config.yaml

# subclass_depth: 3  # default is 3 uncomment to override for fhir json schema


# This limits the top level objects the system will render
# For some output targets, e.g. PFB order of output is important, parents must be rendered before children
dependency_order:
  #
  # gen3 scaffolding required objects
  #
  - _definitions.yaml
  - _terms.yaml
  - Program
  - Project
  #
  # FHIR objects
  #
  - Organization
#  - Location
  - Practitioner
  - PractitionerRole
  - ResearchStudy
  - Patient
  - ResearchSubject
  - Substance
  - Specimen
#  - Encounter
  - Observation
  - DiagnosticReport
  - Condition
  - Medication
  - MedicationAdministration
#  - MedicationStatement
#  - MedicationRequest
  - Procedure
  - DocumentReference
  - Task
  - ImagingStudy
  - FamilyMemberHistory
  - BodyStructure
#  - Immunization


# Properties to 'pluck' from nested objects and render in the parent object
nested_objects:
  Patient:
    - address.postalCode
  Specimen:
    - processing.additive
    - processing.method
  DocumentReference:
    - content.attachment.contentType
    - content.attachment.extension.md5
    - content.attachment.size
    - content.attachment.url
  Task:
    - input.valueReference
    - output.valueReference
  Medication:
    - ingredient.item


# Specify which entities you want to add to a FHIR entities model
extensions:
  Patient:
  - http://hl7.org/fhir/us/core/STU6/StructureDefinition-us-core-race.json
  - http://hl7.org/fhir/us/core/STU6/StructureDefinition-us-core-ethnicity.json
  - http://hl7.org/fhir/us/core/STU6/StructureDefinition-us-core-tribal-affiliation.json
  - http://hl7.org/fhir/us/core/STU6/StructureDefinition-us-core-birthsex.json
  - http://hl7.org/fhir/us/core/STU6/StructureDefinition-us-core-genderIdentity.json
  - http://synthetichealth.github.io/synthea/disability-adjusted-life-years
  - http://synthetichealth.github.io/synthea/quality-adjusted-life-years
  - https://hl7.org/fhir/extensions/StructureDefinition-patient-birthPlace.json
  - https://hl7.org/fhir/extensions/StructureDefinition-patient-mothersMaidenName.json


# Constrain the parent destination links from a Node for the Simplified Model.
limit_links:
  Observation:
    - ResearchStudy
    - Patient
    - Specimen
  Encounter:
    - Patient
  DocumentReference:
    - Patient
    - Specimen
    - ResearchStudy
    - Observation
  Practitioner: []
  ResearchStudy:
    - Project
    - ResearchStudy
  FamilyMemberHistory:
    - Patient
  Procedure:
    - Patient
    - Practitioner
    - Procedure
  MedicationAdministration:
    - Patient
    - Medication

# Add these extra properties to the simplified schema
# These may be used to add extra scalar properties to the simplified schema as well as constrain edge destination types.
extra_properties:

  Patient:
    us_core_race_ombCategory_coding:
      description: extension
      type: array
      items:
        type: string
    us_core_ethnicity_ombCategory_coding:
      description: extension
      type: array
      items:
        type: string
    us_core_race_text:
      description: extension
      type: string
    patient_birthPlace_resourceType:
      description: nested
      type: string
    patient_birthPlace_city:
      description: nested
      type: string
    us_core_ethnicity_text:
      description: nested
      type: string
    patient_birthPlace_state:
      description: nested
      type: string
    patient_birthPlace_country:
      description: nested
      type: string


