From enobacon at gmail.com Thu Apr 1 11:11:54 2010 From: enobacon at gmail.com (Seven till Seven) Date: Thu, 1 Apr 2010 11:11:54 -0700 Subject: [Pdx-pm] April meeting in 1.86 weeks Message-ID: <201004011111.55060.enobacon@gmail.com> Wed. April 14th, 6:53pm at FreeGeek -- 1731 SE 10th Ave. see http://pdx.pm.org/kwiki/ The Amazing Miracle of DBIx::Class speaker: RobertBuels Rob will give an introduction to and overview of DBIx::Class. It's an object-relational mapping framework, much better than the old Class::DBI, and it will make your life easier if you are currently writing a lot of SQL in your Perl. http://search.cpan.org/dist/DBIx-Class As always, the meeting will be followed by social hour at the LuckyLab. -- http://pdx.pm.org From enobacon at gmail.com Wed Apr 7 14:03:36 2010 From: enobacon at gmail.com (Seven till Seven) Date: Wed, 7 Apr 2010 14:03:36 -0700 Subject: [Pdx-pm] DBIx::Class - April meeting next week Message-ID: <201004071403.37098.enobacon@gmail.com> Wed. April 14th, 6:53pm at FreeGeek -- 1731 SE 10th Ave. see http://pdx.pm.org/kwiki/ The Amazing Miracle of DBIx::Class speaker: RobertBuels Rob will give an introduction to and overview of DBIx::Class. It's an object-relational mapping framework, much better than the old Class::DBI, and it will make your life easier if you are currently writing a lot of SQL in your Perl. http://search.cpan.org/dist/DBIx-Class As always, the meeting will be followed by social hour at the LuckyLab. -- http://pdx.pm.org From kellert at ohsu.edu Thu Apr 8 16:27:57 2010 From: kellert at ohsu.edu (Tom Keller) Date: Thu, 8 Apr 2010 16:27:57 -0700 Subject: [Pdx-pm] cpan ExtUtils::MakeMaker issue Message-ID: <53C61B88-A00B-4BAB-BFD5-6E55246FBD98@ohsu.edu> Greetings, I think I got help with this before, but I can't remember the fix. Sorry. I'm getting makefile errors that seem to be related to switching to perl 5.10 but somehow messing up which ExtUtils::MakeMaker gets found? cpan[3]> upgrade /Bio/ Package namespace installed latest in CPAN file Bio::Align::AlignI undef 1.006001 CJFIELDS/BioPerl-1.6.1.tar.gz Bio::Factory::EMBOSS undef 1.006000 CJFIELDS/BioPerl-run-1.6.1.tar.gz Could not eval ' package ExtUtils::MakeMaker::_version; no strict; BEGIN { eval { # Ensure any version() routine which might have leaked # into this package has been deleted. Interferes with # version->import() undef *version; require version; "version"->import; } } local $Graph::VERSION; $Graph::VERSION=undef; do { ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ? }; $Graph::VERSION; ' in /Library/Perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax error at (eval 179) line 17, at EOF Suggestions greatly appreciated. thanks, Tom kellert at ohsu.edu 503-494-2442 -------------- next part -------------- An HTML attachment was scrubbed... URL: From enobacon at gmail.com Fri Apr 9 10:28:09 2010 From: enobacon at gmail.com (Eric Wilhelm) Date: Fri, 9 Apr 2010 10:28:09 -0700 Subject: [Pdx-pm] cpan ExtUtils::MakeMaker issue In-Reply-To: <53C61B88-A00B-4BAB-BFD5-6E55246FBD98@ohsu.edu> References: <53C61B88-A00B-4BAB-BFD5-6E55246FBD98@ohsu.edu> Message-ID: <201004091028.10116.enobacon@gmail.com> # from Tom Keller # on Thursday 08 April 2010 16:27: > $Graph::VERSION=undef; > do { > ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ? where's the rest? --^ > }; > $Graph::VERSION; > ' in /Library/Perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: > syntax error at (eval 179) line 17, at EOF Odd that the error says "in ...GraphAdaptor.pm". >I'm getting makefile errors that seem to be related to switching to >perl 5.10 but somehow messing up which ExtUtils::MakeMaker gets found? Which $INC{"ExtUtils/MakeMaker.pm"} is getting found and is it the right one? perl -E 'say for @INC' perl -E 'say for grep({-e } map {"$_/ExtUtils/MakeMaker.pm"} @INC)' --Eric -- "Insert random misquote here" --------------------------------------------------- http://scratchcomputing.com --------------------------------------------------- From tyler at triddle.us Mon Apr 12 20:00:02 2010 From: tyler at triddle.us (Tyler Riddle) Date: Mon, 12 Apr 2010 20:00:02 -0700 Subject: [Pdx-pm] Road trip to YAPC? Message-ID: I heard a rumor there was someone interested in road tripping to the upcoming YAPC. Is there still interest in that? I'm entertaining the idea of carpooling with a fellow hacker because I think it'd make for some great conversation. Tyler -- If you wish to make an apple pie from scratch you must first invent the universe. -- Carl Sagan From ingy at ingy.net Mon Apr 12 20:03:04 2010 From: ingy at ingy.net (Ingy dot Net) Date: Mon, 12 Apr 2010 20:03:04 -0700 Subject: [Pdx-pm] Road trip to YAPC? In-Reply-To: References: Message-ID: Maybe we can turn it into a big caravan from the West Coast, and pick up people along the way... On Mon, Apr 12, 2010 at 8:00 PM, Tyler Riddle wrote: > I heard a rumor there was someone interested in road tripping to the > upcoming YAPC. Is there still interest in that? I'm entertaining the > idea of carpooling with a fellow hacker because I think it'd make for > some great conversation. > > Tyler > > -- > If you wish to make an apple pie from scratch you must first invent > the universe. -- Carl Sagan > _______________________________________________ > Pdx-pm-list mailing list > Pdx-pm-list at pm.org > http://mail.pm.org/mailman/listinfo/pdx-pm-list > From ingy at ingy.net Mon Apr 12 20:15:01 2010 From: ingy at ingy.net (Ingy dot Net) Date: Mon, 12 Apr 2010 20:15:01 -0700 Subject: [Pdx-pm] C'Dent Talk at pdx.pm Message-ID: Hey all, I've been