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ensembl-test
Commit a305d5ad authored by Tamara El Naboulsi's avatar Tamara El Naboulsi
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Changes for 105 version bump

parent 90d0843b
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    Showing with 55 additions and 43 deletions
    modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
    View file @ a305d5ad
    1 \N schema_version 104
    1 \N schema_version 105
    2 1 assembly.default NCBI34
    3 1 species.taxonomy_id 9606
    26 1 species.classification Homo sapiens
    ......@@ -119,3 +119,4 @@
    193 \N patch patch_101_102_a.sql|schema_version
    194 \N patch patch_102_103_a.sql|schema_version
    195 \N patch patch_103_104_a.sql|schema_version
    196 \N patch patch_104_105_a.sql|schema_version
    modules/t/test-genome-DBs/homo_sapiens/core/table.sql
    View file @ a305d5ad
    ......@@ -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=196 DEFAULT CHARSET=latin1;
    ) ENGINE=MyISAM AUTO_INCREMENT=197 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
    View file @ a305d5ad
    85 \N schema_version 104
    89 \N schema_version 105
    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
    ......@@ -67,3 +67,6 @@
    82 \N patch patch_101_102_c.sql|stn_node_id_bigint
    84 \N patch patch_102_103_a.sql|schema_version
    86 \N patch patch_103_104_a.sql|schema_version
    87 \N patch patch_103_104_b.sql|dnafrag_alt_region
    88 \N patch patch_103_104_c.sql|fix_int_types
    90 \N patch patch_104_105_a.sql|schema_version
    modules/t/test-genome-DBs/multi/compara/table.sql
    View file @ a305d5ad
    ......@@ -14,7 +14,7 @@ CREATE TABLE `CAFE_gene_family` (
    CREATE TABLE `CAFE_species_gene` (
    `cafe_gene_family_id` int(10) unsigned NOT NULL,
    `node_id` bigint(20) unsigned NOT NULL,
    `n_members` int(4) unsigned NOT NULL,
    `n_members` int(10) unsigned NOT NULL,
    `pvalue` double(5,4) DEFAULT NULL,
    PRIMARY KEY (`cafe_gene_family_id`,`node_id`),
    KEY `node_id` (`node_id`)
    ......@@ -32,9 +32,9 @@ CREATE TABLE `conservation_score` (
    CREATE TABLE `constrained_element` (
    `constrained_element_id` bigint(20) unsigned NOT NULL,
    `dnafrag_id` bigint(20) unsigned NOT NULL,
    `dnafrag_start` int(12) unsigned NOT NULL,
    `dnafrag_end` int(12) unsigned NOT NULL,
    `dnafrag_strand` int(2) NOT NULL,
    `dnafrag_start` int(10) unsigned NOT NULL,
    `dnafrag_end` int(10) unsigned NOT NULL,
    `dnafrag_strand` tinyint(4) NOT NULL,
    `method_link_species_set_id` int(10) unsigned NOT NULL,
    `p_value` double NOT NULL DEFAULT '0',
    `score` double NOT NULL DEFAULT '0',
    ......@@ -51,11 +51,18 @@ CREATE TABLE `dnafrag` (
    `coord_system_name` varchar(40) NOT NULL DEFAULT '',
    `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',
    `codon_table_id` tinyint(3) unsigned NOT NULL DEFAULT '1',
    PRIMARY KEY (`dnafrag_id`),
    UNIQUE KEY `name` (`genome_db_id`,`name`)
    ) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1;
    CREATE TABLE `dnafrag_alt_region` (
    `dnafrag_id` bigint(20) unsigned NOT NULL,
    `dnafrag_start` int(10) unsigned NOT NULL,
    `dnafrag_end` int(10) unsigned NOT NULL,
    PRIMARY KEY (`dnafrag_id`)
    ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
    CREATE TABLE `dnafrag_region` (
    `synteny_region_id` int(10) unsigned NOT NULL DEFAULT '0',
    `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
    ......@@ -69,10 +76,10 @@ CREATE TABLE `dnafrag_region` (
    CREATE TABLE `exon_boundaries` (
    `gene_member_id` int(10) unsigned NOT NULL,
    `seq_member_id` int(10) unsigned NOT NULL,
    `dnafrag_start` int(11) NOT NULL,
    `dnafrag_end` int(11) NOT NULL,
    `dnafrag_start` int(10) unsigned NOT NULL,
    `dnafrag_end` int(10) unsigned NOT NULL,
    `sequence_length` int(10) unsigned NOT NULL,
    `left_over` tinyint(1) NOT NULL DEFAULT '0',
    `left_over` tinyint(3) unsigned NOT NULL DEFAULT '0',
    KEY `seq_member_id` (`seq_member_id`),
    KEY `gene_member_id` (`gene_member_id`)
    ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
    ......@@ -117,7 +124,7 @@ CREATE TABLE `gene_align` (
