How to iterate through multiple folders within a folder and export specific CSV filename that begins for example- "abc*.csv" and export them into a new folder directory.
Trying to search similar example in Stack overflow but most examples were reading multiple CSV files within a folder and combine them to one data frame. Thanks.
import os
import shutil
files = []
source_dir = ['./files/']
dest_dir = './export/'
# List all files from all directories within the path
while len(source_dir) > 0:
for (dirpath, dirnames, filenames) in os.walk(source_dir.pop()):
source_dir.extend(dirnames)
files.extend(map(lambda n: os.path.join(
*n), zip([dirpath] * len(filenames), filenames)))
# Loop thru files to copy/move the matching CSVs
for file in files:
if file.startswith('abc') and file.endswith('.csv'):
shutil.copy(file, dest_dir)
# shutil.move(file, dest_dir) # Use .move to move the file instead
If you have this file structure:
files
├── dir1
│ ├── abc789.csv
│ └── abc789.txt
├── dir2
│ ├── abc098.csv
│ └── abc098.txt
└── dir3
├── abc456.csv
└── subdir3
├── abc123.csv
└── abc123.txt
Only the matching files will be exported:
$ ls export/
abc098.csv abc123.csv abc456.csv abc789.csv
Is there a way of importing all the files within folder1? Each csv file is contained within a subfolder. Below is the file structure.
C:/downloads/folder1 > tree /F
C:.
│ tree
│
├───2020-06
│ test1.csv
│
├───2020-07
│ test2.csv
│
├───2020-08
│ test3.csv
│
├───2020-09
│ test4.csv
I'm aware of glob, below, to take all files within a folder. However can this be used for subfolders?
import glob
import pandas as pd
# Get a list of all the csv files
csv_files = glob.____('*.csv')
# List comprehension that loads of all the files
dfs = [pd.read_csv(____) for ____ in ____]
# List comprehension that looks at the shape of all DataFrames
print(____)
Use the recursive keyword argument of the glob.glob() method:
glob.glob('**\\*.csv', recursive=True)
You can use os.walk to find all sub_folder and get the required files
here's a code sample
import os
import pandas as pd
path = '<Insert Path>'
file_extension = '.csv'
csv_file_list = []
for root, dirs, files in os.walk(path):
for name in files:
if name.endswith(file_extension):
file_path = os.path.join(root, name)
csv_file_list.append(file_path)
dfs = [pd.read_csv(f) for f in csv_file_list]
I found this on Kite's website, check it out
path = "./directory/src_folder"
text_files = glob.glob(path + "/**/*.txt", recursive = True)
print(text_files)
OUTPUT
['./directory/src_folder/src_file.txt', './directory/src_folder/subdirectory/subdirectory_file.txt']
This thread here advises to use shutilto zip files:
import shutil
shutil.make_archive(output_filename, 'zip', dir_name)
This zips everything in dir_name and maintains the folder structure in it. Is it possible to use this same library to remove all sub-folders and just zip all files in dir_name into the same level? Or must I introduce a separate code chunk to first consolidate the files? For eg., this is a hypothetical folder structure:
\dir_name
\dir1
\cat1
file1.txt
file2.txt
\cat2
file3.txt
\dir2
\cat3
file4.txt
Output zip should just contain:
file1.txt
file2.txt
file3.txt
file4.txt
shutil.make_archive does not have a way to do what you want without copying files to another directory, which is inefficient. Instead you can use a compression library directly similar to the linked answer you provided. Note this doesn't handle name collisions!
import zipfile
import os
with zipfile.ZipFile('output.zip','w',zipfile.ZIP_DEFLATED,compresslevel=9) as z:
for path,dirs,files in os.walk('dir_name'):
for file in files:
full = os.path.join(path,file)
z.write(full,file) # write the file, but with just the file's name not full path
# print the files in the zipfile
with zipfile.ZipFile('output.zip') as z:
for name in z.namelist():
print(name)
Given:
dir_name
├───dir1
│ ├───cat1
│ │ file1.txt
│ │ file2.txt
│ │
│ └───cat2
│ file3.txt
│
└───dir2
└───cat3
file4.txt
Output:
file1.txt
file2.txt
file3.txt
file4.txt
# The root directory to search for
path = r'dir_name/'
import os
import glob
# List all *.txt files in the root directory
file_paths = [file_path
for root_path, _, _ in os.walk(path)
for file_path in glob.glob(os.path.join(root_path, '*.txt'))]
import tempfile
# Create a temporary directory to copy your files into
with tempfile.TemporaryDirectory() as tmp:
import shutil
for file_path in file_paths:
# Get the basename of the file
basename = os.path.basename(file_path)
# Copy the file to the temporary directory
shutil.copyfile(file_path, os.path.join(tmp, basename))
# Zip the temporary directory to the working directory
shutil.make_archive('output', 'zip', tmp)
This will create a output.zip file in the current working directory. The temporary directory will be deleted when the end of the context manager is reached.
