Additional Functionalities

Visualise Relationships

Parent-child relationships between Objects can be visualised as trees or tables in the ELN.

To see the genealogical tree, select the Hierarchy Graph option from the More… dropdown in an Object form.

Large trees can be pruned, by selecting how many levels of parents and/or children and which types to show.

To view the genealogy of an Object in a tabular format, select the Hierarchy Table option from the More… dropdown.

Copy Objects

To create a copy of an existing entry, select Copy from the More.. drop down menu in the Object page.

When an Object is copied, the user has the following options:

• Copy Comments Log: If the comments log is available in the Object being copied, the user can choose whether to copy this or not.

• Link Parents: the copied Object will keep the links to the parents present in the orginal Object.

• Children:

  • Do NOT Copy or Link: children are not copied nor linked.

  • Link: the copied Object will keep the links to the children present in the orginal Object.

  • Copy into parents collection: children present in the original Object are copied into the same entity (Space, Project, Collection) the Object belongs to and will be linked to the copied Object.

All these options are disabled by default.

Objects are always copied in the entity they belong to (Space, Project, Collection). After copying, you can move entries to a different entity.

Move Objects

Objects can be moved from one entity to another, either from the Object form or from a Collection table, if they belong to a Collection.

Move from entry form

To move Objects to a different entity, select Move from the More… drop down menu in the Object form.

You have the option to move to an existing entity (Space, Project, Collection)

or to move to a new Collection.

Move from Collection Table

It is also possible to move Objects beloging to Collections from Collection tables. You can select one or multiple entries from a table and click on the Move button.

Also in this case you can move to an existing entity or create a new Collection.

Templates

It is possible to have templates for given Object types in openBIS. Templates have prefilled values. This is useful when performing repetitive tasks, where some fields are always the same, or would require only minor changes.

Templates need to be crated by the lab manager in the ELN Settings. If templates have been created for a given Object type, you can choose from the list of available templates by clicking the Template button on the Object form, as shown below.

If the template you use contains predefined Parents/Children and you alreday have some parents/children defined in your Object that you wish to preserve, you should leave the option “Merge current parents/children” selected. This can happen for example in the Lab Notebook, when you register one Object starting from another Object and a parent/child relationship is automatically created. See Lab Notebook.

Browse Entries by Type

The Object Browser under the Tools main menu allows to see all entities of the same type, which may be contained in different Spaces, Projects, Experiments/Collections.

From the Object Browser page, it is also possible to Batch register or Batch update Objects using an XLS or TSV template.

Print PDF

For every entity in openBIS it is possible to generate a pdf using the Print PDF option from the More.. dropdown menu.

The generated pdf file can be printed or downloaded from the browser.

An example for a Space is shown in the picture below.

Trashcan

When Experiments, Objects and Datasets are deleted, they are moved to the openBIS trashcan, under the Utilities menu in the Tools tab. Items can be removed from the trashcan only by someone with Space admin or Instance admin role. Deletion from the trashcan is IRREVERSIBLE.

Note: Spaces and Projects are directly permanently deleted, they are not moved to the trashcan first.

To empty the whole trashcan, click the blue Empty Trash button above the table.

To delete permanently single entries choose one of two options from the Operations dropdown:

• delete permanently: deletes permanently only the selected entry.

• delete permanently (including dependent deletions): if the selected entry had children which are also in the trashcan, this option allows to permanently delete both the entry and its children.

If one entity was unintentionally deleted, the operation can be reverted at this stage by choosing the Revert Deletions option from the Operations drop down in the table.

Visualize Available Storage Space

The storage space available in an openBIS instance can be visualized by navigating to Other Tools in the menu under the Tools tab and clicking on the Show available storage space button.

Before uploading large datasets, the available storage space should always be checked.

Vocabulary Browser

The Vocabulary browser is accessible from the Utilities menu under the Tools tab. This shows all controlled vocabularies registered in openBIS and the terms they contain. Vocabularies are predefined lists of values to choose from in given fields. Vocabularies can be created/modified by an openBIS Instance admin (see New Entity Type Registration).

This information is needed for filling the forms for Batch Upload orBatch Update of Objects via TSV file. If an Object has a property of type Controlled Vocabulary, the codes of the vocabulary have to be entered in the .tsv template file. This is not the case for XLS Batch registration or update, where labels can be used.

Freeze Entities

Each level of the openBIS hierarchy (Space, Project, Experiment/Collection, Object, Dataset) can be frozen, so it can be no longer edited and/or deleted.

At every level, everything contained underneath is selected by default to be frozen. E.g. if I choose to freeze a Space, everything contained in the Space is automatically selected to be frozen. Single entities can be manually unselected.

A Space admin role is necessary to freeze entities in a given Space.

IMPORTANT: the freezing is IRREVERSIBLE!

This operation cannot be undone from any UI, not even by an Instance admin. Please freeze entities only when you are absolutely sure that they should not be further modified!

How to freeze an entity

At each level of the openBIS hierarchy (Space, Project, Experiment/Collection, Object, Dataset) the Freeze Entity option is available under the More.. dropdown menu. See the example for a Space below.

