Merge two lines into one within a configuration file - perl

I have several AIX systems with a configuration file, let's call it /etc/bar/config. The file may or may not have a line declaring values for foo. An example would be:
foo = A_1,GROUP_1,USER_1,USER_2,USER_3
The foo line may or may not be the same on all systems. Different systems may have different values and different a different number of values. My task is to add "bare minimum" values in the config file on all systems. The bare minimum line will look like this.
foo = A_1,USER_1,SYS_1,SYS_2
If the line does not exist, I must create it. If the line does exist, I must merge the two lines. Using my examples, the result would be this. The order of the values does not matter.
foo = A_1,GROUP_1,USER_1,USER_3,USER_2,SYS_1,SYS_2
Obviously I want a script to do my work. I have the standard sh, ksh, awk, sed, grep, perl, cut, etc. Since this is AIX, I do not have access to the GNU versions of these utilities.
Originally, I had a script with these commands to replace the entire foo line.
cp /etc/bar/config /etc/bar/config.$$
sed "s/foo = .*/foo = A_1,USER_1,SYS_1,SYS_2/" /etc/bar/config.$$ > /etc/bar/config
But this simply replaces the line. It does take into consideration any pre-existing configuration, including a line that's missing. And I'm doing other configuration modifications in the script, such as adding completely unique lines to other files and restarting a process, so I'd perfer this be some type of shell-based code snippet I can add to my change script. I am open to other options, especially if the solution is simpler.

Some dirty bash/sed:
#!/usr/bin/bash
input_file="some_filename"
v=$(grep -n '^foo *=' "$input_file")
lineno=$(cut -d: -f1 <<< "${v}0:")
base="A_1,USER_1,SYS_1,SYS_2,"
if [[ "$lineno" == 0 ]]; then
echo "foo = A_1,USER_1,SYS_1,SYS_2" >> "$input_file"
else
all=$(sed -n ${lineno}'s/^foo *= */'"$base"'/p' "$input_file" | \
tr ',' '\n' | sort | uniq | tr '\n' ',' | \
sed -e 's/^/foo = /' -e 's/, *$//' -e 's/ */ /g' <<< "$all")
sed -i "${lineno}"'s/.*/'"$all"'/' "$input_file"
fi

Untested bash, etc.
config=/etc/bar/config
default=A_1,USER_1,SYS_1,SYS_2
pattern='^foo[[:blank:]]*=[[:blank:]]*' # shared with grep and sed
if current=$( grep "$pattern" "$config" | sed "s/$pattern//" )
then
new=$( echo "$current,$default" | tr ',' '\n' | sort | uniq | paste -sd, )
sed "s/$pattern.*/foo = $new/" "$config" > "$config.$$.tmp" &&
mv "$config.$$.tmp" "$config"
else
echo "foo = $default" >> "$config"
fi
A vanilla perl solution:
perl -i -lpe '
BEGIN {%foo = map {$_ => 1} qw/A_1 USER_1 SYS_1 SYS_2/}
if (s/^foo\s*=\s*//) {
$found=1;
$foo{$_}=1 for split /,/;
$_ = "foo = " . join(",", keys %foo);
}
END {print "foo = " . join(",", keys %foo) unless $found}
' /etc/bar/config

This Perl code will do as you ask. It expects the path to the file to be modified as a parameter on the command line.
Note that it reads the entire input file into the array #config and then overwrites the same file with the modified data.
It works by building a hash %values from a combination of the items already present in the foo = line and the list of defaults items in #defaults. The combination is sorted in alphabetical order and joined eith a comma
use strict;
use warnings;
my #defaults = qw/ A_1 USER_1 SYS_1 SYS_2 /;
my ($file) = #ARGV;
my #config = <>;
open my $out_fh, '>', $file or die $!;
select $out_fh;
for ( #config ) {
if ( my ($pfx, $vals) = /^(foo \s* = \s* ) (.+) /x ) {
my %values;
++$values{$_} for $vals =~ /[^,\s]+/g;
++$values{$_} for #defaults;
print $pfx, join(',', sort keys %values), "\n";
}
else {
print;
}
}
close $out_fh;
output
foo = A_1,GROUP_1,SYS_1,SYS_2,USER_1,USER_2,USER_3