working on my latest Acmeist technology called C'Dent. It's a programming language for modules. Write a Perl module and publish it in over a dozen other languages. I gave a talk to pdx.pm last year about TestML, an Acmeist unit test language that complements C'Dent. I'd love to come down from Seattle and give a talk about Acmeism, C'Dent, TestML and a new Acmeist documentation project. Do you have any upcoming dates available? Read about C'Dent here: * http://cdent.org/ * http://pypi.python.org/pypi/cdent/ * http://github.com/ingydotnet/cdent/ * http://ingydotnet.github.com/cdent-seapig2010-talk/ Looking forward, Ingy From tyler at triddle.us Mon Apr 12 20:21:05 2010 From: tyler at triddle.us (Tyler Riddle) Date: Mon, 12 Apr 2010 20:21:05 -0700 Subject: [Pdx-pm] Road trip to YAPC? In-Reply-To: References: Message-ID: On Mon, Apr 12, 2010 at 8:03 PM, Ingy dot Net wrote: > Maybe we can turn it into a big caravan from the West Coast, and pick > up people along the way... Perl Party Train! -- If you wish to make an apple pie from scratch you must first invent the universe. -- Carl Sagan From enobacon at gmail.com Mon Apr 12 22:49:37 2010 From: enobacon at gmail.com (Eric Wilhelm) Date: Mon, 12 Apr 2010 22:49:37 -0700 Subject: [Pdx-pm] C'Dent Talk at pdx.pm In-Reply-To: References: Message-ID: <201004122249.37796.enobacon@gmail.com> # from Ingy dot Net # on Monday 12 April 2010 20:15: >I'd love to come down from Seattle and give a talk about Acmeism, >C'Dent, TestML and a new Acmeist documentation project. Sounds interesting. >Do you have any upcoming dates available? http://pdx.pm.org/kwiki/index.cgi?FutureMeetings Feel free to extend that calendar as needed. Thanks, Eric -- "Insert random misquote here" --------------------------------------------------- http://scratchcomputing.com --------------------------------------------------- From ingy at ingy.net Tue Apr 13 00:26:51 2010 From: ingy at ingy.net (Ingy dot Net) Date: Tue, 13 Apr 2010 00:26:51 -0700 Subject: [Pdx-pm] C'Dent Talk at pdx.pm In-Reply-To: <201004122249.37796.enobacon@gmail.com> References: <201004122249.37796.enobacon@gmail.com> Message-ID: Done. http://pdx.pm.org/kwiki/index.cgi?June2010Meeting Ingy On Mon, Apr 12, 2010 at 10:49 PM, Eric Wilhelm wrote: > # from Ingy dot Net > # on Monday 12 April 2010 20:15: > >>I'd love to come down from Seattle and give a talk about Acmeism, >>C'Dent, TestML and a new Acmeist documentation project. > > Sounds interesting. > >>Do you have any upcoming dates available? > > ?http://pdx.pm.org/kwiki/index.cgi?FutureMeetings > > Feel free to extend that calendar as needed. > > Thanks, > Eric > -- > "Insert random misquote here" > --------------------------------------------------- > ? ?http://scratchcomputing.com > --------------------------------------------------- > _______________________________________________ > Pdx-pm-list mailing list > Pdx-pm-list at pm.org > http://mail.pm.org/mailman/listinfo/pdx-pm-list > From rmb32 at cornell.edu Tue Apr 13 08:31:11 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Tue, 13 Apr 2010 08:31:11 -0700 Subject: [Pdx-pm] projector for pdx.pm meeting tomorrow Message-ID: <4BC48E3F.4020001@cornell.edu> Hi Tom, Can you confirm that you'll be at the pdx.pm meeting tomorrow with a projector? So far I think you're the only source we have for a projector for tomorrow. Thanks! Rob From igal at pragmaticraft.com Wed Apr 14 07:48:47 2010 From: igal at pragmaticraft.com (Igal Koshevoy) Date: Wed, 14 Apr 2010 07:48:47 -0700 Subject: [Pdx-pm] projector for pdx.pm meeting tomorrow In-Reply-To: <4BC48E3F.4020001@cornell.edu> References: <4BC48E3F.4020001@cornell.edu> Message-ID: <4BC5D5CF.3080008@pragmaticraft.com> On 04/13/2010 08:31 AM, Robert Buels wrote: > Can you confirm that you'll be at the pdx.pm meeting tomorrow with a > projector? So far I think you're the only source we have for a > projector for tomorrow. Has this been resolved? Unless I hear otherwise, I'll bring a projector. See you tonight. -igal From rmb32 at cornell.edu Wed Apr 14 08:32:04 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 14 Apr 2010 08:32:04 -0700 Subject: [Pdx-pm] projector for pdx.pm meeting tomorrow In-Reply-To: <4BC5D5CF.3080008@pragmaticraft.com> References: <4BC48E3F.4020001@cornell.edu> <4BC5D5CF.3080008@pragmaticraft.com> Message-ID: <4BC5DFF4.9060007@cornell.edu> Igal Koshevoy wrote: > Has this been resolved? > > Unless I hear otherwise, I'll bring a projector. Tom and Michael said they are bringing projectors too. Igal, if you could bring your projector, that would be great. I'll point it at the back wall and use your laptop to show photos of my cat. Actually, I don't have a cat. But I might use your laptop. What's your password, could you go ahead and CC that on this thread? Rob From triddle at gmail.com Wed Apr 14 08:36:41 2010 From: triddle at gmail.com (Tyler Riddle) Date: Wed, 14 Apr 2010 08:36:41 -0700 Subject: [Pdx-pm] projector for pdx.pm meeting tomorrow In-Reply-To: <4BC5DFF4.9060007@cornell.edu> References: <4BC48E3F.4020001@cornell.edu> <4BC5D5CF.3080008@pragmaticraft.com> <4BC5DFF4.9060007@cornell.edu> Message-ID: Think we can take the projectors to the Lucky Lab and play Quake there? On Wed, Apr 14, 2010 at 8:32 AM, Robert Buels wrote: > Igal Koshevoy wrote: >> Has this been resolved? >> >> Unless I hear otherwise, I'll bring a projector. > > Tom and Michael said they are bringing projectors too. > > Igal, if you could bring your projector, that would be great. ?I'll point it > at the back wall and use your laptop to show photos of my