OPS435 Python Lab 5

LAB OBJECTIVES

So far, you have created Python scripts to prompt a user to input data from the keyboard. When creating Python scripts, you may also need to be able to process large volumes of information, or store processed data for further processing. The first investigation in this lab will focus on file management, opening files, saving data to files, and reading files.

NOTE: Since many tasks that system administrators deal with files, this is a crucial skill to understand.

Python is an object oriented programming language. Object oriented programming languages have great advantages or other programming languages. Some advantages include greater modularity for more effective troubleshooting, the ability to re-use objects, and to provide greater flexibility to allow objects to handle unique situations from various data (for example a date in different formats). The second investigation in this lab will introduce the student to basic object oriented programming. To keep things simple, this investigation will focus more on the concept that objects are primarily used to store data and code.

PYTHON REFERENCE

In previous labs, you have been advised to make notes and use online references. This also relates to working with files and learning about objected oriented programming to help becoming "overwhelmed" with the volume of information in this lab.

Below is a table with links to useful online Python reference sites (by category). You may find these references useful when performing assignments, etc.

Category	Resource Link
Handling Errors & Exceptions	Errors & Exceptions
Built-in Exceptions	Built-in Exceptions
Data Manipulation via Files	Reading & Writing Files
Opening Files	Open File Usage
Using Classes	Classes

INVESTIGATION 1: Working with Files

You will now learn how to write Python scripts in order to open text files, to read the contents within a text file, to process the contents, and finally to write the processed contents back into a file. These operations are very common, and are used extensively in programming. Examples of file operations would include situations such as logging output, logging errors, reading and creating configuration/temporary files, etc.

Files are accessed through the use of file objects. An object is a storage location which stores data in the form of attributes (variables) and methods (functions). Creating our own objects will be covered later in investigation 3.

PART 1 - Reading Data From Files

Perform the Following Steps:

1. Launch your Centos VM, open a shell terminal (as a regular user) and start a new ipython3 session:

   ipython3

2. Create a new text file in the lab5 directory:

   %cd ~/ops435/lab5
   %vim ~/ops435/lab5/data.txt

3. Place the following content inside the new file and save it:

   Hello World
   This is the second liner
   Third line
   Last line

   
   In order to read data from a text file, we need to create a special storage area (or a "buffer") that will be used to access and storage the data in a file. This special storage has different names for various programming languages (like a "file pointer" in the C programming language or as an "object" in object oriented programming languages).
   In Python, we define an object to act as a buffer to help access the data contained within the file. To simplify things for now, you can think of an object as a special variable. You will learn more about object oriented programming later in this lab.
   
   
4. Now lets write some python code from the ipython3 prompt to open this created file for reading. We will define and object called "f" in order to act as a buffer to help retrieve content from our text file. Issue the following:

   f = open('data.txt', 'r')

   
   The open() function takes two string arguments: a path to a file, and a mode option for reading, writing, appending, etc. The open() function will return a special object to us, this object will allow us to read the lines inside the file.
   
   
5. You may recall that we used the dir() function to display library information for our Python library (eg. dir(sys) ). This function can also display other elements such as attributes and methods for an object. Issue the following:

   dir(f)

6. Although the dir(f) function displays a lot of information, we will focus on only a few elements. Separately issue the following commands in order to inspect some of the functions. attributes and methods that we can use with this file object:

   help(f.read)            # help for reading all lines and stores in a string
   help(f.readlines)       # help for reading all lines and stores in a list
   help(f.readline)        # help for reading first line, if run a second time it will read the second line, then third
   help(f.writable)        # help for determining if a file is writable
   help(f.close)           # help for closing the opened file
   f.writable()            # Object method (confirm if file is writable)
   f.name                  # Object attribute (contains name of opened file)
   f.closed                # Object attribute (confirm if file is closed)

7. Next, issue the following commands to read data from the buffer of the opened file and store the contents into a variable called "read_data", and then confirm the contents of the variable "read_data:

   read_data = f.read()
   read_data

   
   After you have completed accessing data within a file, you should close the file in order to free up the computer resources. It is useful to first confirm that the file is still open prior to closing it.
   
