Commit 12dcd869 authored by Ameya Chaubal's avatar Ameya Chaubal

patch test db for 101

parent f320b0f6
Pipeline #65114 passed with stage
in 5 minutes and 46 seconds
1 \N schema_version 100 1 \N schema_version 101
2 1 assembly.default NCBI34 2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606 3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens 26 1 species.classification Homo sapiens
...@@ -114,3 +114,5 @@ ...@@ -114,3 +114,5 @@
188 \N patch patch_98_99_a.sql|schema_version 188 \N patch patch_98_99_a.sql|schema_version
189 \N patch patch_99_100_a.sql|schema_version 189 \N patch patch_99_100_a.sql|schema_version
190 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull 190 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
191 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
192 \N patch patch_100_101_a.sql|schema_version
69 \N schema_version 100 72 \N schema_version 101
2 \N schema_type compara 2 \N schema_type compara
3 \N patch patch_84_85_a.sql|schema_version 3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr 4 \N patch patch_84_85_b.sql|gene_tree_root_attr
...@@ -55,3 +55,9 @@ ...@@ -55,3 +55,9 @@
67 \N patch patch_97_98_b.sql|division_name 67 \N patch patch_97_98_b.sql|division_name
68 \N patch patch_98_99_a.sql|schema_version 68 \N patch patch_98_99_a.sql|schema_version
70 \N patch patch_99_100_a.sql|schema_version 70 \N patch patch_99_100_a.sql|schema_version
71 \N patch patch_99_100_b.sql|homology_id_64-bits
73 \N patch patch_100_101_a.sql|schema_version
74 \N patch patch_100_101_b.sql|genome_db.strain_name
75 \N patch patch_100_101_c.sql|mlss_attr.n_goc_null
76 \N patch patch_100_101_d.sql|gat.node_ids
77 \N patch patch_100_101_e.sql|positive_int
...@@ -24,8 +24,8 @@ CREATE TABLE `conservation_score` ( ...@@ -24,8 +24,8 @@ CREATE TABLE `conservation_score` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL, `genomic_align_block_id` bigint(20) unsigned NOT NULL,
`window_size` smallint(5) unsigned NOT NULL, `window_size` smallint(5) unsigned NOT NULL,
`position` int(10) unsigned NOT NULL, `position` int(10) unsigned NOT NULL,
`expected_score` blob DEFAULT NULL, `expected_score` blob,
`diff_score` blob DEFAULT NULL, `diff_score` blob,
KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`) KEY `genomic_align_block_id` (`genomic_align_block_id`,`window_size`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841; ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=15000000 AVG_ROW_LENGTH=841;
...@@ -36,8 +36,8 @@ CREATE TABLE `constrained_element` ( ...@@ -36,8 +36,8 @@ CREATE TABLE `constrained_element` (
`dnafrag_end` int(12) unsigned NOT NULL, `dnafrag_end` int(12) unsigned NOT NULL,
`dnafrag_strand` int(2) NOT NULL, `dnafrag_strand` int(2) NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL,
`p_value` double NOT NULL DEFAULT 0, `p_value` double NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT 0, `score` double NOT NULL DEFAULT '0',
KEY `dnafrag_id` (`dnafrag_id`), KEY `dnafrag_id` (`dnafrag_id`),
KEY `constrained_element_id_idx` (`constrained_element_id`), KEY `constrained_element_id_idx` (`constrained_element_id`),
KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`) KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`)
...@@ -45,23 +45,23 @@ CREATE TABLE `constrained_element` ( ...@@ -45,23 +45,23 @@ CREATE TABLE `constrained_element` (
CREATE TABLE `dnafrag` ( CREATE TABLE `dnafrag` (
