npm - @openhealth/oht-custom-parser-lib - Versions diffs - 0.5.16 → 0.5.18 - Mend

@openhealth/oht-custom-parser-lib 0.5.16 → 0.5.18

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 (17) hide show

package/dist/index.d.ts +1 -1
package/dist/index.js.map +1 -1
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.d.ts +12 -7
package/dist/service/ohtReportMeasurementsExtractor.service.js +28 -9
package/dist/service/ohtReportMeasurementsExtractor.service.js.map +1 -1
package/dist/types/oht.types.d.ts +87 -1
package/dist/types/oht.types.js.map +1 -1
package/dist/util-ts/dataUtils.js +0 -5
package/dist/util-ts/dataUtils.js.map +1 -1
package/dist/util-ts/extractionUtils.d.ts +34 -2
package/dist/util-ts/extractionUtils.js +110 -0
package/dist/util-ts/extractionUtils.js.map +1 -1
package/package.json +36 -36
package/readme.md +115 -115

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

@@ -1,5 +1,5 @@
 import { UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
-import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey } from "../types/oht.types";
+import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey, PartnerCustomization } from "../types/oht.types";
 import { ErrorMessage } from "../types/error.types";
 type ExamWithSyntheticId = Exam & {
     _syntheticId: string;
@@ -86,10 +86,13 @@ type ApplyTransformationRulesResult = {
  * - Logs warning and marks measurement as incorrectly parsed if value is not plausible
  *
  * ##### 5.3.7: Extract Reference Ranges (for NUMERICAL biomarkers)
- * - Calls `ohtReportExtractReferenceRanges()` which uses `parseRange()` internally
- * - Extracts min/max normal values based on patient age, sex, and range data
- * - Filters ranges by patient demographics and selects most appropriate range
- * - Logs warning and marks measurement as incorrectly parsed if range extraction fails
+ * - Uses `getEffectiveBiomarkerCompatibility()` combined with
+ *   `getRangeForCompatibility()` to decide if and how to extract ranges
+ *   from `ohtReportExtractReferenceRanges()`/`parseRange()`.
+ * - For internal compatibilities or configured fallbacks, it can return
+ *   null ranges with `isRangeParsedCorrectly = true` (no warnings).
+ * - Only scenarios that require a “real” external range
+ *   (`external_strict` and default modes) produce warnings when extraction fails.
  *
  * ##### 5.3.8: Extract Reference Annotation
  * - Calls `ohtReportExtractReferenceAnnotation()` to extract annotation text
@@ -100,7 +103,8 @@ type ApplyTransformationRulesResult = {
  * - Constructs complete `Measurement` object with all extracted data:
  *   - Biomarker ID, value type, value, alphanumeric value
  *   - Unit, original unit, arbitrary unit flag
- *   - Reference range (min/max normal values)
+ *   - Reference range (min/max normal values), respecting effective
+ *     compatibility (internal vs external, no visual range, alphanumerical, etc.)
  *   - Range annotation
  *   - Material, method
  *   - Collection dates (collectionDate, effectiveDate, examCollectionDate, examEffectiveDate)
@@ -149,9 +153,10 @@ type ApplyTransformationRulesResult = {
  * @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
+ * @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
  * @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<{
+declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, transformationRules: TransformationRulesChains, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, errorMessages: ErrorMessage[], partnerCustomization?: PartnerCustomization): Promise<{
     measurements: Measurement[];
     unknownMeasurements: UnknownMeasurement[];
     unknownUnits: UnknownUnits[];

