@openhealth/oht-custom-parser-lib 0.2.52 → 0.2.53
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 +2 -2
- package/dist/index.js +3 -1
- package/dist/index.js.map +1 -1
- package/dist/service/ohtMeasurementsExtractor.service.d.ts +5 -3
- package/dist/service/ohtMeasurementsExtractor.service.js +49 -14
- package/dist/service/ohtMeasurementsExtractor.service.js.map +1 -1
- package/dist/service/reportCreator.service.d.ts +2 -1
- package/dist/service/reportCreator.service.js +13 -1
- package/dist/service/reportCreator.service.js.map +1 -1
- package/dist/types/custom-parser.types.d.ts +22 -0
- package/dist/types/custom-parser.types.js.map +1 -1
- package/dist/util-ts/dataUtils.d.ts +17 -0
- package/dist/util-ts/dataUtils.js +76 -1
- package/dist/util-ts/dataUtils.js.map +1 -1
- package/package.json +34 -34
- package/readme.md +99 -99
package/dist/index.d.ts
CHANGED
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@@ -4,12 +4,12 @@ export { ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenc
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export { getSlackFileIssueNotificationMessage, sendMessageToSlack } from './service/slackMessages.service';
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export { aggregateMessages, aggregateBiMessages, publishToTopic, generateBIMessages } from './service/errorHandling.service';
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export { applyRules as applyTransformationRules, validateJsonataExpression as validateTransformationRuleExpression, } from './service/transformationRules.service';
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export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, ReferenceAsAnnotation, UnitExtraction, RangeExtraction, RangeExtractionResponse, ValueExtraction, unitSynonyms, ValueExtractionResponse, } from './types/custom-parser.types';
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export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, ReferenceAsAnnotation, UnitExtraction, RangeExtraction, RangeExtractionResponse, ValueExtraction, unitSynonyms, ValueExtractionResponse, SynonymUnit, UnknownUnits, } from './types/custom-parser.types';
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export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, } from './types/oht.types';
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export { ErrorMessage } from './types/error.types';
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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 { makeApiCallWithRetry, parseErrorObj } from './util-ts/apiUtils';
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export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings } from './util-ts/dataUtils';
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export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings, fetchSynonymUnits, resolveUnitFromSynonyms } from './util-ts/dataUtils';
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export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStorageUtils';
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export { default as pinoLogger } from './util-ts/pinoLogger';
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export { getGreaterThanPatterns, getLowerThanPatterns } from './util-ts/regexUtils';
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package/dist/index.js
CHANGED
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@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = 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.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postDataImportFileUploadToCore = void 0;
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exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = 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.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postDataImportFileUploadToCore = 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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@@ -59,6 +59,8 @@ Object.defineProperty(exports, "extractValue", { enumerable: true, get: function
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Object.defineProperty(exports, "isBiomarkerValueNumerical", { enumerable: true, get: function () { return dataUtils_1.isBiomarkerValueNumerical; } });
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Object.defineProperty(exports, "isBiomarkerExternalNoVisualRange", { enumerable: true, get: function () { return dataUtils_1.isBiomarkerExternalNoVisualRange; } });
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Object.defineProperty(exports, "processAppendedMappings", { enumerable: true, get: function () { return dataUtils_1.processAppendedMappings; } });
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Object.defineProperty(exports, "fetchSynonymUnits", { enumerable: true, get: function () { return dataUtils_1.fetchSynonymUnits; } });
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Object.defineProperty(exports, "resolveUnitFromSynonyms", { enumerable: true, get: function () { return dataUtils_1.resolveUnitFromSynonyms; } });
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var googleStorageUtils_1 = require("./util-ts/googleStorageUtils");
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Object.defineProperty(exports, "readFileFromBucket", { enumerable: true, get: function () { return googleStorageUtils_1.readFileFromBucket; } });
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Object.defineProperty(exports, "uploadFileBufferToGCS", { enumerable: true, get: function () { return googleStorageUtils_1.uploadFileBufferToGCS; } });
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package/dist/index.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../index.ts"],"names":[],"mappings":";;;;;;AAAA,mBAAmB;AACnB,yEAEyC;AADvC,uIAAA,8BAA8B,OAAA;AAEhC,mFAO8C;AAN5C,oIAAA,sBAAsB,OAAA;AACtB,yHAAA,WAAW,OAAA;AACX,+HAAA,iBAAiB,OAAA;AACjB,6HAAA,eAAe,OAAA;AACf,yIAAA,2BAA2B,OAAA;AAC3B,qIAAA,uBAAuB,OAAA;AAEzB,+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;AAElC,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,
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../index.ts"],"names":[],"mappings":";;;;;;AAAA,mBAAmB;AACnB,yEAEyC;AADvC,uIAAA,8BAA8B,OAAA;AAEhC,mFAO8C;AAN5C,oIAAA,sBAAsB,OAAA;AACtB,yHAAA,WAAW,OAAA;AACX,+HAAA,iBAAiB,OAAA;AACjB,6HAAA,eAAe,OAAA;AACf,yIAAA,2BAA2B,OAAA;AAC3B,qIAAA,uBAAuB,OAAA;AAEzB,+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;AAElC,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,+CAiC2B;AAhCzB,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;AAeH,uGAAA,UAAU,OAAA;AAWZ,kBAAkB;AAClB,+CAAuE;AAA/D,gHAAA,oBAAoB,OAAA;AAAE,yGAAA,aAAa,OAAA;AAC3C,iDAAmL;AAA3K,yGAAA,YAAY,OAAA;AAAE,sHAAA,yBAAyB,OAAA;AAAE,6HAAA,gCAAgC,OAAA;AAAE,oHAAA,uBAAuB,OAAA;AAAE,8GAAA,iBAAiB,OAAA;AAAE,oHAAA,uBAAuB,OAAA;AACtJ,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,iDAA0D;AAAlD,gHAAA,mBAAmB,OAAA"}
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@@ -1,10 +1,11 @@
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import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction } from "../types/custom-parser.types";
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import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction, SynonymUnit, UnknownUnits } from "../types/custom-parser.types";
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import { Biomarker, BiomarkerValueType, Measurement, MeasurementValueComparator, PatientInfo, UnknownMeasurement, Exam } from "../types/oht.types";
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declare function extractUnit(unitExtraction: UnitExtraction | undefined, rawData: any, ohtBiomarker: Biomarker): {
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declare function extractUnit(unitExtraction: UnitExtraction | undefined, rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
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unit: string;
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isUnitParsedCorrectly: boolean;
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originalUnit: string;
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isArbitraryUnit: boolean;
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unknownUnit: string;
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};
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declare function extractReferenceAnnotation(labToOhtMapper: LabToOhtMapper, rawExam: any, patientInfo: PatientInfo, documentDate?: Date, exams?: Exam[]): string;
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declare const getRangeFromPositionAndRegex: (rangeExtraction: RangeExtraction, rawData: any) => {
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isValueParsedCorrectly: boolean;
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};
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declare function checkValueForPlausibleValues(labToOhtMapper: LabToOhtMapper, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean): boolean;
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declare function ohtMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], ohtCoreApiKey: string): Promise<{
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declare function ohtMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{
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measurements: Measurement[];
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unknownMeasurements: UnknownMeasurement[];
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unknownUnits: UnknownUnits[];
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isReportCorrectlyParsed: boolean;
