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Data Upload


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

First the Experiment/Object must be registered in the database, and then Datasets can be added to it. Data can be uploaded via the web user interface or via dropbox mechanism, as explained below.

Upload via web interface

 

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

 

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 Uploader area or browse for files.

5. When uploading a zip file, users have the option to uncompress before import.

6. Save

 

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.zip folder-name  -x “*.DS_Store”
  2. Use an external archiver (e.g. Stuffit Deluxe).


Upload via dropbox


Web upload 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

   Folder 2

         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. 

Folder 2 can be named as wished by the user.

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

Place the correctly named Folder 1 containing your data in the eln-lims-dropbox folder. openBIS continuously monitors this folder and when data are placed here, they are moved to the final storage.