Commit aeeb6039 authored by Marek Szuba's avatar Marek Szuba Committed by Shamika Mohanan
Browse files

Patch test databases for release 97, part 2

The previous test-database update missed some patches for the core and
variation schemas, which is why Travis jobs keep failing these days.
parent d20e7be0
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 15:00:15 2019 -- Created on Tue Apr 2 16:03:53 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code"); ...@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code");
CREATE TABLE "object_xref" ( CREATE TABLE "object_xref" (
"object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, "object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"ensembl_id" integer NOT NULL DEFAULT 0, "ensembl_id" integer NOT NULL DEFAULT 0,
"ensembl_object_type" enum NOT NULL DEFAULT 'RawContig', "ensembl_object_type" enum NOT NULL,
"xref_id" integer NOT NULL, "xref_id" integer NOT NULL,
"linkage_annotation" varchar(255), "linkage_annotation" varchar(255),
"analysis_id" smallint "analysis_id" smallint
...@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" ( ...@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" (
"score" double precision "score" double precision
); );
--
-- Table: "rnaproduct"
--
CREATE TABLE "rnaproduct" (
"rnaproduct_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"rnaproduct_type_id" smallint NOT NULL,
"transcript_id" integer NOT NULL,
"seq_start" integer NOT NULL,
"start_exon_id" integer,
"seq_end" integer NOT NULL,
"end_exon_id" integer,
"stable_id" varchar(128),
"version" smallint,
"created_date" datetime,
"modified_date" datetime
);
--
-- Table: "rnaproduct_attrib"
--
CREATE TABLE "rnaproduct_attrib" (
"rnaproduct_id" integer NOT NULL DEFAULT 0,
"attrib_type_id" smallint NOT NULL DEFAULT 0,
"value" text NOT NULL
);
CREATE UNIQUE INDEX "rnaproduct_attribx" ON "rnaproduct_attrib" ("rnaproduct_id", "attrib_type_id", "value");
--
-- Table: "rnaproduct_type"
--
CREATE TABLE "rnaproduct_type" (
"rnaproduct_type_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"code" varchar(20) NOT NULL DEFAULT '',
"name" varchar(255) NOT NULL DEFAULT '',
"description" text
);
CREATE UNIQUE INDEX "code_idx03" ON "rnaproduct_type" ("code");
-- --
-- Table: "seq_region" -- Table: "seq_region"
-- --
...@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" ( ...@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" (
"new_stable_id" varchar(128), "new_stable_id" varchar(128),
"new_version" smallint, "new_version" smallint,
"mapping_session_id" integer NOT NULL DEFAULT 0, "mapping_session_id" integer NOT NULL DEFAULT 0,
"type" enum NOT NULL DEFAULT 'gene', "type" enum NOT NULL,
"score" float NOT NULL DEFAULT 0 "score" float NOT NULL DEFAULT 0
); );
......
...@@ -128,3 +128,6 @@ ...@@ -128,3 +128,6 @@
128 \N patch patch_95_96_a.sql|schema_version 128 \N patch patch_95_96_a.sql|schema_version
129 \N patch patch_96_97_a.sql|schema_version 129 \N patch patch_96_97_a.sql|schema_version
130 \N patch patch_96_97_b.sql|biotype_so_term 130 \N patch patch_96_97_b.sql|biotype_so_term
131 \N patch patch_96_97_c.sql|rnaproduct_tables
132 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
133 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Mon Mar 18 14:30:07 2019 -- Created on Tue Apr 2 16:03:56 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
......