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}>;
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export { ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan };
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exports.parseExamValue = parseExamValue;
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exports.extractUnit = extractUnit;
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exports.extractValueFromGreaterLowerThan = extractValueFromGreaterLowerThan;
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const custom_parser_types_1 = require("../types/custom-parser.types");
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const dataUtils_1 = require("../util-ts/dataUtils");
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const regexUtils_1 = require("../util-ts/regexUtils");
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const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
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@@ -20,16 +19,16 @@ const oht_types_1 = require("../types/oht.types");
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const logger = (0, pinoLogger_1.default)();
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const OHT_CORE_URL = process.env.OHT_CORE_URL;
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let filename = '';
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function extractUnit(unitExtraction, rawData, ohtBiomarker) {
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function extractUnit(unitExtraction, rawData, ohtBiomarker, synonymUnits = null, partnerId = null) {
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if (!(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
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return { unit: "None", isUnitParsedCorrectly: true, originalUnit: "", isArbitraryUnit: false };
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return { unit: "None", isUnitParsedCorrectly: true, originalUnit: "", isArbitraryUnit: false, unknownUnit: '' };
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}
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const isArbitraryUnit = ohtBiomarker.acf.standardUnitArbUnitLogic === 'default';
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let originalUnit = '';
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// If there's a function to extract the unit, use it
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if (unitExtraction && unitExtraction?.extractionFunc) {
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const extractedUnitExtraction = unitExtraction.extractionFunc(rawData);
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return { unit: extractedUnitExtraction ?? '', isUnitParsedCorrectly: !!extractedUnitExtraction, originalUnit: originalUnit, isArbitraryUnit };
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return { unit: extractedUnitExtraction ?? '', isUnitParsedCorrectly: !!extractedUnitExtraction, originalUnit: originalUnit, isArbitraryUnit, unknownUnit: '' };
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}
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const unit = (0, dataUtils_1.extractValue)(rawData, unitExtraction?.unitPosition);
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let unitLowerCase = unit?.toLowerCase();
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@@ -43,7 +42,7 @@ function extractUnit(unitExtraction, rawData, ohtBiomarker) {
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// If the biomarker uses an arbitrary unit, return standard unit and set the original unit as the unit extracted from the data
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if (isArbitraryUnit) {
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originalUnit = unit;
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return { unit: standardUnit, isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit };
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return { unit: standardUnit, isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
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}
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// First test if the biomarker has the unit explicit in the 'unity' field
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const allUnitContainsJsonUnit = allBmOhtUnits.includes(unitLowerCase);
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unit: unit?.replaceAll(/ /g, ''),
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isUnitParsedCorrectly: true,
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originalUnit: originalUnit,
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isArbitraryUnit: isArbitraryUnit
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isArbitraryUnit: isArbitraryUnit,
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unknownUnit: ''
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};
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}
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// Check if there are any Synonym configured
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if (unitLowerCase?.length > 0) {
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let resolvedUnit = null;
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if (synonymUnits && synonymUnits.length > 0) {
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const resolved = (0, dataUtils_1.resolveUnitFromSynonyms)(unitLowerCase, ohtBiomarker.id, partnerId, synonymUnits);
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if (resolved.found && resolved.targetUnit) {
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resolvedUnit = resolved.targetUnit;
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}
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}
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if (resolvedUnit) {
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const allUnitContainsJsonUnitSynonyms = allBmOhtUnits.includes(resolvedUnit.toLowerCase());
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if (allUnitContainsJsonUnitSynonyms) {
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return { unit: resolvedUnit, isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
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}
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}
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}
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if (unitExtraction?.predefinedUnit) {
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const allUnitContainsUnitFromOhtMap = allBmOhtUnits.includes(unitExtraction.predefinedUnit.toLowerCase());
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// If the 'unity' field is not present, try to get the unit from the biomarker map
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return { unit: unitExtraction?.predefinedUnit, isUnitParsedCorrectly: allUnitContainsUnitFromOhtMap, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit };
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return { unit: unitExtraction?.predefinedUnit, isUnitParsedCorrectly: allUnitContainsUnitFromOhtMap, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
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}
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if (unitExtraction?.extractionRegex) {
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const regex = new RegExp(unitExtraction.extractionRegex);
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const match = rawData.match(regex);
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const allUnitContainsUnitMatch = allBmOhtUnits.includes(match?.[1]?.toLowerCase());
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if (match?.[1] && allUnitContainsUnitMatch) {
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return { unit: match?.[1], isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit };
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return { unit: match?.[1], isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
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}
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}
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// if the unit didnt match any of the cases, add the unit to an unknownUnit list
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return { unit: '', isUnitParsedCorrectly: false, originalUnit: '', isArbitraryUnit: false, unknownUnit: unit };
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}
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78
90
|
function extractReferenceAnnotation(labToOhtMapper, rawExam, patientInfo, documentDate, exams) {
|
|
79
91
|
const annotationExtractionFunc = labToOhtMapper?.referenceAsAnnotation?.extractionFunc;
|
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@@ -279,10 +291,11 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
|
|
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279
291
|
}
|
|
280
292
|
return isPlausibleValue;
|
|
281
293
|
}
|
|
282
|
-
async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey) {
|
|
294
|
+
async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey, partnerId) {
|
|
283
295
|
filename = labToOhtContract.sourceFilename;
|
|
284
296
|
const measurements = [];
|
|
285
297
|
const unknownMeasurements = [];
|
|
298
|
+
const unknownUnits = [];
|
|
286
299
|
let isReportCorrectlyParsed = true;
|
|
287
300
|
const allPossibleOHTBmIds = [];
|
|
288
301
|
[
|
|
@@ -300,6 +313,15 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey)
|
|
|
300
313
|
};
|
|
301
314
|
// api call to ohtCore to find biomarkers.
