I have multiple zip files inside a folder and another zip file exists within each of these zip folders. I would like to unzip the first and the second zip folders and create their own directories.
Here is the structure
Workspace
customer1.zip
application/app1.zip
customer2.zip
application/app2.zip
customer3.zip
application/app3.zip
customer4.zip
application/app4.zip
As shown above, inside the Workspace, we have multiple zip files, and within each of these zip files, there exists another zip file application/app.zip. I would like to unzip app1, app2, app3, and app4 into new folders. I would like to use the same name as the parent zip folder to place each of the results. I tried the following answers but this unzips just the first folder.
sh '''
for zipfile in ${WORKSPACE}/*.zip; do
exdir="${zipfile%.zip}"
mkdir "$exdir"
unzip -d "$exdir" "$zipfile"
done
'''
Btw, I am running this command inside my Jenkins pipeline.
No idea about Jenkins but what you need is a recursive function.
recursiveUnzip.sh
#!/bin/dash
recursiveUnzip () { # $1=directory
local path="$(realpath "$1")"
for file in "$path"/*; do
if [ -d "$file" ]; then
recursiveUnzip "$file"
elif [ -f "$file" -a "${file##*.}" = 'zip' ]; then
# unzip -d "${file%.zip}" "$file" # variation 1
unzip -d "${file%/*}" "$file" # variation 2
rm -f "$file" # comment this if you want to keep the zip files.
recursiveUnzip "${file%.zip}"
fi
done
}
recursiveUnzip "$1"
Then call the script like this
./recursiveUnzip.sh <directory>
In you case, probably like this
./recursiveUnzip.sh "$WORKSPACE"
I am running numerous simulations on a remote server (via ssh). The outcomes of these simulations are stored as .tar archives in an archive directory on this remote server.
What I would like to do, is write a bash script which connects to the remote server via ssh and extracts the required output files from each .tar archive into separate folders on my local hard drive.
These folders should have the same name as the .tar file from which the files come (To give an example, say the output of simulation 1 is stored in the archive S1.tar on the remote server, I want all '.dat' and '.def' files within this .tar archive to be extracted to a directory S1 on my local drive).
For the extraction itself, I was trying:
for f in *.tar; do
(
mkdir ../${f%.tar}
tar -x -f "$f" -C ../${f%.tar} "*.dat" "*.def"
)
done
wait
Every .tar file is around 1GB and there is a lot of them. So downloading everything takes too much time, which is why I only want to extract the necessary files (see the extensions in the code above).
Now the code works perfectly when I have the .tar files on my local drive. However, what I can't figure out is how I can do it without first having to download all the .tar archives from the server.
When I first connect to the remote server via ssh username#host, then the terminal stops with the script and just connects to the server.
Btw I am doing this in VS Code and running the script through terminal on my MacBook.
I hope I have described it clear enough. Thanks for the help!
Stream the results of tar back with filenames via SSH
To get the data you wish to retrieve from .tar files, you'll need to pass the results of tar to a string of commands with the --to-command option. In the example below, we'll run three commands.
# Send the files name back to your shell
echo $TAR_FILENAME
# Send the contents of the file back
cat /dev/stdin
# Send EOF (Ctrl+d) back (note: since we're already in a $'' we don't use the $ again)
echo '\004'
Once the information is captured in your shell, we can start to process the data. This is a three-step process.
Get the file's name
note that, in this code, we aren't handling directories at all (simply stripping them away; i.e. dir/1.dat -> 1.dat)
you can write code to create directories for the file by replacing the forward slashes / with spaces and iterating over each directory name but that seems out-of-scope for this.
