{ "resourceType" : "StructureMap", "id" : "HRExtractLaboratory", "text" : { "status" : "generated", "div" : "

Generated Narrative: StructureMap HRExtractLaboratory

\r\n/// url = 'https://fhir.optimalhealth.org/ig/healthy-route/StructureMap/HRExtractLaboratory'\r\n/// version = '0.2.0'\r\n/// name = 'HRExtractLaboratory'\r\n/// status = 'draft'\r\n\r\nuses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QR as source\r\nuses "http://hl7.org/fhir/StructureDefinition/Bundle" alias Bundle as target\r\nuses "http://hl7.org/fhir/StructureDefinition/Observation" alias Observation as target\r\nuses "http://hl7.org/fhir/StructureDefinition/Specimen" alias Specimen as target\r\nuses "http://hl7.org/fhir/StructureDefinition/DiagnosticReport" alias DiagnosticReport as target\r\n\r\ngroup HRExtractLaboratory(source qr : QR, target bundle : Bundle) {\r\n  qr -> bundle.type = 'transaction' "type";\r\n  qr -> evaluate(qr, id.replaceMatches('/_history/.*$', '').replaceMatches('^.*/', '')) as qid then {\r\n    qr ->  bundle.entry as e,  e.resource = create('Specimen') as sp then {\r\n      qr ->  append(qid, '-specimen-blood') as idText,  sp.id = cast(idText, 'id') "id";\r\n      qr -> e.fullUrl = append('Specimen/', qid, '-specimen-blood') "fullUrl";\r\n      qr -> e.request as rq then {\r\n        qr -> rq.method = 'PUT' "method";\r\n        qr -> rq.url = append('Specimen/', qid, '-specimen-blood') "url";\r\n      } "request";\r\n      qr -> sp then Sample(qr, sp) "shared";\r\n      qr -> sp.type = create('CodeableConcept') as cv then {\r\n        qr -> cv.coding = create('Coding') as cd then {\r\n          qr -> cd.system = 'http://terminology.hl7.org/CodeSystem/v2-0487' "typeSystem";\r\n          qr -> cd.code = 'BLD' "typeCode";\r\n          qr -> cd.display = 'Whole blood' "typeDisplay";\r\n        } "typeCoding";\r\n      } "type";\r\n    } "blood";\r\n    qr ->  bundle.entry as e,  e.resource = create('Specimen') as sp then {\r\n      qr ->  append(qid, '-specimen-urine') as idText,  sp.id = cast(idText, 'id') "id";\r\n      qr -> e.fullUrl = append('Specimen/', qid, '-specimen-urine') "fullUrl";\r\n      qr -> e.request as rq then {\r\n        qr -> rq.method = 'PUT' "method";\r\n        qr -> rq.url = append('Specimen/', qid, '-specimen-urine') "url";\r\n      } "request";\r\n      qr -> sp then Sample(qr, sp) "shared";\r\n      qr -> sp.type = create('CodeableConcept') as cv then {\r\n        qr -> cv.coding = create('Coding') as cd then {\r\n          qr -> cd.system = 'http://terminology.hl7.org/CodeSystem/v2-0487' "typeSystem";\r\n          qr -> cd.code = 'UR' "typeCode";\r\n          qr -> cd.display = 'Urine' "typeDisplay";\r\n        } "typeCoding";\r\n      } "type";\r\n    } "urine";\r\n    qr ->  bundle.entry as re,  re.resource = create('DiagnosticReport') as rep then {\r\n      qr ->  append(qid, '-report') as idText,  rep.id = cast(idText, 'id') "id";\r\n      qr -> re.fullUrl = append('DiagnosticReport/', qid, '-report') "fullUrl";\r\n      qr -> re.request as rq then {\r\n        qr -> rq.method = 'PUT' "method";\r\n        qr -> rq.url = append('DiagnosticReport/', qid, '-report') "url";\r\n      } "request";\r\n      qr ->  rep.meta as m,  m.profile = 'https://fhir.optimalhealth.org/ig/healthy-route/StructureDefinition/hr-diagnostic-report' "profile";\r\n      qr.meta as qm then {\r\n        qm.tag as t ->  rep.meta as m,  m.tag = t;\r\n      } "tags";\r\n      qr.extension as x where (url = 'https://fhir.optimalhealth.org/ig/healthy-route/StructureDefinition/hr-tenant') -> rep.extension = x "tenant";\r\n      qr -> rep.status = 'final' "status";\r\n      qr -> rep.category = create('CodeableConcept') as cv then {\r\n        qr -> cv.coding = create('Coding') as cd then {\r\n          qr -> cd.system = 'http://terminology.hl7.org/CodeSystem/v2-0074' "categorySystem";\r\n          qr -> cd.code = 'LAB' "categoryCode";\r\n          qr -> cd.display = 'Laboratory' "categoryDisplay";\r\n        } "categoryCoding";\r\n      } "category";\r\n      qr -> rep.code = create('CodeableConcept') as cv then {\r\n        qr -> cv.coding = create('Coding') as cd then {\r\n          qr -> cd.system = 'http://loinc.org' "codeSystem";\r\n          qr -> cd.code = '11502-2' "codeCode";\r\n          qr -> cd.display = 'Laboratory report' "codeDisplay";\r\n        } "codeCoding";\r\n      } "code";\r\n      qr.subject as s -> rep.subject = s;\r\n      qr.encounter as en -> rep.encounter = en;\r\n      qr ->  rep.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-blood') "bloodRef";\r\n      qr ->  rep.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-urine') "urineRef";\r\n      qr.item as ci where (linkId = 'samples-collected') then {\r\n        ci.answer first as ca then {\r\n          ca.value as cv -> rep.effective = cv "effective";\r\n        };\r\n      } "collected";\r\n      qr.item as it where (linkId = '2160-0') then {\r\n        it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n          qr -> obs then Result(qr, it, obs, e) "base";\r\n          qr ->  obs.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-blood') "specimen";\r\n          qr.item as u where (linkId = '2160-0.unit') then {\r\n            u.answer first as ua then {\r\n              ua.value : Coding as uv where (code = 'umol/L') -> obs.code = create('CodeableConcept') as cv then {\r\n                qr -> cv.coding = create('Coding') as cd then {\r\n                  qr -> cd.system = 'http://loinc.org' "molarSystem";\r\n                  qr -> cd.code = '14682-9' "molarCode";\r\n                  qr -> cd.display = 'Creatinine [Moles/volume] in Serum or Plasma' "molarDisplay";\r\n                } "molarCoding";\r\n              } "molar";\r\n              ua.value : Coding as uv where (code = 'mg/dL') -> obs.code = create('CodeableConcept') as cv then {\r\n                qr -> cv.coding = create('Coding') as cd then {\r\n                  qr -> cd.system = 'http://loinc.org' "massSystem";\r\n                  qr -> cd.code = '2160-0' "massCode";\r\n                  qr -> cd.display = 'Creatinine [Mass/volume] in Serum or Plasma' "massDisplay";\r\n                } "massCoding";\r\n              } "mass";\r\n              ua.value : Coding as uv then {\r\n                a.value as v -> obs.value = create('Quantity') as q then {\r\n                  v -> q.value = v "value";\r\n                  qr -> q.system = 'http://unitsofmeasure.org' "system";\r\n                  uv.code as c -> q.code = c "unitCode";\r\n                  uv.display as d -> q.unit = d "unit";\r\n                } "quantity";\r\n              } "withUnit";\r\n            } "unitAnswer";\r\n          } "unit";\r\n          qr ->  rep.result = create('Reference') as r,  r.reference = append('Observation/', qid, '-2160-0') "result";\r\n        } "obs";\r\n      } "creatinine";\r\n      qr.item as it where (linkId = '4548-4') then {\r\n        it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n          qr -> obs then Result(qr, it, obs, e) "base";\r\n          qr ->  obs.