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 15:00:22 2019 -- Created on Tue Apr 2 16:03:59 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code"); ...@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code");
CREATE TABLE "object_xref" ( CREATE TABLE "object_xref" (
"object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, "object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"ensembl_id" integer NOT NULL DEFAULT 0, "ensembl_id" integer NOT NULL DEFAULT 0,
"ensembl_object_type" enum NOT NULL DEFAULT 'RawContig', "ensembl_object_type" enum NOT NULL,
"xref_id" integer NOT NULL, "xref_id" integer NOT NULL,
"linkage_annotation" varchar(255), "linkage_annotation" varchar(255),
"analysis_id" smallint "analysis_id" smallint
...@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" ( ...@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" (
"score" double precision "score" double precision
); );
--
-- Table: "rnaproduct"
--
CREATE TABLE "rnaproduct" (
"rnaproduct_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"rnaproduct_type_id" smallint NOT NULL,
"transcript_id" integer NOT NULL,
"seq_start" integer NOT NULL,
"start_exon_id" integer,
"seq_end" integer NOT NULL,
"end_exon_id" integer,
"stable_id" varchar(128),
"version" smallint,
"created_date" datetime,
"modified_date" datetime
);
--
-- Table: "rnaproduct_attrib"
--
CREATE TABLE "rnaproduct_attrib" (
"rnaproduct_id" integer NOT NULL DEFAULT 0,
"attrib_type_id" smallint NOT NULL DEFAULT 0,
"value" text NOT NULL
);
CREATE UNIQUE INDEX "rnaproduct_attribx" ON "rnaproduct_attrib" ("rnaproduct_id", "attrib_type_id", "value");
--
-- Table: "rnaproduct_type"
--
CREATE TABLE "rnaproduct_type" (
"rnaproduct_type_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"code" varchar(20) NOT NULL DEFAULT '',
"name" varchar(255) NOT NULL DEFAULT '',
"description" text
);
CREATE UNIQUE INDEX "code_idx03" ON "rnaproduct_type" ("code");
-- --
-- Table: "seq_region" -- Table: "seq_region"
-- --
...@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" ( ...@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" (
"new_stable_id" varchar(128), "new_stable_id" varchar(128),
"new_version" smallint, "new_version" smallint,
"mapping_session_id" integer NOT NULL DEFAULT 0, "mapping_session_id" integer NOT NULL DEFAULT 0,
"type" enum NOT NULL DEFAULT 'gene', "type" enum NOT NULL,
"score" float NOT NULL DEFAULT 0 "score" float NOT NULL DEFAULT 0
); );
......
...@@ -107,3 +107,6 @@ ...@@ -107,3 +107,6 @@
156 \N patch patch_95_96_a.sql|schema_version 156 \N patch patch_95_96_a.sql|schema_version
157 \N patch patch_96_97_a.sql|schema_version 157 \N patch patch_96_97_a.sql|schema_version
158 \N patch patch_96_97_b.sql|biotype_so_term 158 \N patch patch_96_97_b.sql|biotype_so_term
159 \N patch patch_96_97_c.sql|rnaproduct_tables
160 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
161 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
-- --
-- Created by SQL::Translator::Producer::SQLite -- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 15:00:25 2019 -- Created on Tue Apr 2 16:04:02 2019
-- --
BEGIN TRANSACTION; BEGIN TRANSACTION;
...@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code"); ...@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code");
CREATE TABLE "object_xref" ( CREATE TABLE "object_xref" (
"object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL, "object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"ensembl_id" integer NOT NULL DEFAULT 0, "ensembl_id" integer NOT NULL DEFAULT 0,
"ensembl_object_type" enum NOT NULL DEFAULT 'RawContig', "ensembl_object_type" enum NOT NULL,
"xref_id" integer NOT NULL, "xref_id" integer NOT NULL,
"linkage_annotation" varchar(255), "linkage_annotation" varchar(255),
"analysis_id" smallint "analysis_id" smallint
...@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" ( ...@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" (
"score" double precision "score" double precision
); );
--
-- Table: "rnaproduct"
--
CREATE TABLE "rnaproduct" (
"rnaproduct_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"rnaproduct_type_id" smallint NOT NULL,
"transcript_id" integer NOT NULL,
"seq_start" integer NOT NULL,
"start_exon_id" integer,
"seq_end" integer NOT NULL,
"end_exon_id" integer,
"stable_id" varchar(128),
"version" smallint,
"created_date" datetime,
"modified_date" datetime
);
--
-- Table: "rnaproduct_attrib"
--
CREATE TABLE "rnaproduct_attrib" (
"rnaproduct_id" integer NOT NULL DEFAULT 0,
"attrib_type_id" smallint NOT NULL DEFAULT 0,
"value" text NOT NULL
);
CREATE UNIQUE INDEX "rnaproduct_attribx" ON "rnaproduct_attrib" ("rnaproduct_id", "attrib_type_id", "value");
--
-- Table: "rnaproduct_type"
--
CREATE TABLE "rnaproduct_type" (
"rnaproduct_type_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
"code" varchar(20) NOT NULL DEFAULT '',
"name" varchar(255) NOT NULL DEFAULT '',
"description" text
);
CREATE UNIQUE INDEX "code_idx03" ON "rnaproduct_type" ("code");
-- --
-- Table: "seq_region" -- Table: "seq_region"
-- --
...@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" ( ...@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" (
"new_stable_id" varchar(128), "new_stable_id" varchar(128),
"new_version" smallint, "new_version" smallint,
"mapping_session_id" integer NOT NULL DEFAULT 0, "mapping_session_id" integer NOT NULL DEFAULT 0,
"type" enum NOT NULL DEFAULT 'gene', "type" enum NOT NULL,
"score" float NOT NULL DEFAULT 0 "score" float NOT NULL DEFAULT 0
); );
......