|
|
302
315
|
const biomarkers = await (0, apiUtils_1.makeApiCallWithRetry)('post', `${OHT_CORE_URL}/v1/biomarker/biomarkers`, requestData, ohtCoreApiKey);
|
|
316
|
+
// Fetch synonym units from API if enabled
|
|
317
|
+
let synonymUnits = null;
|
|
318
|
+
if (partnerId) {
|
|
319
|
+
synonymUnits = await (0, dataUtils_1.fetchSynonymUnits)(partnerId, ohtCoreApiKey);
|
|
320
|
+
// If API fetch failed or returned empty, set to null to use hardcoded fallback
|
|
321
|
+
if (synonymUnits.length === 0) {
|
|
322
|
+
synonymUnits = null;
|
|
323
|
+
}
|
|
324
|
+
}
|
|
303
325
|
labToOhtContract.labToOhtList.forEach((labToOhtMapper) => {
|
|
304
326
|
let isMeasurementCorrectlyParsed = true;
|
|
305
327
|
if (!labToOhtMapper.rawExam) {
|
|
@@ -326,7 +348,19 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey)
|
|
|
326
348
|
const bmInfo = ohtBiomarker?.acf?.shortName ?
|
|
327
349
|
`name:${ohtBiomarker.acf.shortName}, bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}` :
|
|
328
350
|
`bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}`;
|
|
329
|
-
const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit } = extractUnit(labToOhtMapper.unitExtraction, rawExamObj, ohtBiomarker);
|
|
351
|
+
const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = extractUnit(labToOhtMapper.unitExtraction, rawExamObj, ohtBiomarker, synonymUnits, partnerId);
|
|
352
|
+
if (unknownUnit.length > 0) {
|
|
353
|
+
unknownUnits.push({
|
|
354
|
+
biomarkerId: ohtBiomarker.id,
|
|
355
|
+
unit: unknownUnit,
|
|
356
|
+
partnerId: partnerId,
|
|
357
|
+
labKey: labToOhtMapper.labKey,
|
|
358
|
+
ohtExam: labToOhtMapper.ohtExam,
|
|
359
|
+
originalExam: labToOhtMapper.originalExam,
|
|
360
|
+
biomarkerName: labToOhtMapper.biomarkerName,
|
|
361
|
+
dataImportFileUploadId: null, // is null it will be set later in the structParser.service.ts
|
|
362
|
+
});
|
|
363
|
+
}
|
|
330
364
|
if (!isUnitParsedCorrectly) {
|
|
331
365
|
logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
|
|
332
366
|
labToOhtContract.errorMessages.push({
|
|
@@ -471,6 +505,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey)
|
|
|
471
505
|
return {
|
|
472
506
|
measurements,
|
|
473
507
|
unknownMeasurements,
|
|
508
|
+
unknownUnits,
|
|
474
509
|
isReportCorrectlyParsed
|
|
475
510
|
};
|
|
476
511
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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;QACZ,uBAAuB;KACxB,CAAA;AACH,CAAC"}
|
|
@@ -1,3 +1,4 @@
|
|
|
1
1
|
import { DataImportFileUpload, UnknownMeasurementsBulk } from '../types/oht.types';
|
|
2
|
-
|
|
2
|
+
import { UnknownUnits } from '../types/custom-parser.types';
|
|
3
|
+
declare function postDataImportFileUploadToCore(dataImportFileUpload: DataImportFileUpload, unknownMeasurements: UnknownMeasurementsBulk, unknownUnits: UnknownUnits[], rejectedStatus: string | undefined, rejectReason: string | undefined, isReportParsedCorrectly: boolean, filename: string, ohtCoreApiKey: string): Promise<DataImportFileUpload | null>;
|
|
3
4
|
export { postDataImportFileUploadToCore };
|
|
@@ -18,7 +18,7 @@ const dataUtils_1 = require("../util-ts/dataUtils");
|
|
|
18
18
|
const apiUtils_1 = require("../util-ts/apiUtils");
|
|
19
19
|
dotenv_1.default.config({ path: `.env.local` });
|
|
20
20
|
const OHT_CORE_URL = process.env.OHT_CORE_URL;
|
|
21
|
-
async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasurements, rejectedStatus, rejectReason, isReportParsedCorrectly, filename, ohtCoreApiKey) {
|
|
21
|
+
async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasurements, unknownUnits, rejectedStatus, rejectReason, isReportParsedCorrectly, filename, ohtCoreApiKey) {
|
|
22
22
|
let status = isReportParsedCorrectly
|
|
23
23
|
? oht_types_1.DataImportFileUploadStatus.PROCESSED
|
|
24
24
|
: oht_types_1.DataImportFileUploadStatus.FOR_REVIEW;
|
|
@@ -78,6 +78,18 @@ async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasu
|
|
|
78
78
|
}, `Failed to send unknown measurements to server, filename: ${filename}`);
|
|
79
79
|
}
|
|
80
80
|
}
|
|
81
|
+
if (unknownUnits.length > 0) {
|
|
82
|
+
try {
|
|
83
|
+
await (0, dataUtils_1.bulkCreateCustomParserUnknownUnits)(dataImportFileUpload.partnerId, unknownUnits, ohtCoreApiKey);
|
|
84
|
+
}
|
|
85
|
+
catch (error) {
|
|
86
|
+
logger.error({
|
|
87
|
+
error: (0, apiUtils_1.parseErrorObj)(error),
|
|
88
|
+
partnerId: dataImportFileUpload.partnerId,
|
|
89
|
+
unknownUnits: unknownUnits
|
|
90
|
+
