I have about 700 text files that consist of config output which uses various special characters. I am using this script to remove the special characters so I can then run a different script referencing an SED file to remove the commands that should be there leaving what should not be in the config.
I got the below from Remove all special characters and case from string in bash but am hitting a wall.
When I run the script it continues to loop and writes the script into the output file. Ideally, it just takes out the special characters and creates a new file with the updated information. I have not gotten to the point to remove the previous text file since it probably wont be needed. Any insight is greatly appreciated.
for file in *.txt for file in *.txt
do
cat * | tr -cd '[:alnum:]\n\r' | tr '[:upper:]' '[:lower:]' >> "$file" >> "$file".new_file.txt
done
A less-broken version of this might look like:
#!/usr/bin/env bash
for file in *.txt; do
[[ $file = *.new_file.txt ]] && continue ## skip files created by this same script
tr -cd '[:alnum:]\n\r' <"$file" \
| tr '[:upper:]' '[:lower:]' \
>> "$file".new_file.txt
done
Note:
We're referring to the "$file" variable being set by for.
We aren't using cat. It slows your script down with no compensating benefits whatsoever. Instead, using <"$file" redirects from the specific input file being iterated over at present.
We're skipping files that already have .new_file.txt extensions.
We only have one output redirection (to the new_file.txt version of the file; you can't safely write to the file you're using as input in the same pipeline).
Using GNU sed:
sed -i 's/[^[:alnum:]\n\r]//g;s/./\l&/g' *.txt
Related
I have these files
NotRequired.txt (having lines which need to be remove)
Need2CleanSED.txt (big file , need to clean)
Need2CleanGRP.txt (big file , need to clean)
content:
more NotRequired.txt
[abc-xyz_pqr-pe2_123]
[lon-abc-tkt_1202]
[wat-7600-1_414]
[indo-pak_isu-5_761]
I am reading above file and want to remove lines from Need2Clean???.txt, trying via SED and GREP but no success.
myFile="NotRequired.txt"
while IFS= read -r HKline
do
sed -i '/$HKline/d' Need2CleanSED.txt
done < "$myFile"
myFile="NotRequired.txt"
while IFS= read -r HKline
do
grep -vE \"$HKline\" Need2CleanGRP.txt > Need2CleanGRP.txt
done < "$myFile"
Looks as if the Variable and characters [] making some problem.
What you're doing is extremely inefficient and error prone. Just do this:
grep -vF -f NotRequired.txt Need2CleanGRP.txt > tmp &&
mv tmp Need2CleanGRP.txt
Thanks to grep -F the above treats each line of NotRequired.txt as a string rather than a regexp so you don't have to worry about escaping RE metachars like [ and you don't need to wrap it in a shell loop - that one command will remove all undesirable lines in one execution of grep.
Never do command file > file btw as the shell might decide to execute the > file first and so empty file before command gets a chance to read it! Always do command file > tmp && mv tmp file instead.
Your assumption is correct. The [...] construct looks for any characters in that set, so you have to preface ("escape") them with \. The easiest way is to do that in your original file:
sed -i -e 's:\[:\\[:' -e 's:\]:\\]:' "${myFile}"
If you don't like that, you can probably put the sed command in where you're directing the file in:
done < replace.txt|sed -e 's:\[:\\[:' -e 's:\]:\\]:'
Finally, you can use sed on each HKline variable:
HKline=$( echo $HKline | sed -e 's:\[:\\[:' -e 's:\]:\\]:' )
try gnu sed:
sed -Ez 's/\n/\|/g;s!\[!\\[!g;s!\]!\\]!g; s!(.*).!/\1/d!' NotRequired.txt| sed -Ef - Need2CleanSED.txt
Two sed process are chained into one by shell pipe
NotRequired.txt is 'slurped' by sed -z all at once and substituted its \n and [ meta-char with | and \[ respectively of which the 2nd process uses it as regex script for the input file, ie. Need2CleanSED.txt. 1st process output;
/\[abc-xyz_pqr-pe2_123\]|\[lon-abc-tkt_1202\]|\[wat-7600-1_414\]|\[indo-pak_isu-5_761\]/d
add -u ie. unbuffered, option to evade from batch process, sort of direct i/o
I have a bash script that iterates over a list of links, curl's down an html page per link, greps for a particular string format (syntax is: CVE-####-####), removes the surrounding html tags (this is a consistent format, no special case handling necessary), searches a changelog file for the resulting string ID, and finally does stuff based on whether the string ID was found or not.
The found string ID is set as a variable. The issue is that when grepping for the variable there are no results, even though I positively know there should be for some of the ID's. Here is the relevant portion of the script:
for link in $(cat links.txt); do
curl -s "$link" | grep 'CVE-' | sed 's/<[^>]*>//g' | while read cve; do
echo "$cve"
grep "$cve" ./changelog.txt
done
done
If I hardcode a known ID in the grep command, the script finds the ID and returns things as expected. I've tried many variations of grepping on this variable (e.g. exporting it and doing command expansion, cat'ing the changelog and piping to grep, setting variable directly via command expansion of the curl chain, single and double quotes surrounding variables, half a dozen other things).
