Bash script optimisation - bash

This is the script in question:
for file in `ls products`
do
echo -n `cat products/$file \
| grep '<td>.*</td>' | grep -v 'img' | grep -v 'href' | grep -v 'input' \
| head -1 | sed -e 's/^ *<td>//g' -e 's/<.*//g'`
done
I'm going to run it on 50000+ files, which would take about 12 hours with this script.
The algorithm is as follows:
Find only lines containing table cells (<td>) that do not contain any of 'img', 'href', or 'input'.
Select the first of them, then extract the data between the tags.
The usual bash text filters (sed, grep, awk, etc.) are available, as well as perl.

Looks like that can all be replace by one gawk command:
gawk '
/<td>.*<\/td>/ && !(/img/ || /href/ || /input/) {
sub(/^ *<td>/,""); sub(/<.*/,"")
print
nextfile
}
' products/*
This uses the gawk extension nextfile.
If the wildcard expansion is too big, then
find products -type f -print | xargs gawk '...'

Here's some quick perl to do the whole thing that should be alot faster.
#!/usr/bin/perl
process_files($ARGV[0]);
# process each file in the supplied directory
sub process_files($)
{
my $dirpath = shift;
my $dh;
opendir($dh, $dirpath) or die "Cant readdir $dirpath. $!";
# get a list of files
my #files;
do {
#files = readdir($dh);
foreach my $ent ( #files ){
if ( -f "$dirpath/$ent" ){
get_first_text_cell("$dirpath/$ent");
}
}
} while ($#files > 0);
closedir($dh);
}
# return the content of the first html table cell
# that does not contain img,href or input tags
sub get_first_text_cell($)
{
my $filename = shift;
my $fh;
open($fh,"<$filename") or die "Cant open $filename. $!";
my $found = 0;
while ( ( my $line = <$fh> ) && ( $found == 0 ) ){
## capture html and text inside a table cell
if ( $line =~ /<td>([&;\d\w\s"'<>]+)<\/td>/i ){
my $cell = $1;
## omit anything with the following tags
if ( $cell !~ /<(img|href|input)/ ){
$found++;
print "$cell\n";
}
}
}
close($fh);
}
Simply invoke it by passing the directory to be searched as the first argument:
$ perl parse.pl /html/documents/

What about this (should be much faster and clearer):
for file in products/*; do
grep -P -o '(?<=<td>).*(?=<\/td>)' $file | grep -vP -m 1 '(img|input|href)'
done
the for will look to every file in products. See the difference with your syntax.
the first grep will output just the text between <td> and </td> without those tags for every cell as long as each cell is in a single line.
finally the second grep will output just the first line (which is what I believe you wanted to achieve with that head -1) of those lines which doesn't contain img, href or input (and will exit right then reducing the overall time allowing to process the next file faster)
I would have loved to use just a single grep, but then the regex will be really awful. :-)
Disclaimer: of course I haven't tested it

Related

How can extract a value from .ini using sed [duplicate]

