Merge branch 'sql-refactoring' into dev

.env.template

@@ -1,12 +1,12 @@
-# MongoDB
-MONGODB_NAME="raccoon-dicom"
-MONGODB_HOSTS=["mongodb"]
-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

.gitignore

@@ -26,4 +26,6 @@
 config/ae-prod.properties
 
 # ignore jscpd output report
-/report
+/report
+
+/jsconfig.json

README.md

@@ -1,29 +1,72 @@
-# raccoon-only-dicom
-Another raccoon focus on dicom. The original raccoon combine the FHIR and DICOM together in MongoDB, I think it will cause performance and maintenance issues. So, here start a new project only for DICOM.
+# raccoon-dicom
+
+<p align="center">
+    <img src="https://user-images.githubusercontent.com/49154622/236814496-a87eb89f-9cbe-4898-a7bf-aa2b27d97596.svg" alt="logo" width="10%"/>
+</p>
+<br/>
+
+Another Raccoon focus on DICOM.
+
+[English](README.md) | [繁體中文](README.zh-TW.md)
+
+---
+
+**Raccoon-DICOM** is a noSQL-based medical image archive designed for managing DICOM images, utilizing MongoDB to store and manage the images while providing RESTful APIs that support [DICOMweb](https://www.dicomstandard.org/dicomweb/") protocols for querying, retrieving, and managing DICOM images.
+
+# Installation
+- [Installation](https://github.com/Chinlinlee/raccoon-dicom/wiki/Installation)
+- Step by Step guide to installing Raccoon-DICOM - Windows (WIP🚧)
+- Step by Step guide to installing Raccoon-DICOM - Ubuntu (WIP🚧)
+
+# Troubleshooting on linux
+- `Unknown VR: Tag not found in data dictionary` when using `STOW-RS`
+    - You need set the `DCMDICTPATH` environment variable
+    - The `dicom.dic` can find in the `/usr/share/libdcmtk{version}` or `./models/DICOM/dcmtk/dicom.dic`
+    > The {version} corresponds to dcmtk version, e.g. 3.6.5 => libdcmtk15
+
+    - Set `DCMDICTPATH` environment variable using command or you can add the command to profile file(`~/.bashrc`,`~/.profile` etc.), example **with dcmtk 3.6.5**:
+    ```sh
+    export DCMDICTPATH=/usr/share/libdcmtk15/dicom.dic
+    ```
+    - Check the environment variable
+    ```sh
+    echo $DCMDICTPATH
+    ```
 
 # Features
 The features implemented here:
-- [QIDO-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.6)
-- [STOW-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.5)
-    - Convert DICOM to ImagingStudy, Endpoint, Patient of FHIR resources and sync FHIR resources to FHIR server
-- [WADO-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.4.1.1.1)
-    - [Retrieve Transaction Instance Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-1)
-    - [Retrieve Transaction Metadata Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-2)
-    - [Retrieve Transaction Rendered Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-3)
-    - [Retrieve Transaction Bulkdata Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1.5-1)
-
-# Environment Requirements
-- node.js >= 16
-- Java JDK >= 11
-
-> **Note**
-> - You should copy opencv_java library to JDK's lib directory
-> - In windows, copy `opencv_java.dll`
-> - In linux, copy `libclib_jiio.so` and `libopencv_java.so`
+## [QIDO-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.6)
+### Support Format (Media Types)
+
+Format | Support |
+---------|----------|
+ application/dicom+json | ✅ | 
+ multipart/related; type="application/dicom+xml | ❌ |
+
+### Support Query Parameter
+
+Query Parameter | Support |
+---------|----------|
+ fuzzymatching | ❌ |
+ includefield | ✅ |
+ limit | ✅ |
+ offset | ✅ |
+
+
+## [STOW-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.5)
+- You can set `SYCN_TO_FHIR_SERVER=true` in .env to convert DICOM to ImagingStudy, Endpoint, Patient of FHIR resources and sync FHIR resources to FHIR server
+## [WADO-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.4.1.1.1)
+- [Retrieve Transaction Instance Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-1)
+- [Retrieve Transaction Metadata Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-2)
+- [Retrieve Transaction Rendered Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-3)
+- [Retrieve Transaction Thumbnail Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-4)
+- [Retrieve Transaction Bulkdata Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1.5-1)
+
 
 # API Documentation
 - raccoon-dicom uses swagger ui hosting openapi.json to generate documentation
 - [API Documentation](https://chinlinlee.github.io/raccoon-dicom/)
 
-
+# Wiki
+Our [wiki](https://github.com/Chinlinlee/raccoon-dicom/wiki) includes a lot of information about raccoon-dicom, we heavily encourage you to take a look!!
 