   
8. Issue the following object attribute will provide a boolean value to confirm that the file is still open (true indicates closed and false indicates open):

   f.closed

9. Finally, issue the following object method and object attribute to close the file, and then verify that the file has been successfully closed:

   f.close()                               # This method will close the file
   f.closed                                # Confirm that the file is closed

   
   Let's take a moment to revisit the file read sequence. The following code sequence will open a file, store the contents of a file into a variable, close the file and provide confirmation that the file has been closed:

   
   f = open('data.txt', 'r') # Open file
   read_data = f.read() # Read from file
   f.close() # Close file
   f.closed # Confirm file is closed
   

   
   Another way to read data from a file is using the with looping statement. The advantage by using the with loop is that the file will automatically close when the data within the file has been completely read
   
   
10. To demonstrate, issue the following code block:

    with open('data.txt', 'r') as f:        # Open file
        read_data = f.read()                # Read from file
    f.closed                                # Confirm file is closed

    
    Let us take a few moments to revisit the data that has been read into the variable called "read_data".
    
    
11. Let's re-issue the following command:

    read_data

    
    This command displays the data from the file in a single long string. The end of each line in the file will show the special character '\n' which represents the newline character in a file used to separate lines (or records in a traditional "flat database file"). It would be convenient to split the line on the new-line characters, so each line can be stored into a separate array elements (or in our case, a list!).
    
    
12. First issue the following commands to get help on the split method:

    dir(read_data)
    help(read_data.split)

13. Next, issue the following commands to store the contents of our file into a list called list_of_lines:

    read_data.split('\n')                       # Returns a list
    list_of_lines = read_data.split('\n')       # Saves returned list in variable
    list_of_lines

    
    Although the above sequence works, there are functions and methods the we can use with our object (called "f") to place lines from our file into a list. This would help to reduce code and is considered a more common method to store multiple lines or records within a list.
    
    
14. Issue both method1 and method2 sequence of commands to see how you can store data into a list more efficiently:

    # METHOD 1:
    
    f = open('data.txt', 'r')
    method1 = list(f)
    f.close()
    method1
    
    # METHOD 2:
    
    f = open('data.txt', 'r')
    method2 = f.readlines()
    f.close()
    method2

    
    Sometimes, you may need to only display retrieved data on the screen as opposed to processing the data. In these simple cases, there is no need to create extra-large variables to store the data, but rather print one line at a time onto the screen. Using this method will save computer resources while reading files.

    <br><br>
    :#To demonstrate, issue the following code sequence:<source lang="python"
    f = open('data.txt', 'r')
    for line in f:
        print(line, end='')
    f.close()

15. The python print() function by default adds the new-line character to the end of the line. Using the end= argument used in print replaces the '\n' at the end with nothing . This allows the print() to use the new-line characters found on each line of the file that was read. Though if desired you can always strip the new-line characters from any lines. The strip() function will remove all leading and trailing whitespace, which may help in processing some lines or data.

    f = open('data.txt', 'r')
    for line in f:
        print(line.strip())
    f.close()

Create a Python Script Demonstrating Reading Files

Perform the Following Instructions

1. Create the ~/ops435/lab5/lab5a.py script.
2. Use the following as a template:

   #!/usr/bin/env python3
   
   def read_file_string(file_name):
       # Takes a filename string, returns a string of all lines in the file
   
   def read_file_list(file_name):
       # Takes a filename string, returns a list of lines without new-line characters
   
   if __name__ == '__main__':
       file_name = 'data.txt'
       print(read_file_string(file_name))
       print(read_file_list(file_name))

• The read_file_string() function should return a string
• The read_file_list() function should return a list
• The read_file_list() function must remove the new-line characters from each line in the list
• Both functions must accept one argument which is a string
• The script should show the exact output as the samples
• The script should contain no errors

Sample Run 1:

python3 lab5a.py 
Hello World
This is the second line
Third line
Last line
['Hello World', 'This is the second line', 'Third line', 'Last line']

