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Commit a6b79aea authored by premanand17's avatar premanand17
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patched test databases for schema_version 91 update

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modules/t/test-genome-DBs/circ/core/SQLite/table.sql
View file @ a6b79aea
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Jun 1 11:16:06 2017
-- Created on Fri Sep 22 15:51:19 2017
--
BEGIN TRANSACTION;
......@@ -729,7 +729,7 @@ CREATE TABLE protein_feature (
seq_end integer NOT NULL DEFAULT 0,
hit_start integer NOT NULL DEFAULT 0,
hit_end integer NOT NULL DEFAULT 0,
hit_name varchar(40) NOT NULL DEFAULT '',
hit_name varchar(40) NOT NULL,
analysis_id integer NOT NULL DEFAULT 0,
score double precision NOT NULL DEFAULT 0,
evalue double precision,
......
modules/t/test-genome-DBs/circ/core/meta.txt
View file @ a6b79aea
......@@ -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 90
2 \N schema_version 91
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
......@@ -110,3 +110,4 @@
110 \N patch patch_89_90_a.sql|schema_version
111 \N patch patch_89_90_b.sql|remove_status
112 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
113 \N patch patch_90_91_a.sql|schema_version
modules/t/test-genome-DBs/circ/core/table.sql
View file @ a6b79aea
......@@ -476,7 +476,7 @@ 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=113 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=114 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
View file @ a6b79aea
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Jun 1 11:16:22 2017
-- Created on Fri Sep 22 15:51:29 2017
--
BEGIN TRANSACTION;
......@@ -729,7 +729,7 @@ CREATE TABLE protein_feature (
seq_end integer NOT NULL DEFAULT 0,
hit_start integer NOT NULL DEFAULT 0,
hit_end integer NOT NULL DEFAULT 0,
hit_name varchar(40) NOT NULL DEFAULT '',
hit_name varchar(40) NOT NULL,
analysis_id integer NOT NULL DEFAULT 0,
score double precision NOT NULL DEFAULT 0,
evalue double precision,
......
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @ a6b79aea
1 \N schema_version 90
1 \N schema_version 91
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
......@@ -89,3 +89,4 @@
156 \N patch patch_89_90_a.sql|schema_version
157 \N patch patch_89_90_b.sql|remove_status
158 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
159 \N patch patch_90_91_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @ a6b79aea
......@@ -476,7 +476,7 @@ 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=159 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 '',
......
modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
View file @ a6b79aea
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Jun 1 11:16:39 2017
-- Created on Fri Sep 22 15:51:38 2017
--
BEGIN TRANSACTION;
......@@ -729,7 +729,7 @@ CREATE TABLE protein_feature (
seq_end integer NOT NULL DEFAULT 0,
hit_start integer NOT NULL DEFAULT 0,
hit_end integer NOT NULL DEFAULT 0,
hit_name varchar(40) NOT NULL DEFAULT '',
hit_name varchar(40) NOT NULL,
analysis_id integer NOT NULL DEFAULT 0,
score double precision NOT NULL DEFAULT 0,
evalue double precision,
......
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @ a6b79aea
1 \N schema_version 90
1 \N schema_version 91
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
......@@ -89,3 +89,4 @@
138 \N patch patch_89_90_a.sql|schema_version
139 \N patch patch_89_90_b.sql|remove_status
140 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
141 \N patch patch_90_91_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @ a6b79aea
......@@ -476,7 +476,7 @@ 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=141 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=142 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
View file @ a6b79aea
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Jun 1 11:16:56 2017
-- Created on Fri Sep 22 15:51:48 2017
--
BEGIN TRANSACTION;
......@@ -729,7 +729,7 @@ CREATE TABLE protein_feature (
seq_end integer NOT NULL DEFAULT 0,
hit_start integer NOT NULL DEFAULT 0,
hit_end integer NOT NULL DEFAULT 0,
hit_name varchar(40) NOT NULL DEFAULT '',
hit_name varchar(40) NOT NULL,
analysis_id integer NOT NULL DEFAULT 0,
score double precision NOT NULL DEFAULT 0,
evalue double precision,
......
