@openhealth/oht-custom-parser-lib 0.5.58 → 0.5.60
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/index.d.ts +1 -0
- package/dist/index.js +4 -1
- package/dist/index.js.map +1 -1
- package/dist/service/auxiliaryFunctions.service.d.ts +1 -1
- package/dist/service/auxiliaryFunctions.service.js +6 -3
- package/dist/service/auxiliaryFunctions.service.js.map +1 -1
- package/dist/service/ohtReportMeasurementsExtractor.service.d.ts +2 -1
- package/dist/service/ohtReportMeasurementsExtractor.service.js +5 -4
- package/dist/service/ohtReportMeasurementsExtractor.service.js.map +1 -1
- package/dist/service/reportCreator.service.d.ts +1 -1
- package/dist/service/reportCreator.service.js +2 -2
- package/dist/service/reportCreator.service.js.map +1 -1
- package/dist/types/oht.types.d.ts +1 -0
- package/dist/types/oht.types.js.map +1 -1
- package/dist/util-ts/dataUtils.d.ts +4 -4
- package/dist/util-ts/dataUtils.js +31 -13
- package/dist/util-ts/dataUtils.js.map +1 -1
- package/dist/util-ts/mapperUtils.d.ts +8 -7
- package/dist/util-ts/mapperUtils.js +11 -8
- package/dist/util-ts/mapperUtils.js.map +1 -1
- package/dist/util-ts/siloPaths.d.ts +13 -0
- package/dist/util-ts/siloPaths.js +24 -0
- package/dist/util-ts/siloPaths.js.map +1 -0
- package/package.json +40 -40
- package/readme.md +115 -115
package/dist/index.d.ts
CHANGED
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@@ -12,6 +12,7 @@ export { handleError, ValidationError, JSON_VALIDATION_ERROR_NAME, shouldSendSla
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export type { TransformationRule, TransformationContext, ApplyRulesResult as TransformationApplyRulesResult, ApplyRulesOptions as TransformationApplyRulesOptions, ValidationResult as TransformationValidationResult, } from './types/transformationRules.types';
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export { processingLogger, ProcessingContext, StageDuration, getRequestIdFromContext, getCurrentRequestId, getRequestScopedFilename, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
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export { parsingErrorService, initParsingErrorRequestState, clearParsingErrorRequestState, } from './service/parsingErrorService.service';
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export { normalizePartnerMappingKey, partnerSiloPath } from './util-ts/siloPaths';
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export { makeApiCallWithRetry, parseErrorObj } from './util-ts/apiUtils';
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export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings, fetchSynonymUnits, resolveUnitFromSynonyms, extractFromPath, applyFormat } from './util-ts/dataUtils';
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export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStorageUtils';
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package/dist/index.js
CHANGED
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@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.ValidationError = exports.handleError = exports.PARSING_ERROR_CATALOG = exports.ParsingErrorType = 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.getPartnerTransformationRules = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.getPatientAge = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
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-
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.clearParsingErrorRequestState = exports.initParsingErrorRequestState = exports.parsingErrorService = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getCurrentRequestId = exports.getRequestIdFromContext = exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = exports.shouldSendSlackNotification = exports.JSON_VALIDATION_ERROR_NAME = void 0;
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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.partnerSiloPath = exports.normalizePartnerMappingKey = exports.clearParsingErrorRequestState = exports.initParsingErrorRequestState = exports.parsingErrorService = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getCurrentRequestId = exports.getRequestIdFromContext = exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = exports.shouldSendSlackNotification = exports.JSON_VALIDATION_ERROR_NAME = void 0;
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// ### SERVICES ###
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var reportCreator_service_1 = require("./service/reportCreator.service");
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Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
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@@ -85,6 +85,9 @@ Object.defineProperty(exports, "parsingErrorService", { enumerable: true, get: f
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Object.defineProperty(exports, "initParsingErrorRequestState", { enumerable: true, get: function () { return parsingErrorService_service_1.initParsingErrorRequestState; } });
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Object.defineProperty(exports, "clearParsingErrorRequestState", { enumerable: true, get: function () { return parsingErrorService_service_1.clearParsingErrorRequestState; } });
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// ### UTIL-TS ###
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var siloPaths_1 = require("./util-ts/siloPaths");
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Object.defineProperty(exports, "normalizePartnerMappingKey", { enumerable: true, get: function () { return siloPaths_1.normalizePartnerMappingKey; } });
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Object.defineProperty(exports, "partnerSiloPath", { enumerable: true, get: function () { return siloPaths_1.partnerSiloPath; } });
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var apiUtils_1 = require("./util-ts/apiUtils");
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Object.defineProperty(exports, "makeApiCallWithRetry", { enumerable: true, get: function () { return apiUtils_1.makeApiCallWithRetry; } });
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Object.defineProperty(exports, "parseErrorObj", { enumerable: true, get: function () { return apiUtils_1.parseErrorObj; } });
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package/dist/index.js.map
CHANGED
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@@ -1 +1 @@
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-
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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,mFAU8C;AAT5C,oIAAA,sBAAsB,OAAA;AACtB,yHAAA,WAAW,OAAA;AACX,+HAAA,iBAAiB,OAAA;AACjB,2HAAA,aAAa,OAAA;AACb,6HAAA,eAAe,OAAA;AACf,yIAAA,2BAA2B,OAAA;AAC3B,qIAAA,uBAAuB,OAAA;AAEvB,2IAAA,6BAA6B,OAAA;AAG/B,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,mEAcqC;AALnC,mHAAA,YAAY,OAAA;AAMd,+CA+C2B;AA9CzB,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;AAad,mDAa6B;AAX3B,wGAAA,SAAS,OAAA;AACT,4GAAA,aAAa,OAAA;AACb,6GAAA,cAAc,OAAA;AACd,8GAAA,eAAe,OAAA;AACf,8GAAA,eAAe,OAAA;AACf,+GAAA,gBAAgB,OAAA;AAEhB,oHAAA,qBAAqB,OAAA;AAKvB,2FAOkD;AANhD,6HAAA,WAAW,OAAA;AACX,iIAAA,eAAe,OAAA;AACf,4IAAA,0BAA0B,OAAA;AAC1B,6IAAA,2BAA2B,OAAA;AAC3B,8IAAA,4BAA4B,OAAA;AAC5B,wIAAA,sBAAsB,OAAA;AAUxB,4BAA4B;AAC5B,+EAS4C;AAR1C,4HAAA,gBAAgB,OAAA;AAGhB,mIAAA,uBAAuB,OAAA;AACvB,+HAAA,mBAAmB,OAAA;AACnB,oIAAA,wBAAwB,OAAA;AACxB,0HAAA,cAAc,OAAA;AACd,+HAAA,mBAAmB,OAAA;AAGrB,qFAI+C;AAH7C,kIAAA,mBAAmB,OAAA;AACnB,2IAAA,4BAA4B,OAAA;AAC5B,4IAAA,6BAA6B,OAAA;AAG/B,kBAAkB;AAClB,iDAAkF;AAAzE,uHAAA,0BAA0B,OAAA;AAAE,4GAAA,eAAe,OAAA;AACpD,+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"}
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rejectReason?: string;
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isArchived?: boolean;
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}, fileUploadId: string, filename: string, ohtCoreApiKey: string): Promise<DataImportFileUpload>;
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declare function getPartnerTransformationRules(partnerId: string, labKeys: string[] | undefined, ohtCoreApiKey: string): Promise<TransformationRulesChains>;
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declare function getPartnerTransformationRules(partnerId: string, labKeys: string[] | undefined, ohtCoreApiKey: string, partnerMappingKey?: string): Promise<TransformationRulesChains>;
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export { parseExternalPatientId, parseGender, isPatientAgeValid, getPatientAge, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, getPartnerTransformationRules, };
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const processingLogger_service_1 = require("./processingLogger.service");
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const parsingErrorService_service_1 = require("./parsingErrorService.service");
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const error_types_1 = require("../types/error.types");
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const siloPaths_1 = require("../util-ts/siloPaths");
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const oht_types_1 = require("../types/oht.types");
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const dayjs_1 = __importDefault(require("dayjs"));
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const customParseFormat_1 = __importDefault(require("dayjs/plugin/customParseFormat"));
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// getPartnerTransformationRules fetches all the available partner transformation rules.
