I am trying to split the output of the following code into two fields and insert it from the 3rd row of a csv file
#!/bin/bash
cid=`git log -n 1 --pretty=format:"%H"`
git diff-tree --no-commit-id --name-only -r $cid | xargs -I {} echo '\'{} | xargs -I {} md5sum > final.csv
Current Output comes as a single line ( need to be separated into fields)
title,Path
l34sdg232f00b434532196298ecf8427e /path/to/file
sg35s3456f00b204e98324998ecsdf3af /path/to/file
Expected Output
final.csv
title,Path
l34sdg232f00b434532196298ecf8427e,/path/to/file
sg35s3456f00b204e98324998ecsdf3af,/path/to/file
I am thinking of placing the output of the script in a third file and then reading that file line by line using awk. Not sure if that's the correct way to proceed.
Thanks in advance.
You seem to be overcomplicating things.
#!/bin/sh
cid=$(git log -n 1 --pretty=format:"%H")
git diff-tree --no-commit-id --name-only -r "$cid" |
xargs md5sum |
sed 's/ /,/' > final.csv
This simply replaces the two spaces in the md5sum output with a comma.
Because nothing here is Bash-specific, I changed the shebang to #!/bin/sh; obviously, still feel free to use Bash if you prefer.
I also switched from the obsolescent `backtick` syntax to modern $(command substitution) syntax.
If you absolutely require the CSV header on top, adding that in the sed script should be trivial. Generally, header lines are more of a nuisance than actually useful, so maybe don't.
This kind of does what you're asking:
#!/bin/bash
cid=$(git log -n 1 --pretty=format:"%H")
git diff-tree --no-commit-id --name-only -r "$cid" | while read -r path
do
md5sum "${path}"
done | awk 'BEGIN{printf "%s,%s\n", "title", "path";printf "\n"}{printf "%s,%s\n",$1,$2}' > final.csv
Related
I need to write a Bash script that achieve the following goals:
1) move the newest n pdf files from folder 1 to folder 2;
2) correctly handles files that could have spaces in file names;
3) output each file name in a specific position in a text file. (In my actual usage, I will use sed to put the file names in a specific position of an existing file.)
I tried to make an array of filenames and then move them and do text output in a loop. However, the following array cannot handle files with spaces in filename:
pdfs=($(find -name "$DOWNLOADS/*.pdf" -print0 | xargs -0 ls -1 -t | head -n$NUM))
Suppose a file has name "Filename with Space". What I get from the above array will have "with" and "Space" in separate array entries.
I am not sure how to avoid these words in the same filename being treated separately.
Can someone help me out?
Thanks!
-------------Update------------
Sorry for being vague on the third point as I thought I might be able to figure that out after achieving the first and second goals.
Basically, it is a text file that have a line start with "%comment" near the end and I will need to insert the filenames before that line in the format "file=PATH".
The PATH is the folder 2 that I have my pdfs moved to.
You can achieve this using mapfile in conjunction with gnu versions of find | sort | cut | head that have options to operate on NUL terminated filenames:
mapfile -d '' -t pdfs < <(find "$DOWNLOADS/*.pdf" -name 'file*' -printf '%T#:%p\0' |
sort -z -t : -rnk1 | cut -z -d : -f2- | head -z -n $NUM)
Commands used are:
mapfile -d '': To read array with NUL as delimiter
find: outputs each file's modification stamp in EPOCH + ":" + filename + NUL byte
sort: sorts reverse numerically on 1st field
cut: removes 1st field from output
head: outputs only first $NUM filenames
find downloads -name "*.pdf" -printf "%T# %p\0" |
sort -z -t' ' -k1 -n |
cut -z -d' ' -f2- |
tail -z -n 3
find all *.pdf files in downloads
for each file print it's modifition date %T with the format specifier # that means seconds since epoch with fractional part, then print space, filename and separate with \0
Sort the null separated stream using space as field separator using only first field using numerical sort
Remove the first field from the stream, ie. creation date, leaving only filenames.
Get the count of the newest files, in this example 3 newest files, by using tail. We could also do reverse sort and use head, no difference.
Don't use ls in scripts. ls is for nice formatted output. You could do xargs -0 stat --printf "%Y %n\0" which would basically move your script forward, as ls isn't meant to be used for scripts. Just that I couldn't make stat output fractional part of creation date.
