/// url = 'https://fhir.slade360.co.ke/fhir/StructureMap/ExtractMedicalReport'
/// name = 'ExtractMedicalReport'
/// title = 'Medical Report Extraction'
/// status = 'active'
/// description = 'A medical report is written once, read as a whole, and handed to whoever asked for it -- an insurer, a court, another hospital -- so it extracts as a Composition under LOINC 34133-9 with one section per printed heading, plus a Condition per diagnosis line so the report does not become the only place the diagnosis is written down. Each section names an Observation carrying its text: Narrative.div is an XhtmlType this engine cannot build from FML, and referencing an Observation is the better shape anyway, because the text becomes something a query can reach rather than a blob inside a document. The stay itself lands in Composition.event.period, which is what makes the report answer \'when was this admission\'.'

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
uses "http://hl7.org/fhir/StructureDefinition/Condition" alias Condition as target

group ExtractMedicalReport(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 = 'Medical report' "title";
    qr.authored as t -> comp.date = t "date";
    qr.encounter as e -> comp.encounter = e;
    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 = 'medical-report' "cd";
        qr -> cg.display = 'Medical report' "dsp";
      } "coding";
    } "category";
    // The doctor who signed it is the author, and the form's own signature
    // block is what says so -- not qr.source, which is whoever keyed it in.
    qr.item as g where (linkId = 'sign-off') then {
      g.item as it where ((linkId = 'sign-off/doctor') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as ref -> comp.author = ref "author";
        };
      } "authorRule";
      g.item as it where ((linkId = 'sign-off/purpose') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as txt ->  comp.note as n,  n.text = txt "purposeNote";
        };
      } "purposeRule";
    } "signOffGroup";
    // ── The admission the report is about ─────────────────────────────────
    // Composition.event.period is a Period of dateTimes and the form asks for
    // dates, hence the casts: a DateType into a dateTime element fails at
    // transform time rather than at compile time.
    qr.item as g where (linkId = 'stay') then {
      g -> comp.event as ev then {
        g -> ev.period as per then {
          g.item as it where ((linkId = 'stay/admitted-on') and answer.value.exists()) then {
            it.answer first as a then {
              a.value as v -> per.start = cast(v, 'dateTime') "start";
            };
          } "admittedRule";
          g.item as it where ((linkId = 'stay/discharged-on') and answer.value.exists()) then {
            it.answer first as a then {
              a.value as v -> per.end = cast(v, 'dateTime') "end";
            };
          } "dischargedRule";
        } "period";
      } "event";
    } "stayGroup";
    qr.item as it where ((linkId = 'clinical-summary') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Clinical summary' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '11329-0' "cd";
          it -> cg.display = 'History general Narrative - Reported' "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 = '11329-0' "cd";
            it -> scg.display = 'History general Narrative - Reported' "dsp";
          } "coding";
          it -> scc.text = 'Clinical summary on the Medical report' "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_clinical_summary";
    qr.item as it where ((linkId = 'past-medical-surgical-history') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Past medical and surgical 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 = 'Past medical and surgical history on the Medical report' "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_past_medical_surgical_history";
    qr.item as it where ((linkId = 'investigations') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Investigations' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '30954-2' "cd";
          it -> cg.display = 'Relevant diagnostic tests/laboratory data 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 = '30954-2' "cd";
            it -> scg.display = 'Relevant diagnostic tests/laboratory data note' "dsp";
          } "coding";
          it -> scc.text = 'Investigations on the Medical report' "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_investigations";
    qr.item as it where ((linkId = 'interventions') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Interventions' "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 = 'Interventions on the Medical report' "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_interventions";
    qr.item as it where ((linkId = 'treatment') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Treatment' "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 = 'Treatment on the Medical report' "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_treatment";