README.zh-TW.md

@@ -0,0 +1,72 @@
+# raccoon-dicom
+
+<p align="center">
+    <img src="https://user-images.githubusercontent.com/49154622/236814496-a87eb89f-9cbe-4898-a7bf-aa2b27d97596.svg" alt="logo" width="10%"/>
+</p>
+<br/>
+
+Another Raccoon focus on DICOM.
+
+[English](README.md) | [繁體中文](README.zh-TW.md)
+
+---
+
+**Raccoon-DICOM** 是使用 no-SQL 資料庫實作的醫學影像儲存系統(DICOMweb PACS)，其使用 MongoDB 管理 DICOM 影像並提供 [DICOMweb](https://www.dicomstandard.org/dicomweb/") RESTful API 功能進行儲存、查詢以及調閱
+
+
+# 安裝
+- [安裝手冊](https://github.com/Chinlinlee/raccoon-dicom/wiki/Installation.zh-TW)
+- [從 0 開始部屬 Raccoon - Windows](https://github.com/Chinlinlee/raccoon-dicom/wiki/From-zero-to-deploy.zh-TW): 在 Windows 上，一步一步從安裝到部屬
+- 從 0 開始部屬 Raccoon - Ubuntu (WIP🚧)
+
+# Troubleshooting on linux
+- `Unknown VR: Tag not found in data dictionary` when using `STOW-RS`
+    - 您必須設定 `DCMDICTPATH` 環境變數
+    - `dicom.dic` 檔案可以在`/usr/share/libdcmtk{version}`或 `./models/DICOM/dcmtk/dicom.dic`找到
+    > {version} 對應到dcmtk的版本, e.g. 3.6.5 => libdcmtk15
+
+    - 使用指令設定 `DCMDICTPATH` 或者您可以將指令加入到profile檔案中(`~/.bashrc`,`~/.profile` etc.), example **with dcmtk 3.6.5**:
+    ```sh
+    export DCMDICTPATH=/usr/share/libdcmtk15/dicom.dic
+    ```
+    - 檢查環境變數
+    ```sh
+    echo $DCMDICTPATH
+    ```
+
+# 提供之功能
+目前以實作的功能如下：
+## [QIDO-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.6)
+### 支援的格式 (Media Types)
+
+Format | Support |
+---------|----------|
+ application/dicom+json | ✅ | 
+ multipart/related; type="application/dicom+xml | ❌ |
+
+### 支援的查詢參數
+
+Query Parameter | Support |
+---------|----------|
+ fuzzymatching | ❌ |
+ includefield | ✅ |
+ limit | ✅ |
+ offset | ✅ |
+
+
+## [STOW-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.5)
+- 您可以在 .env 設定 `SYCN_TO_FHIR_SERVER=true` 以將 DICOM 轉換為 FHIR ImagingStudy, Endpoint 以及 Patient，並同步這些 Resources 至 FHIR server
+## [WADO-RS](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#sect_10.4.1.1.1)
+- [Retrieve Transaction Instance Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-1)
+- [Retrieve Transaction Metadata Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-2)
+- [Retrieve Transaction Rendered Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-3)
+- [Retrieve Transaction Thumbnail Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1-4)
+- [Retrieve Transaction Bulkdata Resources](https://dicom.nema.org/medical/dicom/current/output/html/part18.html#table_10.4.1.5-1)
+
+
+# API Documentation
+- raccoon-dicom uses swagger ui hosting openapi.json to generate documentation
+- [API Documentation](https://chinlinlee.github.io/raccoon-dicom/)
+
+# Wiki
+我們的[Wiki](https://github.com/Chinlinlee/raccoon-dicom/wiki)含有更多與 Raccoon-DICOM 更多的資訊，非常建議您閱讀一下