}, `Failed to send unknown units to server, filename: ${filename}`);
|
|
91
|
+
}
|
|
92
|
+
}
|
|
81
93
|
if (isReportParsedCorrectly && rejectedStatus === undefined) {
|
|
82
94
|
if (dataImportFileUpload?.labOrderId?.length > 0) {
|
|
83
95
|
// deprecate any previous fileUpload with same labOrderId and update current to READY
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"reportCreator.service.js","sourceRoot":"","sources":["../../service/reportCreator.service.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
{"version":3,"file":"reportCreator.service.js","sourceRoot":"","sources":["../../service/reportCreator.service.ts"],"names":[],"mappings":";;;;;AAqNS,wEAA8B;AArNvC,kDAM4B;AAE5B,kDAA0B;AAC1B,uFAA+D;AAC/D,2DAAmC;AACnC,eAAK,CAAC,MAAM,CAAC,2BAAiB,CAAC,CAAC;AAChC,eAAK,CAAC,MAAM,CAAC,aAAG,CAAC,CAAC;AAElB,uEAA+C;AAC/C,MAAM,MAAM,GAAG,IAAA,oBAAU,GAAE,CAAC;AAE5B,oDAA4B;AAC5B,6EAAuE;AACvE,oDAAoH;AACpH,kDAA0E;AAC1E,gBAAM,CAAC,MAAM,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAC;AAEtC,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC;AAE9C,KAAK,UAAU,8BAA8B,CAC3C,oBAA0C,EAC1C,mBAA4C,EAC5C,YAA4B,EAC5B,cAAkC,EAClC,YAAgC,EAChC,uBAAgC,EAChC,QAAgB,EAChB,aAAqB;IAErB,IAAI,MAAM,GAAG,uBAAuB;QAClC,CAAC,CAAC,sCAA0B,CAAC,SAAS;QACtC,CAAC,CAAC,sCAA0B,CAAC,UAAU,CAAC;IAE1C,MAAM,WAAW,GAAG,cAAc,IAAI,MAAM,CAAC;IAC7C,MAAM,0BAA0B,GAAG,GAAG,YAAY,oBAAoB,oBAAoB,CAAC,EAAE,SAAS,CAAC;IACvG,MAAM,oBAAoB,GAAG,GAAG,YAAY,oBAAoB,oBAAoB,CAAC,EAAE,EAAE,CAAC;IAC1F,MAAM,wBAAwB,GAAG,GAAG,YAAY,oBAAoB,oBAAoB,CAAC,EAAE,iBAAiB,CAAC;IAE7G,yEAAyE;IACzE,MAAM,cAAc,GAAG,GAAG,YAAY,4CAA4C,oBAAoB,CAAC,EAAE,EAAE,CAAC;IAC5G,MAAM,mBAAmB,GAAG,MAAM,IAAA,+BAAoB,EACpD,KAAK,EACL,cAAc,EACd,IAAI,EACJ,aAAa,CACd,CAAC;IAEF,MAAM,CAAC,IAAI,CACT,EAAC,QAAQ,EAAE,mBAAmB,CAAC,IAAI,EAAC,EACpC,8DAA8D,oBAAoB,CAAC,EAAE,eAAe,QAAQ,EAAE,CAC/G,CAAC;IAEF,IAAI,CAAC,mBAAmB,EAAE,IAAI,EAAE,WAAW,EAAE,CAAC;QAC5C,MAAM,CAAC,KAAK,CACV,EAAC,QAAQ,EAAE,mBAAmB,EAAE,IAAI,EAAC,EACvC,qEAAqE,oBAAoB,CAAC,EAAE,eAAe,QAAQ,EAAE,CACpH,CAAC;QACF,MAAM,IAAI,KAAK,CAAC,0CAA0C,oBAAoB,CAAC,EAAE,EAAE,CAAC,CAAC;IACvF,CAAC;IAED,MAAM,WAAW,GAAG,mBAAmB,CAAC,IAAI,CAAC,WAAW,CAAC;IAEzD,2CAA2C;IAC3C,MAAM,WAAW,GAAG;QAClB,SAAS,EAAE,oBAAoB,EAAE,WAAW,EAAE,SAAS,IAAI,EAAE;QAC7D,QAAQ,EAAE,oBAAoB,EAAE,WAAW,EAAE,QAAQ,IAAI,EAAE;QAC3D,KAAK,EAAE,oBAAoB,EAAE,WAAW,EAAE,KAAK,IAAI,EAAE;QACrD,SAAS,EAAE,oBAAoB,EAAE,WAAW,EAAE,SAAS,IAAI,IAAI;QAC/D,kEAAkE;QAClE,GAAG,EAAE,oBAAoB,EAAE,WAAW,EAAE,GAAG,IAAI,EAAE;QACjD,GAAG,EAAE,oBAAoB,EAAE,WAAW,EAAE,GAAG,IAAI,IAAI;QACnD,MAAM,EAAE,oBAAoB,EAAE,WAAW,EAAE,MAAM,IAAI,IAAI;QACzD,UAAU,EAAE,oBAAoB,EAAE,WAAW,EAAE,UAAU,IAAI,EAAE;KAChE,CAAC;IAEF,MAAM,OAAO,GAAG,GAAG,YAAY,kBAAkB,WAAW,EAAE,CAAC;IAC/D,MAAM,YAAY,GAAG,MAAM,IAAA,+BAAoB,EAC7C,OAAO,EACP,OAAO,EACP,WAAW,EACX,aAAa,CACd,CAAC;IAEF,MAAM,CAAC,IAAI,CACT,EAAC,QAAQ,EAAE,YAAY,CAAC,IAAI,EAAC,EAC7B,8BAA8B,WAAW,eAAe,QAAQ,EAAE,CACnE,CAAC;IAEF,IAAI,CAAC;QACH,MAAM,eAAe,GAAG,MAAM,IAAA,+BAAoB,EAChD,OAAO,EACP,oBAAoB,EACpB;YACE,GAAG,oBAAoB;YACvB,MAAM,EAAE,WAAW;YACnB,YAAY;YACZ,cAAc,EAAE;gBACd,GAAG,oBAAoB,CAAC,cAAc;gBACtC,YAAY,EAAE,wBAAY,CAAC,eAAe;aAC3C;SACF,EACD,aAAa,CACd,CAAC;QACF,MAAM,CAAC,IAAI,CACT,EAAE,QAAQ,EAAE,eAAe,CAAC,IAAI,EAAE,EAClC,uBAAuB,WAAW,IAAI,oBAAoB,eAAe,QAAQ,EAAE,CACpF,CAAC;QAEF,0CAA0C;QAC1C,IAAI,mBAAmB,CAAC,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACnD,IAAI,CAAC;gBACH,MAAM,IAAA,oDAAwC,EAC5C,oBAAoB,CAAC,SAAS,EAC9B,mBAAmB,EACnB,aAAa,CACd,CAAC;gBACF,MAAM,CAAC,IAAI,CACT;oBACE,SAAS,EAAE,oBAAoB,CAAC,SAAS;oBACzC,mBAAmB,EAAE,mBAAmB,CAAC,eAAe;iBACzD,EACD,+DAA+D,QAAQ,EAAE,CAC1E,CAAC;YACJ,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,CAAC,KAAK,CACV;oBACE,KAAK,EAAE,IAAA,wBAAa,EAAC,KAAK,CAAC;oBAC3B,SAAS,EAAE,oBAAoB,CAAC,SAAS;oBACzC,mBAAmB,EAAE,mBAAmB,CAAC,eAAe;iBACzD,EACD,4DAA4D,QAAQ,EAAE,CACvE,CAAC;YACJ,CAAC;QACH,CAAC;QAED,IAAI,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC5B,IAAI,CAAC;gBACH,MAAM,IAAA,8CAAkC,EACtC,oBAAoB,CAAC,SAAS,EAC9B,YAAY,EACZ,aAAa,CACd,CAAC;YACJ,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,CAAC,KAAK,CACV;oBACE,KAAK,EAAE,IAAA,wBAAa,EAAC,KAAK,CAAC;oBAC3B,SAAS,EAAE,oBAAoB,CAAC,SAAS;oBACzC,YAAY,EAAE,YAAY;iBAC3B,EACD,qDAAqD,QAAQ,EAAE,CAChE,CAAC;YACJ,CAAC;QACH,CAAC;QAED,IAAI,uBAAuB,IAAI,cAAc,KAAK,SAAS,EAAE,CAAC;YAC5D,IAAI,oBAAoB,EAAE,UAAU,EAAE,MAAM,GAAG,CAAC,EAAE,CAAC;gBACjD,qFAAqF;gBACrF,MAAM,IAAA,+BAAoB,EACxB,MAAM,EACN,0BAA0B,EAC1B,EAAE,EACF,aAAa,CACd,CAAC;gBACF,OAAO,IAAI,CAAC;YACd,CAAC;iBAAM,CAAC;gBACN,OAAO,MAAM,IAAA,oDAAuB,EAClC;oBACE,MAAM,EAAE,sCAA0B,CAAC,KAAK;oBACxC,cAAc,