I try to search for files and seperate path and version as variable because each will be needed later for creating a directory and to unzip a .jar in desired path.
file=$(find /home/user/Documents/test/ -path *.jar)
version=$(echo "$file" | grep -P -o '[0-9].[0-9].[0-9].[0-9]')
path=$(echo "$file" | sed 's/\(.*\)[/].*/\1/')
newpath=$(echo "${path}/${version}")
echo "$newpath"
result
> /home/user/Documents/test/gb0500
> /home/user/Documents/test/gb0500 /home/user/Documents/test/gb0500
> /home/user/Documents/test /home/user/Documents/test/1.3.2.0
> 1.3.2.1
> 1.3.2.2
> 1.2.0.0
> 1.3.0.0
It's hilarious that it's only working at one line.
what else I tried:
file=$(find /home/v990549/Dokumente/test/ -path *.jar)
version=$(grep -P -o '[0-9].[0-9].[0-9].[0-9]')
path=$(sed 's/\(.*\)[/].*/\1/')
while read $file
do
echo "$path$version"
done
I have no experience in scripting. Thats what I figured out some days ago. I am just practicing and trying to make life easier.
find output:
/home/user/Documents/test/gb0500/gb0500-koetlin-log4j2-web-1.3.2.0-javadoc.jar
/home/user/Documents/test/gb0500/gb0500-koetlin-log4j2-web-1.3.2.1-javadoc.jar
/home/user/Documents/test/gb0500/gb0500-koetlin-log4j2-web-1.3.2.2-javadoc.jar
/home/user/Documents/test/gb0500-co-log4j2-web-1.2.0.0-javadoc.jar
/home/user/Documents/test/gb0500-commons-log4j2-web-1.3.0.0-javadoc.jar
As the both variables version and path are newline-separated, how about:
file=$(find /home/user/Documents/test/ -path *.jar)
version=$(echo "$file" | grep -P -o '[0-9].[0-9].[0-9].[0-9]')
path=$(echo "$file" | sed 's/\(.*\)[/].*/\1/')
paste -d "/" <(echo "$path") <(echo "$version")
Result:
/home/user/Documents/test/gb0500/1.3.2.0
/home/user/Documents/test/gb0500/1.3.2.1
/home/user/Documents/test/gb0500/1.3.2.2
/home/user/Documents/test/1.2.0.0
/home/user/Documents/test/1.3.0.0
BTW I do not recommend to store multiple filenames in a single variable
as a newline-separated variable due to several reasons:
Filenames may contain a newline character.
It is not easy to manipulate the values of each line.
For instance you could simply say
the third line as path=${file%/*} if file contains just one.
Hope this helps.
How do you use a command line argument as a file path and check for file existence in Bash?
I have the simple Bash script test.sh:
#!/bin/bash
set -e
echo "arg1=$1"
if [ ! -f "$1" ]
then
echo "File $1 does not exist."
exit 1
fi
echo "File exists!"
and in the same directory, I have a data folder containing stuff.txt.
If I run ./test.sh data/stuff.txt I see the expected output:
arg1=data/stuff.txt
"File exists!"
However, if I call this script from a second script test2.sh, in the same directory, like:
#!/bin/bash
fn="data/stuff.txt"
./test.sh $fn
I get the mangled output:
arg1=data/stuff.txt
does not exist
Why does the call work when I run it manually from a terminal, but not when I run it through another Bash script, even though both are receiving the same file path? What am I doing wrong?
Edit: The filename does not have spaces. Both scripts are executable. I'm running this on Ubuntu 18.04.
The filename was getting an extra whitespace character added to it as a result of how I was retrieving it in my second script. I didn't note this in my question, but I was retrieving the filename from folder list over SSH, like:
fn=$(ssh -t "cd /project/; ls -t data | head -n1" | head -n1)
Essentially, I wanted to get the filename of the most recent file in a directory on a remote server. Apparently, head includes the trailing newline character. I fixed it by changing it to:
fn=$(ssh -t "cd /project/; ls -t data | head -n1" | head -n1 | tr -d '\n' | tr -d '\r')
Thanks to #bigdataolddriver for hinting at the problem likely being an extra character.
Am trying to grep pattern from dozen files .tar.gz but its very slow
am using
tar -ztf file.tar.gz | while read FILENAME
do
if tar -zxf file.tar.gz "$FILENAME" -O | grep "string" > /dev/null
then
echo "$FILENAME contains string"
fi
done
If you have zgrep you can use
zgrep -a string file.tar.gz
You can use the --to-command option to pipe files to an arbitrary script. Using this you can process the archive in a single pass (and without a temporary file). See also this question, and the manual.
