/// url = 'https://fhir.slade360.co.ke/fhir/StructureMap/ExtractIcuNeurologicalChart'
/// name = 'ExtractIcuNeurologicalChart'
/// title = 'ICU Neurological Observation Chart Extraction'
/// status = 'active'
/// description = 'Each round of the ICU neurological chart out as: one Observation for the Glasgow Coma Scale under LOINC 9269-2, carrying the total as its value and the three components under their own LOINC codes, with the total computed by the map when the client submits none; one for limb power; one per eye for pupil size and reaction, because a unilaterally dilating pupil is the finding that matters and it has to be findable per side; and the four vitals each as their own Observation. Every one takes the round\'s own time, not the form\'s, because the chart is a time series and a deteriorating conscious level is only visible as one.'

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

group ExtractIcuNeurologicalChart(source qr : QR, target bundle : Bundle) {
  qr -> bundle.type = 'transaction' "setBundleType";
  // Day in unit, as its own Observation. Not a component of anything: it is the
  // denominator for every length-of-stay question anyone asks of critical care.
  qr.item as g where (linkId = 'unit') then {
    g.item as it where ((linkId = 'unit/day-in-unit') and answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetSurveyCategory(qr, obs) "category";
      it -> obs.code as cc then {
        it -> cc.coding as cg then {
          it -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
          it -> cg.code = 'obs-day-in-unit' "cd";
          it -> cg.display = 'Day in unit' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v "set";
      };
    } "measure_labour_stage_duration";
    g.item as it where ((linkId = 'unit/diagnosis') and answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetSurveyCategory(qr, obs) "category";
      it -> obs.code as cc then {
        it -> cc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '11450-4' "cd";
          it -> cg.display = 'Problem list - Reported' "dsp";
        } "coding";
        it -> cc.text = 'Diagnosis on the ICU neurological chart' "codeText";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "text";
      };
    } "narr_11450_4";
  } "unitGroup";
  // ── One round at a time ─────────────────────────────────────────────────
  qr.item as g where (linkId = 'round') then {
    // ── The Glasgow Coma Scale ────────────────────────────────────────────
    // One Observation under LOINC 9269-2, total as the value, the three
    // components under 9267-6, 9270-0 and 9268-4. The answers are the IG's own
    // clinical-score codes -- #gcs-eye-1..4 and so on -- reused rather than
    // minted again, so a GCS charted here and a GCS charted on the pain
    // templates' Glasgow form are the same coded answers.
    // The total prefers what the form submitted and otherwise sums the weights
    // off the tails of the answer codes. Guarded on all three components being
    // answered: a GCS of 8 over two components is not a lower GCS, it is a
    // different number, and nothing in the resource would say which.
    g.item as gcs where ((linkId = 'round/gcs') and (item.answer.value.ofType(Coding).count() = 3)) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetExamCategory(qr, obs) "category";
      gcs -> obs.code as cc then {
        gcs -> cc.coding as cg then {
          gcs -> cg.system = 'http://loinc.org' "sys";
          gcs -> cg.code = '9269-2' "cd";
          gcs -> cg.display = 'Glasgow coma score total' "dsp";
        } "coding";
      } "code";
      gcs -> obs.value = evaluate(gcs, iif(item.where(linkId = 'round/gcs/total').answer.value.exists(), item.where(linkId = 'round/gcs/total').answer.value.truncate(), item.answer.value.ofType(Coding).code.select(iif($this.endsWith('-6'), 6, iif($this.endsWith('-5'), 5, iif($this.endsWith('-4'), 4, iif($this.endsWith('-3'), 3, iif($this.endsWith('-2'), 2, iif($this.endsWith('-1'), 1, 0))))))).aggregate($this + $total, 0))) "totalValue";
      // 8 or less is coma. Stated as the interpretation rather than left to a
      // reader, because that threshold is what triggers intubation.
      gcs -> obs.interpretation as interp then {
        gcs -> interp.coding as icg then {
          gcs -> icg.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation' "sys";
          gcs -> icg.code = evaluate(gcs, iif(iif(item.where(linkId = 'round/gcs/total').answer.value.exists(), item.where(linkId = 'round/gcs/total').answer.value.truncate(), item.answer.value.ofType(Coding).code.select(iif($this.endsWith('-6'), 6, iif($this.endsWith('-5'), 5, iif($this.endsWith('-4'), 4, iif($this.endsWith('-3'), 3, iif($this.endsWith('-2'), 2, iif($this.endsWith('-1'), 1, 0))))))).aggregate($this + $total, 0)) <= 8, 'LL', iif(iif(item.where(linkId = 'round/gcs/total').answer.value.exists(), item.where(linkId = 'round/gcs/total').answer.value.truncate(), item.answer.value.ofType(Coding).code.select(iif($this.endsWith('-6'), 6, iif($this.endsWith('-5'), 5, iif($this.endsWith('-4'), 4, iif($this.endsWith('-3'), 3, iif($this.endsWith('-2'), 2, iif($this.endsWith('-1'), 1, 0))))))).aggregate($this + $total, 0)) < 15, 'A', 'N'))) "cd";
