Merge pull request #52 from Ensembl/103_testdbpatch

103 test db patch

modules/t/test-genome-DBs/homo_sapiens/core/meta.txt

@@ -1,4 +1,4 @@
-1	\N	schema_version	102
+1	\N	schema_version	103
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -117,3 +117,4 @@
 191	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
 192	\N	patch	patch_100_101_a.sql|schema_version
 193	\N	patch	patch_101_102_a.sql|schema_version
+194	\N	patch	patch_102_103_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/core/table.sql

@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=194 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=195 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

modules/t/test-genome-DBs/multi/compara/meta.txt

@@ -1,4 +1,4 @@
-79	\N	schema_version	102
+83	\N	schema_version	103
 2	\N	schema_type	compara
 3	\N	patch	patch_84_85_a.sql|schema_version
 4	\N	patch	patch_84_85_b.sql|gene_tree_root_attr
@@ -63,3 +63,6 @@
 77	\N	patch	patch_100_101_e.sql|positive_int
 78	\N	patch	patch_100_101_f.sql|gab.direction
 80	\N	patch	patch_101_102_a.sql|schema_version
+81	\N	patch	patch_101_102_b.sql|enum_other
+82	\N	patch	patch_101_102_c.sql|stn_node_id_bigint
+84	\N	patch	patch_102_103_a.sql|schema_version

modules/t/test-genome-DBs/multi/compara/table.sql

@@ -1,7 +1,7 @@
 CREATE TABLE `CAFE_gene_family` (
   `cafe_gene_family_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `root_id` int(10) unsigned NOT NULL,
-  `lca_id` int(10) unsigned NOT NULL,
+  `root_id` bigint(20) unsigned NOT NULL,
+  `lca_id` bigint(20) unsigned NOT NULL,
   `gene_tree_root_id` int(10) unsigned NOT NULL,
   `pvalue_avg` double(5,4) DEFAULT NULL,
   `lambdas` varchar(100) DEFAULT NULL,
@@ -13,7 +13,7 @@ CREATE TABLE `CAFE_gene_family` (
 
