@openhealth/oht-custom-parser-lib 0.2.43 → 0.2.45
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 -3
- package/dist/index.js +1 -2
- package/dist/index.js.map +1 -1
- package/dist/types/oht.types.d.ts +0 -1
- package/dist/util-ts/dataUtils.d.ts +0 -40
- package/dist/util-ts/dataUtils.js +4 -71
- package/dist/util-ts/dataUtils.js.map +1 -1
- package/package.json +1 -1
package/dist/index.d.ts
CHANGED
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@@ -7,9 +7,8 @@ export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, Referen
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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 { makeApiCallWithRetry, parseErrorObj } from './util-ts/apiUtils';
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-
export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings
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export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings } 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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export { getMappedBiomarkers } from './util-ts/dataUtils';
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export { AnnotationPreviewResult, AnnotationConfig, ExtractionPath } from './util-ts/dataUtils';
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export { getMappedBiomarkers, } from './util-ts/dataUtils';
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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.
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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.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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@@ -56,7 +56,6 @@ 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, "generateAnnotationPreview", { enumerable: true, get: function () { return dataUtils_1.generateAnnotationPreview; } });
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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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-
{"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;AAGpB,gBAAgB;AAChB,mEAWqC;AAFnC,mHAAA,YAAY,OAAA;AAGd,+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;AAIZ,kBAAkB;AAClB,+CAAuE;AAA/D,gHAAA,oBAAoB,OAAA;AAAE,yGAAA,aAAa,OAAA;AAC3C,
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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;AAGpB,gBAAgB;AAChB,mEAWqC;AAFnC,mHAAA,YAAY,OAAA;AAGd,+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;AAIZ,kBAAkB;AAClB,+CAAuE;AAA/D,gHAAA,oBAAoB,OAAA;AAAE,yGAAA,aAAa,OAAA;AAC3C,iDAAuI;AAA/H,yGAAA,YAAY,OAAA;AAAE,sHAAA,yBAAyB,OAAA;AAAE,6HAAA,gCAAgC,OAAA;AAAE,oHAAA,uBAAuB,OAAA;AAC1G,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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@@ -408,7 +408,6 @@ export interface AnnotationConfig {
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maxLength?: number;
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fallbackValue?: string;
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separator?: string;
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concatenationMode?: 'space' | 'newline' | 'comma';
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}
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/** Main backend biomarker mapping interface */
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export interface BackendBiomarkerMapping {
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@@ -1,31 +1,4 @@
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import { UnknownMeasurementsBulk, AnnotationLabKey } from '../types/oht.types';
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export interface AnnotationPreviewResult {
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success: boolean;
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text: string;
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error?: string;
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extractedValues: Array<{
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labKey: string;
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path: string;
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value: string;
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formatted: string;
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required: boolean;
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used: boolean;
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}>;
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}
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export interface AnnotationConfig {
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enabled: boolean;
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labKeys?: AnnotationLabKey[];
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concatenationMode?: 'space' | 'newline' | 'comma';
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separator?: string;
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maxLength?: number;
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fallbackValue?: string;
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}
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export interface ExtractionPath {
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path: string;
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required: boolean;
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format?: string;
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defaultValue?: string;
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}
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export declare function isBiomarkerValueNumerical(biomarker: any): boolean;
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export declare function isBiomarkerExternalNoVisualRange(biomarker: any): boolean;
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export declare const extractValue: (obj: any, position?: string) => any;
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maxLength?: number;
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fallbackValue?: string;
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separator?: string;
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concatenationMode?: 'space' | 'newline' | 'comma';
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}): {
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success: boolean;
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text: string;
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used: boolean;
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}>;
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};
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/**
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* Generate annotation preview from single exam data (ohapi compatibility)
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* Wrapper function that converts single exam to array format for processAppendedMappings
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* @param examData - Single exam data (OHTExam or JSON blob)
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* @param annotationConfig - Annotation configuration
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* @param targetLabKey - Target lab key for extraction
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* @param extractionPaths - Array of extraction paths
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* @param prefix - Optional prefix for the result
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* @param suffix - Optional suffix for the result
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* @returns AnnotationPreviewResult with extracted text and values
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*/
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export declare function generateAnnotationPreview(examData: any, annotationConfig: AnnotationConfig, targetLabKey: string, extractionPaths: ExtractionPath[], prefix?: string, suffix?: string): AnnotationPreviewResult;
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@@ -7,7 +7,6 @@ exports.updatePartnerCustomParserUnmappedLabKeys = exports.getMappedBiomarkers =
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exports.isBiomarkerValueNumerical = isBiomarkerValueNumerical;
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exports.isBiomarkerExternalNoVisualRange = isBiomarkerExternalNoVisualRange;
