Merge branch 'dev'

Chinlinlee · Jan 24, 2024 · 7988265 · 7988265
2 parents b740097 + 73a4dc7
commit 7988265
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Showing 195 changed files with 8,561 additions and 8,567 deletions.
diff --git a/.dependency-cruiser.js b/.dependency-cruiser.js
diff --git a/.env.template b/.env.template
@@ -1,13 +1,23 @@
 # MongoDB
-MONGODB_NAME="raccoon-dicom"
-MONGODB_HOSTS=["mongodb"]
+MONGODB_NAME="raccoon"
+MONGODB_HOSTS=["127.0.0.1"]
 MONGODB_PORTS=[27017]
 MONGODB_USER="root"
 MONGODB_PASSWORD="root"
 MONGODB_AUTH_SOURCE="admin"
 MONGODB_OPTIONS=""
 MONGODB_IS_SHARDING_MODE=false
 
+# SQL
+SQL_HOST="127.0.0.1"
+SQL_PORT="5432"
+SQL_DB="raccoon"
+SQL_TYPE="postgres"
+SQL_USERNAME="postgres"
+SQL_PASSWORD="postgres"
+SQL_LOGGING=false
+SQL_FORCE_SYNC=false
+
 # Server
 SERVER_PORT=8081
 SERVER_SESSION_SECRET_KEY="secret-key"

diff --git a/.gitignore b/.gitignore
@@ -23,4 +23,7 @@
 /config/logback.xml
 /pm2log/**
 !pm2log/.gitkeep
-config/ae-prod.properties
+config/ae-prod.properties
+
+# ignore jscpd output report
+/report
diff --git a/.jscpd.json b/.jscpd.json
@@ -0,0 +1,19 @@
+{
+    "threshold": 0.1,
+    "reporters": [
+        "html",
+        "console"
+    ],
+    "ignore": [
+        "**/node_modules/**",
+        "models/DICOM/dcm4che/wrapper/**/*.ts",
+        "models/DICOM/dcm4che/wrapper/**/*.js",
+        "docs/**",
+        "test/**"
+    ],
+    "ignorePattern": [
+        "const .* require.*"
+    ],
+    "absolute": true,
+    "gitignore": true
+}
diff --git a/api/WADO-URI/controller/retrieveInstance.js b/api/WADO-URI/controller/retrieveInstance.js
@@ -1,44 +1,46 @@
-const { WadoUriService, NotFoundInstanceError } = require("../service/WADO-URI.service");
+const { WadoUriService } = require("@api/WADO-URI/service/WADO-URI.service");
 const { Controller } = require("../../controller.class");
 const { ApiLogger } = require("../../../utils/logs/api-logger");
+const { ApiErrorArrayHandler } = require("@error/api-errors.handler");
+const { EventOutcomeIndicator } = require("@models/DICOM/audit/auditUtils");
 
 class RetrieveSingleInstanceController extends Controller {
     constructor(req, res) {
         super(req, res);
-        this.service = new WadoUriService(req, res);
         this.logger = new ApiLogger(this.request, "WADO-URI");
+        this.service = new WadoUriService(req, res, this.logger);
     }
 
     async mainProcess() {
-        let { 
+        let {
             contentType
         } = this.request.query;
 
         if (!contentType) contentType = this.request.headers.accept;
 
         try {
 
-            if (contentType === "application/dicom") {
-                this.service.getAndResponseDicomInstance();
+            if (contentType === "application/dicom" || !contentType) {
+
+                let dicomInstanceReadStream = await this.service.getDicomInstanceReadStream();
+                this.response.setHeader("Content-Type", "application/dicom");
+                dicomInstanceReadStream.pipe(this.response);
             } else if (contentType === "image/jpeg") {
-                this.service.getAndResponseJpeg();
-            } else if (!contentType) {
-                this.service.getAndResponseDicomInstance();
+                let jpegBuffer = await this.service.handleRequestQueryAndGetJpeg();
+
+                this.response.setHeader("Content-Type", "image/jpeg");
+
+                this.response.end(jpegBuffer, "buffer");
             }
 
-        } catch(e) {
-            let errorStr = JSON.stringify(e, Object.getOwnPropertyNames(e));
-            this.logger.error(errorStr);
-
-            this.response.writeHead(500, {
-                "Content-Type": "application/dicom+json"
-            });
-            this.response.end(JSON.stringify({
-                code: 500,
-                message: errorStr
-            }));
+            this.response.on("finish", () => this.service.auditInstanceTransferred());
+
+        } catch (e) {
+            this.service.auditInstanceTransferred(EventOutcomeIndicator.MajorFailure);
+            let apiErrorArrayHandler = new ApiErrorArrayHandler(this.response, this.logger, e);
+            return apiErrorArrayHandler.doErrorResponse();
         }
-        
+
     }
 
