@precisa-saude/fhir 0.17.4 → 0.19.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/biomarkers.cjs +2 -2
- package/dist/biomarkers.js +1 -1
- package/dist/{chunk-R6FI2RNB.cjs → chunk-6HKQY6VO.cjs} +6 -6
- package/dist/chunk-6HKQY6VO.cjs.map +1 -0
- package/dist/{chunk-NAUVJPLC.js → chunk-EXG2IU2O.js} +4 -4
- package/dist/chunk-EXG2IU2O.js.map +1 -0
- package/dist/{chunk-NP4YZFUI.cjs → chunk-J3QVVVVH.cjs} +3 -3
- package/dist/{chunk-NP4YZFUI.cjs.map → chunk-J3QVVVVH.cjs.map} +1 -1
- package/dist/{chunk-LPYXISLF.js → chunk-LCXTQE2B.js} +2 -2
- package/dist/{chunk-CBGEU6SG.cjs → chunk-MMO356YH.cjs} +13 -1
- package/dist/chunk-MMO356YH.cjs.map +1 -0
- package/dist/{chunk-7O6VUA2B.js → chunk-MTWOF55H.js} +287 -2
- package/dist/chunk-MTWOF55H.js.map +1 -0
- package/dist/{chunk-LR2OUVOA.js → chunk-XTEKGGYQ.js} +13 -1
- package/dist/{chunk-LR2OUVOA.js.map → chunk-XTEKGGYQ.js.map} +1 -1
- package/dist/{chunk-ONRVND6U.cjs → chunk-Z5VH5QGC.cjs} +287 -2
- package/dist/chunk-Z5VH5QGC.cjs.map +1 -0
- package/dist/cli.js +301 -4
- package/dist/converter.cjs +3 -3
- package/dist/converter.js +2 -2
- package/dist/importer.cjs +3 -3
- package/dist/importer.d.cts +13 -1
- package/dist/importer.d.ts +13 -1
- package/dist/importer.js +2 -2
- package/dist/index.cjs +6 -6
- package/dist/index.js +4 -4
- package/dist/reference-ranges.cjs +2 -2
- package/dist/reference-ranges.js +1 -1
- package/package.json +1 -1
- package/dist/chunk-7O6VUA2B.js.map +0 -1
- package/dist/chunk-CBGEU6SG.cjs.map +0 -1
- package/dist/chunk-NAUVJPLC.js.map +0 -1
- package/dist/chunk-ONRVND6U.cjs.map +0 -1
- package/dist/chunk-R6FI2RNB.cjs.map +0 -1
- /package/dist/{chunk-LPYXISLF.js.map → chunk-LCXTQE2B.js.map} +0 -0
package/dist/biomarkers.cjs
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var _chunkZ5VH5QGCcjs = require('./chunk-Z5VH5QGC.cjs');
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exports.BIOMARKER_DEFINITIONS =
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exports.BIOMARKER_DEFINITIONS = _chunkZ5VH5QGCcjs.BIOMARKER_DEFINITIONS; exports.CAC_INDICATOR_CODES = _chunkZ5VH5QGCcjs.CAC_INDICATOR_CODES; exports.DEXA_CATEGORIES = _chunkZ5VH5QGCcjs.DEXA_CATEGORIES; exports.DEXA_INDICATOR_CODES = _chunkZ5VH5QGCcjs.DEXA_INDICATOR_CODES; exports.codeToLoinc = _chunkZ5VH5QGCcjs.codeToLoinc; exports.filterVisibleBiomarkers = _chunkZ5VH5QGCcjs.filterVisibleBiomarkers; exports.findCodeByName = _chunkZ5VH5QGCcjs.findCodeByName; exports.generateCacFullReference = _chunkZ5VH5QGCcjs.generateCacFullReference; exports.generateDexaFullReference = _chunkZ5VH5QGCcjs.generateDexaFullReference; exports.generateFilteredLLMReference = _chunkZ5VH5QGCcjs.generateFilteredLLMReference; exports.generateLLMReference = _chunkZ5VH5QGCcjs.generateLLMReference; exports.getAllCodes = _chunkZ5VH5QGCcjs.getAllCodes; exports.getAllDefinitions = _chunkZ5VH5QGCcjs.getAllDefinitions; exports.getAllLoincCodes = _chunkZ5VH5QGCcjs.getAllLoincCodes; exports.getAllSearchPatterns = _chunkZ5VH5QGCcjs.getAllSearchPatterns; exports.getBiomarkersByCategory = _chunkZ5VH5QGCcjs.getBiomarkersByCategory; exports.getBiomarkersForCategories = _chunkZ5VH5QGCcjs.getBiomarkersForCategories; exports.getDefinitionByCode = _chunkZ5VH5QGCcjs.getDefinitionByCode; exports.getDefinitionByLoinc = _chunkZ5VH5QGCcjs.getDefinitionByLoinc; exports.getDefinitionsBySex = _chunkZ5VH5QGCcjs.getDefinitionsBySex; exports.getSexForCode = _chunkZ5VH5QGCcjs.getSexForCode; exports.getVisibleDefinitions = _chunkZ5VH5QGCcjs.getVisibleDefinitions; exports.isBiomarkerVisible = _chunkZ5VH5QGCcjs.isBiomarkerVisible; exports.isCacDocument = _chunkZ5VH5QGCcjs.isCacDocument; exports.isDexaDocument = _chunkZ5VH5QGCcjs.isDexaDocument; exports.isValidCode = _chunkZ5VH5QGCcjs.isValidCode; exports.isValidLoinc = _chunkZ5VH5QGCcjs.isValidLoinc; exports.loincToCode = _chunkZ5VH5QGCcjs.loincToCode; exports.normalizeCode = _chunkZ5VH5QGCcjs.normalizeCode; exports.toBiomarkerTests = _chunkZ5VH5QGCcjs.toBiomarkerTests; exports.validateLoincNameMatch = _chunkZ5VH5QGCcjs.validateLoincNameMatch;
