Provide documentation for raw data upload by external submitters (#46)

* Provide documentation on how to request access and upload data as an external data submitter.
# Co-authored-by: KochTobi <[email protected]>

* Fix missing images and renaming

* Streamline documentation and fix minor mistakes

* Update What's new Section

* Slim Update Title

* Typo

Author: Steffengreiner

docs/get_started/process_overview.md

@@ -5,6 +5,6 @@
 3. Specify the [experimental design](../experiment/experiment_introduction.md)
 4. Register [Sample Batches](../batch/sample-batch.md)
 5. Specify the performed [measurements](../measurement/measurement_introduction.md)
-6. Upload your [raw data](../rawdata/raw_data_upload.md).
+6. Upload your [raw data](../rawdata/raw_data_request_server_access.md).
 7. Fine tune the accessibility of your project to [collaborators](../project/project_access.md)!
 8. Share your measurement data [easily](../rawdata/raw_data_download.md)

docs/index.md

@@ -6,11 +6,25 @@ the [Data Manager](https://rdm.qbic.uni-tuebingen.de/login) platform early on in
 
 ## What's new?
 
+### Data Submission from outside the University Tübingen network
+
+<div style="font-size: smaller; color: rgba(122,122,122,1)">October 10th, 2025 </div>
+
+- External Data Submission: Check out how
+  to [request access ](rawdata/raw_data_request_server_access.md)
+  and [submit your data](rawdata/raw_data_upload.md) from outside the University Tübingen network
+- Orcid Linkage documentation: Learn how to [link your orcid account](user/user_edit.md#link-orcid)
+  within the data manager
+
+## Update history
+
 ### Orcid Linkage and Template Registration Overhaul
 
 <div style="font-size: smaller; color: rgba(122,122,122,1)">September 18th, 2025 </div>
 
-📌 Checkout the complete [release notes](https://github.com/qbicsoftware/data-manager-app/releases/tag/1.11.0) on GitHub.
+📌 Checkout the
+complete [release notes](https://github.com/qbicsoftware/data-manager-app/releases/tag/1.11.0) on
+GitHub.
 
 💡 Highlights:
 
@@ -30,16 +44,13 @@ the [Data Manager](https://rdm.qbic.uni-tuebingen.de/login) platform early on in
 - Download Urls for filtered raw data: Triggering the download of dataset URLS provides only the
   URLs of the filtered dataset
 
-## Update history
-
 ### Metadata Examples and Descriptions
 
 <div style="font-size: smaller; color: rgba(122,122,122,1)">September 18th, 2025 </div>
 
 - Glossary: Introduction of a glossary explaining the terms with example values in the research data
   management documentation. Check it out [here](metadata/concepts.md)
 
-
 ### Enable Asynchronous Sample and Experiment Update
 
 <div style="font-size: smaller; color: rgba(122,122,122,1)">June 10th, 2025 </div>

docs/metadata/concepts.md

@@ -269,7 +269,7 @@ registration [template sheet](templates/proteomics_measurement_registration_shee
 
 ### Raw Data
 
-Visit our documentation to find out how to [upload](../rawdata/raw_data_upload.md)
+Visit our documentation to find out how to [upload](../rawdata/raw_data_request_server_access.md)
 or [download](../rawdata/raw_data_download.md) your raw data.
 
 The following concepts are associated with a raw data dataset.

docs/rawdata/images/upload/raw_data_upload_site_manager_submitter_credential_fields.png

@@ -1,6 +1,6 @@
 # Raw Data Introduction
 
-The raw data summary view shows detailed information about the raw data already [registered](raw_data_upload.md) for the measurements within your experiment.
+The raw data summary view shows detailed information about the raw data already [registered](raw_data_request_server_access.md) for the measurements within your experiment.
 Additionally, it enables you to generate the [URLs](#raw-data-url-generation) necessary
 to start the command line based [raw data download](#download-raw-data). 
 