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// When labKeys is undefined, all chains for the partner are returned (no labKey filter applied),
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// which includes ohtReport.* chains used to build the OhtReport from raw JSON.
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async function getPartnerTransformationRules(partnerId, labKeys, ohtCoreApiKey) {
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async function getPartnerTransformationRules(partnerId, labKeys, ohtCoreApiKey, partnerMappingKey) {
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// Fetch every partner transformation rule
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const
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const rulesPath = (0, siloPaths_1.partnerSiloPath)(partnerId, partnerMappingKey, 'transformation-rules/');
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const ohtCoreTransformationRulesUrl = `${OHT_CORE_URL}${rulesPath}`;
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const rulesResponse = await (0, apiUtils_1.makeApiCallWithRetry)('GET', ohtCoreTransformationRulesUrl, null, ohtCoreApiKey);
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const rulesMap = (rulesResponse?.data?.items ?? [])
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.reduce((map, rule) => {
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});
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}, new Map());
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// Fetch the rule chains — when labKeys is provided, filter by them; otherwise fetch all chains
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const
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const chainsPath = (0, siloPaths_1.partnerSiloPath)(partnerId, partnerMappingKey, 'transformation-rules-chains/query');
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const ohtCoreTransformationRulesChainsUrl = `${OHT_CORE_URL}${chainsPath}`;
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const chainsBody = labKeys !== undefined
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? { filters: [{ field: 'labKey', multiSearch: labKeys }] }
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: {};
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{"version":3,"file":"auxiliaryFunctions.service.js","sourceRoot":"","sources":["../../service/auxiliaryFunctions.service.ts"],"names":[],"mappings":";;;;;
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+
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@@ -142,9 +142,10 @@ import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey, Par
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* @param partnerId - Partner ID for fetching biomarker mappings and synonym units
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* @param isReportPreview - isReportPreview Report Simulator
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* @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
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+
* @param partnerMappingKey - Silo key resolved from the pipeline Pub/Sub message (defaults to `'default'`).
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* @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, and parsing status
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*/
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-
declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, partnerCustomization?: PartnerCustomization): Promise<{
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148
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+
declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, partnerCustomization?: PartnerCustomization, partnerMappingKey?: string): Promise<{
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measurements: Measurement[];
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unknownMeasurements: UnknownMeasurement[];
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unknownUnits: UnknownUnits[];
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@@ -232,9 +232,10 @@ function resolveUnknownMeasurementName(parts, fallback) {
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* @param partnerId - Partner ID for fetching biomarker mappings and synonym units
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* @param isReportPreview - isReportPreview Report Simulator
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* @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
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+
* @param partnerMappingKey - Silo key resolved from the pipeline Pub/Sub message (defaults to `'default'`).
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* @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, and parsing status
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*/
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237
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-
async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, partnerCustomization) {
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238
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+
async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, partnerCustomization, partnerMappingKey) {
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filename = sourceFilename;
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const measurements = [];
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const unknownMeasurements = [];
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@@ -260,8 +261,8 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
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processingLogger_service_1.processingLogger.logInfo(`Processing lab file with ${labKeys.length} keys, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`);
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// Call getMappedBiomarkers to get the biomarker mapping for the partner and if reportPreview is true, get the latest version regardless of active status
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const mappedBiomarkers = isReportPreview
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-
? await (0, dataUtils_1.getMappedBiomarkersLatest)(partnerId, ohtCoreApiKey)
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-
: await (0, dataUtils_1.getMappedBiomarkers)(partnerId, ohtCoreApiKey);
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264
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+
? await (0, dataUtils_1.getMappedBiomarkersLatest)(partnerId, ohtCoreApiKey, partnerMappingKey)
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265
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+
: await (0, dataUtils_1.getMappedBiomarkers)(partnerId, ohtCoreApiKey, partnerMappingKey);
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// add "GROUPED_" bms for appended mappings
|
|
266
267
|
if (mappedBiomarkers) {
|
|
267
268
|
const groupedLabKeys = Object.keys(mappedBiomarkers).filter(labKey => labKey.startsWith('GROUPED_'));
|
|
@@ -326,7 +327,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
|
|
|
326
327
|
// Fetch synonym units from API if enabled
|
|
327
328
|
let synonymUnits = null;
|
|
328
329
|
if (partnerId) {
|
|
329
|
-
synonymUnits = await (0, dataUtils_1.fetchSynonymUnits)(partnerId, ohtCoreApiKey);
|
|
330
|
+
synonymUnits = await (0, dataUtils_1.fetchSynonymUnits)(partnerId, ohtCoreApiKey, partnerMappingKey);
|
|
330
331
|
// If API fetch failed or returned empty, set to null to use hardcoded fallback
|
|
331
332
|
if (synonymUnits.length === 0) {
|
|
332
333
|
synonymUnits = null;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -5,5 +5,5 @@ import { UnknownUnits } from '../types/custom-parser.types';
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5
5
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* Uses the shared makeApiCallWithRetry helper (Basic auth) from oht-custom-parser-lib.
