@openhealth/oht-custom-parser-lib 0.5.23 → 0.5.24

package/dist/index.d.ts

@@ -18,3 +18,5 @@ 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 type { LisCsvRow } from './util-ts/mapperUtils';

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.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.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; } });
@@ -100,4 +100,7 @@ Object.defineProperty(exports, "getMappedBiomarkers", { enumerable: true, get: f
 Object.defineProperty(exports, "getMappedBiomarkersLatest", { enumerable: true, get: function () { return dataUtils_2.getMappedBiomarkersLatest; } });
 var extractionUtils_1 = require("./util-ts/extractionUtils");
 Object.defineProperty(exports, "parseRange", { enumerable: true, get: function () { return extractionUtils_1.parseRange; } });
+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; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/util-ts/mapperUtils.d.ts

@@ -0,0 +1,12 @@
+/** One parsed row: keys from the CSV header, values as strings. */
+export type LisCsvRow = Record<string, string>;
+/**
+ * LIS CSV (`;`, quoted multiline fields) → rows. Column names come from the header; one row = one logical line.
+ */
+export declare function lisCsvToExamRows(csv: string): LisCsvRow[];
+/**
+ * LIS / AOL-style XML → plain JS object (xml2js: attrs merged into elements, no trim).
+ * Uses `explicitArray: false` so single text/child nodes are strings/objects, not `[value]`.
+ * Repeated sibling tags (e.g. several `exame`) still parse as arrays.
+ */
+export declare function lisXmlToJson(xml: string): Promise<unknown>;

package/dist/util-ts/mapperUtils.js

@@ -0,0 +1,44 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.lisCsvToExamRows = lisCsvToExamRows;
+exports.lisXmlToJson = lisXmlToJson;
+const sync_1 = require("csv-parse/sync");
+const xml2js_1 = require("xml2js");
+const lisCsvParseOptions = {
+    columns: true,
+    skip_empty_lines: true,
+    bom: true,
+    relax_column_count: true,
+    delimiter: ';',
+};
+function parseLisCsvRaw(csv) {
+    if (typeof csv !== 'string') {
+        throw new TypeError('lisCsvToExamRows: expected a string');
+    }
+    if (csv.trim() === '') {
+        return [];
+    }
+    return (0, sync_1.parse)(csv, lisCsvParseOptions);
+}
+/**
+ * LIS CSV (`;`, quoted multiline fields) → rows. Column names come from the header; one row = one logical line.
+ */
+function lisCsvToExamRows(csv) {
+    return parseLisCsvRaw(csv);
+}
+/**
+ * LIS / AOL-style XML → plain JS object (xml2js: attrs merged into elements, no trim).
+ * Uses `explicitArray: false` so single text/child nodes are strings/objects, not `[value]`.
+ * Repeated sibling tags (e.g. several `exame`) still parse as arrays.
+ */
+async function lisXmlToJson(xml) {
+    if (typeof xml !== 'string') {
+        throw new TypeError('lisXmlToJson: expected a string');
+    }
+    return (0, xml2js_1.parseStringPromise)(xml, {
+        explicitArray: false,
+        mergeAttrs: true,
+        trim: false,
+    });
+}
+//# sourceMappingURL=mapperUtils.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"mapperUtils.js","sourceRoot":"","sources":["../../util-ts/mapperUtils.ts"],"names":[],"mappings":";;AA2BA,4CAEC;AAOD,oCASC;AA7CD,yCAAwE;AACxE,mCAA4C;AAE5C,MAAM,kBAAkB,GAAoB;IAC1C,OAAO,EAAE,IAAI;IACb,gBAAgB,EAAE,IAAI;IACtB,GAAG,EAAE,IAAI;IACT,kBAAkB,EAAE,IAAI;IACxB,SAAS,EAAE,GAAG;CACf,CAAC;AAKF,SAAS,cAAc,CAAC,GAAW;IACjC,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;QAC5B,MAAM,IAAI,SAAS,CAAC,qCAAqC,CAAC,CAAC;IAC7D,CAAC;IACD,IAAI,GAAG,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;QACtB,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,OAAO,IAAA,YAAK,EAAC,GAAG,EAAE,kBAAkB,CAA2B,CAAC;AAClE,CAAC;AAED;;GAEG;AACH,SAAgB,gBAAgB,CAAC,GAAW;IAC1C,OAAO,cAAc,CAAC,GAAG,CAAC,CAAC;AAC7B,CAAC;AAED;;;;GAIG;AACI,KAAK,UAAU,YAAY,CAAC,GAAW;IAC5C,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;QAC5B,MAAM,IAAI,SAAS,CAAC,iCAAiC,CAAC,CAAC;IACzD,CAAC;IACD,OAAO,IAAA,2BAAkB,EAAC,GAAG,EAAE;QAC7B,aAAa,EAAE,KAAK;QACpB,UAAU,EAAE,IAAI;QAChB,IAAI,EAAE,KAAK;KACZ,CAAC,CAAC;AACL,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.23",
+  "version": "0.5.24",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -18,19 +18,23 @@
     "@google-cloud/storage": "^7.7.0",
     "axios": "^1.13.2",
     "bottleneck": "^2.19.5",
+    "csv-parse": "^6.2.1",
     "dayjs": "^1.11.13",
     "dotenv": "^16.4.5",
     "jsonata": "^2.1.0",
     "moment": "^2.30.1",
     "mongodb": "^6.3.0",
     "pino": "^8.19.0",
-    "pino-pretty": "^11.3.0"
+    "pino-pretty": "^11.3.0",
+    "xml2js": "^0.6.2"
   },
   "devDependencies": {
     "@types/jest": "^29.5.14",
+    "@types/xml2js": "^0.4.14",
     "axios-mock-adapter": "^2.1.0",
     "jest": "^29.7.0",
     "ts-jest": "^29.2.5",
+    "tsx": "^4.19.2",
     "typescript": "^5.0.0"
   }
 }