I have a parameters.ini file, such as:
[parameters.ini]
database_user = user
database_version = 20110611142248
I want to read in and use the database version specified in the parameters.ini file from within a bash shell script so I can process it.
#!/bin/sh
# Need to get database version from parameters.ini file to use in script
php app/console doctrine:migrations:migrate $DATABASE_VERSION
How would I do this?
How about grepping for that line then using awk
version=$(awk -F "=" '/database_version/ {print $2}' parameters.ini)
You can use bash native parser to interpret ini values, by:
$ source <(grep = file.ini)
Sample file:
[section-a]
var1=value1
var2=value2
IPS=( "1.2.3.4" "1.2.3.5" )
To access variables, you simply printing them: echo $var1. You may also use arrays as shown above (echo ${IPS[#]}).
If you only want a single value just grep for it:
source <(grep var1 file.ini)
For the demo, check this recording at asciinema.
It is simple as you don't need for any external library to parse the data, but it comes with some disadvantages. For example:
If you have spaces between = (variable name and value), then you've to trim the spaces first, e.g.
$ source <(grep = file.ini | sed 's/ *= */=/g')
Or if you don't care about the spaces (including in the middle), use:
$ source <(grep = file.ini | tr -d ' ')
To support ; comments, replace them with #:
$ sed "s/;/#/g" foo.ini | source /dev/stdin
The sections aren't supported (e.g. if you've [section-name], then you've to filter it out as shown above, e.g. grep =), the same for other unexpected errors.
If you need to read specific value under specific section, use grep -A, sed, awk or ex).
E.g.
source <(grep = <(grep -A5 '\[section-b\]' file.ini))
Note: Where -A5 is the number of rows to read in the section. Replace source with cat to debug.
If you've got any parsing errors, ignore them by adding: 2>/dev/null
See also:
How to parse and convert ini file into bash array variables? at serverfault SE
Are there any tools for modifying INI style files from shell script
Sed one-liner, that takes sections into account. Example file:
[section1]
param1=123
param2=345
param3=678
[section2]
param1=abc
param2=def
param3=ghi
[section3]
param1=000
param2=111
param3=222
Say you want param2 from section2. Run the following:
sed -nr "/^\[section2\]/ { :l /^param2[ ]*=/ { s/[^=]*=[ ]*//; p; q;}; n; b l;}" ./file.ini
will give you
def
Bash does not provide a parser for these files. Obviously you can use an awk command or a couple of sed calls, but if you are bash-priest and don't want to use any other shell, then you can try the following obscure code:
#!/usr/bin/env bash
cfg_parser ()
{
ini="$(<$1)" # read the file
ini="${ini//[/\[}" # escape [
ini="${ini//]/\]}" # escape ]
IFS=$'\n' && ini=( ${ini} ) # convert to line-array
ini=( ${ini[*]//;*/} ) # remove comments with ;
ini=( ${ini[*]/\ =/=} ) # remove tabs before =
ini=( ${ini[*]/=\ /=} ) # remove tabs after =
ini=( ${ini[*]/\ =\ /=} ) # remove anything with a space around =
ini=( ${ini[*]/#\\[/\}$'\n'cfg.section.} ) # set section prefix
ini=( ${ini[*]/%\\]/ \(} ) # convert text2function (1)
ini=( ${ini[*]/=/=\( } ) # convert item to array
ini=( ${ini[*]/%/ \)} ) # close array parenthesis
ini=( ${ini[*]/%\\ \)/ \\} ) # the multiline trick
ini=( ${ini[*]/%\( \)/\(\) \{} ) # convert text2function (2)
ini=( ${ini[*]/%\} \)/\}} ) # remove extra parenthesis
ini[0]="" # remove first element
ini[${#ini[*]} + 1]='}' # add the last brace
eval "$(echo "${ini[*]}")" # eval the result
}
cfg_writer ()
{
IFS=' '$'\n'
fun="$(declare -F)"
fun="${fun//declare -f/}"
for f in $fun; do
[ "${f#cfg.section}" == "${f}" ] && continue
item="$(declare -f ${f})"
item="${item##*\{}"
item="${item%\}}"
item="${item//=*;/}"
vars="${item//=*/}"
eval $f
echo "[${f#cfg.section.}]"
for var in $vars; do
echo $var=\"${!var}\"
done
done
}
Usage:
# parse the config file called 'myfile.ini', with the following
# contents::
# [sec2]
# var2='something'
cfg.parser 'myfile.ini'
# enable section called 'sec2' (in the file [sec2]) for reading
cfg.section.sec2
# read the content of the variable called 'var2' (in the file
# var2=XXX). If your var2 is an array, then you can use
# ${var[index]}
echo "$var2"
Bash ini-parser can be found at The Old School DevOps blog site.
Just include your .ini file into bash body:
File example.ini:
DBNAME=test
DBUSER=scott
DBPASSWORD=tiger
File example.sh
#!/bin/bash
#Including .ini file
. example.ini
#Test
echo "${DBNAME} ${DBUSER} ${DBPASSWORD}"
All of the solutions I've seen so far also hit on commented out lines. This one didn't, if the comment code is ;:
awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /database_version/) print $2}' file.ini
You may use crudini tool to get ini values, e.g.:
DATABASE_VERSION=$(crudini --get parameters.ini '' database_version)
one of more possible solutions
dbver=$(sed -n 's/.*database_version *= *\([^ ]*.*\)/\1/p' < parameters.ini)
echo $dbver
Display the value of my_key in an ini-style my_file:
sed -n -e 's/^\s*my_key\s*=\s*//p' my_file
-n -- do not print anything by default
-e -- execute the expression
s/PATTERN//p -- display anything following this pattern
In the pattern:
^ -- pattern begins at the beginning of the line
\s -- whitespace character
* -- zero or many (whitespace characters)
Example:
$ cat my_file
# Example INI file
something = foo
my_key = bar
not_my_key = baz
my_key_2 = bing
$ sed -n -e 's/^\s*my_key\s*=\s*//p' my_file
bar
So:
Find a pattern where the line begins with zero or many whitespace characters,
followed by the string my_key, followed by zero or many whitespace characters, an equal sign, then zero or many whitespace characters again. Display the rest of the content on that line following that pattern.
Similar to the other Python answers, you can do this using the -c flag to execute a sequence of Python statements given on the command line:
$ python3 -c "import configparser; c = configparser.ConfigParser(); c.read('parameters.ini'); print(c['parameters.ini']['database_version'])"
20110611142248
This has the advantage of requiring only the Python standard library and the advantage of not writing a separate script file.
Or use a here document for better readability, thusly:
#!/bin/bash
python << EOI
import configparser
c = configparser.ConfigParser()
c.read('params.txt')
print c['chassis']['serialNumber']
EOI
serialNumber=$(python << EOI
