Grails 3 Download Saved Documnets/Files (.pdf, .txt, .docx and others) Example.

How to Download different types of files using Grails 3.

If you want to use server-side file download for different types of files like pdf, txt, docx etc then there are different ways to do it.

We can use ServletOutputStream object for it as below:

    def download(){
            def filePath = "/opt/tomcat/webapps/savedFile/filename.pdf" //I am saving files on tomcat.
            def file = new File(filePath)
            if (file.exists()){
                response.setContentType("application/octet-stream")
                response.setHeader("Content-disposition", "filename=${file.getName()}")
                response.outputStream << file.bytes
            }else {
                //handle file not found messages.
            }
}

Here, contentType is "application/octet-stream" for all types of file. If you want to specified for specific one set contentType for specific one.

                response.setContentType("application/pdf")

Or you can do simply like this:

    def download(){
            def filePath = "/opt/tomcat/webapps/savedFile/filename.pdf" //I am saving files on tomcat.
            def file = new File(filePath)
            if (file.exists()){
                response.setContentType("application/octet-stream")
                response.setHeader("Content-disposition", "filename=${file.getName()}")
                response.outputStream << file.newInputStream()
            }else {
                //handle file not found messages.
            }
}

def download(){
            def filePath = "/opt/tomcat/webapps/savedFile/filename.pdf" //I am saving files on tomcat.
            def file = new File(filePath)
            if (file.exists()){
                response.setContentType("application/octet-stream")
                response.setHeader("Content-disposition", "filename=${file.getName()}")
                def outputStream = response.getOutputStream()
                outputStream << file.bytes
                outputStream.flush()
                outputStream.close()
            }else {
                //handle file not found messages.
            }
}

But in grails 3 latter version while deploying the war file to external tomcat(tomcat 7) server then we might get some class not found issue while downloading files.

Error 500: Internal Server Error
URI
/patient/download
Class
java.lang.ClassNotFoundException
Message
Handler dispatch failed; nested exception is java.lang.NoClassDefFoundError: javax/servlet/WriteListener
Caused by
javax.servlet.WriteListener

In order to solve this issue, we need to make the controller's action wrap with @GrailsCompileStatic annotation.

import grails.compiler.GrailsCompileStatic

@GrailsCompileStatic
def download(){
            def filePath = "/opt/tomcat/webapps/savedFile/filename.pdf" //I am saving files on tomcat.
            def file = new File(filePath)
            if (file.exists()){
                response.setContentType("application/octet-stream")
                response.setHeader("Content-disposition", "filename=${file.getName()}")
                def outputStream = response.getOutputStream()
                outputStream << file.bytes
                outputStream.flush()
                outputStream.close()
            }else {
                //handle file not found messages.
            }
}

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Securing Grails Application with Spring Security Rest | Rest API | Grails 3.x

How to Secure Grails Application with Spring Security Rest in Grails 3

Table of Contents

• - Introduction
• - Pre-requisites
• - Create Grails Application
• - Spring Security Core Plugin Configuration
• - Spring Security Rest Plugin Configuration
• - Testing Secured REST API

Introduction:

In this tutorial, we are going to secure our grails application with spring security simply refer to spring security rest login. Here we are using grails version 3.3.0 and Java 8. This tutorial describes the configuration of Spring Security Core, Spring Security Rest with Grails 3 to secure the application.

Pre-requisites:

1. Running Java
2. Running Grails

Create Grails Application:

1. Create App

In order to create grails application, open your terminal or cmd and type following command to create an app.

grails create-app spring-security-rest --profile rest-api

// Application created at (path of app)

Open your favorite text editor or IDE and open the project that we recently created.

Go to a created project folder.

cd spring-security-rest

Run grails interactive mode.

grails 

In order to run and stop an application simply type "run-app" and "stop-app"

2. Create Domain Class

Let's create a dummy class to test security called "Product". You can use either terminal or your IDE.

create-domain-class Product

Add some properties in the domain class.

class Product {
    String name
    Double price
    String companyName
    String description
    Date dateCreated = new Date()
    static constraints = {
    }
}

Add some data using BootStrap.groovy

class BootStrap {

    def init = { servletContext ->
        if (Product.count() == 0){
            new Product(name: "product1", price: 10, companyName: "company1", description:"description1").save(flush:true)
            new Product(name: "product2", price: 100, companyName: "company2", description:"description2").save(flush:true)
            new Product(name: "product3", price: 1000, companyName: "company3", description:"description3").save(flush:true)
            new Product(name: "product4", price: 10000, companyName: "company4", description:"description4").save(flush:true)
        }
    }
    def destroy = {
    }
}

