/// url = 'https://fhir.slade360.co.ke/fhir/StructureMap/ExtractChemotherapyProtocolCycles'
/// name = 'ExtractChemotherapyProtocolCycles'
/// title = 'Chemotherapy Protocol Cycle Extraction'
/// status = 'active'
/// description = 'One laboratory Observation per value per cycle, each taking the cycle\'s own date rather than the form\'s, because the whole reason this sheet exists is to be read as a series: a neutrophil count means one thing on its own and another as the third fall in a row. The absolute neutrophil count carries an interpretation, low below 1.0 and critically low below 0.5, because those are the thresholds that defer a cycle.'

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 ExtractChemotherapyProtocolCycles(source qr : QR, target bundle : Bundle) {
  qr -> bundle.type = 'transaction' "setBundleType";
  qr.item as g where (linkId = 'protocol') then {
    g.item as it where ((linkId = 'protocol/regimen') 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 = 'chemotherapy-regimen' "cd";
          it -> cg.display = 'Chemotherapy regimen' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "text";
      };
    } "narr_chemotherapy_regimen";
    g.item as it where ((linkId = 'protocol/weight') 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 = '29463-7' "cd";
          it -> cg.display = 'Body weight' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v "set";
      };
    } "measure_29463_7";
    g.item as it where ((linkId = 'protocol/height') 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 = '8302-2' "cd";
          it -> cg.display = 'Body height' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v "set";
      };
    } "measure_8302_2";
    g.item as it where ((linkId = 'protocol/body-surface-area') 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 = '8277-6' "cd";
          it -> cg.display = 'Body surface area' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = create('Quantity') as q then {
          v -> q.value = v "qValue";
          v -> q.unit = 'm2' "qUnit";
          v -> q.system = 'http://unitsofmeasure.org' "qSystem";
          v -> q.code = 'm2' "qCode";
        } "quantity";
      };
    } "measureq_8277_6";
  } "protocolGroup";
  // ── One cycle at a time ─────────────────────────────────────────────────
  qr.item as c where (linkId = 'cycle') then {
    c.item as it where ((linkId = 'cycle/haemoglobin') and answer.value.ofType(Quantity).exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetLaboratoryCategory(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 = '718-7' "cd";
          it -> cg.display = 'Hemoglobin [Mass/volume] in Blood' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v;
      };
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cyclelab_haemoglobin";
    c.item as it where ((linkId = 'cycle/platelets') and answer.value.ofType(Quantity).exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetLaboratoryCategory(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 = '777-3' "cd";
          it -> cg.display = 'Platelets [#/volume] in Blood by Automated count' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v;
      };
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cyclelab_platelets";
    c.item as it where ((linkId = 'cycle/creatinine') and answer.value.ofType(Quantity).exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetLaboratoryCategory(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 = '2160-0' "cd";
          it -> cg.display = 'Creatinine [Mass/volume] in Serum or Plasma' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v;
      };
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cyclelab_creatinine";
    c.item as it where ((linkId = 'cycle/urea') and answer.value.ofType(Quantity).exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetLaboratoryCategory(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 = '3094-0' "cd";
          it -> cg.display = 'Urea nitrogen [Mass/volume] in Serum or Plasma' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v;
      };
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cyclelab_urea";
    // The neutrophil count, interpreted. Below 1.0 x10^9/L most protocols
    // defer the cycle and below 0.5 the patient is neutropenic and at risk
    // from an infection they cannot mount a response to. Leaving a reader to
    // notice the number is not good enough on the one value that stops
    // treatment.
    c.item as it where ((linkId = 'cycle/anc') and answer.value.ofType(Quantity).exists()) ->  bundle.entry as entry,  entry.resource = create('Observation') as obs then {
      qr ->  obs,  entry then BuildObsBase(qr, obs, entry) "base";
      qr -> obs then SetLaboratoryCategory(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 = '751-8' "cd";
          it -> cg.display = 'Neutrophils [#/volume] in Blood by Automated count' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v;
      };
      it -> obs.interpretation as interp then {
        it -> interp.coding as icg then {
          it -> icg.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation' "sys";
          it -> icg.code = evaluate(it, iif(answer.value.ofType(Quantity).value < 0.5, 'LL', iif(answer.value.ofType(Quantity).value < 1.0, 'L', 'N'))) "cd";
        } "coding";
      } "interpretation";
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cycleAnc";
    c.item as it where ((linkId = 'cycle/pulse') and answer.value.ofType(Quantity).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;
      };
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cyclePulse";
    c.item as it where ((linkId = 'cycle/weight') and answer.value.ofType(Quantity).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 = '29463-7' "cd";
          it -> cg.display = 'Body weight' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as v -> obs.value = v;
      };
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cycleWeight";
    // Blood pressure travels as typed -- "128/76" on one line. Split into a
    // systolic and a diastolic component it would have to be parsed, and a
    // mis-parsed blood pressure is worse than a legible string.
    c.item as it where ((linkId = 'cycle/blood-pressure') 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 = '85354-9' "cd";
          it -> cg.display = 'Blood pressure panel with all children optional' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "bpText";
      };
      c -> obs then SetCycleContext(c, obs) "cycleContext";
    } "cycleBloodPressure";
    c.item as it where ((linkId = 'cycle/remarks') 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 = 'chemo-remarks-on-a-chemotherapy-cycle' "cd";
          it -> cg.display = 'Remarks on a chemotherapy cycle' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "text";
      };
    } "narr_chemo_remarks_on_a_chemotherapy_cycle";
  } "cycleRows";
}

// The cycle's own date and number, on every Observation from that cycle. The
// date overrides the response's authored time: a sheet written up at the end of
// six cycles would otherwise collapse all six onto one instant and the series
// -- which is the entire point of the sheet -- would be gone.
group SetCycleContext(source c, target obs : Observation) {
  c.item as it where ((linkId = 'cycle/date') and answer.value.exists()) then {
    it.answer first as a then {
      a.value as v -> obs.effective = cast(v, 'dateTime') "effectiveFromCycle";
    };
  } "cycleDateRule";
  c.item as it where ((linkId = 'cycle/number') and answer.value.exists()) then {
    it.answer first as a then {
      a.value as n ->  obs.note as note,  note.text = 'Recorded against a numbered cycle on the chemotherapy protocol sheet' "cycleNote";
    };
  } "cycleNumberRule";
  c.item as it where ((linkId = 'cycle/signed-by') and answer.value.exists()) then {
    it.answer first as a then {
      a.value as ref -> obs.performer = ref "performer";
    };
  } "signedByRule";
}

// ─────────────────────────────────────────────────────────────────────────────
// 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 SetLaboratoryCategory(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 = 'laboratory' "categoryCode";
      qr -> coding.display = 'Laboratory' "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";
}

// ── 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 = 'chemotherapy-protocol-cycles' "provenanceCode";
      qr -> t.display = 'Chemotherapy protocol cycle record' "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";
}