Armed with the above information, you could try something like:
$ tar xf file.tar.gz --to-command "awk '/bar/ { print ENVIRON[\"TAR_FILENAME\"]; exit }'"
bfe2/.bferc
bfe2/CHANGELOG
bfe2/README.bferc
I know this question is 4 years old, but I have a couple different options:
Option 1: Using tar --to-command grep
The following line will look in example.tgz for PATTERN. This is similar to #Jester's example, but I couldn't get his pattern matching to work.
tar xzf example.tgz --to-command 'grep --label="$TAR_FILENAME" -H PATTERN ; true'
Option 2: Using tar -tzf
The second option is using tar -tzf to list the files, then go through them with grep. You can create a function to use it over and over:
targrep () {
for i in $(tar -tzf "$1"); do
results=$(tar -Oxzf "$1" "$i" | grep --label="$i" -H "$2")
echo "$results"
done
}
Usage:
targrep example.tar.gz "pattern"
Both the below options work well.
$ zgrep -ai 'CDF_FEED' FeedService.log.1.05-31-2019-150003.tar.gz | more
2019-05-30 19:20:14.568 ERROR 281 --- [http-nio-8007-exec-360] DrupalFeedService : CDF_FEED_SERVICE::CLASSIFICATION_ERROR:408: Classification failed even after maximum retries for url : abcd.html
$ zcat FeedService.log.1.05-31-2019-150003.tar.gz | grep -ai 'CDF_FEED'
2019-05-30 19:20:14.568 ERROR 281 --- [http-nio-8007-exec-360] DrupalFeedService : CDF_FEED_SERVICE::CLASSIFICATION_ERROR:408: Classification failed even after maximum retries for url : abcd.html
If this is really slow, I suspect you're dealing with a large archive file. It's going to uncompress it once to extract the file list, and then uncompress it N times--where N is the number of files in the archive--for the grep. In addition to all the uncompressing, it's going to have to scan a fair bit into the archive each time to extract each file. One of tar's biggest drawbacks is that there is no table of contents at the beginning. There's no efficient way to get information about all the files in the archive and only read that portion of the file. It essentially has to read all of the file up to the thing you're extracting every time; it can't just jump to a filename's location right away.
The easiest thing you can do to speed this up would be to uncompress the file first (gunzip file.tar.gz) and then work on the .tar file. That might help enough by itself. It's still going to loop through the entire archive N times, though.
If you really want this to be efficient, your only option is to completely extract everything in the archive before processing it. Since your problem is speed, I suspect this is a giant file that you don't want to extract first, but if you can, this will speed things up a lot:
tar zxf file.tar.gz
for f in hopefullySomeSubdir/*; do
grep -l "string" $f
done
Note that grep -l prints the name of any matching file, quits after the first match, and is silent if there's no match. That alone will speed up the grepping portion of your command, so even if you don't have the space to extract the entire archive, grep -l will help. If the files are huge, it will help a lot.
For starters, you could start more than one process:
tar -ztf file.tar.gz | while read FILENAME
do
(if tar -zxf file.tar.gz "$FILENAME" -O | grep -l "string"
then
echo "$FILENAME contains string"
fi) &
done
The ( ... ) & creates a new detached (read: the parent shell does not wait for the child)
process.
After that, you should optimize the extracting of your archive. The read is no problem,
as the OS should have cached the file access already. However, tar needs to unpack
the archive every time the loop runs, which can be slow. Unpacking the archive once
and iterating over the result may help here:
local tempPath=`tempfile`
mkdir $tempPath && tar -zxf file.tar.gz -C $tempPath &&
find $tempPath -type f | while read FILENAME
do
(if grep -l "string" "$FILENAME"
then
echo "$FILENAME contains string"
fi) &
done && rm -r $tempPath
find is used here, to get a list of files in the target directory of tar, which we're iterating over, for each file searching for a string.
Edit: Use grep -l to speed up things, as Jim pointed out. From man grep:
-l, --files-with-matches
Suppress normal output; instead print the name of each input file from which output would
normally have been printed. The scanning will stop on the first match. (-l is specified
by POSIX.)