Since you didn't provide sample input and expected output I couldn't test this but this is the right approach:
awk '
/foo = / { old = ","$3; next }
{ print }
END {
split("A_1,USER_1,SYS_1,SYS_2"old,all,/,/)
for (i in all)
if (!seen[all[i]]++)
new = (new ? new "," : "") all[i]
print "foo =", new
}
' /etc/bar/config > tmp && mv tmp /etc/bar/config

Related

Perl script throws syntax error for awk command

I have a file which contains each users userid and password. I need to fetch userid and password from that file by passing userid as an search element using awk command.
user101,smith,smith#123
user102,jones,passj#007
user103,albert,albpass#01
I am using a awk command inside my perl script like this:
...
...
my $userid = ARGV[0];
my $user_report_file = "report_file.txt";
my $data = `awk -F, '$1 ~ /$userid/ {print $2, $3}' $user_report_file`;
my ($user,$pw) = split(" ",$data);
...
...
Here I am getting the error:
awk: ~ /user101/ {print , }
awk: ^ syntax error
But if I run same command in terminal window its able to give result like below:
$] awk -F, '$1 ~ /user101/ {print $2, $3}' report_file.txt
smith smith#123
What could be the issue here?
The backticks are a double-quoted context, so you need to escape any literal $ that you want awk to interpret.
my $data = `awk -F, '\$1 ~ /$userid/ {print \$2, \$3}' $user_report_file`;
If you don't do that, you're interpolating the capture variables from the last successful Perl match.
When I have these sorts of problems, I try the command as a string first to see if it is what I expect:
my $data = "awk -F, '\$1 ~ /$userid/ {print \$2, \$3}' $user_report_file";
say $data;
Here's the Perl equivalent of that command:
$ perl -aF, -e '$F[0]=~/101/ && print "#F[1,2]"' report_file
But, this is something you probably want to do in Perl instead of creating another process:
Interpolating data into external commands can go wrong, such as a filename that is foo.txt; rm -rf /.
The awk you run is the first one in the path, so someone can make that a completely different program (so use the full path, like /usr/bin/awk).
Taint checking can tell you when you are passing unsanitized data to the shell.
Inside a program you don't get all the shortcuts, but if this is the part of your program that is slow, you probably want to rethink how you are accessing this data because scanning the entire file with any tool isn't going to be that fast:
open my $fh, '<', $user_report_file or die;
while( <$fh> ) {
chomp;
my #F = split /,/;
next unless $F[0] =~ /\Q$userid/;
print "#F[1,2]";
last; # if you only want the first one
}

Any way to find if two adjacent new lines start with certain words?

Say I have a file like so:
+jaklfjdskalfjkdsaj
fkldsjafkljdkaljfsd
-jslakflkdsalfkdls;
+sdjafkdjsakfjdskal
I only want to find and count the amount of times during this file a line that starts with - is immediately followed by a line that starts with +.
Rules:
No external scripts
Must be done from within a bash script
Must be inline
I could figure out how to do this in a Python script, for instance, but I've never had to do something this extensive in Bash.
Could anyone help me out? I figure it'll end up being grep, perl, or maybe a talented sed line -- but these are things I'm still learning.
Thank you all!
grep -A1 "^-" $file | grep "^+" | wc -l
The first grep finds all of the lines starting with -, and the -A1 causes it to also output the line after the match too.
We then grep that output for any lines starting with +. Logically:
We know the output of the first grep is only the -XXX lines and the following lines
We know that a +xxx line cannot also be a -xxx line
Therefore, any +xxx lines must be following lines, and should be counted, which we do with wc -l
Easy in Perl:
perl -lne '$c++ if $p and /^\+/; $p = /^-/ }{ print $c' FILE
awk one-liner:
awk -v FS='' '{x=x sprintf("%s", $1)}END{print gsub(/-\+/,"",x)}' file
e.g.
kent$ cat file
+jaklfjdskalfjkdsaj
fkldsjafkljdkaljfsd
-jslakflkdsalfkdls;
+sdjafkdjsakfjdskal
-
-
-
+
-
+
foo
+
kent$ awk -v FS='' '{x=x sprintf("%s", $1)}END{print gsub(/-\+/,"",x)}' file
3
Another Perl example. Not as terse as choroba's, but more transparent in how it works:
perl -e'while (<>) { $last = $cur; $cur = $_; print $last, $cur if substr($last, 0, 1) eq "-" && substr($cur, 0, 1) eq "+" }' < infile
Output:
-jslakflkdsalfkdls;
+sdjafkdjsakfjdskal
Pure bash:
unset c p
while read line ; do
[[ $line == +* && $p == 0 ]] && (( c++ ))
[[ $line == -* ]]
p=$?
done < FILE
echo $c

