{
   "title": "Rare Disease Report Writing",
   "type": "object",
   "properties": {
      "toplines": {
         "title": "Topline Finding(s)",
         "type": "array",
         "minItems": 1,
         "maxItems": 5,
         "items": {
            "allOf": [
               {
                  "$ref": "../../structs.json#/definitions/ToplineFinding"
               },
               {
                  "properties": {
                     "finding": {
                        "$ref": "../../core.json#/definitions/RareDiseaseToplineFinding"
                     }
                  }
               }
            ]
         }
      },
      "classifications": {
         "title": "Classifications",
         "minItems": 1,
         "type": "array",
         "items": {
            "allOf": [
               {
                  "type": "object",
                  "properties": {
                     "finding_type": {
                        "$ref": "../../core.json#/definitions/FindingType"
                     },
                     "classification": {
                        "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
                     }
                  }
               },
               {
                  "allOf": [
                     {
                        "if": {
                           "properties": {
                              "classification": {
                                 "const": "NEGATIVE"
                              }
                           }
                        },
                        "then": {
                           "$ref": "#/definitions/RareDiseaseNegativeClassification"
                        }
                     },
                     {
                        "if": {
                           "properties": {
                              "finding_type": {
                                 "const": "RARE_DISEASE"
                              }
                           }
                        },
                        "then": {
                           "$ref": "#/definitions/RareDiseaseClassification"
                        }
                     },
                     {
                        "if": {
                           "properties": {
                              "finding_type": {
                                 "const": "RARE_DISEASE_CNV"
                              }
                           }
                        },
                        "then": {
                           "$ref": "#/definitions/RareDiseaseCNVClassification"
                        }
                     },
                     {
                        "if": {
                           "properties": {
                              "finding_type": {
                                 "const": "RARE_DISEASE_MITO"
                              }
                           }
                        },
                        "then": {
                           "$ref": "#/definitions/RareDiseaseMitoClassification"
                        }
                     },
                     {
                        "if": {
                           "properties": {
                              "finding_type": {
                                 "const": "RARE_DISEASE_TRE"
                              }
                           }
                        },
                        "then": {
                           "$ref": "#/definitions/RareDiseaseTREClassification"
                        }
                     }
                  ]
               }
            ]
         }
      },
      "next_steps": {
         "$ref": "../../structs.json#/definitions/ReportNextSteps"
      },
      "sample_limitations": {
         "title": "Sample Limitations",
         "type": "array",
         "items": {
            "type": "string"
         }
      }
   },
   "definitions": {
      "RareDiseaseNegativeClassification": {
         "type": "object",
         "required": [
            "classification"
         ],
         "properties": {
            "classification": {
               "const": "NEGATIVE"
            }
         }
      },
      "RareDiseaseClassification": {
         "type": "object",
         "additionalProperties": false,
         "required": [
            "classification"
         ],
         "properties": {
            "variantfinding_id": {
               "$ref": "../../ids.json#/definitions/VariantFindingId"
            },
            "finding_type": {
               "const": "RARE_DISEASE"
            },
            "gene_symbol": {
               "title": "Location (Gene Symbol)",
               "type": "string"
            },
            "condition": {
               "title": "Condition",
               "type": "string"
            },
            "event": {
               "title": "Variant Event",
               "type": [
                  "string",
                  "null"
               ]
            },
            "inheritance": {
               "type": "object",
               "properties": {
                  "mode": {
                     "title": "Mode of Inheritance",
                     "$ref": "../../core.json#/definitions/Inheritance"
                  },
                  "zygosity": {
                     "title": "Zygosity",
                     "$ref": "../../core.json#/definitions/Zygosity"
                  },
                  "pattern": {
                     "title": "Inherited From",
                     "$ref": "../../core.json#/definitions/VariantInheritance"
                  }
               }
            },
            "classification": {
               "title": "ACMG Classification",
               "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
            },
            "phenotype": {
               "title": "Interpretation Summary",
               "type": "object",
               "properties": {
                  "evidence_summary": {
                     "title": "Description",
                     "type": "string"
                  }
               }
            },
            "variation": {
               "title": "Variant Summary",
               "$ref": "../../structs.json#/definitions/RareDiseaseVariation"
            },
            "variant_description": {
               "title": "Evidence",
               "type": [
                  "string",
                  "null"
               ]
            },
            "gene_info": {
               "title": "Gene Information",
               "type": "string"
            }
         }
      },
      "RareDiseaseCNVClassification": {
         "type": "object",
         "additionalProperties": false,
         "required": [
            "classification"
         ],
         "properties": {
            "variantfinding_id": {
               "$ref": "../../ids.json#/definitions/VariantFindingId"
            },
            "finding_type": {
               "const": "RARE_DISEASE_CNV"
            },
            "cytoband": {
               "title": "Location (Cytoband)",
               "$ref": "../../core.json#/definitions/Cytoband"
            },
            "condition": {
               "title": "Condition",
               "type": "string"
            },
            "event": {
               "title": "Variant Event",
               "$ref": "../../core.json#/definitions/GeneticEventType"
            },
