I have following architecture of files in a directory.
Directory
/A/abc.xyz
/B/abc.xyz
/C/abc.xyz
/D/abc.xyz
/E/abc.xyz
I want to execute a program on acb.xyz in each SubDirectory. Save Output files in different directory i.e. Directory/processed with the name of SubDirectory appended in the name of output files.
Can it be written in following way? Need corrections.
for i in `ls "Directory/"`
do
program.pl $i/abc.xyz > processed/$i-abc.xyz
done
for dir in Directory/*; do
program.pl "$dir/abc.xyz" > "processed/${dir##*/}-abc.xyz"
done
The ${dir##*/} part strips the leading directory names from $dir, so Directory/A becomes just A. I added quotes to ensure directory names with whitespace don't cause issue (a good habit, even if you know there are no spaces).
As an alternative to the string munging you could simplify this if you first change directory:
cd Directory
for dir in *; do
program.pl "$dir/abc.xyz" > "processed/$dir-abc.xyz"
done
Related
I've got (what feels like) a fairly simple problem but my complete lack of experience in bash has left me stumped. I've spent all day trying to synthesize a script from many different SO threads explaining how to do specific things with unintuitive commands, but I can't figure out how to make them work together for the life of me.
Here is my situation: I've got a directory full of nested folders each containing a file with extension .7 and another file with extension .pc, plus a whole bunch of unrelated stuff. It looks like this:
Folder A
Folder 1
Folder x
data_01.7
helper_01.pc
...
Folder y
data_02.7
helper_02.pc
...
...
Folder 2
Folder z
data_03.7
helper_03.pc
...
...
Folder B
...
I've got a script that I need to run in each of these folders that takes in the name of the .7 file as an input.
pc_script -f data.7 -flag1 -other_flags
The current working directory needs to be the folder with the .7 file when running the script and the helper.pc file also needs to be present in it. After the script is finished running, there are a ton of new files and directories. However, I need to take just one of those output files, result.h5, and copy it to a new directory maintaining the same folder structure but with a new name:
Result Folder/Folder A/Folder 1/Folder x/new_result1.h5
I then need to run the same script again with a different flag, flag2, and copy the new version of that output file to the same result directory with a different name, new_result2.h5.
The folders all have pretty arbitrary names, though there aren't any spaces or special characters beyond underscores.
Here is an example of what I've tried:
#!/bin/bash
DIR=".../project/data"
for d in */ ; do
for e in */ ; do
for f in */ ; do
for PFILE in *.7 ; do
echo "$d/$e/$f/$PFILE"
cd "$DIR/$d/$e/$f"
echo "Performing operation 1"
pc_script -f "$PFILE" -flag1
mkdir -p ".../results/$d/$e/$f"
mv "results.h5" ".../project/results/$d/$e/$f/new_results1.h5"
echo "Performing operation 2"
pc_script -f "$PFILE" -flag 2
mv "results.h5" ".../project/results/$d/$e/$f/new_results2.h5"
done
done
done
done
Obviously, this didn't work. I've also tried using find with -execdir but then I couldn't figure out how to insert the name of the file into the script flag. I'd appreciate any help or suggestions on how to carry this out.
Another, perhaps more flexible, approach to the problem is to use the find command with the -exec option to run a short "helper-script" for each file found below a directory path that ends in ".7". The -name option allows find to locate all files ending in ".7" below a given directory using simple file-globbing (wildcards). The helper-script then performs the same operation on each file found by find and handles moving the result.h5 to the proper directory.
The form of the command will be:
find /path/to/search -type f -name "*.7" -exec /path/to/helper-script '{}` \;
Where the -f option tells find to only return files (not directories) ending in ".7". Your helper-script needs to be executable (e.g. chmod +x helper-script) and unless it is in your PATH, you must provide the full path to the script in the find command. The '{}' will be replaced by the filename (including relative path) and passed as an argument to your helper-script. The \; simply terminates the command executed by -exec.
