/// url = 'https://fhir.slade360.co.ke/fhir/StructureMap/ExtractMortalityCommitteeFindings'
/// name = 'ExtractMortalityCommitteeFindings'
/// title = 'Mortality Committee Findings Extraction'
/// status = 'active'
/// description = 'The death review as a Composition under LOINC 34133-9, one section per numbered question, each section naming an Observation that carries its text. A governance document rather than a clinical note, so it is kept whole: the committee\'s opinion means nothing separated from the initial management it is an opinion about.'

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/Composition" alias Composition as target

group ExtractMortalityCommitteeFindings(source qr : QR, target bundle : Bundle) {
  qr -> bundle.type = 'transaction' "setBundleType";
  qr ->  bundle.entry as entry,  entry.resource = create('Composition') as comp then {
    qr ->  comp,  entry then BuildCompositionBase(qr, comp, entry) "base";
    qr -> comp.status = 'final' "status";
    qr -> comp.title = 'Mortality committee findings and recommendations' "title";
    qr.authored as t -> comp.date = t "date";
    qr.source as src -> comp.author = src "author";
    qr -> comp.type as tp then {
      qr -> tp.coding as cg then {
        qr -> cg.system = 'http://loinc.org' "sys";
        qr -> cg.code = '34133-9' "cd";
        qr -> cg.display = 'Summary of episode note' "dsp";
      } "coding";
    } "type";
    qr -> comp.category as cat then {
      qr -> cat.coding as cg then {
        qr -> cg.system = 'https://fhir.slade360.co.ke/fhir/CodeSystem/document-type-codesystem' "sys";
        qr -> cg.code = 'mortality-committee-findings' "cd";
        qr -> cg.display = 'Mortality committee findings and recommendations' "dsp";
      } "coding";
    } "category";
    // Restricted by default. This is a death review, and whether it belongs in
    // the patient's clinical record at all is a policy question -- so it is
    // labelled as the more sensitive of the two possibilities rather than the
    // less, which is the safe direction to be wrong in.
    // R5 removed Composition.confidentiality; the label lives in
    // Resource.meta.security. Restricted rather than normal, deliberately: for
    // a death review and for the mortuary set, whether the record belongs in
    // the patient's clinical file at all is an open policy question, and the
    // safe direction to be wrong in is the more protective one.
    qr ->  comp.meta as m,  m.security as sec then {
      qr -> sec.system = 'http://terminology.hl7.org/CodeSystem/v3-Confidentiality' "sys";
      qr -> sec.code = 'R' "cd";
      qr -> sec.display = 'restricted' "dsp";
    } "confidentiality";
    qr.item as g where (linkId = 'review') then {
      g.item as it where ((linkId = 'review/attendance-or-admission') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as v ->  comp.event as ev,  ev.period as per,  per.start = v "eventStart";
        };
      } "attendanceRule";
      g.item as it where ((linkId = 'review/chairman') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as txt -> comp.attester as att then {
            txt ->  att.mode as am,  am.text = 'Chairman of the mortality committee' "mode";
            txt ->  att.party = create('Reference') as pref,  pref.display = txt "party";
          } "attester";
        };
      } "chairmanRule";
      g.item as it where ((linkId = 'review/secretary') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as txt ->  comp.note as n,  n.text = txt "secretaryNote";
        };
      } "secretaryRule";
    } "reviewGroup";
    qr.item as it where ((linkId = 'presenting-complaints') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Initial presenting complaints' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '10164-2' "cd";
          it -> cg.display = 'History of Present illness Narrative' "dsp";
        } "coding";
      } "code";
      it ->  bundle.entry as sentry,  sentry.resource = create('Observation') as sobs then {
        qr ->  sobs,  sentry then BuildObsBase(qr, sobs, sentry) "base";
        qr -> sobs then SetSurveyCategory(qr, sobs) "category";
        it -> sobs.code as scc then {
          it -> scc.coding as scg then {
            it -> scg.system = 'http://loinc.org' "sys";
            it -> scg.code = '10164-2' "cd";
            it -> scg.display = 'History of Present illness Narrative' "dsp";
          } "coding";
