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ensembl-gh-mirror
ensembl
Commits
6399c37b
Commit
6399c37b
authored
Dec 06, 2018
by
Magali Ruffier
Browse files
ENSCORESW-2967
: update schema to 96
parent
e3f8508b
Changes
43
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20 changed files
with
74 additions
and
28 deletions
+74
-28
misc-scripts/ontology/sql/patch_95_96_a.sql
misc-scripts/ontology/sql/patch_95_96_a.sql
+27
-0
misc-scripts/ontology/sql/tables.sql
misc-scripts/ontology/sql/tables.sql
+2
-2
modules/Bio/EnsEMBL/ApiVersion.pm
modules/Bio/EnsEMBL/ApiVersion.pm
+1
-1
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
+3
-1
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
+3
-1
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
+3
-1
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
+3
-1
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/homo_sapiens/variation/meta.txt
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+2
-1
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+1
-1
modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
+8
-0
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
+3
-1
No files found.
misc-scripts/ontology/sql/patch_95_96_a.sql
0 → 100644
View file @
6399c37b
-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-- Copyright [2016-2018] EMBL-European Bioinformatics Institute
--
-- Licensed under the Apache License, Version 2.0 (the "License");
-- you may not use this file except in compliance with the License.
-- You may obtain a copy of the License at
--
-- http://www.apache.org/licenses/LICENSE-2.0
--
-- Unless required by applicable law or agreed to in writing, software
-- distributed under the License is distributed on an "AS IS" BASIS,
-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-- See the License for the specific language governing permissions and
-- limitations under the License.
#
patch_95_96_a
.
sql
#
#
Title
:
Update
schema
version
.
#
#
Description
:
#
Update
schema_version
in
meta
table
to
96
.
UPDATE
meta
SET
meta_value
=
'96'
WHERE
meta_key
=
'schema_version'
;
#
Patch
identifier
INSERT
INTO
meta
(
species_id
,
meta_key
,
meta_value
)
VALUES
(
NULL
,
'patch'
,
'patch_95_96_a.sql|schema_version'
);
misc-scripts/ontology/sql/tables.sql
View file @
6399c37b
...
...
@@ -31,11 +31,11 @@ CREATE TABLE meta (
#
Add
schema
type
and
schema
version
to
the
meta
table
INSERT
INTO
meta
(
meta_key
,
meta_value
)
VALUES
(
'schema_type'
,
'ontology'
),
(
'schema_version'
,
'9
5
'
);
(
'schema_version'
,
'9
6
'
);
#
Patches
included
in
this
schema
file
INSERT
INTO
meta
(
meta_key
,
meta_value
)
VALUES
(
'patch'
,
'patch_9
4
_9
5
_a.sql|schema_version'
);
VALUES
(
'patch'
,
'patch_9
5
_9
6
_a.sql|schema_version'
);
CREATE
TABLE
ontology
(
...
...
modules/Bio/EnsEMBL/ApiVersion.pm
View file @
6399c37b
...
...
@@ -56,7 +56,7 @@ use base qw( Exporter );
our
@EXPORT
=
qw( software_version )
;
my
$API_VERSION
=
9
5
;
my
$API_VERSION
=
9
6
;
sub
software_version
{
return
$API_VERSION
}
...
...
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
View file @
6399c37b
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Wed Sep 26 16:18
:3
7
2018
-- Created on
Thu Dec 6 13:49
:3
2
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
"analysis_id"
smallint
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
,
"analysis_id"
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
);
--
-- Table: "ontology_xref"
...
...
modules/t/test-genome-DBs/circ/core/meta.txt
View file @
6399c37b
...
...
@@ -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
5
2 \N schema_version 9
6
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
...
...
@@ -124,3 +124,5 @@
124 \N patch patch_93_94_c.sql|default_aln_type
125 \N patch patch_94_95_a.sql|schema_version
126 \N patch patch_94_95_b.sql|vertebrate_division_rename
127 \N patch patch_94_95_c.sql|ox_key_update
128 \N patch patch_95_96_a.sql|schema_version
modules/t/test-genome-DBs/circ/core/table.sql
View file @
6399c37b
...
...
@@ -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
7
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
12
9
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAULT
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`analysis_idx`
(
`analysis_id`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
81424
DEFAULT
CHARSET
=
latin1
COLLATE
=
latin1_bin
;
...
...
modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
View file @
6399c37b
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Wed Sep 26 16:18:44
2018
-- Created on
Thu Dec 6 13:49:43
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
"analysis_id"
smallint
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
,
"analysis_id"
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
);
--
-- Table: "ontology_xref"
...
...
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @
6399c37b
1 \N schema_version 9
5
1 \N schema_version 9
6
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
...
...
@@ -103,3 +103,5 @@
170 \N patch patch_93_94_c.sql|default_aln_type
171 \N patch patch_94_95_a.sql|schema_version
172 \N patch patch_94_95_b.sql|vertebrate_division_rename
173 \N patch patch_94_95_c.sql|ox_key_update
174 \N patch patch_95_96_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @
6399c37b
...
