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  • Why do I get an error when inserting rows with Net::Cassandra::Easy and Cassandra 0.5x?

    - by knorv
    When using the Perl module Net::Cassandra::Easy to interface with Cassandra I use the following code to read colums col[123] from rows row[123] in the column-family Standard1: my $cassandra = Net::Cassandra::Easy->new(keyspace => 'Keyspace1', server => 'localhost'); $cassandra->connect(); my $result = $cassandra->get(['row1', 'row2', 'row3'], family => 'Standard1', byname => ['col1', 'col2', 'col3']); This works as expected. However, when trying to insert row row1 with .. $result = $cassandra->mutate(['row1'], family => 'Standard1', insertions => { "col1" => "Value to set." }); .. I get the error message Can't use string ("0") as a SCALAR ref while "strict refs" in use at .../Net/GenThrift/Thrift/BinaryProtocol.pm line 376. What am I doing wrong?

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  • DBD::CSV: Problem with file-name-extensions

    - by sid_com
    In this script I have problems with file-name-extensions: if I use /home/mm/test_x it works, with file named /home/mm/test_x.csv it doesn't: #!/usr/bin/env perl use warnings; use strict; use 5.012; use DBI; my $table_1 = '/home/mm/test_1.csv'; my $table_2 = '/home/mm/test_2.csv'; #$table_1 = '/home/mm/test_1'; #$table_2 = '/home/mm/test_2'; my $dbh = DBI->connect( "DBI:CSV:" ); $dbh->{RaiseError} = 1; $table_1 = $dbh->quote_identifier( $table_1 ); $table_2 = $dbh->quote_identifier( $table_2 ); my $sth = $dbh->prepare( "SELECT a.id, a.name, b.city FROM $table_1 AS a NATURAL JOIN $table_2 AS b" ); $sth->execute; $sth->dump_results; $dbh->disconnect; Output with file-name-extention: DBD::CSV::st execute failed: Execution ERROR: No such column '"/home/mm/test_1.csv".id' called from /usr/local/lib/perl5/site_perl/5.12.0/x86_64-linux/DBD/File.pm at 570. Output without file-name-extension: '1', 'Brown', 'Laramie' '2', 'Smith', 'Watertown' 2 rows Is this a bug?

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  • How to include frameset under CGI.pm

    - by neversaint
    I want to have a cgi-script that does two things. Take the input from a form. Generate results base on the input values on a frame. Primarily I want the frame exist only after the results is generated/printed. Below is the simplified code of what I want to do. But somehow it doesn't work. What's the right way to do it? #!/usr/local/bin/perl use CGI ':standard'; print header; print start_html('A Simple Example'), h1('A Simple Example'), start_form, "What's your name? ",textfield('name'), p, "What's the combination?", p, checkbox_group(-name=>'words', -values=>['eenie','meenie','minie','moe'], -defaults=>['eenie','minie']), p, "What's your favorite color? ", popup_menu(-name=>'color', -values=>['red','green','blue','chartreuse']), p, submit, end_form, hr; if (param()) { # begin create the frame print <<EOF; <html><head><title>$TITLE</title></head> <frameset rows="10,90"> <frame src="$script_name/query" name="query"> <frame src="$script_name/response" name="response"> </frameset> EOF # Finish creating frame print "Your name is: ",em(param('name')), p, "The keywords are: ",em(join(", ",param('words'))), p, "Your favorite color is: ",em(param('color')), hr; } print end_html;

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  • Bioperl, equivalent of IO::ScalarArray for array of Seq objects?

    - by Ryan Thompson
    In perl, we have IO::ScalarArray for treating the elements of an array like the lines of a file. In BioPerl, we have Bio::SeqIO, which can produce a filehandle that reads and writes Bio::Seq objects instead of strings representing lines of text. I would like to do a combination of the two: I would like to obtain a handle that reads successive Bio::Seq objects from an array of such objects. Is there any way to do this? Would it be trivial for me to implement a module that does this? My reason for wanting this is that I would like to be able to write a subroutine that accepts either a Bio::SeqIO handle or an array of Bio::Seq objects, and I'd like to avoid writing separate loops based on what kind of input I get. Perhaps the following would be better than writing my own IO module? sub process_sequences { my $input = $_[0]; # read either from array of Bio::Seq or from Bio::SeqIO my $nextseq; if (ref $input eq 'ARRAY') { my $pos = 0 $nextseq = sub { return $input->[$pos++] if $pos < @$input}; } } else { $nextseq = sub { $input->getline(); } } while (my $seq = $nextseq->()) { do_cool_stuff_with($seq) } }

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  • Regular expression to match empty HTML tags that may contain embedded JSTL?

