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  • Perl Threads with binmode

    - by jAndy
    Hi Folks, this call my $th = threads->create(\&print, "Hello thread World!\n"); $th->join(); works fine. But as soon as I add binmode(STDOUT, ":encoding(ISO-8859-1)"); to my script file, I get an error like "segmentation fault", "access denied". What is wrong to define an encoding type when trying to call a perl thread? Kind Regards --Andy

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  • How do I use a dependency on a Perl module installed in a non-standard location?

    - by Kinopiko
    I need to install two Perl modules on a web host. Let's call them A::B and X::Y. X::Y depends on A::B (needs A::B to run). Both of them use Module::Install. I have successfully installed A::B into a non-system location using perl Makefile.PL PREFIX=/non/system/location make; make test; make install Now I want to install X::Y, so I try the same thing perl Makefile.PL PREFIX=/non/system/location The output is $ perl Makefile.PL PREFIX=/non/system/location/ Cannot determine perl version info from lib/X/Y.pm *** Module::AutoInstall version 1.03 *** Checking for Perl dependencies... [Core Features] - Test::More ...loaded. (0.94) - ExtUtils::MakeMaker ...loaded. (6.54 >= 6.11) - File::ShareDir ...loaded. (1.00) - A::B ...missing. ==> Auto-install the 1 mandatory module(s) from CPAN? [y] It can't seem to find A::B in the system, although it is installed, and when it tries to auto-install the module from CPAN, it tries to write it into the system directory (ignoring PREFIX). I have tried using variables like PERL_LIB and LIB on the command line, after PREFIX=..., but nothing I have done seems to work. I can do make and make install successfully, but I can't do make test because of this problem. Any suggestions? I found some advice at http://servers.digitaldaze.com/extensions/perl/modules.html to use an environment variable PERL5LIB, but this also doesn't seem to work: export PERL5LIB=/non/system/location/lib/perl5/ didn't solve the problem.

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  • A Perl script and a Perl module are using `use lib` and referencing the same module

    - by miss_a
    I have a Perl script that is using two modules. The first module also uses the second module. If the the first module does use lib 'dir1', and the script does use lib 'dir2': module1.pm use lib "dir1"; use module2; script.pl use lib "dir2"; use module1; use module2; which directory is being used by the first module? Does the script's use lib, 'dir2' override the use lib, 'dir1' in the first module, or do they have different scope?

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  • (PHP vs Python vs Perl) vs Ruby [closed]

    - by Dr.Kameleon
    OK, here's what : I've programmed in over 20 different languages and now, because of a large project I'm currently working on for Mac OS X (in Objective-C/Cocoa), I need to make a final decision on which language to use for my background scripting + plugin functionality. Definitely, one factor that'll ultimately influence my decision is which one I'm most familiar with, which is PHP (one of the ugliest languages around, which I however adore... lol), then Python / Perl (the "proven values"... )... and then Ruby (which, to me, is almost confusing and I've only played with it for some time.) Now, here's my considerations : (As previously mentioned) Being familiar with it (anyway, if X is better in my case, I really don't mind studying it from scratch...) Speed Good interaction with the Shell + ease of integration with my Cocoa application Btw, some of the reasons that made me wonder if Ruby would be a good choice is : The hype around it (although, I still don't get why; but that's probably just me...) My major competitor (we're actually talking about the same type of software here) is using Ruby for its backend scripting almost exclusively (ok, along with some BASH). Isn't Ruby considered slower e.g. than Perl? Why did he choose that? Simply, a matter of personal taste? So... your thoughts?

