/// url = 'https://fhir.slade360.co.ke/fhir/StructureMap/ExtractInpatientNutritionScreening'
/// name = 'ExtractInpatientNutritionScreening'
/// title = 'Inpatient Nutrition Screening (MUST) Extraction'
/// status = 'active'
/// description = 'The MUST score becomes one Observation carrying the total with its three steps as components, plus a RiskAssessment for the band. The nutritional plan becomes a CarePlan, and a score in the high-risk band raises a dietitian referral. That referral is intent `proposal` and status `draft` deliberately: a map should not put an active order in a dietitian\'s queue on its own, so it arrives as something a clinician signs.'

uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QR as source
uses "http://hl7.org/fhir/StructureDefinition/Bundle" alias Bundle as target
uses "http://hl7.org/fhir/StructureDefinition/Observation" alias Observation as target
uses "http://hl7.org/fhir/StructureDefinition/RiskAssessment" alias RiskAssessment as target
uses "http://hl7.org/fhir/StructureDefinition/CarePlan" alias CarePlan as target
uses "http://hl7.org/fhir/StructureDefinition/ServiceRequest" alias ServiceRequest as target

group ExtractInpatientNutritionScreening(source qr : QR, target bundle : Bundle) {
  qr -> bundle.type = 'transaction' "setBundleType";
  // ── MUST score ─────────────────────────────────────────────────────────────
  // LOINC has 101789-6 for the screening itself and 101807-6 for its result
  // indicator, but nothing for the three steps, so those carry local codes.
  qr.item as gM where ((linkId = 'must') and item.answer.value.ofType(Coding).exists()) then {
    gM ->  bundle.entry as entryM,  entryM.resource = create('Observation') as obsM then {
      qr ->  obsM,  entryM then BuildObsBase(qr, obsM, entryM) "mustBase";
      qr -> obsM then SetSurveyCategory(qr, obsM) "mustCategory";
      qr -> obsM.code as code then {
        qr -> code.coding as coding then {
          qr -> coding.system = 'http://loinc.org' "codeSystem";
          qr -> coding.code = '101789-6' "codeCode";
          qr -> coding.display = 'Malnutrition risk screening' "codeDisplay";
        } "codeCoding";
        qr -> code.text = 'MUST score' "codeText";
      } "mustCode";
      // The submitted total wins; otherwise sum the answers, reading each
      // weight off the tail of its code (must-loss-2 is worth 2). Guarded on
      // all three steps being answered -- MUST is a sum of three, and a sum of
      // two banded as low risk would send a wasting patient home.
      gM where (item.answer.value.ofType(Coding).count() = 3) then {
        gM -> obsM.value = evaluate(gM, iif(item.where(linkId = 'must.total').answer.value.exists(), item.where(linkId = 'must.total').answer.value, item.answer.value.ofType(Coding).code.select($this.split('-').last().toInteger()).aggregate($this + $total, 0))) "mustTotalValue";
      } "mustTotalRule";
      gM.item as it where ((linkId = 'must.bmi') and answer.value.exists()) -> obsM.component as comp then {
        it -> comp.code as code then {
          it -> code.coding as coding then {
            it -> coding.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/inpatient-clinical-concept-codesystem' "codeSystem";
            it -> coding.code = 'must-bmi-score' "codeCode";
            it -> coding.display = 'BMI score (MUST)' "codeDisplay";
          } "codeCoding";
        } "bmiCode";
        it -> comp then SetComponentCodedValue(it, comp) "bmiValue";
      } "mustBmiRule";
      gM.item as it where ((linkId = 'must.loss') and answer.value.exists()) -> obsM.component as comp then {
        it -> comp.code as code then {
          it -> code.coding as coding then {
            it -> coding.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/inpatient-clinical-concept-codesystem' "codeSystem";
            it -> coding.code = 'must-weight-loss-score' "codeCode";
            it -> coding.display = 'Unplanned weight loss score (MUST)' "codeDisplay";
          } "codeCoding";
        } "lossCode";
        it -> comp then SetComponentCodedValue(it, comp) "lossValue";
      } "mustLossRule";
      gM.item as it where ((linkId = 'must.acute') and answer.value.exists()) -> obsM.component as comp then {
        it -> comp.code as code then {
          it -> code.coding as coding then {
            it -> coding.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/inpatient-clinical-concept-codesystem' "codeSystem";
            it -> coding.code = 'must-acute-disease-score' "codeCode";
            it -> coding.display = 'Acute disease effect score (MUST)' "codeDisplay";
          } "codeCoding";
        } "acuteCode";
        it -> comp then SetComponentCodedValue(it, comp) "acuteValue";
      } "mustAcuteRule";
      qr ->  obsM,  bundle then AddMustRiskAssessment(obsM, qr, bundle) "mustBand";
      // BAPEN's management guidance for a MUST of 2 or more is to refer to a
      // dietitian, so a high-risk score raises the referral rather than leaving
      // it to be remembered. Draft and proposal: it needs a signature.
      qr ->  obsM,  bundle then AddDietitianReferral(obsM, qr, bundle) "dietitianReferral";
    } "mustObservation";
  } "mustRule";
  // ── Nutritional plan ───────────────────────────────────────────────────────
  qr.item as itP where ((linkId = 'plan') and answer.value.exists()) then {
    itP.answer first as aP then {
      aP ->  bundle.entry as entryC,  entryC.resource = create('CarePlan') as plan then {
        qr -> plan.id = uuid() then SetCarePlanFullUrl(plan, entryC) "idAndFullUrl";
        qr -> entryC.request as request then {
          qr -> request.method = 'POST' "requestMethod";
          qr -> request.url = 'CarePlan' "requestUrl";
        } "entryRequest";
        qr -> plan.status = 'active' "status";
        qr -> plan.intent = 'plan' "intent";
        qr -> plan.category as cat then {
          qr -> cat.coding as coding then {
            qr -> coding.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/inpatient-clinical-concept-codesystem' "categorySystem";
            qr -> coding.code = 'nutrition-care-plan' "categoryCode";
            qr -> coding.display = 'Nutritional plan' "categoryDisplay";
          } "categoryCoding";
        } "category";
        qr -> plan.title = 'Nutritional plan' "title";
        aP.value as v -> plan.description = v "description";
        qr.subject as s -> plan.subject = s;
        qr.encounter as e -> plan.encounter = e;
        qr.authored as t -> plan.created = t "created";
        qr.author as a -> plan.contributor = a "contributorFromAuthor";
        qr where (author.exists().not()) then {
          qr.source as src -> plan.contributor = src "contributorFromSource";
        } "contributorFallback";
        qr -> plan.supportingInfo = create('Reference') as ref then {
          qr.id as qid -> ref.reference = qid "supportingInfoRef";
        } "linkQuestionnaireResponse";
      } "carePlan";
    } "planAnswer";
  } "planRule";
}

