@openhealth/oht-custom-parser-lib 0.4.3 → 0.5.3

package/dist/service/ohtMeasurementsExtractor.service.js

@@ -14,12 +14,11 @@ exports.extractValueFromGreaterLowerThan = extractValueFromGreaterLowerThan;
 const crypto_1 = __importDefault(require("crypto"));
 const dataUtils_1 = require("../util-ts/dataUtils");
 const regexUtils_1 = require("../util-ts/regexUtils");
-const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+const processingLogger_service_1 = require("./processingLogger.service");
 const apiUtils_1 = require("../util-ts/apiUtils");
 const oht_types_1 = require("../types/oht.types");
 const transformationRules_service_1 = require("./transformationRules.service");
 const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
-const logger = (0, pinoLogger_1.default)();
 const OHT_CORE_URL = process.env.OHT_CORE_URL;
 let filename = '';
 function extractUnit(unitExtraction, rawData, ohtBiomarker, synonymUnits = null, partnerId = null) {
@@ -297,7 +296,7 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
     const isPlausibleValue = value >= plausibleLowerValue && value <= plausibleUpperValue;
     // Log if the value is not plausible
     if (!isPlausibleValue) {
-        logger.warn({ labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename }, `Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}", filename: ${filename}`);
+        processingLogger_service_1.processingLogger.logWarn(`Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename: (0, processingLogger_service_1.getRequestScopedFilename)(filename) });
     }
     return isPlausibleValue;
 }
@@ -307,9 +306,9 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
  *
  * @param exams - Array of original exam objects with synthetic IDs
  * @param transformationRules - Mapping of labKey to transformation rule chains
- * @param patientInfo - Patient information
- * @param documentDate - Document date
- * @returns Promise<ApplyTransformationRulesResult> - Array of transformed exams and error messages
+ * @param patientInfo - PatientInfo
+ * @param documentDate - Source DocumentDate
+ * @returns Promise<ApplyTransformationRulesResult[]> - Array of transformed exams
  */
 async function applyTransformationRulesToExams(exams, transformationRules, patientInfo, documentDate) {
     if (transformationRules.size === 0) {
@@ -331,7 +330,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
     const ohtReport = {
         exams: exams.map(e => e.ohtExam),
     };
-    logger.info({ examsCount: exams.length, chainsCount: transformationRules.size, filename }, 'Applying transformation rules to exams...');
+    processingLogger_service_1.processingLogger.logInfo('Applying transformation rules to exams...', { exams_count: exams.length, chains_count: transformationRules.size, filename });
     let labKeysWithRulesCount = 0;
     let transformedLabKeysCount = 0;
     const applicationErrorMessages = [];
@@ -349,7 +348,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
                 contextJson: reportContext,
             });
             if (result.errors.length > 0) {
-                logger.warn({ labKey, errors: result.errors, filename }, 'Errors applying transformation rule(s) for labKey.');
+                processingLogger_service_1.processingLogger.logWarn('Errors applying transformation rule(s) for labKey.', { labKey, errors: result.errors, filename });
                 applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
                 // Keep original exam when transformation fails
                 transformedExams.push(exam);
@@ -358,7 +357,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
                 if (result.appliedRules.length > 0) {
                     transformedLabKeysCount++;
                 }
-                logger.info({ labKey, appliedRules: result.appliedRules.length, filename }, 'Done applying transformation rule(s) for labKey.');
+                processingLogger_service_1.processingLogger.logInfo('Done applying transformation rule(s) for labKey.', { labKey, applied_rules: result.appliedRules.length, filename });
                 // Preserve the synthetic ID through transformation
                 transformedExams.push({
                     _syntheticId: exam._syntheticId,
@@ -368,19 +367,19 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
             }
         }
         catch (error) {
-            logger.error({ labKey, error, filename }, 'Failed to apply transformation rules for labKey.');
+            processingLogger_service_1.processingLogger.logError('Failed to apply transformation rules for labKey.', error instanceof Error ? error : undefined, { labKey, filename });
             applicationErrorMessages.push(`${labKey}: Unhandled error occurred.`);
             // Keep original exam when transformation throws
             transformedExams.push(exam);
         }
     }
-    logger.info({
+    processingLogger_service_1.processingLogger.logInfo('Done applying the transformation rules to exams.', {
         filename,
-        examsCount: exams.length,
-        chainsCount: transformationRules.size,
-        transformedLabKeysCount,
-        labKeysWithRulesCount,
-    }, 'Done applying the transformation rules to exams.');
