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Merge pull request #746 from mgcam/tests_for_staging_monitor
Added tests for top level staging monitor.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,280 @@ | ||
| use strict; | ||
| use warnings; | ||
| use Test::More tests => 7; | ||
| use Test::Exception; | ||
| use File::Path qw/make_path/; | ||
| use File::Copy; | ||
| use File::Temp qw/ tempdir /; | ||
|
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| use t::dbic_util; | ||
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| use_ok('Monitor::RunFolder::Staging'); | ||
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| ######### | ||
| # Tests for high-level functionality, ie the update_run_from_path method | ||
| # of the Monitor::RunFolder::Staging class. In these tests the class | ||
| # instances are created the same way as in the staging_area_monitor script, | ||
| # i.e. by supplying the runfolder_path and npg_tracking_schema attributes. | ||
| # | ||
| # Tests are arranged roughly in the way the code flows. Each subtest | ||
| # corresponds to one loop of the staging monitor. | ||
| # | ||
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| my $schema = t::dbic_util->new->test_schema(); # t/data/dbic_fixtures | ||
| my $dir = tempdir( CLEANUP => 1 ); | ||
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| my $idir = "$dir/incoming"; | ||
| my $adir = "$dir/analysis"; | ||
| my $odir = "$dir/outgoing"; | ||
| make_path($idir, $adir, $odir); | ||
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| # Create bare-bones NovaSeqXPlus run. | ||
| my $id_run = 47539; | ||
| my $run = $schema ->resultset('Run')->create({ | ||
| id_run => $id_run, | ||
| expected_cycle_count => 8, | ||
| actual_cycle_count => 0, | ||
| id_instrument => 70, | ||
| id_instrument_format => 13, | ||
| team => 'A' | ||
| }); | ||
| $run->update_run_status('run pending'); | ||
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| my $runfolder_name = q[20230628_LH00210_0008_B225TGJLT3]; | ||
| # The runfolder is originally in 'incoming' | ||
| my $runfolder_path = join q[/], $idir, $runfolder_name; | ||
| make_path($runfolder_path); | ||
| my $basecalls_path = "$runfolder_path/Data/Intensities/BaseCalls"; | ||
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| copy 't/data/test_staging_daemon/novaseqxplus/RunInfo.xml', | ||
| "$runfolder_path/RunInfo.xml"; | ||
| copy 't/data/test_staging_daemon/novaseqxplus/RunParameters.xml', | ||
| "$runfolder_path/RunParameters.xml"; | ||
|
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||
| subtest 'a new run in incoming' => sub { | ||
| plan tests => 15; | ||
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| my $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| my $size_hash = {}; | ||
| my $done; | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| ok (defined $monitor->tracking_run(), 'run row is cached'); | ||
| my $tracking_run = $monitor->tracking_run(); | ||
| is ($tracking_run->id_run, $id_run, 'correct db record is cached'); | ||
| is ($tracking_run->folder_name(), $runfolder_name, | ||
| 'tracking database - run folder name is set'); | ||
| is ($tracking_run->folder_path_glob(), "$dir/*/", | ||
| 'tracking database - run folder glob is set'); | ||
| is ($tracking_run->actual_cycle_count(), 0, 'cycle count is zero'); | ||
| is ($tracking_run->current_run_status_description(), 'run pending', | ||
| 'the run is still pending'); | ||
| is ($tracking_run->flowcell_id(), '225TGJLT3', | ||
| 'flowcell barcode is recorded'); | ||
| ok ($tracking_run->is_tag_set('staging'), 'staging tag is set'); | ||
| ok ($tracking_run->is_tag_set('fc_slotB'), 'instrument side B is set'); | ||
| ok ($tracking_run->is_tag_set('paired_read'), 'run is tagged as paired'); | ||
| ok ($tracking_run->is_tag_set('multiplex'), 'run is tagged as multiplex'); | ||
| ok (exists $size_hash->{$runfolder_path}, 'runfolder size is cached'); | ||
| is ($size_hash->{$runfolder_path}, 0, 'runfolder size is set to zero'); | ||
| }; | ||
|
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||
| subtest 'run in progress' => sub { | ||
| plan tests => 10; | ||
|
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| # Now the run is half way through to completion. | ||
| for my $i ((1 .. 8)) { | ||
| for my $j ((1 .. 4)) { | ||
| make_path("$basecalls_path/L00${i}/C${j}.1"); | ||
| } | ||
| } | ||
| my $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| my $size_hash = {$runfolder_path => 0}; | ||
| my $done; | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| is ($monitor->tracking_run->actual_cycle_count(), 4, 'cycle count is 4'); | ||
| is ($monitor->tracking_run->current_run_status_description(), 'run in progress', | ||
| 'the run is in progress'); | ||
| is ($size_hash->{$runfolder_path}, 0, 'runfolder size is zero'); | ||
|
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| # Now the run is close to completion. | ||
| for my $i ((1 .. 8)) { | ||
| for my $j ((5 .. 8)) { | ||
| make_path("$basecalls_path/L00${i}/C${j}.1"); | ||
| } | ||
| } | ||
| $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| is ($monitor->tracking_run->actual_cycle_count(), 8, 'cycle count is 8'); | ||
| is ($monitor->tracking_run->current_run_status_description(), 'run in progress', | ||
| 'the run is in progress'); | ||
| is ($size_hash->{$runfolder_path}, 0, 'runfolder size is zero'); | ||
| }; | ||
|
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| subtest 'run is completed' => sub { | ||
| plan tests => 5; | ||
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| for my $f (qw(RTAComplete.txt CopyComplete.txt)) { | ||
| `touch $runfolder_path/$f`; | ||
| } | ||
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| my $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| my $size_hash = {$runfolder_path => 0}; | ||
| my $done; | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| is ($monitor->tracking_run->actual_cycle_count(), 8, 'cycle count is 8'); | ||
