@openhealth/oht-custom-parser-lib 0.5.27 → 0.5.29

package/dist/index.d.ts

@@ -18,5 +18,7 @@ export { default as pinoLogger } from './util-ts/pinoLogger';
 export { getGreaterThanPatterns, getLowerThanPatterns } from './util-ts/regexUtils';
 export { getMappedBiomarkers, getMappedBiomarkersLatest } from './util-ts/dataUtils';
 export { parseRange } from './util-ts/extractionUtils';
-export { lisCsvToExamRows, lisXmlToJson, } from './util-ts/mapperUtils';
+export { lisCsvToExamRows, lisXmlToJson, fetchActiveMappingRules, } from './util-ts/mapperUtils';
 export type { LisCsvRow } from './util-ts/mapperUtils';
+export { mapToOhtReport } from './service/ohtReportMapper.service';
+export type { OhtReportMappingRules, OhtReportMetadataPathRules, OhtReportPatientPathRules, OhtReportExamsPathRules, OhtReportRangePathRules, MapperOptions, FilterCondition, } from './types/mappingRules.types';

package/dist/index.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = exports.shouldSendSlackNotification = exports.ValidationError = exports.handleError = exports.getRejectReason = exports.getErrorMessage = exports.ERROR_MESSAGES = exports.ERROR_CATALOG = exports.ErrorCode = exports.RejectReason = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.validateTransformationRuleExpression = exports.applyTransformationRules = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.ohtReportMeasurementsExtractor = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
-exports.lisXmlToJson = exports.lisCsvToExamRows = exports.parseRange = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getRequestIdFromContext = void 0;
+exports.mapToOhtReport = exports.fetchActiveMappingRules = exports.lisXmlToJson = exports.lisCsvToExamRows = exports.parseRange = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getRequestIdFromContext = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -103,4 +103,8 @@ Object.defineProperty(exports, "parseRange", { enumerable: true, get: function (
 var mapperUtils_1 = require("./util-ts/mapperUtils");
 Object.defineProperty(exports, "lisCsvToExamRows", { enumerable: true, get: function () { return mapperUtils_1.lisCsvToExamRows; } });
 Object.defineProperty(exports, "lisXmlToJson", { enumerable: true, get: function () { return mapperUtils_1.lisXmlToJson; } });
+Object.defineProperty(exports, "fetchActiveMappingRules", { enumerable: true, get: function () { return mapperUtils_1.fetchActiveMappingRules; } });
+// ### OHT REPORT MAPPER ###
+var ohtReportMapper_service_1 = require("./service/ohtReportMapper.service");
+Object.defineProperty(exports, "mapToOhtReport", { enumerable: true, get: function () { return ohtReportMapper_service_1.mapToOhtReport; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../index.ts"],"names":[],"mappings":";;;;;;;AAAA,mBAAmB;AACnB,yEAGyC;AAFvC,uIAAA,8BAA8B,OAAA;AAC9B,gIAAA,uBAAuB,OAAA;AAEzB,mFAQ8C;AAP5C,oIAAA,sBAAsB,OAAA;AACtB,yHAAA,WAAW,OAAA;AACX,+HAAA,iBAAiB,OAAA;AACjB,6HAAA,eAAe,OAAA;AACf,yIAAA,2BAA2B,OAAA;AAC3B,qIAAA,uBAAuB,OAAA;AAIzB,2GAE0D;AADxD,wJAAA,8BAA8B,OAAA;AAGhC,+FASoD;AARlD,4IAAA,wBAAwB,OAAA;AACxB,gJAAA,4BAA4B,OAAA;AAC5B,0IAAA,sBAAsB,OAAA;AACtB,8IAAA,0BAA0B,OAAA;AAC1B,kIAAA,cAAc,OAAA;AACd,gJAAA,4BAA4B,OAAA;AAC5B,+HAAA,WAAW,OAAA;AACX,oJAAA,gCAAgC,OAAA;AAGlC,yEAEyC;AADvC,6IAAA,oCAAoC,OAAA;AAAE,2HAAA,kBAAkB,OAAA;AAE1D,yEAKyC;AAJvC,0HAAA,iBAAiB,OAAA;AACjB,4HAAA,mBAAmB,OAAA;AACnB,uHAAA,cAAc,OAAA;AACd,2HAAA,kBAAkB,OAAA;AAEpB,qFAG+C;AAF7C,uIAAA,UAAU,OAA4B;AACtC,mJAAA,yBAAyB,OAAwC;AAGnE,gBAAgB;AAChB,mEAaqC;AAJnC,mHAAA,YAAY,OAAA;AAKd,+CA8C2B;AA7CzB,6HAAA,gCAAgC,OAAA;AAChC,+HAAA,kCAAkC,OAAA;AAClC,wGAAA,WAAW,OAAA;AACX,mHAAA,sBAAsB,OAAA;AACtB,+GAAA,kBAAkB,OAAA;AAOlB,yGAAA,YAAY,OAAA;AACZ,+GAAA,kBAAkB,OAAA;AAClB,uHAAA,0BAA0B,OAAA;AAC1B,+GAAA,kBAAkB,OAAA;AAClB,uHAAA,0BAA0B,OAAA;AAC1B,gGAAA,GAAG,OAAA;AAgBH,uGAAA,UAAU,OAAA;AAEV,yGAAA,YAAY,OAAA;AAYd,mDAO6B;AAL3B,wGAAA,SAAS,OAAA;AACT,4GAAA,aAAa,OAAA;AACb,6GAAA,cAAc,OAAA;AACd,8GAAA,eAAe,OAAA;AACf,8GAAA,eAAe,OAAA;AAEjB,2FAMkD;AALhD,6HAAA,WAAW,OAAA;AACX,iIAAA,eAAe,OAAA;AACf,6IAAA,2BAA2B,OAAA;AAC3B,8IAAA,4BAA4B,OAAA;AAC5B,wIAAA,sBAAsB,OAAA;AAUxB,4BAA4B;AAC5B,+EAQ4C;AAP1C,4HAAA,gBAAgB,OAAA;AAGhB,mIAAA,uBAAuB,OAAA;AACvB,oIAAA,wBAAwB,OAAA;AACxB,0HAAA,cAAc,OAAA;AACd,+HAAA,mBAAmB,OAAA;AAGrB,kBAAkB;AAClB,+CAAuE;AAA/D,gHAAA,oBAAoB,OAAA;AAAE,yGAAA,aAAa,OAAA;AAC3C,iDAAiN;AAAzM,yGAAA,YAAY,OAAA;AAAE,sHAAA,yBAAyB,OAAA;AAAE,6HAAA,gCAAgC,OAAA;AAAE,oHAAA,uBAAuB,OAAA;AAAE,8GAAA,iBAAiB,OAAA;AAAE,oHAAA,uBAAuB,OAAA;AAAE,4GAAA,eAAe,OAAA;AAAE,wGAAA,WAAW,OAAA;AACpL,mEAAuF;AAA/E,wHAAA,kBAAkB,OAAA;AAAE,2HAAA,qBAAqB,OAAA;AACjD,mDAA2D;AAAnD,yHAAA,OAAO,OAAc;AAC7B,mDAAkF;AAA1E,oHAAA,sBAAsB,OAAA;AAAE,kHAAA,oBAAoB,OAAA;AACpD,iDAAmF;AAA3E,gHAAA,mBAAmB,OAAA;AAAE,sHAAA,yBAAyB,OAAA;AACtD,6DAAqD;AAA7C,6GAAA,UAAU,OAAA;AAClB,qDAI+B;AAH7B,+GAAA,gBAAgB,OAAA;AAChB,2GAAA,YAAY,OAAA;AACZ,sHAAA,uBAAuB,OAAA;AAIzB,4BAA4B;AAC5B,6EAAmE;AAA1D,yHAAA,cAAc,OAAA"}