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  • Mod_Perl configuration for multiple domains

    - by daliaessam
    Reading the Mod_Perl module documentation, can we configure it on per domain basis, what I mean can we configure it to run on every domain or specific domain only. What I see in the docs is: Registry Scripts To enable registry scripts add to httpd.conf: Alias /perl/ /home/httpd/2.0/perl/ <Location /perl/> SetHandler perl-script PerlResponseHandler ModPerl::Registry PerlOptions +ParseHeaders Options +ExecCGI </Location> and now assuming that we have the following script: #!/usr/bin/perl print "Content-type: text/plain\n\n"; print "mod_perl 2.0 rocks!\n"; saved in /home/httpd/httpd-2.0/perl/rock.pl. Make the script executable and readable by everybody: % chmod a+rx /home/httpd/httpd-2.0/perl/rock.pl Of course the path to the script should be readable by the server too. In the real world you probably want to have a tighter permissions, but for the purpose of testing, that things are working, this is just fine. From what I understand above, we can run Perl scripts only from one specific folder that we put the directive above. So the question again, can we make this directive per domain for all domains or for specific number of domains?

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  • Error with perl script using module Mail::Sendmail

    - by Octopus
    I am using below code to connect to SMTP server where authentication is required for connection. While executing script I am getting an error message saying "Error sending mail: Connection error from mail.utiba.com on port 465 ()". However the connection to the mail server is working fine, I can connect to the mail server using other mail clients. Please suggest what I am doing wrong here. Is there any sendmail settings required? #!/usr/bin/perl use strict; use warnings; use Mail::Sendmail; print "Testing Mail::Sendmail version $Mail::Sendmail::VERSION\n"; print "Default server: $Mail::Sendmail::mailcfg{smtp}->[0]\n"; print "Default sender: $Mail::Sendmail::mailcfg{from}\n"; my %mail = ( From=> 'username', Bcc => '[email protected]', Cc=> '[email protected]', Subject => 'Test message', 'X-Mailer' => "Mail::Sendmail version $Mail::Sendmail::VERSION", ); $mail{Smtp} = 'mail.server.com:port'; $mail{auth} = {user=>'username', password=>"password", required=>1 }; $mail{'X-custom'} = 'My custom additionnal header'; $mail{'mESSaGE : '} = "The message key looks terrible, but works."; $mail{Date} = Mail::Sendmail::time_to_date( time() - 86400 ); if (sendmail %mail) { print "Mail sent OK.\n" } else { print "Error sending mail: $Mail::Sendmail::error \n" } print "\n\$Mail::Sendmail::log says:\n", $Mail::Sendmail::log;

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  • Parsing tab delimited file with double quotes in Perl

    - by sfactor
    I have a data set that is tab delimited with the user-agent strings in double quotes. I need to parse each of these columns and based on the answer of my other post I used the Text::CSV module. 94410634 0 GET "Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.1; Trident/4.0; GTB6.6; .NET CLR 2.0.50727; .NET CLR 3.0.04506.648; .NET CLR 3.5.21022; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729; AskTB5.5)" 1 The code is a simple one. #!/usr/bin/perl use strict; use warnings; use Text::CSV; my $csv = Text::CSV->new(sep_char => "\t"); while (<>) { if ($csv->parse($_)) { my @columns = $csv->fields(); print "@columns\n"; } else { my $err = $csv->error_input; print "Failed to parse line: $err"; } } But i get the Failed to parse line: error when I try it on this dataset. what am I doing wrong? I need to extract the 4th column containing the user-agent strings for further processing.

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  • Help passing reference to class subroutine in Perl.

    - by stephenmm
    I am trying to pass a routine to another subroutine within a Perl module. But when I pass the sub reference the passed in ref no longer has the object data. Maybe its not possible to do it this way. The line I have a question about is the "unless" lines below: sub get_flag_end { my $self = shift; return ( -e "$self->{file}" ); } sub wait_for_end { my $self = shift; my $timeout = shift; my $poll_interval = shift; # Is it even possible to pass the oject subroutine and retain the objects data? #unless ( $self->timeout( $timeout, $poll_interval, $self->get_flag_end ) ) { # does not work unless ( $self->timeout( $timeout, $poll_interval, \&get_flag_end ) ) { # call happens but members are empty die "!!!ERROR!!! Timed out while waiting for wait_for_end: timeout=$timeout, poll_interval=$poll_interval \n"; } } sub timeout { my $self = shift; my $timeout = shift; my $poll_interval = shift; my $test_condition = shift; until ($test_condition->() || $timeout <= 0) { $timeout -= $poll_interval; sleep $poll_interval; } return $timeout > 0; # condition was met before timeout } I know that I could change the "get_flag_end" routine to take the value as an argument to the subroutine but what if there was a bunch of stuff done in "get_flag_end" and I needed more members from the object. I simplified the code a bit to make it a little easier to follow.