cat. > > Actually, I don't have a cat. ?But I might use your laptop. ?What's your > ?password, could you go ahead and CC that on this thread? > > Rob > > _______________________________________________ > Pdx-pm-list mailing list > Pdx-pm-list at pm.org > http://mail.pm.org/mailman/listinfo/pdx-pm-list > -- If you wish to make an apple pie from scratch you must first invent the universe. -- Carl Sagan From kellert at ohsu.edu Wed Apr 14 09:08:59 2010 From: kellert at ohsu.edu (Tom Keller) Date: Wed, 14 Apr 2010 09:08:59 -0700 Subject: [Pdx-pm] projector for pdx.pm meeting tomorrow In-Reply-To: References: <4BC48E3F.4020001@cornell.edu> <4BC5D5CF.3080008@pragmaticraft.com> <4BC5DFF4.9060007@cornell.edu> Message-ID: With three projectors, we can create a 3D presentation right? Tom kellert at ohsu.edu 503-494-2442 On Apr 14, 2010, at 8:36 AM, Tyler Riddle wrote: Think we can take the projectors to the Lucky Lab and play Quake there? On Wed, Apr 14, 2010 at 8:32 AM, Robert Buels > wrote: Igal Koshevoy wrote: Has this been resolved? Unless I hear otherwise, I'll bring a projector. Tom and Michael said they are bringing projectors too. Igal, if you could bring your projector, that would be great. I'll point it at the back wall and use your laptop to show photos of my cat. Actually, I don't have a cat. But I might use your laptop. What's your password, could you go ahead and CC that on this thread? Rob _______________________________________________ Pdx-pm-list mailing list Pdx-pm-list at pm.org http://mail.pm.org/mailman/listinfo/pdx-pm-list -- If you wish to make an apple pie from scratch you must first invent the universe. -- Carl Sagan -------------- next part -------------- An HTML attachment was scrubbed... URL: From enobacon at gmail.com Wed Apr 14 09:47:46 2010 From: enobacon at gmail.com (Eric Wilhelm) Date: Wed, 14 Apr 2010 09:47:46 -0700 Subject: [Pdx-pm] projector for meeting tonight -- Rob on DBIx::Class (live, in 3D) In-Reply-To: References: <4BC48E3F.4020001@cornell.edu> Message-ID: <201004140947.46411.enobacon@gmail.com> # from Tom Keller # on Wednesday 14 April 2010 09:08: >With three projectors, we can create a 3D presentation right? You mean 6D, right? I would usually send a reminder about the meeting around this time, so for anyone who forgot what it is about: http://pdx.pm.org/kwiki/ Now I have to find 3 videos of cats playing the etherophone. Thanks, Eric -- Moving pianos is dangerous. Moving pianos are dangerous. Buffalo buffalo buffalo buffalo buffalo buffalo buffalo. --------------------------------------------------- http://scratchcomputing.com --------------------------------------------------- From michael at jamhome.us Thu Apr 15 08:14:05 2010 From: michael at jamhome.us (Michael) Date: Thu, 15 Apr 2010 08:14:05 -0700 (PDT) Subject: [Pdx-pm] use of uninitialized ... Message-ID: <25932.170.135.241.45.1271344445.squirrel@mail.jamhome.us> Well this should be a no brainer: ?Use of uninitialized value in concatenation (.) or string at ? ? ? ? ?/usr/lib/perl5/5.8.5/Net/OUR/DNS.pm line 139 (#1) ? ?Where: ?139 print __LINE__, " our_fqdn called with $host state_code $state_code and thus region of $region_code \n"; ? ?Outputs: ?139 our_fqdn called with scdor44s4q1rr.nw.us.our-dns.com state_code OR and thus region of NW [download] All the values are being printed, indicating to my mind that they were initialized. But Perl says otherwise. Cluestick whack requested. (crosspost warning - this is also perlmonks node 834909) -- Michael Rasmussen http://www.jamhome.us/ Be Appropriate && Follow Your Curiosity -------------- next part -------------- An HTML attachment was scrubbed... URL: From chromatic at wgz.org Thu Apr 15 08:27:45 2010 From: chromatic at wgz.org (chromatic) Date: Thu, 15 Apr 2010 08:27:45 -0700 Subject: [Pdx-pm] use of uninitialized ... In-Reply-To: <25932.170.135.241.45.1271344445.squirrel@mail.jamhome.us> References: <25932.170.135.241.45.1271344445.squirrel@mail.jamhome.us> Message-ID: <201004150827.46018.chromatic@wgz.org> On Thursday 15 April 2010 at 08:14, Michael wrote: > Well this should be a no brainer: > > Use of > uninitialized value in concatenation (.) or string at > > /usr/lib/perl5/5.8.5/Net/OUR/DNS.pm line 139 (#1) If you can run this code on Perl 5.10, the warning message will include the name of the unintialized variable. -- c From dherrington at robertmarktech.com Fri Apr 16 09:31:33 2010 From: dherrington at robertmarktech.com (Daniel Herrington) Date: Fri, 16 Apr 2010 09:31:33 -0700 Subject: [Pdx-pm] Sourcing profile from within cgi script Message-ID: <4BC890E5.4070503@robertmarktech.com> All, I've been looking into ways to source a shell profile from within a perl script to get the shell variables into the perl environment. From comments online it is recommended to source the environment before executing the perl script itself, and then the variables will be accessible to the script. I don't think this solution will work since the script is being executed as a cgi through apache, they would have to source the profile in the environment of the user who started the apache process. As another alternative, I've started to look into the module Shell::EnvImporter but it doesn't mention anything about cgi. HAs anyone worked with this module before? thanks, -- Daniel B. Herrington Director of Field Services Robert Mark Technologies dherrington at robertmarktechnologies.com o: 651-769-2574 m: 503-358-8575 From db at kavod.com Fri Apr 16 09:39:08 2010 From: db at kavod.com (Daniel Browning) Date: Fri, 16 Apr 2010 09:39:08 -0700 Subject: [Pdx-pm] Sourcing profile from within cgi script In-Reply-To: <4BC890E5.4070503@robertmarktech.com> References: <4BC890E5.4070503@robertmarktech.com> Message-ID: <201004160939.08965.db@kavod.com> On Friday 16 April 2010 9:31:33 am Daniel Herrington wrote: > I've been looking into ways to source a shell profile from within a perl > script to get the shell variables into the perl environment. The way I normally get shell variables into the perl environment of CGI scripts is with the Apache PassEnv parameter, e.g.: # In httpd.conf or other apache config file: PassEnv HOME -- DB From dherrington at robertmarktech.com Fri Apr 16 09:51:35 2010 From: dherrington at robertmarktech.com (Daniel Herrington) Date: Fri, 16 Apr 2010 09:51:35 -0700 Subject: [Pdx-pm] Sourcing profile from within cgi script In-Reply-To: <201004160939.08965.db@kavod.com> References: <4BC890E5.4070503@robertmarktech.com> <201004160939.08965.db@kavod.com> Message-ID: <4BC89597.1070603@robertmarktech.com> The issue that sparked this is we're attempting to avoid setting the variables statically anywhere in perl or apache. Since the profile changes each time an upgrade occurs, we're looking to avoid redevelopment efforts in the future. Daniel Browning wrote: > On Friday 16 April 2010 9:31:33 am Daniel Herrington wrote: > >> I've been looking into ways to source a shell profile from within a perl >> script to get the shell variables into the perl environment. >> > > The way I normally get shell variables into the perl environment of CGI > scripts is with the Apache PassEnv parameter, e.g.: > > # In httpd.conf or other apache config file: > PassEnv HOME > > -- > DB > _______________________________________________ > Pdx-pm-list mailing list > Pdx-pm-list at pm.org > http://mail.pm.org/mailman/listinfo/pdx-pm-list > -- Daniel B. Herrington Director of Field Services Robert Mark Technologies dherrington at robertmarktechnologies.com o: 651-769-2574 m: 503-358-8575 -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik at hollensbe.org Fri Apr 16 09:54:09 2010 From: erik at hollensbe.org (Erik Hollensbe) Date: Fri, 16 Apr 2010 12:54:09 -0400 Subject: [Pdx-pm] Sourcing profile from within cgi script In-Reply-To: <4BC89597.1070603@robertmarktech.com> References: <4BC890E5.4070503@robertmarktech.com> <201004160939.08965.db@kavod.com> <4BC89597.1070603@robertmarktech.com> Message-ID: <4BC89631.7070308@hollensbe.org> On 04/16/10 12:51, Daniel Herrington wrote: > The issue that sparked this is we're attempting to avoid setting the > variables statically anywhere in perl or apache. Since the profile > changes each time an upgrade occurs, we're looking to avoid > redevelopment efforts in the future. > > Daniel Browning wrote: >> On Friday 16 April 2010 9:31:33 am Daniel Herrington wrote: >> >>> I've been looking into ways to source a shell profile from within a perl >>> script to get the shell variables into the perl environment. >>> >> >> The way I normally get shell variables into the perl environment of CGI >> scripts is with the Apache PassEnv parameter, e.g.: >> >> # In httpd.conf or other apache config file: >> PassEnv HOME >> >> -- >> DB >> _______________________________________________ >> Pdx-pm-list mailing list >> Pdx-pm-list at pm.org >> http://mail.pm.org/mailman/listinfo/pdx-pm-list >> > > -- > Daniel B. Herrington > Director of Field Services > Robert Mark Technologies > dherrington at robertmarktechnologies.com > o: 651-769-2574 > m: 503-358-8575 > > > _______________________________________________ > Pdx-pm-list mailing list > Pdx-pm-list at pm.org > http://mail.pm.org/mailman/listinfo/pdx-pm-list startup.pl? -------------- next part -------------- An HTML attachment was scrubbed... URL: From enobacon at gmail.com Fri Apr 16 10:28:41 2010 From: enobacon at gmail.com (Eric Wilhelm) Date: Fri, 16 Apr 2010 10:28:41 -0700 Subject: [Pdx-pm] Sourcing profile from within cgi script In-Reply-To: <4BC89597.1070603@robertmarktech.com> References: <4BC890E5.4070503@robertmarktech.com> <201004160939.08965.db@kavod.com> <4BC89597.1070603@robertmarktech.com> Message-ID: <201004161028.41354.enobacon@gmail.com> # from Daniel Herrington # on Friday 16 April 2010 09:51: >The issue that sparked this is we're attempting to avoid setting the >variables statically anywhere in perl or apache. Since the profile >changes each time an upgrade occurs, we're looking to avoid >redevelopment efforts in the future. If the environment is in some easily-parseable file, then you can just parse it as data. But, if it has some interpolations or shell operators, then you probably want the shell to interpret all of that. If you can't squeeze it into the mash of shell scripts from the init.d/apache startup process (/etc/default/apache2?), it might be easiest to read the output of `env` from a short shell script which sources the file. This would add a few subprocesses to the script, so you'll want to do that at server start instead of on each hit. --Eric -- "Insert random misquote here" --------------------------------------------------- http://scratchcomputing.com --------------------------------------------------- From schwern at pobox.com Sat Apr 17 09:03:59 2010 From: schwern at pobox.com (Michael G Schwern) Date: Sat, 17 Apr 2010 19:03:59 +0300 Subject: [Pdx-pm] cpan ExtUtils::MakeMaker issue In-Reply-To: <53C61B88-A00B-4BAB-BFD5-6E55246FBD98@ohsu.edu> References: <53C61B88-A00B-4BAB-BFD5-6E55246FBD98@ohsu.edu> Message-ID: <4BC9DBEF.2000809@pobox.com> Tom Keller wrote: > Greetings, > I think I got help with this before, but I can't remember