From f6697005c35976bb8744e9579390910f73e2945b Mon Sep 17 00:00:00 2001 From: peterjc Date: Mon, 10 Sep 2012 11:18:40 +0100 Subject: [PATCH] MySQLdb is dropping TYPE=INNODB, use ENGINE=INNODB Closes https://redmine.open-bio.org/issues/2568 --- sql/biosqldb-mysql.sql | 56 +++++++++++++++++++++--------------------- 1 file changed, 28 insertions(+), 28 deletions(-) diff --git a/sql/biosqldb-mysql.sql b/sql/biosqldb-mysql.sql index fff65b8..5251963 100644 --- a/sql/biosqldb-mysql.sql +++ b/sql/biosqldb-mysql.sql @@ -53,7 +53,7 @@ CREATE TABLE biodatabase ( description TEXT, PRIMARY KEY (biodatabase_id), UNIQUE (name) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX db_auth on biodatabase(authority); @@ -79,7 +79,7 @@ CREATE TABLE taxon ( UNIQUE (ncbi_taxon_id), UNIQUE (left_value), UNIQUE (right_value) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX taxparent ON taxon(parent_taxon_id); @@ -89,7 +89,7 @@ CREATE TABLE taxon_name ( name VARCHAR(255) BINARY NOT NULL, name_class VARCHAR(32) BINARY NOT NULL, UNIQUE (taxon_id,name,name_class) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX taxnametaxonid ON taxon_name(taxon_id); CREATE INDEX taxnamename ON taxon_name(name); @@ -102,7 +102,7 @@ CREATE TABLE ontology ( definition TEXT, PRIMARY KEY (ontology_id), UNIQUE (name) -) TYPE=INNODB; +) ENGINE=INNODB; -- any controlled vocab term, everything from full ontology -- terms eg GO IDs to the various keys allowed as qualifiers @@ -125,7 +125,7 @@ CREATE TABLE term ( -- obsoleteness into the uniqueness constraint. -- UNIQUE (name,ontology_id) UNIQUE (name,ontology_id,is_obsolete) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX term_ont ON term(ontology_id); @@ -136,7 +136,7 @@ CREATE TABLE term_synonym ( synonym VARCHAR(255) BINARY NOT NULL, term_id INT(10) UNSIGNED NOT NULL, PRIMARY KEY (term_id,synonym) -) TYPE=INNODB; +) ENGINE=INNODB; -- ontology terms to dbxref association: ontology terms have dbxrefs CREATE TABLE term_dbxref ( @@ -144,7 +144,7 @@ CREATE TABLE term_dbxref ( dbxref_id INT(10) UNSIGNED NOT NULL, rank SMALLINT, PRIMARY KEY (term_id, dbxref_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX trmdbxref_dbxrefid ON term_dbxref(dbxref_id); @@ -171,7 +171,7 @@ CREATE TABLE term_relationship ( ontology_id INT(10) UNSIGNED NOT NULL, PRIMARY KEY (term_relationship_id), UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX trmrel_predicateid ON term_relationship(predicate_term_id); CREATE INDEX trmrel_objectid ON term_relationship(object_term_id); @@ -192,7 +192,7 @@ CREATE TABLE term_relationship_term ( term_id INT(10) UNSIGNED NOT NULL, PRIMARY KEY ( term_relationship_id ), UNIQUE ( term_id ) -) TYPE=INNODB; +) ENGINE=INNODB; -- the infamous transitive closure table on ontology term relationships -- this is a warehouse approach - you will need to update this regularly @@ -214,7 +214,7 @@ CREATE TABLE term_path ( distance INT(10) UNSIGNED, PRIMARY KEY (term_path_id), UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id,distance) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX trmpath_predicateid ON term_path(predicate_term_id); CREATE INDEX trmpath_objectid ON term_path(object_term_id); @@ -260,7 +260,7 @@ CREATE TABLE bioentry ( -- within a namespace. -- UNIQUE (identifier) UNIQUE (identifier, biodatabase_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX bioentry_name ON bioentry(name); CREATE INDEX bioentry_db ON bioentry(biodatabase_id); @@ -277,7 +277,7 @@ CREATE TABLE bioentry_relationship ( rank INT(5), PRIMARY KEY (bioentry_relationship_id), UNIQUE (object_bioentry_id,subject_bioentry_id,term_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX bioentryrel_trm ON bioentry_relationship(term_id); CREATE INDEX bioentryrel_child ON bioentry_relationship(subject_bioentry_id); @@ -293,7 +293,7 @@ CREATE TABLE bioentry_path ( term_id INT(10) UNSIGNED NOT NULL, distance INT(10) UNSIGNED, UNIQUE (object_bioentry_id,subject_bioentry_id,term_id,distance) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX bioentrypath_trm ON bioentry_path(term_id); CREATE