    - by Keith Bentrup
    I'm trying to construct a regular expression to look for empty html tags that may have embedded JSTL. I'm using Perl for my matching. So far I can match any empty html tag that does not contain JSTL with the following? /<\w+\b(?!:)[^<]*?>\s*<\/\w+/si The \b(?!:) will avoid matching an opening JTSL tag but that doesn't address the whether JSTL may be within the HTML tag itself (which is allowable). I only want to know if this HTML tag has no children (only whitespace or empty). So I'm looking for a pattern that would match both the following: <div id="my-id"> </div> <div class="<c:out var="${my.property}" />"></div> Currently the first div matches. The second does not. Is it doable? I tried several variations using lookahead assertions, and I'm starting to think it's not. However, I can't say for certain or articulate why it's not. Edit: I'm not writing something to interpret the code, and I'm not interested in using a parser. I'm writing a script to point out potential issues/oversights. And at this point, I'm curious, too, to see if there is something clever with lookaheads or lookbehinds that I may be missing. If it bothers you that I'm trying to "solve" a problem this way, don't think of it as looking for a solution. To me it's more of a challenge now, and an opportunity to learn more about regular expressions. Also, if it helps, you can assume that the html is xhtml strict.

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  • How to delete sentences starting with a lower case letter?

    - by Ron
    Hello: In the example below the following regex (".*?") was used to remove all dialogue first. The next step is to remove all remaining sentences starting with a lower case letter. Only sentences starting with an upper case letter should remain. Example: exclaimed Wade. Indeed, below them were villages, of crude huts made of timber and stone and mud. Rubble work walls, for they needed little shelter here, and the people were but savages. asked Arcot, his voice a bit unsteady with suppressed excitement. replied Morey without turning from his station at the window. Below them now, less than half a mile down on the patchwork of the Nile valley, men were standing, staring up, collecting in little groups, gesticulating toward the strange thing that had materialized in the air above them. In the example above the following should be deleted only: exclaimed Wade. asked Arcot, his voice a bit unsteady with suppressed excitement. replied Morey without turning from his station at the window. A useful regex or simple Perl or python code is appreciated. I'm using version 7 of Textpipe. Thanks.

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  • Why "Not an ARRAY reference" error?

    - by Sandra Schlichting
    I have this script #!/usr/bin/perl use strict; use warnings; use yy; my $data = [ ["aax", "ert", "ddd"], ["asx", "eer", "kkk"], ["xkk", "fff", "lll"], ["xxj", "vtt", "lle"], ]; use Test::More tests => 4; is(yy::type1_to_type2(\$data, 'aax'), 'ert'); is(yy::type1_to_type3(\$data, 'asx'), 'kkk'); is(yy::type2_to_type3(\$data, 'fff'), 'lll'); is(yy::type3_to_type1(\$data, 'lle'), 'xxj'); which uses this module package yy; sub typeX_to_typeY { my ($x, $y, $data, $str) = @_; foreach (@$data) { if ($_->[$x - 1] eq $str) { return $_->[$y - 1]; } } return; } sub type1_to_type2 { typeX_to_typeY(1, 2, @_) } sub type1_to_type3 { typeX_to_typeY(1, 3, @_) } sub type2_to_type1 { typeX_to_typeY(2, 1, @_) } sub type2_to_type3 { typeX_to_typeY(2, 3, @_) } sub type3_to_type1 { typeX_to_typeY(3, 1, @_) } sub type3_to_type2 { typeX_to_typeY(3, 2, @_) } 1; and gives this error Not an ARRAY reference at yy.pm line 6. # Looks like your test died before it could output anything. The line it complains about is foreach (@$data) { Isn't this the way to pass an array reference? What am I doing wrong?

