@openhealth/oht-custom-parser-lib 0.1.11 → 0.1.12

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

@@ -0,0 +1 @@
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package/dist/service/reportCreator.service.d.ts

@@ -0,0 +1,8 @@
+import { DataImportFileUpload } from "../types/oht.types";
+declare function makeApiCallWithRetry(method: string, url: string, data: any, ohtCoreApiKey: string | undefined, retries?: number): Promise<import("axios").AxiosResponse<any, any>>;
+declare function parseErrorObj(resp: any): {
+    message: any;
+    config: any;
+};
+declare function postDataImportFileUploadToCore(dataImportFileUpload: DataImportFileUpload, rejectedStatus: string | undefined, rejectReason: string | undefined, isReportParsedCorrectly: boolean, filename: string, ohtCoreApiKey: string): Promise<DataImportFileUpload | null>;
+export { postDataImportFileUploadToCore, makeApiCallWithRetry, parseErrorObj };

package/dist/service/reportCreator.service.js

@@ -0,0 +1,129 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.postDataImportFileUploadToCore = postDataImportFileUploadToCore;
+exports.makeApiCallWithRetry = makeApiCallWithRetry;
+exports.parseErrorObj = parseErrorObj;
+const https_1 = __importDefault(require("https"));
+const bottleneck_1 = __importDefault(require("bottleneck"));
+const axios_1 = __importDefault(require("axios"));
+const oht_types_1 = require("../types/oht.types");
+const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+const logger = (0, pinoLogger_1.default)();
+const dotenv_1 = __importDefault(require("dotenv"));
+const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
+dotenv_1.default.config({ path: `.env.local` });
+const OHT_CORE_URL = process.env.OHT_CORE_URL;
+const httpsAgent = new https_1.default.Agent({
+    keepAlive: true, // Set keepAlive to true for persistent connections
+    timeout: 60000, // Increase the timeout to 60 seconds
+    secureProtocol: 'TLSv1_2_method',
+});
+// Initialize the rate limiter
+const limiter = new bottleneck_1.default({
+    minTime: 200, // Time in ms between each task (e.g., 200ms)
+    maxConcurrent: 1, // Maximum number of tasks running at the same time
+});
+// Wrap the API call function
+// Wrap the API call function
+const makeApiCall = limiter.wrap(async function (method, url, data, ohtCoreApiKey) {
+    const authHeader = `Basic ${ohtCoreApiKey}`;
+    const headers = {
+        'Authorization': authHeader
+    };
+    return (0, axios_1.default)({
+        method,
+        url,
+        headers,
+        data,
+        httpsAgent,
+    });
+});
+// Function to handle API calls with retries
+async function makeApiCallWithRetry(method, url, data, ohtCoreApiKey, retries = 3) {
+    for (let attempt = 1; attempt <= retries; attempt++) {
+        try {
+            return await makeApiCall(method, url, data, ohtCoreApiKey);
+        }
+        catch (error) {
+            if (attempt === retries) {
+                throw error;
+            }
+            logger.warn({ method, url }, `Attempt ${attempt} failed. Retrying...`);
+        }
+    }
+}
+function parseErrorObj(resp) {
+    let error = {
+        message: resp.message, // Basic error message
+        // stack: resp.stack, // Stack trace for debugging
+        config: resp.config // Axios request config that led to the error
