seqvault: Add support for SQLite databases.

Add the (unreleased by upstream) BioSQL schema for SQLite3. Fix detection of the 'prefix' column.
2 years ago · d08bde1e5a
2 changed files with 400 additions and 1 deletions
--- a/biosql/biosqldb-sqlite.sql
+++ b/biosql/biosqldb-sqlite.sql
@ -0,0 +1,399 @@
+--  BioSQL database schema for SQLite.
+-- 
+--  This file is part of BioSQL.
+--
+--  BioSQL is free software: you can redistribute it and/or modify it
+--  under the terms of the GNU Lesser General Public License as
+--  published by the Free Software Foundation, either version 3 of the
+--  License, or (at your option) any later version.
+--
+--  BioSQL is distributed in the hope that it will be useful,
+--  but WITHOUT ANY WARRANTY; without even the implied warranty of
+--  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+--  GNU Lesser General Public License for more details.
+--
+--  You should have received a copy of the GNU Lesser General Public License
+--  along with BioSQL. If not, see <http://www.gnu.org/licenses/>.
+--
+-- ========================================================================
+--
+-- See MySQL database schema and BioSQL website for table documentation.
+-- This contains notes specific to SQLite
+-- 
+-- A note about Primary Keys in SQLite
+-- SQLite automatically creates a ROWID for each row of a table.
+--   Using this ROWID as the primary key is faster than using a 
+--   user-defined primary key. By declaring a column as an 
+--   INTEGER PRIMARY KEY, you are actually creating an alias to the
+--   ROWID and get the associated speed benefits.  The ROWID effectively
+--   "autoincrements"; however, it can reuse ROWIDs of deleted rows. 
+--   To avoid reusing old ROWIDs would require adding the AUTOINCREMENT
+--   keyword, which also reduces the performance.
+--   ( see http://www.sqlite.org/autoinc.html) 
+
+CREATE TABLE biodatabase (
+  	biodatabase_id 	INTEGER PRIMARY KEY,
+  	name           	VARCHAR(128) NOT NULL,
+	authority	VARCHAR(128),
+	prefix	VARCHAR(3),
+	description	TEXT,
+  	UNIQUE (name),
+  	UNIQUE (prefix)
+);
+
+CREATE INDEX db_auth on biodatabase(authority);
+
+CREATE TABLE taxon (
+       taxon_id		INTEGER PRIMARY KEY,
+       ncbi_taxon_id 	INT(10),
+       parent_taxon_id	INT(10) ,
+       node_rank	VARCHAR(32),
+       genetic_code	TINYINT ,
+       mito_genetic_code TINYINT ,
+       left_value	INT(10) ,
+       right_value	INT(10) ,
+       UNIQUE (ncbi_taxon_id),
+       UNIQUE (left_value),
+       UNIQUE (right_value)
+);
+
+CREATE INDEX taxparent ON taxon(parent_taxon_id);
+
+CREATE TABLE taxon_name (
+       taxon_id		INTEGER,
+       name		VARCHAR(255)  NOT NULL,
+       name_class	VARCHAR(32)  NOT NULL,
+    UNIQUE (taxon_id,name,name_class),
+    FOREIGN KEY ( taxon_id ) REFERENCES taxon ( taxon_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX taxnametaxonid ON taxon_name(taxon_id);
+CREATE INDEX taxnamename    ON taxon_name(name);
+
+CREATE TABLE ontology (
+       	ontology_id        INTEGER PRIMARY KEY,
+       	name	   	   VARCHAR(32)  NOT NULL,
+       	definition	   TEXT,
+	UNIQUE (name)
+);
+
+CREATE TABLE term (
+       	term_id   INTEGER PRIMARY KEY,
+       	name	   	   VARCHAR(255)  NOT NULL,
+       	definition	   TEXT,
+	identifier	   VARCHAR(40) ,
+	is_obsolete	   CHAR(1),
+	ontology_id	   INTEGER,
+	UNIQUE (identifier),
+    UNIQUE (name,ontology_id,is_obsolete),
+    FOREIGN KEY ( ontology_id ) REFERENCES ontology ( ontology_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX term_ont ON term(ontology_id);
+
+CREATE TABLE term_synonym (
+       synonym		  VARCHAR(255)  NOT NULL,
+       term_id		  INTEGER,
+    PRIMARY KEY (term_id,synonym),