import configparser
c = configparser.ConfigParser()
c.read('params.txt')
print c['chassis']['serialNumber']
EOI
)
echo $serialNumber
sed
You can use sed to parse the ini configuration file, especially when you've section names like:
# last modified 1 April 2001 by John Doe
[owner]
name=John Doe
organization=Acme Widgets Inc.
[database]
# use IP address in case network name resolution is not working
server=192.0.2.62
port=143
file=payroll.dat
so you can use the following sed script to parse above data:
# Configuration bindings found outside any section are given to
# to the default section.
1 {
x
s/^/default/
x
}
# Lines starting with a #-character are comments.
/#/n
# Sections are unpacked and stored in the hold space.
/\[/ {
s/\[\(.*\)\]/\1/
x
b
}
# Bindings are unpacked and decorated with the section
# they belong to, before being printed.
/=/ {
s/^[[:space:]]*//
s/[[:space:]]*=[[:space:]]*/|/
G
s/\(.*\)\n\(.*\)/\2|\1/
p
}
this will convert the ini data into this flat format:
owner|name|John Doe
owner|organization|Acme Widgets Inc.
database|server|192.0.2.62
database|port|143
database|file|payroll.dat
so it'll be easier to parse using sed, awk or read by having section names in every line.
Credits & source: Configuration files for shell scripts, Michael Grünewald
Alternatively, you can use this project: chilladx/config-parser, a configuration parser using sed.
For people (like me) looking to read INI files from shell scripts (read shell, not bash) - I've knocked up the a little helper library which tries to do exactly that:
https://github.com/wallyhall/shini (MIT license, do with it as you please. I've linked above including it inline as the code is quite lengthy.)
It's somewhat more "complicated" than the simple sed lines suggested above - but works on a very similar basis.
Function reads in a file line-by-line - looking for section markers ([section]) and key/value declarations (key=value).
Ultimately you get a callback to your own function - section, key and value.
Here is my version, which parses sections and populates a global associative array g_iniProperties with it.
Note that this works only with bash v4.2 and higher.
function parseIniFile() { #accepts the name of the file to parse as argument ($1)
#declare syntax below (-gA) only works with bash 4.2 and higher
unset g_iniProperties
declare -gA g_iniProperties
currentSection=""
while read -r line
do
if [[ $line = [* ]] ; then
if [[ $line = [* ]] ; then
currentSection=$(echo $line | sed -e 's/\r//g' | tr -d "[]")
fi
else
if [[ $line = *=* ]] ; then
cleanLine=$(echo $line | sed -e 's/\r//g')
key=$currentSection.$(echo $cleanLine | awk -F: '{ st = index($0,"=");print substr($0,0,st-1)}')
value=$(echo $cleanLine | awk -F: '{ st = index($0,"=");print substr($0,st+1)}')
g_iniProperties[$key]=$value
fi
fi;
done < $1
}
And here is a sample code using the function above:
parseIniFile "/path/to/myFile.ini"
for key in "${!g_iniProperties[#]}"; do
echo "Found key/value $key = ${g_iniProperties[$key]}"
done
Yet another implementation using awk with a little more flexibility.
function parse_ini() {
cat /dev/stdin | awk -v section="$1" -v key="$2" '
BEGIN {
if (length(key) > 0) { params=2 }
else if (length(section) > 0) { params=1 }
else { params=0 }
}
match($0,/#/) { next }
match($0,/^\[(.+)\]$/){
current=substr($0, RSTART+1, RLENGTH-2)
found=current==section
if (params==0) { print current }
}
match($0,/(.+)=(.+)/) {
if (found) {
if (params==2 && key==$1) { print $3 }
if (params==1) { printf "%s=%s\n",$1,$3 }
}
}'
}
You can use calling passing between 0 and 2 params:
cat myfile1.ini myfile2.ini | parse_ini # List section names
cat myfile1.ini myfile2.ini | parse_ini 'my-section' # Prints keys and values from a section
cat myfile1.ini myfile2.ini | parse_ini 'my-section' 'my-key' # Print a single value
complex simplicity
ini file
test.ini
[section1]
name1=value1
name2=value2
[section2]
name1=value_1
name2 = value_2
bash script with read and execute
/bin/parseini
#!/bin/bash
set +a
while read p; do
reSec='^\[(.*)\]$'
#reNV='[ ]*([^ ]*)+[ ]*=(.*)' #Remove only spaces around name
reNV='[ ]*([^ ]*)+[ ]*=[ ]*(.*)' #Remove spaces around name and spaces before value
if [[ $p =~ $reSec ]]; then
section=${BASH_REMATCH[1]}
elif [[ $p =~ $reNV ]]; then
sNm=${section}_${BASH_REMATCH[1]}
sVa=${BASH_REMATCH[2]}
set -a
eval "$(echo "$sNm"=\""$sVa"\")"
set +a
fi
done < $1
then in another script I source the results of the command and can use any variables within
test.sh
#!/bin/bash
source parseini test.ini
echo $section2_name2
finally from command line the output is thus
# ./test.sh
value_2
Some of the answers don't respect comments. Some don't respect sections. Some recognize only one syntax (only ":" or only "="). Some Python answers fail on my machine because of differing captialization or failing to import the sys module. All are a bit too terse for me.
So I wrote my own, and if you have a modern Python, you can probably call this from your Bash shell. It has the advantage of adhering to some of the common Python coding conventions, and even provides sensible error messages and help. To use it, name it something like myconfig.py (do NOT call it configparser.py or it may try to import itself,) make it executable, and call it like
value=$(myconfig.py something.ini sectionname value)
Here's my code for Python 3.5 on Linux:
#!/usr/bin/env python3
# Last Modified: Thu Aug 3 13:58:50 PDT 2017
"""A program that Bash can call to parse an .ini file"""
import sys
import configparser
import argparse
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="A program that Bash can call to parse an .ini file")
parser.add_argument("inifile", help="name of the .ini file")
parser.add_argument("section", help="name of the section in the .ini file")
parser.add_argument("itemname", help="name of the desired value")
args = parser.parse_args()
config = configparser.ConfigParser()
config.read(args.inifile)
print(config.get(args.section, args.itemname))
I wrote a quick and easy python script to include in my bash script.
For example, your ini file is called food.ini
and in the file you can have some sections and some lines:
[FRUIT]
Oranges = 14
Apples = 6
Copy this small 6 line Python script and save it as configparser.py
#!/usr/bin/python
import configparser
import sys
config = configparser.ConfigParser()
config.read(sys.argv[1])
