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.

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

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

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.

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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.

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Exports

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

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    1. Import Compatible:

      1. 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.

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

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2. Columns:

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

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

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3. Rows:

        1. All Pages. All pages of the table are exported.

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

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

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4. Value:

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

      2. Rich Text. Text fields are exported in HTML format.

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Tables are exported to XLS format. Exported tables can be used for updates via the XLS Batch Update Objects.

Note: Excel has a character limit of 32767 characters in each cell. If you export entries where a field exceeds this limit, you get a warning and the exported Excel file will not contain the content of the cell which is above this limit and the cell is highlighted in red, as shown below.

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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.

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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.

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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.

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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 existing Collection/Experiment or to a new one.

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

  • Update custom barcodes/QR codes: allows to update existing custom barcodes of the selected entries.

  • Clear selection: allows to clear the selection made.

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

  1. Upload a file to the Object

  2. Move the Object to another exiting Experiment/Collection.

  3. Update Barcode/QR code.

  4. Open the hierarchy graph. This is the graph showing parent/child connections of the Object.

  5. Open the hierarchy table. This is the table showing parent/child connections of the Object.

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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.

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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.

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

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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.

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Visualize Available Storage Space

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

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

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.

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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.

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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.

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To freeze one or several entities, you need to provide your login password and save.

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

  1. 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 Utilities in the main menu.

The available custom imports can be selected from the Custom Import Service drop down menu in the Custom Import page (see below).

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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.

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

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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.

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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.

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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.

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History table for Objects

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

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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.

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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

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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:

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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 navigation menu.

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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.