As for the second part, we need to save the null delimetered list to a file
find downloads ........ >"$tmp"
and then:
str='%comment'
{
grep -B$((2**32)) -x "$str" "$out" | grep -v "$str"
# I don't know what you expect to do with newlines in filenames, but I guess you don't have those
cat "$tmp" | sed -z 's/^/file=/' | sed 's/\x0/\n/g'
grep -A$((2**32)) -x "$str" "$out"
} | sponge "$out"
where output is the output file name
assuming output file name is stored in variable "$out"
filter all lines before the %comment and remove the line %comment itself from the file
output each filename with file= on the beginning. I also substituted zeros for newlines.
the filter all lines after %comment including %comment itself
write the output for outfile. Remember to use a temporary file.
Don't use pdf=$(...) on null separated inputs. You can use mapfile to store that to an array, as other answers provided.
Then to move the files, do smth like
<"$tmp" xargs -0 -i mv {} "$outdir"
or faster, with a single move:
{ cat <"$tmp"; printf "%s\0" "$outdir"; } | xargs -0 mv
or alternatively:
<"$tmp" xargs -0 sh -c 'outdir="$1"; shift; mv "$#" "$outdir"' -- "$outdir"
Live example at turorialspoint.
I suppose following code will be close to what you want:
IFS=$'\n' pdfs=($(find -name "$DOWNLOADS/*.pdf" -print0 | xargs -0 -I ls -lt "{}" | tail -n +1 | head -n$NUM))
Then you can access the output through ${pdfs[0]}, ${pdfs[1]}, ...
Explanations
IFS=$'\n' makes the following line to be split only with "\n".
-I option for xargs tells xargs to substitute {} with filenames so it can be quoted as "{}".
tail -n +1 is a trick to suppress an error message saying "xargs: 'ls' terminated by signal 13".
Hope this helps.
Bash v4 has an option globstar, after enabling this option, we can use ** to match zero or more subdirectories.
mapfile is a built-in command, which is used for reading lines into an indexed array variable. -t option removes a trailing newline.
shopt -s globstar
mapfile -t pdffiles < <(ls -t1 **/*.pdf | head -n"$NUM")
typeset -p pdffiles
for f in "${pdffiles[#]}"; do
echo "==="
mv "${f}" /dest/path
sed "/^%comment/i${f}=/dest/path" a-text-file.txt
done
I am facing a problem with a script I need to use for log analysis; let me explain the question:
I have a gzipped file like:
5555_prova.log.gz
Inside the file there are mali lines of log like this one:
2018-06-12 03:34:31 95.245.15.135 GET /hls.playready.vod.mediasetpremium/farmunica/2018/06/218742_163f10da04c7d2/hlsrc/w12/21.ts
I need a script read the gzipped log file which is capable to output on the stdout a modified log line like this one:
5555 2018-06-12 03:34:31 95.245.15.135 GET /hls.playready.vod.mediasetpremium/farmunica/2018/06/218742_163f10da04c7d2/hlsrc/w12/21.ts
As you can see the line of log now start with the number read from the gzip file name.
I need this new line to feed a logstash data crunching chain.
I have tried with a script like this:
echo "./5555_prova.log.gz" | xargs -ISTR -t -r sh -c "gunzip -c STR | awk '{$0="5555 "$0}' "
this is not exactly what I need (the prefix is static and not captured with a regular expression from the file name) but even with this simplified version I receive an error:
sh -c gunzip -c ./5555_prova.log.gz | awk '{-bash=5555 -bash}'
-bash}' : -c: line 0: unexpected EOF while looking for matching `''
-bash}' : -c: line 1: syntax error: unexpected end of file
As you can see from the above output the $0 is no more the whole line passed via pipe to awk but is a strange -bash.
I need to use xargs because the list of gzipped file is fed the the command line from an another tool (i.e. an instantiated inotifywait listening to a directory where the files are written via ftp).
What I am missing? do you have some suggestions to point me in the right direction?
Regards,
S.
