@openhealth/oht-custom-parser-lib 0.3.13 → 0.4.0

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

@@ -1 +1 @@
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package/dist/util-ts/extractionUtils.js

@@ -13,8 +13,12 @@ exports.ohtReportParseExamValue = ohtReportParseExamValue;
 exports.ohtReportCheckValueForPlausibleValues = ohtReportCheckValueForPlausibleValues;
 const oht_types_1 = require("../types/oht.types");
 const moment_1 = __importDefault(require("moment"));
-const processingLogger_service_1 = require("../service/processingLogger.service");
+const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
 const dataUtils_1 = require("./dataUtils");
+/**
+ * Logger instance for the application
+ */
+const logger = (0, pinoLogger_1.default)();
 /**
  * Default range parsing function that extracts range information from exam data
  * @param exam - The OHT exam object containing range information
@@ -419,10 +423,10 @@ function handleBiomarkerId(backendMapping, labKey) {
     const shouldBeUnmapped = backendMapping.keepAsUnmapped === true;
     const finalOhtBmId = shouldBeUnmapped ? -1 : backendMapping.ohtBmId;
     if (isAlreadyUnmapped) {
-        processingLogger_service_1.processingLogger.logInfo(`Processing backend unmapped biomarker: ${labKey} (ohtBmId: -1)`);
+        logger.info(`Processing backend unmapped biomarker: ${labKey} (ohtBmId: -1)`);
     }
     else if (shouldBeUnmapped) {
-        processingLogger_service_1.processingLogger.logInfo(`Overriding biomarker to unmapped: ${labKey} (ohtBmId: ${backendMapping.ohtBmId} -> -1)`);
+        logger.info(`Overriding biomarker to unmapped: ${labKey} (ohtBmId: ${backendMapping.ohtBmId} -> -1)`);
     }
     return {
         ohtBmId: finalOhtBmId,
@@ -655,7 +659,7 @@ function ohtReportCheckValueForPlausibleValues(ohtBmId, labKey, ohtBiomarker, un
     const isPlausibleValue = value >= plausibleLowerValue && value <= plausibleUpperValue;
     // Log if the value is not plausible
     if (!isPlausibleValue) {
-        processingLogger_service_1.processingLogger.logWarn(`Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${ohtBmId}" | "${labKey}", filename: ${filename}`, { ohtBmId, labKey, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename });
+        logger.warn({ ohtBmId, labKey, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename }, `Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${ohtBmId}" | "${labKey}", filename: ${filename}`);
     }
     return isPlausibleValue;
 }

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

@@ -1 +1 @@
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package/dist/util-ts/pinoLogger.js