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exports.processAppendedMappings = processAppendedMappings;
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exports.generateAnnotationPreview = generateAnnotationPreview;
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const apiUtils_1 = require("./apiUtils");
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const pinoLogger_1 = __importDefault(require("./pinoLogger"));
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const logger = (0, pinoLogger_1.default)();
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required: path.required,
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used: !!formatted
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});
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// Handle required paths - if required and no value,
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// Handle required paths - if required and no value, log warning and use fallback
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if (path.required && !rawValue && !path.defaultValue) {
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logger.warn(`Required extraction path ${path.path} not found for labKey ${additionalLabKey.labKey}, filename: ${filename}`);
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success: false,
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text: '',
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error: `Required path '${path.path}' is missing for labKey '${additionalLabKey.labKey}'`,
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extractedValues: allExtractedValues
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};
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parts.push(`appended biomarker information for ${additionalLabKey.labKey} not found`);
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}
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else if (formatted) {
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// Only add non-empty formatted values
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const finalResult = `${additionalLabKey.prefix || ''}${combinedValue}${additionalLabKey.suffix || ''}`;
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labKeyResults.push(finalResult);
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}
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// Join results based on
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let finalText = '';
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if (annotationConfig?.concatenationMode) {
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switch (annotationConfig.concatenationMode) {
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case 'space':
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finalText = labKeyResults.join(' ');
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break;
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case 'newline':
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finalText = labKeyResults.join('\n');
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break;
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case 'comma':
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finalText = labKeyResults.join(', ');
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break;
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default:
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finalText = labKeyResults.join(annotationConfig?.separator || ' ');
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}
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}
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else {
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finalText = labKeyResults.join(annotationConfig?.separator || ' ');
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}
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// Join results based on separator or default to space
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let finalText = labKeyResults.join(annotationConfig?.separator || ' ');
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if (annotationConfig?.maxLength && finalText.length > annotationConfig.maxLength) {
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finalText = finalText.substring(0, annotationConfig.maxLength);
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return null;
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}
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/**
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* Generate annotation preview from single exam data (ohapi compatibility)
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* Wrapper function that converts single exam to array format for processAppendedMappings
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* @param examData - Single exam data (OHTExam or JSON blob)
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* @param annotationConfig - Annotation configuration
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* @param targetLabKey - Target lab key for extraction
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* @param extractionPaths - Array of extraction paths
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* @param prefix - Optional prefix for the result
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* @param suffix - Optional suffix for the result
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* @returns AnnotationPreviewResult with extracted text and values
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*/
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function generateAnnotationPreview(examData, annotationConfig, targetLabKey, extractionPaths, prefix, suffix) {
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if (!examData) {
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return {
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text: '',
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error: 'No exam data provided',
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extractedValues: []
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};
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}
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// Convert single exam to array format expected by processAppendedMappings
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const exams = [{
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ohtExam: examData,
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labKey: targetLabKey
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}];
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// Create AnnotationLabKey from provided parameters
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const labKey = {
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labKey: targetLabKey,
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extractionPaths: extractionPaths,
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required: false, // Not used in this context
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prefix: prefix,
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suffix: suffix
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};
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// Call processAppendedMappings with single exam
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const result = processAppendedMappings(exams, [labKey], 'webapp-preview', // filename for logging
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{
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maxLength: annotationConfig.maxLength,
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fallbackValue: annotationConfig.fallbackValue,
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separator: annotationConfig.separator,
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concatenationMode: annotationConfig.concatenationMode
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});
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return result;
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}
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//# sourceMappingURL=dataUtils.js.map
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{"version":3,"file":"dataUtils.js","sourceRoot":"","sources":["../../util-ts/dataUtils.ts"],"names":[],"mappings":";;;;;;
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