# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: BiblioReferences.t,v 1.9 2002/03/08 13:58:00 senger Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS);
my $error;
BEGIN {
    # to handle systems with no installed Test module
    # we include the t dir (where a copy of Test.pm is located)
    # as a fallback
    eval { require Test; };
    $error = 0;
    if( $@ ) {
        use lib 't';
    }
    use Test;
    $NUMTESTS = 537;
    plan tests => $NUMTESTS;
}
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run. 
my ($biblio, $count, $str, @args);
my ($citation, $provider);
my $format = ($ENV{'TEST_DETAILS'} ? "\t%-45s" : '');
print "Testing 'use Bio::Biblio:: ...'\n";
eval { require Bio::Biblio::Article };
print sprintf ($format, "use Bio::Biblio::Article"); ok (%Bio::Biblio::Article::);
print $@ if $@;
eval { require Bio::Biblio::Book };
print sprintf ($format, "use Bio::Biblio::Book"); ok (%Bio::Biblio::Book::);
print $@ if $@;
eval { require Bio::Biblio::BookArticle };
print sprintf ($format, "use Bio::Biblio::BookArticle"); ok (%Bio::Biblio::BookArticle::);
print $@ if $@;
eval { require Bio::Biblio::Journal };
print sprintf ($format, "use Bio::Biblio::Journal"); ok (%Bio::Biblio::Journal::);
print $@ if $@;
eval { require Bio::Biblio::JournalArticle };
print sprintf ($format, "use Bio::Biblio::JournalArticle"); ok (%Bio::Biblio::JournalArticle::);
print $@ if $@;
eval { require Bio::Biblio::MedlineArticle };
print sprintf ($format, "use Bio::Biblio::MedlineArticle"); ok (%Bio::Biblio::MedlineArticle::);
print $@ if $@;
eval { require Bio::Biblio::MedlineBook };
print sprintf ($format, "use Bio::Biblio::MedlineBook"); ok (%Bio::Biblio::MedlineBook::);
print $@ if $@;
eval { require Bio::Biblio::MedlineBookArticle };
print sprintf ($format, "use Bio::Biblio::MedlineBookArticle"); ok (%Bio::Biblio::MedlineBookArticle::);
print $@ if $@;
eval { require Bio::Biblio::MedlineJournal };
print sprintf ($format, "use Bio::Biblio::MedlineJournal"); ok (%Bio::Biblio::MedlineJournal::);
print $@ if $@;
eval { require Bio::Biblio::MedlineJournalArticle };
print sprintf ($format, "use Bio::Biblio::MedlineJournalArticle"); ok (%Bio::Biblio::MedlineJournalArticle::);
print $@ if $@;
eval { require Bio::Biblio::Organisation };
print sprintf ($format, "use Bio::Biblio::Organisation"); ok (%Bio::Biblio::Organisation::);
print $@ if $@;
eval { require Bio::Biblio::Patent };
print sprintf ($format, "use Bio::Biblio::Patent"); ok (%Bio::Biblio::Patent::);
print $@ if $@;
eval { require Bio::Biblio::Person };
print sprintf ($format, "use Bio::Biblio::Person"); ok (%Bio::Biblio::Person::);
print $@ if $@;
eval { require Bio::Biblio::Proceeding };
print sprintf ($format, "use Bio::Biblio::Proceeding"); ok (%Bio::Biblio::Proceeding::);
print $@ if $@;
eval { require Bio::Biblio::Provider };
print sprintf ($format, "use Bio::Biblio::Provider"); ok (%Bio::Biblio::Provider::);
print $@ if $@;
eval { require Bio::Biblio::Ref };
print sprintf ($format, "use Bio::Biblio::Ref"); ok (%Bio::Biblio::Ref::);
print $@ if $@;
eval { require Bio::Biblio::Service };
print sprintf ($format, "use Bio::Biblio::Service"); ok (%Bio::Biblio::Service::);
print $@ if $@;
eval { require Bio::Biblio::TechReport };
print sprintf ($format, "use Bio::Biblio::TechReport"); ok (%Bio::Biblio::TechReport::);
print $@ if $@;
eval { require Bio::Biblio::Thesis };
print sprintf ($format, "use Bio::Biblio::Thesis"); ok (%Bio::Biblio::Thesis::);
print $@ if $@;
eval { require Bio::Biblio::WebResource };
print sprintf ($format, "use Bio::Biblio::WebResource"); ok (%Bio::Biblio::WebResource::);
print $@ if $@;
eval { require Bio::Biblio::PubmedArticle };
print sprintf ($format, "use Bio::Biblio::PubmedArticle"); ok (%Bio::Biblio::PubmedArticle::);
print $@ if $@;
eval { require Bio::Biblio::PubmedBookArticle };
print sprintf ($format, "use Bio::Biblio::PubmedBookArticle"); ok (%Bio::Biblio::PubmedBookArticle::);
print $@ if $@;
eval { require Bio::Biblio::PubmedJournalArticle };
print sprintf ($format, "use Bio::Biblio::PubmedJournalArticle"); ok (%Bio::Biblio::PubmedJournalArticle::);
print $@ if $@;
print "Testing 'new Bio::Biblio:: ...'\n";
foreach my $object (
                    qw(
                     Bio::Biblio::Article
                     Bio::Biblio::Book
                     Bio::Biblio::BookArticle
                     Bio::Biblio::Journal