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  • Perl module error on solaris-10

    - by ramesh.mimit
    I have installed perl and pm_dbdmysql perl module on solaris-10. I have a perl script which makes the mysql DB connection to a diff server and runs some queries and returns the results. Its working fine on linux(redhat) but when I am running the script on solaris-10 its giving me the below error: 2010-12-14 00:00:00 and 2010-12-14 23:59:59DAILY INSIDE : 2010-12-14 00:00:00 -- 2010-12-14 23:59:59 install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC contains: /usr/local/lib/perl5/5.10.1/i86pc-solaris /usr/local/lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/i86pc-solaris /usr/local/lib/perl5/site_perl/5.10.1 .) at (eval 15) line 3. Perhaps the DBD::mysql perl module hasn't been fully installed, or perhaps the capitalisation of 'mysql' isn't right. Available drivers: DBM, ExampleP, File, Gofer, Multiplex, Proxy, Sponge, Sybase. at cerberus_report.pl line 114 Though dbd-mysql perl module is already installed. PKGINST: CSWpmdbdmysql NAME: pm_dbdmysql - MySQL driver for the Perl5 Database Interface (DBI) Is it something related to the path variables to need some other perl moudule dependency!

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  • conventions for friend methods in Perl

    - by xenoterracide
    Perl doesn't support a friend relationship between objects, nor does it support private or protected methods. What is usually done for private methods is to prefix the name with an underscore. I occasionally have methods that I think of as friend methods. Meaning that I expect them to be used by a specific object, or an object with a specific responsibility, but I'm not sure if I should make that method public (meaning foo ) or private ( _foo ) or if there's a better convention? is there a convention for friend methods?

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  • Perl numerical sorting: how to ignore leading alpha character [migrated]

    - by Luke Sheppard
    I have a 1,660 row array like this: ... H00504 H00085 H00181 H00500 H00103 H00007 H00890 H08793 H94316 H00217 ... And the leading character never changes. It is always "H" then five digits. But when I do what I believe is a numerical sort in Perl, I'm getting strange results. Some segments are sorted in order, but then a different segment starts up. Here is a segment after sorting: ... H01578 H01579 H01580 H01581 H01582 H01583 H01584 H00536 H00537 H00538 H01585 H01586 H01587 H01588 H01589 H01590 ... What I'm trying is this: my @sorted_array = sort {$a <=> $b} @raw_array; But obviously it is not working. Anyone know why?

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  • Installed Perl DBI Module Can't Be Found