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-blood') "specimen";\r\n          qr -> obs.code = create('CodeableConcept') as cv then {\r\n            qr -> cv.coding = create('Coding') as cd then {\r\n              qr -> cd.system = 'http://loinc.org' "codeSystem";\r\n              qr -> cd.code = '4548-4' "codeCode";\r\n              qr -> cd.display = 'Hemoglobin A1c/Hemoglobin.total in Blood' "codeDisplay";\r\n            } "codeCoding";\r\n          } "code";\r\n          a.value as v -> obs.value = create('Quantity') as q then {\r\n            v -> q.value = v "value";\r\n            qr -> q.system = 'http://unitsofmeasure.org' "system";\r\n            qr -> q.code = '%' "unitCode";\r\n            qr -> q.unit = '%' "unit";\r\n          } "quantity";\r\n          qr ->  rep.result = create('Reference') as r,  r.reference = append('Observation/', qid, '-4548-4') "result";\r\n        } "obs";\r\n      } "hba1c";\r\n      qr.item as it where (linkId = '9318-7') then {\r\n        it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n          qr -> obs then Result(qr, it, obs, e) "base";\r\n          qr ->  obs.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-urine') "specimen";\r\n          qr.item as u where (linkId = '9318-7.unit') then {\r\n            u.answer first as ua then {\r\n              ua.value : Coding as uv where (code = 'mg/g') -> obs.code = create('CodeableConcept') as cv then {\r\n                qr -> cv.coding = create('Coding') as cd then {\r\n                  qr -> cd.system = 'http://loinc.org' "massSystem";\r\n                  qr -> cd.code = '9318-7' "massCode";\r\n                  qr -> cd.display = 'Albumin/Creatinine [Mass Ratio] in Urine' "massDisplay";\r\n                } "massCoding";\r\n              } "mass";\r\n              ua.value : Coding as uv where (code = 'mg/mmol') -> obs.code = create('CodeableConcept') as cv then {\r\n                qr -> cv.coding = create('Coding') as cd then {\r\n                  qr -> cd.system = 'http://loinc.org' "ratioSystem";\r\n                  qr -> cd.code = '32294-1' "ratioCode";\r\n                  qr -> cd.display = 'Albumin/Creatinine [Ratio] in Urine' "ratioDisplay";\r\n                } "ratioCoding";\r\n              } "ratio";\r\n              ua.value : Coding as uv then {\r\n                a.value as v -> obs.value = create('Quantity') as q then {\r\n                  v -> q.value = v "value";\r\n                  qr -> q.system = 'http://unitsofmeasure.org' "system";\r\n                  uv.code as c -> q.code = c "unitCode";\r\n                  uv.display as d -> q.unit = d "unit";\r\n                } "quantity";\r\n              } "withUnit";\r\n            } "unitAnswer";\r\n          } "unit";\r\n          qr ->  rep.result = create('Reference') as r,  r.reference = append('Observation/', qid, '-9318-7') "result";\r\n        } "obs";\r\n      } "uacr";\r\n      qr.item as it where (linkId = '20454-5') then {\r\n        it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n          qr -> obs then Result(qr, it, obs, e) "base";\r\n          qr ->  obs.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-urine') "specimen";\r\n          qr -> obs.code = create('CodeableConcept') as cv then {\r\n            qr -> cv.coding = create('Coding') as cd then {\r\n              qr -> cd.system = 'http://loinc.org' "codeSystem";\r\n              qr -> cd.code = '20454-5' "codeCode";\r\n              qr -> cd.display = 'Protein [Presence] in Urine by Test strip' "codeDisplay";\r\n            } "codeCoding";\r\n          } "code";\r\n          a.value as v ->  obs.value = create('CodeableConcept') as concept,  concept.coding = v;\r\n          qr ->  rep.result = create('Reference') as r,  r.reference = append('Observation/', qid, '-20454-5') "result";\r\n        } "obs";\r\n      } "dipstick";\r\n    } "report";\r\n    qr.item as it where (linkId = 'creatinine-converted') then {\r\n      it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n        qr -> obs then Result(qr, it, obs, e) "base";\r\n        qr ->  obs.