7zip - don't add to existing archive, create new archive only - bash

I'm creating a bash script that includes a function to compress a file to a new archive.
Basic example:
archive_path="/foo.7z"
target="/bar.txt"
7z a $archive_path $target
The problem I have is that I only ever want to create a new archive. If there are any existing archives at /foo.7z then bar.txt should not be added to it. Instead, either prompt the user to create a new name for the archive or just append a number on the end and create a new archive (e.g. /foo-1.7z).
I can't find anything in the documentation, on SO or a general internet search that explains how to do this natively with 7zip, which seems strange as I imagine it would be a very common requirement amongst users.
The only solution I can think of is to do this myself manually, something along the lines of:
archive_path="/foo.7z"
target="/bar.txt"
while [ -f $archive_path ]; do
read -p "'$archive_path' already exists. Enter new path for archive: " archive_path
done
7z a $archive_path $target
Is there any other way to do it natively with 7zip or do I need to handle this myself?

There doesn't seem to be any way of doing this with just 7z. While there is a "new archive" switch for the update flag, it will create both the new name and old one, plus you run into the problem of what happens when the new one exists as well. The best option is to do what you've done, or alternatively, something like this could work
arc='archive.7z'
new_arc=${arc}
target='file.txt'
while [[ -f ${new_arc} ]]; do
((i++))
new_arc=${arc%.*}${i}.${arc#*.}
done
7z a "${new_arc}" "${target}"
Which will rename the archive filename with an integer added before the extension (+1 each loop) until no file is found by that name. So you'll get archive.7z archive1.7z archive2.7z archive3.7z and so forth.

Related

How to recursively rename all files and folder including specific part of the filename with Windows Bash?

This has to be a duplicate but I have read and tried at least a dozen of Q&As here on SO, and I cannot get any of them working for my case.
Really hope this won't result in downvotes because of it.
So I'm on Windows (10) and have a Bash terminal that I want to use for my task. The MINGW64 one I downloaded when I started working with Git.
I would prefer the solution with this program, but will be perfectly happy with one in Command Prompt Terminal or even PowerShell.
I created a TemplateApp which is in C:\Apps\TemplateApp folder which has multiple folders and subfolders named TemplateApp or TemplateApp.something as well as a lot of files that have TemplateApp as a part of their name.
Could be:
TemplateApp.ext
TemplateApp.something.ext
something.TemplateApp.something.ext
Then I copied the uppermost folder to C:\Apps\TemplateApp - Copy and in turn renamed it to C:\Apps\ProductionApplication.
Now for the love of whomever, I cannot make any of the scripts I found on SO to work for my case, ie. to rename all the above mentioned files and folders by replacing TemplateApp with ProductionApplication.
Here is a bash function I wrote that I think does very much like what you are wanting to do.
function func_CreateSourceAndDestination() {
#
for (( i = 0 ; i < ${#files_syncSource[#]} ; i++ )) ; do
files_syncDestination[${i}]="${files_syncSource[${i}]#${directory_MusicLibraryRoot_source}}"
file_destinationPath="$( dirname -- "${directory_PMPRoot_destination}${files_syncDestination[${i}]}" )"
if [ ! -d "${file_destinationPath}" ] ; then
mkdir -p "${file_destinationPath}"
fi
rsync -rltDvPmz "${files_syncSource[${i}]}" "${directory_PMPRoot_destination}${files_syncDestination[${i}]}"
done
}
In my case I'm feeding into rsync for a source and a destination. I'm pulling all the file paths from an array that has been split into path segments. I have to make certain character substitutions for FAT and NTFS file systems. I do this recursively.
files_syncDestination[${i}]="${files_syncDestination[${i}]//\:/__}"
That's the magic. I load a new array with the character substituted. You could do the same with a loaded variable including your phrases for change.
files_syncDestination[${i}]="${files_syncDestination[${i}]//${targetPhrase}/${subPhrase}}"
After that change in the function, you could use rsync or cp or mv as you prefer to go from your source array to your destination array.
(The double-slash in the substitution makes the substitution global.)