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @ a6b79aea
1 \N schema_version 90
1 \N schema_version 91
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
......@@ -94,3 +94,4 @@
2101 \N patch patch_89_90_a.sql|schema_version
2102 \N patch patch_89_90_b.sql|remove_status
2103 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
2104 \N patch patch_90_91_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @ a6b79aea
......@@ -476,7 +476,7 @@ 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=2104 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=2105 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/meta.txt
View file @ a6b79aea
......@@ -21,3 +21,4 @@
21 \N patch patch_89_90_a.sql|schema version
22 \N patch patch_89_90_b.sql|add start_retained_variant to consequence_types in variation_feature and transcript_variation
23 \N patch patch_89_90_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
24 \N patch patch_90_91_b.sql|extend the characters supported in the publication.authors column
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
View file @ a6b79aea
......@@ -168,7 +168,7 @@ 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=24 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=25 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -306,7 +306,7 @@ CREATE TABLE `protein_function_predictions_attrib` (
CREATE TABLE `publication` (
`publication_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`title` varchar(255) DEFAULT NULL,
`authors` varchar(255) DEFAULT NULL,
`authors` varchar(255) CHARACTER SET latin2 DEFAULT NULL,
`pmid` int(10) DEFAULT NULL,
`pmcid` varchar(255) DEFAULT NULL,
`year` int(10) unsigned DEFAULT NULL,
......
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
View file @ a6b79aea
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Jun 1 11:17:12 2017
-- Created on Fri Sep 22 15:51:57 2017
--
BEGIN TRANSACTION;
......@@ -729,7 +729,7 @@ CREATE TABLE protein_feature (
seq_end integer NOT NULL DEFAULT 0,
hit_start integer NOT NULL DEFAULT 0,
hit_end integer NOT NULL DEFAULT 0,
hit_name varchar(40) NOT NULL DEFAULT '',
hit_name varchar(40) NOT NULL,
analysis_id integer NOT NULL DEFAULT 0,
score double precision NOT NULL DEFAULT 0,
evalue double precision,
......
modules/t/test-genome-DBs/mapping/core/meta.txt
View file @ a6b79aea
1 \N schema_version 90
1 \N schema_version 91
2 1 assembly.default MULTIMAP
3 1 species.taxonomy_id 1
4 1 assembly.mapping chromosome:MULTIMAP#contig
......@@ -50,3 +50,4 @@
143 \N patch patch_89_90_a.sql|schema_version
144 \N patch patch_89_90_b.sql|remove_status
145 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
146 \N patch patch_90_91_a.sql|schema_version
modules/t/test-genome-DBs/mapping/core/table.sql
View file @ a6b79aea
......@@ -476,7 +476,7 @@ 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=146 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=147 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
View file @ a6b79aea
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Jun 1 11:17:43 2017
-- Created on Fri Sep 22 15:52:04 2017
--
BEGIN TRANSACTION;
......@@ -49,7 +49,7 @@ CREATE TABLE constrained_element (
dnafrag_end integer NOT NULL,
dnafrag_strand integer NOT NULL,
method_link_species_set_id integer NOT NULL,
p_value double precision,
p_value double precision NOT NULL DEFAULT 0,
score double precision NOT NULL DEFAULT 0
);
......@@ -364,8 +364,8 @@ CREATE TABLE genomic_align_tree (
root_id bigint NOT NULL DEFAULT 0,
left_index integer NOT NULL DEFAULT 0,
right_index integer NOT NULL DEFAULT 0,
left_node_id bigint NOT NULL DEFAULT 0,
right_node_id bigint NOT NULL DEFAULT 0,
left_node_id bigint,
right_node_id bigint,
distance_to_parent double precision NOT NULL DEFAULT 1
);
......@@ -609,6 +609,23 @@ CREATE TABLE seq_member (
CREATE UNIQUE INDEX stable_id04 ON seq_member (stable_id);
--
-- Table: seq_member_projection
--
CREATE TABLE seq_member_projection (
target_seq_member_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
source_seq_member_id integer NOT NULL,
identity float(5,2) NOT NULL
);
--
-- Table: seq_member_projection_stable_id
--
CREATE TABLE seq_member_projection_stable_id (
target_seq_member_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
source_stable_id varchar(128) NOT NULL
);
--
-- Table: sequence
--
......
modules/t/test-genome-DBs/multi/compara/meta.txt
View file @ a6b79aea
......@@ -35,3 +35,4 @@
40 \N patch patch_89_90_d.sql|genomic_align_tree_left_node_id_null
41 \N patch patch_89_90_e.sql|seq_member_projection
42 \N patch patch_89_90_f.sql|gene_member_missing_biotype_groups
43 \N patch patch_90_91_b.sql|gene_member_qc.seq_member_id.unsigned
modules/t/test-genome-DBs/multi/compara/table.sql
View file @ a6b79aea
......@@ -172,7 +172,7 @@ CREATE TABLE `gene_member_hom_stats` (
CREATE TABLE `gene_member_qc` (
`gene_member_stable_id` varchar(128) NOT NULL,
`genome_db_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) DEFAULT NULL,
`seq_member_id` int(10) unsigned DEFAULT NULL,
`n_species` int(11) DEFAULT NULL,
`n_orth` int(11) DEFAULT NULL,
`avg_cov` float DEFAULT NULL,
......@@ -434,7 +434,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`meta_value`(255))
) ENGINE=MyISAM AUTO_INCREMENT=43 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=44 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......
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