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

@@ -254,10 +254,13 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
  * - Logs warning and marks measurement as incorrectly parsed if value is not plausible
  *
  * ##### 5.3.7: Extract Reference Ranges (for NUMERICAL biomarkers)
- * - Calls `ohtReportExtractReferenceRanges()` which uses `parseRange()` internally
- * - Extracts min/max normal values based on patient age, sex, and range data
- * - Filters ranges by patient demographics and selects most appropriate range
- * - Logs warning and marks measurement as incorrectly parsed if range extraction fails
+ * - Uses `getEffectiveBiomarkerCompatibility()` combined with
+ *   `getRangeForCompatibility()` to decide if and how to extract ranges
+ *   from `ohtReportExtractReferenceRanges()`/`parseRange()`.
+ * - For internal compatibilities or configured fallbacks, it can return
+ *   null ranges with `isRangeParsedCorrectly = true` (no warnings).
+ * - Only scenarios that require a “real” external range
+ *   (`external_strict` and default modes) produce warnings when extraction fails.
  *
  * ##### 5.3.8: Extract Reference Annotation
  * - Calls `ohtReportExtractReferenceAnnotation()` to extract annotation text
@@ -268,7 +271,8 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
  * - Constructs complete `Measurement` object with all extracted data:
  *   - Biomarker ID, value type, value, alphanumeric value
  *   - Unit, original unit, arbitrary unit flag
- *   - Reference range (min/max normal values)
+ *   - Reference range (min/max normal values), respecting effective
+ *     compatibility (internal vs external, no visual range, alphanumerical, etc.)
  *   - Range annotation
  *   - Material, method
  *   - Collection dates (collectionDate, effectiveDate, examCollectionDate, examEffectiveDate)
@@ -317,9 +321,10 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
  * @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
+ * @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
  * @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) {
+async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, transformationRules, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, errorMessages, partnerCustomization) {
     filename = sourceFilename;
     const measurements = [];
     const unknownMeasurements = [];
@@ -441,11 +446,16 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             synonymUnits = null;
         }
     }
+    // Collect reference range extraction log entries to log once at the end
+    const referenceRangeLogEntries = [];
     // Process each exam directly using the exams with synthetic IDs
     for (const examWithId of examsWithIds) {
         const labKey = examWithId.ohtExam.labKey;
         const examObj = examWithId.ohtExam;
         const originalExam = examWithId.originalExam;
+        // Get the partner customisation for this labKey.
+        const partnerPanelCustomization = partnerCustomization?.panelCustomisation;
+        const partnerReportCustomization = partnerCustomization?.reportCustomisation;
         // Get the transformed exam by synthetic UUID (supports duplicate labKeys)
         const transformedExamWithId = transformedExamsMap.get(examWithId._syntheticId);
         const transformedExamObj = transformedExamWithId ? transformedExamWithId.ohtExam : examObj;
@@ -489,7 +499,6 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 fallbackValue: backendMapping.annotationConfig?.fallbackValue,
                 separator: backendMapping.annotationConfig?.separator,
             };
-            processingLogger_service_1.processingLogger.logInfo(`Using mappings from custom parser studio (oht-core backend) for labKey: ${labKey} (ohtBmId: ${backendMapping.ohtBmId})`);
         }
         else {
             processingLogger_service_1.processingLogger.logDebug(`No backend mapping found for labKey: ${labKey}, will process as unmapped`);
@@ -531,6 +540,10 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             const bmInfo = ohtBiomarker?.acf?.shortName ?
                 `name:${ohtBiomarker.acf.shortName}, bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}` :
                 `bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}`;
+            // Determine effective biomarker compatibility, combining ACF
+            // with reportCustomisation rules when present.
+            const effectiveCompatibility = (0, extractionUtils_1.getEffectiveBiomarkerCompatibility)(ohtBiomarker, partnerPanelCustomization, partnerReportCustomization);
+            // extract the unit
             const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = (0, extractionUtils_1.ohtReportExtractUnit)(transformedExamObj, ohtBiomarker, synonymUnits, partnerId);
             if (unknownUnit.length > 0) {
                 unknownUnits.push({
@@ -610,9 +623,9 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             }
             let from = null, to = null;
             let isRangeParsedCorrectly = true;
-            // If the biomarker is numerical, extract the reference range
+            // Extract reference range respecting biomarker compatibility.
             if ((0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
-                const extractedRange = (0, extractionUtils_1.ohtReportExtractReferenceRanges)(transformedExamObj, patientInfo);
+                const extractedRange = (0, extractionUtils_1.getRangeForCompatibility)(ohtBiomarker, effectiveCompatibility, transformedExamObj, patientInfo, referenceRangeLogEntries);
                 from = extractedRange.from ?? null;
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
@@ -712,6 +725,12 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             unknownMeasurements.push(unknownMeasurement);
         }
     }
+    // Log reference range extraction summary once with all labkeys
+    if (referenceRangeLogEntries.length > 0) {
+        processingLogger_service_1.processingLogger.logInfo('LabKey compatibility list', {
+            labKeyCompatibilityList: referenceRangeLogEntries.map((e) => `processed labkey ${e.labkey} with compatibility ${e.compatibility}`),
+        });
+    }
     // Log summary of processing
     const backendMappedCount = measurements.length;
     const unmappedCount = unknownMeasurements.length;

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

	@@ -1 +1 @@
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package/dist/types/oht.types.d.ts CHANGED Viewed

