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ensembl-gh-mirror
ensembl
Commits
fc4990b5
Commit
fc4990b5
authored
Feb 12, 2019
by
Tiago Grego
Browse files
patched test dbs with patch_96_97_b and updated fixtures
parent
5415237e
Changes
31
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20 changed files
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39 additions
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22 deletions
+39
-22
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+3
-2
modules/t/test-genome-DBs/circ/core/meta.txt
modules/t/test-genome-DBs/circ/core/meta.txt
+1
-0
modules/t/test-genome-DBs/circ/core/table.sql
modules/t/test-genome-DBs/circ/core/table.sql
+2
-1
modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+3
-2
modules/t/test-genome-DBs/homo_sapiens/core/biotype.txt
modules/t/test-genome-DBs/homo_sapiens/core/biotype.txt
+3
-3
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+1
-0
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+2
-1
modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
...les/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+3
-2
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+1
-0
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+2
-1
modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
...les/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+3
-2
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+1
-0
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+2
-1
modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
+1
-1
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+3
-2
modules/t/test-genome-DBs/mapping/core/meta.txt
modules/t/test-genome-DBs/mapping/core/meta.txt
+1
-0
modules/t/test-genome-DBs/mapping/core/table.sql
modules/t/test-genome-DBs/mapping/core/table.sql
+2
-1
modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
+1
-1
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
+3
-2
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+1
-0
No files found.
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
View file @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:04
2019
-- Created on Tue Feb 12 1
5:00:15
2019
--
BEGIN
TRANSACTION
;
...
...
@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id"
integer
,
"description"
text
,
"biotype_group"
enum
,
"so_acc"
varchar
(
64
)
"so_acc"
varchar
(
64
),
"so_term"
varchar
(
1023
)
);
CREATE
UNIQUE
INDEX
"name_type_idx"
ON
"biotype"
(
"name"
,
"object_type"
);
...
...
modules/t/test-genome-DBs/circ/core/meta.txt
View file @
fc4990b5
...
...
@@ -127,3 +127,4 @@
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
130 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/circ/core/table.sql
View file @
fc4990b5
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +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
=
13
0
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
13
1
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 @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:08
2019
-- Created on Tue Feb 12 1
5:00:19
2019
--
BEGIN
TRANSACTION
;
...
...
@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id"
integer
,
"description"
text
,
"biotype_group"
enum
,
"so_acc"
varchar
(
64
)
"so_acc"
varchar
(
64
),
"so_term"
varchar
(
1023
)
);
CREATE
UNIQUE
INDEX
"name_type_idx"
ON
"biotype"
(
"name"
,
"object_type"
);
...
...
modules/t/test-genome-DBs/homo_sapiens/core/biotype.txt
View file @
fc4990b5
64 protein_coding gene core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0001217
65 protein_coding transcript core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0000234
87 tRNA gene core,otherfeatures,presite 76 \N snoncoding SO:0001263
64 protein_coding gene core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0001217
protein_coding_gene
65 protein_coding transcript core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0000234
mRNA
87 tRNA gene core,otherfeatures,presite 76 \N snoncoding SO:0001263
ncRNA_gene
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @
fc4990b5
...
...
@@ -106,3 +106,4 @@
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
176 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @
fc4990b5
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
88
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +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
=
17
6
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
17
7
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 @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:11
2019
-- Created on Tue Feb 12 1
5:00:22
2019
--
BEGIN
TRANSACTION
;
...
...
@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id"
integer
,
"description"
text
,
"biotype_group"
enum
,
"so_acc"
varchar
(
64
)
"so_acc"
varchar
(
64
),
"so_term"
varchar
(
1023
)
);
CREATE
UNIQUE
INDEX
"name_type_idx"
ON
"biotype"
(
"name"
,
"object_type"
);
...
...
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @
fc4990b5
...
...
@@ -106,3 +106,4 @@
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
158 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @
fc4990b5
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +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
=
15
8
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
15
9
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 @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:14
2019
-- Created on Tue Feb 12 1
5:00:25
2019
--
BEGIN
TRANSACTION
;
...
...
@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id"
integer
,
"description"
text
,
"biotype_group"
enum
,
"so_acc"
varchar
(
64
)
"so_acc"
varchar
(
64
),
"so_term"
varchar
(
1023
)
);
CREATE
UNIQUE
INDEX
"name_type_idx"
ON
"biotype"
(
"name"
,
"object_type"
);
...
...
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @
fc4990b5
...
...
@@ -111,3 +111,4 @@
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
2121 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @
fc4990b5
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +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
=
212
1
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
212
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/xref/SQLite/table.sql
View file @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:15
2019
-- Created on Tue Feb 12 1
5:00:26
2019
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
View file @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:18
2019
-- Created on Tue Feb 12 1
5:00:29
2019
--
BEGIN
TRANSACTION
;
...
...
@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id"
integer
,
"description"
text
,
"biotype_group"
enum
,
"so_acc"
varchar
(
64
)
"so_acc"
varchar
(
64
),
"so_term"
varchar
(
1023
)
);
CREATE
UNIQUE
INDEX
"name_type_idx"
ON
"biotype"
(
"name"
,
"object_type"
);
...
...
modules/t/test-genome-DBs/mapping/core/meta.txt
View file @
fc4990b5
...
...
@@ -67,3 +67,4 @@
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
163 \N patch patch_96_97_b.sql|biotype_so_term
modules/t/test-genome-DBs/mapping/core/table.sql
View file @
fc4990b5
...
...
@@ -114,6 +114,7 @@ CREATE TABLE `biotype` (
`description`
text
,
`biotype_group`
enum
(
'coding'
,
'pseudogene'
,
'snoncoding'
,
'lnoncoding'
,
'mnoncoding'
,
'LRG'
,
'undefined'
,
'no_group'
)
DEFAULT
NULL
,
`so_acc`
varchar
(
64
)
DEFAULT
NULL
,
`so_term`
varchar
(
1023
)
DEFAULT
NULL
,
PRIMARY
KEY
(
`biotype_id`
),
UNIQUE
KEY
`name_type_idx`
(
`name`
,
`object_type`
)
)
ENGINE
=
MyISAM
DEFAULT
CHARSET
=
latin1
;
...
...
@@ -489,7 +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
=
16
3
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
16
4
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 @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:21
2019
-- Created on Tue Feb 12 1
5:00:32
2019
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
View file @
fc4990b5
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Tue Feb 12 1
1:45:24
2019
-- Created on Tue Feb 12 1
5:00:36
2019
--
BEGIN
TRANSACTION
;
...
...
@@ -142,7 +142,8 @@ CREATE TABLE "biotype" (
"attrib_type_id"
integer
,
"description"
text
,
"biotype_group"
enum
,
"so_acc"
varchar
(
64
)
"so_acc"
varchar
(
64
),
"so_term"
varchar
(
1023
)
);
CREATE
UNIQUE
INDEX
"name_type_idx"
ON
"biotype"
(
"name"
,
"object_type"
);
...
...
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
View file @
fc4990b5
...
...
@@ -184,3 +184,4 @@
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
1699 \N patch patch_96_97_b.sql|biotype_so_term
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