package/dist/service/ohtReportMapper.service.d.ts

@@ -0,0 +1,20 @@
+import { OhtReport } from '../types/oht.types';
+import { OhtReportMappingRules, OhtReportMetadataPathRules, OhtReportPatientPathRules, OhtReportExamsPathRules, OhtReportRangePathRules, MapperOptions } from '../types/mappingRules.types';
+export type { OhtReportMappingRules, OhtReportMetadataPathRules, OhtReportPatientPathRules, OhtReportExamsPathRules, OhtReportRangePathRules, MapperOptions, };
+/**
+ * Map a raw file (JSON, XML or CSV) to an OhtReport using the provided path rules.
+ *
+ * Behaviour:
+ * - If the parsed content already satisfies the OhtReport shape, it is returned as-is.
+ * - XML content is converted via `lisXmlToJson`.
+ * - CSV content is converted via `lisCsvToExamRows` and wrapped in `{ rows: [...] }`.
+ * - All field paths support `[*]` array-iteration notation.
+ * - The `labKey` exam path supports compound `"pathA:pathB"` notation to join two
+ *   values (potentially from different array depths) with a colon separator.
+ *
+ * @param fileContent  Raw string content of the source file.
+ * @param rules        Path rules describing where each OhtReport field lives in the source.
+ * @param options      Optional context (e.g. filename for logging).
+ * @throws             On invalid input, parse failure, or unrecoverable mapping error.
+ */
+export declare function mapToOhtReport(fileContent: string, rules: OhtReportMappingRules, options?: MapperOptions): Promise<OhtReport>;