`dnafrag_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `dnafrag_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`length` int(11) NOT NULL DEFAULT 0, `length` int(10) unsigned NOT NULL DEFAULT '0',
`name` varchar(255) NOT NULL DEFAULT '', `name` varchar(255) NOT NULL DEFAULT '',
`genome_db_id` int(10) unsigned NOT NULL, `genome_db_id` int(10) unsigned NOT NULL,
`coord_system_name` varchar(40) NOT NULL DEFAULT '', `coord_system_name` varchar(40) NOT NULL DEFAULT '',
`cellular_component` enum('NUC','MT','PT') NOT NULL DEFAULT 'NUC', `cellular_component` enum('NUC','MT','PT') NOT NULL DEFAULT 'NUC',
`is_reference` tinyint(1) NOT NULL DEFAULT 1, `is_reference` tinyint(1) NOT NULL DEFAULT '1',
`codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT 1, `codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT '1',
PRIMARY KEY (`dnafrag_id`), PRIMARY KEY (`dnafrag_id`),
UNIQUE KEY `name` (`genome_db_id`,`name`) UNIQUE KEY `name` (`genome_db_id`,`name`)
) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1;
CREATE TABLE `dnafrag_region` ( CREATE TABLE `dnafrag_region` (
`synteny_region_id` int(10) unsigned NOT NULL DEFAULT 0, `synteny_region_id` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT 0, `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`dnafrag_start` int(10) unsigned NOT NULL DEFAULT 0, `dnafrag_start` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_end` int(10) unsigned NOT NULL DEFAULT 0, `dnafrag_end` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_strand` tinyint(4) NOT NULL DEFAULT 0, `dnafrag_strand` tinyint(4) NOT NULL DEFAULT '0',
KEY `synteny` (`synteny_region_id`,`dnafrag_id`), KEY `synteny` (`synteny_region_id`,`dnafrag_id`),
KEY `synteny_reversed` (`dnafrag_id`,`synteny_region_id`) KEY `synteny_reversed` (`dnafrag_id`,`synteny_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -72,7 +72,7 @@ CREATE TABLE `exon_boundaries` ( ...@@ -72,7 +72,7 @@ CREATE TABLE `exon_boundaries` (
`dnafrag_start` int(11) NOT NULL, `dnafrag_start` int(11) NOT NULL,
`dnafrag_end` int(11) NOT NULL, `dnafrag_end` int(11) NOT NULL,
`sequence_length` int(10) unsigned NOT NULL, `sequence_length` int(10) unsigned NOT NULL,
`left_over` tinyint(1) NOT NULL DEFAULT 0, `left_over` tinyint(1) NOT NULL DEFAULT '0',
KEY `seq_member_id` (`seq_member_id`), KEY `seq_member_id` (`seq_member_id`),
KEY `gene_member_id` (`gene_member_id`) KEY `gene_member_id` (`gene_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -87,7 +87,7 @@ CREATE TABLE `external_db` ( ...@@ -87,7 +87,7 @@ CREATE TABLE `external_db` (
`type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL, `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
`secondary_db_name` varchar(255) DEFAULT NULL, `secondary_db_name` varchar(255) DEFAULT NULL,
`secondary_db_table` varchar(255) DEFAULT NULL, `secondary_db_table` varchar(255) DEFAULT NULL,
`description` text DEFAULT NULL, `description` text,
PRIMARY KEY (`external_db_id`), PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`) UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -97,7 +97,7 @@ CREATE TABLE `family` ( ...@@ -97,7 +97,7 @@ CREATE TABLE `family` (
`stable_id` varchar(40) NOT NULL, `stable_id` varchar(40) NOT NULL,
`version` int(10) unsigned NOT NULL, `version` int(10) unsigned NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL,
`description` text DEFAULT NULL, `description` text,
`description_score` double DEFAULT NULL, `description_score` double DEFAULT NULL,
PRIMARY KEY (`family_id`), PRIMARY KEY (`family_id`),
