Merge pull request #162 from thomasmaurel/ontology_db_patch_87

New schema patches to allow the ensembl_ontology schema to work on ne…

misc-scripts/ontology/sql/patch_86_87_b.sql

+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016] 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_86_87_b.sql
+#
+# Title: Increase dbxref field length 
+#
+# Description:
+#   Update synonym table to increase size of dbxref column
+
+ALTER TABLE synonym MODIFY COLUMN dbxref VARCHAR(256) NOT NULL;
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_86_87_b.sql|longer_dbxref');

misc-scripts/ontology/sql/patch_86_87_c.sql

+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016] 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_86_87_c.sql
+#
+# Title: Increase dbxref field length 
+#
+# Description:
+#   Update synonym table to allow UTF8 Unicode characters
+
+ALTER TABLE synonym CONVERT TO CHARACTER SET utf8 COLLATE utf8_swedish_ci;
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_86_87_c.sql|make_table_utf8');

misc-scripts/ontology/sql/patch_86_87_d.sql

+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016] 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_86_87_d.sql
+#
+# Title: Default value for confident_relationship
+#
+# Description:
+#   Adding default value for the confident_relationship column in the closure table
+
+ALTER TABLE closure ALTER COLUMN confident_relationship SET DEFAULT 0;
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+  VALUES (NULL, 'patch', 'patch_86_87_d.sql|default_value_confident_relationship');

misc-scripts/ontology/sql/tables.sql

@@ -35,7 +35,7 @@ INSERT INTO meta (meta_key, meta_value) VALUES
 
 # Patches included in this schema file
 INSERT INTO meta (meta_key, meta_value)
-  VALUES ('patch', 'patch_86_87_a.sql|schema_version');
+  VALUES ('patch', 'patch_86_87_d.sql|default_value_confident_relationship');
 
 
 CREATE TABLE ontology (
@@ -78,12 +78,12 @@ CREATE TABLE synonym (
   term_id       INT UNSIGNED NOT NULL,
   name          TEXT NOT NULL,
   type		ENUM('EXACT', 'BROAD', 'NARROW', 'RELATED'),
-  dbxref        VARCHAR(64)  NULL,
+  dbxref        VARCHAR(258)  NULL,
 
   PRIMARY KEY (synonym_id),
   UNIQUE INDEX term_synonym_idx (term_id, synonym_id),
   INDEX name_idx (name(50))
-) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
+) COLLATE=utf8_swedish_ci ENGINE=MyISAM;
 
 CREATE TABLE alt_id (
   alt_id        INT UNSIGNED NOT NULL AUTO_INCREMENT,
@@ -124,7 +124,7 @@ CREATE TABLE closure (
   subparent_term_id INT UNSIGNED,
   distance          TINYINT UNSIGNED NOT NULL,
   ontology_id       INT UNSIGNED NOT NULL,
-  confident_relationship BOOL NOT NULL,
+  confident_relationship BOOL NOT NULL DEFAULT 0,
 
   PRIMARY KEY (closure_id),
   UNIQUE INDEX child_parent_idx