print config.get(sys.argv[2],sys.argv[3])
Now, in your bash script you could do this for example.
OrangeQty=$(python configparser.py food.ini FRUIT Oranges)
or
ApplesQty=$(python configparser.py food.ini FRUIT Apples)
echo $ApplesQty
This presupposes:
you have Python installed
you have the configparser library installed (this should come with a std python installation)
Hope it helps
:¬)
The explanation to the answer for the one-liner sed.
[section1]
param1=123
param2=345
param3=678
[section2]
param1=abc
param2=def
param3=ghi
[section3]
param1=000
param2=111
param3=222
sed -nr "/^\[section2\]/ { :l /^\s*[^#].*/ p; n; /^\[/ q; b l; }" ./file.ini
To understand, it will be easier to format the line like this:
sed -nr "
# start processing when we found the word \"section2\"
/^\[section2\]/ { #the set of commands inside { } will be executed
#create a label \"l\" (https://www.grymoire.com/Unix/Sed.html#uh-58)
:l /^\s*[^#].*/ p;
# move on to the next line. For the first run it is the \"param1=abc\"
n;
# check if this line is beginning of new section. If yes - then exit.
/^\[/ q
#otherwise jump to the label \"l\"
b l
}
" file.ini
This script will get parameters as follow :
meaning that if your ini has :
pars_ini.ksh < path to ini file > < name of Sector in Ini file > < the name in name=value to return >
eg. how to call it :
[ environment ]
a=x
[ DataBase_Sector ]
DSN = something
Then calling :
pars_ini.ksh /users/bubu_user/parameters.ini DataBase_Sector DSN
this will retrieve the following "something"
the script "pars_ini.ksh" :
\#!/bin/ksh
\#INI_FILE=path/to/file.ini
\#INI_SECTION=TheSection
\# BEGIN parse-ini-file.sh
\# SET UP THE MINIMUM VARS FIRST
alias sed=/usr/local/bin/sed
INI_FILE=$1
INI_SECTION=$2
INI_NAME=$3
INI_VALUE=""
eval `sed -e 's/[[:space:]]*\=[[:space:]]*/=/g' \
-e 's/;.*$//' \
-e 's/[[:space:]]*$//' \
-e 's/^[[:space:]]*//' \
-e "s/^\(.*\)=\([^\"']*\)$/\1=\"\2\"/" \
< $INI_FILE \
| sed -n -e "/^\[$INI_SECTION\]/,/^\s*\[/{/^[^;].*\=.*/p;}"`
TEMP_VALUE=`echo "$"$INI_NAME`
echo `eval echo $TEMP_VALUE`
This implementation uses awk and has the following advantages:
Will only return the first matching entry
Ignores lines that start with a ;
Trims leading and trailing whitespace, but not internal whitespace
Formatted version:
awk -F '=' '/^\s*database_version\s*=/ {
sub(/^ +/, "", $2);
sub(/ +$/, "", $2);
print $2;
exit;
}' parameters.ini
One-liner:
awk -F '=' '/^\s*database_version\s*=/ { sub(/^ +/, "", $2); sub(/ +$/, "", $2); print $2; exit; }' parameters.ini
You can use a CSV parser xsv as parsing INI data.
cargo install xsv
$ cat /etc/*release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
$ xsv select -d "=" - <<< "$( cat /etc/*release )" | xsv search --no-headers --select 1 "DISTRIB_CODENAME" | xsv select 2
xenial
or from a file.
$ xsv select -d "=" - file.ini | xsv search --no-headers --select 1 "DISTRIB_CODENAME" | xsv select 2
My version of the one-liner
#!/bin/bash
#Reader for MS Windows 3.1 Ini-files
#Usage: inireader.sh
# e.g.: inireader.sh win.ini ERRORS DISABLE
# would return value "no" from the section of win.ini
#[ERRORS]
#DISABLE=no
INIFILE=$1
SECTION=$2
ITEM=$3
cat $INIFILE | sed -n /^\[$SECTION\]/,/^\[.*\]/p | grep "^[:space:]*$ITEM[:space:]*=" | sed s/.*=[:space:]*//
Just finished writing my own parser. I tried to use various parser found here, none seems to work with both ksh93 (AIX) and bash (Linux).
It's old programming style - parsing line by line. Pretty fast since it used few external commands. A bit slower because of all the eval required for dynamic name of the array.
The ini support 3 special syntaxs:
includefile=ini file -->
Load an additionnal ini file. Useful for splitting ini in multiple files, or re-use some piece of configuration
includedir=directory -->
Same as includefile, but include a complete directory
includesection=section -->
Copy an existing section to the current section.
I used all thoses syntax to have pretty complex, re-usable ini file. Useful to install products when installing a new OS - we do that a lot.
Values can be accessed with ${ini[$section.$item]}. The array MUST be defined before calling this.
Have fun. Hope it's useful for someone else!
function Show_Debug {
[[ $DEBUG = YES ]] && echo "DEBUG $#"
}
function Fatal {
echo "$#. Script aborted"
exit 2
}
#-------------------------------------------------------------------------------
# This function load an ini file in the array "ini"
# The "ini" array must be defined in the calling program (typeset -A ini)
#
# It could be any array name, the default array name is "ini".
#
# There is heavy usage of "eval" since ksh and bash do not support
# reference variable. The name of the ini is passed as variable, and must
# be "eval" at run-time to work. Very specific syntax was used and must be
# understood before making any modifications.
#
# It complexify greatly the program, but add flexibility.
#-------------------------------------------------------------------------------
function Load_Ini {
Show_Debug "$0($#)"
typeset ini_file="$1"
# Name of the array to fill. By default, it's "ini"
typeset ini_array_name="${2:-ini}"
typeset section variable value line my_section file subsection value_array include_directory all_index index sections pre_parse
typeset LF="
"
if [[ ! -s $ini_file ]]; then
Fatal "The ini file is empty or absent in $0 [$ini_file]"
fi
include_directory=$(dirname $ini_file)
include_directory=${include_directory:-$(pwd)}
Show_Debug "include_directory=$include_directory"
section=""
# Since this code support both bash and ksh93, you cannot use
# the syntax "echo xyz|while read line". bash doesn't work like
# that.
# It forces the use of "<<<", introduced in bash and ksh93.
Show_Debug "Reading file $ini_file and putting the results in array $ini_array_name"
pre_parse="$(sed 's/^ *//g;s/#.*//g;s/ *$//g' <$ini_file | egrep -v '^$')"
while read line; do
if [[ ${line:0:1} = "[" ]]; then # Is the line starting with "["?
# Replace [section_name] to section_name by removing the first and last character
section="${line:1}"
section="${section%\]}"
eval "sections=\${$ini_array_name[sections_list]}"
sections="$sections${sections:+ }$section"
eval "$ini_array_name[sections_list]=\"$sections\""
Show_Debug "$ini_array_name[sections_list]=\"$sections\""
eval "$ini_array_name[$section.exist]=YES"
Show_Debug "$ini_array_name[$section.exist]='YES'"
else