UNIQUE KEY `stable_id` (`stable_id`), UNIQUE KEY `stable_id` (`stable_id`),
...@@ -108,7 +108,7 @@ CREATE TABLE `family` ( ...@@ -108,7 +108,7 @@ CREATE TABLE `family` (
CREATE TABLE `family_member` ( CREATE TABLE `family_member` (
`family_id` int(10) unsigned NOT NULL, `family_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned NOT NULL,
`cigar_line` mediumtext DEFAULT NULL, `cigar_line` mediumtext,
PRIMARY KEY (`family_id`,`seq_member_id`), PRIMARY KEY (`family_id`,`seq_member_id`),
KEY `seq_member_id` (`seq_member_id`) KEY `seq_member_id` (`seq_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -117,14 +117,14 @@ CREATE TABLE `gene_align` ( ...@@ -117,14 +117,14 @@ CREATE TABLE `gene_align` (
`gene_align_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `gene_align_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`seq_type` varchar(40) DEFAULT NULL, `seq_type` varchar(40) DEFAULT NULL,
`aln_method` varchar(40) NOT NULL DEFAULT '', `aln_method` varchar(40) NOT NULL DEFAULT '',
`aln_length` int(10) NOT NULL DEFAULT 0, `aln_length` int(10) NOT NULL DEFAULT '0',
PRIMARY KEY (`gene_align_id`) PRIMARY KEY (`gene_align_id`)
) ENGINE=MyISAM AUTO_INCREMENT=100000189 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=100000189 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_align_member` ( CREATE TABLE `gene_align_member` (
`gene_align_id` int(10) unsigned NOT NULL, `gene_align_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned NOT NULL, `seq_member_id` int(10) unsigned NOT NULL,
`cigar_line` mediumtext DEFAULT NULL, `cigar_line` mediumtext,
PRIMARY KEY (`gene_align_id`,`seq_member_id`), PRIMARY KEY (`gene_align_id`,`seq_member_id`),
KEY `seq_member_id` (`seq_member_id`) KEY `seq_member_id` (`seq_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -132,13 +132,13 @@ CREATE TABLE `gene_align_member` ( ...@@ -132,13 +132,13 @@ CREATE TABLE `gene_align_member` (
CREATE TABLE `gene_member` ( CREATE TABLE `gene_member` (
`gene_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `gene_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`stable_id` varchar(128) NOT NULL, `stable_id` varchar(128) NOT NULL,
`version` int(10) DEFAULT 0, `version` int(10) DEFAULT '0',
`source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL, `source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL,
`taxon_id` int(10) unsigned NOT NULL, `taxon_id` int(10) unsigned NOT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL, `genome_db_id` int(10) unsigned DEFAULT NULL,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group','current_notdumped','notcurrent') NOT NULL DEFAULT 'coding', `biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group','current_notdumped','notcurrent') NOT NULL DEFAULT 'coding',
`canonical_member_id` int(10) unsigned DEFAULT NULL, `canonical_member_id` int(10) unsigned DEFAULT NULL,
`description` text DEFAULT NULL, `description` text,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL, `dnafrag_id` bigint(20) unsigned DEFAULT NULL,
`dnafrag_start` int(10) DEFAULT NULL, `dnafrag_start` int(10) DEFAULT NULL,
`dnafrag_end` int(10) DEFAULT NULL, `dnafrag_end` int(10) DEFAULT NULL,
...@@ -159,12 +159,12 @@ CREATE TABLE `gene_member` ( ...@@ -159,12 +159,12 @@ CREATE TABLE `gene_member` (
CREATE TABLE `gene_member_hom_stats` ( CREATE TABLE `gene_member_hom_stats` (
`gene_member_id` int(10) unsigned NOT NULL, `gene_member_id` int(10) unsigned NOT NULL,