...@@ -112,3 +112,6 @@ ...@@ -112,3 +112,6 @@
2119 \N patch patch_95_96_a.sql|schema_version 2119 \N patch patch_95_96_a.sql|schema_version
2120 \N patch patch_96_97_a.sql|schema_version 2120 \N patch patch_96_97_a.sql|schema_version
2121 \N patch patch_96_97_b.sql|biotype_so_term 2121 \N patch patch_96_97_b.sql|biotype_so_term
2122 \N patch patch_96_97_c.sql|rnaproduct_tables
2123 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
2124 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
1 \N schema_type variation 1 \N schema_type variation
2 \N schema_version 96 2 \N schema_version 97
3 \N patch patch_84_85_a.sql|schema version 3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym 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 5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
...@@ -39,3 +39,6 @@ ...@@ -39,3 +39,6 @@
39 \N patch patch_95_96_c.sql|add new entries to the failed_description table 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 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. 41 \N patch patch_95_96_e.sql|Rename motif_name to binding_matrix_stable_id.
42 \N patch patch_96_97_a.sql|schema version
43 \N patch patch_96_97_b.sql|move ancestral allele column to variation_feature
44 \N patch patch_96_97_c.sql|add an unique index on the name column
...@@ -38,24 +38,24 @@ CREATE TABLE `associate_study` ( ...@@ -38,24 +38,24 @@ CREATE TABLE `associate_study` (
CREATE TABLE `attrib` ( CREATE TABLE `attrib` (
`attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT, `attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0', `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
`value` text NOT NULL, `value` text NOT NULL,
PRIMARY KEY (`attrib_id`), PRIMARY KEY (`attrib_id`),
UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80)) UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_set` ( CREATE TABLE `attrib_set` (
`attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0', `attrib_set_id` int(11) unsigned NOT NULL DEFAULT 0,
`attrib_id` int(11) unsigned NOT NULL DEFAULT '0', `attrib_id` int(11) unsigned NOT NULL DEFAULT 0,
UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`), UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
KEY `attrib_idx` (`attrib_id`) KEY `attrib_idx` (`attrib_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `attrib_type` ( CREATE TABLE `attrib_type` (
`attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0', `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT 0,
`code` varchar(20) NOT NULL DEFAULT '', `code` varchar(20) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '', `name` varchar(255) NOT NULL DEFAULT '',
`description` text, `description` text DEFAULT NULL,
PRIMARY KEY (`attrib_type_id`), PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`) UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -66,7 +66,7 @@ CREATE TABLE `compressed_genotype_region` ( ...@@ -66,7 +66,7 @@ CREATE TABLE `compressed_genotype_region` (
`seq_region_start` int(11) NOT NULL, `seq_region_start` int(11) NOT NULL,
`seq_region_end` int(11) NOT NULL, `seq_region_end` int(11) NOT NULL,
`seq_region_strand` tinyint(4) NOT NULL, `seq_region_strand` tinyint(4) NOT NULL,
`genotypes` blob, `genotypes` blob DEFAULT NULL,
KEY `pos_idx` (`seq_region_id`,`seq_region_start`), KEY `pos_idx` (`seq_region_id`,`seq_region_start`),
KEY `sample_idx` (`sample_id`) KEY `sample_idx` (`sample_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -74,14 +74,14 @@ CREATE TABLE `compressed_genotype_region` ( ...@@ -74,14 +74,14 @@ CREATE TABLE `compressed_genotype_region` (
CREATE TABLE `compressed_genotype_var` ( CREATE TABLE `compressed_genotype_var` (
`variation_id` int(11) unsigned NOT NULL, `variation_id` int(11) unsigned NOT NULL,
`subsnp_id` int(11) unsigned DEFAULT NULL, `subsnp_id` int(11) unsigned DEFAULT NULL,
`genotypes` blob, `genotypes` blob DEFAULT NULL,
KEY `variation_idx` (`variation_id`), KEY `variation_idx` (`variation_id`),
KEY `subsnp_idx` (`subsnp_id`) KEY `subsnp_idx` (`subsnp_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` ( CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned NOT NULL DEFAULT '1', `species_id` int(10) unsigned NOT NULL DEFAULT 1,
