Merge pull request #283 from CristiGuijarro/fix/compara_fks

Remove duplicate fk tests and fix constraint issues
Ensembl · Aug 3, 2020 · 3a4cd63 · 3a4cd63
2 parents e989e1a + 0105f52
commit 3a4cd63
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Showing 5 changed files with 169 additions and 72 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/CheckConstrainedElementTable.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/CheckConstrainedElementTable.pm
@@ -24,6 +24,7 @@ use strict;
 use Moose;
 use Test::More;
 use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+use Bio::EnsEMBL::Utils::SqlHelper;
 
 extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
@@ -33,17 +34,54 @@ use constant {
   GROUPS         => ['compara', 'compara_genome_alignments'],
   DATACHECK_TYPE => 'critical',
   DB_TYPES       => ['compara'],
-  TABLES         => ['constrained_elements']
+  TABLES         => ['constrained_elements', 'method_link_species_set']
 };
 
+sub skip_tests {
+  my ($self) = @_;
+  my $mlss_adap = $self->dba->get_MethodLinkSpeciesSetAdaptor;
+  my $mlss = $mlss_adap->fetch_all_by_method_link_type('GERP_CONSTRAINED_ELEMENT');
+  my $db_name = $self->dba->dbc->dbname;
+
+  if ( scalar(@$mlss) == 0 ) {
+    return( 1, "There are no GERP_CONSTRAINED_ELEMENT MLSS in $db_name" );
+  }
+}
+
 sub tests {
   my ($self) = @_;
   my $dba = $self->dba;
-
+  my $helper = $dba->dbc->sql_helper;
+
   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);
-
+
+  my $mlsss = $self->dba->get_MethodLinkSpeciesSetAdaptor->fetch_all_by_method_link_type('GERP_CONSTRAINED_ELEMENT');
+
+  my $expected_ce_count;
+
+  foreach my $mlss ( @$mlsss ) {
+
+    my $mlss_id   = $mlss->dbID;
+    my $mlss_name = $mlss->name;
+
+    my $sql = qq/
+      SELECT COUNT(*)
+        FROM constrained_element
+      WHERE method_link_species_set_id = $mlss_id
+    /;
+
+    $expected_ce_count += $helper->execute_single_result(-SQL => $sql);
+
+    my $desc_1 = "The constrained elements for $mlss_id ($mlss_name) are present as expected";
+    is_rows_nonzero($dba, $sql, $desc_1);
+  }
+
+  my $desc_2 = "All the constrained elements with corresponding method_link_species_sets are expected";
+  my $row_count_sql = "SELECT COUNT(*) FROM constrained_element";
+  is_rows($dba, $row_count_sql, $expected_ce_count, $desc_2);
+
 }
 
 1;

diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/CheckGenomicAlignments.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/CheckGenomicAlignments.pm
@@ -0,0 +1,98 @@
+=head1 LICENSE
+
+Copyright [2018-2020] 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::CheckGenomicAlignments;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+use Bio::EnsEMBL::Utils::SqlHelper;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'CheckGenomicAlignments',
+  DESCRIPTION    => 'The expected number of genomic alignments have been merged',
+  GROUPS         => ['compara', 'compara_genome_alignments'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['compara'],
+  TABLES         => ['method_link_species_set', 'genomic_align', 'genomic_align_block']
+};
+
+sub skip_tests {
+  my ($self) = @_;
+  my $mlss_adap = $self->dba->get_MethodLinkSpeciesSetAdaptor;
+
+  my @method_links = qw(LASTZ_NET LASTZ_PATCH EPO EPO_EXTENDED PECAN);
+  my @mlsss;
+  foreach my $method (@method_links) {
+    my $mlss = $mlss_adap->fetch_all_by_method_link_type($method);
+    push @mlsss, @$mlss;
+  }
+
+  my $db_name = $self->dba->dbc->dbname;
+
+  if ( scalar(@mlsss) == 0 ) {
+    return( 1, "There are no genomic alignment MLSS in $db_name" );
+  }
+}
+
+sub tests {
+  my ($self) = @_;
+  my $dba    = $self->dba;
+  my $helper = $dba->dbc->sql_helper;
+  my @method_links = qw(LASTZ_NET LASTZ_PATCH EPO EPO_EXTENDED PECAN);
+
+  my $expected_align_count;
+  my @tables    = qw(genomic_align genomic_align_block);
+
+  foreach my $table (@tables) {
+    foreach my $method_link_type ( @method_links ) {
+
+      my $mlsss = $self->dba->get_MethodLinkSpeciesSetAdaptor->fetch_all_by_method_link_type($method_link_type);
+      # Only check from the method_links that have mlsss there are other datachecks to check if mlsss are correct
+      next if scalar(@$mlsss) == 0;
+
+      foreach my $mlss ( @$mlsss ) {
+
+        my $mlss_id   = $mlss->dbID;
+        my $mlss_name = $mlss->name;
+
+        my $sql = qq/
+          SELECT COUNT(*)
+            FROM $table
+          WHERE method_link_species_set_id = $mlss_id
+        /;
+
+        $expected_align_count += $helper->execute_single_result(-SQL => $sql) if $table eq "genomic_align";
+
+        my $desc_1 = "The $table for $mlss_id ($mlss_name) has rows as expected";
+        is_rows_nonzero($dba, $sql, $desc_1);
+      }
+    }
+  }
+    # Check that all the genomic_aligns correspond to a method_link_species_set that should have an alignment
+    my $desc_2 = "All the genomic_align rows with corresponding method_link_species_sets are expected";
+    my $row_count_sql = "SELECT COUNT(*) FROM genomic_align";
+    is_rows($dba, $row_count_sql, $expected_align_count, $desc_2);
+}
+
+1;
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/CheckSynteny.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/CheckSynteny.pm
@@ -29,7 +29,7 @@ extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
 use constant {
   NAME           => 'CheckSynteny',
-  DESCRIPTION    => 'Every synteny_region_id should be seen more than once',
+  DESCRIPTION    => 'Every synteny_region_id should be seen more than once and correspond to an mlss',
   GROUPS         => ['compara', 'compara_syntenies'],
   DATACHECK_TYPE => 'critical',
   DB_TYPES       => ['compara'],
@@ -64,6 +64,24 @@ sub tests {
 
   my $desc_2 = "All synteny_region_ids have been seen more than once";
   is_one_to_many( $dbc, "dnafrag_region", "synteny_region_id", $desc_2 );
+
+  my $mlss_adap = $self->dba->get_MethodLinkSpeciesSetAdaptor;
+  my $mlsss     = $mlss_adap->fetch_all_by_method_link_type('SYNTENY');
+
+  foreach my $mlss ( @$mlsss ) {
+
+    my $mlss_id   = $mlss->dbID;
+    my $mlss_name = $mlss->name;
+
+    my $sql = qq/
+      SELECT COUNT(*)
+        FROM synteny_region
+      WHERE method_link_species_set_id = $mlss_id
+    /;
+
+    my $desc_3 = "The syntenies for $mlss_id ($mlss_name) are present as expected";
+    is_rows_nonzero($dbc, $sql, $desc_3);
+  }
 }
 
 1;

diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/ForeignKeysCompara.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/ForeignKeysCompara.pm
@@ -95,14 +95,9 @@ sub compara_fk {
   # in the "table.sql" file.
 