`collection` varchar(40) NOT NULL, `collection` varchar(40) NOT NULL,
`families` int(10) unsigned NOT NULL DEFAULT 0, `families` int(10) unsigned NOT NULL DEFAULT '0',
`gene_trees` tinyint(1) unsigned NOT NULL DEFAULT 0, `gene_trees` tinyint(1) unsigned NOT NULL DEFAULT '0',
`gene_gain_loss_trees` tinyint(1) unsigned NOT NULL DEFAULT 0, `gene_gain_loss_trees` tinyint(1) unsigned NOT NULL DEFAULT '0',
`orthologues` int(10) unsigned NOT NULL DEFAULT 0, `orthologues` int(10) unsigned NOT NULL DEFAULT '0',
`paralogues` int(10) unsigned NOT NULL DEFAULT 0, `paralogues` int(10) unsigned NOT NULL DEFAULT '0',
`homoeologues` int(10) unsigned NOT NULL DEFAULT 0, `homoeologues` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`gene_member_id`,`collection`) PRIMARY KEY (`gene_member_id`,`collection`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -184,9 +184,9 @@ CREATE TABLE `gene_tree_node` ( ...@@ -184,9 +184,9 @@ CREATE TABLE `gene_tree_node` (
`node_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `node_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` int(10) unsigned DEFAULT NULL, `parent_id` int(10) unsigned DEFAULT NULL,
`root_id` int(10) unsigned DEFAULT NULL, `root_id` int(10) unsigned DEFAULT NULL,
`left_index` int(10) NOT NULL DEFAULT 0, `left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT '0',
`distance_to_parent` double NOT NULL DEFAULT 1, `distance_to_parent` double NOT NULL DEFAULT '1',
`seq_member_id` int(10) unsigned DEFAULT NULL, `seq_member_id` int(10) unsigned DEFAULT NULL,
PRIMARY KEY (`node_id`), PRIMARY KEY (`node_id`),
KEY `parent_id` (`parent_id`), KEY `parent_id` (`parent_id`),
...@@ -281,10 +281,10 @@ CREATE TABLE `genome_db` ( ...@@ -281,10 +281,10 @@ CREATE TABLE `genome_db` (
`name` varchar(128) NOT NULL DEFAULT '', `name` varchar(128) NOT NULL DEFAULT '',
`assembly` varchar(100) NOT NULL DEFAULT '', `assembly` varchar(100) NOT NULL DEFAULT '',
`genebuild` varchar(100) NOT NULL DEFAULT '', `genebuild` varchar(100) NOT NULL DEFAULT '',
`has_karyotype` tinyint(1) NOT NULL DEFAULT 0, `has_karyotype` tinyint(1) NOT NULL DEFAULT '0',
`is_good_for_alignment` tinyint(1) NOT NULL DEFAULT 0, `is_good_for_alignment` tinyint(1) NOT NULL DEFAULT '0',
`genome_component` varchar(5) DEFAULT NULL, `genome_component` varchar(5) DEFAULT NULL,
`strain_name` varchar(40) DEFAULT NULL, `strain_name` varchar(100) DEFAULT NULL,
`display_name` varchar(255) DEFAULT NULL, `display_name` varchar(255) DEFAULT NULL,
`locator` varchar(400) DEFAULT NULL, `locator` varchar(400) DEFAULT NULL,
`first_release` smallint(6) DEFAULT NULL, `first_release` smallint(6) DEFAULT NULL,
...@@ -297,13 +297,13 @@ CREATE TABLE `genome_db` ( ...@@ -297,13 +297,13 @@ CREATE TABLE `genome_db` (
CREATE TABLE `genomic_align` ( CREATE TABLE `genomic_align` (
`genomic_align_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `genomic_align_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`genomic_align_block_id` bigint(20) unsigned NOT NULL, `genomic_align_block_id` bigint(20) unsigned NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT 0, `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
`dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT 0, `dnafrag_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`dnafrag_start` int(10) NOT NULL DEFAULT 0, `dnafrag_start` int(10) NOT NULL DEFAULT '0',
`dnafrag_end` int(10) NOT NULL DEFAULT 0, `dnafrag_end` int(10) NOT NULL DEFAULT '0',