+
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE
+);
+
+CREATE TABLE term_dbxref (
+       	term_id	          INTEGER,
+       	dbxref_id         INTEGER,
+	rank		  SMALLINT,
+    PRIMARY KEY (term_id, dbxref_id),
+
+    FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX trmdbxref_dbxrefid ON term_dbxref(dbxref_id);
+
+CREATE TABLE term_relationship (
+        term_relationship_id INTEGER PRIMARY KEY,
+       	subject_term_id	INTEGER,
+       	predicate_term_id    INTEGER,
+       	object_term_id       INTEGER,
+	ontology_id	INTEGER,
+    UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id),
+
+    FOREIGN KEY ( subject_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
+    FOREIGN KEY ( predicate_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
+    FOREIGN KEY ( object_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
+    FOREIGN KEY ( ontology_id ) REFERENCES ontology ( ontology_id ) ON DELETE CASCADE
+
+);
+
+CREATE INDEX trmrel_predicateid ON term_relationship(predicate_term_id);
+CREATE INDEX trmrel_objectid ON term_relationship(object_term_id);
+CREATE INDEX trmrel_ontid ON term_relationship(ontology_id);
+
+CREATE TABLE term_relationship_term (
+        term_relationship_id INTEGER PRIMARY KEY,
+        term_id              INTEGER,
+    UNIQUE ( term_id ),
+
+    FOREIGN KEY (term_relationship_id) REFERENCES term_relationship(term_relationship_id) ON DELETE CASCADE,
+    FOREIGN KEY (term_id) REFERENCES term(term_id) ON DELETE CASCADE
+);
+
+CREATE TABLE term_path (
+        term_path_id         INTEGER PRIMARY KEY,
+       	subject_term_id	     INTEGER,
+       	predicate_term_id    INTEGER,
+       	object_term_id       INTEGER,
+	ontology_id          INTEGER,
+	distance	     INT(10) ,
+    UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id,distance),
+    FOREIGN KEY ( subject_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
+    FOREIGN KEY ( predicate_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
+    FOREIGN KEY ( object_term_id ) REFERENCES term ( term_id ) ON DELETE CASCADE ,
+    FOREIGN KEY ( ontology_id ) REFERENCES ontology ( ontology_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX trmpath_predicateid ON term_path(predicate_term_id);
+CREATE INDEX trmpath_objectid ON term_path(object_term_id);
+CREATE INDEX trmpath_ontid ON term_path(ontology_id);
+
+CREATE TABLE bioentry (
+	bioentry_id	    INTEGER PRIMARY KEY,
+  	biodatabase_id  INTEGER,
+  	taxon_id     	INT(10) ,
+  	name		VARCHAR(40) NOT NULL,
+  	accession    	VARCHAR(128)  NOT NULL,
+  	identifier   	VARCHAR(40) ,
+	division	VARCHAR(6),
+  	description  	TEXT,
+  	version 	SMALLINT  NOT NULL, 
+  	UNIQUE (accession,biodatabase_id,version),
+    UNIQUE (identifier, biodatabase_id),
+
+    FOREIGN KEY ( taxon_id ) REFERENCES taxon ( taxon_id ),
+    FOREIGN KEY ( biodatabase_id ) REFERENCES biodatabase ( biodatabase_id )
+);
+
+CREATE INDEX bioentry_name ON bioentry(name);
+CREATE INDEX bioentry_db   ON bioentry(biodatabase_id);
+CREATE INDEX bioentry_tax  ON bioentry(taxon_id);
+
+CREATE TABLE bioentry_relationship (
+        bioentry_relationship_id INTEGER PRIMARY KEY,
+        object_bioentry_id 	 INTEGER,
+   	subject_bioentry_id 	 INTEGER,
+   	term_id 		 INTEGER,
+   	rank 			 INT(5),
+    UNIQUE (object_bioentry_id,subject_bioentry_id,term_id),
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
+    FOREIGN KEY ( object_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( subject_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX bioentryrel_trm   ON bioentry_relationship(term_id);
+CREATE INDEX bioentryrel_child ON bioentry_relationship(subject_bioentry_id);
+