`name` varchar(40) NOT NULL, `name` varchar(40) NOT NULL,
`version` varchar(255) DEFAULT NULL, `version` varchar(255) DEFAULT NULL,
`rank` int(11) NOT NULL, `rank` int(11) NOT NULL,
...@@ -151,11 +151,11 @@ CREATE TABLE `genotype_code` ( ...@@ -151,11 +151,11 @@ CREATE TABLE `genotype_code` (
CREATE TABLE `individual` ( CREATE TABLE `individual` (
`individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL, `name` varchar(255) DEFAULT NULL,
`description` text, `description` text DEFAULT NULL,
`gender` enum('Male','Female','Unknown') NOT NULL DEFAULT 'Unknown', `gender` enum('Male','Female','Unknown') NOT NULL DEFAULT 'Unknown',
`father_individual_id` int(10) unsigned DEFAULT NULL, `father_individual_id` int(10) unsigned DEFAULT NULL,
`mother_individual_id` int(10) unsigned DEFAULT NULL, `mother_individual_id` int(10) unsigned DEFAULT NULL,
`individual_type_id` int(10) unsigned NOT NULL DEFAULT '0', `individual_type_id` int(10) unsigned NOT NULL DEFAULT 0,
PRIMARY KEY (`individual_id`), PRIMARY KEY (`individual_id`),
KEY `father_individual_idx` (`father_individual_id`), KEY `father_individual_idx` (`father_individual_id`),
KEY `mother_individual_idx` (`mother_individual_id`) KEY `mother_individual_idx` (`mother_individual_id`)
...@@ -174,19 +174,19 @@ CREATE TABLE `individual_synonym` ( ...@@ -174,19 +174,19 @@ CREATE TABLE `individual_synonym` (
CREATE TABLE `individual_type` ( CREATE TABLE `individual_type` (
`individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) NOT NULL, `name` varchar(255) NOT NULL,
`description` text, `description` text DEFAULT NULL,
PRIMARY KEY (`individual_type_id`) PRIMARY KEY (`individual_type_id`)
) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
CREATE TABLE `meta` ( CREATE TABLE `meta` (
`meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`species_id` int(10) unsigned DEFAULT '1', `species_id` int(10) unsigned DEFAULT 1,
`meta_key` varchar(40) NOT NULL, `meta_key` varchar(40) NOT NULL,
`meta_value` varchar(255) NOT NULL, `meta_value` varchar(255) NOT NULL,
PRIMARY KEY (`meta_id`), PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`), UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`) KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1; ) ENGINE=MyISAM AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` ( CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL, `table_name` varchar(40) NOT NULL,
...@@ -200,14 +200,14 @@ CREATE TABLE `motif_feature_variation` ( ...@@ -200,14 +200,14 @@ CREATE TABLE `motif_feature_variation` (
`variation_feature_id` int(11) unsigned NOT NULL, `variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL, `feature_stable_id` varchar(128) DEFAULT NULL,
`motif_feature_id` int(11) unsigned NOT NULL, `motif_feature_id` int(11) unsigned NOT NULL,
`allele_string` text, `allele_string` text DEFAULT NULL,
`somatic` tinyint(1) NOT NULL DEFAULT '0', `somatic` tinyint(1) NOT NULL DEFAULT 0,
`consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL, `consequence_types` set('TF_binding_site_variant','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation') DEFAULT NULL,
`binding_matrix_stable_id` varchar(60) DEFAULT NULL, `binding_matrix_stable_id` varchar(60) DEFAULT NULL,
`motif_start` int(11) unsigned DEFAULT NULL, `motif_start` int(11) unsigned DEFAULT NULL,
`motif_end` int(11) unsigned DEFAULT NULL, `motif_end` int(11) unsigned DEFAULT NULL,
`motif_score_delta` float DEFAULT NULL, `motif_score_delta` float DEFAULT NULL,
`in_informative_position` tinyint(1) NOT NULL DEFAULT '0', `in_informative_position` tinyint(1) NOT NULL DEFAULT 0,
PRIMARY KEY (`motif_feature_variation_id`), PRIMARY KEY (`motif_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`), KEY `variation_feature_idx` (`variation_feature_id`),
KEY `consequence_type_idx` (`consequence_types`), KEY `consequence_type_idx` (`consequence_types`),
...@@ -233,7 +233,7 @@ CREATE TABLE `phenotype_feature` ( ...@@ -233,7 +233,7 @@ CREATE TABLE `phenotype_feature` (
`study_id` int(11) unsigned DEFAULT NULL, `study_id` int(11) unsigned DEFAULT NULL,
