/// url = 'https://fhir.slade360.co.ke/fhir/StructureMap/ExtractPatientReferral'
/// name = 'ExtractPatientReferral'
/// title = 'Patient Referral Extraction'
/// status = 'active'
/// description = 'A referral extracts as a ServiceRequest -- the thing the receiving unit has to act on -- carrying the destination, the specialty sought, the priority and who is asking. Everything the receiving clinician needs to read lands in Observations alongside it: the history and investigations, the treatment already given, the reason for referral under LOINC 42349-1, and any further comments. The working diagnosis becomes a Condition with clinicalStatus active and verificationStatus provisional, because a referral is precisely the case where the diagnosis is not yet confirmed and saying so is the point.'

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

group ExtractPatientReferral(source qr : QR, target bundle : Bundle) {
  qr -> bundle.type = 'transaction' "setBundleType";
  qr.item as g where (linkId = 'referral') then {
    g ->  bundle.entry as entry,  entry.resource = create('ServiceRequest') as sr then {
      qr ->  sr,  entry then BuildServiceRequestBase(qr, sr, entry) "base";
      g -> sr.status = 'active' "status";
      g -> sr.intent = 'order' "intent";
      qr.encounter as e -> sr.encounter = e;
      qr.authored as t -> sr.authoredOn = t "authoredOn";
      g ->  sr.code as cr,  cr.concept as cc then {
        g -> cc.coding as cg then {
          g -> cg.system = 'http://snomed.info/sct' "sys";
          g -> cg.code = '3457005' "cd";
          g -> cg.display = 'Patient referral' "dsp";
        } "coding";
      } "code";
      // Priority is a code on ServiceRequest, not a Coding: it takes the code
      // alone and has nowhere to record which system it came from. The form
      // binds the request-priority value set directly, so the codes line up.
      g.item as it where ((linkId = 'referral/priority') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as cv then {
            cv.code as c -> sr.priority = c "priorityCode";
          } "coding";
        };
      } "priorityRule";
      g.item as it where ((linkId = 'referral/referred-by') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as ref -> sr.requester = ref "requester";
        };
      } "requesterRule";
      // Where the patient is going is typed, not picked, so the performer is a
      // display-only reference. Better than dropping it: the display is what a
      // human reads off the referral and what an audit of onward referrals
      // counts.
      g.item as it where ((linkId = 'referral/referred-to') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as txt ->  sr.performer = create('Reference') as pref,  pref.display = txt "referredTo";
        };
      } "referredToRule";
      g.item as it where ((linkId = 'referral/speciality-sought') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as txt ->  sr.performerType as pt,  pt.text = txt "specialtySought";
        };
      } "specialtyRule";
      g.item as it where ((linkId = 'referral/date') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as v -> sr.occurrence = cast(v, 'dateTime') "occurrence";
        };
      } "dateRule";
      // The reason rides as a plain note as well as its own Observation. The
      // SGHI ServiceRequest profile binds `reason` required to a LOINC value
      // set and the form takes free text, so a coded reason is not available.
      qr.item as it where ((linkId = 'reasons-for-referral') and answer.value.exists()) then {
        it.answer first as a then {
          a.value as txt ->  sr.note as n,  n.text = txt "reasonNote";
        };
      } "reasonNoteRule";
    } "referralRequest";
  } "referralGroup";
  qr.item as it where ((linkId = 'reasons-for-referral') 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 = '42349-1' "cd";
        it -> cg.display = 'Reason for referral (narrative)' "dsp";
      } "coding";
      it -> cc.text = 'Reason the patient is being referred on' "codeText";
    } "code";
    it.answer first as a then {
      a.value as txt ->  obs.note as n,  n.text = txt "text";
    };
  } "narr_42349_1";
  qr.item as it where ((linkId = 'brief-history-and-investigations') 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 = '11329-0' "cd";
        it -> cg.display = 'History general Narrative - Reported' "dsp";
      } "coding";
      it -> cc.text = 'Brief history and investigations on the referral form' "codeText";
    } "code";
    it.answer first as a then {
      a.value as txt ->  obs.note as n,  n.text = txt "text";
    };
  } "narr_11329_0";
  qr.item as it where ((linkId = 'treatment-given') 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 = '18776-5' "cd";
        it -> cg.display = 'Plan of care note' "dsp";
      } "coding";
      it -> cc.text = 'Treatment already given before referral' "codeText";
    } "code";
    it.answer first as a then {
      a.value as txt ->  obs.note as n,  n.text = txt "text";
    };
  } "narr_18776_5";
  qr.item as it where ((linkId = 'other-pertinent-comments') 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 = 'referral-other-pertinent-comments-on-referral' "cd";
        it -> cg.display = 'Other pertinent comments on referral' "dsp";
      } "coding";
    } "code";
    it.answer first as a then {
      a.value as txt ->  obs.note as n,  n.text = txt "text";
    };
  } "narr_referral_other_pertinent_comments_on_referral";
  // ── The working diagnosis ───────────────────────────────────────────────
  // verificationStatus provisional, deliberately. A referral is the case where
  // the diagnosis is a working one, and a Condition that does not say so reads
  // as confirmed to everything downstream that looks at it.
  qr.item as g where (linkId = 'working-diagnosis') then {
    g.item as it where ((linkId = 'working-diagnosis/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.verificationStatus as vs then {
        it -> vs.coding as cg then {
          it -> cg.system = 'http://terminology.hl7.org/CodeSystem/condition-ver-status' "sys";
          it -> cg.code = 'provisional' "cd";
          it -> cg.display = 'Provisional' "dsp";
        } "coding";
      } "verificationStatus";
      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;
      g.item as ex where ((linkId = 'working-diagnosis/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";
    } "workingDiagnosisCondition";
  } "workingDiagnosisGroup";
}

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

group SetServiceRequestFullUrl(source r : ServiceRequest, target entry) {
  r.id as id -> entry.fullUrl = append('https://fhir.slade360.co.ke/fhir/ServiceRequest/', 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 = 'patient-referral' "provenanceCode";
      qr -> t.display = 'Patient referral form' "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";
}