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Dropped uqc QC type for the review check
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@mgcam
mgcam committed Sep 12, 2024
1 parent 130ab92 commit 160c326
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Showing 6 changed files with 21 additions and 199 deletions.
11 changes: 7 additions & 4 deletions Changes
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,13 @@ LIST OF CHANGES FOR NPG-QC PACKAGE
the checksum of the downloaded script to the expected value. We now store
an updated expected checksum value, which corresponds to the latest release.
- npg_qc::autoqc::check::review:
The forthcoming lane-level evaluations are impossible if the code continues
to error when library_type attribute is not defined for the entity under
consideration. The library_type attribute is now set when possible, no error
if it is undefined.
- The forthcoming lane-level evaluations are impossible if the code continues
to error when library_type attribute is not defined for the entity under
consideration. The library_type attribute is now set when possible, no error
if it is undefined.
- Ability to set UQC outcomes was introduced for the Heron project. This
functionality was never used and is unlikely to be used in future. It is
now removed.

release 72.2.0 (2024-08-30)
- npg_qc::autoqc::check::review:
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1 change: 0 additions & 1 deletion MANIFEST
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Expand Up @@ -521,7 +521,6 @@ t/data/autoqc/review/no_criteria_section/product_release.yml
t/data/autoqc/review/not_hash/product_release.yml
t/data/autoqc/review/mqc_type/product_release.yml
t/data/autoqc/review/unknown_qc_type/product_release.yml
t/data/autoqc/review/uqc_type/product_release.yml
t/data/autoqc/review/default_and_study_section/product_release.yml
t/data/autoqc/review/default_section/product_release.yml
t/data/autoqc/review/wrong_default_and_study_section/product_release.yml
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30 changes: 9 additions & 21 deletions lib/npg_qc/autoqc/checks/review.pm
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Expand Up @@ -32,7 +32,7 @@ Readonly::Scalar my $SEQ_APPLICABILITY_CRITERIA_KEY => q[sequencing_run];
Readonly::Scalar my $ACCEPTANCE_CRITERIA_KEY => q[acceptance_criteria];

Readonly::Scalar my $QC_TYPE_DEFAULT => q[mqc];
Readonly::Array my @VALID_QC_TYPES => ($QC_TYPE_DEFAULT, q[uqc]);
Readonly::Array my @VALID_QC_TYPES => ($QC_TYPE_DEFAULT);

Readonly::Scalar my $TIMESTAMP_FORMAT_WOFFSET => q[%Y-%m-%dT%T%z];

Expand Down Expand Up @@ -103,11 +103,6 @@ marked as 'Preliminary' (examples: 'Accepted Final',
'Rejected Preliminary'). By default the final_qc_outcome flag is
false and the produced outcomes are preliminary.
A valid User QC outcome is one of the values from the
uqc_outcome_dict table of the npg_qc database. A concept of
the finality and, hence, immutability of the outcome is not
applicable to user QC outcome.
The type of QC outcome can be configured within the Robo QC
section of product configuration. The default type is library
Manual QC.
Expand Down Expand Up @@ -329,8 +324,9 @@ sub execute {
}

$self->result->criteria($self->_criteria);
my $md5 = $self->result->generate_checksum4data($self->result->criteria);
$self->result->criteria_md5($md5);
$self->result->criteria_md5(
$self->result->generate_checksum4data($self->result->criteria)
);
my $err;

try {
Expand All @@ -341,7 +337,7 @@ sub execute {
$self->result->add_comment($err);
};
not $err and $self->result->qc_outcome(
$self->generate_qc_outcome($self->_outcome_type(), $md5));
$self->generate_qc_outcome($self->_outcome_type()));

return;
}
Expand All @@ -368,34 +364,26 @@ sub evaluate {
Returns a hash reference representing the QC outcome.
my $u_outcome = $r->generate_qc_outcome('uqc', $md5);
my $m_outcome = $r->generate_qc_outcome('mqc');
=cut

sub generate_qc_outcome {
my ($self, $outcome_type, $md5) = @_;
my ($self, $outcome_type) = @_;

$outcome_type or croak 'outcome type should be defined';

my $package_name = 'npg_qc::Schema::Mqc::OutcomeDict';
my $pass = $self->result->pass;
#####
# Any of Accepted, Rejected, Undecided outcomes can be returned here
my $outcome = ($outcome_type eq $QC_TYPE_DEFAULT)
? $package_name->generate_short_description(
$self->final_qc_outcome ? 1 : 0, $pass)
: $package_name->generate_short_description_prefix($pass);
my $outcome = $package_name->generate_short_description(
$self->final_qc_outcome ? 1 : 0, $pass);