Am trying to grep pattern from dozen files .tar.gz but its very slow
tar -ztf file.tar.gz | while read FILENAME
do
if tar -zxf file.tar.gz "$FILENAME" -O | grep "string" > /dev/null
then
echo "$FILENAME contains string"
fi
done
That's actually very easy with ugrep option -z:
-z, --decompress
Decompress files to search, when compressed. Archives (.cpio,
.pax, .tar, and .zip) and compressed archives (e.g. .taz, .tgz,
.tpz, .tbz, .tbz2, .tb2, .tz2, .tlz, and .txz) are searched and
matching pathnames of files in archives are output in braces. If
-g, -O, -M, or -t is specified, searches files within archives
whose name matches globs, matches file name extensions, matches
file signature magic bytes, or matches file types, respectively.
Supported compression formats: gzip (.gz), compress (.Z), zip,
bzip2 (requires suffix .bz, .bz2, .bzip2, .tbz, .tbz2, .tb2, .tz2),
lzma and xz (requires suffix .lzma, .tlz, .xz, .txz).
Which requires just one command to search file.tar.gz as follows:
ugrep -z "string" file.tar.gz
This greps each of the archived files to display matches. Archived filenames are shown in braces to distinguish them from ordinary filenames. For example:
$ ugrep -z "Hello" archive.tgz
{Hello.bat}:echo "Hello World!"
Binary file archive.tgz{Hello.class} matches
{Hello.java}:public class Hello // prints a Hello World! greeting
{Hello.java}: { System.out.println("Hello World!");
{Hello.pdf}:(Hello)
{Hello.sh}:echo "Hello World!"
{Hello.txt}:Hello
If you just want the file names, use option -l (--files-with-matches) and customize the filename output with option --format="%z%~" to get rid of the braces:
$ ugrep -z Hello -l --format="%z%~" archive.tgz
Hello.bat
Hello.class
Hello.java
Hello.pdf
Hello.sh
Hello.txt
All of the code above was really helpful, but none of it quite answered my own need: grep all *.tar.gz files in the current directory to find a pattern that is specified as an argument in a reusable script to output:
The name of both the archive file and the extracted file
The line number where the pattern was found
The contents of the matching line
It's what I was really hoping that zgrep could do for me and it just can't.
Here's my solution:
pattern=$1
for f in *.tar.gz; do
echo "$f:"
tar -xzf "$f" --to-command 'grep --label="`basename $TAR_FILENAME`" -Hin '"$pattern ; true";
done
You can also replace the tar line with the following if you'd like to test that all variables are expanding properly with a basic echo statement:
tar -xzf "$f" --to-command 'echo "f:`basename $TAR_FILENAME` s:'"$pattern\""
Let me explain what's going on. Hopefully, the for loop and the echo of the archive filename in question is obvious.
tar -xzf: x extract, z filter through gzip, f based on the following archive file...
"$f": The archive file provided by the for loop (such as what you'd get by doing an ls) in double-quotes to allow the variable to expand and ensure that the script is not broken by any file names with spaces, etc.
--to-command: Pass the output of the tar command to another command rather than actually extracting files to the filesystem. Everything after this specifies what the command is (grep) and what arguments we're passing to that command.
Let's break that part down by itself, since it's the "secret sauce" here.
'grep --label="`basename $TAR_FILENAME`" -Hin '"$pattern ; true"
First, we use a single-quote to start this chunk so that the executed sub-command (basename $TAR_FILENAME) is not immediately expanded/resolved. More on that in a moment.
grep: The command to be run on the (not actually) extracted files
--label=: The label to prepend the results, the value of which is enclosed in double-quotes because we do want to have the grep command resolve the $TAR_FILENAME environment variable passed in by the tar command.
basename $TAR_FILENAME: Runs as a command (surrounded by backticks) and removes directory path and outputs only the name of the file
-Hin: H Display filename (provided by the label), i Case insensitive search, n Display line number of match
Then we "end" the first part of the command string with a single quote and start up the next part with a double quote so that the $pattern, passed in as the first argument, can be resolved.
Realizing which quotes I needed to use where was the part that tripped me up the longest. Hopefully, this all makes sense to you and helps someone else out. Also, I hope I can find this in a year when I need it again (and I've forgotten about the script I made for it already!)
And it's been a bit a couple of weeks since I wrote the above and it's still super useful... but it wasn't quite good enough as files have piled up and searching for things has gotten more messy. I needed a way to limit what I looked at by the date of the file (only looking at more recent files). So here's that code. Hopefully it's fairly self-explanatory.
if [ -z "$1" ]; then
echo "Look within all tar.gz files for a string pattern, optionally only in recent files"
echo "Usage: targrep <string to search for> [start date]"
fi
pattern=$1
startdatein=$2
startdate=$(date -d "$startdatein" +%s)
for f in *.tar.gz; do
filedate=$(date -r "$f" +%s)
if [[ -z "$startdatein" ]] || [[ $filedate -ge $startdate ]]; then
echo "$f:"
tar -xzf "$f" --to-command 'grep --label="`basename $TAR_FILENAME`" -Hin '"$pattern ; true"
fi
done
And I can't stop tweaking this thing. I added an argument to filter by the name of the output files in the tar file. Wildcards work, too.