`dnafrag_strand` tinyint(4) NOT NULL DEFAULT 0, `dnafrag_strand` tinyint(4) NOT NULL DEFAULT '0',
`cigar_line` mediumtext NOT NULL, `cigar_line` mediumtext NOT NULL,
`visible` tinyint(2) unsigned NOT NULL DEFAULT 1, `visible` tinyint(2) unsigned NOT NULL DEFAULT '1',
`node_id` bigint(20) unsigned DEFAULT NULL, `node_id` bigint(20) unsigned DEFAULT NULL,
PRIMARY KEY (`genomic_align_id`), PRIMARY KEY (`genomic_align_id`),
KEY `genomic_align_block_id` (`genomic_align_block_id`), KEY `genomic_align_block_id` (`genomic_align_block_id`),
...@@ -314,12 +314,12 @@ CREATE TABLE `genomic_align` ( ...@@ -314,12 +314,12 @@ CREATE TABLE `genomic_align` (
CREATE TABLE `genomic_align_block` ( CREATE TABLE `genomic_align_block` (
`genomic_align_block_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `genomic_align_block_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT 0, `method_link_species_set_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double DEFAULT NULL, `score` double DEFAULT NULL,
`perc_id` tinyint(3) unsigned DEFAULT NULL, `perc_id` tinyint(3) unsigned DEFAULT NULL,
`length` int(10) NOT NULL, `length` int(10) NOT NULL,
`group_id` bigint(20) unsigned DEFAULT NULL, `group_id` bigint(20) unsigned DEFAULT NULL,
`level_id` tinyint(2) unsigned NOT NULL DEFAULT 0, `level_id` tinyint(2) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`genomic_align_block_id`), PRIMARY KEY (`genomic_align_block_id`),
KEY `method_link_species_set_id` (`method_link_species_set_id`) KEY `method_link_species_set_id` (`method_link_species_set_id`)
) ENGINE=MyISAM AUTO_INCREMENT=6770001148336 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=6770001148336 DEFAULT CHARSET=latin1;
...@@ -327,12 +327,12 @@ CREATE TABLE `genomic_align_block` ( ...@@ -327,12 +327,12 @@ CREATE TABLE `genomic_align_block` (
CREATE TABLE `genomic_align_tree` ( CREATE TABLE `genomic_align_tree` (
`node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT, `node_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` bigint(20) unsigned DEFAULT NULL, `parent_id` bigint(20) unsigned DEFAULT NULL,
`root_id` bigint(20) unsigned NOT NULL DEFAULT 0, `root_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`left_index` int(10) NOT NULL DEFAULT 0, `left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT '0',
`left_node_id` bigint(10) DEFAULT NULL, `left_node_id` bigint(20) unsigned DEFAULT NULL,
`right_node_id` bigint(10) DEFAULT NULL, `right_node_id` bigint(20) unsigned DEFAULT NULL,
`distance_to_parent` double NOT NULL DEFAULT 1, `distance_to_parent` double NOT NULL DEFAULT '1',
PRIMARY KEY (`node_id`), PRIMARY KEY (`node_id`),
KEY `parent_id` (`parent_id`), KEY `parent_id` (`parent_id`),
KEY `left_index` (`root_id`,`left_index`) KEY `left_index` (`root_id`,`left_index`)
...@@ -350,8 +350,8 @@ CREATE TABLE `hmm_curated_annot` ( ...@@ -350,8 +350,8 @@ CREATE TABLE `hmm_curated_annot` (
`seq_member_stable_id` varchar(40) NOT NULL, `seq_member_stable_id` varchar(40) NOT NULL,
`model_id` varchar(40) DEFAULT NULL, `model_id` varchar(40) DEFAULT NULL,
`library_version` varchar(40) NOT NULL, `library_version` varchar(40) NOT NULL,
`annot_date` timestamp NOT NULL DEFAULT current_timestamp(), `annot_date` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
`reason` mediumtext DEFAULT NULL, `reason` mediumtext,
PRIMARY KEY (`seq_member_stable_id`), PRIMARY KEY (`seq_member_stable_id`),