@@ -16,14 +16,6 @@ const SeverityLookup = {
     warn: 'WARNING',
     error: 'ERROR',
 };
-/** True when logs should be pretty-printed for terminal (local/dev). GCP/production keeps JSON. */
-function usePrettyLogs() {
-    if (process.env.LOG_PRETTY === 'true')
-        return true;
-    if (process.env.LOG_PRETTY === 'false')
-        return false;
-    return process.env.NODE_ENV !== 'production';
-}
 // Define the default Pino configuration
 const defaultPinoConfig = {
     messageKey: 'message',
@@ -54,27 +46,8 @@ const defaultPinoConfig = {
         }
     },
 };
-/** Options for pino-pretty when running locally (readable terminal output). */
-const prettyTransportOptions = {
-    target: 'pino-pretty',
-    options: {
-        colorize: true,
-        translateTime: 'SYS:HH:MM:ss',
-        messageKey: 'message',
-        singleLine: false,
-        errorLikeObjectKeys: ['err', 'error'],
-        ignore: 'pid,hostname',
-    },
-};
 // Export a function that creates a Pino logger instance with the provided configuration overrides
 exports.default = (pinoConfigOverrides = {}) => {
-    const baseConfig = { ...defaultPinoConfig, ...pinoConfigOverrides };
-    if (usePrettyLogs()) {
-        return (0, pino_1.default)({
-            ...baseConfig,
-            transport: prettyTransportOptions,
-        });
-    }
-    return (0, pino_1.default)(baseConfig);
+    return (0, pino_1.default)({ ...defaultPinoConfig, ...pinoConfigOverrides });
 };
 //# sourceMappingURL=pinoLogger.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"pinoLogger.js","sourceRoot":"","sources":["../../util-ts/pinoLogger.ts"],"names":[],"mappings":";;;;;AAAA,gDAAwB;AACxB,qDAA+E;AAO/E,oCAAoC;AACpC,MAAM,cAAc,GAAuB;IACzC,OAAO,EAAE,SAAS;IAClB,KAAK,EAAE,SAAS;IAChB,OAAO,EAAE,OAAO;IAChB,KAAK,EAAE,OAAO;IACd,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,MAAM;IACZ,IAAI,EAAE,SAAS;IACf,KAAK,EAAE,OAAO;CACf,CAAC;AAEF,wCAAwC;AACxC,MAAM,iBAAiB,GAAG;IACxB,UAAU,EAAE,SAAS;IACrB,UAAU,EAAE;QACV,KAAK,CAAC,KAAsB,EAAE,MAAW;YACvC,OAAO,EAAE,QAAQ,EAAE,cAAc,CAAC,KAAK,CAAC,IAAI,SAAS,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QACzE,CAAC;KACF;IACD,WAAW,EAAE;QACX,KAAK,EAAE,cAAI,CAAC,cAAc,CAAC,GAAG,EAAE,6BAA6B;KAC9D;IACD,MAAM,EAAE;QACN,KAAK,EAAE,IAAA,kCAAiB,GAAE;QAC1B,MAAM,EAAE,YAAY;KACrB;IACD,KAAK,EAAE;QACL,SAAS,CAAC,IAA4B,EAAE,MAAgB;YACtD,IAAI,CAAC;gBACH,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,IAAI,OAAO,IAAI,CAAC,CAAC,CAAC,KAAK,QAAQ,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;oBACvE,MAAM,SAAS,GAAG,IAAA,yCAAwB,EAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;oBACpD,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC;gBACtB,CAAC;gBACD,MAAM,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;YAC3B,CAAC;YAAC,MAAM,CAAC;gBACP,MAAM,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC,CAAC,uCAAuC;YACnE,CAAC;QACH,CAAC;KACF;CACF,CAAC;AAEF,kGAAkG;AAClG,kBAAe,CAAC,sBAA2B,EAAE,EAAe,EAAE;IAC5D,OAAO,IAAA,cAAI,EAAC,EAAE,GAAG,iBAAiB,EAAE,GAAG,mBAAmB,EAAE,CAAC,CAAC;AAChE,CAAC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.3.13",
+  "version": "0.4.0",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -8,7 +8,6 @@
     "/dist"
   ],
   "scripts": {
-    "build": "tsc",
     "test": "jest"
   },
   "keywords": [],
@@ -24,14 +23,12 @@
     "jsonata": "^2.1.0",
     "moment": "^2.30.1",
     "mongodb": "^6.3.0",
-    "pino": "^8.19.0",
-    "pino-pretty": "^11.3.0"
+    "pino": "^8.19.0"
   },
   "devDependencies": {
     "@types/jest": "^29.5.14",
     "axios-mock-adapter": "^2.1.0",
     "jest": "^29.7.0",
-    "ts-jest": "^29.2.5",
-    "typescript": "^5.0.0"
+    "ts-jest": "^29.2.5"
   }
 }