|
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6
6
|
*/
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7
7
|
declare function postReportPreviewToCore(reportPreviewId: string, measurements: Measurement[], unknownMeasurements: UnknownMeasurement[], filename: string, unknownUnits: UnknownUnits[], partnerId: string, isReportParsedCorrectly: boolean, notes: string, ohtCoreApiKey: string): Promise<void>;
|
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8
|
-
declare function postDataImportFileUploadToCore(dataImportFileUpload: DataImportFileUpload, unknownMeasurements: UnknownMeasurementsBulk, unknownUnits: UnknownUnits[], rejectedStatus: string | undefined, rejectReason: string | undefined, isReportParsedCorrectly: boolean, filename: string, ohtCoreApiKey: string): Promise<DataImportFileUpload | null>;
|
|
8
|
+
declare function postDataImportFileUploadToCore(dataImportFileUpload: DataImportFileUpload, unknownMeasurements: UnknownMeasurementsBulk, unknownUnits: UnknownUnits[], rejectedStatus: string | undefined, rejectReason: string | undefined, isReportParsedCorrectly: boolean, filename: string, ohtCoreApiKey: string, partnerMappingKey?: string): Promise<DataImportFileUpload | null>;
|
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9
9
|
export { postDataImportFileUploadToCore, postReportPreviewToCore };
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@@ -79,7 +79,7 @@ async function postReportPreviewToCore(reportPreviewId, measurements, unknownMea
|
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|
79
79
|
throw apiError;
|
|
80
80
|
}
|
|
81
81
|
}
|
|
82
|
-
async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasurements, unknownUnits, rejectedStatus, rejectReason, isReportParsedCorrectly, filename, ohtCoreApiKey) {
|
|
82
|
+
async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasurements, unknownUnits, rejectedStatus, rejectReason, isReportParsedCorrectly, filename, ohtCoreApiKey, partnerMappingKey) {
|
|
83
83
|
let status = isReportParsedCorrectly
|
|
84
84
|
? oht_types_1.DataImportFileUploadStatus.PROCESSED
|
|
85
85
|
: oht_types_1.DataImportFileUploadStatus.FOR_REVIEW;
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@@ -114,7 +114,7 @@ async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasu
|
|
|
114
114
|
// Send unknown measurements if they exist (before ingestion)
|
|
115
115
|
if (unknownMeasurements.unmappedlabkeys.length > 0) {
|
|
116
116
|
try {
|
|
117
|
-
await (0, dataUtils_1.updatePartnerCustomParserUnmappedLabKeys)(dataImportFileUpload.partnerId, unknownMeasurements, ohtCoreApiKey);
|
|
117
|
+
await (0, dataUtils_1.updatePartnerCustomParserUnmappedLabKeys)(dataImportFileUpload.partnerId, unknownMeasurements, ohtCoreApiKey, partnerMappingKey);
|
|
118
118
|
processingLogger_service_1.processingLogger.logInfo(`Successfully sent unknown measurements to server, filename: ${filename}`, {
|
|
119
119
|
partner_id: dataImportFileUpload.partnerId,
|
|
120
120
|
unknown_measurements_count: unknownMeasurements.unmappedlabkeys.length,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"reportCreator.service.js","sourceRoot":"","sources":["../../service/reportCreator.service.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
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@@ -1 +1 @@
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|
1
|
-
{"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;
|
|
1
|
+
{"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;AAkWA,IAAY,GAIX;AAJD,WAAY,GAAG;IACb,oBAAa,CAAA;IACb,wBAAiB,CAAA;IACjB,sBAAe,CAAA;AACjB,CAAC,EAJW,GAAG,mBAAH,GAAG,QAId;AAED,IAAY,UAGX;AAHD,WAAY,UAAU;IACpB,qDAAuC,CAAA;IACvC,6BAAe,CAAA;AACjB,CAAC,EAHW,UAAU,0BAAV,UAAU,QAGrB;AAED,IAAY,0BAYX;AAZD,WAAY,0BAA0B;IACpC,mDAAqB,CAAA;IACrB,iDAAmB,CAAA;IACnB,uDAAyB,CAAA;IACzB,uDAAyB,CAAA;IACzB,qDAAuB,CAAA;IACvB,qDAAuB,CAAA;IACvB,6CAAe,CAAA;IACf,iDAAmB,CAAA;IACnB,mDAAqB,CAAA;IACrB,mDAAqB,CAAA;IACrB,2DAA6B,CAAA;AAC/B,CAAC,EAZW,0BAA0B,0CAA1B,0BAA0B,QAYrC;AAED,IAAY,kBAGX;AAHD,WAAY,kBAAkB;IAC5B,uDAAiC,CAAA;IACjC,6CAAuB,CAAA;AACzB,CAAC,EAHW,kBAAkB,kCAAlB,kBAAkB,QAG7B;AAED,IAAY,0BAIX;AAJD,WAAY,0BAA0B;IACpC,6CAAe,CAAA;IACf,2DAA6B,CAAA;IAC7B,qDAAuB,CAAA;AACzB,CAAC,EAJW,0BAA0B,0CAA1B,0BAA0B,QAIrC;AAED,IAAY,kBAOX;AAPD,WAAY,kBAAkB;IAC5B,yCAAmB,CAAA;IACnB,yCAAmB,CAAA;IACnB,+CAAyB,CAAA;IACzB,mCAAa,CAAA;IACb,qCAAe,CAAA;IACf,2CAAqB,CAAA;AACvB,CAAC,EAPW,kBAAkB,kCAAlB,kBAAkB,QAO7B;AAED,IAAY,YASX;AATD,WAAY,YAAY;IACtB,6CAA6B,CAAA;IAC7B,mDAAmC,CAAA;IACnC,yDAAyC,CAAA;IACzC,2DAA2C,CAAA;IAC3C,2DAA2C,CAAA;IAC3C,+DAA+C,CAAA;IAC/C,2DAA2C,CAAA;IAC3C,mDAAmC,CAAA;AACrC,CAAC,EATW,YAAY,4BAAZ,YAAY,QASvB;AAED,IAAY,YAsBX;AAtBD,WAAY,YAAY;IACtB,mFAAmE,CAAA;IACnE,uDAAuC,CAAA;IACvC,+DAA+C,CAAA;IAC/C,mDAAmC,CAAA;IACnC,iEAAiD,CAAA;IACjD,uDAAuC,CAAA;IACvC,uDAAuC,CAAA;IACvC,6DAA6C,CAAA;IAC7C,2EAA2D,CAAA;IAC3D,2DAA2C,CAAA;IAC3C,uEAAuD,CAAA;IACvD,yDAAyC,CAAA;IACzC,uEAAuD,CAAA;IACvD,iEAAiD,CAAA;IACjD,oHAAoG,CAAA;IACpG,qGAAqG;IACrG,gEAAgD,CAAA;IAChD,wFAAwF;IACxF,uEAAuD,CAAA;IACvD,gGAAgG;IAChG,6HAA6G,CAAA;AAC/G,CAAC,EAtBW,YAAY,4BAAZ,YAAY,QAsBvB;AA0CD,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,+BAAe,CAAA;IACf,iCAAiB,CAAA;IACjB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,4BAAZ,YAAY,QAIvB;AAsCD,IAAY,kBAIX;AAJD,WAAY,kBAAkB;IAC5B,6CAAuB,CAAA;IACvB,2CAAqB,CAAA;IACrB,uDAAiC,CAAA;AACnC,CAAC,EAJW,kBAAkB,kCAAlB,kBAAkB,QAI7B;AAED,IAAY,sBAOX;AAPD,WAAY,sBAAsB;IAChC,+CAAqB,CAAA;IACrB,+CAAqB,CAAA;IACrB,4EAAkD,CAAA;IAClD,4EAAkD,CAAA;IAClD,4DAAkC,CAAA;IAClC,2CAAiB,CAAA;AACnB,CAAC,EAPW,sBAAsB,sCAAtB,sBAAsB,QAOjC;AAED,IAAY,WAGX;AAHD,WAAY,WAAW;IACrB,wBAAS,CAAA;IACT,sCAAuB,CAAA;AACzB,CAAC,EAHW,WAAW,2BAAX,WAAW,QAGtB;AAED,IAAY,kCAGX;AAHD,WAAY,kCAAkC;IAC5C,6DAAuB,CAAA;IACvB,iEAA2B,CAAA;AAC7B,CAAC,EAHW,kCAAkC,kDAAlC,kCAAkC,QAG7C;AAED,IAAY,gCAMX;AAND,WAAY,gCAAgC;IAC1C,2DAAuB,CAAA;IACvB,6EAAyC,CAAA;IACzC,+EAA2C,CAAA;IAC3C,2FAAuD,CAAA;IACvD,uFAAmD,CAAA;AACrD,CAAC,EANW,gCAAgC,gDAAhC,gCAAgC,QAM3C"}
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@@ -13,16 +13,16 @@ export declare function resolveUnitFromSynonyms(unitLowerCase: string, biomarker
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13
13
|
export declare function isBiomarkerValueNumerical(biomarker: any): boolean;
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14
14
|
export declare function isBiomarkerExternalNoVisualRange(biomarker: any): boolean;
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|
15
15
|
export declare const extractValue: (obj: any, position?: string) => any;
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16
|
-
export declare const getMappedBiomarkers: (partnerId: string, ohtCoreApiKey: string) => Promise<any>;
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17
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-
export declare const getMappedBiomarkersLatest: (partnerId: string, ohtCoreApiKey: string) => Promise<any>;
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18
|
-
export declare const updatePartnerCustomParserUnmappedLabKeys: (partnerId: string, unknownMeasurementsBulk: UnknownMeasurementsBulk, ohtCoreApiKey: string) => Promise<void>;
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16
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+
export declare const getMappedBiomarkers: (partnerId: string, ohtCoreApiKey: string, partnerMappingKey?: string) => Promise<any>;
