npm - @openhealth/oht-custom-parser-lib - Versions diffs - 0.5.42 → 0.5.45 - Mend

@openhealth/oht-custom-parser-lib 0.5.42 → 0.5.45

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.

Files changed (9) hide show

package/dist/service/ohtAgnosticMeasurementsExtractor.service.d.ts +59 -0
package/dist/service/ohtAgnosticMeasurementsExtractor.service.js +603 -0
package/dist/service/ohtAgnosticMeasurementsExtractor.service.js.map +1 -0
package/dist/service/ohtReportMeasurementsExtractor.service.js +51 -16
package/dist/service/ohtReportMeasurementsExtractor.service.js.map +1 -1
package/dist/service/reportCreator.service.js +4 -45
package/dist/service/reportCreator.service.js.map +1 -1
package/package.json +40 -40
package/readme.md +115 -115

package/dist/service/ohtAgnosticMeasurementsExtractor.service.js.map ADDED Viewed

@@ -0,0 +1 @@

+ 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package/dist/service/ohtReportMeasurementsExtractor.service.js CHANGED Viewed

@@ -572,20 +572,6 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 isMeasurementCorrectlyParsed = false;
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = (0, extractionUtils_1.ohtReportParseExamValue)(transformedExamObj, ohtBiomarker);
-            if (!isValueParsedCorrectly) {
-                processingLogger_service_1.processingLogger.addWarning(`Value not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, 'extract_measurements', {
-                    warningType: 'value_extraction_failed',
-                    warningCategory: 'measurements',
-                    warningSeverity: 'degraded',
-                    data: { ohtBmId: finalOhtBmId, labKey },
-                });
-                errorMessages.push({
-                    destination: { slack: true, notes: true, bi: true },
-                    message: `Value not extracted correctly for:[PLACEHOLDER]`,
-                    item: `${bmInfo}`
-                });
-                isMeasurementCorrectlyParsed = false;
-            }
             if ((0, dataUtils_1.isNumericalWithoutValidResult)(valueType, numberValue, alphanumericalValue)) {
                 const alphanumericalValueTrimmed = alphanumericalValue?.trim() ?? '';
                 const unknownMeasurement = {
@@ -609,16 +595,65 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 unknownMeasurements.push(unknownMeasurement);
                 continue;
             }
+            if (!isValueParsedCorrectly) {
+                processingLogger_service_1.processingLogger.addWarning(`Value not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, 'extract_measurements', {
+                    warningType: 'value_extraction_failed',
+                    warningCategory: 'measurements',
+                    warningSeverity: 'degraded',
+                    data: { ohtBmId: finalOhtBmId, labKey },
+                });
+                errorMessages.push({
+                    destination: { slack: true, notes: true, bi: true },
+                    message: `Value not extracted correctly for:[PLACEHOLDER]`,
+                    item: `${bmInfo}`
+                });
+                isMeasurementCorrectlyParsed = false;
+            }
             // Check if the value is plausible
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && (0, extractionUtils_1.ohtReportCheckValueForPlausibleValues)(finalOhtBmId, transformedExamObj.labKey, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly, filename);
                 if (!isPlausibleValue) {
                     errorMessages.push({
-                        destination: { slack: true, notes: true, bi: true },
+                        destination: { slack: false, notes: true, bi: true },
                         message: `Value is not plausible for:[PLACEHOLDER]`,
                         item: `${bmInfo}, value:${numberValue}${unit}`
                     });
-                    isMeasurementCorrectlyParsed = false;
+                    // Resolve name with fallbacks
+                    const implausibleName = transformedExamObj.examName ||
+                        transformedExamObj.mnemonic ||
+                        transformedExamObj.description ||
+                        '';
+                    // Extract range inline (no error reporting) to include in annotation
+                    const implausibleAnnotationParts = [];
+                    if (transformedExamObj.annotation) {
+                        implausibleAnnotationParts.push(transformedExamObj.annotation);
+                    }
+                    if ((0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
+                        const implausibleRange = (0, extractionUtils_1.getRangeForCompatibility)(ohtBiomarker, effectiveCompatibility, transformedExamObj, patientInfo, referenceRangeLogEntries);
+                        const implausibleFrom = implausibleRange.from ?? null;
+                        const implausibleTo = implausibleRange.to ?? null;
+                        if (implausibleFrom !== null || implausibleTo !== null) {
+                            implausibleAnnotationParts.push(`Report.OHTStudio.UngroupedImplausibleRange ${implausibleFrom ?? 'n/a'} - ${implausibleTo ?? 'n/a'}`);
+                        }
+                    }
+                    implausibleAnnotationParts.push('Report.OHTStudio.UngroupedImplausibleAnnotation');
+                    const implausibleUnknownMeasurement = {
+                        biomarkerName: implausibleName,
+                        value: transformedExamObj.value || String(numberValue) || '',
+                        unit: unit ?? '',
+                        annotation: implausibleAnnotationParts.join('\n'),
+                        dataOrigin: [{
+                                itemExtracted: 'measurement',
+                                method: 'custom-parser',
+                                methodVersion: `oht-custom-parser-lib-v${ohtCustomParserLibVersion}`,
+                                path: 'exams',
+                            }],
+                        originalName: transformedExamObj.examName || labKey.split(':')[1] || '',
+                        originalExam: originalExam ? originalExam : undefined,
+                        ohtExam: transformedExamObj,
+                    };
+                    unknownMeasurements.push(implausibleUnknownMeasurement);
+                    continue;
                 }
             }
             let from = null, to = null;