(note there is another form for -exec called -execdir and another terminator '+' that can be used to process the command on all files in a given directory -- that is a bit safer, but has additional PATH requirements for the command being run. Since you have only one ".7" file per-directory -- there isn't much benefit here)
The helper-script just does what you need to do in each directory. Based on your description it could be something like the following:
#!/bin/bash
dir="${1%/*}" ## trim file.7 from end of path
cd "$dir" || { ## change to directory or handle error
printf "unable to change to directory %s\n" "$dir" >&2
exit 1
}
destdir="/Result_Folder/$dir" ## set destination dir for result.h5
mkdir -p "$destdir" || { ## create with all parent dirs or exit
printf "unable to create directory %s\n" "$dir" >&2
exit 1
}
ls *.pc 2>/dev/null || exit 1 ## check .pc file exists or exit
file7="${1##*/}" ## trim path from file.7 name
pc_script -f "$file7" -flags1 -other_flags ## first run
## check result.h5 exists and non-empty and copy to destdir
[ -s "result.h5" ] && cp -a "result.h5" "$destdir/new_result1.h5"
pc_script -f "$file7" -flags2 -other_flags ## second run
## check result.h5 exists and non-empty and copy to destdir
[ -s "result.h5" ] && cp -a "result.h5" "$destdir/new_result2.h5"
Which essentially stores the path part of the file.7 argument in dir and changes to that directory. If unable to change to the directory (due to read-permissions, etc..) the error is handled and the script exits. Next the full directory structure is created below your Result_Folder with mkdir -p with the same error handling if the directory cannot be created.
ls is used as a simple check to verify that a file ending in ".pc" exits in that directory. There are other ways to do this by piping the results to wc -l, but that spawns additional subshells that are best avoided.
(also note that Linux and Mac have files ending in ".pc" for use by pkg-config used when building programs from source -- they should not conflict with your files -- but be aware they exists in case you start chasing why weird ".pc" files are found)
After all tests are performed, the path is trimmed from the current ".7" filename storing just the filename in file7. The file7 variabli is then used in your pc_script command (which should also include the full path to the script if not in you PATH). After the pc_script is run [ -s "result.h5" ] is used to verify that result.h5 exists and is non-empty before moving that file to your Result_Folder location.
That should get you started. Using find to locate all .7 files is a simple way to let the tool designed to find the files for you do its job -- rather than trying to hand-roll your own solution. That way you only have to concentrate on what should be done for each file found. (note: I don't have pc_script or the files, so I have not testes this end-to-end, but it should be very close if not right-on-the-money)
There is nothing wrong in writing your own routine, but using find eliminates a lot of area where bugs can hide in your own solution.
Let me know if you have further questions.
I have a folder /home/user/Document/filepath where I have three files namely file1-1.1.0.txt, file2-1.1.1.txt, file3-1.1.2.txt
and another folder named /home/user/Document/backuppath where I have to move files from /home/user/Document/folderpath which has file1-1.0.0.txt, file2-1.0.1.txt and file3-1.0.2.txt
task is to copy the specific files from folder path to backup path.
To summarize:
the below is the files.txt where I listed the files which has to be copied:
file1-*.txt
file2-*.txt
The below is the move.sh script that execute the movements
for file in `cat files.txt`; do cp "/home/user/Document/folderpath/$file" "/home/user/Documents/backuppath/" ; done
for the above script I am getting the error like
cp: cannot stat '/home/user/Document/folderpath/file1-*.txt': No such file or directory found
cp: cannot stat '/home/user/Document/folderpath/file2-*.txt': No such file or directory found
what I would like to accomplish is that I would like to use the script to copy specific files using * in the place of version numbers., since the version number may vary in the future.
You have wildcard characters in your files.txt. In your cp command, you are using quotes. These quotes prevent the wildcards to be expanded, as you can clearly see from the error message.
