How to search all file types in directory for regular expression

Question

So, I want to search my whole directory for files that contain a list of regular expressions. That includes: directories, pdfs, and csv files. I can succesfully do this task when searching for only text files but search all file types is the struggle. Below is my work so far:

import glob
import re
import PyPDF2
#-------------------------------------------------Input----------------------------------------------------------------------------------------------
folder_path = "/home/"
file_pattern = "/*"
folder_contents = glob.glob(folder_path + file_pattern)


#Search for Emails
regex1= re.compile(r'\S+@\S+')
#Search for Phone Numbers
regex2 = re.compile(r'\d\d\d[-]\d\d\d[-]\d\d\d\d')
#Search for Locations
regex3 =re.compile("([A-Z]\w+), ([A-Z]{2})")


for file in folder_contents:
    read_file = open(file, 'rt').read()
if readile_file == pdf:

    pdfFileObj = open('pdf.pdf', 'rb') 

    pdfReader = PyPDF2.PdfFileReader(pdfFileObj) 

    pageObj = pdfReader.getPage(0)  

    content= pageObj.extractText()) 

    if regex1.findall(read_file) or regex2.findall(read_file) or regex3.findall(read_file):
        print ("YES, This file containts PHI")
        print(file)
    else:
        print("No, This file DOES NOT contain PHI")
        print(file)

When I run this i get this error:

YES, This file containts PHI
/home/e136320/sample.txt
No, This file DOES NOT contain PHI
/home/e136320/medicalSample.txt

---------------------------------------------------------------------------
UnicodeDecodeError                        Traceback (most recent call last)
<ipython-input-129-be0b68229c20> in <module>()
     19 
     20 for file in folder_contents:
---> 21     read_file = open(file, 'rt').read()
     22 if readile_file == pdf:
     23     # creating a pdf file object
---------------------------------------------------------------------------
UnicodeDecodeError                        Traceback (most recent call last)
<ipython-input-128-1537605cf636> in <module>()
     18 
     19 for file in folder_contents:
---> 20     read_file = open(file, 'rt').read()
     21     if regex1.findall(read_file) or regex2.findall(read_file) or regex3.findall(read_file):
     22         print ("YES, This file containts PHI")

/jupyterhub_env/lib/python3.5/codecs.py in decode(self, input, final)
    319         # decode input (taking the buffer into account)
    320         data = self.buffer + input
--> 321         (result, consumed) = self._buffer_decode(data, self.errors, final)
    322         # keep undecoded input until the next call
    323         self.buffer = data[consumed:]

UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc7 in position 10: invalid continuation byte

Any suggestions?

Answer 1

You can't open a pdf file like that, it is expecting a plain text file. You could use something like this:

fn, ext = os.path.splitext(file)

if ext == '.pdf':
    open_function = PyPDF2.PdfFileReader
else:  # plain text
    open_function = open

with open_function(file, 'rt') as open_file:
    # Do something with open file...

This snippet checks the file extension then assigns an open function depending on what it finds, this is a bit naive and could be done better in a method similar to the one shown in this answer.