
   ![Alt](duma_9.png "Title") <br/>
-You will be prompted for encryption passphrase which you should already have received from the repository administrator. <br/>
+You will be prompted for encryption passphrase which is present on the file browser. <br/>
   ![Alt](duma_10.png "Title") <br/>
 Encrypted files are by default kept on your disc after decryption. If you want to change this behaviour, navigate to Options->Settings and check "Delete encrypted files when finished" box.
 
 
+7. You can also navigate to the help section on the top right of the browser. It contains information and links to get support.
 
-<a name="DUMA_CLI"></a>
-## Accessing DUMA via Command-Line Tool
-In the following steps we describe instructions on how to use DUMA web interface.
-
-1. **Install the aspera command line client.** The _ascp_ tool, which can be found [here](https://downloads.asperasoft.com/en/downloads/62) as instructed.
-
-1. **Obtain tokens.** You will need **tokens** while using _ascp_. You will need a **download token** for download and a separate **upload token** for upload. Your tokens can be viewed by clicking the **Help** icon on your access link (see below).<br/>
-     ![Alt](duma_help_link.png "Title") <br/><br/><br/>
-     ![Alt](duma_cli_tokens.png "Title")
-
-1. **Obtain encryption passphrase.** You should receive corresponding passphrase from repository administrator.
-
-1. **Obtain SSH key.** You will also need an **SSH private key** to authenticate. This is the Aspera key that comes with the Aspera Connect installation named `asperaweb_id_dsa.openssh`. Below are locations where the ssh_key can be found:
-
-
-    * On MAC
-	  * Local installation of Aspera connect:
-	    * `/Users/username/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.openssh`
-	  * System wide installation of Connect:
-	    * `/Applications/Aspera  Connect.app/Contents/Resources/asperaweb_id_dsa.openssh` 	
-
-    * On WINDOWS
-	  * Local installation of Aspera connect:
-	    * `C:\\Users\username\AppData\Local\Programs\Aspera\Aspera Connect\etc\asperaweb_id_dsa.openssh` 	
-	  * System wide installation of Connect:
-	    * `C:\\Program Files (x86)\Aspera\Aspera Connect\etc\asperaweb_id_dsa.openssh`
-
-    * On LINUX
-	  * Local installation of Aspera connect:
-	    * `/home/username/.aspera/connect/etc/asperaweb_id_dsa.openssh` 	
-	  * System wide installation of Connect:
-	    * `/opt/aspera/etc/asperaweb_id_dsa.openssh`
-
-1. **Set necessary environment variables**.  `KEY` and `TOKEN` environment variables should be set as follows. If you do not have any of the tokens use `None` as the value.
-
-	* `KEY=<path to the ssh key>`
-	* `DTOKEN=<<<<YOUR DOWNLOAD TOKEN>>>>>>`
-	* `UTOKEN=<<<<YOUR UPLOAD TOKEN>>>>>>`
-	* `export ASPERA_SCP_FILEPASS=<<<<<YOUR ENCRYPTION PASSPHRASE>>>>>`
+<a name="ASPERAWEB_CLI"></a>
+## Accessing AsperaWEB via Command-Line Tool
 
-1. **Run the relevant _ascp_ commands**.
 
+Go to the help section of your access link 
 
-     * Upload:
-		* To upload all *png* files to the root of the share:
-		  * `ascp -d -i $KEY -P 33001 --file-crypt=encrypt -W $UTOKEN *.png app_duma_public_read@aspera.lcsb.uni.lu:/`
-		* To upload *document.txt* to a subfolder:
-		  * `ascp -d -i $KEY -P 33001 --file-crypt=encrypt -W $UTOKEN document.txt app_duma_public_read@aspera.lcsb.uni.lu:/subfolder`
-	 * Download:
-		* To download *subfolder* and all it's content to the current directory:
-		  * `ascp -d -i $KEY -P 33001 --file-crypt=decrypt -W $DTOKEN app_duma_public_read@aspera.lcsb.uni.lu:subfolder`
+<br/> ![Alt](duma_help_link.png "Title") <br/><br/><br/>
 
+And follow the steps in the **Using the command line** section.
 
-You can find more information also on the [Aspera website](https://downloads.asperasoft.com/en/documentation/62).
+<br/> ![Alt](duma_cli_tokens.png "Title") <br/><br/><br/>
\ No newline at end of file

external/exchange-channels/owncloud.md

@@ -6,7 +6,7 @@
 
 ## Obtaining a LUMS account
 
-A LUMS (LCSB User Management System) account is needed in order to use LCSB ownCloud. LUMS accounts for LCSB staff are normally created within the first few days of starting work at the LCSB. In addition to staff, researchers at Partner Institutes may be given LUMS accounts. If you want to create a LUMS account, or require support, you should contact [LCSB admin team](lcsb-sysadmins@uni.lu).
+A LUMS (LCSB User Management System) account is needed in order to use LCSB ownCloud. LUMS accounts for LCSB staff are normally created within the first few days of starting work at the LCSB. In addition to staff, researchers at Partner Institutes may be given LUMS accounts. If you want to create a LUMS account, or require support, you should contact [LCSB admin team](mailto:lcsb-sysadmins@uni.lu).
 
 ## Using LCSB ownCloud
 
@@ -35,4 +35,3 @@ When sharing research data, one should observe the following guidance using Ownc
  **IMPORTANT NOTE: Whenever the LCSB shares an ownCloud folder with you (collaborator), the share password will be reachable via link, which will expire. Therefore you should make a record of your password once you view it.**
 
  
-