The computer cluster he details is the same cluster I ran large stacks of Perl on for my "mutation grid" project whose name I stole when I formed Mutation Grid, Inc. A little trip down memory lane for me, and a good read for curious minds. :)
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Usually.
Unfortunately today the table names "Order" and "Service-tier2" blow up:
Bad table or view 'Order', ignoring: DBIx::Class::Schema::Loader::make_schema_at(): DBI Exception: DBD::mysql::st execute failed: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'Order WHERE ( 1 = 0 )' at line 1 [for Statement "SELECT * FROM Order WHERE ( 1 = 0 )"] at refresh_schema.pl line 9
Apparently "Order" is semi-reserved by MySQL, and dashes are trouble:
SELECT * FROM Order # syntax error
SELECT * FROM `Order` # works
SELECT * FROM Service-tier2 # syntax error
SELECT * FROM `Service-tier2` # works
Another point for irc.perl.org #dbix-class, as ilmari pointed me to quote_char as the cure for what ailed me.
use strict;
use DBIx::Class::Schema::Loader qw( make_schema_at );
make_schema_at(
"P3::Schema", {
dump_directory => ".",
},
[ "dbi:mysql:protec", $user, $password, {
quote_char => '`'
} ],
);
Beauty. I'm still hitting this new warning because the column name 'can' (Client Access Number) collides with UNIVERSAL::can():
Column can in table ClContact collides with an inherited method.
See "COLUMN ACCESSOR COLLISIONS" in perldoc DBIx::Class::Schema::Loader::Base .
Oops! :) But that's an easy work-around in my Result/ class. I just have to pick anything that's not reserved:
"can",
{ accessor => "cant", data_type => "varchar", is_nullable => 0, size => 10 },
So to access that column I now call $clcontact->cant(). Why? Because now I can. :)
->can() is already spoken for. Since DBIx::Class::Schema::Loader creates an accessor method for each column of each table in your database, things went sideways on me today when I tried to auto-generate classes for all tables in that database.
Luckily irc.perl.org #dbix-class came to the rescue again, and Caelum was quick to patch the bug. So if you have clients like mine, rest assured the next push to CPAN will cure what ails ya. :)
]]>The front content was WYSIWYG'd by their previous ISP. Prolific position:absolute CSS makes that content painful to edit. But links to the shiny new backend are all Catalyst, Template Toolkit, and lots of jQuery.
It's an alpha release. Feedback welcome. :)
]]>.change() event tied to bar works as I expected, but baz is a global variable.
function addARow() {
var i = $('#next_id').val();
var d = $("div"), //COMMA then foo
foo = $("<input>",{id:"foo" + i,size:"3"}).appendTo(d)
.change(function() { bar.val($(this).val() * 2); })
.change(function() { baz.val($(this).val() * 2); }), //COMMA then bar
bar = $("<input>",{id:"bar" + i,size:"3"}).appendTo(d);//SEMICOLON then baz
baz = $("<input>",{id:"baz" + i,size:"3"}).appendTo(d);
$("<br>").appendTo(d);
$('#next_id').val(i - 1 + 2); // + 1 would concat 1 onto the string :)
};
See it in action here. jQuery creates a set of 3 input fields (foo, bar, baz) on each click of "add". When foo is changed by the user, bar and baz are updated. But the wrong baz gets the update.
Live and learn. :)
]]>The computer cluster he details is the same cluster I ran large stacks of Perl on for my "mutation grid" project whose name I stole when I formed Mutation Grid, Inc. A little trip down memory lane for me, and a good read for curious minds. :)
]]>
ctlPagePlaceHolder makes the simplest navigation beyond the reach of WWW::Mechanize as far as I can tell. Luckily Selenium came to my rescue.
If you haven't experienced Selenium automation, it's quite impressive. From a normal shell window (OS X Terminal.app in my case) you launch a Java server
selenium-remote-control-1.0.3/selenium-server-1.0.3
$ java -jar selenium-server.jar
and then use WWW::Selenium in your Perl program. As your Perl program runs it launches Firefox on your local workstation and performs whatever commands you issue. In my case this was simply "click 'Next Page'". :)
The Selenium IDE Firefox plugin is great for quickly mocking up what commands you need. Once it's working, drop those commands into your program to get the job done.
It's disturbing to me that ASP.NET is so convoluted by default that I need Selenium for some operations. (I can't imagine anyone went out of their way to make automation of their site this difficult intentionally.) But I sure am glad it's available when I need it. What should have been ?page=2 turned into me harnessing untold volumes of source code (Selenium + Firefox!) to get the job done.
Oh well. Such is the way of the world sometimes. :)
The nice weather is holding out here in Omaha, Nebraska, USA. Still motorcycle weather, and the trees are pretty in the light industrial park Mutation Grid now calls home.
castaway blew my mind this morning in irc.perl.org #axkit-dahut.
Convert an XML file to Perl data structure:
perl -MXML::Simple -MData::Dumper -le'print Dumper XMLin("foo.xml")'
Convert an XML file to JSON:
perl -MJSON::Any -MXML::Simple \
-le'print JSON::Any->new()->objToJson(XMLin("foo.xml"))'
"How do I do X?" Like this! Poof!
Some days Perl feels like a Las Vegas magic show. :)
]]>(1) Code blocks. If you choose Format: Markdown, leave a blank line, indent text with 4 spaces, then another blank line
you will get code blocks like this
# with some
$rudimentary = "syntax highlighting";
(2) Blog subtitle. Erez Schatz was kind enough to point out how to set your blog subtitle (e.g.: Mutation Grid, Inc. "Controlled software evolution." above): From the blogs.perl.org page, click on Post, then, on the top menu bar: Preferences - General, the subtitle is "description".
]]>irc.perl.org #perl-help posed a good question tonight. Why does this only find some of the matches?
my $sequence = "ggg atg aaa tgt tcc cgg taa atg aat gcc cgg gaa ata tag cct gac ctg a";
$sequence =~ tr/ //d;
print "Input sequence is: $sequence \n";
while ($sequence =~ /(atg(...)*?(taa|tag|tga))/g) {print "$1 \n";}
Because, by default, regex /g begins each subsequent search after the end of the last match, so overlapping hits are not found. As this blog post explains, a negative lookahead assertion is the key to finding all of them. This works great:
while ($sequence =~ /(?=(atg.*?(taa|tag|tga)))/g) {
print "$1\n";
}
I'm partial to bioinformatics homework after 4 years of hacking on the stuff. :)
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