+    };
+    if (resp.response) {
+        error = {
+            ...error,
+            // @ts-expect-error: adding response data and status to error message
+            responseData: resp.response.data,
+            status: resp.response.status,
+        };
+    }
+    else if (resp.request) {
+        error = {
+            ...error,
+            // @ts-expect-error: adding request to error message
+            error: resp.request
+        };
+    }
+    return error;
+}
+async function postDataImportFileUploadToCore(dataImportFileUpload, rejectedStatus, rejectReason, isReportParsedCorrectly, filename, ohtCoreApiKey) {
+    let status = isReportParsedCorrectly ?
+        oht_types_1.DataImportFileUploadStatus.PROCESSED :
+        oht_types_1.DataImportFileUploadStatus.FOR_REVIEW;
+    const patchStatus = rejectedStatus ?? status;
+    const ohtCoreFileUploadUrl = `${OHT_CORE_URL}/v1/file-uploads/${dataImportFileUpload.id}`;
+    const ohtCoreFileUploadSetStatusUrl = `${OHT_CORE_URL}/v1/file-uploads/status/set/${dataImportFileUpload.id}`;
+    const ohtCoreDigitalizationUrl = `${OHT_CORE_URL}/v1/file-uploads/${dataImportFileUpload.id}/digitalization`;
+    try {
+        const initialResponse = await makeApiCallWithRetry('patch', ohtCoreFileUploadUrl, {
+            ...dataImportFileUpload,
+            status: patchStatus,
+            rejectReason,
+            digitalization: {
+                ...dataImportFileUpload.digitalization,
+                pipelineStep: `${dataImportFileUpload.notes}: Render Report`
+            },
+        }, ohtCoreApiKey);
+        logger.info({ response: initialResponse }, `Resp: PATCH status: ${patchStatus} ${ohtCoreFileUploadUrl}, filename: ${filename}`);
+        if (isReportParsedCorrectly && rejectedStatus === undefined) {
+            try {
+                return await (0, auxiliaryFunctions_service_1.postFileUploadSetStatus)(oht_types_1.DataImportFileUploadStatus.READY, dataImportFileUpload.id, filename, ohtCoreApiKey);
+            }
+            catch (error) {
+                const errorDetail = parseErrorObj(error);
+                logger.error({ resp: errorDetail }, `ERROR: POST status: READY ${ohtCoreFileUploadSetStatusUrl}, filename: ${filename}`);
+                throw error;
+            }
+        }
+        logger.warn({
+            isReportParsedCorrectly,
+            rejectedStatus,
+            initialResponse
+        }, `Report not parsed correctly fileUploadID ${dataImportFileUpload.id}, filename: ${filename}`);
+        return initialResponse?.data;
+    }
+    catch (error) {
+        const errorDetail = parseErrorObj(error);
+        logger.error({ resp: errorDetail }, `ERROR: PATCH status: ${patchStatus} ${ohtCoreFileUploadUrl}, rejectedStatus: ${rejectedStatus} filename: ${filename}`);
+        // set digitalization error
+        await makeApiCallWithRetry('patch', ohtCoreDigitalizationUrl, {
+            status: oht_types_1.DigitizationStatus.ERROR,
+            pipelineStep: oht_types_1.PipelineStep.EXAM_DETAIL_EXTRACTION_STEP,
+            pipelineStepData: rejectReason,
+        }, ohtCoreApiKey);
+        return null; // TODO check which dataImportFileUpload should we return
+    }
+}
+//# sourceMappingURL=reportCreator.service.js.map