+        exams_count: exams.length,
+        chains_count: transformationRules.size,
+        transformed_lab_keys_count: transformedLabKeysCount,
+        lab_keys_with_rules_count: labKeysWithRulesCount,
+    });
     return {
         transformedExams,
         applicationErrorMessages
@@ -414,10 +413,10 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
         transformedExamsResult = await applyTransformationRulesToExams(examsWithIds, transformationRules, labToOhtContract.patientInfo, labToOhtContract.documentDate);
     }
     catch (error) {
-        logger.error({ error, filename }, 'Unhandled error while applying transformation rules to exams.');
+        processingLogger_service_1.processingLogger.logError('Unhandled error while applying transformation rules to exams.', error instanceof Error ? error : undefined, { filename: (0, processingLogger_service_1.getRequestScopedFilename)(filename) });
         labToOhtContract.errorMessages.push({
             destination: { slack: true, notes: true, bi: false },
-            message: `Failed applying the transformation rules for filename ${filename}. ${error instanceof Error ? error.message : error}`,
+            message: `Failed applying the transformation rules for filename ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}. ${error instanceof Error ? error.message : error}`,
         });
     }
     if (transformedExamsResult.applicationErrorMessages.length > 0) {
@@ -460,7 +459,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
         if (!labToOhtMapper.rawExam) {
             labToOhtContract.errorMessages.push({
                 destination: { slack: true, notes: false, bi: false },
-                message: `Missing rawExam for labKey: ${labToOhtMapper.labKey} filename: ${filename}`,
+                message: `Missing rawExam for labKey: ${labToOhtMapper.labKey} filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`,
             });
             return;
         }
@@ -476,7 +475,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
         if (labToOhtMapper?.ohtBmId && labToOhtMapper?.ohtBmId !== -1) {
             // if BM is already in measurements, continue to the next one
             if (measurements.some(measurement => measurement.biomarkerId === labToOhtMapper.ohtBmId)) {
-                logger.warn({ labToOhtMapper }, `Biomarker already in measurements array, should investigate, filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Biomarker already in measurements array, should investigate, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { labToOhtMapper });
                 labToOhtContract.errorMessages.push({
                     destination: { slack: false, notes: false, bi: true },
                     message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
@@ -503,7 +502,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 });
             }
             if (!isUnitParsedCorrectly) {
-                logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { labToOhtMapper });
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Unit not extracted correctly for:[PLACEHOLDER]`,
@@ -513,7 +512,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(examObj, labToOhtMapper.valueExtraction, ohtBiomarker);
             if (!isValueParsedCorrectly) {
-                logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { labToOhtMapper });
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Value not extracted correctly for:[PLACEHOLDER]`,
@@ -549,7 +548,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly);
                 if (!isPlausibleValue) {
-                    logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                    processingLogger_service_1.processingLogger.logWarn(`Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { labToOhtMapper });
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Value is not plausible for:[PLACEHOLDER]`,
@@ -567,7 +566,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
                 if (!isRangeParsedCorrectly) {
-                    logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                    processingLogger_service_1.processingLogger.logWarn(`Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { labToOhtMapper });
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Range not extracted correctly for:[PLACEHOLDER]`,
@@ -624,7 +623,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             measurements.push(measurement);
         }
         else {
-            logger.warn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${filename}`);
+            processingLogger_service_1.processingLogger.logWarn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`);
             labToOhtContract.errorMessages.push({
                 destination: { slack: false, notes: false, bi: true },
                 message: `Created ungroupedBiomarkers for:[PLACEHOLDER]`,

package/dist/service/ohtMeasurementsExtractor.service.js.map

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package/dist/service/ohtReportMeasurementsExtractor.service.d.ts

@@ -148,6 +148,7 @@ type ApplyTransformationRulesResult = {
  * @param ohtCoreApiKey - API key for OHT Core API calls