 }
@@ -48,7 +50,7 @@ class RetrieveSingleInstanceController extends Controller {
  * @param {import("http").IncomingMessage} req 
  * @param {import("http").ServerResponse} res 
  */
-module.exports = async function(req, res) {
+module.exports = async function (req, res) {
     let controller = new RetrieveSingleInstanceController(req, res);
 
     await controller.doPipeline();

diff --git a/api/WADO-URI/service/WADO-URI.service.js b/api/WADO-URI/service/WADO-URI.service.js
@@ -1,17 +1,20 @@
 const mongoose = require("mongoose");
 const fs = require("fs");
 const _ = require("lodash");
-const renderedService = require("../../dicom-web/controller/WADO-RS/service/rendered.service");
+const { RenderedImageProcessParameterHandler, getInstanceFrameObj } = require("../../dicom-web/controller/WADO-RS/service/rendered.service");
 const { Dcm2JpgExecutor } = require("../../../models/DICOM/dcm4che/wrapper/org/github/chinlinlee/dcm2jpg/Dcm2JpgExecutor");
 const { Dcm2JpgExecutor$Dcm2JpgOptions } = require("../../../models/DICOM/dcm4che/wrapper/org/github/chinlinlee/dcm2jpg/Dcm2JpgExecutor$Dcm2JpgOptions");
-const sharp = require('sharp');
+const imageSizeOf = require("image-size");
+const { promisify } = require("util");
+const imageSizeOfPromise = promisify(imageSizeOf);
 const Magick = require("../../../models/magick");
 const { NotFoundInstanceError, InvalidFrameNumberError, InstanceGoneError } = require("../../../error/dicom-instance");
-const dicomModel = require("../../../models/mongodb/models/dicom");
+const { InstanceModel } = require("@dbModels/instance.model");
 const { AuditManager } = require("@models/DICOM/audit/auditManager");
 const { EventType } = require("@models/DICOM/audit/eventType");
 const { EventOutcomeIndicator } = require("@models/DICOM/audit/auditUtils");
 const { DicomWebService } = require("@root/api/dicom-web/service/dicom-web.service");
+const { ApiErrorArrayHandler } = require("@error/api-errors.handler");
 
 class WadoUriService {
 
@@ -20,95 +23,17 @@ class WadoUriService {
      * @param {import("http").IncomingMessage} req 
      * @param {import("http").ServerResponse} res 
      */
-    constructor(req, res) {
+    constructor(req, res, apiLogger) {
         this.request = req;
         this.response = res;
+        this.apiLogger = apiLogger;
         this.auditBeginTransferring();
-    }
-
-    async getAndResponseDicomInstance() {
-        try {
-
-            let dicomInstanceReadStream = await this.getDicomInstanceReadStream();
-
-            this.response.setHeader("Content-Type", "application/dicom");
-            dicomInstanceReadStream.pipe(this.response);
-            this.auditInstanceTransferred();
-
-        } catch (e) {
-            this.auditInstanceTransferred(EventOutcomeIndicator.MajorFailure);
-
-            if (e instanceof NotFoundInstanceError) {
-                this.response.writeHead(404, {
-                    "Content-Type": "application/dicom+json"
-                });
-                return this.response.end();
-            } else if (e instanceof InstanceGoneError) {
-                this.response.writeHead(410, {
-                    "Content-Type": "application/dicom+json"
-                });
-                return this.response.end(JSON.stringify({
-                    Details: e.message,
-                    HttpStatus: 410,
-                    Message: "Image Gone",
-                    Method: "GET"
-                }));
-            }
 
-            throw e;
-        }
+        let clonedRequestQuery = _.cloneDeep(this.request?.query);
+        _.set(clonedRequestQuery, "imageQuality", _.get(this.request.query, "imageQuality", ""));
+        this.renderedImageProcessParameterHandler = new RenderedImageProcessParameterHandler(clonedRequestQuery);
     }
 
-    async getAndResponseJpeg() {
-        try {
-
-            let jpegBuffer = await this.handleRequestQueryAndGetJpeg();
-
-            this.response.setHeader("Content-Type", "image/jpeg");
-
-            this.response.end(jpegBuffer, "buffer");
-            this.auditInstanceTransferred();
-
-        } catch (e) {
-            this.auditInstanceTransferred(EventOutcomeIndicator.MajorFailure);
-
-            if (e instanceof NotFoundInstanceError) {
-
-                this.response.writeHead(404, {
-                    "Content-Type": "application/dicom+json"
-                });
-                return this.response.end();
-
-            } else if (e instanceof InvalidFrameNumberError) {
-
-                this.response.writeHead(400, {
-                    "Content-Type": "application/dicom+json"
-                });
-
-                return this.response.end(JSON.stringify({
-                    Details: e.message,
-                    HttpStatus: 400,
-                    Message: "Bad request",
-                    Method: "GET"
-                }));
-
-            } else if (e instanceof InstanceGoneError) {
-                this.response.writeHead(410, {
-                    "Content-Type": "application/dicom+json"
-                });
-                return this.response.end(JSON.stringify({
-                    Details: e.message,
-                    HttpStatus: 410,
-                    Message: "Image Gone",
-                    Method: "GET"
-                }));
-            }
-
-            throw e;
-        }
-    }
-
-
     /**
      * @throws {NotFoundInstanceError}
      * @returns {Promise<fs.ReadStream>}
@@ -127,7 +52,7 @@ class WadoUriService {
             objectUID: instanceUID
         } = this.request.query;
 