Create Controller for product domain.

create-restful-controller Product

It will create controller like this:

class ProductController extends RestfulController {
    static responseFormats = ['json', 'xml']
    ProductController() {
        super(Product)
    }
}

Run application. And simply make get request, as following endpoint will results "product" data in Json format that we created in BootStrap.groovy.

http://localhost:8080/product

Spring Security Core Plugin Configuration:

Under build.gradle file within dependencies add the following configuration and run command "compile"

dependencies {
    compile 'org.grails.plugins:spring-security-core:3.2.0'
}

Now its time to create user related tables,  for this exit from the interactive console.

exit
grails s2-quickstart spring.security.rest User Role

You can see:

CONFIGURE SUCCESSFUL
Total time: 2.965 secs
| Creating User class 'User' and Role class 'Role' in package 'spring.security.rest'
| Rendered template PersonWithoutInjection.groovy.template to destination grails-app/domain/spring/security/rest/User.groovy
| Rendered template PersonPasswordEncoderListener.groovy.template to destination src/main/groovy/spring/security/rest/UserPasswordEncoderListener.groovy
| Rendered template Authority.groovy.template to destination grails-app/domain/spring/security/rest/Role.groovy
| Rendered template PersonAuthority.groovy.template to destination grails-app/domain/spring/security/rest/UserRole.groovy
| 
************************************************************
* Created security-related domain classes. Your            *
* grails-app/conf/application.groovy has been updated with *
* the class names of the configured domain classes;        *
* please verify that the values are correct.               *
************************************************************

Which will create User.groovy, Role.groovy, and UserRole.groovy Domain classes.

Now let's create a user data for testing purpose using BootStrap.groovy.

def role1 = new Role(authority:"ROLE_USER").save flush:true
        def user1 = new User(username:"user@gmail.com",password:"pwd@123").save flush:true
        UserRole.create(user1,role1)

Spring Security Rest Plugin Configuration:
Under build.gradle file within dependencies add the following configuration and run command "compile"

dependencies {
    compile "org.grails.plugins:spring-security-rest:2.0.0.M2"
}

Go to application.groovy and add chainMap configuration:

grails.plugin.springsecurity.filterChain. chainMap = [
  [pattern: '/**',filters: 'JOINED_FILTERS,-anonymousAuthenticationFilter,-exceptionTranslationFilter,-authenticationProcessingFilter,-securityContextPersistenceFilter'],
  [pattern: '/**', filters: 'JOINED_FILTERS,-restTokenValidationFilter,-restExceptionTranslationFilter'] 
]

Note: If your endpoint start with https://address.com/api or /othername then your chainMap look like

grails.plugin.springsecurity.filterChain. chainMap = [
  [pattern: '/api**',filters: 'JOINED_FILTERS,-anonymousAuthenticationFilter,-exceptionTranslationFilter,-authenticationProcessingFilter,-securityContextPersistenceFilter'],
  [pattern: '/**', filters: 'JOINED_FILTERS,-restTokenValidationFilter,-restExceptionTranslationFilter'] 
]

The final configuration looks like

// Added by the Spring Security Core plugin:
grails.plugin.springsecurity.userLookup.userDomainClassName = 'spring.security.rest.User'
grails.plugin.springsecurity.userLookup.authorityJoinClassName = 'spring.security.rest.UserRole'
grails.plugin.springsecurity.authority.className = 'spring.security.rest.Role'
grails.plugin.springsecurity.controllerAnnotations.staticRules = [
 [pattern: '/',               access: ['permitAll']],
 [pattern: '/error',          access: ['permitAll']],
 [pattern: '/index',          access: ['permitAll']],
 [pattern: '/index.gsp',      access: ['permitAll']],
 [pattern: '/shutdown',       access: ['permitAll']],
 [pattern: '/assets/**',      access: ['permitAll']],
 [pattern: '/**/js/**',       access: ['permitAll']],
 [pattern: '/**/css/**',      access: ['permitAll']],
 [pattern: '/**/images/**',   access: ['permitAll']],
 [pattern: '/**/favicon.ico', access: ['permitAll']],
 [pattern: '/**',             access: ['isFullyAuthenticated()']]
]

grails.plugin.springsecurity.filterChain. chainMap = [
  [pattern: '/**',filters: 'JOINED_FILTERS,-anonymousAuthenticationFilter,-exceptionTranslationFilter,-authenticationProcessingFilter,-securityContextPersistenceFilter'],
  [pattern: '/**', filters: 'JOINED_FILTERS,-restTokenValidationFilter,-restExceptionTranslationFilter'] 
]

Testing Secured REST API:
Now re-run the application and request the endpoint "http://localhost:8080/product"

which is our application is secured. I will make a tutorial for customizing this message format.