  * @param partnerId - Partner ID for fetching biomarker mappings and synonym units
  * @param errorMessages - Array to accumulate error messages (modified in-place)
+ * @param isReportPreview - isReportPreview Report Simulator
  * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, parsing status, and transformation errors
  */
 declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, transformationRules: TransformationRulesChains, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, errorMessages: ErrorMessage[]): Promise<{

package/dist/service/ohtReportMeasurementsExtractor.service.js

@@ -40,17 +40,13 @@ exports.ohtReportMeasurementsExtractor = ohtReportMeasurementsExtractor;
 const crypto_1 = __importDefault(require("crypto"));
 const dataUtils_1 = require("../util-ts/dataUtils");
 const extractionUtils_1 = require("../util-ts/extractionUtils");
-const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+const processingLogger_service_1 = require("./processingLogger.service");
 const apiUtils_1 = require("../util-ts/apiUtils");
 const oht_types_1 = require("../types/oht.types");
 const transformationRules_service_1 = require("./transformationRules.service");
 const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
 const path = __importStar(require("path"));
 const fs = __importStar(require("fs"));
-/**
- * Logger instance for the application
- */
-const logger = (0, pinoLogger_1.default)();
 // Import version from package.json file
 // Handle multiple possible paths: compiled (dist/service/), development (service/), or when used as dependency
 function getPackageJsonVersion() {
@@ -70,12 +66,11 @@ function getPackageJsonVersion() {
             }
             catch {
                 // Continue to next path if this one fails
-                continue;
             }
         }
     }
     // Fallback to a default version if package.json cannot be found
-    logger.warn('Could not find package.json, using default version');
+    processingLogger_service_1.processingLogger.logWarn('Could not find package.json, using default version');
     return '0.0.0';
 }
 const ohtCustomParserLibVersion = getPackageJsonVersion();
@@ -117,7 +112,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
     const ohtReport = {
         exams: exams.map(e => e.ohtExam),
     };
-    logger.info({ examsCount: exams.length, chainsCount: transformationRules.size, filename }, 'Applying transformation rules to exams...');
+    processingLogger_service_1.processingLogger.logInfo('Applying transformation rules to exams...', { exams_count: exams.length, chains_count: transformationRules.size, filename });
     let labKeysWithRulesCount = 0;
     let transformedLabKeysCount = 0;
     const applicationErrorMessages = [];
@@ -135,7 +130,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
                 contextJson: reportContext,
             });
             if (result.errors.length > 0) {
-                logger.warn({ labKey, errors: result.errors, filename }, 'Errors applying transformation rule(s) for labKey.');
+                processingLogger_service_1.processingLogger.logWarn('Errors applying transformation rule(s) for labKey.', { labKey, errors: result.errors, filename });
                 applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
                 // Keep original exam when transformation fails
                 transformedExams.push(exam);
@@ -144,7 +139,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
                 if (result.appliedRules.length > 0) {
                     transformedLabKeysCount++;
                 }
-                logger.info({ labKey, appliedRules: result.appliedRules.length, filename }, 'Done applying transformation rule(s) for labKey.');
+                processingLogger_service_1.processingLogger.logInfo('Done applying transformation rule(s) for labKey.', { labKey, applied_rules: result.appliedRules.length, filename });
                 // Preserve the synthetic ID through transformation
                 transformedExams.push({
                     _syntheticId: exam._syntheticId,
@@ -154,19 +149,19 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
             }
         }
         catch (error) {
-            logger.error({ labKey, error, filename }, 'Failed to apply transformation rules for labKey.');
+            processingLogger_service_1.processingLogger.logError('Failed to apply transformation rules for labKey.', error instanceof Error ? error : undefined, { labKey, filename });
             applicationErrorMessages.push(`${labKey}: Unhandled error occurred.`);
             // Keep original exam when transformation throws
             transformedExams.push(exam);
         }
     }
-    logger.info({
+    processingLogger_service_1.processingLogger.logInfo('Done applying the transformation rules to exams.', {
         filename,
-        examsCount: exams.length,
-        chainsCount: transformationRules.size,
-        transformedLabKeysCount,
-        labKeysWithRulesCount,
-    }, 'Done applying the transformation rules to exams.');
+        exams_count: exams.length,
+        chains_count: transformationRules.size,
+        transformed_lab_keys_count: transformedLabKeysCount,