package/dist/service/ohtReportMapper.service.js

@@ -0,0 +1,61 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mapToOhtReport = mapToOhtReport;
+const processingLogger_service_1 = require("./processingLogger.service");
+const mapperUtils_1 = require("../util-ts/mapperUtils");
+/**
+ * Map a raw file (JSON, XML or CSV) to an OhtReport using the provided path rules.
+ *
+ * Behaviour:
+ * - If the parsed content already satisfies the OhtReport shape, it is returned as-is.
+ * - XML content is converted via `lisXmlToJson`.
+ * - CSV content is converted via `lisCsvToExamRows` and wrapped in `{ rows: [...] }`.
+ * - All field paths support `[*]` array-iteration notation.
+ * - The `labKey` exam path supports compound `"pathA:pathB"` notation to join two
+ *   values (potentially from different array depths) with a colon separator.
+ *
+ * @param fileContent  Raw string content of the source file.
+ * @param rules        Path rules describing where each OhtReport field lives in the source.
+ * @param options      Optional context (e.g. filename for logging).
+ * @throws             On invalid input, parse failure, or unrecoverable mapping error.
+ */
+async function mapToOhtReport(fileContent, rules, options) {
+    const filename = options?.filename ?? 'unknown';
+    if (typeof fileContent !== 'string' || fileContent.trim() === '') {
+        const err = new Error('mapToOhtReport: fileContent must be a non-empty string');
+        processingLogger_service_1.processingLogger.logError('OhtReportMapper: invalid file content', err, { filename });
+        throw err;
+    }
+    if (!rules || typeof rules !== 'object') {
+        const err = new Error('mapToOhtReport: rules must be a valid OhtReportMappingRules object');
+        processingLogger_service_1.processingLogger.logError('OhtReportMapper: invalid rules', err, { filename });
+        throw err;
+    }
+    // ── Parse raw content to JSON ─────────────────────────────────────────────
+    let parsed;
+    try {
+        parsed = await (0, mapperUtils_1.parseFileToJson)(fileContent);
+    }
+    catch (e) {
+        const err = e instanceof Error ? e : new Error(String(e));
+        processingLogger_service_1.processingLogger.logError('OhtReportMapper: failed to parse file content', err, { filename });
+        throw err;
+    }
+    // ── Short-circuit: already an OhtReport ──────────────────────────────────
+    if ((0, mapperUtils_1.isOhtReport)(parsed)) {
+        return parsed;
+    }
+    // ── Map source JSON → OhtReport ───────────────────────────────────────────
+    try {
+        const metadata = (0, mapperUtils_1.mapMetadata)(parsed, rules.metadata);
+        const patient = (0, mapperUtils_1.mapPatient)(parsed, rules.patient);
+        const exams = (0, mapperUtils_1.mapExams)(parsed, rules.exams);
+        return { metadata, patient, exams };
+    }
+    catch (e) {
+        const err = e instanceof Error ? e : new Error(String(e));
+        processingLogger_service_1.processingLogger.logError('OhtReportMapper: mapping failed', err, { filename, error: err.message });
+        throw err;
+    }
+}
+//# sourceMappingURL=ohtReportMapper.service.js.map

package/dist/service/ohtReportMapper.service.js.map

@@ -0,0 +1 @@
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package/dist/types/mappingRules.types.d.ts

