I have a 680 million rows (19gig) file that I need the datetime appended onto every line. I get this file every night and I have to add the time that I processed it to the end of each line. I have tried many ways to do this including sed/awk and loading it into a SQL database with the last column being defaulted to the current timestamp.
I was wondering if there is a fast way to do this? My fastest way so far takes two hours and that is just not fast enough given the urgency of the information in this file. It is a flat CSV file.
edit1:
Here's what I've done so far:
awk -v date="$(date +"%Y-%m-%d %r")" '{ print $0","date}' lrn.ae.txt > testoutput.txt
Time = 117 minutes
perl -ne 'chomp; printf "%s.pdf\n", $_' EXPORT.txt > testoutput.txt
Time = 135 minutes
mysql load data local infile '/tmp/input.txt' into table testoutput
Time = 211 minutes
You don't specify if the timestamps have to be different for each of the lines. Would a "start of processing" time be enough?
If so, a simple solution is to use the paste command, with a pre-generated file of timestamps, exactly the same length as the file you're processing. Then just paste the whole thing together. Also, if the whole process is I/O bound, as others are speculating, then maybe running this on a box with an SSD drive would help speed up the process.
I just tried it locally on a 6 million row file (roughly 1% of yours), and it's actually able to do it in less than one second, on Macbook Pro, with an SSD drive.
~> date; time paste file1.txt timestamps.txt > final.txt; date
Mon Jun 5 10:57:49 MDT 2017
real 0m0.944s
user 0m0.680s
sys 0m0.222s
Mon Jun 5 10:57:49 MDT 2017
I'm going to now try a ~500 million row file, and see how that fares.
Updated:
Ok, the results are in. Paste is blazing fast compared to your solution, it took just over 90 seconds total to process the whole thing, 600M rows of simple data.
~> wc -l huge.txt
600000000 huge.txt
~> wc -l hugetimestamps.txt
600000000 hugetimestamps.txt
~> date; time paste huge.txt hugetimestamps.txt > final.txt; date
Mon Jun 5 11:09:11 MDT 2017
real 1m35.652s
user 1m8.352s
sys 0m22.643s
Mon Jun 5 11:10:47 MDT 2017
You still need to prepare the timestamps file ahead of time, but that's a trivial bash loop. I created mine in less than one minute.
A solution that simplifies mjuarez' helpful approach:
yes "$(date +"%Y-%m-%d %r")" | paste -d',' file - | head -n "$(wc -l < file)" > out-file
Note that, as with the approach in the linked answer, you must know the number of input lines in advance - here I'm using wc -l to count them, but if the number is fixed, simply use that fixed number.
yes keeps repeating its argument indefinitely, each on its own output line, until it is terminated.
paste -d',' file - pastes a corresponding pair of lines from file and stdin (-) on a single output line, separated with ,
Since yes produces "endless" output, head -n "$(wc -l < file)" ensures that processing stops once all input lines have been processed.
The use of a pipeline acts as a memory throttle, so running out of memory shouldn't be a concern.
Another alternative to test is
$ date +"%Y-%m-%d %r" > timestamp
$ join -t, -j9999 file timestamp | cut -d, -f2-
or time stamp can be generated in place as well <(date +"%Y-%m-%d %r")
join creates a cross product of the first file and second file using the non-existing field (9999), and since second file is only one line, practically appending it to the first file. Need the cut to get rid of the empty key field generated by join
If you want to add the same (current) datetime to each row in the file, you might as well leave the file as it is, and put the datetime in the filename instead. Depending on the use later, the software that processes the file could then first get the datetime from the filename.
To put the same datetime at the end of each row, some simple code could be written:
Make a string containing a separator and the datetime.
Read the lines from the file, append the above string and write back to a new file.
This way a conversion from datetime to string is only done once, and converting the file should not take much longer than copying the file on disk.
I am using orgmode on Emacs and want to automatically update parts of an orgmode file using cron scheduling.
I know how to get the cron job to run at the times I choose but now I am faced with the issue of selecting certain parts of the file to change.
I would like to increment numbers at a certain locations in a file everyday (like every day at 3am or something).
So say I have the file fruit.org:
* Apple
age: 2
* Bananas
age: 1
A really bad fruit
* Cranberry
* Death
* Easter
A cool day
I want to select all the numerical values after age and then increment them every day. How would I do this selection and replacing. I believe it would involve regexp and some tool (maybe awk) but I am relatively clueless from there on.