          it -> scc.text = 'Initial presenting complaints on the Mortality committee review' "codeText";
        } "code";
        it.answer first as a then {
          a.value as txt ->  sobs.note as n,  n.text = txt "text";
        };
        it ->  sec.entry = create('Reference') as sref,  sref.reference = reference(sobs) "linkEntry";
      } "sectionObservation";
    } "section_presenting_complaints";
    qr.item as it where ((linkId = 'previous-history') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Previous available medical history' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '11348-0' "cd";
          it -> cg.display = 'History of Past illness note' "dsp";
        } "coding";
      } "code";
      it ->  bundle.entry as sentry,  sentry.resource = create('Observation') as sobs then {
        qr ->  sobs,  sentry then BuildObsBase(qr, sobs, sentry) "base";
        qr -> sobs then SetSurveyCategory(qr, sobs) "category";
        it -> sobs.code as scc then {
          it -> scc.coding as scg then {
            it -> scg.system = 'http://loinc.org' "sys";
            it -> scg.code = '11348-0' "cd";
            it -> scg.display = 'History of Past illness note' "dsp";
          } "coding";
          it -> scc.text = 'Previous available medical history on the Mortality committee review' "codeText";
        } "code";
        it.answer first as a then {
          a.value as txt ->  sobs.note as n,  n.text = txt "text";
        };
        it ->  sec.entry = create('Reference') as sref,  sref.reference = reference(sobs) "linkEntry";
      } "sectionObservation";
    } "section_previous_history";
    qr.item as it where ((linkId = 'initial-management') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Initial management' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '18776-5' "cd";
          it -> cg.display = 'Plan of care note' "dsp";
        } "coding";
      } "code";
      it ->  bundle.entry as sentry,  sentry.resource = create('Observation') as sobs then {
        qr ->  sobs,  sentry then BuildObsBase(qr, sobs, sentry) "base";
        qr -> sobs then SetSurveyCategory(qr, sobs) "category";
        it -> sobs.code as scc then {
          it -> scc.coding as scg then {
            it -> scg.system = 'http://loinc.org' "sys";
            it -> scg.code = '18776-5' "cd";
            it -> scg.display = 'Plan of care note' "dsp";
          } "coding";
          it -> scc.text = 'Initial management on the Mortality committee review' "codeText";
        } "code";
        it.answer first as a then {
          a.value as txt ->  sobs.note as n,  n.text = txt "text";
        };
        it ->  sec.entry = create('Reference') as sref,  sref.reference = reference(sobs) "linkEntry";
      } "sectionObservation";
    } "section_initial_management";
    qr.item as it where ((linkId = 'complications') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Observed complications' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '55109-3' "cd";
          it -> cg.display = 'Complications Document' "dsp";
        } "coding";
      } "code";
      it ->  bundle.entry as sentry,  sentry.resource = create('Observation') as sobs then {
        qr ->  sobs,  sentry then BuildObsBase(qr, sobs, sentry) "base";
        qr -> sobs then SetSurveyCategory(qr, sobs) "category";
        it -> sobs.code as scc then {
          it -> scc.coding as scg then {
            it -> scg.system = 'http://loinc.org' "sys";
            it -> scg.code = '55109-3' "cd";
            it -> scg.display = 'Complications Document' "dsp";
          } "coding";
          it -> scc.text = 'Observed complications on the Mortality committee review' "codeText";
        } "code";
        it.answer first as a then {
          a.value as txt ->  sobs.note as n,  n.text = txt "text";
        };
        it ->  sec.entry = create('Reference') as sref,  sref.reference = reference(sobs) "linkEntry";
      } "sectionObservation";
    } "section_complications";
    qr.item as it where ((linkId = 'committee-opinion') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Opinion of the committee' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '51848-0' "cd";
          it -> cg.display = 'Evaluation note' "dsp";
        } "coding";
      } "code";
      it ->  bundle.entry as sentry,  sentry.resource = create('Observation') as sobs then {
        qr ->  sobs,  sentry then BuildObsBase(qr, sobs, sentry) "base";
