Introduction

Activating your Computer Science (CS) Lab account

The very first time (and only the first time) you use a computer in the lab, you need to activate your account. Your Computer Science (CS) Lab account will have a DIFFERENT login ID and password than the one you use for other UWP access.

• Preparation

  Have the following information ready before you start:

  1. Your UWP login ID (the one you use for SOLAR, RangerMail, etc.)
  2. Your UWP password
  3. Your choice for a LAB account password. Lab passwords must contain between 8 and 255 characters and have at least 2 characters that are not letters, and at least one character that is not alphanumeric (not a letter or digit). Also, it cannot contain any common English words or match your UWP password.
  
  
• Please wait at your machine while each student activates his/her account individually. Once activated, the system will need a few minutes to process the activation.
• The system will assign a login name to you. This might / might not match your last name.

  Remember your LAB login name and your LAB password.

Logging In

1. The computer system you use in the Computer Science Laboratory runs the Linux operating system. Linux is a variant of UNIX, and our lab currently uses CentOS linux.
2. If the screen is blank, press any key to bring it to life. The monitor may be turned off; turn it on if necessary (our monitors will go to sleep after a short time with no computer use). PLEASE keep your fingers from touching the screens - they are not easily cleanable. You should now see a screen with the current date and time. Press the Enter key (or roll the mouse wheel). Now you should see a dialogue box where you can enter your "Username:". Enter your CS department login name and press Enter. Then, one more dialogue box appears asking for your password. Type your password in the box and then press the Enter key.
3. If your login is successful, there will be a short delay (needed to load your profile) followed by the display of some startup Gnome windows (Gnome is your Desktop Manager Program.) Close any windows that show up by clicking on the X in the upper right corner of the window.
4. Look in the upper left corner and click Applications. You can use this menu item to reach just about anything you need to use. In the Favorites list which appears, click Terminal. You will now see a window whose title includes your login, machine name (login-name@vegetable-name) and current directory location (~, which means your home directory, /home/student/login-name). The cursor should appear to the right of a prompt which looks like: "[login-name@vegetable-name~]$".

Logging Out

First, close all browsers and application programs currently running. Logging out while certain applications are running can leave them running even after you log out, tying up resources and leaving a potential security risk.

Click on your name (found in the upper right corner of the screen). Select the option, "Log out". Another dialogue box will appear, from which you can confirm that you want to log out. DO NOT shut the machine down; others may be using it remotely.

Working in X Windows and Linux

Linux Commands

[smith@cabbage~]$

Linux commands are case sensitive. Most commands are typed in all lower case, but make certain you type them exactly as they appear below.

• The Directory Structure

  Almost all operating systems use the basic notions of directories (folders) and files stored within the directories. Linux is no exception. When you login to your account, you are in your home directory. Your home directory has a parent directory, and as you will see, you can also create subdirectories within your home directory. All together the directories form a large (upside down) tree. The root of the tree is named: /

  When typing commands several directories have special abbreviations.
  The current directory is referred to as: .
  The parent of the current directory is: ..
  Your home directory is: ~
  

  
  
  1. pwd prints the name of the working directory.
     At the $ prompt, enter: pwd.
     Assuming that your account is named 'smith' and that you have just logged in, the machine will respond with:
     /home/student/smith
     This may be interpreted as:
     / contains a subdirectory named home,
     home contains a subdirectory named student,
     and student contains a subdirectory named smith, which is your home directory.
     
     
  2. cd changes the working directory.
     cd (typed by itself) returns you to your home directory.
     cd .. moves you up one level in the directory tree.
     cd directory path - changes directory to location specified.
     
     
  3. ls lists the files and subdirectories within the current directory (that's a letter L in lowercase followed by s).
     ls lists the filenames.
     ls -l is a long listing (the letter after the - (dash) is also a lowercase L). It includes permissions on the files, the owner of each file, when they were created and their names.
     ls -a lists all files, including those beginning with . (files usually hidden from view; generally containing setup or configuration information). The current directory is always named . (by itself), but other files may begin with . as well.
     
     
  4. mkdir makes directories.
     mkdir Lab01 creates a subdirectory named Lab01
     
     
  5. rmdir removes empty directories.
     rmdir Lab01 removes the directory named Lab01

• File Manipulation

  Files exist within directories. They are typically created using an editor. There are many editors available in the CS lab, including gedit, vi and emacs. gedit is the most intuitive, with many of the same commands you use in Microsoft's WordPad. There are specialized handouts available in MOLN D120 to learn about vi and emacs.

  Once files exist, they can be copied, moved, deleted and viewed via various Linux commands.

  Linux uses the wild card character, *, to match any string of characters in a file name. Warning: Using an asterisk (*) can affect more files than you expect if unintended files match your wild card specification.
  