the fix. Sorry. > I'm getting makefile errors that seem to be related to switching to perl > 5.10 but somehow messing up which ExtUtils::MakeMaker gets found? Executive summary: You can ignore it. This is "normal" behavior". The upgrade should still work. Long story short, you asked CPAN to upgrade every installed module matching /Bio/ so it had to scan the versions of all the installed .pm files which match. It uses MM->parse_version to do that. MakeMaker (MM) has to use heuristics to find the line where $VERSION is defined for each .pm file and eval that line. In the case of Bio::Ontology::SimpleGOEngine::GraphAdaptor it does not define a $VERSION for itself, which is fine, but it does mention it later on. sub new { my( $class ) = @_; $class = ref $class || $class; my $self= ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ? bless ( {}, $class ) : bless ( {}, 'Bio::Ontology::SimpleGOEngine::GraphAdaptor02' ); $self->{_graph}=new Graph::Directed; $self->{_vertex_attributes}={}; $self->{_edge_attributes}={}; return $self; } MM->parse_version picked up on that, tried to eval it, and it blew up. > cpan[3]> upgrade /Bio/ > > > Package namespace installed latest in CPAN file > Bio::Align::AlignI undef 1.006001 CJFIELDS/BioPerl-1.6.1.tar.gz > Bio::Factory::EMBOSS undef 1.006000 > CJFIELDS/BioPerl-run-1.6.1.tar.gz > Could not eval ' > package ExtUtils::MakeMaker::_version; > no strict; > BEGIN { eval { > # Ensure any version() routine which might have leaked > # into this package has been deleted. Interferes with > # version->import() > undef *version; > require version; > "version"->import; > } } > > local $Graph::VERSION; > $Graph::VERSION=undef; > do { > ( defined $Graph::VERSION && $Graph::VERSION >= > 0.5 ) ? > }; > $Graph::VERSION; > ' in > /Library/Perl/5.10.0/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm: syntax > error at (eval 179) line 17, at EOF -- Look at me talking when there's science to do. When I look out there it makes me glad I'm not you. I've experiments to be run. There is research to be done On the people who are still alive. -- Jonathan Coulton, "Still Alive" From joshua at keroes.com Wed Apr 21 16:36:17 2010 From: joshua at keroes.com (Joshua Keroes) Date: Wed, 21 Apr 2010 16:36:17 -0700 Subject: [Pdx-pm] DBIC "Can't find source" error Message-ID: I'm trying to put last week's DBIC lecture to use and have most of the obvious stuff done. I'm getting hung up by the error message: "DBIx::Class::Schema::resultset(): Can't find source for Interface at ...". For the record, dbicadmin will generate the same error message (but still generate SQL.) There are two tables: ECCKT and interface. An ECCKT is a circuit ID. Each ECCKT can have many interfaces. I'm not finding much about fixing this particular error and the DBIC source code is a little dry for me to see how it relates. Ideas? Thanks, Joshua Source code from one script and three modules: --------- # This is the program that uses the DBIC schema: use Integra::UBI::Schema; my $schema = Integra::UBI::Schema->connect( ...redacted...); my $row = $schema->resultset('ECCKT')->create({ 'ecckt' => 'ABCD0123456ABCDEF', 'customer' => 'John Johnsonson', 'end' => 1269644794, 'interface' => 'GigabitEthernet10/1', 'last_updated' => 1269644794, 'router' => 'ar11.slkcutxd.example.com', 'speed' => 1000000000, 'start' => 1265958902, 'state' => 'active', }); $row->update; --------- package Integra::UBI::Schema; use base qw/DBIx::Class::Schema/; our $VERSION = '0.01'; __PACKAGE__->load_namespaces(); __PACKAGE__->load_components(qw/Schema::Versioned/); --------- package Integra::UBI::Schema::Result::ECCKT; use base qw/DBIx::Class::Core/; __PACKAGE__->table('ecckt'); __PACKAGE__->add_columns( ecckt_id => { data_type => 'integer', size => 8, is_nullable => 0, is_auto_increment => 1, }, ecckt => { data_type => 'varchar', size => 64, is_nullable => 0, }, if_id => { data_type => 'integer', size => 8, is_nullable => 0, is_foreign_key => 1, } ); __PACKAGE__->set_primary_key('ecckt_id'); __PACKAGE__->has_many('interfaces', 'Integra::UBI::Schema::Result::Interface', 'if_id'); --------- package Integra::UBI::Schema::Result::Interface; use base qw/DBIx::Class::Core/; __PACKAGE__->table('interface'); __PACKAGE__->add_columns( if_id => { data_type => 'integer', is_nullable => 0, is_auto_increment => 1, }, customer => { data_type => 'varchar', size => 256, is_nullable => 1, default_value => '', }, state => { data_type => 'varchar', size => 12, is_nullable => 1, }, router => { data_type => 'varchar', size => 128, }, interface => { data_type => 'varchar', size => 128, }, speed => { data_type => 'integer', is_nullable => 1, }, start => { data_type => 'integer', is_nullable => 1, }, end => { data_type => 'integer', is_nullable => 1, }, last_updated => { data_type => 'integer', is_nullable => 1, }, valid_router => { data_type => 'tinyint', is_nullable => 1, }, valid_it => { data_type => 'tinyint', is_nullable => 1, }, ecckt_id => { data_type => 'integer', is_nullable => 0, is_foreign_key => 1, }, ); __PACKAGE__->set_primary_key('if_id'); __PACKAGE__->belongs_to('ecckt', 'Integra::UBI::Schema::Result::ECCKT', 'ecckt_id'); __END__ -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmb32 at cornell.edu Wed Apr 21 17:11:10 2010 From: rmb32 at cornell.edu (Robert Buels) Date: Wed, 21 Apr 2010 17:11:10 -0700 Subject: [Pdx-pm] DBIC "Can't find source" error In-Reply-To: References: Message-ID: <4BCF941E.6040105@cornell.edu> I don't get that error using that code. Are all your modules in different files? load_namespaces is actually based