@@ -16,8 +16,51 @@ export interface OHTPartner {
     reportCustomisation?: ReportCustomisation;
     style: ReportStyleConfig[];
 }
+export type PartnerCustomization = {
+    panelCustomisation?: PartnerCustomPanel;
+    reportCustomisation?: ReportCustomisation;
+};
+/**
+ * Lightweight type describing report rules used by checkOhtBiomarkerCompatibility.
+ *
+ * The current implementation only relies on a subset of fields:
+ * - objectType: must be "BIOMARKER" for biomarker rules
+ * - objectIds: optional list of biomarker IDs (as strings) that the rule applies to
+ * - includeAllObjects: when true, rule applies to all biomarkers of the given objectType
+ * - objectsFilter.compatibility: list of ACF compatibilities that this rule may override
+ * - config.compatibilityOverrideMap: map from current compatibility to the overridden compatibility
+ *
+ * Other properties can exist on the rule object and will be ignored by the compatibility helper.
+ */
+export type BiomarkerReportRule = {
+    /** Type of object the rule targets, e.g. "BIOMARKER" */
+    objectType: string;
+    /** Explicit list of biomarker IDs (as strings) this rule targets */
+    objectIds?: string[];
+    /** When true, rule applies to all objects of the given type */
+    includeAllObjects?: boolean;
+    objectsFilter?: {
+        /**
+         * List of compatibilities from ACF that this rule can override.
+         * Values come from BiomarkerCompatibility but we keep it permissive
+         * to stay forward‑compatible with backend-defined strings.
+         */
+        compatibility?: (BiomarkerCompatibility | string)[];
+    };
+    config?: {
+        /**
+         * Map where the key is the current compatibility and the value
+         * is the compatibility that should be applied.
+         */
+        compatibilityOverrideMap?: Record<string, BiomarkerCompatibility | string>;
+    };
+};
 export type ReportCustomisation = {
-    rules: any[];
+    /**
+     * Ordered list of report rules that can override biomarker compatibility.
+     * Only a subset of the shape is required by the compatibility helper, see BiomarkerReportRule.
+     */
+    rules: BiomarkerReportRule[];
     displaySettings: ReportDisplaySettings;
     enableHistoricalData: boolean;
     enableHistoricalMode: boolean;
@@ -188,6 +231,49 @@ export interface OriginalExam {
     contentType: string;
     exam: string;
 }
+export interface OhtMetadata {
+    /** REQUIRED: Unique identifier for the report/order. Must be a non-empty string. */
+    labOrderId: string;
+    /** REQUIRED: Collection date in ISO 8601 format (2006-01-02T15:04:05.000Z). Must be a non-empty string. */
+    collectionDate: string;
+    /** Exam date */
+    examDate: string;
+    /** Order date */
+    documentDate: string;
+}
+export interface OhtPatient {
+    /** REQUIRED: Patient unique identifier. Must be a non-empty string. */
+    id: string;
+    /** Patient name (PacienteNome) */
+    name: string;
+    /** Patient first name */
+    firstName: string;
+    /** Patient last name */
+    lastName: string;
+    /** Patient birth date (DataNascimento) */
+    birthdate: string;
+    /** REQUIRED: Patient sex/gender. Must be one of: "MALE", "FEMALE", or "OTHER". Case-insensitive. */
+    sex: string;
+    /** Patient gender (alternative field) */
+    gender: string;
+    /** Patient social name */
+    socialName: string;
+    /** Patient email */
+    email: string;
+    /** Patient CPF */
+    cpf: string;
+    /** Patient Document ID */
+    documentId: string;
+    /** Patient address */
+    address: string;
+    /** Patient phone number */
+    phoneNumber: string;
+}
+export interface OhtReport {
+    metadata: OhtMetadata;
+    patient: OhtPatient;
+    exams: Exam[];
+}
 export interface UnmappedLabKey extends UnknownMeasurement {
     jsonBlob?: string;
     labKey?: string;