    - by Russell C.
    I'm trying to setup a Perl development environment on my Mac laptop and have been having a really hard time getting it working. I thought I had everything configured correctly but when I try to run a sample script it is reporting errors with the DBI module and can't access the DB. Here is what is reported in the Apache error logs: [Fri Apr 30 23:11:33 2010] [error] [client 127.0.0.1] Can't locate DBI.pm in @INC (@INC contains: /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at main.pm line 5. I downloaded and installed both modules manually to work with MAMP using the following commands as specified in this forum post: For DBI 1. cd /Library/Perl/DBI-1.611 2. sudo Perl Makefile.PL 3. sudo make 4. sudo make install For DBD 1. cd /Library/Perl/DBD-mysql-4.014 2. sudo Perl Makefile.PL --mysql_config=/Applications/MAMP/Library/bin/mysql_config 3. sudo make 4. sudo make install What I noticed while running the above commands is that the files seems to be getting installed in the '/opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/' directory which doesn't seem to be one of the search directories that Apache mentions in the error at the beginning of this post. Here is what I'm seeing during the install: $ sudo make install Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/auto/DBI/DBI.bundle Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/auto/DBI/dbipport.h Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/auto/DBI/DBIXS.h Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/auto/DBI/dbixs_rev.h Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/auto/DBI/Driver.xst Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/auto/DBI/Driver_xst.h Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBI.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/TASKS.pod Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBD/DBM.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBD/File.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBD/Gofer.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBI/Changes.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBI/DBD.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBI/Profile.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBI/ProxyServer.pm Installing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/DBI/PurePerl.pm Installing /opt/local/share/man/man3/DBD::DBM.3pm Installing /opt/local/share/man/man3/DBD::File.3pm Installing /opt/local/share/man/man3/DBD::Gofer.3pm Installing /opt/local/share/man/man3/DBI.3pm Installing /opt/local/share/man/man3/DBI::DBD.3pm Installing /opt/local/share/man/man3/DBI::Profile.3pm Installing /opt/local/share/man/man3/DBI::ProxyServer.3pm Installing /opt/local/share/man/man3/DBI::PurePerl.3pm Installing /opt/local/share/man/man3/TASKS.3pm Installing /opt/local/bin/dbiprof Installing /opt/local/bin/dbiproxy Writing /opt/local/lib/perl5/site_perl/5.8.9/darwin-2level/auto/DBI/.packlist Appending installation info to /opt/local/lib/perl5/5.8.9/darwin-2level/perllocal.pod My question is, what am I doing wrong and how can I either 1) Get Apache to look in the right directory where the DBD & DBI modules are installed or 2) Update the way I'm installing the module to install them into one of the search directories. I honestly don't know what option makes more sense and could use guidance on that as well. As you can probably tell I'm pretty lost at the moment. Please help!!!

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  • Perl - How to use a process Handle created in a Module in another Perl Script

    - by Zwik
    Ultimately, what I want to do is to start a process in a module and parse the output in real time in another script. What I want to do : Open a process Handler (IPC) Use this attribute outside of the Module How I'm trying to do it and fail : Open the process handler Save the handler in a module's attribute Use the attribute outside the module. Code example : #module.pm self->{PROCESS_HANDLER}; sub doSomething{ ... open( self->{PROCESS_HANDLER}, "run a .jar 2>&1 |" ); ... } #perlScript.pl my $module = new module(...); ... $module->doSomething(); ... while( $module->{PROCESS_HANDLER} ){ ... }

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  • Tailing 'Jobs' with Perl under mod_perl

    - by Matthew
    Hi everyone, I've got this project running under mod_perl shows some information on a host. On this page is a text box with a dropdown that allows users to ping/nslookup/traceroute the host. The output is shown in the text box like a tail -f. It works great under CGI. When the user requests a ping it would make an AJAX call to the server, where it essentially starts the ping with the output going to a temp file. Then subsequent ajax calls would 'tail' the file so that the output was updated until the ping finished. Once the job finished, the temp file would be removed. However, under mod_perl no matter what I do I can's stop it from creating zombie processes. I've tried everything, double forking, using IPC::Run etc. In the end, system calls are not encouraged under mod_perl. So my question is, maybe there's a better way to do this? Is there a CPAN module available for creating command line jobs and tailing output that will work under mod_perl? I'm just looking for some suggestions. I know I could probably create some sort of 'job' daemon that I signal with details and get updates from. It would run the commands and keep track of their status etc. But is there a simpler way? Thanks in advance.

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  • jQuery + Perl CGI to vb.net transition

    - by user1257458
    I've been developing oracle database-heavy "web applications" forever by building my html by hand, adding some jquery to handle ajax requests (html inserts for forms processing etc), and always did my server side stuff in perl cgi. I really love how easy it is to read some form input, execute some select statements through dbi (SO EASY), and generate HTML to be inserted by the jquery request. That's a web application to me. However, my new boss builds everything in visual studio 2010, vb.net, usually webforms. So, for work reasons, I now need to start developing in vb.net so it can be collectively maintained, and I'm just seeking advice on where to start learning/how to approach this. I know I could at least learn ASP.net and VB.net, and create a webform, have it read parameters, return HTML, etc. which would allow me to use my previously written HTML and client-side scripts (jQuery). Although- since we're moving heavily to mobile applications I really need to reduce client-side processing load. Is there any advantage to my boss' method? Thanks a ton.