variable=${line%%=*} # content before the =
value=${line#*=} # content after the =
if [[ $variable = includefile ]]; then
# Include a single file
Load_Ini "$include_directory/$value" "$ini_array_name"
continue
elif [[ $variable = includedir ]]; then
# Include a directory
# If the value doesn't start with a /, add the calculated include_directory
if [[ $value != /* ]]; then
value="$include_directory/$value"
fi
# go thru each file
for file in $(ls $value/*.ini 2>/dev/null); do
if [[ $file != *.ini ]]; then continue; fi
# Load a single file
Load_Ini "$file" "$ini_array_name"
done
continue
elif [[ $variable = includesection ]]; then
# Copy an existing section into the current section
eval "all_index=\"\${!$ini_array_name[#]}\""
# It's not necessarily fast. Need to go thru all the array
for index in $all_index; do
# Only if it is the requested section
if [[ $index = $value.* ]]; then
# Evaluate the subsection [section.subsection] --> subsection
subsection=${index#*.}
# Get the current value (source section)
eval "value_array=\"\${$ini_array_name[$index]}\""
# Assign the value to the current section
# The $value_array must be resolved on the second pass of the eval, so make sure the
# first pass doesn't resolve it (\$value_array instead of $value_array).
# It must be evaluated on the second pass in case there is special character like $1,
# or ' or " in it (code).
eval "$ini_array_name[$section.$subsection]=\"\$value_array\""
Show_Debug "$ini_array_name[$section.$subsection]=\"$value_array\""
fi
done
fi
# Add the value to the array
eval "current_value=\"\${$ini_array_name[$section.$variable]}\""
# If there's already something for this field, add it with the current
# content separated by a LF (line_feed)
new_value="$current_value${current_value:+$LF}$value"
# Assign the content
# The $new_value must be resolved on the second pass of the eval, so make sure the
# first pass doesn't resolve it (\$new_value instead of $new_value).
# It must be evaluated on the second pass in case there is special character like $1,
# or ' or " in it (code).
eval "$ini_array_name[$section.$variable]=\"\$new_value\""
Show_Debug "$ini_array_name[$section.$variable]=\"$new_value\""
fi
done <<< "$pre_parse"
Show_Debug "exit $0($#)\n"
}
When I use a password in base64, I put the separator ":" because the base64 string may has "=". For example (I use ksh):
> echo "Abc123" | base64
QWJjMTIzCg==
In parameters.ini put the line pass:QWJjMTIzCg==, and finally:
> PASS=`awk -F":" '/pass/ {print $2 }' parameters.ini | base64 --decode`
> echo "$PASS"
Abc123
If the line has spaces like "pass : QWJjMTIzCg== " add | tr -d ' ' to trim them:
> PASS=`awk -F":" '/pass/ {print $2 }' parameters.ini | tr -d ' ' | base64 --decode`
> echo "[$PASS]"
[Abc123]
This uses the system perl and clean regular expressions:
cat parameters.ini | perl -0777ne 'print "$1" if /\[\s*parameters\.ini\s*\][\s\S]*?\sdatabase_version\s*=\s*(.*)/'
The answer of "Karen Gabrielyan" among another answers was the best but in some environments we dont have awk, like typical busybox, i changed the answer by below code.
trim()
{
local trimmed="$1"
# Strip leading space.
trimmed="${trimmed## }"
# Strip trailing space.
trimmed="${trimmed%% }"
echo "$trimmed"
}
function parseIniFile() { #accepts the name of the file to parse as argument ($1)
#declare syntax below (-gA) only works with bash 4.2 and higher
unset g_iniProperties
declare -gA g_iniProperties
currentSection=""
while read -r line
do
if [[ $line = [* ]] ; then
if [[ $line = [* ]] ; then
currentSection=$(echo $line | sed -e 's/\r//g' | tr -d "[]")
fi
else
if [[ $line = *=* ]] ; then
cleanLine=$(echo $line | sed -e 's/\r//g')
key=$(trim $currentSection.$(echo $cleanLine | cut -d'=' -f1'))
value=$(trim $(echo $cleanLine | cut -d'=' -f2))
g_iniProperties[$key]=$value
fi
fi;
done < $1
}
If Python is available, the following will read all the sections, keys and values and save them in variables with their names following the format "[section]_[key]". Python can read .ini files properly, so we make use of it.
#!/bin/bash
eval $(python3 << EOP
from configparser import SafeConfigParser
config = SafeConfigParser()
config.read("config.ini"))
for section in config.sections():
for (key, val) in config.items(section):
print(section + "_" + key + "=\"" + val + "\"")
EOP
)
echo "Environment_type: ${Environment_type}"
echo "Environment_name: ${Environment_name}"
config.ini
[Environment]
type = DEV
name = D01
If using sections, this will do the job :
Example raw output :
$ ./settings
[section]
SETTING_ONE=this is setting one
SETTING_TWO=This is the second setting
ANOTHER_SETTING=This is another setting
Regexp parsing :
$ ./settings | sed -n -E "/^\[.*\]/{s/\[(.*)\]/\1/;h;n;};/^[a-zA-Z]/{s/#.*//;G;s/([^ ]*) *= *(.*)\n(.*)/\3_\1='\2'/;p;}"
section_SETTING_ONE='this is setting one'
section_SETTING_TWO='This is the second setting'
section_ANOTHER_SETTING='This is another setting'
Now all together :
$ eval "$(./settings | sed -n -E "/^\[.*\]/{s/\[(.*)\]/\1/;h;n;};/^[a-zA-Z]/{s/#.*//;G;s/([^ ]*) *= *(.*)\n(.*)/\3_\1='\2'/;p;}")"
$ echo $section_SETTING_TWO
This is the second setting
I have nice one-liner (assuimng you have php and jq installed):
cat file.ini | php -r "echo json_encode(parse_ini_string(file_get_contents('php://stdin'), true, INI_SCANNER_RAW));" | jq '.section.key'
This thread does not have enough solutions to choose from, thus here my solution, it does not require tools like sed or awk :
grep '^\[section\]' -A 999 config.ini | tail -n +2 | grep -B 999 '^\[' | head -n -1 | grep '^key' | cut -d '=' -f 2
If your are to expect sections with more than 999 lines, feel free to adapt the example above. Note that you may want to trim the resulting value, to remove spaces or a comment string after the value. Remove the ^ if you need to match keys that do not start at the beginning of the line, as in the example of the question. Better, match explicitly for white spaces and tabs, in such a case.
If you have multiple values in a given section you want to read, but want to avoid reading the file multiple times:
CONFIG_SECTION=$(grep '^\[section\]' -A 999 config.ini | tail -n +2 | grep -B 999 '^\[' | head -n -1)
KEY1=$(echo ${CONFIG_SECTION} | tr ' ' '\n' | grep key1 | cut -d '=' -f 2)
echo "KEY1=${KEY1}"
KEY2=$(echo ${CONFIG_SECTION} | tr ' ' '\n' | grep key2 | cut -d '=' -f 2)
echo "KEY2=${KEY2}"

