Search icon CANCEL
Subscription
0
Cart icon
Your Cart (0 item)
Close icon
You have no products in your basket yet
Save more on your purchases! discount-offer-chevron-icon
Savings automatically calculated. No voucher code required.
Arrow left icon
Explore Products
Best Sellers
New Releases
Books
Videos
Audiobooks
Learning Hub
Newsletter Hub
Free Learning
Arrow right icon
timer SALE ENDS IN
0 Days
:
00 Hours
:
00 Minutes
:
00 Seconds
Java Data Science Cookbook
Java Data Science Cookbook

Java Data Science Cookbook: Explore the power of MLlib, DL4j, Weka, and more

Arrow left icon
Profile Icon Shams
Arrow right icon
$19.99 per month
Paperback Mar 2017 372 pages 1st Edition
eBook
$38.99 $43.99
Paperback
$54.99
Subscription
Free Trial
Renews at $19.99p/m
Arrow left icon
Profile Icon Shams
Arrow right icon
$19.99 per month
Paperback Mar 2017 372 pages 1st Edition
eBook
$38.99 $43.99
Paperback
$54.99
Subscription
Free Trial
Renews at $19.99p/m
eBook
$38.99 $43.99
Paperback
$54.99
Subscription
Free Trial
Renews at $19.99p/m

What do you get with a Packt Subscription?

Free for first 7 days. $19.99 p/m after that. Cancel any time!
Product feature icon Unlimited ad-free access to the largest independent learning library in tech. Access this title and thousands more!
Product feature icon 50+ new titles added per month, including many first-to-market concepts and exclusive early access to books as they are being written.
Product feature icon Innovative learning tools, including AI book assistants, code context explainers, and text-to-speech.
Product feature icon Thousands of reference materials covering every tech concept you need to stay up to date.
Subscribe now
View plans & pricing
Table of content icon View table of contents Preview book icon Preview Book

Java Data Science Cookbook

Chapter 1. Obtaining and Cleaning Data

In this chapter, we will cover the following recipes:

  • Retrieving all file names from hierarchical directories using Java
  • Retrieving all file names from hierarchical directories using Apache Commons IO
  • Reading contents from text files all at once using Java 8
  • Reading contents from text files all at once using Apache Commons IO
  • Extracting PDF text using Apache Tika
  • Cleaning ASCII text files using Regular Expressions
  • Parsing Comma Separated Value files using Univocity
  • Parsing Tab Separated Value files using Univocity
  • Parsing XML files using JDOM
  • Writing JSON files using JSON.simple
  • Reading JSON files using JSON.simple
  • Extracting web data from a URL using JSoup
  • Extracting web data from a website using Selenium Webdriver
  • Reading table data from MySQL database

Introduction

Every data scientist needs to deal with data that is stored on disks in several formats, such as ASCII text, PDF, XML, JSON, and so on. Also, data can be stored in database tables. The first and foremost task for a data scientist before doing any analysis is to obtain data from these data sources and of these formats, and apply data-cleaning techniques to get rid of noises present in them. In this chapter, we will see recipes to accomplish this important task.

We will be using external Java libraries (Java archive files or simply JAR files) not only for this chapter but throughout the book. These libraries are created by developers or organizations to make everybody's life easier. We will be using Eclipse IDE for code development, preferably on the Windows platform, and execution throughout the book. Here is how you can include any external JAR file, and in many recipes, where I instruct you to include external JAR files into your project, this is what you need to do.

You can add a JAR file in a project in Eclipse by right-clicking on the Project | Build Path | Configure Build Path. Under the Libraries tab, click on Add External JARs..., and select the external JAR file(s) that you are going to use for a particular project:

Introduction

Retrieving all filenames from hierarchical directories using Java

This recipe (and the following) is for the data scientist who wants to retrieve the file paths and names (for some future analysis) from a complex directory structure that contains numerous directories and files inside a root directory.