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  • Perl - can't flush STDOUT or STDERR

    - by Jim Salter
    Perl 5.14 from stock Ubuntu Precise repos. Trying to write a simple wrapper to monitor progress on copying from one stream to another: use IO::Handle; while ($bufsize = read (SOURCE, $buffer, 1048576)) { STDERR->printflush ("Transferred $xferred of $sendsize bytes\n"); $xferred += $bufsize; print TARGET $buffer; } This does not perform as expected (writing a line each time the 1M buffer is read). I end up seeing the first line (with a blank value of $xferred), and then the 7th and 8th lines (on an 8MB transfer). Been pounding my brains out on this for hours - I've read the perldocs, I've read the classic "Suffering from Buffering" article, I've tried everything from select and $|++ to IO::Handle to binmode (STDERR, "::unix") to you name it. I've also tried flushing TARGET with each line using IO::Handle (TARGET-flush). No dice. Has anybody else ever encountered this? I don't have any ideas left. Sleeping one second "fixes" the problem, but obviously I don't want to sleep a second every time I read a buffer just so my progress will output on the screen! FWIW, the problem is exactly the same whether I'm outputting to STDERR or STDOUT.

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  • Perl: Negative look behind regex question [migrated]

    - by James
    The Perlre in Perldoc didn't go into much detail on negative look around but I tried testing it, and didn't work as expected. I want to see if I can differentiate a C preprocessor macro definition (e.g. #define MAX(X) ....) from actual usage (y = MAX(x);), but it didn't work as expected. my $macroName = 'MAX'; my $macroCall = "y = MAX(X);"; my $macroDef = "# define MAX(X)"; my $boundary = qr{\b$macroName\b}; my $bstr = " MAX(X)"; if($bstr =~ /$boundary/) { print "boundary: $bstr matches: $boundary\n"; } else { print "Error: no match: boundary: $bstr, $boundary\n"; } my $negLookBehind = qr{(?<!define)\b$macroName\b}; if($macroCall =~ /$negLookBehind/) # "y = MAX(X)" matches "(?<!define)\bMAX\b" { print "negative look behind: $macroCall matches: $negLookBehind\n"; } else { print "no match: negative look behind: $macroCall, $negLookBehind\n"; } if($macroDef =~ /$negLookBehind/) # "#define MAX(X)" should not match "(?<!define)\bMAX\b" { print "Error: negative look behind: $macroDef matches: $negLookBehind\n"; } else { print "no match: negative look behind: $macroDef, $negLookBehind\n"; } It seems that both $macroDef and $macroCall seem to match regex /(?<!define)\b$macroName\b/. I backed off from the original /(?<\#)\s*(?<!define)\b$macroName\b/ since that didn't work either. So what did I screw up? Also does Perl allow chaining of multiple look around expressions?

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  • What is a good starter-project in Perl?

    - by Vivin Paliath
    A buddy of mine wants to learn Perl. He asked me how to go about it. I told him: To learn Perl, you must first write Perl code. This was seconded by another buddy of mine who writes a lot of good Perl code. It's very zen, but not helpful. The problem is that this is exactly how I learnt to write Perl. At my very first job I had to implement something in Perl and I pretty much just jumped into it and waded and stumbled around until I figured it out. I was thinking that the best way for him to learn Perl would be to do a small project in Perl. The problem is, I can't think of anything that would be a good starter-project in Perl. For just basic learning and understanding concepts, I have recommended going to PerlMonks, to read Learning Perl, and also to look at Perl Best Practices. Aside from this, I think a good starter-project would be useful for him to get a grasp of the language. Any suggestions?