Next test the login endpoint with our existing user created in BootStrap.groovy. Here I am using Post-man.

Now access data via authorization.

Here, for authorization key use "Bearer access_token". You can see data as shown above. Because in our application.groovy we configure in such a way that all the login users can access data.

[pattern: '/**',             access: ['isFullyAuthenticated()']]

In the next tutorial I am going to create different customization for configuration and describe about different annotations.

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Splitting resources.groovy configuration in Grails applications

Splitting resources.groovy configuration in Grails applications

Table Of Contents

• 1. Introduction
  
• 2. How to split resources.groovy
• 3. Import external bean file

1. Introduction:

In grails, when our resources.groovy file is growing then it is better to split some logical bean configuration with a separate file and import that file in resources.groovy.  For this, Grails provides a neat way to specify Spring bean definitions with its custom Beans DSL by using importBeans or loadBeans.

2. How to split resources.groovy

You can simply create resources file under  "grails-app/conf/spring/" package: e.g

firstBean.groovy:

beans {
  beanConfiguration: yourBeanConfiguration
}

3. Import external bean file

Grails provide importBeans or loadBeans to import custom external bean file which can be done inside resources.groovy as bellow:

beans = { 
  importBeans('file:grails-app/conf/spring/firstBean.groovy') 
}

The problem is that this seems to work, but only if you run the application via  grails run-app with the embedded servlet container.

As soon we create a WAR file and deploy it into tomcat we are getting into trouble. The problem is Spring Bean Configuration file is moved on the different folder in tomcat "WEB-INF/classes/spring/" so we can get file-not-found-exception.

In order to resolve this problem, we need to locate custom resource path in resources.groovy.

def loadFromFile = { name ->
        importBeans("file:grails-app/conf/spring/"+name)
    }

    def loadFromWar = { name ->
        def resource = application.parentContext.getResource("WEB-INF/classes/spring/"+name)
        loadBeans(resource)
    }
    def loadResource = application.isWarDeployed() ? loadFromWar : loadFromFile

    loadResource "firstBean.groovy"
    loadResource "secondBean.groovy"

Here if the application is running via grails run-app then it will use the path "grails-app/conf/spring/". And if it is via external tomcat with deploying the WAR file then it uses the path "WEB-INF/classes/spring/".

Note: Be sure that your resource file is packaged on WAR with the right path.

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How to resolve grails-resolving-server-failed-to-start-for-port-8080-address-already-in-use

On Linux:

step1: if your server port already running at port 8080 then, firstly we have to kill this process for this open your terminal and type

lsof -w -n -i tcp:8080

which shows all the list of open file which is running at port 8080. if you type
lsof -w -n -i tcp:9090 if your server is running with port 9090 which shows all the list of open file which are running at port 9090. Here, lsof stand for ls = list and of = opened file. You can see list with pid number.

step2: type sudo kill -9 6911 where 6911 is pid number. Here 9 has its own meaning which is defined as kill command "SIGKILL" you can see this by type in terminal as kill -l . You can use -SIGKILL instead of -9.

step3: run your application. 

On Windows:

- Open and run command prompt as administrator and type following command:

   

   netstat -ano | findstr :8080

This command will find and list the process that uses this port.

Now, we need to kill the process, for this use following command:

   taskkill /pid 5884 /f

Where 5884 is the PID number. Use your PID number which is obtained previously.

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Error: ENOENT: no such file or directory, stat '../pancake-swap-periphery/node_modules/@uniswap/v2-core/contracts/interfaces/IPancakeFactory.sol

While trying to do pancake-swap clone, we might get the following issue while building a contract.

Error: ENOENT: no such file or directory, stat '../pancake-swap-periphery/node_modules/@uniswap/v2-core/contracts/interfaces/IPancakeFactory.sol'

It is due to the file is not found in node modules as suggested in error. If you go to the package.json file you can see the following dependency is injected inside the dependencies

"@uniswap/v2-core": "^1.0.1"

So here, pancake-swap core dependency files are not found which is imported in the contract we are building.

Let's add the required dependency from the git panackage-swap-core

replace the above dependency:

"@uniswap/v2-core": "git://github.com/pancakeswap/pancake-swap-core.git"

Now install the added dependency

npm install

After that, we can try building the contract.