api-sql/WADO-URI/service/WADO-URI.service.js

@@ -0,0 +1,99 @@
+const fs = require("fs");
+const _ = require("lodash");
+const renderedService = 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 Magick = require("@models/magick");
+const { NotFoundInstanceError, InvalidFrameNumberError, InstanceGoneError } = require("@error/dicom-instance");
+const { WadoUriService } = require("@root/api/WADO-URI/service/WADO-URI.service");
+const { InstanceModel } = require("@models/sql/models/instance.model");
+const { ApiLogger } = require("@root/utils/logs/api-logger");
+class SqlWadoUriService extends WadoUriService{
+
+    /**
+     * 
+     * @param {import("http").IncomingMessage} req 
+     * @param {import("http").ServerResponse} res 
+     */
+    constructor(req, res, apiLogger) {
+        super(req, res);
+        this.apiLogger = apiLogger;
+    }
+
+    async getDicomInstancePathObj() {
+        let {
+            studyUID,
+            seriesUID,
+            objectUID: instanceUID
+        } = this.request.query;
+
+        let imagePathObj = await InstanceModel.getPathOfInstance({
+            studyUID,
+            seriesUID,
+            instanceUID
+        });
+
+        if (imagePathObj) {
+
+            try {
+                await fs.promises.access(imagePathObj.instancePath, fs.constants.F_OK);
+            } catch(e) {
+                console.error(e);
+                throw new InstanceGoneError("The image is deleted permanently, but meta data remain");
+            }
+
+            return imagePathObj;
+        }
+
+        throw new NotFoundInstanceError("Not found instance");
+    }
+
+    async handleFrameNumberAndGetImageObj() {
+        let imagePathObj = await this.getDicomInstancePathObj();
+        let instanceFramesObj = await renderedService.getInstanceFrameObj(imagePathObj);
+        let instanceTotalFrameNumber = _.get(instanceFramesObj, "x00280008") ? _.get(instanceFramesObj, "x00280008") : 1;
+
+        let windowCenter = _.get(instanceFramesObj, "x00281050.0", "");
+        let windowWidth = _.get(instanceFramesObj, "x00281051.0", "");
+
+        let transferSyntax = _.get(instanceFramesObj, "x00020010");
+        let frameNumber = parseInt(_.get(this.request.query, "frameNumber", 1));
+
+        if (frameNumber > instanceTotalFrameNumber) {
+            throw new InvalidFrameNumberError(`Invalid Frame Number, total ${instanceTotalFrameNumber}, but requested ${frameNumber}`);
+        }
+
+        /** @type {Dcm2JpgExecutor$Dcm2JpgOptions} */
+        let options = await Dcm2JpgExecutor$Dcm2JpgOptions.newInstanceAsync();
+        options.frameNumber = frameNumber;
+
+        if (windowCenter && windowWidth) {
+            options.windowCenter = windowCenter;
+            options.windowWidth = windowWidth;
+        }
+
+        let dicomFilename = instanceFramesObj.instancePath;
+        let jpegFile = dicomFilename.replace(/\.dcm\b/gi , `.${frameNumber-1}.jpg`);
+
+        let getFrameImageStatus = await Dcm2JpgExecutor.convertDcmToJpgFromFilename(
+            dicomFilename,
+            jpegFile,
+            options
+        );
+
+        if (getFrameImageStatus.status) {
+
+            return {
+                imageSharp: sharp(jpegFile),
+                magick: new Magick(jpegFile)
+            };
+        }
+
+        throw new NotFoundInstanceError("Not found DICOM Instance's Jpeg, may convert error");
+    }
+
+}
+
+module.exports.WadoUriService = SqlWadoUriService;
+module.exports.NotFoundInstanceError = NotFoundInstanceError;

