Bash beginner: Error when tries to copy directory itself when making subdirectories

I have a directory with 4 directories in it.
I want to make a 5th directory (cx1_date) and create 4 empty directories with the same names as those of the original directory
I then want to copy two files from each of the original directories to the new subdirectories with their respective names

I think I am getting an error because it tries to copy the PWD itself (as this shows up as a result of the find call), so I tried to include an if statement but I think that it doesn't work

now=$(date +"%m_%d_%Y")

PWD="/nmr/charlie"

mkdir $PWD/cx1_$now

for name in $(find $PWD -maxdepth 1 -type d); do
if [[ "$name" = "$PWD" && "$PWD" = "$name" ]];
then 
    :
else 
    cd $PWD/cx1_$now
    mkdir $PWD/$name
    cd $PWD/$name 
    cp file1.ext $PWD/cx1_$now/$name
    cp file2.ext $PWD/cx1_$now/$name
fi 
done

First line of the error

mkdir: cannot create directory `/nmr/charlie/cx1_05_15_2012//nmr/charlie/cx1_05_15_2012': No such file or directory

Thanking you in advance for any help you can give!

Charlie

Solution

The second mkdir doesn't want the $PWD:

now=$(date +"%m_%d_%Y")

DIR="/nmr/charlie"

mkdir $DIR/cx1_$now

for name in $(find $DIR -maxdepth 1 -type d)
do
    if [[ "$name" != "$DIR" ]]
    then 
        (cd $DIR/cx1_$now; mkdir $name)
        (cd $DIR/$name 
         cp file1.ext $DIR/cx1_$now/$name
         cp file2.ext $DIR/cx1_$now/$name
        )
    fi
done

Also, PWD is a built-in variable; you shouldn't set it (except via the cd command).

You don't need the symmetric test in the if; you can use != instead of = to avoid an empty then clause (OK, it contains a nice anodyne : command; you don't need it if you invert the test).

I usually put cd operations into sub-shells; that way, I get less confused. An alternative for the second mkdir line is this, which doesn't need the cd or subshell:

mkdir -p $DIR/cx1_$now/$name

I recommend using the ISO 8601 format for dates, such as:

now=$(date +"%Y_%m_%d")

That way, the directories will sort in date order automatically.

I still get the error:

mkdir: cannot create directory `/nmr/charlie/directory_name_1': File exists
/home/charlie/Desktop/scripts/test.sh: line 16: cd: /nmr/charlie//nmr/charlie/directory_name_1: No such file or directory

The problem likely means we've not filtered correctly yet. For example, each time you create a back up directory, all the previous backup directories will be backed up into the new one, which a little excessive. So, the other part of the exercise is filtering the output of find better.

...And we should be using the base name of the directory, and we can avoid all cd operations too:

now=$(date +"%m_%d_%Y")

DIR="/nmr/charlie"

mkdir $DIR/cx1_$now

for name in $(find $DIR -maxdepth 1 -type d | grep -v '/cx1_[^/]*$')
do
    if [[ "$name" != "$DIR" ]]
    then
        targetdir=$DIR/cx1_$now/$(basename $name)
        mkdir -p $targetdir
        cp $name/file1.ext $name/file2.ext $targetdir
    fi
done

You do know about using 'sh -x script.sh' or 'bash -x script.sh' to run the script and see what it is doing. I'm not even sure that we need the if condition with the grep filtering out anything that looks like a backup directory from the list.

I note that this only works if the directory paths are sane and contain no spaces. Things go wrong rather rapidly if you use non-portable files names (where portable names use [-_.A-Za-z0-9] only). Newlines and spaces really make a mess.

Note that this would be simpler if you made the backup in directories under /nmr/backup/charlie or anywhere other than under /nmr/charlie itself. However, with care, it can be done in situ as requested.