Unscramble words Challenge - improve my bash solution

There is a Capture the Flag challenge
I have two files; one with scrambled text like this with about 550 entries
dnaoyt
cinuertdso
bda
haey
tolpap
...
The second file is a dictionary with about 9,000 entries
radar
ccd
gcc
fcc
historical
...
The goal is to find the right, unscrambled version of the word, which is contained in the dictionary file.
My approach is to sort the characters from the first word from the first file and then look up if the first word from the second file has the same length. If so then sort that too and compare them.
This is my fully functional bash script, but it is very slow.
#!/bin/bash
while IFS="" read -r p || [ -n "$p" ]
do
var=0
ro=$(echo $p | perl -F -lane 'print sort #F')
len_ro=${#ro}
while IFS="" read -r o || [ -n "$o" ]
do
ro2=$(echo $o | perl -F -lane 'print sort # F')
len_ro2=${#ro2}
let "var+=1"
if [ $len_ro == $len_ro2 ]; then
if [ $ro == $ro2 ]; then
echo $o >> new.txt
echo $var >> whichline.txt
fi
fi
done < dictionary.txt
done < scrambled-words.txt
I have also tried converting all characters to ASCII integers and sum each word, but while comparing I realized that the sum of a different char pattern may have the same sum.
[edit]
For the records:
- no anagrams contained in dictionary
- to get the flag, you need to export the unscrambled words as one blob and ans make a SHA-Hash out of it (thats the flag)
- link to ctf for guy who wanted the files https://challenges.reply.com/tamtamy/user/login.action
You're better off creating a lookup dictionary (keyed by the sorted word) from the dictionary file.
Your loop body is executed 550 * 9,000 = 4,950,000 times (O(N*M)).
The solution I propose executes two loops of at most 9,000 passes each (O(N+M)).
Bonus: It finds all possible solutions at no cost.
#!/usr/bin/perl
use strict;
use warnings qw( all );
use feature qw( say );
my $dict_qfn = "dictionary.txt";
my $scrambled_qfn = "scrambled-words.txt";
sub key { join "", sort split //, $_[0] }
my %dict;
{
open(my $fh, "<", $dict_qfn)
or die("Can't open \"$dict_qfn\": $!\n");
while (<$fh>) {
chomp;
push #{ $dict{key($_)} }, $_;
}
}
{
open(my $fh, "<", $scrambled_qfn)
or die("Can't open \"$scrambled_qfn\": $!\n");
while (<$fh>) {
chomp;
my $matches = $dict{key($_)};
say "$_ matches #$matches" if $matches;
}
}
I wouldn't be surprised if this only takes one millionths of the time of your solution for the sizes you provided (and it scales so much better than yours if you were to increase the sizes).
I would do something like this with gawk
gawk '
NR == FNR {
dict[csort()] = $0
next
}
{
print dict[csort()]
}
function csort( chars, sorted) {
split($0, chars, "")
asort(chars)
for (i in chars)
sorted = sorted chars[i]
return sorted
}' dictionary.txt scrambled-words.txt
Here's perl-free solution I came up with using sort and join:
sort_letters() {
# Splits each letter onto a line, sorts the letters, then joins them
# e.g. "hello" becomes "ehllo"
echo "${1}" | fold-b1 | sort | tr -d '\n'
}
# For each input file...
for input in "dict.txt" "words.txt"; do
# Convert each line to [sorted] [original]
# then sort and save the results with a .sorted extension
while read -r original; do
sorted=$(sort_letters "${original}")
echo "${sorted} ${original}"
done < "${input}" | sort > "${input}.sorted"
done
# Join the two files on the [sorted] word
# outputting the scrambled and unscrambed words
join -j 1 -o 1.2,2.2 "words.txt.sorted" "dict.txt.sorted"
I tried something very alike, but a bit different.
#!/bin/bash
exec 3<scrambled-words.txt
while read -r line <&3; do
printf "%s" ${line} | perl -F -lane 'print sort #F'
done>scrambled-words_sorted.txt
exec 3>&-
exec 3<dictionary.txt
while read -r line <&3; do
printf "%s" ${line} | perl -F -lane 'print sort #F'
done>dictionary_sorted.txt
exec 3>&-
printf "" > whichline.txt
exec 3<scrambled-words_sorted.txt
while read -r line <&3; do
counter="$((++counter))"
grep -n -e "^${line}$" dictionary_sorted.txt | cut -d ':' -f 1 | tr -d '\n' >>whichline.txt printf "\n" >>whichline.txt
done
exec 3>&-
As you can see I don't create a new.txt file; instead I only create whichline.txt with a blank line where the word doesn't match. You can easily paste them up to create new.txt.
The logic behind the script is nearly the logic behind yours, with the exception that I called perl less times and I save two support files.
I think (but I am not sure) that creating them and cycle only one file will be better than ~5kk calls of perl. This way "only" ~10k times is called.
Finally, I decided to use grep because it's (maybe) the fastest regex matcher, and searching for the entire line the lenght is intrinsic in the regex.
Please, note that what #benjamin-w said is still valid and, in that case, grep will reply badly and I did not managed it!
I hope this could help [:

Find if null exists in csv file

I have a csv file. The file has some anomalies as it contains some unknown characters.
The characters appear at line 1535 in popular editors (images attached below). The sed command in the terminal for this linedoes not show anything.
$ sed '1535!d' sample.csv
"sample_id","sample_column_text_1","sample_"sample_id","sample_column_text_1","sample_column_text_2","sample_column_text_3"
However below are the snapshots of the file in various editors.
Sublime Text
Nano
Vi
The directory has various csv files that contain this character/chain of characters.
I need to write a bash script to determine the files that have such characters. How can I achieve this?
The following is from;
http://www.linuxquestions.org/questions/programming-9/how-to-check-for-null-characters-in-file-509377/
#!/usr/bin/perl -w
use strict;
my $null_found = 0;
foreach my $file (#ARGV) {
if ( ! open(F, "<$file") ) {
warn "couldn't open $file for reading: $!\n";
next;
}
while(<F>) {
if ( /\000/ ) {
print "detected NULL at line $. in file $file\n";
$null_found = 1;
last;
}
}
close(F);
}
exit $null_found;
If it works as desired, you can save it to a file, nullcheck.pl and make it executable;
chmod +x nullcheck.pl
It seems to take an array of files names as input, but will fail if it finds in any, so I'd only pass in one at a time. The command below is used to run the script.
for f in $(find . -type f -exec grep -Iq . {} \; -and -print) ; do perl ./nullcheck.pl $f || echo "$f has nulls"; done
The above find command is lifted from Linux command: How to 'find' only text files?
You can try tr :
grep '\000' filename to find if the files contain the \000 characters.
You can use this to remove NULL and make it non-NULL file :
tr < file-with-nulls -d '\000' > file-without-nulls