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Modify Dicom file metadata using dcm4che in Java

How to modify Dicom file metadata using dcm4che.

Please follow our previous tutorials on dcm4che.

Read the Dicom header information using dcm4che in Java

Read Dicom file metadata using dcm4che in Java

Let's create a sample java class ModifyMetadata.java to modify the available metadata in the given Dicom file.

 public static void main(String[] args) {
        String inputDicomPath = "path/to/dicom/N2D_0001.dcm";
        String outputDicomPath = "output/path/to/dicom/N2D_0001.dcm";
        try {
            modifyMetadata(inputDicomPath, outputDicomPath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

 private static void modifyMetadata(String inputDicomPath, String outputDicomPath) throws IOException {
        File file = new File(inputDicomPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        if (attributes.contains(Tag.PatientID))
            attributes.setString(Tag.PatientID, VR.LO, "L500400");
        if (attributes.contains(Tag.PatientName))
            attributes.setString(Tag.PatientName, VR.PN, "Test name");
        DicomOutputStream dos = new DicomOutputStream(new File(outputDicomPath));
        attributes.writeTo(dos);
        dis.close();
        dos.close();
    }

Here we are using the dcm4che standard library classes. Please follow our previous tutorial to set up dcm4che jar files. We have created modifyMetadata() method which accepts two arguments one for input Dicom image path and another is output Dicom image path where we are writing the file after modification.

DicomInputStream will read the file. We are reading all the available data set to get the attributes and try to modify the patient ID and the patient name.

After modification, DicomOutputStream will write the modified attributes to the output path. If we open the image and see, the name and patient id are changed. We can modify any available metadata similar to the above example. For Tag and VR follow the Dicom tag library

The overall code implementation looks as below

package dicom.dcm4che;

import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.VR;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.io.DicomOutputStream;

import java.io.File;
import java.io.IOException;

public class ModifyMetadata {

    public static void main(String[] args) {
        String inputDicomPath = "path/to/dicom/N2D_0001.dcm";
        String outputDicomPath = "output/path/to/dicom/N2D_0001.dcm";
        try {
            modifyMetadata(inputDicomPath, outputDicomPath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

    private static void modifyMetadata(String inputDicomPath, String outputDicomPath) throws IOException {
        File file = new File(inputDicomPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        if (attributes.contains(Tag.PatientID))
            attributes.setString(Tag.PatientID, VR.LO, "L500400");
        if (attributes.contains(Tag.PatientName))
            attributes.setString(Tag.PatientName, VR.PN, "Test name");
        DicomOutputStream dos = new DicomOutputStream(new File(outputDicomPath));
        attributes.writeTo(dos);
        dis.close();
        dos.close();
    }
}

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Read Dicom file meatadata using dcm4che in Java

How to read Dicom file metadata using dcm4che in Java.

dcm4che is a collection of open-source applications and utilities for the healthcare enterprise application for processing, manipulating, and analysis of medical images.

Please follow the tutorial for setting the dcm4che in our java application.

Let's create a java class DicomMetadataReader.java to read the available metadata in the given Dicom file.

public static void main(String[] args) {
        String inputDicomFilePath = "path/to/dicom/N2D_0001.dcm";
        try {
            readMetadata(inputDicomFilePath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

private static void readMetadata(String dicomFilePath) throws IOException {
        File file = new File(dicomFilePath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String tagValue = attributes.getString(tag);
            System.out.println("Tag Address: " + tagAddress + " Value: " + tagValue);
        }
        dis.close();
    }

Here, we are using standard classes from the dcm4che core library jar file. DicomInputStream will read the file. We are reading the available dataset of the file and getting tags. After that, we are looping through the available tags and get the tag address and corresponding tag value.

The sample Output:

