More Python modules
Contents
11. More Python modules¶
gzip- compresses/decompresses binary data, reads/writes data into *.gzip file.zipfile- creates, adds, reads, writes to zip archives.getpass- reads password from keyboard.glob- finds files with matched regexp patterns.argparse- passes parameters to a python script.
11.1. Module gzip (Exercise)¶
The module is utilized to
compress/decompress binary data
write data into compressed *.gz file
read data from compressed *.gz file
## See all the methods in the module
import gzip
data = '''
Create some data. \nIn this particular case, \nthe data is just two sentences stored in a string\n
Line 4 \n
Line 5 \n
Line 6 \n
Line 7
'''
print(data)
## Store data into gzip file, data.txt.gz. The procedure is very similar to writing data into a regular file.
## Notice the write option 'wt' is for writing text:
with gzip.open("data.txt.gz","wt") as f:
f.write(data)
## Check if file data.txt.gz shows up in the directory:
import os
os.listdir()
%ls data.txt.gz
## Let's check if we can read data back from the file. Notice the read option 'rt' is for reading text:
with gzip.open("data.txt.gz","rt") as f:
data_read = f.read()
print(data_read)
## We cal also convert the data into a binary form, then write it into gzip file with 'wb' option
#data_byte = bytes(data, 'utf-8')
data_byte = data.encode('utf-8')
type(data_byte)
print(data_byte)
## Store the binary data into gzip file
with gzip.open("data.txt.gz","wb") as f:
f.write(data_byte)
## This also can be done with GzipFile method:
with gzip.GzipFile("data.txt.gz","wb") as f:
f.write(data_byte)
## We can also read the gzip file into binary data type by using "rb" option:
with gzip.open("data.txt.gz","rb") as f:
out_byte = f.read()
print(out_byte)
## Compressing/decompressing data. It can be applied to binary data only.
## Check the sizes of text data, byte data, and compressed byte data:
import sys
size_txt = sys.getsizeof(data)
out_byte = data.encode('utf-8')
size_bin = sys.getsizeof(out_byte)
out_compressed = gzip.compress(out_byte)
size_compressed = sys.getsizeof(out_compressed)
print(size_txt, '>', size_bin, '>', size_compressed)
11.2. Module zipfile (Exercise)¶
Works with zip archives:
Reads list of files and directories from zip archive
Extracts files from an archive
Reads specific file from an archive
Creates a new archive
Adds/appends file to the archive
11.2.1. Download a zip file:¶
%wget https://linuxcourse.rutgers.edu/2024/html/files/test.zip
import zipfile
with zipfile.ZipFile('test.zip') as file:
# printing all the information of archive file contents using 'printdir' method
print(file.printdir())
with zipfile.ZipFile('test.zip') as file:
# ZipFile.namelist() returns a list containing all the members with names of an archive file
print(file.namelist())
with zipfile.ZipFile('test.zip') as file:
# Open and read the content of a file from the list:
with file.open(name = file.namelist()[0], mode = 'r') as text_file:
print(text_file.read().decode('utf-8'))
with zipfile.ZipFile('test.zip') as file:
# ZipFile.infolist() returns a list containing all the members of an archive file
print(file.infolist())
## Extract the content of zip file into a new directory, EXTRACT_DIR
with zipfile.ZipFile('test.zip') as f:
f.extractall('EXTRACT_DIR')
import os
os.listdir('EXTRACT_DIR')
## Create an empty zipfile:
archive_name = 'new_test.zip'
f = zipfile.ZipFile(archive_name, 'w')
f.close()
## Add a new file, /etc/hosts, to the existing archive. Ovewrite existing files there.
with zipfile.ZipFile('new_test.zip', 'w') as f:
f.write('/etc/hosts')
## Append a new file, /etc/passwd. This doesn't overwrite the existing files.
with zipfile.ZipFile('new_test.zip', 'a') as f:
f.write('/etc/passwd')
## Check the content of archive new_test.zip
with zipfile.ZipFile('new_test.zip','r') as f:
print(f.printdir())
11.3. Module getpass (Exercise)¶
Promps for password and reads it from stdin
Figures out the user name from the environment
import getpass
## Prompt for password and read user password:
p = getpass.getpass(prompt='Enter the password: ')
if p == 'this':
print('correct password')
else:
print('password incorrect')
## identify the user and prompt in the loop until success. Maximum 10 attempts
user = getpass.getuser()
count = 0
max_count = 10
#while True:
while count <= max_count:
pwd = getpass.getpass("User Name : %s" % user)
count += 1
if pwd == 'password1':
print("login successful")
break
else:
print("The password you entered is incorrect.")
