Schema of tables not added by the bootstrap_master.pl script.

misc-scripts/production_database/tables.sql

+-- Schema of tables not added by the bootstrap_master.pl script.
+
+-- NB: Additional tables are added by the web team to support storing
+-- declarations of intentions etc.  Thos tables are not even mentioned
+-- here.
+
+-- The 'species' table.
+-- Lists the species for which there is a Core database.
+CREATE TABLE species (
+  species_id    INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+  db_name       VARCHAR(32) NOT NULL,   -- Name used in database names.
+  common_name   VARCHAR(32) NOT NULL,   -- What we often refer to it as.
+  web_name      VARCHAR(32) NOT NULL,   -- Name that the web site is using.
+  is_current    BOOLEAN NOT NULL DEFAULT true,
+
+  PRIMARY KEY (species_id),
+  UNIQUE INDEX db_name_idx (db_name)
+);
+
+
+-- The 'db' table.
+-- This table contains all species-specific databases for this release.
+CREATE TABLE db (
+  db_id         INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+  species_id    INTEGER UNSIGNED NOT NULL,  -- FK into 'species_list'.
+  db_type       ENUM('cdna', 'core', 'coreexpressionatlas',
+                     'coreexpressionest', 'coreexpressiongnf',
+                     'funcgen', 'otherfeatures', 'variation', 'vega')
+                     NOT NULL DEFAULT 'core',
+  db_release    INTEGER NOT NULL,
+  db_assembly   INTEGER NOT NULL,
+  db_suffix     CHAR(1) DEFAULT '',
+  db_host       VARCHAR(32) DEFAULT NULL,
+
+  PRIMARY KEY (db_id),
+  UNIQUE INDEX species_release_idx (species_id, db_type, db_release)
+);
+
+
+-- The 'biotype' table.
+-- Contains all the valid biotypes used for genes and transcripts.
+CREATE TABLE biotype (
+  biotype_id    INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+  name          VARCHAR(64) NOT NULL,
+  is_current    BOOLEAN NOT NULL DEFAULT true,
+  is_dumped     BOOLEAN NOT NULL DEFAULT true,
+  object_type   ENUM('gene', 'transcript') NOT NULL DEFAULT 'gene',
+  db_type       SET('cdna', 'core', 'coreexpressionatlas',
+                    'coreexpressionest', 'coreexpressiongnf', 'funcgen',
+                    'otherfeatures', 'variation', 'vega')
+                    NOT NULL DEFAULT 'core',
+  description   TEXT,
+
+  PRIMARY KEY (biotype_id),
+  UNIQUE INDEX name_type_idx (name, object_type, db_type)
+);
+
+-- The 'meta_key' table.
+-- Contains the meta keys that may or must be available in the 'meta'
+-- table in the Core databases.
+CREATE TABLE meta_key (
+  meta_key_id       INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+  name              VARCHAR(64) NOT NULL,
+  is_optional       BOOLEAN NOT NULL DEFAULT false,
+  is_current        BOOLEAN NOT NULL DEFAULT true,
+  db_type           SET('cdna', 'core', 'funcgen', 'otherfeatures',
+                      'variation', 'vega') NOT NULL DEFAULT 'core',
+  only_for_species  TEXT,
+  description       TEXT,
+
+  PRIMARY KEY (meta_key_id),
+  UNIQUE INDEX name_type_idx (name, db_type)
+);
+
+-- The 'analysis_description' table.
+-- TODO: ANY DATA FOUND IN THIS TABLE IS NOT YET "REAL".
+--       DEVELOPMENT IS STILL UNDERWAY.
+-- Contains the analysis logic name along with the data that should
+-- be available in the 'analysis_description' table, except for the
+-- 'web_data' column.
+CREATE TABLE analysis_description (
+  analysis_description_id   INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+  analysis_id               INTEGER UNSIGNED NOT NULL,
+  logic_name                VARCHAR(128) NOT NULL,
+  description               TEXT,
+  display_label             VARCHAR(256) NOT NULL,
+  displayable               BOOLEAN,
+
+  PRIMARY KEY (analysis_description_id),
+  UNIQUE INDEX analysis_id_idx (analysis_id),
+  UNIQUE INDEX logic_name_idx (logic_name)
+);
+
+-- The 'web_data' table.
+-- TODO: ANY DATA FOUND IN THIS TABLE IS NOT YET "REAL".
+--       DEVELOPMENT IS STILL UNDERWAY.
+-- Contains the data for the 'web_data' column in the
+-- 'analysis_description' table.
+-- The 'web_data' is a hash and we store this as key-value pairs
+-- ('hash_key' and 'hash_value').  The 'hash_key' might contain double
+-- colons ('::') to distinguish sub-hash keys, e.g. 'default::MultiTop'.
+CREATE TABLE web_data (
+  web_data_id   INTEGER UNSIGNED NOT NULL AUTO_INCREMENT,
+  hash_key      VARCHAR(32) NOT NULL,
+  hash_value    VARCHAR(128),
+
+  PRIMARY KEY (web_data_id)
+);
+
+-- The 'analysis_web_data' table.
+-- TODO: ANY DATA FOUND IN THIS TABLE IS NOT YET "REAL".
+--       DEVELOPMENT IS STILL UNDERWAY.
+-- This table connects the 'analysis_description' table with the
+-- 'web_data' and 'db' tables.
+CREATE TABLE analysis_web_data (
+  analysis_description_id   INTEGER UNSIGNED NOT NULL,
+  web_data_id               INTEGER UNSIGNED NOT NULL,
+  db_id                     INTEGER UNSIGNED NOT NULL,
+
+  UNIQUE KEY analysis_web_data_db_idx
+    (analysis_description_id, web_data_id, db_id)
+);
+
+-- VIEWS
+
+CREATE VIEW db_list AS
+SELECT  CONCAT(
+          CONCAT_WS('_', db_name, db_type, db_release, db_assembly),
+        db_suffix) AS full_db_name
+FROM    species
+  JOIN  db USING (species_id);
+
+-- CREATE VIEW readable_web_data AS
+-- SELECT  CONCAT('{',
+--           GROUP_CONCAT(data SEPARATOR ','),
+--         '}') AS web_data
+-- FROM    analysis_web_data awd
+--   JOIN  web_data wd USING (web_data_id)
+-- GROUP BY