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17
|
+
export declare const getMappedBiomarkersLatest: (partnerId: string, ohtCoreApiKey: string, partnerMappingKey?: string) => Promise<any>;
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|
18
|
+
export declare const updatePartnerCustomParserUnmappedLabKeys: (partnerId: string, unknownMeasurementsBulk: UnknownMeasurementsBulk, ohtCoreApiKey: string, partnerMappingKey?: string) => Promise<void>;
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|
19
19
|
export declare const bulkUpsertCustomParserErrorProfiles: (partnerId: string, errorProfiles: import("../types/error.types").ErrorProfilePayload[], ohtCoreApiKey: string) => Promise<void>;
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20
20
|
export declare const bulkCreateCustomParserUnknownUnits: (partnerId: string, unknownUnits: UnknownUnits[], ohtCoreApiKey: string) => Promise<void>;
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/**
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* Fetch synonym units from oht-core API endpoint
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* Returns all approved resolved synonym units (backend already filters and returns all results)
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*/
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export declare const fetchSynonymUnits: (partnerId: string | null | undefined, ohtCoreApiKey: string) => Promise<SynonymUnit[]>;
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export declare const fetchSynonymUnits: (partnerId: string | null | undefined, ohtCoreApiKey: string, partnerMappingKey?: string) => Promise<SynonymUnit[]>;
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/**
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* Processes appended biomarker mappings by extracting values from additional labKeys.
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* Compatible with AnnotationPreviewService interface and returns object with text property.
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@@ -11,6 +11,7 @@ exports.isNumericalWithoutValidResult = isNumericalWithoutValidResult;
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const oht_types_1 = require("../types/oht.types");
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const apiUtils_1 = require("./apiUtils");
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const processingLogger_service_1 = require("../service/processingLogger.service");
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+
const siloPaths_1 = require("./siloPaths");
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/**
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* Normalize unit string for comparison (lowercase, remove spaces)
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*/
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@@ -69,10 +70,11 @@ const extractValue = (obj, position) => {
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};
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exports.extractValue = extractValue;
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const OHT_CORE_URL = process.env.OHT_CORE_URL;
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// function that uses GET request at /v1/customparser/partner/{partnerId}/active to get the mapping for the biomarker
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-
const getMappedBiomarkers = async (partnerId, ohtCoreApiKey) => {
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// function that uses GET request at /v1/customparser/partner/{partnerId}/mappings/{key}/active to get the mapping for the biomarker
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+
const getMappedBiomarkers = async (partnerId, ohtCoreApiKey, partnerMappingKey) => {
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try {
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-
const
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+
const path = (0, siloPaths_1.partnerSiloPath)(partnerId, partnerMappingKey, 'active');
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+
const response = await (0, apiUtils_1.makeApiCallWithRetry)('get', `${OHT_CORE_URL}${path}`, null, ohtCoreApiKey);
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return response?.data?.biomarkerMappings ?? {};
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}
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80
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catch (error) {
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@@ -83,11 +85,12 @@ const getMappedBiomarkers = async (partnerId, ohtCoreApiKey) => {
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}
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};
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|
exports.getMappedBiomarkers = getMappedBiomarkers;
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|
-
// function that uses GET request at /v1/customparser/partner/{partnerId}/latest to get the latest mapping version for the biomarker
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+
// function that uses GET request at /v1/customparser/partner/{partnerId}/mappings/{key}/latest to get the latest mapping version for the biomarker
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// Used when reportPreview is true to get the latest version regardless of active status
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-
const getMappedBiomarkersLatest = async (partnerId, ohtCoreApiKey) => {
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90
|
+
const getMappedBiomarkersLatest = async (partnerId, ohtCoreApiKey, partnerMappingKey) => {
|
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91
|
try {
|
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90
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-
const
|
|
92
|
+
const path = (0, siloPaths_1.partnerSiloPath)(partnerId, partnerMappingKey, 'latest');
|
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93
|
+
const response = await (0, apiUtils_1.makeApiCallWithRetry)('get', `${OHT_CORE_URL}${path}`, null, ohtCoreApiKey);
|
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94
|
return response?.data?.biomarkerMappings ?? {};
|
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92
95
|
}
|
|
93
96
|
catch (error) {
|
|
@@ -98,15 +101,18 @@ const getMappedBiomarkersLatest = async (partnerId, ohtCoreApiKey) => {
|
|
|
98
101
|
}
|
|
99
102
|
};
|
|
100
103
|
exports.getMappedBiomarkersLatest = getMappedBiomarkersLatest;
|
|
101
|
-
// function that uses POST request at /v1/customparser/partners/{partnerId}/unmapped/bulk to send the unknownMeasurements to the server
|
|
102
|
-
const updatePartnerCustomParserUnmappedLabKeys = async (partnerId, unknownMeasurementsBulk, ohtCoreApiKey) => {
|
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103
|
-
const
|
|
104
|
+
// function that uses POST request at /v1/customparser/partners/{partnerId}/mappings/{key}/unmapped/bulk to send the unknownMeasurements to the server
|
|
105
|
+
const updatePartnerCustomParserUnmappedLabKeys = async (partnerId, unknownMeasurementsBulk, ohtCoreApiKey, partnerMappingKey) => {
|
|
106
|
+
const path = (0, siloPaths_1.partnerSiloPath)(partnerId, partnerMappingKey, 'unmapped/bulk');
