I've been trying to get a script working to backup some files from one machine to another but have been running into an issue.
Basically what I want to do is copy two files, one .log and one (or more) .dmp. Their format is always as follows:
something_2022_01_24.log
something_2022_01_24.dmp
I want to do three things with these files:
find the second to last one .log file (i.e. something_2022_01_24.log is the latest,I want to find the one before that say something_2022_01_22.log)
get a substring with just the date (2022_01_22)
copy every .dmp that matches the date (i.e something_2022_01_24.dmp, something01_2022_01_24.dmp)
For the first one from what I could find the best way is to do: ls -t *.log | head-2 as it displays the second to last file created.
As for the second one I'm more at a loss because I'm not sure how to parse the output of the first command.
The third one I think I could manage with something of the sort:
[ -f "/var/www/my_folder/*$capturedate.dmp" ] && cp "/var/www/my_folder/*$capturedate.dmp" /tmp/
What do you guys think is there any way to do this? How can I compare the substring?
Thanks!
Would you please try the following:
#!/bin/bash
dir="/var/www/my_folder"
second=$(ls -t "$dir/"*.log | head -n 2 | tail -n 1)
if [[ $second =~ .*_([0-9]{4}_[0-9]{2}_[0-9]{2})\.log ]]; then
capturedate=${BASH_REMATCH[1]}
cp -p "$dir/"*"$capturedate".dmp /tmp
fi
second=$(ls -t "$dir"/*.log | head -n 2 | tail -n 1) will pick the
second to last log file. Please note it assumes that the timestamp
of the file is not modified since it is created and the filename
does not contain special characters such as a newline. This is an easy
solution and we may need more improvement for the robustness.
The regex .*_([0-9]{4}_[0-9]{2}_[0-9]{2})\.log will match the log
filename. It extracts the date substring (enclosed with the parentheses) and assigns the bash variable
${BASH_REMATCH[1]} to it.
Then the next cp command will do the job. Please be cateful
not to include the widlcard * within the double quotes so that
the wildcard is properly expanded.
FYI here are some alternatives to extract the date string.
With sed:
capturedate=$(sed -E 's/.*_([0-9]{4}_[0-9]{2}_[0-9]{2})\.log/\1/' <<< "$second")
With parameter expansion of bash (if something does not include underscores):
capturedate=${second%.log}
capturedate=${capturedate#*_}
With cut command (if something does not include underscores):
capturedate=$(cut -d_ -f2,3,4 <<< "${second%.log}")
Related
I have 2 files that I needed to grep in a separate file.
The two files are in this directory /var/list
TB.1234.txt
TB.135325.txt
I have to grep them in another file in another directory which is in /var/sup/. I used the command below:
for i in TB.*; do grep "$i" /var/sup/logs.txt; done
what I want to do is, if the result of the grep command contains the word "ERROR" the files which is found in /var/list will be moved to another directory /var/last.
for example I grep this file TB.1234.txt to /var/sup/logs.txt then the result is like this:
ERROR: TB.1234.txt
TB.1234.txt will be move to /var/last.
please help. I don't know how to construct the logic on how to move the files, I'm stuck in that I provided, I am also trying to use two greps in a for loop but I am encountering an error.
I am new in coding and really appreciates any help and suggestions. Thank you so much.
If you are asking how to move files which contain "ERROR", this should be extremely straightforward.
for file in TB.*; do
grep -q 'ERROR' "$file" &&
mv "$file" /var/last/
done
The notation this && that is a convenient shorthand for
if this; then
that
fi
The -q option to grep says to not print the matches, and quit as soon as you find one. Like all well-defined commands, grep sets its exit code to reflect whether it succeeded (the status is visible in $?, but usually you would not examine it directly; perhaps see also Why is testing ”$?” to see if a command succeeded or not, an anti-pattern?)
Your question is rather unclear, but if you want to find either of the matching files in a third file, perhaps something like
awk 'FNR==1 && (++n < ARGC-1) { a[n] = FILENAME; nextfile }
/ERROR/ { for(j=1; j<=n; ++j) if ($0 ~ a[j]) b[a[j]]++ }
END { for(f in b) print f }' TB*.txt /var/sup/logs.txt |
xargs -r mv -t /var/last/
This is somewhat inefficient in that it will read all the lines in the log file, and brittle in that it will only handle file names which do not contain newlines. (The latter restriction is probably unimportant here, as you are looking for file names which occur on the same line as the string "ERROR" in the first place.)
