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medizininformatik-initiative / sq2cql

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Fix Translation of Consent #68

Closed juliangruendner closed 10 months ago

juliangruendner commented 10 months ago

Consent ist not translated correctly. Instead of using the "termCodeFhirPath": "provision.provision.code" it alway creates Consent as: exists [Consent: Code '2.16.840.1.113883.3.1937.777.24.5.3.8' from consent]

Input SQ:

{
  "version": "http://to_be_decided.com/draft-1/schema#",
  "display": "",
  "inclusionCriteria": [
    [
      {
        "context": {
          "code": "Einwilligung",
          "display": "Einwilligung",
          "system": "fdpg.mii.cds",
          "version": "1.0.0"
        },
        "termCodes": [
          {
            "code": "2.16.840.1.113883.3.1937.777.24.5.3.8",
            "display": "MDAT wissenschaftlich nutzen EU DSGVO NIVEAU",
            "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3"
          }
        ]
      }
    ]
  ]
}

Current CQL:

library Retrieve version '1.0.0'
using FHIR version '4.0.0'
include FHIRHelpers version '4.0.0'

codesystem consent: 'urn:oid:2.16.840.1.113883.3.1937.777.24.5.3'

context Patient

define InInitialPopulation:
  exists [Consent: Code '2.16.840.1.113883.3.1937.777.24.5.3.8' from consent]

Instead CQL should contain:

C.provision.provision.code.coding contains Code '2.16.840.1.113883.3.1937.777.24.5.3.8'' from consent

