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ensembl-gh-mirror
ensembl
Commits
1e80fb15
Commit
1e80fb15
authored
Apr 25, 2018
by
Magali Ruffier
Browse files
ENSCORESW-2377
: make analysis_id nullable in object_xref
parent
53e6da4f
Changes
32
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20 changed files
with
647 additions
and
641 deletions
+647
-641
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
+1
-0
modules/t/test-genome-DBs/circ/core/table.sql
modules/t/test-genome-DBs/circ/core/table.sql
+2
-2
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
+1
-0
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+2
-2
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
+1
-0
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+2
-2
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
+1
-0
modules/t/test-genome-DBs/homo_sapiens/patch/object_xref.txt
modules/t/test-genome-DBs/homo_sapiens/patch/object_xref.txt
+616
-616
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
modules/t/test-genome-DBs/homo_sapiens/patch/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
+1
-0
modules/t/test-genome-DBs/mapping/core/table.sql
modules/t/test-genome-DBs/mapping/core/table.sql
+2
-2
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
+2
-2
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+1
-0
modules/t/test-genome-DBs/mus_musculus/core/table.sql
modules/t/test-genome-DBs/mus_musculus/core/table.sql
+2
-2
No files found.
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
View file @
1e80fb15
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Tue
Apr 2
4 11:41:38
2018
-- Created on
Wed
Apr 2
5 09:28:02
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
ensembl_object_type
enum
NOT
NULL
DEFAULT
'RawContig'
,
xref_id
integer
NOT
NULL
,
linkage_annotation
varchar
(
255
),
analysis_id
smallint
NOT
NULL
analysis_id
smallint
);
CREATE
UNIQUE
INDEX
xref_idx
ON
object_xref
(
xref_id
,
ensembl_object_type
,
ensembl_id
,
analysis_id
);
...
...
modules/t/test-genome-DBs/circ/core/meta.txt
View file @
1e80fb15
...
...
@@ -120,3 +120,4 @@
120 \N patch patch_92_93_b.sql|biotype_table
121 \N patch patch_92_93_c.sql|collate_index_interpro
122 \N patch patch_93_94_a.sql|schema_version
123 \N patch patch_93_94_c.sql|nullable_ox_analysis
modules/t/test-genome-DBs/circ/core/table.sql
View file @
1e80fb15
...
...
@@ -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
=
12
3
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
12
4
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
`ensembl_object_type`
enum
(
'RawContig'
,
'Transcript'
,
'Gene'
,
'Translation'
,
'regulatory_factor'
,
'regulatory_feature'
,
'Marker'
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
'RawContig'
,
`xref_id`
int
(
10
)
unsigned
NOT
NULL
,
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
NO
T
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAUL
T
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
...
...
modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
View file @
1e80fb15
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Tue
Apr 2
4 11:41:49
2018
-- Created on
Wed
Apr 2
5 09:28:13
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
ensembl_object_type
enum
NOT
NULL
DEFAULT
'RawContig'
,
xref_id
integer
NOT
NULL
,
linkage_annotation
varchar
(
255
),
analysis_id
smallint
NOT
NULL
analysis_id
smallint
);
CREATE
UNIQUE
INDEX
xref_idx
ON
object_xref
(
xref_id
,
ensembl_object_type
,
ensembl_id
,
analysis_id
);
...
...
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @
1e80fb15
...
...
@@ -99,3 +99,4 @@
166 \N patch patch_92_93_b.sql|biotype_table
167 \N patch patch_92_93_c.sql|collate_index_interpro
168 \N patch patch_93_94_a.sql|schema_version
169 \N patch patch_93_94_c.sql|nullable_ox_analysis
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @
1e80fb15
...
...
@@ -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
=
1
69
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
1
70
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
`ensembl_object_type`
enum
(
'RawContig'
,
'Transcript'
,
'Gene'
,
'Translation'
,
'regulatory_factor'
,
'regulatory_feature'
,
'Marker'
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
'RawContig'
,
`xref_id`
int
(
10
)
unsigned
NOT
NULL
,
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
NO
T
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAUL
T
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
...
...
modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
View file @
1e80fb15
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Tue
Apr 2
4 11:42:00
2018
-- Created on
Wed
Apr 2
5 09:28:23
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
ensembl_object_type
enum
NOT
NULL
DEFAULT
'RawContig'
,
xref_id
integer
NOT
NULL
,
linkage_annotation
varchar
(
255
),
analysis_id
smallint
NOT
NULL
analysis_id
smallint
);
CREATE
UNIQUE
INDEX
xref_idx
ON
object_xref
(
xref_id
,
ensembl_object_type
,
ensembl_id
,
analysis_id
);
...
...
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @
1e80fb15
...
...
@@ -99,3 +99,4 @@
148 \N patch patch_92_93_b.sql|biotype_table
149 \N patch patch_92_93_c.sql|collate_index_interpro
150 \N patch patch_93_94_a.sql|schema_version
151 \N patch patch_93_94_c.sql|nullable_ox_analysis
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @
1e80fb15
...
...
