Bio-Das-ProServer
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lib/Bio/Das/ProServer.pm  view on Meta::CPAN 

File::Spec
Sys::Hostname
Bio::Das::ProServer::SourceAdaptor
Bio::Das::ProServer::SourceHydra
Socket
English
Carp

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: Roger Pettett$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/Authenticator.pm  view on Meta::CPAN 

  Simply returns an undefined value.

=head2 init : Executed upon construction

This stub method does nothing.

=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS

None reported.

=head1 DEPENDENCIES

=over

=item L<Carp|Carp>

=item L<HTTP::Response|HTTP::Response>

lib/Bio/Das/ProServer/Authenticator/http.pm  view on Meta::CPAN 

=over

=item L<Carp|Carp>

=item L<Bio::Das::ProServer::Authenticator|Bio::Das::ProServer::Authenticator>

=item L<LWP::UserAgent|LWP::UserAgent>

=back

=head1 BUGS AND LIMITATIONS

This authenticator implementation may only be used to ask yes/no questions,
such as "does this token identify a user with sufficient privileges?". Questions
such as "which user does this token identify?" have additional security
implications and are therefore not supported.

=head1 INCOMPATIBILITIES

None reported.

lib/Bio/Das/ProServer/Authenticator/ip.pm  view on Meta::CPAN 

=item L<Carp|Carp>

=item L<Net::IP|Net::IP>

=item L<Socket|Socket>

=item L<Bio::Das::ProServer::Authenticator|Bio::Das::ProServer::Authenticator>

=back

=head1 BUGS AND LIMITATIONS

Clients that are separated from the server by an anonymising HTTP proxy (i.e.
one that does not reveal the client's IP address in the X-Forwarded-For HTTP
header) will always fail this method of authentication.

Note that clients may spoof an IP address in the X-Forwarded-For header.
Therefore this method of authentication is not a robust security precaution.

=head1 INCOMPATIBILITIES

lib/Bio/Das/ProServer/Config.pm  view on Meta::CPAN 

=head2 log - log to STDERR with timestamp

  $oConfig->log('a message');

=head1 DIAGNOSTICS

=head1 DEPENDENCIES

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Roger Pettett <rmp@sanger.ac.uk>.

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2006 The Sanger Institute

This library is free software; you can redistribute it and/or modify

lib/Bio/Das/ProServer/SourceAdaptor.pm  view on Meta::CPAN 

=item L<English|English>

=item L<Carp|Carp>

=back

=head1 INCOMPATIBILITIES

None reported

=head1 BUGS AND LIMITATIONS

None reported

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2008 The Sanger Institute

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/Transport/bed12.pm  view on Meta::CPAN 

=item L<DBI|DBI>

=item L<Carp|Carp>

=back

=head1 INCOMPATIBILITIES

None reported.

=head1 BUGS AND LIMITATIONS

BED is mapped to DAS in the following manner:

1. The BED format allows for "blocks" within each line. Where these are present
   it is assumed that the line represents a group of features, with each block
   representing a single feature within the group. Lines without blocks are
   treated as if they contain a single full-length block.

2. DAS fields are mapped from BED fields as follows:

lib/Bio/Das/ProServer/SourceAdaptor/Transport/bioseqio.pm  view on Meta::CPAN 

              Bio::DB::Flat::new().

  dbroot      The directory where the database index is
              or will be located.  Corresponds to the
              '-directory' option of Bio::DB::Flat::new().

=head1 DEPENDENCIES

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Andreas Kahari, andreas.kahari@ebi.ac.uk

=head1 LICENSE AND COPYRIGHT

lib/Bio/Das/ProServer/SourceAdaptor/Transport/csv.pm  view on Meta::CPAN 

  $csvtransport->last_modified();

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Jody Clements <jc3@sanger.ac.uk>

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2005 The Sanger Institute

lib/Bio/Das/ProServer/SourceAdaptor/Transport/dbi.pm  view on Meta::CPAN 

=over

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::generic|Bio::Das::ProServer::SourceAdaptor::Transport::generic>

=item L<DBI|DBI>

=back

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Roger Pettett <rmp@sanger.ac.uk>.

