@openhealth/oht-custom-parser-lib 0.2.54 → 0.2.57
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.
- package/dist/service/auxiliaryFunctions.service.d.ts +4 -1
- package/dist/service/auxiliaryFunctions.service.js +57 -2
- package/dist/service/auxiliaryFunctions.service.js.map +1 -1
- package/dist/service/ohtMeasurementsExtractor.service.d.ts +8 -3
- package/dist/service/ohtMeasurementsExtractor.service.js +119 -10
- package/dist/service/ohtMeasurementsExtractor.service.js.map +1 -1
- package/dist/service/transformationRules.service.js +21 -4
- package/dist/service/transformationRules.service.js.map +1 -1
- package/dist/types/custom-parser.types.d.ts +2 -0
- package/dist/types/custom-parser.types.js.map +1 -1
- package/dist/types/oht.types.d.ts +21 -0
- package/dist/util-ts/dataUtils.js +2 -1
- package/dist/util-ts/dataUtils.js.map +1 -1
- package/dist/util-ts/regexUtils.js +28 -10
- package/dist/util-ts/regexUtils.js.map +1 -1
- package/package.json +1 -1
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@@ -1,6 +1,8 @@
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import { ErrorMessage } from '../types/error.types';
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import { DataImportFileUpload, DataImportFileUploadStatus, Sex } from "../types/oht.types";
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import dayjs from 'dayjs';
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import { TransformationRulesChains } from "../types/custom-parser.types";
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declare function getPatientAge(documentDate?: Date, patientBirthdate?: Date): number | null;
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declare function isPatientAgeValid(documentDate?: Date, patientBirthdate?: Date): boolean;
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declare function parseExternalPatientId(patientExternalId?: string): boolean;
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declare function parseGender(patientGender?: string): {
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@@ -23,4 +25,5 @@ declare function postFileUploadSetStatus(payload: {
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lastUpdated: dayjs.Dayjs;
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};
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}, fileUploadId: string, filename: string, ohtCoreApiKey: string): Promise<DataImportFileUpload>;
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declare function getPartnerTransformationRules(partnerId: string, labKeys: string[], ohtCoreApiKey: string): Promise<TransformationRulesChains>;
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export { parseExternalPatientId, parseGender, isPatientAgeValid, getPatientAge, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, getPartnerTransformationRules, };
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@@ -6,9 +6,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
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exports.parseExternalPatientId = parseExternalPatientId;
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exports.parseGender = parseGender;
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exports.isPatientAgeValid = isPatientAgeValid;
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exports.getPatientAge = getPatientAge;
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exports.handleRejection = handleRejection;
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exports.queryFileUploadsWithFilters = queryFileUploadsWithFilters;
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exports.postFileUploadSetStatus = postFileUploadSetStatus;
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exports.getPartnerTransformationRules = getPartnerTransformationRules;
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const moment_1 = __importDefault(require("moment/moment"));
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const apiUtils_1 = require("../util-ts/apiUtils");
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const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
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@@ -19,10 +21,20 @@ const utc_1 = __importDefault(require("dayjs/plugin/utc"));
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dayjs_1.default.extend(customParseFormat_1.default);
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dayjs_1.default.extend(utc_1.default);
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const logger = (0, pinoLogger_1.default)();
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-
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const OHT_CORE_URL = process.env.OHT_CORE_URL;
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function getPatientAge(documentDate, patientBirthdate) {
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if (!patientBirthdate || !documentDate)
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return null;
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// Normalize dates to start of day to avoid timezone issues
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const docDate = (0, moment_1.default)(documentDate).startOf('day');
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const birthDate = (0, moment_1.default)(patientBirthdate).startOf('day');
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return docDate.diff(birthDate, 'years');
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}
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function isPatientAgeValid(documentDate, patientBirthdate) {
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const patientAge = getPatientAge(documentDate, patientBirthdate);
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if (patientAge === null) {
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return false;
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-
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}
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return patientAge >= 18 && patientAge <= 130;
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}
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function parseExternalPatientId(patientExternalId) {
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@@ -68,4 +80,47 @@ async function postFileUploadSetStatus(payload, fileUploadId, filename, ohtCoreA
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logger.info({ resp: processingResponse?.data }, `Resp: POST status: ${payload.status} /file-uploads/${fileUploadId}, filename: ${filename}`);
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return processingResponse?.data;
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}
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// getPartnerTransformationRules fetches all the available partner transformation rules
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async function getPartnerTransformationRules(partnerId, labKeys, ohtCoreApiKey) {
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// Fetch every partner transformation rule
