Find the name of subdirectories and process files in each - linux

Let's say /tmp has subdirectories /test1, /test2, /test3 and so on,
and each has multiple files inside.
I have to run a while loop or for loop to find the name of the directories (in this case /test1, /test2, ...)
and run a command that processes all the files inside of each directory.
So, for example,
I have to get the directory names under /tmp which will be test1, test2, ...
For each subdirectory, I have to process the files inside of it.
How can I do this?
Clarification:
This is the command that I want to run:
find /PROD/140725_D0/ -name "*.json" -exec /tmp/test.py {} \;
where 140725_D0 is an example of one subdirectory to process - there are multiples, with different names.
So, by using a for or while loop, I want to find all subdirectories and run a command on the files in each.
The for or while loop should iteratively replace the hard-coded name 140725_D0 in the find command above.

You should be able to do with a single find command with an embedded shell command:
find /PROD -type d -execdir sh -c 'for f in *.json; do /tmp/test.py "$f"; done' \;
Note: -execdir is not POSIX-compliant, but the BSD (OSX) and GNU (Linux) versions of find support it; see below for a POSIX alternative.
The approach is to let find match directories, and then, in each matched directory, execute a shell with a file-processing loop (sh -c '<shellCmd>').
If not all subdirectories are guaranteed to have *.json files, change the shell command to for f in *.json; do [ -f "$f" ] && /tmp/test.py "$f"; done
Update: Two more considerations; tip of the hat to kenorb's answer:
By default, find processes the entire subtree of the input directory. To limit matching to immediate subdirectories, use -maxdepth 1[1]:
find /PROD -maxdepth 1 -type d ...
As stated, -execdir - which runs the command passed to it in the directory currently being processed - is not POSIX compliant; you can work around this by using -exec instead and by including a cd command with the directory path at hand ({}) in the shell command:
find /PROD -type d -exec sh -c 'cd "{}" && for f in *.json; do /tmp/test.py "$f"; done' \;
[1] Strictly speaking, you can place the -maxdepth option anywhere after the input file paths on the find command line - as an option, it is not positional. However, GNU find will issue a warning unless you place it before tests (such as -type) and actions (such as -exec).

Try the following usage of find:
find . -type d -exec sh -c 'cd "{}" && echo Do some stuff for {}, files are: $(ls *.*)' ';'
Use -maxdepth if you'd like to limit your directory levels.

You can do this using bash's subshell feature like so
for i in /tmp/test*; do
# don't do anything if there's no /test directory in /tmp
[ "$i" != "/tmp/test*" ] || continue
for j in $i/*.json; do
# don't do anything if there's nothing to run
[ "$j" != "$i/*.json" ] || continue
(cd $i && ./file_to_run)
done
done
When you wrap a command in ( and ) it starts a subshell to run the command. A subshell is exactly like starting another instance of bash except it's slightly more optimal.

You can also simply ask the shell to expand the directories/files you need, e.g. using command xargs:
echo /PROD/*/*.json | xargs -n 1 /tmp/test.py
or even using your original find command:
find /PROD/* -name "*.json" -exec /tmp/test.py {} \;
Both command will process all JSON files contained into any subdirectory of /PROD.

Another solution is to change slightly the Python code inside your script in order to accept and process multiple files.
For example, if your script contains something like:
def process(fname):
print 'Processing file', fname
if __name__ == '__main__':
import sys
process(sys.argv[1])
you could replace the last line with:
for fname in sys.argv[1:]:
process(fname)
After this simple modification, you can call your script this way:
/tmp/test.py /PROD/*/*.json
and have it process all the desired JSON files.

Related

Loop through a directory with any level of depth

I want to execute a command on all files present on all levels in the directory. It may have any number of files and sub directories. Even these sub directories may contain any number of files and subdirectories. I want to do this using shell script. As I am new to this field can any one suggest me a way out.
You can use the command "find" with "xargs" after "|"(pipe).
Example: Suppose that I want to remove all files that have ".txt" extension on "Documents" directory:
find Documents -iname *.txt |xargs rm -f
Helps?
You can use a recursive command that uses wildcard characters (*) like so:
for dir in ~/dev/myproject/*; do (cd "$dir" && git status); done
If you want to apply commands on the individual files you should use the find command and execute commands on it like so:
find yourdirectory -type f -exec echo "File found: '{}'" \;
What this does:
finds all the items in the directory yourdirectory
that have the type f - so are a file
runs an exec on each file
Use find:
find -type f -exec COMMAND {} \;
-f applies the command only to files, not to directories. The command is recursive by default.