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2007 The Sanger Institute

This library is free software; you can redistribute it and/or modify

lib/Bio/Das/ProServer/SourceAdaptor/Transport/ensembl.pm  view on Meta::CPAN 

=item Ensembl core API

=item Additional Ensembl APIs if used

=back

=head1 INCOMPATIBILITIES

None reported

=head1 BUGS AND LIMITATIONS

None reported

=head1 REFERENCES

=over

=item L<http://www.ensembl.org/info/software/Pdoc/ensembl/|http://www.ensembl.org/info/software/Pdoc/ensembl/> Ensembl API

=back

lib/Bio/Das/ProServer/SourceAdaptor/Transport/file.pm  view on Meta::CPAN 

=over

=item L<File::stat|File::stat>

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::generic|Bio::Das::ProServer::SourceAdaptor::Transport::generic>

=back

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

Only AND compound queries are supported.

=head1 AUTHOR

Roger Pettett <rmp@sanger.ac.uk> and Andy Jenkinson <aj@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2008 The Sanger Institute and EMBL-EBI

lib/Bio/Das/ProServer/SourceAdaptor/Transport/generic.pm  view on Meta::CPAN 

  my $resultref = $transport->query(...);

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Roger Pettett <rmp@sanger.ac.uk>.

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2007 The Sanger Institute

This library is free software; you can redistribute it and/or modify

lib/Bio/Das/ProServer/SourceAdaptor/Transport/getz.pm  view on Meta::CPAN 


=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

Bio::Das::ProServer::SourceAdaptor::Transport::generic
Carp

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: Roger Pettett$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/Transport/martservice.pm  view on Meta::CPAN 

=item List::MoreUtils

=item LWP::UserAgent

=item XML::Writer

=back

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Ray Miller <rm7@sanger.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2009 Wellcome Trust Sanger Institute

This library is free software; you can redistribute it and/or modify

lib/Bio/Das/ProServer/SourceAdaptor/Transport/oracle.pm  view on Meta::CPAN 

  my $dbh = Bio::Das::ProServer::SourceAdaptor::Transport::oracle->dbh();

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Roger Pettett <rmp@sanger.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2005 The Sanger Institute

This library is free software; you can redistribute it and/or modify

lib/Bio/Das/ProServer/SourceAdaptor/Transport/sif.pm  view on Meta::CPAN 

=head1 DEPENDENCIES

=over

=item L<Carp|Carp>

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::file|Bio::Das::ProServer::SourceAdaptor::Transport::file>

=back

=head1 BUGS AND LIMITATIONS

The Simple Interaction Format is very simple, and therefore only supports a
limited range of DAS annotation details. It also only handles binary
interactions (i.e. those with exactly two interactors).

=head1 INCOMPATIBILITIES

None reported.

=head1 AUTHOR

lib/Bio/Das/ProServer/SourceAdaptor/Transport/wgetz.pm  view on Meta::CPAN 

=item strict

=item warnings

=item base

=back

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Andreas Kahari, <andreas.kahari@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/all_in_group.pm  view on Meta::CPAN 

=item strict

=item warnings

=item base

=back

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: jws, dj3$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/bed12.pm  view on Meta::CPAN 

=head1 DESCRIPTION

Serves up features DAS responses from BED files.
See L<http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED|http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED>
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
for details of the file format.

The BED and DAS formats contain an intersection of information. That is, not all
DAS fields are supported in BED, and vice versa. In order to be adapted to the
DAS protocol, some basic assumptions need to be made and some configurability is
lost. See the BUGS AND LIMITATIONS section for more details.

=head1 CONFIGURATION AND ENVIRONMENT

  [mybed]
  state       = on
  adaptor     = bed12
  path        = /data/
  filename    = example.bed
  ; coordinates -> test segment
  coordinates = NCBI_36,Chromosome,Homo sapiens -> X:1,100

lib/Bio/Das/ProServer/SourceAdaptor/bed12.pm  view on Meta::CPAN 

=over

=item L<Bio::Das::ProServer::SourceAdaptor|Bio::Das::ProServer::SourceAdaptor> 

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::bed12|Bio::Das::ProServer::SourceAdaptor::Transport::bed12>

=item L<Carp|Carp>

=back

=head1 BUGS AND LIMITATIONS

See the BUGS AND LIMITATIONS section of
Bio::ProServer::SourceAdaptor::Transport::bed12 for details.