                     Bio::Biblio::JournalArticle
                     Bio::Biblio::MedlineArticle
                     Bio::Biblio::MedlineBook
                     Bio::Biblio::MedlineBookArticle
                     Bio::Biblio::MedlineJournal
                     Bio::Biblio::MedlineJournalArticle
                     Bio::Biblio::Organisation
                     Bio::Biblio::Patent
                     Bio::Biblio::Person
                     Bio::Biblio::Proceeding
                     Bio::Biblio::Provider
                     Bio::Biblio::Ref
                     Bio::Biblio::Service
                     Bio::Biblio::TechReport
                     Bio::Biblio::Thesis
                     Bio::Biblio::WebResource
                     Bio::Biblio::PubmedArticle
                     Bio::Biblio::PubmedBookArticle
                     Bio::Biblio::PubmedJournalArticle
                       )) {
    print sprintf ($format, "new $object"); ok defined ($biblio = new $object);
}
my @scalar_methods_for_ref =
    qw(
     abstract
     abstract_language
     abstract_type
     author_list_complete
     cross_references_list_complete
     date
     date_completed
     date_created
     date_revised
     format
     identifier
     language
     last_modified_date
     repository_subset
     rights
     spatial_location
     subject_headings_source
     temporal_period
     title
     toc
     toc_type
     type
     );
my @other_methods_for_ref =
    qw(
     authors
     cross_references
     codes
     contributors
     keywords
     publisher
     subject_headings
    );
my @scalar_methods_for_book =
    qw(
     edition
     isbn
     series
     volume
     );
my @other_methods_for_book =
    qw(
     editor
     );
my @scalar_methods_for_bookarticle =
    qw(
     );
my @other_methods_for_bookarticle =
    qw(
     book
     );
my @scalar_methods_for_article =
    qw(
     first_page
     last_page
     );
my @other_methods_for_article =
    qw(
     );
my @scalar_methods_for_journalarticle =
    qw(
     issue
     issue_supplement
     volume
     );
my @other_methods_for_journalarticle =
    qw(
     journal
     );
my @scalar_methods_for_medlinearticle =
    qw(
     affiliation
     citation_owner
     date_of_electronic_publication
     gene_symbols
     grant_list_complete
     medline_date
     medline_id
     medline_page
     number_of_references
     other_languages
     pmid
     season
     status
     vernacular_title
     );
my @other_methods_for_medlinearticle =
    qw(
     chemicals
     comment_ins
     comment_ons
     erratum_fors
     erratum_ins
     general_notes
     grants
     mesh_headings
     original_report_ins
     other_abstracts
     other_ids
     republished_froms
     republished_ins
     retraction_ins
     retraction_ofs
     summary_for_patients_ins
     update_ins
     update_ofs
     );
my @scalar_methods_for_medlinejournalarticle =
    qw(
     );
my @other_methods_for_medlinejournalarticle =
    qw(
     journal
     );
my @scalar_methods_for_medlinebookarticle =
    qw(
     );
my @other_methods_for_medlinebookarticle =
    qw(
     book
     );
my @scalar_methods_for_medlinebook =
    qw(
     );
my @other_methods_for_medlinebook =
    qw(
     );
my @scalar_methods_for_pubmedarticle =
    qw(
     pubmed_status
     pubmed_provider_id
     );
my @other_methods_for_pubmedarticle =
    qw(
     pubmed_history_list
     pubmed_article_id_list
     pubmed_url_list
     );
my @scalar_methods_for_journal =
    qw(
     abbreviation
     issn
     name
     );
my @other_methods_for_journal =
    qw(
     );
my @scalar_methods_for_medlinejournal =
    qw(
     coden
     country
     medline_code
     medline_ta
     nlm_unique_id
     );
my @other_methods_for_medlinejournal =
    qw(
     );
my @scalar_methods_for_patent =
    qw(
     doc_number
     doc_office
     doc_type
     );
my @other_methods_for_patent =
    qw(
     applicants
     );
my @scalar_methods_for_webresource =
    qw(
     url
     estimated_size
     cost
     );
my @other_methods_for_webresource =
    qw(
     );
my @scalar_methods_for_provider =
    qw(
     type
     );
my @scalar_methods_for_person =
    qw(
     affiliation
     email
     firstname
     forename
     initials
     lastname
     middlename
     postal_address
     suffix
     );