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//# sourceMappingURL=biomarkers.cjs.map
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package/dist/biomarkers.js
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"use strict";Object.defineProperty(exports, "__esModule", {value: true}); function _optionalChain(ops) { let lastAccessLHS = undefined; let value = ops[0]; let i = 1; while (i < ops.length) { const op = ops[i]; const fn = ops[i + 1]; i += 2; if ((op === 'optionalAccess' || op === 'optionalCall') && value == null) { return undefined; } if (op === 'access' || op === 'optionalAccess') { lastAccessLHS = value; value = fn(value); } else if (op === 'call' || op === 'optionalCall') { value = fn((...args) => value.call(lastAccessLHS, ...args)); lastAccessLHS = undefined; } } return value; }
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var _chunkZ5VH5QGCcjs = require('./chunk-Z5VH5QGC.cjs');
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var _chunk3ILBFLVQcjs = require('./chunk-3ILBFLVQ.cjs');
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// src/importer.ts
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var MAX_OBSERVATIONS =
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var MAX_FILE_SIZE =
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var MAX_OBSERVATIONS = 5e3;
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var MAX_FILE_SIZE = 15 * 1024 * 1024;
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function extractLoincCode(observation) {
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if (!_optionalChain([observation, 'access', _ => _.code, 'optionalAccess', _2 => _2.coding])) return void 0;
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const loincCoding = observation.code.coding.find((c) => c.system === "http://loinc.org");
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};
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}
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const internalCode =
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const internalCode = _chunkZ5VH5QGCcjs.loincToCode.call(void 0, loincCode);
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return {
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}
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const definition =
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const definition = _chunkZ5VH5QGCcjs.getDefinitionByLoinc.call(void 0, loincCode);
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let value;
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let unit = "";
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let isQualitative = false;
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exports.MAX_OBSERVATIONS = MAX_OBSERVATIONS; exports.MAX_FILE_SIZE = MAX_FILE_SIZE; exports.extractObservationsFromBundle = extractObservationsFromBundle; exports.mapFHIRObservationToInternal = mapFHIRObservationToInternal; exports.processImportBundle = processImportBundle;
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//# sourceMappingURL=chunk-
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//# sourceMappingURL=chunk-6HKQY6VO.cjs.map
