StructureMap for PGx result by omarisgreat · Pull Request #160 · NHSDigital/NHSDigital-FHIR-Genomics-ImplementationGuide

omarisgreat · 2025-04-22T12:38:31Z

No description provided.

ryma2fhir · 2025-05-22T14:47:50Z

Hi @omarisgreat. Using HAPI-FHIR v 8.0.0 locally I get the following issues for StructureMap/StructureMap-PharmacogeneticTestResult-Genomics.json

{
  "resourceType": "OperationOutcome",
  "issue": [
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 2
        }
      ],
      "severity": "warning",
      "code": "processing",
      "diagnostics": "Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)",
      "location": [
        "StructureMap",
        "Line[1] Col[2]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 85
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[0].input[0]",
        "Line[85] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 90
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type GenomicVariantResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3759 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[0].input[1]",
        "Line[90] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 185
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 18
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
        }
      ],
      "severity": "error",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
          }
        ]
      },
      "diagnostics": "The FHIRPath expression passed as the evaluate parameter is invalid: Unknown context evaluating FHIRPath expression: Procedure.extension (@char 1)",
      "location": [
        "StructureMap.group[0].rule[1].target[1]",
        "Line[185] Col[18]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 439
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 18
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
        }
      ],
      "severity": "error",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
          }
        ]
      },
      "diagnostics": "The FHIRPath expression passed as the evaluate parameter is invalid: Unknown context evaluating FHIRPath expression: Observation.component.extension (@char 1)",
      "location": [
        "StructureMap.group[0].rule[6].target[4]",
        "Line[439] Col[18]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 790
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 14
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_NOT_CHECKED"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_NOT_CHECKED"
          }
        ]
      },
      "diagnostics": "Transform qty not checked yet",
      "location": [
        "StructureMap.group[0].rule[13].target[2]",
        "Line[790] Col[14]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 961
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 18
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
        }
      ],
      "severity": "error",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
          }
        ]
      },
      "diagnostics": "The FHIRPath expression passed as the evaluate parameter is invalid: Unknown context evaluating FHIRPath expression: Observation.component.extension (@char 1)",
      "location": [
        "StructureMap.group[0].rule[16].target[4]",
        "Line[961] Col[18]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1167
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 18
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
        }
      ],
      "severity": "error",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
          }
        ]
      },
      "diagnostics": "The FHIRPath expression passed as the evaluate parameter is invalid: Unknown context evaluating FHIRPath expression: Observation.component.extension (@char 1)",
      "location": [
        "StructureMap.group[0].rule[20].target[4]",
        "Line[1167] Col[18]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1417
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[1].input[0]",
        "Line[1417] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1422
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type KnowledgeBaseReference which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3748 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[1].input[1]",
        "Line[1422] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1582
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 18
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
        }
      ],
      "severity": "error",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
          }
        ]
      },
      "diagnostics": "The FHIRPath expression passed as the evaluate parameter is invalid: Unknown context evaluating FHIRPath expression: Observation.component.extension (@char 1)",
      "location": [
        "StructureMap.group[1].rule[2].target[5]",
        "Line[1582] Col[18]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1732
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 14
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_NOT_CHECKED"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_NOT_CHECKED"
          }
        ]
      },
      "diagnostics": "Transform pointer not checked yet",
      "location": [
        "StructureMap.group[1].rule[6].target[0]",
        "Line[1732] Col[14]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1751
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[2].input[0]",
        "Line[1751] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1756
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type GenomicVariantResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3759 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[2].input[1]",
        "Line[1756] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1860
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[3].input[0]",
        "Line[1860] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1938
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type GenomicVariantResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3759 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[4].input[0]",
        "Line[1938] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1999
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 18
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
        }
      ],
      "severity": "error",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
          }
        ]
      },
      "diagnostics": "The FHIRPath expression passed as the evaluate parameter is invalid: Unknown context evaluating FHIRPath expression: Observation.component.extension (@char 1)",
      "location": [
        "StructureMap.group[4].rule[0].target[3]",
        "Line[1999] Col[18]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 2116
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 18
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
        }
      ],
      "severity": "error",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_EXPRESSION_ERROR"
          }
        ]
      },
      "diagnostics": "The FHIRPath expression passed as the evaluate parameter is invalid: Unknown context evaluating FHIRPath expression: Observation.component.extension (@char 1)",
      "location": [
        "StructureMap.group[4].rule[3].target[4]",
        "Line[2116] Col[18]"
      ]
    }
  ]
}

omarisgreat · 2025-05-23T13:38:20Z

HI @ryma2fhir, would you be able to check again, I've run the validation locally after fixing the above errors using HAPI-FHIR v8.2.0 without issues, just making sure I haven't missed anything

ryma2fhir · 2025-05-27T10:29:40Z

Looks fine to me (using 8.2.0)