        } "coding";
      } "interpretation";
      g.item as tm where ((linkId = 'round/time') and answer.value.exists()) then {
        tm.answer first as a then {
          a.value as t ->  obs.note as n,  n.text = 'Round taken at the time recorded on the chart' "timeNote";
        };
      } "roundTimeRule";
      gcs.item as it where ((linkId = 'round/gcs/eyes-open') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'http://loinc.org' "sys";
            it -> cg.code = '9267-6' "cd";
            it -> cg.display = 'Glasgow coma score eye opening' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentCodedValue(it, comp) "value";
      } "comp_9267_6";
      gcs.item as it where ((linkId = 'round/gcs/verbal-response') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'http://loinc.org' "sys";
            it -> cg.code = '9270-0' "cd";
            it -> cg.display = 'Glasgow coma score verbal' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentCodedValue(it, comp) "value";
      } "comp_9270_0";
      gcs.item as it where ((linkId = 'round/gcs/motor-response') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'http://loinc.org' "sys";
            it -> cg.code = '9268-4' "cd";
            it -> cg.display = 'Glasgow coma score motor' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentCodedValue(it, comp) "value";
      } "comp_9268_4";
    } "gcsObservation";
    // ── Limb power ────────────────────────────────────────────────────────
    // One Observation with arms and legs as components. Together, because the
    // finding that matters is asymmetry and a reader compares them.
    g.item as lm where ((linkId = 'round/limb-movement') and item.answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetExamCategory(qr, obs) "category";
      lm -> obs.code as cc then {
        lm -> cc.coding as cg then {
          lm -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
          lm -> cg.code = 'limb-power' "cd";
          lm -> cg.display = 'Limb power' "dsp";
        } "coding";
      } "code";
      lm.item as it where ((linkId = 'round/limb-movement/arms') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
            it -> cg.code = 'neuro-arm-power' "cd";
            it -> cg.display = 'Arm power' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentCodedValue(it, comp) "value";
      } "comp_neuro_arm_power";
      lm.item as it where ((linkId = 'round/limb-movement/legs') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
            it -> cg.code = 'neuro-leg-power' "cd";
            it -> cg.display = 'Leg power' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentCodedValue(it, comp) "value";
      } "comp_neuro_leg_power";
    } "limbPowerObservation";
    // ── Pupils, one Observation per eye ───────────────────────────────────
    // Per eye and not one panel of four. A unilaterally dilating unreactive
    // pupil is the sign of an expanding mass on that side, and "which side" is
    // the whole question -- so each eye carries its own bodySite and a query
    // can ask about the right pupil alone.
    g.item as pg where ((linkId = 'round/pupils') and item.where(linkId = 'round/pupils/right-reaction').answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetExamCategory(qr, obs) "category";
      pg -> obs.code as cc then {
        pg -> cc.coding as cg then {
          pg -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
          pg -> cg.code = 'pupil-assessment' "cd";
          pg -> cg.display = 'Pupil assessment' "dsp";
        } "coding";
        pg -> cc.text = 'Right pupil' "codeText";
      } "code";
      pg -> obs.bodySite as bsc then {
        pg -> bsc.coding as bcg then {
          pg -> bcg.system = 'http://snomed.info/sct' "sys";
          pg -> bcg.code = '18944008' "cd";
          pg -> bcg.display = 'Right eye structure' "dsp";
        } "coding";
      } "bodySite";
      pg.item as it where ((linkId = 'round/pupils/right-size') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
            it -> cg.code = 'neuro-pupil-size' "cd";
            it -> cg.display = 'Pupil size' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentValue(it, comp) "value";
      } "comp_neuro_pupil_size";
      pg.item as it where ((linkId = 'round/pupils/right-reaction') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
            it -> cg.code = 'neuro-pupil-reaction' "cd";
            it -> cg.display = 'Pupil reaction' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentCodedValue(it, comp) "value";
      } "comp_neuro_pupil_reaction";
    } "pupil_right";
    g.item as pg where ((linkId = 'round/pupils') and item.where(linkId = 'round/pupils/left-reaction').answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetExamCategory(qr, obs) "category";
      pg -> obs.code as cc then {