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const ohtCoreTransformationRulesUrl = `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/transformation-rules`;
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const rulesResponse = await (0, apiUtils_1.makeApiCallWithRetry)('GET', ohtCoreTransformationRulesUrl, null, ohtCoreApiKey);
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const rulesMap = (rulesResponse?.data?.items ?? [])
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.reduce((map, rule) => {
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return map.set(rule.id, {
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id: rule.id,
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name: rule.name,
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description: rule.description,
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conditionExpression: rule.conditionExpression,
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valueExpression: rule.valueExpression,
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targetExpression: rule.targetExpression,
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tags: [],
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createdAt: dayjs_1.default.utc(rule.createdAt).toDate(),
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updatedAt: dayjs_1.default.utc(rule.updatedAt).toDate(),
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});
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}, new Map());
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// Fetch the rule chains for the requested labKeys
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const ohtCoreTransformationRulesChainsUrl = `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/transformation-rules-chains/query`;
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const rulesChainsResponse = await (0, apiUtils_1.makeApiCallWithRetry)('POST', ohtCoreTransformationRulesChainsUrl, {
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filters: [
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{
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field: 'labKey',
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multiSearch: labKeys,
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}
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],
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}, ohtCoreApiKey);
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// Hydrate the rules chains with the actual rules
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return (rulesChainsResponse?.data?.items ?? [])
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.reduce((map, chainItem) => {
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return map.set(chainItem.labKey, chainItem.ruleIds
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.map((ruleId) => {
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const rule = rulesMap.get(ruleId);
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if (!rule) {
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throw new Error(`Transformation rule with ID ${ruleId} for labKey ${chainItem.labKey} not found for partner ${partnerId}.`);
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}
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return rule;
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})
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.filter((rule) => rule !== undefined));
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}, new Map());
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}
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//# sourceMappingURL=auxiliaryFunctions.service.js.map
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@@ -1 +1 @@
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-
{"version":3,"file":"auxiliaryFunctions.service.js","sourceRoot":"","sources":["../../service/auxiliaryFunctions.service.ts"],"names":[],"mappings":";;;;;
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import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction, SynonymUnit, UnknownUnits } from "../types/custom-parser.types";
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import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction, SynonymUnit, UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
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import { Biomarker, BiomarkerValueType, Measurement, MeasurementValueComparator, PatientInfo, UnknownMeasurement, Exam } from "../types/oht.types";
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declare function extractUnit(unitExtraction: UnitExtraction | undefined, rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
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isValueParsedCorrectly: boolean;
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};
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declare function checkValueForPlausibleValues(labToOhtMapper: LabToOhtMapper, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean): boolean;
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type ApplyTransformationRulesResult = {
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transformedExams: Exam[];
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applicationErrorMessages: string[];
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};
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declare function ohtMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{
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measurements: Measurement[];
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unknownMeasurements: UnknownMeasurement[];
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unknownUnits: UnknownUnits[];
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isReportCorrectlyParsed: boolean;
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transformationRulesErrors: string[];
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}>;
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export { ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan };
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export { ApplyTransformationRulesResult, ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan };
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const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
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const apiUtils_1 = require("../util-ts/apiUtils");
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const oht_types_1 = require("../types/oht.types");
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const transformationRules_service_1 = require("./transformationRules.service");
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const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
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const logger = (0, pinoLogger_1.default)();
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const OHT_CORE_URL = process.env.OHT_CORE_URL;