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  • Generic dataset handling library

    - by Pep.
    Hello, I want to build a generic Perl module for handling and analysing biomedical character separated datasets and which can, most certain, be used on any kind of datasets that contain a mixture of categorical (A,B,C,..) and continuous (1.2,3,881..) and identifier (XXX1,XXX2...). The plan is to have people initialize the module and then use some arguments to point to the data file(s), the place were the analysis reports should be placed and the structure of the data. By structure of data I mean which variable is in which place and its name/type. And this is where I need some enlightenment. I am baffled how to do this in a clean way. Obviously, having people create a simple schema file, be it XML or some other format would be the cleanest but maybe not all people enjoy doing something like this. The solutions I can think of are: Create a configuration file in XML or similar and with a prespecified format. Pass the information during initialization of the module. Use the first row of the data as headers and try to guess types (ouch) Surely there must be a "canonical" way of doing this that is also usable and efficient. Thanks p.

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  • Is there a reason to use the XML::LibXML::Number-object in my XML::LibXML-example?

    - by sid_com
    In this example I get to times '96'. Is there a possible case where I would need a XML::LibXML-Number-object to to achieve the goal? #!/usr/bin/env perl use warnings; use strict; use 5.012; use XML::LibXML; my $xml_string =<<EOF; <?xml version="1.0" encoding="UTF-8"?> <filesystem> <path> <dirname>/var</dirname> <files> <action>delete</action> <age units="hours">10</age> </files> <files> <action>delete</action> <age units="hours">96</age> </files> </path> </filesystem> EOF #/ my $doc = XML::LibXML->load_xml( string => $xml_string ); my $root = $doc->documentElement; my $result = $root->find( '//files/age[@units="hours"]' ); $result = $result->get_node( 1 ); say ref $result; # XML::LibXML::Element say $result->textContent; # 96 $result = $root->find ( 'number( //files/age[@units="hours"] )' ); say ref $result; # XML::LibXML::Number say $result; # 96

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  • How to extract block of XML from a log file on Linux

    - by dragonmantank
    I have a log file that looks like the following: 2010-05-12 12:23:45 Some sort of log entry 2010-05-12 01:45:12 Request XML: <RootTag> <Element>Value</Element> <Element>Another Value</Element> </RootTag> 2010-05-12 01:45:32 Response XML: <ResponseRoot> <Element>Value</Element> </ResponseRoot> 2010-05-12 01:45:49 Another log entry What I want to do is extract the Request and Response XML (and ultimately dump them into their own single files). I had a similar parser that used egrep but the XML was all on one line, not multiple ones like above. The log files are also somewhat large, hitting 500-600 megs a log. Smaller logs I would read in via a PHP script and use regex matching, but the amount of memory required for such a large file would more than likely kill the script. Is there an easy way using the built-in tools on a Linux box (CentOS in this case) to extract multiple lines or am I going to have to bite the bullet and use Perl or PHP to read in the entire file to extract it?

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  • How do I include a frameset under CGI.pm?

    - by neversaint
    I want to have a cgi-script that does two things. Take the input from a form. Generate results base on the input values on a frame. I also want the frame to exist only after the result is generated/printed. Below is the simplified code of what I want to do. But somehow it doesn't work. What's the right way to do it? #!/usr/local/bin/perl use CGI ':standard'; print header; print start_html('A Simple Example'), h1('A Simple Example'), start_form, "What's your name? ",textfield('name'), p, "What's the combination?", p, checkbox_group(-name=>'words', -values=>['eenie','meenie','minie','moe'], -defaults=>['eenie','minie']), p, "What's your favorite color? ", popup_menu(-name=>'color', -values=>['red','green','blue','chartreuse']), p, submit, end_form, hr; if (param()) { # begin create the frame print <<EOF; <html><head><title>$TITLE</title></head> <frameset rows="10,90"> <frame src="$script_name/query" name="query"> <frame src="$script_name/response" name="response"> </frameset> EOF # Finish creating frame print "Your name is: ",em(param('name')), p, "The keywords are: ",em(join(", ",param('words'))), p, "Your favorite color is: ",em(param('color')), hr; } print end_html;

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  • What is wrong with accessing DBI directly?