+CREATE TABLE bioentry_path (
+   	object_bioentry_id 	INTEGER PRIMARY KEY,
+   	subject_bioentry_id 	INTEGER,
+   	term_id 		INTEGER,
+	distance	     	INT(10) ,
+    UNIQUE (object_bioentry_id,subject_bioentry_id,term_id,distance),
+
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
+    FOREIGN KEY ( object_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( subject_bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX bioentrypath_trm   ON bioentry_path(term_id);
+CREATE INDEX bioentrypath_child ON bioentry_path(subject_bioentry_id);
+
+CREATE TABLE biosequence (
+  	bioentry_id     INTEGER PRIMARY KEY,
+  	version     	SMALLINT, 
+  	length      	INT(10),
+  	alphabet        VARCHAR(10),
+    seq 		LONGTEXT,
+    FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
+);
+
+CREATE TABLE dbxref (
+        dbxref_id	INTEGER PRIMARY KEY,
+        dbname          VARCHAR(40)  NOT NULL,
+        accession       VARCHAR(128)  NOT NULL,
+	version		SMALLINT  NOT NULL,
+        UNIQUE(accession, dbname, version)
+);
+
+CREATE INDEX dbxref_db  ON dbxref(dbname);
+
+CREATE TABLE dbxref_qualifier_value (
+       	dbxref_id 		INTEGER,
+       	term_id 		INTEGER,
+  	rank  		   	SMALLINT NOT NULL DEFAULT 0,
+       	value			TEXT,
+    PRIMARY KEY (dbxref_id,term_id,rank),
+
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
+    FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX dbxrefqual_dbx ON dbxref_qualifier_value(dbxref_id);
+CREATE INDEX dbxrefqual_trm ON dbxref_qualifier_value(term_id);
+
+CREATE TABLE bioentry_dbxref ( 
+       	bioentry_id        INTEGER,
+       	dbxref_id          INTEGER,
+  	rank  		   SMALLINT,
+    PRIMARY KEY (bioentry_id,dbxref_id),
+    FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE
+
+);
+
+CREATE INDEX dblink_dbx  ON bioentry_dbxref(dbxref_id);
+
+CREATE TABLE reference (
+  	reference_id       INTEGER PRIMARY KEY,
+	dbxref_id	   INT(10) ,
+  	location 	   TEXT NOT NULL,
+  	title    	   TEXT,
+  	authors  	   TEXT,
+  	crc	   	   VARCHAR(32),
+	UNIQUE (dbxref_id),
+    UNIQUE (crc),
+    FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id )
+);
+
+CREATE TABLE bioentry_reference (
+  	bioentry_id 	INTEGER,
+  	reference_id 	INTEGER,
+  	start_pos	INT(10),
+  	end_pos	  	INT(10),
+  	rank  		SMALLINT NOT NULL DEFAULT 0,
+    PRIMARY KEY(bioentry_id,reference_id,rank),
+    FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
+    FOREIGN KEY ( reference_id ) REFERENCES reference ( reference_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX bioentryref_ref ON bioentry_reference(reference_id);
+
+CREATE TABLE comment (
+  	comment_id  	INTEGER PRIMARY KEY,
+  	bioentry_id    	INTEGER,
+  	comment_text   	TEXT NOT NULL,
+  	rank   		SMALLINT NOT NULL DEFAULT 0,
+    UNIQUE(bioentry_id, rank),
+    FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
+);
+
+CREATE TABLE bioentry_qualifier_value (
+	bioentry_id   		INTEGER,
+   	term_id  		INTEGER,
+   	value         		TEXT,
+	rank			INT(5) NOT NULL DEFAULT 0,
+    UNIQUE (bioentry_id,term_id,rank),
+    FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
+);
+
+CREATE INDEX bioentryqual_trm ON bioentry_qualifier_value(term_id);
+
+CREATE TABLE seqfeature (
+   	seqfeature_id 		INTEGER PRIMARY KEY,
+   	bioentry_id   		INTEGER,
+   	type_term_id		INTEGER,
+   	source_term_id  	INTEGER,
+	display_name		VARCHAR(64),
+   	rank 			SMALLINT  NOT NULL DEFAULT 0,
+    UNIQUE (bioentry_id,type_term_id,source_term_id,rank),
+    FOREIGN KEY ( type_term_id ) REFERENCES term ( term_id ),
+    FOREIGN KEY ( source_term_id ) REFERENCES term ( term_id ),