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let filename = '';
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}
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return isPlausibleValue;
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}
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/**
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* Apply transformation rules to exams
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* This function applies transformation rules chain to each exam, passing all exams as context
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*
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* @param exams - Array of original exam objects
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* @param transformationRules - Mapping of labKey to transformation rule chains
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* @param labToOhtContract - The contract containing patient info and other context
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* @returns Promise<Exam[]> - Array of transformed exams
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*/
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async function applyTransformationRulesToExams(exams, transformationRules, patientInfo, documentDate) {
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if (transformationRules.size === 0) {
|
|
307
|
+
return {
|
|
308
|
+
transformedExams: exams,
|
|
309
|
+
applicationErrorMessages: []
|
|
310
|
+
};
|
|
311
|
+
}
|
|
312
|
+
const transformedExams = [];
|
|
313
|
+
// Prepare context for transformation rules
|
|
314
|
+
const reportContext = {
|
|
315
|
+
patient: {
|
|
316
|
+
sex: patientInfo.sex,
|
|
317
|
+
birthdate: patientInfo.birthdate,
|
|
318
|
+
age: (0, auxiliaryFunctions_service_1.getPatientAge)(documentDate, patientInfo.birthdate),
|
|
319
|
+
}
|
|
320
|
+
};
|
|
321
|
+
// Prepare the OHT exam data
|
|
322
|
+
const ohtReport = {
|
|
323
|
+
exams: exams.map(e => e.ohtExam),
|
|
324
|
+
};
|
|
325
|
+
logger.info({ examsCount: exams.length, chainsCount: transformationRules.size, filename }, 'Applying transformation rules to exams...');
|
|
326
|
+
let labKeysWithRulesCount = 0;
|
|
327
|
+
let transformedLabKeysCount = 0;
|
|
328
|
+
const applicationErrorMessages = [];
|
|
329
|
+
for (const exam of exams) {
|
|
330
|
+
const labKey = exam.ohtExam.labKey;
|
|
331
|
+
const rulesChain = transformationRules.get(labKey);
|
|
332
|
+
if (!rulesChain || rulesChain.length === 0) {
|
|
333
|
+
transformedExams.push(exam);
|
|
334
|
+
continue;
|
|
335
|
+
}
|
|
336
|
+
labKeysWithRulesCount++;
|
|
337
|
+
try {
|
|
338
|
+
const result = await (0, transformationRules_service_1.applyRules)(rulesChain, exam.ohtExam, {
|
|
339
|
+
ohtReportJson: ohtReport,
|
|
340
|
+
contextJson: reportContext,
|
|
341
|
+
});
|
|
342
|
+
if (result.errors.length > 0) {
|
|
343
|
+
logger.warn({ labKey, errors: result.errors, filename }, 'Errors applying transformation rule(s) for labKey.');
|
|
344
|
+
applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
|
|
345
|
+
}
|
|
346
|
+
else {
|
|
347
|
+
if (result.appliedRules.length > 0) {
|
|
348
|
+
transformedLabKeysCount++;
|
|
349
|
+
}
|
|
350
|
+
logger.info({ labKey, appliedRules: result.appliedRules.length, filename }, 'Done applying transformation rule(s) for labKey.');
|
|
351
|
+
// Add the transformed exam to the result array only if there are no errors in the chain
|
|
352
|
+
transformedExams.push({
|
|
353
|
+
ohtExam: result.data,
|
|
354
|
+
originalExam: exam.originalExam
|
|
355
|
+
});
|
|
356
|
+
}
|
|
357
|
+
}
|
|
358
|
+
catch (error) {
|
|
359
|
+
logger.error({ labKey, error, filename }, 'Failed to apply transformation rules for labKey.');
|
|
360
|
+
applicationErrorMessages.push(`${labKey}: Unhandled error occurred.`);
|
|
361
|
+
}
|
|
362
|
+
}
|
|
363
|
+
logger.info({
|
|
364
|
+
filename,
|
|
365
|
+
examsCount: exams.length,
|
|
366
|
+
chainsCount: transformationRules.size,
|
|
367
|
+
transformedLabKeysCount,
|
|
368
|
+
labKeysWithRulesCount,
|
|
369
|
+
}, 'Done applying the transformation rules to exams.');
|
|
370
|
+
return {
|
|
371
|
+
transformedExams,
|
|
372
|
+
applicationErrorMessages
|
|
373
|
+
};
|
|
374
|
+
}
|
|
375
|
+
async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationRules, ohtCoreApiKey, partnerId) {
|
|
295
376
|
filename = labToOhtContract.sourceFilename;
|
|
296
377
|
const measurements = [];
|
|
297
378
|
const unknownMeasurements = [];
|
|
298
379
|
const unknownUnits = [];
|
|
299
380
|
let isReportCorrectlyParsed = true;
|
|
381
|
+
let transformationRulesErrors = [];
|
|
382
|
+
// Apply transformation rules to all exams
|
|
383
|
+
let transformedExamsResult = { transformedExams: [], applicationErrorMessages: [] };
|
|
384
|
+
try {
|
|
385
|
+
transformedExamsResult = await applyTransformationRulesToExams(exams, transformationRules, labToOhtContract.patientInfo, labToOhtContract.documentDate);
|
|
386
|
+
}
|
|
387
|
+
catch (error) {
|
|
388
|
+
logger.error({ error, filename }, 'Unhandled error while applying transformation rules to exams.');
|
|
389
|
+
labToOhtContract.errorMessages.push({
|
|
390
|
+
destination: { slack: true, notes: true, bi: false },
|
|
391
|
+
message: `Failed applying the transformation rules for filename ${filename}. ${error instanceof Error ? error.message : error}`,
|
|
392
|
+
});
|
|
393
|
+
}
|
|
394
|
+
if (transformedExamsResult.applicationErrorMessages.length > 0) {
|
|
395
|
+
transformationRulesErrors = transformedExamsResult.applicationErrorMessages;
|
|
396
|
+
labToOhtContract.errorMessages.push({
|
|
397
|
+
destination: { slack: false, notes: true, bi: false },
|
|
398
|
+
message: `Failed applying some transformation rules:\n${transformedExamsResult.applicationErrorMessages.map((e) => ` - ${e}`).join("\n\n")}`,
|
|
399
|
+
});
|
|
400
|
+
}
|
|
401
|
+
const transformedExams = transformedExamsResult.transformedExams;
|
|
402
|
+
const transformedExamsMap = transformedExams.reduce((map, exam) => map.set(exam.ohtExam.labKey, exam), new Map());
|
|
300
403
|
const allPossibleOHTBmIds = [];
|
|
301
404
|
[
|
|
302
405
|
...Object.values(labToOhtContract.labToOhtList)
|
|
@@ -331,7 +434,12 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
|
|
|
331
434
|
});
|
|
332
435
|
return;
|
|
333
436
|
}
|
|
334
|
-
|
|
437
|
+
let examObj = JSON.parse(labToOhtMapper.rawExam);
|
|
438
|
+
// Get the transformed exam for this labKey
|
|
439
|
+
const transformedExam = transformedExamsMap.get(labToOhtMapper.labKey);
|
|
440
|
+
if (transformedExam) {
|
|
441
|
+
examObj = transformedExam.ohtExam;
|
|
442
|
+
}
|
|
335
443
|
if (labToOhtMapper?.ohtBmId && labToOhtMapper?.ohtBmId !== -1) {
|
|
336
444
|
// if BM is already in measurements, continue to the next one
|
|
337
445
|
if (measurements.some(measurement => measurement.biomarkerId === labToOhtMapper.ohtBmId)) {
|
|
@@ -348,7 +456,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
|
|
|
348
456
|
const bmInfo = ohtBiomarker?.acf?.shortName ?
