properties-handled-by-scripts.md

Properties Handled By Scripts

Introduction

One of the reasons why openBIS is easily extensible and adjustible is the concept of generic entities like samples, experiments, materials and data sets. By adding domain specific properties to the mentioned objects, instance administrator creates a data model specific to given field of study. Values of configured properties will be defined by the user upon creation or update of the entities (samples etc.).

In most cases values of properties must be provided directly by the user. The default way of handling a property in openBIS can be changed by instance admin defining a property that should be handled by a script written in Jython or Predeployed Plugin written in Java. Jython plugins use Jython version configured by the service.properties property jython-version which can be either 2.5 or 2.7.

Types of Scripts

There are two types of plugins that can be used for handling properties, and one script type to perform validations on entities:

1. Dynamic Property Evaluator (for properties referred to as Dynamic Properties)
   • for properties that can't be modified by users,
   • values of such properties will be evaluated automatically using metadata already stored in openBIS (e.g. values of other properties of the same entity or connected entities),
   • the script defines an expression or a function that returns a value for a Dynamic Property specified in the script
2. Managed Property Handler (for properties referred to as Managed Properties)

 

1. • for properties that will be indirectly modified by users,
   • the script alters default handling of a property by openBIS by defining functions that specify e.g.:
     • how the property should be displayed in entity detail view (e.g. as a table),
     • input fields for modifying the property,

    

   • • translation and/or validation of user input.

2. Entity Validation

   1. performed after each update or creation of a given entity type.
   2. the user provided script performs a validation, which can cancel the operation if the validation fails

Defining properties

To create a property that should be handled by a script perform the following steps.

1. Define a property type with appropriate name and data type (Administration->Property Types->New).
2. Define a script that will handle the property (Administration->Scripts) or deploy a Java plugin. For details and examples of usage go to pages:
   • Dynamic Properties
   • Managed Properties
   • Entity validation scripts
3. Assign the created property type to chosen entity type using the created script (e.g. for samples: Administration->Property Types->Assign to Sample Type):
   • select Handled By Script checkbox,
   • select the appropriate Script Type
   • choose the Script
4. The validation scripts are assigned to the type in the "Edit Type" section. (e.g Admin->Types->Samples. Select sample and click edit.)

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Dynamic Properties

Introduction

Dynamic Properties are one of two types of properties that use Jython scripts for providing special functionality to OpenBIS. To understand the basic concept read about Properties Handled By Scripts.

Defining dynamic properties

To create a dynamic property:

• Define a property type with appropriate name and data type (Admin->Plugins→Add Plugin)
  
• Choose Dynamic Property Evaluator from Plugin type dropdown list in the upper left corner.
  
• You may evaluate script on chosen entity in Script Tester section.

Creating scripts

To edit existing dynamic property script, edit dynamic property (Admin→Plugins→(click on dynamic property)→Edit plugin)

The scripts should be written using standard Jython syntax. Unlike custom columns and filters (which also require Jython syntax), dynamic properties can have more than one line of code. If the Script contains only one line, it will be evaluated and used as the value of appropriate dynamic property. If on the other hand a multi line script is needed, the function named "calculate" will be expected and the the result will be used as property value.

To access the entity object from the script, use the following syntax:

entity.<requested method>

Currently available methods that can be called on all kinds of entities include:

• code()
• property(propertyTypeCode)
• propertyValue(propertyTypeCode)
• propertyRendered(propertyTypeCode)
• properties()

For more details see IEntityAdaptor (interface implemented by entity) and IEntityPropertyAdaptor (interface implemented by each property).

It is also possible to acces the complete Java Object by calling "entityPE()" method, but this is appropach is not recomended, as the returned value is not a part of a well defined API and may change at any point. You may use it as a workaround, in case some data are not accessible via well defined API, but you should contact OpenBIS helpdesk and comunicate your needs, so the appropriate methods can be added to the official API.

You can test your script on selected entities (samples/experiments/materials/data sets) using the testing environment