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Nesse tamanho, 5000 Observations dão 6,0MB\n * compactos ou 13,1MB indentados, e por isso o teto de arquivo é 15MB: cobre\n * as duas formas com folga.\n *\n * Na densidade desse mesmo histórico (16 Observations por laudo), 5000\n * equivalem a cerca de 300 laudos.\n */\nconst MAX_OBSERVATIONS = 5000;\nconst MAX_FILE_SIZE = 15 * 1024 * 1024; // 15MB\n\n/**\n * Extract LOINC code from an Observation's code.coding array\n */\nfunction extractLoincCode(observation: FHIRObservation): string | undefined {\n if (!observation.code?.coding) return undefined;\n const loincCoding = observation.code.coding.find((c) => c.system === 'http://loinc.org');\n return loincCoding?.code;\n}\n\n/**\n * Extract interpretation flag from Observation\n */\nfunction extractFlag(observation: FHIRObservation): 'H' | 'L' | '' {\n const code = observation.interpretation?.[0]?.coding?.[0]?.code;\n if (code === 'H' || code === 'HH') return 'H';\n if (code === 'L' || code === 'LL') return 'L';\n return '';\n}\n\n/**\n * Extract Observation resources from a FHIR Bundle\n */\nexport function extractObservationsFromBundle(bundle: FHIRBundle): {\n observations: FHIRObservation[];\n skipped: SkippedEntry[];\n} {\n const observations: FHIRObservation[] = [];\n const skipped: SkippedEntry[] = [];\n\n for (let i = 0; i < bundle.entry.length; i++) {\n const entry = bundle.entry[i]!;\n if (!entry.resource) {\n skipped.push({ index: i, reason: 'Entry has no resource' });\n continue;\n }\n\n if (entry.resource.resourceType !== 'Observation') {\n // Non-observation resources are silently skipped (Patient, DiagnosticReport, etc.)\n continue;\n }\n\n if (observations.length >= MAX_OBSERVATIONS) {\n skipped.push({ index: i, reason: `Maximum of ${MAX_OBSERVATIONS} observations exceeded` });\n continue;\n }\n\n observations.push(entry.resource as FHIRObservation);\n }\n\n return { observations, skipped };\n}\n\n/**\n * Map a FHIR Observation to internal format using LOINC→biomarker code lookup\n */\nexport function mapFHIRObservationToInternal(\n observation: FHIRObservation,\n index: number,\n): { observation: ImportedObservation } | { skipped: SkippedEntry } {\n const loincCode = extractLoincCode(observation);\n\n if (!loincCode) {\n return {\n skipped: {\n index,\n reason: 'No LOINC code found in observation coding',\n resourceType: 'Observation',\n },\n };\n }\n\n const internalCode = loincToCode(loincCode);\n if (!internalCode) {\n return {\n skipped: {\n index,\n loincCode,\n reason: `Unknown LOINC code: ${loincCode}`,\n resourceType: 'Observation',\n },\n };\n }\n\n const definition = getDefinitionByLoinc(loincCode);\n\n // Extract value\n let value: number | string;\n let unit = '';\n let isQualitative = false;\n\n if (observation.valueQuantity?.value !== undefined) {\n value = observation.valueQuantity.value;\n unit = observation.valueQuantity.unit || observation.valueQuantity.code || '';\n } else if (observation.valueString) {\n value = observation.valueString;\n isQualitative = true;\n } else {\n return {\n skipped: {\n index,\n loincCode,\n reason: 'Observation has no value (valueQuantity or valueString)',\n resourceType: 'Observation',\n },\n };\n }\n\n // Extract collection date (effectiveDateTime or effectivePeriod.start)\n const collectionDate = observation.effectiveDateTime || observation.effectivePeriod?.start || '';\n if (!collectionDate) {\n return {\n skipped: {\n index,\n loincCode,\n reason: 'Observation has no effectiveDateTime or effectivePeriod.start',\n resourceType: 'Observation',\n },\n };\n }\n\n // Extract reference ranges\n let referenceMin: number | undefined;\n let referenceMax: number | undefined;\n if (observation.referenceRange?.