Awk/Perl/Sed column substitution based on a text code

I have a text file with the following content
L,4m,06/03/2013
L,33GJm,06/03/2013,G
L,44Bm,06/03/2013,B
L,4q,08/03/2013
J,4m,04/03/2013
J,3GU,04/03/2013,G
J,3jm,04/03/2013
J,3GJ,04/03/2013,G
J,44Bm,06/03/2013,B
J,34Bq,08/03/2013,B
M,4v,12/03/2013
D,3GU,12/03/2013,G
D,4B,11/03/2013,B
D,4m,12/03/2013
D,3GJ,13/03/2013,G
D,3GU,13/03/2013,G
D,4B,14/03/2013,B
D,4B,14/03/2013,B
D,34Bm,14/03/2013,B
L,33BUq,11/03/2013,B
L,3BJUq,11/03/2013,B
L,44Bq,14/03/2013,B
L,44Bq,14/03/2013,B
L,3Bq,15/03/2013,B
L,3q,15/03/2013
J,34Bjq,11/03/2013,B
J,33GUm,12/03/2013,G
J,4q,13/03/2013
J,33GUq,13/03/2013,G
J,33GUq,13/03/2013,G
J,4q,13/03/2013
M,3BU,18/03/2013,B
M,4B,18/03/2013,B
M,4B,18/03/2013,B
M,3GJ,19/03/2013,G
M,3GJ,19/03/2013,G
D,4B,22/03/2013,B
D,3BU,22/03/2013,B
L,34Bv,18/03/2013,B
L,3jm,19/03/2013
L,4m,19/03/2013
L,33GJm,19/03/2013,G
L,33GUm,19/03/2013,G
J,33BUm,18/03/2013,B
J,4m,18/03/2013
J,4B,18/03/2013,B
J,33BUm,18/03/2013,B
J,4q,22/03/2013
J,4q,22/03/2013
A,3GJ,28/03/2013,G
M,4B,27/03/2013,B
D,4B,25/03/2013,B
L,44Bq,25/03/2013,B
L,34Bq,25/03/2013,B
L,34Bq,25/03/2013,B
L,33BUa,26/03/2013,B
L,33BUq,26/03/2013,B
L,33BUq,26/03/2013,B
L,34Bq,27/03/2013,B
L,34Bq,27/03/2013,B
L,4B,27/03/2013,B
L,34Bq,27/03/2013,B
L,4a,28/03/2013
I want to translate the second column based on the following coding system.
If $2 starts with a 1 or 2 - Change $2 to Excellent
If $2 contains 3BU or 3GU - Change $2 to Good
if $2 contains 3BJ or 3GJ - Change $2 to OK
If $2 starts with a 4 - Change $2 to Poor
If $2 starts with a 5 - Change $2 Terrible
I can find and change the 3BUs to Good easy enough using the following command
awk 'BEGIN{FS=",";OFS=","} {if ($2~ /3(B|G)U/)print $1,"Good",$3}' file | sponge file
Though I use all other non 3(B|G)U lines. I could use if else terminology though this seems inelegant. I have tried to use gensub to solve the problem
awk -F, '{gensub(/3(B|G)U/,Good,"",2)}1' file
But this prints the file contents without substitution. Any hints
Desired output
L,Poor,06/03/2013
L,Ok,06/03/2013,G
L,Poor,06/03/2013,B
L,Poor,08/03/2013
J,Poor,04/03/2013
J,Good,04/03/2013,G
A perl or sed one-liner would also be helpful as this code forms part of a bash shell script
If you want to stick with shell:
(
IFS=,
while read -ra f; do # pick more appropriate variable names
case ${f[1]} in
[12]*) f[1]=Excellent ;;
*3[BG]U*) f[1]=Good ;;
*3[BG]J*) f[1]=OK ;;
4*) f[1]=Poor ;;
5*) f[1]=Terrible ;;
esac
echo "${f[*]}"
done < file
) > tmp && mv tmp file
I ran that in a subshell to localize changes to $IFS
a sed solutions too
sed -e 's/\(^.,\)\(1\|2\)[^,]*/\1Excellent/g' -e 's/\(^.,\)3[BG]U[^,]*/\1Good/g' -e 's/\(^.,\)3[BG]J[^,]*/\1OK/g' -e 's/\(^.,\)4[^,]*/\1Poor/g' -e 's/\(^.,\)5[^,]*/\1Terrible/g' <filename>
$ awk '
BEGIN { FS=OFS="," }
$2 ~ /^(1|2)/ { $2 = "Excellent" }
$2 ~ /3(B|G)U/ { $2 = "Good" }
$2 ~ /3(B|G)J/ { $2 = "OK" }
$2 ~ /^4/ { $2 = "Poor" }
$2 ~ /^5/ { $2 = "Terrible" }
1
' foo.txt | head -n 10
L,Poor,06/03/2013
L,OK,06/03/2013,G
L,Poor,06/03/2013,B
L,Poor,08/03/2013
J,Poor,04/03/2013
J,Good,04/03/2013,G
J,3jm,04/03/2013
J,OK,04/03/2013,G
J,Poor,06/03/2013,B
J,34Bq,08/03/2013,B
perl -pe 's{,(\w+)}{ $_ = /^[12]/ ?"Excellent" :/3[BG]U/ ?"Good" :/3[BG]J/ ?"OK" :/^4/ ?"Poor" :/^5/ ?"Terrible" :$_ for $v=$1; ",$v" }e'
More readable version,
s{,(\w+)}{
for ($v = $1) {
$_ = /^[12]/ ?"Excellent"
:/3[BG]U/ ?"Good"
:/3[BG]J/ ?"OK"
:/^4/ ?"Poor"
:/^5/ ?"Terrible"
:$_;
}
",$v";
}e;