    `gene_align_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
    `seq_type` varchar(40) DEFAULT NULL,
    `aln_method` varchar(40) NOT NULL DEFAULT '',
    `aln_length` int(10) NOT NULL DEFAULT '0',
    `aln_length` int(10) unsigned NOT NULL DEFAULT '0',
    PRIMARY KEY (`gene_align_id`)
    ) ENGINE=MyISAM AUTO_INCREMENT=100000189 DEFAULT CHARSET=latin1;
    ......@@ -132,7 +139,7 @@ CREATE TABLE `gene_align_member` (
    CREATE TABLE `gene_member` (
    `gene_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
    `stable_id` varchar(128) NOT NULL,
    `version` int(10) DEFAULT '0',
    `version` int(10) unsigned DEFAULT '0',
    `source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL,
    `taxon_id` int(10) unsigned NOT NULL,
    `genome_db_id` int(10) unsigned DEFAULT NULL,
    ......@@ -140,8 +147,8 @@ CREATE TABLE `gene_member` (
    `canonical_member_id` int(10) unsigned DEFAULT NULL,
    `description` text,
    `dnafrag_id` bigint(20) unsigned DEFAULT NULL,
    `dnafrag_start` int(10) DEFAULT NULL,
    `dnafrag_end` int(10) DEFAULT NULL,
    `dnafrag_start` int(10) unsigned DEFAULT NULL,
    `dnafrag_end` int(10) unsigned DEFAULT NULL,
    `dnafrag_strand` tinyint(4) DEFAULT NULL,
    `display_label` varchar(128) DEFAULT NULL,
    PRIMARY KEY (`gene_member_id`),
    ......@@ -184,8 +191,8 @@ CREATE TABLE `gene_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,
    `left_index` int(10) NOT NULL DEFAULT '0',
    `right_index` int(10) NOT NULL DEFAULT '0',
    `left_index` int(10) unsigned NOT NULL DEFAULT '0',
    `right_index` int(10) unsigned NOT NULL DEFAULT '0',
    `distance_to_parent` double NOT NULL DEFAULT '1',
    `seq_member_id` int(10) unsigned DEFAULT NULL,
    PRIMARY KEY (`node_id`),
    ......@@ -299,11 +306,11 @@ CREATE TABLE `genomic_align` (
    `genomic_align_block_id` bigint(20) unsigned NOT NULL,
    `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
    `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
    `dnafrag_start` int(10) NOT NULL DEFAULT '0',
    `dnafrag_end` int(10) NOT NULL DEFAULT '0',
    `dnafrag_start` int(10) unsigned NOT NULL DEFAULT '0',
    `dnafrag_end` int(10) unsigned NOT NULL DEFAULT '0',
    `dnafrag_strand` tinyint(4) NOT NULL DEFAULT '0',
    `cigar_line` mediumtext NOT NULL,
    `visible` tinyint(2) unsigned NOT NULL DEFAULT '1',
    `visible` tinyint(3) unsigned NOT NULL DEFAULT '1',
    `node_id` bigint(20) unsigned DEFAULT NULL,
    PRIMARY KEY (`genomic_align_id`),
    KEY `genomic_align_block_id` (`genomic_align_block_id`),
    ......@@ -317,10 +324,10 @@ CREATE TABLE `genomic_align_block` (
    `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
    `score` double DEFAULT NULL,
    `perc_id` tinyint(3) unsigned DEFAULT NULL,
    `length` int(10) NOT NULL,
    `length` int(10) unsigned NOT NULL,
    `group_id` bigint(20) unsigned DEFAULT NULL,
    `level_id` tinyint(2) unsigned NOT NULL DEFAULT '0',
    `direction` tinyint(1) unsigned DEFAULT NULL,
    `level_id` tinyint(3) unsigned NOT NULL DEFAULT '0',
    `direction` tinyint(3) unsigned DEFAULT NULL,
    PRIMARY KEY (`genomic_align_block_id`),
    KEY `method_link_species_set_id` (`method_link_species_set_id`)
    ) ENGINE=MyISAM AUTO_INCREMENT=6770001148336 DEFAULT CHARSET=latin1;
    ......@@ -329,8 +336,8 @@ CREATE TABLE `genomic_align_tree` (
    `node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
    `parent_id` bigint(20) unsigned DEFAULT NULL,
    `root_id` bigint(20) unsigned NOT NULL DEFAULT '0',
    `left_index` int(10) NOT NULL DEFAULT '0',
    `right_index` int(10) NOT NULL DEFAULT '0',
    `left_index` int(10) unsigned NOT NULL DEFAULT '0',
    `right_index` int(10) unsigned NOT NULL DEFAULT '0',
    `left_node_id` bigint(20) unsigned DEFAULT NULL,
    `right_node_id` bigint(20) unsigned DEFAULT NULL,
    `distance_to_parent` double NOT NULL DEFAULT '1',
    ......@@ -429,7 +436,7 @@ 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=87 DEFAULT CHARSET=latin1;
    ) ENGINE=MyISAM AUTO_INCREMENT=91 DEFAULT CHARSET=latin1;
    CREATE TABLE `method_link` (
    `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
    ......@@ -504,7 +511,7 @@ CREATE TABLE `ncbi_taxa_node` (