        qr -> sobs then SetSurveyCategory(qr, sobs) "category";
        it -> sobs.code as scc then {
          it -> scc.coding as scg then {
            it -> scg.system = 'http://loinc.org' "sys";
            it -> scg.code = '51848-0' "cd";
            it -> scg.display = 'Evaluation note' "dsp";
          } "coding";
          it -> scc.text = 'Opinion of the committee on the Mortality committee review' "codeText";
        } "code";
        it.answer first as a then {
          a.value as txt ->  sobs.note as n,  n.text = txt "text";
        };
        it ->  sec.entry = create('Reference') as sref,  sref.reference = reference(sobs) "linkEntry";
      } "sectionObservation";
    } "section_committee_opinion";
    qr.item as it where ((linkId = 'recommendation') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Recommendation' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '62387-6' "cd";
          it -> cg.display = 'Interventions Narrative' "dsp";
        } "coding";
      } "code";
      it ->  bundle.entry as sentry,  sentry.resource = create('Observation') as sobs then {
        qr ->  sobs,  sentry then BuildObsBase(qr, sobs, sentry) "base";
        qr -> sobs then SetSurveyCategory(qr, sobs) "category";
        it -> sobs.code as scc then {
          it -> scc.coding as scg then {
            it -> scg.system = 'http://loinc.org' "sys";
            it -> scg.code = '62387-6' "cd";
            it -> scg.display = 'Interventions Narrative' "dsp";
          } "coding";
          it -> scc.text = 'Recommendation on the Mortality committee review' "codeText";
        } "code";
        it.answer first as a then {
          a.value as txt ->  sobs.note as n,  n.text = txt "text";
        };
        it ->  sec.entry = create('Reference') as sref,  sref.reference = reference(sobs) "linkEntry";
      } "sectionObservation";
    } "section_recommendation";
  } "mortalityReviewComposition";
  // Who saw the patient first, and what they thought it was. Its own
  // Observation because the whole point of a mortality review is whether the
  // right grade of clinician saw the patient early enough, and that question is
  // asked across deaths, not within one.
  qr.item as g where (linkId = 'first-clinician') then {
    g.item as it where ((linkId = 'first-clinician/rank') 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 = 'mortality-review-rank-of-the-first-clinician-who-attended' "cd";
          it -> cg.display = 'Rank of the first clinician who attended' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "text";
      };
    } "narr_mortality_review_rank_of_the_first_clinician_who_attended";
    g.item as it where ((linkId = 'first-clinician/provisional-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 = 'https://fhir.slade360.co.ke/fhir/CodeSystem/concept-codesystem' "sys";
          it -> cg.code = 'mortality-review-provisional-diagnosis-made-by-the-first-clinician' "cd";
          it -> cg.display = 'Provisional diagnosis made by the first clinician' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "text";
      };
    } "narr_mortality_review_provisional_diagnosis_made_by_the_first_clinician";
  } "firstClinicianGroup";
  qr.item as it where ((linkId = 'senior-review') 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 = 'mortality-review-time-of-first-senior-clinician-review' "cd";
        it -> cg.display = 'Time of first senior clinician review' "dsp";
      } "coding";
    } "code";
    it.answer first as a then {
      a.value as v -> obs.value = v;
    };
  } "seniorReviewObservation";
}

// ─────────────────────────────────────────────────────────────────────────────
// 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 BuildCompositionBase(source qr : QR, target r : Composition, target entry) {
  qr -> r then SetResponseProvenance(qr, r) "responseProvenance";
  qr -> r.id = uuid() then SetCompositionFullUrl(r, entry) "idAndFullUrl";
  qr -> entry.request as request then {
    qr -> request.method = 'POST' "requestMethod";
    qr -> request.url = 'Composition' "requestUrl";
  } "entryRequest";
  qr.subject as s -> r.subject = s;
}

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

// ── 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 = 'mortality-committee-findings' "provenanceCode";
      qr -> t.display = 'Mortality committee findings and recommendations' "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";
}