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Update list validation to allow variable names without CO number #4631

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merged 3 commits into from
Oct 12, 2023
Merged

Update list validation to allow variable names without CO number #4631

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d128409
Update list validation to allow observationVariable names without CO …
timparsons Aug 30, 2023
dd5944a
The call to refresh the mat. view was changed from asynchronous to sy…
timparsons Aug 31, 2023
87d7fb9
Adding feature flag
timparsons Oct 10, 2023
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16 changes: 1 addition & 15 deletions lib/CXGN/BrAPI/v2/ObservationUnits.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -858,21 +858,7 @@ sub _refresh_matviews {
my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );

# Refresh materialized view so data can be retrieved
my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'phenotypes', 'concurrent', $c->config->{basepath});
# Wait until materialized view is reset. Wait 5 minutes total, then throw an error
my $refreshing = 1;
my $refresh_time = 0;
while ($refreshing && $refresh_time < $timeout) {
my $refresh_status = $bs->matviews_status();
if (!$refresh->{connection}->alive) {
$refreshing = 0;
} elsif ($refresh_time >= $timeout) {
return {error => CXGN::BrAPI::JSONResponse->return_error($self->status, "Refreshing materialized views is taking too long to return a response", 500)};
} else {
sleep 1;
$refresh_time += 1;
}
}
$bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'phenotypes', 'concurrent', $c->config->{basepath}, 0);
}

sub _order {
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25 changes: 20 additions & 5 deletions lib/CXGN/List/Validate/Plugin/Traits.pm
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Expand Up @@ -13,6 +13,7 @@ sub validate {
my $schema = shift;
my $list = shift;
my $validator = shift;
my $context = SGN::Context->new;
my @missing;
my @wrong_ids;

Expand All @@ -27,6 +28,9 @@ sub validate {
my @parts = split (/\|/ , $term);
my ($db_name, $accession) = split ":", pop @parts;
my $trait_name = join '|', @parts;
if(!$context->get_conf('list_trait_require_id')) {
$trait_name = $term;
}

$accession =~ s/\s+$//;
$accession =~ s/^\s+//;
Expand All @@ -35,30 +39,41 @@ sub validate {
$trait_name =~ s/\s+$//;
$trait_name =~ s/^\s+//;

print STDERR $db_name."\n";
print STDERR $trait_name."\n";
if (!$context->get_conf('list_trait_require_id') && ($db_name eq '' || $db_name eq $trait_name)) {
$db_name = $context->get_conf('trait_ontology_db_name');
}

my $db_rs = $schema->resultset("General::Db")->search( { 'me.name' => $db_name });
if ($db_rs->count() == 0) {
#print STDERR "Problem found with term $term at db $db_name\n";
print STDERR "Problem found with term $term at db $db_name\n";
push @missing, $term;
} else {
my $db = $db_rs->first();
my $query = {
'dbxref.db_id' => $db->db_id(),
'dbxref.accession' => $accession,
};

if (!$context->get_conf('list_trait_require_id') && $accession eq '') {
$query->{'me.name'} = $trait_name;
} else {
$query->{'dbxref.accession'} = $accession;
}
if ( $db_name eq 'COMP' && $validator->{composable_validation_check_name} ) {
$query->{'me.name'} = $trait_name;
}
my $rs = $schema->resultset("Cv::Cvterm")->search($query, {'join' => 'dbxref'});

my $is_missing = 0;
if ($rs->count == 0) {
#print STDERR "Problem found with term $term at cvterm rs from accession $accession point 2\n";
print STDERR "Problem found with term $term at cvterm rs from accession $accession point 2\n";
push @missing, $term;
$is_missing = 1;
} else {
my $rs_var = $rs->search_related('cvterm_relationship_subjects', {'type.name' => 'VARIABLE_OF'}, { 'join' => 'type'});
if ($rs_var->count == 0) {
#print STDERR "Problem found with term $term at variable check point 3\n";
print STDERR "Problem found with term $term at variable check point 3\n";
push @missing, $term;
$is_missing = 1;
}
Expand Down Expand Up @@ -89,7 +104,7 @@ sub validate {
}

}
# print STDERR Dumper \@missing;
print STDERR Dumper \@missing;
print STDERR Dumper \@wrong_ids;
return {
missing => \@missing,
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2 changes: 2 additions & 0 deletions sgn.conf
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Expand Up @@ -79,6 +79,8 @@ allow_repeat_measures 0
#export trait names as synonyms (1) or the original trait name (0)
fieldbook_trait_synonym 1

list_trait_require_id 1

# Cluster backend
backend Slurm

Expand Down