Raw content of Bio::DB::Biblio::soap # $Id: soap.pm,v 1.5 2002/10/22 07:45:14 lapp Exp $ # # BioPerl module Bio::DB::Biblio::soap.pm # # Cared for by Martin Senger <senger@ebi.ac.uk> # For copyright and disclaimer see below. # POD documentation - main docs before the code =head1 NAME Bio::DB::Biblio::soap - A SOAP-based access to a bibliographic query service =head1 SYNOPSIS Do not use this object directly, it is recommended to access it and use it through the I<Bio::Biblio> module: use Bio::Biblio; my $biblio = new Bio::Biblio (-access => 'soap'); =head1 DESCRIPTION This object contains the real implementation of a Bibliographic Query Service as defined in L<Bio::DB::BiblioI> - using a SOAP protocol to access a WebService (a remote server) that represents a bibliographic repository. =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/MailList.shtml - About the mailing lists =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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR Martin Senger (senger@ebi.ac.uk) =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 BUGS AND LIMITATIONS =over =item * Methods returning a boolean value (I<has_next>, I<exists> and I<contains>) can be used only with SOAP::Lite version 0.52 and newer (probably due to a bug in the older SOAP::Lite). =item * It does not use WSDL. Coming soon... =item * There is an open question to discuss: should the service return citations as type I<string> or rather as type I<base64>? What is faster? What is better for keeping non-ASCII characters untouched? How the decision would be influenced if the transparent compression support is introduced? =item * More testing and debugging needed to ensure that returned citations are properly transferred even if they contain foreign characters. =back =head1 APPENDIX The main documentation details are to be found in L<Bio::DB::BiblioI>. Here is the rest of the object methods. Internal methods are preceded with an underscore _. =cut # Let the code begin... package Bio::DB::Biblio::soap; use vars qw(@ISA $VERSION $Revision $DEFAULT_SERVICE $DEFAULT_NAMESPACE); use strict; use Bio::Biblio; # TBD: ?? WHY SHOULD I DO THIS ?? use SOAP::Lite on_fault => sub { my $soap = shift; my $res = shift; my $msg = ref $res ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring : "--- TRANSPORT ERROR ---\n" . $soap->transport->status; Bio::DB::Biblio::soap->throw ( -text => $msg ); } ; @ISA = qw(Bio::Biblio); BEGIN { # set the version for version checking $VERSION = do { my @r = (q$Revision: 1.5 $ =~ /\d+/g); sprintf "%d.%-02d", @r }; $Revision = q$Id: soap.pm,v 1.5 2002/10/22 07:45:14 lapp Exp $; # where to go... $DEFAULT_SERVICE = 'http://industry.ebi.ac.uk/soap/openBQS'; # ...and what to find there $DEFAULT_NAMESPACE = 'http://industry.ebi.ac.uk/openBQS'; } # ----------------------------------------------------------------------------- =head2 _initialize Usage : my $obj = new Bio::Biblio (-access => 'soap' ...); (_initialize is internally called from this constructor) Returns : nothing interesting Args : This module recognises and uses following arguments: -namespace => 'urn' The namespace used by the WebService that is being accessed. It is a string which guarantees its world-wide uniqueness - therefore it often has a style of a URL - but it does not mean that such pseudo-URL really exists. Default is 'http://industry.ebi.ac.uk/openBQS' (which well corresponds with the default '-location' - see module Bio::Biblio). -destroy_on_exit => '0' Default value is '1' which means that all Bio::Biblio objects - when being finalised - will send a request to the remote WebService to forget the query collections they represent. If you change it to '0' make sure that you know the query collection identification - otherwise you will not be able to re-established connection with it. This can be done by calling method get_collection_id. -collection_id => '...' It defines what query collection will this object work with. Use this argument when you know a collection ID of an existing query collection and when you wish to re-established connection with it. By default, the collection IDs are set automatically by the query methods - they return Bio::Biblio objects already having a collection ID. A missing or undefined collection ID means that the object represents the whole bibliographic repository (which again means that some methods, like get_all, will be probably refused). -soap => a SOAP::Lite object Usually all Bio::Biblio objects share an instance of the underlying SOAP::Lite module. But you are free to have more - perhaps with different characteristics. See the code for attributes of the default SOAP::Lite object. -httpproxy => 'http://server:port' In addition to the 'location' parameter, you may need