Running a script in terminal using Linux

Im trying to run this script in the terminal but its not working and says permission denied. scriptEmail is filename.
% find . -type d -exec ./scriptEmail {} \;
scriptEmail is written as follows:
# !/bin/bash
# Mail Script
find gang-l -type f -name "*" -exec sh -c ' file = "$0" java RemoveHeaders "$file" > processed/$file ' {} ';'
My read write permission
-rwxr-xr-x
As for permissions:
Check that your shebang is at the very top of your file, and that it starts exactly with #!; # ! will not work.
Check that your files are given execute permissions; chmod 750 scriptEmail will do.
Check that your file uses UNIX newlines -- with DOS newlines, your shebang may have a hidden character making it point to an interpreter which doesn't actually exist.
Check that the directory your file is stored in is in a directory where executable scripts are allowed (not mounted with the noexec flag, or in a SELinux context disallowing execution).
If your mount point is noexec or your ability to create executable scripts is blocked by SELinux or similar, then use find . -type d -exec bash ./scriptEmail {} \; to explicitly specify an interpreter rather than attempting to execute your script.
Second: Since you're executing your script with find already -- and using that to recurse through directories -- you don't need a second find inside (which would have you potentially operating on processed/dirA/dirB/file as well as processed/dirB/file and processed/file -- with errors for all of these where the directory doesn't exist).
#!/bin/sh
cd "$1" || exit # if we can't cd to directory given in argument, exit.
mkdir -p processed || exit # if we can't create our output directory, exit.
for f in *; do # ...iterate through all directory contents...
[ -f "$f" ] || continue # ...if they aren't files, skip them...
java RemoveHeaders "$f" >processed/"$f" # run the processing for one item
done
Try
sudo find . -type d -exec ./scriptEmail {} \;

Linux recursive copy files to its parent folder

I want to copy recursively files to its parent folder for a specific file extension. For example:
./folderA/folder1/*.txt to ./folderA/*.txt
./folderB/folder2/*.txt to ./folderB/*.txt
etc.
I checked cp and find commands but couldn't get it working.
I suspect that while you say copy, you actually mean to move the files up to their respective parent directories. It can be done easily using find:
$ find . -name '*.txt' -type f -execdir mv -n '{}' ../ \;
The above command recurses into the current directory . and then applies the following cascade of conditionals to each item found:
-name '*.txt' will filter out only files that have the .txt extension
-type f will filter out only regular files (eg, not directories that – for whatever reason – happen to have a name ending in .txt)
-execdir mv -n '{}' ../ \; executes the command mv -n '{}' ../ in the containing directory where the {} is a placeholder for the matched file's name and the single quotes are needed to stop the shell from interpreting the curly braces. The ; terminates the command and again has to be escaped from the shell interpreting it.
I have passed the -n flag to the mv program to avoid accidentally overwriting an existing file.
The above command will transform the following file system tree
dir1/
dir11/
file3.txt
file4.txt
dir12/
file2.txt
dir2/
dir21/
file6.dat
dir22/
dir221/
dir221/file8.txt
file7.txt
file5.txt
dir3/
file9.dat
file1.txt
into this one:
dir1/
dir11/
dir12/
file3.txt
file4.txt
dir2/
dir21/
file6.dat
dir22/
dir221/
file8.txt
file7.txt
dir3/
file9.dat
file2.txt
file5.txt
To get rid of the empty directories, run
$ find . -type d -empty -delete
Again, this command will traverse the current directory . and then apply the following:
-type d this time filters out only directories
-empty filters out only those that are empty
-delete deletes them.
Fine print: -execdir is not specified by POSIX, though major implementations (at least the GNU and BSD one) support it. If you need strict POSIX compliance, you'll have to make do with the less safe -exec which would need additional thought to be applied correctly in this case.
Finally, please try your commands in a test directory with dummy files, not your actual data. Especially with the -delete option of find, you can loose all your data quicker than you might imaging. Read the man page and, if that is not enough, the reference manual of find. Never blindly copy shell commands from random strangers posted on the internet if you don't understand them.
$cp ./folderA/folder1/*.txt ./folderA
Try this commnad
Run something like this from the root(ish) directory:
#! /bin/bash
BASE_DIR=./
new_dir() {
LOC_DIR=`pwd`
for i in "${LOC_DIR}"/*; do
[[ -f "${i}" ]] && cp "${i}" ../
[[ -d "${i}" ]] && cd "${i}" && new_dir
cd ..
done
return 0
}
new_dir
This will search each directory. When a file is encountered, it copies the file up a directory. When a directory is found, it will move down into the directory and start the process over again. I think it'll work for you.
Good luck.