I am trying to create a backup script in Python 3.5 that will zip all the contents of a specified folder. Here is what I am doing now:
import shutil
import datetime
import os
import os.path
import dropbox
INPUT_FOLDER = '~/Documents/db-backup-test/'
ARCHIVE_PATH = '~/Documents/tmp/'
ARCHIVE_FILE_NAME = "db-backup_iOS__"
def compress_folder(origem, destino):
try:
arq = shutil.make_archive(destino, 'zip', root_dir=origem, base_dir=origem)
except Exception as e:
print('\n\nAn error was found during compression:')
print(e)
timestamp = str(datetime.datetime.now())
input_path = os.path.expanduser(INPUT_FOLDER)
archive_path = os.path.expanduser(ARCHIVE_PATH + ARCHIVE_FILE_NAME + timestamp)
compress_folder(input_path, archive_path)
I goes well, except for one thing: the resulting zip archive extracts its contents with a reproduction of the full original path. What I would like is to get is a simple copy of the folder, with its original name and its contents with relative paths, when extracting the archive.
I was looking into a simple and short solution that would not require to iterate through the folder contents.
Is this possible with shutil.make_archive(), or will I need to dig into other modules, like zipfile?
Use the arcname parameter to control the name/path in the zip file.
#!/usr/bin/env python2.7
import os
import zipfile
def zip(src, dst):
zf = zipfile.ZipFile("%s.zip" % (dst), "w", zipfile.ZIP_DEFLATED)
abs_src = os.path.abspath(src)
for dirname, subdirs, files in os.walk(src):
for filename in files:
absname = os.path.abspath(os.path.join(dirname, filename))
arcname = absname[len(abs_src) + 1:]
print 'zipping %s as %s' % (os.path.join(dirname, filename), arcname)
zf.write(absname, arcname)
zf.close()
zip("src", "dst")
With a directory structure like this:
src
└── a
├── b
│ └── bar
└── foo
I have a Python script that zips a file (new.txt):
tofile = "/root/files/result/"+file
targetzipfile = new.zip # This is how I want my zip to look like
zf = zipfile.ZipFile(targetzipfile, mode='w')
try:
#adding to archive
zf.write(tofile)
finally:
zf.close()
When I do this I get the zip file. But when I try to unzip the file I get the text file inside of a series of directories corresponding to the path of the file i.e I see a folder called root in the result directory and more directories within it, i.e. I have
/root/files/result/new.zip
and when I unzip new.zip I have a directory structure that looks like
/root/files/result/root/files/result/new.txt
Is there a way I can zip such that when I unzip I only get new.txt?
In other words I have /root/files/result/new.zip and when I unzip new.zip, it should look like
/root/files/results/new.txt
The zipfile.write() method takes an optional arcname argument that specifies what the name of the file should be inside the zipfile
I think you need to do a modification for the destination, otherwise it will duplicate the directory. Use :arcname to avoid it. try like this:
import os
import zipfile
def zip(src, dst):
zf = zipfile.ZipFile("%s.zip" % (dst), "w", zipfile.ZIP_DEFLATED)
abs_src = os.path.abspath(src)
for dirname, subdirs, files in os.walk(src):
for filename in files:
absname = os.path.abspath(os.path.join(dirname, filename))
arcname = absname[len(abs_src) + 1:]
print 'zipping %s as %s' % (os.path.join(dirname, filename),
arcname)
zf.write(absname, arcname)
zf.close()
zip("src", "dst")
zf.write(tofile)
to change
zf.write(tofile, zipfile_dir)
for example
zf.write("/root/files/result/root/files/result/new.txt", "/root/files/results/new.txt")
To illustrate most clearly,
directory structure:
/Users
└── /user
. ├── /pixmaps
. │ ├── pixmap_00.raw
. │ ├── pixmap_01.raw
│ ├── /jpeg
│ │ ├── pixmap_00.jpg
│ │ └── pixmap_01.jpg
│ └── /png
│ ├── pixmap_00.png
│ └── pixmap_01.png
├── /docs
├── /programs
├── /misc
.
