# $Id: Biblio.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module Bio::Biblio # # Please direct questions and support issues to # # Cared for by Martin Senger # For copyright and disclaimer see below. # # POD documentation - main docs before the code =head1 NAME Bio::Biblio - A Bibliographic Query Service module =head1 SYNOPSIS use Bio::Biblio; my $biblio = Bio::Biblio->new(); print $biblio->find ('perl')->get_count . "\n"; my $collection = $biblio->find ('brazma', 'authors'); while ( $collection->has_next ) { print $collection->get_next; } # The new() method can accept parameters, for example: $biblio = Bio::Biblio->new (-access => 'soap', -location => 'http://www.ebi.ac.uk/openbqs/services/MedlineSRS', -destroy_on_exit => '0'); # See below for some one-liners =head1 DESCRIPTION This is a class whose instances can access bibliographic repositories. It allows to query a bibliographic database (such as MEDLINE) and then to retrieve resulting citations from it. The citations are returned in an XML format which is native to the repository but there are also supporting modules for converting them into Perl objects. The detailed descriptions of all query and retrieval methods are in L (an interface). All those methods should be called on instances of this (Bio::Biblio) module. The module complies (with some simplifications) with the specification described in the B project. Its home page is at L. The module also gives an access to a set of controlled vocabularies and their values. It allows to introspect bibliographic repositories and to find what citation resource types (such as journal and book articles, patents or technical reports) are provided, and what attributes they have, eventually what attribute values are allowed. Here are some one-liners: perl -MBio::Biblio -e 'print new Bio::Biblio->get_by_id ("12368254")' perl -MBio::Biblio \ -e 'print join ("\n", @{ Bio::Biblio->new->find ("brazma")->get_all_ids })' perl -MBio::Biblio \ -e 'print Bio::Biblio->new->find ("Java")->find ("perl")->get_count' =head1 OVERVIEW OF CLASSES AND PACKAGES =over =item L This is the main class to be used by the end users. It loads a real implementation for a particular access protocol according to the argument I<-access>. At the time of writing this documentation there is only one available access module implementing all query and retrieval methods: -access => soap This module implements all methods defined in the interface I (see L) by delegating calls to a loaded low-level module (e.g. see L). Note that there are other modules which do not use the SOAP protocol and do not implement all query methods - nevertheless they have retrieval methods and can be used in the same way: -access => biofetch Lacking documentation: -access => eutils =item Bio::DB::BiblioI This is an interface defining all methods that can be called on I instances. =item Bio::DB::Biblio::soap This is a real implementation of all methods defined in Bio::DB::BiblioI using SOAP protocol (calling a WebService based on SOAP). This class should not be instantiated directly (use I instead). See L for details. =item Bio::Biblio::IO This module instantiates and uses a converter of the citations read by any of the access methods mentioned above. See L for details. =item Bio::Biblio::IO::medlinexml and Bio::Biblio::IO::medline2ref A converter of MEDLINE citations in XML into Perl objects. =item Bio::Biblio::IO::pubmedxml and Bio::Biblio::IO::pubmed2ref A converter of PUBMED citations in XML into Perl objects. =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.open-bio.org/ =head1 AUTHOR Martin Senger (martin.senger@gmail.com) =head1 COPYRIGHT Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. =head1 DISCLAIMER This software is provided "as is" without warranty of any kind. =head1 SEE ALSO =over =item * OpenBQS home page: http://www.ebi.ac.uk/~senger/openbqs/ =item * Comments to the Perl client: http://www.ebi.ac.uk/~senger/openbqs/Client_perl.html =back =head1 APPENDIX The main documentation details are to be found in L. Here is the rest of the object methods. Internal methods are preceded with an underscore _. =cut # Let the code begin... package Bio::Biblio; use strict; use base qw(Bio::Root::Root Bio::DB::BiblioI); # ----------------------------------------------------------------------------- =head2 new Usage : my $obj = Bio::Biblio->new(@args); Returns : Bio::Biblio object on success, or undef on failure Args : This module recognizes and uses: -access => 'soap' It indicates what lower-level module to load. Default is 'soap'. -location => 'http://...' It says where to find a bibliographic query service. The format and contents of this argument is dependent on the '-access' argument. For 'soap' access it is a URL of a WebService. Default is http://www.ebi.ac.uk/openbqs/services/MedlineSRS Other arguments can be given here but they are recognized by the lower-level module (e.g. see Bio::DB::Biblio::soap). It builds, populates and returns a new I object. This is how it is seen from the outside. But in fact, it builds, populates and returns a more specific lower-level object, for example I object - which one it is depends on the parameter I<-access>. The real initialization is done in the method I<_initialize> of the lower-level object. This method can also be used for I an existing object and changing or adding new attributes to it in the same time. This is, however, not particulary useful for the casual users of this module, because the query methods (see L) themselves already return cloned objects with more refined query collections. Anyway this is how the cloning can be done: use Bio::Biblio; my $biblio = Bio::Biblio->new(); # this will create a new object which will NOT send a 'destroy' # message to the remote server when its life ends my $clone = $biblio->new (-destroy-on-exit => '0'); =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # if $caller is an object, or if it is an underlying # 'real-work-doing' class (e.g. Bio::DB::Biblio::soap) then # we want to call SUPER to create and bless an object if ($class =~ /Bio::DB::Biblio::(\S+)/) { my ($self) = $class->SUPER::new (@args); # now the $self is an empty object - we will populate it from # the $caller - if $caller is an object if (ref ($caller)) { %{ $self } = %{ $caller }; } # and finally add values from '@args' into the newly created # object (the values will overwrite the values copied above) $self->_initialize (@args); return $self; # this is called only the first time when somebody calls: 'new # Bio::Biblio (...)', and it actually loads a 'real-work-doing' # module and call this new() method again (unless the loaded # module has its own new() method) } else { my %param = @args; @param { map { lc $_ } keys %param } = values %param; # lowercase keys my $access = $param {'-access'} || $class->_guess_access ( $param {'-location'} ) || 'soap'; $access = "\L$access"; # normalize capitalization to lower case # load module with the real implementation - as defined in $access return unless (&_load_access_module ($access)); # this will call this same method new() - but rather its the # upper (object) branche return "Bio::DB::Biblio::$access"->new (@args); } } # ----------------------------------------------------------------------------- =head2 _load_access_module Usage : $class->_load_access_module ($access) Returns : 1 on success, undef on failure Args : 'access' should contain the last part of the name of a module who does the real implementation It does (in run-time) a similar thing as require Bio::DB::Biblio::$access It prints an error on STDERR if it fails to find and load the module (for example, because of the compilation errors in the module). =cut sub _load_access_module { my ($access) = @_; my ($module, $load, $m); $module = "_throw (<_guess_access ($location) Returns : string with a guessed access protocol (e.g. 'soap') Args : 'location' defines where to find a bibliographic service in a protocol-dependent manner (e.g. for SOAP it is a URL of a bibliographic WebService) It makes an expert guess what kind of access/transport protocol should be used based on the I of the service (e.g. if the I looks like an IOR then the access protocol is probably CORBA). =cut # this is kept here for the future when more access protocols # (e.g. CORBA) may be available for accessing bibliographic query # services sub _guess_access { # my ($class, $location) = @_; return 'soap'; } =head2 VERSION and Revision Usage : print $Bio::Biblio::VERSION; print $Bio::Biblio::Revision; =cut 1; __END__