$outcome_type .= '_outcome';
my $outcome_info = { $outcome_type => $outcome,
timestamp => create_current_timestamp(),
username => $ROBO_KEY};
if ($outcome_type =~ /\Auqc/xms) {
my @r = ($ROBO_KEY, $VERSION);
$md5 and push @r, $md5;
$outcome_info->{'rationale'} = join q[ ], @r;
}

return $outcome_info;
}
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124 changes: 3 additions & 121 deletions t/50-schema-result-Review.t
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@@ -1,6 +1,6 @@
use strict;
use warnings;
use Test::More tests => 6;
use Test::More tests => 5;
use Test::Exception;
use Moose::Meta::Class;
use Digest::MD5 qw/md5_hex/;
Expand Down Expand Up @@ -306,135 +306,17 @@ subtest 'a full insert/update record with mqc outcome' => sub {
is ($rs->next->description, 'Accepted final', 'outcome has not changed');
};

subtest 'a full insert/update record with uqc outcome' => sub {
plan tests => 36;

my $initial_num_records = $schema->resultset($table)->search({})->count();

my $uqc_table = 'UqcOutcomeEnt';
my $id_seq_composition = t::autoqc_util::find_or_save_composition(
$schema, {'id_run' => 1111,
'position' => 1,
'tag_index' => 33});

my $uqc_rs = $schema->resultset($uqc_table)->search({id_seq_composition => $id_seq_composition});
is ($uqc_rs->count, 0, 'no uqc records for this entity');
my $rs = $schema->resultset($table)->search({id_seq_composition => $id_seq_composition});
is ($rs->count, 0, 'no review records for this entity');

my $qc_outcome = {"uqc_outcome" => "Rejected",
"timestamp" => "2018-06-03T12:53:46+0000",
"username" => "robo_qc",
"rationale" => "testrobo"};
my $values = {
id_seq_composition => $id_seq_composition,
library_type => 'common_type',
evaluation_results => {"e1"=>1,"e2"=>0},
criteria => {"and"=>["e1","e2"]},
qc_outcome => $qc_outcome,
pass => 0,
path => 't/data'
};
my $cmd5 = md5_hex(JSON::XS->new()->canonical(1)->encode($values->{criteria}));

isa_ok($schema->resultset($table)->create($values), 'npg_qc::Schema::Result::' . $table);
is ($schema->resultset($table)->search({})->count(), $initial_num_records + 1,
'total number of records in teh review table went up by one');
$rs = $schema->resultset($table)->search({id_seq_composition => $id_seq_composition});
is ($rs->count, 1, 'one row created in the review table');
my $row = $rs->next;
is_deeply ($row->qc_outcome, $qc_outcome, 'qc outcome saved');
is_deeply ($row->evaluation_results, {"e1"=>1,"e2"=>0}, 'evaluation results saved');
is_deeply ($row->criteria, {"and"=>["e1","e2"]}, 'criteria saved');
is ($row->criteria_md5, $cmd5, 'checksum saved');
$uqc_rs = $schema->resultset($uqc_table)->search({id_seq_composition => $id_seq_composition});
is ($uqc_rs->count, 1, 'one row created in the uqc table');
my $outcome = $uqc_rs->next;
is ($outcome->rationale, 'testrobo', 'rationale recorded');
is ($outcome->description, 'Rejected', 'correct uqc outcome');
is ($outcome->modified_by, $ENV{USER}, 'correct user');
is ($outcome->username, 'robo_qc', 'correct user');
my $dt = $outcome->last_modified();
is ($dt->year, 2018, 'correct year');
is ($dt->month, '6', 'correct month');
is ($dt->minute, '53', 'correct minute');
is ($dt->second, '46', 'correct second');

$qc_outcome = {"uqc_outcome" => "Accepted",
"timestamp" => "2018-08-05T12:53:46+0000",
"username" => "robo_qc",
"rationale" => "testrobo1"};
$values = {
id_seq_composition => $id_seq_composition,
library_type => 'common_type',
evaluation_results => {"e1"=>1,"e2"=>1},
criteria => {"and"=>["e1","e2"]},
qc_outcome => $qc_outcome,
};
$row->update($values);
is_deeply ($row->evaluation_results, {"e1"=>1,"e2"=>1}, 'evaluation results updated');
is_deeply ($row->qc_outcome, $qc_outcome, 'qc outcome updated');
$outcome = $schema->resultset($uqc_table)->search({id_seq_composition => $id_seq_composition})
->next;
is ($outcome->rationale, 'testrobo1', 'rationale updated');
is ($outcome->description, 'Accepted', 'uqc outcome updated');
is ($outcome->last_modified()->month, 8, 'month updated');
is ($outcome->last_modified()->year, 2018, 'correct year');