| is ($monitor->tracking_run->current_run_status_description(), 'run complete', | ||
| 'the run has completed'); | ||
| is ($size_hash->{$runfolder_path}, 0, 'runfolder size is zero'); | ||
| }; | ||
|
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| subtest 'run is mirrored' => sub { | ||
| plan tests => 10; | ||
|
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| for my $i ((1 .. 8)) { | ||
| for my $j ((1 .. 8)) { | ||
| for my $s ((1 .. 2)) { | ||
| `touch $basecalls_path/L00${i}/C${j}.1/L00${i}_${s}.cbcl`; | ||
| } | ||
| } | ||
| } | ||
| my $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| my $size_hash = {$runfolder_path => 0}; | ||
| my $done; | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| my $size = $size_hash->{$runfolder_path}; | ||
| ok ($size > 0, 'runfolder size is not zero'); | ||
| is ($monitor->tracking_run->current_run_status_description(), 'run complete', | ||
| 'the run is still marked as completed'); | ||
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| $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| ok ($done, 'correct return value'); | ||
| is ($size_hash->{$runfolder_path}, $size, 'runfolder size does not change'); | ||
| is ($monitor->tracking_run->current_run_status_description(), 'analysis pending', | ||
| 'the run is marked as mirrored and automatically moved to pending analysis'); | ||
| ok (!-e $runfolder_path, 'the old run folder path is invalid'); | ||
| $runfolder_path = join q[/], $adir, $runfolder_name; | ||
| ok (-e $runfolder_path, q[the folder has been moved to 'analysis']); | ||
| }; | ||
|
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| subtest q[move to 'outgoing'] => sub { | ||
| plan tests => 10; | ||
|
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| # Run is now in the 'analysis' directory' | ||
| $run->update_run_status('secondary analysis in progress'); | ||
| my $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| my $done; | ||
| lives_ok { $done = $monitor->update_run_from_path({}) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| ok (-e $runfolder_path, q[run folder is still in 'analysis']); | ||
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| $run->update_run_status('qc complete'); | ||
| $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| my $inhibit_folder_move = 1; | ||
| lives_ok { $done = $monitor->update_run_from_path({}, $inhibit_folder_move ) } | ||
| 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| ok (-e $runfolder_path, q[run folder is still in 'analysis']); | ||
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| lives_ok { $done = $monitor->update_run_from_path({}) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| ok (!-e $runfolder_path, 'the old run folder path is invalid'); | ||
| $runfolder_path = join q[/], $odir, $runfolder_name; | ||
| ok (-e $runfolder_path, q[the folder has been moved to 'outgoing']); | ||
| }; | ||
|
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| subtest q[wait for DRAGEN analysis to finish] => sub { | ||
| plan tests => 13; | ||
|
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| # Change the run status. | ||
| sleep 1; # Ensure a different timestamp for the new status. | ||
| $run->update_run_status('run complete'); | ||
|
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| my $new_path = join q[/], $idir, $runfolder_name; | ||
| `mv $runfolder_path $new_path`; # Move the run folder back to 'incoming'. | ||
| $runfolder_path = $new_path; | ||
| # Copy the file with the DRAGEN analysis section. | ||
| copy('t/data/run_params/RunParameters.novaseqx.onboard.xml', | ||
| "$runfolder_path/RunParameters.xml"); | ||
| my $dpath = "$runfolder_path/Analysis/1"; | ||
| make_path($dpath); # Create DRAGEN analysis directory. | ||
|
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| my $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| my $size_hash = {$runfolder_path => 0}; | ||
| my $done; | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } | ||
| 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| ok ($monitor->onboard_analysis_planned(), 'onboard analysis is planned'); | ||
| ok (!$monitor->is_onboard_analysis_output_copied(), | ||
| 'onboard analysis data is not copied across yet'); | ||
| ok (-e $runfolder_path, q[run folder is in 'incoming']); | ||
| my $size = $size_hash->{$runfolder_path}; | ||
|
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| $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| ok (!$done, 'correct return value'); | ||
| ok (-e $runfolder_path, q[run folder is still in 'incoming']); | ||
| ok ($size_hash->{$runfolder_path} == $size, 'the run folder size is stable'); | ||
| ok (!$monitor->is_onboard_analysis_output_copied(), | ||
| 'onboard analysis data is not copied across yet'); | ||
|
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| # Mark DRAGEN analysis as copied across. | ||
| open my $fh, q[>], "$dpath/CopyComplete.txt" or die 'Cannot open the file'; | ||
| print $fh 'Mark DRAGEN analysis as copied' or die 'Cannot write'; | ||
| close $fh or die 'Cannot close the filehandle'; | ||
|
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| $monitor = Monitor::RunFolder::Staging->new( | ||
| runfolder_path => $runfolder_path, | ||
| npg_tracking_schema => $schema | ||
| ); | ||
| lives_ok { $done = $monitor->update_run_from_path($size_hash) } 'run the monitor'; | ||
| # Sometimes the runfolder size comes out differently at this point, | ||
| # and and extra round is needed. | ||
| if (!$done) { | ||
| $monitor->update_run_from_path($size_hash); | ||
| } | ||
| ok (!-e $runfolder_path, 'the old run folder path is invalid'); | ||
| $runfolder_path = join q[/], $adir, $runfolder_name; | ||
| ok (-e $runfolder_path, q[the folder has been moved to 'analysis']); | ||
| }; | ||
|
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| 1; | ||
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