=head1 INCOMPATIBILITIES

None reported.

=head1 AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

lib/Bio/Das/ProServer/SourceAdaptor/bioseq.pm  view on Meta::CPAN 

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

 Bio::Das::ProServer::SourceAdaptor

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Andreas Kahari, andreas.kahari@ebi.ac.uk

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/file.pm  view on Meta::CPAN 

  typereference group_id grouplabel grouptype groupnote grouplink grouplinktxt

It is also possible for such properties to include placeholders, which will be
dynamically substituted for the appropriate column in each feature:

  [mysource]
  ...
  # Fill-in properties:
  link   = http://example.com?chromosome=%segment;type=%type

=head1 BUGS AND LIMITATIONS

Although this module supports the "filling in" of feature properties from the
source's INI configuration, it only supports the setting of scalar values.
It is therefore not possible to set more than one note, link or group.

Also, the setting of "target" properties in this way is at present not supported
(each feature's target is likely to be dynamic anyway).

=head1 DIAGNOSTICS

lib/Bio/Das/ProServer/SourceAdaptor/grouped_db.pm  view on Meta::CPAN 

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

Bio::Das::ProServer::SourceAdaptor

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: Roger Pettett$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/proxy.pm  view on Meta::CPAN 


=head1 DEPENDENCIES

HTTP::Request
LWP::UserAgent
Bio::Das::Lite
Bio::Das::ProServer::SourceAdaptor

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: Roger M Pettett$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/sif.pm  view on Meta::CPAN 

=over

=item L<Carp|Carp> 

=item L<Bio::Das::ProServer::SourceAdaptor|Bio::Das::ProServer::SourceAdaptor> 

=item L<Bio::Das::ProServer::SourceAdaptor::Transport::sif|Bio::Das::ProServer::SourceAdaptor::Transport::sif>

=back

=head1 BUGS AND LIMITATIONS

The Simple Interaction Format is very simple, and therefore only supports a
limited range of DAS annotation details. It also only handles binary
interactions (i.e. those with exactly two interactors).

=head1 INCOMPATIBILITIES

None reported.

=head1 AUTHOR

lib/Bio/Das/ProServer/SourceAdaptor/simple.pm  view on Meta::CPAN 

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

 Bio::Das::ProServer::SourceAdaptor
 Carp
 POSIX

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/simple_interaction.pm  view on Meta::CPAN 

=over

=item L<Bio::Das::ProServer::SourceAdaptor|Bio::Das::ProServer::SourceAdaptor>

=back

=head1 INCOMPATIBILITIES

None reported

=head1 BUGS AND LIMITATIONS

None reported

=head1 AUTHOR

  Andy Jenkinson <andy.jenkinson@ebi.ac.uk>

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2007 EMBL-EBI

lib/Bio/Das/ProServer/SourceAdaptor/simple_volmap.pm  view on Meta::CPAN 

=item L<Bio::Das::ProServer::SourceAdaptor|Bio::Das::ProServer::SourceAdaptor>

=back

=head1 DIAGNOSTICS

=head1 INCOMPATIBILITIES

None reported

=head1 BUGS AND LIMITATIONS

None reported

=head1 LICENSE AND COPYRIGHT

Copyright (c) 2007 EMBL-EBI

=cut

lib/Bio/Das/ProServer/SourceAdaptor/simpledb.pm  view on Meta::CPAN 

  dbhost    = mysql.example.com
  dbuser    = proserverro
  dbpass    = topscret

=head1 DEPENDENCIES

 Bio::Das::ProServer::SourceAdaptor

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: Roger M Pettett$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or

lib/Bio/Das/ProServer/SourceAdaptor/styletest.pm  view on Meta::CPAN 

=head1 DIAGNOSTICS

=head1 CONFIGURATION AND ENVIRONMENT

=head1 DEPENDENCIES

 Bio::Das::ProServer::SourceAdaptor

=head1 INCOMPATIBILITIES

=head1 BUGS AND LIMITATIONS

=head1 AUTHOR

$Author: Jim Stalker$

=head1 LICENSE AND COPYRIGHT

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or



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