Sample Run 2 (with import):

import lab5a        
file_name = 'data.txt'                             
lab5a.read_file_string(file_name)
'Hello World\nThis is the second line\nThird line\nLast line\n'
lab5a.read_file_list(file_name)
['Hello World', 'This is the second line', 'Third line', 'Last line']

3. Exit the ipython3 shell, download the checking script and check your work. Enter the following commands from the bash shell.

cd ~/ops435/lab5/
pwd #confirm that you are in the right directory
ls CheckLab5.py || wget matrix.senecac.on.ca/~acoatley-willis/CheckLab5.py
python3 ./CheckLab5.py -f -v lab5a

4. Before proceeding, make certain that you identify any and all errors in lab5a.py. When the checking script tells you everything is OK before proceeding to the next step.

PART 2 - Writing To Files

There is a danger involved in this next section, when opening files for writing, Python assumes content in the file is no longer wanted and it's immediately deleted. If the file contents are important, append to the file instead.

Perform the Following Steps:

1. To start, open the ipython3 shell:

   ipython3

2. When opening a file the 'w' option can be give to open(). When 'w' is provided the previous contents inside the file are deleted, this deleting takes place the moment the open() function is executed, not during the write. If the file that is being written to doesn't exit, it will be created.

   f = open('file1.txt', 'w')

3. To add lines of text to the file, use the write() method for the file object. For safe file management, always end every line with a '\n'. Multiple lines may also be placed inside a single write, simply put the '\n' wherever a line should end.

   f.write('Line 1\nLine 2 is a little longer\nLine 3 is too\n')

4. Once the write() has been run, the final step would be to close() the file. The file MUST be closed properly or else data will not consistently be written to the file. Not closing a file can lead to corruption or not changes being made.

   f.close()

5. View the contents of the file to make sure the write data was saved. We can use the ipython bash alias %cat to do this.

   %cat file1.txt
   Line 1
   Line 2 is a little longer
   Line 3 is too

6. Create another file but this time, run multiple write() methods together. The ability to write() multiple lines like this allows for writes to take place inside loops and more complex programs to continuously write to a file.

   f = open('file2.txt', 'w')
   f.write('Line 1\nLine 2 is a little longer\nLine 3 is too\n')
   f.write('This is the 4th line\n')
   f.write('Last line in file\n')
   f.close()

7. View the contents of the file2.txt to make sure the write data was saved.

   %cat file2.txt
   Line 1
   Line 2 is a little longer
   Line 3 is too
   This is the 4th line
   Last line in file

8. View the contents of the file1.txt to make sure it has the original data and has not been changed

   %cat file1.txt
   Line 1
   Line 2 is a little longer
   Line 3 is too

9. In the event that the data in the file is important and should not be overwritten, we can append data to the end of the file instead. Use the option 'a' instead of 'w' to perform appending.

   f = open('file1.txt', 'a')
   f.write('This is the 4th line\n')
   f.write('Last line in file\n')
   f.close()

10. The final point to make when writing to files is to make sure that the values being written are strings. This means that before trying to place integers, floats, lists, or dictionaries into a file, first either convert the value using str() or extract the specific strings from items in the list.

    my_number = 1000
    my_list = [1,2,3,4,5]
    f = open('file3.txt', 'w')
    f.write(str(my_number) + '\n')
    for num in my_list:
        f.write(str(num) + '\n')
    f.close()

11. View the contents of the file3.txt to make sure the write data was saved.

    %cat file3.txt       
    1000                          
    1                             
    2                             
    3                             
    4                             
    5

Create a Python Script Demonstrating Writing to Files

Perform the Following Instructions

1. Copy ~/ops435/lab5/lab5a.py script to ~/ops435/lab5/lab5b.py script. We need the previous read functions written.
2. Use the following as a template:

