Validate Annotations

Warning: This is a beta implementation and is subject to change. Use at your own risk.

Validate annotations on your Synapse entities by leveraging the JSON schema services. Here are the steps you must take to set up the JSON Schema service.

Create a JSON Schema organization

Set up Synapse client and JSON Schema service:

import synapseclient
syn = synapseclient.login()
syn.get_available_services()  # Output: ['json_schema']
js = syn.service("json_schema")

Create, manage, and delete a JSON Schema organization:

my_org_name = <your org name here>
my_org = js.JsonSchemaOrganization(my_org_name)
my_org  # Output: JsonSchemaOrganization(name=my_org_name)
my_org.create()
my_org.get_acl()
my_org.set_acl([syn.getUserProfile().ownerId])
# my_org.update_acl([syn.getUserProfile().ownerId])
my_org.delete()

Retrieve existing organization and associated JSON schemas:

orgs     = js.list_organizations()
sage_org = js.JsonSchemaOrganization("sage.annotations")
schemas  = sage_org.list_json_schemas()
schema1  = next(schemas)
schema2  = sage_org.get_json_schema(schema1.name)
assert schema1 is schema2  # True
schema1  # Output: JsonSchema(org='sage.annotations', name='analysis.alignmentMethod')

Manage a specific version of a JSON schema:

versions  = schema1.list_versions()
version1  = next(versions)
raw_body  = version1.body
full_body = version1.expand()
version1
# Output: JsonSchemaVersion(org='sage.annotations', name='analysis.alignmentMethod', version='0.0.1')

Create a new JSON schema version for an existing organization:

from random import randint
rint = randint(0, 100000)
schema_name = "my.schema"

# Method 1
my_org          = js.JsonSchemaOrganization(my_org_name)
new_version1    = my_org.create_json_schema(raw_body, schema_name, f"0.{rint}.1")

# Method 2
my_schema    = js.JsonSchema(my_org, schema_name)
new_version2 = my_schema.create(raw_body, f"0.{rint}.2")

# Method 3
my_version   = js.JsonSchemaVersion(my_org, schema_name, f"0.{rint}.3")
new_version3 = my_version.create(raw_body)

Test validation on a Synapse entity:

from time import sleep
synapse_id = "syn25922647"
js.bind_json_schema(new_version1.uri, synapse_id)
js.get_json_schema(synapse_id)
sleep(3)
js.validate(synapse_id)
js.validate_children(synapse_id)
js.validation_stats(synapse_id)
js.unbind_json_schema(synapse_id)

Access to low-level API functions:

js.create_organization(organization_name)
js.get_organization(organization_name)
js.list_organizations()
js.delete_organization(organization_id)
js.get_organization_acl(organization_id)
js.update_organization_acl(organization_id, resource_access, etag)
js.list_json_schemas(organization_name)
js.list_json_schema_versions(organization_name, json_schema_name)
js.create_json_schema(json_schema_body, dry_run)
js.get_json_schema_body(json_schema_uri)
js.delete_json_schema(json_schema_uri)
js.json_schema_validation(json_schema_uri)
js.bind_json_schema_to_entity(synapse_id, json_schema_uri)
js.get_json_schema_from_entity(synapse_id)
js.delete_json_schema_from_entity(synapse_id)
js.validate_entity_with_json_schema(synapse_id)
js.get_json_schema_validation_statistics(synapse_id)
js.get_invalid_json_schema_validation(synapse_id)