package/dist/types/oht.types.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;~~AA+OA~~,IAAY,GAIX;AAJD,WAAY,GAAG;IACb,oBAAa,CAAA;IACb,wBAAiB,CAAA;IACjB,sBAAe,CAAA;AACjB,CAAC,EAJW,GAAG,mBAAH,GAAG,QAId;AAED,IAAY,UAGX;AAHD,WAAY,UAAU;IACpB,qDAAuC,CAAA;IACvC,6BAAe,CAAA;AACjB,CAAC,EAHW,UAAU,0BAAV,UAAU,QAGrB;AAED,IAAY,0BAYX;AAZD,WAAY,0BAA0B;IACpC,mDAAqB,CAAA;IACrB,iDAAmB,CAAA;IACnB,uDAAyB,CAAA;IACzB,uDAAyB,CAAA;IACzB,qDAAuB,CAAA;IACvB,qDAAuB,CAAA;IACvB,6CAAe,CAAA;IACf,iDAAmB,CAAA;IACnB,mDAAqB,CAAA;IACrB,mDAAqB,CAAA;IACrB,2DAA6B,CAAA;AAC/B,CAAC,EAZW,0BAA0B,0CAA1B,0BAA0B,QAYrC;AAED,IAAY,kBAGX;AAHD,WAAY,kBAAkB;IAC5B,uDAAiC,CAAA;IACjC,6CAAuB,CAAA;AACzB,CAAC,EAHW,kBAAkB,kCAAlB,kBAAkB,QAG7B;AAED,IAAY,0BAIX;AAJD,WAAY,0BAA0B;IACpC,6CAAe,CAAA;IACf,2DAA6B,CAAA;IAC7B,qDAAuB,CAAA;AACzB,CAAC,EAJW,0BAA0B,0CAA1B,0BAA0B,QAIrC;AAED,IAAY,kBAOX;AAPD,WAAY,kBAAkB;IAC5B,yCAAmB,CAAA;IACnB,yCAAmB,CAAA;IACnB,+CAAyB,CAAA;IACzB,mCAAa,CAAA;IACb,qCAAe,CAAA;IACf,2CAAqB,CAAA;AACvB,CAAC,EAPW,kBAAkB,kCAAlB,kBAAkB,QAO7B;AAED,IAAY,YASX;AATD,WAAY,YAAY;IACtB,6CAA6B,CAAA;IAC7B,mDAAmC,CAAA;IACnC,yDAAyC,CAAA;IACzC,2DAA2C,CAAA;IAC3C,2DAA2C,CAAA;IAC3C,+DAA+C,CAAA;IAC/C,2DAA2C,CAAA;IAC3C,mDAAmC,CAAA;AACrC,CAAC,EATW,YAAY,4BAAZ,YAAY,QASvB;AAED,IAAY,YAoBX;AApBD,WAAY,YAAY;IACtB,mFAAmE,CAAA;IACnE,uDAAuC,CAAA;IACvC,+DAA+C,CAAA;IAC/C,mDAAmC,CAAA;IACnC,iEAAiD,CAAA;IACjD,uDAAuC,CAAA;IACvC,uDAAuC,CAAA;IACvC,6DAA6C,CAAA;IAC7C,2EAA2D,CAAA;IAC3D,2DAA2C,CAAA;IAC3C,uEAAuD,CAAA;IACvD,yDAAyC,CAAA;IACzC,uEAAuD,CAAA;IACvD,iEAAiD,CAAA;IACjD,oHAAoG,CAAA;IACpG,wFAAwF;IACxF,uEAAuD,CAAA;IACvD,gGAAgG;IAChG,6HAA6G,CAAA;AAC/G,CAAC,EApBW,YAAY,4BAAZ,YAAY,QAoBvB;AA6CD,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,+BAAe,CAAA;IACf,iCAAiB,CAAA;IACjB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,4BAAZ,YAAY,QAIvB;AAsCD,IAAY,kBAIX;AAJD,WAAY,kBAAkB;IAC5B,6CAAuB,CAAA;IACvB,2CAAqB,CAAA;IACrB,uDAAiC,CAAA;AACnC,CAAC,EAJW,kBAAkB,kCAAlB,kBAAkB,QAI7B;AAED,IAAY,sBAOX;AAPD,WAAY,sBAAsB;IAChC,+CAAqB,CAAA;IACrB,+CAAqB,CAAA;IACrB,4EAAkD,CAAA;IAClD,4EAAkD,CAAA;IAClD,4DAAkC,CAAA;IAClC,2CAAiB,CAAA;AACnB,CAAC,EAPW,sBAAsB,sCAAtB,sBAAsB,QAOjC;AAED,IAAY,WAGX;AAHD,WAAY,WAAW;IACrB,wBAAS,CAAA;IACT,sCAAuB,CAAA;AACzB,CAAC,EAHW,WAAW,2BAAX,WAAW,QAGtB;AAED,IAAY,kCAGX;AAHD,WAAY,kCAAkC;IAC5C,6DAAuB,CAAA;IACvB,iEAA2B,CAAA;AAC7B,CAAC,EAHW,kCAAkC,kDAAlC,kCAAkC,QAG7C;AAED,IAAY,gCAMX;AAND,WAAY,gCAAgC;IAC1C,2DAAuB,CAAA;IACvB,6EAAyC,CAAA;IACzC,+EAA2C,CAAA;IAC3C,2FAAuD,CAAA;IACvD,uFAAmD,CAAA;AACrD,CAAC,EANW,gCAAgC,gDAAhC,gCAAgC,QAM3C"}