|
|
349
457
|
`name:${ohtBiomarker.acf.shortName}, bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}` :
|
|
350
458
|
`bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}`;
|
|
351
|
-
const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = extractUnit(labToOhtMapper.unitExtraction,
|
|
459
|
+
const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = extractUnit(labToOhtMapper.unitExtraction, examObj, ohtBiomarker, synonymUnits, partnerId);
|
|
352
460
|
if (unknownUnit.length > 0) {
|
|
353
461
|
unknownUnits.push({
|
|
354
462
|
biomarkerId: ohtBiomarker.id,
|
|
@@ -370,7 +478,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
|
|
|
370
478
|
});
|
|
371
479
|
isMeasurementCorrectlyParsed = false;
|
|
372
480
|
}
|
|
373
|
-
let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(
|
|
481
|
+
let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(examObj, labToOhtMapper.valueExtraction, ohtBiomarker);
|
|
374
482
|
if (!isValueParsedCorrectly) {
|
|
375
483
|
logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
|
|
376
484
|
labToOhtContract.errorMessages.push({
|
|
@@ -397,7 +505,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
|
|
|
397
505
|
let isRangeParsedCorrectly = true;
|
|
398
506
|
// If the biomarker is numerical, extract the reference range
|
|
399
507
|
if ((0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
|
|
400
|
-
const extractedRange = extractReferenceRanges(labToOhtMapper,
|
|
508
|
+
const extractedRange = extractReferenceRanges(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate);
|
|
401
509
|
from = extractedRange.from ?? null;
|
|
402
510
|
to = extractedRange.to ?? null;
|
|
403
511
|
isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
|
|
@@ -413,16 +521,16 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
|
|
|
413
521
|
}
|
|
414
522
|
let extractedAnnotation;
|
|
415
523
|
if (labToOhtMapper?.referenceAsAnnotation?.use || labToOhtMapper?.annotationConfig?.enabled) {
|
|
416
|
-
extractedAnnotation = extractReferenceAnnotation(labToOhtMapper,
|
|
524
|
+
extractedAnnotation = extractReferenceAnnotation(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate, transformedExams);
|
|
417
525
|
}
|
|
418
|
-
const material = (0, dataUtils_1.extractValue)(
|
|
419
|
-
const method = (0, dataUtils_1.extractValue)(
|
|
526
|
+
const material = (0, dataUtils_1.extractValue)(examObj, labToOhtMapper.material);
|
|
527
|
+
const method = (0, dataUtils_1.extractValue)(examObj, labToOhtMapper.method);
|
|
420
528
|
let alphaValue = !(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) && alphanumericalValue
|
|
421
529
|
? alphanumericalValue.trim()
|
|
422
530
|
: '';
|
|
423
531
|
// adding unit for alphanumerical values as number.
|
|
424
532
|
if (!Number.isNaN(parseFloat(alphaValue))) {
|
|
425
|
-
let originalUnit = (0, dataUtils_1.extractValue)(
|
|
533
|
+
let originalUnit = (0, dataUtils_1.extractValue)(examObj, labToOhtMapper?.unitExtraction?.unitPosition);
|
|
426
534
|
originalUnit = originalUnit?.replaceAll(/ /g, '') ?? '';
|
|
427
535
|
alphaValue = alphaValue && unit?.length > 0 ? `${alphaValue} ${originalUnit}`.trim() : alphaValue;
|
|
428
536
|
}
|
|
@@ -506,7 +614,8 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
|
|
|
506
614
|
measurements,
|
|
507
615
|
unknownMeasurements,
|
|
508
616
|
unknownUnits,
|
|
509
|
-
isReportCorrectlyParsed
|
|
617
|
+
isReportCorrectlyParsed,
|
|
618
|
+
transformationRulesErrors,
|
|
510
619
|
};
|
|
511
620
|
}
|
|
512
621
|
//# sourceMappingURL=ohtMeasurementsExtractor.service.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -6,6 +6,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
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6
6
|
exports.validateJsonataExpression = exports.applyRules = void 0;
|
|
7
7
|
const jsonata_1 = __importDefault(require("jsonata"));
|
|
8
8
|
const transformationRules_1 = require("../util-ts/transformationRules");
|
|
9
|
+
const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
|
|
10
|
+
const logger = (0, pinoLogger_1.default)();
|
|
9
11
|
/**
|
|
10
12
|
* JSON Transformation Rules Engine
|
|
11
13
|
*
|
|
@@ -38,7 +40,10 @@ const evaluateCondition = async (condition, context) => {
|
|
|
38
40
|
return Boolean(result);
|
|
39
41
|
}
|
|
40
42
|
catch (error) {
|
|
41
|
-
|
|
43
|
+
logger.error({
|
|
44
|
+
error: error instanceof Error ? error.message : String(error),
|
|
45
|
+
condition,
|
|
46
|
+
}, 'Error evaluating condition.');
|
|
42
47
|
return false;
|
|
43
48
|
}
|
|
44
49
|
};
|
|
@@ -57,7 +62,10 @@ const evaluateValueExpression = async (valueExpression, context) => {
|
|
|
57
62
|
return result;
|
|
58
63
|
}
|
|
59
64
|
catch (error) {
|
|
60
|
-
|
|
65
|
+
logger.error({
|
|
66
|
+
error: error instanceof Error ? error.message : String(error),
|
|
67
|
+
valueExpression,
|
|
68
|
+
}, 'Error evaluating value expression.');
|
|
61
69
|
throw error;
|
|
62
70
|
}
|
|
63
71
|
};
|
|
@@ -139,11 +147,20 @@ const applyRules = async (rules, inputData, options = {}) => {
|
|
|
139
147
|
appliedRules: [],
|
|
140
148
|
errors: [],
|
|
141
149
|
}));
|
|
150
|
+
// In case of errors, do not return partial transformed input.