In some more detail, the Awk script collects the wildcard matches into the array a, then processes all lines in the last file, looking for ones with "ERROR" in them. On these lines, it checks if any of the file names in a are also found, and if so, also adds them to b. When all lines have been processed, print the entries in b, which are then piped to a simple shell command to move them.
xargs is a neat command to read some arguments from standard input, and run another command with those arguments added to its command line. The -r option says to not run the other command if there are no arguments.
(mv -t is a GNU extension; it's convenient, but not crucial to have here. If you need portable code, you could replace xargs with a simple while read -r loop.)
The FNR==1 condition requires that the input files are non-empty.
If the text file is small, or you expect a match near its beginning most of the time, perhaps just live with grepping it multiple times:
for file in TB.*; do
grep -Eq "ERROR.*$file|$file.*ERROR" /var/sup/logs.txt &&
mv "$file" /var/last/
done
Notice how we now need double quotes, not single, around the regular expression so that the variable $file gets substituted in the string.
grep has an -l switch, showing only the filename of the file which contains a pattern. It should not be too difficult to write something like (this is pseudocode, it won't work, it's just for giving you an idea):
if $(grep -l "ERROR" <directory> | wc -l) > 0
then foreach (f in $(grep -l "ERROR")
do cp f <destination>
end if
The wc -l is to check if there are any files which contain the word "ERROR". If not, nothing needs to be done.
Edit after Tripleee's comment:
My proposal can be simplified as:
if grep -lq "ERROR" TB.*;
then foreach (f in $(grep -l "ERROR")
do cp f <destination>
end if
Edit after Tripleee's second comment:
This is even shorter:
for f in $(grep -l "ERROR" TB.*);
do cp "$f" destination;
done
I have over 100 files in a directory with format xxx_1_sequence.fastq.gz and xxx_2_sequence.fastq.gz
The goal is to create a TAB file with 3 columns in this format:
xxx ---> xxx_1_sequence.fastq.gz ---> xxx_2_sequence.fastq.gz
where ---> is a tab.
I was thinking of creating a for loop or maybe using string manipulation in order to achieve this. My knowledge is rudimentary at this stage, so any help would be much appreciated.
Would you please try the following:
shopt -s extglob # enable extended pattern matching
suffix="sequence.fastq.gz"
for f in !(*"$suffix"); do # files which does not match the pattern
if [[ -f ${f}_1_$suffix && -f ${f}_2_$suffix ]]; then
# check the existence of the files just in case
printf "%s\t%s\t%s\n" "$f" "${f}_1_$suffix" "${f}_2_$suffix"
fi
done
If your files are in a directory called files:
paste -d '\t' \
<(printf "%s\n" files/*_1_sequence.fastq.gz | sort) \
<(printf "%s\n" files/*_2_sequence.fastq.gz | sort) \
| sed 's/\(.*\)_1_sequence.fastq.gz/\1\t\1_1_sequence.fastq.gz/' \
> out.tsv
Explanation:
printf "%s\n" will print every argument in a new line. So:
printf "%s\n" files/*_1_sequence.fastq.gz | sort
prints a sorted list of the first type of files (the second column in your output). And of course it's symmetrical with *_2_sequence.fastq.gz (the third column).
(We probably don't need the sort part, but it helps clarify the intention.)
The syntax <(some shell command) runs some shell command, puts its output into a temporary input file, and passes that file as an argument. You can see the temporary file like so:
$ echo <(echo a) <(echo b)
/dev/fd/63 /dev/fd/62
So we are passing 2 (temporary) files to paste. If each output file has N lines, then paste outputs N lines, where line number K is a concatenation of line K of each of the files, in order.
For example, if line 4 of the first file is hello and line 4 if the second file is world, paste will have hello\tworld as line 4 of the output. But instead of trusting the default, we're setting the delimiter to TAB explicitly with -d '\t'.
That gives us the last 2 columns of our tab-separated-values file, but the first column is the * part of *_1_sequence.fastq.gz, which is where sed comes in.
We tell sed to replace \(.*\)_1_sequence.fastq.gz with \1\t\1_1_sequence.fastq.gz. .* will match anything, and \(some-pattern\) tells sed to remember the text that matched the pattern.
The first parentheses in sed's regex are can be read back into the replacement pattern as \1, which is why we have \1_1_sequence.fastq.gz in the replacement pattern.
But now we can also use \1 to create the first column of our tsv, which is why we have \1\t.
Thankyou for the help guys- I was thrown into a coding position a week ago with no prior experience and have been struggling.
I ended up with this printf "%s\n" *_1_sequence.fastq.gz | sort | sed 's/\(.*\)_1_sequence.fastq.gz/\1\t\1_1_sequence.fastq.gz\t\1_2_sequence.fastq.gz/ ' > NULLARBORformat.tab
and it does the job perfectly!