KEY `model_id` (`model_id`) KEY `model_id` (`model_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -360,16 +360,16 @@ CREATE TABLE `hmm_profile` ( ...@@ -360,16 +360,16 @@ CREATE TABLE `hmm_profile` (
`model_id` varchar(40) NOT NULL, `model_id` varchar(40) NOT NULL,
`name` varchar(40) DEFAULT NULL, `name` varchar(40) DEFAULT NULL,
`type` varchar(40) NOT NULL, `type` varchar(40) NOT NULL,
`compressed_profile` mediumblob DEFAULT NULL, `compressed_profile` mediumblob,
`consensus` mediumtext DEFAULT NULL, `consensus` mediumtext,
PRIMARY KEY (`model_id`,`type`) PRIMARY KEY (`model_id`,`type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `homology` ( CREATE TABLE `homology` (
`homology_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `homology_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`method_link_species_set_id` int(10) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL,
`description` enum('ortholog_one2one','ortholog_one2many','ortholog_many2many','within_species_paralog','other_paralog','gene_split','between_species_paralog','alt_allele','homoeolog_one2one','homoeolog_one2many','homoeolog_many2many') NOT NULL, `description` enum('ortholog_one2one','ortholog_one2many','ortholog_many2many','within_species_paralog','other_paralog','gene_split','between_species_paralog','alt_allele','homoeolog_one2one','homoeolog_one2many','homoeolog_many2many') NOT NULL,
`is_tree_compliant` tinyint(1) NOT NULL DEFAULT 0, `is_tree_compliant` tinyint(1) NOT NULL DEFAULT '0',
`dn` float(10,5) DEFAULT NULL, `dn` float(10,5) DEFAULT NULL,
`ds` float(10,5) DEFAULT NULL, `ds` float(10,5) DEFAULT NULL,
`n` float(10,1) DEFAULT NULL, `n` float(10,1) DEFAULT NULL,
...@@ -389,13 +389,13 @@ CREATE TABLE `homology` ( ...@@ -389,13 +389,13 @@ CREATE TABLE `homology` (
) ENGINE=MyISAM AUTO_INCREMENT=100990070 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=100990070 DEFAULT CHARSET=latin1;
CREATE TABLE `homology_member` ( CREATE TABLE `homology_member` (
`homology_id` int(10) unsigned NOT NULL, `homology_id` bigint(20) unsigned NOT NULL,
`gene_member_id` int(10) unsigned NOT NULL, `gene_member_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned DEFAULT NULL, `seq_member_id` int(10) unsigned DEFAULT NULL,
`cigar_line` mediumtext DEFAULT NULL, `cigar_line` mediumtext,
`perc_cov` float unsigned DEFAULT 0, `perc_cov` float unsigned DEFAULT '0',
`perc_id` float unsigned DEFAULT 0, `perc_id` float unsigned DEFAULT '0',
`perc_pos` float unsigned DEFAULT 0, `perc_pos` float unsigned DEFAULT '0',
PRIMARY KEY (`homology_id`,`gene_member_id`), PRIMARY KEY (`homology_id`,`gene_member_id`),
KEY `gene_member_id` (`gene_member_id`), KEY `gene_member_id` (`gene_member_id`),
KEY `seq_member_id` (`seq_member_id`) KEY `seq_member_id` (`seq_member_id`)
...@@ -404,7 +404,7 @@ CREATE TABLE `homology_member` ( ...@@ -404,7 +404,7 @@ CREATE TABLE `homology_member` (
CREATE TABLE `mapping_session` ( CREATE TABLE `mapping_session` (
`mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `mapping_session_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`type` enum('family','tree','hmm') DEFAULT NULL, `type` enum('family','tree','hmm') DEFAULT NULL,
`when_mapped` timestamp NOT NULL DEFAULT current_timestamp(), `when_mapped` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
`rel_from` int(10) unsigned DEFAULT NULL, `rel_from` int(10) unsigned DEFAULT NULL,
`rel_to` int(10) unsigned DEFAULT NULL, `rel_to` int(10) unsigned DEFAULT NULL,
`prefix` char(4) NOT NULL, `prefix` char(4) NOT NULL,