In awk, you could say:
awk '/age:/ { $2++ } { print }' foo.org
If you have a recent version of GNU awk, you can edit the file in-place using the option -i inplace. Otherwise, just do the usual, i.e. redirect to a temporary file and then replace the original:
awk '/age:/ { $2++ } { print }' foo.org > foo.org.tmp && mv foo.org{.tmp,}
That's basically what the inplace option of awk or sed does behind the scenes anyway.
for example
I want to add 13.29s to 2013-4-24 3:10:50.50
how to handle the milisecond ?
I've tried to use mktime and strftime, but it seems that can only deal with seconds...
awk is really a powerful tool, but I don't think awk was the best choice here, I would go with gnu date.
see the test with your example data:
#add 13.29s to date 2013-4-24 3:10:50.50
kent$ date -d'+13.29 second 2013-4-24 3:10:50.50' +"%F %T.%N"
2013-04-24 03:11:03.790000000
well I know that there are trailing zeros for nano seconds. but I think it wouldn't be problem for you if you want to remove them.
you can invoke external command from awk, if using awk is a must for you.
Not simple thing to do, but here we go:
time="2013-4-24 3:10:50.50"
echo "13.29" | awk '{split(v,a,"[ -:.]");t=mktime(a[1]" "a[2]" "a[3]" "a[4]" "a[5]" "a[6])+(a[7]/100)+$1;print strftime("%Y-%m-%d %H:%M:%S",t)"."(t-int(t))*100}' v="$time"
2013-04-24 03:11:03.79
With explanation
echo "13.29" | awk '
{
split(v,a,"[ -:.]") # Split the date string into separate parts
t=mktime(a[1]" "a[2]" "a[3]" "a[4]" "a[5]" "a[6])+(a[7]/100)+$1 # Convert to epoch time and add milliseconds and calcualte the new value
print strftime("%Y-%m-%d %H:%M:%S",t)"."(t-int(t))*100 # Convert back to normal time format and print it out
}
' v="$time" # Read the variable
Here is the simple perl script fetching data from SQL.
Read data and write on a file OUTFILE, and print the data on screen for every 10000th line.
One thing I am curious is that the printing the data on screen terminates very quickly(in 30 seconds), however, data fetching and writing on a file ends very slowly(30 minutes later).
The amount of data is not large. The output files size is less than 100Mbyte.
while ( my ($a,$b) = $curSqlEid->fetchrow_array() )
{
printf OUTFILE ("%s,%d\n", $a,$b);
$counter ++;
if($counter % 10000 == 0){
printf ("%s,%d\n", $a,$b);
}
}
$curSqlEid->finish();
$dbh->disconnect();
close(OUTFILE);
You are suffering from buffering.
Handles other than STDERR are buffered by default, and most handles use a block buffering. That means Perl will wait until there is 8KB* of data to write before sending anything to the system.
STDOUT is special. When is attached to a terminal (and only then), it uses a different kind of buffering: line buffering. When using line buffering, the data is flushed every time a newline is encountered in the data to write.
You can see this by running
$ perl -e'print "abc"; print "def"; sleep 5; print "\n"; sleep 5;'
[ 5 seconds pass ]
abcdef
[ 5 seconds pass ]
$ perl -e'print "abc"; print "def"; sleep 5; print "\n"; sleep 5;' | cat
[ 10 seconds pass ]
abcdef
The solution is to turn off buffering.
use IO::Handle qw( ); # Not needed on Perl 5.14 or later
OUTFILE->autoflush(1);
* — 8KB is the default. It can be configured when Perl is compiled. It used to be a non-configurable 4KB until 5.14.
I think you are seeing the output file size as 0 while the script is running and displaying on the console. Do not go by that. The file size will show up only once the script has finished. This is due to output buffering.
Anyways, the delay cannot be as large as 30 min. Once the script is done, you should see the output file data.
I tried various things, but the final conclusion is that python and perl has basically different handling data flow from DB. It looks like in perl, it is possible to handle data line by line while the data is transferred from DB. However, in Python it needs to wait until the entire data download from the server to process it.
It's the first great virtue of programmers. All of us have, at one time or another automated a task with a bit of throw-away code. Sometimes it takes a couple seconds tapping out a one-liner, sometimes we spend an exorbitant amount of time automating away a two-second task and then never use it again.