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-blood') "specimen";\r\n        qr -> obs.code = create('CodeableConcept') as cv then {\r\n          qr -> cv.coding = create('Coding') as cd then {\r\n            qr -> cd.system = 'https://fhir.optimalhealth.org/ig/healthy-route/CodeSystem/hr-measurement' "codeSystem";\r\n            qr -> cd.code = 'creatinine-converted' "codeCode";\r\n            qr -> cd.display = 'Serum creatinine, converted' "codeDisplay";\r\n          } "codeCoding";\r\n        } "code";\r\n        a.value as v -> obs.value = create('Quantity') as q then {\r\n          v -> q.value = v "value";\r\n          qr -> q.system = 'http://unitsofmeasure.org' "system";\r\n          qr -> q.code = 'mg/dL' "unitCode";\r\n          qr -> q.unit = 'mg/dL' "unit";\r\n        } "quantity";\r\n        qr ->  obs.derivedFrom = create('Reference') as r,  r.reference = append('Observation/', qid, '-2160-0') "creatinine";\r\n      } "obs";\r\n    } "creatinineConverted";\r\n    qr.item as it where (linkId = 'egfr-age') then {\r\n      it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n        qr -> obs then Result(qr, it, obs, e) "base";\r\n        qr -> obs.code = create('CodeableConcept') as cv then {\r\n          qr -> cv.coding = create('Coding') as cd then {\r\n            qr -> cd.system = 'https://fhir.optimalhealth.org/ig/healthy-route/CodeSystem/hr-measurement' "codeSystem";\r\n            qr -> cd.code = 'egfr-age' "codeCode";\r\n            qr -> cd.display = 'Age used for the eGFR' "codeDisplay";\r\n          } "codeCoding";\r\n        } "code";\r\n        a.value as v -> obs.value = create('Quantity') as q then {\r\n          v -> q.value = v "value";\r\n          qr -> q.system = 'http://unitsofmeasure.org' "system";\r\n          qr -> q.code = 'a' "unitCode";\r\n          qr -> q.unit = 'years' "unit";\r\n        } "quantity";\r\n      } "obs";\r\n    } "egfrAge";\r\n    qr.item as it where (linkId = 'egfr-sex') then {\r\n      it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n        qr -> obs then Result(qr, it, obs, e) "base";\r\n        qr -> obs.code = create('CodeableConcept') as cv then {\r\n          qr -> cv.coding = create('Coding') as cd then {\r\n            qr -> cd.system = 'https://fhir.optimalhealth.org/ig/healthy-route/CodeSystem/hr-measurement' "codeSystem";\r\n            qr -> cd.code = 'egfr-sex' "codeCode";\r\n            qr -> cd.display = 'Sex used for the eGFR' "codeDisplay";\r\n          } "codeCoding";\r\n        } "code";\r\n        a.value as v -> obs.value = v;\r\n      } "obs";\r\n    } "egfrSex";\r\n    qr.item as it where (linkId = '98979-8') then {\r\n      it.answer first as a ->  bundle.entry as e,  e.resource = create('Observation') as obs then {\r\n        qr -> obs then Result(qr, it, obs, e) "base";\r\n        qr -> obs then Derived(qr, obs) "derivedCategory";\r\n        qr ->  obs.specimen = create('Reference') as r,  r.reference = append('Specimen/', qid, '-specimen-blood') "specimen";\r\n        qr -> obs.code = create('CodeableConcept') as cv then {\r\n          qr -> cv.coding = create('Coding') as cd then {\r\n            qr -> cd.system = 'http://loinc.org' "codeSystem";\r\n            qr -> cd.code = '98979-8' "codeCode";\r\n            