docs/rawdata/raw_data_download.md

@@ -0,0 +1,88 @@
+# Request Server Access
+
+This section gives an overview on how to request access to our upload server to submit data from outside of the University Tübingen network.
+
+!!! tip
+    Should you be a member of the university of Tübingen you can immediately [upload your data](raw_data_upload.md) and skip this process.
+
+## Prerequisites
+
+- An `ed25519` encrypted public and private keypair on the connecting machine
+- The static and public `IPv4` address of the connecting machine
+- The name and affiliation of the data submitting party
+
+## Procedure
+
+To minimize security risk, access to our upload server is restricted to temporary whitelisted IP addresses from outside of the university network.
+!!! note
+    Please make sure to provide a **public** and **static** IP address from the machine you want to connect from.
+    Check with your IT department on details on how to obtain such an IP address.
+
+As an additional security layer, data submitters have to authenticate using [strong cryptographic keys](#generate-cryptographic-keys).
+Once these technical details are resolved, feel free to contact us to [request access to our server](#get-in-contact)
+
+### Generate Cryptographic Keys
+
+For account creation a public key is required. Please generate an ssh keypair via your system specific command and make sure to specify your email address:
+
+=== "Linux"
+
+    Open your terminal
+    ``` bash
+    ssh-keygen -t ed25519 -a 420 -f ~/.ssh/qbic-upload.ed25519 -C "<[email protected]>"
+    ```
+
+=== "MacOS"
+
+    Open Terminal [as described by Apple](https://support.apple.com/guide/terminal/open-or-quit-terminal-apd5265185d-f365-44cb-8b09-71a064a42125/mac)
+    ``` bash
+    ssh-keygen -t ed25519 -a 420 -f ~/.ssh/qbic-upload.ed25519 -C "<[email protected]>"
+    ```
+
+=== "Windows"
+
+    Open PowerShell [as described by Microsoft](https://learn.microsoft.com/en-us/powershell/scripting/windows-powershell/starting-windows-powershell?view=powershell-7.5#run-from-the-start-menu)
+    ``` bash
+    ssh-keygen -t ed25519 -a 420 -f $HOME/.ssh/qbic-upload.ed25519 -C "<[email protected]>"
+    ```
+
+with the name `qbic-upload.ed25519` and a public key named `qbic-upload.ed25519.pub` within your `.ssh` directory.
+
+### Get in Contact
+
+After you have [generated your ssh key](#generate-cryptographic-keys) and setup a public static IP address, 
+please write an email to [[email protected]](mailto:[email protected]) and attach the public (.pub) key file similar to the provided template:
+
+!!! warning 
+    Make sure you **only** send us the public key file ending with .pub 
+
+    **Do not send us the private key!**
+
+```txt
+Dear QBiC Team
+
+I would like to upload measurement data to your data manager. 
+Can you please provide me with an account on your upload server. 
+
+Below you can find the requested information
+
+Name: <Max Mustermann>
+E-Mail: <[email protected]>
+Affiliation: <My Research Institute>, <https://ror.org/03a1kwz48>
+Project: <Q2EXAMPLE>
+Access Duration: 30 days
+
+IP-Address: <Your static public IPV4 Adress>
+For accessing your upload server I would like to use the attached key.
+
+Attachments: qbic-upload.ed25519.pub
+```
+
+### Wait for a reply
+After you have [established contact](#get-in-contact) with our support team, 
+we will create an account for you on our upload server and contact you with confirmation and your assigned username.
+
+!!! note 
+    Please note down the username as this will be the username you will use to connect to our upload server.
+
+### Proceed by [uploading data](raw_data_upload.md)

docs/rawdata/raw_data_request_server_access.md

@@ -3,16 +3,26 @@
 After creating measurements in the Data Manager, you can upload measured data to our platform.
 This section gives an overview on how to upload data to measurements from QBiC's Data Manager.
 
+!!! info
+    If you are not a member of the University of Tübingen, please [request access as a data submitter](raw_data_request_server_access.md) 
+
 ## Prerequisites
 
-The following is required in order to successfully execute the measurement data upload.
+The following is required in order to successfully execute the measurement data upload dependent on your affiliation.
+
+=== "University Tübingen member"
+    - A connection to the University Of Tübingen network (
+    e.g. [using the University VPN](https://uni-tuebingen.de/en/facilities/zentrum-fuer-datenverarbeitung/services/network-services/network-access/remote-access-vpn/))
+    - An LDAP account of the University Of Tübingen
+    - Access to the project of interest
+    - OpenSSH package or a SFTP **client** software (e.g. [FileZilla](https://filezilla-project.org/download.php?type=client)
+    or [WinSCP](https://winscp.net))
 
-- A connection to the University Of Tübingen network (
-  e.g. [using the University VPN](https://uni-tuebingen.de/en/facilities/zentrum-fuer-datenverarbeitung/services/network-services/network-access/remote-access-vpn/))
-- An LDAP account of the University Of Tübingen
-- Access to the project of interest
-- OpenSSH package or a SFTP **client** software (e.g. [FileZilla](https://filezilla-project.org/download.php?type=client)
-  or [WinSCP](https://winscp.net))
+=== "External data submitter"
+    - [Granted access and authorization to our upload server](raw_data_request_server_access.md)
+    - Access to the project of interest
+    - OpenSSH package or a SFTP **client** software (e.g. [FileZilla](https://filezilla-project.org/download.php?type=client)
+    or [WinSCP](https://winscp.net))
 
