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.

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.
aeeb6039 · Marek Szuba · Shamika Mohanan · d20e7be0 · aeeb6039 · aeeb6039
Commit aeeb6039 authored Apr 02, 2019 by Marek Szuba Committed by Shamika Mohanan Apr 17, 2019
20 changed files
--- a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
 -- 
 -- 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;
@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code");
 CREATE TABLE "object_xref" (
  "object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
  "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,
  "linkage_annotation" varchar(255),
  "analysis_id" smallint
@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" (
  "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"
 --
@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" (
  "new_stable_id" varchar(128),
  "new_version" smallint,
  "mapping_session_id" integer NOT NULL DEFAULT 0,
-  "type" enum NOT NULL DEFAULT 'gene',
+  "type" enum NOT NULL,
  "score" float NOT NULL DEFAULT 0
 );


--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -128,3 +128,6 @@
 128	\N	patch	patch_95_96_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
+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
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
--- a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
 -- 
 -- 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;

--- a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
 -- 
 -- 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;
@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code");
 CREATE TABLE "object_xref" (
  "object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
  "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,
  "linkage_annotation" varchar(255),
  "analysis_id" smallint
@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" (
  "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"
 --
@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" (
  "new_stable_id" varchar(128),
  "new_version" smallint,
  "mapping_session_id" integer NOT NULL DEFAULT 0,
-  "type" enum NOT NULL DEFAULT 'gene',
+  "type" enum NOT NULL,
  "score" float NOT NULL DEFAULT 0
 );


--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -107,3 +107,6 @@
 156	\N	patch	patch_95_96_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
+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
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
 -- 
 -- 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;
@@ -615,7 +615,7 @@ CREATE UNIQUE INDEX "code_idx02" ON "misc_set" ("code");
 CREATE TABLE "object_xref" (
  "object_xref_id" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
  "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,
  "linkage_annotation" varchar(255),
  "analysis_id" smallint
@@ -787,6 +787,46 @@ CREATE TABLE "repeat_feature" (
  "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"
 --
@@ -854,7 +894,7 @@ CREATE TABLE "stable_id_event" (
  "new_stable_id" varchar(128),
  "new_version" smallint,
  "mapping_session_id" integer NOT NULL DEFAULT 0,
-  "type" enum NOT NULL DEFAULT 'gene',
+  "type" enum NOT NULL,
  "score" float NOT NULL DEFAULT 0
 );


--- a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
@@ -112,3 +112,6 @@
 2119	\N	patch	patch_95_96_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
+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
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
 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
 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
@@ -39,3 +39,6 @@
 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.
+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
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
@@ -38,24 +38,24 @@ CREATE TABLE `associate_study` (

 CREATE TABLE `attrib` (
  `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,
  PRIMARY KEY (`attrib_id`),
  UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
 ) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1;

 CREATE TABLE `attrib_set` (
-  `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
-  `attrib_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,
  UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
  KEY `attrib_idx` (`attrib_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;

 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 '',
  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text,
+  `description` text DEFAULT NULL,
  PRIMARY KEY (`attrib_type_id`),
  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -66,7 +66,7 @@ CREATE TABLE `compressed_genotype_region` (
  `seq_region_start` int(11) NOT NULL,
  `seq_region_end` int(11) 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 `sample_idx` (`sample_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -74,14 +74,14 @@ CREATE TABLE `compressed_genotype_region` (
 CREATE TABLE `compressed_genotype_var` (
  `variation_id` int(11) unsigned NOT NULL,
  `subsnp_id` int(11) unsigned DEFAULT NULL,
-  `genotypes` blob,
+  `genotypes` blob DEFAULT NULL,
  KEY `variation_idx` (`variation_id`),
  KEY `subsnp_idx` (`subsnp_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;