|
|
107
|
+
const response = await (0, apiUtils_1.makeApiCallWithRetry)('post', `${OHT_CORE_URL}${path}`, {
|
|
104
108
|
partnerId: partnerId,
|
|
105
109
|
unmappedLabKeys: unknownMeasurementsBulk.unmappedlabkeys,
|
|
106
110
|
}, ohtCoreApiKey);
|
|
107
111
|
const unmappedData = response?.data;
|
|
108
|
-
|
|
112
|
+
const key = (0, siloPaths_1.normalizePartnerMappingKey)(partnerMappingKey);
|
|
113
|
+
processingLogger_service_1.processingLogger.logInfo(`Resp: POST ${path}`, {
|
|
109
114
|
partner_id: partnerId,
|
|
115
|
+
partner_mapping_key: key,
|
|
110
116
|
unmapped_count: unknownMeasurementsBulk.unmappedlabkeys?.length ?? 0,
|
|
111
117
|
http_status: response?.status,
|
|
112
118
|
response_message: typeof unmappedData?.message === 'string' ? unmappedData.message : undefined,
|
|
@@ -146,15 +152,26 @@ exports.bulkCreateCustomParserUnknownUnits = bulkCreateCustomParserUnknownUnits;
|
|
|
146
152
|
* Fetch synonym units from oht-core API endpoint
|
|
147
153
|
* Returns all approved resolved synonym units (backend already filters and returns all results)
|
|
148
154
|
*/
|
|
149
|
-
const fetchSynonymUnits = async (partnerId, ohtCoreApiKey) => {
|
|
155
|
+
const fetchSynonymUnits = async (partnerId, ohtCoreApiKey, partnerMappingKey) => {
|
|
150
156
|
try {
|
|
151
|
-
const
|
|
157
|
+
const params = new URLSearchParams();
|
|
158
|
+
if (partnerId)
|
|
159
|
+
params.set('partnerId', partnerId);
|
|
160
|
+
if (partnerMappingKey) {
|
|
161
|
+
params.set('partnerMappingKey', (0, siloPaths_1.normalizePartnerMappingKey)(partnerMappingKey));
|
|
162
|
+
}
|
|
163
|
+
const queryString = params.toString();
|
|
164
|
+
const url = `${OHT_CORE_URL}/v1/synonym/synonym-units/resolved${queryString ? `?${queryString}` : ''}`;
|
|
152
165
|
const response = await (0, apiUtils_1.makeApiCallWithRetry)('get', url, null, ohtCoreApiKey);
|
|
153
166
|
// Backend returns array directly (already filtered for approved status and non-null targetUnit)
|
|
154
167
|
const synonymUnits = Array.isArray(response?.data)
|
|
155
168
|
? response.data
|
|
156
169
|
: response?.data?.items || [];
|
|
157
|
-
processingLogger_service_1.processingLogger.logInfo(`Fetched ${synonymUnits.length} synonym units from API`, {
|
|
170
|
+
processingLogger_service_1.processingLogger.logInfo(`Fetched ${synonymUnits.length} synonym units from API`, {
|
|
171
|
+
partner_id: partnerId,
|
|
172
|
+
partner_mapping_key: (0, siloPaths_1.normalizePartnerMappingKey)(partnerMappingKey),
|
|
173
|
+
count: synonymUnits.length,
|
|
174
|
+
});
|
|
158
175
|
return synonymUnits;
|
|
159
176
|
}
|
|
160
177
|
catch (error) {
|
|
@@ -164,6 +181,7 @@ const fetchSynonymUnits = async (partnerId, ohtCoreApiKey) => {
|
|
|
164
181
|
warningSeverity: 'degraded',
|
|
165
182
|
data: {
|
|
166
183
|
partner_id: partnerId,
|
|
184
|
+
partner_mapping_key: (0, siloPaths_1.normalizePartnerMappingKey)(partnerMappingKey),
|
|
167
185
|
error: error.message,
|
|
168
186
|
},
|
|
169
187
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -17,16 +17,17 @@ export declare function lisXmlToJson(xml: string): Promise<unknown>;
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/**
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* Fetch the active mapping rules for a partner from the OHT Core API.
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*
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-
* Calls `GET {
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* and returns the raw response payload, which the caller can cast to
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-
*
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20
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+
* Calls `GET {ohtCoreUrl}/v1/customparser/partners/{partnerId}/mappings/{key}/mapping-rules/active`
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21
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* and returns the raw response payload, which the caller can cast to `OhtReportMappingRules`.
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* Returns `null` when the API returns no data.
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*
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-
* @param
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* @param apiKey
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* @param partnerId
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+
* @param ohtCoreUrl Base URL of the OHT Core API (e.g. process.env.OHT_CORE_URL).
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+
* @param apiKey API key used for Basic auth.
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* @param partnerId Partner identifier.
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* @param partnerMappingKey Optional silo key (default: `'default'`).
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* @throws When the HTTP request itself fails (network error, non-2xx status, etc.).
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*/
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-
export declare function fetchActiveMappingRules(ohtCoreUrl: string, apiKey: string, partnerId: string): Promise<ActiveMappingRulesApiResponse | null>;
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30
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+
export declare function fetchActiveMappingRules(ohtCoreUrl: string, apiKey: string, partnerId: string, partnerMappingKey?: string): Promise<ActiveMappingRulesApiResponse | null>;
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/**
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31
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* Parse raw file content to a plain JS value, auto-detecting the format.
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32
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* CSV rows are wrapped in { rows: [...] } so downstream path rules can target them.
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@@ -11,6 +11,7 @@ exports.mapExams = mapExams;
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11
11
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const sync_1 = require("csv-parse/sync");
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12
12
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const xml2js_1 = require("xml2js");
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13
13
|
const apiUtils_1 = require("./apiUtils");
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14
|
+
const siloPaths_1 = require("./siloPaths");
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14
15
|
const lisCsvParseOptions = {
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15
16
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columns: true,
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16
17
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skip_empty_lines: true,
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@@ -60,17 +61,19 @@ async function lisXmlToJson(xml) {
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60
61
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/**
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61
62
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* Fetch the active mapping rules for a partner from the OHT Core API.