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,eAAK,CAAC,GAAG,EAAE,EAAE;iBAC7D,EACD,oBAAoB,CAAC,EAAE,EACvB,QAAQ,EACR,aAAa,CACd,CAAC;YACJ,CAAC;QACH,CAAC;QACD,MAAM,CAAC,IAAI,CACT;YACE,uBAAuB;YACvB,cAAc;YACd,eAAe,EAAE,eAAe;SACjC,EACD,4CAA4C,oBAAoB,CAAC,EAAE,eAAe,QAAQ,EAAE,CAC7F,CAAC;QAEF,OAAO,eAAe,EAAE,IAAI,CAAC;IAC/B,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,WAAW,GAAG,IAAA,wBAAa,EAAC,KAAK,CAAC,CAAC;QACzC,MAAM,CAAC,KAAK,CACV,EAAE,WAAW,EAAE,IAAI,EAAE,WAAW,EAAE,EAClC,mCAAmC,oBAAoB,cAAc,QAAQ,EAAE,CAChF,CAAC;QACF,2BAA2B;QAC3B,MAAM,IAAA,+BAAoB,EACxB,OAAO,EACP,wBAAwB,EACxB;YACE,MAAM,EAAE,8BAAkB,CAAC,KAAK;YAChC,YAAY,EAAE,wBAAY,CAAC,qBAAqB;YAChD,gBAAgB,EAAE,YAAY;SAC/B,EACD,aAAa,CACd,CAAC;QACF,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC"}
|
|
@@ -1,5 +1,24 @@
|
|
|
1
1
|
import { ErrorMessage } from "./error.types";
|
|
2
2
|
import { AnnotationConfig, DataOrigin, MeasurementValueComparator, OhtExam, PatientInfo } from "./oht.types";
|
|
3
|
+
export interface SynonymUnit {
|
|
4
|
+
id: string;
|
|
5
|
+
partnerId: string | null;
|
|
6
|
+
biomarkerId: number;
|
|
7
|
+
unknownUnit: string;
|
|
8
|
+
targetUnit: string;
|
|
9
|
+
conversionFactor: number;
|
|
10
|
+
status: 'pending' | 'in_review' | 'approved' | 'ignored';
|
|
11
|
+
}
|
|
12
|
+
export interface UnknownUnits {
|
|
13
|
+
biomarkerId: number;
|
|
14
|
+
unit: string;
|
|
15
|
+
partnerId: string;
|
|
16
|
+
dataImportFileUploadId: string;
|
|
17
|
+
labKey: string;
|
|
18
|
+
ohtExam?: OhtExam;
|
|
19
|
+
originalExam?: OriginalExam;
|
|
20
|
+
biomarkerName?: string;
|
|
21
|
+
}
|
|
3
22
|
export declare const unitSynonyms: Record<string, string>;
|
|
4
23
|
export interface ValueExtraction {
|
|
5
24
|
valuePosition?: string;
|
|
@@ -52,6 +71,7 @@ export interface OriginalExam {
|
|
|
52
71
|
}
|
|
53
72
|
export interface LabToOhtMapper {
|
|
54
73
|
ohtBmId?: number;
|
|
74
|
+
biomarkerName?: string;
|
|
55
75
|
labKey: string;
|
|
56
76
|
rawExam?: string;
|
|
57
77
|
material?: string;
|
|
@@ -67,6 +87,8 @@ export interface LabToOhtMapper {
|
|
|
67
87
|
unknownMeasurement?: UnknownMeasurementExtraction;
|
|
68
88
|
annotationConfig?: AnnotationConfig;
|
|
69
89
|
originalName?: string;
|
|
90
|
+
originalExam?: OriginalExam;
|
|
91
|
+
ohtExam?: OhtExam;
|
|
70
92
|
}
|
|
71
93
|
export interface LabToOhtContract {
|
|
72
94
|
labToOhtList: LabToOhtMapper[];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"custom-parser.types.js","sourceRoot":"","sources":["../../types/custom-parser.types.ts"],"names":[],"mappings":";;;
|
|
1
|
+
{"version":3,"file":"custom-parser.types.js","sourceRoot":"","sources":["../../types/custom-parser.types.ts"],"names":[],"mappings":";;;AA0Ba,QAAA,YAAY,GAA2B;IAClD,KAAK,EAAE,MAAM;IACb,KAAK,EAAE,MAAM;IACb,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,MAAM;IACf,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,OAAO;IAChB,WAAW,EAAE,aAAa;IAC1B,YAAY,EAAE,aAAa;IAC3B,IAAI,EAAE,KAAK;IACX,MAAM,EAAE,KAAK;IACb,UAAU,EAAE,SAAS;IACrB,SAAS,EAAE,QAAQ;IACnB,SAAS,EAAE,QAAQ;IACnB,QAAQ,EAAE,QAAQ;IAClB,eAAe,EAAE,eAAe;IAChC,KAAK,EAAE,GAAG;IACV,IAAI,EAAE,MAAM;IACZ,IAAI,EAAE,MAAM;IACZ,EAAE,EAAE,MAAM;IACV,MAAM,EAAE,KAAK;IACb,KAAK,EAAE,MAAM;IACb,QAAQ,EAAE,OAAO;IACjB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,SAAS;IACnB,SAAS,EAAE,SAAS;IACpB,SAAS,EAAE,SAAS;IACpB,QAAQ,EAAE,SAAS;IACnB,gBAAgB,EAAE,YAAY;IAC9B,iBAAiB,EAAE,YAAY;IAC/B,UAAU,EAAE,SAAS;IACrB,OAAO,EAAE,OAAO;IAChB,OAAO,EAAE,OAAO;IAChB,QAAQ,EAAE,OAAO;IACjB,OAAO,EAAE,OAAO;IAChB,IAAI,EAAE,MAAM;IACZ,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,MAAM;IACf,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,MAAM;IACf,OAAO,EAAE,MAAM;IACf,SAAS,EAAE,QAAQ;IACnB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,SAAS;IACnB,QAAQ,EAAE,SAAS;IACnB,WAAW,EAAE,OAAO;IACpB,UAAU,EAAE,OAAO;IACnB,WAAW,EAAE,OAAO;IACpB,UAAU,EAAE,OAAO;IACnB,IAAI,EAAE,aAAa;IACnB,IAAI,EAAE,aAAa;IACnB,aAAa,EAAE,QAAQ;IAEvB,kCAAkC;IAElC,OAAO,EAAE,OAAO;IAEhB,OAAO,EAAE,OAAO;IAEhB,OAAO,EAAE,OAAO;IAEhB,MAAM,EAAE,MAAM;IACd,MAAM,EAAE,MAAM;IACd,KAAK,EAAE,MAAM;IACb,KAAK,EAAE,MAAM;IAEb,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAElB,aAAa,EAAE,SAAS;IACxB,WAAW,EAAE,SAAS;IACtB,cAAc,EAAE,SAAS;IACzB,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,cAAc,EAAE,SAAS;IACzB,SAAS,EAAE,SAAS;IACpB,UAAU,EAAE,SAAS;IACrB,QAAQ,EAAE,SAAS;IACnB,WAAW,EAAE,SAAS;IAEtB,UAAU,EAAE,SAAS;IACrB,SAAS,EAAE,SAAS;IACpB,QAAQ,EAAE,SAAS;IAEnB,eAAe,EAAE,eAAe;IAChC,gBAAgB,EAAE,eAAe;IACjC,gBAAgB,EAAE,eAAe;IACjC,eAAe,EAAE,eAAe;IAChC,eAAe,EAAE,eAAe;IAEhC,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,sBAAsB,EAAE,eAAe;IACvC,sBAAsB,EAAE,eAAe;IACvC,sBAAsB,EAAE,eAAe;IAEvC,KAAK,EAAE,GAAG;IACV,IAAI,EAAE,GAAG;IACT,KAAK,EAAE,GAAG;IACV,SAAS,EAAE,GAAG;IACd,UAAU,EAAE,GAAG;IACf,SAAS,EAAE,GAAG;IAEd,OAAO,EAAE,WAAW;IACpB,QAAQ,EAAE,YAAY;IACtB,YAAY,EAAE,YAAY;IAC1B,gBAAgB,EAAE,YAAY;IAC9B,iBAAiB,EAAE,YAAY;IAC/B,iBAAiB,EAAE,YAAY;IAC/B,WAAW,EAAE,YAAY;IACzB,eAAe,EAAE,YAAY;IAC7B,gBAAgB,EAAE,YAAY;IAC9B,gBAAgB,EAAE,YAAY;IAE9B,KAAK,EAAE,KAAK;IACZ,MAAM,EAAE,KAAK;IACb,MAAM,EAAE,KAAK;IACb,mBAAmB,EAAE,KAAK;IAE1B,KAAK,EAAE,MAAM;IACb,KAAK,EAAE,MAAM;IAEb,WAAW,EAAE,cAAc;IAC3B,WAAW,EAAE,cAAc;IAC3B,UAAU,EAAE,cAAc;IAC1B,UAAU,EAAE,cAAc;IAC1B,MAAM,EAAE,MAAM;IACd,MAAM,EAAE,MAAM;CACf,CAAC"}
|
|
@@ -1,9 +1,26 @@
|
|
|
1
1
|
import { UnknownMeasurementsBulk, AnnotationLabKey } from '../types/oht.types';
|
|
2
|
+
import { SynonymUnit, UnknownUnits } from '../types/custom-parser.types';
|
|
3
|
+
/**
|
|
4
|
+
* Resolve unit from synonym units following priority:
|
|
5
|
+
* 1. Biomarker-specific partner synonym
|
|
6
|
+
* 2. Partner-specific synonym
|
|
7
|
+
* 3. Global synonym
|
|
8
|
+
*/
|
|
9
|
+
export declare function resolveUnitFromSynonyms(unitLowerCase: string, biomarkerId: number, partnerId: string | null | undefined, synonymUnits: SynonymUnit[]): {
|
|
10
|
+
targetUnit: string | null;
|
|
11
|
+
found: boolean;
|
|
12
|
+
};
|
|
2
13
|
export declare function isBiomarkerValueNumerical(biomarker: any): boolean;
|
|
3
14
|
export declare function isBiomarkerExternalNoVisualRange(biomarker: any): boolean;
|
|
4
15
|
export declare const extractValue: (obj: any, position?: string) => any;
|
|
5
16
|
export declare const getMappedBiomarkers: (partnerId: string, ohtCoreApiKey: string) => Promise<any>;
|
|
6
17
|
export declare const updatePartnerCustomParserUnmappedLabKeys: (partnerId: string, unknownMeasurementsBulk: UnknownMeasurementsBulk, ohtCoreApiKey: string) => Promise<void>;
|
|
18
|
+
export declare const bulkCreateCustomParserUnknownUnits: (partnerId: string, unknownUnits: UnknownUnits[], ohtCoreApiKey: string) => Promise<void>;
|
|
19
|
+
/**
|
|
20
|
+
* Fetch synonym units from oht-core API endpoint
|
|
21
|
+
* Returns all approved resolved synonym units (backend already filters and returns all results)
|
|
22
|
+
*/
|
|
23
|
+
export declare const fetchSynonymUnits: (partnerId: string | null | undefined, ohtCoreApiKey: string) => Promise<SynonymUnit[]>;
|
|
7
24
|
/**
|
|
8
25
|
* Processes appended biomarker mappings by extracting values from additional labKeys
|
|
9
26
|
* Compatible with AnnotationPreviewService interface but returns object with text property
|
|
@@ -3,13 +3,58 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.updatePartnerCustomParserUnmappedLabKeys = exports.getMappedBiomarkers = exports.extractValue = void 0;
|
|
6
|
+
exports.fetchSynonymUnits = exports.bulkCreateCustomParserUnknownUnits = exports.updatePartnerCustomParserUnmappedLabKeys = exports.getMappedBiomarkers = exports.extractValue = void 0;
|
|
7
|
+
exports.resolveUnitFromSynonyms = resolveUnitFromSynonyms;
|
|
7
8
|
exports.isBiomarkerValueNumerical = isBiomarkerValueNumerical;
|
|
8
9
|
exports.isBiomarkerExternalNoVisualRange = isBiomarkerExternalNoVisualRange;
|
|
9
10
|
exports.processAppendedMappings = processAppendedMappings;
|
|
10
11
|
const apiUtils_1 = require("./apiUtils");
|
|
11
12
|
const pinoLogger_1 = __importDefault(require("./pinoLogger"));
|
|
12
13
|
const logger = (0, pinoLogger_1.default)();
|
|
14
|
+
/**
|
|
15
|
+
* Normalize unit string for comparison (lowercase, remove spaces)
|
|
16
|
+
*/
|
|
17
|
+
function normalizeUnit(unit) {
|
|
18
|
+
return unit?.toLowerCase().replaceAll(/ /g, '') ?? '';
|
|
19
|
+
}
|
|
20
|
+
/**
|
|
21
|
+
* Resolve unit from synonym units following priority:
|
|
22
|
+
* 1. Biomarker-specific partner synonym
|
|
23
|
+
* 2. Partner-specific synonym
|
|
24
|
+
* 3. Global synonym
|
|
25
|
+
*/
|
|
26
|
+
function resolveUnitFromSynonyms(unitLowerCase, biomarkerId, partnerId, synonymUnits) {
|
|
27
|
+
if (!synonymUnits || synonymUnits.length === 0) {
|
|
28
|
+
return { targetUnit: '', found: false };
|
|
29
|
+
}
|
|
30
|
+
const normalizedUnit = normalizeUnit(unitLowerCase);
|
|
31
|
+
// Priority 1: Biomarker-specific partner synonym
|
|
32
|
+
if (biomarkerId && partnerId) {
|
|
33
|
+
const biomarkerPartnerMatch = synonymUnits.find((unit) => unit.biomarkerId === biomarkerId &&
