feat: add bulkdata API

- Add `writeBulkData` method for bulk data at `multipartWriter` class. - Add bulk data object type definition - Use multipartWriter refactoring of original **single** bulkdata API - Add `bulkdata` API in `api/diocm-web` directory - Fix incorrect multipart structure. Remove `CRLF` in `writeContentLength` and move in `writeBufferData` to avoid the content-length is not last header. > The correct structure --++++CRLF Content-Type: media-type CRLF Content-Location: url CRLF (Content-Length: uint CRLF / Content-Encoding: encoding CRLF) [Content-Description: {description} CRLF] CRLF payload CRLF --++++CRLF Content-Type: media-type CRLF . . . payload CRLF --++++CRLF zh_TW: - 在 `multipartWriter` 新增 `writeBulkData` 功能以處理 bulkdata 的 multipart 資料 - 新增 bulk data 物件聲明 - 使用 multipartWriter 重構原本取得單個 bulkdata 的 API - `api/diocm-web` 新增 `bulkdata` 的 API - 修正錯誤的 multipart 結構。移除在`writeContentLength`內的一個 `CRLF`並搬移到`writeBufferData` 以防 content-length 不是最後一個 header。 > 正確的 multipart 結構 --++++CRLF Content-Type: media-type CRLF Content-Location: url CRLF (Content-Length: uint CRLF / Content-Encoding: encoding CRLF) [Content-Description: {description} CRLF] CRLF payload CRLF --++++CRLF Content-Type: media-type CRLF . . . payload CRLF --++++CRLF
cylab-tw · Apr 20, 2022 · e2d3d9a · e2d3d9a
1 parent eec3d8a
commit e2d3d9a
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Showing 6 changed files with 157 additions and 27 deletions.
diff --git a/api/dicom-web/controller/bulkdata.js b/api/dicom-web/controller/bulkdata.js
@@ -0,0 +1,51 @@
+const mongodb = require("../../../models/mongodb");
+const _ = require('lodash');
+const uuid = require('uuid');
+const fs = require('fs');
+const {
+    MultipartWriter
+} = require('../../../utils/multipartWriter');
+
+/**
+ * 
+ * @param {import('express').Request} req 
+ * @param {import('express').Response} res 
+ * @returns 
+ */
+module.exports = async function (req, res) {
+    let {
+        studyID,
+        seriesID,
+        instanceID
+    } = req.params;
+    let bulkDataList = await mongodb["dicomBulkData"].find({
+        $and: [
+            {
+                $or : [
+                    {
+                        studyUID: studyID
+                    },
+                    {
+                        seriesUID: seriesID
+                    },
+                    {
+                        instanceUID: instanceID
+                    }
+                ]
+
+            }
+        ]
+    })
+    .exec();
+
+    let multipartWriter = new MultipartWriter([], res, req);
+    multipartWriter.setHeaderMultipartRelatedContentType("application/octet-stream");
+    let isFirst = true;
+    for (let bulkData of bulkDataList) {
+        await multipartWriter.writeBulkData(bulkData, isFirst);
+        isFirst = false;
+    }
+    await multipartWriter.writeFinalBoundary();
+
+    return res.end();
+}
diff --git a/api/dicom-web/index.js b/api/dicom-web/index.js
@@ -76,4 +76,13 @@ router.get('/studies/:studyID/instances' , require('./controller/qido-rs-study-i
 router.get('/series' , require('./controller/qido-rs-series'));
 //#endregion
 
+//#region bulk data
+
+router.get('/studies/:studyID/bulkdata', require('./controller/bulkdata'));
+router.get('/studies/:studyID/series/:seriesID/bulkdata', require('./controller/bulkdata'));
+router.get('/studies/:studyID/series/:seriesID/instances/:instanceID/bulkdata', require('./controller/bulkdata'));
+
+//#endregion
+
+
 module.exports = router;
diff --git a/api/dicom/controller/bulkData.js b/api/dicom/controller/bulkData.js
@@ -1,18 +1,16 @@
 const mongodb = require("../../../models/mongodb");
-const _ = require('lodash');
-const uuid = require('uuid');
-const fs = require('fs');
+const { MultipartWriter } = require('../../../utils/multipartWriter');
 
