New test for valid foreign keys in InnoDB applications. foreign_keys.sql...

New test for valid foreign keys in InnoDB applications. foreign_keys.sql cleaned. Tabs assassinated.

modules/t/schema.t

@@ -20,6 +20,7 @@ use Test::More;
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Utils::IO qw/slurp/;
 use File::Spec::Functions qw/updir catfile catdir/;
+use File::Temp qw/tempfile/;
 
 my $db = Bio::EnsEMBL::Test::MultiTestDB->new();
 my $dba = $db->get_DBAdaptor('core');
@@ -42,7 +43,7 @@ SKIP: {
   my $table_string = slurp $sql_file;  
   my @fks = sort grep /FOREIGN[\s\n]+?KEY[\s\n]+?\(.+?\)[\s\n]+?REFERENCES/i, $table_string;
   if(@fks) {
-    fail("Definition of foreign keys detected in SQL schema file");
+    fail("Definition of foreign keys detected in SQL schema file\n".join(', ',@fks));
   } else {
     pass("SQL schema file does not define foreign keys");
   }
@@ -62,6 +63,38 @@ SKIP: {
   
   note 'Dropping database '.$new_db_name;
   $dba->dbc()->do("drop database $new_db_name");
+
+  # Check viability of foreign_keys.sql 
+
+  $table_string =~ s/ENGINE=MyISAM/ENGINE=InnoDB/g;
+  my $fk_file = catfile($sql_dir, 'foreign_keys.sql');
+  $table_string .= slurp $fk_file;
+
+  my ($temp_fh,$temp_filename) = tempfile;
+  {
+    local $| = 1;
+    print $temp_fh $table_string;
+  }
+  $new_db_name = $db->create_db_name('fkschematemp');
+  note 'Creating database with foreign keys '.$new_db_name;
+  $dba->dbc()->do("create database $new_db_name");
+
+  %args = ( host => $dbc->host(), port => $dbc->port(), user => $dbc->username(), password => $dbc->password());
+  $cmd_args = join(q{ }, map { "--${_}=$args{$_}" } keys %args);
+  $cmd = "mysql $cmd_args $new_db_name < $temp_filename 2>&1";
+  $output = `$cmd`;
+  $ec = ($? >> 8);
+  if($ec != 0) {
+    note($output);
+    fail("MySQL (InnoDB) command failed with error code '$ec'");
+  }
+  else {
+    pass("MySQL (InnoDB) was able to load the Ensembl core schema with foreign keys");
+  }
+  
+  note 'Dropping database '.$new_db_name;
+  $dba->dbc()->do("drop database $new_db_name");
 }
 
+
 done_testing();
\ No newline at end of file

sql/foreign_keys.sql

@@ -23,8 +23,8 @@
 # key constraints on MyISAM tables.
 
 ALTER table alt_allele ADD FOREIGN KEY (gene_id) REFERENCES gene(gene_id);
-ALTER table alt_allele ADD FOREIGN KEY (alt_allele_group_id) REFERENCES alt_allele_group(alt_allele_group_id)
-ALTER table alt_allele_id ADD FOREIGN KEY (alt_allele_id) REFERENCES alt_allele(alt_allele_id);
+ALTER table alt_allele ADD FOREIGN KEY (alt_allele_group_id) REFERENCES alt_allele_group(alt_allele_group_id);
+ALTER table alt_allele ADD FOREIGN KEY (alt_allele_id) REFERENCES alt_allele(alt_allele_id);
 