package/dist/service/ohtReportMeasurementsExtractor.service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/service/reportCreator.service.js CHANGED Viewed

@@ -10,7 +10,6 @@ const processingLogger_service_1 = require("./processingLogger.service");
 const dotenv_1 = __importDefault(require("dotenv"));
 const dataUtils_1 = require("../util-ts/dataUtils");
 const apiUtils_1 = require("../util-ts/apiUtils");
-const errorHandling_service_1 = require("./errorHandling.service");
 dotenv_1.default.config({ path: `.env.local` });
 const OHT_CORE_URL = process.env.OHT_CORE_URL;
 /**
@@ -147,9 +146,8 @@ async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasu
         // - Handle LabOrderID version deprecation (if labOrderId is present)
         // - Set status to READY
         // - Trigger all notifications and webhooks
-        // OHT Core `fileuploadspubsub.IngestionMessage` (see oht-core pkg/fileuploads/pubsub/message.go).
-        // Minimal `userToken`: core uses userId → LoggedUserID; audit uses id, partnerId (TenantID).
-        const ingestionBody = {
+        // Use ingestion endpoint - handles report creation and READY status automatically
+        const ingestionResponse = await (0, apiUtils_1.makeApiCallWithRetry)('patch', ohtCoreIngestionUrl, {
             ...dataImportFileUpload,
             status: patchStatus,
             rejectReason,
@@ -157,47 +155,8 @@ async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasu
                 ...dataImportFileUpload.digitalization,
                 pipelineStep: oht_types_1.PipelineStep.SENDING_RESULTS,
             },
-        };
-        const ingestionMessage = {
-            schemaVersion: 1,
-            dataImportFileUploadId: dataImportFileUpload.id,
-            body: ingestionBody,
-            userToken: {
-                id: ownerUserId,
-                userId: ownerUserId,
-                partnerId: dataImportFileUpload.partnerId,
-            },
-        };
-        // const ingestionResponse = await makeApiCallWithRetry(
-        //   'patch',
-        //   ohtCoreIngestionUrl,
-        //   ingestionBody,
-        //   ohtCoreApiKey
-        // );
-        // processingLogger.logInfo(
-        //   `Resp: PATCH ingestion status: ${patchStatus} ${ohtCoreIngestionUrl}, filename: ${filename}`,
-        //   { response: ingestionResponse.data }
-        // );
-        const pubsubIngestionTopic = process.env.PUBSUB_FILE_UPLOADS_INGESTION_TOPIC ?? '';
-        const pubsubProjectId = process.env.PUBSUB_FILE_UPLOADS_INGESTION_PROJECT_ID ?? '';
-        if (pubsubIngestionTopic && pubsubProjectId) {
-            if (!dataImportFileUpload.id?.trim()) {
-                processingLogger_service_1.processingLogger.logError(`Pub/Sub: skipping file-uploads ingestion publish — missing dataImportFileUpload.id, filename: ${filename}`, undefined, { topic: pubsubIngestionTopic });
-            }
-            else {
-                try {
-                    await (0, errorHandling_service_1.publishToTopic)(pubsubIngestionTopic, Buffer.from(JSON.stringify(ingestionMessage), 'utf8'), pubsubProjectId);
-                    processingLogger_service_1.processingLogger.logInfo(`Pub/Sub: published file-uploads ingestion message, topic: ${pubsubIngestionTopic}, filename: ${filename}`, { file_upload_id: dataImportFileUpload.id });
-                }
-                catch (pubsubError) {
-                    processingLogger_service_1.processingLogger.logError(`Pub/Sub: failed to publish file-uploads ingestion message, filename: ${filename}`, pubsubError instanceof Error ? pubsubError : undefined, {
-                        file_upload_id: dataImportFileUpload.id,
-                        topic: pubsubIngestionTopic,
-                        error_details: (0, apiUtils_1.parseErrorObj)(pubsubError),
-                    });
-                }
-            }
-        }
+        }, ohtCoreApiKey);
+        processingLogger_service_1.processingLogger.logInfo(`Resp: PATCH ingestion status: ${patchStatus} ${ohtCoreIngestionUrl}, filename: ${filename}`, { response: ingestionResponse.data });
         // Return null since ingestion is asynchronous and we don't have the updated file upload object
         // The caller should not rely on the returned value for status checking
         return null;

