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Explicit check for availability of core db - datacheck fails, as befo…
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…re, but with a more easily interpreted error message.
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James Allen committed May 12, 2021
1 parent a2ae6ef commit e247c70
Showing 1 changed file with 82 additions and 74 deletions.
156 changes: 82 additions & 74 deletions lib/Bio/EnsEMBL/DataCheck/Checks/ForeignKeysMultiDB.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -51,44 +51,48 @@ sub variation_core_fk {
# Core <-> Variation database relationships. We cannot assume that the dbs
# are on the same server, so need to compare in Perl rather than SQL.

my $desc_dna_dba = 'Core database found';
my $dna_dba = $self->get_dna_dba();
my $pass = ok(defined $dna_dba, $desc_dna_dba);

if ($pass) {
my ($stable_ids) = $self->col_array($dna_dba, 'transcript', 'stable_id');
my @stable_id_tables = qw/
transcript_variation
/;
foreach my $table (@stable_id_tables) {
my $desc = "All stable IDs in $table exist in core database";

my ($ids, $label) = $self->col_array($self->dba, $table, 'feature_stable_id');
my $diff = array_diff($ids, $stable_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}

my ($stable_ids) = $self->col_array($dna_dba, 'transcript', 'stable_id');
my @stable_id_tables = qw/
transcript_variation
/;
foreach my $table (@stable_id_tables) {
my $desc = "All stable IDs in $table exist in core database";

my ($ids, $label) = $self->col_array($self->dba, $table, 'feature_stable_id');
my $diff = array_diff($ids, $stable_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}
my ($seq_region_ids) = $self->col_array($dna_dba, 'seq_region', 'seq_region_id');
my @seq_region_id_tables = qw/
variation_feature
structural_variation_feature
/;
foreach my $table (@seq_region_id_tables) {
my $desc = "All seq_region IDs in $table exist in core database";

my ($seq_region_ids) = $self->col_array($dna_dba, 'seq_region', 'seq_region_id');
my @seq_region_id_tables = qw/
variation_feature
structural_variation_feature
/;
foreach my $table (@seq_region_id_tables) {
my $desc = "All seq_region IDs in $table exist in core database";

my ($ids, $label) = $self->col_array($self->dba, $table, 'seq_region_id');
my $diff = array_diff($ids, $seq_region_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}
my ($ids, $label) = $self->col_array($self->dba, $table, 'seq_region_id');
my $diff = array_diff($ids, $seq_region_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}

{
my $desc = "seq_region IDs and names are consistent with the core database";
my ($sr_variation, $label) = $self->col_hash($self->dba, 'seq_region', 'seq_region_id', 'name');
my ($sr_core) = $self->col_hash($dna_dba, 'seq_region', 'seq_region_id', 'name');
my $diff = hash_diff($sr_variation, $sr_core, $label);
my @diffs = keys %{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
@diffs = keys %{$$diff{"Different values"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
{
my $desc = "seq_region IDs and names are consistent with the core database";
my ($sr_variation, $label) = $self->col_hash($self->dba, 'seq_region', 'seq_region_id', 'name');
my ($sr_core) = $self->col_hash($dna_dba, 'seq_region', 'seq_region_id', 'name');
my $diff = hash_diff($sr_variation, $sr_core, $label);
my @diffs = keys %{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
@diffs = keys %{$$diff{"Different values"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}
}
}

Expand Down Expand Up @@ -130,50 +134,54 @@ sub funcgen_core_fk {
# Core <-> Funcgen database relationships. We cannot assume that the dbs
# are on the same server, so need to compare in Perl rather than SQL.

my $desc_dna_dba = 'Core database found';
my $dna_dba = $self->get_dna_dba();
my $pass = ok(defined $dna_dba, $desc_dna_dba);

if ($pass) {
my ($stable_ids) = $self->col_array($dna_dba, 'transcript', 'stable_id');
my @stable_id_tables = qw/
probe_feature_transcript
probe_set_transcript
probe_transcript
/;
foreach my $table (@stable_id_tables) {
my $desc = "All stable IDs in $table exist in core database";

my ($ids, $label) = $self->col_array($self->dba, $table, 'stable_id');
my $diff = array_diff($ids, $stable_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}

my ($stable_ids) = $self->col_array($dna_dba, 'transcript', 'stable_id');
my @stable_id_tables = qw/
probe_feature_transcript
probe_set_transcript
probe_transcript
/;
foreach my $table (@stable_id_tables) {
my $desc = "All stable IDs in $table exist in core database";

my ($ids, $label) = $self->col_array($self->dba, $table, 'stable_id');
my $diff = array_diff($ids, $stable_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}

my ($gene_stable_ids) = $self->col_array($dna_dba, 'gene', 'stable_id');
my @gene_stable_id_tables = ('mirna_target_feature');
my ($gene_stable_ids) = $self->col_array($dna_dba, 'gene', 'stable_id');
my @gene_stable_id_tables = ('mirna_target_feature');

for my $table (@gene_stable_id_tables){
my $desc = "All gene stable IDs in $table exist in core database";
my ($ids, $label) = $self->col_array($self->dba, $table, 'gene_stable_id');
my $diff = array_diff($ids, $gene_stable_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}
for my $table (@gene_stable_id_tables){
my $desc = "All gene stable IDs in $table exist in core database";
my ($ids, $label) = $self->col_array($self->dba, $table, 'gene_stable_id');
my $diff = array_diff($ids, $gene_stable_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}

my ($seq_region_ids) = $self->col_array($dna_dba, 'seq_region', 'seq_region_id');
my @seq_region_id_tables = qw/
external_feature
mirna_target_feature
motif_feature
peak
probe_feature
regulatory_feature
/;
foreach my $table (@seq_region_id_tables) {
my $desc = "All seq_region IDs in $table exist in core database";

my ($ids, $label) = $self->col_array($self->dba, $table, 'seq_region_id');
my $diff = array_diff($ids, $seq_region_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
my ($seq_region_ids) = $self->col_array($dna_dba, 'seq_region', 'seq_region_id');
my @seq_region_id_tables = qw/
external_feature
mirna_target_feature
motif_feature
peak
probe_feature
regulatory_feature
/;
foreach my $table (@seq_region_id_tables) {
my $desc = "All seq_region IDs in $table exist in core database";

my ($ids, $label) = $self->col_array($self->dba, $table, 'seq_region_id');
my $diff = array_diff($ids, $seq_region_ids, $label);
my @diffs = @{$$diff{"In $label only"}};
is(scalar(@diffs), 0, $desc) || diag explain \@diffs;
}
}
}

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