@@ -0,0 +1,74 @@
+export interface OhtReportMappingRules {
+    metadata: OhtReportMetadataPathRules;
+    patient: OhtReportPatientPathRules;
+    exams: OhtReportExamsPathRules;
+}
+export interface OhtReportMetadataPathRules {
+    labOrderId: string;
+    collectionDate?: string;
+    examDate?: string;
+    documentDate?: string;
+    pdfBase64?: string;
+    prescriberExternalId?: string;
+}
+export interface OhtReportPatientPathRules {
+    id: string;
+    name?: string;
+    firstName?: string;
+    lastName?: string;
+    birthdate: string;
+    sex: string;
+    gender?: string;
+    socialName?: string;
+    email?: string;
+    cpf?: string;
+    documentId?: string;
+    address?: string;
+    phoneNumber?: string;
+}
+export interface OhtReportExamsPathRules {
+    labKey: string;
+    value: string;
+    unit: string;
+    mnemonic: string;
+    examName: string;
+    range: OhtReportRangePathRules;
+    method?: string;
+    material?: string;
+    collectionDate?: string;
+    effectiveDate?: string;
+    examCollectionDate?: string;
+    examEffectiveDate?: string;
+    documentDate?: string;
+    description?: string;
+    annotation?: string;
+    /** When true, emit a single range with noSourceRanges: true and skip source range mapping */
+    noSourceRanges?: boolean;
+}
+export interface OhtReportRangePathRules {
+    text: string;
+    from?: string;
+    to?: string;
+    age?: string;
+    sex?: string;
+}
+export interface MapperOptions {
+    filename?: string;
+}
+/**
+ * Filter condition used in conditional path syntax: [key=[pattern]].
+ *
+ * Patterns without regex metacharacters (^$.*+?()[]{}|\) perform strict === comparison.
+ * Patterns with metacharacters are compiled as RegExp; falls back to strict equality on error.
+ *
+ * Examples:
+ *   items[code=[A1]].val      → exact match "A1"
+ *   items[code=[^TSH]].val    → regex: starts with "TSH"
+ *   items[code=[^TSH$]].val   → regex: exactly "TSH"
+ */
+export interface FilterCondition {
+    /** Dot-path key to read from each array element for comparison. */
+    key: string;
+    /** Pattern to match against the resolved key value. */
+    pattern: string;
+}

package/dist/types/mappingRules.types.js

@@ -0,0 +1,4 @@
+"use strict";
+// ─── Public types — mirror of Go OhtReportMappingRuleSet ──────────────────────
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=mappingRules.types.js.map

package/dist/types/mappingRules.types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"mappingRules.types.js","sourceRoot":"","sources":["../../types/mappingRules.types.ts"],"names":[],"mappings":";AAAA,iFAAiF"}

package/dist/util-ts/mapperUtils.d.ts

@@ -1,3 +1,6 @@
+import { OhtReport, OhtMetadata, OhtPatient, Exam } from '../types/oht.types';
+export type { OhtReportMappingRules, OhtReportMetadataPathRules, OhtReportPatientPathRules, OhtReportExamsPathRules, OhtReportRangePathRules, MapperOptions, FilterCondition, } from '../types/mappingRules.types';
+import type { OhtReportMetadataPathRules, OhtReportPatientPathRules, OhtReportExamsPathRules } from '../types/mappingRules.types';
 /** One parsed row: keys from the CSV header, values as strings. */
 export type LisCsvRow = Record<string, string>;
 /**
@@ -10,3 +13,35 @@ export declare function lisCsvToExamRows(csv: string): LisCsvRow[];
  * Repeated sibling tags (e.g. several `exame`) still parse as arrays.
  */
 export declare function lisXmlToJson(xml: string): Promise<unknown>;
+/**
+ * Fetch the active mapping rules for a partner from the OHT Core API.
+ *
+ * Calls `GET {apiUrl}/mapping-rules/active` (with an optional `partnerId` query param)
+ * and returns the raw response payload, which the caller can cast to
+ * `OhtReportMappingRules`.  Returns `null` when the API returns no data.
+ *
+ * @param apiUrl   Base URL of the OHT Core API (e.g. process.env.OHAPI_URL).
+ * @param apiKey   API key used for Basic auth (e.g. process.env.OHT_CORE_AGNOSTIC_PARSER_API_KEY).
+ * @param partnerId  Optional partner identifier forwarded as a query parameter.
+ * @throws When the HTTP request itself fails (network error, non-2xx status, etc.).
+ */
+export declare function fetchActiveMappingRules(ohtCoreUrl: string, apiKey: string, partnerId: string): Promise<unknown>;
+/**
+ * Parse raw file content to a plain JS value, auto-detecting the format.
+ * CSV rows are wrapped in { rows: [...] } so downstream path rules can target them.
+ */
+export declare function parseFileToJson(content: string): Promise<unknown>;
+/** Returns true when data already conforms to the OhtReport structure. */
+export declare function isOhtReport(data: unknown): data is OhtReport;
+export declare function mapMetadata(source: any, rules: OhtReportMetadataPathRules): OhtMetadata;
+export declare function mapPatient(source: any, rules: OhtReportPatientPathRules): OhtPatient;
+/**
+ * Map all exams from the source object using the exam path rules.
+ *
+ * Algorithm:
+ *  1. Collect every path referenced in examRules (expanding compound labKey paths).
+ *  2. Determine the maximum [*] depth across all paths.
+ *  3. Resolve every leaf ArrayItem at that depth (each becomes one exam).
+ *  4. Fields from shallower depths are resolved via the ancestors chain.
+ */
+export declare function mapExams(source: any, examRules: OhtReportExamsPathRules): Exam[];

