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Migrate custom resources defined with Zen to FHIR Schema

Prerequisites

The materials in this section describe what to do next with the resulting FHIR Schema resource or set of resources. They explain how to load them into Aidbox, either one by one or via IG. Additionally, they outline the requirements for FHIR Schema to define a Custom Resource and provide a detailed FHIR Schema specification.

FHIR Schema ValidatorCustom resources using FHIR SchemaHow to create FHIR NPM packageUpload FHIR Implementation Guide

Obtain FHIRSchema

In the following sections, we will describe how to obtain the FHIR Schema from a Zen resource definition.

Semi-Automated approach

You can use a special REST API endpoint to migrate specific Zen definitions to the FHIR schema. The endpoint requires a Zen namespace and symbol under which the custom resource definition is described. Internally, it attempts to compile the Zen definition to the FHIR schema.

GET /ZenSchema/<zen-namespace>/<zen-definition-symbol>/$dump-as-fhir-schema

If the compilation succeeds, the endpoint returns the resulting FHIR Schema. If it fails, it provides a list of errors detailing what went wrong. Most errors occur because you've used keys on your Zen definition that are not recognized by our compiler. In this case, you can contact us to potentially extend the compiler. Alternatively, you can manually rewrite your custom resource using FHIR Schema.

Please double-check the compilation results, as they may contain transformation errors. This tool is intended to reduce manual effort during the migration process and is not meant for fully automated resource migration.

Example: EmailSchedule custom resource

Here's an example of migrating a custom resource EmailSchedulethat describes the schedule for email notifications about appointments. Let's imagine it is described in main namespace of our Aidbox configuration project.

{ns main
    import #{aidbox
             zenbox
             zen.fhir}

    EmailSchedule
    {:zen/tags #{zen/schema zenbox/persistent zen.fhir/base-schema}
     :zen.fhir/type "EmailSchedule"
     :zen.fhir/version "0.5.3"
     :resourceType "EmailSchedule"
     :type zen/map
     :confirms #{zenbox/Resource}
     :require  #{:reports}
     :keys {:name {:type zen/string}
            :days {:type zen/vector :every {:type zen/string
                                            :enum [{:value "mon"}
                                                   {:value "tue"}
                                                   {:value "wed"}
                                                   {:value "thu"}
                                                   {:value "fri"}
                                                   {:value "sat"}
                                                   {:value "sun"}]}}
            :data {:type zen/any}
            :parameters {:type zen/map :validation-type :open}
            :time {:type zen/string}
            :timezone {:type zen/string}
            :reports {:type zen/vector
                      :minItems 1
                      :every {:type zen/map
                              :require #{:enabled :fileFormat :campaignTypes :reportType}
                              :keys {:enabled {:type zen/boolean}
                                     :reportType {:type zen/string :enum [{:value "campaign"} {:value "summary"} {:value "combined-campaign"}]}
                                     :fileFormat {:type zen/map
                                                  :keys {:csvPartial {:type zen/boolean}
                                                         :pdfPartial {:type zen/boolean}
                                                         :csvFull {:type zen/boolean}
                                                         :csv {:type zen/boolean}
                                                         :pdf {:type zen/boolean}}}
                                     :campaignTypes {:type zen/vector
                                                     :minItems 1
                                                     :every {:type zen/string
                                                             :enum [{:value "appointment-reminder"}
                                                                    {:value "appointment-notification"}
                                                                    {:value "appointment-noshow"}
                                                                    {:value "appointment-alert"}
                                                                    {:value "recall"}
                                                                    {:value "broadcast"}]}}}}}
            :recipients {:type zen/vector :every {:type zen/string}}}}

    box
    {:zen/tags #{aidbox/system}}}

Convert this Zen definition to FHIRSchema using API:

GET /ZenSchema/main/EmailSchedule/$dump-as-fhir-schema
content-type: application/json
accept: application/json

Manual Approach

If the compiler doesn't support certain instructions for your Zen definitions, if you want full control during the migration process, or if you want to extend your custom resources using unique FHIR Schema features, you can manually rewrite your custom resource definitions from scratch using the FHIR Schema.

In the following steps, we will use the same custom resource example, EmailSchedule. Although it is just an example, it covers most aspects of resource definition with Zen. If this guide misses any features of Zen resource definition, please contact us.

Get Zen definition

Open your Aidbox configuration project and find custom resource definitions. It should look similar to EmailSchedule definition example.