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  • Simple perl program failing to execute

    - by yves Baumes
    Here is a sample that fails: #!/usr/bin/perl -w # client.pl #---------------- use strict; use Socket; # initialize host and port my $host = shift || 'localhost'; my $port = shift || 55555; my $server = "10.126.142.22"; # create the socket, connect to the port socket(SOCKET,PF_INET,SOCK_STREAM,(getprotobyname('tcp'))[2]) or die "Can't create a socket $!\n"; connect( SOCKET, pack( 'Sn4x8', AF_INET, $port, $server )) or die "Can't connect to port $port! \n"; my $line; while ($line = <SOCKET>) { print "$line\n"; } close SOCKET or die "close: $!"; with the error: Argument "10.126.142.22" isn't numeric in pack at D:\send.pl line 16. Can't connect to port 55555! I am using this version of Perl: This is perl, v5.10.1 built for MSWin32-x86-multi-thread (with 2 registered patches, see perl -V for more detail) Copyright 1987-2009, Larry Wall Binary build 1006 [291086] provided by ActiveState http://www.ActiveState.com Built Aug 24 2009 13:48:26 Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using "man perl" or "perldoc perl". If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page. While I am running the netcat command on the server side. Telnet does work.

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  • Crawling engine architecture - Java/ Perl integration

    - by Bigtwinz
    Hi all, I am looking to develop a management and administration solution around our webcrawling perl scripts. Basically, right now our scripts are saved in SVN and are manually kicked off by SysAdmin/devs etc. Everytime we need to retrieve data from new sources we have to create a ticket with business instructions and goals. As you can imagine, not an optimal solution. There are 3 consistent themes with this system: the retrieval of data has a "conceptual structure" for lack of a better phrase i.e. the retrieval of information follows a particular path we are only looking for very specific information so we dont have to really worry about extensive crawling for awhile (think thousands-tens of thousands of pages vs millions) crawls are url-based instead of site-based. As I enhance this alpha version to a more production-level beta I am looking to add automation and management of the retrieval of data. Additionally our other systems are Java (which I'm more proficient in) and I'd like to compartmentalize the perl aspects so we dont have to lean heavily on outside help. I've evaluated the usual suspects Nutch, Droid etc but the time spent on modifying those frameworks to suit our specific information retrieval cant be justified. So I'd like your thoughts regarding the following architecture. I want to create a solution which use Java as the interface for managing and execution of the perl scripts use Java for configuration and data access stick with perl for retrieval An example use case would be a data analyst delivers us a requirement for crawling perl developer creates the required script and uses this webapp to submit the script (which gets saved to the filesystem) the script gets kicked off from the webapp with specific parameters .... Webapp should be able to create multiple threads of the perl script to initiate multiple crawlers. So questions are what do you think how solid is integration between Java and Perl specifically from calling perl from java has someone used such a system which actually is part perl repository The goal really is to not have a whole bunch of unorganized perl scripts and put some management and organization on our information retrieval. Also, I know I can use perl do do the web part of what we want - but as I mentioned before - trying to keep perl focused. But it seems assbackwards I'm not adverse to making it an all perl solution. Open to any all suggestions and opinions. Thanks

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  • Perl syntax error [closed]