Append part of folder name to all .gz within

I have a folder of data folders with the following structure:
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/data1.gz
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/data2.gz
sampleName2-randomNumbers/subfolder1/subfolder2/subfolder3/data1.gz
I want to modify all the data.gz within each sample folder by appending the sample name but not the random numbers to get:
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/sampleName1_data1.gz
sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/sampleName1_data2.gz
sampleName2-randomNumbers/subfolder1/subfolder2/subfolder3/sampleName2_data1.gz
It seems like this should be a simple mv for loop but I haven't been able to figure out how to pull part of a folder name using basename.
for i in */Data/Intensities/BaseCalls/*.gz; do mv $i "fastq""/"${i%%-*}"."`basename $i`; done
I couldn't figure out how to make the files stay in their original folder but for my purposes it works to have all the files go to a new folder ("fastq")
I suppose the "sampleName" part doesn't include dashes. In that case, use the standard pattern removal expansion: %%. That is, suppose your full path (relative to directory root) is stored in $path, just do ${path%%-*} to extract the "sampleName" part. Search for %% in the Bash Reference Manual for more details. As a simple example:
> path=sampleName1-randomNumbers/subfolder1/subfolder2/subfolder3/data1.gz
> echo ${path%%-*}
sampleName1
Otherwise, you could also use more advanced substring extraction based on regex. See BashFAQ/100 or Manipulating Strings from the TLDP Advanced Bash Scripting Guide.
Update. Here's the full command to perform the job described, and it is entirely native to the shell:
for file in */Data/Intensities/BaseCalls/*.gz; do
mv "$file" "${file%/*}/${file%%-*}_${file##*/}"
done

looping files with bash

I'm not very good in shell scripting and would like to ask you some question about looping of files big dataset: in my example I have alot of files with the common .pdb extension in the work dir. I need to loop all of them and i) to print name (w.o pdb extension) of each looped file and make some operation after this. E.g I need to make new dir for EACH file outside of the workdir with the name of each file and copy this file to that dir. Below you can see example of my code which are not worked- it's didn't show me the name of the file and didn't create folder for each of them. Please correct it and show me where I was wrong
#!/bin/bash
# set the work dir
receptors=./Receptors
for pdb in $receptors
do
filename=$(basename "$pdb")
echo "Processing of $filename file"
cd ..
mkdir ./docking_$filename
done
Many thanks for help,
Gleb
If all your files are contained within the .Repectors folder, you can loop each of them like so:
#!/bin/bash
for pdb in ./Receptors/*.pdb ; do
filename=$(basename "$pdb")
filenamenoextention=${filename/.pdb/}
mkdir "../docking_${filenamenoextention}"
done
Btw:
filenamenoextention=${filename/.pdb/}
Does a search replace in the variable $pdb. The syntax is ${myvariable/FOO/BAR}, and replaces all "FOO" substrings in $myvariable with "BAR". In your case it replaces ".pdb" with nothing, effectively removing it.
Alternatively, and safer (in case $filename contains multiple ".pdb"-substrings) is to remove the last four characters, like so: filenamenoextention=${filename:0:-4}
The syntax here is ${myvariable:s:e} where s and e correspond to numbers for the start and end index (not inclusive). It also let's you use negative numbers, which are offsets from the end. In other words: ${filename:0:-4} says: extract the substring from $filename starting from index 0, until you reach fourth-to-the-last character.
A few problems you have had with your script:
for pdb in ./Receptors loops only "./Receptors", and not each of the files within the folder.
When you change to parent directory (cd ..), you do so for the current shell session. This means that you keep going to the parent directory each time. Instead, you can specify the parent directory in the mkdir call. E.g mkdir ../thedir
You're looping over a one-item list, I think what you wanted to get is the list of the content of ./Receptors:
...
for pdb in $receptors/*
...
to list only file with .pdb extension use $receptors/*.pdb
So instead of just giving the path in for loop, give this:
for pdb in $receptors/*.pdb
To remove the extension :
set the variable ext to the extension you want to remove and using shell expansion operator "%" remove the extension from your filename eg:
ext=.pdb
filename=${filename%${ext}}
You can create the new directory without changing your current directory:
So to create a directory outside your current directory use the following command
mkdir ../docking_$filename
And to copy the file in the new directory use cp command
After correction
Your script should look like:
receptors=./Receptors
ext=.pdb
for pdb in $receptors/*.pdb
do
filename=$(basename "$pdb")
filename=${filename%${ext}}
echo "Processing of $filename file"
mkdir ../docking_$filename
cp $pdb ../docking_$filename
done

Create new files from existing ones but change their extension

In shell, what is a good way to duplicating files in an existing directory so that the result gives the same file but with a different extension? So taking something like:
path/view/blah.html.erb
And adding:
path/view/blah.mobile.erb
So that in the path/view directory, there would be:
path/view/blah.html.erb
path/view/blah.mobile.erb
I'd ideally like to perform this at a directory level and not create the file if it already has both extensions but that isn't necessary.
You can do:
cd /path/view/
for f in *.html.erb; do
cp "$f" "${f/.html./.mobile.}"
done
PS: This replaces first instance of .html. with .mobile., syntax is bash specific (let me know if you're not using BASH).