 ## Process Overview
 
@@ -132,10 +142,19 @@ measurement data registration, select `SFTP - SSH File Transfer Protocol` and
 enter `upload.qbic.uni-tuebingen.de` into the `Host` field.
 ![An image showing the users site manager highlighting the host and connection field](images/upload/raw_data_upload_site_manager_host-fields.png){.screenshot}
 
-You can log in with your _University of Tübingen_ credentials. Enter your university user account
-into the `User` field.
-![An image showing the users site manager highlighting the user and password field](images/upload/raw_data_upload_site_manager_credential-fields.png){.screenshot}
-**Connect to the server:** Make sure you are in the network of the _University of Tübingen_. You can connect to the server by pressing `Connect` in
+Afterwards, choose the affiliation dependent login method to connect to our upload server. 
+
+=== "University Tübingen member"
+    Login with your _University of Tübingen_ credentials. Enter your university provided username
+    into the `User` field.
+    ![An image showing the users site manager highlighting the user and password field](images/upload/raw_data_upload_site_manager_credential-fields.png){.screenshot}
+
+=== "External data submitter"
+    Login with your username and key file. Enter your username
+    into the `User` field and select your private key file from within your local `.ssh` directory by pressing the browse button.
+    ![An image showing the users site manager highlighting the user field](images/upload/raw_data_upload_site_manager_submitter_credential_fields.png){.screenshot}
+
+**Connect to the server:** You can connect to the server by pressing `Connect` in
 the _Site Manager_. After connecting to the server, _FileZilla_ shows you the contents of your home directory on the server side.
 ![An image showing the users home folder. You can see three directories named registration, error and upload.](images/upload/raw_data_upload_remote_filesystem.png){.screenshot}
 !!! warning
@@ -165,38 +184,43 @@ The OpenSSH SFTP program is supported natively by most operating systems.
 In this section we will go through the process of connecting to our server
 using the [OpenSSH SFTP](https://man.openbsd.org/sftp) program.
 
+!!! note
+    This section requires commandline knowledge within your operating system.
+    We recommend to get in contact with your local IT department should you need assistance
+    or upload your data via a [dedicated sftp client](#upload-your-dataset-via-sftp-client)
+
 ### Install OpenSSH SFTP
 
 #### Linux/Mac
 Linux and Mac systems do typically have the OpenSSH package containing SFTP pre-installed.
 Should this not be the case, try to install the openSSH package with the package manager employed by your system.
-We recommend to get in contact with your local IT department should you need assistance.
 
 #### Windows
 Newer Windows Versions (Windows10 version 1803 and newer and Windows 11) do typically have the OpenSSH package containing SFTP preinstalled.
-Should this not be the case, check your system settings to see if the **OpenSSH server feature** is installed within the windows optional features. 
-We recommend to get in contact with your local IT department should you need assistance.
+Should this not be the case, check your system settings to see if the **OpenSSH server feature** is installed within the windows optional features.
 
 ### Connect and upload your dataset 
 
-!!! note
-    This section requires basic command line knowledge of your operating system. 
+!!! tip
+
     Check the OpenSSH sftp [manpage](https://man.openbsd.org/sftp) for information on how to use the sftp program.
 
 Start by opening the command line within your operating system of choice. 
 Next navigate to the local working directory containing the dataset you wish to upload.
-From within this directory connect to our upload server with the **sftp** command, replacing <your-user> with your university account credentials:
+From within this directory connect to our upload server with the **sftp** command, replacing <your-user> with your university account credentials 
+or tbe username granted to you after [requesting access](raw_data_request_server_access.md) to our upload server from outside the university network:
 
-``` bash
-sftp <your-user>@upload.qbic.uni-tuebingen.de
-```
-Upon successful connection you will be prompted for your university account password.
+=== "External Data Submitter"
+    ``` bash
+    sftp -i <your private key file> <username>@upload.qbic.uni-tuebingen.de
+    ```
 
-!!! Warning
-    Keep in mind that you need to be within the university network and 
-    have a valid university account to connect to our upload server 
+=== "University Tübingen Member"
+    ``` bash
+    sftp <username>@upload.qbic.uni-tuebingen.de
+    ```
 
-If everything goes well, you'll be connected to the remote working directory within our upload server.
+If everything goes well, you'll be connected to your remote home directory within our upload server.
 You can check out the directory structure of this directory with the following **ls** command:
 
 ``` bash