From 5ad40c1d15721949c54132324cc38aec104c093a Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 10 May 2016 13:16:05 +0100
Subject: [PATCH] ontology updated for release 85
---
misc-scripts/ontology/sql/patch_84_85_a.sql | 26 +++++++++++++++++++
misc-scripts/ontology/sql/tables.sql | 10 +++++--
.../ontology/ontology/meta.txt | 3 ++-
3 files changed, 36 insertions(+), 3 deletions(-)
create mode 100644 misc-scripts/ontology/sql/patch_84_85_a.sql
diff --git a/misc-scripts/ontology/sql/patch_84_85_a.sql b/misc-scripts/ontology/sql/patch_84_85_a.sql
new file mode 100644
index 0000000000..e2ed93c541
--- /dev/null
+++ b/misc-scripts/ontology/sql/patch_84_85_a.sql
@@ -0,0 +1,26 @@
+-- Copyright [1999-2016] Wellcome Trust Sanger Institute and the 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_84_85_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+# Update schema_version in meta table to 85.
+
+UPDATE meta SET meta_value='85' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+ VALUES (NULL, 'patch', 'patch_84_85_a.sql|schema_version');
diff --git a/misc-scripts/ontology/sql/tables.sql b/misc-scripts/ontology/sql/tables.sql
index efa8b35523..82832a92b3 100644
--- a/misc-scripts/ontology/sql/tables.sql
+++ b/misc-scripts/ontology/sql/tables.sql
@@ -30,11 +30,15 @@ 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', '84');
+ ('schema_version', '85');
# Patches included in this schema file
INSERT INTO meta (meta_key, meta_value)
- VALUES ('patch', 'patch_83_84_a.sql|schema_version');
+ VALUES ('patch', 'patch_84_85_a.sql|schema_version');
+INSERT INTO meta (meta_key, meta_value)
+ VALUES ('patch', 'patch_84_85_b.sql|confident_relationship');
+INSERT INTO meta (meta_key, meta_value)
+ VALUES ('patch', 'patch_84_85_c.sql| add synonym dbxref');
CREATE TABLE ontology (
@@ -76,6 +80,7 @@ CREATE TABLE synonym (
term_id INT UNSIGNED NOT NULL,
name TEXT NOT NULL,
type ENUM('EXACT', 'BROAD', 'NARROW', 'RELATED'),
+ dbxref VARCHAR(64) NULL,
PRIMARY KEY (synonym_id),
UNIQUE INDEX term_synonym_idx (term_id, synonym_id),
@@ -121,6 +126,7 @@ CREATE TABLE closure (
subparent_term_id INT UNSIGNED,
distance TINYINT UNSIGNED NOT NULL,
ontology_id INT UNSIGNED NOT NULL,
+ confident_relationship BOOL NOT NULL,
PRIMARY KEY (closure_id),
UNIQUE INDEX child_parent_idx
diff --git a/modules/t/test-genome-DBs/ontology/ontology/meta.txt b/modules/t/test-genome-DBs/ontology/ontology/meta.txt
index 5df37bd58e..e5d025d256 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/meta.txt
+++ b/modules/t/test-genome-DBs/ontology/ontology/meta.txt
@@ -9,7 +9,7 @@
10 patch patch_72_73_b.sql|meta \N
12 patch patch_73_74_a.sql|schema_version \N
14 patch patch_74_75_a.sql|schema_version \N
-15 schema_version 84 \N
+15 schema_version 85 \N
16 patch patch_75_76_a.sql|schema_version \N
17 patch patch_76_77_a.sql|schema_version \N
18 patch patch_77_78_a.sql|schema_version \N
@@ -22,3 +22,4 @@
25 patch patch_83_84_a.sql|schema_version \N
26 patch patch_84_85_b.sql|confident_relationship \N
27 patch patch_84_85_c.sql| add synonym dbxref \N
+28 patch patch_84_85_a.sql|schema_version \N
--
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