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

@@ -0,0 +1 @@
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package/dist/service/slackMessages.service.d.ts

@@ -0,0 +1,9 @@
+import { SlackMessage } from "../types/slackMessages.types";
+declare function aggregateMessages(slackMsgErrors: SlackMessage[]): string;
+declare function getSlackFileIssueNotificationMessage(message: string, lab: string, fileUrl: string): Record<string, any>;
+/**
+ * Sends a message to a Slack channel.
+ * @param {Record<string, any>} payload - The message payload to be sent.
+ */
+declare function sendMessageToSlack(payload: Record<string, any>): Promise<void>;
+export { getSlackFileIssueNotificationMessage, sendMessageToSlack, aggregateMessages };

package/dist/service/slackMessages.service.js

@@ -0,0 +1,92 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getSlackFileIssueNotificationMessage = getSlackFileIssueNotificationMessage;
+exports.sendMessageToSlack = sendMessageToSlack;
+exports.aggregateMessages = aggregateMessages;
+const axios_1 = __importDefault(require("axios"));
+const dotenv_1 = __importDefault(require("dotenv"));
+const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+const logger = (0, pinoLogger_1.default)();
+dotenv_1.default.config({ path: `.env.local` });
+// Get the Slack webhook URL from the environment variable
+const slackWebhookUrl = process.env.SLACK_WEBHOOK_URL;
+function aggregateMessages(slackMsgErrors) {
+    const messageMap = slackMsgErrors.reduce((acc, { message, item }) => {
+        if (item) {
+            if (!acc[message]) {
+                acc[message] = [];
+            }
+            acc[message].push(item);
+        }
+        else {
+            if (!acc[message]) {
+                acc[message] = null;
+            }
+        }
+        return acc;
+    }, {});
+    return Object.entries(messageMap)
+        .map(([message, items]) => {
+        if (items) {
+            const joinedItems = items.map(item => `-> ${item}`).join('\n');
+            return message.replace('[PLACEHOLDER]', `[\n${joinedItems}\n]`);
+        }
+        else {
+            return message;
+        }
+    })
+        .join('\n');
+}
+// Function to generate a Slack notification message for file issues
+function getSlackFileIssueNotificationMessage(message, lab, fileUrl) {
+    return {
+        blocks: [
+            {
+                type: 'section',
+                text: {
+                    type: 'mrkdwn',
+                    text: `*Issue processing file from <${lab}>*`,
+                },
+            },
+            {
+                type: 'section',
+                text: {
+                    type: 'mrkdwn',
+                    text: `*File:* <${fileUrl}|View File>`,
+                },
+            },
+            {
+                type: 'divider',
+            },
+            {
+                type: 'section',
+                text: {
+                    type: 'mrkdwn',
+                    text: message,
+                },
+            },
+        ],
+    };
+}
+/**
+ * Sends a message to a Slack channel.
+ * @param {Record<string, any>} payload - The message payload to be sent.
+ */
+async function sendMessageToSlack(payload) {
+    try {
+        const response = await axios_1.default.post(slackWebhookUrl, payload);
+        if (response.status === 200) {
+            logger.info('Message successfully sent to Slack.');
+        }
+        else {
+            logger.info('Error sending message to Slack:', response.status, response.statusText);
+        }
+    }
+    catch (error) {
+        logger.warn('Error sending message to Slack:', error);
+    }
+}
+//# sourceMappingURL=slackMessages.service.js.map

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

@@ -0,0 +1 @@
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package/dist/types/custom-parser.types.d.ts

@@ -0,0 +1,56 @@
+import { SlackMessage } from "./slackMessages.types";
+import { PatientInfo } from "./oht.types";
+export declare const unitSynonyms: Record<string, string>;
+export interface ValueExtraction {
+    valuePosition?: string;
+    defaultValueExtractionFunc?: (value: string) => string | null;
+}
+export interface RangeExtractionResponse {
+    from: number | null;
+    to: number | null;
+    isRangeParsedCorrectly: boolean;
+}
+export interface RangeExtraction {
+    useInternalRange: boolean;
+    rangePosition?: string;
+    extractionRegex?: RegExp;
+    extractionFunc?: (exam: any, labToOhtMapper: LabToOhtMapper, patientInfo: PatientInfo, documentDate?: Date) => RangeExtractionResponse;
+    defaultRangeExtractionFunc?: (labToOhtMapper: LabToOhtMapper, exam: any) => RangeExtractionResponse;
+}
+export interface UnitExtraction {
+    predefinedUnit?: string;
+    unitPosition?: string;
+    extractionRegex?: RegExp;
+    extractionFunc?: (examResult: any) => string | null;
+}
+export interface ReferenceAsAnnotation {
+    use: boolean;
+    position?: string;
+    extractionFunc?: (exam: any, labToOhtMapper: LabToOhtMapper, patientInfo: PatientInfo, documentDate?: Date) => string | null;
+}
+export interface UnknownMeasurementExtraction {
+    biomarkerName?: string;
+    value?: string;
+    unit?: string;
+    annotation?: string;
+}
+export interface LabToOhtMapper {
+    ohtBmId?: number;
+    labKey: string;
+    rawExam?: string;
+    material?: string;
+    method?: string;
+    valueExtraction?: ValueExtraction;
+    unitExtraction?: UnitExtraction;
+    rangeExtraction?: RangeExtraction;
+    referenceAsAnnotation?: ReferenceAsAnnotation;
+    unknownMeasurement?: UnknownMeasurementExtraction;
+}
+export interface LabToOhtContract {
+    labToOhtList: LabToOhtMapper[];
+    slackMessages: SlackMessage[];
+    patientInfo: PatientInfo;
+    documentDate?: Date;
+    sourceFilename: string;
+    externalPatientId: string;
+}