   #!/usr/bin/env python3
   
   def read_file_string(file_name):
       # This is the same code from lab5a.py
   
   def read_file_list(file_name):
       # This is the same code from lab5a.py
   
   def append_file_string(file_name, string_of_lines):
       # Takes two strings, appends the string to the end of the file
   
   def write_file_list(file_name, list_of_lines):
       # Takes a string and list, writes all items from list to file where each item is one line
   
   def copy_file_add_line_numbers(file_name_read, file_name_write):
       # Takes two strings, reads data from first file, writes data to new file, adds line number to new file
   
   if __name__ == '__main__':
       file1 = 'seneca1.txt'
       file2 = 'seneca2.txt'
       file3 = 'seneca3.txt'
       string1 = 'First Line\nSecond Line\nThird Line\n'
       list1 = ['Line 1', 'Line 2', 'Line 3']
       append_file_string(file1, string1)
       print(read_file_string(file1))
       write_file_list(file2, list1)
       print(read_file_string(file2))
       copy_file_add_line_numbers(file2, file3)
       print(read_file_string(file3))

append_file_string()

1. Takes two string arguments
2. Appends to the file(Argument 1) all data from the string(Argument 2)

write_file_list()

1. Takes two arguments, a string and a list
2. Writes to file(Argument 1) all lines of data found in the list(Argument 2)

copy_file_add_line_numbers()

1. Takes two arguments, both strings, both filesnames
2. Reads all data from first file(Argument 1), writes all lines into secon file(Argument 2) adding line numbers
3. Line numbers should be added to the beginning of each line with a colon next to them(see sample output)
4. Hint: review len() and range() functions from lab 3 and lab 4

Sample Run 1:

python3 lab5b.py 
First Line
Second Line
Third Line

Line 1
Line 2
Line 3

1:Line 1
2:Line 2
3:Line 3

Sample Run 2 (with import):

import lab5b
file1 = 'seneca1.txt'
file2 = 'seneca2.txt'
file3 = 'seneca3.txt'
string1 = 'First Line\nSecond Line\nThird Line\n'
list1 = ['Line 1', 'Line 2', 'Line 3']

lab5b.append_file_string(file1, string1)

lab5b.read_file_string(file1)
'First Line\nSecond Line\nThird Line\nFirst Line\nSecond Line\nThird Line\n'

lab5b.write_file_list(file2, list1)

lab5b.read_file_string(file2)
'Line 1\nLine 2\nLine 3\n'

lab5b.copy_file_add_line_numbers(file2, file3)

lab5b.read_file_string(file3)
'1:Line 1\n2:Line 2\n3:Line 3\n'

3. Exit the ipython3 shell, download the checking script and check your work. Enter the following commands from the bash shell.

cd ~/ops435/lab5/
pwd #confirm that you are in the right directory
ls CheckLab5.py || wget matrix.senecac.on.ca/~acoatley-willis/CheckLab5.py
python3 ./CheckLab5.py -f -v lab5b

4. Before proceeding, make certain that you identify any and all errors in lab5b.py. When the checking script tells you everything is OK before proceeding to the next step.

INVESTIGATION 2: Exceptions and Error Handling

Running into errors in programming will be a common occurrence. In python when a error occurs, python raises a python object called an exception, which represents the error that occured. These exceptions are raised when python is no long able to handle what the code is trying to do. This section will give the programmer the ability to catch these exceptions when they happen and allow the program to continue running, however in many cases it might be a good idea to stop the program when an exception happens anyway.

PART 1 - Handling Errors

There are a massive amount of exceptions, way too many to cover. But if you are searching for a specific exception check out the Python Exception Documentation.

Perform the Following Steps:

1. To start, open the ipython3 shell:

   ipython3

2. Before we try and catch and detect exceptions, lets make sure we know a few ways to make errors in python. The following code will create an error:

   print('5' + 10)

3. Immediately the following error occurs:

   ---------------------------------------------------------------------------
   TypeError                                 Traceback (most recent call last)
   <ipython-input-3-1b929b80ca50> in <module>()
   ----> 1 print('5' + 10)
   
   TypeError: Can't convert 'int' object to str implicitly

4. Firstly, what to look for here is the exception name 'TypeError.' The Type error means a mismatch of a type(string, int, float, list, etc). Python doesn't know how to handle it, should it change the number into a string or change the string into a number?
5. If we want to write this program safely, we can catch this error while it's happening. This is done with a specific block of code called a try clause where you place code inbetween the try: and 'except:. If no error occurs in the code the except portion will be skipped.
6. No Exception:

   try:
       print(5 + 10)
   except TypeError:
       print('not an integer')
   