Am I missing something nuanced with the outputted variable from the curl | grep | sed chain? When it is echo'd to stdout or >> to a file, things look fine (a single ID with no odd characters or carriage returns etc.).
Any hints or alternate solutions would be much appreciated. Thanks!
FYI:
OSX:$bash --version
GNU bash, version 3.2.57(1)-release (x86_64-apple-darwin14)
Edit:
The html file that I was curl'ing was chock full of carriage returns. Running the script with set -x was helpful because it revealed the true string being grepped: $'CVE-2011-2716\r'.
+ read -r link
+ curl -s http://localhost:8080/link1.html
+ sed -n '/CVE-/s/<[^>]*>//gp'
+ read -r cve
+ grep -q -F $'CVE-2011-2716\r' ./kernelChangelog.txt
Also investigating from another angle, opening the curled file in vim showed ^M and doing a printf %s "$cve" | xxd also showed the carriage return hex code 0d appended to the grep'd variable. Relying on 'echo' stdout was a wrong way of diagnosing things. Writing a simple html page with a valid CVE-####-####, but then adding a carriage return (in vim insert mode just type ctrl-v ctrl-m to insert the carriage return) will create a sample file that fails with the original script snippet above.
This is pretty standard string sanitization stuff that I should have figured out. The solution is to remove carriage returns, piping to tr -d '\r' is one method of doing that. I'm not sure there is a specific duplicate on SO for this series of steps, but in any case here is my now working script:
while read -r link; do
curl -s "$link" | sed -n '/CVE-/s/<[^>]*>//gp' | tr -d '\r' | while read -r cve; do
if grep -q -F "$cve" ./changelog.txt; then
echo "FOUND: $cve";
else
echo "NOT FOUND: $cve";
fi;
done
done < links.txt
HTML files can contain carriage returns at the ends of lines, you need to filter those out.
curl -s "$link" | sed -n '/CVE-/s/<[^>]*>//gp' | tr -d '\r' | while read cve; do
Notice that there's no need to use grep, you can use a regular expression filter in the sed command. (You can also use the tr command in sed to remove characters, but doing this for \r is cumbersome, so I piped to tr instead).
It should look like this:
# First: Care about quoting your variables!
# Use read to read the file line by line
while read -r link ; do
# No grep required. sed can do that.
curl -s "$link" | sed -n '/CVE-/s/<[^>]*>//gp' | while read -r cve; do
echo "$cve"
# grep -F searches for fixed strings instead of patterns
grep -F "$cve" ./changelog.txt
done
done < links.txt
I have a bash script which parses a file line by line, extracts the date using a cut command and then makes a folder using that date. However, it seems like my variables are not being populated properly. Do I have a syntax issue? Any help or direction to external resources is very appreciated.
#!/bin/bash
ls | grep .mp3 | cut -d '.' -f 1 > filestobemoved
cat filestobemoved | while read line
do
varYear= $line | cut -d '_' -f 3
varMonth= $line | cut -d '_' -f 4
varDay= $line | cut -d '_' -f 5
echo $varMonth
mkdir $varMonth'_'$varDay'_'$varYear
cp ./$line'.mp3' ./$varMonth'_'$varDay'_'$varYear/$line'.mp3'
done
You have many errors and non-recommended practices in your code. Try the following:
for f in *.mp3; do
f=${f%%.*}
IFS=_ read _ _ varYear varMonth varDay <<< "$f"
echo $varMonth
mkdir -p "${varMonth}_${varDay}_${varYear}"
cp "$f.mp3" "${varMonth}_${varDay}_${varYear}/$f.mp3"
done
The actual error is that you need to use command substitution. For example, instead of
varYear= $line | cut -d '_' -f 3
you need to use
varYear=$(cut -d '_' -f 3 <<< "$line")
A secondary error there is that $foo | some_command on its own line does not mean that the contents of $foo gets piped to the next command as input, but is rather executed as a command, and the output of the command is passed to the next one.
Some best practices and tips to take into account:
Use a portable shebang line - #!/usr/bin/env bash (disclaimer: That's my answer).
Don't parse ls output.
Avoid useless uses of cat.
Use More Quotes™
Don't use files for temporary storage if you can use pipes. It is literally orders of magnitude faster, and generally makes for simpler code if you want to do it properly.
If you have to use files for temporary storage, put them in the directory created by mktemp -d. Preferably add a trap to remove the temporary directory cleanly.
There's no need for a var prefix in variables.
grep searches for basic regular expressions by default, so .mp3 matches any single character followed by the literal string mp3. If you want to search for a dot, you need to either use grep -F to search for literal strings or escape the regular expression as \.mp3.
You generally want to use read -r (defined by POSIX) to treat backslashes in the input literally.
