@openhealth/oht-custom-parser-lib 0.5.15 → 0.5.16

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

@@ -1 +1 @@
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package/dist/service/slackMessages.service.js

@@ -85,7 +85,14 @@ async function sendMessageToSlack(payload) {
         }
     }
     catch (error) {
-        processingLogger_service_1.processingLogger.addWarning(`Error sending message to Slack (error=${error instanceof Error ? error.message : String(error)})`, 'slack_message_sending');
+        processingLogger_service_1.processingLogger.addWarning(`Error sending message to Slack (error=${error instanceof Error ? error.message : String(error)})`, 'slack_message_sending', {
+            warningType: 'slack_notification_failed',
+            warningCategory: 'infrastructure',
+            warningSeverity: 'degraded',
+            data: {
+                error: error instanceof Error ? error.message : String(error),
+            },
+        });
     }
 }
 //# sourceMappingURL=slackMessages.service.js.map

package/dist/service/slackMessages.service.js.map

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

@@ -16,51 +16,8 @@ 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 = {
-    /**
-     * 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[];
+    rules: any[];
     displaySettings: ReportDisplaySettings;
     enableHistoricalData: boolean;
     enableHistoricalMode: boolean;
@@ -231,49 +188,6 @@ 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

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package/dist/util-ts/apiUtils.js

@@ -43,7 +43,12 @@ async function makeApiCallWithRetry(method, url, data, ohtCoreApiKey, retries =
             if (attempt === retries) {
                 throw error;
             }
-            processingLogger_service_1.processingLogger.addWarning(`Attempt ${attempt} failed. Retrying... (method=${method}, url=${url})`, 'api_call_retry');
+            processingLogger_service_1.processingLogger.addWarning(`Attempt ${attempt} failed. Retrying... (method=${method}, url=${url})`, 'api_call_retry', {
+                warningType: 'oht_core_api_error',
+                warningCategory: 'infrastructure',
+                warningSeverity: 'degraded',
+                data: { attempt, method, url },
+            });
         }
     }
 }

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

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

@@ -145,8 +145,13 @@ const fetchSynonymUnits = async (partnerId, ohtCoreApiKey) => {
     }
     catch (error) {
         processingLogger_service_1.processingLogger.addWarning(`Failed to fetch synonym units from API, falling back to hardcoded synonyms`, 'fetch_synonym_units', {
-            partner_id: partnerId,
-            error: error.message,
+            warningType: 'synonym_units_fetch_failed',
+            warningCategory: 'infrastructure',
+            warningSeverity: 'degraded',
+            data: {
+                partner_id: partnerId,
+                error: error.message,
+            },
         });
         return [];
     }
@@ -173,22 +178,27 @@ 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
@@ -211,9 +221,14 @@ function processAppendedMappings(exams, labKeys, filename, annotationConfig) {
             // Handle required paths - if required and no value, log warning and use fallback
             if (path.required && !rawValue && !path.defaultValue) {
                 processingLogger_service_1.processingLogger.addWarning(`Required extraction path ${path.path} not found for labKey ${additionalLabKey.labKey}`, 'process_append_mappings', {
-                    labKey: additionalLabKey.labKey,
-                    path: path.path,
-                    filename: filenameForLogging,
+                    warningType: 'required_extraction_path_missing',
+                    warningCategory: 'mapping',
+                    warningSeverity: 'degraded',
+                    data: {
+                        labKey: additionalLabKey.labKey,
+                        path: path.path,
+                        filename: filenameForLogging,
+                    },
                 });
                 parts.push(`appended biomarker information for ${additionalLabKey.labKey} not found`);
             }

