merge stable_id tables with their object tables, create views for old stable_id tables

sql/patch_64_65_b.sql

+# patch_64_65_b.sql
+#
+# Title: Incorporate stable_id tables into exon, gene, operon, operon_transcript, translation and transcript tables.
+#
+# Description: 
+
+# Add stable_id, version, stable_id_created_date, stable_id_modified_date columns to tables exon, 
+# gene, operon, operon_transcript, transcript and translation. Add index on stable_id and version to each table.
+# Move data from the stable_id tables into their related object tables.
+# Delete stable_id tables. Create views like the stable_id tables.
+
+
+ALTER TABLE exon ADD COLUMN (stable_id VARCHAR(128) NOT NULL DEFAULT '', version INT(10) NOT NULL DEFAULT 0, created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00', modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00');
+ALTER TABLE exon ADD INDEX stable_id_idx (stable_id, version);
+
+ALTER TABLE gene ADD COLUMN (stable_id VARCHAR(128) NOT NULL DEFAULT '', version INT(10) NOT NULL DEFAULT 0, created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00', modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00');
+ALTER TABLE gene ADD INDEX stable_id_idx (stable_id, version);
+
+ALTER TABLE operon ADD COLUMN (stable_id VARCHAR(128) NOT NULL DEFAULT '', version INT(10) NOT NULL DEFAULT 0, created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00', modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00');
+ALTER TABLE operon ADD INDEX stable_id_idx (stable_id, version);
+
+ALTER TABLE operon_transcript ADD COLUMN (stable_id VARCHAR(128) NOT NULL DEFAULT '', version INT(10) NOT NULL DEFAULT 0, created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00', modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00');
+ALTER TABLE operon_transcript ADD INDEX stable_id_idx (stable_id, version);
+
+ALTER TABLE transcript ADD COLUMN (stable_id VARCHAR(128) NOT NULL DEFAULT '', version INT(10) NOT NULL DEFAULT 0, created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00', modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00');
+ALTER TABLE transcript ADD INDEX stable_id_idx (stable_id, version);
+  
+ALTER TABLE translation ADD COLUMN (stable_id VARCHAR(128) NOT NULL DEFAULT '', version INT(10) NOT NULL DEFAULT 0, created_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00', modified_date DATETIME NOT NULL DEFAULT '0000-00-00 00:00:00');
+ALTER TABLE translation ADD INDEX stable_id_idx (stable_id, version);
+
+UPDATE exon o, exon_stable_id s SET o.stable_id = s.stable_id, o.version = s.version, o.created_date = s.created_date, o.modified_date = s.modified_date WHERE o.exon_id = s.exon_id;
+
+UPDATE gene o, gene_stable_id s SET o.stable_id = s.stable_id, o.version = s.version, o.created_date = s.created_date, o.modified_date = s.modified_date WHERE o.gene_id = s.gene_id;
+
+UPDATE operon o, operon_stable_id s SET o.stable_id = s.stable_id, o.version = s.version, o.created_date = s.created_date, o.modified_date = s.modified_date WHERE o.operon_id = s.operon_id;
+
+UPDATE operon_transcript o, operon_transcript_stable_id s SET o.stable_id = s.stable_id, o.version = s.version, o.created_date = s.created_date, o.modified_date = s.modified_date WHERE o.operon_transcript_id = s.operon_transcript_id;
+
+UPDATE translation o, translation_stable_id s SET o.stable_id = s.stable_id, o.version = s.version, o.created_date = s.created_date, o.modified_date = s.modified_date WHERE o.translation_id = s.translation_id;
+
+UPDATE transcript o, transcript_stable_id s SET o.stable_id = s.stable_id, o.version = s.version, o.created_date = s.created_date, o.modified_date = s.modified_date WHERE o.transcript_id = s.transcript_id;
+
+DROP TABLE exon_stable_id;
+
+DROP TABLE gene_stable_id;
+
+DROP TABLE operon_stable_id;
+
+DROP TABLE operon_transcript_stable_id;
+
+DROP TABLE translation_stable_id;
+
+DROP TABLE transcript_stable_id;
+
+CREATE VIEW exon_stable_id (exon_id, stable_id, version, created_date, modified_date) AS (SELECT exon_id, stable_id, version, created_date, modified_date FROM exon);
+
+CREATE VIEW gene_stable_id (gene_id, stable_id, version, created_date, modified_date) AS (SELECT gene_id, stable_id, version, created_date, modified_date FROM gene);
+
+CREATE VIEW operon_stable_id (operon_id, stable_id, version, created_date, modified_date) AS (SELECT operon_id, stable_id, version, created_date, modified_date FROM operon);
+
+CREATE VIEW operon_transcript_stable_id (operon_transcript_id, stable_id, version, created_date, modified_date) AS (SELECT operon_transcript_id, stable_id, version, created_date, modified_date FROM operon_transcript);
+
+CREATE VIEW translation_stable_id (translation_id, stable_id, version, created_date, modified_date) AS (SELECT translation_id, stable_id, version, created_date, modified_date FROM translation);
+
+CREATE VIEW transcript_stable_id (transcript_id, stable_id, version, created_date, modified_date) AS (SELECT transcript_id, stable_id, version, created_date, modified_date FROM transcript);
+
+
+# Patch identifier
+#INSERT INTO meta (species_id, meta_key, meta_value)
+#  VALUES (NULL, 'patch', 'patch_64_65_b.sql|merge_stable_id_with_object');
+