Commit db95ae42 authored by Andreas Tille's avatar Andreas Tille

Skip tests for soap

parent 010919bf
......@@ -6,3 +6,4 @@ skip_tests_for_muscle.patch
skip_tests_for_ncbi-blast+.patch
hyphy.patch
remove_tests_for_ensembl.patch
skip_tests_for_soap.patch
Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 11 Feb 2019 19:34:04 +0100
Description: Somehow these tests are failing - no idea why
--- a/t/AnalysisFactory_soap.t
+++ /dev/null
@@ -1,56 +0,0 @@
-# -*-Perl-*-
-# $id$
-## Bioperl Test Harness Script for Modules
-
-use strict;
-
-BEGIN {
- use Bio::Root::Test;
-
- # The EMBL-EBI Soaplab server has been decommissioned on 1st February 2013
- # (https://www.ebi.ac.uk/Tools/webservices/about/news).
- # Website "http://www.ebi.ac.uk/soaplab/services" dont exists anymore,
- # so tests will fail with "404 Not Found" if executed
- test_begin(-tests => 0,
- -requires_networking => 1);
- use_ok('Bio::Tools::Run::AnalysisFactory');
-}
-
-
-# setup global objects that are to be used in more than one test
-# Also test they were initialised correctly
-# test new with default access
-my $factory = Bio::Tools::Run::AnalysisFactory->new();
-isa_ok( $factory, 'Bio::Tools::Run::AnalysisFactory');
-
-# test new with explicit access
-$factory = Bio::Tools::Run::AnalysisFactory->new(-access=>'soap');
-isa_ok( $factory, 'Bio::Tools::Run::AnalysisFactory');
-
-# test new with non-existing access
-throws_ok { Bio::Tools::Run::AnalysisFactory->new(-access=>'non_existing') } qr/cannot be found or loaded/, 'Non existant access method threw an error';
-
-# test default factory values
-
-# Now onto the nitty gritty tests of the modules methods
-SKIP: {
- test_skip(-tests => 9, -requires_module => 'SOAP::Lite');
- use_ok('SOAP::Lite');
-
- my $array_ref = $factory->available_categories;
- isa_ok( $array_ref, 'ARRAY' );
- ok( grep(/protein/i, @$array_ref), 'available_categories returned category with protein' );
-
- $array_ref = $factory->available_analyses;
- isa_ok( $array_ref, 'ARRAY' );
- ok( grep(/seqret/i, @$array_ref), 'available_analyses returned category with seqret' );
-
- $array_ref = $factory->available_analyses('edit');
- isa_ok( $array_ref, 'ARRAY' );
- ok( grep(/seqret/i, @$array_ref), 'available_analyses("edit") returned something' );
-
- my $service;
- lives_ok {$service = $factory->create_analysis('edit.seqret')};
- skip ("create_analysis failed :$@", 1) if $@;
- isa_ok( $service, 'Bio::Tools::Run::Analysis::soap' );
-}
--- a/t/Analysis_soap.t
+++ /dev/null
@@ -1,72 +0,0 @@
-# -*-Perl-*-
-# $id$
-## Bioperl Test Harness Script for Modules
-
-use strict;
-
-BEGIN {
- use Bio::Root::Test;
-
- # The EMBL-EBI Soaplab server has been decommissioned on 1st February 2013
- # (https://www.ebi.ac.uk/Tools/webservices/about/news).
- # Website "http://www.ebi.ac.uk/soaplab/services" dont exists anymore,
- # so tests will fail with "404 Not Found" if executed
- test_begin(-tests => 0,
- -requires_networking => 1);
- use_ok('Bio::Tools::Run::Analysis');
- use_ok('File::Spec');
-}
-
-SKIP: {
- test_skip(-tests => 15, -requires_module => 'SOAP::Lite');
- use_ok('SOAP::Lite');
-
- my $seqret = Bio::Tools::Run::Analysis->new(-name=>'edit.seqret');
- my $seq = 'tatacga';
-
- SKIP: {
- # condition used to skip this block of tests
- #skip($why, $how_many_in_block);
- skip("Failed to create the analysis object", 1)
- unless isa_ok( $seqret, 'Bio::Tools::Run::Analysis::soap');
-
- # test seqret service with some testing data
- # TODO: use BIOPERLDEBUG to skip these tests
- my %input = (
- 'sequence_direct_data' => $seq,
- 'osformat' => 'raw',
- );
- is( $seqret->analysis_name, 'seqret', 'analysis_name returned seqret' );
- isa_ok( $seqret->analysis_spec, 'HASH');
-
- my $input_spec = $seqret->input_spec;
- isa_ok( $input_spec, 'ARRAY' );
- ok( @$input_spec > 0, 'input_spec returned an array with something in it' );
- isa_ok( $input_spec->[0], 'HASH' );
- my $result_spec = $seqret->result_spec;
- isa_ok( $result_spec, 'ARRAY' );
- ok( @$result_spec > 0, 'result_spec returned an array with something in it' );
- like( $seqret->describe, '/^<\?xml /', 'describe seems to have returned the correct thing' );
- my $job = $seqret->create_job (\%input);
- SKIP: {
- skip("Object not created correctly", 6) unless isa_ok( $job, 'Bio::Tools::Run::Analysis::Job' );
-
- is( $job->status, 'CREATED', 'Job status correct' );
- # TODO: not goot to use private methods
- my $cloned_job = $seqret->create_job ($job->{'_id'});
-
- SKIP: {
- skip( "Couldn't clone the job", 2 )
- unless isa_ok( $cloned_job, 'Bio::Tools::Run::Analysis::Job',
- 'Job cloned successfully' );
-
- like( $cloned_job->last_event, '/^<\?xml /',
- 'last_event seems to have returned the correct thing' );
- $cloned_job->remove;
- # TODO: not good to use private methods
- is( $cloned_job->{'_destroy_on_exit'}, 1,
- 'Cloned job removed successfully' );
- }
- }
- }
-}
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