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Before we look at the definition of our Example.json let's first look at the definition of our new VertebrateOrganType.json. For this example we want to use the Basic Vertebrate Anatomy ontology to define the valid values for Organs:
VertebrateOrganType.json

Code Block

{
        "type":"string",
   	 "format":"uri",
  	  "enum":[
        "XQUERY":
		"doc(http://rest.bioontology.org/bioportal/concepts/4531?conceptid=tbio:Organ&light=1&apikey=2fb9306a-7f3f-477a-821e-e3ccd7356a18)/success/data/classBean/relations/entry[string=Subclass]/list/classBean/fullId"
	]    ]
}

In this example, the enumeration values are defined by an XQuery that is used to get the "fullId" (URIs) of all Sub-classes of the Term "Organ" using the XML returned from NCBO's BioPortal Term services. Here is the XML returned by the term service for this exampl: http://rest.bioontology.org/bioportal/concepts/4531?conceptid=tbio:Organ&light=1&apikey=2fb9306a-7f3f-477a-821e-e3ccd7356a18.
Assuming the XQuery is setup correctly, the effective enum definition for this type would be"

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Now that we have defined an Annotation Type for Organ using the ontology we can use this type in the definition of the entity.
Here is our definition of our example Entity:
Example.json

Code Block

{
    "extends":"org/sagebionetworks/entity/type/Entity.json"
"name":"Product",
    "properties":{
        "id":{
            "type":"number",
            "description":"Example identifier",
            "required":true
        },
        "name":{
            "description":"Name of the Example",
            "type":"string",
            "required":true
        },
        "organ":{
	
            "$ref":"org/sagebionetworks/annotation/types/VertebrateOrganType.json"
        }
    },
}

The first thing to point out about our Example.json is that it extends Entity.json, which makes it a Synapse Entity. This implies it inherits all of its values from the base Entity. The second thing to point out is that the "organ" property is defined using the annotation type we created earlier.

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Since we still want Java POJOs to represent all entities, we will use the schema-to-pojo-maven-plugin to build these POJOs. This is done by simply added the following to the lib-auto-generated/pom.xml file:

Code Block

<\!-\- This plugin builds the POJOs from JSON schemas. \-->
<plugins>
<plugin>
<groupId>org.sagebionetworks</groupId>
<plugin>
	<groupId>org.sagebionetworks</groupId>
	<artifactId>schema-to-pojo-maven-plugin</artifactId>
	<version>${schema-to-pojo.version}</version>
	<executions>
		<execution>
			<goals>
				<goal>generate</goal>
			</goals>
			<configuration>
				<sourceDirectory>src/main/resources</sourceDirectory>
				<packageName>org.sagebionetworks</packageName>
<outputDirectory>target				<outputDirectory>target/auto-generated-pojos</outputDirectory>
			</configuration>
		</execution>
	</executions>
</plugin>
</plugins>

The plugin will automatically create a POJOs class for each JSON schema found in the resource directory. These POJOs will be placed in the target/auto-generated-pojos directory.

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Code Block
root/schemas/org/sagebionetworks/entity/type/Example.json root/schemas/org/sagebionetworks/annotation/types/BioOntologyTissueTypeVertebrateOrganType.json

Folder entities will be created as need to create each path. By giving each SchemaEntity a unique path, we can use this path to reference a schema before we have an entity to represent it.

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We want to add a new required primary field called "status". Since "status" is required, we must provide a default value. This is a requirement because we already have instances of Example entities deployed to Synapse, and each of these must be given a default value. We will cover how these default values are applied shortly. Here is our new Example.json:
Example.json

code

Code Block

{
    "extends":"org/sagebionetworks/entity/type/Entity.json"
"name":"Product",
    "properties":{
        "id":{
            "type":"number",
            "description":"Example identifier",
            "required":true
        },
        "name":{
            "description":"Name of the Example",
            "type":"string",
            "required":true
        },
        "statusorgan":{
            "type$ref":"string"org/sagebionetworks/annotation/types/VertebrateOrganType.json"
        },
         "requiredstatus":true,
	"enum":[ "PROTOTYPE", "RELEASED", "RECALLED", "DEPRECIATED"],
	"default":"PROTOTYPE"{
            "type":"string",
            "required":true,
            "enum":[
                "PROTOTYPE",
                "RELEASED",
                "RECALLED",
                "DEPRECIATED"
            ],
        }, }, "additionalProperties":{ "tissue":{ 	"typedefault":"objectPROTOTYPE",
	"$ref":"org/sagebionetworks/annotation/types/BioOntologyTissueType.json"        }
    }
}

Compile POJOs (Nth Time)

This time when we compile the new Example.java POJO, the resulting POJO will have a new field called "status" with a default value of "PROTYPE".

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