Lets say I have a folder of .txt files that have a dd-MM-yyyy_HH-mm-ss time followed by _name.txt. I want to be able to sort by name first then time after. Example:
BEFORE
15-2-2010_10-01-55_greg.txt
10-2-1999_10-01-55_greg.txt
10-2-1999_10-01-55_jason.txt
AFTER
greg_1_10-2-1999_10-01-55
greg_2_15-2-2010_10-01-55
jason_1_10-2-1999_10-01-55
Edit: Apologies, from my "cp" line I was meant to copy them into another directory with a different name to them.
Something I tried to do is make a copy with the count, but it doesn't sort the files with the same name properly in terms of dates:
cd data/unfilteredNames
for filename in *.txt; do
n=${filename%.*}
n=${filename##*_}
filteredName=${n%.*}
count=0
find . -type f -name "*_$n" | while read name; do
count=$(($count+1))
cp -p $name ../filteredNames/"$filteredName"_"$count"
done
done
Not sure that the renaming of files is one of your expectation. At least for only sorting file name, you don't need to.
You can do this by only using GNU sort command:
sort -t- -k5.4 -k3.1,3.4 -k2.1,2.1 -k1.1,1.2 -k3.6,3.13 <(printf "%s\n" *.txt)
-t sets the field separator to a dash -.
-k enables to sort based on fields. As explained in man sort page, the syntax is -k<start>,<stop> where <start> or is composed of <field number>.<position>. Adding several -k option to the command allows to sort on multiple fields; the first in he command line having more precedence than the other.
For example, the first -k5.4 tells to sort based on the 5th fields with an offset of 4 characters. There isn't a stop field because this is the end of the filename.
The -k3.1,3.4 option sorts based on the 3rd field starting from offset 1 to 4.
The same principle applies to other -k options.
In your example the month field only has 1 digit. If you have files with a month coded with 2 digits, you might want to pad with 0 all month filenames. This can be done by adding to the printf statement this <(... | sed 's/-0\?\([0-9]\)/-0\1/') and change the -k 2.1,2.1 by -k2.1,2.2.
Lets say i have multiple filesnames e.g. R014-20171109-1159.log.20171109_1159.
I want to create a shell script which creates for every given date a folder and moves the files matching the date to it.
Is this possible?
For the example a folder "20171109" should be created and has the file "R014-20171109-1159.log.20171109_1159" on it.
Thanks
This is a typical application of a for-loop in bash to iterate thru files.
At the same time, this solution utilizes GNU [ shell param substitution ].
for file in /path/to/files/*\.log\.*
do
foldername=${file#*-}
foldername=${foldername%%-*}
mkdir -p "${foldername}" # -p suppress errors if folder already exists
[ $? -eq 0 ] && mv "${file}" "${foldername}" # check last cmd status and move
done
Since you want to write a shell script, use commands. To get date, use cut cmd like ex:
cat 1.txt
R014-20171109-1159.log.20171109_1159
cat 1.txt | cut -d "-" -f2
Output
20171109
is your date and create folder. This way you can loop and create as many folders as you want
Its actually quite easy(my Bash syntax might be a bit off) -
for f in /path/to/your/files*; do
## Check if the glob gets expanded to existing files.
## If not, f here will be exactly the pattern above
## and the exists test will evaluate to false.
[ -e "$f" ] && echo $f > #grep the file name for "*.log."
#and extract 8 charecters after "*.log." .
#Next check if a folder exists already with the name of 8 charecters.
#If not { create}
#else just move the file to that folder path
break
done
Main idea is from this post link. Sorry for not providing the actual code as i havent worked anytime recently on Bash
Below commands can be put in script to achieve this,
Assign a variable with current date as below ( use --date='n day ago' option if need to have an older date).
if need to get it from File name itself, get files in a loop then use cut command to get the date string,
dirVar=$(date +%Y%m%d) --> for current day,
dirVar=$(date +%Y%m%d --date='1 day ago') --> for yesterday,
dirVar=$(echo $fileName | cut -c6-13) or
dirVar=$(echo $fileName | cut -d- -f2) --> to get from $fileName
Create directory with the variable value as below, (-p : create directory if doesn't exist.)
mkdir -p ${dirVar}
Move files to directory to the directory with below line,
mv *log.${dirVar}* ${dirVar}/
I use DJing software on linux (xwax) which uses a 'scanning' script (visible here) that compiles all the music files available to the software and outputs a string which contains a path to the filename and then the title of the mp3. For example, if it scans path-to-mp3/Artist - Test.mp3, it will spit out a string like so:
path-to-mp3/Artist - Test.mp3[tab]Artist - Test
I have tagged all my mp3s with BPM information via the id3v2 tool and have a commandline method for extracting that information as follows:
id3v2 -l name-of-mp3.mp3 | grep TBPM | cut -D: -f2
That spits out JUST the numerical BPM to me. What I'd like to do is prepend the BPM number from the above command as part of the xwax scanning script, but I'm not sure how to insert that command in the midst of the script. What I'd want it to generate is:
path-to-mp3/Artist - Test.mp3[tab][bpm]Artist - Test
Any ideas?