|
|
34
|
+
unit.partnerId === partnerId &&
|
|
35
|
+
normalizeUnit(unit.unknownUnit) === normalizedUnit);
|
|
36
|
+
if (biomarkerPartnerMatch) {
|
|
37
|
+
return { targetUnit: biomarkerPartnerMatch.targetUnit, found: true };
|
|
38
|
+
}
|
|
39
|
+
}
|
|
40
|
+
// Priority 2: Partner-specific synonym (biomarkerId is 0 or not set)
|
|
41
|
+
if (partnerId) {
|
|
42
|
+
const partnerMatch = synonymUnits.find((unit) => (unit.biomarkerId === 0 || !unit.biomarkerId) &&
|
|
43
|
+
unit.partnerId === partnerId &&
|
|
44
|
+
normalizeUnit(unit.unknownUnit) === normalizedUnit);
|
|
45
|
+
if (partnerMatch) {
|
|
46
|
+
return { targetUnit: partnerMatch.targetUnit, found: true };
|
|
47
|
+
}
|
|
48
|
+
}
|
|
49
|
+
// Priority 3: Global synonym (partnerId is null, biomarkerId is 0 or not set)
|
|
50
|
+
const globalMatch = synonymUnits.find((unit) => unit.partnerId === null &&
|
|
51
|
+
(unit.biomarkerId === 0 || !unit.biomarkerId) &&
|
|
52
|
+
normalizeUnit(unit.unknownUnit) === normalizedUnit);
|
|
53
|
+
if (globalMatch) {
|
|
54
|
+
return { targetUnit: globalMatch.targetUnit, found: true };
|
|
55
|
+
}
|
|
56
|
+
return { targetUnit: '', found: false }; //TODO target unit is empty ''
|
|
57
|
+
}
|
|
13
58
|
function isBiomarkerValueNumerical(biomarker) {
|
|
14
59
|
return biomarker?.acf?.compatibility !== 'external_alphanumerical';
|
|
15
60
|
}
|
|
@@ -47,6 +92,36 @@ const updatePartnerCustomParserUnmappedLabKeys = async (partnerId, unknownMeasur
|
|
|
47
92
|
logger.info(response.data, `Resp: POST /v1/customparser/partners/${partnerId}/unmapped/bulk`);
|
|
48
93
|
};
|
|
49
94
|
exports.updatePartnerCustomParserUnmappedLabKeys = updatePartnerCustomParserUnmappedLabKeys;
|
|
95
|
+
// function that uses POST request at /v1/synonym/partners/{partnerId}/unknown-units/bulk to send the unknownUnits to the server
|
|
96
|
+
const bulkCreateCustomParserUnknownUnits = async (partnerId, unknownUnits, ohtCoreApiKey) => {
|
|
97
|
+
const response = await (0, apiUtils_1.makeApiCallWithRetry)('post', `${OHT_CORE_URL}/v1/synonym/partners/${partnerId}/unknown-units/bulk`, {
|
|
98
|
+
partnerId: partnerId,
|
|
99
|
+
unknownUnits: unknownUnits,
|
|
100
|
+
}, ohtCoreApiKey);
|
|
101
|
+
logger.info(response.data, `Resp: POST /v1/synonym/partners/${partnerId}/unknown-units/bulk`);
|
|
102
|
+
};
|
|
103
|
+
exports.bulkCreateCustomParserUnknownUnits = bulkCreateCustomParserUnknownUnits;
|
|
104
|
+
/**
|
|
105
|
+
* Fetch synonym units from oht-core API endpoint
|
|
106
|
+
* Returns all approved resolved synonym units (backend already filters and returns all results)
|
|
107
|
+
*/
|
|
108
|
+
const fetchSynonymUnits = async (partnerId, ohtCoreApiKey) => {
|
|
109
|
+
try {
|
|
110
|
+
const url = `${OHT_CORE_URL}/v1/synonym/synonym-units/resolved${partnerId ? `?partnerId=${partnerId}` : ''}`;
|
|
111
|
+
const response = await (0, apiUtils_1.makeApiCallWithRetry)('get', url, null, ohtCoreApiKey);
|
|
112
|
+
// Backend returns array directly (already filtered for approved status and non-null targetUnit)
|
|
113
|
+
const synonymUnits = Array.isArray(response?.data)
|
|
114
|
+
? response.data
|
|
115
|
+
: response?.data?.items || [];
|
|
116
|
+
logger.info({ partnerId, count: synonymUnits.length }, `Fetched ${synonymUnits.length} synonym units from API`);
|
|
117
|
+
return synonymUnits;
|
|
118
|
+
}
|
|
119
|
+
catch (error) {
|
|
120
|
+
logger.warn({ partnerId, error: error.message }, `Failed to fetch synonym units from API, falling back to hardcoded synonyms`);
|
|
121
|
+
return [];
|
|
122
|
+
}
|
|
123
|
+
};
|
|
124
|
+
exports.fetchSynonymUnits = fetchSynonymUnits;
|
|
50
125
|
/**
|
|
51
126
|
* Processes appended biomarker mappings by extracting values from additional labKeys
|
|
52
127
|
* Compatible with AnnotationPreviewService interface but returns object with text property
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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package/package.json
CHANGED
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@@ -1,34 +1,34 @@
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1
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-
{
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2
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-
"name": "@openhealth/oht-custom-parser-lib",
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3
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-
"version": "0.2.
