Commit 4b0f8b6e authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Incorporate the changes from patch 'd' (multispecies).

Correct the name of patch 'c' (meta --> meta_coord).

Adjust the insertion of patch identifiers to take into account the
species_id column in the meta table (needs explicit NULL).
parent 1a34e448
...@@ -868,14 +868,14 @@ CREATE TABLE prediction_transcript ( ...@@ -868,14 +868,14 @@ CREATE TABLE prediction_transcript (
CREATE TABLE meta ( CREATE TABLE meta (
meta_id INT NOT NULL AUTO_INCREMENT, meta_id INT NOT NULL AUTO_INCREMENT,
species_id INT UNSIGNED DEFAULT 1,
meta_key VARCHAR(40) NOT NULL, meta_key VARCHAR(40) NOT NULL,
meta_value VARCHAR(255) NOT NULL, meta_value VARCHAR(255) NOT NULL,
PRIMARY KEY (meta_id), PRIMARY KEY (meta_id),
UNIQUE KEY key_value (meta_key, meta_value), UNIQUE KEY species_key_value_idx (species_id, meta_key, meta_value),
KEY meta_key_index (meta_key), KEY species_value_idx (species_id, meta_value)
KEY meta_value_index (meta_value)
) COLLATE=latin1_swedish_ci TYPE=MyISAM; ) COLLATE=latin1_swedish_ci TYPE=MyISAM;
...@@ -885,9 +885,10 @@ INSERT INTO meta (meta_key, meta_value) VALUES ("schema_version", "51"); ...@@ -885,9 +885,10 @@ INSERT INTO meta (meta_key, meta_value) VALUES ("schema_version", "51");
# patches included in this schema file # patches included in this schema file
# NOTE: at beginning of release cycle, remove patch entries from last release # NOTE: at beginning of release cycle, remove patch entries from last release
INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_50_51_a.sql|schema_version'); INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_50_51_a.sql|schema_version');
INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_50_51_b.sql|protein_feature_hit_name'); INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_50_51_b.sql|protein_feature_hit_name');
INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_50_51_c.sql|meta_index'); INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_50_51_c.sql|meta_coord_index');
INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_50_51_d.sql|multispecies');
################################################################################ ################################################################################
# #
...@@ -1338,14 +1339,16 @@ CREATE TABLE assembly_exception ( ...@@ -1338,14 +1339,16 @@ CREATE TABLE assembly_exception (
CREATE TABLE coord_system ( CREATE TABLE coord_system (
coord_system_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT, coord_system_id INT(10) UNSIGNED NOT NULL AUTO_INCREMENT,
species_id INT(10) UNSIGNED NOT NULL DEFAULT 1,
name VARCHAR(40) NOT NULL, name VARCHAR(40) NOT NULL,
version VARCHAR(40) DEFAULT NULL, version VARCHAR(40) DEFAULT NULL,
rank INT NOT NULL, rank INT NOT NULL,
attrib SET('default_version', 'sequence_level'), attrib SET('default_version', 'sequence_level'),
UNIQUE (name, version), PRIMARY KEY (coord_system_id),
UNIQUE (rank), UNIQUE KEY rank_idx (rank, species_id),
PRIMARY KEY (coord_system_id) UNIQUE KEY name_idx (name, version, species_id),
KEY species_idx (species_id)
) COLLATE=latin1_swedish_ci TYPE=MyISAM; ) COLLATE=latin1_swedish_ci TYPE=MyISAM;
......
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