[Bioperl-l] Adding namespace support toBio::DB::SeqFeature::Store::DBI::Pg

Chris Fields cjfields at illinois.edu
Fri Feb 12 08:38:19 EST 2010


Code for post-test cleanup is found in Build.PL file; look for the code re: Bio::DB::Seqfeature::Store tests for BDB, Pg, MySQL, etc.

chris

On Feb 12, 2010, at 7:25 AM, Adam Witney wrote:

> 
> Hi Mark,
> 
> What is the general approach for creating a database in the tests and where does that test database then get deleted? My test runs, but it leaves the database in place.
> 
> thanks
> 
> adam
> 
> 
> On 11 Feb 2010, at 14:34, Mark A. Jensen wrote:
> 
>> Hey Adam,
>> The SeqFeature tests are slightly complex in the Build-- during Build.PL execution,
>> the user specifies the DBMS, which is dynamically incorporated during the test.
>> So, any new tests you want to make, you can probably just add to SeqFeature.t,
>> and the Build script will make sure these are routed to the right handler. Jason/Chris
>> will certainly correct me if I'm wrong....
>> cheers MAJ
>> ----- Original Message ----- From: "Adam Witney" <awitney at sgul.ac.uk>
>> To: "Scott Cain" <scott at scottcain.net>
>> Cc: "BioPerl" <bioperl-l at lists.open-bio.org>
>> Sent: Thursday, February 11, 2010 9:21 AM
>> Subject: Re: [Bioperl-l] Adding namespace support toBio::DB::SeqFeature::Store::DBI::Pg
>> 
>> 
>>> 
>>> Hi Scott,
>>> 
>>> ok I now have a version working with PostgreSQL schemas.
>>> 
>>> I was looking for the SFS tests, but can only find SeqFeature.t which only tests the "memory" adaptor. Are there any tests for the mysql/Pg adaptors?
>>> 
>>> thanks
>>> 
>>> adam
>>> 
>>> On 10 Feb 2010, at 19:35, Scott Cain wrote:
>>> 
>>>> Hi Adam,
>>>> 
>>>> I don't have a problem with this approach. Can you verify that this
>>>> patch still passes the Pg SFS tests? I don't generally use
>>>> schemas/name spaces (same thing,right?) much, so I wouldn't feel
>>>> comfortable evaluting it completely.  And, even better, could you add
>>>> to the tests that exercise this behavior?
>>>> 
>>>> Thanks,
>>>> Scott
>>>> 
>>>> 
>>>> On Wednesday, February 10, 2010, Adam Witney <awitney at sgul.ac.uk> wrote:
>>>>> 
>>>>> I noticed that namespace's didn't work with Bio::DB::SeqFeature::Store::DBI::Pg because when creating the database the CREATE INDEX statements didn't pass through _qualify to add the namespace prefix, thus giving a "relation "typelist_tab" already exists" error.
>>>>> 
>>>>> The patch below fixes this, but the question is does this seem like a good approach?
>>>>> 
>>>>> thanks
>>>>> 
>>>>> adam
>>>>> 
>>>>> 
>>>>> Index: Pg.pm
>>>>> ===================================================================
>>>>> --- Pg.pm       (revision 16551)
>>>>> +++ Pg.pm       (working copy)
>>>>> @@ -256,22 +256,20 @@
>>>>> indexed  int default 1,
>>>>> object     bytea not null
>>>>> );
>>>>> -  CREATE INDEX feature_stuff ON feature(seqid,tier,bin,typeid);
>>>>> -  CREATE INDEX feature_typeid ON feature(typeid);
>>>>> END
>>>>> 
>>>>>        locationlist => <<END,
>>>>> (
>>>>> id         serial primary key,
>>>>> seqname    varchar(256)   not null
>>>>> -); CREATE INDEX locationlist_seqname ON locationlist(seqname);
>>>>> +);
>>>>> END
>>>>> 
>>>>>        typelist => <<END,
>>>>> (
>>>>> id       serial primary key,
>>>>> tag      varchar(256)  not null
>>>>> -); CREATE INDEX typelist_tab ON typelist(tag);
>>>>> +);
>>>>> END
>>>>>        name => <<END,
>>>>> (
>>>>> @@ -279,8 +277,6 @@
>>>>> name         varchar(256)  not null,
>>>>> display_name int       default 0
>>>>> );
>>>>> -  CREATE INDEX name_id ON name(id);
>>>>> -  CREATE INDEX name_name ON name(name);
>>>>> END
>>>>> 
>>>>>        attribute => <<END,
>>>>> @@ -289,8 +285,6 @@
>>>>> attribute_id     int   not null,
>>>>> attribute_value  text
>>>>> );
>>>>> -  CREATE INDEX attribute_id ON attribute(id);
>>>>> -  CREATE INDEX attribute_id_val ON attribute(attribute_id,SUBSTR(attribute_value, 1, 10));
>>>>> END
>>>>> 
>>>>>        attributelist => <<END,
>>>>> @@ -298,14 +292,12 @@
>>>>> id       serial primary key,
>>>>> tag      varchar(256)  not null
>>>>> );
>>>>> -  CREATE INDEX attributelist_tag ON attributelist(tag);
>>>>> END
>>>>>        parent2child => <<END,
>>>>> (
>>>>> id               int       not null,
>>>>> child            int       not null
>>>>> );
>>>>> -  CREATE INDEX parent2child_id_child ON parent2child(id,child);
>>>>> END
>>>>> 
>>>>>        meta => <<END,
>>>>> @@ -325,6 +317,22 @@
>>>>>       };
>>>>> }
>>>>> 
>>>>> +sub index_definitions {
>>>>> +  my $self = shift;
>>>>> +  return {
>>>>> +         feature_stuff  => "feature(seqid,tier,bin,typeid)",
>>>>> +         feature_typeid => "feature(typeid)",
>>>>> +         locationlist_seqname => "locationlist(seqname)",
>>>>> +      typelist_tab => "typelist(tag)",
>>>>> +      name_id => "name(id)",
>>>>> +      name_name => "name(name)",
>>>>> +      attribute_id => "attribute(id)",
>>>>> +      attribute_id_val => "attribute(attribute_id,SUBSTR(attribute_value, 1, 10))",
>>>>> +      attributelist_tag =>  "attributelist(tag)",
>>>>> +      parent2child_id_child => "parent2child(id,child)",
>>>>> +        };
>>>>> +}
>>>>> +
>>>>> sub schema {
>>>>> my ($self, $schema) = @_;
>>>>> $self->{'schema'} = $schema if defined($schema);
>>>>> @@ -354,6 +362,18 @@
>>>>>                      $dbh->do($query) or $self->throw($dbh->errstr);
>>>>>              }
>>>>> }
>>>>> +
>>>>> +  my $indexes = $self->index_definitions;
>>>>> +  foreach (keys %$indexes) {
>>>>> +    my $index = $self->_qualify($_);
>>>>> +    my $index_def = $self->_qualify($indexes->{$_});
>>>>> +    $dbh->do("DROP INDEX IF EXISTS $index") if $erase;
>>>>> +    my @index_exists = $dbh->selectrow_array("SELECT * FROM pg_indexes WHERE indexname = '$index'");
>>>>> +               if (!scalar(@index_exists)) {
>>>>> +                       my $query = "CREATE INDEX $index ON $index_def";
>>>>> +                       $dbh->do($query) or $self->throw($dbh->errstr);
>>>>> +               }
>>>>> +  }
>>>>> $self->subfeatures_are_indexed(1) if $erase;
>>>>> 1;
>>>>> }
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
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>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
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>> 
> 
> 
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