Translate zen definition :keys to FHIRSchema element entry

The FHIRSchema elements is similar to :keys field in Zen definition, serving the same purpose: defining properties for a resource.

For example, we have name key in EmailSchedule custom resource:

{...
:keys {:name {:type zen/string}}
...}

It states that the name property must be a string. This property is located on the top level, indicating it is the root field in the resource.

To describe it as a FHIRSchema element, do the following:

{"elements": {"name": {"type": "string"}}}

For nested keys like reports.enabled in the EmailSchedule resource, nest the "elements" statements accordingly. Note that "elements" repeats each time you nest a property:

{"elements": {"name": {"type": "string"}
              "reports": {"elements": {"enabled": {"type": "boolean"}},
                          "array": true}}}

Handling Enums

Enums (:enum) were a handy tool for limiting possible values directly within the Zen definition model. However, this approach conflicts with FHIR, which has its own well-defined methods for limiting value sets.

Using FHIRPath Constraints

Enums can be described using FHIRPath constraints. Here's an example of days property in EmailSchedule resource:

{"elements":
 "days": {
    "array": true,
    "type": "string",
    "constraints": {
    "<your-constraint-id>": {
      "expression": "%context.subsetOf('mon' | 'tue' | 'wed' | 'thu' | 'fri' | 'sat' | 'sun')",
      "severity": "error"
    }}}}

Constraint id must be unique across one resource definition. While this method allows for defining possible values in place, it has downsides. It makes it difficult to reuse or implement lookups for these values. Here is the FHIRSchema reference specification describing the constraints property.

Using ValueSets

Alternatively, you can create a ValueSet and bind it to the coded value. FHIR resources extensively utilize this approach. This involves creating a ValueSet as a resource and delivering it to an external terminology server. However, this is beyond the scope of this guide.

{"elements":
 {"days":
  {"type": "string",
   "binding": {"valueSet": "<your-vs-url>",
               "strength": "required"}}}}

In FHIR, terminology bindings occur in four gradations: required, extensible, preferred, and example. The FHIRSchema validator checks bindings only with the strength of "required"; all other binding strengths are ignored.

This approach leverages FHIR's capabilities for managing value sets, ensuring consistency and reusability across different resources.

Handling :validation-type :open

The :validation-type :open with :type zen/map instruction for a Zen definition indicates that value is an arbitrary map with arbitrary key/value pairs.

Example: parameters property in EmailSchedule resource

{...
:keys {:parameters {:type zen/map :validation-type :open}}
...}

FHIRSchema Equivalent

With FHIRSchema, you can express identical semantics using additionalProperties and any: true. However, note that resource definitions using these instructions are not compatible with FHIR. This means you cannot convert FHIRSchema with these instructions back to StructureDefinition, as FHIR doesn't naturally describe arbitrary key/value nodes.

To express :validation-type :open with :type zen/map in FHIRSchema:

{
  "elements": {
    "parameters": {
      "additionalProperties": {
        "any": true
      }
    }
  }
}

  • additionalProperties indicates that any property not described in elements will be validated against the schema provided in additionalProperties.

  • any: true indicates that the value is arbitrary and may be of any type.

You can also include more complex schemas within additionalProperties. For example:

{"elements": {
    "parameters": {
      "elements": {
        "someField": {
          "type": "integer"
        }
      },
      "additionalProperties": {
        "type": "string",
        "constraints": {
          // Define constraints here
        }
      }
    }
  }
}

This means any keys not described in elements must have a string value and pass the defined constraints. For more details about these FHIRSchema instructions, please refer to the reference specification section.

Handling zen/any

The zen/any type for a Zen definition indicates that the value is arbitrary and may be of any type.

Example: data property in EmailSchedule resource

{...
:keys {:data {:type zen/any}}
...}

FHIRSchema Equivalent

To describe zen/any use any without additionalProperties. 

{"elements":
 {"data": {"any": true}}}

Handling :require

The :require instruction indicates that the described property is required and must be present in a resource instance.

Example: reports property in EmailSchedule resource

{...
:require  #{:reports}
:keys {:reports {:type zen/vector
                ...}}
...}

FHIRSchema Equivalent

To express :require in FHIRSchema, use the required property at the same level as elements. It is an array of fields that must be present in the data instance.

{"required": ["reports"],
 "elements":
 {"reports": {"array": true,
              ...}}

For more information about this instruction, please refer to the relevant section in the FHIRSchema specification.

Handling zen/vector

The zen/vector type indicates that the described property represents a collection of items.