Total tag found in dicom file: 54
Tag Address: (0008,0008) Value: DERIVED
Tag Address: (0008,0016) Value: 1.2.840.10008.5.1.4.1.1.4
Tag Address: (0008,0018) Value: 1.2.826.0.1.3680043.2.1143.1590429688519720198888333603882344634
Tag Address: (0008,0020) Value: 20130717
Tag Address: (0008,0021) Value: 20130717
Tag Address: (0008,0022) Value: 20130717
Tag Address: (0008,0023) Value: 20130717
Tag Address: (0008,0030) Value: 141500
Tag Address: (0008,0031) Value: 142035.93000
Tag Address: (0008,0032) Value: 132518
Tag Address: (0008,0033) Value: 142035.93
Tag Address: (0008,0050) Value: null
Tag Address: (0008,0060) Value: MR
Tag Address: (0008,0070) Value: BIOLAB
Tag Address: (0008,0080) Value: null
Tag Address: (0008,0090) Value: null
Tag Address: (0008,1030) Value: Hanke_Stadler^0024_transrep
Tag Address: (0008,103E) Value: anat-T1w
Tag Address: (0008,1090) Value: nifti2dicom
Tag Address: (0010,0010) Value: Jane_Doe
Tag Address: (0010,0020) Value: 02
Tag Address: (0010,0030) Value: 19660101
Tag Address: (0010,0040) Value: F
Tag Address: (0010,1000) Value: null
Tag Address: (0010,1010) Value: 42
Tag Address: (0010,1030) Value: 75
Tag Address: (0010,21C0) Value: 4
Tag Address: (0018,0050) Value: 0.666666686534882
Tag Address: (0018,0088) Value: 0.666666686534882
Tag Address: (0018,1020) Value: 0.4.11
Tag Address: (0018,1030) Value: anat-T1w
Tag Address: (0020,000D) Value: 1.2.826.0.1.3680043.2.1143.2592092611698916978113112155415165916
Tag Address: (0020,000E) Value: 1.2.826.0.1.3680043.2.1143.515404396022363061013111326823367652
Tag Address: (0020,0010) Value: 433724515
Tag Address: (0020,0011) Value: 401
Tag Address: (0020,0012) Value: 1
Tag Address: (0020,0013) Value: 1
Tag Address: (0020,0020) Value: L
Tag Address: (0020,0032) Value: -91.4495864331908
Tag Address: (0020,0037) Value: 0.999032176441525
Tag Address: (0020,0052) Value: 1.2.826.0.1.3680043.2.1143.6856184167807409206647724161920598374
Tag Address: (0028,0002) Value: 1
Tag Address: (0028,0004) Value: MONOCHROME2
Tag Address: (0028,0010) Value: 384
Tag Address: (0028,0011) Value: 274
Tag Address: (0028,0030) Value: 0.666666686534882
Tag Address: (0028,0100) Value: 16
Tag Address: (0028,0101) Value: 16
Tag Address: (0028,0102) Value: 15
Tag Address: (0028,0103) Value: 1
Tag Address: (0028,1052) Value: 0
Tag Address: (0028,1053) Value: 1
Tag Address: (0028,1054) Value: US
Tag Address: (7FE0,0010) Value: 0

Please follow the Dicom standard library for tag and its description.

The overall code implementation looks as below:

package dicom.dcm4che;

import org.dcm4che3.data.Attributes;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.util.TagUtils;

import java.io.File;
import java.io.IOException;

public class DicomMetadataReader {

    public static void main(String[] args) {
        String inputDicomFilePath = "path/to/dicom/N2D_0001.dcm";
        try {
            readMetadata(inputDicomFilePath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

    private static void readMetadata(String dicomFilePath) throws IOException {
        File file = new File(dicomFilePath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String tagValue = attributes.getString(tag);
            System.out.println("Tag Address: " + tagAddress + " Value: " + tagValue);
        }
        dis.close();
    }
}

Read More

Read the Dicom header information using dcm4che in Java

In this tutorial, we are going to learn how to get the Dicom file header information using dcm4che.

DICOM (Digital Imaging and Communications in Medicine) is the ubiquitous standard in the radiology and cardiology imaging industry for the exchange and management of images and image-related information.

For Dicom standard information please visit Dicom Library.

Before start writing code we need to use a couple of jar files. Download all the Dicom library files from the bundle. This bundle contains a lot of jar files we will use only the desired one.

Extract the downloaded file, go to the lib folder and grab two jar files. dcm4che-core-5.25.1.jar and another is slf4j-api-1.7.32.jar, the verison might be different at the time of implementation.

Now, create a folder called libs inside the project directory and add the jar file and load it from the IDE.

Loading Jar file in Maven Project:

<dependency>
          <groupId>com.dcm4che</groupId>
          <artifactId>dcm4che</artifactId>
          <version>20220117</version>
          <scope>system</scope>
          <systemPath>${basedir}/libs/dcm4che-core-5.25.1.jar</systemPath>
      </dependency>

<dependency>
          <groupId>com.slf4j</groupId>
          <artifactId>slf4j</artifactId>
          <version>20220217</version>
          <scope>system</scope>
          <systemPath>${basedir}/libs/slf4j-api-1.7.32.jar</systemPath>
      </dependency>

Note: use the downloaded jar file name.