Find files in a dir, executing a command with execdir and redirecting

It seems like I am unable to find a direct answer to this question.
I appreciate your help.
I'm trying to find all files with a specific name in a directory, read the last 1000 lines of the file and copy it in to a new file in the same directory. As an example:
Find all files names xyz.log in the current directory, copy the last 1000 lines to file abc.log (which doesn't exist).
I tried to use the following command with no luck:
find . -name "xyz.log" -execdir tail -1000 {} > abc.log \;
The problem I'm having is that for all the files in the current directory, they all write to abc.log in the CURRENT directory and not in the directory where xyz.log resides. Clearly the find with execdir is first executed and then the output is redirected to abc.log.
Can you guys suggest a way to fix this? I appreciate any information/help.
EDIT- I tried find . -name "xyz.log" -execdir sh -c "tail -1000 {} > abc.log" \; as suggested by some of the friends, but it gives me this error: sh: ./tail: No such file or directory error message. Do you guys have any idea what the problem is?
Luckily the solution to use -printf is working fine.
The simplest way is this:
find . -name "xyz.log" -execdir sh -c 'tail -1000 "{}" >abc.log' \;
A more flexible alternative is to first print out the commands and then execute them all with sh:
find . -name "xyz.log" -printf 'tail -1000 "%p" >"%h/abc.log"\n' | sh
You can remove the | sh from the end when you're trying it out/debugging.
There is a bug in some versions of findutils (4.2 and 4.3, though it was fixed in some 4.2.x and 4.3.x versions) that cause execdir arguments that contain {} to be prefixed with ./ (instead of the prefix being applied only to {} it is applied to the whole quoted string). To work around this you can use:
find . -name "xyz.log" -execdir sh -c 'tail -1000 "$1" >abc.log' sh {} \;
sh -c 'script' arg0 arg1 runs the sh script with arg0, arg1, etc. passed to it. By convention, arg0 is the name of the executable (here, "sh"). From the script you can access the arguments using $0 (corresponding to "sh"), $1 (corresponding to find's expansion of {}), etc.
The redirect isn't passed into execdir, so abc.log shows up in the directory you run the command in. -execdir also doesn't like embedded redirects. but you can workaround the problem by passing -execdir a shell command with a redirect embedded, like this:
find . -name "xyz.log" -execdir sh -c '/usr/bin/tail -1000 {} > abc.log' \;
Much credit to this blog post (not mine):
http://www.microhowto.info/howto/act_on_all_files_in_a_directory_tree_using_find.html
Edit
I put the full path to tail in the command (assuming it's in /usr/bin on your system), since sh may load a .profile with a PATH that differs from your current shell.
Here's another non-find (well, sorta - it still uses find but doesn't try to shoehorn find into doing the whole thing):
while read f
do
d=$(dirname "${f}")
tail -n 1000 "${f}" > "${d}/abc.log"
done < <(find . -type f -name xyz.log -print)