Usage:
targrep.sh [-d <start date>] [-f <filename to include>] <string to search for>
Example:
targrep.sh -d "1/1/2019" -f "*vehicle_models.csv" ford
while getopts "d:f:" opt; do
case $opt in
d) startdatein=$OPTARG;;
f) targetfile=$OPTARG;;
esac
done
shift "$((OPTIND-1))" # Discard options and bring forward remaining arguments
pattern=$1
echo "Searching for: $pattern"
if [[ -n $targetfile ]]; then
echo "in filenames: $targetfile"
fi
startdate=$(date -d "$startdatein" +%s)
for f in *.tar.gz; do
filedate=$(date -r "$f" +%s)
if [[ -z "$startdatein" ]] || [[ $filedate -ge $startdate ]]; then
echo "$f:"
if [[ -z "$targetfile" ]]; then
tar -xzf "$f" --to-command 'grep --label="`basename $TAR_FILENAME`" -Hin '"$pattern ; true"
else
tar -xzf "$f" --no-anchored "$targetfile" --to-command 'grep --label="`basename $TAR_FILENAME`" -Hin '"$pattern ; true"
fi
fi
done
zgrep works fine for me, only if all files inside is plain text.
it looks nothing works if the tgz file contains gzip files.
You can mount the TAR archive with ratarmount and then simply search for the pattern in the mounted view:
pip install --user ratarmount
ratarmount large-archive.tar mountpoint
grep -r '<pattern>' mountpoint/
This is much faster than iterating over each file and piping it to grep separately, especially for compressed TARs. Here are benchmark results in seconds for a 55 MiB uncompressed and 42 MiB compressed TAR archive containing 40 files:
Compression
Ratarmount
Bash Loop over tar -O
none
0.31 +- 0.01
0.55 +- 0.02
gzip
1.1 +- 0.1
13.5 +- 0.1
bzip2
1.2 +- 0.1
97.8 +- 0.2
Of course, these results are highly dependent on the archive size and how many files the archive contains. These test examples are pretty small because I didn't want to wait too long. But, they already exemplify the problem well enough. The more files there are, the longer it takes for tar -O to jump to the correct file. And for compressed archives, it will be quadratically slower the larger the archive size is because everything before the requested file has to be decompressed and each file is requested separately. Both of these problems are solved by ratarmount.
This is the code for benchmarking:
function checkFilesWithRatarmount()
{
local pattern=$1
local archive=$2
ratarmount "$archive" "$archive.mountpoint"
'grep' -r -l "$pattern" "$archive.mountpoint/"
}
function checkEachFileViaStdOut()
{
local pattern=$1
local archive=$2
tar --list --file "$archive" | while read -r file; do
if tar -x --file "$archive" -O -- "$file" | grep -q "$pattern"; then
echo "Found pattern in: $file"
fi
done
}
function createSampleTar()
{
for i in $( seq 40 ); do
head -c $(( 1024 * 1024 )) /dev/urandom | base64 > $i.dat
done
tar -czf "$1" [0-9]*.dat
}
createSampleTar myarchive.tar.gz
time checkEachFileViaStdOut ABCD myarchive.tar.gz
time checkFilesWithRatarmount ABCD myarchive.tar.gz
sleep 0.5s
fusermount -u myarchive.tar.gz.mountpoint
In my case the tarballs have a lot of tiny files and I want to know what archived file inside the tarball matches. zgrep is fast (less than one second) but doesn't provide the info I want, and tar --to-command grep is much, much slower (many minutes)1.
So I went the other direction and had zgrep tell me the byte offsets of the matches in the tarball and put that together with the list of offsets in the tarball of all archived files to find the matching archived files.