1	+ {"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;AAgVA,IAAY,GAIX;AAJD,WAAY,GAAG;IACb,oBAAa,CAAA;IACb,wBAAiB,CAAA;IACjB,sBAAe,CAAA;AACjB,CAAC,EAJW,GAAG,mBAAH,GAAG,QAId;AAED,IAAY,UAGX;AAHD,WAAY,UAAU;IACpB,qDAAuC,CAAA;IACvC,6BAAe,CAAA;AACjB,CAAC,EAHW,UAAU,0BAAV,UAAU,QAGrB;AAED,IAAY,0BAYX;AAZD,WAAY,0BAA0B;IACpC,mDAAqB,CAAA;IACrB,iDAAmB,CAAA;IACnB,uDAAyB,CAAA;IACzB,uDAAyB,CAAA;IACzB,qDAAuB,CAAA;IACvB,qDAAuB,CAAA;IACvB,6CAAe,CAAA;IACf,iDAAmB,CAAA;IACnB,mDAAqB,CAAA;IACrB,mDAAqB,CAAA;IACrB,2DAA6B,CAAA;AAC/B,CAAC,EAZW,0BAA0B,0CAA1B,0BAA0B,QAYrC;AAED,IAAY,kBAGX;AAHD,WAAY,kBAAkB;IAC5B,uDAAiC,CAAA;IACjC,6CAAuB,CAAA;AACzB,CAAC,EAHW,kBAAkB,kCAAlB,kBAAkB,QAG7B;AAED,IAAY,0BAIX;AAJD,WAAY,0BAA0B;IACpC,6CAAe,CAAA;IACf,2DAA6B,CAAA;IAC7B,qDAAuB,CAAA;AACzB,CAAC,EAJW,0BAA0B,0CAA1B,0BAA0B,QAIrC;AAED,IAAY,kBAOX;AAPD,WAAY,kBAAkB;IAC5B,yCAAmB,CAAA;IACnB,yCAAmB,CAAA;IACnB,+CAAyB,CAAA;IACzB,mCAAa,CAAA;IACb,qCAAe,CAAA;IACf,2CAAqB,CAAA;AACvB,CAAC,EAPW,kBAAkB,kCAAlB,kBAAkB,QAO7B;AAED,IAAY,YASX;AATD,WAAY,YAAY;IACtB,6CAA6B,CAAA;IAC7B,mDAAmC,CAAA;IACnC,yDAAyC,CAAA;IACzC,2DAA2C,CAAA;IAC3C,2DAA2C,CAAA;IAC3C,+DAA+C,CAAA;IAC/C,2DAA2C,CAAA;IAC3C,mDAAmC,CAAA;AACrC,CAAC,EATW,YAAY,4BAAZ,YAAY,QASvB;AAED,IAAY,YAoBX;AApBD,WAAY,YAAY;IACtB,mFAAmE,CAAA;IACnE,uDAAuC,CAAA;IACvC,+DAA+C,CAAA;IAC/C,mDAAmC,CAAA;IACnC,iEAAiD,CAAA;IACjD,uDAAuC,CAAA;IACvC,uDAAuC,CAAA;IACvC,6DAA6C,CAAA;IAC7C,2EAA2D,CAAA;IAC3D,2DAA2C,CAAA;IAC3C,uEAAuD,CAAA;IACvD,yDAAyC,CAAA;IACzC,uEAAuD,CAAA;IACvD,iEAAiD,CAAA;IACjD,oHAAoG,CAAA;IACpG,wFAAwF;IACxF,uEAAuD,CAAA;IACvD,gGAAgG;IAChG,6HAA6G,CAAA;AAC/G,CAAC,EApBW,YAAY,4BAAZ,YAAY,QAoBvB;AA6CD,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,+BAAe,CAAA;IACf,iCAAiB,CAAA;IACjB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,4BAAZ,YAAY,QAIvB;AAsCD,IAAY,kBAIX;AAJD,WAAY,kBAAkB;IAC5B,6CAAuB,CAAA;IACvB,2CAAqB,CAAA;IACrB,uDAAiC,CAAA;AACnC,CAAC,EAJW,kBAAkB,kCAAlB,kBAAkB,QAI7B;AAED,IAAY,sBAOX;AAPD,WAAY,sBAAsB;IAChC,+CAAqB,CAAA;IACrB,+CAAqB,CAAA;IACrB,4EAAkD,CAAA;IAClD,4EAAkD,CAAA;IAClD,4DAAkC,CAAA;IAClC,2CAAiB,CAAA;AACnB,CAAC,EAPW,sBAAsB,sCAAtB,sBAAsB,QAOjC;AAED,IAAY,WAGX;AAHD,WAAY,WAAW;IACrB,wBAAS,CAAA;IACT,sCAAuB,CAAA;AACzB,CAAC,EAHW,WAAW,2BAAX,WAAW,QAGtB;AAED,IAAY,kCAGX;AAHD,WAAY,kCAAkC;IAC5C,6DAAuB,CAAA;IACvB,iEAA2B,CAAA;AAC7B,CAAC,EAHW,kCAAkC,kDAAlC,kCAAkC,QAG7C;AAED,IAAY,gCAMX;AAND,WAAY,gCAAgC;IAC1C,2DAAuB,CAAA;IACvB,6EAAyC,CAAA;IACzC,+EAA2C,CAAA;IAC3C,2FAAuD,CAAA;IACvD,uFAAmD,CAAA;AACrD,CAAC,EANW,gCAAgC,gDAAhC,gCAAgC,QAM3C"}