    - by canavanin
    Hi everyone! I'm currently reading Effective Perl Programming (2nd edition). I have come across a piece of code which was described as being poorly written, but I don't yet understand what's so bad about it, or how it should be improved. It would be great if someone could explain the matter to me. Here's the code in question: sub sum_values_per_key { my ( $class, $dsn, $user, $password, $parameters ) = @_; my %results; my $dbh = DBI->connect( $dsn, $user, $password, $parameters ); my $sth = $dbh->prepare( 'select key, calculate(value) from my_table'); $sth->execute(); # ... fill %results ... $sth->finish(); $dbh->disconnect(); return \%results; } The example comes from the chapter on testing your code (p. 324/325). The sentence that has left me wondering about how to improve the code is the following: Since the code was poorly written and accesses DBI directly, you'll have to create a fake DBI object to stand in for the real thing. I have probably not understood a lot of what the book has so far been trying to teach me, or I have skipped the section relevant for understanding what's bad practice about the above code... Well, thanks in advance for your help!

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  • Checking if any of a list of values falls within a table of ranges

    - by Conspicuous Compiler
    I'm looking to check whether any of a list of integers fall in a list of ranges. The ranges are defined in a table defined something like: # Extra Type Field Default Null Key 0 int(11) rangeid 0 NO PRI 1 int(11) max 0 NO MUL 2 int(11) min 0 NO MUL Using MySQL 5.1 and Perl 5.10. I can check whether a single value, say 7, is in any of the ranges with a statement like SELECT 1 FROM range WHERE 7 BETWEEN min AND max If 7 is in any of those ranges, I get a single row back. If it isn't, no rows are returned. Now I have a list of, say, 50 of these values, not stored in a table at present. I assemble them using map: my $value_list = '(' . ( join ', ', map { int $_ } @values ) . ')' ; I want to see if any of the items in the list fall inside of any of the ranges, but am not particularly concerned with which number nor which range. I'd like to use a syntax such as: SELECT 1 FROM range WHERE (1, 2, 3, 4, 5, 6, 7, 42, 309, 10000) BETWEEN min AND max MySQL kindly chastises me for such syntax: Operand should contain 1 column(s) I pinged #mysql who were quite helpful. However, having already written this up by the time they responded and thinking it'd be helpful to fix the answer in a more permanent medium, I figured I'd post the question anyhow. Maybe SO will provide a different solution?

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  • Connections hanging on read()

    - by viraptor
    Hi, Short version: I've got a strange issue with a server accepting TCP connections. Even though there are normally some processes waiting, at some volume of connections it hangs. Long version: The server is written in Perl and binds a $srv socket with the reuse flag and listen == 5. Afterwards, it forks into 10 processes with a loop of $clt=$srv->accept(); do_processing($clt); $clt->shutdown(2); The client written in C is also very simple - it sends some lines, then receives all lines available and does a shutdown(sockfd, 2); There's nothing async going on and at the end both send and receive queues are empty (as reported by netstat). Connections last only ~20ms. All clients behave the same way, are the same implementation, etc. Now let's say I'm accepting X connections from client 1 and another X from client 2. Processes still report that they're idle all the time. If I add another X connections from client 3, suddenly the server processes start hanging just after accepting. The first blocking thing they do after accept(); is while (<$clt>) ... - but they don't get any data (on the first try already). Suddenly all 10 processes are in this state and do not stop waiting. On strace, the server processes seem to hang on read(), which makes sense. There are loads of connections in TIME_WAIT state belonging to that server (~100 when the problem starts to manifest), but this might be a red herring. What could be happening here?