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4
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-
"description": "Shared nodejs lib with with reusable functions",
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|
5
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-
"main": "dist/index.js",
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|
6
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-
"types": "dist/index.d.ts",
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7
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-
"files": [
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8
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-
"/dist"
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9
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-
],
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10
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-
"scripts": {
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11
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-
"test": "jest"
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12
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-
},
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|
13
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-
"keywords": [],
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|
14
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-
"author": "",
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|
15
|
-
"license": "ISC",
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|
16
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-
"dependencies": {
|
|
17
|
-
"@google-cloud/pubsub": "^4.10.0",
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|
18
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-
"@google-cloud/storage": "^7.7.0",
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|
19
|
-
"axios": "^1.6.7",
|
|
20
|
-
"bottleneck": "^2.19.5",
|
|
21
|
-
"dayjs": "^1.11.13",
|
|
22
|
-
"dotenv": "^16.4.5",
|
|
23
|
-
"jsonata": "^2.1.0",
|
|
24
|
-
"moment": "^2.30.1",
|
|
25
|
-
"mongodb": "^6.3.0",
|
|
26
|
-
"pino": "^8.19.0"
|
|
27
|
-
},
|
|
28
|
-
"devDependencies": {
|
|
29
|
-
"@types/jest": "^29.5.14",
|
|
30
|
-
"axios-mock-adapter": "^2.1.0",
|
|
31
|
-
"jest": "^29.7.0",
|
|
32
|
-
"ts-jest": "^29.2.5"
|
|
33
|
-
}
|
|
34
|
-
}
|
|
1
|
+
{
|
|
2
|
+
"name": "@openhealth/oht-custom-parser-lib",
|
|
3
|
+
"version": "0.2.53",
|
|
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": "^1.6.7",
|
|
20
|
+
"bottleneck": "^2.19.5",
|
|
21
|
+
"dayjs": "^1.11.13",
|
|
22
|
+
"dotenv": "^16.4.5",
|
|
23
|
+
"jsonata": "^2.1.0",
|
|
24
|
+
"moment": "^2.30.1",
|
|
25
|
+
"mongodb": "^6.3.0",
|
|
26
|
+
"pino": "^8.19.0"
|
|
27
|
+
},
|
|
28
|
+
"devDependencies": {
|
|
29
|
+
"@types/jest": "^29.5.14",
|
|
30
|
+
"axios-mock-adapter": "^2.1.0",
|
|
31
|
+
"jest": "^29.7.0",
|
|
32
|
+
"ts-jest": "^29.2.5"
|
|
33
|
+
}
|
|
34
|
+
}
|
package/readme.md
CHANGED
|
@@ -1,99 +1,99 @@
|
|
|
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
|
-
## Development
|
|
37
|
-
|
|
38
|
-
### Patch Versions
|
|
39
|
-
|
|
40
|
-
When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
|
|
41
|
-
|
|
42
|
-
1. **Update the version number**: Use npm's version command to bump the version:
|
|
43
|
-
- **Patch** for bug fixes:
|
|
44
|
-
```bash
|
|
45
|
-
npm version patch
|
|
46
|
-
```
|
|
47
|
-
- **Minor** for new features:
|
|
48
|
-
```bash
|
|
49
|
-
npm version minor
|
|
50
|
-
```
|
|
51
|
-
- **Major** for breaking changes:
|
|
52
|
-
```bash
|
|
53
|
-
npm version major
|
|
54
|
-
```
|
|
55
|
-
|
|
56
|
-
This command will automatically update the version in the `package.json` and create a git tag.
|
|
57
|
-
|
|
58
|
-
2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
|
|
59
|
-
|
|
60
|
-
### Publish to npm Registry
|
|
61
|
-
|
|
62
|
-
After updating the version, you can publish the library to the npm registry:
|
|
63
|
-
|
|
64
|
-
1. **Login to npm** (if you haven't already):
|
|
65
|
-
```bash
|
|
66
|
-
npm login
|
|
67
|
-
```
|
|
68
|
-
|
|
69
|
-
2. **Publish the package**:
|
|
70
|
-
```bash
|
|
71
|
-
npm publish
|
|
72
|
-
```
|
|
73
|
-
|
|
74
|
-
If this is a private package, use:
|
|
75
|
-
```bash
|
|
76
|
-
npm publish --access restricted
|
|
77
|
-
```
|
|
78
|
-
|
|
79
|
-
3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
|
|
80
|
-
|
|
81
|
-
## Using the Library in Cloud Functions
|
|
82
|
-
|
|
83
|
-
To use `oht-custom-parser-lib` in your cloud functions:
|
|
84
|
-
|
|
85
|
-
1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
|
|
86
|
-
|
|
87
|
-
```json
|
|
88
|
-
{
|
|
89
|
-
"dependencies": {
|
|
90
|
-
"oht-custom-parser-lib": "^1.0.0"
|
|
91
|
-
}
|
|
92
|
-
}
|
|
93
|
-
```
|
|
94
|
-
|
|
95
|
-
Replace `^1.0.0` with the appropriate version as needed.
|
|
96
|
-
|
|
97
|
-
2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
|
|
98
|
-
|
|
99
|
-
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
|
+
## Development
|
|
37
|
+
|
|
38
|
+
### Patch Versions
|
|
39
|
+
|
|
40
|
+
When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
|
|
41
|
+
|
|
42
|
+
1. **Update the version number**: Use npm's version command to bump the version:
|
|
43
|
+
- **Patch** for bug fixes:
|
|
44
|
+
```bash
|
|
45
|
+
npm version patch
|
|
46
|
+
```
|
|
47
|
+
- **Minor** for new features:
|
|
48
|
+
```bash
|
|
49
|
+
npm version minor
|
|
50
|
+
```
|
|
51
|
+
- **Major** for breaking changes:
|
|
52
|
+
```bash
|
|
53
|
+
npm version major
|
|
54
|
+
```
|
|
55
|
+
|
|
56
|
+
This command will automatically update the version in the `package.json` and create a git tag.
|
|
57
|
+
|
|
58
|
+
2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
|
|
59
|
+
|
|
60
|
+
### Publish to npm Registry
|
|
61
|
+
|
|
62
|
+
After updating the version, you can publish the library to the npm registry:
|
|
63
|
+
|
|
64
|
+
1. **Login to npm** (if you haven't already):
|
|
65
|
+
```bash
|
|
66
|
+
npm login
|
|
67
|
+
```
|
|
68
|
+
|
|
69
|
+
2. **Publish the package**:
|
|
70
|
+
```bash
|
|
71
|
+
npm publish
|
|
72
|
+
```
|
|
73
|
+
|
|
74
|
+
If this is a private package, use:
|
|
75
|
+
```bash
|
|
76
|
+
npm publish --access restricted
|
|
77
|
+
```
|
|
78
|
+
|
|
79
|
+
3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
|
|
80
|
+
|
|
81
|
+
## Using the Library in Cloud Functions
|
|
82
|
+
|
|
83
|
+
To use `oht-custom-parser-lib` in your cloud functions:
|
|
84
|
+
|
|
85
|
+
1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
|
|
86
|
+
|
|
87
|
+
```json
|
|
88
|
+
{
|
|
89
|
+
"dependencies": {
|
|
90
|
+
"oht-custom-parser-lib": "^1.0.0"
|
|
91
|
+
}
|
|
92
|
+
}
|
|
93
|
+
```
|
|
94
|
+
|
|
95
|
+
Replace `^1.0.0` with the appropriate version as needed.
|
|
96
|
+
|
|
97
|
+
2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
|
|
98
|
+
|
|
99
|
+
3. **Deploy Your Function**: Deploy your cloud function as usual, ensuring that the updated dependencies are included.
|