  
  
  1. cp
  is used to copy files.
  cp Ball.java Ball.bak copies the file Ball.java into a new file named Ball.bak
  
  At the beginning of each week's lab exercise, you will copy a directory of files. For example, here is the command for the first week:
  cp -r /home/student/Classes/Cs241/Labs/Lab01 .

  This command has several parts to it, including a "from" and a "to" location.

  Specifically, it copies the directory named Lab01 (and all folders and files it holds) from its location inside of /home/student/Classes/Cs241/Labs. The -r option (or "flag") says to do the copy recursively (meaning take the contents of the directory as well). It copies all of this group to the current directory (the location from which you typed the command, represented by the dot (.)).
  As a rule of thumb, when copying a directory, use the -r flag. When copying individual files, do not.
  
  
  2. more
  lists files to the window, one windowful at a time.
  more Ball.java lists the file Ball.java to the window. If the file is more than one window long, more waits for the user to press the spacebar for the next windowful.
  
  
  3. rm
  removes files.
  rm Ball.java removes the file Ball.java
  Warning! Use rm with caution. Once a file is removed, it is gone forever. For example,
  rm -rf * will remove all the files in the current directory.
  
  
  4. chmod
  changes the access permissions on files or directories. Security on UNIX systems is based on granting permissions to the file owner (u), the file's group (g) and all others (o). You are the owner of files you create. All students belong to a group named student.

  The permissions are read (r), write (w) and execute (x). Anyone with read permission may see the contents of the file. Anyone with write permission may change the file. For programs, anyone with execute permission may run the program. The permissions are a bit different for directories. In particular, execute permission on a directory enables one to access the contents of the directory.
  chmod g+x a.out adds execute permission to all members of the group to enable them to run the program a.out.
  chmod go-r Ball.java removes read permission from the file Ball.java, so that group members and others can no longer read it.

  Now ls -l discussed above makes more sense.
  ls -l /home/student/Classes/Cs241/Labs/Lab01 returns something like:
  

  -rw-r--r-- 1 hansen staff 123 Sep 7 2001 LabOne.ctxt
  -rw-r--r-- 1 hansen staff 788 Sep 7 2001 LabOne.java
  -rw-r--r-- 1 eddy staff 471 Sep 7 2001 README.TXT
  -rw-r--r-- 1 hansen staff 285 Sep 7 2001 bluej.pkg
  -rw-r--r-- 1 hansen staff 285 Sep 7 2001 bluej.pkh
   

  Most of the files belong to Professor Hansen, except for README.TXT which belongs to Ms. Eddy. The group of each file is staff. The first 10 characters of each line show the permissions on the file. The first character is a - for ordinary files and a d for directories. The next three characters show the owner's permissions, the next three the group's permissions and the last three all other's permissions. In our example, the owner has read and write permissions. The group and others have only read permissions. There are no executable files in this directory.

Linux Printing Commands

1. lp prints a copy of a file to the printer.
   lp LabOne.java prints the file LabOne.java to the printer. It prints one logical page per physical sheet of paper.
2. To submit your assignments, you will NOT need to give a printout to your instructor. You will upload a copy of your .java file(s) to Canvas. However, if you wish to print for your own review, we recommend printing files through BlueJ. BlueJ also allows you to print 2 logical pages on one physical sheet of paper (used to save paper while work is in progress). Most applications (like BlueJ, mentioned earlier) have a print command in their menu system. This is generally the easiest way to print.

   Warning!
   Do not print binary files. In particular, do not print files with a .class extension. The results are unpredictable, including possibly printing hundreds of pages and/or hanging the printer.
   
   

3. lpq displays the jobs currently waiting in the print queue. You can see if your file is still waiting to be printed.

 
4. Most applications (like BlueJ, mentioned earlier) have a print command in their menu system. This is generally the easiest way to print.

Submitting a Programming Assignment Electronically (two required ways)

1. Submit your projects through a BlueJ menu option. You MUST be running BlueJ in our lab to do the submission; it does NOT work with your home computer BlueJ installation. This process copies your BlueJ project, and all its files, into a directory that your instructor uses for grading.
   Each submission is time-stamped so that we will know it has arrived on time. From here, your instructor can compile your program(s) as well as run it/them with test data.
2. Upload each .java (source file) you create/modify to Canvas. Your instructor can write comments on this copy and assign points.

If, after submitting a project, you discover that you want to change what you have submitted, you may simply submit through the menu option again. The earlier version(s) of your program(s) will be replaced by the new version(s).

Using a USB Storage Device

To begin:

1. Insert the USB device on the front of the computer underneath the table.
2. After a brief delay, a window will appear listing the contents of this device. An icon for the device will also appear on your desktop.
3. Stored files will be found inside a directory at:
   /media
   The name of the directory where the files are located depends on the brand name of your flash drive. For example, if the brand is Kingston, you might find the files at this location:
   /media/KINGSTON/*
   These files can be accessed with normal Linux commands like cd, ls, cp, etc.