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

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

@@ -1,5 +1,5 @@
 import { RangeExtractionResponse, SynonymUnit } from "../types/custom-parser.types";
-import { AnnotationLabKey, BackendBiomarkerMapping, OhtExam, PatientInfo, Biomarker, BiomarkerValueType, MeasurementValueComparator, AnnotationConfig, Exam, ReportCustomisation, PartnerCustomPanel, BiomarkerCompatibility } from "../types/oht.types";
+import { AnnotationLabKey, BackendBiomarkerMapping, OhtExam, PatientInfo, Biomarker, BiomarkerValueType, MeasurementValueComparator, AnnotationConfig, Exam } from "../types/oht.types";
 /**
  * Default range parsing function that extracts range information from exam data
  * @param exam - The OHT exam object containing range information
@@ -49,37 +49,6 @@ 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;
@@ -97,5 +66,4 @@ 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;
-declare function checkOhtBiomarkerCompatibility(ohtBiomarker: Biomarker, panelCustomisation?: PartnerCustomPanel, reportCustomisation?: ReportCustomisation): BiomarkerCompatibility | undefined;
-export { parseRange, handleBiomarkerId, ohtReportExtractUnit, ohtReportExtractReferenceAnnotation, ohtReportExtractReferenceRanges, ohtReportExtractValueFromGreaterLowerThan, ohtReportParseExamValue, ohtReportCheckValueForPlausibleValues, checkOhtBiomarkerCompatibility, getEffectiveBiomarkerCompatibility, getRangeForCompatibility, };
+export { parseRange, handleBiomarkerId, ohtReportExtractUnit, ohtReportExtractReferenceAnnotation, ohtReportExtractReferenceRanges, ohtReportExtractValueFromGreaterLowerThan, ohtReportParseExamValue, ohtReportCheckValueForPlausibleValues, };

package/dist/util-ts/extractionUtils.js

@@ -11,9 +11,6 @@ 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");
@@ -372,7 +369,7 @@ function parsePtNumber(raw) {
 * @returns Array of RegExp objects for "less than" pattern matching
 */
 function getLessThanPatternsLocal() {
-    const patterns = [
+    return [
         /<=\s*([\d\.,]+)/, // Universal: "<="
         /at[eé]\s*([\d\.,]+)/, // Portuguese: "até"
         /inferior\s+[AaÀà]\s+([\d\.,]+)/, // Portuguese: "inferior a/à"
@@ -386,14 +383,13 @@ function getLessThanPatternsLocal() {
         /inferior\s+ou\s+igual\s+(?:[AaÀà]\s+)?([\d\.,]+)/, // Portuguese: "inferior ou igual a/à"
         /less\s+than\s+or\s+equal\s+to\s+([\d\.,]+)/i, // English: "less than or equal to"
     ];
-    return patterns;
 }
 /**
  * Gets an array of regular expressions for matching "greater than" patterns in various languages
  * @returns Array of RegExp objects for "greater than" pattern matching
  */
 function getGreaterThanPatternsLocal() {
-    const patterns = [
+    return [
         />=\s*([\d\.,]+)/, // Universal: ">="
         /superior\s+[AaÀà]\s+([\d\.,]+)/, // Spanish/Portuguese: "superior a/à"
         />\s?([\d\.,]+)/, // Universal: ">"
@@ -407,7 +403,6 @@ function getGreaterThanPatternsLocal() {
         /maior\s+ou\s+igual\s+(?:[AaÀà]\s+)?([\d\.,]+)/, // Portuguese: "maior ou igual a/à"
         /greater\s+than\s+or\s+equal\s+to\s+([\d\.,]+)/i, // English: "greater than or equal to"
     ];
-    return patterns;
 }
 /**
 * Converts backend biomarker id to know if it should be mapped or unmapped
@@ -542,70 +537,6 @@ 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,
-    };
-    // 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;
-    }
-    if (logEntries) {
-        logEntries.push({
-            labkey: ohtExam.labKey ?? '',
-            compatibility: compatibility ?? 'undefined',
-        });
-    }
-    switch (compatibility) {
-        case oht_types_1.BiomarkerCompatibility.Internal:
-            // Internal ranges are handled downstream, not here
-            return nullRangeTrue;
-        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?
@@ -724,61 +655,21 @@ function ohtReportCheckValueForPlausibleValues(ohtBmId, labKey, ohtBiomarker, un
     // Log if the value is not plausible
     if (!isPlausibleValue) {
         processingLogger_service_1.processingLogger.addWarning(`Value "${value} ${unit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${ohtBmId}" | "${labKey}"`, 'plausibility_check', {
-            ohtBmId,
-            labKey,
-            value,
-            unit,
-            standardUnit,
-            plausibleLowerValue,
-            plausibleUpperValue,
-            filename,
+            warningType: 'plausibility_check_failed',
+            warningCategory: 'measurements',
+            warningSeverity: 'degraded',
+            data: {
+                ohtBmId,
+                labKey,
+                value,
+                unit,
+                standardUnit,
+                plausibleLowerValue,
+                plausibleUpperValue,
+                filename,
+            },
         });
     }
     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;
-}
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