package/dist/util-ts/mapperUtils.js

@@ -2,8 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.lisCsvToExamRows = lisCsvToExamRows;
 exports.lisXmlToJson = lisXmlToJson;
+exports.fetchActiveMappingRules = fetchActiveMappingRules;
+exports.parseFileToJson = parseFileToJson;
+exports.isOhtReport = isOhtReport;
+exports.mapMetadata = mapMetadata;
+exports.mapPatient = mapPatient;
+exports.mapExams = mapExams;
 const sync_1 = require("csv-parse/sync");
 const xml2js_1 = require("xml2js");
+const apiUtils_1 = require("./apiUtils");
 const lisCsvParseOptions = {
     columns: true,
     skip_empty_lines: true,
@@ -41,4 +48,420 @@ async function lisXmlToJson(xml) {
         trim: false,
     });
 }
+/**
+ * Fetch the active mapping rules for a partner from the OHT Core API.
+ *
+ * Calls `GET {apiUrl}/mapping-rules/active` (with an optional `partnerId` query param)
+ * and returns the raw response payload, which the caller can cast to
+ * `OhtReportMappingRules`.  Returns `null` when the API returns no data.
+ *
+ * @param apiUrl   Base URL of the OHT Core API (e.g. process.env.OHAPI_URL).
+ * @param apiKey   API key used for Basic auth (e.g. process.env.OHT_CORE_AGNOSTIC_PARSER_API_KEY).
+ * @param partnerId  Optional partner identifier forwarded as a query parameter.
+ * @throws When the HTTP request itself fails (network error, non-2xx status, etc.).
+ */
+async function fetchActiveMappingRules(ohtCoreUrl, apiKey, partnerId) {
+    const url = `${ohtCoreUrl}/v1/customparser/partners/${partnerId}/mapping-rules/active`;
+    const response = await (0, apiUtils_1.makeApiCallWithRetry)('GET', url, null, apiKey, 2);
+    return response?.data ?? null;
+}
+// ─── Path utilities ────────────────────────────────────────────────────────────
+/** Coerce any value to string; null/undefined → ''. Objects are JSON-serialised. */
+function coerceString(val) {
+    if (val == null)
+        return '';
+    if (typeof val === 'object') {
+        try {
+            return JSON.stringify(val);
+        }
+        catch {
+            return '';
+        }
+    }
+    return String(val);
+}
+/**
+ * Navigate a simple dot-path on obj without any [*] handling.
+ * e.g. resolveDotPath(obj, "datos.idpaciente") → obj.datos.idpaciente
+ */
+function resolveDotPath(obj, dotPath) {
+    if (!dotPath || obj == null)
+        return undefined;
+    return dotPath.split('.').reduce((acc, key) => {
+        if (acc == null)
+            return undefined;
+        return acc[key];
+    }, obj);
+}
+/** Returns true when the path contains any array annotation ([*] or [key=[...]]). */
+function hasArrayNotation(path) {
+    return /\[\*\]|\[[^\]=]+=\[/.test(path);
+}
+/**
+ * Test whether an array element satisfies a FilterCondition.
+ *
+ * Matching rules:
+ *   - Pattern with no regex metacharacters → strict string equality (===).
+ *   - Pattern with regex metacharacters    → compiled as RegExp, tested with .test().
+ *   - If RegExp compilation throws          → fallback to strict equality.
+ */
+function testFilter(item, filter) {
+    const value = coerceString(resolveDotPath(item, filter.key));
+    const hasMetaChars = /[\\^$.*+?()[\]{}|]/.test(filter.pattern);
+    if (!hasMetaChars) {
+        return value === filter.pattern;
+    }
+    try {
+        return new RegExp(filter.pattern).test(value);
+    }
+    catch {
+        return value === filter.pattern;
+    }
+}
+/**
+ * Parse a path with array annotations into ordered segments.
+ * Supports both wildcard [*] and conditional filter [key=[pattern]].
+ *
+ * "datos.pruebas[*].resultados[code=[A1]].valor" →
+ *   [{ segment: "datos.pruebas",  isArray: true                              },
+ *    { segment: "resultados",     isArray: true, filter: {key:"code", pattern:"A1"} },
+ *    { segment: "valor",          isArray: false                             }]
+ */
+function parseArraySegments(path) {
+    if (!path)
+        return [];
+    // Matches either [*] or a conditional filter [key=[pattern]]
+    const ANNOTATION_RE = /\[\*\]|\[([^\]=]+)=\[([^\]]*)\]\]/g;
+    const segments = [];
+    let lastIndex = 0;
+    let match;
+    while ((match = ANNOTATION_RE.exec(path)) !== null) {
+        const rawBefore = path.slice(lastIndex, match.index);
+        const segText = rawBefore.startsWith('.') ? rawBefore.slice(1) : rawBefore;