When finished, you will need to remove the device using these steps:

1. Close any windows displaying the contents of the device.
2. Right-click on the device's icon and choose Eject Volume.
3. Unplug the device from the cable before logging out and turning off the monitor.

Other Useful Linux Commands

Although a Linux command exists to change your password, it is easier do so by opening a browser and navigating to:
https://www.cs.uwp.edu/account/activate  Follow the directions on the screen.
1. who tells you who is currently logged onto the system.

2. ps -u tells you the status of all your active processes (i.e., the programs that are running on the machine in front of you).
   Here is sample output from ps -u:

    USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
   hansen 26902 0.0 0.1 1740 988 pts/8 S 13:00 0:00 -bash
   hansen 26963 0.1 1.0 8192 5296 pts/8 S 13:01 0:05 emacs -font 10x20
   hansen 28737 0.0 0.1 2324 688 pts/8 R 13:49 0:00 ps -u
   

   Professor Hansen has three processes running: a command shell (bash), an editor (emacs) and the ps command. The first two are stopped. The status of the last one is running. The PID (Process ID) column tells you the unique number assigned to each process.

3. kill -9 PID kills processes.
   kill -9 26963 will kill the emacs session that Professor Hansen is running.

   Warning! Use kill judiciously. There is almost always a more natural way to terminate a program. Only use kill when a program is so hung there is no other alternative.

Sending Labs to Your Partner's Account

For the following instructions, the student currently logged in will be referred to as "Student1", and the student who will receive a copy of the files will be referred to as "Student2". We will assume you want to copy all the files in the Lab01 directory. So that only one file need be transferred, the first part of these instructions explain how to create a zip file:

Student1:

1. Make certain you are in the directory that contains the Lab01 directory. You may need to cd to the proper level (to go up one level, type cd ..).
2. Enter one of these commands:

        zip -r Lab01.zip Lab01   

   OR

        zip -r Lab01.zipp Lab01   

   This creates a zip (compressed) file containing all of the Lab01 directory contents, including any subdirectories that might exist. For security reasons, our campus email does not allow .zip files to be attached to email messages. If you wish to use RangerMail, you should name your file with the slightly different file extension (zipp). You'll rename it later.

Here are two sets of instructions (you can use either one) to transfer this zipped file to Student2. The first way is by attaching the file to an email message, and the second way is by using secure file transfer protocol (sftp).

1. The following instructions use the campus RangerMail program as the email client (program). Very similar directions apply if you use a different email server such as yahoo or hotmail. This method of file transfer is handy if Student2 wishes to get a copy of the lab files on their home computer. It is also a good way to send files to yourself to retrieve at home.
   1. Using Firefox, go to the UWP Logins page and log into RangerMail.
   2. Choose to send a new message.
   3. Enter your partner's email address in the To box.
   4. Type "Lab01 Files" in the Subject box.
   5. Look for the "Attach files" button (with the paper clip) above the "From:" field. Choose Browse and navigate to your Lab01.zipp file, and click Open.
   6. Important! You must click the Attach button.
   7. Click the Send button.
   8. Log out of RangerMail.

   To receive the lab files, Student2 should follow the procedure below:

   1. Log in to any lab machine.
   2. Using Firefox, go to the UWP Logins page and log into RangerMail.
   3. Select the message containing the attachment.
   4. On the Parts line you should see Lab01.zipp. Click on it.
   5. A window will appear asking if you want to save the file. Make certain "Save to Disk" is selected, then either save to your desktop (the default) or click on the Desktop button to navigate to the location where you wish to save the file.
   6. Rename the ".zipp" file as ".zip".
   7. Log out of RangerMail and close Firefox.

2. The two students can also use secure file transfer protocol to transfer the zipped file directly into another lab account.
   1. Assume that the two lab partners are working on the machine named radish. Student1 types the following command on his/her machine:
      sftp student2@radish.cs.uwp.edu
      note: this assumes student2 is the person's login name
   2. A prompt will appear asking for Student2's password. Student2 should type this in, then press Enter.
   3. The terminal window doesn't look quite the same as a normal terminal window, but Student2 can still use Linux commands such as cd, ls, etc. to go to the location where she wants the copied file to be placed.
   4. Student2 then types
      put Lab01.zip
   5. The zipped file will then be placed in the proper location. Student2 is still logged in to her account at this time.
   6. Student2 should type exit to stop running sftp and return the machine to Student1's account.

Student2 should log in as usual to her account, then:

1. In a terminal window, cd to the directory where you saved the Lab01.zip file.
2. Type the command unzip Lab01.zip to unzip the file.

