I have a bash script that contains:
for i in $(stuff);
do other-stuff; cp -r $i $p;
done
but I don't have read permissions to a specific log dump file type, let's call it .txt
Currently I get:
cp: cannot open `file.txt' for reading: Permission denied
Without changing any permissions, is there an easy way to copy everything except those files?
cp doesn't hang when it generates that message. It just skips the file. Add in verbose (cp -vr $i $p) and you'll see that its either busy copying other files, or alternatively something else in your script is hanging.
cp doesn't really have a way to exclude files its recursing over. If you want that, you'll have to switch to something more featureful, like tar (possibly with find) or rsync.
Also, you should really quote your arguments, just in case they contain spaces: cp -r "$i" "$p"
Test if the file is readable by the current user with if [ -r "$i" ]:
for i in $(stuff);
if [ -r "$i" ]; do
cp -r $i $p
fi
done
More info here: File test operators
Flag Returns true if...
-rfile has read permission (for the user running the test)
-wfile has write permission (for the user running the test)
-xfile has execute permission (for the user running the test)
do other-stuff; $i =~ "*.txt" || cp -r $i $p;
You may need grouping here; I didn't check the operator precedences and I can't keep them all in my head. But ~= does a regex. If it succeeds the copy will be skipped.
Related
In shell, I want to check if a file exists or not then create if it doesn't exist or delete if it exists. For this I need a one liner and am trying to do something like:
ls | awk '\filename\' <if exist delete else create>
I need the ls as my problem has some command that outputs a list of strings that need to be pipelined to awk then possibly touch/mkdir.
#!/bin/bash
if [ -z "$1" ] || [ ! -f "$1" ] # $1 is input filename and -f check if $1 is a regular file
then
rm "$1" #delete the file
else
touch "$1" #create the file
fi
save the file as filecreator.sh
change the permission to allow execution with sudo chmod a+rx
while running the script use ./filecreator.sh yourfile.extension
You can see the file in your directory.
Using oc projects and oc new-project instad of ls and touch as indicated in a comment.
oc projects |
while read -r proj; do
if [ -d "$proj" ]; then
rm -rf "$proj"
else
oc new-project "$proj"
fi
done
I don't think there is a useful way to write this as a one-liner. If you like, you can replace the newlines with semicolons, except after then and else.
You really should put your actual requirements in the question itself. ls is a superbly useless example because it cannot list a file which doesn't already exist, and you should not use ls in scripts at all.
rm yourfile 2>/dev/null || touch yourfile
If the file existed before, rm will succeed and erase the file, and the touch won't be executed. You end up with no file afterwards.
If the file did not exist before, rm will fail (but the error message is not visible, since it is directed to the bitbucket), and due to the non-zero exit code of rm, the touch will be executed. You end up with an empty file afterwards.
Caveat: If the file exists, but you don't have permissions to remove it, you won't notice this error, due to the redirection of stderr. Hence, for debugging and later diagnosis, it might be better to redirect stderr to some file instead.
I am working on some stuff where I am storing data in a file.
But each time I run the script it gets appended to the previous file.
I want help on how I can remove the file if it already exists.
Don't bother checking if the file exists, just try to remove it.
rm -f /p/a/t/h
# or
rm /p/a/t/h 2> /dev/null
Note that the second command will fail (return a non-zero exit status) if the file did not exist, but the first will succeed owing to the -f (short for --force) option. Depending on the situation, this may be an important detail.
But more likely, if you are appending to the file it is because your script is using >> to redirect something into the file. Just replace >> with >. It's hard to say since you've provided no code.
Note that you can do something like test -f /p/a/t/h && rm /p/a/t/h, but doing so is completely pointless. It is quite possible that the test will return true but the /p/a/t/h will fail to exist before you try to remove it, or worse the test will fail and the /p/a/t/h will be created before you execute the next command which expects it to not exist. Attempting this is a classic race condition. Don't do it.
Another one line command I used is:
[ -e file ] && rm file
You can use this:
#!/bin/bash
file="file_you_want_to_delete"
if [ -f "$file" ] ; then
rm "$file"
fi
If you want to ignore the step to check if file exists or not, then you can use a fairly easy command, which will delete the file if exists and does not throw an error if it is non-existing.
rm -f xyz.csv
A one liner shell script to remove a file if it already exist (based on Jindra Helcl's answer):
[ -f file ] && rm file
or with a variable:
#!/bin/bash
file="/path/to/file.ext"
[ -f $file ] && rm $file
Something like this would work
#!/bin/sh
if [ -fe FILE ]
then
rm FILE
fi
-f checks if it's a regular file
-e checks if the file exist
Introduction to if for more information
EDIT : -e used with -f is redundant, fo using -f alone should work too
if [ $( ls <file> ) ]; then rm <file>; fi
Also, if you redirect your output with > instead of >> it will overwrite the previous file
So in my case I wanted to remove a FIFO file before I create it again, so this worked for me:
#!/bin/bash
file="/tmp/test"
rm -rf $file | true
mkfifo $file
| true will continue the script even if file is not found.