[0]) {\n referenceMin = observation.referenceRange[0].low?.value;\n referenceMax = observation.referenceRange[0].high?.value;\n }\n\n const imported: ImportedObservation = {\n biomarkerCode: internalCode,\n biomarkerName:\n definition?.names.pt[0] || definition?.names.en[0] || observation.code.text || internalCode,\n collectionDate,\n flag: extractFlag(observation),\n isQualitative,\n loincCode,\n referenceMax,\n referenceMin,\n unit: unit || definition?.unit || '',\n value,\n };\n\n return { observation: imported };\n}\n\n/**\n * Process a complete FHIR Bundle for import\n */\nexport function processImportBundle(data: unknown): FHIRImportResult {\n // Structural validation\n const validationErrors = validateFHIRImportBundle(data);\n if (validationErrors.length > 0) {\n return {\n errors: validationErrors,\n imported: [],\n skipped: [],\n totalProcessed: 0,\n };\n }\n\n const bundle = data as FHIRBundle;\n\n // Extract observations\n const { observations, skipped } = extractObservationsFromBundle(bundle);\n\n // Map each observation to internal format\n const imported: ImportedObservation[] = [];\n const allSkipped: SkippedEntry[] = [...skipped];\n\n for (let i = 0; i < observations.length; i++) {\n const result = mapFHIRObservationToInternal(observations[i]!, i);\n\n if ('observation' in result) {\n imported.push(result.observation);\n } else {\n allSkipped.push(result.skipped);\n }\n }\n\n return {\n errors: [],\n imported,\n skipped: allSkipped,\n totalProcessed: observations.length,\n };\n}\n\nexport { MAX_FILE_SIZE, MAX_OBSERVATIONS };\n"]}
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// src/importer.ts
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{"version":3,"sources":["../src/importer.ts"],"sourcesContent":["/**\n * FHIR Importer\n *\n * Parses FHIR R4 Bundles and extracts Observation resources with known LOINC codes,\n * mapping them to internal biomarker codes for storage as lab results.\n */\n\nimport { getDefinitionByLoinc, loincToCode } from './biomarkers';\nimport type { FHIRBundle, FHIRObservation } from './fhir-types';\nimport { validateFHIRImportBundle } from './validators';\n\nexport interface ImportedObservation {\n biomarkerCode: string;\n biomarkerName: string;\n collectionDate: string;\n flag: 'H' | 'L' | '';\n isQualitative: boolean;\n loincCode: string;\n referenceMax?: number;\n referenceMin?: number;\n unit: string;\n value: number | string;\n}\n\nexport interface SkippedEntry {\n index: number;\n loincCode?: string;\n reason: string;\n resourceType?: string;\n}\n\nexport interface ImportError {\n details: string;\n field: string;\n}\n\nexport interface FHIRImportResult {\n errors: ImportError[];\n imported: ImportedObservation[];\n skipped: SkippedEntry[];\n totalProcessed: number;\n}\n\n/**\n * Limites de importação.\n *\n * Uma Observation exportada ocupa cerca de 1,25KB em JSON compacto e 2,75KB\n * quando o arquivo vem indentado, medido sobre um histórico real de 998\n * Observations em 61 laudos. 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exports.labObservationToFHIR = labObservationToFHIR; exports.labReportToFHIR = labReportToFHIR; exports.userProfileToFHIR = userProfileToFHIR; exports.labResultToFHIRBundle = labResultToFHIRBundle;
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[\n {\n city: profile.address.city,\n country: profile.address.country || 'BR',\n line: [\n profile.address.street && profile.address.number\n ? `${profile.address.street}, ${profile.address.number}`\n : profile.address.street,\n profile.address.complement,\n ].filter(Boolean) as string[],\n postalCode: profile.address.postalCode,\n state: profile.address.state,\n },\n ]\n : undefined,\n birthDate: profile.birthDate,\n gender: profile.gender,\n id: profile.userId,\n name: [\n {\n family,\n given: given.length > 0 ? given : undefined,\n text: profile.name,\n },\n ],\n resourceType: 'Patient',\n telecom:\n [\n ...(profile.email ? [{ system: 'email' as const, value: profile.email }] : []),\n ...(profile.phone ? [{ system: 'phone' as const, value: profile.phone }] : []),\n ].length > 0\n ? [\n ...(profile.email ? [{ system: 'email' as const, value: profile.email }] : []),\n ...(profile.phone ? 