package/dist/service/fileUploadErrorHandler.service.d.ts

@@ -1,26 +0,0 @@
-import { RejectReason } from '../types/oht.types';
-/**
- * Validation error for parser/report validation (rejectReason + optional field).
- * Used by mapErrorToRejectReason and handleError.
- */
-export declare class ValidationError extends Error {
-    rejectReason: RejectReason;
-    fieldName?: string;
-    constructor(message: string, rejectReason: RejectReason, fieldName?: string);
-}
-/**
- * Whether to send Slack notification for this reject reason (not in silent list).
- */
-export declare function shouldSendSlackNotification(rejectReason: RejectReason | undefined, silentRejectReasons: RejectReason[]): boolean;
-/**
- * Formats reject reason with field name and context for better client messages.
- */
-export declare function extractFormattedRejectReason(rejectReason: RejectReason, fieldName?: string, errorMessage?: string): string;
-/**
- * Maps error to an appropriate RejectReason.
- */
-export declare function mapErrorToRejectReason(error: Error, errorMessage: string, statusCode?: number, responseData?: any): RejectReason;
-/**
- * Handles file-upload processing errors: updates status, notifies Slack, logs with error_code.
- */
-export declare function handleError(error: Error, fileName: string, signedUploadId: string | undefined, apiKey: string, ohapiUrl: string, cloudEventId?: string, partnerName?: string, silentRejectReasons?: RejectReason[]): Promise<void>;

