diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index 00ce8bde9bb03bff391db01aee85f6f439d6e714..096dda511139b42299cbc117c63eaecb8fd5d2e7 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -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
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..81def2134aea4bc36091193716cb813ef5946917 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -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;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 46c541821a5f1e1a41b9ad75baeb4491e67cdbd4..f212829508d3e57c0373ec4f183add82a3dc5fb4 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -1,4 +1,4 @@
-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
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..56b9a4545e81d0251e3d96eb7f37ecf9053c3ac3 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -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;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 10e58422b2bd58add1324082289242d7061c864c..05d29613febd0682a2f0680a6b487e425b2618e8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -1,4 +1,4 @@
-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
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..c5bb959fb33f4229ad4843192a90d95c05285f97 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -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`),
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;
@@ -869,7 +868,7 @@ CREATE TABLE `unmapped_reason` (
`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,
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
index ff7d5c3720256a76c7e3c65119a2328899eb3c19..a985cea4a247c432b1ecabcbb08ed3b2d4dfc908 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
@@ -1,4 +1,4 @@
-1 \N schema_version 84
+1 \N schema_version 85
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
@@ -79,3 +79,5 @@
2086 \N patch patch_83_84_c.sql|protein_feature_unique
2087 \N patch patch_83_84_d.sql|longer_synonym
2088 \N patch patch_83_84_e.sql|nullable_versions
+2089 \N patch patch_84_85_a.sql|schema_version
+2090 \N patch patch_84_85_b.sql|remove_duplicated_key
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..c1cc8e202e0bda8c2f20963ed518bc240168ca0b 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -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=11 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=5213 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=8449 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=155 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `associated_group` (
`associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -103,7 +103,7 @@ CREATE TABLE `attrib_type` (
`description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=405 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_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=1004 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=16758826 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=110 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=1366612 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=1221449 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=29387404 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=7296966 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=633706 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -334,9 +334,8 @@ 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`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=71 DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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=852 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=13 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=394 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=27 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=27 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=716771 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=2091 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=93001 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=19 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=17375428 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `ontology_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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=250655 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=394607 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=54799 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=19573639 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=7821872 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=595635 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=31576665 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=1001161224 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=177 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=968471 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=2047756 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=1044748 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=12401901 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=139 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=7795492 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
diff --git a/modules/t/test-genome-DBs/mapping/core/meta.txt b/modules/t/test-genome-DBs/mapping/core/meta.txt
index bf9db054d2ffc5b19401ceab22392e3983adc6c7..a9cd008f1e6eaae6097525db9e6944db4cfc34d5 100644
--- a/modules/t/test-genome-DBs/mapping/core/meta.txt
+++ b/modules/t/test-genome-DBs/mapping/core/meta.txt
@@ -1,4 +1,4 @@
-1 \N schema_version 84
+1 \N schema_version 85
2 1 assembly.default MULTIMAP
3 1 species.taxonomy_id 1
4 1 assembly.mapping chromosome:MULTIMAP#contig
@@ -35,3 +35,5 @@
128 \N patch patch_83_84_c.sql|protein_feature_unique
129 \N patch patch_83_84_d.sql|longer_synonym
130 \N patch patch_83_84_e.sql|nullable_versions
+131 \N patch patch_84_85_a.sql|schema_version
+132 \N patch patch_84_85_b.sql|remove_duplicated_key
diff --git a/modules/t/test-genome-DBs/mapping/core/table.sql b/modules/t/test-genome-DBs/mapping/core/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..9d726286678d89d780a1c53bc3d5eee818c635e0 100644
--- a/modules/t/test-genome-DBs/mapping/core/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/table.sql
@@ -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=133 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;