Check for the EOF (end-of-file)
Add content to file
# Get the files via ssh and tar
files=$(ssh -n <user#server> $'tar -xf <tar-file> --wildcards \'*\' --to-command=$\'echo $TAR_FILENAME; cat /dev/stdin; echo \'\004\'\'')
# Keeps track of what state we're in (filename or content)
state="filename"
filename=""
# Each line is one of these:
# - file's name
# - file's data
# - EOF
while read line; do
if [[ $state == "filename" ]]; then
filename=${line/*\//}
touch $filename
echo "Copying: $filename"
state="content"
elif [[ $state == "content" ]]; then
# look for EOF (ctrl+d)
if [[ $line == $'\004' ]]; then
filename=""
state="filename"
else
# append data to file
echo $line >> <output-folder>/$filename
fi
fi
# Double quotes here are very important
done < <(echo -e "$files")
Alternative: tar + scp
If the above example seems overly complex for what it's doing, it is. An alternative that touches the disk more and requires to separate ssh connections would be to extract the files you need from your .tar file to a folder and scp that folder back to your workstation.
ssh -n <username>#<server> 'mkdir output/; tar -C output/ -xf <tar-file> --wildcards *.dat *.def'
scp -r <username>#<server>:output/ ./
The breakdown
First, we'll make a place to keep our outputted files. You can skip this if you already know the folder they'll be in.
mkdir output/
Then, we'll extract the matching files to this folder we created (if you don't want them to be in a different folder remove the -C output/ option).
tar -C output/ -xf <tar-file> --wildcards *.dat *.def
Lastly, now that we're running commands on our machine again, we can run scp to reconnect to the remote machine and pull the files back.
scp -r <username>#<server>:output/ ./
Am trying to grep pattern from dozen files .tar.gz but its very slow
am using
tar -ztf file.tar.gz | while read FILENAME
do
if tar -zxf file.tar.gz "$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 will download a lot of files from a server with wget. But the files should only be stored when the file name is in a given list. Otherwise wget should stop getting these file and start the next one.
I tried the following:
#!/bin/bash
etsienURL="http://www.etsi.org/deliver/etsi_en"
etsitsURL="http://www.etsi.org/deliver/etsi_ts"
listOfStandards=("en_302571" "en_3023630401" "en_3023630501" "en_3023630601" "en_30263702" "en_30263703" "en_302663" "en_302931" "ts_10153901" "ts_10153903" "ts_1026360501" "ts_1027331" "ts_10286801" "ts_10287103" "ts_10289401" "ts_10289402" "ts_102940" "ts_102941" "ts_102942" "ts_102943" "ts_103097" "ts_10324601" "ts_10324603")
wget -r -nd -nc -e robots=off -A.pdf $etsienURL
wget -r -nd -nc -e robots=off -A.pdf $etsitsURL
for file in *.pdf
do
relevant=false
for t in "${listOfStandards[#]}"
do
if [[ $(basename "$file" .pdf) == *"$t"* ]]
then
relevant=true
break
fi
done
if [ $relevant == false ]
then
rm "$file"
fi
done
With this code all files will be downloaded. After the download the script checks, if the filename or a part of this is in the list. Otherwise the script delete the file. But this cost a lot of disc space. I will only download a file, if the file name contains one if the list items.
Perhaps somebody can help to find a solution.
Found the solution. I forgot the --no-parent tag for wget.
I want to unzip file automatically after being uploaded into server.
I'm not experienced in bash but I've tried this
for file in *.zip
do
unzip -P pcp9100 "$file" -d ./
done
It's not working as I want.
Okay, assuming you want this to be continuously done in a loop, you can do something like:
while true; do
for file in *.zip; do
unzip -P pcp9100 "${file}" -d ./
rm "${file}"
done
sleep 3
done
Of course there are several things that can go wrong here.
File has an incorrect password
The file inside is also a zip file and does not have the same password
Permissions are incorrect
First, your permissions should be correct. Secondly, you can create a directory called "ExtractedFiles" and one called "IncorrectPasswords" which you can do something like:
while true; do
for file in *.zip; do
unzip -P pcp9100 "${file}" -d ./ExtractedFiles || mv "${file}" ./IncorrectPasswords
rm "${file}"
done
sleep 3
done