   # Standard FK constraints that are missing from "table.sql".
-  fk($self->dba, 'species_tree_node', 'parent_id', 'species_tree_node', 'node_id');
-  fk($self->dba, 'species_tree_node', 'root_id', 'species_tree_node', 'node_id');
   fk($self->dba, 'species_tree_node', 'root_id', 'species_tree_root');
 
-  fk($self->dba, 'genomic_align_tree', 'parent_id', 'genomic_align_tree', 'node_id');
   fk($self->dba, 'genomic_align_tree', 'root_id', 'genomic_align_tree', 'node_id');
-  fk($self->dba, 'genomic_align_tree', 'left_node_id', 'genomic_align_tree', 'node_id');
-  fk($self->dba, 'genomic_align_tree', 'right_node_id', 'genomic_align_tree', 'node_id');
 
   # Cases in which we want to check for the reverse direction of the FK constraint
   fk($self->dba, 'family',              'family_id',              'family_member');
@@ -118,68 +113,6 @@ sub compara_fk {
   }
 
   # Cases in which we need to restrict to a subset of rows, using a constraint
-  my $genomic_align_constraint = q/
-    method_link_id IN (
-      SELECT method_link_id FROM method_link
-      WHERE
-        method_link_id < 100 AND
-        class LIKE "GenomicAlign%" AND
-        type NOT LIKE "CACTUS_HAL%"
-    )
-  /;
-  fk($self->dba, 'genomic_align',       'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $genomic_align_constraint);
-  fk($self->dba, 'genomic_align_block', 'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $genomic_align_constraint);
-
-  my $constrained_element_constraint = q/
-    method_link_id IN (
-      SELECT method_link_id FROM method_link
-      WHERE
-        method_link_id < 100 AND
-        class LIKE "ConstrainedElement.%"
-    )
-  /;
-  fk($self->dba, 'constrained_element', 'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $constrained_element_constraint);
-
-  my $synteny_region_constraint = q/
-    method_link_id IN (
-      SELECT method_link_id FROM method_link
-      WHERE
-        method_link_id > 100 AND
-        method_link_id < 200
-    )
-  /;
-  fk($self->dba, 'synteny_region', 'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $synteny_region_constraint);
-
-  my $homology_constraint = q/
-    method_link_id IN (
-      SELECT method_link_id FROM method_link
-      WHERE
-        method_link_id > 200 AND
-        method_link_id < 300
-    )
-  /;
-  fk($self->dba, 'homology', 'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $homology_constraint);
-
-  my $family_constraint = q/
-    method_link_id IN (
-      SELECT method_link_id FROM method_link
-      WHERE
-        method_link_id > 300 AND
-        method_link_id < 400
-    )
-  /;
-  fk($self->dba, 'family', 'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $family_constraint);
-
-  my $tree_constraint = q/
-    method_link_id IN (
-      SELECT method_link_id FROM method_link
-      WHERE
-        method_link_id > 400 AND
-        method_link_id < 500
-    )
-  /;
-  fk($self->dba, 'gene_tree_root',    'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $tree_constraint);
-  fk($self->dba, 'species_tree_root', 'method_link_species_set_id', 'method_link_species_set', 'method_link_species_set_id', $tree_constraint);
 
   my $hom_stats_constraint = q/
     tree_type = 'tree' AND 

diff --git a/lib/Bio/EnsEMBL/DataCheck/index.json b/lib/Bio/EnsEMBL/DataCheck/index.json
@@ -343,6 +343,16 @@
       "name" : "CheckGenomicAlignTreeTable",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::CheckGenomicAlignTreeTable"
    },
+   "CheckGenomicAlignments" : {
+      "datacheck_type" : "critical",
+      "description" : "The expected number of genomic alignments have been merged",
+      "groups" : [
+         "compara",
+         "compara_genome_alignments"
+      ],
+      "name" : "CheckGenomicAlignments",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::CheckGenomicAlignments"
+   },
    "CheckHomology" : {
       "datacheck_type" : "critical",
       "description" : "Check homology_id are all one-to-many for homology_members",
@@ -519,7 +529,7 @@
    },
    "CheckSynteny" : {
       "datacheck_type" : "critical",
-      "description" : "Every synteny_region_id should be seen more than once",
+      "description" : "Every synteny_region_id should be seen more than once and correspond to an mlss",
       "groups" : [
          "compara",
          "compara_syntenies"