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

package/dist/types/oht.types.js

@@ -0,0 +1,90 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AcfBiomarkerRangeAnnotationCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.ManualCheck = exports.BiomarkerCompatibility = exports.ReferenceRangeType = exports.GoLiveStatus = exports.PipelineStep = exports.DigitizationStatus = exports.MeasurementValueComparator = exports.BiomarkerValueType = exports.DataImportFileUploadStatus = exports.Sex = void 0;
+var Sex;
+(function (Sex) {
+    Sex["MALE"] = "MALE";
+    Sex["FEMALE"] = "FEMALE";
+    Sex["OTHER"] = "OTHER";
+})(Sex || (exports.Sex = Sex = {}));
+var DataImportFileUploadStatus;
+(function (DataImportFileUploadStatus) {
+    DataImportFileUploadStatus["UPLOADED"] = "UPLOADED";
+    DataImportFileUploadStatus["PENDING"] = "PENDING";
+    DataImportFileUploadStatus["PROCESSING"] = "PROCESSING";
+    DataImportFileUploadStatus["FOR_REVIEW"] = "FOR_REVIEW";
+    DataImportFileUploadStatus["IN_REVIEW"] = "IN_REVIEW";
+    DataImportFileUploadStatus["PROCESSED"] = "PROCESSED";
+    DataImportFileUploadStatus["READY"] = "READY";
+    DataImportFileUploadStatus["EDITING"] = "EDITING";
+    DataImportFileUploadStatus["APPROVED"] = "APPROVED";
+    DataImportFileUploadStatus["REJECTED"] = "REJECTED";
+    DataImportFileUploadStatus["MISSING_DATA"] = "MISSING_DATA";
+})(DataImportFileUploadStatus || (exports.DataImportFileUploadStatus = DataImportFileUploadStatus = {}));
+var BiomarkerValueType;
+(function (BiomarkerValueType) {
+    BiomarkerValueType["ALPHANUMERICAL"] = "ALPHANUMERICAL";
+    BiomarkerValueType["NUMERICAL"] = "NUMERICAL";
+})(BiomarkerValueType || (exports.BiomarkerValueType = BiomarkerValueType = {}));
+var MeasurementValueComparator;
+(function (MeasurementValueComparator) {
+    MeasurementValueComparator["EQUAL"] = "EQUAL";
+    MeasurementValueComparator["GREATER_THAN"] = "GREATER_THAN";
+    MeasurementValueComparator["LESS_THAN"] = "LESS_THAN";
+})(MeasurementValueComparator || (exports.MeasurementValueComparator = MeasurementValueComparator = {}));
+var DigitizationStatus;
+(function (DigitizationStatus) {
+    DigitizationStatus["PENDING"] = "PENDING";
+    DigitizationStatus["WAITING"] = "WAITING";
+    DigitizationStatus["PROCESSING"] = "PROCESSING";
+    DigitizationStatus["DONE"] = "DONE";
+    DigitizationStatus["ERROR"] = "ERROR";
+    DigitizationStatus["DISABLED"] = "DISABLED";
+})(DigitizationStatus || (exports.DigitizationStatus = DigitizationStatus = {}));
+var PipelineStep;
+(function (PipelineStep) {
+    PipelineStep["REPORT_ANALYSIS_STEP"] = "REPORT_ANALYSIS_STEP";
+    PipelineStep["EXAMS_LIST_STEP"] = "EXAMS_LIST_STEP";
+    PipelineStep["EXAM_DETAIL_EXTRACTION_STEP"] = "EXAM_DETAIL_EXTRACTION_STEP";
+    PipelineStep["BIOMARKER_MAPPING_STEP"] = "BIOMARKER_MAPPING_STEP";
+})(PipelineStep || (exports.PipelineStep = PipelineStep = {}));
+var GoLiveStatus;
+(function (GoLiveStatus) {
+    GoLiveStatus["Green"] = "green";
+    GoLiveStatus["Yellow"] = "yellow";
+    GoLiveStatus["Red"] = "red";
+})(GoLiveStatus || (exports.GoLiveStatus = GoLiveStatus = {}));
+var ReferenceRangeType;
+(function (ReferenceRangeType) {
+    ReferenceRangeType["NUMERICAL"] = "numerical";
+    ReferenceRangeType["GREATER_THAN"] = "> XX";
+    ReferenceRangeType["ALPHANUMERICAL"] = "alphanumerical";
+})(ReferenceRangeType || (exports.ReferenceRangeType = ReferenceRangeType = {}));
+var BiomarkerCompatibility;
+(function (BiomarkerCompatibility) {
+    BiomarkerCompatibility["Internal"] = "internal";
+    BiomarkerCompatibility["External"] = "external";
+    BiomarkerCompatibility["ExternalAlphanumerical"] = "external_alphanumerical";
+    BiomarkerCompatibility["ExternalNoVisualRange"] = "external_no_visual_range";
+    BiomarkerCompatibility["ExternalStrict"] = "external_strict";
+    BiomarkerCompatibility["Custom"] = "custom";
+})(BiomarkerCompatibility || (exports.BiomarkerCompatibility = BiomarkerCompatibility = {}));
+var ManualCheck;
+(function (ManualCheck) {
+    ManualCheck["NO"] = "No";
+    ManualCheck["MANDATORY"] = "Mandatory";
+})(ManualCheck || (exports.ManualCheck = ManualCheck = {}));
+var AcfBiomarkerGenericDisclaimerLogic;
+(function (AcfBiomarkerGenericDisclaimerLogic) {
+    AcfBiomarkerGenericDisclaimerLogic["DONT_SHOW"] = "DONT_SHOW";
+    AcfBiomarkerGenericDisclaimerLogic["SHOW_ALWAYS"] = "SHOW_ALWAYS";
+})(AcfBiomarkerGenericDisclaimerLogic || (exports.AcfBiomarkerGenericDisclaimerLogic = AcfBiomarkerGenericDisclaimerLogic = {}));
+var AcfBiomarkerRangeAnnotationCheck;
+(function (AcfBiomarkerRangeAnnotationCheck) {
+    AcfBiomarkerRangeAnnotationCheck["DONT_SHOW"] = "DONT_SHOW";
+    AcfBiomarkerRangeAnnotationCheck["SHOW_WITH_EXTERNAL"] = "SHOW_WITH_EXTERNAL";
+    AcfBiomarkerRangeAnnotationCheck["SHOW_IF_NO_EXTERNAL"] = "SHOW_IF_NO_EXTERNAL";
+    AcfBiomarkerRangeAnnotationCheck["SHOW_WOMEN_IF_NO_EXTERNAL"] = "SHOW_WOMEN_IF_NO_EXTERNAL";
+    AcfBiomarkerRangeAnnotationCheck["SHOW_MEN_IF_NO_EXTERNAL"] = "SHOW_MEN_IF_NO_EXTERNAL";
+})(AcfBiomarkerRangeAnnotationCheck || (exports.AcfBiomarkerRangeAnnotationCheck = AcfBiomarkerRangeAnnotationCheck = {}));
+//# sourceMappingURL=oht.types.js.map

