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Fix: missing schema param in inferred id run test #478

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merged 3 commits into from
Nov 26, 2024
Merged

Fix: missing schema param in inferred id run test #478

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aefd27a
Add undef tracking schema to inferred ID Run test in log_publisher
marcomoscasgr Nov 21, 2024
a4a87a3
Fix indentation
marcomoscasgr Nov 21, 2024
07b306c
Add comments about test fix
marcomoscasgr Nov 22, 2024
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12 changes: 9 additions & 3 deletions t/lib/WTSI/NPG/HTS/Illumina/LogPublisherTest.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -63,10 +63,16 @@ sub publish_logs : Test(12) {
# test the RunPublisher
my $runfolder_path2 =
"t/data/illumina/sequence/150910_HS40_17550_A_C75BCANXX";

# The tracking database handle must be specified, otherwise when
# the tracking schema file exists in .npg folder it tries to retrieve
# the db credentials from it and connect to the database defined there.
# By setting it to 'undef', the code avoids the database route.
my $pub2 = WTSI::NPG::HTS::Illumina::LogPublisher->new
(irods => $irods,
runfolder_path => $runfolder_path2,
dest_collection => "$irods_tmp_coll/publish_logs_inferred_id_run");
(irods => $irods,
runfolder_path => $runfolder_path2,
npg_tracking_schema => undef,
dest_collection => "$irods_tmp_coll/publish_logs_inferred_id_run");

my $log_archive2 = $pub2->publish_logs;
ok($log_archive2, 'Log archive created given a runfolder path');
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