+    FOREIGN KEY ( bioentry_id ) REFERENCES bioentry ( bioentry_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX seqfeature_trm  ON seqfeature(type_term_id);
+CREATE INDEX seqfeature_fsrc ON seqfeature(source_term_id);
+
+CREATE TABLE seqfeature_relationship (
+        seqfeature_relationship_id INTEGER PRIMARY KEY,
+   	object_seqfeature_id	INTEGER,
+   	subject_seqfeature_id 	INTEGER,
+   	term_id 	        INTEGER,
+   	rank 			INT(5),
+    UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id),
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
+    FOREIGN KEY ( object_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( subject_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX seqfeaturerel_trm   ON seqfeature_relationship(term_id);
+CREATE INDEX seqfeaturerel_child ON seqfeature_relationship(subject_seqfeature_id);
+
+CREATE TABLE seqfeature_path (
+   	object_seqfeature_id	INTEGER,
+   	subject_seqfeature_id 	INTEGER,
+   	term_id 		INTEGER,
+	distance	     	INT(10) ,
+    UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id,distance),
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
+    FOREIGN KEY ( object_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( subject_seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX seqfeaturepath_trm   ON seqfeature_path(term_id);
+CREATE INDEX seqfeaturepath_child ON seqfeature_path(subject_seqfeature_id);
+
+CREATE TABLE seqfeature_qualifier_value (
+	seqfeature_id 		INTEGER,
+   	term_id 		INTEGER,
+   	rank 			SMALLINT NOT NULL DEFAULT 0,
+   	value  			TEXT NOT NULL,
+    PRIMARY KEY (seqfeature_id,term_id,rank),
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id ),
+    FOREIGN KEY ( seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX seqfeaturequal_trm ON seqfeature_qualifier_value(term_id);
+   
+CREATE TABLE seqfeature_dbxref ( 
+       	seqfeature_id      INTEGER,
+       	dbxref_id          INTEGER,
+  	rank  		   SMALLINT,
+    PRIMARY KEY (seqfeature_id,dbxref_id),
+    FOREIGN KEY ( seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ON DELETE CASCADE
+);
+
+CREATE INDEX feadblink_dbx  ON seqfeature_dbxref(dbxref_id);
+
+CREATE TABLE location (
+	location_id		INTEGER PRIMARY KEY,
+   	seqfeature_id		INTEGER,
+	dbxref_id		INT(10),
+	term_id			INT(10),
+   	start_pos              	INT(10),
+   	end_pos                	INT(10),
+   	strand             	TINYINT NOT NULL DEFAULT 0,
+   	rank          		SMALLINT NOT NULL DEFAULT 0,
+    UNIQUE (seqfeature_id, rank),
+    FOREIGN KEY ( seqfeature_id ) REFERENCES seqfeature ( seqfeature_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ),
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
+);
+
+CREATE INDEX seqfeatureloc_start ON location(start_pos, end_pos);
+CREATE INDEX seqfeatureloc_dbx   ON location(dbxref_id);
+CREATE INDEX seqfeatureloc_trm   ON location(term_id);
+
+CREATE TABLE location_qualifier_value (
+	location_id		INTEGER,
+   	term_id 		INTEGER,
+   	value  			VARCHAR(255) NOT NULL,
+   	int_value 		INT(10),
+    PRIMARY KEY (location_id,term_id),
+    FOREIGN KEY ( location_id ) REFERENCES location ( location_id ) ON DELETE CASCADE,
+    FOREIGN KEY ( term_id ) REFERENCES term ( term_id )
+);
+
+CREATE INDEX locationqual_trm ON location_qualifier_value(term_id);
--- a/incenp/bio/seq/vault.py
+++ b/incenp/bio/seq/vault.py
@ -96,7 +96,7 @@ class Server(DBServer):
            return self._is_prefixed
        except AttributeError:
            self.adaptor.execute('SELECT * FROM biodatabase LIMIT 1')
-            columns = [desc.name for desc in self.adaptor.cursor.description]
+            columns = [desc[0] for desc in self.adaptor.cursor.description]
            self._is_prefixed = 'prefix' in columns
            return self._is_prefixed