Piping output from awk to perl

I want to make an array in Perl with the values obtained from my awk script. Then I can do math on them in Perl.
Here is my Perl, which runs a program, which saves a text file:
my $unix_command_dsc = (`./program -s test.fasta saved_file.txt`);
my $dsc_run = qx($unix_command_dsc);
Now I have some Awk that parses that data saved in the text file:
#!/usr/bin/awk -f
BEGIN{ # Initialize the values to zero. Note, done automatically also.
sumc4 = 0
sumc5 = 0
sumc6 = 0
}
/^[1-9][0-9]* residue/ {next} #Match line that begins with number and has word 'residue', skip it.
/^[1-9]/ { #Match line that begins with number.
sumc4 += $4 #Add up the values of the nth column into the variables.
sumc5 += $5
sumc6 += $6
print $4 "\t" $5 "\t" $6 #This will show the whole columns.
}
END{
print "sum H" "\t" "sum E" "\t" "sum C"
print sumc4 "\t" sumc5 "\t" sumc6
}
I run this Awk from terminal with the following commands:
./awk_program.txt saved_file.txt
Any ideas how I would gather this data from the print statements in awk into arrays in perl?
What I've tried is to just run that awk script in perl:
my $unix_command_awk = (`./awk_program.txt saved_file.txt`);
my $awk_run = qx($unix_command_awk);
But perl gives me errors and commands not found, like it thinks the data are commands. Should there be a STDOUT in the awk that I'm missing, rather than print?
It should just be:
my $awk_run = `./awk_program.txt saved_file.txt`;
Backticks tell perl to run the command and return the output. So your assignment to $unix_command_awk is running the command, and then qx($unix_command_awk) executes the output as a new command.
Pipe from awk to your perl script:
./awk_program file.txt | perl perl-script.pl
Then read from stdin inside the perl:
while (<>) {
# do stuff with $_
my #cols = split(/\t/);
}