Argument list too long error for rm, cp, mv commands

I have several hundred PDFs under a directory in UNIX. The names of the PDFs are really long (approx. 60 chars).
When I try to delete all PDFs together using the following command:
rm -f *.pdf
I get the following error:
/bin/rm: cannot execute [Argument list too long]
What is the solution to this error?
Does this error occur for mv and cp commands as well? If yes, how to solve for these commands?
The reason this occurs is because bash actually expands the asterisk to every matching file, producing a very long command line.
Try this:
find . -name "*.pdf" -print0 | xargs -0 rm
Warning: this is a recursive search and will find (and delete) files in subdirectories as well. Tack on -f to the rm command only if you are sure you don't want confirmation.
You can do the following to make the command non-recursive:
find . -maxdepth 1 -name "*.pdf" -print0 | xargs -0 rm
Another option is to use find's -delete flag:
find . -name "*.pdf" -delete
tl;dr
It's a kernel limitation on the size of the command line argument. Use a for loop instead.
Origin of problem
This is a system issue, related to execve and ARG_MAX constant. There is plenty of documentation about that (see man execve, debian's wiki, ARG_MAX details).
Basically, the expansion produce a command (with its parameters) that exceeds the ARG_MAX limit.
On kernel 2.6.23, the limit was set at 128 kB. This constant has been increased and you can get its value by executing:
getconf ARG_MAX
# 2097152 # on 3.5.0-40-generic
Solution: Using for Loop
Use a for loop as it's recommended on BashFAQ/095 and there is no limit except for RAM/memory space:
Dry run to ascertain it will delete what you expect:
for f in *.pdf; do echo rm "$f"; done
And execute it:
for f in *.pdf; do rm "$f"; done
Also this is a portable approach as glob have strong and consistant behavior among shells (part of POSIX spec).
Note: As noted by several comments, this is indeed slower but more maintainable as it can adapt more complex scenarios, e.g. where one want to do more than just one action.
Solution: Using find
If you insist, you can use find but really don't use xargs as it "is dangerous (broken, exploitable, etc.) when reading non-NUL-delimited input":
find . -maxdepth 1 -name '*.pdf' -delete
Using -maxdepth 1 ... -delete instead of -exec rm {} + allows find to simply execute the required system calls itself without using an external process, hence faster (thanks to #chepner comment).
References
I'm getting "Argument list too long". How can I process a large list in chunks? # wooledge
execve(2) - Linux man page (search for ARG_MAX) ;
Error: Argument list too long # Debian's wiki ;
Why do I get “/bin/sh: Argument list too long” when passing quoted arguments? # SuperUser
find has a -delete action:
find . -maxdepth 1 -name '*.pdf' -delete
Another answer is to force xargs to process the commands in batches. For instance to delete the files 100 at a time, cd into the directory and run this:
echo *.pdf | xargs -n 100 rm
If you’re trying to delete a very large number of files at one time (I deleted a directory with 485,000+ today), you will probably run into this error:
/bin/rm: Argument list too long.
The problem is that when you type something like rm -rf *, the * is replaced with a list of every matching file, like “rm -rf file1 file2 file3 file4” and so on. There is a relatively small buffer of memory allocated to storing this list of arguments and if it is filled up, the shell will not execute the program.
To get around this problem, a lot of people will use the find command to find every file and pass them one-by-one to the “rm” command like this:
find . -type f -exec rm -v {} \;
My problem is that I needed to delete 500,000 files and it was taking way too long.
I stumbled upon a much faster way of deleting files – the “find” command has a “-delete” flag built right in! Here’s what I ended up using:
find . -type f -delete
Using this method, I was deleting files at a rate of about 2000 files/second – much faster!
You can also show the filenames as you’re deleting them:
find . -type f -print -delete
…or even show how many files will be deleted, then time how long it takes to delete them:
root#devel# ls -1 | wc -l && time find . -type f -delete
100000
real 0m3.660s
user 0m0.036s
sys 0m0.552s
Or you can try:
find . -name '*.pdf' -exec rm -f {} \;
you can try this:
for f in *.pdf
do
rm "$f"
done
EDIT:
ThiefMaster comment suggest me not to disclose such dangerous practice to young shell's jedis, so I'll add a more "safer" version (for the sake of preserving things when someone has a "-rf . ..pdf" file)
echo "# Whooooo" > /tmp/dummy.sh
for f in '*.pdf'
do
echo "rm -i \"$f\""
done >> /tmp/dummy.sh