$id_seq_composition = t::autoqc_util::find_or_save_composition(
$schema, {'id_run' => 1111,
'position' => 1,
'tag_index' => 34});
$uqc_rs = $schema->resultset($uqc_table)->search({id_seq_composition => $id_seq_composition});
is ($uqc_rs->count, 0, 'no uqc records for this entity');
my $new_uqc = $schema->resultset($uqc_table)
->new_result({id_seq_composition => $id_seq_composition});
$new_uqc->update_outcome({uqc_outcome => 'Accepted', rationale => 'test1'}, 'user1', 'test');
$uqc_rs = $schema->resultset($uqc_table)->search({id_seq_composition => $id_seq_composition});
is ($uqc_rs->count, 1, 'record created');

$values = {
id_seq_composition => $id_seq_composition,
library_type => 'common_type',
evaluation_results => '{"e1":1,"e2":1}',
criteria => '{"and":["e1","e2"]}',
qc_outcome => {"uqc_outcome" => "Undecided",
"timestamp" => "2018-09-03T12:58:43+0000",
"username" => "robo_qc",
"rationale" => "testrobo2"},
pass => undef
};
my $created=$schema->resultset($table)->create($values);

is ($schema->resultset($table)->search({})->count(), $initial_num_records + 2,
'total number of records in teh review table went up by one');
$uqc_rs = $schema->resultset($uqc_table)->search({id_seq_composition => $id_seq_composition});
is ($uqc_rs->count, 1, 'one uqc record for the entity');
$outcome = $uqc_rs->next;
is ($outcome->rationale, 'testrobo2', 'rationale updated');
is ($outcome->description, 'Undecided', 'outcome updated');
is ($outcome->modified_by, $ENV{USER}, 'correct user');
is ($outcome->username, 'robo_qc', 'correct user');
$dt = $outcome->last_modified();
is ($dt->year, 2018, 'correct year');
is ($dt->month, '9', 'correct month');
is ($dt->minute, '58', 'correct minute');
is ($dt->second, '43', 'correct second');
};


subtest 'unknown outcome type should give an error' => sub {
plan tests => 5;

my $uqc_table = 'UqcOutcomeEnt';
my $id_seq_composition = t::autoqc_util::find_or_save_composition(
$schema, {'id_run' => 1111,
'position' => 1,
'tag_index' => 43});

my $no_records = sub {
is ($schema->resultset($uqc_table)->search({id_seq_composition => $id_seq_composition})->count,
0, 'no uqc records for this entity');
is ($schema->resultset($mqc_table)->search({id_seq_composition => $id_seq_composition})->count,
0, 'no mqc records for this entity');
is ($schema->resultset($table)->search({id_seq_composition => $id_seq_composition})->count,
0, 'no review records for this entity');
};
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16 changes: 2 additions & 14 deletions t/60-autoqc-checks-review.t
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Original file line number Diff line number Diff line change
Expand Up @@ -401,7 +401,7 @@ subtest 'single expression evaluation' => sub {
};

subtest 'evaluation within the execute method' => sub {
plan tests => 48;
plan tests => 40;

local $ENV{NPG_CACHED_SAMPLESHEET_FILE} =
't/data/autoqc/review/samplesheet_29524.csv';
Expand All @@ -420,7 +420,6 @@ subtest 'evaluation within the execute method' => sub {
is ($o->result->pass, undef, 'result pass attribute is unset');

my @check_objects = ();

push @check_objects, npg_qc::autoqc::checks::review->new(
runfolder_path => $rf_path,
conf_path => $test_data_dir,
Expand All @@ -430,12 +429,7 @@ subtest 'evaluation within the execute method' => sub {
conf_path => "$test_data_dir/mqc_type",
qc_in => $dir,
rpt_list => $rpt_list);
push @check_objects, npg_qc::autoqc::checks::review->new(
conf_path => "$test_data_dir/uqc_type",
qc_in => $dir,
rpt_list => $rpt_list);

my $count = 0;
foreach my $check (@check_objects) {
lives_ok { $check->execute } 'execute method runs OK';
is ($check->result->pass, 1, 'result pass attribute is set to 1');
Expand All @@ -445,15 +439,9 @@ subtest 'evaluation within the execute method' => sub {
is_deeply ($check->result->evaluation_results(), \%expected,
'evaluation results are saved');
my $outcome = $check->result->qc_outcome;
if ($count < 2) {
is ($outcome->{'mqc_outcome'} , 'Accepted preliminary', 'correct outcome string');
} elsif ($count == 2) {
is ($outcome->{'uqc_outcome'} , 'Accepted', 'correct outcome string');
ok ($outcome->{'rationale'} , 'rationale is set');
}
is ($outcome->{'mqc_outcome'} , 'Accepted preliminary', 'correct outcome string');
is ($outcome->{'username'}, 'robo_qc', 'correct process id');
ok ($outcome->{'timestamp'}, 'timestamp saved');
$count++;
}

# Undefined library type should not be a problem.
Expand Down
38 changes: 0 additions & 38 deletions t/data/autoqc/review/uqc_type/product_release.yml
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