        pg -> cc.coding as cg then {
          pg -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
          pg -> cg.code = 'pupil-assessment' "cd";
          pg -> cg.display = 'Pupil assessment' "dsp";
        } "coding";
        pg -> cc.text = 'Left pupil' "codeText";
      } "code";
      pg -> obs.bodySite as bsc then {
        pg -> bsc.coding as bcg then {
          pg -> bcg.system = 'http://snomed.info/sct' "sys";
          pg -> bcg.code = '8966001' "cd";
          pg -> bcg.display = 'Left eye structure' "dsp";
        } "coding";
      } "bodySite";
      pg.item as it where ((linkId = 'round/pupils/left-size') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
            it -> cg.code = 'neuro-pupil-size' "cd";
            it -> cg.display = 'Pupil size' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentValue(it, comp) "value";
      } "comp_neuro_pupil_size2";
      pg.item as it where ((linkId = 'round/pupils/left-reaction') and answer.value.exists()) -> obs.component as comp then {
        it -> comp.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
            it -> cg.code = 'neuro-pupil-reaction' "cd";
            it -> cg.display = 'Pupil reaction' "dsp";
          } "coding";
        } "code";
        it -> comp then SetComponentCodedValue(it, comp) "value";
      } "comp_neuro_pupil_reaction2";
    } "pupil_left";
    // ── The four vitals the chart graphs ──────────────────────────────────
    g.item as vg where (linkId = 'round/vitals') then {
      vg.item as it where ((linkId = 'round/vitals/pulse') and answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
        qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
        qr -> obs then SetVitalSignsCategory(qr, obs) "category";
        it -> obs.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'http://loinc.org' "sys";
            it -> cg.code = '8867-4' "cd";
            it -> cg.display = 'Heart rate' "dsp";
          } "coding";
        } "code";
        it.answer first as a then {
          a.value as v -> obs.value = v "set";
        };
      } "vital_8867_4";
      vg.item as it where ((linkId = 'round/vitals/respiratory-rate') and answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
        qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
        qr -> obs then SetVitalSignsCategory(qr, obs) "category";
        it -> obs.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'http://loinc.org' "sys";
            it -> cg.code = '9279-1' "cd";
            it -> cg.display = 'Respiratory rate' "dsp";
          } "coding";
        } "code";
        it.answer first as a then {
          a.value as v -> obs.value = v "set";
        };
      } "vital_9279_1";
      vg.item as it where ((linkId = 'round/vitals/temperature') and answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
        qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
        qr -> obs then SetVitalSignsCategory(qr, obs) "category";
        it -> obs.code as cc then {
          it -> cc.coding as cg then {
            it -> cg.system = 'http://loinc.org' "sys";
            it -> cg.code = '8310-5' "cd";
            it -> cg.display = 'Body temperature' "dsp";
          } "coding";
        } "code";
        it.answer first as a then {
          a.value as v -> obs.value = v "set";
        };
      } "vital_8310_5";
      vg.item as bp where ((linkId = 'round/vitals/blood-pressure') and item.answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
        qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
        qr -> obs then SetVitalSignsCategory(qr, obs) "category";
        bp -> obs.code as cc then {
          bp -> cc.coding as cg then {
            bp -> cg.system = 'http://loinc.org' "sys";
            bp -> cg.code = '85354-9' "cd";
            bp -> cg.display = 'Blood pressure panel with all children optional' "dsp";
          } "coding";
        } "code";
        bp.item as it where ((linkId = 'round/vitals/blood-pressure/systolic') and answer.value.exists()) -> obs.component as comp then {
          it -> comp.code as cc then {
            it -> cc.coding as cg then {
              it -> cg.system = 'http://loinc.org' "sys";
              it -> cg.code = '8480-6' "cd";
              it -> cg.display = 'Systolic blood pressure' "dsp";
            } "coding";
          } "code";
          it -> comp then SetComponentValue(it, comp) "value";
        } "comp_8480_6";
        bp.item as it where ((linkId = 'round/vitals/blood-pressure/diastolic') and answer.value.exists()) -> obs.component as comp then {
          it -> comp.code as cc then {
            it -> cc.coding as cg then {
              it -> cg.system = 'http://loinc.org' "sys";
              it -> cg.code = '8462-4' "cd";
              it -> cg.display = 'Diastolic blood pressure' "dsp";
            } "coding";
          } "code";
          it -> comp then SetComponentValue(it, comp) "value";
        } "comp_8462_4";
      } "bloodPressureObservation";
    } "vitalsGroup";
  } "roundGroup";
}