Example: recipients property in EmailSchedule resource

{...
:keys {:recipients {:type zen/vector :every {:type zen/string}}}
...}

This definition specifies that recipients is a property within the EmailSchedule resource, where each item in the collection is of type string.

FHIRSchema Equivalent

To express zen/vector in FHIRSchema, use array: true.

{"elements":
 {"recipients": {"array": true, "type": "string"}}

For more information about this instruction, please refer to the relevant section in the FHIRSchema specification.

Handling :refers

The :refers instruction indicates that a node will contain a reference to another resource and limits the possible target resource types to a predefined list.

Example:

{...
:keys {:organization {:confirms #{zenbox/Reference}
                      :zen.fhir/reference {:refers #{my-resources.organization/Organization}}}}
...}

In this example, the organization property refers to a resource of type Organization.

FHIRSchema Equivalent

To express this in FHIRSchema, use the refers instruction and specify the "Reference" type. This will be handled as a regular FHIR reference. Additionally, in the refers property, you can reference not only resource types but also profiles on some resources.

{
  "elements": {
    "organization": {
      "type": "Reference",
      "refers": ["Organization"]
    }
  }
}

In this schema, organization is defined as a reference to resources of type Organization.

For more information about this instruction, refer to the relevant section of the FHIR Schema reference specification.

Handling :fhir/polymorphic

The :fhir/polymorphic instruction indicates a choice of datatypes that allows values of different types for specific fields.

Example:

{...
 :keys {:effective
         {:type zen/map
          :fhir/polymorphic true
          :exclusive-keys #{#{:dateTime :Period}}
          :keys {:dateTime {:confirms #{my-types/DateTime}}
                 :period {:confirms #{my-types/Period}}}}}
...}

In this example, the effective property can be either effectiveDateTime or effectivePeriod.

FHIRSchema Equivalent

To express this in FHIRSchema, use the choiceOf instruction:

{
  "elements": {
    "effectiveDateTime": {
      "choiceOf": "effective",
      "type": "DateTime"
    },
    "effectivePeriod": {
      "type": "Period",
      "choiceOf": "effective"
    }
  }
}

For more information about this instruction, refer to the relevant section of the FHIR Schema reference specification.

Resulting FHIRSchema

{ "derivation": "specialization",
  "id": "EmailSchedule",
  "kind": "resource",
  "datatype": "EmailSchedule",
  "url": "EmailSchedule",
  "required": [
    "reports"
  ],
  "type": "EmailSchedule",
  "elements": {
    "name": {
      "type": "string"
    },
    "data": {"any": true},
    "parameters": {
      "additionalProperties": {
        "any": true
      }
    },
    "organization": {
      "type": "Reference",
      "refers": ["Organization"]
    },
    "effectiveDateTime": {
      "choiceOf": "effective",
      "type": "DateTime"
    },
    "effectivePeriod": {
      "type": "Period",
      "choiceOf": "effective"
    },
    "recipients": {"array": true, "type": "string"},
    "days": {
      "array": true,
      "type": "string",
      "constraints": {
        "enum-7": {
          "expression": "%context.subsetOf('mon' | 'tue' | 'wed' | 'thu' | 'fri' | 'sat' | 'sun')",
          "severity": "error"
        }
      }
    }
  }
}

Handling resulting FHIR Schemas

To deliver the FHIR Schema(s) and related Entities you authored to Aidbox, follow these steps. Ensure that your Aidbox is configured to run with the FHIRSchema validation engine. Here's a guide describing how to achieve that:

Setup Aidbox with FHIR Schema validation engine

Single FHIRSchema Delivery

If you have only one FHIRSchema that replaces your custom-defined Zen definition, follow this guide to deliver a single FHIRSchema to Aidbox.

Custom resources using FHIR Schema

Multiple Schemas as a Package

If you have multiple schemas replacing a set of resources and want to work with this set of entities as a package (ImplementationGuide), refer to this guide on how to create your own FHIR NPM package with ImplementationGuide entities.

How to create FHIR NPM package

Loading the FHIR NPM Package

Upload FHIR Implementation Guide

Important Notes:

Schema Precedence: Uploaded FHIRSchemas with your resource definitions have higher precedence than Zen definitions, so validation will be performed using the FHIRSchema. You can delete your Zen definition after creating the FHIRSchema with resource definitions.

SearchParameters: SearchParameters described for custom resources won't work in FHIRSchema validation mode. You need to redefine them as regular FHIR SearchParameters, not Aidbox Search Parameters. See the migration guide.

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