// ─────────────────────────────────────────────────────────────────────────────
// MUST bands (BAPEN): 0 low risk, 1 medium risk, 2 or more high risk.
// ─────────────────────────────────────────────────────────────────────────────
group AddMustRiskAssessment(source obs : Observation, source qr : QR, target bundle : Bundle) {
  obs where (value.ofType(integer) = 0) ->  bundle.entry as entry,  entry.resource = create('RiskAssessment') as ra then {
    qr ->  ra,  entry then BuildRiskBase(qr, obs, ra, entry) "riskBase";
    qr -> ra then SetMustRiskCode(qr, ra) "riskCode";
    qr -> ra.prediction as pred then {
      qr -> pred.qualitativeRisk as risk then {
        qr -> risk.coding as coding then {
          qr -> coding.system = 'http://terminology.hl7.org/CodeSystem/risk-probability' "riskSystem";
          qr -> coding.code = 'low' "riskCode";
          qr -> coding.display = 'Low likelihood' "riskDisplay";
        } "riskCoding";
        qr -> risk.text = 'Low risk' "riskText";
      } "qualitativeRisk";
    } "prediction";
  } "mustLow";
  obs where (value.ofType(integer) = 1) ->  bundle.entry as entry,  entry.resource = create('RiskAssessment') as ra then {
    qr ->  ra,  entry then BuildRiskBase(qr, obs, ra, entry) "riskBase";
    qr -> ra then SetMustRiskCode(qr, ra) "riskCode";
    qr -> ra.prediction as pred then {
      qr -> pred.qualitativeRisk as risk then {
        qr -> risk.coding as coding then {
          qr -> coding.system = 'http://terminology.hl7.org/CodeSystem/risk-probability' "riskSystem";
          qr -> coding.code = 'moderate' "riskCode";
          qr -> coding.display = 'Moderate likelihood' "riskDisplay";
        } "riskCoding";
        qr -> risk.text = 'Medium risk' "riskText";
      } "qualitativeRisk";
    } "prediction";
  } "mustMedium";
  obs where (value.ofType(integer) >= 2) ->  bundle.entry as entry,  entry.resource = create('RiskAssessment') as ra then {
    qr ->  ra,  entry then BuildRiskBase(qr, obs, ra, entry) "riskBase";
    qr -> ra then SetMustRiskCode(qr, ra) "riskCode";
    qr -> ra.prediction as pred then {
      qr -> pred.qualitativeRisk as risk then {
        qr -> risk.coding as coding then {
          qr -> coding.system = 'http://terminology.hl7.org/CodeSystem/risk-probability' "riskSystem";
          qr -> coding.code = 'high' "riskCode";
          qr -> coding.display = 'High likelihood' "riskDisplay";
        } "riskCoding";
        qr -> risk.text = 'High risk' "riskText";
      } "qualitativeRisk";
    } "prediction";
  } "mustHigh";
}