qr -> cd.display = 'Glomerular filtration rate [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI 2021)/1.73 sq M' "codeDisplay";\r\n          } "codeCoding";\r\n        } "code";\r\n        a.value as v -> obs.value = create('Quantity') as q then {\r\n          v -> q.value = v "value";\r\n          qr -> q.system = 'http://unitsofmeasure.org' "system";\r\n          qr -> q.code = 'mL/min/{1.73_m2}' "unitCode";\r\n          qr -> q.unit = 'mL/min/1.73m2' "unit";\r\n        } "quantity";\r\n        qr ->  obs.derivedFrom = create('Reference') as r,  r.reference = append('Observation/', qid, '-creatinine-converted') "creatinine";\r\n        qr ->  obs.derivedFrom = create('Reference') as r,  r.reference = append('Observation/', qid, '-egfr-age') "age";\r\n        qr ->  obs.derivedFrom = create('Reference') as r,  r.reference = append('Observation/', qid, '-egfr-sex') "sex";\r\n      } "obs";\r\n    } "egfr";\r\n  } "response";\r\n}\r\n\r\n// The category a value worked out on this form carries beside its FHIR one.\r\ngroup Derived(source qr : QR, target obs : Observation) {\r\n  qr -> obs.category = create('CodeableConcept') as cv then {\r\n    qr -> cv.coding = create('Coding') as cd then {\r\n      qr -> cd.system = 'https://fhir.optimalhealth.org/ig/healthy-route/CodeSystem/hr-observation-category' "derivedSystem";\r\n      qr -> cd.code = 'derived' "derivedCode";\r\n      qr -> cd.display = 'Derived' "derivedDisplay";\r\n    } "derivedCoding";\r\n  } "category";\r\n}\r\n\r\n// What both specimens share: the response's identity and the sample time.\r\ngroup Sample(source qr : QR, target sp : Specimen) {\r\n  qr ->  sp.meta as m,  m.profile = 'https://fhir.optimalhealth.org/ig/healthy-route/StructureDefinition/hr-specimen' "profile";\r\n  qr.meta as qm then {\r\n    qm.tag as t ->  sp.meta as m,  m.tag = t;\r\n  } "tags";\r\n  qr.extension as x where (url = 'https://fhir.optimalhealth.org/ig/healthy-route/StructureDefinition/hr-tenant') -> sp.extension = x "tenant";\r\n  qr -> sp.status = 'available' "status";\r\n  qr.subject as s -> sp.subject = s;\r\n  qr.item as ci where (linkId = 'samples-collected') then {\r\n    ci.answer first as ca then {\r\n      ca.value as cv ->  sp.collection as col,  col.collected = cv "collected";\r\n    };\r\n  } "collected";\r\n  qr.author as au ->  sp.collection as col,  col.collector = au "collector";\r\n}\r\n\r\n// What every result shares: identity, tags, tenant, the laboratory category,\r\n// and the sample time as its effective time.\r\ngroup Result(source qr : QR, source it, target obs : Observation, target e) {\r\n  qr -> evaluate(qr, id.replaceMatches('/_history/.*$', '').replaceMatches('^.*/', '')) as qid then {\r\n    it.linkId as k ->  append(qid, '-', k) as idText,  obs.id = cast(idText, 'id') "id";\r\n    it.linkId as k -> e.fullUrl = append('Observation/', qid, '-', k) "fullUrl";\r\n    it.linkId as k -> e.request as rq then {\r\n      qr -> rq.method = 'PUT' "method";\r\n      qr -> rq.url = append('Observation/', qid, '-', k) "url";\r\n    } "request";\r\n  } "ids";\r\n  qr ->  obs.meta as m,  m.profile = 'https://fhir.optimalhealth.org/ig/healthy-route/StructureDefinition/hr-observation' "profile";\r\n  qr.meta as qm then {\r\n    qm.tag as t ->  obs.meta as m,  m.tag = t;\r\n  } "tags";\r\n  qr.extension as x where (url = 'https://fhir.optimalhealth.org/ig/healthy-route/StructureDefinition/hr-tenant') -> obs.extension = x "tenant";\r\n  qr -> obs.status = 'final' "status";\r\n  qr -> obs.category = create('CodeableConcept') as cv then {\r\n    qr -> cv.coding = create('Coding') as