If you select this, a list of entities contained or connected to the one selected will be presented to you, as shown below. By default everything is selected, so you need to unselect entries that you do not want to freeze.

To freeze one or several entities, you need to enter the result of The operation presented in the widget.

Rules for freezing

1. Freeze Space only

	Allowed	Not allowed
Create new Project		x
Create new Experiment/Collection	x
Create new Object		x
Create new Dataset in existing Experiment/Collection	x
Create new Dataset in existing Object	x
Edit existing Project	x
Edit existing Experiment/Collection	x
Edit existing Object	x
Edit existing Dataset	x
Delete Space		x
Delete Project		x
Delete Experiment/Collection	x
Delete Object	x
Delete Dataset	x
Move Experiment/Collection	x
Move Object	x
Copy Object		x
Export	x

2. Freeze Project only

	Allowed	Not allowed
Create new Experiment/Collection		x
Create new Object		x
Create new Dataset in existing Experiment/Collection	x
Create new Dataset in existing Object	x
Edit Project		x
Edit existing Experiment/Collection	x
Edit existing Object	x
Edit existing Dataset	x
Delete Project		x
Delete Experiment/Collection		x
Delete Object		x
Delete Dataset		x
Move Experiment/Collection		x
Move Object		x
Copy Object		x
Export	x

3. Freeze Experiment/Collection only

	Allowed	Not allowed
Create new Object		x
Create new Dataset in existing Experiment/Collection		x
Create new Dataset in existing Object		x
Edit existing Experiment/Collection		x
Edit existing Object	x
Edit existing Dataset	x
Delete Experiment/Collection		x
Delete Object		x
Delete Dataset		x
Move Experiment/Collection		x
Move Object		x
Copy Object		x
Export	x

4. Freeze Object only

	Allowed	Not allowed
Create new Dataset in existing Object		x
Edit existing Object		x
Edit existing Dataset in Object	x
Delete Object		x
Delete Dataset		x
Move Object		x
Copy Object	x (only if the Experiment is not frozen)
Export	x

5. Freeze Dataset only

	Allowed	Not allowed
Edit existing Dataset		x
Delete Dataset		x
Move Dataset		x
Export	x

Custom Imports

From openBIS version 20.10.4, Custom Imports, previously available only in the core UI, are available in the ELN UI.

Custom imports allow users to import metadata in a custom way, by using a dropbox script in the background. You can use this if you want to parse a file in a given format and import the information from this file as metadata in openBIS.

Custom imports are not available by default, but need to be enabled on the server side by a system admin, and a dropbox script needs to be associated with an import (see Custom Imports).

If one or more custom imports are configured in openBIS, the Custom Import option is available under the Tools in the navigation menu.

The available custom imports can be selected from the Custom Import Service drop down menu in the Custom Import page.   If the available custom import provides a template that can be used as input for the import, the template will be available to download from the Custom Import page.

If the custom import is not configured to provide a template, no download link is shown in the Custom Import page.

Entity history

Whenever an entity of type Collection/Experiment, Object or Dataset is modified in openBIS, the changes are stored in the database. The stored changes are modifications to property fields, addition and deletion of parents/children for Objects and Datasets, changes of Space/Project/Experiment/Object ownership if an entity is moved.

The History of changes of each entity is now available in the ELN UI. In versions prior to openBIS 20.10.3 this was only available in the core UI.

History table for Collections

In a Collection page, the History can be accessed from the More.. dropdown list.

The History table shows the version number of the changes, the author of the changes, the changes made (with the values before- in red, and after the change – in green), and the timestamp, i.e. the time when the changes were made.

For a Collection, the PermID (Permanent Identifier) of the Project it belongs to is shown. If a Collection is moved from one Project to another, the PermID of the old and new Projects are shown in the history table.

The show option in Full Document shows the full metadata of the entry (not only the changed fields) when changes were applied. This is displayed in JSON format.

History table for Objects

For every Object, the history of changes can be accessed from the More.. dropdown on the Object page.

For an Object, the PermID (Permanent Identifier) of the Collection it belongs to is shown. If an Object is moved from one Collection to another, the PermID of the old and new Collections are shown in the history table.

History table for Datasets

For every dataset, the history of changes can be accessed from the More.. dropdown on the Dataset page.

For a Dataset, the PermID (Permanent Identifier) of the Object/Collection it belongs to is shown. If a Dataset is moved from one Object/Collection to another, the PermID of the old and new Objects/Collections are shown in the history table.

Spreadsheet

The spreadsheet component needs to be enabled by a group admin or lab manager who can edit the ELN Settings, as described here: Enable Rich Text Editor or Spreadsheet Widgets

The spreadsheet supports some basic Excel functionalities, such as mathematical formulas (e.g. =SUM(A1+A2)). It is possible to import an openBIS Object into the spreadsheet, with the import button, on the spreadsheet itself:

Please note that if the Object is updated in openBIS, it will NOT be automatically updated in the spreadsheet.

Session Token

When users log in to openBIS, a session token is generated. The session token is visible in the ELN UI, under the User Profile, in the Tools navigation menu.

The session token is needed to connect to openBIS via pyBIS or obis, in cases where SSO (e.g. SWITCHaai) is used for authentication. See pyBIS.