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Raccoon is a NoSQL-based medical image archive for managing the DICOM images.

License: MIT License

Python 1.21% Dockerfile 0.12% JavaScript 86.49% CSS 4.18% HTML 7.95% Shell 0.04% Batchfile 0.01%
dicomweb fhir-server mongodb fhir-resources wado-uri fhir-imagingstudy qido-rs pathology wsi bluelight

raccoon's People

Contributors

chinlinlee avatar cylien avatar lorex avatar luckypig3400 avatar

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Forkers

yjsyyyjszf vb6hobbyst7 jibrel luckypig3400 mbilalsh lorex johnny990628 gigakiller eternityjh yang-jiaxiang

raccoon's Issues

同学，您这个项目引入了441个开源组件，存在5个漏洞，辛苦升级一下

检测到 cylab-tw/raccoon 一共引入了441个开源组件，存在5个漏洞

漏洞标题：validator.js 安全漏洞
缺陷组件：[email protected]
漏洞编号：CVE-2021-3765
漏洞描述：Validator.js是一个字符串验证器
validator.js存在安全漏洞，该漏洞源于网络系统或产品的代码开发过程中存在设计或实现不当的问题。
影响范围：(∞, 13.7.0)
最小修复版本：13.7.0
缺陷组件引入路径：[email protected]>[email protected]>[email protected]

另外还有5个漏洞，详细报告：https://mofeisec.com/jr?p=ifdb83

Incorrect way to convert 00080061 to FHIR

In DICOM2FHIRImagingStudy.js line 213

studyobj.modality = DCMstring(json, '00080061');

The code read 00080061 tag of DICOM which the tag is only used for querying.
Need to find another way to convert the value of 00080061 tag to modalities in the study of FHIR ImagingStudy.

Please support python without Anaconda in windows configuration! Thanks a lot 😄

Hello author, thanks for your amazing project!

A few bugs occurred while I was deploying this project on my laptop(Win10).

I tried to install Anaconda and set up 'gdcm' environment with python 3.7 but in the end, it all lead to the same Error: "ImportError: DLL load failed:"

Package 'pydicom' & 'gdcm' may support windows without Anaconda

So, I tried to install the required python packages with the python (which was installed on my laptop directly)
Then I found this great news, it could be installed with python 3.7.9 without Anaconda environment!
🔽 more information below 🔽

Please support python without Anaconda in windows configuration! Thanks a lot 😄

Config examples for Raccoon+Bluelight in Win10/11 localhost deployment

This is my note for deploying at localhost:8081 in Win10/11

You may look at my config files if you have some issues during the configurations.
Hopes this may help you! 😺

Environment

  • System: Windows11 Pro 22H2 22621.963

All Programs were installed in the default location

  • Node.JS: 16.14.0
  • Python: 3.7.9
  • MongoDB: 6.0.3
  • ImageMagick: 7.1.0-55
  • Xampp (Optional for virtual host config): 8.1.12

My Raccoon Config files

.env

MONGODB_NAME="raccoon"
MONGODB_HOSTS=["localhost"] 
# If your NodeJS version >= 17.x then change localhost to 127.0.0.1
# https://www.mongodb.com/community/forums/t/mongooseserverselectionerror-connect-econnrefused-127-0-0-1-27017/123421
MONGODB_PORTS=[27017]
MONGODB_USER="yourMongoDBuser"
MONGODB_PASSWORD="yourDBuserPassword"
MONGODB_SLAVEMODE=false

SERVER_HOST="localhost"
SERVER_PORT=8081

DICOM_STORE_ROOTPATH='C:/Services/RaccoonDicomImages/'
DICOMWEB_HOST="localhost"
DICOMWEB_PORT=8081
DICOMWEB_API="dicom-web"

FHIRSERVER_HTTP="http"
FHIRSERVER_APIPATH="api/fhir"
FHIRSERVER_HOST="localhost"
FHIRSERVER_PORT=8081
FHIR_NEED_PARSE_PATIENT=true

USE_CONDA=false
CONDA_PATH="path/conda.exe"
CONDA_GDCM_ENV_NAME ="gdcm"

USE_DCM2JPEG_PYTHONAPI=true
DCM2JPEG_PYTHONAPI_HOST="127.0.0.1"
DCM2JPEG_PYTHONAPI_PORT=5000

ENABLE_OAUTH_LOGIN=true

plugins\config.js

No changes
Just copy the config.template.js and rename it to config.js

public\scripts\config.js

var envConfig = {
    QIDO: {
        hostName: "localhost",
        port: "8081",
        api: "dicom-web",
        http: "http"
    },
    WADO: {
        hostName: "localhost",
        port: "8081",
        api: "dicom-web",
        http: "http"
    },
    FHIR: {
        hostName: "localhost",
        port: "8081",
        api: "api/fhir",
        http: "http"
    },
    login: {
        enable: false,
        jwt: false //*If true, get token from localStorage and add headers for every requests
    },
    backend: {
        baseUrl: "http://localhost:8081"
    }
};

