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Enable datacheck Jira ticket CSV output #871

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Enable datacheck Jira ticket CSV output #871

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e5858a3
Enable datacheck Jira ticket CSV output
twalsh-ebi Oct 27, 2024
8c866dd
Expect failure in createDCJiraTickets.t
twalsh-ebi Oct 27, 2024
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21 changes: 17 additions & 4 deletions modules/Bio/EnsEMBL/Compara/RunnableDB/CreateDCJiraTickets.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -36,30 +36,43 @@ sub param_defaults {
my $self = shift;
return {
%{$self->SUPER::param_defaults},
'merge_ticket_key' => undef,
'test_mode' => 0,
'csv_mode' => 0,
}
}

sub run {
my $self = shift;

my $jira_exe = $self->param_required('create_datacheck_tickets_exe');
my $tap_file = $self->param_required('output_results');

my $merge_ticket_key_param = $self->param_is_defined('merge_ticket_key')
? sprintf('--merge_ticket_key %s', $self->param('merge_ticket_key'))
: '';

my $csv_param = $self->param('csv_mode')
? sprintf('--csv %s.csv', $tap_file)
: '';

my $command = join(" ", (
$jira_exe, $self->param_required('output_results'), "--update",
$jira_exe, $tap_file, "--update",
"--division", $self->param_required('division'),
( $self->param('datacheck_type') ? '--label ' . $self->param('datacheck_type') : '' ),
( $self->param('dry_run') ? '--dry_run' : '')
( $self->param('dry_run') ? '--dry_run' : ''),
$merge_ticket_key_param,
$csv_param,
));
$self->warning( "Command: " . $command );

return if $self->param('test_mode');

if (defined $ENV{'JIRA_AUTH_TOKEN'}) {
if (defined $ENV{'JIRA_AUTH_TOKEN'} || $self->param('csv_mode')) {
$self->run_command($command, { die_on_failure => 1, });
}
else {
$self->warning( "ERROR: ENV variable not defined: \$JIRA_AUTH_TOKEN. Define with:\nexport JIRA_AUTH_TOKEN=$(echo -n 'user:pass' | openssl base64)" );
$self->die_no_retry( "ERROR: ENV variable not defined: \$JIRA_AUTH_TOKEN. Define with:\nexport JIRA_AUTH_TOKEN=$(echo -n 'user:pass' | openssl base64)" );
}

}
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23 changes: 8 additions & 15 deletions modules/t/createDCJiraTickets.t
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Original file line number Diff line number Diff line change
Expand Up @@ -36,14 +36,11 @@ standaloneJob(
'dry_run' => 1,
'create_datacheck_tickets_exe' => '$ENSEMBL_ROOT_DIR/ensembl-compara/scripts/jira_tickets/create_datacheck_tickets.pl',
'division' => 'vertebrates',
'test_mode' => 1,
},
[
[
'WARNING',
"Command: \$ENSEMBL_ROOT_DIR/ensembl-compara/scripts/jira_tickets/create_datacheck_tickets.pl $test_infile --update --division vertebrates --dry_run",
],
]
undef,
{
'expect_failure' => 1,
},
);

standaloneJob(
Expand All @@ -54,15 +51,11 @@ standaloneJob(
'dry_run' => 1,
'create_datacheck_tickets_exe' => '$ENSEMBL_ROOT_DIR/ensembl-compara/scripts/jira_tickets/create_datacheck_tickets.pl',
'division' => 'vertebrates',
'test_mode' => 1,

},
[
[
'WARNING',
"Command: \$ENSEMBL_ROOT_DIR/ensembl-compara/scripts/jira_tickets/create_datacheck_tickets.pl $test_infile --update --division vertebrates --label critical --dry_run",
],
]
undef,
{
'expect_failure' => 1,
},
);

done_testing();
67 changes: 49 additions & 18 deletions scripts/jira_tickets/create_datacheck_tickets.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,16 @@ =head1 OPTIONS
In dry-run mode, the JIRA tickets will not be submitted to the JIRA
server. By default, dry-run mode is off.

=item B<-csv> <PATH>

Optional. Instead of creating JIRA tickets,
output to a CSV file to be imported to JIRA.

=item B<-merge_ticket_key> <STR>

Optional. Merge ticket key. If specified, datacheck
tickets will be created as subtasks of this ticket.