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
index 0c78bd9131f06a5866fe84594e25c512e16cfb77..00ddfe208770d156787da2e7a9bbe537e6adef61 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
@@ -1,5 +1,5 @@
1 \N schema_type core
-2 \N schema_version 84
+2 \N schema_version 85
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
@@ -152,3 +152,5 @@
1664 \N patch patch_83_84_c.sql|protein_feature_unique
1665 \N patch patch_83_84_d.sql|longer_synonym
1666 \N patch patch_83_84_e.sql|nullable_versions
+1667 \N patch patch_84_85_a.sql|schema_version
+1668 \N patch patch_84_85_b.sql|remove_duplicated_key
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..379b3cc0916730e867709300c3b727c7a13aa238 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
@@ -103,7 +103,7 @@ CREATE TABLE `attrib_type` (
`description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=508 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_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=112 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=1669 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=20603 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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;
@@ -869,7 +868,7 @@ CREATE TABLE `unmapped_reason` (
`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=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
diff --git a/modules/t/test-genome-DBs/nameless/core/meta.txt b/modules/t/test-genome-DBs/nameless/core/meta.txt
index 1c9d944bb6b180fa13bea6167abb27a5b5926b99..be15c0a7cb2b25a774526950e7f9a040f75dfd64 100644
--- a/modules/t/test-genome-DBs/nameless/core/meta.txt
+++ b/modules/t/test-genome-DBs/nameless/core/meta.txt
@@ -1,4 +1,4 @@
-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
@@ -73,3 +73,5 @@
127 \N patch patch_83_84_c.sql|protein_feature_unique
128 \N patch patch_83_84_d.sql|longer_synonym
129 \N patch patch_83_84_e.sql|nullable_versions
+130 \N patch patch_84_85_a.sql|schema_version
+131 \N patch patch_84_85_b.sql|remove_duplicated_key
diff --git a/modules/t/test-genome-DBs/nameless/core/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..fac36ecdc1484ba14f521f969ea6a2182fe13049 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -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=132 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;
diff --git a/modules/t/test-genome-DBs/polyploidy/core/meta.txt b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
index 5877a7bd3a84a62a6414b241c6ed928726972432..745c6e6bb54df0a5f9b7067adc2e4c007c95c101 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/meta.txt
+++ b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
@@ -1,5 +1,5 @@
1 \N schema_type core
-2 \N schema_version 84
+2 \N schema_version 85
3 \N patch patch_68_69_a.sql|schema_version
4 1 species.taxonomy_id 4565
6 1 species.alias bread wheat
@@ -128,3 +128,5 @@
208 \N patch patch_83_84_c.sql|protein_feature_unique
209 \N patch patch_83_84_d.sql|longer_synonym
210 \N patch patch_83_84_e.sql|nullable_versions
+211 \N patch patch_84_85_a.sql|schema_version
+212 \N patch patch_84_85_b.sql|remove_duplicated_key
diff --git a/modules/t/test-genome-DBs/polyploidy/core/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..8236ec09cd8af033f491a43b478a4a94dcbe78cd 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/table.sql
@@ -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=201 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `analysis_description` (
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -103,7 +103,7 @@ CREATE TABLE `attrib_type` (
`description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=437 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_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=11 DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned 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=23 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
@@ -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` (
@@ -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=382467 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=40234 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -334,9 +334,8 @@ 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`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+ UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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=213 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -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=24 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -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;
@@ -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=3502933 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=1163919 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=10446798 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=3495795 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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=124988 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=124988 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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;
@@ -869,7 +868,7 @@ CREATE TABLE `unmapped_reason` (
`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=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
diff --git a/modules/t/test-genome-DBs/test_collection/core/meta.txt b/modules/t/test-genome-DBs/test_collection/core/meta.txt
index f6fbef56a121fe7553b8dfff62bb826522da94da..cd6ca91efccfb2f13ee4e83701ce990ee850e61c 100644
--- a/modules/t/test-genome-DBs/test_collection/core/meta.txt
+++ b/modules/t/test-genome-DBs/test_collection/core/meta.txt
@@ -39,7 +39,7 @@
190 \N patch patch_83_84_c.sql|protein_feature_unique
191 \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
@@ -148,3 +148,5 @@
131 2 species.url Bacillus_thuringiensis_hd_790
155 2 transcriptbuild.level toplevel
192 \N patch patch_83_84_e.sql|nullable_versions
+193 \N patch patch_84_85_a.sql|schema_version
+194 \N patch patch_84_85_b.sql|remove_duplicated_key
diff --git a/modules/t/test-genome-DBs/test_collection/core/table.sql b/modules/t/test-genome-DBs/test_collection/core/table.sql
index edab34555c34887837fa6702d3977f55e9d467ec..0e62c409e9bc594ceaec45323dc41c70876e2750 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -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=195 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;