My Bluelight Config file

public\html\BL\bluelight\data\config.json

{
    "DICOMWebServersConfig": [
        {
            "AETitle": "localhost",
            "enableHTTPS": false,
            "hostname": "localhost",
            "PORT": 8081,
            "contentType": "application/json",
            "timeout": 80000,
            "charset": "UTF=8",
            "QIDO": "dicom-web",
            "WADO-URI": "wado",
            "WADO-RS": "dicom-web",
            "WADO-RS/RUI":"RS",
            "STOW": "stow",
            "enableRetrieveURI": false,
            "includefield": false,
            "enableXml2Dcm":false,
            "Xml2DcmUrl":"/upload",
            "target": "http://localhost:8081/html/BL/bluelight/html/start.html",
            "token": ""
        },
        {
            "AETitle": "ldcmPACS",
            "enableHTTPS": true,
            "hostname": "orthanc.dicom.tw",
            "PORT": 443,
            "contentType": "application/json",
            "timeout": 80000,
            "charset": "UTF=8",
            "QIDO": "dicom-web",
            "WADO-URI": "wado",
            "WADO-RS": "dicom-web",
            "WADO-RS/RUI":"URI",
            "STOW": "stow",
            "enableRetrieveURI": false,
            "includefield": false,
            "enableXml2Dcm":false,
            "Xml2DcmUrl":"/upload",
            "target": "https://cylab-tw.github.io/bluelight/bluelight/html/start.html",
            "token": ""
        }
    ],
    "//_thumnail_witdth": "縮圖寬度",
    "thumnail_witdth": 70,
    "//_study_comparison": "進片模式",
    "study_comparison": false
}

Virtual host config files

Windows Host file

Add the line below in C:\Windows\System32\drivers\etc\hosts

127.0.0.1  raccoon.localhost.net  www.raccoon.localhost.net

REF: https://stackoverflow.com/questions/3660066/hosting-multiple-local-sites-with-xampp

XAMPP Apache vhost config

Add the following lines in C:\xampp\apache\conf\extra\httpd-vhosts.conf

<VirtualHost *:80>
	ProxyPass / http://localhost:8081/
	ProxyPassReverse / http://localhost:8081/
	
	ServerName raccoon.localhost.net
	ServerAlias www.raccoon.localhost.net
	DocumentRoot "c:/xampp/htdocs/raccoon.localhost.net"
</VirtualHost>

REF1: https://www.how2lab.com/programming/php/multiple-websites.php
REF2: https://httpd.apache.org/docs/2.4/howto/reverse_proxy.html
REF3: https://dotblogs.com.tw/jses88001/2014/04/17/144782

dicom影像沒有顯示出來

學長(們) 好:

我有兩個問題想請教

  1. 本院自行上傳的dicom影像無法於bluelight顯示?
  2. 為了執行mainecoon專案，請問如何確認DICOMWeb已經成功安裝?

謝謝

以下是操作過程：

我按照安裝步驟在本機完成raccoon & Bluelight兩個專案的安裝

接著從raccoon上傳dicom影像，分別有【手冊提供的測試影像】以及【本院的dicom影像】
(本院的dicom影像是三組去識別的CT影像)

dicom影像上傳過程順利無異常

執行按鈕後，只有【手冊提供的測試影像】可於bluelight顯示
(Philips Amy的影像有密集的直線線條，Robert Huron則正常顯示)

【本院的dicom影像】無法於Bluelight顯示

我在Bluelight點擊資料夾圖案手動載入【本院的dicom影像】可以顯示出來

為了確認raccoon 有將dicom影像儲存下在。我從網址複製StudyInstanceUID，到資料表dicomBulkData查詢，資料庫紀錄的filename確實可以在資料夾內找到相同名稱的檔案

再來，為了確認是否因程式碼出錯，造成影像無法呈現，我開啟瀏覽器<開發者模式>並重新整理視窗多次，都沒有看到錯誤訊息出現。命令提示字元(cmd)同樣沒有錯誤訊息。

Problem with raccon initiation in docker

I tried to build raccoon and mongo by cloning the repository and then starting the two docker container using the command in the terminal

docker-compose up

However it gives me the following error when starting the raccoon container

raccoon    | SyntaxError: Unexpected token u in JSON at position 0
raccoon    |     at JSON.parse (<anonymous>)
raccoon    |     at exports (/nodejs/raccoon/models/mongodb/connector.js:13:24)
raccoon    |     at Object.<anonymous> (/nodejs/raccoon/models/mongodb/index.js:8:52)
raccoon    |     at Module._compile (internal/modules/cjs/loader.js:1114:14)
raccoon    |     at Object.Module._extensions..js (internal/modules/cjs/loader.js:1143:10)
raccoon    |     at Module.load (internal/modules/cjs/loader.js:979:32)
raccoon    |     at Function.Module._load (internal/modules/cjs/loader.js:819:12)
raccoon    |     at Module.require (internal/modules/cjs/loader.js:1003:19)
raccoon    |     at Module.Hook._require.Module.require (/usr/local/lib/node_modules/pm2/node_modules/require-in-the-middle/index.js