Beyond the Basics

BlueJ

You'll use BlueJ in the very first lab.

• Starting BlueJ To start BlueJ, enter the command (after the $ prompt)

   bluej& 

  The ampersand (&) allows you to toggle back-and-forth between BlueJ and the terminal window. You can also reach BlueJ through the Applications->Programming menu.
  A few moments after entering this command, the main BlueJ window will open.

• Exiting BlueJ To exit BlueJ select Project -> Quit from BlueJ's menu.
  

• BlueJ Projects BlueJ, like most IDEs, collects Java files together into projects. A project is a directory that contains one or more Java programs and other related files. For example, when you copy files for use in a lab exercise, you typically copy one or more BlueJ projects.
  • Creating and Opening Projects
    When you start working you will either want to create a new BlueJ project or open a pre-existing project. Both options appear in BlueJ's Project menu.

    When you select either option the system gives you a list of what is available in your current subdirectory. Each icon on the 'Look In:' line represents a way to either move to a different directory level, or change the way the directory listings are displayed in this window. Move your mouse pointer onto each icon, one at a time, to see (after a brief delay) a short description of the action that icon performs. Instead of using the mouse, you can also type the file name you want in the area labeled 'File Name:' located below the directory listing.
    
    To create a new project select Project -> New Project and enter the name of the project in the 'File Name:' area.
    
    To open an existing project select Project -> Open Project. In the Open Project window, choose the folder with the project name, then click Open. Your BlueJ window now displays a paper icon and a class icon for each class in the project. If you opened a new project, there are no classes currently displayed.

  • Adding Classes to Projects
    To add a class to a project, click on the New Class button. A dialog box appears asking for a class name. Enter the name of your choice.

• Editing Java Files
  BlueJ uses a text editor named moe to edit Java source code. To open the editor, use the right mouse button, click on the class icon for LabOne and select "Open Editor" from the menu displayed. (Alternatively, you can double-click the class icon to edit the implementation.) The Java code for this class is now displayed.

  The editor is fairly intuitive. You can move around the file using the arrow keys. Text is inserted when you type. The editor also uses syntax highlighting. Right now we don't know much Java, but as the semester proceeds, you will see that different language structures appear in different colors in the editor.

  To close the editor, first choose Class -> Save, then choose Class -> Close.

• Compiling Java Files
  Java source code needs to be translated into byte code before it can be run. The Java files that we edit are called source code. Source code is easy for humans to read and interpret. Byte code, a.k.a. machine language, is binary. It is very difficult for humans to read but easy for the computer to interpret. In Java, source code files always have a .java suffix. Byte code files always have a .class suffix.
  Warning! Never print a byte code (or any other binary) file.

  To successfully compile, a Java file must be syntactically correct. This means that it must contain only legal Java statements. If there are syntactic errors the compiler cannot generate byte code, but can generate error messages. One nice feature of BlueJ's IDE is that when the compiler finds an error, it highlights the line where the error was detected and displays an error message, hopefully making the error easier to correct. The error may occur on the highlighted line or on one earlier in the program.
  Warning! Logical errors are mistakes in the program's logic, not its syntax. The Java compiler has no way of detecting these.

  To compile a class while you are editing it, click the Compile button that appears at the upper left of the window. If the compile is successful, you will receive a message saying, "Class compiled - no syntax errors."

  To compile a class when not editing, right click the class icon and choose compile. If the compile is successful, you will see a message saying, "Compiling ... Done".

• Running Java Code from Within BlueJ
  Java is an object-oriented language. The basic idea behind object-oriented programming is to define classes and then make instances of those classes named objects. BlueJ gives us three ways to create and use objects.
  1. The BlueJ Object Bench
     It is possible in BlueJ to create (instantiate) an object and manipulate it directly. Right click on the class you wish to instantiate and choose new classname. A window appears with a name for the object. You may simply click okay, or rename the object as you wish. A red object icon appears in the object bench at the bottom of the BlueJ window.

     An object contains methods that may be invoked to make the object do things. Right click on the object icon and choose the method. If the method requires arguments, i.e., data, another window will appear asking you to enter it.

  2. Java Programs
     Most Java programs are made up of many objects working together to accomplish some task. Java programs are invoked (start running) from the class icon, not object icon. Right click on the class icon and choose Run Main Method. The program begins running.
     Note: Alternatively, you can run the main method by choosing void main(String []). You will then see a second window with { } symbols in the textbox. Simply choose OK to run the program.

  3. Java Applets
     There is a third way to manipulate objects in BlueJ. Applets are Java programs that are meant to run in a web browser. Applets require both extensive knowledge of Java and some knowledge of html. While we may explore applets at some point during the semester, they are not covered further here.