.
.
Directory of interest: /Users/user/pixmaps
First attemp
import os
import zipfile
TARGET_DIRECTORY = "/Users/user/pixmaps"
ZIPFILE_NAME = "CompressedDir.zip"
def zip_dir(directory, zipname):
"""
Compress a directory (ZIP file).
"""
if os.path.exists(directory):
outZipFile = zipfile.ZipFile(zipname, 'w', zipfile.ZIP_DEFLATED)
for dirpath, dirnames, filenames in os.walk(directory):
for filename in filenames:
filepath = os.path.join(dirpath, filename)
outZipFile.write(filepath)
outZipFile.close()
if __name__ == '__main__':
zip_dir(TARGET_DIRECTORY, ZIPFILE_NAME)
ZIP file structure:
CompressedDir.zip
.
└── /Users
└── /user
└── /pixmaps
├── pixmap_00.raw
├── pixmap_01.raw
├── /jpeg
│ ├── pixmap_00.jpg
│ └── pixmap_01.jpg
└── /png
├── pixmap_00.png
└── pixmap_01.png
Avoiding the full directory path
def zip_dir(directory, zipname):
"""
Compress a directory (ZIP file).
"""
if os.path.exists(directory):
outZipFile = zipfile.ZipFile(zipname, 'w', zipfile.ZIP_DEFLATED)
# The root directory within the ZIP file.
rootdir = os.path.basename(directory)
for dirpath, dirnames, filenames in os.walk(directory):
for filename in filenames:
# Write the file named filename to the archive,
# giving it the archive name 'arcname'.
filepath = os.path.join(dirpath, filename)
parentpath = os.path.relpath(filepath, directory)
arcname = os.path.join(rootdir, parentpath)
outZipFile.write(filepath, arcname)
outZipFile.close()
if __name__ == '__main__':
zip_dir(TARGET_DIRECTORY, ZIPFILE_NAME)
ZIP file structure:
CompressedDir.zip
.
└── /pixmaps
├── pixmap_00.raw
├── pixmap_01.raw
├── /jpeg
│ ├── pixmap_00.jpg
│ └── pixmap_01.jpg
└── /png
├── pixmap_00.png
└── pixmap_01.png
The arcname parameter in the write method specifies what will be the name of the file inside the zipfile:
import os
import zipfile
# 1. Create a zip file which we will write files to
zip_file = "/home/username/test.zip"
zipf = zipfile.ZipFile(zip_file, 'w', zipfile.ZIP_DEFLATED)
# 2. Write files found in "/home/username/files/" to the test.zip
files_to_zip = "/home/username/files/"
for file_to_zip in os.listdir(files_to_zip):
file_to_zip_full_path = os.path.join(files_to_zip, file_to_zip)
# arcname argument specifies what will be the name of the file inside the zipfile
zipf.write(filename=file_to_zip_full_path, arcname=file_to_zip)
zipf.close()
You can isolate just the file name of your sources files using:
name_file_only= name_full_path.split(os.sep)[-1]
For example, if name_full_path is /root/files/results/myfile.txt, then name_file_only will be myfile.txt. To zip myfile.txt to the root of the archive zf, you can then use:
zf.write(name_full_path, name_file_only)
Check out the documentation for Zipfile.write.
ZipFile.write(filename[, arcname[, compress_type]]) Write the file
named filename to the archive, giving it the archive name arcname (by
default, this will be the same as filename, but without a drive letter
and with leading path separators removed)
https://docs.python.org/2/library/zipfile.html#zipfile.ZipFile.write
Try the following:
import zipfile
import os
filename = 'foo.txt'
# Using os.path.join is better than using '/' it is OS agnostic
path = os.path.join(os.path.sep, 'tmp', 'bar', 'baz', filename)
zip_filename = os.path.splitext(filename)[0] + '.zip'
zip_path = os.path.join(os.path.dirname(path), zip_filename)
# If you need exception handling wrap this in a try/except block
with zipfile.ZipFile(zip_path, 'w') as zf:
zf.write(path, zip_filename)
The bottom line is that if you do not supply an archive name then the filename is used as the archive name and it will contain the full path to the file.