my @scalar_methods_for_organisation =
    qw(
     name
     );
my @scalar_methods_for_service =
    qw(
     name
     );
#
# Bio::Biblio::MedlineJournalArticle
#
print "Testing Bio::Biblio::MedlineJournalArticle ...\n";
$citation = new Bio::Biblio::MedlineJournalArticle;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_ref,
                    @scalar_methods_for_article,
                    @scalar_methods_for_journalarticle,
                    @scalar_methods_for_medlinearticle,
                    @scalar_methods_for_medlinejournalarticle) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $citation->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $citation->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::MedlineJournalArticle (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $citation->$method(), $args[$i+1];
}
foreach my $method (@other_methods_for_ref,
                    @other_methods_for_article,
                    @other_methods_for_journalarticle,
                    @other_methods_for_medlinearticle,
                    @other_methods_for_medlinejournalarticle) {
    print sprintf ($format, "get '$method' "); ok $citation->$method(), undef;
}
my ($me) = new Bio::Biblio::Person (-lastname => 'me');
my ($you) = new Bio::Biblio::Person (-lastname => 'you');
print sprintf ($format, "add_author 1"); ok $citation->add_author ($me);
print sprintf ($format, "add_author 2"); ok $citation->add_author ($you);
print sprintf ($format, "get authors");  ok ${ $citation->authors }[1]->lastname, 'you';
print sprintf ($format, "add_contributor 1"); ok $citation->add_contributor ($me);
print sprintf ($format, "add_contributor 2"); ok $citation->add_contributor ($you);
print sprintf ($format, "get contributors");  ok ${ $citation->contributors }[1]->lastname, 'you';
use Bio::Annotation::DBLink;
my $link1 = new Bio::Annotation::DBLink(-database => 'here',
                                        -primary_id => '001'
                                        );
my $link2 = new Bio::Annotation::DBLink(-database => 'there',
                                        -primary_id => '002'
                                        );
print sprintf ($format, "add_cross_reference 1"); ok $citation->add_cross_reference ($link1);
print sprintf ($format, "add_cross_reference 2"); ok $citation->add_cross_reference ($link2);
print sprintf ($format, "get cross_references");  ok ${ $citation->cross_references }[0]->database, 'here';
print sprintf ($format, "get cross_references");  ok ${ $citation->cross_references }[1]->primary_id, '002';
#
# Bio::Biblio::MedlineBookArticle
#
print "Testing Bio::Biblio::MedlineBookArticle ...\n";
$citation = new Bio::Biblio::MedlineBookArticle;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_ref,
                    @scalar_methods_for_article,
                    @scalar_methods_for_bookarticle,
                    @scalar_methods_for_medlinearticle,
                    @scalar_methods_for_medlinebookarticle) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $citation->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $citation->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::MedlineBookArticle (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $citation->$method(), $args[$i+1];
}
foreach my $method (@other_methods_for_ref,
                    @other_methods_for_article,
                    @other_methods_for_bookarticle,
                    @other_methods_for_medlinearticle,
                    @other_methods_for_medlinebookarticle) {
    print sprintf ($format, "get '$method' "); ok $citation->$method(), undef;
}
#
# Bio::Biblio::MedlineBook
#
print "Testing Bio::Biblio::MedlineBook ...\n";
$citation = new Bio::Biblio::MedlineBook;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_ref,
                    @scalar_methods_for_book,
                    @scalar_methods_for_medlinebook) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $citation->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $citation->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::MedlineBook (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $citation->$method(), $args[$i+1];
}
foreach my $method (@other_methods_for_ref,
                    @other_methods_for_book,
                    @other_methods_for_medlinebook) {
    print sprintf ($format, "get '$method' "); ok $citation->$method(), undef;