...@@ -422,13 +422,13 @@ CREATE TABLE `member_xref` ( ...@@ -422,13 +422,13 @@ CREATE TABLE `member_xref` (
CREATE TABLE `meta` ( CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT, `meta_id` int(11) NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT 1, `species_id` int(10) unsigned DEFAULT '1',
`meta_key` varchar(40) NOT NULL, `meta_key` varchar(40) NOT NULL,
`meta_value` text NOT NULL, `meta_value` text NOT NULL,
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`meta_value`(255)) KEY `species_value_idx` (`species_id`,`meta_value`(255))
) ENGINE=MyISAM AUTO_INCREMENT=71 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=78 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` ( CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
...@@ -455,7 +455,6 @@ CREATE TABLE `method_link_species_set` ( ...@@ -455,7 +455,6 @@ CREATE TABLE `method_link_species_set` (
CREATE TABLE `method_link_species_set_attr` ( CREATE TABLE `method_link_species_set_attr` (
`method_link_species_set_id` int(10) unsigned NOT NULL, `method_link_species_set_id` int(10) unsigned NOT NULL,
`n_goc_null` int(11) DEFAULT NULL,
`n_goc_0` int(11) DEFAULT NULL, `n_goc_0` int(11) DEFAULT NULL,
`n_goc_25` int(11) DEFAULT NULL, `n_goc_25` int(11) DEFAULT NULL,
`n_goc_50` int(11) DEFAULT NULL, `n_goc_50` int(11) DEFAULT NULL,
...@@ -490,10 +489,10 @@ CREATE TABLE `ncbi_taxa_node` ( ...@@ -490,10 +489,10 @@ CREATE TABLE `ncbi_taxa_node` (
`taxon_id` int(10) unsigned NOT NULL, `taxon_id` int(10) unsigned NOT NULL,
`parent_id` int(10) unsigned NOT NULL, `parent_id` int(10) unsigned NOT NULL,
`rank` char(32) NOT NULL DEFAULT '', `rank` char(32) NOT NULL DEFAULT '',
`genbank_hidden_flag` tinyint(1) NOT NULL DEFAULT 0, `genbank_hidden_flag` tinyint(1) NOT NULL DEFAULT '0',
`left_index` int(10) NOT NULL DEFAULT 0, `left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT '0',
`root_id` int(10) NOT NULL DEFAULT 1, `root_id` int(10) NOT NULL DEFAULT '1',
PRIMARY KEY (`taxon_id`), PRIMARY KEY (`taxon_id`),
KEY `parent_id` (`parent_id`), KEY `parent_id` (`parent_id`),
KEY `rank` (`rank`), KEY `rank` (`rank`),
...@@ -515,11 +514,11 @@ CREATE TABLE `peptide_align_feature` ( ...@@ -515,11 +514,11 @@ CREATE TABLE `peptide_align_feature` (
`hmember_id` int(10) unsigned NOT NULL, `hmember_id` int(10) unsigned NOT NULL,
`qgenome_db_id` int(10) unsigned DEFAULT NULL, `qgenome_db_id` int(10) unsigned DEFAULT NULL,
`hgenome_db_id` int(10) unsigned DEFAULT NULL, `hgenome_db_id` int(10) unsigned DEFAULT NULL,
`qstart` int(10) NOT NULL DEFAULT 0, `qstart` int(10) NOT NULL DEFAULT '0',
`qend` int(10) NOT NULL DEFAULT 0, `qend` int(10) NOT NULL DEFAULT '0',
`hstart` int(11) NOT NULL DEFAULT 0, `hstart` int(10) unsigned NOT NULL DEFAULT '0',
`hend` int(11) NOT NULL DEFAULT 0, `hend` int(10) unsigned NOT NULL DEFAULT '0',
`score` double(16,4) NOT NULL DEFAULT 0.0000, `score` double(16,4) NOT NULL DEFAULT '0.0000',
`evalue` double NOT NULL, `evalue` double NOT NULL,
`align_length` int(10) NOT NULL, `align_length` int(10) NOT NULL,
`identical_matches` int(10) NOT NULL, `identical_matches` int(10) NOT NULL,
...@@ -527,22 +526,22 @@ CREATE TABLE `peptide_align_feature` ( ...@@ -527,22 +526,22 @@ CREATE TABLE `peptide_align_feature` (
`positive_matches` int(10) NOT NULL, `positive_matches` int(10) NOT NULL,
`perc_pos` int(10) NOT NULL, `perc_pos` int(10) NOT NULL,
`hit_rank` int(10) NOT NULL, `hit_rank` int(10) NOT NULL,
`cigar_line` mediumtext DEFAULT NULL, `cigar_line` mediumtext,