Getting ready

In order to perform this recipe, we will require the following:

  1. Create directories within directories (as many layers as you want).
  2. Create text files in some of these directories while leaving some directories empty for more excitement.

How to do it...

  1. We are going to create a static method that takes a File argument, which is eventually the root directory or the directory to start with. The method will return a set of files that are found within this root directory (and in all other subsequent directories):
            public static Set<File> listFiles(File rootDir) {  
    
  2. First, create a HashSet that will contain the file information:
            Set<File> fileSet = new HashSet<File>(); 
    
  3. Once the HashSet is created, we need to check whether the root directory or the directories within it are null. For such cases, we do not need to proceed further:
            if (rootDir == null || rootDir.listFiles() == null){ 
                         return fileSet; 
               } 
    
  4. We consider one directory (or file) from the root directory at a time and check whether we are dealing with a file or with a directory. In the case of a file, we add that to our HashSet. In the case of a directory, we recursively call this method again by sending the path and name of the directory:
            for (File fileOrDir : rootDir.listFiles()) { 
                         if (fileOrDir.isFile()){ 
                           fileSet.add(fileOrDir); 
                         } 
                         else{ 
                           fileSet.addAll(listFiles(fileOrDir)); 
                         } 
                 } 
    
  5. Finally, we return the HashSet to the caller of this method:
           return fileSet; 
              } 
    

    The complete method, with the class and the driver method to run it, is as follows:

    import java.io.File; 
    import java.util.HashSet; 
    import java.util.Set; 
     
    public class TestRecursiveDirectoryTraversal { 
       public static void main(String[] args){ 
          System.out.println(listFiles(new File("Path for root 
              directory")).size()); 
       } 
        
       public static Set<File> listFiles(File rootDir) { 
           Set<File> fileSet = new HashSet<File>(); 
           if(rootDir == null || rootDir.listFiles()==null){ 
               return fileSet; 
           } 
           for (File fileOrDir : rootDir.listFiles()) { 
                 if (fileOrDir.isFile()){ 
                   fileSet.add(fileOrDir); 
                 } 
                 else{ 
                   fileSet.addAll(listFiles(fileOrDir)); 
                 } 
         } 
     
           return fileSet; 
       } 
    } 
    

Note

Note the use of HashSet to store the paths and names of the files. This means that we will not have any duplicates since the Set data structures in Java do not contain duplicate entries.

Retrieving all filenames from hierarchical directories using Apache Commons IO

Listing of file names in hierarchical directories can be done recursively as demonstrated in the previous recipe. However, this can be done in a much easier and convenient way and with less coding using the Apache Commons IO library.

Getting ready

In order to perform this recipe, we will require the following:

  1. In this recipe, we will be using a Java library from Apache named Commons IO. Throughout the book, we will be using version 2.5. Download the JAR file of your choice from here: https://commons.apache.org/proper/commons-io/download_io.cgi
  2. Include the JAR file in your project an external JAR in Eclipse.

How to do it...

  1. Create a method that takes the root directory in the hierarchy of directories as input:
            public void listFiles(String rootDir){ 
    
  2. Create a file object with the root directory name:
            File dir = new File(rootDir); 
    
  3. The FileUtils class of the Apache Commons library contains a method named listFiles(). Use this method to retrieve all the file names, and put the names in a list variable with <File> generics. Use TrueFileFilter.INSTANCE to match all directories:
            List<File> files = (List<File>) FileUtils.listFiles(dir,   
              TrueFileFilter.INSTANCE, TrueFileFilter.INSTANCE); 
    
  4. The file names can be displayed on the standard output as follows. As we now have the names in a list, we have a means to process the data in these files further:
            for (File file : files) { 
               System.out.println("file: " + file.getAbsolutePath()); 
            } 
    