...
@@ -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
=
17
3
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
17
5
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAULT
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`analysis_idx`
(
`analysis_id`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
253694
DEFAULT
CHARSET
=
latin1
COLLATE
=
latin1_bin
;
...
...
modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
View file @
6399c37b
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Wed Sep 26 16:18
:5
2
2018
-- Created on
Thu Dec 6 13:49
:5
4
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
"analysis_id"
smallint
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
,
"analysis_id"
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
);
--
-- Table: "ontology_xref"
...
...
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @
6399c37b
1 \N schema_version 9
5
1 \N schema_version 9
6
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
...
...
@@ -103,3 +103,5 @@
152 \N patch patch_93_94_c.sql|default_aln_type
153 \N patch patch_94_95_a.sql|schema_version
154 \N patch patch_94_95_b.sql|vertebrate_division_rename
155 \N patch patch_94_95_c.sql|ox_key_update
156 \N patch patch_95_96_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @
6399c37b
...
...
@@ -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
5
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
''
,
...
...
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAULT
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`analysis_idx`
(
`analysis_id`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
81424
DEFAULT
CHARSET
=
latin1
COLLATE
=
latin1_bin
;
...
...
modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
View file @
6399c37b
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Wed Sep 26 16:18:59
2018
-- Created on
Thu Dec 6 13:50:04
2018
--
BEGIN
TRANSACTION
;
...
...
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
"analysis_id"
smallint
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
,
"analysis_id"
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
);
--
-- Table: "ontology_xref"
...
...
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @
6399c37b
1 \N schema_version 9
5
1 \N schema_version 9
6
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
...
...
@@ -108,3 +108,5 @@
2115 \N patch patch_93_94_c.sql|default_aln_type
2116 \N patch patch_94_95_a.sql|schema_version
2117 \N patch patch_94_95_b.sql|vertebrate_division_rename
2118 \N patch patch_94_95_c.sql|ox_key_update
2119 \N patch patch_95_96_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @
6399c37b
...
...
@@ -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
=
21
18
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
21
20
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
@@ -543,7 +543,7 @@ CREATE TABLE `object_xref` (
`linkage_annotation`
varchar
(
255
)
COLLATE
latin1_bin
DEFAULT
NULL
,
`analysis_id`
smallint
(
5
)
unsigned
DEFAULT
NULL
,
PRIMARY
KEY
(
`object_xref_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
,
`analysis_id`
),
UNIQUE
KEY
`xref_idx`
(
`xref_id`
,
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`ensembl_idx`
(
`ensembl_object_type`
,
`ensembl_id`
),
KEY
`analysis_idx`
(
`analysis_id`
)
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
17375428
DEFAULT
CHARSET
=
latin1
COLLATE
=
latin1_bin
;
...
...
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
View file @
6399c37b
1 \N schema_type variation
2 \N schema_version 9
5
2 \N schema_version 9
6
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
...
...
@@ -34,3 +34,4 @@
34 \N patch patch_93_94_a.sql|schema version
35 \N patch patch_94_95_a.sql|schema version
36 \N patch patch_94_95_b.sql|create table to store allele synonyms
37 \N patch patch_95_96_a.sql|schema_version
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
View file @
6399c37b
...
...
@@ -178,7 +178,7 @@ 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
=
3
7
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
3
8
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
NOT
NULL
,
...
...
modules/t/test-genome-DBs/homo_sapiens/xref/SQLite/table.sql
0 → 100644
View file @
6399c37b
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Dec 6 13:50:07 2018
--
BEGIN
TRANSACTION
;
COMMIT
;
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
View file @
6399c37b
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Wed Sep 26 16:19:0
7 2018
-- Created on
Thu Dec 6 13:50:1
7 2018
--
BEGIN
TRANSACTION
;
...
...
@@ -620,7 +620,7 @@ CREATE TABLE "object_xref" (
"analysis_id"
smallint
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
,
"analysis_id"
);
CREATE
UNIQUE
INDEX
"xref_idx"
ON
"object_xref"
(
"xref_id"
,
"ensembl_object_type"
,
"ensembl_id"
);
--
-- Table: "ontology_xref"
...
...
modules/t/test-genome-DBs/mapping/core/meta.txt
View file @
6399c37b
1 \N schema_version 9
5
1 \N schema_version 9
6
2 1 assembly.default MULTIMAP
3 1 species.taxonomy_id 1
4 1 assembly.mapping chromosome:MULTIMAP#contig
...
...
@@ -64,3 +64,5 @@
157 \N patch patch_93_94_c.sql|default_aln_type
158 \N patch patch_94_95_a.sql|schema_version
159 \N patch patch_94_95_b.sql|vertebrate_division_rename
160 \N patch patch_94_95_c.sql|ox_key_update
161 \N patch patch_95_96_a.sql|schema_version
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