docs(wiki): add Step by Step guideline to installing - Ubuntu

Chinlinlee · Jan 25, 2024 · 6983c0e · 6983c0e
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diff --git a/wiki/_Sidebar.md b/wiki/_Sidebar.md
@@ -7,7 +7,7 @@
 - **[🏠 Home](https://github.com/Chinlinlee/raccoon-dicom/wiki/Home)**
 - **[🔧 Installation](https://github.com/Chinlinlee/raccoon-dicom/wiki/Installation)**
     - **[👨‍💻 Step by Step guideline to installing - Windows](https://github.com/Chinlinlee/raccoon-dicom/wiki/From-zero-to-deploy)**
-
+    - **[👨‍💻 Step by Step guideline to installing - Ubuntu](https://github.com/Chinlinlee/raccoon-dicom/wiki/step-by-step-installation-ubuntu)**
 ## Developer
 - **[🧪 Test Workflow](https://github.com/Chinlinlee/raccoon-dicom/wiki/DICOM-Instance-Test-Info)**
 

diff --git a/wiki/step-by-step-installation-ubuntu.md b/wiki/step-by-step-installation-ubuntu.md
@@ -1,4 +1,267 @@
 # Step by Step to installing - Ubuntu
-In the following, we will use ubuntu 20.04 to install.
+In the following, we will use `ubuntu 22.04` to install.
+
+## Install Environment Requirement
+The following is a list of requirements, we will install each software next.
+- git
+- Node.js
+- Imagemagick
+- openJDK >= 11
+
+## Install git
+```bash
+sudo apt install -y git
+```
+
+## Install Node.js
+```bash
+curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash - &&\
+sudo apt-get install -y nodejs
+```
+
+## Install MongoDB
+- From a terminal, install gnupg and curl if they are not already available:
+```bash
+sudo apt-get install -y gnupg curl
+```
+- To import the MongoDB public GPG key from 
+https://pgp.mongodb.com/server-6.0.asc
+, run the following command:
+```bash
+curl -fsSL https://pgp.mongodb.com/server-6.0.asc | \
+   sudo gpg -o /usr/share/keyrings/mongodb-server-6.0.gpg \
+   --dearmor
+```
+- Create the list file /etc/apt/sources.list.d/mongodb-org-6.0.list for your version of Ubuntu.
+```bash
+echo "deb [ arch=amd64,arm64 signed-by=/usr/share/keyrings/mongodb-server-6.0.gpg ] https://repo.mongodb.org/apt/ubuntu jammy/mongodb-org/6.0 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-6.0.list
+```
+- Reload local package database
+```bash
+sudo apt-get update
+```
+- To install the latest stable version, issue the following
+```bash
+sudo apt-get install -y mongodb-org
+```
+### Start MongoDB
+You can start the mongod process by issuing the following command:
+```bash
+sudo systemctl start mongod
+```
+[Additional Info, if you got problems](https://www.mongodb.com/docs/v6.0/tutorial/install-mongodb-on-ubuntu/#start-mongodb)
+
+### Create User in MongoDB
+Since the MongoDB connection with Raccoon-DICOM requires username and password. You need to create a user in the MongoDB to use Raccoon-DICOM.
+- connect to mongodb
+```bash
+mongosh --host localhost --port 27017
+```
+- Enter the following command to switch to admin database
+```bash
+use admin;
+```
+- Enter the following command to create root user
+
+> [!CAUTION]
+> Please change the username and password to a secure one by yourself!
+
+```bash
+db.createUser({
+    user : "root",
+    pwd : "root" ,
+    roles : [{role : "root" , db:"admin"}]
+});
+```
+
+> If present `{ ok: 1 }`, it means the creation was successful!