 CREATE TABLE `CAFE_species_gene` (
   `cafe_gene_family_id` int(10) unsigned NOT NULL,
-  `node_id` int(10) unsigned NOT NULL,
+  `node_id` bigint(20) unsigned NOT NULL,
   `n_members` int(4) unsigned NOT NULL,
   `pvalue` double(5,4) DEFAULT NULL,
   PRIMARY KEY (`cafe_gene_family_id`,`node_id`),
@@ -49,7 +49,7 @@ CREATE TABLE `dnafrag` (
   `name` varchar(255) NOT NULL DEFAULT '',
   `genome_db_id` int(10) unsigned NOT NULL,
   `coord_system_name` varchar(40) NOT NULL DEFAULT '',
-  `cellular_component` enum('NUC','MT','PT') NOT NULL DEFAULT 'NUC',
+  `cellular_component` enum('NUC','MT','PT','OTHER') NOT NULL DEFAULT 'NUC',
   `is_reference` tinyint(1) NOT NULL DEFAULT '1',
   `codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT '1',
   PRIMARY KEY (`dnafrag_id`),
@@ -197,7 +197,7 @@ CREATE TABLE `gene_tree_node` (
 CREATE TABLE `gene_tree_node_attr` (
   `node_id` int(10) unsigned NOT NULL,
   `node_type` enum('duplication','dubious','speciation','sub-speciation','gene_split') DEFAULT NULL,
-  `species_tree_node_id` int(10) unsigned DEFAULT NULL,
+  `species_tree_node_id` bigint(20) unsigned DEFAULT NULL,
   `bootstrap` tinyint(3) unsigned DEFAULT NULL,
   `duplication_confidence_score` double(5,4) DEFAULT NULL,
   PRIMARY KEY (`node_id`),
@@ -225,7 +225,7 @@ CREATE TABLE `gene_tree_root` (
   `tree_type` enum('clusterset','supertree','tree') NOT NULL,
   `clusterset_id` varchar(20) NOT NULL DEFAULT 'default',
   `method_link_species_set_id` int(10) unsigned NOT NULL,
-  `species_tree_root_id` int(10) unsigned DEFAULT NULL,
+  `species_tree_root_id` bigint(20) unsigned DEFAULT NULL,
   `gene_align_id` int(10) unsigned DEFAULT NULL,
   `ref_root_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(40) DEFAULT NULL,
@@ -259,7 +259,7 @@ CREATE TABLE `gene_tree_root_attr` (
   `tree_num_dup_nodes` int(10) unsigned DEFAULT NULL,
   `tree_num_leaves` int(10) unsigned DEFAULT NULL,
   `tree_num_spec_nodes` int(10) unsigned DEFAULT NULL,
-  `lca_node_id` int(10) unsigned DEFAULT NULL,
+  `lca_node_id` bigint(20) unsigned DEFAULT NULL,
   `taxonomic_coverage` float DEFAULT NULL,
   `ratio_species_genes` float DEFAULT NULL,
   `model_name` varchar(40) DEFAULT NULL,
@@ -376,7 +376,7 @@ CREATE TABLE `homology` (
   `n` float(10,1) DEFAULT NULL,
   `s` float(10,1) DEFAULT NULL,
   `lnl` float(10,3) DEFAULT NULL,
-  `species_tree_node_id` int(10) unsigned DEFAULT NULL,
+  `species_tree_node_id` bigint(20) unsigned DEFAULT NULL,
   `gene_tree_node_id` int(10) unsigned DEFAULT NULL,
   `gene_tree_root_id` int(10) unsigned DEFAULT NULL,
   `goc_score` tinyint(3) unsigned DEFAULT NULL,
@@ -429,7 +429,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=81 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=85 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -609,9 +609,9 @@ CREATE TABLE `species_set_tag` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `species_tree_node` (
-  `node_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `parent_id` int(10) unsigned DEFAULT NULL,
-  `root_id` int(10) unsigned DEFAULT NULL,
+  `node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
+  `parent_id` bigint(20) unsigned DEFAULT NULL,
+  `root_id` bigint(20) unsigned DEFAULT NULL,
   `left_index` int(10) NOT NULL DEFAULT '0',
   `right_index` int(10) NOT NULL DEFAULT '0',
   `distance_to_parent` double DEFAULT '1',
@@ -626,7 +626,7 @@ CREATE TABLE `species_tree_node` (
 ) ENGINE=MyISAM AUTO_INCREMENT=40102221 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `species_tree_node_attr` (
-  `node_id` int(10) unsigned NOT NULL,
+  `node_id` bigint(20) unsigned NOT NULL,
   `nb_long_genes` int(11) DEFAULT NULL,
   `nb_short_genes` int(11) DEFAULT NULL,
   `avg_dupscore` float DEFAULT NULL,
@@ -656,15 +656,15 @@ CREATE TABLE `species_tree_node_attr` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `species_tree_node_tag` (
-  `node_id` int(10) unsigned NOT NULL,
+  `node_id` bigint(20) unsigned NOT NULL,
   `tag` varchar(50) NOT NULL,
   `value` mediumtext NOT NULL,
   KEY `node_id_tag` (`node_id`,`tag`),
   KEY `tag` (`tag`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `species_tree_root` (
-  `root_id` int(10) unsigned NOT NULL,
+  `root_id` bigint(20) unsigned NOT NULL DEFAULT '0',
   `method_link_species_set_id` int(10) unsigned NOT NULL,
   `label` varchar(256) NOT NULL DEFAULT 'default',
   PRIMARY KEY (`root_id`),

modules/t/test-genome-DBs/mus_musculus/core/meta.txt

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	102
+2	\N	schema_version	103
 3	\N	patch	patch_65_66_a.sql|schema_version
 4	\N	patch	patch_65_66_b.sql|fix_external_db_id
 5	\N	patch	patch_65_66_c.sql|reorder_unmapped_obj_index
@@ -195,3 +195,4 @@
 1707	\N	patch	patch_99_100_c.sql|alter_mapping_session_assembly_length
 1708	\N	patch	patch_100_101_a.sql|schema_version
 1709	\N	patch	patch_101_102_a.sql|schema_version
+1710	\N	patch	patch_102_103_a.sql|schema_version

modules/t/test-genome-DBs/mus_musculus/core/table.sql

@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=1710 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1711 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

scripts/runtests.pl

@@ -94,14 +94,15 @@
 
 clean();
 
-if($results->has_errors()) {
   my $count = $results->failed();
   $count   += $results->parse_errors();
   $count   += $results->exit();
   $count   += $results->wait();
   $count = 255 if $count > 255;
+  use Data::Dumper;
+  printf(Dumper($results));
+  printf($count)
   exit $count;
-}
 
 sub usage {
     print <<EOT;