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  • Online file storage similar to Amazon S3

    - by Joel G
    I am looking to code a file storage application in perl similar to amazon s3. I already have a amazon s3 clone that I found online called parkplace but its in ruby and is old also isn't built for high loads. I am not really sure what modules and programs I should use so id like some help picking them out. My requirements are listed below (yes I know there are lots but I could start simple then add more once I get it going): Easy API implementation for client side apps. (maybe RESTful but extras like mkdir and cp (?) Centralized database server for the USERDB (maybe PostgreSQL (?). Logging of all connections, bandwidth used, well pretty much everything to a centralized server (maybe PostgreSQL again (?). Easy server side configuration (config file(s) stored on the servers). Web based control panel for admin(s) and user(s) to show logs. (could work just running queries from the databases) Fast High Uptime Low memory usage Some sort of load distribution/load balancer (maybe a dns based or pound or perlbal or something else (?). Maybe a cache of some sort (memcached or parlbal or something else (?). Thanks in advance

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  • Is it safe to read regular expressions from a file?

    - by Zilk
    Assuming a Perl script that allows users to specify several text filter expressions in a config file, is there a safe way to let them enter regular expressions as well, without the possibility of unintended side effects or code execution? Without actually parsing the regexes and checking them for problematic constructs, that is. There won't be any substitution, only matching. As an aside, is there a way to test if the specified regex is valid before actually using it? I'd like to issue warnings if something like /foo (bar/ was entered. Thanks, Z. EDIT: Thanks for the very interesting answers. I've since found out that the following dangerous constructs will only be evaluated in regexes if the use re 'eval' pragma is used: (?{code}) (??{code}) ${code} @{code} The default is no re 'eval'; so unless I'm missing something, it should be safe to read regular expressions from a file, with the only check being the eval/catch posted by Axeman. At least I haven't been able to hide anything evil in them in my tests. Thanks again. Z.

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  • Creating multiple csv files from data within a csv file.

    - by S1syphus
    System OSX or Linux I'm trying to automate my work flow at work, each week I receive an excel file, which I convert to a csv. An example is: ,,L1,,,L2,,,L3,,,L4,,,L5,,,L6,,,L7,,,L8,,,L9,,,L10,,,L11, Title,r/t,needed,actual,Inst,needed,actual,Inst,needed,actual,Inst,needed,actual,Inst,neede d,actual,Inst,needed,actual,Inst,needed,actual,Inst,needed,actual,Inst,needed,actual,Inst,needed,actual,Inst,needed,actual,Inst EXAMPLEfoo,60,6,6,6,0,0,0,0,0,0,6,6,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 EXAMPLEbar,30,6,6,12,6,7,14,6,6,12,6,6,12,6,8,16,6,7,14,6,7.5,15,6,6,12,6,8,16,6,0,0,6,7,14 EXAMPLE1,60,3,3,3,3,5,5,3,4,4,3,3,3,3,6,6,3,4,4,3,3,3,3,4,4,3,8,8,3,0,0,3,4,4 EXAMPLE2,120,6,6,3,0,0,0,6,8,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 EXAMPLE3,60,6,6,6,6,8,8,6,6,6,6,6,6,0,0,0,0,0,0,6,8,8,6,6,6,0,0,0,0,0,0,0,10,10 EXAMPLE4,30,6,6,12,6,7,14,6,6,12,6,6,12,3,5.5,11,6,7.5,15,6,6,12,6,0,0,6,9,18,6,0,0,6,6.5,13 And so you can get a picture of how it looks in excel: What I need to do, is create multiple csv files for each instance in row 1, so L1, L2, L3, L4... And within that each csv file it needs to contain the title, r/t, needed So for L1 an example out put would look like: EXAMPLEfoo,60,6 EXAMPLEbar,30,6 EXAMPLE1,60,3 EXAMPLE2,120,6 EXAMPLE3,60,6 EXAMPLE4,30,6 And for L2: EXAMPLEfoo,60,0 EXAMPLEbar,30,6 EXAMPLE1,60,3 EXAMPLE2,120,0 EXAMPLE3,60,6 EXAMPLE4,30,6 And so on. I have tried playing around with sed and awk and hit google but I have found nothing that really solves the issue. I'd imagine perl would be particular suited to this or maybe python, so I would be more than happy to accept suggestions from users. So, any suggestions? Thanks in advance.