+        lab_keys_with_rules_count: labKeysWithRulesCount,
+    });
     return {
         transformedExams,
         applicationErrorMessages
@@ -312,6 +307,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
  * @param ohtCoreApiKey - API key for OHT Core API calls
  * @param partnerId - Partner ID for fetching biomarker mappings and synonym units
  * @param errorMessages - Array to accumulate error messages (modified in-place)
+ * @param isReportPreview - isReportPreview Report Simulator
  * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, parsing status, and transformation errors
  */
 async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, transformationRules, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, errorMessages) {
@@ -325,8 +321,8 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
     // Check if we have exams
     const labKeys = exams.map(e => e.ohtExam.labKey);
     if (labKeys.length === 0) {
-        const errorMsg = `No lab keys found, filename: ${filename}`;
-        logger.error(errorMsg);
+        const errorMsg = `No lab keys found, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`;
+        processingLogger_service_1.processingLogger.logError(errorMsg);
         errorMessages.push({
             destination: { slack: true, notes: false, bi: false },
             message: errorMsg,
@@ -340,7 +336,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             transformationRulesErrors,
         };
     }
-    logger.info(`Processing lab file with ${labKeys.length} keys, filename: ${filename}`);
+    processingLogger_service_1.processingLogger.logInfo(`Processing lab file with ${labKeys.length} keys, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`);
     // Call getMappedBiomarkers to get the biomarker mapping for the partner and if reportPreview is true, get the latest version regardless of active status
     const mappedBiomarkers = isReportPreview
         ? await (0, dataUtils_1.getMappedBiomarkersLatest)(partnerId, ohtCoreApiKey)
@@ -370,14 +366,14 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             exams.push(emptyExam);
         }
         if (groupedLabKeys.length > 0) {
-            logger.info(`Added ${groupedLabKeys.length} empty OhtExam objects for GROUPED_ biomarkers to check for appended mappings`);
+            processingLogger_service_1.processingLogger.logInfo(`Added ${groupedLabKeys.length} empty OhtExam objects for GROUPED_ biomarkers to check for appended mappings`);
         }
     }
     if (mappedBiomarkers) {
-        logger.info(`Retrieved ${Object.keys(mappedBiomarkers).length} biomarker mappings from backend for partner: ${partnerId}`);
+        processingLogger_service_1.processingLogger.logInfo(`Retrieved ${Object.keys(mappedBiomarkers).length} biomarker mappings from backend for partner: ${partnerId}`);
     }
     else {
-        logger.info(`No biomarker mappings found in backend for partner: ${partnerId}`);
+        processingLogger_service_1.processingLogger.logInfo(`No biomarker mappings found in backend for partner: ${partnerId}`);
     }
     // Assign UUIDs to exams for tracking through transformation.
     // This enables support for duplicate labKeys (double-hits).
@@ -391,10 +387,10 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         transformedExamsResult = await applyTransformationRulesToExams(examsWithIds, transformationRules, patientInfo, documentDate);
     }
     catch (error) {
-        logger.error({ error, filename }, 'Unhandled error while applying transformation rules to exams.');
+        processingLogger_service_1.processingLogger.logError('Unhandled error while applying transformation rules to exams.', error instanceof Error ? error : undefined, { filename });
         errorMessages.push({
             destination: { slack: true, notes: true, bi: false },
-            message: `Failed applying the transformation rules for filename ${filename}. ${error instanceof Error ? error.message : error}`,
+            message: `Failed applying the transformation rules for filename ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}. ${error instanceof Error ? error.message : error}`,
         });
     }
     if (transformedExamsResult.applicationErrorMessages.length > 0) {
@@ -468,7 +464,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         const backendMapping = mappedBiomarkers?.[labKey];
         // Skip processing if biomarker is marked as ignored
         if (backendMapping?.isIgnored === true) {
-            logger.info(`Skipping ignored biomarker: ${labKey}`);
+            processingLogger_service_1.processingLogger.logInfo(`Skipping ignored biomarker: ${labKey}`);
             continue;
         }
         // Handle biomarker id
@@ -484,17 +480,17 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 fallbackValue: backendMapping.annotationConfig?.fallbackValue,
                 separator: backendMapping.annotationConfig?.separator,
             };
-            logger.info(`Using mappings from custom parser studio (oht-core backend) for labKey: ${labKey} (ohtBmId: ${backendMapping.ohtBmId})`);
+            processingLogger_service_1.processingLogger.logInfo(`Using mappings from custom parser studio (oht-core backend) for labKey: ${labKey} (ohtBmId: ${backendMapping.ohtBmId})`);