|
|
151
|
+
if (result.errors.length > 0) {
|
|
152
|
+
return {
|
|
153
|
+
success: false,
|
|
154
|
+
data: inputData,
|
|
155
|
+
appliedRules: [],
|
|
156
|
+
errors: result.errors,
|
|
157
|
+
};
|
|
158
|
+
}
|
|
142
159
|
return {
|
|
143
|
-
success:
|
|
160
|
+
success: true,
|
|
144
161
|
data: result.data,
|
|
145
162
|
appliedRules: result.appliedRules,
|
|
146
|
-
errors:
|
|
163
|
+
errors: [],
|
|
147
164
|
};
|
|
148
165
|
};
|
|
149
166
|
exports.applyRules = applyRules;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"transformationRules.service.js","sourceRoot":"","sources":["../../service/transformationRules.service.ts"],"names":[],"mappings":";;;;;;AAAA,sDAA8B;AAI9B,wEAEwC;
|
|
1
|
+
{"version":3,"file":"transformationRules.service.js","sourceRoot":"","sources":["../../service/transformationRules.service.ts"],"names":[],"mappings":";;;;;;AAAA,sDAA8B;AAI9B,wEAEwC;AACxC,uEAA+C;AAE/C,MAAM,MAAM,GAAG,IAAA,oBAAU,GAAE,CAAC;AAE5B;;;;;;;GAOG;AAEH,MAAM,gBAAgB,GAAG,CAAC,cAAsB,EAAE,OAA8B,EAAE,EAAE;IAClF,MAAM,UAAU,GAAG,IAAA,iBAAO,EAAC,cAAc,CAAC,CAAC;IAC3C,UAAU,CAAC,MAAM,CAAC,QAAQ,EAAE,OAAO,CAAC,SAAS,CAAC,CAAC;IAC/C,UAAU,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,OAAO,CAAC,CAAC;IAC3C,UAAU,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,OAAO,CAAC,CAAC;IAE9C,OAAO,UAAU,CAAC;AACpB,CAAC,CAAC;AAEF;;;;;;GAMG;AACH,MAAM,iBAAiB,GAAG,KAAK,EAAE,SAAiB,EAAE,OAA8B,EAAoB,EAAE;IACtG,IAAI,CAAC;QACH,IAAI,CAAC,SAAS,IAAI,SAAS,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;YAC1C,OAAO,IAAI,CAAC;QACd,CAAC;QAED,MAAM,UAAU,GAAG,gBAAgB,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACxD,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QAE1D,OAAO,OAAO,CAAC,MAAM,CAAC,CAAC;IACzB,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,CAAC,KAAK,CAAC;YACX,KAAK,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC;YAC7D,SAAS;SACV,EAAE,6BAA6B,CAAC,CAAC;QAElC,OAAO,KAAK,CAAC;IACf,CAAC;AACH,CAAC,CAAC;AAEF;;;;;;;GAOG;AACH,MAAM,uBAAuB,GAAG,KAAK,EAAE,eAAuB,EAAE,OAA8B,EAAoB,EAAE;IAClH,IAAI,CAAC;QACH,MAAM,UAAU,GAAG,gBAAgB,CAAC,eAAe,EAAE,OAAO,CAAC,CAAC;QAC9D,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QAC1D,OAAO,MAAM,CAAC;IAChB,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,CAAC,KAAK,CAAC;YACX,KAAK,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC;YAC7D,eAAe;SAChB,EAAE,oCAAoC,CAAC,CAAC;QAEzC,MAAM,KAAK,CAAC;IACd,CAAC;AACH,CAAC,CAAC;AAEF;;;;;;;GAOG;AACH,MAAM,SAAS,GAAG,KAAK,EACrB,IAAwB,EACxB,IAA6B,EAC7B,UAA6B,EAAE,EACG,EAAE;IACpC,MAAM,OAAO,GAA0B;QACrC,SAAS,EAAE,OAAO,CAAC,aAAa,IAAI,EAAE;QACtC,OAAO,EAAE,IAAI;QACb,OAAO,EAAE,OAAO,CAAC,WAAW,IAAI,EAAE;KACnC,CAAC;IAEF,MAAM,WAAW,GAAG,MAAM,iBAAiB,CAAC,IAAI,CAAC,mBAAmB,EAAE,OAAO,CAAC,CAAC;IAC/E,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,OAAO,IAAI,CAAC;IACd,CAAC;IAED,MAAM,QAAQ,GAAG,MAAM,uBAAuB,CAAC,IAAI,CAAC,eAAe,EAAE,OAAO,CAAC,CAAC;IAE9E,MAAM,eAAe,GAAG,EAAE,GAAG,IAAI,EAAE,CAAC;IAEpC,IAAI,IAAI,CAAC,gBAAgB,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;QAC3C,MAAM,YAAY,GAAG,IAAA,+BAAS,EAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC;QACtD,IAAA,oCAAc,EAAC,eAAe,EAAE,YAAY,EAAE,QAAQ,CAAC,CAAC;IAC1D,CAAC;IAED,OAAO,eAAe,CAAC;AACzB,CAAC,CAAC;AAEF;;;;;;;;;;;;GAYG;AACI,MAAM,UAAU,GAAG,KAAK,EAC7B,KAA2B,EAC3B,SAAkC,EAClC,UAA6B,EAAE,EACJ,EAAE;IAC7B,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,MAAM,CAC/B,KAAK,EAAE,UAAU,EAAE,IAAI,EAAE,EAAE;QACzB,MAAM,GAAG,GAAG,MAAM,UAAU,CAAC;QAE7B,IAAI,CAAC;YACH,MAAM,OAAO,GAA0B;gBACrC,SAAS,EAAE,OAAO,CAAC,aAAa,IAAI,EAAE;gBACtC,OAAO,EAAE,GAAG,CAAC,IAAI;gBACjB,OAAO,EAAE,OAAO,CAAC,WAAW,IAAI,EAAE;aACnC,CAAC;YAEF,MAAM,WAAW,GAAG,MAAM,iBAAiB,CAAC,IAAI,CAAC,mBAAmB,EAAE,OAAO,CAAC,CAAC;YAC/E,IAAI,WAAW,EAAE,CAAC;gBAChB,MAAM,eAAe,GAAG,MAAM,SAAS,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;gBAEjE,OAAO;oBACL,IAAI,EAAE,eAAe;oBACrB,YAAY,EAAE,CAAC,GAAG,GAAG,CAAC,YAAY,EAAE,IAAI,CAAC,EAAE,CAAC;oBAC5C,MAAM,EAAE,GAAG,CAAC,MAAM;iBACnB,CAAC;YACJ,CAAC;YAED,OAAO,GAAG,CAAC;QACb,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,OAAO;gBACL,IAAI,EAAE,GAAG,CAAC,IAAI;gBACd,YAAY,EAAE,GAAG,CAAC,YAAY;gBAC9B,MAAM,EAAE;oBACN,GAAG,GAAG,CAAC,MAAM;oBACb;wBACE,MAAM,EAAE,IAAI,CAAC,EAAE;wBACf,QAAQ,EAAE,IAAI,CAAC,IAAI;wBACnB,KAAK,EAAE,IAAA,qCAAe,EAAC,KAAK,CAAC;qBAC9B;iBACF;aACF,CAAC;QACJ,CAAC;IACH,CAAC,EACD,OAAO,CAAC,OAAO,CAAC;QACd,IAAI,EAAE,EAAE,GAAG,SAAS,EAAE;QACtB,YAAY,EAAE,EAAc;QAC5B,MAAM,EAAE,EAAgE;KACzE,CAAC,CACH,CAAC;IAEF,8DAA8D;IAC9D,IAAI,MAAM,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC7B,OAAO;YACL,OAAO,EAAE,KAAK;YACd,IAAI,EAAE,SAAS;YACf,YAAY,EAAE,EAAE;YAChB,MAAM,EAAE,MAAM,CAAC,MAAM;SACtB,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE,IAAI;QACb,IAAI,EAAE,MAAM,CAAC,IAAI;QACjB,YAAY,EAAE,MAAM,CAAC,YAAY;QACjC,MAAM,EAAE,EAAE;KACX,CAAC;AACJ,CAAC,CAAC;AAlEW,QAAA,UAAU,cAkErB;AAEF;;;;;GAKG;AACI,MAAM,yBAAyB,GAAG,CAAC,UAAkB,EAAoB,EAAE;IAChF,IAAI,CAAC;QACH,IAAI,CAAC,UAAU,IAAI,UAAU,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;YAC5C,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;QACzB,CAAC;QAED,IAAA,iBAAO,EAAC,UAAU,CAAC,CAAC;QACpB,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;IACzB,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO;YACL,KAAK,EAAE,KAAK;YACZ,KAAK,EAAE,IAAA,qCAAe,EAAC,KAAK,CAAC;SAC9B,CAAC;IACJ,CAAC;AACH,CAAC,CAAC;AAdW,QAAA,yBAAyB,6BAcpC"}
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@@ -1,5 +1,6 @@
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1
1
|
import { ErrorMessage } from "./error.types";
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2
2
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import { AnnotationConfig, DataOrigin, MeasurementValueComparator, OhtExam, PatientInfo } from "./oht.types";
|
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3
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+
import { TransformationRule } from "./transformationRules.types";
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3
4
|
export interface SynonymUnit {
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4
5
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id: string;
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5
6
|
partnerId: string | null;
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@@ -98,3 +99,4 @@ export interface LabToOhtContract {
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98
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|
sourceFilename: string;
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99
100
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externalPatientId: string;
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100
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}
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102
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+
export type TransformationRulesChains = Map<string, TransformationRule[]>;
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@@ -1 +1 @@