    qr.item as it where ((linkId = 'discharge-instructions-and-medications') and answer.value.exists()) -> comp.section as sec then {
      it -> sec.title = 'Discharge instructions and medications' "title";
      it -> sec.code as sc then {
        it -> sc.coding as cg then {
          it -> cg.system = 'http://loinc.org' "sys";
          it -> cg.code = '8653-8' "cd";
          it -> cg.display = 'Hospital Discharge instructions' "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 = '8653-8' "cd";
            it -> scg.display = 'Hospital Discharge instructions' "dsp";
          } "coding";
          it -> scc.text = 'Discharge instructions and medications on the Medical report' "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_discharge_instructions_and_medications";
  } "medicalReportComposition";
  // ── The diagnoses ───────────────────────────────────────────────────────
  // One Condition per line. Where the writer picked a Condition the patient
  // already has, the reference travels as evidence rather than forking the
  // problem list -- a report written for an insurer should not add a second
  // copy of a diagnosis that is already on the record.
  qr.item as g where (linkId = 'diagnosis') then {
    g.item as d where (linkId = 'diagnosis/entry') then {
      d.item as it where ((linkId = 'diagnosis/entry/text') and answer.value.exists()) ->  bundle.entry as entry,  entry.resource = create('Condition') as cond then {
        qr ->  cond,  entry then BuildConditionBase(qr, cond, entry) "base";
        it -> cond.clinicalStatus as cs then {
          it -> cs.coding as cg then {
            it -> cg.system = 'http://terminology.hl7.org/CodeSystem/condition-clinical' "sys";
            it -> cg.code = 'active' "cd";
            it -> cg.display = 'Active' "dsp";
          } "coding";
        } "clinicalStatus";
        it -> cond.category as cat then {
          it -> cat.coding as cg then {
            it -> cg.system = 'http://terminology.hl7.org/CodeSystem/condition-category' "sys";
            it -> cg.code = 'encounter-diagnosis' "cd";
            it -> cg.display = 'Encounter Diagnosis' "dsp";
          } "coding";
        } "category";
        it.answer first as a then {
          a.value as txt ->  cond.code as cc,  cc.text = txt "codeText";
        };
        qr.authored as t -> cond.recordedDate = t "recordedDate";
        qr.encounter as e -> cond.encounter = e;
        d.item as ex where ((linkId = 'diagnosis/entry/condition') and answer.value.exists()) then {
          ex.answer first as ea then {
            ea.value as existing ->  cond.evidence as ev,  ev.reference = existing "evidenceReference";
          };
        } "existingRule";
      } "diagnosisCondition";
    } "diagnosisRows";
  } "diagnosisGroup";
  // ── The wards ───────────────────────────────────────────────────────────
  // Observations rather than anything on the Composition. Which ward a patient
  // was admitted to and which one they left from is a fact about the stay that
  // gets asked in aggregate, and there is nowhere on a Composition to put it
  // where a query would find it.
  qr.item as g where (linkId = 'stay') then {
    g.item as it where ((linkId = 'stay/ward-of-admission') 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 = 'discharge-ward-of-admission' "cd";
          it -> cg.display = 'Ward of admission' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "text";
      };
    } "narr_discharge_ward_of_admission";
    g.item as it where ((linkId = 'stay/ward-of-discharge') 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 = 'discharge-ward-of-discharge' "cd";
          it -> cg.display = 'Ward of discharge' "dsp";
        } "coding";
      } "code";
      it.answer first as a then {
        a.value as txt ->  obs.note as n,  n.text = txt "text";
      };
    } "narr_discharge_ward_of_discharge";
  } "wardGroup";
}

// ─────────────────────────────────────────────────────────────────────────────
// 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";
}

group BuildConditionBase(source qr : QR, target r : Condition, target entry) {
  qr -> r then SetResponseProvenance(qr, r) "responseProvenance";
  qr -> r.id = uuid() then SetConditionFullUrl(r, entry) "idAndFullUrl";
  qr -> entry.request as request then {
    qr -> request.method = 'POST' "requestMethod";
    qr -> request.url = 'Condition' "requestUrl";
  } "entryRequest";
  qr.subject as s -> r.subject = s;
}

group SetConditionFullUrl(source r : Condition, target entry) {
  r.id as id -> entry.fullUrl = append('https://fhir.slade360.co.ke/fhir/Condition/', 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 = 'medical-report' "provenanceCode";
      qr -> t.display = 'Medical report' "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";
}