to specify also a location/URL of a HTTP proxy server (if your site requires one). Additionally, the main module Bio::Biblio recognises also: -access => '...' -location => '...' It populates calling object with the given arguments, and then - for some attributes and only if they are not yet populated - it assigns some default values. This is an actual new() method (except for the real object creation and its blessing which is done in the parent class Bio::Root::Root in method _create_object). Note that this method is called always as an I<object> method (never as a I<class> method) - and that the object who calls this method may already be partly initiated (from Bio::Biblio::new method); so if you need to do some tricks with the 'class invocation' you need to change Bio::Biblio::new method, not this one. =cut sub _initialize { my ($self, @args) = @_; # make a hashtable from @args my %param = @args; @param { map { lc $_ } keys %param } = values %param; # lowercase keys # copy all @args into this object (overwriting what may already be # there) - changing '-key' into '_key' my $new_key; foreach my $key (keys %param) { ($new_key = $key) =~ s/^-/_/; $self->{ $new_key } = $param { $key }; } # finally add default values for those keys who have default value # and who are not yet in the object $self->{'_location'} = $DEFAULT_SERVICE unless $self->{'_location'}; $self->{'_namespace'} = $DEFAULT_NAMESPACE unless $self->{'_namespace'}; $self->{'_destroy_on_exit'} = 1 unless defined $self->{'_destroy_on_exit'}; unless ($self->{'_soap'}) { if (defined $self->{'_httpproxy'}) { $self->{'_soap'} = SOAP::Lite -> uri ($self->{'_namespace'}) -> proxy ($self->{'_location'}, proxy => ['http' => $self->{'_httpproxy'}]); } else { $self->{'_soap'} = SOAP::Lite -> uri ($self->{'_namespace'}) -> proxy ($self->{'_location'}); } } } # ----------------------------------------------------------------------------- # # objects representing query collections are being destroyed if they # have attribute '_destroy_on_exit' set to true - which is a default # value # sub DESTROY { my $self = shift; my $soap = $self->{'_soap'}; my $destroy = $self->{'_destroy_on_exit'}; return unless $destroy; my $collection_id = $self->{'_collection_id'}; return unless $collection_id; # ignore all errors here eval { $soap->destroy (SOAP::Data->type (string => $collection_id)); } } # # some methods must be called with an argument containing a collection # ID; here we return a proper error message explaining it # sub _no_id_msg { my $self = shift; my $package = ref $self; my $method = (caller(1))[3]; my $strip_method = $method; $strip_method =~ s/^$package\:\://; return <<"END_OF_MSG"; Method '$method' works only if its object has a query collection ID. Perhaps you need to use: \tnew Bio::Biblio (-collection_id => '1234567')->$strip_method; or to obtain a collection ID indirectly from a query method: \tnew Bio::Biblio->find ('keyword')->$strip_method; END_OF_MSG } # # some methods do not work with older SOAP::Lite version; here we #return message explaining it # sub _old_version_msg { my $self = shift; my $method = (caller(1))[3]; return <<"END_OF_MSG"; Method '$method' works only with SOAP::Lite version 0.52 and newer (the problem is with returning a boolean value from the server). END_OF_MSG } # # some controlled vocabulary methods needs two parameters; here we # return message explaining it # sub _two_params_msg { my $self = shift; my $method = (caller(1))[3]; return <<"END_OF_MSG"; Method '$method' expects two parameters: vocabulary name and a value. END_OF_MSG } # # some controlled vocabulary methods needs a vocabulary name; here we # return message explaining it # sub _missing_name_msg { my $self = shift; my $method = (caller(1))[3]; return <<"END_OF_MSG"; Method '$method' expects vocabulary name as parameter. END_OF_MSG } # # return a copy of a given array, with all its elements replaced # with the SOAP-Data objects defining elements type as 'string' # sub _as_strings { my ($ref_input_array) = @_; my (@result) = map { SOAP::Data->new (type => 'string', value => $_) } @$ref_input_array; return \@result; } # --------------------------------------------------------------------- # # Here are the methods implementing Bio::DB::BiblioI interface # (documentation is in Bio::DB::BiblioI) # # --------------------------------------------------------------------- sub get_collection_id { my ($self) = @_; $self->{'_collection_id'}; } sub get_count { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; if ($collection_id) { $soap->getBibRefCount (SOAP::Data->type (string => $collection_id))->result; } else { $soap->getBibRefCount->result; } } # try: 94033980 sub get_by_id { my ($self, $citation_id) = @_; $self->throw ("Citation ID is expected as a parameter of method 'get_by_id'.") unless $citation_id; my $soap = $self->{'_soap'}; $soap->getById (SOAP::Data->type (string => $citation_id))->result; } sub find { my ($self, $keywords, $attrs) = @_; my (@keywords, @attrs); # $keywords can be a comma-delimited scalar or a reference to an array if ($keywords) { my $ref = ref $keywords; @keywords = split (/,/, $keywords) unless $ref; @keywords = @$keywords if $ref =~ /ARRAY/; } $self->throw ("No keywords given in 'find' method.