Here is the condition:
I have a file with all packages installed.
I have a folder with all kinds of other packages, but they include all of the ones in the list, plus more.
I need a bash script that will read the file and check a folder for packages that don't exist in the list then remove them, they are not needed, but keep the packages that are on the list in that folder.
Or perhaps the bash should read folder then if packages in the folder aren't on the list them rm -f that or those packages.
I am familiar with writing if then conditional statements, I just don't know how to do if making the items in the list a variable or variables (in a loop).
thanks!
I would move the packages on the list to a new folder, delete the original folder, and move the temporary folder back:
DIR=directory-name
mkdir "$DIR-tmp"
while read pkgname; do
if [[ -f "$DIR/$pkgname" ]]; then
mv "$DIR/$pkgname" "$DIR-tmp"
fi
done < package-list.txt
# Confirm $DIR-tmp has the files you want first!
rm -rf "$DIR"
mv "$DIR-tmp" "$DIR"
I think you want something like this:
for file in $(ls folder) ; do
grep -E "$file" install-list-file >/dev/null || \
echo $file
done > rm-list
vi rm-list # view file to ensure correct
rm $(<rm_list)
There are ways to make this faster (using parameter substitution to avoid fork/exec's), but I recommend avoiding fancy shell stuff [${file##*/}] until you've got the basics down. Also, this script basically translates the description into a script and is not intended to be much more than a guide on how to approach the problem.
I have a file that contains some keywords and I intend to create subdirectories into the same directory of the same keyword using a bash script. Here is the code I am using but it doesn't seem to be working.
I don't know where I have gone wrong. Help me out
for i in `cat file.txt`
do
# if [[ ! -e $path/$i ]]; then
echo "creating" $i "directory"
mkdir $path/$i
# fi
grep $i file >> $path/$i/output.txt
done
echo "created the files in "$path/$TEMP/output.txt
You've gone wrong here, and you've gone wrong here.
while read i
do
echo "Creating $i directory"
mkdir "$path/$i"
grep "$i" file >> "$path/$i"/output.txt
done < file.txt
echo "created the files in $path/$TEMP/output.txt"
78mkdir will refuse to create a directory, if parts of it do not exist.
e.g. if there is no /foo/bar directory, then mkdir /foo/bar/baz will fail.
you can relax this a bit by using the -p flag, which will create parent directories if necessary (in the example, it might create /foo and /foo/bar).
you should also use quotes, in case your paths contain blanks.
mkdir -p "${path}/${i}"
finally, make sure that you are actually allowed to create directories in $path
I have many files' path, but I need to copy all files into other location /sample, and I want to copy files into different folders:
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59329/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59329/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_2.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59329/clean_111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz.total.info
I want to copy those files into AS34_59329 folder inside /sample
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_2.fq.gz
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/clean_111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz.total.info
I want to copy those file into AS34_59328 folder inside /sample
I write codes to scp all file into /sample folder, but I don't know how to put each files into different sub-directory, like:
/ifshk5/BC_IP/PROJECT/T11073/T11073_RICekkR/Fq/AS34_59328/clean_111220_I631_FCC0E5EACXX_L4_RICwdsRSYHSD11-2-IPAAPEK-93_1.fq.gz.total.info
put into AS34_59328
#! /bin/bash
while read myline
do
for i in $myline
do
if [ -f $i]; then
#how to put different files into different sub-directory
scp -r $i xxx#191.168.174.43:/sample
fi
done
done < data.list
new changed part
#! /bin/bash
while read myline
do
for i in $myline
do
if [ -f $i ]
then
relname=$(echo $i | sed 's%\(/[^/][^/]*\)\{5\}/%%')
echo $relname
fi
done
done < /home/jesse/T11073_all_3254.fq.list
It appears you need to strip the leading 5 components of the pathname off the filename. Since you don't have spaces in your names (the way you're using for i in $myline precludes that possibility), you can use:
#! /bin/bash
while read myline
do
for i in $myline
do
if [ -f $i ]
then
relname=$(echo $i | sed 's%\(/[^/][^/]*\)\{5\}/%%')
scp -r $i xxx#191.168.174.43:/sample/$relname
fi
done
done < data.list
The regex is just a way of looking for a sequence of five sets of slash followed by one or more non-slashes plus one more slash and deleting them. Since slashes figure prominently in the search, I used % to mark the sections of the s/// operation instead.
For example, given the input:
/a/b/c/d/e/f/g
the output from the sed is:
f/g
Note that this code does not explicitly create directories on the remote machine; it just specifies where the file is to go. If you need to create them too, you will have to investigate ssh, probably, to run mkdir -p /sample/$(dirname $relname) on the remote machine (where the dirname operation can be run either locally or remotely).
Note that scp has a recursive copy mode (-r) which would simplify things considerably if you knew you needed to copy all the files from the local directory to the remote.