From 591b4c768f6c64d0e2a1cb781cd481c73f1bd5af Mon Sep 17 00:00:00 2001
From: Tiago Grego <tgrego@ebi.ac.uk>
Date: Tue, 23 Apr 2019 10:34:23 +0100
Subject: [PATCH] patched test dbs
---
.../homo_sapiens/core/meta.txt | 3 ++
.../homo_sapiens/core/table.sql | 44 +++++++++++++++++--
.../homo_sapiens/empty/meta.txt | 3 ++
.../homo_sapiens/empty/table.sql | 42 ++++++++++++++++--
.../homo_sapiens/patch/meta.txt | 3 ++
.../homo_sapiens/patch/table.sql | 42 ++++++++++++++++--
6 files changed, 127 insertions(+), 10 deletions(-)
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 058f8ca5..6d8ae3f5 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -105,3 +105,6 @@
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
+175 \N patch patch_96_97_c.sql|rnaproduct_tables
+176 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
+177 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
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 55e35ba2..b9ecd5ae 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -117,7 +117,7 @@ CREATE TABLE `biotype` (
`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;
+) ENGINE=MyISAM AUTO_INCREMENT=88 DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -490,7 +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=175 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=178 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -539,7 +539,7 @@ CREATE TABLE `misc_set` (
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned DEFAULT NULL,
@@ -716,6 +716,42 @@ CREATE TABLE `repeat_feature` (
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM AUTO_INCREMENT=922516 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+CREATE TABLE `rnaproduct` (
+ `rnaproduct_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `rnaproduct_type_id` smallint(5) unsigned NOT NULL,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `seq_start` int(10) NOT NULL,
+ `start_exon_id` int(10) unsigned DEFAULT NULL,
+ `seq_end` int(10) NOT NULL,
+ `end_exon_id` int(10) unsigned DEFAULT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned DEFAULT NULL,
+ `created_date` datetime DEFAULT NULL,
+ `modified_date` datetime DEFAULT NULL,
+ PRIMARY KEY (`rnaproduct_id`),
+ KEY `transcript_idx` (`transcript_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_attrib` (
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `rnaproduct_idx` (`rnaproduct_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_type` (
+ `rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(20) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text,
+ PRIMARY KEY (`rnaproduct_type_id`),
+ UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
@@ -774,7 +810,7 @@ CREATE TABLE `stable_id_event` (
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
`mapping_session_id` int(10) NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
+ `type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
`score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
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 66ae1c0a..9a3dc037 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -105,3 +105,6 @@
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
+157 \N patch patch_96_97_c.sql|rnaproduct_tables
+158 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
+159 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
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 fda1d489..d0dc0873 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -490,7 +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=157 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=160 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -539,7 +539,7 @@ CREATE TABLE `misc_set` (
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned DEFAULT NULL,
@@ -716,6 +716,42 @@ CREATE TABLE `repeat_feature` (
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+CREATE TABLE `rnaproduct` (
+ `rnaproduct_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `rnaproduct_type_id` smallint(5) unsigned NOT NULL,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `seq_start` int(10) NOT NULL,
+ `start_exon_id` int(10) unsigned DEFAULT NULL,
+ `seq_end` int(10) NOT NULL,
+ `end_exon_id` int(10) unsigned DEFAULT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned DEFAULT NULL,
+ `created_date` datetime DEFAULT NULL,
+ `modified_date` datetime DEFAULT NULL,
+ PRIMARY KEY (`rnaproduct_id`),
+ KEY `transcript_idx` (`transcript_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_attrib` (
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `rnaproduct_idx` (`rnaproduct_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_type` (
+ `rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(20) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text,
+ PRIMARY KEY (`rnaproduct_type_id`),
+ UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
@@ -774,7 +810,7 @@ CREATE TABLE `stable_id_event` (
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
`mapping_session_id` int(10) NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
+ `type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
`score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
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 0b0f8560..a89ba992 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
@@ -110,3 +110,6 @@
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
+2120 \N patch patch_96_97_c.sql|rnaproduct_tables
+2121 \N patch patch_96_97_d.sql|add_object_type_rnaproduct
+2122 \N patch patch_96_97_e.sql|add_stable_id_event_type_rnaproduct
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 f4c739da..c8acbc72 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -490,7 +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=2120 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2123 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -539,7 +539,7 @@ CREATE TABLE `misc_set` (
CREATE TABLE `object_xref` (
`object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
`ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
- `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
+ `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','Operon','OperonTranscript','Marker','RNAProduct') COLLATE latin1_bin NOT NULL,
`xref_id` int(10) unsigned NOT NULL,
`linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
`analysis_id` smallint(5) unsigned DEFAULT NULL,
@@ -716,6 +716,42 @@ CREATE TABLE `repeat_feature` (
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM AUTO_INCREMENT=31576665 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+CREATE TABLE `rnaproduct` (
+ `rnaproduct_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `rnaproduct_type_id` smallint(5) unsigned NOT NULL,
+ `transcript_id` int(10) unsigned NOT NULL,
+ `seq_start` int(10) NOT NULL,
+ `start_exon_id` int(10) unsigned DEFAULT NULL,
+ `seq_end` int(10) NOT NULL,
+ `end_exon_id` int(10) unsigned DEFAULT NULL,
+ `stable_id` varchar(128) DEFAULT NULL,
+ `version` smallint(5) unsigned DEFAULT NULL,
+ `created_date` datetime DEFAULT NULL,
+ `modified_date` datetime DEFAULT NULL,
+ PRIMARY KEY (`rnaproduct_id`),
+ KEY `transcript_idx` (`transcript_id`),
+ KEY `stable_id_idx` (`stable_id`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_attrib` (
+ `rnaproduct_id` int(10) unsigned NOT NULL DEFAULT '0',
+ `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
+ `value` text NOT NULL,
+ UNIQUE KEY `rnaproduct_attribx` (`rnaproduct_id`,`attrib_type_id`,`value`(500)),
+ KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
+ KEY `val_only_idx` (`value`(40)),
+ KEY `rnaproduct_idx` (`rnaproduct_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
+CREATE TABLE `rnaproduct_type` (
+ `rnaproduct_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
+ `code` varchar(20) NOT NULL DEFAULT '',
+ `name` varchar(255) NOT NULL DEFAULT '',
+ `description` text,
+ PRIMARY KEY (`rnaproduct_type_id`),
+ UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`name` varchar(255) COLLATE latin1_bin NOT NULL,
@@ -774,7 +810,7 @@ CREATE TABLE `stable_id_event` (
`new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
`new_version` smallint(6) DEFAULT NULL,
`mapping_session_id` int(10) NOT NULL DEFAULT '0',
- `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
+ `type` enum('gene','transcript','translation','rnaproduct') COLLATE latin1_bin NOT NULL,
`score` float NOT NULL DEFAULT '0',
UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
KEY `new_idx` (`new_stable_id`),
--
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