=item B<-h[elp]>

Print usage information.
Expand All @@ -77,7 +87,7 @@ =head1 OPTIONS

use Bio::EnsEMBL::Compara::Utils::JIRA;

my ( $release, $division, @labels, $update, $dry_run, $help );
my ( $release, $division, @labels, $update, $dry_run, $csv, $merge_ticket_key, $help );
$update = 0;
$dry_run = 0;
$help = 0;
Expand All @@ -87,6 +97,8 @@ =head1 OPTIONS
"label=s" => \@labels,
"update" => \$update,
'dry_run|dry-run' => \$dry_run,
'csv=s' => \$csv,
'merge_ticket_key=s' => \$merge_ticket_key,
"h|help" => \$help,
);
pod2usage(1) if $help;
Expand All @@ -97,15 +109,19 @@ =head1 OPTIONS
my $dc_abs_path = abs_path($dc_file);
# Get a new Utils::JIRA object to create the tickets for the given division and
# release
my $jira_adaptor = Bio::EnsEMBL::Compara::Utils::JIRA->new(-DIVISION => $division, -RELEASE => $release);
my $jira_adaptor = Bio::EnsEMBL::Compara::Utils::JIRA->new(-DIVISION => $division, -RELEASE => $release, -CSV => $csv);
# Parse Datacheck information from input TAP file
my $testcase_failures = parse_datachecks($dc_file);
unless ( %$testcase_failures ) {
print "No failed DCs found in $dc_file\n";
exit;
}

if (!defined $merge_ticket_key) {
$merge_ticket_key = find_labeled_ticket($jira_adaptor, 'Merge_anchor');
}

# Create a task ticket for each datacheck subtest failure
my $merge_ticket_key = find_labeled_ticket($jira_adaptor, 'Merge_anchor');
my @json_subtasks;
foreach my $testcase ( keys %$testcase_failures ) {
my $failure_subtask_json = {
Expand All @@ -117,21 +133,36 @@ =head1 OPTIONS
}
my $components = ['Datachecks', 'Production tasks'];
my $categories = ['Bug::Internal', 'Production::Tasks'];
# Create all JIRA tickets
my $dc_task_keys = $jira_adaptor->create_tickets(
-JSON_OBJ => \@json_subtasks,
-DEFAULT_ISSUE_TYPE => 'Sub-task',
-DEFAULT_PRIORITY => 'Blocker',
-EXTRA_COMPONENTS => $components,
-EXTRA_CATEGORIES => $categories,
-EXTRA_LABELS => \@labels,
-UPDATE => $update,
-DRY_RUN => $dry_run
);
# Create a blocker issue link between the newly created datacheck ticket and the
# handover ticket if it doesn't already exist
my $blocked_ticket_key = find_labeled_ticket($jira_adaptor, 'Handover_anchor');
$jira_adaptor->link_tickets('Blocks', $dc_task_keys->[0], $blocked_ticket_key, $dry_run);

if ($csv) {
$jira_adaptor->create_ticket_csv(
-JSON_OBJ => \@json_subtasks,
-DEFAULT_ISSUE_TYPE => 'Sub-task',
-DEFAULT_PRIORITY => 'Blocker',
-EXTRA_COMPONENTS => $components,
-EXTRA_CATEGORIES => $categories,
-EXTRA_LABELS => \@labels,
-DRY_RUN => $dry_run,
-CSV_FILE => $csv,
-PARENT_LINK => $merge_ticket_key,
);
} else {
# Create all JIRA tickets
my $dc_task_keys = $jira_adaptor->create_tickets(
-JSON_OBJ => \@json_subtasks,
-DEFAULT_ISSUE_TYPE => 'Sub-task',
-DEFAULT_PRIORITY => 'Blocker',
-EXTRA_COMPONENTS => $components,
-EXTRA_CATEGORIES => $categories,
-EXTRA_LABELS => \@labels,
-UPDATE => $update,
-DRY_RUN => $dry_run
);
# Create a blocker issue link between the newly created datacheck ticket and the
# handover ticket if it doesn't already exist
my $blocked_ticket_key = find_labeled_ticket($jira_adaptor, 'Handover_anchor');
$jira_adaptor->link_tickets('Blocks', $dc_task_keys->[0], $blocked_ticket_key, $dry_run);
}

sub parse_datachecks {
my $dc_file = shift;
Expand Down