package/dist/service/fileUploadErrorHandler.service.js

@@ -1,257 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ValidationError = void 0;
-exports.shouldSendSlackNotification = shouldSendSlackNotification;
-exports.extractFormattedRejectReason = extractFormattedRejectReason;
-exports.mapErrorToRejectReason = mapErrorToRejectReason;
-exports.handleError = handleError;
-const oht_types_1 = require("../types/oht.types");
-const slackMessages_service_1 = require("./slackMessages.service");
-const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
-const apiUtils_1 = require("../util-ts/apiUtils");
-const processingLogger_service_1 = require("./processingLogger.service");
-const error_types_1 = require("../types/error.types");
-const dayjs_1 = __importDefault(require("dayjs"));
-const utc_1 = __importDefault(require("dayjs/plugin/utc"));
-dayjs_1.default.extend(utc_1.default);
-/**
- * Validation error for parser/report validation (rejectReason + optional field).
- * Used by mapErrorToRejectReason and handleError.
- */
-class ValidationError extends Error {
-    constructor(message, rejectReason, fieldName) {
-        super(message);
-        this.name = 'ValidationError';
-        this.rejectReason = rejectReason;
-        this.fieldName = fieldName;
-    }
-}
-exports.ValidationError = ValidationError;
-/**
- * Whether to send Slack notification for this reject reason (not in silent list).
- */
-function shouldSendSlackNotification(rejectReason, silentRejectReasons) {
-    if (!rejectReason || silentRejectReasons.length === 0) {
-        return true;
-    }
-    return !silentRejectReasons.includes(rejectReason);
-}
-/**
- * Formats reject reason with field name and context for better client messages.
- */
-function extractFormattedRejectReason(rejectReason, fieldName, errorMessage) {
-    const baseRejectReason = String(rejectReason);
-    if (rejectReason === oht_types_1.RejectReason.INVALID_DATA_FORMAT && errorMessage) {
-        const formattedMatch = errorMessage.match(/Invalid Data Format \[expected: ([^\]]+), received: ([^\]]+)\]/);
-        if (formattedMatch) {
-            const expectedFormat = formattedMatch[1];
-            const receivedFormat = formattedMatch[2];
-            const fieldPart = fieldName ? ` for '${fieldName}'` : '';
-            return `Invalid Data Format${fieldPart} [expected: ${expectedFormat}, received: ${receivedFormat}]`;
-        }
-    }
-    if (fieldName) {
-        switch (rejectReason) {
-            case oht_types_1.RejectReason.INCOMPLETE_DATA:
-                if (fieldName === 'patient.id') {
-                    return `Patient external ID conflict: '${fieldName}' does not match user's external reference`;
-                }
-                return `${baseRejectReason} - Missing or invalid '${fieldName}'`;
-            case oht_types_1.RejectReason.MISSING_EXAM_DATE:
-                return `${baseRejectReason} - Missing '${fieldName}'`;
-            case oht_types_1.RejectReason.MISSING_LAB_ORDER_ID:
-                return `${baseRejectReason} - Missing '${fieldName}'`;
-            case oht_types_1.RejectReason.MISSING_EXTERNAL_PATIENT_ID:
-                return `${baseRejectReason} - Missing '${fieldName}'`;
-            case oht_types_1.RejectReason.MISSING_PATIENT_SEX:
-                return `${baseRejectReason} - Missing '${fieldName}'`;
-            case oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA:
-                return `${baseRejectReason} - Invalid '${fieldName}'`;
-            default:
-                return `${baseRejectReason} - Issue with '${fieldName}'`;
-        }
-    }
-    return baseRejectReason;
-}
-function isPatientExternalIdConflict(statusCode, errorMessage, responseData) {
-    const lowerMessage = errorMessage.toLowerCase();
-    const is409Error = statusCode === 409 ||
-        lowerMessage.includes('status code 409') ||
-        lowerMessage.includes('409');
-    if (!is409Error)
-        return false;
-    const isExplicitlyNotPatientConflict = lowerMessage.includes('duplicate') &&
-        !lowerMessage.includes('patient') &&
-        !lowerMessage.includes('external');
-    return !isExplicitlyNotPatientConflict;
-}
-/**
- * Maps error to an appropriate RejectReason.
- */
-function mapErrorToRejectReason(error, errorMessage, statusCode, responseData) {
-    if (isPatientExternalIdConflict(statusCode, errorMessage, responseData)) {
-        return oht_types_1.RejectReason.INCOMPLETE_DATA;
-    }
-    const hasRejectReason = error instanceof ValidationError || 'rejectReason' in error;
-    if (hasRejectReason) {
-        const rejectReason = error.rejectReason;
-        if (rejectReason !== undefined && rejectReason !== null && rejectReason !== '') {