Loading Jar in Gradle Project:

Add the following inside dependencies in build.gradle file.

dependencies {
//other dependencies
 
compile fileTree(dir: 'libs', include: '*.jar')
}

Let's create the java class ReadHeaderInfo.java to read the header information

public static void main(String[] args) {
        String inputDicomFilePath = "path/to/dicom/N2D_0001.dcm";
        try {
            readHeader(inputDicomFilePath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

private static void readHeader(String inputPath) throws IOException {
        File file = new File(inputPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in the given dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String vr = attributes.getVR(tag).toString();
            System.out.println("Tag Address: " + tagAddress + " VR: " + vr);
        }
    }

Basically, we are using the Dicom-core classes from the jar file to read the file information. We are providing the sample Dicom file and reading the Tag Address and VR available in that file. 

DicomInputStream is used to read the file. dis.readDataset() read all the tags available in that file and finally, we are getting Tag Address and VR and outputting the values.

Output:

Total tag found in the given dicom file: 54
Tag Address: (0008,0008) VR: CS
Tag Address: (0008,0016) VR: UI
Tag Address: (0008,0018) VR: UI
Tag Address: (0008,0020) VR: DA
Tag Address: (0008,0021) VR: DA
Tag Address: (0008,0022) VR: DA
Tag Address: (0008,0023) VR: DA
Tag Address: (0008,0030) VR: TM
Tag Address: (0008,0031) VR: TM
Tag Address: (0008,0032) VR: TM
Tag Address: (0008,0033) VR: TM
Tag Address: (0008,0050) VR: SH
Tag Address: (0008,0060) VR: CS
Tag Address: (0008,0070) VR: LO
Tag Address: (0008,0080) VR: LO
Tag Address: (0008,0090) VR: PN
Tag Address: (0008,1030) VR: LO
Tag Address: (0008,103E) VR: LO
Tag Address: (0008,1090) VR: LO
Tag Address: (0010,0010) VR: PN
Tag Address: (0010,0020) VR: LO
Tag Address: (0010,0030) VR: DA
Tag Address: (0010,0040) VR: CS
Tag Address: (0010,1000) VR: LO
Tag Address: (0010,1010) VR: AS
Tag Address: (0010,1030) VR: DS
Tag Address: (0010,21C0) VR: US
Tag Address: (0018,0050) VR: DS
Tag Address: (0018,0088) VR: DS
Tag Address: (0018,1020) VR: LO
Tag Address: (0018,1030) VR: LO
Tag Address: (0020,000D) VR: UI
Tag Address: (0020,000E) VR: UI
Tag Address: (0020,0010) VR: SH
Tag Address: (0020,0011) VR: IS
Tag Address: (0020,0012) VR: IS
Tag Address: (0020,0013) VR: IS
Tag Address: (0020,0020) VR: CS
Tag Address: (0020,0032) VR: DS
Tag Address: (0020,0037) VR: DS
Tag Address: (0020,0052) VR: UI
Tag Address: (0028,0002) VR: US
Tag Address: (0028,0004) VR: CS
Tag Address: (0028,0010) VR: US
Tag Address: (0028,0011) VR: US
Tag Address: (0028,0030) VR: DS
Tag Address: (0028,0100) VR: US
Tag Address: (0028,0101) VR: US
Tag Address: (0028,0102) VR: US
Tag Address: (0028,0103) VR: US
Tag Address: (0028,1052) VR: DS
Tag Address: (0028,1053) VR: DS
Tag Address: (0028,1054) VR: LO
Tag Address: (7FE0,0010) VR: OW

Extracting the header information is important to visualize the Dicom file information.

The overall code implementation looks as below:

package dicom.dcm4che;

import org.dcm4che3.data.Attributes;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.util.TagUtils;

import java.io.File;
import java.io.IOException;

public class ReadHeaderInfo {

    public static void main(String[] args) {
        String inputDicomFilePath = "path/to/dicom/N2D_0001.dcm";
        try {
            readHeader(inputDicomFilePath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

    private static void readHeader(String inputPath) throws IOException {
        File file = new File(inputPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in the given dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String vr = attributes.getVR(tag).toString();
            System.out.println("Tag Address: " + tagAddress + " VR: " + vr);
        }
        dis.close();
    }

}

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Read the files inside directory(folder) and subdirectory(sub folder) using Java 8+

In this tutorial, we are going to learn how we can read all the files and specific files inside the directory and subdirectory.