package/dist/util-ts/dataUtils.js CHANGED Viewed

@@ -178,27 +178,22 @@ function processAppendedMappings(exams, labKeys, filename, annotationConfig) {
     }
     // Use request-scoped fileName so log message and structured context (file_name, file_upload_id) always match; avoids cross-request leakage under concurrency.
     const filenameForLogging = (0, processingLogger_service_1.getRequestScopedFilename)(filename);
-    processingLogger_service_1.processingLogger.logInfo(`Processing appended mapping with ${labKeys.length} additional labKeys. filename: ${filenameForLogging}`);
     const allExtractedValues = [];
     const labKeyResults = [];
     for (const additionalLabKey of labKeys) {
-        processingLogger_service_1.processingLogger.logInfo(`Processing labKey: ${additionalLabKey.labKey}, filename: ${filenameForLogging}`);
         // First try: Find exam by direct labKey match
         let exam = exams.find(exam => exam?.labKey === additionalLabKey.labKey ||
             exam?.ohtExam?.labKey === additionalLabKey.labKey);
         let examData = null;
         if (exam) {
-            processingLogger_service_1.processingLogger.logInfo(`Found exam by direct labKey match for: ${additionalLabKey.labKey}`);
             // Use ohtExam data if available, otherwise use exam directly
             examData = exam.ohtExam || exam;
         }
         else {
-            processingLogger_service_1.processingLogger.logInfo(`Direct labKey not found, trying complex search for: ${additionalLabKey.labKey}`);
             // Second try: labKey search for "labKeyFirstHalf:labKeySecondHalf" format
             examData = findExamByLabKey(exams, additionalLabKey.labKey);
             if (!examData)
                 continue;
-            processingLogger_service_1.processingLogger.logInfo(`Found exam by complex search for: ${additionalLabKey.labKey}`);
         }
         const parts = [];
         // Process each extraction path