    - by Linny
    I am a beginner taking a Perl programming course. We are trying to write a basic program for counting nucleotides in a DNA string. I'm getting syntax errors on the lines that have a single bracket on lines 28 & 70 and don't know why. It also reads that I have compilation errors. I have no idea where to start figuring that out. # The purpose of this program is to count the number of nucleotides in a strand. Each protein is counted separately # print "/n NOTE: Nucleotide counting /n"; # use strict; # enforce variable declarations use warnings; # enable compiler warnings # Display number of A,a,T,t,G,g,C,c, nucleotides in a word or sequence of letters. # my ($base) = ''; # an extracted letter from a string my ($nuceotide_count) = 0 ; # the current position within the word my ($position) = 0 ; # number of vowels in user-supplied word my ($word) = ''; # word to be processed my ($A_count) = 0 ; # of A nucleotides in the user-supplied sequence my ($a_count) = 0 ; # of A nucleotides in the user-supplied sequence my ($C_count) = 0 ; # of C nucleotides in the user-supplied sequence my ($c_count) = 0 ; # of C nucleotides in the user-supplied sequence my ($G_count) = 0 ; # of G nucleotides in the user-supplied sequence my ($g_count) = 0 ; # of G nucleotides in the user-supplied sequence my ($T_count) = 0 ; # of T nucleotides in the user-supplied sequence my ($t_count) = 0 ; # of T nucleotides in the user-supplied sequence word = (STDIN) for ($position = 0);($position if (($base eq 'a') or ($base eq 'A')) { ++$A_count; } # end if ++$position; if (($base eq 'T') or ($base eq 't')) { ++$T_count; } end if ++$position; if (($base eq 'G') or ($base eq 'g')) { ++$G_count; } # end if ++$position; if (($base eq 'C') or ($base eq 'c')) { ++$C_count; } # end if ++$position; } # end for # Display final results. # print " \n The number of A or a neucleotides is: $A_count"; print " \n The number of T or t neucleotides is: $T_count"; print " \n The number of G or g neucleotides is: $G_count"; print " \n The number of C or c neucleotides is: $C_count"; print " \n\n Program completed successfully. \n" ; exit ;

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  • perl comparing 2 data file as array 2D for finding match one to one [migrated]

    - by roman serpa
    I'm doing a program that uses combinations of variables ( combiData.txt 63 rows x different number of columns) for analysing a data table ( j1j2_1.csv, 1000filas x 19 columns ) , to choose how many times each combination is repeated in data table and which rows come from (for instance, tableData[row][4]). I have tried to compile it , however I get the following message : Use of uninitialized value $val in numeric eq (==) at rowInData.pl line 34. Use of reference "ARRAY(0x1a2eae4)" as array index at rowInData.pl line 56. Use of reference "ARRAY(0x1a1334c)" as array index at rowInData.pl line 56. Use of uninitialized value in subtraction (-) at rowInData.pl line 56. Modification of non-creatable array value attempted, subscript -1 at rowInData.pl line 56. nothing This is my code: #!/usr/bin/perl use strict; use warnings; my $line_match; my $countTrue; open (FILE1, "<combiData.txt") or die "can't open file text1.txt\n"; my @tableCombi; while(<FILE1>) { my @row = split(' ', $_); push(@tableCombi, \@row); } close FILE1 || die $!; open (FILE2, "<j1j2_1.csv") or die "can't open file text1.txt\n"; my @tableData; while(<FILE2>) { my @row2 = split(/\s*,\s*/, $_); push(@tableData, \@row2); } close FILE2 || die $!; #function transform combiData.txt variable (position ) to the real value that i have to find in the data table. sub trueVal($){ my ($val) = $_[0]; if($val == 7){ return ('nonsynonymous_SNV'); } elsif( $val == 14) { return '1'; } elsif( $val == 15) { return '1';} elsif( $val == 16) { return '1'; } elsif( $val == 17) { return '1'; } elsif( $val == 18) { return '1';} elsif( $val == 19) { return '1';} else { print 'nothing'; } } #function IntToStr ( ) , i'm not sure if it is necessary) that transforms $ to strings , to use the function <eq> in the third loop for the array of combinations compared with the data array . sub IntToStr { return "$_[0]"; } for my $combi (@tableCombi) { $line_match = 0; for my $sheetData (@tableData) { $countTrue=0; for my $cell ( @$combi) { #my $temp =\$tableCombi[$combi][$cell] ; #if ( trueVal($tableCombi[$combi][$cell] ) eq $tableData[$sheetData][ $tableCombi[$combi][$cell] - 1 ] ){ #if ( IntToStr(trueVal($$temp )) eq IntToStr( $tableData[$sheetData][ $$temp-1] ) ){ if ( IntToStr(trueVal($tableCombi[$combi][$cell]) ) eq IntToStr($tableData[$sheetData][ $tableCombi[$combi][$cell] -1]) ){ $countTrue++;} if ($countTrue==@$combi){ $line_match++; #if ($line_match < 50){ print $tableData[$sheetData][4]." "; #} } } } print $line_match." \n"; }

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