[ENSCORESW-493]. Fixing a number of naming issues in ontology schema. Also had...

[ENSCORESW-493]. Fixing a number of naming issues in ontology schema. Also had to introduce a patch for is_obsolete

misc-scripts/ontology/sql/patch_71_72b.sql → misc-scripts/ontology/sql/patch_71_72_b.sql

@@ -12,4 +12,4 @@ CREATE TABLE alt_id (
 
 -- Patch identifier
 INSERT INTO meta (meta_key, meta_value)
-  VALUES ('patch', 'patch_71_72b.sql|alt_id table');
+  VALUES ('patch', 'patch_71_72_b.sql|alt_id table');

misc-scripts/ontology/sql/patch_71_72c.sql → misc-scripts/ontology/sql/patch_71_72_c.sql

--- patch_71_72c.sql
+-- patch_71_72_c.sql
 --
 -- Title: Insert schema version.
 --
@@ -11,6 +11,6 @@ INSERT INTO meta (meta_key, meta_value)
 
 -- Patch identifier
 INSERT INTO meta (meta_key, meta_value)
-  VALUES ('patch', 'patch_71_72c.sql|schema_version');
+  VALUES ('patch', 'patch_71_72_c.sql|schema_version');
 
 

misc-scripts/ontology/sql/patch_71_72_d.sql

+-- patch_71_72_d.sql
+--
+-- Title: Fix patch versions
+--
+-- Description:
+--   Fixes the existing patch meta items as their versioning was not correct
+
+update meta set meta_value = 'patch_71_72_b.sql|alt_id table'
+  where meta_key = 'patch'
+  and meta_value = 'patch_71_72b.sql|alt_id table';
+
+update meta set meta_value = 'patch_71_72_c.sql|schema_version'
+  where meta_key = 'patch'
+  and meta_value = 'patch_71_72c.sql|schema_version';
+
+-- Patch identifier
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_71_72_d.sql|patch_version_fix');
+
+

misc-scripts/ontology/sql/patch_71_72_e.sql

+-- patch_71_72_e.sql
+--
+-- Title: Add is_obsolete
+--
+-- Description:
+--   Adds the is_obsolete flag to the term table
+
+ALTER TABLE TERM
+ADD COLUMN is_obsolete INT NOT NULL DEFAULT 0;
+
+-- Patch identifier
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_71_72_e.sql|is_obsolete');
+
+

misc-scripts/ontology/sql/tables.sql

@@ -22,6 +22,10 @@ INSERT INTO meta (meta_key, meta_value)
   VALUES ('patch', 'patch_71_72b.sql|alt_id table');
 INSERT INTO meta (meta_key, meta_value)
   VALUES ('patch', 'patch_71_72c.sql|schema_version');
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_71_72_d.sql|patch_version_fix');
+INSERT INTO meta (meta_key, meta_value)
+  VALUES ('patch', 'patch_71_72_e.sql|is_obsolete');
 
 CREATE TABLE ontology (
   ontology_id   INT UNSIGNED NOT NULL AUTO_INCREMENT,
@@ -48,8 +52,8 @@ CREATE TABLE term (
   accession     VARCHAR(64) NOT NULL,
   name          VARCHAR(255) NOT NULL,
   definition    TEXT,
-  is_root       INT,
-  is_obsolete   INT,
+  is_root       INT NOT NULL DEFAULT 0,
+  is_obsolete   INT NOT NULL DEFAULT 0,
 
   PRIMARY KEY (term_id),
   UNIQUE INDEX accession_idx (accession),