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Data Access


Datasets are displayed on the left hand-side of the Experiment/Object form, as shown below.


To navigate and open data registered in openBIS via Finder or Explorer, open the Dataset folder and click on the drive icon next to the Dataset type name (see above). If SFTP has been configured by a system admin, you will be provided with a link to copy/paste in an application such as Cyberduck or other.

Please check our documentation for SFTP server configuration: Installation and Administrators Guide of the openBIS Data Store Server

 

For native access through Windows Explorer or Mac Finder we recommend the following:

 

 


Example of SFTP Net Drive connection:

1. open SFTP Net Drive and click on New:

 

2. Edit the drive with the following info, as shown below:

     a. Drive name: choose any name you want. Can be the same as your openBIS server, but does not have to be.

     b. Remote Host: the name of your openBIS. For example, if the url of your openBIS is https://openbis- demo.ethz.ch/openbis/webapp/eln-lims, then openbis-demo.ethz.ch is the name you want to enter.

    c. Remote port: enter 2222.

    d. Authentication type: Password (this is selected by default).

    e. Username: the username you use to login to openBIS.

    f. Password: the password you use to login to openBIS.

    g. Root folder on server: you can leave the default, User’s home folder.

    h. Press OK after filling in all the information above. 

 

 

3. After saving the drive, select it in the drivers’ window and click Connect.

 

3. openBIS will now appear as a drive in your Explorer window. Click on the ELN-LIMS folder and navigate to the folder containing the data you want to access.

 

 

Note: if you encounter the error message “SSH connection failed: Could not find a part of the path.” you can fix this by disabling the cache (Drives -> Advanced -> Enable Caching), and disabling log files. The error is caused by an attempt to create files in a folder not available to Windows.

 

 

Example of Cyber Duck configuration

 

Create a new connection in cyberduck:

  1. select SFTP (SSH File Transfer Protocol)
  2. Nickname: the name you want to use for the server
  3. Server: the name of the server you want to connect to. In the example below openbis-training.ethz.ch. Replace this with the name of your own openBIS server.
  4. Port: 2222 
  5. Username: this is the username with which you connect to your openBIS
  6. Password: this is the password you use to connect to your openBIS
  7. SSH private Key: none

 

Save the specifications and connect to the server.

You will see the folders of your own openBIS in the Cyberduck window and you can navigate to your data from there.

 

Example of  Dolphin File Manager configuration

To access the Dataset form and edit the Dataset metadata, click on the Dataset code or Name (if provided).

 

SFTP access via session token

To access via session token (for example when using SSO authentication) you need to provide the following credentials:

 

Username: ?

Password: session token.

 

The session token can be copied from the User Profile under Utilities in the main menu, as shown below.