  5. Close the method:
           } 
    

    The method in this recipe, the class for it, and the driver method to run it are as follows:

    import java.io.File; 
    import java.util.List; 
    import org.apache.commons.io.FileUtils; 
    import org.apache.commons.io.filefilter.TrueFileFilter; 
     
    public class FileListing{ 
       public static void main (String[] args){ 
          FileListing fileListing = new FileListing(); 
          fileListing.listFiles("Path for the root directory here"); 
       } 
       public void listFiles(String rootDir){ 
          File dir = new File(rootDir); 
     
          List<File> files = (List<File>) FileUtils.listFiles(dir,  
            TrueFileFilter.INSTANCE, TrueFileFilter.INSTANCE); 
          for (File file : files) { 
             System.out.println("file: " + file.getAbsolutePath()); 
          } 
       } 
    

Tip

If you want to list files with some particular extensions, there is a method in Apache Commons library called listFiles, too. However, the parameters are different; the method takes three parameters, namely, file directory, String[] extensions, boolean recursive. Another interesting method in this library is listFilesAndDirs (File directory, IOFileFilter fileFilter, IOFileFilter dirFilter) if someone is interested in listing not only files but also directories. Detailed information can be found at https://commons.apache.org/proper/commons-io/javadocs/.

Reading contents from text files all at once using Java 8

On many occasions, data scientists have their data in text format. There are many different ways to read text file contents, and they each have their own pros and cons: some of them consume time and memory, while some are fast and do not require much computer memory; some read the text contents all at once, while some read text files line by line. The choice depends on the task at hand and a data scientist's approach to that task.

This recipe demonstrates how to read text file contents all at once using Java 8.

How to do it...

  1. First, create a String object to hold the path and name of the text file you are going to read:
            String file = "C:/dummy.txt";  
    
  2. Using the get() method of the Paths class, we get to the path of the file we are trying to read. The parameter for this method is the String object that points to the name of the file. The output of this method is fed to another method named lines(), which is in the Files class. This method reads all lines from a file as a Stream, and therefore, the output of this method is directed to a Stream variable. Because our dummy.txt file contains string data, the generics of the Stream variable is set to String.

The entire process of reading needs a try...catch block for attempts such as reading a file that does not exist or damaged and so on.

The following code segment displays the contents of our dummy.txt file. The stream variable contains the lines of the text file, and therefore, the forEach() method of the variable is used to display each line content:

        try (Stream<String> stream = Files.lines(Paths.get(file))) { 
        stream.forEach(System.out::println); } catch (IOException e) { 
        System.out.println("Error reading " +  file.getAbsolutePath()); 
        } 
Left arrow icon Right arrow icon
Download code icon Download Code

Key benefits

  • This book provides modern recipes in small steps to help an apprentice cook become a master chef in data science
  • Use these recipes to obtain, clean, analyze, and learn from your data
  • Learn how to get your data science applications to production and enterprise environments effortlessly

Description

If you are looking to build data science models that are good for production, Java has come to the rescue. With the aid of strong libraries such as MLlib, Weka, DL4j, and more, you can efficiently perform all the data science tasks you need to. This unique book provides modern recipes to solve your common and not-so-common data science-related problems. We start with recipes to help you obtain, clean, index, and search data. Then you will learn a variety of techniques to analyze, learn from, and retrieve information from data. You will also understand how to handle big data, learn deeply from data, and visualize data. Finally, you will work through unique recipes that solve your problems while taking data science to production, writing distributed data science applications, and much more - things that will come in handy at work.

Who is this book for?

This book is for Java developers who are familiar with the fundamentals of data science and want to improve their skills to become a pro.