}
#
# Bio::Biblio::MedlineJournal
#
print "Testing Bio::Biblio::MedlineJournal ...\n";
$citation = new Bio::Biblio::MedlineJournal;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_journal,
                    @scalar_methods_for_medlinejournal) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $citation->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $citation->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::MedlineJournal (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $citation->$method(), $args[$i+1];
}
foreach my $method (@other_methods_for_journal,
                    @other_methods_for_medlinejournal) {
    print sprintf ($format, "get '$method' "); ok $citation->$method(), undef;
}
#
# Bio::Biblio::Patent
#
print "Testing Bio::Biblio::Patent ...\n";
$citation = new Bio::Biblio::Patent;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_patent) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $citation->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $citation->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::Patent (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $citation->$method(), $args[$i+1];
}
foreach my $method (@other_methods_for_patent) {
    print sprintf ($format, "get '$method' "); ok $citation->$method(), undef;
}
#
# Bio::Biblio::WebResource
#
print "Testing Bio::Biblio::WebResource ...\n";
$citation = new Bio::Biblio::WebResource;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_webresource) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $citation->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $citation->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::WebResource (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $citation->$method(), $args[$i+1];
}
foreach my $method (@other_methods_for_webresource) {
    print sprintf ($format, "get '$method' "); ok $citation->$method(), undef;
}
#
# Bio::Biblio::Person
#
print "Testing Bio::Biblio::Person ...\n";
$provider = new Bio::Biblio::Person;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_provider,
                    @scalar_methods_for_person) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $provider->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $provider->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::Person (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $provider->$method(), $args[$i+1];
}
#
# Bio::Biblio::Organisation
#
print "Testing Bio::Biblio::Organisation ...\n";
$provider = new Bio::Biblio::Organisation;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_provider,
                    @scalar_methods_for_organisation) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $provider->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $provider->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::Organisation (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $provider->$method(), $args[$i+1];
}
#
# Bio::Biblio::Service
#
print "Testing Bio::Biblio::Service ...\n";
$provider = new Bio::Biblio::Service;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_provider,
                    @scalar_methods_for_organisation) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $provider->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $provider->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::Service (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $provider->$method(), $args[$i+1];
}
#
# Bio::Biblio::PubmedJournalArticle
#
print "Testing Bio::Biblio::PubmedJournalArticle ...\n";
$citation = new Bio::Biblio::PubmedJournalArticle;
@args = ();
$count = 1;
foreach my $method (@scalar_methods_for_pubmedarticle) {
    $str = 'string' . ($count++);
    print sprintf ($format, "set '$method' "); ok $citation->$method ($str), $str;
    print sprintf ($format, "get '$method' "); ok $citation->$method(), $str;
    push (@args, ("-$method" => $str));
}
print sprintf ($format, "set all attributes in a constructor");
ok defined ($biblio = new Bio::Biblio::PubmedJournalArticle (@args));
for (my $i = 0; $i < @args; $i += 2) {
    my $method = substr ($args[$i], 1);
    print sprintf ($format, "   $method"); ok $citation->$method(), $args[$i+1];
}
foreach my $method (@other_methods_for_pubmedarticle) {
    print sprintf ($format, "get '$method' "); ok $citation->$method(), undef;
}
__END__