Is this error occured previously? How can i fix this?
Thanks in advance

npm ERR

When I do npm install, I get:

npm WARN EBADENGINE Unsupported engine {
npm WARN EBADENGINE   package: '[email protected]',
npm WARN EBADENGINE   required: { node: '>=14' },
npm WARN EBADENGINE   current: { node: 'v12.22.9', npm: '8.5.1' }
npm WARN EBADENGINE }
npm WARN deprecated [email protected]: This package is no longer supported. It's now a built-in Node module. If you've depended on crypto, you should switch to the one that's built-in.
npm WARN deprecated [email protected]: this library is no longer supported
npm WARN deprecated [email protected]: Please upgrade to latest, formidable@v2 or formidable@v3! Check these notes: https://bit.ly/2ZEqIau
npm WARN deprecated [email protected]: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
npm WARN deprecated [email protected]: request has been deprecated, see https://github.com/request/request/issues/3142
npm ERR! code 1
npm ERR! path /home/user/raccoon/node_modules/dicom-to-json
npm ERR! command failed
npm ERR! command sh -c run-script-os
npm ERR! > [email protected] install:linux
npm ERR! > npx prebuild-install -r napi || npx cmake-js compile --CDWITH_LIBICONVINC:PATH="/usr/local/apps" --CDDCMTK_ENABLE_CHARSET_CONVERSION:STRING="libiconv" --CDDCMTK_WITH_ICONV:BOOL=1 --CDnapi_build_version=4
npm ERR! prebuild-install WARN install No prebuilt binaries found (target=4 runtime=napi arch=arm64 libc= platform=linux)
npm ERR! internal/modules/cjs/loader.js:818
npm ERR!   throw err;
npm ERR!   ^
npm ERR! 
npm ERR! Error: Cannot find module 'bluebird'
npm ERR! Require stack:
npm ERR! - /home/user/raccoon/node_modules/cmake-js/lib/downloader.js
npm ERR! - /home/user/raccoon/node_modules/cmake-js/lib/dist.js
npm ERR! - /home/user/raccoon/node_modules/cmake-js/lib/cMake.js
npm ERR! - /home/user/raccoon/node_modules/cmake-js/lib/buildSystem.js
npm ERR! - /home/user/raccoon/node_modules/cmake-js/lib/index.js
npm ERR! - /home/user/raccoon/node_modules/cmake-js/bin/cmake-js
npm ERR!     at Function.Module._resolveFilename (internal/modules/cjs/loader.js:815:15)
npm ERR!     at Function.Module._load (internal/modules/cjs/loader.js:667:27)
npm ERR!     at Module.require (internal/modules/cjs/loader.js:887:19)
npm ERR!     at require (internal/modules/cjs/helpers.js:74:18)
npm ERR!     at Object.<anonymous> (/home/user/raccoon/node_modules/cmake-js/lib/downloader.js:2:15)
npm ERR!     at Module._compile (internal/modules/cjs/loader.js:999:30)
npm ERR!     at Object.Module._extensions..js (internal/modules/cjs/loader.js:1027:10)
npm ERR!     at Module.load (internal/modules/cjs/loader.js:863:32)
npm ERR!     at Function.Module._load (internal/modules/cjs/loader.js:708:14)
npm ERR!     at Module.require (internal/modules/cjs/loader.js:887:19) {
npm ERR!   code: 'MODULE_NOT_FOUND',
npm ERR!   requireStack: [
npm ERR!     '/home/user/raccoon/node_modules/cmake-js/lib/downloader.js',
npm ERR!     '/home/user/raccoon/node_modules/cmake-js/lib/dist.js',
npm ERR!     '/home/user/raccoon/node_modules/cmake-js/lib/cMake.js',
npm ERR!     '/home/user/raccoon/node_modules/cmake-js/lib/buildSystem.js',
npm ERR!     '/home/user/raccoon/node_modules/cmake-js/lib/index.js',
npm ERR!     '/home/user/raccoon/node_modules/cmake-js/bin/cmake-js'
npm ERR!   ]
npm ERR! }

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/user/.npm/_logs/2024-03-04T22_33_19_361Z-debug-0.log

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