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

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

@@ -0,0 +1,5 @@
+export interface SlackMessage {
+    type: string;
+    message: string;
+    item?: string;
+}

package/dist/types/slackMessages.types.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=slackMessages.types.js.map

package/dist/types/slackMessages.types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"slackMessages.types.js","sourceRoot":"","sources":["../../types/slackMessages.types.ts"],"names":[],"mappings":""}

package/dist/util-ts/dataUtils.d.ts

@@ -0,0 +1,3 @@
+export declare function isBiomarkerValueNumerical(biomarker: any): boolean;
+export declare function isBiomarkerExternalNoVisualRange(biomarker: any): boolean;
+export declare const extractValue: (obj: any, position?: string) => any;

package/dist/util-ts/dataUtils.js

@@ -0,0 +1,19 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.extractValue = void 0;
+exports.isBiomarkerValueNumerical = isBiomarkerValueNumerical;
+exports.isBiomarkerExternalNoVisualRange = isBiomarkerExternalNoVisualRange;
+function isBiomarkerValueNumerical(biomarker) {
+    return biomarker?.acf?.compatibility !== 'external_alphanumerical';
+}
+function isBiomarkerExternalNoVisualRange(biomarker) {
+    return biomarker?.acf?.compatibility === 'external_no_visual_range';
+}
+const extractValue = (obj, position) => {
+    if (!position)
+        return null;
+    const keys = position.split('.');
+    return keys.reduce((acc, key) => acc?.[key], obj);
+};
+exports.extractValue = extractValue;
+//# sourceMappingURL=dataUtils.js.map

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

@@ -0,0 +1 @@
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package/dist/util-ts/googleStorageUtils.d.ts