One obvious possibility is to not use quotes:
cp /home/user/Document/folderpath/$file /home/user/Documents/backuppath/
Or not use a loop at all:
cp $(<files.txt) /home/user/Documents/backuppath/
However, this would of course break if one line in your files.txt is a filename pattern which contains white spaces. Therefore, I would recommend a second loop over the expanded pattern:
while read file # Puts the next line into 'file'
do
for f in $file # This expands the pattern in 'file'
do
cp "/home/user/Document/folderpath/$f" /home/user/Documents/backuppath
done
done < files.txt
I have created a test directory structure:
t1.html
t2.php
a/t1.html
a/t2.php
b/t1.html
b/t2.php
All files contain the string "HELLO".
The following commands are run from the root folder above:
> grep -r "HELLO" *
b/t1.html:HELLO
b/t2.php:HELLO
c/t1.html:HELLO
c/t2.php:HELLO
t1.html:HELLO
t2.php:HELLO
> grep -r --include=*.html "HELLO" *
b/t1.html:HELLO
c/t1.html:HELLO
t2.php:HELLO
Why is it including the correct .html files from the sub-directories, but the .php file from the current directory?
If I pop up a level to the directory above my whole structure, then it gives following result:
grep -r --include=*.html "HELLO" *
a/t1.html:HELLO
a/c/t1.html:HELLO
a/b/t1.html:HELLO
This is what I expected when ran from within my structure.
I assume I can achieve the goal using find+grep together, but I thought this was valid usage of grep.
Thanks for any help.
Andy
Use a dot instead of the asterisk:
grep -r HELLO .
Asterisk gets evaluated by the shell and replaced with the list of all the files in the current directory (whose names don't start with a dot). All of them are then grepped recursively.
I need to unzip a bunch of student assignment (jar) files so that I can use a script to submit the contents to the Moss (Stanford) plagiarism detection server. I did the same thing in Java which was trivial but I'm trying to re-implement to as a bash script.
I am trying to do the following:
Get a list of student names (each student has a directory).
In each student directory, sub-directories exist numbered from 1 to the
latest submission. I need to get the directory with the highest
number.
Inside of each of those submission directories contains a
jar file that I need. I copy each jar into a temp directory with the
same name as the student and unzip it.
I need that temp directory listing formatted as a string in the form
/tempDir/studentName1/.languageExt /tempDir/studentName2/.languageExt
The student directory has the basic structure:
Student_Root_Directory:
Student1
Student2
Student1
Sub-Directories: 1 2 3 4 5
1: student1.jar
2: student1.jar
...
Student2
Sub-Directories: 1 2 3
1. student2.jar
...
To do the first 3 steps above I did:
#!/bin/bash
# Extract all jar files into a temp directory called /home/moss/tempJarFiles/studentName
# $1 is the command line argument that contains the path to the institution submission dir.
# $2 is the language extension: .c, .cpp, .java, .py
students=`ls $1`
student_dir=$1
languageExt=$2
mossDir="/home/moss"
tempDir="/home/moss/tempJarStorage"
for student in $students
do
latestSubmissionDir=`ls -t $student_dir/$student | head -1`
for jarDir in $latestSubmissionDir
do
mkdir $tempDir/$student
cp $student_dir/$student/$jarDir/*.jar $tempDir/$student
unzip -d $tempDir/$student/ -o -j $tempDir/$student/$student.jar *.$languageExt
rm $tempDir/$student/$student.jar
done
done
...which results in a number of student directories being created in a temp directory that contains only the unzipped contents for the student submissions.