Let's create a sample class FileReader.java

Read all the directory subdirectory and files:

 public static void main(String[] args) {
        String directoryPath = "path_to_directory";
        try {
            List<String> allFiles = listFiles(directoryPath);
            for (String filePath : allFiles) {
                System.out.println(filePath);
            }
        } catch (IOException e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

    public static List<String> listFiles(String directoryPath) throws IOException {
        Path start = Paths.get(directoryPath);
        try (Stream<Path> stream = Files.walk(start, Integer.MAX_VALUE)) {
            return stream
                    .map(String::valueOf)
                    .sorted()
                    .collect(Collectors.toList());
        }
    }

listFiles() method list all the directory, subdirectory, and files present inside the given directory. We are using Files.walk which will return stream API; list the files, directory and subdirectory by walking through the start directory to the max level of the subdirectory. Integer.MAX_VALUE will go through the maximum level of subdirectories available.

Read all the files and folders inside the current directory:

    public static List<String> listFiles(String directoryPath) throws IOException {
        Path start = Paths.get(directoryPath);
        try (Stream<Path> stream = Files.walk(start, 1)) {
            return stream
                    .map(String::valueOf)
                    .sorted()
                    .collect(Collectors.toList());
        }
    }

Here, we are using 1 as a maximum level value instead of Integer.MAX_VALUE, so it will read the current directory.

Only read the files inside the directory and subdirectory:

    public static List<String> listFiles(String directoryPath) throws IOException {
        Path start = Paths.get(directoryPath);
        try (Stream<Path> stream = Files.walk(start, Integer.MAX_VALUE)) {
            return stream
                    .map(String::valueOf)
                    .filter(file -> !new File(file).isDirectory())
                    .sorted()
                    .collect(Collectors.toList());
        }
    }

We are adding the filter that will only read files but not the directory or subdirectory and returns only files present inside the given directory.

Read Specific files inside directory and subdirectory

Suppose we want to only read .jpg or .png or .zip files present inside the directory and subdirectory. In this case, we will apply the filter to read only the desired extension file.

public static void main(String[] args) {
        String directoryPath = "path_to_directory";
        try {
            String fileExtensionToRead = ".png";
            List<String> pngFiles = listFiles(directoryPath, fileExtensionToRead);
            for (String filePath : pngFiles) {
                System.out.println(filePath);
            }
        } catch (IOException e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

private static List<String> listFiles(String directoryPath, String ext) throws IOException {
        Path start = Paths.get(directoryPath);
        try (Stream<Path> stream = Files.walk(start, Integer.MAX_VALUE)) {
            return stream
                    .map(String::valueOf)
                    .filter(file -> file.contains(ext))
                    .sorted()
                    .collect(Collectors.toList());
        }
    }

We are using a filter such that it will list the file if the filename contains the given extension. We can customize this filter as per our requirements.

The overall code implementation looks as below:

package io;

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;

public class FileReader {

    public static void main(String[] args) {
        String directoryPath = "path_to_directory";
        try {
            List<String> allFiles = listFiles(directoryPath);
            for (String filePath : allFiles) {
                System.out.println(filePath);
            }
            String fileExtensionToRead = ".png";
            List<String> pngFiles = listFiles(directoryPath, fileExtensionToRead);
            for (String filePath : pngFiles) {
                System.out.println(filePath);
            }
        } catch (IOException e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

    public static List<String> listFiles(String directoryPath) throws IOException {
        Path start = Paths.get(directoryPath);
        try (Stream<Path> stream = Files.walk(start, Integer.MAX_VALUE)) {
            return stream
                    .map(String::valueOf)
                    .filter(file -> !new File(file).isDirectory())
                    .sorted()
                    .collect(Collectors.toList());
        }
    }

    private static List<String> listFiles(String directoryPath, String ext) throws IOException {
        Path start = Paths.get(directoryPath);
        try (Stream<Path> stream = Files.walk(start, Integer.MAX_VALUE)) {
            return stream
                    .map(String::valueOf)
                    .filter(file -> file.contains(ext))
                    .sorted()
                    .collect(Collectors.toList());
        }
    }
}

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How to unzip the zip file and zip the folder in Java

In this tutorial, we are going to learn how to zip the given folder and unzip the zip file using Java.