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|
|
1
|
-
{"version":3,"file":"custom-parser.types.js","sourceRoot":"","sources":["../../types/custom-parser.types.ts"],"names":[],"mappings":";;;
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1
|
+
{"version":3,"file":"custom-parser.types.js","sourceRoot":"","sources":["../../types/custom-parser.types.ts"],"names":[],"mappings":";;;AA2Ba,QAAA,YAAY,GAA2B;IAClD,KAAK,EAAE,MAAM;IACb,KAAK,EAAE,MAAM;IACb,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,MAAM;IACf,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,OAAO;IAChB,WAAW,EAAE,aAAa;IAC1B,YAAY,EAAE,aAAa;IAC3B,IAAI,EAAE,KAAK;IACX,MAAM,EAAE,KAAK;IACb,UAAU,EAAE,SAAS;IACrB,SAAS,EAAE,QAAQ;IACnB,SAAS,EAAE,QAAQ;IACnB,QAAQ,EAAE,QAAQ;IAClB,eAAe,EAAE,eAAe;IAChC,KAAK,EAAE,GAAG;IACV,IAAI,EAAE,MAAM;IACZ,IAAI,EAAE,MAAM;IACZ,EAAE,EAAE,MAAM;IACV,MAAM,EAAE,KAAK;IACb,KAAK,EAAE,MAAM;IACb,QAAQ,EAAE,OAAO;IACjB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,SAAS;IACnB,SAAS,EAAE,SAAS;IACpB,SAAS,EAAE,SAAS;IACpB,QAAQ,EAAE,SAAS;IACnB,gBAAgB,EAAE,YAAY;IAC9B,iBAAiB,EAAE,YAAY;IAC/B,UAAU,EAAE,SAAS;IACrB,OAAO,EAAE,OAAO;IAChB,OAAO,EAAE,OAAO;IAChB,QAAQ,EAAE,OAAO;IACjB,OAAO,EAAE,OAAO;IAChB,IAAI,EAAE,MAAM;IACZ,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,MAAM;IACf,MAAM,EAAE,MAAM;IACd,OAAO,EAAE,MAAM;IACf,OAAO,EAAE,MAAM;IACf,SAAS,EAAE,QAAQ;IACnB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,SAAS;IACnB,QAAQ,EAAE,SAAS;IACnB,WAAW,EAAE,OAAO;IACpB,UAAU,EAAE,OAAO;IACnB,WAAW,EAAE,OAAO;IACpB,UAAU,EAAE,OAAO;IACnB,IAAI,EAAE,aAAa;IACnB,IAAI,EAAE,aAAa;IACnB,aAAa,EAAE,QAAQ;IAEvB,kCAAkC;IAElC,OAAO,EAAE,OAAO;IAEhB,OAAO,EAAE,OAAO;IAEhB,OAAO,EAAE,OAAO;IAEhB,MAAM,EAAE,MAAM;IACd,MAAM,EAAE,MAAM;IACd,KAAK,EAAE,MAAM;IACb,KAAK,EAAE,MAAM;IAEb,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAElB,aAAa,EAAE,SAAS;IACxB,WAAW,EAAE,SAAS;IACtB,cAAc,EAAE,SAAS;IACzB,aAAa,EAAE,SAAS;IACxB,aAAa,EAAE,SAAS;IACxB,cAAc,EAAE,SAAS;IACzB,SAAS,EAAE,SAAS;IACpB,UAAU,EAAE,SAAS;IACrB,QAAQ,EAAE,SAAS;IACnB,WAAW,EAAE,SAAS;IAEtB,UAAU,EAAE,SAAS;IACrB,SAAS,EAAE,SAAS;IACpB,QAAQ,EAAE,SAAS;IAEnB,eAAe,EAAE,eAAe;IAChC,gBAAgB,EAAE,eAAe;IACjC,gBAAgB,EAAE,eAAe;IACjC,eAAe,EAAE,eAAe;IAChC,eAAe,EAAE,eAAe;IAEhC,QAAQ,EAAE,QAAQ;IAClB,QAAQ,EAAE,QAAQ;IAClB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,eAAe,EAAE,QAAQ;IACzB,sBAAsB,EAAE,eAAe;IACvC,sBAAsB,EAAE,eAAe;IACvC,sBAAsB,EAAE,eAAe;IAEvC,KAAK,EAAE,GAAG;IACV,IAAI,EAAE,GAAG;IACT,KAAK,EAAE,GAAG;IACV,SAAS,EAAE,GAAG;IACd,UAAU,EAAE,GAAG;IACf,SAAS,EAAE,GAAG;IAEd,OAAO,EAAE,WAAW;IACpB,QAAQ,EAAE,YAAY;IACtB,YAAY,EAAE,YAAY;IAC1B,gBAAgB,EAAE,YAAY;IAC9B,iBAAiB,EAAE,YAAY;IAC/B,iBAAiB,EAAE,YAAY;IAC/B,WAAW,EAAE,YAAY;IACzB,eAAe,EAAE,YAAY;IAC7B,gBAAgB,EAAE,YAAY;IAC9B,gBAAgB,EAAE,YAAY;IAE9B,KAAK,EAAE,KAAK;IACZ,MAAM,EAAE,KAAK;IACb,MAAM,EAAE,KAAK;IACb,mBAAmB,EAAE,KAAK;IAE1B,KAAK,EAAE,MAAM;IACb,KAAK,EAAE,MAAM;IAEb,WAAW,EAAE,cAAc;IAC3B,WAAW,EAAE,cAAc;IAC3B,UAAU,EAAE,cAAc;IAC1B,UAAU,EAAE,cAAc;IAC1B,MAAM,EAAE,MAAM;IACd,MAAM,EAAE,MAAM;CACf,CAAC"}
|
|
@@ -432,3 +432,24 @@ export interface BackendBiomarkerMapping {
|
|
|
432
432
|
/** Optional tagged LOINC code */
|
|
433
433
|
taggedLoincCode?: string;
|
|
434
434
|
}
|
|
435
|
+
/** Custom parser transformation rules */
|
|
436
|
+
export type TransformationRule = {
|
|
437
|
+
id: string;
|
|
438
|
+
partnerId: string;
|
|
439
|
+
name: string;
|
|
440
|
+
description: string;
|
|
441
|
+
conditionExpression: string;
|
|
442
|
+
targetExpression: string;
|