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62
63
|
*
|
|
63
|
-
* Calls `GET {
|
|
64
|
-
* and returns the raw response payload, which the caller can cast to
|
|
65
|
-
*
|
|
64
|
+
* Calls `GET {ohtCoreUrl}/v1/customparser/partners/{partnerId}/mappings/{key}/mapping-rules/active`
|
|
65
|
+
* and returns the raw response payload, which the caller can cast to `OhtReportMappingRules`.
|
|
66
|
+
* Returns `null` when the API returns no data.
|
|
66
67
|
*
|
|
67
|
-
* @param
|
|
68
|
-
* @param apiKey
|
|
69
|
-
* @param partnerId
|
|
68
|
+
* @param ohtCoreUrl Base URL of the OHT Core API (e.g. process.env.OHT_CORE_URL).
|
|
69
|
+
* @param apiKey API key used for Basic auth.
|
|
70
|
+
* @param partnerId Partner identifier.
|
|
71
|
+
* @param partnerMappingKey Optional silo key (default: `'default'`).
|
|
70
72
|
* @throws When the HTTP request itself fails (network error, non-2xx status, etc.).
|
|
71
73
|
*/
|
|
72
|
-
async function fetchActiveMappingRules(ohtCoreUrl, apiKey, partnerId) {
|
|
73
|
-
const
|
|
74
|
+
async function fetchActiveMappingRules(ohtCoreUrl, apiKey, partnerId, partnerMappingKey) {
|
|
75
|
+
const path = (0, siloPaths_1.partnerSiloPath)(partnerId, partnerMappingKey, 'mapping-rules/active');
|
|
76
|
+
const url = `${ohtCoreUrl}${path}`;
|
|
74
77
|
const response = await (0, apiUtils_1.makeApiCallWithRetry)('GET', url, null, apiKey, 2);
|
|
75
78
|
return (response?.data ?? null);
|
|
76
79
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -0,0 +1,13 @@
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|
|
1
|
+
/**
|
|
2
|
+
* Normalize a partnerMappingKey to a canonical lowercase form.
|
|
3
|
+
* Mirrors oht-core `silo.NormalizeKey`: trim + lowercase, empty → "default".
|
|
4
|
+
*/
|
|
5
|
+
export declare function normalizePartnerMappingKey(key: string | undefined | null): string;
|
|
6
|
+
/**
|
|
7
|
+
* Build a silo-scoped path under `/v1/customparser/partners/{partnerId}/mappings/{key}/`.
|
|
8
|
+
*
|
|
9
|
+
* @param partnerId - Partner ObjectID string
|
|
10
|
+
* @param mappingKey - Raw silo key (will be normalized)
|
|
11
|
+
* @param suffix - Path segment(s) after the key, e.g. `'active'`, `'unmapped/bulk'`
|
|
12
|
+
*/
|
|
13
|
+
export declare function partnerSiloPath(partnerId: string, mappingKey: string | undefined | null, suffix: string): string;
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.normalizePartnerMappingKey = normalizePartnerMappingKey;
|
|
4
|
+
exports.partnerSiloPath = partnerSiloPath;
|
|
5
|
+
/**
|
|
6
|
+
* Normalize a partnerMappingKey to a canonical lowercase form.
|
|
7
|
+
* Mirrors oht-core `silo.NormalizeKey`: trim + lowercase, empty → "default".
|
|
8
|
+
*/
|
|
9
|
+
function normalizePartnerMappingKey(key) {
|
|
10
|
+
const k = (key ?? '').trim().toLowerCase();
|
|
11
|
+
return k === '' ? 'default' : k;
|
|
12
|
+
}
|
|
13
|
+
/**
|
|
14
|
+
* Build a silo-scoped path under `/v1/customparser/partners/{partnerId}/mappings/{key}/`.
|
|
15
|
+
*
|
|
16
|
+
* @param partnerId - Partner ObjectID string
|
|
17
|
+
* @param mappingKey - Raw silo key (will be normalized)
|
|
18
|
+
* @param suffix - Path segment(s) after the key, e.g. `'active'`, `'unmapped/bulk'`
|
|
19
|
+
*/
|
|
20
|
+
function partnerSiloPath(partnerId, mappingKey, suffix) {
|
|
21
|
+
const key = normalizePartnerMappingKey(mappingKey);
|
|
22
|
+
return `/v1/customparser/partners/${partnerId}/mappings/${encodeURIComponent(key)}/${suffix}`;
|
|
23
|
+
}
|
|
24
|
+
//# sourceMappingURL=siloPaths.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"siloPaths.js","sourceRoot":"","sources":["../../util-ts/siloPaths.ts"],"names":[],"mappings":";;AAIA,gEAGC;AASD,0CAOC;AAvBD;;;GAGG;AACH,SAAgB,0BAA0B,CAAC,GAA8B;IACvE,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IAC3C,OAAO,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC;AAClC,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,eAAe,CAC7B,SAAiB,EACjB,UAAqC,EACrC,MAAc;IAEd,MAAM,GAAG,GAAG,0BAA0B,CAAC,UAAU,CAAC,CAAC;IACnD,OAAO,6BAA6B,SAAS,aAAa,kBAAkB,CAAC,GAAG,CAAC,IAAI,MAAM,EAAE,CAAC;AAChG,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,40 +1,40 @@
|
|
|
1
|
-
{
|
|
2
|
-
"name": "@openhealth/oht-custom-parser-lib",
|
|
3
|
-
"version": "0.5.
|
|
4
|
-
"description": "Shared nodejs lib with with reusable functions",
|
|
5
|
-
"main": "dist/index.js",
|
|
6
|
-
"types": "dist/index.d.ts",
|
|
7
|
-
"files": [
|
|
8
|
-
"/dist"
|
|
9
|
-
],
|
|
10
|
-
"scripts": {
|
|
11
|
-
"test": "jest"
|
|
12
|
-
},
|
|
13
|
-
"keywords": [],
|
|
14
|
-
"author": "",
|
|
15
|
-
"license": "ISC",
|
|
16
|
-
"dependencies": {
|
|
17
|
-
"@google-cloud/pubsub": "^4.10.0",
|
|
18
|
-
"@google-cloud/storage": "^7.7.0",
|
|
19
|
-
"axios": "^1.13.2",
|
|
20
|
-
"bottleneck": "^2.19.5",
|
|
21
|
-
"csv-parse": "^6.2.1",
|
|
22
|
-
"dayjs": "^1.11.13",
|
|
23
|
-
"dotenv": "^16.4.5",
|
|
24
|
-
"jsonata": "^2.1.0",
|
|
25
|
-
"moment": "^2.30.1",
|
|
26
|
-
"mongodb": "^6.3.0",
|
|
27
|
-
"pino": "^8.19.0",
|
|
28
|
-
"pino-pretty": "^11.3.0",
|
|
29
|
-
"xml2js": "^0.6.2"
|
|
30
|
-
},
|
|
31
|
-
"devDependencies": {
|
|
32
|
-
"@types/jest": "^29.5.14",
|
|
33
|
-
"@types/xml2js": "^0.4.14",
|
|
34
|
-
"axios-mock-adapter": "^2.1.0",
|
|
35
|
-
"jest": "^29.7.0",
|
|
36
|
-
"ts-jest": "^29.2.5",
|
|
37
|
-
"tsx": "^4.19.2",
|
|
38
|
-
"typescript": "^5.0.0"
|
|
39
|
-
}
|
|
40
|
-
}
|
|
1
|
+
{
|
|
2
|
+
"name": "@openhealth/oht-custom-parser-lib",
|
|
3
|
+
"version": "0.5.60",
|
|
4
|
+
"description": "Shared nodejs lib with with reusable functions",
|
|
5
|
+
"main": "dist/index.js",
|
|
6
|
+
"types": "dist/index.d.ts",
|
|
7
|
+
"files": [
|
|
8
|
+
"/dist"
|
|
9
|
+
],
|
|
10
|
+
"scripts": {
|
|
11
|
+
"test": "jest"
|
|
12
|
+
},
|
|
13
|
+
"keywords": [],
|
|
14
|
+
"author": "",
|
|
15
|
+
"license": "ISC",
|
|
16
|
+
"dependencies": {
|
|
17
|
+
"@google-cloud/pubsub": "^4.10.0",
|
|
18
|
+
"@google-cloud/storage": "^7.7.0",
|
|
19
|
+
"axios": "^1.13.2",
|
|
20
|
+
"bottleneck": "^2.19.5",
|
|
21
|
+
"csv-parse": "^6.2.1",
|
|
22
|
+
"dayjs": "^1.11.13",
|
|
23
|
+
"dotenv": "^16.4.5",
|
|
24
|
+
"jsonata": "^2.1.0",
|
|
25
|
+
"moment": "^2.30.1",
|
|
26
|
+
"mongodb": "^6.3.0",
|
|
27
|
+
"pino": "^8.19.0",
|
|
28
|
+
"pino-pretty": "^11.3.0",
|
|
29
|
+
"xml2js": "^0.6.2"
|
|
30
|
+
},
|
|
31
|
+
"devDependencies": {
|
|
32
|
+
"@types/jest": "^29.5.14",
|
|
33
|
+
"@types/xml2js": "^0.4.14",
|
|
34
|
+
"axios-mock-adapter": "^2.1.0",
|
|
35
|
+
"jest": "^29.7.0",
|
|
36
|
+
"ts-jest": "^29.2.5",
|
|
37
|
+
"tsx": "^4.19.2",
|
|
38
|
+
"typescript": "^5.0.0"
|
|
39
|
+
}
|
|
40
|
+
}
|
package/readme.md
CHANGED
|
@@ -1,115 +1,115 @@
|
|
|
1
|
-
# oht-custom-parser-lib
|
|
2
|
-
|
|
3
|
-
`oht-custom-parser-lib` is a shared library designed for use across multiple Node.js cloud functions. It contains common MongoDB connectors and data utilities that can be reused to avoid code duplication and ensure consistency.