After running the above, just open the /tmp/dummy.sh file in your favorite editor and check every single line for dangerous filenames, commenting them out if found.
Then copy the dummy.sh script in your working dir and run it.
All this for security reasons.
For somone who doesn't have time.
Run the following command on terminal.
ulimit -S -s unlimited
Then perform cp/mv/rm operation.
I'm surprised there are no ulimit answers here. Every time I have this problem I end up here or here. I understand this solution has limitations but ulimit -s 65536 seems to often do the trick for me.
You could use a bash array:
files=(*.pdf)
for((I=0;I<${#files[#]};I+=1000)); do
rm -f "${files[#]:I:1000}"
done
This way it will erase in batches of 1000 files per step.
you can use this commend
find -name "*.pdf" -delete
The rm command has a limitation of files which you can remove simultaneous.
One possibility you can remove them using multiple times the rm command bases on your file patterns, like:
rm -f A*.pdf
rm -f B*.pdf
rm -f C*.pdf
...
rm -f *.pdf
You can also remove them through the find command:
find . -name "*.pdf" -exec rm {} \;
If they are filenames with spaces or special characters, use:
find -name "*.pdf" -delete
For files in current directory only:
find -maxdepth 1 -name '*.pdf' -delete
This sentence search all files in the current directory (-maxdepth 1) with extension pdf (-name '*.pdf'), and then, delete.
i was facing same problem while copying form source directory to destination
source directory had files ~3 lakcs
i used cp with option -r and it's worked for me
cp -r abc/ def/
it will copy all files from abc to def without giving warning of Argument list too long
Try this also If you wanna delete above 30/90 days (+) or else below 30/90(-) days files/folders then you can use the below ex commands
Ex: For 90days excludes above after 90days files/folders deletes, it means 91,92....100 days
find <path> -type f -mtime +90 -exec rm -rf {} \;
Ex: For only latest 30days files that you wanna delete then use the below command (-)
find <path> -type f -mtime -30 -exec rm -rf {} \;
If you wanna giz the files for more than 2 days files
find <path> -type f -mtime +2 -exec gzip {} \;
If you wanna see the files/folders only from past one month .
Ex:
find <path> -type f -mtime -30 -exec ls -lrt {} \;
Above 30days more only then list the files/folders
Ex:
find <path> -type f -mtime +30 -exec ls -lrt {} \;
find /opt/app/logs -type f -mtime +30 -exec ls -lrt {} \;
And another one:
cd /path/to/pdf
printf "%s\0" *.[Pp][Dd][Ff] | xargs -0 rm
printf is a shell builtin, and as far as I know it's always been as such. Now given that printf is not a shell command (but a builtin), it's not subject to "argument list too long ..." fatal error.
So we can safely use it with shell globbing patterns such as *.[Pp][Dd][Ff], then we pipe its output to remove (rm) command, through xargs, which makes sure it fits enough file names in the command line so as not to fail the rm command, which is a shell command.
The \0 in printf serves as a null separator for the file names wich are then processed by xargs command, using it (-0) as a separator, so rm does not fail when there are white spaces or other special characters in the file names.
Argument list too long
As this question title for cp, mv and rm, but answer stand mostly for rm.
Un*x commands
Read carefully command's man page!
For cp and mv, there is a -t switch, for target:
find . -type f -name '*.pdf' -exec cp -ait "/path to target" {} +
and
find . -type f -name '*.pdf' -exec mv -t "/path to target" {} +
Script way
There is an overall workaroung used in bash script:
#!/bin/bash
folder=( "/path to folder" "/path to anther folder" )
if [ "$1" != "--run" ] ;then
exec find "${folder[#]}" -type f -name '*.pdf' -exec $0 --run {} +
exit 0;
fi
shift
for file ;do
printf "Doing something with '%s'.\n" "$file"
done
What about a shorter and more reliable one?
for i in **/*.pdf; do rm "$i"; done
I had the same problem with a folder full of temporary images that was growing day by day and this command helped me to clear the folder
find . -name "*.png" -mtime +50 -exec rm {} \;
The difference with the other commands is the mtime parameter that will take only the files older than X days (in the example 50 days)
Using that multiple times, decreasing on every execution the day range, I was able to remove all the unnecessary files
You can create a temp folder, move all the files and sub-folders you want to keep into the temp folder then delete the old folder and rename the temp folder to the old folder try this example until you are confident to do it live:
mkdir testit
cd testit
mkdir big_folder tmp_folder
touch big_folder/file1.pdf
touch big_folder/file2.pdf
mv big_folder/file1,pdf tmp_folder/