Adding a status (file integrity)check to a cbr cbz converting bash script

First post, so Hi! Let me start by saying I'm a total noob regarding programming. I understand very basic stuff, but when it comes to checking exit codes or what the adequate term is, I'm at a loss. Apparently my searchfoo is really weak in this area, I guess it's a question of terminology.
Thanks in advance for taking your time to reading this/answering my question!
Description: I found a script that converts/repack .cbr files to .cbz files. These files are basically your average rar and zip files, however renamed to another extension as they are used for (comic)book applications such as comicrack, qcomicbook and what not. Surprisingly enough there no cbr -> cbz converters out there. The advantages of .cbz is besides escaping the proprietary rar file format, that one can store the metadata from Comic Vine with e. g comictagger.
Issue: Sometimes the repackaging of the files doesn't end well and would hopefully be alleviated by a integrity check & another go. I modified said script slightly to use p7zip as it can both pack/unpack 7z, zip-files and some others, i. e great for options. p7zip can test the archive by:
7z t comicfile.cbz tmpworkingdir
I guess it's a matter of using if & else here(?) to check the integrity and then give it another go, if there are any error.
Question/tl;dr: What would be the "best"/adequate approach to add a integrity file check to the script below?
#!/bin/bash
#Source: http://comicrack.cyolito.com/forum/13-scripts/30013-cbr3cbz-rar-to-zip-conversion-for-linux
echo "Converting CBRs to CBZs"
# Set the "field separator" to something other than spaces/newlines" so that spaces
# in the file names don't mess things up. I'm using the pipe symbol ("|") as it is very
# unlikely to appear in a file name.
IFS="|"
# Set working directory where to create the temp dir. The user you are using must have permission
# to write into this directory.
# For performance reasons I'm using ram disk (/dev/shm/) in Ubuntu server.
WORKDIR="/dev/shm/"
# Set name for the temp dir. This directory will be created under WORDDIR
TEMPDIR="cbr2cbz"
# The script should be invoked as "cbr2cbz {directory}", where "{directory}" is the
# top-level directory to be searched. Just to be paranoid, if no directory is specified,
# then default to the current working directory ("."). Let's put the name of the
# directory into a shell variable called SOURCEDIR.
# Note: "$1" = "The first command line argument"
if test -z "$1"; then
SOURCEDIR=`pwd`
else
SOURCEDIR="$1"
fi
echo "Working from directory $SOURCEDIR"
# We need an empty directory to work in, so we'll create a temp directory here
cd "$WORKDIR"
mkdir "$TEMPDIR"
# and step into it
cd "$TEMPDIR"
# Now, execute a loop, based on a "find" command in the specified directory. The
# "-printf "$p|" will cause the file names to be separated by the pipe symbol, rather than
# the default newline. Note the backtics ("`") (the key above the tab key on US
# keyboards).
for CBRFILE in `find "$SOURCEDIR" -name "*.cbr" -printf "%p|while read line; do
# Now for the actual work. First, extract the base file name (without the extension)
# using the "basename" command. Warning: more backtics.
BASENAME=`basename $CBRFILE ".cbr"`
# And the directory path for that file, so we know where to put the finished ".cbz"
# file.
DIRNAME=`dirname $CBRFILE`
# Now, build the "new" file name,
NEWNAME="$BASENAME.cbz"
# We use RAR file's name to create folder for unpacked files
echo "Processing $CBRFILE"
mkdir "$BASENAME"
# and unpack the rar file into it
7z x "$CBRFILE" -O"$BASENAME"
cd "$BASENAME"
# Lets ensure the permissions allow us to pack everything
sudo chmod 777 -R ./*
# Put all the extracted files into new ".cbz" file
7z a -tzip -mx=9 "$NEWNAME" *
# And move it to the directory where we found the original ".cbr" file
mv "$NEWNAME" $DIRNAME/"$NEWNAME"
# Finally, "cd" back to the original working directory, and delete the temp directory
# created earlier.
cd ..
rm -r "$BASENAME"
# Delete the RAR file also
rm "$CBRFILE"
done
# At the end we cleanup by removing the temp folder from ram disk
cd ..
echo "Conversion Done"
rm -r "$TEMPDIR"
Oh the humanity, not posting more than two links before 10 reputation and I linked the crap out of OP.. [edit]ah.. mh-mmm.. there we go..
[edit 2] I removed unrar as an dependency and use p7zip instead, as it can extract rar-files.
You will need two checks:
7z t will test the integrity of the archive
You should also test the integrity of all the image files in the archive. You can use at tools like ImageMagick for this.
A simple test would be identify file but that might read only the header. I'd use convert file -resize 5x5 png:- > /dev/null
This scales the image down to 5x5 pixels, converts it to PNG and then pipes the result to /dev/null (discarding it). For the scaling, the whole image has to be read. If this command fails with an error, something is wrong with the image file.

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