HL7 v2 pipeline with Patient mapping

Since the 2405 release, using Aidbox in FHIR schema validation engine is recommended, which is incompatible with zen or Entity/Attribute options.

Setup Aidbox with FHIR Schema validation engine

In this tutorial we will create an HL7 v2 pipeline to parse, map and persist Patient resources to your Aidbox database.

This tutorial is also available with a sample aidbox configuration project.

Mapping definition

Define your mapping tagged by lisp/mapping.

The :mapping value is confirmed as lisp/expr, so you may use Lisp expressions to define which intermediate format properties should be included in the Bundle resource.

{ns my-mappings
 import #{hl7v2.api
          lisp}

 patient-fhir-mapping
 {:zen/tags #{lisp/mapping}
  :mapping  {:resourceType "Bundle"
             :type "transaction"
             :id (get-in [:parsed :message :proc_id :id])
             :entry [{:request {:url "/fhir/Patient"
                                :method "POST"}

                      :resource {:resourceType "Patient"

                                 :extension
                                 [(when (get-in [:parsed :patient_group :patient :race])
                                    {:url "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
                                     :extension (for [i (get-in [:parsed :patient_group :patient :race])]
                                                  {:url "text"
                                                   :valueCoding (select-keys i [:display :system :code])})})]

                                 :identifier   (for [i (get-in [:parsed :patient_group :patient :identifier])]
                                                 (select-keys i [:value :system :type]))

                                 :name         (for [i (get-in [:parsed :patient_group :patient :name])]
                                                 (select-keys i [:family :given :middle :suffix :prefix]))

                                 :birthDate    (get-in [:parsed :patient_group :patient :birthDate])

                                 :gender       (get {"M" "male"
                                                     "F" "female"
                                                     "A" "other"
                                                     "O" "other"
                                                     "U" "unknown"}
                                                    (get-in [:parsed :patient_group :patient :gender]))

                                 :address      (for [i (get-in [:parsed :patient_group :patient :address])]
                                                 (select-keys i [:line :city :state :postalCode :country]))

                                 :telecom      (for [i (get-in [:parsed :patient_group :patient :telecom])]
                                                 (select-keys i [:value :use :system]))

                                 :martialStatus (when (get-in [:parsed :patient_group :patient :martialStatus])
                                                  {:coding (select-keys (get-in [:parsed :patient_group :patient :martialStatus])
                                                                        [:code :display :system])})}}
                     ]}
  }
 }

Mapping with several functions on empty intermediate fields may cause exceptions. To avoid such cases, use when Lisp function or refrain from using such mappings if not necessary.

Api definition

Create a namespace with your API definition with operation tagged by aidbox.rest/op. You should use hl7v2.api/in-op as :engine for every pipeline operation.

Aidbox provides a predefined parser configuration, so you may use hl7v2.config/default-config for most types of messages. :mapping property should use mapping defined in previous step.

{ns my-hl7-api
 import #{aidbox.rest
          hl7v2.config
          hl7v2.api}

 adt-in
 {:zen/tags #{aidbox.rest/op}
  :engine           hl7v2.api/in-op
  :mapping          my-mappings/patient-fhir-mapping
  :parser-config    hl7v2.config/default-config
  }

 api
 {:zen/tags #{aidbox.rest/api}
  "hl7in" {"ADT" {:POST adt-in}}
  }
}

Aidbox definition

Add your API in :apis set of Aidbox server definition.

To properly validate the resulting resource, import the appropriate fhir profiles.

{ns box
 import #{zenbox
          aidbox
          my-hl7-api
          hl7-fhir-r4-core
          hl7-fhir-us-core}

 server
 {:zen/tags #{aidbox/service}
  :engine   aidbox/http
  :apis     #{my-hl7-api/api}}

 box
 {:zen/tags #{aidbox/system}
  :services {:http server}}
}

Running instance

If your configuration was loaded correctly - you should see a new option when creating the HL7 v2 message.