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  • php automatically commented with apache

    - by clement
    We have installed apache 2.2, and activeperl to run bugzilla, all that on a Windows Server 2003. Here We want to install PHP on the server to install a wiki. I followed those steps: tutorial to install PHP and enable it from Apache. After all those steps, I restart couples of times, and When I try a simple phpinfo() on PHP, the whole PHP code is commented: < ! - - ?php phpinfo(); ? - - Now, the httpd.conf was already edited for the PERL and it can be those edits that make the mistake. Here is the whole httpd.conf file: ServerRoot "C:/Program Files/Apache Software Foundation/Apache2.2" Listen 6969 LoadModule actions_module modules/mod_actions.so LoadModule alias_module modules/mod_alias.so LoadModule asis_module modules/mod_asis.so LoadModule auth_basic_module modules/mod_auth_basic.so LoadModule php5_module "c:/php/php5apache2_2.dll" LoadModule authn_default_module modules/mod_authn_default.so LoadModule authn_file_module modules/mod_authn_file.so LoadModule authz_default_module modules/mod_authz_default.so LoadModule authz_groupfile_module modules/mod_authz_groupfile.so LoadModule authz_host_module modules/mod_authz_host.so LoadModule authz_user_module modules/mod_authz_user.so LoadModule autoindex_module modules/mod_autoindex.so LoadModule cgi_module modules/mod_cgi.so LoadModule dir_module modules/mod_dir.so LoadModule env_module modules/mod_env.so LoadModule include_module modules/mod_include.so LoadModule isapi_module modules/mod_isapi.so LoadModule log_config_module modules/mod_log_config.so LoadModule mime_module modules/mod_mime.so LoadModule negotiation_module modules/mod_negotiation.so LoadModule setenvif_module modules/mod_setenvif.so User daemon Group daemon ServerAdmin [email protected] DocumentRoot C:/bugzilla-4.4.2/ Options FollowSymLinks AllowOverride None Order deny,allow Deny from all Options Indexes FollowSymLinks ExecCGI AllowOverride All Order allow,deny Allow from all ScriptInterpreterSource Registry-Strict DirectoryIndex index.html index.html.var index.cgi index.php Order allow,deny Deny from all Satisfy All ErrorLog "logs/error.log" LogLevel warn LogFormat "%h %l %u %t \"%r\" %s %b \"%{Referer}i\" \"%{User-Agent}i\"" combined LogFormat "%h %l %u %t \"%r\" %s %b" common <IfModule logio_module> LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %I %O" combinedio </IfModule> ScriptAlias /cgi-bin/ "C:/Program Files/Apache Software Foundation/Apache2.2/cgi-bin/" AllowOverride None Options None Order allow,deny Allow from all DefaultType text/plain AddType application/x-compress .Z AddType application/x-gzip .gz .tgz AddHandler cgi-script .cgi AddType application/x-httpd-php .php SSLRandomSeed startup builtin SSLRandomSeed connect builtin PHPIniDir "c:/php"

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  • Try::Tiny-Question

    - by sid_com
    Why doesn't the subroutine with try/catch give me the same results as the eval-version does. #!/usr/bin/env perl use warnings; use strict; use 5.012; use Try::Tiny; sub shell_command_1 { my $command = shift; my $timeout_alarm = shift; my @array; eval { local $SIG{ALRM} = sub { die "timeout '$command'\n" }; alarm $timeout_alarm; @array = qx( $command ); alarm 0; }; die $@ if $@ && $@ ne "timeout '$command'\n"; warn $@ if $@ && $@ eq "timeout '$command'\n"; return @array; } shell_command_1( 'sleep 4', 3 ); say "Test_1"; sub shell_command_2 { my $command = shift; my $timeout_alarm = shift; my @array; try { local $SIG{ALRM} = sub { die "timeout '$command'\n" }; alarm $timeout_alarm; @array = qx( $command ); alarm 0; } catch { die $_ if $_ ne "timeout '$command'\n"; warn $_ if $_ eq "timeout '$command'\n"; } return @array; } shell_command_2( 'sleep 4', 3 ); say "Test_2"

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  • In DBD::CSV what does a /r in the f_ext attribute mean?