11.4. Module glob (Exercise)¶
Finds files matching a specified pattern and returns them in a list [ ]
*matches zero or more characters?matches one character[0-9] matches any number
[a-z] matches any low case character
[A-Z] matches any upper case character
import glob
glob.glob('*.zip')
glob.glob('*[0-9].zip')
glob.glob('*[a-z].zip')
glob.glob('[A-Z]*[0-9].zip')
glob.glob('[n,I]e*')
## Search for files specifically in /etc
glob.glob('/etc/*.conf')
## Search for files in directory and subdirectories /etc
glob.glob('/etc/*/*.conf')
## Recursive search in a directory tree
glob.glob('/etc/**/*.conf', recursive=True)
## For recursive search, it is better using iterative method `iglob` to save space in RAM.
## The iglob runs iteratively so doesn't buffer the output unlike glob.
for filename in glob.iglob('/etc/**/*.conf', recursive=True):
print(filename)
11.5. Exception handling in Python (Exercise)¶
## Example: find all conf files that contain keyword `network`.
## This will throw an error since some files in /etc are not readable by the user.
for filename in glob.iglob('/etc/**/*.conf', recursive=True):
with open(filename) as f:
line = f.read()
if 'network' in line:
print(filename)
To allow the script to run and prompt us about errors, we run it within block
try:
...
except ...
## Lets handle the exception above
for filename in glob.iglob('/etc/**/*.conf', recursive=True):
try:
with open(filename) as f:
line = f.read()
if 'network' in line:
print(filename)
except PermissionError as e:
print(f"can't read {filename}: {e}")
There is another, FileNotFoundError, error due to a symbolic link to a missing file.
We can handle multipple exceptions:
for filename in glob.iglob('/etc/**/*.conf', recursive=True):
try:
with open(filename) as f:
line = f.read()
if 'network' in line:
print(filename)
except (PermissionError, FileNotFoundError) as e:
print(f"can't read {filename}: {e}")
The last two exceptions we can catch with a generic OSError:
except OSError as e:
In numerical computations, you may need to deal with the division by zero. For example:
denominator = [1.2, 4.0, 0.001, 45.0, 0.0]
numerator = 0.1
for i in denominator:
s = numerator / i
print(s)
We need to put safe guards with
except ZeroDivisionError as e:
try:
for i in denominator:
s = numerator / i
print(s)
except ZeroDivisionError as e:
print('Division by zero, i = ', i)
11.6. Parsing arguments with argparse (Exercise)¶
It allows to pass parameters to a python script.
All the exercises below should run in the Linux command prompt. There are 3 python scripts in the directory: parser_1.py, parser_2.py, and parser_3.py
Exersizes:
# Import the library
import argparse
# Create the parser
parser = argparse.ArgumentParser()
# Add an argument
parser.add_argument('--alpha', type=int, required=True)
# Parse the argument
args = parser.parse_args()
# use and print the argument
value = args.alpha * 10
print('alpha = ', args.alpha, f', value = {args.alpha} * 10 = ', value)
11.6.1. Run the script¶
Save the above cell in a script, say parser_1.py, specify that it is a python script in the header:
#!/home/hostadm/miniconda3/bin/python3
Make it executable:
chmod a+x parser_1.py
Run the script with the parameter:
./parser_1.py --alpha 15
11.6.2. Multiple arguments with help options¶
11.6.3. More arguments¶
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--a1', type = str, required=True, help = 'First coefficient')
parser.add_argument('--a2', type = str, required=True, help = 'Second coefficient')
parser.add_argument('--a3', type = str, help = 'Third coefficient')
args = parser.parse_args()
s = f'{args.a1}*x^2 + {args.a2}*x + {args.a2}'
print(s)
11.6.4. Invoking help¶
Save the content of the cell above in file, say, parser_2.py, then run as follows:
./parser_2.py -h
./parser_2.py --a1 34 --a2 55 --a3 56
11.6.5. Multiple arguments¶
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--values', type=int, nargs=3)
args = parser.parse_args()
sum = sum(args.values)
print('Sum:', sum)
Run it with values:
./parser_3.py --values 4 8 9
For any number of values, set nargs = '+'