{
  "resourceType": "OperationOutcome",
  "issue": [
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 2
        }
      ],
      "severity": "warning",
      "code": "processing",
      "diagnostics": "Constraint failed: dom-6: 'A resource should have narrative for robust management' (defined in http://hl7.org/fhir/StructureDefinition/DomainResource) (Best Practice Recommendation)",
      "location": [
        "StructureMap",
        "Line[1] Col[2]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 85
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[0].input[0]",
        "Line[85] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 90
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type GenomicVariantResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3759 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[0].input[1]",
        "Line[90] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 790
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 14
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_NOT_CHECKED"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_NOT_CHECKED"
          }
        ]
      },
      "diagnostics": "Transform qty not checked yet",
      "location": [
        "StructureMap.group[0].rule[13].target[2]",
        "Line[790] Col[14]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1417
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[1].input[0]",
        "Line[1417] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1422
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type KnowledgeBaseReference which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3748 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[1].input[1]",
        "Line[1422] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1732
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 14
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_TARGET_TRANSFORM_NOT_CHECKED"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_TARGET_TRANSFORM_NOT_CHECKED"
          }
        ]
      },
      "diagnostics": "Transform pointer not checked yet",
      "location": [
        "StructureMap.group[1].rule[6].target[0]",
        "Line[1732] Col[14]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1751
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[2].input[0]",
        "Line[1751] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1756
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type GenomicVariantResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3759 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[2].input[1]",
        "Line[1756] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1860
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type PharmacogeneticTestResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.7066 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[3].input[0]",
        "Line[1860] Col[10]"
      ]
    },
    {
      "extension": [
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-line",
          "valueInteger": 1938
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col",
          "valueInteger": 10
        },
        {
          "url": "http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id",
          "valueString": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
        }
      ],
      "severity": "warning",
      "code": "processing",
      "details": {
        "coding": [
          {
            "system": "http://hl7.org/fhir/java-core-messageId",
            "code": "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE"
          }
        ]
      },
      "diagnostics": "The type GenomicVariantResult which maps to the canonical URL https://ckm.openehr.org/ckm/archetypes/1013.1.3759 is not known, so the paths cannot be validated",
      "location": [
        "StructureMap.group[4].input[0]",
        "Line[1938] Col[10]"
      ]
    }
  ]
}

omarisgreat · 2025-05-27T10:55:47Z

Many thanks, I'll hold off on merging until we have a strategic direction on what to do regarding the validator issues.

Needs criteria to differentiate requests that are for Duo/Trio vs. other child test scenarios

This reverts commit 047177d.

…ureMap-PharmacogeneticTestResult-Genomics Removing file extension to bypass validation issues (to be rectified once validation issues are sorted out)

omarisgreat added 5 commits April 22, 2025 13:36

StructureMap for PGx result

5a0ad3c

Correction to SNOMED display term

ad726df

Removal of unneeded targets

5b92526

Removal of placeholders and Range function

77a6046

Removal of TherapeuticImplication target

5dab576

omarisgreat added 2 commits May 23, 2025 09:23

Merge branch 'main' into Issue-2671

4877e83

Removal of evaluate operation

dbdab8a

omarisgreat requested a review from ryma2fhir May 23, 2025 13:37

omarisgreat and others added 4 commits May 30, 2025 17:18

First draft of Graph definition for child requests

047177d

Needs criteria to differentiate requests that are for Duo/Trio vs. other child test scenarios

Revert "First draft of Graph definition for child requests"

0b20fb4

This reverts commit 047177d.

Merge branch 'main' into Issue-2671

5f6e318

Rename StructureMap-PharmacogeneticTestResult-Genomics.json to Struct…

1e8d021

…ureMap-PharmacogeneticTestResult-Genomics Removing file extension to bypass validation issues (to be rectified once validation issues are sorted out)

omarisgreat merged commit 7705bf7 into main Jan 26, 2026
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StructureMap for PGx result#160

StructureMap for PGx result#160
omarisgreat merged 11 commits intomainfrom
Issue-2671

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