|
|
4
|
-
|
|
5
|
-
## Table of Contents
|
|
6
|
-
|
|
7
|
-
- [Installation](#installation)
|
|
8
|
-
- [Usage](#usage)
|
|
9
|
-
- [Development](#development)
|
|
10
|
-
- [Patch Versions](#patch-versions)
|
|
11
|
-
- [Publish to npm Registry](#publish-to-npm-registry)
|
|
12
|
-
- [Using the Library in Cloud Functions](#using-the-library-in-cloud-functions)
|
|
13
|
-
|
|
14
|
-
## Installation
|
|
15
|
-
|
|
16
|
-
To install `oht-custom-parser-lib`, you can add it as a dependency in your project using npm:
|
|
17
|
-
|
|
18
|
-
```bash
|
|
19
|
-
npm install oht-custom-parser-lib
|
|
20
|
-
```
|
|
21
|
-
|
|
22
|
-
Or, if you want to install a specific version:
|
|
23
|
-
|
|
24
|
-
```bash
|
|
25
|
-
npm install oht-custom-parser-lib@<version>
|
|
26
|
-
```
|
|
27
|
-
|
|
28
|
-
## Usage
|
|
29
|
-
|
|
30
|
-
After installing, you can import and use the library in your cloud functions:
|
|
31
|
-
|
|
32
|
-
```javascript
|
|
33
|
-
const { connectToMongoDB } = require('oht-custom-parser-lib');
|
|
34
|
-
```
|
|
35
|
-
|
|
36
|
-
## Logging
|
|
37
|
-
|
|
38
|
-
- **Production / GCP**: Logs are emitted as JSON (one line per log) for Cloud Logging.
|
|
39
|
-
- **Local / development**: When `NODE_ENV !== 'production'`, logs are pretty-printed in the terminal (colors, timestamps, readable structure). You can override: `LOG_PRETTY=true` to force pretty output, or `LOG_PRETTY=false` to force JSON when not in production.
|
|
40
|
-
|
|
41
|
-
### Processing logger: request-scoped state
|
|
42
|
-
|
|
43
|
-
The processing logger (`processingLogger`, `runWithContextAsync`, `getRequestIdFromContext`) uses a **registry + facade** so each request has isolated state and logs never leak context between concurrent invocations (e.g. in Cloud Functions).
|
|
44
|
-
|
|
45
|
-
- **Registry**: One `ProcessingState` per request, keyed by request id (`fileUploadId ?? messageId ?? cloudEventId ?? generatedId`). The same id is used for the whole request.
|
|
46
|
-
- **AsyncLocalStorage**: Holds only the current request id; state is resolved via `registry.get(id)`.
|
|
47
|
-
- **Entry point**: Wrap your handler in `runWithContextAsync(context, async () => { ... })`. The lib creates a registry entry, runs your callback with the id in AsyncLocalStorage, and removes the entry in a `finally` block.
|
|
48
|
-
- **Clear-state rule**: If there is no request id or the id is not in the registry (e.g. logging outside `runWithContextAsync` or after teardown), the logger uses a **transient empty state** for that call only (never stored). That way one request never overwrites another’s context.
|
|
49
|
-
|
|
50
|
-
Use `processingLogger.logInfo`, `logWarn`, `logError`, `logProgress`, etc. inside the callback so logs include the same context and are searchable by `fileUploadId` / filename.
|
|
51
|
-
|
|
52
|
-
## Development
|
|
53
|
-
|
|
54
|
-
### Patch Versions
|
|
55
|
-
|
|
56
|
-
When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
|
|
57
|
-
|
|
58
|
-
1. **Update the version number**: Use npm's version command to bump the version:
|
|
59
|
-
- **Patch** for bug fixes:
|
|
60
|
-
```bash
|
|
61
|
-
npm version patch
|
|
62
|
-
```
|
|
63
|
-
- **Minor** for new features:
|
|
64
|
-
```bash
|
|
65
|
-
npm version minor
|
|
66
|
-
```
|
|
67
|
-
- **Major** for breaking changes:
|
|
68
|
-
```bash
|
|
69
|
-
npm version major
|
|
70
|
-
```
|
|
71
|
-
|
|
72
|
-
This command will automatically update the version in the `package.json` and create a git tag.
|
|
73
|
-
|
|
74
|
-
2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
|
|
75
|
-
|
|
76
|
-
### Publish to npm Registry
|
|
77
|
-
|
|
78
|
-
After updating the version, you can publish the library to the npm registry:
|
|
79
|
-
|
|
80
|
-
1. **Login to npm** (if you haven't already):
|
|
81
|
-
```bash
|
|
82
|
-
npm login
|
|
83
|
-
```
|
|
84
|
-
|
|
85
|
-
2. **Publish the package**:
|
|
86
|
-
```bash
|
|
87
|
-
npm publish
|
|
88
|
-
```
|
|
89
|
-
|
|
90
|
-
If this is a private package, use:
|
|
91
|
-
```bash
|
|
92
|
-
npm publish --access restricted
|
|
93
|
-
```
|
|
94
|
-
|
|
95
|
-
3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
|
|
96
|
-
|
|
97
|
-
## Using the Library in Cloud Functions
|
|
98
|
-
|
|
99
|
-
To use `oht-custom-parser-lib` in your cloud functions:
|
|
100
|
-
|
|
101
|
-
1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
|
|
102
|
-
|
|
103
|
-
```json
|
|
104
|
-
{
|
|
105
|
-
"dependencies": {
|
|
106
|
-
"oht-custom-parser-lib": "^1.0.0"
|
|
107
|
-
}
|
|
108
|
-
}
|
|
109
|
-
```
|
|
110
|
-
|
|
111
|
-
Replace `^1.0.0` with the appropriate version as needed.