cd then {\r\n      qr -> cd.system = 'http://terminology.hl7.org/CodeSystem/observation-category' "categorySystem";\r\n      qr -> cd.code = 'laboratory' "categoryCode";\r\n      qr -> cd.display = 'Laboratory' "categoryDisplay";\r\n    } "categoryCoding";\r\n  } "category";\r\n  qr.subject as s -> obs.subject = s;\r\n  qr.encounter as en -> obs.encounter = en;\r\n  qr.item as ci where (linkId = 'samples-collected') then {\r\n    ci.answer first as ca then {\r\n      ca.value as cv -> obs.effective = cv "effective";\r\n    };\r\n  } "collected";\r\n}\r\n\r\n
" }, "url" : "https://fhir.optimalhealth.org/ig/healthy-route/StructureMap/HRExtractLaboratory", "version" : "0.2.0", "name" : "HRExtractLaboratory", "status" : "draft", "date" : "2026-11-12T10:14:36+00:00", "publisher" : "Savannah Informatics", "contact" : [{ "name" : "Savannah Informatics", "telecom" : [{ "system" : "url", "value" : "https://optimalhealth.org" }] }, { "name" : "Savannah Informatics", "telecom" : [{ "system" : "url", "value" : "https://optimalhealth.org" }] }], "structure" : [{ "url" : "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse", "mode" : "source", "alias" : "QR" }, { "url" : "http://hl7.org/fhir/StructureDefinition/Bundle", "mode" : "target", "alias" : "Bundle" }, { "url" : "http://hl7.org/fhir/StructureDefinition/Observation", "mode" : "target", "alias" : "Observation" }, { "url" : "http://hl7.org/fhir/StructureDefinition/Specimen", "mode" : "target", "alias" : "Specimen" }, { "url" : "http://hl7.org/fhir/StructureDefinition/DiagnosticReport", "mode" : "target", "alias" : "DiagnosticReport" }], "group" : [{ "name" : "HRExtractLaboratory", "input" : [{ "name" : "qr", "type" : "QR", "mode" : "source" }, { "name" : "bundle", "type" : "Bundle", "mode" : "target" }], "rule" : [{ "name" : "type", "source" : [{ "context" : "qr" }], "target" : [{ "context" : "bundle", "element" : "type", "transform" : "copy", "parameter" : [{ "valueString" : "transaction" }] }] }, { "name" : "response", "source" : [{ "context" : "qr" }], "target" : [{ "variable" : "qid", "transform" : "evaluate", "parameter" : [{ "valueId" : "qr" }, { "valueString" : "id.replaceMatches('/_history/.*$', '').replaceMatches('^.*/', '')" }] }], "rule" : [{ "name" : "blood", "source" : [{ "context" : "qr" }], "target" : [{ "context" : "bundle", "element" : "entry", "variable" : "e" }, { "context" : "e", "element" : "resource", "variable" : "sp", "transform" : "create", "parameter" : [{ "valueString" : "Specimen" }] }], "rule" : [{ "name" : "id", "source" : [{ "context" : "qr" }], "target" : [{ "variable" : "idText", "transform" : "append", "parameter" : [{ "valueId" : "qid" }, { "valueString" : "-specimen-blood" }] }, { "context" : "sp", "element" : "id", "transform" : "cast", "parameter" : [{ "valueId" : "idText" }, { "valueString" : "id" }] }] }, { "name" : "fullUrl", "source" : [{ "context" : "qr" }], "target" : [{ "context" : "e", "element" : "fullUrl", "transform" : "append", "parameter" : [{ "valueString" : "Specimen/" }, { "valueId" : "qid" }, { "valueString" : "-specimen-blood" }] }] }, { "name" : "request", "source" : [{ "context" : "qr" }], "target" : [{ "context" : "e", "element" : "request", "variable" : "rq" }], "rule" : [{ "name" : "method", "source" : [{ "context" : "qr" }], "target" : [{ "context" : "rq", "element" : "method", "transform" : "copy", "parameter" : [{ "valueString" : "PUT" }] }] }, { "name" : "url", "source" : [{ "context" : "qr" }], "target" : [{ "context" : "rq", "element" : "url", "transform" : "append", "parameter" : 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