-        let imagePathObj = await dicomModel.getPathOfInstance({
+        let imagePathObj = await InstanceModel.getPathOfInstance({
             studyUID,
             seriesUID,
             instanceUID
@@ -154,13 +79,13 @@ class WadoUriService {
     async handleRequestQueryAndGetJpeg() {
 
         let {
-            imageSharp,
+            imageSize,
             magick
         } = await this.handleFrameNumberAndGetImageObj();
 
         await this.handleImageQuality(magick);
-        await this.handleRegion(this.request.query, imageSharp, magick);
-        await this.handleRowsAndColumns(this.request.query, imageSharp, magick);
+        await this.handleRegion(this.request.query, imageSize, magick);
+        await this.handleRowsAndColumns(this.request.query, imageSize, magick);
         await this.handleImageICCProfile(this.request.query, magick, this.request.query.objectUID);
 
         await magick.execCommand();
@@ -170,10 +95,7 @@ class WadoUriService {
 
     async handleFrameNumberAndGetImageObj() {
         let imagePathObj = await this.getDicomInstancePathObj();
-        let instanceFramesObj = await renderedService.getInstanceFrameObj(imagePathObj, {
-            "00281050": 1,
-            "00281051": 1
-        });
+        let instanceFramesObj = await getInstanceFrameObj(imagePathObj);
         let instanceTotalFrameNumber = _.get(instanceFramesObj, "00280008.Value.0", 1);
         let windowCenter = _.get(instanceFramesObj, "00281050.Value.0", "");
         let windowWidth = _.get(instanceFramesObj, "00281051.Value.0", "");
@@ -206,7 +128,7 @@ class WadoUriService {
         if (getFrameImageStatus.status) {
 
             return {
-                imageSharp: sharp(jpegFile),
+                imageSize: await imageSizeOfPromise(jpegFile),
                 magick: new Magick(jpegFile)
             };
         }
@@ -215,17 +137,21 @@ class WadoUriService {
     }
 
     async handleImageQuality(magick) {
-        renderedService.handleImageQuality({
-            quality: _.get(this.request.query, "imageQuality", "")
-        }, magick);
+        this.renderedImageProcessParameterHandler.handleImageQuality(magick);
     }
 
-    async handleRegion(param, imageSharp, magick) {
+    /**
+     * 
+     * @param {Object} param 
+     * @param {string} param.region
+     * @param {{height: number, width: number}} imageSize 
+     * @param {Magick} magick 
+     */
+    async handleRegion(param, imageSize, magick) {
         if (param.region) {
             let [xMin, yMin, xMax, yMax] = param.region.split(",").map(v => parseFloat(v));
-            let imageMetadata = await imageSharp.metadata();
-            let imageWidth = imageMetadata.width;
-            let imageHeight = imageMetadata.height;
+            let imageWidth = imageSize.width;
+            let imageHeight = imageSize.height;
             let extractLeft = imageWidth * xMin;
             let extractTop = imageHeight * yMin;
             let extractWidth = imageWidth * xMax - extractLeft;
@@ -234,21 +160,28 @@ class WadoUriService {
         }
     }
 
-    async handleRowsAndColumns(param, imageSharp, magick) {
-        let imageMetadata = await imageSharp.metadata();
+    /**
+     * 
+     * @param {Object} param 
+     * @param {string} param.rows
+     * @param {string} param.columns
+     * @param {{height: number, width: number}} imageSize 
+     * @param {Magick} magick 
+     */
+    async handleRowsAndColumns(param, imageSize, magick) {
         let rows = Number(param.rows);
         let columns = Number(param.columns);
         if (param.rows && param.columns) {
             magick.resize(rows, columns);
         } else if (param.rows) {
-            magick.resize(rows, imageMetadata.height);
+            magick.resize(rows, imageSize.height);
         } else if (param.columns) {
-            magick.resize(imageMetadata.width, columns);
+            magick.resize(imageSize.width, columns);
         }
     }
 
     async handleImageICCProfile(magick) {
-        await renderedService.handleImageICCProfile(this.request.query, magick, this.request.query.objectUID);
+        await this.renderedImageProcessParameterHandler.handleImageICCProfile(magick, this.request.query.objectUID);
     }
 
     async auditBeginTransferring() {