+        if (match[0] === '[*]') {
+            if (segText)
+                segments.push({ segment: segText, isArray: true });
+        }
+        else {
+            // conditional filter: match[1] = key, match[2] = pattern
+            if (segText)
+                segments.push({ segment: segText, isArray: true, filter: { key: match[1], pattern: match[2] } });
+        }
+        lastIndex = ANNOTATION_RE.lastIndex;
+    }
+    // trailing leaf segment after the last annotation
+    const rawTrailing = path.slice(lastIndex);
+    const trailing = rawTrailing.startsWith('.') ? rawTrailing.slice(1) : rawTrailing;
+    if (trailing)
+        segments.push({ segment: trailing, isArray: false });
+    return segments;
+}
+/** Count array iteration levels in path — both [*] wildcards and [key=[pattern]] filters. */
+function countArrayDepth(path) {
+    return (path.match(/\[\*\]|\[[^\]=]+=\[[^\]]*\]\]/g) ?? []).length;
+}
+/**
+ * Traverse all [*]-marked segments of path on source, producing one ArrayItem
+ * per leaf element. The first non-array (leaf field) segment terminates traversal.
+ *
+ * For "datos.pruebas[*].resultados[*].valor":
+ *   – iterates datos.pruebas[*] → for each prueba, iterates resultados[*]
+ *   – returns { item: resultadoItem, ancestors: [pruebaItem] } per resultado
+ */
+function resolveArrayChain(source, path) {
+    const arraySegments = parseArraySegments(path).filter(s => s.isArray);
+    let workList = [{ ctx: source, collected: [] }];
+    for (const seg of arraySegments) {
+        const next = [];
+        for (const { ctx, collected } of workList) {
+            const arr = resolveDotPath(ctx, seg.segment);
+            if (!Array.isArray(arr))
+                continue;
+            const candidates = seg.filter
+                ? arr.filter(child => testFilter(child, seg.filter))
+                : arr;
+            for (const child of candidates) {
+                next.push({ ctx: child, collected: [...collected, child] });
+            }
+        }
+        workList = next;
+    }
+    return workList.map(({ collected }) => ({
+        item: collected[collected.length - 1],
+        ancestors: collected.slice(0, -1),
+    }));
+}
+/**
+ * Resolve a scalar string from a path that may contain [*].
+ * For scalar-context fields (metadata, patient): returns the FIRST non-empty value found.
+ */
+function resolveScalar(source, path) {
+    if (!path)
+        return '';
+    if (!hasArrayNotation(path)) {
+        return coerceString(resolveDotPath(source, path));
+    }
+    const leafSeg = parseArraySegments(path).find(s => !s.isArray);
+    const items = resolveArrayChain(source, path);
+    for (const { item } of items) {
+        const val = coerceString(leafSeg ? resolveDotPath(item, leafSeg.segment) : item);
+        if (val !== '')
+            return val;
+    }
+    return '';
+}
+/**
+ * Given all field paths, find the deepest [*] level and return ArrayItems for
+ * every leaf element. Fields at shallower depths are resolved via `ancestors`.
+ */
+function resolveDeepestArrayItems(source, allPaths) {
+    let maxDepth = 0;
+    let deepestPath = '';
+    for (const p of allPaths) {
+        const d = countArrayDepth(p);
+        if (d > maxDepth) {
+            maxDepth = d;
+            deepestPath = p;
+        }
+    }
+    if (maxDepth === 0) {
+        return [{ item: source, ancestors: [] }];
+    }
+    return resolveArrayChain(source, deepestPath);
+}
+// ─── labKey compound notation ("pathA:pathB") ──────────────────────────────────
+/** True when a labKey rule path uses compound "pathA:pathB" notation. */
+function isCompoundLabKey(path) {
+    return path.includes(':');
+}
+/** Split "pathA:pathB" on the FIRST ':' into its two component paths. */
+function splitCompoundLabKey(path) {
+    const idx = path.indexOf(':');
+    return [path.substring(0, idx).trim(), path.substring(idx + 1).trim()];
+}
+// ─── Atomic field extractors ───────────────────────────────────────────────────
+/**
+ * Resolve a single field path for an ArrayItem in the context of a known maxDepth.
+ *
+ * The depth of the path determines which context to use:
+ *   depth >= maxDepth → item (leaf)
+ *   depth  < maxDepth → ancestors[depth - 1]