package/dist/service/reportCreator.service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/package.json CHANGED Viewed

@@ -1,40 +1,40 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.42",
-  "description": "Shared nodejs lib with with reusable functions",
-  "main": "dist/index.js",
-  "types": "dist/index.d.ts",
-  "files": [
-    "/dist"
-  ],
-  "scripts": {
-    "test": "jest"
-  },
-  "keywords": [],
-  "author": "",
-  "license": "ISC",
-  "dependencies": {
-    "@google-cloud/pubsub": "^4.10.0",
-    "@google-cloud/storage": "^7.7.0",
-    "axios": "^1.13.2",
-    "bottleneck": "^2.19.5",
-    "csv-parse": "^6.2.1",
-    "dayjs": "^1.11.13",
-    "dotenv": "^16.4.5",
-    "jsonata": "^2.1.0",
-    "moment": "^2.30.1",
-    "mongodb": "^6.3.0",
-    "pino": "^8.19.0",
-    "pino-pretty": "^11.3.0",
-    "xml2js": "^0.6.2"
-  },
-  "devDependencies": {
-    "@types/jest": "^29.5.14",
-    "@types/xml2js": "^0.4.14",
-    "axios-mock-adapter": "^2.1.0",
-    "jest": "^29.7.0",
-    "ts-jest": "^29.2.5",
-    "tsx": "^4.19.2",
-    "typescript": "^5.0.0"
-  }
-}
+{
+  "name": "@openhealth/oht-custom-parser-lib",
+  "version": "0.5.45",
+  "description": "Shared nodejs lib with with reusable functions",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "/dist"
+  ],
+  "scripts": {
+    "test": "jest"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "dependencies": {
+    "@google-cloud/pubsub": "^4.10.0",
+    "@google-cloud/storage": "^7.7.0",
+    "axios": "^1.13.2",
+    "bottleneck": "^2.19.5",
+    "csv-parse": "^6.2.1",
+    "dayjs": "^1.11.13",
+    "dotenv": "^16.4.5",
+    "jsonata": "^2.1.0",
+    "moment": "^2.30.1",
+    "mongodb": "^6.3.0",
+    "pino": "^8.19.0",
+    "pino-pretty": "^11.3.0",
+    "xml2js": "^0.6.2"
+  },
+  "devDependencies": {
+    "@types/jest": "^29.5.14",
+    "@types/xml2js": "^0.4.14",
+    "axios-mock-adapter": "^2.1.0",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.2.5",
+    "tsx": "^4.19.2",
+    "typescript": "^5.0.0"
+  }
+}