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Batch register entries in a Collection

 

It is possible to register several samples at once via file upload. Two methods are currently available:

  1. Batch registration via Excel template file (XLS Batch Register Objects)
  2. Batch registration via TSV template file (Batch Register Objects)

 

 

Batch registration via Excel template file 

 

To register several entries of the same type with an Excel file:

  1. Navigate to the relevant collection (e.g. Samples).
  2. Select XLS Batch Register Objects from the More drop-down menu (see figure above)
  3. Download the template file and fill in the relevant information. (Example file: SAMPLE-COLLECTION-REGISTRATION-SAMPLE-STORAGE_POSITION-template)
  4. Upload the file.

 

Controlled vocabularies

 

For Controlled Vocabularies fields, i.e. fields with a drop down menu, you can enter either the code or the label of the terms in the Excel file.

Please note that codes are not case-sensitive, but labels are.

Codes and labels of vocabulary terms can be seen under Utilities -> Vocabulary Browser.

 

Registration of parents

 

In the Parents column of the Excel file, you can set parents of the objects you are uploading, by using their identifier (/SPACE code/PROJECT code/OBJECT code). If you want to add multiple parents to one Object, every identifier should be in a new line in the corresponding Excel cell. A new line in an Excel cell is entered with the keyboard shortcuts Alt + Enter.

Example file: SAMPLE-COLLECTION-REGISTRATION-ANTIBODY-STORAGE_POSITION-template

 

 Note: no other separators (e.g “,” or  “;”) should be used, otherwise an error will be thrown.

 

Register storage positions and samples in the same XLS file

 

A sample and its storage position can be registered together, as shown in the template provided above:

 

  • The info in the $ column of the sample spreadsheet should match the Parents column in Storage Positions spreadsheet. In the $ column you can enter numbers or names.

 

Batch registration via TSV template file

 

  1. Select Batch Register Objects from the More drop-down menu
  2. Select the Object type (E.g. Sample or Storage)
  3. Download the template file and fill in the relevant information
  4. Upload the file

 

Rules to follow to fill in the template .tsv file

 

  1. Identifiers:
    1. Identifiers are given by /SPACE/PROJECT/OBJECT_CODE, e.g /MATERIALS/EQUIPMENT/INS1. Users can provide their own identifiers, or these can be automatically generated by openBIS.
    2. To have identifiers automatically generated by openBIS, completely remove the identifier column from the file.
  2. Lists. In fields that have lists to choose from (called Controlled Vocabularies), the code of the term needs to be entered. Term codes can be seen under Utilities -> Vocabulary Browser.
  3. Parents. Use the following syntax to enter parents: identifier1, identifier2, identifier3.
  4. Parents annotations. Use the following syntax to annotate parents: identifier:xxx;COMMENTS:xxxx\identifier:yyy;COMMENTS:yyyy. Where COMMENTS is the property used for the annotation in this case (to be replaced with the actual property used).

 

Advantages of XLS batch registration vs the old batch registration

 

  1. XLS batch registration uses labels instead of codes in the column headers in the template file.
  2. Fields which are Controlled Vocabularies can use labels instead of codes.
  3. The template can be used as it is, and no modifications are necessary by removing the identifier column, as it was in case of the old batch registration.
  4. Upload of samples and storage positions can now be performed using single template file. 

 

The old batch register mode is being maintained for backward compatibility and will be phased out.