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ensembl-gh-mirror
ensembl
Commits
a6b79aea
Commit
a6b79aea
authored
Sep 22, 2017
by
premanand17
Browse files
patched test databases for schema_version 91 update
parent
3c02af28
Changes
37
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20 changed files
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52 additions
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28 deletions
+52
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modules/t/test-genome-DBs/circ/core/SQLite/table.sql
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+2
-2
modules/t/test-genome-DBs/circ/core/meta.txt
modules/t/test-genome-DBs/circ/core/meta.txt
+2
-1
modules/t/test-genome-DBs/circ/core/table.sql
modules/t/test-genome-DBs/circ/core/table.sql
+1
-1
modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+2
-2
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+2
-1
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+1
-1
modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
...les/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+2
-2
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+2
-1
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+1
-1
modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
...les/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+2
-2
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+2
-1
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+1
-1
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+1
-0
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+2
-2
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+2
-2
modules/t/test-genome-DBs/mapping/core/meta.txt
modules/t/test-genome-DBs/mapping/core/meta.txt
+2
-1
modules/t/test-genome-DBs/mapping/core/table.sql
modules/t/test-genome-DBs/mapping/core/table.sql
+1
-1
modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
+21
-4
modules/t/test-genome-DBs/multi/compara/meta.txt
modules/t/test-genome-DBs/multi/compara/meta.txt
+1
-0
modules/t/test-genome-DBs/multi/compara/table.sql
modules/t/test-genome-DBs/multi/compara/table.sql
+2
-2
No files found.
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 9
0
2 \N schema_version 9
1
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
=
11
3
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
11
4
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
:2
2
2017
-- Created on
Fri Sep 22 15:51
:2
9
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 9
0
1 \N schema_version 9
1
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
=
1
59
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
1
60
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
:3
9
2017
-- Created on
Fri Sep 22 15:51
:3
8
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 9
0
1 \N schema_version 9
1
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
=
14
1
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
14
2
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 9
0
1 \N schema_version 9
1
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
=
210
4
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
210
5
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
=
2
4
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
2
5
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 9
0
1 \N schema_version 9
1
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
=
14
6
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
14
7
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
=
4
3
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
4
4
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`method_link`
(
`method_link_id`
int
(
10
)
unsigned
NOT
NULL
AUTO_INCREMENT
,
...
...
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