|
443
|
+
valueExpression: string;
|
|
444
|
+
createdAt: string;
|
|
445
|
+
updatedAt: string;
|
|
446
|
+
};
|
|
447
|
+
/** Custom parser transformation rules chain for a labkey */
|
|
448
|
+
export type TransformationRuleChain = {
|
|
449
|
+
id: string;
|
|
450
|
+
partnerId: string;
|
|
451
|
+
labKey: string;
|
|
452
|
+
ruleIds: string[];
|
|
453
|
+
createdAt: string;
|
|
454
|
+
updatedAt: string;
|
|
455
|
+
};
|
|
@@ -311,7 +311,8 @@ function findObjectWithValue(obj, targetValue) {
|
|
|
311
311
|
return false;
|
|
312
312
|
// Check if any direct property has the target value
|
|
313
313
|
for (const key in obj) {
|
|
314
|
-
|
|
314
|
+
const value = obj[key];
|
|
315
|
+
if (typeof value === 'string' && value.trim() === targetValue.trim())
|
|
315
316
|
return true;
|
|
316
317
|
}
|
|
317
318
|
return false;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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@@ -4,17 +4,35 @@ exports.getGreaterThanPatterns = getGreaterThanPatterns;
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|
4
4
|
exports.getLowerThanPatterns = getLowerThanPatterns;
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|
5
5
|
// utils/patterns.ts
|
|
6
6
|
function getGreaterThanPatterns() {
|
|
7
|
-
|
|
8
|
-
const
|
|
9
|
-
|
|
10
|
-
const
|
|
11
|
-
|
|
7
|
+
// Check >= pattern first to avoid partial matches with >
|
|
8
|
+
const pattern1 = />=\s*([\d,]+)/;
|
|
9
|
+
// Then check > patterns
|
|
10
|
+
const pattern2 = /superior\s+a\s+([\d,]+)/;
|
|
11
|
+
const pattern3 = />\s?([\d,]+)/;
|
|
12
|
+
const pattern4 = /maior\s+que\s+([\d,]+)/;
|
|
13
|
+
const pattern5 = /mais\s+que\s+([\d,]+)/;
|
|
14
|
+
return [
|
|
15
|
+
pattern1,
|
|
16
|
+
pattern2,
|
|
17
|
+
pattern3,
|
|
18
|
+
pattern4,
|
|
19
|
+
pattern5
|
|
20
|
+
];
|
|
12
21
|
}
|
|
13
22
|
function getLowerThanPatterns() {
|
|
14
|
-
|
|
15
|
-
const
|
|
16
|
-
|
|
17
|
-
const
|
|
18
|
-
|
|
23
|
+
// Check <= pattern first to avoid partial matches with <
|
|
24
|
+
const pattern1 = /<=\s*([\d,.]+)/;
|
|
25
|
+
// Then check < patterns
|
|
26
|
+
const pattern2 = /inferior\s+a\s+([\d,]+)/;
|
|
27
|
+
const pattern3 = /<\s*([\d,.]+)/;
|
|
28
|
+
const pattern4 = /menor\s+que\s+([\d,]+)/;
|
|
29
|
+
const pattern5 = /menos\s+que\s+([\d,]+)/;
|
|
30
|
+
return [
|
|
31
|
+
pattern1,
|
|
32
|
+
pattern2,
|
|
33
|
+
pattern3,
|
|
34
|
+
pattern4,
|
|
35
|
+
pattern5
|
|
36
|
+
];
|
|
19
37
|
}
|
|
20
38
|
//# sourceMappingURL=regexUtils.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"regexUtils.js","sourceRoot":"","sources":["../../util-ts/regexUtils.ts"],"names":[],"mappings":";;AACA,
|
|
1
|
+
{"version":3,"file":"regexUtils.js","sourceRoot":"","sources":["../../util-ts/regexUtils.ts"],"names":[],"mappings":";;AACA,wDAiBC;AAED,oDAiBC;AArCD,oBAAoB;AACpB,SAAgB,sBAAsB;IAClC,yDAAyD;IACzD,MAAM,QAAQ,GAAG,eAAe,CAAC;IAEjC,wBAAwB;IACxB,MAAM,QAAQ,GAAG,yBAAyB,CAAC;IAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC;IAChC,MAAM,QAAQ,GAAG,wBAAwB,CAAC;IAC1C,MAAM,QAAQ,GAAG,uBAAuB,CAAC;IAEzC,OAAO;QACH,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;KACX,CAAC;AACN,CAAC;AAED,SAAgB,oBAAoB;IAChC,yDAAyD;IACzD,MAAM,QAAQ,GAAG,gBAAgB,CAAC;IAElC,wBAAwB;IACxB,MAAM,QAAQ,GAAG,yBAAyB,CAAC;IAC3C,MAAM,QAAQ,GAAG,eAAe,CAAC;IACjC,MAAM,QAAQ,GAAG,wBAAwB,CAAC;IAC1C,MAAM,QAAQ,GAAG,wBAAwB,CAAC;IAE1C,OAAO;QACH,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;KACX,CAAC;AACN,CAAC"}
|