-            return rejectReason;
-        }
-    }
-    const lowerMessage = errorMessage.toLowerCase();
-    if (lowerMessage.includes('invalid data format') || lowerMessage.includes('invalid format') || lowerMessage.includes('iso 8601 format')) {
-        return oht_types_1.RejectReason.INVALID_DATA_FORMAT;
-    }
-    if (lowerMessage.includes('no biomarker') || lowerMessage.includes('invalid input') || lowerMessage.includes('no measurements')) {
-        return oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA;
-    }
-    if (lowerMessage.includes('image quality') || lowerMessage.includes('low quality')) {
-        return oht_types_1.RejectReason.LOW_IMAGE_QUALITY;
-    }
-    if (lowerMessage.includes('underage') || (lowerMessage.includes('age') && lowerMessage.includes('invalid'))) {
-        return oht_types_1.RejectReason.UNDERAGE_PERSON;
-    }
-    if (lowerMessage.includes('language') || lowerMessage.includes('unsupported language')) {
-        return oht_types_1.RejectReason.LANGUAGE_NOT_SUPPORTED;
-    }
-    if (lowerMessage.includes('implausible') || lowerMessage.includes('invalid value')) {
-        return oht_types_1.RejectReason.IMPLAUSIBLE_DATA;
-    }
-    if (lowerMessage.includes('missing exam date') || lowerMessage.includes('no date') || lowerMessage.includes('date')) {
-        return oht_types_1.RejectReason.MISSING_EXAM_DATE;
-    }
-    if (lowerMessage.includes('missing unit') || lowerMessage.includes('incomplete') || lowerMessage.includes('missing data')) {
-        return oht_types_1.RejectReason.INCOMPLETE_DATA;
-    }
-    if (lowerMessage.includes('not an official') || lowerMessage.includes('not official')) {
-        return oht_types_1.RejectReason.NOT_AN_OFFICIAL_REPORT;
-    }
-    if (lowerMessage.includes('missing external patient') || lowerMessage.includes('missing patient id')) {
-        return oht_types_1.RejectReason.MISSING_EXTERNAL_PATIENT_ID;
-    }
-    if (lowerMessage.includes('unsupported') || lowerMessage.includes('not supported')) {
-        return oht_types_1.RejectReason.UNSUPPORTED_UPLOAD;
-    }
-    return oht_types_1.RejectReason.UNSUPPORTED_UPLOAD;
-}
-/**
- * Handles file-upload processing errors: updates status, notifies Slack, logs with error_code.
- */
-async function handleError(error, fileName, signedUploadId, apiKey, ohapiUrl, cloudEventId, partnerName, silentRejectReasons = []) {
-    const errorDetails = (0, apiUtils_1.parseErrorObj)(error);
-    const responseData = errorDetails.responseData;
-    const statusCode = errorDetails.status;
-    const axiosStatusCode = error.response?.status;
-    const finalStatusCode = statusCode || axiosStatusCode;
-    const errorMessage = responseData
-        ? `${error.message} - Response: ${JSON.stringify(responseData)}`
-        : error.message || 'Unknown error occurred';
-    const isIngestionError = finalStatusCode === 409 ||
-        errorMessage.toLowerCase().includes('ingestion') ||
-        errorDetails.config?.url?.includes('/ingestion');
-    const pipelineStep = isIngestionError
-        ? oht_types_1.PipelineStep.SENDING_RESULTS
-        : oht_types_1.PipelineStep.EXTRACTING_METADATA;
-    const errorType = error.constructor.name;
-    const rejectReason = mapErrorToRejectReason(error, errorMessage, finalStatusCode, responseData);
-    let fieldName;
-    if (error instanceof ValidationError) {
-        fieldName = error.fieldName;
-    }
-    else if (finalStatusCode === 409 && rejectReason === oht_types_1.RejectReason.INCOMPLETE_DATA) {
-        fieldName = 'patient.id';
-    }
-    const formattedRejectReason = extractFormattedRejectReason(rejectReason, fieldName, errorMessage);
-    if (!signedUploadId) {
-        const noUploadError = new Error((0, error_types_1.getErrorMessage)(error_types_1.ErrorCode.UPLOAD_MISSING_SIGNED_UPLOAD_ID));
-        processingLogger_service_1.processingLogger.addError(noUploadError, 'error_handling');
-        processingLogger_service_1.processingLogger.logError('Processing failed: Missing signed upload ID', noUploadError, {
-            error_code: error_types_1.ErrorCode.UPLOAD_MISSING_SIGNED_UPLOAD_ID,
-            cloud_event_id: cloudEventId,
-            partner_name: partnerName,
-        });
-        processingLogger_service_1.processingLogger.logEnd(false);
-        throw noUploadError;
-    }
-    try {
-        processingLogger_service_1.processingLogger.addError(error, 'error_handling');
-        const fileUploads = await (0, auxiliaryFunctions_service_1.queryFileUploadsWithFilters)([{ field: 'signedUploadId', search: signedUploadId }], apiKey);
-        const fileUploadId = fileUploads[0]?.id;