            "copy_number": {
               "title": "Copy Number",
               "$ref": "../../core.json#/definitions/CopyNumber"
            },
            "inheritance": {
               "type": "object",
               "properties": {
                  "mode": {
                     "title": "Mode of Inheritance",
                     "$ref": "../../core.json#/definitions/Inheritance"
                  },
                  "zygosity": {
                     "title": "Zygosity",
                     "$ref": "../../core.json#/definitions/Zygosity"
                  },
                  "pattern": {
                     "title": "Inherited From",
                     "$ref": "../../core.json#/definitions/VariantInheritance"
                  }
               }
            },
            "classification": {
               "title": "ACMG Classification",
               "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
            },
            "phenotype": {
               "title": "Interpretation Summary",
               "type": "object",
               "properties": {
                  "evidence_summary": {
                     "title": "Description",
                     "type": "string"
                  }
               }
            },
            "variation": {
               "title": "Variant Summary",
               "$ref": "../../structs.json#/definitions/RareDiseaseVariation"
            },
            "iscn_nomenclature": {
               "title": "ISCN Nomenclature",
               "$ref": "../../core.json#/definitions/ISCNNomenclature"
            },
            "variant_description": {
               "title": "Evidence",
               "type": [
                  "string",
                  "null"
               ]
            }
         }
      },
      "RareDiseaseMitoClassification": {
         "type": "object",
         "additionalProperties": false,
         "required": [
            "classification"
         ],
         "properties": {
            "variantfinding_id": {
               "$ref": "../../ids.json#/definitions/VariantFindingId"
            },
            "finding_type": {
               "const": "RARE_DISEASE_MITO"
            },
            "gene_symbol": {
               "title": "Location (Gene Symbol)",
               "type": "string"
            },
            "condition": {
               "title": "Condition",
               "type": "string"
            },
            "event": {
               "title": "Variant Event",
               "type": [
                  "string",
                  "null"
               ]
            },
            "inheritance": {
               "type": "object",
               "properties": {
                  "mode": {
                     "title": "Mode of Inheritance",
                     "$ref": "../../core.json#/definitions/Inheritance"
                  },
                  "zygosity": {
                     "title": "Zygosity",
                     "$ref": "../../core.json#/definitions/Zygosity"
                  },
                  "pattern": {
                     "title": "Inherited From",
                     "$ref": "../../core.json#/definitions/VariantInheritance"
                  },
                  "percent_heteroplasmy": {
                     "title": "Percent Heteroplasmy",
                     "$ref": "../../core.json#/definitions/PercentHeteroplasmy"
                  }
               }
            },
            "classification": {
               "title": "ACMG Classification",
               "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
            },
            "phenotype": {
               "title": "Interpretation Summary",
               "type": "object",
               "properties": {
                  "evidence_summary": {
                     "title": "Description",
                     "type": "string"
                  }
               }
            },
            "variation": {
               "title": "Variant Summary",
               "$ref": "../../structs.json#/definitions/RareDiseaseVariation"
            },
            "variant_description": {
               "title": "Evidence",
               "type": [
                  "string",
                  "null"
               ]
            },
            "gene_info": {
               "title": "Gene Information",
               "type": "string"
            }
         }
      },
      "RareDiseaseTREClassification": {
         "type": "object",
         "additionalProperties": false,
         "required": [
            "classification"
         ],
         "properties": {
            "variantfinding_id": {
               "$ref": "../../ids.json#/definitions/VariantFindingId"
            },
            "finding_type": {
               "const": "RARE_DISEASE_TRE"
            },
            "gene_symbol": {
               "title": "Location (Gene Symbol)",
               "type": "string"
            },
            "condition": {
               "title": "Condition",
               "type": "string"
            },
            "alleles": {
               "title": "Alleles",
               "type": "array",
               "items": {
                  "type": "object",
                  "properties": {
                     "event": {
                        "title": "Variant Event",
                        "type": "string"
                     },
                     "classification": {
                        "title": "Allele Classification",
                        "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
                     },
                     "number": {
                        "type": "integer"
                     }
                  }
               }
            },
            "inheritance": {
               "type": "object",
               "properties": {
                  "mode": {
                     "title": "Mode of Inheritance",
                     "$ref": "../../core.json#/definitions/Inheritance"
                  },
                  "zygosity": {
                     "title": "Zygosity",
                     "$ref": "../../core.json#/definitions/Zygosity"
                  },
                  "pattern": {
                     "title": "Inherited From",
                     "$ref": "../../core.json#/definitions/VariantInheritance"
                  }
               }
            },
            "classification": {
               "title": "ACMG Classification",
               "$ref": "../../core.json#/definitions/ACMGPlusNegativeClassification"
            },
            "phenotype": {
               "title": "Interpretation Summary",
               "type": "object",
               "properties": {
                  "evidence_summary": {
                     "title": "Description",
                     "type": "string"
                  }
               }
            },
            "variation": {
               "title": "Variant Summary",
               "$ref": "../../structs.json#/definitions/RareDiseaseVariation"
            },
            "variant_description": {
               "title": "Evidence",
               "type": [
                  "string",
                  "null"
               ]
            },
            "gene_info": {
               "title": "Gene Information",
               "type": "string"
            }
         }
      }
   }
}