What tiny hack have you found useful enough to reuse? To make go so far as to make an alias for?
Note: before answering, please check to make sure it's not already on favourite command-line tricks using BASH or perl/ruby one-liner questions.
i found this on dotfiles.org just today. it's very simple, but clever. i felt stupid for not having thought of it myself.
###
### Handy Extract Program
###
extract () {
if [ -f $1 ] ; then
case $1 in
*.tar.bz2) tar xvjf $1 ;;
*.tar.gz) tar xvzf $1 ;;
*.bz2) bunzip2 $1 ;;
*.rar) unrar x $1 ;;
*.gz) gunzip $1 ;;
*.tar) tar xvf $1 ;;
*.tbz2) tar xvjf $1 ;;
*.tgz) tar xvzf $1 ;;
*.zip) unzip $1 ;;
*.Z) uncompress $1 ;;
*.7z) 7z x $1 ;;
*) echo "'$1' cannot be extracted via >extract<" ;;
esac
else
echo "'$1' is not a valid file"
fi
}
Here's a filter that puts commas in the middle of any large numbers in standard input.
$ cat ~/bin/comma
#!/usr/bin/perl -p
s/(\d{4,})/commify($1)/ge;
sub commify {
local $_ = shift;
1 while s/^([ -+]?\d+)(\d{3})/$1,$2/;
return $_;
}
I usually wind up using it for long output lists of big numbers, and I tire of counting decimal places. Now instead of seeing
-rw-r--r-- 1 alester alester 2244487404 Oct 6 15:38 listdetail.sql
I can run that as ls -l | comma and see
-rw-r--r-- 1 alester alester 2,244,487,404 Oct 6 15:38 listdetail.sql
This script saved my career!
Quite a few years ago, i was working remotely on a client database. I updated a shipment to change its status. But I forgot the where clause.
I'll never forget the feeling in the pit of my stomach when I saw (6834 rows affected). I basically spent the entire night going through event logs and figuring out the proper status on all those shipments. Crap!
So I wrote a script (originally in awk) that would start a transaction for any updates, and check the rows affected before committing. This prevented any surprises.
So now I never do updates from command line without going through a script like this. Here it is (now in Python):
import sys
import subprocess as sp
pgm = "isql"
if len(sys.argv) == 1:
print "Usage: \nsql sql-string [rows-affected]"
sys.exit()
sql_str = sys.argv[1].upper()
max_rows_affected = 3
if len(sys.argv) > 2:
max_rows_affected = int(sys.argv[2])
if sql_str.startswith("UPDATE"):
sql_str = "BEGIN TRANSACTION\\n" + sql_str
p1 = sp.Popen([pgm, sql_str],stdout=sp.PIPE,
shell=True)
(stdout, stderr) = p1.communicate()
print stdout
# example -> (33 rows affected)
affected = stdout.splitlines()[-1]
affected = affected.split()[0].lstrip('(')
num_affected = int(affected)
if num_affected > max_rows_affected:
print "WARNING! ", num_affected,"rows were affected, rolling back..."
sql_str = "ROLLBACK TRANSACTION"
ret_code = sp.call([pgm, sql_str], shell=True)
else:
sql_str = "COMMIT TRANSACTION"
ret_code = sp.call([pgm, sql_str], shell=True)
else:
ret_code = sp.call([pgm, sql_str], shell=True)
I use this script under assorted linuxes to check whether a directory copy between machines (or to CD/DVD) worked or whether copying (e.g. ext3 utf8 filenames -> fusebl
k) has mangled special characters in the filenames.
#!/bin/bash
## dsum Do checksums recursively over a directory.
## Typical usage: dsum <directory> > outfile
export LC_ALL=C # Optional - use sort order across different locales
if [ $# != 1 ]; then echo "Usage: ${0/*\//} <directory>" 1>&2; exit; fi
cd $1 1>&2 || exit
#findargs=-follow # Uncomment to follow symbolic links
find . $findargs -type f | sort | xargs -d'\n' cksum
Sorry, don't have the exact code handy, but I coded a regular expression for searching source code in VS.Net that allowed me to search anything not in comments. It came in very useful in a particular project I was working on, where people insisted that commenting out code was good practice, in case you wanted to go back and see what the code used to do.