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

	@@ -1 +1 @@
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package/dist/util-ts/extractionUtils.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import { RangeExtractionResponse, SynonymUnit } from "../types/custom-parser.types";
-import { AnnotationLabKey, BackendBiomarkerMapping, OhtExam, PatientInfo, Biomarker, BiomarkerValueType, MeasurementValueComparator, AnnotationConfig, Exam } from "../types/oht.types";
+import { AnnotationLabKey, BackendBiomarkerMapping, OhtExam, PatientInfo, Biomarker, BiomarkerValueType, MeasurementValueComparator, AnnotationConfig, Exam, ReportCustomisation, PartnerCustomPanel, BiomarkerCompatibility } from "../types/oht.types";
 /**
  * Default range parsing function that extracts range information from exam data
  * @param exam - The OHT exam object containing range information
@@ -49,6 +49,37 @@ declare function ohtReportExtractReferenceAnnotation(annotationConfig: Annotatio
  * Always uses parseRange function from extractionUtils for range extraction
  */
 declare function ohtReportExtractReferenceRanges(ohtExam: OhtExam, patientInfo: PatientInfo): RangeExtractionResponse;
+/**
+ * Computes the effective compatibility for a biomarker, taking into account
+ * report customisation rules when present and falling back to the ACF
+ * compatibility when there are no applicable rules.
+ *
+ * This is a thin wrapper around checkOhtBiomarkerCompatibility that:
+ * - Uses reportCustomisation rules if present
+ * - Falls back to ohtBiomarker.acf.compatibility when rules are absent
+ */
+declare function getEffectiveBiomarkerCompatibility(ohtBiomarker: Biomarker, panelCustomisation?: PartnerCustomPanel, reportCustomisation?: ReportCustomisation): BiomarkerCompatibility | undefined;
+/**
+ * Centralizes reference range selection according to the biomarker's
+ * effective compatibility.
+ *
+ * Main rules:
+ * - external_strict: uses ohtReportExtractReferenceRanges; parse failures keep
+ *   isRangeParsedCorrectly = false (warnings are generated as today).
+ * - external / external_no_visual_range: tries ohtReportExtractReferenceRanges;
+ *   if it fails, returns { null, null, true } (no warnings, no parse error).
+ * - internal: never extracts an external range; always returns { null, null, true }.
+ * - external_alphanumerical: does not extract ranges or call parseRange;
+ *   always returns { null, null, true }.
+ * - custom / undefined / others: keeps current behaviour, calling
+ *   ohtReportExtractReferenceRanges once and respecting its
+ *   isRangeParsedCorrectly value.
+ */
+export type ReferenceRangeLogEntry = {
+    labkey: string;
+    compatibility: string;
+};
+declare function getRangeForCompatibility(ohtBiomarker: Biomarker, compatibility: BiomarkerCompatibility | undefined, ohtExam: OhtExam, patientInfo: PatientInfo, logEntries?: ReferenceRangeLogEntry[]): RangeExtractionResponse;
 declare function ohtReportExtractValueFromGreaterLowerThan(value: string): {
     extractedValue: number | null;
     extractedValueComparator: MeasurementValueComparator | null;
@@ -66,4 +97,5 @@ declare function ohtReportParseExamValue(ohtExam: OhtExam, ohtBiomarker: Biomark
     isValueParsedCorrectly: boolean;
 };
 declare function ohtReportCheckValueForPlausibleValues(ohtBmId: number, labKey: string, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean, filename: string): boolean;
-export { parseRange, handleBiomarkerId, ohtReportExtractUnit, ohtReportExtractReferenceAnnotation, ohtReportExtractReferenceRanges, ohtReportExtractValueFromGreaterLowerThan, ohtReportParseExamValue, ohtReportCheckValueForPlausibleValues, };
+declare function checkOhtBiomarkerCompatibility(ohtBiomarker: Biomarker, panelCustomisation?: PartnerCustomPanel, reportCustomisation?: ReportCustomisation): BiomarkerCompatibility | undefined;
+export { parseRange, handleBiomarkerId, ohtReportExtractUnit, ohtReportExtractReferenceAnnotation, ohtReportExtractReferenceRanges, ohtReportExtractValueFromGreaterLowerThan, ohtReportParseExamValue, ohtReportCheckValueForPlausibleValues, checkOhtBiomarkerCompatibility, getEffectiveBiomarkerCompatibility, getRangeForCompatibility, };