#!/bin/bash
set -e
set -o pipefail
function tar_offsets() {
# Get the byte offsets of all the files in a given tarball
# based on https://stackoverflow.com/a/49865044/60422
[ $# -eq 1 ]
tar -tvf "$1" -R | awk '
BEGIN{
getline;
f=$8;
s=$5;
}
{
offset = int($2) * 512 - and((s+511), compl(512)+1)
print offset,s,f;
f=$8;
s=$5;
}'
}
function tar_byte_offsets_to_files() {
[ $# -eq 1 ]
# Convert the search results of a tarball with byte offsets
# to search results with archived file name and offset, using
# the provided tar_offsets output (single pass, suitable for
# process substitution)
offsets_file="$1"
prev_offset=0
prev_offset_filename=""
IFS=' ' read -r last_offset last_len last_offset_filename < "$offsets_file"
while IFS=':' read -r search_result_offset match_text
do
while [ $last_offset -lt $search_result_offset ]; do
prev_offset=$last_offset
prev_offset_filename="$last_offset_filename"
IFS=' ' read -r last_offset last_len last_offset_filename < "$offsets_file"
# offsets increasing safeguard
[ $prev_offset -le $last_offset ]
done
# now last offset is the first file strictly after search result offset so prev offset is
# the one at or before it, and must be the one it is in
result_file_offset=$(( $search_result_offset - $prev_offset ))
echo "$prev_offset_filename:$result_file_offset:$match_text"
done
}
# Putting it together e.g.
zgrep -a --byte-offset "your search here" some.tgz | tar_byte_offsets_to_files <(tar_offsets some.tgz)
1 I'm running this in Git for Windows' minimal MSYS2 fork unixy environment, so it's possible that the launch overhead of grep is much much higher than on any kind of real Unix machine and would make `tar --to-command grep` good enough there; benchmark solutions for your own needs and platform situation before selecting.
I want to make UNIX script, which will automatically move my working directory files to newly created directories.
Example: In you dir you got files:
001-file.html,
001-file.rb,
002-file.html,
002-file.rb
And 2 files will be moved to ./NewDir/001-file and another 2 to ./NewDir/002-file
My problem is that after I get correct string from Unix commands I cannot assign it to variable.
Here is my code:
clear
echo "Starting script"
echo "Dir = "$(pwd)
read -p "Please enter count(max '999') of different file groups:" max_i
read -p "Enter new dir name:" outer_dir_name
for ((i=0; i<=$max_i;i++)) do
a1=$(($i/100))
a2=$((($i-$a1*100)/10))
a3=$(($i-($a2*10)-($a1*100)))
inner_dir_name=$((ls *[$a1][$a2][$a3]* 2>/dev/null | head -n 1 | cut -f1 -d"."))
echo $inner_dir_name
echo "--------------"
done
One pair of round parentheses is enough for command substitution.
inner_dir_name=$(ls *[$a1][$a2][$a3]* 2>/dev/null | head -n 1 | cut -f1 -d".")
It looks like you're going about the operation the hard way. I would probably do something like this, assuming that there are no spaces in the file names:
ls | sed 's/\..*$//' | sort -u |
while read prefix
do
mkdir -p $outer_dir_name/$prefix
mv $prefix.* $outer_dir_name/$prefix
done
The ls could be made more precise with:
ls [0-9][0-9][0-9]-file.*
If I was worried about blanks and other odd-ball characters in the file names, I'd have to use something more careful:
for file in [0-9][0-9][0-9]-file.*
do
prefix=${file%%.*}
[ -d "$outer_dir_name/$prefix" ] || mkdir -p "$outer_dir_name/$prefix"
mv "$file" "$outer_dir_name/$prefix"
done
This executes more mv commands, in general.
I have written a bash script that finds any executable files in our scripts directory, then performs a grep on the resulting files to display a description, if it was included in the file.
A "description" is identified in each file as a line beginning with "# DESC:"
For some reason, the script also includes the grep command that is being run (but only once). Does anyone know why this is?
Script and output shown below. Why does the second line in the output happen?
Script
#!/bin/bash
# Find any FILES that are EXECUTABLE in the SCRIPTS
# directory and display any description, if there is one
find /opt/scripts/. -perm -111 -type f -maxdepth 1 | while read line ;
do
file=$(basename "$line")
printf "\033[1m%10s\033[0m : " $file
grep "# DESC:" "$line" | cut -c 9-
done
Output
desc : Displays all the scripts and their descriptions
DESC:" "$line" | cut -c 9-
showhelp : Displays the script help file
test : Script to perform system testing
Reason
Presumably your grepping script is also in /opt/scripts?
So it finds itself, and finds the grep subject '#DESC' and prints that.
You could fix that by adding a # DESC line to the top of your grep script, and just outputting the first result found by each grep using 'grep -m1'
grep -m1 '# DESC' "$line" | cut -c 9-
<humour>Otherwise its just turtles all the way down... ;-) </humour>
Alternative Fix
You could also improve the grep by using a regular expression and anchoring to the beginning of the line:
egrep -m1 '^# DESC' "$line" | cut -c 9-