+ *   depth == 0        → resolve directly on item (path has no [*])
+ */
+function extractFieldFromItem(arrayItem, path, maxDepth) {
+    if (!path)
+        return '';
+    const depth = countArrayDepth(path);
+    const leafSeg = parseArraySegments(path).find(s => !s.isArray);
+    const relativePath = leafSeg?.segment ?? '';
+    if (depth === 0) {
+        return coerceString(resolveDotPath(arrayItem.item, path));
+    }
+    let context;
+    if (depth >= maxDepth) {
+        context = arrayItem.item;
+    }
+    else {
+        context = arrayItem.ancestors[depth - 1];
+    }
+    if (context == null)
+        return '';
+    return coerceString(resolveDotPath(context, relativePath));
+}
+/**
+ * Extract the labKey for one exam item.
+ * Handles both plain paths and compound "pathA:pathB" notation
+ * (where each part may reference different array depths).
+ */
+function extractLabKey(arrayItem, labKeyPath, maxDepth) {
+    if (!labKeyPath)
+        return '';
+    if (isCompoundLabKey(labKeyPath)) {
+        const [pathA, pathB] = splitCompoundLabKey(labKeyPath);
+        const partA = extractFieldFromItem(arrayItem, pathA, maxDepth);
+        const partB = extractFieldFromItem(arrayItem, pathB, maxDepth);
+        if (partA && partB)
+            return `${partA}:${partB}`;
+        return partA || partB;
+    }
+    return extractFieldFromItem(arrayItem, labKeyPath, maxDepth);
+}
+// ─── File type detection & conversion ─────────────────────────────────────────
+/** Detect the content type of a raw file string. */
+function detectContentType(content) {
+    const trimmed = content.trimStart();
+    if (trimmed.startsWith('<'))
+        return 'xml';
+    if (trimmed.startsWith('{') || trimmed.startsWith('['))
+        return 'json';
+    try {
+        JSON.parse(trimmed);
+        return 'json';
+    }
+    catch {
+        // not valid JSON
+    }
+    return 'csv';
+}
+/**
+ * Parse raw file content to a plain JS value, auto-detecting the format.
+ * CSV rows are wrapped in { rows: [...] } so downstream path rules can target them.
+ */
+async function parseFileToJson(content) {
+    const type = detectContentType(content);
+    switch (type) {
+        case 'xml':
+            return lisXmlToJson(content);
+        case 'csv': {
+            const rows = lisCsvToExamRows(content);
+            return { rows };
+        }
+        case 'json':
+        default:
+            return JSON.parse(content);
+    }
+}
+// ─── OhtReport guard ───────────────────────────────────────────────────────────
+/** Returns true when data already conforms to the OhtReport structure. */
+function isOhtReport(data) {
+    if (typeof data !== 'object' || data === null)
+        return false;
+    const obj = data;
+    return ('metadata' in obj &&
+        'patient' in obj &&
+        'exams' in obj &&
+        typeof obj['metadata']?.labOrderId === 'string' &&
+        Array.isArray(obj['exams']));
+}
+// ─── Section mappers ───────────────────────────────────────────────────────────
+function mapMetadata(source, rules) {
+    const get = (path) => resolveScalar(source, path ?? '');
+    return {
+        labOrderId: get(rules.labOrderId),
+        collectionDate: get(rules.collectionDate),
+        examDate: get(rules.examDate),
+        documentDate: get(rules.documentDate),
+        ...(rules.pdfBase64 ? { pdfBase64: get(rules.pdfBase64) || undefined } : {}),
+        ...(rules.prescriberExternalId ? { prescriberExternalId: get(rules.prescriberExternalId) || undefined } : {}),
+    };
+}
+function mapPatient(source, rules) {
+    const get = (path) => resolveScalar(source, path ?? '');
+    return {
+        id: get(rules.id),
+        name: get(rules.name),
+        firstName: get(rules.firstName),
+        lastName: get(rules.lastName),
+        birthdate: get(rules.birthdate),
+        sex: get(rules.sex),
+        gender: get(rules.gender),
+        socialName: get(rules.socialName),
+        email: get(rules.email),
+        cpf: get(rules.cpf),
+        documentId: get(rules.documentId),
+        address: get(rules.address),
+        phoneNumber: get(rules.phoneNumber),
+    };
+}
+function mapRanges(arrayItem, rangeRules, maxDepth, rangeSeparator, noSourceRanges) {
+    if (noSourceRanges) {
+        return [{ from: '', to: '', text: '', noSourceRanges: true }];