@@ -0,0 +1,3 @@
+declare function readFileFromBucket(bucketName: string, fileName: string): Promise<string>;
+declare function uploadFileBufferToGCS(bucketName: string, filename: string, fileBuffer: Buffer): Promise<void>;
+export { readFileFromBucket, uploadFileBufferToGCS };

package/dist/util-ts/googleStorageUtils.js

@@ -0,0 +1,47 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readFileFromBucket = readFileFromBucket;
+exports.uploadFileBufferToGCS = uploadFileBufferToGCS;
+const storage_1 = require("@google-cloud/storage");
+// Function to read a file from a Google Cloud Storage bucket
+async function readFileFromBucket(bucketName, fileName) {
+    const storage = new storage_1.Storage();
+    const bucket = storage.bucket(bucketName);
+    const file = bucket.file(fileName);
+    return new Promise((resolve, reject) => {
+        let fileContent = '';
+        const readStream = file.createReadStream();
+        readStream.setEncoding('utf-8');
+        readStream
+            .on('error', (error) => {
+            reject(error);
+        })
+            .on('data', (chunk) => {
+            fileContent += chunk;
+        })
+            .on('end', () => {
+            resolve(fileContent);
+        });
+    });
+}
+// Function to upload a file buffer to Google Cloud Storage
+function uploadFileBufferToGCS(bucketName, filename, fileBuffer) {
+    return new Promise(async (resolve, reject) => {
+        const writeStream = createWriteStream(bucketName, filename);
+        writeStream.on('finish', resolve);
+        writeStream.on('error', reject);
+        writeStream.write(fileBuffer);
+        writeStream.end();
+    });
+}
+// Function to create a writable stream to upload a file
+const createWriteStream = (bucketName, filename, contentType) => {
+    const storage = new storage_1.Storage();
+    const bucket = storage.bucket(bucketName);
+    const file = bucket.file(filename);
+    return file.createWriteStream({
+        gzip: true,
+        contentType,
+    });
+};
+//# sourceMappingURL=googleStorageUtils.js.map

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

@@ -0,0 +1 @@
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package/dist/util-ts/pinoLogger.d.ts

@@ -0,0 +1,12 @@
+import pino from 'pino';
+type PinoConfig = {
+    messageKey?: string;
+    formatters?: {
+        level?: (label: string, number: number) => {
+            severity: string;
+            level: number;
+        };
+    };
+};
+declare const _default: (pinoConfigOverrides?: PinoConfig) => pino.Logger;
+export default _default;

package/dist/util-ts/pinoLogger.js

@@ -0,0 +1,31 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const pino_1 = __importDefault(require("pino"));
+// Define the severity lookup object
+const SeverityLookup = {
+    'default': 'DEFAULT',
+    'silly': 'DEFAULT',
+    'verbose': 'DEBUG',
+    'debug': 'DEBUG',
+    'http': 'notice',
+    'info': 'INFO',
+    'warn': 'WARNING',
+    'error': 'ERROR',
+};
+// Define the default Pino configuration
+const defaultPinoConfig = {
+    messageKey: 'message',
+    formatters: {
+        level(label, number) {
+            return { severity: SeverityLookup[label] || 'DEFAULT', level: number };
+        },
+    },
+};
+// Export a function that creates a Pino logger instance with the provided configuration overrides
+exports.default = (pinoConfigOverrides = {}) => {
+    return (0, pino_1.default)({ ...defaultPinoConfig, ...pinoConfigOverrides });
+};
+//# sourceMappingURL=pinoLogger.js.map

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

@@ -0,0 +1 @@
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package/dist/util-ts/regexUtils.d.ts

@@ -0,0 +1,2 @@
+export declare function getGreaterThanPatterns(): RegExp[];
+export declare function getLowerThanPatterns(): RegExp[];

package/dist/util-ts/regexUtils.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getGreaterThanPatterns = getGreaterThanPatterns;
+exports.getLowerThanPatterns = getLowerThanPatterns;
+// utils/patterns.ts
+function getGreaterThanPatterns() {
+    const pattern1 = /superior\s+a\s+([\d,]+)/;
+    const pattern2 = />\s?([\d,]+)/;
+    const pattern3 = /maior\s+que\s+([\d,]+)/;
+    const pattern4 = /mais\s+que\s+([\d,]+)/;
+    return [pattern1, pattern2, pattern3, pattern4];
+}
+function getLowerThanPatterns() {
+    const pattern1 = /inferior\s+a\s+([\d,]+)/;
+    const pattern2 = /<\s?(\d+[.,]\d+)/;
+    const pattern3 = /menor\s+que\s+([\d,]+)/;
+    const pattern4 = /menos\s+que\s+([\d,]+)/;
+    return [pattern1, pattern2, pattern3, pattern4];
+}
+//# sourceMappingURL=regexUtils.js.map

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

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.1.11",
+  "version": "0.1.12",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",