\n") unless (@keywords); # ...and the same with $attrs if ($attrs) { my $ref = ref $attrs; @attrs = split (/,/, $attrs) unless $ref; @attrs = @$attrs if $ref =~ /ARRAY/; } my $soap = $self->{'_soap'}; my $collection_id = $self->{'_collection_id'}; my $new_id; if ($collection_id) { if (@attrs) { $new_id = $soap->find (SOAP::Data->type (string => $collection_id), &_as_strings (\@keywords), &_as_strings (\@attrs))->result; } else { $new_id = $soap->find (SOAP::Data->type (string => $collection_id), &_as_strings (\@keywords))->result; } } else { if (@attrs) { $new_id = $soap->find (&_as_strings (\@keywords), &_as_strings (\@attrs))->result; } else { $new_id = $soap->find (&_as_strings (\@keywords))->result; } } # clone itself but change the collection ID to a new one return $self->new (-collection_id => $new_id, -parent_collection_d => $collection_id); } sub get_all_ids { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; $soap->getAllIDs (SOAP::Data->type (string => $collection_id))->result; } sub get_all { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; $soap->getAllBibRefs (SOAP::Data->type (string => $collection_id))->result; } sub has_next { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; $self->throw ($self->_old_version_msg) if $SOAP::Lite::VERSION < 0.52; $soap->hasNext (SOAP::Data->type (string => $collection_id))->result; } sub get_next { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; my $ra = $soap->getNext (SOAP::Data->type (string => $collection_id))->result; $self->{'_collection_id'} = shift @{ $ra }; shift @{ $ra }; } sub get_more { my ($self, $how_many) = @_; my $soap = $self->{'_soap'}; my $collection_id = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; unless (defined ($how_many) and $how_many =~ /^\d+$/) { warn ("Method 'get_more' expects a numeric argument. Changing to 1.\n"); $how_many = 1; } unless ($how_many > 0) { warn ("Method 'get_more' expects a positive argument. Changing to 1.\n"); $how_many = 1; } my $ra = $soap->getMore (SOAP::Data->type (string => $collection_id), SOAP::Data->type (int => $how_many))->result; $self->{'_collection_id'} = shift @{ $ra }; $ra; } sub reset_retrieval { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; $self->{'_collection_id'} = $soap->resetRetrieval (SOAP::Data->type (string => $collection_id))->result; } sub exists { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; $self->throw ($self->_old_version_msg) if $SOAP::Lite::VERSION < 0.52; $soap->exists (SOAP::Data->type (string => $collection_id))->result; } sub destroy { my ($self) = @_; my $soap = $self->{'_soap'}; my ($collection_id) = $self->{'_collection_id'}; $self->throw ($self->_no_id_msg) unless $collection_id; $soap->destroy (SOAP::Data->type (string => $collection_id)); } sub get_vocabulary_names { my ($self) = @_; my $soap = $self->{'_soap'}; $soap->getAllVocabularyNames->result; } sub contains { my ($self, $vocabulary_name, $value) = @_; my $soap = $self->{'_soap'}; $self->throw ($self->_old_version_msg) if $SOAP::Lite::VERSION < 0.52; $self->throw ($self->_two_params_msg) unless defined $vocabulary_name and defined $value; $soap->contains (SOAP::Data->type (string => $vocabulary_name), SOAP::Data->type (string => $value))->result; } sub get_entry_description { my ($self, $vocabulary_name, $value) = @_; my $soap = $self->{'_soap'}; $self->throw ($self->_two_params_msg) unless defined $vocabulary_name and defined $value; $soap->getEntryDescription (SOAP::Data->type (string => $vocabulary_name), SOAP::Data->type (string => $value))->result; } sub get_all_values { my ($self, $vocabulary_name) = @_; my $soap = $self->{'_soap'}; $self->throw ($self->_missing_name_msg) unless defined $vocabulary_name; $soap->getAllValues (SOAP::Data->type (string => $vocabulary_name))->result; } sub get_all_entries { my ($self, $vocabulary_name) = @_; my $soap = $self->{'_soap'}; $self->throw ($self->_missing_name_msg) unless defined $vocabulary_name; $soap->getAllEntries (SOAP::Data->type (string => $vocabulary_name))->result; } =head2 VERSION and Revision Usage : print $Bio::DB::Biblio::soap::VERSION; print $Bio::DB::Biblio::soap::Revision; =cut =head2 Defaults Usage : print $Bio::DB::Biblio::soap::DEFAULT_SERVICE; print $Bio::DB::Biblio::soap::DEFAULT_NAMESPACE; =cut 1; __END__