@@ -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
=
15
1
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
15
2
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
`ensembl_object_type`
enum
(
'RawContig'
,
'Transcript'
,
'Gene'
,
'Translation'
,
'regulatory_factor'
,
'regulatory_feature'
,
'Marker'
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
'RawContig'
,
`xref_id`
int
(
10
)
unsigned
NOT
NULL
,
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
NO
T
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAUL
T
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
...
...
modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
View file @
1e80fb15
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Tue
Apr 2
4 11:42:12
2018
-- Created on
Wed
Apr 2
5 09:28:34
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
ensembl_object_type
enum
NOT
NULL
DEFAULT
'RawContig'
,
xref_id
integer
NOT
NULL
,
linkage_annotation
varchar
(
255
),
analysis_id
smallint
NOT
NULL
analysis_id
smallint
);
CREATE
UNIQUE
INDEX
xref_idx
ON
object_xref
(
xref_id
,
ensembl_object_type
,
ensembl_id
,
analysis_id
);
...
...
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @
1e80fb15
...
...
@@ -104,3 +104,4 @@
2111 \N patch patch_92_93_b.sql|biotype_table
2112 \N patch patch_92_93_c.sql|collate_index_interpro
2113 \N patch patch_93_94_a.sql|schema_version
2114 \N patch patch_93_94_c.sql|nullable_ox_analysis
modules/t/test-genome-DBs/homo_sapiens/patch/object_xref.txt
View file @
1e80fb15
This diff is collapsed.
Click to expand it.
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @
1e80fb15
...
...
@@ -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
=
211
4
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
211
5
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
`ensembl_object_type`
enum
(
'RawContig'
,
'Transcript'
,
'Gene'
,
'Translation'
,
'regulatory_factor'
,
'regulatory_feature'
,
'Marker'
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
'RawContig'
,
`xref_id`
int
(
10
)
unsigned
NOT
NULL
,
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
NO
T
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAUL
T
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
...
...
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
View file @
1e80fb15
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Tue
Apr 2
4 11:42:2
4 2018
-- Created on
Wed
Apr 2
5 09:28:4
4 2018
--
BEGIN
TRANSACTION
;
...
...
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
ensembl_object_type
enum
NOT
NULL
DEFAULT
'RawContig'
,
xref_id
integer
NOT
NULL
,
linkage_annotation
varchar
(
255
),
analysis_id
smallint
NOT
NULL
analysis_id
smallint
);
CREATE
UNIQUE
INDEX
xref_idx
ON
object_xref
(
xref_id
,
ensembl_object_type
,
ensembl_id
,
analysis_id
);
...
...
modules/t/test-genome-DBs/mapping/core/meta.txt
View file @
1e80fb15
...
...
@@ -60,3 +60,4 @@
153 \N patch patch_92_93_b.sql|biotype_table
154 \N patch patch_92_93_c.sql|collate_index_interpro
155 \N patch patch_93_94_a.sql|schema_version
156 \N patch patch_93_94_c.sql|nullable_ox_analysis
modules/t/test-genome-DBs/mapping/core/table.sql
View file @
1e80fb15
...
...
@@ -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
=
15
6
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
15
7
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
`ensembl_object_type`
enum
(
'RawContig'
,
'Transcript'
,
'Gene'
,
'Translation'
,
'regulatory_factor'
,
'regulatory_feature'
,
'Marker'
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
'RawContig'
,
`xref_id`
int
(
10
)
unsigned
NOT
NULL
,
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
NO
T
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAUL
T
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
...
...
modules/t/test-genome-DBs/multi/compara/SQLite/table.sql
View file @
1e80fb15
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Tue
Apr 2
4 11:42:3
3 2018
-- Created on
Wed
Apr 2
5 09:28:5
3 2018
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
View file @
1e80fb15
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Tue
Apr 2
4 11:42:43
2018
-- Created on
Wed
Apr 2
5 09:29:04
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -617,7 +617,7 @@ CREATE TABLE object_xref (
ensembl_object_type
enum
NOT
NULL
DEFAULT
'RawContig'
,
xref_id
integer
NOT
NULL
,
linkage_annotation
varchar
(
255
),
analysis_id
smallint
NOT
NULL
analysis_id
smallint
);
CREATE
UNIQUE
INDEX
xref_idx
ON
object_xref
(
xref_id
,
ensembl_object_type
,
ensembl_id
,
analysis_id
);
...
...
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
View file @
1e80fb15
...
...
@@ -177,3 +177,4 @@
1689 \N patch patch_92_93_b.sql|biotype_table
1690 \N patch patch_92_93_c.sql|collate_index_interpro
1691 \N patch patch_93_94_a.sql|schema_version
1692 \N patch patch_93_94_c.sql|nullable_ox_analysis
modules/t/test-genome-DBs/mus_musculus/core/table.sql
View file @
1e80fb15
...
...
@@ -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
=
169
2
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
169
3
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -541,7 +541,7 @@ CREATE TABLE `object_xref` (
`ensembl_object_type`
enum
(
'RawContig'
,
'Transcript'
,
'Gene'
,
'Translation'
,
'regulatory_factor'
,
'regulatory_feature'
,
'Marker'
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
'RawContig'
,
`xref_id`
int
(
10
)
unsigned
NOT
NULL
,
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
NO
T
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAUL
T
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
...
...
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