Zip the folder or directory:

Let's create a java class ZipUnzip.java and create the main method.

public static void main(String[] args) {
        String folderInputPath = "path/of/folder/to/zip";
        String outputPath = "output/path/compressed.zip";
        try {
            zip(folderInputPath, outputPath);
        } catch (IOException e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

Now, create a method to zip the folder.

private static void zip(String folderInputPath, String outputPath) throws IOException {
        Path sourceFolderPath = Paths.get(folderInputPath);
        File zipPath = new File(outputPath);
        ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(zipPath));
        Files.walkFileTree(sourceFolderPath, new SimpleFileVisitor<Path>() {
            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                zos.putNextEntry(new ZipEntry(sourceFolderPath.relativize(file).toString()));
                Files.copy(file, zos);
                zos.closeEntry();
                return FileVisitResult.CONTINUE;
            }
        });
        zos.close();
    }

We are using java standard core library classes to zip. Files.walkFileTree() is used to navigate recursively through the directory tree. Once we execute the code we can see the zip file is created inside the output path provided. We can verify the compression manually by extracting it.

Unzip the zip file:

Let's create a method unzip() for unzipping the compressed file

 public static void main(String[] args) {
        String zipFilePath = "zip/file/path/compressed.zip";
        String zipOutputPath = "output/path/to/unzip";
        try {
            unzip(zipFilePath, zipOutputPath);
        } catch (IOException e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

private static void unzip(String zipFilePath, String outputDir) throws IOException {
        byte[] buffer = new byte[1024];
        ZipInputStream zis = new ZipInputStream(new FileInputStream(zipFilePath));
        ZipEntry zipEntry = zis.getNextEntry();
        while (zipEntry != null) {
            File newFile = new File(outputDir + File.separator, zipEntry.getName());
            if (zipEntry.isDirectory()) {
                if (!newFile.isDirectory() && !newFile.mkdirs()) {
                    throw new IOException("Failed to create directory " + newFile);
                }
            } else {
                File parent = newFile.getParentFile();
                if (!parent.isDirectory() && !parent.mkdirs()) {
                    throw new IOException("Failed to create directory " + parent);
                }
                FileOutputStream fos = new FileOutputStream(newFile);
                int len = 0;
                while ((len = zis.read(buffer)) > 0) {
                    fos.write(buffer, 0, len);
                }
                fos.close();
            }
            zipEntry = zis.getNextEntry();
        }
        zis.closeEntry();
        zis.close();
    }

Here, we are using ZipInputStream to read the file and FileOutputStream to write the file to the provided output directory.

The overall code implementation looks like below:

package io;

import java.io.*;
import java.nio.file.*;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import java.util.zip.ZipOutputStream;

public class ZipUnzip {

    public static void main(String[] args) {
        String folderInputPath = "path/of/folder/to/zip";
        String outputPath = "output/path/compressed.zip";

        String zipFilePath = "zip/file/path/compressed.zip";
        String zipOutputPath = "output/path/to/unzip";
        try {
            zip(folderInputPath, outputPath);
            unzip(zipFilePath, zipOutputPath);
        } catch (IOException e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

    private static void zip(String folderInputPath, String outputPath) throws IOException {
        Path sourceFolderPath = Paths.get(folderInputPath);
        File zipPath = new File(outputPath);
        ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(zipPath));
        Files.walkFileTree(sourceFolderPath, new SimpleFileVisitor<Path>() {
            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                zos.putNextEntry(new ZipEntry(sourceFolderPath.relativize(file).toString()));
                Files.copy(file, zos);
                zos.closeEntry();
                return FileVisitResult.CONTINUE;
            }
        });
        zos.close();
    }

    private static void unzip(String zipFilePath, String outputDir) throws IOException {
        byte[] buffer = new byte[1024];
        ZipInputStream zis = new ZipInputStream(new FileInputStream(zipFilePath));
        ZipEntry zipEntry = zis.getNextEntry();
        while (zipEntry != null) {
            File newFile = new File(outputDir + File.separator, zipEntry.getName());
            if (zipEntry.isDirectory()) {
                if (!newFile.isDirectory() && !newFile.mkdirs()) {
                    throw new IOException("Failed to create directory " + newFile);
                }
            } else {
                File parent = newFile.getParentFile();
                if (!parent.isDirectory() && !parent.mkdirs()) {
                    throw new IOException("Failed to create directory " + parent);
                }
                FileOutputStream fos = new FileOutputStream(newFile);
                int len = 0;
                while ((len = zis.read(buffer)) > 0) {
                    fos.write(buffer, 0, len);
                }
                fos.close();
            }
            zipEntry = zis.getNextEntry();
        }
        zis.closeEntry();
        zis.close();
    }
}

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