It is much simpler than expected, I configured the module using the parameter "arcname" as "file_to_be_zipped.txt", so the folders do not appear in my final zipped file:
mmpk_zip_file = zipfile.ZipFile("c:\\Destination_folder_name\newzippedfilename.zip", mode='w', compression=zipfile.ZIP_DEFLATED)
mmpk_zip_file.write("c:\\Source_folder_name\file_to_be_zipped.txt", "file_to_be_zipped.txt")
mmpk_zip_file.close()
We can use this
import os
# single File
os.system(f"cd {destinationFolder} && zip fname.zip fname")
# directory
os.system(f"cd {destinationFolder} && zip -r folder.zip folder")
For me, This is working.
Specify the arcname input of the write method as following:
tofile = "/root/files/result/"+file
NewRoot = "files/result/"
zf.write(tofile, arcname=tofile.split(NewRoot)[1])
More info:
ZipFile.write(filename, arcname=None, compress_type=None,
compresslevel=None)
https://docs.python.org/3/library/zipfile.html
I face the same problem and i solve it with writestr. You can use it like this:
zipObject.writestr(<filename> , <file data, bytes or string>)
If you want an elegant way to do it with pathlib you can use it this way:
from pathlib import Path
import zipfile
def zip_dir(path_to_zip: Path):
zip_file = Path(path_to_zip).with_suffix('.zip')
z = zipfile.ZipFile(zip_file, 'w', zipfile.ZIP_DEFLATED)
for f in list(path_to_zip.rglob('*.*')):
z.write(f, arcname=f.relative_to(path_to_zip))
To get rid of the absolute path, I came up with this:
def create_zip(root_path, file_name, ignored=[], storage_path=None):
"""Create a ZIP
This function creates a ZIP file of the provided root path.
Args:
root_path (str): Root path to start from when picking files and directories.
file_name (str): File name to save the created ZIP file as.
ignored (list): A list of files and/or directories that you want to ignore. This
selection is applied in root directory only.
storage_path: If provided, ZIP file will be placed in this location. If None, the
ZIP will be created in root_path
"""
if storage_path is not None:
zip_root = os.path.join(storage_path, file_name)
else:
zip_root = os.path.join(root_path, file_name)
zipf = zipfile.ZipFile(zip_root, 'w', zipfile.ZIP_DEFLATED)
def iter_subtree(path, layer=0):
# iter the directory
path = Path(path)
for p in path.iterdir():
if layer == 0 and p.name in ignored:
continue
zipf.write(p, str(p).replace(root_path, '').lstrip('/'))
if p.is_dir():
iter_subtree(p, layer=layer+1)
iter_subtree(root_path)
zipf.close()
Maybe it isn't the most elegant solution, but this works. If we just use p.name when providing the file name to write() method, then it doesn't create the proper directory structure.
Moreover, if it's needed to ignore the selected directories or files from the root path, this ignores those selections too.
This is an example I used. I have one excel file, Treport where I am using python + pandas in my dowork function to create pivot tables, etc. for each of the companies in CompanyNames. I create a zip file of the csv and a non-zip file so I can check as well.
The writer specifies the path where I want my .xlsx to go and for my zip files, I specify that in the zip.write(). I just specify the name of the xlsx file that was recently created, and that is what gets zipped up, not the whole directory. Beforehand I was just specifying 'writer' and would zip up the whole directory. This allows me to zip up just the recently created excel file.
Treport = 'TestReportData.csv'
CompanyNames = ['Company1','Company2','Company3']
for CompName in CompanyNames:
strcomp = str(CompName)
#Writer Creates pathway to output report to. Each company gets unique file.
writer = pd.ExcelWriter(f"C:\\Users\\MyUser\\Documents\\{strcomp}addReview.xlsx", engine='xlsxwriter')
DoWorkFunction(CompName, Treport, writer)
writer.save()
with ZipFile(f"C:\\Users\\MyUser\\Documents\\{strcomp}addR.zip", 'w') as zip:
zip.write(writer, f"{strcomp}addReview.xlsx")