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expect_failure can now be a regexp to test the error message
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@muffato
muffato committed Nov 27, 2020
1 parent cc48f80 commit 28d80c6
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Showing 2 changed files with 32 additions and 3 deletions.
31 changes: 30 additions & 1 deletion modules/Bio/EnsEMBL/Hive/Utils/Test.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ use warnings;
no warnings qw( redefine );

use Exporter;
use Capture::Tiny 'tee_stderr';
use Carp qw{croak};
use File::Spec;
use File::Temp qw{tempfile};
Expand Down Expand Up @@ -168,6 +169,8 @@ sub standaloneJob {
Arg[4] : (optional) Arrayref $tweaks. Tweaks to be applied to the database (as with the -tweak command-line option)
Arg[5] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : init_pipeline(
'Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMultServer_conf',
$server_url,
Expand Down Expand Up @@ -218,6 +221,8 @@ sub init_pipeline {
Arg[4] : String $test_name (optional). The name of the test
Arg[5] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Description : Generic method that can run any eHive script and check its return status
Returntype : None
Exceptions : TAP-style
Expand All @@ -232,10 +237,16 @@ sub _test_ehive_script {
$flags ||= {};
my @ext_args = ( defined($url) ? (-url => $url) : (), @$args );

my $rc = system($ENV{'EHIVE_ROOT_DIR'}.'/scripts/'.$script_name.'.pl', @ext_args);
my $rc;
my $stderr = tee_stderr {
$rc = system($ENV{'EHIVE_ROOT_DIR'}.'/scripts/'.$script_name.'.pl', @ext_args);
};
if ($flags->{expect_failure}) {
$test_name ||= $script_name.' fails'.(@ext_args ? ' with the command-line options: '.join(' ', @ext_args) : '');
ok($rc, $test_name);
if (re::is_regexp($flags->{expect_failure})) {
like($stderr, $flags->{expect_failure}, 'error message as expected');
}
} else {
$test_name ||= 'Can run '.$script_name.(@ext_args ? ' with the command-line options: '.join(' ', @ext_args) : '');
is($rc, 0, $test_name);
Expand All @@ -250,6 +261,8 @@ sub _test_ehive_script {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : runWorker($url, [ -can_respecialize => 1 ]);
Description : Run a worker on the given pipeline in the current process.
The worker options have been divided in three groups: the ones affecting its specialization,
Expand Down Expand Up @@ -284,6 +297,8 @@ sub runWorker {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : $seed_pipeline($url, [$arg1, $arg2], 'Run seed_pipeline with two arguments');
Description : Very generic function to run seed_pipeline on the given database with the given arguments
Returntype : None
Expand All @@ -306,6 +321,8 @@ sub seed_pipeline {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : beekeeper($url, [$arg1, $arg2], 'Run beekeeper with two arguments');
Description : Very generic function to run beekeeper on the given database with the given arguments
Returntype : None
Expand All @@ -326,6 +343,8 @@ sub beekeeper {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : tweak_pipeline($url, [$arg1, $arg2], 'Run tweak_pipeline with two arguments');
Description : Very generic function to run tweak_pipeline on the given database with the given arguments
Returntype : None
Expand All @@ -347,6 +366,8 @@ sub tweak_pipeline {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : generate_graph($url, [-output => 'lm_analyses.png'], 'Generate a PNG A-diagram');
Description : Very generic function to run generate_graph.pl on the given database with the given arguments
Returntype : None
Expand All @@ -368,6 +389,8 @@ sub generate_graph {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : visualize_jobs($url, [-output => 'lm_jobs.png', -accu_values], 'Generate a PNG J-diagram with accu values');
Description : Very generic function to run visualize_jobs.pl on the given database with the given arguments
Returntype : None
Expand All @@ -388,6 +411,8 @@ sub visualize_jobs {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : peekJob($url, [-job_id => 1], 'Check params for job 1');
Description : Very generic function to run peekJob.pl on the given database with the given arguments
Returntype : None
Expand All @@ -409,6 +434,8 @@ sub peekJob {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : db_cmd($url, [-sql => 'DROP DATABASE'], 'Drop the database');
Description : Very generic function to run db_cmd.pl on the given database with the given arguments
Returntype : None
Expand All @@ -430,6 +457,8 @@ sub db_cmd {
Arg[3] : String $test_name (optional). The name of the test
Arg[4] : (optional) Hashref $flags. Flags given to the text framework. Currently the only
key that is understood is "expect_failure" to reverse the expectation of the test.
It is primarily used as a boolean, but can be a regular expression to test the standard
error of the script.
Example : run_sql_on_db($url, 'INSERT INTO sweets (name, quantity) VALUES (3, 'Snickers')');
Description : Execute an SQL command on the given database and test its execution. This expects the
command-line client to return a non-zero code in case of a failure.
Expand Down
4 changes: 2 additions & 2 deletions t/03.scripts/beekeeper_opts.t
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ my $pipeline_url = get_test_url_or_die();
beekeeper($hive_dba->dbc->url,
['-run', -job_id => 98765],
'beekeeper complained that the job cannot be found',
{'expect_failure' => 1},
{'expect_failure' => qr/Could not fetch Job with dbID=98765/},
);

$beekeeper_rows = $beekeeper_nta->fetch_all();
Expand All @@ -88,7 +88,7 @@ my $pipeline_url = get_test_url_or_die();
$hive_dba->dbc->url,
['-loop', -analyses_pattern => 'this_matches_no_analysis'],
'beekeeper complained that no analysis could be matched',
{'expect_failure' => 1},
{'expect_failure' => qr/the -analyses_pattern 'this_matches_no_analysis' did not match any Analyses/},
);

$beekeeper_rows = $beekeeper_nta->fetch_all();
Expand Down

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