-        if (!fileUploadId) {
-            const notFoundError = new Error((0, error_types_1.getErrorMessage)(error_types_1.ErrorCode.UPLOAD_FILE_NOT_FOUND));
-            processingLogger_service_1.processingLogger.addError(notFoundError, 'error_handling');
-            processingLogger_service_1.processingLogger.logError('Processing failed: File upload not found', notFoundError, {
-                error_code: error_types_1.ErrorCode.UPLOAD_FILE_NOT_FOUND,
-                signed_upload_id: signedUploadId,
-                partner_name: partnerName,
-            });
-            processingLogger_service_1.processingLogger.logEnd(false);
-            return;
-        }
-        const fileUrl = `${ohapiUrl}/data-import/file-uploads/${fileUploadId}`;
-        const sendSlack = shouldSendSlackNotification(rejectReason, silentRejectReasons);
-        const fieldInfo = fieldName ? `\n*Field:* \`${fieldName}\`` : '';
-        const slackMessage = (0, slackMessages_service_1.getSlackFileIssueNotificationMessage)(`🚨 *AgnosticParser Processing Error*\n\n` +
-            `*Error:* ${errorType}: ${errorMessage}\n` +
-            `*Reject Reason:* ${formattedRejectReason}${fieldInfo}\n` +
-            `*File:* \`${fileName}\`\n` +
-            `*Partner:* ${partnerName || 'Unknown'}\n` +
-            `*File Upload ID:* \`${fileUploadId}\`\n` +
-            (cloudEventId ? `*Event ID:* \`${cloudEventId}\`\n` : ''), `AgnosticParser - ${partnerName || 'Unknown Partner'}`, fileUrl);
-        const [slackResult, statusResult] = await Promise.allSettled([
-            sendSlack ? (0, slackMessages_service_1.sendMessageToSlack)(slackMessage) : Promise.resolve(),
-            (0, auxiliaryFunctions_service_1.postFileUploadSetStatus)({
-                status: oht_types_1.DataImportFileUploadStatus.REJECTED,
-                digitalization: {
-                    status: oht_types_1.DigitizationStatus.ERROR,
-                    pipelineStep: pipelineStep,
-                    pipelineStepData: formattedRejectReason,
-                    timestamp: dayjs_1.default.utc().toISOString(),
-                },
-                ...(formattedRejectReason && { rejectReason: formattedRejectReason }),
-            }, fileUploadId, fileName, apiKey),
-        ]);
-        if (slackResult.status === 'rejected') {
-            processingLogger_service_1.processingLogger.logWarn('Slack notification failed', {
-                error_code: error_types_1.ErrorCode.UPLOAD_SLACK_FAILED,
-                file_upload_id: fileUploadId,
-                slack_error: (0, apiUtils_1.parseErrorObj)(slackResult.reason),
-            });
-        }
-        if (statusResult.status === 'rejected') {
-            const statusErrorDetails = (0, apiUtils_1.parseErrorObj)(statusResult.reason);
-            const statusResponseData = statusErrorDetails.responseData;
-            processingLogger_service_1.processingLogger.logError(`Failed to update file upload status: ${statusErrorDetails.message}${statusResponseData ? ` - ${JSON.stringify(statusResponseData)}` : ''}`, undefined, {
-                error_code: error_types_1.ErrorCode.UPLOAD_STATUS_UPDATE_FAILED,
-                file_upload_id: fileUploadId,
-                status_error: statusErrorDetails,
-            });
-        }
-        // Single "Processing failed" log from logEnd(false), with full error detail in processing_summary.errors (message, step, stack, error_type)
-        processingLogger_service_1.processingLogger.logEnd(false);
-    }
-    catch (handleErrorException) {
-        const exceptionMessage = handleErrorException instanceof Error
-            ? handleErrorException.message
-            : String(handleErrorException);
-        const handlingError = handleErrorException instanceof Error
-            ? handleErrorException
-            : new Error(String(handleErrorException));
-        processingLogger_service_1.processingLogger.addError(handlingError, 'error_handling_failure');
-        processingLogger_service_1.processingLogger.logError(`Error handling failed: ${exceptionMessage}`, handlingError, {
-            error_code: error_types_1.ErrorCode.UPLOAD_HANDLING_FAILED,
-            signed_upload_id: signedUploadId,
-            partner_name: partnerName,
-            original_error: errorMessage,
-            original_error_type: errorType,
-            handling_error: exceptionMessage,
-        });
-        processingLogger_service_1.processingLogger.logEnd(false);
-        throw error;
-    }
-}
-//# sourceMappingURL=fileUploadErrorHandler.service.js.map

package/dist/service/fileUploadErrorHandler.service.js.map

@@ -1 +0,0 @@
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