+
+## Install Imagemagick
+```bash
+sudo apt install -y imagemagick
+```
+- Checking the installed version of ImageMagick 
+```bash
+convert --version
+```
+- It should bring something similar to this:
+```bash
+Version: ImageMagick 6.9.11-60 Q16 x86_64 2021-01-25 https://imagemagick.org
+Copyright: (C) 1999-2021 ImageMagick Studio LLC
+License: https://imagemagick.org/script/license.php
+Features: Cipher DPC Modules OpenMP(4.5) 
+Delegates (built-in): bzlib djvu fftw fontconfig freetype heic jbig jng jp2 jpeg lcms lqr ltdl lzma openexr pangocairo png tiff webp wmf x xml zlib
+```
+
+## Install JAVA JDK
+```bash
+sudo apt install -y openjdk-11-jdk
+```
+- Checking java jdk version
+```bash
+java -version
+```
+- It should bring something similar to this:
+```bash
+openjdk version "11.0.21" 2023-10-17
+OpenJDK Runtime Environment (build 11.0.21+9-post-Ubuntu-0ubuntu122.04)
+OpenJDK 64-Bit Server VM (build 11.0.21+9-post-Ubuntu-0ubuntu122.04, mixed mode, sharing)
+```
+
+## Raccoon-DICOM Installation
+### Download Raccoon
+#### Use git
+```bash
+git clone https://github.com/Chinlinlee/raccoon-dicom.git
+```
+
+### Install Node.js Packages
+- go to Raccoon-DICOM directory
+```bash
+cd raccoon-dicom
+```
+- install node packages
+```bash
+npm install
+```
+### Copy opencv_java
+```bash
+sudo cp models/DICOM/dcm4che/javaNode/dcm4chee/lib/linux-x86-64/*.so /usr/lib/jvm/java-11-openjdk-amd64/lib
+```
+
+### Configure dotenv .env file
+- copy `.env.template` to `.env`
+```bash
+cp .env.template .env
+```
+- Modify .env
+```text
+# MongoDB
+MONGODB_NAME="raccoon-dicom"
+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
+
+# Server
+SERVER_PORT=8081
+SERVER_SESSION_SECRET_KEY="secret-key"
+
+# DICOM Web
+DICOM_STORE_ROOTPATH="/home/test/dicomFiles"
+DICOMWEB_HOST="{host}"
+DICOMWEB_PORT=8081
+DICOMWEB_API="dicom-web"
+
+# DICOM DIMSE
+ENABLE_DIMSE=true
+DIMSE_AE_TITLE="RACCOONQRSCP" # default: RACCOONQRSCP
+DIMSE_HOSTNAME="0.0.0.0" # default: 127.0.0.1
+DIMSE_PORT=11112 # default: 11112
+DIMSE_MAX_PDULEN_RCV=16378
+DIMSE_MAX_PDULEN_SND=16378
+DIMSE_NOT_ASYNC=false
+DIMSE_MAX_OPS_INVOKED=0
+DIMSE_MAX_OPS_PERFORMED=0
+DIMSE_NOT_PACK_PDV=false
+DIMSE_CONNECT_TIMEOUT=0
+DIMSE_REQUEST_TIMEOUT=0
+DIMSE_ACCEPT_TIMEOUT=0
+DIMSE_RELEASE_TIMEOUT=0
+DIMSE_SEND_TIMEOUT=0
+DIMSE_STORE_TIMEOUT=0
+DIMSE_RESPONSE_TIMEOUT=0
+DIMSE_RETRIEVE_TIMEOUT=0
+DIMSE_RETRIEVE_TIMEOUT_TOTAL=0
+DIMSE_IDLE_TIMEOUT=0
+DIMSE_SOCLOSE_DELAY=50
+DIMSE_SOSND_BUFFER=0
+DIMSE_SORCV_BUFFER=0
+DIMSE_TCP_DELAY=false
+
+# DIMSE TLS
+DIMSE_TLS=false
+DIMSE_TLS_NULL=false
+DIMSE_TLS_3DES=false
+DIMSE_TLS_AES=false
+DIMSE_TLS_CIPHER=""
+
+DIMSE_TLS13=false
+DIMSE_TLS12=false
+DIMSE_TLS11=false
+DIMSE_TLS1=false
+DIMSE_SSL3=false
+DIMSE_SSL2HELLO=false
+DIMSE_TLS_PROTOCOL=""
+DIMSE_TLS_EIA_HTTPS=false
+DIMSE_TLS_EIA_LDAPS=false
+DIMSE_TLS_NOAUTH=false
+DIMSE_KEY_STORE="./config/certs/key.p12"
+DIMSE_KEY_STORE_TYPE="PKCS12"
+DIMSE_KEY_STORE_PASS="secret"
+DIMSE_KEY_PASS="secret"
+DIMSE_TRUST_STORE="./config/certs/cacerts.p12"
+DIMSE_TRUST_STORE_TYPE="PKCS12"
+DIMSE_TRUST_STORE_PASS="secret"
+
+# FHIR
