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ensembl-gh-mirror
ensembl
Commits
53e6da4f
Commit
53e6da4f
authored
Apr 24, 2018
by
Magali Ruffier
Browse files
updated to version 94
parent
6f882c15
Changes
36
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20 changed files
with
52 additions
and
20 deletions
+52
-20
misc-scripts/ontology/sql/patch_93_94_a.sql
misc-scripts/ontology/sql/patch_93_94_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
+1
-1
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
+1
-1
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
+1
-1
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
+1
-1
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/mapping/core/SQLite/table.sql
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+1
-1
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
+1
-1
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
+1
-1
No files found.
misc-scripts/ontology/sql/patch_93_94_a.sql
0 → 100644
View file @
53e6da4f
-- 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_93_94_a
.
sql
#
#
Title
:
Update
schema
version
.
#
#
Description
:
#
Update
schema_version
in
meta
table
to
94
.
UPDATE
meta
SET
meta_value
=
'94'
WHERE
meta_key
=
'schema_version'
;
#
Patch
identifier
INSERT
INTO
meta
(
species_id
,
meta_key
,
meta_value
)
VALUES
(
NULL
,
'patch'
,
'patch_93_94_a.sql|schema_version'
);
misc-scripts/ontology/sql/tables.sql
View file @
53e6da4f
...
...
@@ -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
3
'
);
(
'schema_version'
,
'9
4
'
);
#
Patches
included
in
this
schema
file
INSERT
INTO
meta
(
meta_key
,
meta_value
)
VALUES
(
'patch'
,
'patch_9
2
_9
3
_a.sql|schema_version'
);
VALUES
(
'patch'
,
'patch_9
3
_9
4
_a.sql|schema_version'
);
CREATE
TABLE
ontology
(
...
...
modules/Bio/EnsEMBL/ApiVersion.pm
View file @
53e6da4f
...
...
@@ -56,7 +56,7 @@ use base qw( Exporter );
our
@EXPORT
=
qw( software_version )
;
my
$API_VERSION
=
9
3
;
my
$API_VERSION
=
9
4
;
sub
software_version
{
return
$API_VERSION
}
...
...
modules/t/test-genome-DBs/circ/core/SQLite/table.sql
View file @
53e6da4f
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Fri
Apr
6 15:15:57
2018
-- Created on
Tue
Apr
24 11:41:38
2018
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/circ/core/meta.txt
View file @
53e6da4f
...
...
@@ -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
3
2 \N schema_version 9
4
8 1 assembly.accession GCA_000292705.1
10 1 assembly.date 2012-08
7 1 assembly.default GCA_000292705.1
...
...
@@ -119,3 +119,4 @@
119 \N patch patch_92_93_a.sql|schema_version
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
modules/t/test-genome-DBs/circ/core/table.sql
View file @
53e6da4f
...
...
@@ -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
2
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
12
3
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 @
53e6da4f
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Fri
Apr
6 15:16:01
2018
-- Created on
Tue
Apr
24 11:41:49
2018
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @
53e6da4f
1 \N schema_version 9
3
1 \N schema_version 9
4
2 1 assembly.default NCBI34
3 1 species.taxonomy_id 9606
26 1 species.classification Homo sapiens
...
...
@@ -98,3 +98,4 @@
165 \N patch patch_92_93_a.sql|schema_version
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
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @
53e6da4f
...
...
@@ -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
=
16
8
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
16
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/empty/SQLite/table.sql
View file @
53e6da4f
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Fri
Apr
6 15:16
:0
4
2018
-- Created on
Tue
Apr
24 11:42
:0
0
2018
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @
53e6da4f
1 \N schema_version 9
3
1 \N schema_version 9
4
2 1 assembly.default NCBI34
33 1 species.classification Chordata
32 1 species.classification Vertebrata
...
...
@@ -98,3 +98,4 @@
147 \N patch patch_92_93_a.sql|schema_version
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
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @
53e6da4f
...
...
@@ -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
0
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
15
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/patch/SQLite/table.sql
View file @
53e6da4f
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Fri
Apr
6 15:16:07
2018
-- Created on
Tue
Apr
24 11:42:12
2018
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @
53e6da4f
1 \N schema_version 9
3
1 \N schema_version 9
4
2014 1 species.classification Haplorrhini
40 1 assembly.default GRCh37
41 1 assembly.date 2009-02
...
...
@@ -103,3 +103,4 @@
2110 \N patch patch_92_93_a.sql|schema_version
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
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @
53e6da4f
...
...
@@ -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
3
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
211
4
DEFAULT
CHARSET
=
latin1
;
CREATE
TABLE
`meta_coord`
(
`table_name`
varchar
(
40
)
COLLATE
latin1_bin
NOT
NULL
DEFAULT
''
,
...
...
modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
View file @
53e6da4f
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Fri
Apr
6 15:16:11
2018
-- Created on
Tue
Apr
24 11:42:24
2018
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/mapping/core/meta.txt
View file @
53e6da4f
1 \N schema_version 9
3
1 \N schema_version 9
4
2 1 assembly.default MULTIMAP
3 1 species.taxonomy_id 1
4 1 assembly.mapping chromosome:MULTIMAP#contig
...
...
@@ -59,3 +59,4 @@
152 \N patch patch_92_93_a.sql|schema_version
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
modules/t/test-genome-DBs/mapping/core/table.sql
View file @
53e6da4f
...
...
@@ -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
6
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 @
53e6da4f
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Fri
Apr
6 15:16:1
3 2018
-- Created on
Tue
Apr
24 11:42:3
3 2018
--
BEGIN
TRANSACTION
;
...
...
modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
View file @
53e6da4f
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on
Fri
Apr
6 15:16:17
2018
-- Created on
Tue
Apr
24 11:42:43
2018
--
BEGIN
TRANSACTION
;
...
...
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