 CREATE TABLE `coord_system` (
  `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,
  `version` varchar(255) DEFAULT NULL,
  `rank` int(11) NOT NULL,
@@ -151,11 +151,11 @@ CREATE TABLE `genotype_code` (
 CREATE TABLE `individual` (
  `individual_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
-  `description` text,
+  `description` text DEFAULT NULL,
  `gender` enum('Male','Female','Unknown') NOT NULL DEFAULT 'Unknown',
  `father_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`),
  KEY `father_individual_idx` (`father_individual_id`),
  KEY `mother_individual_idx` (`mother_individual_id`)
@@ -174,19 +174,19 @@ CREATE TABLE `individual_synonym` (
 CREATE TABLE `individual_type` (
  `individual_type_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) NOT NULL,
-  `description` text,
+  `description` text DEFAULT NULL,
  PRIMARY KEY (`individual_type_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;

 CREATE TABLE `meta` (
  `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_value` varchar(255) NOT NULL,
  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=42 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;

 CREATE TABLE `meta_coord` (
  `table_name` varchar(40) NOT NULL,
@@ -200,14 +200,14 @@ CREATE TABLE `motif_feature_variation` (
  `variation_feature_id` int(11) unsigned NOT NULL,
  `feature_stable_id` varchar(128) DEFAULT NULL,
  `motif_feature_id` int(11) unsigned NOT NULL,
-  `allele_string` text,
-  `somatic` tinyint(1) NOT NULL DEFAULT '0',
+  `allele_string` text DEFAULT NULL,
+  `somatic` tinyint(1) NOT NULL DEFAULT 0,
  `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,
  `motif_start` int(11) unsigned DEFAULT NULL,
  `motif_end` int(11) unsigned 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`),
  KEY `variation_feature_idx` (`variation_feature_id`),
  KEY `consequence_type_idx` (`consequence_types`),
@@ -233,7 +233,7 @@ CREATE TABLE `phenotype_feature` (
  `study_id` int(11) unsigned DEFAULT NULL,
  `type` enum('Gene','Variation','StructuralVariation','SupportingStructuralVariation','QTL','RegulatoryFeature') 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_start` int(11) unsigned DEFAULT NULL,
  `seq_region_end` int(11) unsigned DEFAULT NULL,
@@ -267,8 +267,8 @@ CREATE TABLE `population` (
  `population_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  `size` int(10) DEFAULT NULL,
-  `description` text,
-  `collection` tinyint(1) DEFAULT '0',
+  `description` text DEFAULT NULL,
+  `collection` tinyint(1) DEFAULT 0,
  `freqs_from_gts` tinyint(1) DEFAULT NULL,
  `display` enum('LD','MARTDISPLAYABLE','UNDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
  `display_group_id` tinyint(1) DEFAULT NULL,
@@ -310,7 +310,7 @@ CREATE TABLE `population_synonym` (
 CREATE TABLE `protein_function_predictions` (
  `translation_md5_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`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;

@@ -318,7 +318,7 @@ CREATE TABLE `protein_function_predictions_attrib` (
  `translation_md5_id` int(11) unsigned NOT NULL,
  `analysis_attrib_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`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;

@@ -350,9 +350,9 @@ CREATE TABLE `regulatory_feature_variation` (
  `regulatory_feature_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `variation_feature_id` int(11) unsigned NOT NULL,
  `feature_stable_id` varchar(128) DEFAULT NULL,
-  `feature_type` text,
-  `allele_string` text,
-  `somatic` tinyint(1) NOT NULL DEFAULT '0',
+  `feature_type` text DEFAULT NULL,
+  `allele_string` text DEFAULT NULL,
+  `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,
  PRIMARY KEY (`regulatory_feature_variation_id`),
  KEY `variation_feature_idx` (`variation_feature_id`),
@@ -365,10 +365,10 @@ CREATE TABLE `sample` (
  `sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `individual_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
-  `description` text,
+  `description` text DEFAULT NULL,
  `study_id` int(10) unsigned DEFAULT NULL,
  `display` enum('REFERENCE','DEFAULT','DISPLAYABLE','UNDISPLAYABLE','LD','MARTDISPLAYABLE') DEFAULT 'UNDISPLAYABLE',
-  `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT '0',
+  `has_coverage` tinyint(1) unsigned NOT NULL DEFAULT 0,
  `variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') DEFAULT NULL,
  PRIMARY KEY (`sample_id`),
  KEY `individual_idx` (`individual_id`),
@@ -421,7 +421,8 @@ CREATE TABLE `source` (
  `type` enum('chip','lsdb') DEFAULT NULL,
  `somatic_status` enum('germline','somatic','mixed') DEFAULT 'germline',
  `data_types` set('variation','variation_synonym','structural_variation','phenotype_feature','study') DEFAULT NULL,
-  PRIMARY KEY (`source_id`)
+  PRIMARY KEY (`source_id`),
+  UNIQUE KEY `name_idx` (`name`)
 ) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;