variable for field separator in perl

In awk I can write: awk -F: 'BEGIN {OFS = FS} ...'
In Perl, what's the equivalent of FS? I'd like to write
perl -F: -lane 'BEGIN {$, = [what?]} ...'
update with an example:
echo a:b:c:d | awk -F: 'BEGIN {OFS = FS} {$2 = 42; print}'
echo a:b:c:d | perl -F: -ane 'BEGIN {$, = ":"} $F[1] = 42; print #F'
Both output a:42:c:d
I would prefer not to hard-code the : in the Perl BEGIN block, but refer to wherever the -F option saves its argument.
To sum up, what I'm looking for does not exist:
there's no variable that holds the argument for -F, and more importantly
Perl's "FS" is fundamentally a different data type (regular expression) than the "OFS" (string) -- it does not make sense to join a list of strings using a regex.
Note that the same holds true in awk: FS is a string but acts as regex:
echo a:b,c:d | awk -F'[:,]' 'BEGIN {OFS=FS} {$2=42; print}'
outputs "a[:,]42[:,]c[:,]d"
Thanks for the insight and workarounds though.
You can use perl's -s (similar to awk's -v) to pass a "FS" variable, but the split becomes manual:
echo a:b:c:d | perl -sne '
BEGIN {$, = $FS}
#F = split $FS;
$F[1] = 42;
print #F;
' -- -FS=":"
If you know the exact length of input, you could do this:
echo a:b:c:d | perl -F'(:)' -ane '$, = $F[1]; #F = #F[0,2,4,6]; $F[1] = 42; print #F'
If the input is of variable lengths, you'll need something more sophisticated than #f[0,2,4,6].
EDIT: -F seems to simply provide input to an automatic split() call, which takes a complete RE as an expression. You may be able to find something more suitable by reading the perldoc entries for split, perlre, and perlvar.
You can sort of cheat it, because perl is actually using the split function with your -F argument, and you can tell split to preserve what it splits on by including capturing parens in the regex:
$ echo a:b:c:d | perl -F'(:)' -ane 'print join("/", #F);'
a/:/b/:/c/:/d
You can see what perl's doing with some of these "magic" command-line arguments by using -MO=Deparse, like this:
$ perl -MO=Deparse -F'(:)' -ane 'print join("/", #F);'
LINE: while (defined($_ = <ARGV>)) {
our(#F) = split(/(:)/, $_, 0);
print join('/', #F);
}
-e syntax OK
You'd have to change your #F subscripts to double what they'd normally be ($F[2] = 42).
Darnit...
The best I can do is:
echo a:b:c:d | perl -ne '$v=":";#F = split("$v"); $F[1] = 42; print join("$v", #F) . "\n";'
You don't need the -F: this way, and you're only stating the colon once. I was hoping there was someway of setting variables on the command line like you can with Awk's -v switch.
For one liners, Perl is usually not as clean as Awk, but I remember using Awk before I knew of Perl and writing 1000+ line Awk scripts.
Trying things like this made people think Awk was either named after the sound someone made when they tried to decipher such a script, or stood for AWKward.
There is no input record separator in Perl. You're basically emulating awk by using the -a and -F flags. If you really don't want to hard code the value, then why not just use an environmental variable?
$ export SPLIT=":"
$ perl -F$SPLIT -lane 'BEGIN { $, = $ENV{SPLIT}; } ...'