 /**
  * 
  * @param {import('express').Request} req 
  * @param {import('express').Response} res 
  * @returns 
  */
-module.exports = async function (req , res) {
+module.exports = async function (req, res) {
     let key = req.params.objKey;
     let instanceUID = req.params.instanceUID;
-    let metadata = await mongodb["dicomBulkData"].findOne({
+    let bulkData = await mongodb["dicomBulkData"].findOne({
         $and: [
             {
                 instanceUID: instanceUID
@@ -21,15 +19,11 @@ module.exports = async function (req , res) {
                 filename: new RegExp(key , "gi")
             }
         ]
-    });
-    let bulkData = fs.readFileSync(`${process.env.DICOM_STORE_ROOTPATH}${metadata._doc.filename}`);
+    }).exec();
 
-    const BOUNDARY = `${uuid.v4()}-${uuid.v4()}`;
-    res.set("Content-Type" , `multipart/related; type=application/octet-stream; boundary=${BOUNDARY}`);
-    res.write(`--${BOUNDARY}\r\n`);
-    res.write(`Content-Type:multipart/related; type=application/octet-stream; boundary=${BOUNDARY}\r\n`);
-    res.write('Content-length: ' + bulkData.length + '\r\n\r\n');
-    res.write(bulkData);
-    res.write(`\r\n--${BOUNDARY}--`);
+    let multipartWriter = new MultipartWriter([],res, req);
+    await multipartWriter.setHeaderMultipartRelatedContentType("application/octet-stream");
+    await multipartWriter.writeBulkData(bulkData);
+    await multipartWriter.writeFinalBoundary();
     return res.end();
 }
diff --git a/models/mongodb/model/dicomBulkData.js b/models/mongodb/model/dicomBulkData.js
@@ -1,5 +1,15 @@
 module.exports = function (mongodb) {
     let dicomBulkDataSchema =  mongodb.Schema({  
+        studyUID: {
+            type: String,
+            default: void 0,
+            index: true
+        },
+        seriesUID: {
+            type: String,
+            default: void 0,
+            index: true
+        },
         instanceUID: {
             type: String,
             default: void 0,
@@ -8,6 +18,10 @@ module.exports = function (mongodb) {
         filename: {
             type: String,
             default: void 0
+        },
+        binaryValuePath: {
+            type: String,
+            default: void 0
         }
     }, { 
         strict: false,

diff --git a/utils/multipartWriter.js b/utils/multipartWriter.js
@@ -1,10 +1,20 @@
-const { logger } = require('../utils/log');
+const {
+    logger
+} = require('../utils/log');
 const uuid = require('uuid');
 const fs = require('fs');
 const _ = require('lodash');
 const dicomParser = require('dicom-parser');
-const { streamToBuffer } = require('@jorgeferrero/stream-to-buffer');
-const { dcm2jpegCustomCmd } = require('../models/dcmtk');
+const {
+    streamToBuffer
+} = require('@jorgeferrero/stream-to-buffer');
+const {
+    dcm2jpegCustomCmd
+} = require('../models/dcmtk');
+const {
+    URL
+} = require('url');
+const path =require('path');
 const DICOM_STORE_ROOTPATH = process.env.DICOM_STORE_ROOTPATH;
 
 class MultipartWriter {
@@ -14,7 +24,7 @@ class MultipartWriter {
      * @param {import('express').Response} res The express response
      * @param {import('express').Request} req
      */
-    constructor(pathsOfImages, res, req={}) {
+    constructor(pathsOfImages, res, req = {}) {
         this.BOUNDARY = `${uuid.v4()}-${uuid.v4()}-raccoon`;
         this.pathsOfImages = pathsOfImages;
         this.res = res;
@@ -26,11 +36,11 @@ class MultipartWriter {
      * Write the boundary
      * @param {boolean} isFirst Do not write \r\n\r\n when start if true
      */
-    async writeBoundary(isFirst=false) {
+    async writeBoundary(isFirst = false) {
         if (isFirst) {
             this.res.write(`--${this.BOUNDARY}\r\n`);
         } else {
-            this.res.write(`\r\n\r\n--${this.BOUNDARY}\r\n`);
+            this.res.write(`\r\n--${this.BOUNDARY}\r\n`);
         }
     }
 
@@ -46,7 +56,7 @@ class MultipartWriter {
      * @param {string} type 
      * @param {string} transferSyntax 
      */
-    async writeContentType(type, transferSyntax="") {
+    async writeContentType(type, transferSyntax = "") {
         if (transferSyntax) {
             this.res.write(`Content-Type: ${type};transfer-syntax=${transferSyntax}\r\n`);
         } else {
@@ -59,18 +69,24 @@ class MultipartWriter {
      * @param {number} length length of content
      */
     async writeContentLength(length) {
-        this.res.write('Content-length: ' + length + '\r\n\r\n');
+        this.res.write('Content-length: ' + length + '\r\n');
     }
 