on .pm files on disk, not just package names. Rob Joshua Keroes wrote: > I'm trying to put last week's DBIC lecture to use and have most of the > obvious stuff done. I'm getting hung up by the error message: > "DBIx::Class::Schema::resultset(): Can't find source for Interface at > ...". For the record, dbicadmin will generate the same error message > (but still generate SQL.) > > There are two tables: ECCKT and interface. An ECCKT is a circuit ID. > Each ECCKT can have many interfaces. > > I'm not finding much about fixing this particular error and the DBIC > source code is a little dry for me to see how it relates. > > Ideas? > > Thanks, > Joshua > > Source code from one script and three modules: > > --------- > > # This is the program that uses the DBIC schema: > > use Integra::UBI::Schema; > > my $schema = Integra::UBI::Schema->connect( ...redacted...); > my $row = $schema->resultset('ECCKT')->create({ > 'ecckt' => 'ABCD0123456ABCDEF', > 'customer' => 'John Johnsonson', > 'end' => 1269644794, > 'interface' => 'GigabitEthernet10/1', > 'last_updated' => 1269644794, > 'router' => 'ar11.slkcutxd.example.com > ', > 'speed' => 1000000000, > 'start' => 1265958902, > 'state' => 'active', > }); > $row->update; > > --------- > > package Integra::UBI::Schema; > use base qw/DBIx::Class::Schema/; > > our $VERSION = '0.01'; > > __PACKAGE__->load_namespaces(); > __PACKAGE__->load_components(qw/Schema::Versioned/); > > --------- > > package Integra::UBI::Schema::Result::ECCKT; > use base qw/DBIx::Class::Core/; > > __PACKAGE__->table('ecckt'); > __PACKAGE__->add_columns( > ecckt_id => { > data_type => 'integer', > size => 8, > is_nullable => 0, > is_auto_increment => 1, > }, > ecckt => { > data_type => 'varchar', > size => 64, > is_nullable => 0, > }, > if_id => { > data_type => 'integer', > size => 8, > is_nullable => 0, > is_foreign_key => 1, > } > ); > __PACKAGE__->set_primary_key('ecckt_id'); > __PACKAGE__->has_many('interfaces', > 'Integra::UBI::Schema::Result::Interface', 'if_id'); > > --------- > > package Integra::UBI::Schema::Result::Interface; > use base qw/DBIx::Class::Core/; > > __PACKAGE__->table('interface'); > __PACKAGE__->add_columns( > if_id => { > data_type => 'integer', > is_nullable => 0, > is_auto_increment => 1, > }, > customer => { > data_type => 'varchar', > size => 256, > is_nullable => 1, > default_value => '', > }, > state => { > data_type => 'varchar', > size => 12, > is_nullable => 1, > }, > router => { > data_type => 'varchar', > size => 128, > }, > interface => { > data_type => 'varchar', > size => 128, > }, > speed => { > data_type => 'integer', > is_nullable => 1, > }, > start => { > data_type => 'integer', > is_nullable => 1, > }, > end => { > data_type => 'integer', > is_nullable => 1, > }, > last_updated => { > data_type => 'integer', > is_nullable => 1, > }, > valid_router => { > data_type => 'tinyint', > is_nullable => 1, > }, > valid_it => { > data_type => 'tinyint', > is_nullable => 1, > }, > ecckt_id => { > data_type => 'integer', > is_nullable => 0, > is_foreign_key => 1, > }, > ); > __PACKAGE__->set_primary_key('if_id'); > __PACKAGE__->belongs_to('ecckt', 'Integra::UBI::Schema::Result::ECCKT', > 'ecckt_id'); > > __END__ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pdx-pm-list mailing list > Pdx-pm-list at pm.org > http://mail.pm.org/mailman/listinfo/pdx-pm-list From joshua at keroes.com Wed Apr 21 17:19:13 2010 From: joshua at keroes.com (Joshua Keroes) Date: Wed, 21 Apr 2010 17:19:13 -0700 Subject: [Pdx-pm] DBIC "Can't find source" error In-Reply-To: <4BCF941E.6040105@cornell.edu> References: <4BCF941E.6040105@cornell.edu> Message-ID: On Wed, Apr 21, 2010 at 5:11 PM, Robert Buels wrote: > I don't get that error using that code. > > Are all your modules in different files? load_namespaces is actually based > on .pm files on disk, not just package names. > Separate files: jkeroes at water:~/svn/modules/Integra-UBI-Schema [Thu Apr 22, 00:18:21 | 526] $ tree . ??? lib/ ? ??? Integra/ ? ??? UBI/ ? ??? Schema/ ? ? ??? Result/ ? ? ??? ECCKT.pm ? ? ??? Interface.pm ? ??? Schema.pm ??? t/ ? ??? 00-load.t ? ??? boilerplate.t ? ??? pod-coverage.t ? ??? pod.t ??? .cvsignore ??? Changes ??? MANIFEST ??? Makefile.PL ??? README 6 directories, 12 files -------------- next part -------------- An HTML attachment was scrubbed... URL: From joshua at keroes.com Wed Apr 21 18:04:35 2010 From: joshua at keroes.com (Joshua Keroes) Date: Wed, 21 Apr 2010 18:04:35 -0700 Subject: [Pdx-pm] DBIC "Can't find source" error In-Reply-To: References: <4BCF941E.6040105@cornell.edu> Message-ID: More silliness; these two commands should be the same (--upgrade and -u are synonyms). They're returning different results. jkeroes at jkeroes ~/svn/modules/Integra-UBI-Schema [1233] % dbicadmin --schema=Integra::UBI::Schema --connect='["dbi:mysql:ubi:water.integra.engr","ubi","pass"]' -u -q . Performig action update... DBIx::Class::Admin::update(): resultset() expects a source name at /opt/local/bin/dbicadmin line 72 jkeroes at jkeroes ~/svn/modules/Integra-UBI-Schema [1234:255] % dbicadmin --schema=Integra::UBI::Schema --connect='["dbi:mysql:ubi:water.integra.engr","ubi","pass"]' --upgrade -q . Performig action upgrade... DBIx::Class::Admin::upgrade(): Upgrade not necessary On Wed, Apr 21, 2010 at 5:19 PM, Joshua Keroes wrote: > On Wed, Apr 21, 2010 at 5:11 PM, Robert Buels wrote: > >> I don't get that error using that code. >> >> Are all your modules in different files? load_namespaces is actually >> based on .pm files on disk, not just package names. >> > > Separate files: > > jkeroes at water:~/svn/modules/Integra-UBI-Schema > [Thu Apr 22, 00:18:21 | 526] $ tree > . > ??? lib/ > ? ??? Integra/ > ? ??? UBI/ > ? ??? Schema/ > ? ? ??? Result/ > ? ? ??? ECCKT.pm > ? ? ??? Interface.pm > ? ??? Schema.pm > ??? t/ > ? ??? 