Commit 3c4b3878 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

patch for release 85

parent a79c5469
......@@ -39,7 +39,7 @@
95 \N patch patch_83_84_c.sql|protein_feature_unique
96 \N patch patch_83_84_d.sql|longer_synonym
1 \N schema_type core
2 \N schema_version 84
2 \N schema_version 85
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
......@@ -95,3 +95,5 @@
31 1 species.url Bacillus_thuringiensis
55 1 transcriptbuild.level toplevel
97 \N patch patch_83_84_e.sql|nullable_versions
98 \N patch patch_84_85_a.sql|schema_version
99 \N patch patch_84_85_b.sql|remove_duplicated_key
......@@ -190,7 +190,7 @@ CREATE TABLE `ditag_feature` (
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
KEY `ditag_pair_id` (`ditag_pair_id`),
KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
......@@ -285,7 +285,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
`status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
......@@ -334,8 +334,7 @@ CREATE TABLE `genome_statistics` (
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (`genome_statistics_id`),
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
......@@ -468,7 +467,7 @@ 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=98 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=100 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -522,8 +521,8 @@ CREATE TABLE `object_xref` (
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
PRIMARY KEY (`object_xref_id`),
UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......@@ -775,7 +774,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
......@@ -858,9 +857,9 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
KEY `id_idx` (`identifier`(50)),
KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`),
KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......
1 \N schema_version 84
1 \N schema_version 85
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
......@@ -74,3 +74,5 @@
134 \N patch patch_83_84_c.sql|protein_feature_unique
135 \N patch patch_83_84_d.sql|longer_synonym
136 \N patch patch_83_84_e.sql|nullable_versions
137 \N patch patch_84_85_a.sql|schema_version
138 \N patch patch_84_85_b.sql|remove_duplicated_key
......@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
PRIMARY KEY (`alt_allele_id`),
UNIQUE KEY `gene_idx` (`gene_id`),
KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
CREATE TABLE `alt_allele_attrib` (
`alt_allele_id` int(10) unsigned DEFAULT NULL,
......@@ -16,7 +16,7 @@ CREATE TABLE `alt_allele_attrib` (
CREATE TABLE `alt_allele_group` (
`alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`alt_allele_group_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
CREATE TABLE `analysis` (
`analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -35,7 +35,7 @@ CREATE TABLE `analysis` (
`gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
UNIQUE KEY `logic_name_idx` (`logic_name`)
) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=8409 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -72,7 +72,7 @@ CREATE TABLE `assembly_exception` (
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -116,7 +116,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -143,7 +143,7 @@ CREATE TABLE `density_feature` (
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -153,7 +153,7 @@ CREATE TABLE `density_type` (
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
......@@ -171,7 +171,7 @@ CREATE TABLE `ditag` (
`tag_count` smallint(6) DEFAULT '1',
`sequence` text,
PRIMARY KEY (`ditag_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=3278357 DEFAULT CHARSET=latin1;
CREATE TABLE `ditag_feature` (
`ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -190,8 +190,8 @@ CREATE TABLE `ditag_feature` (
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
KEY `ditag_pair_id` (`ditag_pair_id`),
KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
) ENGINE=MyISAM AUTO_INCREMENT=4828763 DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -223,7 +223,7 @@ CREATE TABLE `dna_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
) ENGINE=MyISAM AUTO_INCREMENT=29797140 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `exon` (
`exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=162036 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
`exon_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -285,7 +285,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
`status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
......@@ -299,7 +299,7 @@ CREATE TABLE `gene` (
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`),
KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=18277 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -334,8 +334,7 @@ CREATE TABLE `genome_statistics` (
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (`genome_statistics_id`),
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
......@@ -384,13 +383,13 @@ CREATE TABLE `karyotype` (
`stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`karyotype_id`),
KEY `region_band_idx` (`seq_region_id`,`band`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `map` (
`map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
PRIMARY KEY (`map_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_session` (
`mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -402,7 +401,7 @@ CREATE TABLE `mapping_session` (
`new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
`created` datetime NOT NULL,
PRIMARY KEY (`mapping_session_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `mapping_set` (
`mapping_set_id` int(10) unsigned NOT NULL,
......@@ -424,7 +423,7 @@ CREATE TABLE `marker` (
PRIMARY KEY (`marker_id`),
KEY `marker_idx` (`marker_id`,`priority`),
KEY `display_idx` (`display_marker_synonym_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_feature` (
`marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -437,7 +436,7 @@ CREATE TABLE `marker_feature` (
PRIMARY KEY (`marker_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `marker_map_location` (
`marker_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -458,7 +457,7 @@ CREATE TABLE `marker_synonym` (
PRIMARY KEY (`marker_synonym_id`),
KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
KEY `marker_idx` (`marker_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `meta` (
`meta_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -468,7 +467,7 @@ 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=98 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -495,7 +494,7 @@ CREATE TABLE `misc_feature` (
`seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `misc_feature_misc_set` (
`misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -512,7 +511,7 @@ CREATE TABLE `misc_set` (
`max_length` int(10) unsigned NOT NULL DEFAULT '0',
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -522,10 +521,10 @@ CREATE TABLE `object_xref` (
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
PRIMARY KEY (`object_xref_id`),
UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=253685 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -552,7 +551,7 @@ CREATE TABLE `operon` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `name_idx` (`display_label`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript` (
`operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -571,7 +570,7 @@ CREATE TABLE `operon_transcript` (
KEY `operon_idx` (`operon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `operon_transcript_gene` (
`operon_transcript_id` int(10) unsigned DEFAULT NULL,
......@@ -585,7 +584,7 @@ CREATE TABLE `peptide_archive` (
`peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
PRIMARY KEY (`peptide_archive_id`),
KEY `checksum` (`md5_checksum`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_exon` (
`prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -601,7 +600,7 @@ CREATE TABLE `prediction_exon` (
PRIMARY KEY (`prediction_exon_id`),
KEY `prediction_transcript_id` (`prediction_transcript_id`),
KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=192 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `prediction_transcript` (
`prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -614,7 +613,7 @@ CREATE TABLE `prediction_transcript` (
PRIMARY KEY (`prediction_transcript_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=18084 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `protein_align_feature` (
`protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -638,7 +637,7 @@ CREATE TABLE `protein_align_feature` (
KEY `hit_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`),
KEY `external_db_idx` (`external_db_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
) ENGINE=MyISAM AUTO_INCREMENT=11554505 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `protein_feature` (
`protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -659,7 +658,7 @@ CREATE TABLE `protein_feature` (
KEY `translation_idx` (`translation_id`),
KEY `hitname_idx` (`hit_name`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=242847 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -672,7 +671,7 @@ CREATE TABLE `repeat_consensus` (
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=1018 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -689,7 +688,7 @@ CREATE TABLE `repeat_feature` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
) ENGINE=MyISAM AUTO_INCREMENT=922515 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -699,7 +698,7 @@ CREATE TABLE `seq_region` (
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -726,7 +725,7 @@ CREATE TABLE `seq_region_synonym` (
PRIMARY KEY (`seq_region_synonym_id`),
UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
KEY `seq_region_idx` (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -741,7 +740,7 @@ CREATE TABLE `simple_feature` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `analysis_idx` (`analysis_id`),
KEY `hit_idx` (`display_label`)
) ENGINE=MyISAM AUTO_INCREMENT=37 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `stable_id_event` (
`old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
......@@ -775,7 +774,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
......@@ -790,7 +789,7 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=21742 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -833,7 +832,7 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=21742 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -858,18 +857,18 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),
KEY `id_idx` (`identifier`(50)),
KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
KEY `ext_db_identifier_idx` (`external_db_id`,`identifier`),
KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `unmapped_reason` (
`unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -884,5 +883,5 @@ CREATE TABLE `xref` (
UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
KEY `display_index` (`display_label`),
KEY `info_type_idx` (`info_type`)
) ENGINE=MyISAM AUTO_INCREMENT=91703 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=1000000 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
1 \N schema_version 84
1 \N schema_version 85
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
......@@ -74,3 +74,5 @@
123 \N patch patch_83_84_c.sql|protein_feature_unique
124 \N patch patch_83_84_d.sql|longer_synonym
125 \N patch patch_83_84_e.sql|nullable_versions
126 \N patch patch_84_85_a.sql|schema_version
127 \N patch patch_84_85_b.sql|remove_duplicated_key
......@@ -35,7 +35,7 @@ CREATE TABLE `analysis` (
`gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`analysis_id`),
UNIQUE KEY `logic_name_idx` (`logic_name`)
) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -72,7 +72,7 @@ CREATE TABLE `assembly_exception` (
PRIMARY KEY (`assembly_exception_id`),
KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -116,7 +116,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -190,7 +190,7 @@ CREATE TABLE `ditag_feature` (
PRIMARY KEY (`ditag_feature_id`),
KEY `ditag_id` (`ditag_id`),
KEY `ditag_pair_id` (`ditag_pair_id`),
KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dna` (
......@@ -285,7 +285,7 @@ CREATE TABLE `gene` (
`seq_region_strand` tinyint(2) NOT NULL,
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL,
`status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_transcript_id` int(10) unsigned NOT NULL,
......@@ -334,8 +334,7 @@ CREATE TABLE `genome_statistics` (
`attrib_type_id` int(10) unsigned DEFAULT NULL,
`timestamp` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
PRIMARY KEY (`genome_statistics_id`),
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
......@@ -468,7 +467,7 @@ 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=98 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=128 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -522,8 +521,8 @@ CREATE TABLE `object_xref` (
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned NOT NULL,
PRIMARY KEY (`object_xref_id`),
UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
UNIQUE KEY `xref_idx` (`xref_id`,`ensembl_object_type`,`ensembl_id`,`analysis_id`),
KEY `ensembl_idx` (`ensembl_object_type`,`ensembl_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
......@@ -699,7 +698,7 @@ CREATE TABLE `seq_region` (
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -726,7 +725,7 @@ CREATE TABLE `seq_region_synonym` (
PRIMARY KEY (`seq_region_synonym_id`),
UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
KEY `seq_region_idx` (`seq_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
CREATE TABLE `simple_feature` (
`simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -775,7 +774,7 @@ CREATE TABLE `transcript` (
`display_xref_id` int(10) unsigned DEFAULT NULL,
`source` varchar(40) NOT NULL DEFAULT 'ensembl',
`biotype` varchar(40) NOT NULL,
`status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
`status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN','ANNOTATED') DEFAULT NULL,
`description` text,
`is_current` tinyint(1) NOT NULL DEFAULT '1',
`canonical_translation_id` int(10) unsigned DEFAULT NULL,
......@@ -858,9 +857,9 @@ CREATE TABLE `unmapped_object` (
`ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
`parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
PRIMARY KEY (`unmapped_object_id`),
UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`,`ensembl_object_type`,`identifier`,`unmapped_reason_id`,`parent`,`external_db_id`),