additional-functionalities.md



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 entity 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.
Updated on March 4, 2022

Tables
All tables in the ELN have a similar format and functionalities. The
tables have been redesigned for the 20.10.3 release of openBIS.
Here we give an overview of the main functionalities of the tables.
 

Filters
Two filter options are available form the Filters button: Filter
Per Column and Global Filter. The first allows to filter on
individual columns, or multiple columns, whereas the second filters
terms across the entire table using the AND or OR operator. 


Sorting
It is possible to sort individual columns or also multiple columns. For
multi-column sorting, you should click on the column header and press
the Cmd keyboard key. The order of sorting is shown by a number in
each column, as shown below.
 

Exports
Tables can be exported in different ways, using the export button shown
below.


Import Compatible:


Yes: in this case some columns which are incompatible
with imports (i.e. registration date, registrator,
modification date, modifier) are not exported even if
selected; some columns that are required by openBIS for
imports are added to the exported file even if not
selected (i.e. code, identifier, $ column). Moreover text
fields are exported in HTML, to keep the formatting upon
import.

No: in this case all columns or selected columns are
exported.


2. Columns:


All (default order). All columns are exported, in
accordance with the selection explained above for import
compatibility.

Selected (shown order). Selected columns are exported,
in accordance with the selection explained above for
import compatibility.


 3. Rows:


All Pages. All pages of the table are exported.

Current Page. Only the currently visible page of
the table is exported.

Selected Rows. Only selected rows in the table are
exported.


4. Value:


Plain Text. Text fields are exported in plain text,
without any formatting. This option is not available if
the export is import-compatible.

Rich Text. Text fields are exported in HTML format.


Tables are exported to XLS format. Exported tables can be used for
updates via the XLS Batch Update Objects. 
 
 
Columns
Users can select which properties to display in the table clicking on
the Columns button. It is also possible to show all properties or
hide all properties. The position of the columns can also be changed by
placing the cursor next to the = sign in the list and moving the fields.
This information is stored in the database for each user.
 

Spreadsheets

If a table contains Objects which have a spreadsheet field which is
filled in, a spreadsheet icon is displayed in the table. Upon clicking
on the icon, the content of the spreadsheet can be expanded.  

 
Text fields
If a table contains Objects which have long text fields, only the
beginning of the text is shown and can be expanded. If the text contains
a picture or a table, an icon is shown in the table and the content of
the text becomes visible by clicking on the icon.

 
Selection of entries in table

Single entries in a table can be selected using the checkbox in the row.
By clicking the checkbox in the table header, all entries of the table
are selected. After selection of entries, some actions become available:


Delete: allows to move the selected entries to the trashcan.

Move: allows to move the selected entries to a different
Collection/Experiment.


Generate barcodes: allows to generate custom barcodes for the
selected entries.

Update custom barcodes: allows to update existing custom
barcodes of the selected entries.

Clear selection: allows to clear the selection made.


In Object tables inside Experiments/Collections there is an
Operations column, which allow users to perform certain tasks on an
Object:


Upload a file to the Object

Move the Object to another Experiment/Collection.
Update Barcode.
Open the hierarchy graph. This is the graph showing parent/child
connections of the Object.
Open the hierarchy table. This is the table showing parent/child
connections of the Object.


Updated on April 26, 2023

Browse Entries by Type
The Object Browser under the Utilities main menu allows to see
all entries of the same type and all Experimental Steps, which may be
contained in different Experiments/Collections and Projects. 

This is useful when there are entries of a certain type that belong to
different Collections (e.g. protocols of the same type stored in two
different protocol collections), or to have an overview of all
Experimental Steps, independently of the Experiment they belong to.
 

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

Updated on April 25, 2023

Trashcan
When Experiments, Objects and Datasets are deleted, they are moved
to the openBIS trashcan, under the Utilities main menu. 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.
 

Updated on October 9, 2022

Vocabulary Browser
The Vocabulary browser is accessible from the Utilities main
menu. 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.
 

Updated on April 25, 2023

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.