   15

7. TypeError Exception:

   try:
       print(5 + 'ten')
   except TypeError:
       print('not an integer')
   
   not an integer

8. Try and open a file that doesn't exist:

   f = open('filethatdoesnotexist', 'r')

9. To catch this error specific error we could simply use:

   try:
       f = open('filethatdoesnotexist', 'r')
       f.write('hello world\n')
       f.close()
   except FileNotFoundError:
       print('no file found')

10. Multiple exceptions can also be caught at the same time, such as does not exist, is a directory, or we don't have permission. Try removing permissions from the file, or creating a directory and opening it.

    try:
        f = open('filethatdoesnotexist', 'r')
        f.write('hello world\n')
        f.close()
    except (FileNotFoundError, PermissionError, IsADirectory): 
        print('failed to open file')

11. If you spend some time looking at the Python Exception Hierarchy we can see exactly how errors get caught in python. FileNotFoundError, PermissionError, and IsADirectory all inherit from OSError, this means that while using more specific errors might be useful for better error messages and handling, it's not always possible to catch every error all the time.::#Another way to catch multiple exceptions:

    try:
        f = open(abc, 'r')
        f.write('hello world\n')
        f.close()
    except (FileNotFoundError, PermissionError): 
        print('file does not exist or wrong permissions')
    except IsADirectoryError:
        print('file is a directory')
    except OSError:
        print('unable to open file')
    except:
        print('unknown error occured')
        raise

12. When catching multiple exceptions, make sure to catch the lowest ones on the hierarchy first. If you put 'Exception' first, both 'OSError' and 'FileNotFoundError', would never get caught.
13. In python it's usually best to 'try:' and 'except:' code rather than to try and determine everything that could go wrong with logic and if statements. For example, instead of checking to see if a file exists and we have read permissions, it can be better to just try and read the file and fail and catch any errors with 'OSError'.

Create a Python Script Which Handles Errors

Perform the Following Instructions

1. Create the ~/ops435/lab5/lab5c.py script.
2. Use the following as a template:

   #!/usr/bin/env python3
   
   def add(number1, number2):
       # Add two numbers together, return the result, if error return string 'error: could not add numbers'
   
   def read_file(filename):
       # Read a file, return a list of all lines, if error return string 'error: could not read file'
   
   if __name__ == '__main__':
       print(add(10,5))                        # works
       print(add('10',5))                      # works
       print(add('abc',5))                     # exception
       print(read_file('seneca2.txt'))         # works
       print(read_file('file10000.txt'))       # exception

Sample Run 1:

python3 lab5c.py 
15
15
error: could not add numbers
['Line 1\n', 'Line 2\n', 'Line 3\n']
error: could not read file

Sample Run 2 (with import):

import lab5c                

lab5c.add(10,5)             
15                          

lab5c.add('10',5)           
15                          

lab5c.add('10','5')         
15                          

lab5c.add('abc','5')                                                                                                                     
'error: could not add numbers'                                  

lab5c.add('hello','world')                                                                                                               
'error: could not add numbers'                                  

lab5c.read_file('seneca2.txt')
['Line 1\n', 'Line 2\n', 'Line 3\n']           

lab5c.read_file('file10000.txt')   
error: could not read file'

3. Exit the ipython3 shell, download the checking script and check your work. Enter the following commands from the bash shell.

cd ~/ops435/lab5/
pwd #confirm that you are in the right directory
ls CheckLab5.py || wget matrix.senecac.on.ca/~acoatley-willis/CheckLab5.py
python3 ./CheckLab5.py -f -v lab5c

4. Before proceeding, make certain that you identify any and all errors in lab5c.py. When the checking script tells you everything is OK before proceeding to the next step.

LAB 5 SIGN-OFF (SHOW INSTRUCTOR)

Have Ready to Show Your Instructor:

✓ Output of: ./CheckLab5.py -f -v

✓ Output of: cat lab5a.py lab5b.py lab5c.py

Practice For Quizzes, Tests, Midterm & Final Exam

1. x
2. x
3. x