Data Upload

Data can be uploaded to Datasets in openBIS to Experiments and Objects (e.g., Experimental Steps). openBIS is agnostic of file formats and types.

Small data files can be uploaded via the web user interface, larger data files can be uploaded via dropbox mechanism.

Data upload via web UI

To upload data via the web interface:

1.Click the Upload button in the form, as shown below.

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2. Select the dataset type (e.g. Attachment).

3. Fill in the relevant fields in the form. It is advisable to always enter a Name, because this is shown in the menu. If the name is not provided, the dataset code is shown.

4. Drag and drop files in the Files Uploader area or browse for files.

5. When uploading a zip file, the option to uncompress before import will be presented in the form.

6. Save.

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Note for MacOS users: the default MacOS archiver generates hidden folders that become visible in openBIS upon unarchive. To avoid this there are two options:

  1. Zip using  the following command on the command-line: zip -r folder-name/\*  -x “\.DS\_Store”

  2. Use an external archiver (e.g. Stuffit Deluxe).

Updated on March 23, 2023

Data upload via dropbox

Web upload of data files is only suitable for files of limited size (few GB). To upload larger data, openBIS uses dropbox scripts that run in the background (see Dropboxes). A default dropbox script is provided with the openBIS ELN-LIMS plugin, and the dropbox folder needs to be set up by a system admin.

If this is available, users need to organise their data in a specific way:

Folder 1

Data (can be single files or folders)

Folder 1 needs to have a specific name that encodes the information of where the data should be uploaded to openBIS.

The name of Folder 1 can be generated from the ELN interface:

  1. From the page where you want to upload data, select Dataset upload helper tool for eln-lims dropbox from the More… dropdown and follow the instructions on screen.

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  1. Select:

    1. The dataset type from the list of available types (mandatory);

    2. Enter the name of your dataset (optional, but recommended);

    3. Copy the generated name of the folder using the copy to clipboard icon.

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3. In your finder/explorer, create a new folder and paste the name you copied from openBIS. Place your data in this folder.

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4. Place this folder containing your data inside the eln-lims-dropbox folder. openBIS continuously monitors this folder and when data are placed here, they are moved to the final storage. The move happens after a predefined (and customisable) inactivity period on the eln-lims-dropbox folder.

Dropbox with markerfile

In case of uploads of data >100GB we recommend to configure the eln-lims-dropbox-marker. The set up and configuration need to be done by a system admin. The process of data preparation is the same as described above, however in this case the data move to the openBIS final storage only starts when a markerfile is placed in the eln-lims-dropbox-marker folder. The marker file is an empty file with this name: .MARKER_is_finished_. Please note the “.” at the start of the name, which indicates that this is a hidden file. This file should also not have any extension. For example, if the folder to be uploaded has the following name:


The marker file should be named:


How to create the Marker file in Windows

You can create the Marker file in Windows using a text editor such as Editor. Any other text editor will  also work.

  1. open Editor.

  2. Save the file with a name such as .MARKER_is_finished_O+BARILLAC+PROJECT_1+EXP1+RAW_DATA+test.

  3. The file is automatically saved with a “.txt” extension. This needs to be removed.

  4. Use the Rename option to remove the extension from the file.

How to create the Marker file on Mac

If you are not familiar with the command line, you can create an empty text file using for example the TextEdit application in a Mac. Any other text editor will also work.

  1. Open the TextEdit application and save an empty file with a name such as .MARKER_is_finished_O+BARILLAC+PROJECT_1+EXP1+RAW_DATA+test.

  2. Save to any format.

  3. You will get a message to say that files starting with “.” are reserved for the system and will be hidden. Confirm that you want to use “.”

  4. To show these hidden files, open the Finder and press Command + Shift + . (period).

  5. The file you saved before has an extension, that needs to be removed. If the extension is not shown in your Finder, go to Finder

    Preferences menu, select the Advanced tab, and check the “Show all filename extensions” box.

  6. Remove the extension from the file.

Dropbox monitor

It is possible to check the status of the upload via dropbox using the Dropbox Monitor under Utilities in the main menu.

The Dropbox Monitor shows a table with all available dropboxes for a given openBIS instance. By default, default-dropbox, eln-lims-dropbox and eln-lims-dropbox-marker are shown.

If data are uploaded in a dropbox folder, users can see the status of the data upload in the table. A red face in the column Last Status indicates a failure of data import, a green face indicates successful data import.

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If you click on the row of the table above, you can see the details of every upload attempt for a given dropbox, as shown below. For failures, the log with the error is shown.

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Registration of metadata for datasets via dropbox

Starting from openBIS version 20.10.2, the default eln-lims dropbox supports the registration of metadata for datasets. The metadata needs to be provided in a file called metadata.json. This file should be placed inside the folder with the openBIS-generated name described above, together with the data. This is shown in the example below.


is the folder with the openBIS-generated name. Inside this folder there is the metadata.json file, and the data, which consists of a few files and 2 folders.

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For example, the metadata.json file for the default RAW_DATA dataset type would be:

{ “properties” :

{ “$NAME” : “my raw data”,

“NOTES” : “This is a test for metadata upload via dropbox” }


It is possible to download the template metadata.json file for each dataset type from the Other Tools section under the Utilities in the main menu.

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In Other Tools, there is also the Show available storage space button, which shows the available storage space on the openBIS instance. This is helpful in calculating how much space one might require for future data upload, especially large data.

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Updated on April 26, 2023