I am using the below script. When I have it echo $f as shown below, it gives the correct result:
#/bin/bash
var="\/home\/"
while read p; do
f=$(echo $p | sed "s/${var}/\\n/g")
f=${f%.sliced.bam}.fastq
echo $f
~/bin/samtools view $p | awk '{print "#"$1"\n"$10"\n+\n"$11}' > $f
./run.sh $f ${f%.fastq}
rm ${f%.sliced.bam}.fastq
done < $1
I get the output as expected
test.fastq
But the file being created by awk > $f has the name
?test.fastq
Note that the overall goal here is to run this loop on every file listed in a file with absolute paths but then write locally (which is what the sed call is for)
edit: Run directly on the command line (without variables) the samtools | awk line runs correctly.
Awk cannot possibly have anything to do with your problem. The shell is completely responsible for file redirection, so f MUST have a weird character in it.
Most likely whatever you are sending to this script has a special character in it (e.g. perhaps a UTF character, and your terminal is showing ASCII only). When you do the echo, the shell doesn't know how to display the char, and probably just shows it as whitespace, and when you send it through ls (which might be doing things like colorization) it combines in a strange way and ends up showing the ?.
Oh wait...why are you putting a newline into the filename with sed??? That is possibly your problem...try just:
sed "s/${var}//g"
I am trying to modify a bash script to remove a glob of malicious code from a large number of files.
The community will benefit from this, so here it is:
#!/bin/bash
grep -r -l 'var createDocumentFragm' /home/user/Desktop/infected_site/* > /home/user/Desktop/filelist.txt
for i in $(cat /home/user/Desktop/filelist.txt)
do
cp -f $i $i.bak
done
for i in $(cat /home/user/Desktop/filelist.txt)
do
$i | sed 's/createDocumentFragm.*//g' > $i.awk
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
This is where the script bombs out with this message:
+ for i in '$(cat /home/user/Desktop/filelist.txt)'
+ sed 's/createDocumentFragm.*//g'
+ /home/user/Desktop/infected_site/index.htm
I get 2 errors and the script stops.
/home/user/Desktop/infected_site/index.htm: line 1: syntax error near unexpected token `<'
/home/user/Desktop/infected_site/index.htm: line 1: `<html><head><script>(function (){ '
I have the first 2 parts done.
The files containing createDocumentfragm have been enumerated in a text file correctly.
The files in the textfile.txt have been duplicated, in their original location with a .bak added to them IE: infected_site/some_directory/infected_file.htm and infected_file.htm.bak
effectively making sure we have a backup.
All I need to do now is write an AWK command that will use the list of files in filelist.txt, use the entire glob of malicious text as a pattern, and remove it from the files. Using just the uppercase script as the starting point, and the lower case script is too generic and could delete legitimate text
I suspect this may help me, but I don't know how to use it correctly.
http://backreference.org/2010/03/13/safely-escape-variables-in-awk/
Once I have this part figured out, and after you have verified that the files weren't mangled you can do this to clean out the bak files:
for i in $(cat /home/user/Desktop/filelist.txt)
do
rm -f $i.bak
done
Several things:
You have:
$i | sed 's/var createDocumentFragm.*//g' > $i.awk
You should probably meant this (using your use of cat which we'll talk about in a moment):
cat $i | sed 's/var createDocumentFragm.*//g' > $i.awk
You're treating each file in your file list as if it was a command and not a file.
Now, about your use of cat. If you're using cat for almost anything but concatenating multiple files together, you probably are doing something not quite right. For example, you could have done this:
sed 's/var createDocumentFragm.*//g' "$i" > $i.awk
I'm also a bit confused about the awk statement. Exactly what file are you using awk on? Your awk statement is using STDIN and STDOUT, so it's reading file names from the for loop and then printing the output on the screen. Is the sed statement suppose to feed into the awk statement?
Note that I don't have to print out my file to STDOUT, then pipe that into sed. The sed command can take the file name directly.
You also want to avoid for loops over a list of files. That is very inefficient, and can cause problems with the command line getting overloaded. Not a big issue today, but can affect you when you least suspect it. What happens is that your $(cat /home/user/Desktop/filelist.txt) must execute first before the for loop can even start.
A little rewriting of your program:
cd ~/Desktop
grep -r -l 'var createDocumentFragm' infected_site/* > filelist.txt
while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" > "$i.awk"
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
done < filelist.txt
We can use one loop, and we made it a while loop. I could even feed the grep into that while loop:
grep -r -l 'var createDocumentFragm' infected_site/* | while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" > "$i.awk"
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
done < filelist.txt
and then I don't even have to create a temporary file.
Let me know what's going on with the awk. I suspect you wanted something like this:
grep -r -l 'var createDocumentFragm' infected_site/* | while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" \
| awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p' > "$i.awk"
done < filelist.txt
Also note I put quotes around file names. This helps prevent problems if file name has a space in it.