`type` enum('Gene','Variation','StructuralVariation','SupportingStructuralVariation','QTL','RegulatoryFeature') DEFAULT NULL, `type` enum('Gene','Variation','StructuralVariation','SupportingStructuralVariation','QTL','RegulatoryFeature') DEFAULT NULL,
`object_id` varchar(255) DEFAULT NULL, `object_id` varchar(255) DEFAULT NULL,
`is_significant` tinyint(1) unsigned DEFAULT '1', `is_significant` tinyint(1) unsigned DEFAULT 1,
`seq_region_id` int(11) unsigned DEFAULT NULL, `seq_region_id` int(11) unsigned DEFAULT NULL,
`seq_region_start` int(11) unsigned DEFAULT NULL, `seq_region_start` int(11) unsigned DEFAULT NULL,
`seq_region_end` int(11) unsigned DEFAULT NULL, `seq_region_end` int(11) unsigned DEFAULT NULL,
...@@ -267,8 +267,8 @@ CREATE TABLE `population` ( ...@@ -267,8 +267,8 @@ CREATE TABLE `population` (
`population_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `population_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) DEFAULT NULL, `name` varchar(255) DEFAULT NULL,
`size` int(10) DEFAULT NULL, `size` int(10) DEFAULT NULL,
`description` text, `description` text DEFAULT NULL,
`collection` tinyint(1) DEFAULT '0', `collection` tinyint(1) DEFAULT 0,
`freqs_from_gts` tinyint(1) DEFAULT NULL, `freqs_from_gts` tinyint(1) DEFAULT NULL,
`display` enum('LD','MARTDISPLAYABLE','UNDISPLAYABLE') DEFAULT 'UNDISPLAYABLE', `display` enum('LD','MARTDISPLAYABLE','UNDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
`display_group_id` tinyint(1) DEFAULT NULL, `display_group_id` tinyint(1) DEFAULT NULL,
...@@ -310,7 +310,7 @@ CREATE TABLE `population_synonym` ( ...@@ -310,7 +310,7 @@ CREATE TABLE `population_synonym` (
CREATE TABLE `protein_function_predictions` ( CREATE TABLE `protein_function_predictions` (
`translation_md5_id` int(11) unsigned NOT NULL, `translation_md5_id` int(11) unsigned NOT NULL,
`analysis_attrib_id` int(11) unsigned NOT NULL, `analysis_attrib_id` int(11) unsigned NOT NULL,
`prediction_matrix` mediumblob, `prediction_matrix` mediumblob DEFAULT NULL,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`) PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -318,7 +318,7 @@ CREATE TABLE `protein_function_predictions_attrib` ( ...@@ -318,7 +318,7 @@ CREATE TABLE `protein_function_predictions_attrib` (
`translation_md5_id` int(11) unsigned NOT NULL, `translation_md5_id` int(11) unsigned NOT NULL,
`analysis_attrib_id` int(11) unsigned NOT NULL, `analysis_attrib_id` int(11) unsigned NOT NULL,
`attrib_type_id` int(11) unsigned NOT NULL, `attrib_type_id` int(11) unsigned NOT NULL,
`position_values` blob, `position_values` blob DEFAULT NULL,
PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`,`attrib_type_id`) PRIMARY KEY (`translation_md5_id`,`analysis_attrib_id`,`attrib_type_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1; ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
...@@ -350,9 +350,9 @@ CREATE TABLE `regulatory_feature_variation` ( ...@@ -350,9 +350,9 @@ CREATE TABLE `regulatory_feature_variation` (
`regulatory_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT, `regulatory_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
`variation_feature_id` int(11) unsigned NOT NULL, `variation_feature_id` int(11) unsigned NOT NULL,
`feature_stable_id` varchar(128) DEFAULT NULL, `feature_stable_id` varchar(128) DEFAULT NULL,
`feature_type` text, `feature_type` text DEFAULT NULL,
`allele_string` text, `allele_string` text DEFAULT NULL,
`somatic` tinyint(1) NOT NULL DEFAULT '0', `somatic` tinyint(1) NOT NULL DEFAULT 0,
`consequence_types` set('regulatory_region_variant','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation') DEFAULT NULL, `consequence_types` set('regulatory_region_variant','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation') DEFAULT NULL,
PRIMARY KEY (`regulatory_feature_variation_id`), PRIMARY KEY (`regulatory_feature_variation_id`),
KEY `variation_feature_idx` (`variation_feature_id`), KEY `variation_feature_idx` (`variation_feature_id`),
...@@ -365,10 +365,10 @@ CREATE TABLE `sample` ( ...@@ -365,10 +365,10 @@ CREATE TABLE `sample` (
`sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT, `sample_id` int(10) unsigned