[Bioperl-l] Bioblio_biofetch.t failure on windows

Nathan Haigh nathanhaigh at ukonline.co.uk
Fri Oct 22 06:12:11 EDT 2004

When running nmake I get an exception error "retrieval type pipeline unsupported"


I have narrowed down the bug to Bio::DB::WebDBSeqI.pm which sets the default retrieval_type to pipeline. Needless to say pipes and
forks are not well implemented on windows (if at all)!

I've notice in the CVS that has been several attempts to fix bug such as this - I don't know if they were to address this particular
problem. But as far as I see, there seems to be several attempts at a workaround in the get_seq_stream. Could the line:

      $self->retrieval_type('io_string') if $self->retrieval_type =~ /pipeline/ && $^O =~ /^MSWin/;

be simply moved into the "new" sub after setting the retrieval type or would this break something else? For the time being copying
the line into the "new" sub fixes things in the Biblio_biofetch test; except for reporting inconsistence between the actual and
expected identifier numbers (but this loos like it's due to the comparison between two different id's .


So that it reads:


    $params        && $self->url_params($params);

    $db            && $self->db($db);

    $ret_type      && $self->retrieval_type($ret_type);

    # workaround for MSWin systems

    $self->retrieval_type('io_string') if $self->retrieval_type =~ /pipeline/ && $^O =~ /^MSWin/;

    $delay          = $self->delay_policy unless defined $delay;


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