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Upload Data

After creating measurements in the data manager, you can upload measured data to our platform. This section gives an overview of how to upload data to measurements from QBiC's data manager.

Prerequisites

The following is required in order to successfully execute the measurement data upload.

  • Access to the project of interest
  • A SFTP client software (e.g. FileZilla or WinSCP)
  • A LDAP account of the University Of Tübingen
  • A connection to the University Of Tübingen network ( e.g. using the University VPN)

Process Overview

graph LR
  A(Prepare your data 
  📝) --> B(Upload your data
  ⇧)
  B --> D{{Data upload successful?}}
  D -- No --> A
  D --> F("Well Done 
  👍")

Connect to the SFTP server

Uploading your files to us was never this easy! SFTP is a broadly used file transfer protocol. The wide-spread use ensures that there exists many client software products that support uploading files to us. In this section we will go through the process of connecting to our server using the FileZilla client as an example.

Open the Site Manager: You need to add the QBiC's upload server as a site to FileZilla within its site manager. To open the site manager select it from the menu or press on the highlighted icon. An image showing the button leading to the site manager

Add the upload server: In the Site Manager you can add sites to which you want to connect. For 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

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 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 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.

Warning

When you first log in, the server will create some folders. Do not delete these folders!

Prepare your data for upload

You need to prepare your data for us to know to which measurement to attach it. Uploading data to a measurement is called data registration in the following section. Folders with a given structure that are moved into the registration folder, are automatically registered in our system. For every registration task, the data needs to reside in a folder with the following structure:

|- my-registration-batch  // folder name is irrelevant
 |- metadata.txt  // mandatory!
 |- file1_1.fastq.gz // all files except for metadata.txt serve as examples
 |- file1_2.fastq
 |- report.pdf
 |- summary.html

Warning

Ensure that the uploaded folder name and files do not have a whitespace within their name

You can upload folders in the same way. Everything at the top level of your created folder is considered. For uploading folders, specify the name of the folder instead of a file name. Uploading only specific files from a subdirectory is not supported at the moment.

To register a folder the data needs to reside in a folder with the following structure:

|- upload-example  // folder name is irrelevant
 |- metadata.txt  // mandatory!
 |- my-registration-batch/

The metadata.txt file for the folder example would look like this: 

NGSQTN23015AS-1225978199074484 my-registration-batch

The folder my-registration-batch represents an atomic registration unit and must contain the metadata.txt with information about the measurements identifier and the files belonging to this measurement dataset. One registration task can register data for multiple measurements. The metadata.txt file for the previous example would look like this:

NGSQTN23015AS-1225978199074484  file1_1.fastq.gz
NGSQTN23015AS-1225978199074484  file1_2.fastq
NGSQTN23015AS-1225978199074484  report.pdf
NGSQTN23015AS-1225978199074484  summary.html

Note

Ensure that measurement identifier and filename are separated by a TAB \t character and not by spaces.

Upload your data

Once you have prepared your folder, upload it to your user directory on our server. Please do not upload directly to the registration folder but stage it instead in your user directory. Once your folder is prepared and uploaded to upload.qbic.uni-tuebingen.de, move it to the registration folder.

Tip

You can easily drag and drop the folder via your mouse from your local filesystem to our server within filezilla

Our system will then transfer the folder and proceed with data registration.

Success

Congratulations you have uploaded your data!

Finally, you can view summarized information for your uploaded data within the raw data view of the data manager. raw_data_upload_shown_in_view.png

Handle failed uploads

Uploading data to a measurement can fail in certain cases. When an upload fails, a folder is created in /home/<your-user>/error. An image showing the error folder. It contains a directory with a long name. In this new folder, you can find an error.txt file describing the error, and the data you tried to upload. You can then try to fix the error. To retry the upload of the fixed folder, move it to the registration folder again.