00-load.t > ? ??? boilerplate.t > ? ??? pod-coverage.t > ? ??? pod.t > ??? .cvsignore > ??? Changes > ??? MANIFEST > ??? Makefile.PL > ??? README > > 6 directories, 12 files > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joshua at keroes.com Wed Apr 21 18:12:41 2010 From: joshua at keroes.com (Joshua Keroes) Date: Wed, 21 Apr 2010 18:12:41 -0700 Subject: [Pdx-pm] DBIC "Can't find source" error In-Reply-To: References: <4BCF941E.6040105@cornell.edu> Message-ID: Test code's working now. The trick was that DBIC wasn't autopopulating the FK in the related table. I had to do that on my own: use Integra::UBI::Schema; my $schema = Integra::UBI::Schema->connect("dbi:mysql:ubi:water.integra.engr","ubi","F1ng3r!"); my $row = $schema->resultset('ECCKT')->create({ 'ecckt' => 'ABCD0123456ABCDEF', }); $row->create_related( interfaces => { 'ecckt_id' => $row->ecckt_id, # not auto-populated 'customer' => 'John Johnsonson', 'end' => 1269644794, 'interface' => 'GigabitEthernet10/1', 'router' => 'ar11.slkcutxd.example.com', 'speed' => 1000000000, 'start' => 1265958902, 'state' => 'active', } ); $row->update; Is there a DBIC way to call create() just once and have it populate both tables simulaneously? With both ecckt.ecckt_id = interfaces.ecckt_id and ecckt.if_id = interfaces.if_id ? Cheers, Joshua On Wed, Apr 21, 2010 at 6:04 PM, Joshua Keroes wrote: > More silliness; these two commands should be the same (--upgrade and -u are > synonyms). They're returning different results. > > jkeroes at jkeroes ~/svn/modules/Integra-UBI-Schema [1233] > % dbicadmin --schema=Integra::UBI::Schema > --connect='["dbi:mysql:ubi:water.integra.engr","ubi","pass"]' -u -q . > Performig action update... > DBIx::Class::Admin::update(): resultset() expects a source name at > /opt/local/bin/dbicadmin line 72 > > jkeroes at jkeroes ~/svn/modules/Integra-UBI-Schema [1234:255] > % dbicadmin --schema=Integra::UBI::Schema > --connect='["dbi:mysql:ubi:water.integra.engr","ubi","pass"]' --upgrade -q . > Performig action upgrade... > DBIx::Class::Admin::upgrade(): Upgrade not necessary > > > On Wed, Apr 21, 2010 at 5:19 PM, Joshua Keroes wrote: > >> On Wed, Apr 21, 2010 at 5:11 PM, Robert Buels wrote: >> >>> I don't get that error using that code. >>> >>> Are all your modules in different files? load_namespaces is actually >>> based on .pm files on disk, not just package names. >>> >> >> Separate files: >> >> jkeroes at water:~/svn/modules/Integra-UBI-Schema >> [Thu Apr 22, 00:18:21 | 526] $ tree >> . >> ??? lib/ >> ? ??? Integra/ >> ? ??? UBI/ >> ? ??? Schema/ >> ? ? ??? Result/ >> ? ? ??? ECCKT.pm >> ? ? ??? Interface.pm >> ? ??? Schema.pm >> ??? t/ >> ? ??? 00-load.t >> ? ??? boilerplate.t >> ? ??? pod-coverage.t >> ? ??? pod.t >> ??? .cvsignore >> ??? Changes >> ??? MANIFEST >> ??? Makefile.PL >> ??? README >> >> 6 directories, 12 files >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From enobacon at gmail.com Wed Apr 28 17:24:05 2010 From: enobacon at gmail.com (Seven till Seven) Date: Wed, 28 Apr 2010 17:24:05 -0700 Subject: [Pdx-pm] Fennec - May meeting in 2 weeks Message-ID: <201004281724.05613.enobacon@gmail.com> Wed. May 12th, 6:53pm at FreeGeek -- 1731 SE 10th Ave. Introduction to, and call for feedback on the Fennec testing framework speaker: Chad 'Exodist' Granum Chad will demonstrate what he has so far, and request feedback. From the fennec docs: Fennec - Framework upon which inter-compatible testing solutions can be built. Fennec provides a solid base that is highly extendable. It allows for the writing of custom nestable workflows (like RSPEC), Custom Asserts (like Test::Exception), Custom output handlers (Alternatives to TAP), Custom file types, and custom result passing (collectors). In Fennec all test files are objects. Fennec also solves the forking problem, that's it, forking just plain works. This framework is what has come from a discussion around modern testing in Perl. It is an attempt to address, or make addressable the desires and needs expressed therein. It is also an attempt to make glue for all future solutions to current and future problems. As always, the meeting will be followed by social hour at the Lucky Lab. -- http://pdx.pm.org From dherrington at robertmarktech.com Thu Apr 29 23:42:37 2010 From: dherrington at robertmarktech.com (Daniel Herrington) Date: Thu, 29 Apr 2010 23:42:37 -0700 Subject: [Pdx-pm] sqlite and chomp Message-ID: <4BDA7BDD.7050106@robertmarktech.com> All, I'm parsing through an array that was produced by slurping a file. One of the first things I do in the array is chomp the line to remove the newline character. I then do an insert into a sqlite table: while (@caJIL) { my $line = shift(@caJIL); chomp($line); my ($jc,$jv) = split (':',$line); if ($jc =~ /insert_job/) { $jv = substr $jv, 1; my $sth = $dbh->prepare_cached("INSERT INTO atJobs (jobName) VALUES (?)"); $sth->execute($jv); } .... } However, the chomp seems to be doing something funny to the line that sqlite doesn't like. Here is the output of a select on the table with the chomp: dan at blackswan:~/Documents/RobertMark/BofA/work/foo/VA2$ sqlite3 VA2-bofa.db SQLite version 3.5.9 Enter ".help" for instructions sqlite> select * from atJobs; |||||||||||||||||||||||||||||||||||||||||||||||||||| sqlite> .quit And here is the output without the chomp: dan