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// High\n case 'L':\n return 'L'; // Low\n default:\n return 'N'; // Normal\n }\n}\n\n/**\n * Convert Flag to FHIR interpretation display\n */\nfunction interpretationDisplay(flag: Flag): string {\n switch (flag) {\n case 'H':\n return 'High';\n case 'L':\n return 'Low';\n default:\n return 'Normal';\n }\n}\n\n/**\n * Convert generic lab observation to FHIR Observation\n */\nexport function labObservationToFHIR(\n observation: LabObservationData,\n patientId: string,\n laboratoryName?: string,\n): FHIRObservation {\n const loincCode = codeToLoinc(observation.biomarkerCode) || '99999-9';\n // Use default unit if source unit is empty\n const sourceUnit =\n observation.unit || getDefaultUnit(observation.biomarkerCode) || observation.unit;\n const ucumUnit = unitToUCUM(sourceUnit);\n const isQualitative = observation.isQualitative || typeof observation.value === 'string';\n\n // Base observation structure\n const fhirObs: FHIRObservation = {\n category: [\n {\n coding: [\n {\n code: 'laboratory',\n display: 'Laboratory',\n system: 'http://terminology.hl7.org/CodeSystem/observation-category',\n },\n ],\n },\n ],\n code: {\n coding: [\n {\n code: loincCode,\n display: observation.biomarkerName,\n system: 'http://loinc.org',\n },\n {\n code: observation.biomarkerCode,\n display: observation.biomarkerName,\n system: 'http://fhir-brasil.dev/biomarker-codes',\n },\n ],\n text: observation.biomarkerName,\n },\n effectiveDateTime: observation.collectionDate,\n id: `${observation.reportId}-${observation.biomarkerCode}`,\n interpretation: [\n {\n coding: [\n {\n code: interpretationCode(observation.flag),\n display: interpretationDisplay(observation.flag),\n system: 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',\n },\n ],\n },\n ],\n performer: laboratoryName ? [{ display: laboratoryName }] : undefined,\n resourceType: 'Observation',\n status: 'final',\n subject: {\n reference: `Patient/${patientId}`,\n },\n };\n\n // Add value based on type (qualitative = string, quantitative = number)\n if (isQualitative) {\n fhirObs.valueString = String(observation.value);\n } else {\n fhirObs.valueQuantity = {\n code: ucumUnit,\n system: 'http://unitsofmeasure.org',\n unit: sourceUnit,\n value: observation.value as number,\n };\n\n // Reference range only applies to quantitative values\n if (observation.referenceMin !== undefined && observation.referenceMax !== undefined) {\n fhirObs.referenceRange = [\n {\n high: {\n code: ucumUnit,\n system: 'http://unitsofmeasure.org',\n unit: sourceUnit,\n value: observation.referenceMax,\n },\n low: {\n code: ucumUnit,\n system: 'http://unitsofmeasure.org',\n unit: sourceUnit,\n value: observation.referenceMin,\n },\n },\n ];\n }\n }\n\n return fhirObs;\n}\n\n/**\n * Convert generic lab report to FHIR DiagnosticReport\n */\nexport function labReportToFHIR(\n report: LabReportData,\n patientId: string,\n observationIds: string[],\n): FHIRDiagnosticReport {\n // Map processing status to FHIR status\n let status: FHIRDiagnosticReport['status'];\n switch (report.processingStatus) {\n case 'complete':\n status = 'final';\n break;\n case 'partial':\n status = 'partial';\n break;\n case 'pending_review':\n status = 'preliminary';\n break;\n default:\n status = 'final';\n }\n\n return {\n category: [\n {\n coding: [\n {\n code: 'LAB',\n display: 'Laboratory',\n system: 'http://terminology.hl7.org/CodeSystem/v2-0074',\n },\n ],\n },\n ],\n code: {\n coding: [\n {\n code: '11502-2', // Laboratory report\n display: 'Laboratory report',\n system: 'http://loinc.org',\n },\n ],\n text: 'Laboratory Results',\n },\n conclusion:\n report.overallStatus === 'NORMAL'\n ? 