Merge pull request #363 from Ensembl/schema_update_97

Schema update 97

misc-scripts/ontology/sql/patch_95_96_b.sql

@@ -40,4 +40,8 @@ CREATE INDEX ix_closure_ontology_id ON closure (`ontology_id`);
 
 CREATE INDEX `ix_relation_parent_term_id` ON relation (`parent_term_id`);
 CREATE INDEX `ix_relation_relation_type_id` ON relation (`relation_type_id`);
-CREATE INDEX `ix_relation_ontology_id` ON relation (`ontology_id`);
+CREATE INDEX `ix_relation_ontology_id` ON relation (`ontology_id`);
+
+-- Patch identifier
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_95_96_b.sql|term_ontology_update');

misc-scripts/ontology/sql/patch_96_97_a.sql

@@ -0,0 +1,27 @@
+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2019] EMBL-European Bioinformatics Institute
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_96_97_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 97.
+
+UPDATE meta SET meta_value='97' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_96_97_a.sql|schema_version');

misc-scripts/ontology/sql/tables.sql

@@ -30,12 +30,11 @@ CREATE TABLE `meta` (
 # Add schema type and schema version to the meta table
 INSERT INTO meta (meta_key, meta_value) VALUES
   ('schema_type', 'ontology'),
-  ('schema_version', '96');
+  ('schema_version', '97');
 
 # Patches included in this schema file
 INSERT INTO meta (meta_key, meta_value)
-  VALUES ('patch', 'patch_95_96_a.sql|schema_version');
-
+  VALUES ('patch', 'patch_96_97_a.sql|schema_version');
 
 CREATE TABLE `ontology` (
   `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,

modules/Bio/EnsEMBL/ApiVersion.pm

@@ -56,7 +56,7 @@ use base qw( Exporter );
 
 our @EXPORT = qw( software_version );
 
-my $API_VERSION = 96;
+my $API_VERSION = 97;
 
 sub software_version { return $API_VERSION }
 

modules/t/test-genome-DBs/circ/core/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:49:32 2018
+-- Created on Tue Feb 12 11:45:04 2019
 -- 
 
 BEGIN TRANSACTION;

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	96
+2	\N	schema_version	97
 8	1	assembly.accession	GCA_000292705.1
 10	1	assembly.date	2012-08
 7	1	assembly.default	GCA_000292705.1
@@ -126,3 +126,4 @@
 126	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 127	\N	patch	patch_94_95_c.sql|ox_key_update
 128	\N	patch	patch_95_96_a.sql|schema_version
+129	\N	patch	patch_96_97_a.sql|schema_version

modules/t/test-genome-DBs/circ/core/table.sql

@@ -489,7 +489,7 @@ 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=129 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=130 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:49:43 2018
+-- Created on Tue Feb 12 11:45:08 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/homo_sapiens/core/meta.txt

@@ -1,4 +1,4 @@
-1	\N	schema_version	96
+1	\N	schema_version	97
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -105,3 +105,4 @@
 172	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 173	\N	patch	patch_94_95_c.sql|ox_key_update
 174	\N	patch	patch_95_96_a.sql|schema_version
+175	\N	patch	patch_96_97_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/core/table.sql

@@ -489,7 +489,7 @@ 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=175 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=176 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/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:49:54 2018
+-- Created on Tue Feb 12 11:45:11 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt

@@ -1,4 +1,4 @@
-1	\N	schema_version	96
+1	\N	schema_version	97
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -105,3 +105,4 @@
 154	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 155	\N	patch	patch_94_95_c.sql|ox_key_update
 156	\N	patch	patch_95_96_a.sql|schema_version
+157	\N	patch	patch_96_97_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/empty/table.sql

@@ -489,7 +489,7 @@ 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=157 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=158 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/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:50:04 2018
+-- Created on Tue Feb 12 11:45:14 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt

@@ -1,4 +1,4 @@
-1	\N	schema_version	96
+1	\N	schema_version	97
 2014	1	species.classification	Haplorrhini
 40	1	assembly.default	GRCh37
 41	1	assembly.date	2009-02
@@ -110,3 +110,4 @@
 2117	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 2118	\N	patch	patch_94_95_c.sql|ox_key_update
 2119	\N	patch	patch_95_96_a.sql|schema_version
+2120	\N	patch	patch_96_97_a.sql|schema_version

modules/t/test-genome-DBs/homo_sapiens/patch/table.sql

@@ -489,7 +489,7 @@ 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=2120 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2121 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

@@ -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

@@ -35,3 +35,7 @@
 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

@@ -113,7 +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,
@@ -131,6 +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,
@@ -178,7 +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=38 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -195,7 +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,
@@ -675,7 +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`)

modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:50:07 2018
+-- Created on Tue Feb 12 11:45:15 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/mapping/core/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:50:17 2018
+-- Created on Tue Feb 12 11:45:18 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/mapping/core/meta.txt

@@ -1,4 +1,4 @@
-1	\N	schema_version	96
+1	\N	schema_version	97
 2	1	assembly.default	MULTIMAP
 3	1	species.taxonomy_id	1
 4	1	assembly.mapping	chromosome:MULTIMAP#contig
@@ -66,3 +66,4 @@
 159	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 160	\N	patch	patch_94_95_c.sql|ox_key_update
 161	\N	patch	patch_95_96_a.sql|schema_version
+162	\N	patch	patch_96_97_a.sql|schema_version

modules/t/test-genome-DBs/mapping/core/table.sql

@@ -489,7 +489,7 @@ 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=162 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=163 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

modules/t/test-genome-DBs/multi/compara/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:50:26 2018
+-- Created on Tue Feb 12 11:45:21 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:50:36 2018
+-- Created on Tue Feb 12 11:45:24 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/mus_musculus/core/meta.txt

@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	96
+2	\N	schema_version	97
 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
@@ -183,3 +183,4 @@
 1695	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 1696	\N	patch	patch_94_95_c.sql|ox_key_update
 1697	\N	patch	patch_95_96_a.sql|schema_version
+1698	\N	patch	patch_96_97_a.sql|schema_version

modules/t/test-genome-DBs/mus_musculus/core/table.sql

@@ -489,7 +489,7 @@ 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=1698 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1699 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',

modules/t/test-genome-DBs/mus_musculus/variation/failed_description.txt

@@ -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/mus_musculus/variation/meta.txt

@@ -62,3 +62,7 @@
 68	\N	patch	patch_94_95_a.sql|schema version
 69	\N	patch	patch_94_95_b.sql|create table to store allele synonyms
 70	\N	patch	patch_95_96_a.sql|schema_version
+71	\N	patch	patch_95_96_b.sql|modify index on variation_synonym
+72	\N	patch	patch_95_96_c.sql|add new entries to the failed_description table
+73	\N	patch	patch_95_96_d.sql|create table to store failed variation features
+74	\N	patch	patch_95_96_e.sql|Rename motif_name to binding_matrix_stable_id.

modules/t/test-genome-DBs/mus_musculus/variation/table.sql

@@ -113,7 +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,
@@ -131,6 +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,
@@ -178,7 +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=71 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=75 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -195,7 +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,
@@ -681,7 +689,7 @@ 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`)

modules/t/test-genome-DBs/nameless/core/SQLite/table.sql

@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Thu Dec  6 13:50:47 2018
+-- Created on Tue Feb 12 11:45:27 2019
 -- 
 
 BEGIN TRANSACTION;

modules/t/test-genome-DBs/nameless/core/meta.txt

@@ -1,4 +1,4 @@
-1	\N	schema_version	96
+1	\N	schema_version	97
 2	1	assembly.default	NCBI34
 3	1	species.taxonomy_id	9606
 26	1	species.classification	Homo sapiens
@@ -104,3 +104,4 @@
 158	\N	patch	patch_94_95_b.sql|vertebrate_division_rename
 159	\N	patch	patch_94_95_c.sql|ox_key_update
 160	\N	patch	patch_95_96_a.sql|schema_version
+161	\N	patch	patch_96_97_a.sql|schema_version