package/dist/types/custom-parser.types.js

@@ -0,0 +1,28 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.unitSynonyms = void 0;
+exports.unitSynonyms = {
+    'mm³': '/mm³',
+    '/mm3': '/mm³',
+    'mg/dl': 'mg/dL',
+    'milh./mm3': 'milhões/mm³',
+    'milh./mm3³': 'milhões/mm³',
+    'u3': 'µm³',
+    'µm ³': 'µm³',
+    '10^6/µ L': '10^6/µL',
+    'mUI/ mL': 'mIU/mL',
+    'miu/ mL': 'mIU/mL',
+    'mui/ml': 'mIU/mL',
+    'ml/min/1,73m2': 'mL/min',
+    'ml/min': 'mL/min/1,73m2',
+    'seg': 's',
+    'NA': 'None',
+    'na': 'None',
+    '': 'None',
+    'IU/L': 'U/L',
+    'u/l': 'IU/L',
+    'mcg/dl': 'µg/dL',
+    'µui/ml': 'µIU/mL',
+    'tera/L': '10^6/µL',
+};
+//# sourceMappingURL=custom-parser.types.js.map

package/dist/types/custom-parser.types.js.map

@@ -0,0 +1 @@
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package/dist/types/oht.types.d.ts

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+export interface OHTPartner {
+    id?: string;
+    _id: string;
+    createdAt: string;
+    updatedAt: string;
+    name: string;
+    countryCode: string;
+    pipeline: string;
+    language: string;
+    labProfileId?: string;
+    reportStyle: string;
+    apiVersion: string;
+    requiredFields: string[];
+    outputTypes: string[];
+    panelCustomisation?: PartnerCustomPanel;
+    reportCustomisation?: ReportCustomisation;
+    style: ReportStyleConfig[];
+}
+export type ReportCustomisation = {
+    rules: any[];
+    displaySettings: ReportDisplaySettings;
+    enableHistoricalData: boolean;
+    enableHistoricalMode: boolean;
+    includeLOINCCodes: boolean;
+};
+export type ReportDisplaySettings = {
+    displayExternalCompatibilityDisclaimer: boolean;
+    displayInternalCompatibilityDisclaimer: boolean;
+    displayBiomarkerSpecificDisclaimer: boolean;
+    displayInternalAnnotations: boolean;
+    displayCalculations: boolean;
+    displayHistoricalGenericDisclaimer: boolean;
+};
+export type PartnerCustomPanel = {
+    includedBiomarkerIds: number[];
+    biomarkerCustomisations: BiomarkerCustomisation[];
+    hubGroupViewEnabled: boolean;
+};
+export type BiomarkerCustomisation = {
+    biomarkerId: number;
+    key: string;
+    targetUnit: string;
+};
+export type LanguageCode = 'en' | 'es' | 'fr' | 'pt';
+export type ReportStyleConfig = {
+    name: string;
+    logoPath?: string;
+    footerLogoPath?: string;
+    showSummary: boolean;
+    showUserImage: boolean;
+    showEvaluation: boolean;
+    generateEvaluation: boolean;
+    language?: LanguageCode;
+    default: boolean;
+    keyPath: string;
+    keyValue: string;
+    originalDownloadEnabled: boolean;
+    showOnlyFirstName: boolean;
+    headless?: boolean;
+};
+export interface SignedUpload {
+    id?: string;
+    _id: string;
+    contentType: string;
+    createdAt: string;
+    partnerId: string;
+    path: string;
+    status: string;
+    updatedAt: string;
+    userId: string;
+    externalId: string;
+}
+export interface MessagePayload {
+    contentType: string;
+    name: string;
+    partnerConfig: OHTPartner;
+    signedUpload: SignedUpload;
+}