    - by sid_com
    Why does only the second example append the extension to the filename and what is the "/r" in ".csv/r" for. #!/usr/bin/env perl use warnings; use strict; use 5.012; use DBI; my $dbh = DBI->connect( "DBI:CSV:f_dir=/home/mm", { RaiseError => 1, f_ext => ".csv/r"} ); my $table = 'new_1'; $dbh->do( "DROP TABLE IF EXISTS $table" ); $dbh->do( "CREATE TABLE $table ( id INT, name CHAR, city CHAR )" ); my $sth_new = $dbh->prepare( "INSERT INTO $table( id, name, city ) VALUES ( ?, ?, ?, )" ); $sth_new->execute( 1, 'Smith', 'Greenville' ); $dbh->disconnect(); # -------------------------------------------------------- $dbh = DBI->connect( "DBI:CSV:f_dir=/home/mm", { RaiseError => 1 } ); $dbh->{f_ext} = ".csv/r"; $table = 'new_2'; $dbh->do( "DROP TABLE IF EXISTS $table" ); $dbh->do( "CREATE TABLE $table ( id INT, name CHAR, city CHAR )" ); $sth_new = $dbh->prepare( "INSERT INTO $table( id, name, city ) VALUES ( ?, ?, ?, )" ); $sth_new->execute( 1, 'Smith', 'Greenville' ); $dbh->disconnect();

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  • regular expression code

    - by Gaia Andreoletti
    Deal all, I need to find match between two tab delimited files files like this: File 1: ID1 1 65383896 65383896 G C PCNXL3 ID1 2 56788990 55678900 T A ACT1 ID1 1 56788990 55678900 T A PRO55 File 2 ID2 34 65383896 65383896 G C MET5 ID2 2 56788990 55678900 T A ACT1 ID2 2 56788990 55678900 T A HLA what I would like to do is to retrive the matching line between the two file. What I would like to match is everyting after the gene ID So far I have written this code but unfortunately perl keeps giving me the error: use of "Use of uninitialized value in pattern match (m//)" Could you please help me figure out where i am doing it wrong? Thank you in advance! use strict; open (INA, $ARGV[0]) || die "cannot to open gene file"; open (INB, $ARGV[1]) || die "cannot to open coding_annotated.var files"; my @sample1 = <INA>; my @sample2 = <INB>; foreach my $line (@sample1) { my @tab = split (/\t/, $line); my $chr = $tab[1]; my $start = $tab[2]; my $end = $tab[3]; my $ref = $tab[4]; my $alt = $tab[5]; my $name = $tab[6]; foreach my $item (@sample2){ my @fields = split (/\t/,$item); if ($fields[1]=~ m/$chr(.*)/ && $fields[2]=~ m/$start(.*)/ && $fields[4]=~ m/$ref(.*)/ && $fields[5]=~ m/$alt(.*)/&& $fields[6]=~ m/$name(.*)/){ print $line,"\n",$item; } } }

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  • Checking if an SSH tunnel is up and running

    - by Jarmund
    I have a perl script which, when destilled a bit, looks like this: my $randport = int(10000 + rand(1000)); # Random port as other scripts like this run at the same time my $localip = '192.168.100.' . ($port - 4000); # Don't ask... backwards compatibility system("ssh -NL $randport:$localip:23 root\@$ip -o ConnectTimeout=60 -i somekey &"); # create the tunnel in the background sleep 10; # Give the tunnel some time to come up # Create the telnet object my $telnet = new Net::Telnet( Timeout => 10, Host => 'localhost', Port => $randport, Telnetmode => 0, Errmode => \&fail, ); # SNIPPED... a bunch of parsing data from $telnet The thing is that the target $ip is on a link with very unpredictable bandwidth, so the tunnel might come up right away, it might take a while, it might not come up at all. So a sleep is necessary to give the tunnel some time to get up and running. So the question is: How can i test if the tunnel is up and running? 10 seconds is a really undesirable delay if the tunnel comes up straight away. Ideally, i would like to check if it's up and continue with creating the telnet object once it is, to a maximum of, say, 30 seconds.