Fast grep on huge csv files

I have a file (queryids.txt) with a list of 847 keywords to search. I have to grep the keywords from about 12 huge csv files (the biggest has 2,184,820,000 lines). Eventually we will load it into a database of some sort but for now, we just want certain keywords to be grep'ed.
My command is:
LC_ALL=C fgrep -f queryids.txt subject.csv
I am thinking of writing a bash script like this:
#!/bin/bash
for f in *.csv
do
( echo "Processing $f"
filename=$(basename "$f")
filename="${filename%.*}"
LC_ALL=C fgrep -f queryids.txt $f > $filename"_goi.csv" ) &
done
and I will run it using: nohup bash myscript.sh &
The queryids.txt looks like this:
ENST00000401850
ENST00000249005
ENST00000381278
ENST00000483026
ENST00000465765
ENST00000269080
ENST00000586539
ENST00000588458
ENST00000586292
ENST00000591459
The subject file looks like this:
target_id,length,eff_length,est_counts,tpm,id
ENST00000619216.1,68,2.65769E1,0.5,0.300188,00065a62-5e18-4223-a884-12fca053a109
ENST00000473358.1,712,5.39477E2,8.26564,0.244474,00065a62-5e18-4223-a884-12fca053a109
ENST00000469289.1,535,3.62675E2,4.82917,0.212463,00065a62-5e18-4223-a884-12fca053a109
ENST00000607096.1,138,1.92013E1,0,0,00065a62-5e18-4223-a884-12fca053a109
ENST00000417324.1,1187,1.01447E3,0,0,00065a62-5e18-4223-a884-12fca053a109
I am concerned this will take a long time. Is there a faster way to do this?
Thanks!
Few things I can suggest to improve the performance:
No need to spawn a sub-shell using ( .. ) &, you can use braces { ... } & if needed.
Use grep -F (non-regex or fixed string search) to make grep run faster
Avoid basename command and use bash string manipulation
Try this script:
#!/bin/bash
for f in *.csv; do
echo "Processing $f"
filename="${f##*/}"
LC_ALL=C grep -Ff queryids.txt "$f" > "${filename%.*}_goi.csv"
done
I suggest you run this on a smaller dataset to compare the performance gain.
You could try this instead:
awk '
BEGIN {
while ( (getline line < "queryids.txt") > 0 ) {
re = ( re=="" ? "" : re "|") line
}
}
FNR==1 { close(out); out=FILENAME; sub(/\.[^.]+$/,"_goi&",out) }
$0 ~ re { print > out }
' *.csv
It's using a regexp rather than string comparison - whether or not that matters and, if so, what we can do about it depends on the values in queryids.txt. In fact there may be a vastly faster and more robust way to do this depending on what your files contain so if you edit your question to include some examples of your file contents we could be of more help.
I see you have now posted some sample input and indeed we can do this much faster and more robustly by using a hash lookup:
awk '
BEGIN {
FS="."
while ( (getline line < "queryids.txt") > 0 ) {
ids[line]
}
}
FNR==1 { close(out); out=FILENAME; sub(/\.[^.]+$/,"_goi&",out) }
$1 in ids { print > out }
' *.csv

Better way of extracting data from file for comparison

Problem: Comparison of files from Pre-check status and Post-check status of a node for specific parameters.
With some help from community, I have written the following solution which extracts the information from files from directories pre and post and based on the "Node-ID" (which happens to be unique and is to be extracted from the files as well). After extracting the data from Pre/post folder, I have created folders based on the node-id and dumped files into the folders.
My Code to extract data (The data is extracted from Pre and Post folders)
FILES=$(find postcheck_logs -type f -name *.log)
for f in $FILES
do
NODE=`cat $f | grep -m 1 ">" | awk '{print $1}' | sed 's/[>]//g'` ##Generate the node-id
echo "Extracting Post check information for " $NODE
mkdir temp/$NODE-post ## create a temp directory
cat $f | awk 'BEGIN { RS=$NODE"> "; } /^param1/ { foo=RS $0; } END { print foo ; }' > temp/$NODE-post/param1.txt ## extract data
cat $f | awk 'BEGIN { RS=$NODE"> "; } /^param2/ { foo=RS $0; } END { print foo ; }' > temp/$NODE-post/param2.txt
cat $f | awk 'BEGIN { RS=$NODE"> "; } /^param3/ { foo=RS $0; } END { print foo ; }' > temp/$NODE-post/param3.txt
done
After this I have a structure as:
/Node1-pre/param1.txt
/Node1-post/param1.txt
and so on.
Now I am stuck to compare $NODE-pre and $NODE-post files,
I have tried to do it using recursive grep, but I am not finding a suitable way to do so. What is the best possible way to compare these files using diff?
Moreover, I find the above data extraction program very slow. I believe it's not the best possible way (using least resources) to do so. Any suggestions?
Look askance at any instance of cat one-file — you could use I/O redirection on the next command in the pipeline instead.
You can do the whole thing more simply with:
for f in $(find postcheck_logs -type f -name *.log)
do
NODE=$(sed '/>/{ s/ .*//; s/>//g; p; q; }' $f) ##Generate the node-id
echo "Extracting Post check information for $NODE"
mkdir temp/$NODE-post
awk -v NODE="$NODE" -v DIR="temp/$NODE-post" \
'BEGIN { RS=NODE"> " }
/^param1/ { param1 = $0 }
/^param2/ { param2 = $0 }
/^param3/ { param3 = $0 }
END {
print RS param1 > DIR "/param1.txt"
print RS param2 > DIR "/param2.txt"
print RS param3 > DIR "/param3.txt"
}' $f
done
The NODE finding process is much better done by a single sed command than cat | grep | awk | sed, and you should plan to use $(...) rather than back-quotes everywhere.
The main processing of the log file should be done once; a single awk command is sufficient. The script is passed to variables — NODE and the directory name. The BEGIN is cleaned up; the $ before NODE was probably not what you intended. The main actions are very similar; each looks for the relevant parameter name and saves it in an appropriate variable. At the end, it write the saved values to the relevant files, decorated with the value of RS. Semicolons are only needed when there's more than one statement on a line; there's just one statement per line in this expanded script. It looks bigger than the original, but that's only because I'm using vertical space.
As to comparing the before and after files, you can do it in many ways, depending on what you want to know. If you've got a POSIX-compliant diff (you probably do), you can use:
diff -r temp/$NODE-pre temp/$NODE-post
to report on the differences, if any, between the contents of the two directories. Alternatively, you can do it manually:
for file in param1.txt param2.txt param3.txt
do
if cmp -s temp/$NODE-pre/$file temp/$NODE-post/$file
then : No difference
else diff temp/$NODE-pre/$file temp/$NODE-post/$file
fi
done
Clearly, you can wrap that in a 'for each node' loop. And, if you are going to need to do that, then you probably do want to capture the output of the find command in a variable (as in the original code) so that you do not have to repeat that operation.

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