+export type DataImportFileUpload = {
+    id: string;
+    description: string;
+    signedUploadId: string;
+    filename: string;
+    mimeType: string;
+    fileSizeBytes: number;
+    uploadedByUserId: string;
+    status: DataImportFileUploadStatus;
+    isArchived: boolean;
+    isDeleted: boolean;
+    lastProcessedByUserId?: string;
+    rejectReason?: string;
+    patientInfo: PatientInfo;
+    documentDate?: Date;
+    labProfileId?: string;
+    labId?: string;
+    partnerId: string;
+    externalPatientId: string;
+    digitalization: Digitization;
+    unknownMeasurements: UnknownMeasurement[];
+    measurements: Measurement[];
+    notes: string;
+    reportStyle: string;
+    createdAt: Date;
+    updatedAt: Date;
+    reportExternalId?: string;
+    documentFingerprint?: string;
+};
+export interface Measurement {
+    biomarkerId: number;
+    valueType: BiomarkerValueType;
+    alphanumericValue: string | null;
+    alphanumericRiskLevelId?: string;
+    value: number | null;
+    comparator: MeasurementValueComparator;
+    minNormalValue: number | null;
+    maxNormalValue: number | null;
+    rangeAnnotation?: string;
+    unit: string;
+    showVisualisationIfAnnotated: boolean;
+    score?: number;
+    method?: string;
+    material?: string;
+    collectionDate?: Date;
+    isDigitalizationApproved?: boolean;
+    isManualChecked?: boolean;
+    isAiParsed?: boolean;
+    isHumanParsed?: boolean;
+}
+export interface UnknownMeasurement {
+    biomarkerName: string;
+    value: string;
+    unit?: string;
+    annotation?: string;
+    isAiParsed?: boolean;
+    isHumanParsed?: boolean;
+}
+export interface PatientInfo {
+    firstName: string;
+    sex: Sex;
+    birthdate?: Date;
+    lastName?: string;
+    cpf?: string;
+    address?: string;
+    height?: number;
+    weight?: number;
+    isDigitalizationApproved: boolean;
+}
+export type Digitization = {
+    status: DigitizationStatus;
+    pipelineStep?: string;
+    pipelineStepPercentageCompleted?: number;
+    pipelineStepData?: Record<string, any>;
+    lastUpdated?: string;
+};
+export declare enum Sex {
+    MALE = "MALE",
+    FEMALE = "FEMALE",
+    OTHER = "OTHER"
+}
+export declare enum DataImportFileUploadStatus {
+    UPLOADED = "UPLOADED",
+    PENDING = "PENDING",
+    PROCESSING = "PROCESSING",
+    FOR_REVIEW = "FOR_REVIEW",
+    IN_REVIEW = "IN_REVIEW",
+    PROCESSED = "PROCESSED",
+    READY = "READY",
+    EDITING = "EDITING",
+    APPROVED = "APPROVED",
+    REJECTED = "REJECTED",
+    MISSING_DATA = "MISSING_DATA"
+}
+export declare enum BiomarkerValueType {
+    ALPHANUMERICAL = "ALPHANUMERICAL",
+    NUMERICAL = "NUMERICAL"
+}
+export declare enum MeasurementValueComparator {
+    EQUAL = "EQUAL",
+    GREATER_THAN = "GREATER_THAN",
+    LESS_THAN = "LESS_THAN"
+}
+export declare enum DigitizationStatus {
+    PENDING = "PENDING",
+    WAITING = "WAITING",
+    PROCESSING = "PROCESSING",
+    DONE = "DONE",
+    ERROR = "ERROR",
+    DISABLED = "DISABLED"
+}
+export declare enum PipelineStep {
+    REPORT_ANALYSIS_STEP = "REPORT_ANALYSIS_STEP",
+    EXAMS_LIST_STEP = "EXAMS_LIST_STEP",