    CREATE TABLE `other_member_sequence` (
    `seq_member_id` int(10) unsigned NOT NULL,
    `seq_type` varchar(40) NOT NULL,
    `length` int(10) NOT NULL,
    `length` int(10) unsigned NOT NULL,
    `sequence` mediumtext NOT NULL,
    PRIMARY KEY (`seq_member_id`,`seq_type`)
    ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=10000000 AVG_ROW_LENGTH=60000;
    ......@@ -515,18 +522,18 @@ CREATE TABLE `peptide_align_feature` (
    `hmember_id` int(10) unsigned NOT NULL,
    `qgenome_db_id` int(10) unsigned DEFAULT NULL,
    `hgenome_db_id` int(10) unsigned DEFAULT NULL,
    `qstart` int(10) NOT NULL DEFAULT '0',
    `qend` int(10) NOT NULL DEFAULT '0',
    `qstart` int(10) unsigned NOT NULL DEFAULT '0',
    `qend` int(10) unsigned NOT NULL DEFAULT '0',
    `hstart` int(10) unsigned NOT NULL DEFAULT '0',
    `hend` int(10) unsigned NOT NULL DEFAULT '0',
    `score` double(16,4) NOT NULL DEFAULT '0.0000',
    `evalue` double NOT NULL,
    `align_length` int(10) NOT NULL,
    `identical_matches` int(10) NOT NULL,
    `perc_ident` int(10) NOT NULL,
    `positive_matches` int(10) NOT NULL,
    `perc_pos` int(10) NOT NULL,
    `hit_rank` int(10) NOT NULL,
    `align_length` int(10) unsigned NOT NULL,
    `identical_matches` int(10) unsigned NOT NULL,
    `perc_ident` tinyint(3) unsigned NOT NULL,
    `positive_matches` int(10) unsigned NOT NULL,
    `perc_pos` tinyint(3) unsigned NOT NULL,
    `hit_rank` smallint(5) unsigned NOT NULL,
    `cigar_line` mediumtext,
    PRIMARY KEY (`peptide_align_feature_id`)
    ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=133;
    ......@@ -534,7 +541,7 @@ CREATE TABLE `peptide_align_feature` (
    CREATE TABLE `seq_member` (
    `seq_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
    `stable_id` varchar(128) NOT NULL,
    `version` int(10) DEFAULT '0',
    `version` int(10) unsigned DEFAULT '0',
    `source_name` enum('ENSEMBLPEP','ENSEMBLTRANS','Uniprot/SPTREMBL','Uniprot/SWISSPROT','EXTERNALPEP','EXTERNALTRANS','EXTERNALCDS') NOT NULL,
    `taxon_id` int(10) unsigned NOT NULL,
    `genome_db_id` int(10) unsigned DEFAULT NULL,
    ......@@ -544,8 +551,8 @@ CREATE TABLE `seq_member` (
    `has_translation_edits` tinyint(1) NOT NULL DEFAULT '0',
    `description` text,
    `dnafrag_id` bigint(20) unsigned DEFAULT NULL,
    `dnafrag_start` int(10) DEFAULT NULL,
    `dnafrag_end` int(10) DEFAULT NULL,
    `dnafrag_start` int(10) unsigned DEFAULT NULL,
    `dnafrag_end` int(10) unsigned DEFAULT NULL,
    `dnafrag_strand` tinyint(4) DEFAULT NULL,
    `display_label` varchar(128) DEFAULT NULL,
    PRIMARY KEY (`seq_member_id`),
    ......@@ -577,7 +584,7 @@ CREATE TABLE `seq_member_projection_stable_id` (
    CREATE TABLE `sequence` (
    `sequence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
    `length` int(10) NOT NULL,
    `length` int(10) unsigned NOT NULL,
    `md5sum` char(32) NOT NULL,
    `sequence` longtext NOT NULL,
    PRIMARY KEY (`sequence_id`),
    ......@@ -612,8 +619,8 @@ CREATE TABLE `species_tree_node` (
    `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',
    `left_index` int(10) unsigned NOT NULL DEFAULT '0',
    `right_index` int(10) unsigned NOT NULL DEFAULT '0',
    `distance_to_parent` double DEFAULT '1',
    `taxon_id` int(10) unsigned DEFAULT NULL,
    `genome_db_id` int(10) unsigned DEFAULT NULL,
    ......
    modules/t/test-genome-DBs/mus_musculus/core/meta.txt
    View file @ a305d5ad
    1 \N schema_type core
    2 \N schema_version 104
    2 \N schema_version 105
    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
    ......@@ -197,3 +197,4 @@
    1709 \N patch patch_101_102_a.sql|schema_version
    1710 \N patch patch_102_103_a.sql|schema_version
    1711 \N patch patch_103_104_a.sql|schema_version
    1712 \N patch patch_104_105_a.sql|schema_version
    modules/t/test-genome-DBs/mus_musculus/core/table.sql
    View file @ a305d5ad
    ......@@ -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=1712 DEFAULT CHARSET=latin1;
    ) ENGINE=MyISAM AUTO_INCREMENT=1713 DEFAULT CHARSET=latin1;
    CREATE TABLE `meta_coord` (
    `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
    ......
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