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  • DBD::CSV: Append-extension-question

    - by sid_com
    Why does only the second example append the extension to the filename and what is the "/r" in ".csv/r" for. #!/usr/bin/env perl use warnings; use strict; use 5.012; use DBI; my $dbh = DBI->connect( "DBI:CSV:f_dir=/home/mm", { RaiseError => 1, f_ext => ".csv/r"} ); my $table = 'new_1'; $dbh->do( "DROP TABLE IF EXISTS $table" ); $dbh->do( "CREATE TABLE $table ( id INT, name CHAR, city CHAR )" ); my $sth_new = $dbh->prepare( "INSERT INTO $table( id, name, city ) VALUES ( ?, ?, ?, )" ); $sth_new->execute( 1, 'Smith', 'Greenville' ); $dbh->disconnect(); # -------------------------------------------------------- $dbh = DBI->connect( "DBI:CSV:f_dir=/home/mm", { RaiseError => 1 } ); $dbh->{f_ext} = ".csv/r"; $table = 'new_2'; $dbh->do( "DROP TABLE IF EXISTS $table" ); $dbh->do( "CREATE TABLE $table ( id INT, name CHAR, city CHAR )" ); $sth_new = $dbh->prepare( "INSERT INTO $table( id, name, city ) VALUES ( ?, ?, ?, )" ); $sth_new->execute( 1, 'Smith', 'Greenville' ); $dbh->disconnect();

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  • google maps api keys to be set webserver-wide, (as env var? inside apache?)

    - by ~knb
    I have a web site with many virtual hosts and each registered with several domain names (ending in .org, .de), site1.mysite.de, site2.mysite.org Then I have different templating systems based on several programming languages (perl and php) in use on the web server. The Google Maps Api requires a unique Google Maps api key for each vhost. I want to have something like a web-server wide variable $goomapkey that I can call from inside my code. In PHP code, Now I have a kludgy case-analysis solution like $domain = substr($_SERVER['SERVER_NAME'], -3); if (".de" == $domain){ //if ("xxxxxx" eq substr($ENV{SERVER_NAME}, 0, 5)){ // $gookey = "ABQIAAA..."; //} else { //site1.de $gookey = "ABQIAAAA1Js..."; //} } elseif ("dev" == substr($_SERVER['SERVER_NAME'], 0, 3)){ //dev.mysite.org $gookey = "ABQIAAAA1JsSb..."; } else { //www.mysite.org $gookey = "ABQIAAAA1JsS..."; //TODO: Add more keys for each virtual host, for my.machinename.de, IP-address based URL, ... } ... inside my php-based CMS. A non-ideal solution, because it is, php-only, and I still have to set it at several html templates inside the CMS, and there are too many cases. I want the google maps api key to be set by the apache web server who examines the request *early in the request loop before any php page template code is constructed and evaluated. is an environment variable a good solution? which technology should be used to set the $goomapkey variable? I'd prefer mod_perl2 Apache request handler, but the documentation is confusing (many API changes in the past ). Which Apache module could I use? Is there a built-in Apache module that does the same thing?

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  • DBIx::Class base result class

    - by Rob
    Hi there, I am trying to create a model for Catalyst by using DBIx::Class::Schema::Loader. I want the result classes to have a base class I can add methods to. So MyTable.pm inherits from Base.pm which inherits from DBIx::Class::core (default). Somehow I cannot figure out how to do this. my create script is below, can anyone tell me what I am doing wrong? The script creates my model ok, but all resultset classes just directly inherit from DBIx::Class::core without my Base class in between. #!/usr/bin/perl use DBIx::Class::Schema::Loader qw/ make_schema_at /; #specifically for the entities many-2-many relation $ENV{DBIC_OVERWRITE_HELPER_METHODS_OK} = 1; make_schema_at( 'MyApp::Schema', { dump_directory => '/tmp', debug => 1, overwrite_modifications => 1, components => ['EncodedColumn'], #encoded password column use_namespaces => 1, default_resultset_class => 'Base' }, [ 'DBI:mysql:database=mydb;host=localhost;port=3306','rob', '******' ], );

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