api-sql/dicom-web/controller/MWL-RS/service/change-filtered-mwlItem-status.js

@@ -0,0 +1,52 @@
+const { MwlItemModel } = require("@models/sql/models/mwlitems.model");
+const { ChangeFilteredMwlItemStatusService } = require("@root/api/dicom-web/controller/MWL-RS/service/change-filtered-mwlItem-status");
+const { cloneDeep, set } = require("lodash");
+const { convertAllQueryToDicomTag } = require("@root/api/dicom-web/service/base-query.service");
+const { MwlQueryBuilder } = require("./query/mwlQueryBuilder");
+const { DicomWebServiceError, DicomWebStatusCodes } = require("@error/dicom-web-service");
+const { dictionary } = require("@models/DICOM/dicom-tags-dic");
+
+class SqlChangeFilteredMwlItemStatusService extends ChangeFilteredMwlItemStatusService {
+    constructor(req, res) {
+        super(req, res);
+    }
+
+    async changeMwlItemsStatus() {
+        let { status } = this.request.params;
+        let mwlItems = await this.getMwlItems();
+
+        if (mwlItems.length === 0) {
+            throw new DicomWebServiceError(DicomWebStatusCodes.NoSuchObjectInstance, "Can not found any MWL item from query", 404);
+        }
+
+        for (let mwlItem of mwlItems) {
+            mwlItem.status = status;
+            set(mwlItem.json, `${dictionary.keyword.ScheduledProcedureStepSequence}.Value.0.${dictionary.keyword.ScheduledProcedureStepStatus}.Value.0`, status);
+            mwlItem.changed("json", true);
+            await mwlItem.save();
+        }
+
+        return mwlItems.length;
+    }
+
+    async getMwlItems() {
+        let queryBuilder = new MwlQueryBuilder({
+            query: this.query
+        });
+        let q = queryBuilder.build();
+        return await MwlItemModel.findAll(q);
+    }
+
+    initQuery_() {
+        let query = cloneDeep(this.request.query);
+        let queryKeys = Object.keys(query).sort();
+        for (let i = 0; i < queryKeys.length; i++) {
+            let queryKey = queryKeys[i];
+            if (!query[queryKey]) delete query[queryKey];
+        }
+
+        this.query = convertAllQueryToDicomTag(query, false);
+    }
+}
+
+module.exports.ChangeFilteredMwlItemStatusService = SqlChangeFilteredMwlItemStatusService;

api-sql/dicom-web/controller/MWL-RS/service/change-mwlItem-status.js

@@ -0,0 +1,44 @@
+const _ = require("lodash");
+const { DicomWebServiceError, DicomWebStatusCodes } = require("@error/dicom-web-service");
+const { dictionary } = require("@models/DICOM/dicom-tags-dic");
+const { ChangeMwlItemStatusService } = require("@root/api/dicom-web/controller/MWL-RS/service/change-mwlItem-status");
+const { MwlItemModel } = require("@models/sql/models/mwlitems.model");
+const { Op } = require("sequelize");
+
+class SqlChangeMwlItemStatusService extends ChangeMwlItemStatusService {
+    constructor(req, res) {
+        super(req, res);
+    }
+
+    async changeMwlItemsStatus() {
+        let { status } = this.request.params;
+        let mwlItem = await this.getMwlItemByStudyUIDAndSpsID();
+        if (!mwlItem) {
+            throw new DicomWebServiceError(DicomWebStatusCodes.NoSuchObjectInstance, "No such object instance", 404);
+        }
+
+        mwlItem.sps_status = status;
+        _.set(mwlItem.json, `${dictionary.keyword.ScheduledProcedureStepSequence}.Value.0.${dictionary.keyword.ScheduledProcedureStepStatus}.Value.0`, status);
+        mwlItem.changed("json", true);
+        await mwlItem.save();
+
+        return mwlItem.json;
+    }
+
+    async getMwlItemByStudyUIDAndSpsID() {
+        return await MwlItemModel.findOne({
+            where: {
+                [Op.and]: [
+                    {
+                        sps_id: this.request.params.spsID
+                    },
+                    {
+                        study_instance_uid: this.request.params.studyUID
+                    }
+                ]
+            }
+        });
+    }
+}
+
+module.exports.ChangeMwlItemStatusService = SqlChangeMwlItemStatusService;