 CREATE TABLE `structural_variation` (
@@ -430,11 +431,11 @@ CREATE TABLE `structural_variation` (
  `alias` varchar(255) DEFAULT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `study_id` int(10) unsigned DEFAULT NULL,
-  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
+  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
  `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
  `validation_status` enum('validated','not validated','high quality') DEFAULT NULL,
-  `is_evidence` tinyint(4) DEFAULT '0',
-  `somatic` tinyint(1) NOT NULL DEFAULT '0',
+  `is_evidence` tinyint(4) DEFAULT 0,
+  `somatic` tinyint(1) NOT NULL DEFAULT 0,
  `copy_number` tinyint(2) DEFAULT NULL,
  PRIMARY KEY (`structural_variation_id`),
  UNIQUE KEY `variation_name` (`variation_name`),
@@ -465,10 +466,10 @@ CREATE TABLE `structural_variation_feature` (
  `variation_name` varchar(255) DEFAULT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `study_id` int(10) unsigned DEFAULT NULL,
-  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `allele_string` longtext,
-  `is_evidence` tinyint(1) NOT NULL DEFAULT '0',
-  `somatic` tinyint(1) NOT NULL DEFAULT '0',
+  `class_attrib_id` int(10) unsigned NOT NULL DEFAULT 0,
+  `allele_string` longtext DEFAULT NULL,
+  `is_evidence` tinyint(1) NOT NULL DEFAULT 0,
+  `somatic` tinyint(1) NOT NULL DEFAULT 0,
  `breakpoint_order` tinyint(4) DEFAULT NULL,
  `length` int(10) DEFAULT NULL,
  `variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
@@ -495,7 +496,7 @@ CREATE TABLE `study` (
  `study_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
-  `description` text,
+  `description` text DEFAULT NULL,
  `url` varchar(255) DEFAULT NULL,
  `external_reference` varchar(255) DEFAULT NULL,
  `study_type` varchar(255) DEFAULT NULL,
@@ -538,8 +539,8 @@ CREATE TABLE `transcript_variation` (
  `transcript_variation_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
  `variation_feature_id` int(11) unsigned NOT NULL,
  `feature_stable_id` varchar(128) DEFAULT NULL,
-  `allele_string` text,
-  `somatic` tinyint(1) NOT NULL DEFAULT '0',
+  `allele_string` text DEFAULT NULL,
+  `somatic` tinyint(1) NOT NULL DEFAULT 0,
  `consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant') DEFAULT NULL,
  `cds_start` int(11) unsigned DEFAULT NULL,
  `cds_end` int(11) unsigned DEFAULT NULL,
@@ -548,16 +549,16 @@ CREATE TABLE `transcript_variation` (
  `translation_start` int(11) unsigned DEFAULT NULL,
  `translation_end` int(11) unsigned DEFAULT NULL,
  `distance_to_transcript` int(11) unsigned DEFAULT NULL,
-  `codon_allele_string` text,
-  `pep_allele_string` text,
-  `hgvs_genomic` text,
-  `hgvs_transcript` text,
-  `hgvs_protein` text,
+  `codon_allele_string` text DEFAULT NULL,
+  `pep_allele_string` text DEFAULT NULL,
+  `hgvs_genomic` text DEFAULT NULL,
+  `hgvs_transcript` text DEFAULT NULL,
+  `hgvs_protein` text DEFAULT NULL,
  `polyphen_prediction` enum('unknown','benign','possibly damaging','probably damaging') DEFAULT NULL,