at blackswan:~/Documents/RobertMark/BofA/work/foo/VA2$ sqlite3 VA2-bofa.db SQLite version 3.5.9 Enter ".help" for instructions sqlite> select * from atJobs; 1|WCM_WGCIB_MON_FW_1 |||||||||||||||||||||||||||||||||||||||||||||||||||| sqlite> .quit I looked at the file in binary, and the line ends with a 0D 0A, which is CR/LF? If so, shouldn't perl simply look at it as a \n and move along? If I run the perl oneliner: perl -pi -e 's/\r\n/\n/g' file.txt against the file and then run my script, everything works fine. Isn't chomp supposed to remove the \r\n? thanks, -- Daniel B. Herrington Director of Field Services Robert Mark Technologies dherrington at robertmarktechnologies.com o: 651-769-2574 m: 503-358-8575 From merlyn at stonehenge.com Fri Apr 30 04:44:18 2010 From: merlyn at stonehenge.com (Randal L. Schwartz) Date: Fri, 30 Apr 2010 04:44:18 -0700 Subject: [Pdx-pm] sqlite and chomp In-Reply-To: <4BDA7BDD.7050106@robertmarktech.com> (Daniel Herrington's message of "Thu, 29 Apr 2010 23:42:37 -0700") References: <4BDA7BDD.7050106@robertmarktech.com> Message-ID: <86d3xh9ncd.fsf@red.stonehenge.com> >>>>> "Daniel" == Daniel Herrington writes: Daniel> I looked at the file in binary, and the line ends with a 0D 0A, which is Daniel> CR/LF? If so, shouldn't perl simply look at it as a \n and move Daniel> along? Are you on windows or unix? -- Randal L. Schwartz - Stonehenge Consulting Services, Inc. - +1 503 777 0095 Smalltalk/Perl/Unix consulting, Technical writing, Comedy, etc. etc. See http://methodsandmessages.vox.com/ for Smalltalk and Seaside discussion From ssandv at gmail.com Fri Apr 30 00:45:47 2010 From: ssandv at gmail.com (Steve Sandvik) Date: Fri, 30 Apr 2010 00:45:47 -0700 Subject: [Pdx-pm] sqlite and chomp In-Reply-To: <4BDA7BDD.7050106@robertmarktech.com> References: <4BDA7BDD.7050106@robertmarktech.com> Message-ID: sounds like your $/ eq "\n", not "\r\n", based on the behavior after running the one-liner. ----- >From the perldoc: This safer version of "chop" removes any trailing string that corresponds to the current value of $/ (also known as $INPUT_RECORD_SEPARATOR in the English module). It returns the total number of characters removed from all its arguments. It's often used to remove the newline from the end of an input record when you're worried that the final record may be missing its newline. When in paragraph mode ($/ = "" ), it removes all trailing newlines from the string. When in slurp mode ($/ = undef ) or fixed-length record mode ($/ is a reference to an integer or the like, see perlvar) chomp() won't remove anything. ----- Steve Sandvik On Thu, Apr 29, 2010 at 11:42 PM, Daniel Herrington wrote: > All, > > I'm parsing through an array that was produced by slurping a file. One of > the first things I do in the array is chomp the line to remove the newline > character. I then do an insert into a sqlite table: > > ? ?while (@caJIL) { > ? ? ? ?my $line = shift(@caJIL); > ? ? ? ?chomp($line); > ? ? ? ?my ($jc,$jv) = split (':',$line); > ? ? ? ?if ($jc =~ /insert_job/) { > ? ? ? ? ? ?$jv = substr $jv, 1; > ? ? ? ? ? ?my $sth = $dbh->prepare_cached("INSERT INTO atJobs (jobName) > VALUES (?)"); > ? ? ? ? ? ?$sth->execute($jv); > ? ? ? ?} > ? ?.... > ? ?} > > However, the chomp seems to be doing something funny to the line that sqlite > doesn't like. Here is the output of a select on the table with the chomp: > dan at blackswan:~/Documents/RobertMark/BofA/work/foo/VA2$ sqlite3 VA2-bofa.db > SQLite version 3.5.9 > Enter ".help" for instructions > sqlite> select * from atJobs; > |||||||||||||||||||||||||||||||||||||||||||||||||||| > sqlite> .quit > > And here is the output without the chomp: > dan at blackswan:~/Documents/RobertMark/BofA/work/foo/VA2$ sqlite3 VA2-bofa.db > SQLite version 3.5.9 > Enter ".help" for instructions > sqlite> select * from atJobs; > 1|WCM_WGCIB_MON_FW_1 > |||||||||||||||||||||||||||||||||||||||||||||||||||| > sqlite> .quit > > I looked at the file in binary, and the line ends with a 0D 0A, which is > CR/LF? If so, shouldn't perl simply look at it as a \n and move along? If I > run the perl oneliner: > > perl -pi -e 's/\r\n/\n/g' file.txt > > against the file and then run my script, everything works fine. Isn't chomp > supposed to remove the \r\n? > > thanks, > > -- > Daniel B. Herrington > Director of Field Services > Robert Mark Technologies > dherrington at robertmarktechnologies.com > o: 651-769-2574 > m: 503-358-8575 > > _______________________________________________ > Pdx-pm-list mailing list > Pdx-pm-list at pm.org > http://mail.pm.org/mailman/listinfo/pdx-pm-list > From dherrington at robertmarktech.com Fri Apr 30 11:51:29 2010 From: dherrington at robertmarktech.com (Daniel Herrington) Date: Fri, 30 Apr 2010 11:51:29 -0700 Subject: [Pdx-pm] sqlite and chomp In-Reply-To: <86d3xh9ncd.fsf@red.stonehenge.com> References: <4BDA7BDD.7050106@robertmarktech.com> <86d3xh9ncd.fsf@red.stonehenge.com> Message-ID: <4BDB26B1.5070008@robertmarktech.com> I'm running this on Ubuntu 8.1 with perl 5.10.0 Thanks for the help. I came across a perlmonks question that answered my questions. Dan H. On 04/30/2010 04:44 AM, Randal L. Schwartz wrote: >>>>>> "Daniel" == Daniel Herrington writes: >>>>>> > Daniel> I looked at the file in binary, and the line ends with a 0D 0A, which is > Daniel> CR/LF? If so, shouldn't perl simply look at it as a \n and move > Daniel> along? > > Are you on windows or unix? > > -- Daniel B. Herrington Director of Field Services Robert Mark Technologies dherrington at robertmarktechnologies.com o: 651-769-2574 m: 503-358-8575