+    EXAM_DETAIL_EXTRACTION_STEP = "EXAM_DETAIL_EXTRACTION_STEP",
+    BIOMARKER_MAPPING_STEP = "BIOMARKER_MAPPING_STEP"
+}
+export type Biomarker = {
+    id: number;
+    title: string;
+    link: string;
+    modifiedAt: string;
+    acf: BiomarkerAcf;
+    createdAt: string;
+    updatedAt: string;
+};
+export type BiomarkerAcf = {
+    goLiveStatus: GoLiveStatus;
+    bm_historical_view_active: boolean;
+    fullName: string;
+    shortName: string;
+    abbreviationName: string;
+    key: string;
+    aliasNames: NameAlias[];
+    standardUnit: string;
+    alternativeUnits: AlternativeUnit[];
+    longDescription: string;
+    shortDescription: string;
+    defaultType: string;
+    priority: string;
+    compatibility: BiomarkerCompatibility;
+    manualCheck: ManualCheck;
+    genericDisclaimerText: string;
+    genericDisclaimerLogic: AcfBiomarkerGenericDisclaimerLogic;
+    customCompatibilityDescription: string;
+    visualRanges: VisualRange[];
+    displayDecimals: number;
+    plausibilityRangeCheck: number;
+    plausibilityRangeCheckHigh: number;
+    referenceRanges: AcfReferenceRange[];
+    greatersmallerthanAllowed: boolean;
+    rangeAnnotation: string;
+    rangeAnnotationCheck: AcfBiomarkerRangeAnnotationCheck;
+    reviewStatus: string;
+    workPrio: string;
+    workingOrder: number;
+};
+export declare enum GoLiveStatus {
+    Green = "green",
+    Yellow = "yellow",
+    Red = "red"
+}
+export type AlternativeUnit = {
+    name: string;
+    conversionFactor: number;
+    displayDecimals: number;
+    isVisible: boolean;
+};
+export type NameAlias = {
+    name: string;
+};
+export type VisualRange = {
+    min: number;
+    max: number;
+    appliesTo: string;
+};
+export type AcfReferenceRange = {
+    from: number;
+    to: number;
+    greaterThan: number;
+    type: ReferenceRangeType;
+    alphanumericalMatch: string;
+    sex: Sex;
+    ageFrom: number;
+    ageTo: number;
+    riskLevel: string;
+    isStandard: boolean;
+    isVisible: boolean;
+    isCriticial: boolean;
+    exceptionCompatibility: string;
+    exceptionUnit: string;
+    exceptionAlphanumericalMatch: string;
+    description: string;
+};
+export declare enum ReferenceRangeType {
+    NUMERICAL = "numerical",
+    GREATER_THAN = "> XX",
+    ALPHANUMERICAL = "alphanumerical"
+}
+export declare enum BiomarkerCompatibility {
+    Internal = "internal",
+    External = "external",
+    ExternalAlphanumerical = "external_alphanumerical",
+    ExternalNoVisualRange = "external_no_visual_range",
+    ExternalStrict = "external_strict",
+    Custom = "custom"
+}
+export declare enum ManualCheck {
+    NO = "No",
+    MANDATORY = "Mandatory"
+}
+export declare enum AcfBiomarkerGenericDisclaimerLogic {
+    DONT_SHOW = "DONT_SHOW",
+    SHOW_ALWAYS = "SHOW_ALWAYS"
+}
+export declare enum AcfBiomarkerRangeAnnotationCheck {
+    DONT_SHOW = "DONT_SHOW",
+    SHOW_WITH_EXTERNAL = "SHOW_WITH_EXTERNAL",
+    SHOW_IF_NO_EXTERNAL = "SHOW_IF_NO_EXTERNAL",
+    SHOW_WOMEN_IF_NO_EXTERNAL = "SHOW_WOMEN_IF_NO_EXTERNAL",
+    SHOW_MEN_IF_NO_EXTERNAL = "SHOW_MEN_IF_NO_EXTERNAL"
+}