+SYCN_TO_FHIR_SERVER=false
+FHIRSERVER_BASE_URL="http://localhost:8088/fhir"
+```
+
+### Start Raccoon-DICOM
+- start raccoon-dicom
+```bash
+node server.js
+```
+
+## Test Raccoon-DICOM features
+### Upload DICOM Instance (STOW-RS)
+- The following steps will use the file test/dicomFiles/jpeg2000/example-jpeg-2000.dcm for uploading test
+- Use curl for uploading
+
+```bash
+curl --location --request POST "http://localhost:8081/dicom-web/studies" \
+--header "Accept: application/dicom+json" \
+--header "Content-Type: multipart/related; type=\"application/dicom\"" \
+--form "[email protected]; type=\"application/dicom\""
+```
+
+- If present message following, congrats upload successful!!
+
+```json
+{"00081190":{"vr":"UT","Value":["http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543"]},"00081198":{"vr":"SQ","Value":[]},"00081199":{"vr":"SQ","Value":[{"00081150":{"vr":"UI","Value":["1.2.840.10008.5.1.4.1.1.77.1.6"]},"00081155":{"vr":"UI","Value":["1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0"]},"00081190":{"vr":"UT","Value":["http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543/series/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560606509.3/instances/1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0"]}}]}}
+```
+
+### Get Image info (QIDO-RS)
+```bash
+curl http://localhost:8081/dicom-web/studies
+```
+- The following output will be shown
+```json
+[{"00080020":{"vr":"DA","Value":["20181003"]},"00080030":{"vr":"TM","Value":["095253"]},"00080050":{"vr":"SH","Value":["D18-1001"]},"00080054":{"vr":"AE","Value":["RACCOONQRSCP"]},"00080061":{"vr":"CS","Value":["SM"]},"00080090":{"vr":"PN","Value":[]},"00081190":{"vr":"UR","Value":["http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543"]},"00100010":{"vr":"PN","Value":[{"Alphabetic":"Philips^Amy"}]},"00100020":{"vr":"LO","Value":["123456"]},"00100030":{"vr":"DA","Value":["20010101"]},"00100040":{"vr":"CS","Value":["O"]},"0020000D":{"vr":"UI","Value":["1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543"]},"00200010":{"vr":"SH","Value":[]},"00201206":{"vr":"IS","Value":["1"]},"00201208":{"vr":"IS","Value":["1"]}}]
+```
+
+### Retrieve Image (WADO-RS)
+- Retrieve frame
+```bash
+curl http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543/series/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560606509.3/instances/1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0/frames/1/rendered --output image.jpg
+```
+
+> Result
+>
+> ![frame](https://user-images.githubusercontent.com/49154622/236471229-5ea2fad0-3781-4075-a755-66712d9ef44f.png)
+
+- You can also test imagemagick is working normally
+```bash
+curl http://localhost:8081/dicom-web/studies/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560373543/series/1.3.46.670589.45.1.1.4993912214784.1.5436.1538560606509.3/instances/1.3.6.1.4.1.5962.99.1.3002151337.1017604488.1540600476073.6.0/frames/1/rendered?iccprofile=rommrgb --output image.jpg
+```
+
+> Result
+>
+> ![iccprofile-frame](https://user-images.githubusercontent.com/49154622/236471143-9af313c4-e6ca-42c8-a5e7-6a5de66e2005.png)
+
 
-##