-    async writeContentLocation() {
-        this.res.write(`Content-Location : ${this.req.protocol}://${this.req.headers.host}${this.req.originalUrl}\r\n`);
+    async writeContentLocation(subPath = "") {
+        if (subPath) {
+            let urlObj = new URL(subPath, `${this.req.protocol}://${this.req.headers.host}`);
+            this.res.write(`Content-Location: ${urlObj.href}\r\n`);
+        } else {
+            this.res.write(`Content-Location: ${this.req.protocol}://${this.req.headers.host}${this.req.originalUrl}\r\n`);
+        }
     }
 
     /**
      * Write the buffer in response
      * @param {Buffer} buffer 
      */
     async writeBufferData(buffer) {
+        this.res.write("\r\n");
         this.res.write(buffer);
     }
 
@@ -82,14 +98,18 @@ class MultipartWriter {
         this.res.set("content-type", `multipart/related; type="${type}"; boundary=${this.BOUNDARY}`);
     }
 
+    /**
+     * Write the files of DICOM in multipart content
+     * @param {string} type
+     */
     async writeDICOMFiles(type) {
         try {
             if (this.pathsOfImages) {
                 this.setHeaderMultipartRelatedContentType(type);
                 for (let i = 0; i < this.pathsOfImages.length; i++) {
                     console.log(`${DICOM_STORE_ROOTPATH}${this.pathsOfImages[i]}`);
                     let fileBuffer = await streamToBuffer(fs.createReadStream(`${DICOM_STORE_ROOTPATH}${this.pathsOfImages[i]}`));
-                    this.writeBoundary(i===0);
+                    this.writeBoundary(i === 0);
                     this.writeContentType(type);
                     this.writeContentLength(fileBuffer.length);
                     this.writeBufferData(fileBuffer);
@@ -98,12 +118,18 @@ class MultipartWriter {
                 return true;
             }
             return false;
-        } catch(e) {
+        } catch (e) {
             logger.error(e);
             return false;
         }
     }
 
+    /**
+     * Write image files of frames in multipart content
+     * @param {string} type 
+     * @param {Array<number>} frameList 
+     * @returns 
+     */
     async writeFrames(type, frameList) {
         this.setHeaderMultipartRelatedContentType();
         let dicomFilename = `${DICOM_STORE_ROOTPATH}${this.pathsOfImages[0]}`;
@@ -130,7 +156,7 @@ class MultipartWriter {
                     untilTag: "x7fe00010"
                 });
                 let transferSyntax = dicomDataSet.string('x00020010');
-                this.writeBoundary(x==0);
+                this.writeBoundary(x == 0);
                 this.writeContentType(type, transferSyntax);
                 this.writeContentLength(fileBuffer.length);
                 this.writeContentLocation();
@@ -141,6 +167,29 @@ class MultipartWriter {
         }
         return false;
     }
+
+    /**
+     * Write multipart/related of multiple bulk data.
+     * @param {import('./typeDef/bulkdata.js').BulkData} bulkDataObj
+     * @returns 
+     */
+    async writeBulkData(bulkDataObj, isFirst=true) {
+        try {
+            let filename = path.join(DICOM_STORE_ROOTPATH, bulkDataObj.filename);
+            let fileStream = fs.createReadStream(filename);
+            let fileBuffer = await streamToBuffer(fileStream);
+            this.writeBoundary(isFirst);
+            this.writeContentType("application/octet-stream");
+            this.writeContentLength(fileBuffer.length);
+            let bulkDataUrlPath = `/api/dicom/instance/${bulkDataObj.instanceUID}/bulkdata/${bulkDataObj.binaryValuePath}`;
+            this.writeContentLocation(bulkDataUrlPath);
+            this.writeBufferData(fileBuffer);
+            return true;
+        } catch (e) {
+            logger.error(e);
+            return false;
+        }
+    }
 }
 
 

diff --git a/utils/typeDef/bulkdata.js b/utils/typeDef/bulkdata.js
@@ -0,0 +1,13 @@
+/**
+ * @typedef {object} BulkData
+ * @property {string} studyUID
+ * @property {string} seriesUID
+ * @property {string} instanceUID
+ * @property {string} filename
+ * @property {string} binaryValuePath The json path of the binary value
+ * 
+ */
+
+const BulkData = true;
+
+export {BulkData};