package/dist/util-ts/extractionUtils.js CHANGED Viewed

@@ -11,6 +11,9 @@ exports.ohtReportExtractReferenceRanges = ohtReportExtractReferenceRanges;
 exports.ohtReportExtractValueFromGreaterLowerThan = ohtReportExtractValueFromGreaterLowerThan;
 exports.ohtReportParseExamValue = ohtReportParseExamValue;
 exports.ohtReportCheckValueForPlausibleValues = ohtReportCheckValueForPlausibleValues;
+exports.checkOhtBiomarkerCompatibility = checkOhtBiomarkerCompatibility;
+exports.getEffectiveBiomarkerCompatibility = getEffectiveBiomarkerCompatibility;
+exports.getRangeForCompatibility = getRangeForCompatibility;
 const oht_types_1 = require("../types/oht.types");
 const moment_1 = __importDefault(require("moment"));
 const processingLogger_service_1 = require("../service/processingLogger.service");
@@ -537,6 +540,68 @@ function ohtReportExtractReferenceRanges(ohtExam, patientInfo) {
     }
     return nullRangeNotParsedCorrectly;
 }
+/**
+ * Computes the effective compatibility for a biomarker, taking into account
+ * report customisation rules when present and falling back to the ACF
+ * compatibility when there are no applicable rules.
+ *
+ * This is a thin wrapper around checkOhtBiomarkerCompatibility that:
+ * - Uses reportCustomisation rules if present
+ * - Falls back to ohtBiomarker.acf.compatibility when rules are absent
+ */
+function getEffectiveBiomarkerCompatibility(ohtBiomarker, panelCustomisation, reportCustomisation) {
+    const compatibilityFromRules = checkOhtBiomarkerCompatibility(ohtBiomarker, panelCustomisation, reportCustomisation);
+    return compatibilityFromRules ?? ohtBiomarker.acf?.compatibility;
+}
+function getRangeForCompatibility(ohtBiomarker, compatibility, ohtExam, patientInfo, logEntries) {
+    const nullRangeTrue = {
+        from: null,
+        to: null,
+        isRangeParsedCorrectly: true,
+    };
+    const nullRangeFalse = {
+        from: null,
+        to: null,
+        isRangeParsedCorrectly: false,
+    };
+    if (logEntries) {
+        logEntries.push({
+            labkey: ohtExam.labKey ?? '',
+            compatibility: compatibility ?? 'undefined',
+        });
+    }
+    // external_alphanumerical: forces alphanumerical behaviour, never extracts a range
+    if (compatibility === oht_types_1.BiomarkerCompatibility.ExternalAlphanumerical) {
+        return nullRangeTrue;
+    }
+    // If the biomarker is not numerical, we should not extract a range
+    if (!(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
+        return nullRangeTrue;
+    }
+    switch (compatibility) {
+        case oht_types_1.BiomarkerCompatibility.Internal:
+        case oht_types_1.BiomarkerCompatibility.External:
+        case oht_types_1.BiomarkerCompatibility.ExternalNoVisualRange: {
+            const extracted = ohtReportExtractReferenceRanges(ohtExam, patientInfo);
+            if (extracted.isRangeParsedCorrectly) {
+                return extracted;
+            }
+            // Internal fallback: do not call parseRange again, just clear the range
+            // and keep isRangeParsedCorrectly = true to avoid warnings.
+            return nullRangeTrue;
+        }
+        case oht_types_1.BiomarkerCompatibility.ExternalStrict: {
+            const extracted = ohtReportExtractReferenceRanges(ohtExam, patientInfo);
+            // Strict behaviour: if extraction fails, we keep the error.
+            return extracted.isRangeParsedCorrectly ? extracted : nullRangeFalse;
+        }
+        case oht_types_1.BiomarkerCompatibility.Custom:
+        default: {
+            // Default/custom behaviour: keep the current extraction logic
+            return ohtReportExtractReferenceRanges(ohtExam, patientInfo);
+        }
+    }
+}
 function ohtReportExtractValueFromGreaterLowerThan(value) {
     // Checks first if any greater than pattern is present
     const greaterThanPatterns = getGreaterThanPatternsLocal(); // TODO: CAN USE THE SAME PATTERNS AS PARSE RANGE FUNCTION?
@@ -672,4 +737,49 @@ function ohtReportCheckValueForPlausibleValues(ohtBmId, labKey, ohtBiomarker, un
     }
     return isPlausibleValue;
 }
+function checkOhtBiomarkerCompatibility(ohtBiomarker, panelCustomisation, reportCustomisation) {
+    const biomarkerId = ohtBiomarker.id;
+    const biomarkerAcfCompatibility = ohtBiomarker.acf?.compatibility;
+    // If no ACF compatibility, return undefined
+    if (!biomarkerAcfCompatibility) {
+        return undefined;
+    }
+    // If no rules exist, return ACF compatibility
+    if (!reportCustomisation?.rules || reportCustomisation.rules.length === 0) {
+        return biomarkerAcfCompatibility;
+    }
+    // Convert biomarkerId to string for comparison (objectIds are strings in the rules)
+    const biomarkerIdString = String(biomarkerId);
+    // Helper function to apply compatibility override map
+    const applyOverrideMap = (compatibility, overrideMap) => {
+        if (overrideMap && overrideMap[compatibility]) {
+            // Cast to BiomarkerCompatibility as override map values might be custom strings
+            return overrideMap[compatibility];
+        }
+        return compatibility;
+    };
+    // Start with ACF compatibility - this will be modified by applying rules in sequence
+    let currentCompatibility = biomarkerAcfCompatibility;
+    // 1. Apply all specific rules where objectIds contains the biomarkerId (in order)
+    const specificRules = reportCustomisation.rules.filter(rule => rule.objectType === "BIOMARKER" &&
+        rule.objectIds?.includes(biomarkerIdString));
+    for (const rule of specificRules) {
+        const overrideMap = rule.config?.compatibilityOverrideMap;
+        currentCompatibility = applyOverrideMap(currentCompatibility, overrideMap);
+    }
+    // 2. Apply all general rules with includeAllObjects: true (in order)
+    // Check if objectsFilter.compatibility includes the original ACF compatibility
+    const generalRules = reportCustomisation.rules.filter(rule => rule.objectType === "BIOMARKER" &&
+        rule.includeAllObjects === true);
+    for (const rule of generalRules) {
+        const filterCompatibility = rule.objectsFilter?.compatibility;
+        // Check if the filter includes the original ACF compatibility
+        if (Array.isArray(filterCompatibility) && filterCompatibility.includes(biomarkerAcfCompatibility)) {
+            const overrideMap = rule.config?.compatibilityOverrideMap;
+            currentCompatibility = applyOverrideMap(currentCompatibility, overrideMap);
+        }
+    }
+    // Return the final compatibility after applying all rules in sequence
+    return currentCompatibility;
+}
 //# sourceMappingURL=extractionUtils.js.map