Trying to following the #Charles Duffy suggestion I have written this code:
#/bin/bash
#
# Usage: sendToLogstash.sh [pattern]
#
# Executes a command whenever files matching the pattern are closed in write
# mode or moved to. "{}" in the command is replaced with the matching filename (via xargs).
# Requires inotifywait from inotify-tools.
#
# For example,
#
# whenever.sh '/usr/local/myfiles/'
#
#
DIR="$1"
PATTERN="\.gz$"
script=$(cat <<'EOF'
awk -v filename="$file" 'BEGIN{split(filename,array,"_")}{$0=array[1] OFS $0} 1' < $(gunzip -dc "$DIR/$file")
EOF
)
inotifywait -q --format '%f' -m -r -e close_write -e moved_to "$DIR" \
| grep --line-buffered $PATTERN | xargs -I{} -r sh -c "file={}; $script"
But I got the error:
[root#ms-felogstash ~]# ./test.sh ./poppo
gzip: /1111_test.log.gz: No such file or directory
gzip: /1111_test.log.gz: No such file or directory
sh: $(gunzip -dc "$DIR/$file"): ambiguous redirect
Thanks for your help, I feel very lost writing bash scripts.
Regards,
S.
EDIT: Also in case you are dealing with multiple .gz files and want to print their content along with their file names(first column _ delimited) then following may help you.
for file in *.gz; do
awk -v filename="$file" 'BEGIN{split(filename,array,"_")}{$0=array[1] OFS $0} 1' <(gzip -dc "$file")
done
I haven't tested your code(couldn't completely understand also), so trying to give here a way like in case your code could pass file name to awk then it will be pretty simple to append the file's first digits like as follows(just an example).
awk 'FNR==1{split(FILENAME,array,"_")} {$0=array[1] OFS $0} 1' 5555_prova.log_file
So here I am taking FILENAME out of the box variable for awk(only in first line of file) and then by splitting it into array named array and then adding it in each line of the file.
Also wrap "gunzip -c STR this with ending " which seems to be missing before you pass its output to awk too.
NEVER, EVER use xargs -I with a string substituted into sh -c (or bash -c or any other context where that string is interpreted as code). This allows malicious filenames to run arbitrary commands -- think about what happens if someone runs touch $'$(rm -rf ~)\'$(rm -rf ~)\'.gz', and gets that file into your log.
Instead, let xargs append arguments after your script text, and write your script to iterate over / read those arguments as data, rather than having them substituted into code.
To show how to use xargs safely (well, safely if we assume that you've filtered out filenames with literal newlines):
# This way you don't need to escape the quotes in your script by hand
script=$(cat <<'EOF'
for arg; do gunzip -c <"$arg" | awk '{$0="5555 "$0}'; done
EOF
)
# if you **did** want to escape them by hand, it would look like this:
# script='for arg; do gunzip -c <"$arg" | awk '"'"'{$0="5555 "$0}'"'"'; done'
echo "./5555_prova.log.gz" | xargs -d $'\n' sh -c "$script" _
To be safer with all possible filenames, you'd instead use:
printf '%s\0' "./5555_prova.log.gz" | xargs -0 sh -c "$script" _
Note the use of NUL-delimited input (created with printf '%s\0') and xargs -0 to consume it.
I am interested in concatenate many files together based on the numeric number and also remove the first line.
e.g. chr1_smallfiles then chr2_smallfiles then chr3_smallfiles.... etc (each without the header)
Note that chr10_smallfiles needs to come after chr9_smallfiles -- that is, this needs to be numeric sort order.
When separate the two command awk and ls -v1, each does the job properly, but when put them together, it doesn't work. Please help thanks!
awk 'FNR>1' | ls -v1 chr*_smallfiles > bigfile
The issue is with the way that you're trying to pass the list of files to awk. At the moment, you're piping the output of awk to ls, which makes no sense.
Bear in mind that, as mentioned in the comments, ls is a tool for interactive use, and in general its output shouldn't be parsed.
If sorting weren't an issue, you could just use:
awk 'FNR > 1' chr*_smallfiles > bigfile
The shell will expand the glob chr*_smallfiles into a list of files, which are passed as arguments to awk. For each filename argument, all but the first line will be printed.
Since you want to sort the files, things aren't quite so simple. If you're sure the full range of files exist, just replace chr*_smallfiles with chr{1..99}_smallfiles in the original command.