I need the ls output of the new temp directories formatted as a string that contains:
/tempDir/studentName1/\*.languageExt /tempDir/studentName2/\*.languageExt
I have tried variations on
find "$tempDir" -iname "*.$languageExt" -printf "%p/*.$languageExt"
using iname and not - but I either have output that contains extra directory information such as $tempDir/*.languageExt (when I just need the subdirectories $tempDir/$studentName/*.languageExt) or I have output where the path for every source file is also listed such as:
$tempDir/$studentName/studentNameA.java
$tempDir/$studentName/studentNameB.java
when I only need
$tempDir/$studentName/*.java
I think this should be really easy and I'm just over thinking it. Any hints for improving the script also appreciated.
Here's a revised version of the script hat may work:
#/bin/bash
# Extract all jar files into a temp directory called /home/moss/tempJarFiles/studentName
# $1 is the command line argument that contains the path to the institution submission dir.
# $2 is the language extension: c, cpp, java, py
students_dir=$1
languageExt=$2
studentPathsT=( "$students_dir"/*/ )
mossDir='/home/moss'
tempDir='/home/moss/tempJarStorage'
for studentPathT in "${studentPathsT[#]}"; do
student=$(basename "$studentPathT")
mkdir "$tempDir/$student"
submissionDirsT=( "$studentPathT"*/ )
latestSubmissionDirT=${submissionDirsT[${#submissionDirsT[#]-1]}
cp "$latestSubmissionDirT"*.jar "$tempDir/$student/"
unzip -d "$tempDir/$student/" -o -j "$tempDir/$student/*.jar" "*.$languageExt"
rm "$tempDir/$student"/*.jar
done
# Note that at this point `"$tempDir"/*/*.$languageExt` would expand
# to all extracted submission files, across all students.
# Finally, output each student's extracted files as an unexpanded glob à la
# /{tempDir}/{studentName1}/*.{languageExt}
for pT in "$tempDir"/*/; do
echo "$pT*.$languageExt"
# Note: If there is a chance that your filenames contain
# embedded newlines (rare in practice) using `echo` won't work properly
# as #Charles Duffy points out.
# If that is a concern, use
# printf '%s\0' "$pT*.$languageExt"
# and process the output with a utility that can process NUL characters
# as separators, such as `xargs -0`.
done
It avoids using ls and only uses pathname expansion and array variables so as to properly deal with paths that contain embedded spaces and other shell metacharacters.
suffix ...T in variable names indicates that a particular path or array of paths is *T*erminated, i.e, that it ends in a /.
The assumption is that the numbered subdirectories do not go beyond 9, as the implicit lexical sorting of pathname expansion is relied upon; if the numbers go higher, explicit numerical sorting must be applied.
Note that the globs (pathname patterns) passed to unzip are intentionally double-quoted, as they should be interpreted by unzip, not the shell.
Note that, based on your original code, I've assumed that $languageExt does NOT start with . (e.g., cpp rather than .cpp), despite what your comment says.
I working with linux, bash.
I have one directory with 100 folders in it, each one named different.
In each of these 100 folders, there is a file called first.bars (so I have 100 files named first.bars). Although all named first.bars, the files are actually slightly different.
I want to get all these files moved to one new folder and rename/number these files so that I know which file comes from which folder. So the first first.bars file must be renamed to 001.bars, the second to 002.bars.. etc.
I have tried the following:
ls -d * >> /home/directorywiththe100folders/list.txt
cat list.txt | while read line;
do cd $line;
mv first.bars /home/newfolder
This does not work because I can't have 100 files, named the same, in one folder. So I only need to know how to rename them. The renaming must be connected to the cat list.txt, because the first line is the folder containing the first file wich is moved and renamed. That file will be called 001.bars.
Try doing this :
$ rename 's/^.*?\./sprintf("%03d.", $c++)/e' *.bar
If you want more information about this command, see this recent response I gave earlier : How do I rename multiple files beginning with a Unix timestamp - imapsync issue
If the rename command is not available,
for d in /home/directorywiththe100folders/*/; do
newfile=$(printf "/home/newfolder/%d.bars" $(( c++ )) )
mv "$d/first.bars" "$newfile"
done