clean_code.py

# run this as "python clean_code.py $PWD" 
import os
import re
import sys
import glob
import codecs
import chardet
import fileinput

list_of_r_files = glob.glob("*.R")
list_of_r_files.extend(glob.glob('*.r'))

def detect_encoding(input):
    result = chardet.detect(input)
    return result['encoding'], result['confidence']

def parse_dependencies(line):
    ''' finds libs between two brackets 
    library(ABC) should be transformed into require(ABC)
    and if not accessible install ABC'''

    lib = line.replace(" ", "") 
    lib = line[line.find("(")+1:line.find(")")]
    lib = lib.strip('"')
    lib = lib.strip("'")

    return_str = 'if (!require(\"{}\")) install.packages(\"{}\")\n'.format(lib, lib)

    if "," in lib: # there are unparced arguments
        return line 
    return return_str


def fix_abs_paths(line, index):
    ''' returns file name without absolute path '''
    rest = line[index:]

    count = 0 # when -1 add ")"
    for i,w in enumerate(rest):
        if w == "(":
            count = count +1
        if w == ")":
            count = count -1
        if count == -1:
            break
    newline = line[:index]+"basename("+rest[:i]+")"+rest[i:]   
    return newline


def fix_abs_path_in_readcsv(line):
    index = line.find('read.csv')+8
    rest = line[index:]
    # find (
    b = rest.find("(")+1
    rest = line[index + b:]

    count = 0 # when -1 add ")"
    for i,w in enumerate(rest):
        if w == "," and count == 0: # in this case there are arguments
            break
        if w == "(":
            count = count +1
        if w == ")":
            count = count -1
        if count == -1: # found both open and closed brackets
            break
    newline = line[:index + b]+"basename("+rest[:i]+")"+rest[i:]
    return newline


def main():

    for r_file in list_of_r_files:

        # encode to ascii
        allcode = open(r_file, 'r').read()
        encoding, confidence = detect_encoding(allcode)
        if encoding != 'ascii':
            allcode = allcode.decode(encoding).encode('ascii', 'ignore')
            with codecs.open(r_file, 'w', encoding='ascii') as f:
                f.write(allcode)     

        for linenum, line in enumerate(fileinput.input(r_file, inplace=True)):

            # avoid setwd error
            if linenum == 0:
                wd = sys.argv[1]
                print("setwd('{}')\n".format(wd))

            # setwd already set, remove it to avoid absolute paths
            if "setwd(" in temp_line: 
                print(line.replace(line, ''))
                continue

            # ignore empty lines
            if not line.strip():
                print(line.rstrip())
                continue

            # ignore comments
            if line.strip().startswith('#') or line.strip().startswith('"'):
                print(line.rstrip())
                continue

            # ignore cases that already have install.packages command
            if "library(" in temp_line and "install.packages" in line and "#" not in line:
                print(line.rstrip())
                continue

            elif "require" in line and "install.packages" in line and "#" not in line:
                print(line.rstrip())
                continue

            elif "library(" in temp_line:
                for match in re.finditer("library", line):
                    print(line.replace(line, parse_dependencies(line[match.start():])))
                continue

            elif line.strip().startswith("install.packages"):
                # install packages should work as is when default CRAN mirror is set
                print(line.rstrip())
                continue
                
            elif temp_line.strip().startswith("require("):
                print(line.replace(line, parse_dependencies(line)))
                continue

            # all following IFs are for fixing fixed paths
            if "file.path(" in temp_line:
                index = line.find('file.path')
                print(line.replace(line, fix_abs_paths(line, index)))

            elif "source(" in temp_line and "/" in line:
                if "http" not in line:
                    index = line.find('source')+6
                    rest = line[index:]
                    # finding (
                    b = rest.find("(")+1
                    index = index + b
                    print(line.replace(line, fix_abs_paths(line, index)))

            elif "read.csv(" in temp_line and "/" in line:
                print(line.replace(line, fix_abs_path_in_readcsv(line)))

            else: # for all other lines
                print(line.rstrip())

if __name__ == "__main__":
    main()