# $Id: BiblioI.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::DB::BiblioI # # 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::DB::BiblioI - An interface to a Bibliographic Query Service =head1 SYNOPSIS This is an interface module - you do not instantiate it. Use I module: use Bio::Biblio; my $biblio = Bio::Biblio->new(@args); =head1 DESCRIPTION This interface describes the methods for accessing a bibliographic repository, for quering it and for retrieving citations from it. The retrieved citations are in XML format and can be converted to perl objects using I. The interface complies (with some simplifications) with the specification described in the B project. Its home page is at http://www.ebi.ac.uk/~senger/openbqs/. =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 APPENDIX This is actually the main documentation... If you try to call any of these methods directly on this Bio::DB::BiblioI object you will get a I error message. You need to call them on a Bio::Biblio object. =cut # Let the code begin... package Bio::DB::BiblioI; use strict; use base qw(Bio::Root::RootI); # ----------------------------------------------------------------------------- =head2 get_collection_id Usage : my $collection_id = $biblio->get_collection_id; Returns : string identifying a query collection represented by the $biblio object Args : none Every query collection is uniquely identify-able by its collection ID. The returned value can be used to populate another $biblio object and then to access that collection. =cut sub get_collection_id { my ($self,@args) = @_; $self->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 get_count Usage : my $count = $biblio->get_count; Returns : integer Args : none, or a string identifying a query collection It returns a number of citations in the query collection represented by the calling $biblio object, or in the collection whose ID is given as an argument. =cut sub get_count { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 find Usage : my $new_biblio = $biblio->find ($keywords, $attrs); my $new_biblio = $biblio->find ('perl', 'abstract'); my $new_biblio = $biblio->find ( [ 'perl', 'Java' ] ); Returns : new Bio::Biblio object representing a new query collection Args : $keywords - what to look for (mandatory) - a comma-delimited list of keywords, or - an array reference with keywords as elements $attrs - where to look in (optional) - a comma-delimited list of attribute names, or - an array reference with attribute names as elements This is the main query method. It looks for the $keywords in a default set of attributes, or - if $attrs given - only in the given attributes. Because it returns a new Bio::Biblio object which can be again queried it is possible to chain together several invocations: $biblio->find ('Brazma')->find ('Robinson')->get_collection_id; =cut sub find { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- # TBD: AFAIK this method is not implemented on the server side. # Let's comment it out for the time being... #sub query { shift->throw_not_implemented(); } # ----------------------------------------------------------------------------- =head2 reset_retrieval Usage : $biblio->reset_retrieval; Returns : nothing Args : none It sets an iterator stored in the $biblio object back to its beginning. After this, the retrieval methods I, I and I start to iterate the underlying query collection again from its start. It throws an exception if this object does not represent any query result (e.i. it does not contain a collection ID). Note that a collection ID is created automatically when this object was returned by a I method, or it can be assigned in a constructor using argument I<-collection_id>. =cut sub reset_retrieval { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_next Usage : my $citation = $biblio->get_next; Returns : a citation in an XML format Args : none It returns the next available citation from the underlying query collection. It throws an exception if there are no more citations. In order to avoid this, use it together with the I method: my $result = $biblio->find ('brazma', 'authors'); while ( $result->has_next ) { print $result->get_next; } It also throws an exception if this object does not represent any query result - see explanation in the I elsewhere in this document. =cut sub get_next { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_more Usage : my $r_citations = $biblio->get_more (5); Returns : an array reference - each element has a citation in an XML format Args : an integer 'how_many' citations to return; default is 1 - but it is assigned with warning It returns the next I available citations from the underlying query collection. It does not throw any exception if 'how_many' is more than currently available - it simply returns less. However, it throws an exception if used again without calling first I. It also throws an exception if this object does not represent any query result - see explanation in method I elsewhere in this document. =cut sub get_more { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 has_next Usage : my $is = $biblio->has_next; Returns : 1 or undef Args : none It returns 1 if there is a next citation available in the underlying query collection. Otherwise it returns undef. It throws an exception if this object does not represent any query result - see explanation in method I elsewhere in this document. =cut sub has_next { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_all_ids Usage : my $r_ids = $biblio->get_all_ids; Returns : an array reference - each element has a citation identifier Args : none The identifiers of all citations in the underlying query collection are returned. A usual pattern