I have two ruby scripts that I modify regularly to download all of various webcomics. Extremely handy! Note: They require wget, so probably linux. Note2: read these before you try them, they need a little bit of modification for each site.
Date based downloader:
#!/usr/bin/ruby -w
Day = 60 * 60 * 24
Fromat = "hjlsdahjsd/comics/st%Y%m%d.gif"
t = Time.local(2005, 2, 5)
MWF = [1,3,5]
until t == Time.local(2007, 7, 9)
if MWF.include? t.wday
`wget #{t.strftime(Fromat)}`
sleep 3
end
t += Day
end
Or you can use the number based one:
#!/usr/bin/ruby -w
Fromat = "http://fdsafdsa/comics/%08d.gif"
1.upto(986) do |i|
`wget #{sprintf(Fromat, i)}`
sleep 1
end
Instead of having to repeatedly open files in SQL Query Analyser and run them, I found the syntax needed to make a batch file, and could then run 100 at once. Oh the sweet sweet joy! I've used this ever since.
isqlw -S servername -d dbname -E -i F:\blah\whatever.sql -o F:\results.txt
This goes back to my COBOL days but I had two generic COBOL programs, one batch and one online (mainframe folks will know what these are). They were shells of a program that could take any set of parameters and/or files and be run, batch or executed in an IMS test region. I had them set up so that depending on the parameters I could access files, databases(DB2 or IMS DB) and or just manipulate working storage or whatever.
It was great because I could test that date function without guessing or test why there was truncation or why there was a database ABEND. The programs grew in size as time went on to include all sorts of tests and become a staple of the development group. Everyone knew where the code resided and included them in their unit testing as well. Those programs got so large (most of the code were commented out tests) and it was all contributed by people through the years. They saved so much time and settled so many disagreements!
I coded a Perl script to map dependencies, without going into an endless loop, For a legacy C program I inherited .... that also had a diamond dependency problem.
I wrote small program that e-mailed me when I received e-mails from friends, on an rarely used e-mail account.
I wrote another small program that sent me text messages if my home IP changes.
To name a few.
Years ago I built a suite of applications on a custom web application platform in PERL.
One cool feature was to convert SQL query strings into human readable sentences that described what the results were.
The code was relatively short but the end effect was nice.
I've got a little app that you run and it dumps a GUID into the clipboard. You can run it /noui or not. With UI, its a single button that drops a new GUID every time you click it. Without it drops a new one and then exits.
I mostly use it from within VS. I have it as an external app and mapped to a shortcut. I'm writing an app that relies heavily on xaml and guids, so I always find I need to paste a new guid into xaml...
Any time I write a clever list comprehension or use of map/reduce in python. There was one like this:
if reduce(lambda x, c: locks[x] and c, locknames, True):
print "Sub-threads terminated!"
The reason I remember that is that I came up with it myself, then saw the exact same code on somebody else's website. Now-adays it'd probably be done like:
if all(map(lambda z: locks[z], locknames)):
print "ya trik"
I've got 20 or 30 of these things lying around because once I coded up the framework for my standard console app in windows I can pretty much drop in any logic I want, so I got a lot of these little things that solve specific problems.
I guess the ones I'm using a lot right now is a console app that takes stdin and colorizes the output based on xml profiles that match regular expressions to colors. I use it for watching my log files from builds. The other one is a command line launcher so I don't pollute my PATH env var and it would exceed the limit on some systems anyway, namely win2k.
I'm constantly connecting to various linux servers from my own desktop throughout my workday, so I created a few aliases that will launch an xterm on those machines and set the title, background color, and other tweaks:
alias x="xterm" # local
alias xd="ssh -Xf me#development_host xterm -bg aliceblue -ls -sb -bc -geometry 100x30 -title Development"
alias xp="ssh -Xf me#production_host xterm -bg thistle1 ..."
I have a bunch of servers I frequently connect to, as well, but they're all on my local network. This Ruby script prints out the command to create aliases for any machine with ssh open:
#!/usr/bin/env ruby
require 'rubygems'
require 'dnssd'
handle = DNSSD.browse('_ssh._tcp') do |reply|
print "alias #{reply.name}='ssh #{reply.name}.#{reply.domain}';"
end
sleep 1
handle.stop
Use it like this in your .bash_profile:
eval `ruby ~/.alias_shares`