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Commit 43251e25 authored by Tiago Grego's avatar Tiago Grego
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patched core test schema to version 97

parent f2339548
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Showing with 51 additions and 11 deletions
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @ 43251e25
1 \N schema_version 95
1 \N schema_version 97
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
......@@ -102,3 +102,6 @@
169 \N patch patch_93_94_c.sql|default_aln_type
170 \N patch patch_94_95_a.sql|schema_version
171 \N patch patch_94_95_b.sql|vertebrate_division_rename
172 \N patch patch_95_96_a.sql|schema_version
173 \N patch patch_96_97_a.sql|schema_version
174 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @ 43251e25
......@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM AUTO_INCREMENT=66 DEFAULT CHARSET=latin1;
......@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=172 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=175 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @ 43251e25
1 \N schema_version 95
1 \N schema_version 97
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
......@@ -102,3 +102,6 @@
151 \N patch patch_93_94_c.sql|default_aln_type
152 \N patch patch_94_95_a.sql|schema_version
153 \N patch patch_94_95_b.sql|vertebrate_division_rename
154 \N patch patch_95_96_a.sql|schema_version
155 \N patch patch_96_97_a.sql|schema_version
156 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @ 43251e25
......@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=154 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=157 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @ 43251e25
1 \N schema_version 95
1 \N schema_version 97
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
......@@ -107,3 +107,6 @@
2114 \N patch patch_93_94_c.sql|default_aln_type
2115 \N patch patch_94_95_a.sql|schema_version
2116 \N patch patch_94_95_b.sql|vertebrate_division_rename
2117 \N patch patch_95_96_a.sql|schema_version
2118 \N patch patch_96_97_a.sql|schema_version
2119 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @ 43251e25
......@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description` text,
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group') DEFAULT NULL,
`so_acc` varchar(64) DEFAULT NULL,
`so_term` varchar(1023) DEFAULT NULL,
PRIMARY KEY (`biotype_id`),
UNIQUE KEY `name_type_idx` (`name`,`object_type`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
......@@ -489,7 +490,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=2117 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=2120 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt
View file @ 43251e25
......@@ -17,3 +17,5 @@
18 Supporting evidence can not be re-mapped to the current assembly
19 Variant maps to more than one genomic location
20 Variant at first base in sequence
21 Reference allele does not match the bases at this genome location
22 Alleles cannot be resolved
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
View file @ 43251e25
1 \N schema_type variation
2 \N schema_version 93
2 \N schema_version 96
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
......@@ -31,3 +31,11 @@
31 \N patch patch_92_93_a.sql|schema version
32 \N patch patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
33 \N patch patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
34 \N patch patch_93_94_a.sql|schema version
35 \N patch patch_94_95_a.sql|schema version
36 \N patch patch_94_95_b.sql|create table to store allele synonyms
37 \N patch patch_95_96_a.sql|schema version
38 \N patch patch_95_96_b.sql|modify index on variation_synonym
39 \N patch patch_95_96_c.sql|add new entries to the failed_description table
40 \N patch patch_95_96_d.sql|create table to store failed variation features
41 \N patch patch_95_96_e.sql|Rename motif_name to binding_matrix_stable_id.
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
View file @ 43251e25
......@@ -20,6 +20,16 @@ CREATE TABLE `allele_code` (
UNIQUE KEY `allele_idx` (`allele`(1000))
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `allele_synonym` (
`allele_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`variation_id` int(10) unsigned NOT NULL,
`hgvs_genomic` varchar(600) NOT NULL,
`name` varchar(255) NOT NULL,
PRIMARY KEY (`allele_synonym_id`),
UNIQUE KEY `variation_name_idx` (`variation_id`,`name`),
KEY `name_idx` (`name`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `associate_study` (
`study1_id` int(10) unsigned NOT NULL,
`study2_id` int(10) unsigned NOT NULL,
......@@ -103,7 +113,7 @@ CREATE TABLE `failed_description` (
`failed_description_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`description` text NOT NULL,
PRIMARY KEY (`failed_description_id`)
) ENGINE=MyISAM AUTO_INCREMENT=21 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=23 DEFAULT CHARSET=latin1;
CREATE TABLE `failed_structural_variation` (
`failed_structural_variation_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -121,6 +131,14 @@ CREATE TABLE `failed_variation` (
UNIQUE KEY `variation_idx` (`variation_id`,`failed_description_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `failed_variation_feature` (
`failed_variation_feature_id` int(11) NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(10) unsigned NOT NULL,
`failed_description_id` int(10) unsigned NOT NULL,
PRIMARY KEY (`failed_variation_feature_id`),
UNIQUE KEY `variation_feature_idx` (`variation_feature_id`,`failed_description_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `genotype_code` (
`genotype_code_id` int(11) unsigned NOT NULL,
`allele_code_id` int(11) unsigned NOT NULL,
......@@ -168,7 +186,7 @@ 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=34 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -185,7 +203,7 @@ CREATE TABLE `motif_feature_variation` (
`allele_string` text,
`somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
`motif_name` varchar(60) DEFAULT NULL,
`binding_matrix_stable_id` varchar(60) DEFAULT NULL,
`motif_start` int(11) unsigned DEFAULT NULL,
`motif_end` int(11) unsigned DEFAULT NULL,
`motif_score_delta` float DEFAULT NULL,
......@@ -665,7 +683,7 @@ CREATE TABLE `variation_synonym` (
`source_id` int(10) unsigned NOT NULL,
`name` varchar(255) DEFAULT NULL,
PRIMARY KEY (`variation_synonym_id`),
UNIQUE KEY `name` (`name`,`source_id`),
UNIQUE KEY `name_idx` (`name`,`source_id`,`variation_id`),
KEY `variation_idx` (`variation_id`),
KEY `subsnp_idx` (`subsnp_id`),
KEY `source_idx` (`source_id`)
......
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