is to use them then in the I method: my $biblio = $repository->find ('brazma')->find ('robinson'); foreach my $id ( @{ $biblio->get_all_ids } ) { print $biblio->get_by_id ($id); } It throws an exception if this object does not represent any query result - see explanation in method I elsewhere in this document. =cut sub get_all_ids { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_by_id Usage : my $citation = $biblio->get_by_id ('12368254'); Returns : a citation in an XML format Args : a citation identifier (PMID for Medline) It returns a citation - disregarding if the citation is or is not in the underlying query collection (of course, it must be in the repository). =cut sub get_by_id { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_all Usage : my $all = $biblio->get_all; Returns : a (big) string with all citations in an XML format Args : none It returns an XML valid string (which means that individual citations are also surrounded by a "set" XML tag) representing all citations from the underlying query collection. Note that some servers may limit the number of citations which can be returned by this method. In such case you need either to refine further your query collection (using I method) or to retrieve results by iteration (methods I, I, I). It throws an exception if this object does not represent any query result - see explanation in method I elsewhere in this document. =cut sub get_all { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 exists Usage : my $exists = $biblio->exists; Returns : 1 or undef Args : none It returns 1 if the underlying query collection represented by the $biblio object still exists (on the server side). If you have a collection ID (e.g. stored or printed in a previous session) but you do not have anymore a C object representing it this is how you can check the collection existence: use Bio::Biblio; print Bio::Biblio->new(-collection_id => '1014324148861')->exists; It throws an exception if this object does not represent any query result - see explanation in method I elsewhere in this document. =cut sub exists { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 destroy Usage : $biblio->destroy; Returns : nothing Args : none It sends a message to the remote server to forget (or free, or destroy - whatever server choose to do) the query collection represented by this object. It throws an exception if this object does not represent any query collection. =cut sub destroy { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_vocabulary_names Usage : print join ("\n", @{ $biblio->get_vocabulary_names }); Returns : an array reference - each element has a name of a controlled vocabulary Args : none The controlled vocabularies allow to introspect bibliographic repositories and to find what citation resource types (such as journal and book articles, patents or technical reports) are provided by the repository, what attributes they have, eventually what attribute values are allowed. This method returns names of all available controlled vocabularies. The names can than be used in other methods dealing with vocabularies: I, I, I, and I. =cut sub get_vocabulary_names { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 contains Usage : my $yes = $biblio->contains ($vocabulary_name, $value); Returns : 1 or undef Args : $vocabulary_name defines a vocabulary where to look, and a $value defines what to look for It returns 1 if the given controlled vocabulary contains the given value. For example, when you know, that a vocabulary C contains value C you can use it in the I method: $biblio->find ('United States', 'COUNTRY'); =cut sub contains { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_entry_description Usage : $biblio->get_entry_description ($voc_name, $value); Returns : a string with a desciption Args : $voc_name defines a vocabulary where to look, and a $value defines whose description to return Each vocabulary entry has its value (mandatory attribute), and can have a description (optional attribute). The description may be just a human readable explanation of an attribute, or it can have more exact meaning. For example, the server implementation of the bibliographic query service provided by the EBI puts into attribute descriptions words I and/or I to distinguish the role of the attributes. It throws an exception if either vocabulary or value do not exist. =cut sub get_entry_description { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_all_values Usage : $biblio->get_all_values ($vocabulary_name); Returns : an array reference - each element has a value (scalar) from the given controlled vocabulary Args : $vocabulary_name defines a vocabulary whose values are being returned It returns all values of the given vocabulary. It throws an exception if the vocabulary does not exist. =cut sub get_all_values { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 get_all_entries Usage : $biblio->get_all_entries ($vocabulary_name); Returns : a hash reference - keys are vocabulary values and values are their descriptions Args : $vocabulary_name defines a vocabulary whose entries are being returned It returns pairs of values and their descriptions of the whole vocabulary. It throws an exception if the vocabulary does not exist. This is one way how to get it and print it: my $name = 'MEDLINE2005/JournalArticle/properties'; use Data::Dumper; print Data::Dumper->Dump ( [$biblio->get_all_entries ($name)], ['All entries']); =cut sub get_all_entries { shift->throw_not_implemented; } # ----------------------------------------------------------------------------- =head2 VERSION and Revision Usage : print $Bio::DB::BiblioI::VERSION; print $Bio::DB::BiblioI::Revision; =cut 1; __END__