group SetMustRiskCode(source qr : QR, target ra : RiskAssessment) {
  qr -> ra.code as code then {
    qr -> code.coding as coding then {
      qr -> coding.system = 'http://loinc.org' "codeSystem";
      qr -> coding.code = '101807-6' "codeCode";
      qr -> coding.display = 'Malnutrition risk screen results indicator' "codeDisplay";
    } "codeCoding";
  } "code";
}

group AddDietitianReferral(source obs : Observation, source qr : QR, target bundle : Bundle) {
  obs where (value.ofType(integer) >= 2) ->  bundle.entry as entry,  entry.resource = create('ServiceRequest') as sr then {
    qr -> sr.id = uuid() then SetServiceRequestFullUrl(sr, entry) "idAndFullUrl";
    qr -> entry.request as request then {
      qr -> request.method = 'POST' "requestMethod";
      qr -> request.url = 'ServiceRequest' "requestUrl";
    } "entryRequest";
    qr -> sr.status = 'draft' "status";
    qr -> sr.intent = 'proposal' "intent";
    qr -> sr.priority = 'routine' "priority";
    // R5 ServiceRequest.code is a CodeableReference, so the concept sits one
    // level down.
    qr -> sr.code as codeRef then {
      qr -> codeRef.concept as concept then {
        qr -> concept.coding as coding then {
          qr -> coding.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/inpatient-clinical-concept-codesystem' "codeSystem";
          qr -> coding.code = 'dietitian-referral' "codeCode";
          qr -> coding.display = 'Referral to a dietitian' "codeDisplay";
        } "codeCoding";
        qr -> concept.text = 'Referral to a dietitian' "codeText";
      } "codeConcept";
    } "serviceRequestCode";
    qr -> sr.performerType as pt then {
      qr -> pt.coding as coding then {
        qr -> coding.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/practitioner-specialty-codesystem' "performerTypeSystem";
        qr -> coding.code = 'nutritionist' "performerTypeCode";
      } "performerTypeCoding";
      qr -> pt.text = 'Nutritionist' "performerTypeText";
    } "performerType";
    qr.subject as s -> sr.subject = s;
    qr.encounter as e -> sr.encounter = e;
    qr.authored as t -> sr.authoredOn = t "authoredOn";
    qr.author as a -> sr.requester = a "requesterFromAuthor";
    qr where (author.exists().not()) then {
      qr.source as src -> sr.requester = src "requesterFromSource";
    } "requesterFallback";
    // Why this referral exists: the score that triggered it.
    obs.id as oid -> sr.reason as reason then {
      oid -> reason.reference = create('Reference') as ref then {
        oid -> ref.reference = append('Observation/', oid) "reasonRef";
      } "reasonTarget";
    } "reason";
    qr -> sr.supportingInfo as si then {
      qr -> si.reference = create('Reference') as ref then {
        qr.id as qid -> ref.reference = qid "supportingInfoRef";
      } "supportingInfoTarget";
    } "linkQuestionnaireResponse";
  } "dietitianReferral";
}