INDEX bioentrypath_child ON bioentry_path(subject_bioentry_id); @@ -311,7 +311,7 @@ CREATE TABLE biosequence ( alphabet VARCHAR(10), seq LONGTEXT, PRIMARY KEY (bioentry_id) -) TYPE=INNODB; +) ENGINE=INNODB; -- CONFIG: add these only if you want them: -- ALTER TABLE biosequence ADD COLUMN ( isoelec_pt NUMERIC(4,2) ); @@ -334,7 +334,7 @@ CREATE TABLE dbxref ( version SMALLINT UNSIGNED NOT NULL, PRIMARY KEY (dbxref_id), UNIQUE(accession, dbname, version) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX dbxref_db ON dbxref(dbname); @@ -352,7 +352,7 @@ CREATE TABLE dbxref_qualifier_value ( rank SMALLINT NOT NULL DEFAULT 0, value TEXT, PRIMARY KEY (dbxref_id,term_id,rank) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX dbxrefqual_dbx ON dbxref_qualifier_value(dbxref_id); CREATE INDEX dbxrefqual_trm ON dbxref_qualifier_value(term_id); @@ -368,7 +368,7 @@ CREATE TABLE bioentry_dbxref ( dbxref_id INT(10) UNSIGNED NOT NULL, rank SMALLINT, PRIMARY KEY (bioentry_id,dbxref_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX dblink_dbx ON bioentry_dbxref(dbxref_id); @@ -388,7 +388,7 @@ CREATE TABLE reference ( PRIMARY KEY (reference_id), UNIQUE (dbxref_id), UNIQUE (crc) -) TYPE=INNODB; +) ENGINE=INNODB; -- bioentry to reference associations CREATE TABLE bioentry_reference ( @@ -398,7 +398,7 @@ CREATE TABLE bioentry_reference ( end_pos INT(10), rank SMALLINT NOT NULL DEFAULT 0, PRIMARY KEY(bioentry_id,reference_id,rank) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX bioentryref_ref ON bioentry_reference(reference_id); @@ -413,7 +413,7 @@ CREATE TABLE comment ( rank SMALLINT NOT NULL DEFAULT 0, PRIMARY KEY (comment_id), UNIQUE(bioentry_id, rank) -) TYPE=INNODB; +) ENGINE=INNODB; -- tag/value and ontology term annotation for bioentries goes here @@ -423,7 +423,7 @@ CREATE TABLE bioentry_qualifier_value ( value TEXT, rank INT(5) NOT NULL DEFAULT 0, UNIQUE (bioentry_id,term_id,rank) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX bioentryqual_trm ON bioentry_qualifier_value(term_id); @@ -441,7 +441,7 @@ CREATE TABLE seqfeature ( rank SMALLINT UNSIGNED NOT NULL DEFAULT 0, PRIMARY KEY (seqfeature_id), UNIQUE (bioentry_id,type_term_id,source_term_id,rank) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX seqfeature_trm ON seqfeature(type_term_id); CREATE INDEX seqfeature_fsrc ON seqfeature(source_term_id); @@ -461,7 +461,7 @@ CREATE TABLE seqfeature_relationship ( rank INT(5), PRIMARY KEY (seqfeature_relationship_id), UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX seqfeaturerel_trm ON seqfeature_relationship(term_id); CREATE INDEX seqfeaturerel_child ON seqfeature_relationship(subject_seqfeature_id); @@ -477,7 +477,7 @@ CREATE TABLE seqfeature_path ( term_id INT(10) UNSIGNED NOT NULL, distance INT(10) UNSIGNED, UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id,distance) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX seqfeaturepath_trm ON seqfeature_path(term_id); CREATE INDEX seqfeaturepath_child ON seqfeature_path(subject_seqfeature_id); @@ -492,7 +492,7 @@ CREATE TABLE seqfeature_qualifier_value ( rank SMALLINT NOT NULL DEFAULT 0, value TEXT NOT NULL, PRIMARY KEY (seqfeature_id,term_id,rank) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX seqfeaturequal_trm ON seqfeature_qualifier_value(term_id); @@ -506,7 +506,7 @@ CREATE TABLE seqfeature_dbxref ( dbxref_id INT(10) UNSIGNED NOT NULL, rank SMALLINT, PRIMARY KEY (seqfeature_id,dbxref_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX feadblink_dbx ON seqfeature_dbxref(dbxref_id); @@ -536,7 +536,7 @@ CREATE TABLE location ( rank SMALLINT NOT NULL DEFAULT 0, PRIMARY KEY (location_id), UNIQUE (seqfeature_id, rank) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX seqfeatureloc_start ON location(start_pos, end_pos); CREATE INDEX seqfeatureloc_dbx ON location(dbxref_id); @@ -556,7 +556,7 @@ CREATE TABLE location_qualifier_value ( value VARCHAR(255) NOT NULL, int_value INT(10), PRIMARY KEY (location_id,term_id) -) TYPE=INNODB; +) ENGINE=INNODB; CREATE INDEX locationqual_trm ON location_qualifier_value(term_id);