|
|
112
|
-
|
|
113
|
-
2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
|
|
114
|
-
|
|
115
|
-
3. **Deploy Your Function**: Deploy your cloud function as usual, ensuring that the updated dependencies are included.
|
|
1
|
+
# oht-custom-parser-lib
|
|
2
|
+
|
|
3
|
+
`oht-custom-parser-lib` is a shared library designed for use across multiple Node.js cloud functions. It contains common MongoDB connectors and data utilities that can be reused to avoid code duplication and ensure consistency.
|
|
4
|
+
|
|
5
|
+
## Table of Contents
|
|
6
|
+
|
|
7
|
+
- [Installation](#installation)
|
|
8
|
+
- [Usage](#usage)
|
|
9
|
+
- [Development](#development)
|
|
10
|
+
- [Patch Versions](#patch-versions)
|
|
11
|
+
- [Publish to npm Registry](#publish-to-npm-registry)
|
|
12
|
+
- [Using the Library in Cloud Functions](#using-the-library-in-cloud-functions)
|
|
13
|
+
|
|
14
|
+
## Installation
|
|
15
|
+
|
|
16
|
+
To install `oht-custom-parser-lib`, you can add it as a dependency in your project using npm:
|
|
17
|
+
|
|
18
|
+
```bash
|
|
19
|
+
npm install oht-custom-parser-lib
|
|
20
|
+
```
|
|
21
|
+
|
|
22
|
+
Or, if you want to install a specific version:
|
|
23
|
+
|
|
24
|
+
```bash
|
|
25
|
+
npm install oht-custom-parser-lib@<version>
|
|
26
|
+
```
|
|
27
|
+
|
|
28
|
+
## Usage
|
|
29
|
+
|
|
30
|
+
After installing, you can import and use the library in your cloud functions:
|
|
31
|
+
|
|
32
|
+
```javascript
|
|
33
|
+
const { connectToMongoDB } = require('oht-custom-parser-lib');
|
|
34
|
+
```
|
|
35
|
+
|
|
36
|
+
## Logging
|
|
37
|
+
|
|
38
|
+
- **Production / GCP**: Logs are emitted as JSON (one line per log) for Cloud Logging.
|
|
39
|
+
- **Local / development**: When `NODE_ENV !== 'production'`, logs are pretty-printed in the terminal (colors, timestamps, readable structure). You can override: `LOG_PRETTY=true` to force pretty output, or `LOG_PRETTY=false` to force JSON when not in production.
|
|
40
|
+
|
|
41
|
+
### Processing logger: request-scoped state
|
|
42
|
+
|
|
43
|
+
The processing logger (`processingLogger`, `runWithContextAsync`, `getRequestIdFromContext`) uses a **registry + facade** so each request has isolated state and logs never leak context between concurrent invocations (e.g. in Cloud Functions).
|
|
44
|
+
|
|
45
|
+
- **Registry**: One `ProcessingState` per request, keyed by request id (`fileUploadId ?? messageId ?? cloudEventId ?? generatedId`). The same id is used for the whole request.
|
|
46
|
+
- **AsyncLocalStorage**: Holds only the current request id; state is resolved via `registry.get(id)`.
|
|
47
|
+
- **Entry point**: Wrap your handler in `runWithContextAsync(context, async () => { ... })`. The lib creates a registry entry, runs your callback with the id in AsyncLocalStorage, and removes the entry in a `finally` block.
|
|
48
|
+
- **Clear-state rule**: If there is no request id or the id is not in the registry (e.g. logging outside `runWithContextAsync` or after teardown), the logger uses a **transient empty state** for that call only (never stored). That way one request never overwrites another’s context.
|
|
49
|
+
|
|
50
|
+
Use `processingLogger.logInfo`, `logWarn`, `logError`, `logProgress`, etc. inside the callback so logs include the same context and are searchable by `fileUploadId` / filename.
|
|
51
|
+
|
|
52
|
+
## Development
|
|
53
|
+
|
|
54
|
+
### Patch Versions
|
|
55
|
+
|
|
56
|
+
When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
|
|
57
|
+
|
|
58
|
+
1. **Update the version number**: Use npm's version command to bump the version:
|
|
59
|
+
- **Patch** for bug fixes:
|
|
60
|
+
```bash
|
|
61
|
+
npm version patch
|
|
62
|
+
```
|
|
63
|
+
- **Minor** for new features:
|
|
64
|
+
```bash
|
|
65
|
+
npm version minor
|
|
66
|
+
```
|
|
67
|
+
- **Major** for breaking changes:
|
|
68
|
+
```bash
|
|
69
|
+
npm version major
|
|
70
|
+
```
|
|
71
|
+
|
|
72
|
+
This command will automatically update the version in the `package.json` and create a git tag.
|
|
73
|
+
|
|
74
|
+
2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
|
|
75
|
+
|
|
76
|
+
### Publish to npm Registry
|
|
77
|
+
|
|
78
|
+
After updating the version, you can publish the library to the npm registry:
|
|
79
|
+
|
|
80
|
+
1. **Login to npm** (if you haven't already):
|
|
81
|
+
```bash
|
|
82
|
+
npm login
|
|
83
|
+
```
|
|
84
|
+
|
|
85
|
+
2. **Publish the package**:
|
|
86
|
+
```bash
|
|
87
|
+
npm publish
|
|
88
|
+
```
|
|
89
|
+
|
|
90
|
+
If this is a private package, use:
|
|
91
|
+
```bash
|
|
92
|
+
npm publish --access restricted
|
|
93
|
+
```
|
|
94
|
+
|
|
95
|
+
3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
|
|
96
|
+
|
|
97
|
+
## Using the Library in Cloud Functions
|
|
98
|
+
|
|
99
|
+
To use `oht-custom-parser-lib` in your cloud functions:
|
|
100
|
+
|
|
101
|
+
1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
|
|
102
|
+
|
|
103
|
+
```json
|
|
104
|
+
{
|
|
105
|
+
"dependencies": {
|
|
106
|
+
"oht-custom-parser-lib": "^1.0.0"
|
|
107
|
+
}
|
|
108
|
+
}
|
|
109
|
+
```
|
|
110
|
+
|
|
111
|
+
Replace `^1.0.0` with the appropriate version as needed.
|
|
112
|
+
|
|
113
|
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2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
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114
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115
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3. **Deploy Your Function**: Deploy your cloud function as usual, ensuring that the updated dependencies are included.
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