+    }
+    const text = extractFieldFromItem(arrayItem, rangeRules.text ?? '', maxDepth);
+    const from = extractFieldFromItem(arrayItem, rangeRules.from ?? '', maxDepth);
+    const to = extractFieldFromItem(arrayItem, rangeRules.to ?? '', maxDepth);
+    const age = rangeRules.age ? extractFieldFromItem(arrayItem, rangeRules.age, maxDepth) || undefined : undefined;
+    const sex = rangeRules.sex ? extractFieldFromItem(arrayItem, rangeRules.sex, maxDepth) || undefined : undefined;
+    if (!text && !from && !to) {
+        return [{ from: '', to: '', text: '', noSourceRanges: true }];
+    }
+    if (text && rangeSeparator) {
+        const sep = rangeSeparator.replace(/\\n/g, '\n').replace(/\\t/g, '\t');
+        const parts = text.split(sep).filter(p => p !== '');
+        if (parts.length > 0) {
+            return parts.map(part => ({ from, to, text: part, age, sex }));
+        }
+    }
+    return [{ from, to, text, age, sex }];
+}
+function serializeOriginalExam(item) {
+    let exam = '';
+    try {
+        exam = JSON.stringify(item);
+    }
+    catch {
+        exam = String(item);
+    }
+    return { contentType: 'application/json', exam };
+}
+function mapSingleExam(arrayItem, examRules, maxDepth) {
+    const extract = (path) => path ? extractFieldFromItem(arrayItem, path, maxDepth) : '';
+    const ohtExam = {
+        labKey: extractLabKey(arrayItem, examRules.labKey, maxDepth),
+        value: extract(examRules.value),
+        unit: extract(examRules.unit),
+        method: extract(examRules.method) || undefined,
+        material: extract(examRules.material) || undefined,
+        collectionDate: extract(examRules.collectionDate) || undefined,
+        effectiveDate: extract(examRules.effectiveDate) || undefined,
+        examCollectionDate: extract(examRules.examCollectionDate) || undefined,
+        examEffectiveDate: extract(examRules.examEffectiveDate) || undefined,
+        documentDate: extract(examRules.documentDate),
+        description: extract(examRules.description),
+        mnemonic: extract(examRules.mnemonic),
+        examName: extract(examRules.examName),
+        range: mapRanges(arrayItem, examRules.range, maxDepth, undefined, examRules.noSourceRanges),
+        annotation: extract(examRules.annotation) || undefined,
+    };
+    return { ohtExam, originalExam: serializeOriginalExam(arrayItem.item) };
+}
+/**
+ * Map all exams from the source object using the exam path rules.
+ *
+ * Algorithm:
+ *  1. Collect every path referenced in examRules (expanding compound labKey paths).
+ *  2. Determine the maximum [*] depth across all paths.
+ *  3. Resolve every leaf ArrayItem at that depth (each becomes one exam).
+ *  4. Fields from shallower depths are resolved via the ancestors chain.
+ */
+function mapExams(source, examRules) {
+    const rawPaths = [
+        examRules.labKey,
+        examRules.value,
+        examRules.unit,
+        examRules.mnemonic,
+        examRules.examName,
+        examRules.range.text,
+        ...[
+            examRules.method,
+            examRules.material,
+            examRules.collectionDate,
+            examRules.effectiveDate,
+            examRules.examCollectionDate,
+            examRules.examEffectiveDate,
+            examRules.documentDate,
+            examRules.description,
+            examRules.annotation,
+            examRules.range.from,
+            examRules.range.to,
+            examRules.range.age,
+            examRules.range.sex,
+        ].filter((p) => !!p),
+    ];
+    const allPaths = [];
+    for (const p of rawPaths) {
+        if (isCompoundLabKey(p)) {
+            const [pA, pB] = splitCompoundLabKey(p);
+            allPaths.push(pA, pB);
+        }
+        else {
+            allPaths.push(p);
+        }
+    }
+    const maxDepth = allPaths.reduce((m, p) => Math.max(m, countArrayDepth(p)), 0);
+    const arrayItems = resolveDeepestArrayItems(source, allPaths);
+    if (arrayItems.length === 0)
+        return [];
+    return arrayItems.map(ai => mapSingleExam(ai, examRules, maxDepth));
+}
 //# sourceMappingURL=mapperUtils.js.map

package/dist/util-ts/mapperUtils.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.27",
+  "version": "0.5.29",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",