rm -r big_folder
mv tmp_folder big_folder
the rm -r big_folder will remove all files in the big_folder no matter how many. You just have to be super careful you first have all the files/folders you want to keep, in this case it was file1.pdf
To delete all *.pdf in a directory /path/to/dir_with_pdf_files/
mkdir empty_dir # Create temp empty dir
rsync -avh --delete --include '*.pdf' empty_dir/ /path/to/dir_with_pdf_files/
To delete specific files via rsync using wildcard is probably the fastest solution in case you've millions of files. And it will take care of error you're getting.
(Optional Step): DRY RUN. To check what will be deleted without deleting. `
rsync -avhn --delete --include '*.pdf' empty_dir/ /path/to/dir_with_pdf_files/
.
.
.
Click rsync tips and tricks for more rsync hacks
I found that for extremely large lists of files (>1e6), these answers were too slow. Here is a solution using parallel processing in python. I know, I know, this isn't linux... but nothing else here worked.
(This saved me hours)
# delete files
import os as os
import glob
import multiprocessing as mp
directory = r'your/directory'
os.chdir(directory)
files_names = [i for i in glob.glob('*.{}'.format('pdf'))]
# report errors from pool
def callback_error(result):
print('error', result)
# delete file using system command
def delete_files(file_name):
os.system('rm -rf ' + file_name)
pool = mp.Pool(12)
# or use pool = mp.Pool(mp.cpu_count())
if __name__ == '__main__':
for file_name in files_names:
print(file_name)
pool.apply_async(delete_files,[file_name], error_callback=callback_error)
If you want to remove both files and directories, you can use something like:
echo /path/* | xargs rm -rf
I only know a way around this.
The idea is to export that list of pdf files you have into a file. Then split that file into several parts. Then remove pdf files listed in each part.
ls | grep .pdf > list.txt
wc -l list.txt
wc -l is to count how many line the list.txt contains. When you have the idea of how long it is, you can decide to split it in half, forth or something. Using split -l command
For example, split it in 600 lines each.
split -l 600 list.txt
this will create a few file named xaa,xab,xac and so on depends on how you split it.
Now to "import" each list in those file into command rm, use this:
rm $(<xaa)
rm $(<xab)
rm $(<xac)
Sorry for my bad english.
I ran into this problem a few times. Many of the solutions will run the rm command for each individual file that needs to be deleted. This is very inefficient:
find . -name "*.pdf" -print0 | xargs -0 rm -rf
I ended up writing a python script to delete the files based on the first 4 characters in the file-name:
import os
filedir = '/tmp/' #The directory you wish to run rm on
filelist = (os.listdir(filedir)) #gets listing of all files in the specified dir
newlist = [] #Makes a blank list named newlist
for i in filelist:
if str((i)[:4]) not in newlist: #This makes sure that the elements are unique for newlist
newlist.append((i)[:4]) #This takes only the first 4 charcters of the folder/filename and appends it to newlist
for i in newlist:
if 'tmp' in i: #If statment to look for tmp in the filename/dirname
print ('Running command rm -rf '+str(filedir)+str(i)+'* : File Count: '+str(len(os.listdir(filedir)))) #Prints the command to be run and a total file count
os.system('rm -rf '+str(filedir)+str(i)+'*') #Actual shell command
print ('DONE')
This worked very well for me. I was able to clear out over 2 million temp files in a folder in about 15 minutes. I commented the tar out of the little bit of code so anyone with minimal to no python knowledge can manipulate this code.
I have faced a similar problem when there were millions of useless log files created by an application which filled up all inodes. I resorted to "locate", got all the files "located"d into a text file and then removed them one by one. Took a while but did the job!
I solved with for
I am on macOS with zsh
I moved thousands only jpg files. Within mv in one line command.
Be sure there are no spaces or special characters in the name of the files you are trying to move
for i in $(find ~/old -type f -name "*.jpg"); do mv $i ~/new; done
A bit safer version than using xargs, also not recursive:
ls -p | grep -v '/$' | grep '\.pdf$' | while read file; do rm "$file"; done
Filtering our directories here is a bit unnecessary as 'rm' won't delete it anyway, and it can be removed for simplicity, but why run something that will definitely return error?
Using GNU parallel (sudo apt install parallel) is super easy
It runs the commands multithreaded where '{}' is the argument passed
E.g.
ls /tmp/myfiles* | parallel 'rm {}'
For remove first 100 files:
rm -rf 'ls | head -100'

Resources