  `polyphen_score` float DEFAULT NULL,
  `sift_prediction` enum('tolerated','deleterious','tolerated - low confidence','deleterious - low confidence') DEFAULT NULL,
  `sift_score` float DEFAULT NULL,
-  `display` int(1) DEFAULT '1',
+  `display` int(1) DEFAULT 1,
  PRIMARY KEY (`transcript_variation_id`),
  KEY `variation_feature_idx` (`variation_feature_id`),
  KEY `consequence_type_idx` (`consequence_types`),
@@ -575,16 +576,15 @@ CREATE TABLE `variation` (
  `variation_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `source_id` int(10) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
-  `ancestral_allele` varchar(255) DEFAULT NULL,
  `flipped` tinyint(1) unsigned DEFAULT NULL,
-  `class_attrib_id` int(10) unsigned DEFAULT '0',
-  `somatic` tinyint(1) NOT NULL DEFAULT '0',
+  `class_attrib_id` int(10) unsigned DEFAULT 0,
+  `somatic` tinyint(1) NOT NULL DEFAULT 0,
  `minor_allele` varchar(50) DEFAULT NULL,
  `minor_allele_freq` float DEFAULT NULL,
  `minor_allele_count` int(10) unsigned DEFAULT NULL,
  `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
  `evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
-  `display` int(1) DEFAULT '1',
+  `display` int(1) DEFAULT 1,
  PRIMARY KEY (`variation_id`),
  UNIQUE KEY `name` (`name`),
  KEY `source_idx` (`source_id`)
@@ -612,21 +612,22 @@ CREATE TABLE `variation_feature` (
  `seq_region_strand` tinyint(4) NOT NULL,
  `variation_id` int(10) unsigned NOT NULL,
  `allele_string` varchar(50000) DEFAULT NULL,
+  `ancestral_allele` varchar(50) DEFAULT NULL,
  `variation_name` varchar(255) DEFAULT NULL,
  `map_weight` int(11) NOT NULL,
  `flags` set('genotyped') DEFAULT NULL,
  `source_id` int(10) unsigned NOT NULL,
  `consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant') NOT NULL DEFAULT 'intergenic_variant',
  `variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
-  `class_attrib_id` int(10) unsigned DEFAULT '0',
-  `somatic` tinyint(1) NOT NULL DEFAULT '0',
+  `class_attrib_id` int(10) unsigned DEFAULT 0,
+  `somatic` tinyint(1) NOT NULL DEFAULT 0,
  `minor_allele` varchar(50) DEFAULT NULL,
  `minor_allele_freq` float DEFAULT NULL,
  `minor_allele_count` int(10) unsigned DEFAULT NULL,
  `alignment_quality` double DEFAULT NULL,
  `evidence_attribs` set('367','368','369','370','371','372','418','421','573','585') DEFAULT NULL,
  `clinical_significance` set('uncertain significance','not provided','benign','likely benign','likely pathogenic','pathogenic','drug response','histocompatibility','other','confers sensitivity','risk factor','association','protective') DEFAULT NULL,
-  `display` int(1) DEFAULT '1',
+  `display` int(1) DEFAULT 1,
  PRIMARY KEY (`variation_feature_id`),
  KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
  KEY `variation_idx` (`variation_id`),
@@ -650,7 +651,7 @@ CREATE TABLE `variation_hgvs` (
 CREATE TABLE `variation_set` (
  `variation_set_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
-  `description` text,
+  `description` text DEFAULT NULL,