 
 ALTER table analysis_description ADD FOREIGN KEY (analysis_id) REFERENCES analysis(analysis_id);
@@ -58,9 +58,6 @@ ALTER table dna ADD FOREIGN KEY (seq_region_id) REFERENCES seq_region(seq_region
 ALTER table dna_align_feature ADD FOREIGN KEY (analysis_id) REFERENCES analysis(analysis_id);
 ALTER table dna_align_feature ADD FOREIGN KEY (seq_region_id) REFERENCES seq_region(seq_region_id);
 ALTER table dna_align_feature ADD FOREIGN KEY (external_db_id) REFERENCES external_db(external_db_id);
-ALTER table dna_align_feature ADD FOREIGN KEY (pair_dna_align_feature_id) REFERENCES dna_align_feature(dna_align_feature_id);
-
-ALTER table dnac ADD FOREIGN KEY (seq_region_id) REFERENCES seq_region(seq_region_id);
 
 ALTER table exon ADD FOREIGN KEY (seq_region_id) REFERENCES seq_region(seq_region_id);
 
@@ -138,16 +135,6 @@ ALTER table protein_align_feature ADD FOREIGN KEY (external_db_id) REFERENCES ex
 ALTER table protein_feature ADD FOREIGN KEY (analysis_id) REFERENCES analysis(analysis_id);
 ALTER table protein_feature ADD FOREIGN KEY (translation_id) REFERENCES translation(translation_id);
 
-ALTER table qtl ADD FOREIGN KEY (flank_marker_id_1) REFERENCES marker(marker_id);
-ALTER table qtl ADD FOREIGN KEY (flank_marker_id_2) REFERENCES marker(marker_id);
-ALTER table qtl ADD FOREIGN KEY (peak_marker_id) REFERENCES marker(marker_id);
-
-ALTER table qtl_feature ADD FOREIGN KEY (analysis_id) REFERENCES analysis(analysis_id);
-ALTER table qtl_feature ADD FOREIGN KEY (qtl_id) REFERENCES qtl(qtl_id);
-ALTER table qtl_feature ADD FOREIGN KEY (seq_region_id) REFERENCES seq_region(seq_region_id);
-
-ALTER table qtl_synonym ADD FOREIGN KEY (qtl_id) REFERENCES qtl(qtl_id);
-
 ALTER table repeat_feature ADD FOREIGN KEY (analysis_id) REFERENCES analysis(analysis_id);
 ALTER table repeat_feature ADD FOREIGN KEY (repeat_consensus_id) REFERENCES repeat_consensus(repeat_consensus_id);
 ALTER table repeat_feature ADD FOREIGN KEY (seq_region_id) REFERENCES seq_region(seq_region_id);
@@ -196,9 +183,6 @@ ALTER table translation ADD FOREIGN KEY (transcript_id) REFERENCES transcript(tr
 ALTER table translation_attrib ADD FOREIGN KEY (attrib_type_id) REFERENCES attrib_type(attrib_type_id);
 ALTER table translation_attrib ADD FOREIGN KEY (translation_id) REFERENCES translation(translation_id);
 
-ALTER table unconventional_transcript_association ADD FOREIGN KEY (gene_id) REFERENCES gene(gene_id);
-ALTER table unconventional_transcript_association ADD FOREIGN KEY (transcript_id) REFERENCES transcript(transcript_id);
-
 ALTER table unmapped_object ADD FOREIGN KEY (analysis_id) REFERENCES analysis(analysis_id);
 ALTER table unmapped_object ADD FOREIGN KEY (external_db_id) REFERENCES external_db(external_db_id);
 ALTER table unmapped_object ADD FOREIGN KEY (unmapped_reason_id) REFERENCES unmapped_reason(unmapped_reason_id);

sql/table.sql

@@ -969,8 +969,8 @@ CREATE TABLE splicing_event (
 @column splicing_event_id                   Foreign key references to the @link splicing_event table.
 @column exon_id                             Foreign key references to the @link exon table.
 @column transcript_id                       Foreign key references to the @link transcript table.
-@column feature_order             	    Feature order number according to genomic location.
-@column transcript_association    	    Transcript sequence.
+@column feature_order                       Feature order number according to genomic location.
+@column transcript_association              Transcript sequence.
 @column type                                E.g. 'constitutive_exon','exon','flanking_exon'.
 @column start                               Sequence start.
 @column end                                 Sequence end.