// ─────────────────────────────────────────────────────────────────────────────
// Shared scaffolding. Repeated in each map rather than imported: the transform
// engine resolves `imports` against whatever StructureMaps happen to be on the
// server, and a form that stops extracting because a shared map was not
// uploaded is a worse failure than a duplicated group.
// ─────────────────────────────────────────────────────────────────────────────
// Two notes on what the publisher's StructureMap validator says about this file.
// Source parameters below are left untyped on purpose. Writing `: Element` makes
// the validator compare QuestionnaireResponse.item against the literal 'Element'
// and report them as incompatible with each other, which is noise, not a finding.
// Untyped, it says only that it cannot check the paths.
// `evaluate(context, expression)` is flagged as "takes 1 parameter but 2 were
// found". Leave it. The FML parser in the same jar refuses the one-argument form
// outright -- it wants a parameter, a comma, then the FHIRPath -- so the publisher
// is objecting to what its own compiler emits. Two arguments is the only form that
// compiles, and it is what the R5 transform engine executes.
group BuildObsBase(source qr : QR, target obs : Observation, target entry) {
  qr -> obs.id = uuid() then SetObservationFullUrl(obs, entry) "idAndFullUrl";
  qr -> entry.request as request then {
    qr -> request.method = 'POST' "requestMethod";
    qr -> request.url = 'Observation' "requestUrl";
  } "entryRequest";
  qr -> obs.status = 'final' "status";
  qr.subject as s -> obs.subject = s;
  qr.encounter as e -> obs.encounter = e;
  qr.authored as t -> obs.effective = t "effective";
  qr.source as src -> obs.performer = src "performerFromSource";
  qr where (source.exists().not()) then {
    qr.author as a -> obs.performer = a "performerFromAuthor";
  } "performerFallback";
  qr -> obs.derivedFrom = create('Reference') as ref then {
    qr.id as qid -> ref.reference = qid "derivedFromRef";
  } "linkQuestionnaireResponse";
}

group BuildRiskBase(source qr : QR, source obs : Observation, target ra : RiskAssessment, target entry) {
  qr -> ra.id = uuid() then SetRiskAssessmentFullUrl(ra, entry) "idAndFullUrl";
  qr -> entry.request as request then {
    qr -> request.method = 'POST' "requestMethod";
    qr -> request.url = 'RiskAssessment' "requestUrl";
  } "entryRequest";
  qr -> ra.status = 'final' "status";
  qr.subject as s -> ra.subject = s;
  qr.encounter as e -> ra.encounter = e;
  qr.authored as t -> ra.occurrence = t "occurrence";
  qr.author as a -> ra.performer = a "performerFromAuthor";
  qr where (author.exists().not()) then {
    qr.source as src -> ra.performer = src "performerFromSource";
  } "performerFallback";
  qr -> ra.basis = create('Reference') as qref then {
    qr.id as qid -> qref.reference = qid "basisQuestionnaireResponse";
  } "basisResponse";
  obs.id as oid -> ra.basis = create('Reference') as oref then {
    oid -> oref.reference = append('Observation/', oid) "basisObservationRef";
  } "basisObservation";
}

group SetComponentCodedValue(source it, target comp) {
  it.answer first as a then {
    a.value as cv -> comp.value = create('CodeableConcept') as cc then {
      cv -> cc.coding = cv "valueCoding";
      cv.display as d -> cc.text = d "valueText";
    } "codedValue";
  } "componentAnswer";
}

group SetSurveyCategory(source qr : QR, target obs : Observation) {
  qr -> obs.category as cat then {
    qr -> cat.coding as coding then {
      qr -> coding.system = 'http://terminology.hl7.org/CodeSystem/observation-category' "categorySystem";
      qr -> coding.code = 'survey' "categoryCode";
      qr -> coding.display = 'Survey' "categoryDisplay";
    } "categoryCoding";
  } "category";
}

group SetObservationFullUrl(source obs : Observation, target entry) {
  obs.id as id -> entry.fullUrl = append('https://fhir.slade360.co.ke/fhir/Observation/', id) "assignFullUrl";
}

group SetRiskAssessmentFullUrl(source ra : RiskAssessment, target entry) {
  ra.id as id -> entry.fullUrl = append('https://fhir.slade360.co.ke/fhir/RiskAssessment/', id) "assignFullUrl";
}

group SetCarePlanFullUrl(source plan : CarePlan, target entry) {
  plan.id as id -> entry.fullUrl = append('https://fhir.slade360.co.ke/fhir/CarePlan/', id) "assignFullUrl";
}

group SetServiceRequestFullUrl(source sr : ServiceRequest, target entry) {
  sr.id as id -> entry.fullUrl = append('https://fhir.slade360.co.ke/fhir/ServiceRequest/', id) "assignFullUrl";
}