PRIMARY KEY (`peptide_align_feature_id`) PRIMARY KEY (`peptide_align_feature_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=133; ) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=133;
CREATE TABLE `seq_member` ( CREATE TABLE `seq_member` (
`seq_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `seq_member_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`stable_id` varchar(128) NOT NULL, `stable_id` varchar(128) NOT NULL,
`version` int(10) DEFAULT 0, `version` int(10) DEFAULT '0',
`source_name` enum('ENSEMBLPEP','ENSEMBLTRANS','Uniprot/SPTREMBL','Uniprot/SWISSPROT','EXTERNALPEP','EXTERNALTRANS','EXTERNALCDS') NOT NULL, `source_name` enum('ENSEMBLPEP','ENSEMBLTRANS','Uniprot/SPTREMBL','Uniprot/SWISSPROT','EXTERNALPEP','EXTERNALTRANS','EXTERNALCDS') NOT NULL,
`taxon_id` int(10) unsigned NOT NULL, `taxon_id` int(10) unsigned NOT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL, `genome_db_id` int(10) unsigned DEFAULT NULL,
`sequence_id` int(10) unsigned DEFAULT NULL, `sequence_id` int(10) unsigned DEFAULT NULL,
`gene_member_id` int(10) unsigned DEFAULT NULL, `gene_member_id` int(10) unsigned DEFAULT NULL,
`has_transcript_edits` tinyint(1) NOT NULL DEFAULT 0, `has_transcript_edits` tinyint(1) NOT NULL DEFAULT '0',
`has_translation_edits` tinyint(1) NOT NULL DEFAULT 0, `has_translation_edits` tinyint(1) NOT NULL DEFAULT '0',
`description` text DEFAULT NULL, `description` text,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL, `dnafrag_id` bigint(20) unsigned DEFAULT NULL,
`dnafrag_start` int(10) DEFAULT NULL, `dnafrag_start` int(10) DEFAULT NULL,
`dnafrag_end` int(10) DEFAULT NULL, `dnafrag_end` int(10) DEFAULT NULL,
...@@ -612,9 +611,9 @@ CREATE TABLE `species_tree_node` ( ...@@ -612,9 +611,9 @@ CREATE TABLE `species_tree_node` (
`node_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `node_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` int(10) unsigned DEFAULT NULL, `parent_id` int(10) unsigned DEFAULT NULL,
`root_id` int(10) unsigned DEFAULT NULL, `root_id` int(10) unsigned DEFAULT NULL,
`left_index` int(10) NOT NULL DEFAULT 0, `left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT 0, `right_index` int(10) NOT NULL DEFAULT '0',
`distance_to_parent` double DEFAULT 1, `distance_to_parent` double DEFAULT '1',
`taxon_id` int(10) unsigned DEFAULT NULL, `taxon_id` int(10) unsigned DEFAULT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL, `genome_db_id` int(10) unsigned DEFAULT NULL,
`node_name` varchar(255) DEFAULT NULL, `node_name` varchar(255) DEFAULT NULL,
......
1 \N schema_type core 1 \N schema_type core
2 \N schema_version 100 2 \N schema_version 101
3 \N patch patch_65_66_a.sql|schema_version 3 \N patch patch_65_66_a.sql|schema_version
4 \N patch patch_65_66_b.sql|fix_external_db_id 4 \N patch patch_65_66_b.sql|fix_external_db_id
5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index 5 \N patch patch_65_66_c.sql|reorder_unmapped_obj_index
...@@ -192,3 +192,5 @@ ...@@ -192,3 +192,5 @@
1704 \N patch patch_98_99_a.sql|schema_version 1704 \N patch patch_98_99_a.sql|schema_version
1705 \N patch patch_99_100_a.sql|schema_version 1705 \N patch patch_99_100_a.sql|schema_version
1706 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull 1706 \N patch patch_99_100_b.sql|alter_externaldb_type_notnull
1707 \N patch patch_99_100_c.sql|alter_mapping_session_assembly_length
1708 \N patch patch_100_101_a.sql|schema_version
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