// ─────────────────────────────────────────────────────────────────────────────
// 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.
// `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 then SetResponseProvenance(qr, obs) "responseProvenance";
  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";
  // A stored response's id already reads "QuestionnaireResponse/<id>", so it is
  // a relative reference as it stands. The hasValue() guard is what stops an
  // unsaved response -- one posted straight to $extract rather than saved first
  // -- from writing "QuestionnaireResponse/null" into the record.
  qr.id as qid where ($this.hasValue()) ->  obs.derivedFrom = create('Reference') as ref,  ref.reference = qid "linkQuestionnaireResponse";
}

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

// The two answer shapes a component can carry. Both read the answer through the
// untyped `.value` accessor: reading `valueCoding` or `valueQuantity` by its
// typed property name fails at transform time on HAPI R5 with "Attempt to read
// invalid property ... on QuestionnaireResponse.item.answer".
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 SetComponentValue(source it, target comp) {
  it.answer first as a then {
    a.value as v -> comp.value = v "plainValue";
  } "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 SetVitalSignsCategory(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 = 'vital-signs' "categoryCode";
      qr -> coding.display = 'Vital Signs' "categoryDisplay";
    } "categoryCoding";
  } "category";
}

group SetExamCategory(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 = 'exam' "categoryCode";
      qr -> coding.display = 'Exam' "categoryDisplay";
    } "categoryCoding";
  } "category";
}

// ── Provenance and tenancy ───────────────────────────────────────────────────
// Two tags on everything this map creates. The first says which questionnaire
// produced it, so a form that reopens mid-admission recalls its own earlier
// entries and not another form's. The second copies the tenant tags off the
// response, because nothing else on the path puts them there.
// The code is the form's document type, not the questionnaire's id: every
// environment mints its own ids, and there is only one set of maps, so an id
// here would tie the tag to whichever environment stamped it.
// ── Provenance and tenancy ───────────────────────────────────────────────────
group SetResponseProvenance(source qr : QR, target r) {
  qr -> r.meta as m then {
    qr -> m.tag as t then {
      qr -> t.system = 'http://slade360edi.com/questionnaire-provenance' "provenanceSystem";
      qr -> t.code = 'icu-neurological-chart' "provenanceCode";
      qr -> t.display = 'ICU neurological observation chart' "provenanceDisplay";
    } "provenanceTag";
  } "provenanceMeta";
  // Every tag the response carries, onto the resource. `meta` is 0..1, so this
  // lands on the same meta the rule above created rather than a second one.
  qr.meta as qm then {
    qm.tag as qt ->  r.meta as m,  m.tag = qt "copyTag";
  } "tenantTags";
}