'All results within normal limits'\n : 'One or more abnormal results detected',\n conclusionCode:\n report.overallStatus === 'ANORMAL'\n ? [\n {\n coding: [\n {\n code: 'A',\n display: 'Abnormal',\n system: 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',\n },\n ],\n },\n ]\n : undefined,\n effectiveDateTime: report.collectionDate,\n id: report.reportId,\n issued: report.createdAt,\n performer: report.laboratoryName ? [{ display: report.laboratoryName }] : undefined,\n resourceType: 'DiagnosticReport',\n result: observationIds.map((id) => ({ reference: `Observation/${id}` })),\n status,\n subject: {\n reference: `Patient/${patientId}`,\n },\n };\n}\n\n/**\n * Convert user profile to FHIR Patient\n * NOTE: CPF is intentionally excluded for privacy (LGPD compliance)\n */\nexport function userProfileToFHIR(profile: UserProfileData): FHIRPatient {\n const nameParts = profile.name.split(' ');\n const given = nameParts.slice(0, -1);\n const family = nameParts[nameParts.length - 1] || '';\n\n return {\n address: profile.address\n ? [\n {\n city: profile.address.city,\n country: profile.address.country || 'BR',\n line: [\n profile.address.street && profile.address.number\n ? `${profile.address.street}, ${profile.address.number}`\n : profile.address.street,\n profile.address.complement,\n ].filter(Boolean) as string[],\n postalCode: profile.address.postalCode,\n state: profile.address.state,\n },\n ]\n : undefined,\n birthDate: profile.birthDate,\n gender: profile.gender,\n id: profile.userId,\n name: [\n {\n family,\n given: given.length > 0 ? given : undefined,\n text: profile.name,\n },\n ],\n resourceType: 'Patient',\n telecom:\n [\n ...(profile.email ? [{ system: 'email' as const, value: profile.email }] : []),\n ...(profile.phone ? [{ system: 'phone' as const, value: profile.phone }] : []),\n ].length > 0\n ? [\n ...(profile.email ? [{ system: 'email' as const, value: profile.email }] : []),\n ...(profile.phone ? [{ system: 'phone' as const, value: profile.phone }] : []),\n ]\n : undefined,\n };\n}\n\n/**\n * Convert complete lab result to FHIR Bundle\n * This is the main function for exporting lab results to FHIR R4 format\n */\nexport function labResultToFHIRBundle(\n report: LabReportData,\n observations: LabObservationData[],\n userProfile: UserProfileData,\n): FHIRBundle {\n const patientId = userProfile.userId;\n\n // Convert observations\n const fhirObservations = observations.map((obs) => ({\n fullUrl: `urn:uuid:observation-${obs.reportId}-${obs.biomarkerCode}`,\n resource: labObservationToFHIR(\n { ...obs, collectionDate: report.collectionDate },\n patientId,\n report.laboratoryName,\n ),\n }));\n\n const observationIds = observations.map(\n (obs) => `observation-${obs.reportId}-${obs.biomarkerCode}`,\n );\n\n // Convert report\n const diagnosticReport = labReportToFHIR(report, patientId, observationIds);\n\n // Convert patient\n const fhirPatient = userProfileToFHIR(userProfile);\n\n return {\n entry: [\n {\n fullUrl: `urn:uuid:${patientId}`,\n resource: fhirPatient,\n },\n {\n fullUrl: `urn:uuid:diagnostic-report-${report.reportId}`,\n resource: diagnosticReport,\n },\n ...fhirObservations,\n ],\n resourceType: 'Bundle',\n type: 'collection',\n };\n}\n"]}
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// Revisão sistemática de 78 estudos, catorze países, incluindo população
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// centro-americana: o limite médio ficou em 0,50 para homens e para
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exports.biomarkerRangeDefinitions = biomarkerRangeDefinitions; exports.defaultReferenceRanges = defaultReferenceRanges; exports.getReferenceRange = getReferenceRange; exports.getRangeDirection = getRangeDirection; exports.getFallbackReferenceRange = getFallbackReferenceRange; exports.applyFallbackReferenceRanges = applyFallbackReferenceRanges;
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//# sourceMappingURL=chunk-MMO356YH.cjs.map
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