What you will learn

  • Find out how to clean and make datasets ready so you can acquire actual insights by removing noise and outliers
  • Develop the skills to use modern machine learning techniques to retrieve information and transform data to knowledge. retrieve information from large amount of data in text format.
  • Familiarize yourself with cutting-edge techniques to store and search large volumes of data and retrieve information from large amounts of data in text format
  • Develop basic skills to apply big data and deep learning technologies on large volumes of data
  • Evolve your data visualization skills and gain valuable insights from your data
  • Get to know a step-by-step formula to develop an industry-standard, large-scale, real-life data product
  • Gain the skills to visualize data and interact with users through data insights

Product Details

Country selected
Publication date, Length, Edition, Language, ISBN-13
Publication date : Mar 28, 2017
Length: 372 pages
Edition : 1st
Language : English
ISBN-13 : 9781787122536
Category :
Languages :
Concepts :
Tools :

What do you get with a Packt Subscription?

Free for first 7 days. $19.99 p/m after that. Cancel any time!
Product feature icon Unlimited ad-free access to the largest independent learning library in tech. Access this title and thousands more!
Product feature icon 50+ new titles added per month, including many first-to-market concepts and exclusive early access to books as they are being written.
Product feature icon Innovative learning tools, including AI book assistants, code context explainers, and text-to-speech.
Product feature icon Thousands of reference materials covering every tech concept you need to stay up to date.
Subscribe now
View plans & pricing

Product Details

Publication date : Mar 28, 2017
Length: 372 pages
Edition : 1st
Language : English
ISBN-13 : 9781787122536
Category :
Languages :
Concepts :
Tools :

Packt Subscriptions

See our plans and pricing
Modal Close icon
$19.99 billed monthly
Feature tick icon Unlimited access to Packt's library of 7,000+ practical books and videos
Feature tick icon Constantly refreshed with 50+ new titles a month
Feature tick icon Exclusive Early access to books as they're written
Feature tick icon Solve problems while you work with advanced search and reference features
Feature tick icon Offline reading on the mobile app
Feature tick icon Simple pricing, no contract
$199.99 billed annually
Feature tick icon Unlimited access to Packt's library of 7,000+ practical books and videos
Feature tick icon Constantly refreshed with 50+ new titles a month
Feature tick icon Exclusive Early access to books as they're written
Feature tick icon Solve problems while you work with advanced search and reference features
Feature tick icon Offline reading on the mobile app
Feature tick icon Choose a DRM-free eBook or Video every month to keep
Feature tick icon PLUS own as many other DRM-free eBooks or Videos as you like for just $5 each
Feature tick icon Exclusive print discounts
$279.99 billed in 18 months
Feature tick icon Unlimited access to Packt's library of 7,000+ practical books and videos
Feature tick icon Constantly refreshed with 50+ new titles a month
Feature tick icon Exclusive Early access to books as they're written
Feature tick icon Solve problems while you work with advanced search and reference features
Feature tick icon Offline reading on the mobile app
Feature tick icon Choose a DRM-free eBook or Video every month to keep
Feature tick icon PLUS own as many other DRM-free eBooks or Videos as you like for just $5 each
Feature tick icon Exclusive print discounts

Frequently bought together


Stars icon
Total $ 164.97
Java Data Science Cookbook
$54.99
Mastering Java for Data Science
$54.99
Java for Data Science
$54.99
Total $ 164.97 Stars icon

Table of Contents

9 Chapters
1. Obtaining and Cleaning Data Chevron down icon Chevron up icon
2. Indexing and Searching Data Chevron down icon Chevron up icon
3. Analyzing Data Statistically Chevron down icon Chevron up icon
4. Learning from Data - Part 1 Chevron down icon Chevron up icon
5. Learning from Data - Part 2 Chevron down icon Chevron up icon
6. Retrieving Information from Text Data Chevron down icon Chevron up icon
7. Handling Big Data Chevron down icon Chevron up icon
8. Learn Deeply from Data Chevron down icon Chevron up icon
9. Visualizing Data Chevron down icon Chevron up icon
Get free access to Packt library with over 7500+ books and video courses for 7 days!
Start Free Trial

FAQs

What is included in a Packt subscription? Chevron down icon Chevron up icon

A subscription provides you with full access to view all Packt and licnesed content online, this includes exclusive access to Early Access titles. Depending on the tier chosen you can also earn credits and discounts to use for owning content

How can I cancel my subscription? Chevron down icon Chevron up icon

To cancel your subscription with us simply go to the account page - found in the top right of the page or at https://subscription.packtpub.com/my-account/subscription - From here you will see the ‘cancel subscription’ button in the grey box with your subscription information in.