Using some Bash-specific and GNU sort features, you can also achieve the sorting like this:
printf '%s\0' chr*_smallfiles | sort -z -n -k1.4 | xargs -0 awk 'FNR > 1' > bigfile
printf '%s\0' prints each filename followed by a null-byte
sort -z sorts records separated by null-bytes
-n -k1.4 does a numeric sort, starting from the 4th character (the numeric part of the filename)
xargs -0 passes the sorted, null-separated output as arguments to awk
Otherwise, if you want to go through the files in numerical order, and you're not sure whether all the files exist, then you can use a shell loop (although it'll be significantly slower than a single awk invocation):
for file in chr{1..99}_smallfiles; do # 99 is the maximum file number
[ -f "$file" ] || continue # skip missing files
awk 'FNR > 1' "$file"
done > bigfile
You can also use tail to concatenate all the files without header
tail -q -n+2 chr*_smallfiles > bigfile
In case you want to concatenate the files in a natural sort order as described in your quesition, you can pipe the result of ls -v1 to xargs using
ls -v1 chr*_smallfiles | xargs -d $'\n' tail -q -n+2 > bigfile
(Thanks to Charles Duffy) xargs -d $'\n' sets the delimiter to a newline \n in case the filename contains white spaces or quote characters
Using a bash 4 associative array to extract only the numeric substring of each filename; sort those individually; and then retrieve and concatenate the full names in the resulting order:
#!/usr/bin/env bash
case $BASH_VERSION in ''|[123].*) echo "Requires bash 4.0 or newer" >&2; exit 1;; esac
# when this is done, you'll have something like:
# files=( [1]=chr_smallfiles1.txt
# [10]=chr_smallfiles10.txt
# [9]=chr_smallfiles9.txt )
declare -A files=( )
for f in chr*_smallfiles.txt; do
files[${f//[![:digit:]]/}]=$f
done
# now, emit those indexes (1, 10, 9) to "sort -n -z" to sort them as numbers
# then read those numbers, look up the filenames associated, and pass to awk.
while read -r -d '' key; do
awk 'FNR > 1' <"${files[$key]}"
done < <(printf '%s\0' "${!files[#]}" | sort -n -z) >bigfile
You can do with a for loop like below, which is working for me:-
for file in chr*_smallfiles
do
tail +2 "$file" >> bigfile
done
How will it work? For loop read all the files from current directory with wild chard character * chr*_smallfiles and assign the file name to variable file and tail +2 $file will output all the lines of that file except the first line and append in file bigfile. So finally all files will be merged (accept the first line of each file) into one i.e. file bigfile.
Just for completeness, how about a sed solution?
for file in chr*_smallfiles
do
sed -n '2,$p' $file >> bigfile
done
Hope it helps!
I have two csv files a.csv and b.csv. I 'cut' one column from the a.csv file and now I want to grep for each one of the string from this column in second file b.csv.
Can someone please help me in writing a shell script for this?
You want the -f (and likely -F and possibly -w) flags to grep for this sort of task.
$ cut ... a.csv > tmp
$ grep -Ff tmp b.csv
You can do this without the temporary file on shells that support process substitution.
$ grep -Ff <(cut ... a.csv) b.csv
I have >100 files that I need to merge, but for each file the first line has to be removed. What is the most efficient way to do this under Unix? I suspect it's probably a command using cat and sed '1d'. All files have the same extension and are in the same folder, so we probably could use *.extension to point to the files. Many thanks!
Assuming your filenames are sorted in the order you want your files appended, you can use:
ls *.extension | xargs -n 1 tail -n +2
EDIT: After Sorin and Gilles comments about the possible dangers of piping ls output, you could use:
find . -name "*.extension" | xargs -n 1 tail -n +2
Everyone has to be complicated. This is really easy:
tail -q -n +2 file1 file2 file3
And so on. If you have a large number of files you can load them in to an array first:
list=(file1 file2 file3)
tail -q -n +2 "${list[#]}"
All the files with a given extension in the current directory?
list=(*.extension)
tail -q -n +2 "${list[#]}"
Or just
tail -q -n +2 *.extension
Just append each file after removing the first line.
#!/bin/bash
DEST=/tmp/out
FILES=space separated list of files
echo "" >$DEST
for FILE in $FILES
do
sed -e'1d' $FILE >>$DEST
done
tail outputs the last lines of a file. You can tell it how many lines to print, or how many lines to omit at the beginning (-n +N where N is the number of the first line to print, counting from 1 — so +2 omits one line). With GNU utilities (i.e. under Linux or Cygwin), FreeBSD or other systems that have the -q option:
tail -q -n +2 *.extension
tail prints a header before each file, and -q is not standard. If your implementation doesn't have it, or to be portable, you need to iterate over the files.
for x in *.extension; do tail -n +2 <"$x"; done
Alternatively, you can call Awk, which has a way to identify the first line of each file. This is likely to be faster if you have a lot of small files and slower if you have many large files.
awk 'FNR != 1' *.extension
ls -1 file*.txt | xargs nawk 'FNR!=1'