It's not clear to me where in that script you want to insert the BPM number, but the idea is this:
To embed the output of one command into the arguments of another, you can use the "command substitution" notation `...` or $(...). For example, this:
rm $(echo abcd)
runs the command echo abcd and substitutes its output (abcd) into the overall command; so that's equivalent to just rm abcd. It will remove the file named abcd.
The above doesn't work inside single-quotes. If you want, you can just put it outside quotes, as I did in the above example; but it's generally safer to put it inside double-quotes (so as to prevent some unwanted postprocessing). Either of these:
rm "$(echo abcd)"
rm "a$(echo bc)d"
will remove the file named abcd.
In your case, you need to embed the command substitution into the middle of an argument that's mostly single-quoted. You can do that by simply putting the single-quoted strings and double-quoted strings right next to each other with no space in between, so that Bash will combine them into a single argument. (This also works with unquoted strings.) For example, either of these:
rm a"$(echo bc)"d
rm 'a'"$(echo bc)"'d'
will remove the file named abcd.
Edited to add: O.K., I think I understand what you're trying to do. You have a command that either (1) outputs out all the files in a specified directory (and any subdirectories and so on), one per line, or (2) outputs the contents of a file, where the contents of that file is a list of files, one per line. So in either case, it's outputting a list of files, one per line. And you're piping that list into this command:
sed -n '
{
# /[<num>[.]] <artist> - <title>.ext
s:/\([0-9]\+.\? \+\)\?\([^/]*\) \+- \+\([^/]*\)\.[A-Z0-9]*$:\0\t\2\t\3:pi
t
# /<artist> - <album>[/(Disc|Side) <name>]/[<ABnum>[.]] <title>.ext
s:/\([^/]*\) \+- \+\([^/]*\)\(/\(disc\|side\) [0-9A-Z][^/]*\)\?/\([A-H]\?[A0-9]\?[0-9].\? \+\)\?\([^/]*\)\.[A-Z0-9]*$:\0\t\1\t\6:pi
t
# /[<ABnum>[.]] <name>.ext
s:/\([A-H]\?[A0-9]\?[0-9].\? \+\)\?\([^/]*\)\.[A-Z0-9]*$:\0\t\t\2:pi
}
'
which runs a sed script over that list. What you want is for all of the replacement-strings to change from \0\t... to \0\tBPM\t..., where BPM is the BPM number computed from your command. Right? And you need to compute that BPM number separately for each file, so instead of relying on seds implicit line-by-line looping, you need to handle the looping yourself, and process one line at a time. Right?
So, you should change the above command to this:
while read -r LINE ; do # loop over the lines, saving each one as "$LINE"
BPM=$(id3v2 -l "$LINE" | grep TBPM | cut -D: -f2) # save BPM as "$BPM"
sed -n '
{
# /[<num>[.]] <artist> - <title>.ext
s:/\([0-9]\+.\? \+\)\?\([^/]*\) \+- \+\([^/]*\)\.[A-Z0-9]*$:\0\t'"$BPM"'\t\2\t\3:pi
t
# /<artist> - <album>[/(Disc|Side) <name>]/[<ABnum>[.]] <title>.ext
s:/\([^/]*\) \+- \+\([^/]*\)\(/\(disc\|side\) [0-9A-Z][^/]*\)\?/\([A-H]\?[A0-9]\?[0-9].\? \+\)\?\([^/]*\)\.[A-Z0-9]*$:\0\t'"$BPM"'\t\1\t\6:pi
t
# /[<ABnum>[.]] <name>.ext
s:/\([A-H]\?[A0-9]\?[0-9].\? \+\)\?\([^/]*\)\.[A-Z0-9]*$:\0\t'"$BPM"'\t\t\2:pi
}
' <<<"$LINE" # take $LINE as input, rather than reading more lines
done
(where the only change to the sed script itself was to insert '"$BPM"'\t in a few places to switch from single-quoting to double-quoting, then insert the BPM, then switch back to single-quoting and add a tab).