  # Add gen3 file scaffolding expected properties
  DocumentReference:
    $ref: "_definitions.yaml#/data_file_properties"
    data_category:
      term:
        $ref: "_terms.yaml#/data_category"
      type: string
    data_type:
      term:
        $ref: "_terms.yaml#/data_type"
      type: string
    data_format:
      term:
        $ref: "_terms.yaml#/data_format"
      type: string
    auth_resource_path:
        type: string
        description: Gen3 scaffolding
#    # from content attachment
#    content_url:
#        type: string
#        description: from content attachment
#    content_contentType:
#        type: string
#        description: from content attachment
#    content_size:
#        type: number
#        description: from content attachment
#    content_md5:
#        type: string
#        description: from content attachment
    # from denormalization
    patient_id:
      type: string
      description: Denormalized patient id
    patient_identifier:
      description: Denormalized patient identifier
      type: array
      items:
        type: string
    specimen_identifier:
      description: Denormalized specimen identifier
      type: array
      items:
        type: string
    task_identifier:
      description: Denormalized task identifier
      type: array
      items:
        type: string


    subject:
      description: Who/what is the subject of the document.
      $ref: Reference.yaml
      backref: subject_DocumentReference
      enum_reference_types:
      - ResearchStudy
      - Patient
      - Specimen
      - Observation
      title: The item that this DocumentReference is about.


  # a link that does not exist in the FHIR schema, in this case from ResearchStudy to Project
  ResearchStudy:
    gen3_project:
      description: The Gen3 project this study belongs to.  Used to generate link.
      $ref: Reference.yaml
      backref: research_study
      enum_reference_types:
      - Project
      title: The Gen3 project this study belongs to.


  # Create edges from references typed as ANY
  # In this case Task we hint that Task inputs will point to Specimen and outputs point to DocumentReferences
  # see:
  # * https://build.fhir.org/task-definitions.html#Task.input.value_x_
  # * https://build.fhir.org/task-definitions.html#Task.output.value_x_

  Task:
    specimen:
      description: The specimen input to this task.  Used to generate link.
      $ref: Reference.yaml
      backref: task
      enum_reference_types:
      - Specimen
      title: The specimen input to this task.
    document_reference:
      description: The output from this task.  Used to generate link.
      $ref: Reference.yaml
      backref: task
      enum_reference_types:
      - DocumentReference
      title: The output from this task.

  # explicitly limit edge `focus` to ResearchStudy
  Observation:
    focus:
      backref: focus_observation
      description: The actual focus of an observation when it is not the patient of
        record representing something or someone associated with the patient such as
        a spouse, parent, fetus, or donor.
      element_property: true
      enum_reference_types:
      - ResearchStudy
      items:
        $ref: Reference.yaml
      title: What the observation is about, when it is not about the subject of record
      type: array
    patient_identifier:
      description: Denormalized patient identifier
      type: array
      items:
        type: string
    specimen_identifier:
      description: Denormalized specimen identifier
      type: array
      items:
        type: string
    condition_identifier:
      description: Denormalized condition identifier
      type: array
      items:
        type: string

  # add a link from a sub-object collection.bodySite
  Specimen:
    bodySite:
      backref: specimen
      $ref: CodeableReference.yaml
      binding_description: SNOMED CT Body site concepts
      binding_strength: example
      binding_uri: http://hl7.org/fhir/ValueSet/body-site
      binding_version: null
      description: Anatomical location from which the specimen was collected (if subject
        is a patient). This is the target site.  This element is not used for environmental
        specimens.
      element_property: true
      enum_reference_types:
      - BodyStructure
      title: Anatomical collection site
    patient_identifier:
      description: Denormalized patient identifier
      type: array
      items:
        type: string

# Add a `category` field to the simplified schema: defaults to Clinical
categories:
  DocumentReference: data_file
  Location: Administrative
  Organization: Administrative
  Patient: Administrative
  Practitioner: Administrative
  PractitionerRole: Administrative
  ResearchStudy: Administrative
  ResearchSubject: Administrative
  Specimen: Biospecimen
  Task: Analysis


# Ignore these properties in all objects
ignored_properties:
  - contained
  - meta
  - implicitRules
  - language
  - contained
  - modifierExtension
  - assigner
  - fhir_comments
  - text


# Rename these properties
renamed_properties:
  label: label_ # https://cdis.slack.com/archives/CDDPLU1NU/p1682393064223499
  for: for_fhir  # https://github.com/nazrulworld/fhir.resources/blob/main/fhir/resources/task.py#L145
  class: class_fhir