Test bundle which schould return exactly one patient if query male

{
  "resourceType": "Bundle",
  "type": "transaction",
  "entry": [ {
    "fullUrl": "Patient/VHF00017",
    "resource": {
      "resourceType": "Patient",
      "id": "VHF00017",
      "meta": {
        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/Patient" ]
      },
      "identifier": [ {
        "use": "usual",
        "type": {
          "coding": [ {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
            "code": "MR"
          } ]
        },
        "system": "https://VHF.de/pid",
        "value": "VHF00017"
      } ],
      "name": [ {
        "use": "official",
        "family": "DUMMY_SURNAME",
        "given": [ "DUMMY_NAME" ]
      } ],
      "gender": "male",
      "birthDate": "2000-07-01",
      "address": [ {
        "extension": [ {
          "url": "http://terminology.hl7.org/CodeSystem/data-absent-reason",
          "valueCode": "unknown"
        } ]
      } ]
    },
    "request": {
      "method": "PUT",
      "url": "Patient/VHF00017"
    }
  }, {
    "fullUrl": "Encounter/VHF00017-E-1",
    "resource": {
      "resourceType": "Encounter",
      "id": "VHF00017-E-1",
      "meta": {
        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/StructureDefinition/KontaktGesundheitseinrichtung" ]
      },
      "identifier": [ {
        "type": {
          "coding": [ {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
            "code": "VN"
          } ]
        },
        "_system": {
          "extension": [ {
            "url": "http://terminology.hl7.org/CodeSystem/data-absent-reason",
            "valueCode": "unknown"
          } ]
        },
        "value": "VHF00017-E-1",
        "assigner": {
          "identifier": {
            "system": "https://www.medizininformatik-initiative.de/fhir/core/NamingSystem/org-identifier",
            "value": "VHF"
          }
        }
      } ],
      "status": "finished",
      "class": {
        "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
        "code": "IMP",
        "display": "inpatient encounter"
      },
      "type": [ {
        "coding": [ {
          "code": "einrichtungskontakt",
          "display": "Einrichtungskontakt"
        } ]
      } ],
      "subject": {
        "reference": "Patient/VHF00017"
      },
      "period": {
        "start": "2021-01-01T00:00:00+01:00",
        "end": "2021-01-02T00:00:00+01:00"
      },
      "diagnosis": [ {
        "condition": {
          "reference": "Condition/VHF00017-CD-1"
        },
        "use": {
          "coding": [ {
            "system": "http://terminology.hl7.org/CodeSystem/diagnosis-role",
            "code": "CC",
            "display": "Chief complaint"
          } ]
        }
      } ]
    },
    "request": {
      "method": "PUT",
      "url": "Encounter/VHF00017-E-1"
    }
  }, {
    "fullUrl": "Encounter/VHF00017-E-1-A-1",
    "resource": {
      "resourceType": "Encounter",
      "id": "VHF00017-E-1-A-1",
      "meta": {
        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/StructureDefinition/KontaktGesundheitseinrichtung" ]
      },
      "status": "finished",
      "class": {
        "extension": [ {
          "url": "http://terminology.hl7.org/CodeSystem/data-absent-reason",
          "valueCode": "unknown"
        } ]
      },
      "type": [ {
        "coding": [ {
          "code": "abteilungskontakt",
          "display": "Abteilungskontakt"
        } ]
      } ],
      "serviceType": {
        "coding": [ {
          "system": "http://fhir.de/CodeSystem/dkgev/Fachabteilungsschluessel",
          "code": "0300",
          "display": "Kardiologie"
        } ]
      },
      "subject": {
        "reference": "Patient/VHF00017"
      },
      "period": {
        "start": "2021-01-01T00:00:00+01:00",
        "end": "2021-01-02T00:00:00+01:00"
      },
      "diagnosis": [ {
        "condition": {
          "_reference": {
            "extension": [ {
              "url": "http://terminology.hl7.org/CodeSystem/data-absent-reason",
              "valueCode": "unknown"
            } ]
          }
        }
      } ],
      "partOf": {
        "reference": "Encounter/VHF00017-E-1"
      }
    },
    "request": {
      "method": "PUT",
      "url": "Encounter/VHF00017-E-1-A-1"
    }
  }, {
    "fullUrl": "Observation/VHF00017-E-1-OL-1",
    "resource": {
      "resourceType": "Observation",
      "id": "VHF00017-E-1-OL-1",
      "meta": {
        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/ObservationLab" ]
      },
      "identifier": [ {
        "type": {
          "coding": [ {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
            "code": "OBI"
          } ]
        },
        "system": "https://VHF.de/befund",
        "value": "VHF00017-E-1-OL-1",
        "assigner": {
          "identifier": {
            "system": "https://www.medizininformatik-initiative.de/fhir/core/NamingSystem/org-identifier",
            "value": "VHF"
          }
        }
      } ],
      "status": "final",
      "category": [ {
        "coding": [ {
          "system": "http://terminology.hl7.org/CodeSystem/observation-category",
          "code": "laboratory",
          "display": "Laboratory"
        }, {
          "system": "http://loinc.org",
          "code": "26436-6",
          "display": "Laboratory studies (set)"
        } ]
      } ],
      "code": {
        "coding": [ {
          "system": "http://loinc.org",
          "code": "33762-6"
        } ],
        "text": "NT-proBNP SerPl-mCnc"
      },
      "subject": {
        "reference": "Patient/VHF00017"
      },
      "encounter": {
        "reference": "Encounter/VHF00017-E-1"
      },
      "effectiveDateTime": "2021-01-01T00:00:00+01:00",
      "valueQuantity": {
        "value": 17.8,
        "unit": "picogram per milliliter",
        "system": "http://unitsofmeasure.org",
        "code": "pg/mL"
      }
    },
    "request": {
      "method": "PUT",
      "url": "Observation/VHF00017-E-1-OL-1"
    }
  }, {
    "fullUrl": "Condition/VHF00017-CD-1",
    "resource": {
      "resourceType": "Condition",
      "id": "VHF00017-CD-1",
      "meta": {
        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose" ]
      },
      "identifier": [ {
        "value": "VHF00017-CD-1"
      } ],
      "code": {
        "coding": [ {
          "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
          "version": "2020",
          "code": "I95.0"
        } ],
        "text": "Idiopathische Hypotonie"
      },
      "subject": {
        "reference": "Patient/VHF00017"
      },
      "recordedDate": "2021-01-01T00:00:00+01:00"
    },
    "request": {
      "method": "PUT",
      "url": "Condition/VHF00017-CD-1"
    }
  }, {
    "fullUrl": "Consent/VHF00017-CO-1",
    "resource": {
      "resourceType": "Consent",
      "id": "VHF00017-CO-1",
      "meta": {
        "profile": [ "http://fhir.de/ConsentManagement/StructureDefinition/Consent" ]
      },
      "status": "active",
      "scope": {
        "coding": [ {
          "system": "http://terminology.hl7.org/CodeSystem/consentscope",
          "code": "research"
        } ]
      },
      "category": [ {
        "coding": [ {
          "system": "http://loinc.org",
          "code": "59284-0"
        } ]
      } ],
      "patient": {
        "reference": "Patient/VHF00017"
      },
      "dateTime": "2021-01-01T00:00:00+01:00",
      "policy": [ {
        "uri": "https://www.medizininformatik-initiative.de/sites/default/files/2020-04/MII_AG-Consent_Einheitlicher-Mustertext_v1.6d.pdf"
      } ],
      "provision": {
        "type": "deny",
        "period": {
          "start": "2021-01-01T00:00:00+01:00",
          "end": "2050-12-31T00:00:00+01:00"
        },
        "provision": [ {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.2",
              "display": "IDAT_erheben"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.3",
              "display": "IDAT_speichern_verarbeiten"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.4",
              "display": "IDAT_zusammenfuehren_Dritte"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.5",
              "display": "IDAT_bereitstellen_EU_DSGVO_NIVEAU"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2025-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.6",
              "display": "MDAT_erheben"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.7",
              "display": "MDAT_speichern_verarbeiten"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.8",
              "display": "MDAT_wissenschaftlich_nutzen_EU_DSGVO_NIVEAU"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.9",
              "display": "MDAT_zusammenfuehren_Dritte"
            } ]
          } ]
        }, {
          "type": "permit",
          "period": {
            "start": "2021-01-01T00:00:00+01:00",
            "end": "2050-12-31T00:00:00+01:00"
          },
          "code": [ {
            "coding": [ {
              "system": "urn:oid:2.16.840.1.113883.3.1937.777.24.5.3",
              "code": "2.16.840.1.113883.3.1937.777.24.5.3.37",
              "display": "Rekontaktierung_Ergebnisse_erheblicher_Bedeutung"
            } ]
          } ]
        } ]
      }
    },
    "request": {
      "method": "PUT",
      "url": "Consent/VHF00017-CO-1"
    }
  } ]
}