Java: Read .csv file and save into arrays

This should do the trick: it basically creates a matrix representation of the csv file.

LinkedList<String[]> rows = new LinkedList<String[]>();
String dataRow = CSVFile.readLine();
// Read the number of the lines in .csv file 
// i = row of the .csv file
int i = 0; 
while ((datarow = CSVFile.readLine()) != null){
    i++;
    rows.addLast(dataRow.split(","));
}

String[][] csvMatrix = rows.toArray(new String[rows.size()][]);

In csvMatrix[row][col]...

When accessing to a column, assert that the col number you are trying to access is in range by doing :

if(col < csvMatrix[row].length)

There are several problems with your code. The exception is caused by the fact that one of the lines doesn't contain enough of the ';' separated values.

The strange thing about your code is this bit:

  for (String item:dataArray) {
    customer_id[i] = dataArray[0];

This simply means you repeat the same assignments 15 times (just remove the for (String item: ...)).

If I were you, I'd do the following:

create a class; something like this:

public class Customer {
    private String customerId;
    private String companyName;

    // ...
    public static Customer create(final String... args) {
        if (args.length != 15) {
            return null; // or throw an exception
        }
        final Customer rv = new Customer();
        rv.setCustomerId(args[0]);
        rv.setCompanyName(args[1]);
        // ...
        return rv;
    }

    public String getCustomerId() {
        return customerId;
    }

    public void setCustomerId(final String customerId) {
        this.customerId = customerId;
    }

    public String getCompanyName() {
        return companyName;
    }

    public void setCompanyName(final String companyName) {
        this.companyName = companyName;
    }
}

use collection (as suggested in post above):

    BufferedReader csv = new BufferedReader(new FileReader("Sub-Companies.csv"));
    List<Customer> customers = new LinkedList<Customer>();

    String data;
    while ((data = csv.readLine()) != null){
        Customer customer = Customer.create(data.split(";"));
        if (customer != null) {
            customers.add(customer);
        }
    }

If you require array instead of collection, you can do:

Customer[] arr = customers.toArray(new Customer[customers.size()]);

Use a library to to read the file... You can try http://opencsv.sourceforge.net/ for example.

department[i] = dataArray[2];  

The exception means that the dataArray does not have that much elements (i.e. 3).
If you want to parse your CSV file you can make your life easier by specifying that for any missing elements there must be a placeholder.
What I mean is that you can have a record like:

a;b;c;d;e;f;g;h;j
Where each of the characters represent the values of your columns but when an element is missing the format must be:
a;;;;;f;g;h;j and not a;f;g;h;j

This is not an unusual expectation but the norm in CSV files and would simplify your code a lot and would avoid array index exception as your line will always have the expected columns

Using ArrayList:

public ArrayList<ArrayList<String>> parseDataFromCsvFile()
{
     ArrayList<ArrayList<String>> dataFromFile=new ArrayList<ArrayList<String>>();
     try{
         Scanner scanner=new Scanner(new FileReader("CSV_FILE_PATH"));
         scanner.useDelimiter(";");

         while(scanner.hasNext())
         {
            String dataInRow=scanner.nextLine();
            String []dataInRowArray=dataInRow.split(";");
            ArrayList<String> rowDataFromFile=new ArrayList<String>(Arrays.asList(dataInRowArray));
            dataFromFile.add(rowDataFromFile);
         }
         scanner.close();
     }catch (FileNotFoundException e){
        e.printStackTrace();
     }
     return dataFromFile;
}

Calling the method(displaying csv content):

ArrayList<ArrayList<String>> csvFileData=parseDataFromCsvFile();

public void printCsvFileContent(ArrayList<ArrayList<String>> csvFileData)
{
    for(ArrayList<String> rowInFile:csvFileData)
    {
        System.out.println(rowInFile);
    }
}

If you want to load data into a Parameterized JUnit test using Gradle ( instead of Maven) , here is the method:

// import au.com.bytecode.opencsv.CSVReader;
@Parameters(name = "{0}: {1}: {2}")
public static Iterable<String[]> loadTestsFromFile2() {
    String separator = System.getProperty("file.separator");
    File tFile = loadGradleResource( System.getProperty("user.dir") + 
        separator +  "build" + separator + "resources" + separator +  "test" + 
            separator + "testdata2.csv" );
    List<String[]> rows = null;
    if ( tFile.exists() ) {
        CSVReader reader = null;
        try {
            reader = new CSVReader( new FileReader( tFile ), ',' );
            rows = reader.readAll();
        } catch (FileNotFoundException e) {
                e.printStackTrace();
        } catch (IOException e) {
                e.printStackTrace();
        }   
    }
    staticlogger.info("Finished loadTestsFromFile2()");
    return rows;
} 

Please check if java.util.StringTokenizer helps

Example:

StringTokenizer tokenizer = new StringTokenizer(inputString, ";")

Manual: StringTokenizer docs