What are credits? Chevron down icon Chevron up icon

Credits can be earned from reading 40 section of any title within the payment cycle - a month starting from the day of subscription payment. You also earn a Credit every month if you subscribe to our annual or 18 month plans. Credits can be used to buy books DRM free, the same way that you would pay for a book. Your credits can be found in the subscription homepage - subscription.packtpub.com - clicking on ‘the my’ library dropdown and selecting ‘credits’.

What happens if an Early Access Course is cancelled? Chevron down icon Chevron up icon

Projects are rarely cancelled, but sometimes it's unavoidable. If an Early Access course is cancelled or excessively delayed, you can exchange your purchase for another course. For further details, please contact us here.

Where can I send feedback about an Early Access title? Chevron down icon Chevron up icon

If you have any feedback about the product you're reading, or Early Access in general, then please fill out a contact form here and we'll make sure the feedback gets to the right team. 

Can I download the code files for Early Access titles? Chevron down icon Chevron up icon

We try to ensure that all books in Early Access have code available to use, download, and fork on GitHub. This helps us be more agile in the development of the book, and helps keep the often changing code base of new versions and new technologies as up to date as possible. Unfortunately, however, there will be rare cases when it is not possible for us to have downloadable code samples available until publication.

When we publish the book, the code files will also be available to download from the Packt website.

How accurate is the publication date? Chevron down icon Chevron up icon

The publication date is as accurate as we can be at any point in the project. Unfortunately, delays can happen. Often those delays are out of our control, such as changes to the technology code base or delays in the tech release. We do our best to give you an accurate estimate of the publication date at any given time, and as more chapters are delivered, the more accurate the delivery date will become.

How will I know when new chapters are ready? Chevron down icon Chevron up icon

We'll let you know every time there has been an update to a course that you've bought in Early Access. You'll get an email to let you know there has been a new chapter, or a change to a previous chapter. The new chapters are automatically added to your account, so you can also check back there any time you're ready and download or read them online.

I am a Packt subscriber, do I get Early Access? Chevron down icon Chevron up icon

Yes, all Early Access content is fully available through your subscription. You will need to have a paid for or active trial subscription in order to access all titles.

How is Early Access delivered? Chevron down icon Chevron up icon

Early Access is currently only available as a PDF or through our online reader. As we make changes or add new chapters, the files in your Packt account will be updated so you can download them again or view them online immediately.

How do I buy Early Access content? Chevron down icon Chevron up icon

Early Access is a way of us getting our content to you quicker, but the method of buying the Early Access course is still the same. Just find the course you want to buy, go through the check-out steps, and you’ll get a confirmation email from us with information and a link to the relevant Early Access courses.

What is Early Access? Chevron down icon Chevron up icon

Keeping up to date with the latest technology is difficult; new versions, new frameworks, new techniques. This feature gives you a head-start to our content, as it's being created. With Early Access you'll receive each chapter as it's written, and get regular updates throughout the product's development, as well as the final course as soon as it's ready.We created Early Access as a means of giving you the information you need, as soon as it's available. As we go through the process of developing a course, 99% of it can be ready but we can't publish until that last 1% falls in to place. Early Access helps to unlock the potential of our content early, to help you start your learning when you need it most. You not only get access to every chapter as it's delivered, edited, and updated, but you'll also get the finalized, DRM-free product to download in any format you want when it's published. As a member of Packt, you'll also be eligible for our exclusive offers, including a free course every day, and discounts on new and popular titles.