         }
         else {
-            logger.debug(`No backend mapping found for labKey: ${labKey}, will process as unmapped`);
+            processingLogger_service_1.processingLogger.logDebug(`No backend mapping found for labKey: ${labKey}, will process as unmapped`);
         }
         // Process as mapped biomarker if ohtBmId is valid
         if (finalOhtBmId !== undefined && finalOhtBmId !== -1) {
             let isMeasurementCorrectlyParsed = true;
             // if BM is already in measurements and multiple measurements are not allowed, continue to the next one
             if (!allowMultiMeasurementsPerBiomarker && measurements.some(measurement => measurement.biomarkerId === finalOhtBmId)) {
-                logger.warn({ ohtBmId: finalOhtBmId, labKey }, `Biomarker already in measurements array, should investigate, filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Biomarker already in measurements array, should investigate, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { ohtBmId: finalOhtBmId, labKey });
                 errorMessages.push({
                     destination: { slack: false, notes: false, bi: true },
                     message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
@@ -504,7 +500,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             }
             const ohtBiomarker = biomarkers?.data?.items.find((bm) => bm.id === finalOhtBmId);
             if (!ohtBiomarker) {
-                logger.warn({ ohtBmId: finalOhtBmId, labKey }, `Biomarker not found in API response for ohtBmId: ${finalOhtBmId}, labKey: ${transformedExamObj.labKey}, filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Biomarker not found in API response for ohtBmId: ${finalOhtBmId}, labKey: ${transformedExamObj.labKey}, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { ohtBmId: finalOhtBmId, labKey });
                 errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Biomarker not found for:[PLACEHOLDER]`,
@@ -530,7 +526,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 });
             }
             if (!isUnitParsedCorrectly) {
-                logger.warn({ ohtBmId: finalOhtBmId, labKey }, `Unit not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Unit not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { ohtBmId: finalOhtBmId, labKey });
                 errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Unit not extracted correctly for:[PLACEHOLDER]`,
@@ -540,7 +536,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = (0, extractionUtils_1.ohtReportParseExamValue)(transformedExamObj, ohtBiomarker);
             if (!isValueParsedCorrectly) {
-                logger.warn({ ohtBmId: finalOhtBmId, labKey }, `Value not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Value not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { ohtBmId: finalOhtBmId, labKey });
                 errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Value not extracted correctly for:[PLACEHOLDER]`,
@@ -575,7 +571,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && (0, extractionUtils_1.ohtReportCheckValueForPlausibleValues)(finalOhtBmId, transformedExamObj.labKey, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly, filename);
                 if (!isPlausibleValue) {
-                    logger.warn({ ohtBmId: finalOhtBmId, labKey }, `Value [${numberValue} ${unit}] is not plausible for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${filename}`);
+                    processingLogger_service_1.processingLogger.logWarn(`Value [${numberValue} ${unit}] is not plausible for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { ohtBmId: finalOhtBmId, labKey });
                     errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Value is not plausible for:[PLACEHOLDER]`,
@@ -593,7 +589,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
                 if (!isRangeParsedCorrectly) {
-                    logger.warn({ ohtBmId: finalOhtBmId, labKey }, `Range not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${filename}`);
+                    processingLogger_service_1.processingLogger.logWarn(`Range not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, { ohtBmId: finalOhtBmId, labKey });
                     errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Range not extracted correctly for:[PLACEHOLDER]`,
@@ -686,11 +682,11 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
     // Log summary of processing
     const backendMappedCount = measurements.length;
     const unmappedCount = unknownMeasurements.length;
-    logger.info(`Processing completed for ${filename}:`, {
-        totalLabKeys: labKeys.length,
-        backendMappedBiomarkers: backendMappedCount,
-        unmappedBiomarkers: unmappedCount,
-        totalProcessed: exams.length,
+    processingLogger_service_1.processingLogger.logInfo(`Processing completed for ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}:`, {
+        total_lab_keys: labKeys.length,
+        backend_mapped_biomarkers: backendMappedCount,
+        unmapped_biomarkers: unmappedCount,
+        total_processed: exams.length,
         errors: errorMessages.length,
     });
     return {