Merge 0ae92a1 into 783236e

lib/Bio/EnsEMBL/DataCheck/Checks/AlignmentCoordinates.pm

@@ -0,0 +1,62 @@
+=head1 LICENSE
+
+Copyright [2018-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::AlignmentCoordinates;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'AlignmentCoordinates',
+  DESCRIPTION    => 'Alignment coordinates are within the length of their dnafrag',
+  DATACHECK_TYPE => 'critical',
+  GROUPS         => ['compara', 'compara_pairwise_alignments', 'compara_multiple_alignments'],
+  DB_TYPES       => ['compara'],
+  TABLES         => ['dnafrag', 'genomic_align']
+};
+
+sub tests {
+  my ($self) = @_;
+
+  my $desc_1 = "All dnafrag_starts are >= 1";
+  my $sql_1 = q/
+    SELECT * 
+      FROM genomic_align 
+    WHERE dnafrag_start < 1
+  /;
+  is_rows_zero($self->dba, $sql_1, $desc_1);
+
+  my $desc_2 = "Alignment coordinates are within the length of their dnafrag";
+  my $sql_2 = q/
+    SELECT * 
+      FROM genomic_align ga 
+        JOIN dnafrag df 
+          USING (dnafrag_id) 
+    WHERE ga.dnafrag_end > length
+  /;
+  is_rows_zero($self->dba, $sql_2, $desc_2);
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/Checks/CheckCAFETable.pm

@@ -0,0 +1,49 @@
+=head1 LICENSE
+
+Copyright [2018-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::CheckCAFETable;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'CheckCAFETable',
+  DESCRIPTION    => 'Each row should show a one-to-many relationship',
+  GROUPS         => ['compara', 'compara_protein_trees'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['compara'],
+  TABLES         => ['cafe_species_gene']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $dba = $self->dba;
+
+  my $desc = "All the rows in CAFE_species_gene have a one-to-many relationship for cafe_gene_family_id";
+
+  is_one_to_many($dba->dbc, "CAFE_species_gene", "cafe_gene_family_id", $desc);
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/Checks/CheckComparaStableIDs.pm

@@ -0,0 +1,61 @@
+=head1 LICENSE
+
+Copyright [2018-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::CheckComparaStableIDs;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'CheckComparaStableIDs',
+  DESCRIPTION    => 'gene trees in gene_tree_root and family all have stable_ids generated',
+  GROUPS         => ['compara', 'compara_families', 'compara_protein_trees'],
+  DATACHECK_TYPE => 'critical',
+  TABLES         => ['family', 'gene_tree_root']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $desc_1 = "There are no NULL stable_ids in family";
+  my $sql_1 = q/
+    SELECT * 
+      FROM family 
+    WHERE stable_id IS NULL
+  /;
+  is_rows_zero($self->dba, $sql_1, $desc_1);
+
+  my $desc_2 = "There are no NULL stable_ids for gene trees in gene_tree_root";
+  my $sql_2 = q/
+    SELECT * FROM gene_tree_root 
+      WHERE member_type = 'protein' 
+        AND tree_type = 'tree' 
+        AND clusterset_id='default' 
+        AND stable_id IS NULL
+  /;
+  is_rows_zero($self->dba, $sql_2, $desc_2);
+
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/Checks/CheckConservationScore.pm

@@ -0,0 +1,73 @@
+=head1 LICENSE
+
+Copyright [2018-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::CheckConservationScore;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'CheckConservationScore',
+  DESCRIPTION    => 'The MLSS for GERP_CONSERVATION_SCORE should have conservation score entries',
+  GROUPS         => ['compara', 'compara_pairwise_alignments'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['compara'],
+  TABLES         => ['conservation_score', 'genomic_align_block', 'method_link', 'method_link_species_set', 'method_link_species_set_tag']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $dba = $self->dba;
+  my $mlss_adap = $dba->get_MethodLinkSpeciesSetAdaptor;
+  my $mlss = $mlss_adap->fetch_all_by_method_link_type("GERP_CONSERVATION_SCORE");
+  my $helper = $dba->dbc->sql_helper;
+
+  foreach my $mlss ( @$mlss ) {
+    my $mlss_name = $mlss->name;
+    my $mlss_id = $mlss->dbID;
+    my $sql_1 = qq/
+      SELECT value 
+        FROM method_link_species_set_tag 
+      WHERE tag = "msa_mlss_id" 
+        AND method_link_species_set_id = $mlss_id
+    /;
+    my $desc_1 = "There is an msa_mlss_id tag for $mlss_name";
+    my $msa_mlss_id = $helper->execute_single_result( -SQL => $sql_1 );
+
+    my $sql_2 = qq/
+      SELECT COUNT(*) 
+        FROM genomic_align_block 
+          JOIN conservation_score 
+            USING (genomic_align_block_id) 
+      WHERE method_link_species_set_id = $msa_mlss_id
+    /;
+
+    my $desc_2 = "There are conservation scores for multiple alignment mlss_id $msa_mlss_id in $mlss_name";
+    is_rows_nonzero($dba, $sql_2, $desc_2);
+
+  }
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/Checks/CheckConstrainedElementTable.pm

@@ -0,0 +1,50 @@
+=head1 LICENSE
+
+Copyright [2018-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::CheckConstrainedElementTable;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'CheckConstrainedElementTable',
+  DESCRIPTION    => 'Each row should show a one-to-many relationship',
+  GROUPS         => ['compara', 'compara_multiple_alignments'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['compara'],
+  TABLES         => ['constrained_elements']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $dba = $self->dba;
+
+  my $desc = "All the rows in constrained_element have a one-to-many relationship for constrained_element_id";
+
+  is_one_to_many($dba->dbc, "constrained_element", "constrained_element_id", $desc);
+
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/Checks/CheckDuplicatedTaxaNames.pm

@@ -0,0 +1,57 @@
+=head1 LICENSE
+
+Copyright [2018-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::CheckDuplicatedTaxaNames;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'CheckDuplicatedTaxaNames',
+  DESCRIPTION    => 'Check that the ncbi_taxa_name contains only unique rows',
+  GROUPS         => ['compara'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['compara'],
+  TABLES         => ['ncbi_taxa_name']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $dbc = $self->dba->dbc;
+
+  my $sql = qq/
+    SELECT taxon_id, name, name_class, count(*) 
+      FROM ncbi_taxa_name 
+        GROUP BY taxon_id, name, name_class 
+      HAVING count(*) > 1;
+  /;
+
+  my $desc = "All the rows in ncbi_taxa_name are unique";
+
+  is_rows_zero($dbc, $sql, $desc);
+
+}
+
+1;
+