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# -*-Perl-*- Test Harness script for Bioperl
# $Id: epost.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
use warnings;
use Data::Dumper;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 60,
-requires_module => 'XML::Simple');
use_ok('Bio::Tools::EUtilities');
use_ok('Bio::Tools::EUtilities::EUtilParameters');
}
# check -correspondence => 0 (default) - this is set up to return the
# exact same thing as correspondece = 1, tested below)
my $eutil = Bio::Tools::EUtilities->new(
-eutil => 'elink',
-file => test_input_file('eutils','elink_ncheck.xml'));
isa_ok($eutil, 'Bio::Tools::EUtilities::Link');
# for lcheck, db are not returned (check is for external link in, not out)
is(join(',',$eutil->get_databases), '');
# for elinks, IDs are globbed together when called from the parser
# unless a database is specified. Since no database is specified, all
# ids are lumped together regardless
is(join(',',$eutil->get_ids), '730439,68536103,1621261,20807972', 'get_ids');
my @ls = $eutil->get_LinkSets;
is(scalar(@ls), 4, 'uncorrelated LinkSets lump everything together');
is(join(',',$ls[1]->get_databases), '');
isa_ok($ls[0], 'Bio::Tools::EUtilities::EUtilDataI');
isa_ok($ls[0], 'Bio::Tools::EUtilities::Link::LinkSet');
# check data in LinkSets
is(join(',',$ls[0]->get_ids), '730439');
is(join(',',$ls[0]->get_databases), '');
is(join(',',$ls[0]->get_submitted_ids), '730439');
is($ls[0]->get_dbfrom, 'protein');
is(join(',',$ls[0]->get_link_names), '');
is($ls[0]->has_scores, 0);
is($ls[0]->has_linkout, 0);
is($ls[0]->has_neighbor, 1);
# no LinkInfo
my @info = $ls[0]->get_LinkInfo;
is(scalar(@info), 0);
my @urls = $ls[0]->get_UrlLinks;
is(scalar(@urls), 0);
is(join(',',$ls[1]->get_ids), '68536103');
is(join(',',$ls[1]->get_databases), '');
is(join(',',$ls[1]->get_submitted_ids), '68536103');
is(join(',',$ls[1]->get_link_names), '');
is($ls[1]->get_dbfrom, 'protein');
is($ls[1]->has_scores, 0);
is($ls[1]->has_linkout, 0);
is($ls[1]->has_neighbor, 1);
# no LinkInfo
@info = $ls[1]->get_LinkInfo;
is(scalar(@info), 0);
# no UrlLinks
@urls = $ls[1]->get_UrlLinks;
is(scalar(@urls), 0);
# check -correspondence => 1
$eutil = Bio::Tools::EUtilities->new(
-eutil => 'elink',
-file => test_input_file('eutils','elink_ncheck_corr.xml'));
isa_ok($eutil, 'Bio::Tools::EUtilities::Link');
is(join(',',$eutil->get_databases), '');
# for elinks, IDs are globbed together when called from the parser unless a database is specified
is(join(',',$eutil->get_ids), '1621261,68536103,20807972,730439', 'get_ids');
@ls = $eutil->get_LinkSets;
is(scalar(@ls), 4, 'correlated LinkSets separate ID data');
is(join(',',$ls[1]->get_databases), '');
isa_ok($ls[0], 'Bio::Tools::EUtilities::EUtilDataI');
isa_ok($ls[0], 'Bio::Tools::EUtilities::Link::LinkSet');
# check data in LinkSets
is(join(',',$ls[0]->get_ids), '1621261');
is(join(',',$ls[0]->get_databases), '');
is(join(',',$ls[0]->get_submitted_ids), '1621261');
is(join(',',$ls[0]->get_link_names), '');
is($ls[0]->get_dbfrom, 'protein');
is($ls[0]->has_scores, 0);
is($ls[0]->has_linkout, 0);
is($ls[0]->has_neighbor, 1);
# no LinkInfo
@info = $ls[0]->get_LinkInfo;
is(scalar(@info), 0);
# no UrlLinks
@urls = $ls[0]->get_UrlLinks;
is(scalar(@urls), 0);
# HistoryI
is($ls[0]->get_webenv, undef);
is($ls[0]->get_query_key, undef);
is(join(',',$ls[1]->get_ids), '68536103');
is(join(',',$ls[1]->get_databases), '');
is(join(',',$ls[1]->get_submitted_ids), '68536103');
is($ls[1]->get_dbfrom, 'protein');
is(join(',',$ls[1]->get_link_names), '');
is($ls[1]->has_scores, 0);
is($ls[1]->has_linkout, 0);
is($ls[1]->has_neighbor, 1);
# no LinkInfo
@info = $ls[1]->get_LinkInfo;
is(scalar(@info), 0);
# no UrlLinks
@urls = $ls[1]->get_UrlLinks;
is(scalar(@urls), 0);
# HistoryI
is($ls[1]->get_webenv, undef);
is($ls[1]->get_query_key, undef);
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