[Bioperl-l] problem with t/LocalDB/SeqFeature.t when host ne localhost

[Chris Fields]

Dan,

Can you file this as a BioPerl bug?  I'm planning on driving towards  
releasing 1.6.1 alpha1 soon (next few weeks) and I would like to get  
this one fixed.

chris

On Jul 31, 2009, at 7:13 AM, Dan Bolser wrote:

> Hi,
>
> Whenever I try to do the Bio::DB::GFF or Bio::DB::SeqFeature::Store
> live database tests:
>
>  - will run tests with database driver 'mysql' and these settings:
>    Database test
>    Host     our.mysql.host
>    DSN      dbi:mysql:database=test;host=our.mysql.host
>    User     me
>    Password secret
>
>
> I get the following error:
>
> DBI connect('database=test','',...) failed: Can't connect to local
> MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at
> Bio/DB/SeqFeature/Store/DBI/mysql.pm line 212
> sh: -user: command not found
>
>
> The clue is the sh error that follows. The contents of the
> t/LocalDB/SeqFeature_mysql.t file looks like this:
>
> system '/usr/bin/perl t/LocalDB/SeqFeature.t -adaptor DBI::mysql
> -create 1 -temp 1 -dsn dbi:mysql:database=test;host=our.mysql.host
> -user me -password secret';
>
>
> I tried the following diff to 'work around' the problem created by the
> ';' character in the dsn:
>
> diff -u  t/LocalDB/SeqFeature.t~  t/LocalDB/SeqFeature.t
> --- t/LocalDB/SeqFeature.t~     2009-05-11 15:22:07.000000000 +0100
> +++ t/LocalDB/SeqFeature.t      2009-07-31 12:56:53.554227455 +0100
> @@ -25,7 +25,7 @@
> @args = (-adaptor => 'memory') unless @args;
>
> SKIP: {
> -my $db = eval { Bio::DB::SeqFeature::Store->new(@args) };
> +my $db = eval { Bio::DB::SeqFeature::Store->new(-adaptor =>
> "DBI::mysql", -create => 1, -temp => 1, -dsn =>
> "dbi:mysql:database=test;host=our.mysql.host", -user => "me",
> -password => "secret") };
> skip "DB load failed? Skipping all! $@", (TEST_COUNT - 2) if $@;
> ok($db);
>
>
> However, running the above script creates the following error:
>
> DBD::mysql::db do failed: BLOB/TEXT column 'tag' used in key
> specification without a key length at
> Bio/DB/SeqFeature/Store/DBI/mysql.pm line 450.
> ok 3 # skip DB load failed? Skipping all!
> # -------------------- EXCEPTION --------------------
> # MSG: BLOB/TEXT column 'tag' used in key specification without a  
> key length
> # STACK Bio::DB::SeqFeature::Store::DBI::mysql::_create_table
> Bio/DB/SeqFeature/Store/DBI/mysql.pm:450
> # STACK Bio::DB::SeqFeature::Store::DBI::mysql::init_tmp_database
> Bio/DB/SeqFeature/Store/DBI/mysql.pm:439
> # STACK Bio::DB::SeqFeature::Store::DBI::mysql::init
> Bio/DB/SeqFeature/Store/DBI/mysql.pm:223
> # STACK Bio::DB::SeqFeature::Store::new Bio/DB/SeqFeature/Store.pm:360
> # STACK (eval) t/LocalDB/SeqFeature.t:28
> # STACK toplevel t/LocalDB/SeqFeature.t:28
> # -------------------------------------------
> #
>
>
> I'm not sure how to proceed from here.
>
> Thanks for any hints,
>
> Dan.
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