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SQLAlchemy definitions for BioSQL; partial implementation
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‎biosql/BioSQL-SQLAlchemy_definitions.py‎

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"""SQLAlchemy definitions for the BioSQL database of biological items.
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This provides a non-Seq-based interface to the BioSQL database through python.
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This is useful if you have non-seq items to put into BioSQL, and should also
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expose things not touched on with the Biopython BioSQL interface. Eventually
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this would be a good target for merging.
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http://www.biosql.org/wiki/Main_Page
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Useful URLs for declarative style:
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https://www.bitbucket.org/stephane/model2/src/tip/transifex/model.py
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http://www.sqlalchemy.org/docs/05/sqlalchemy_ext_declarative.html
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"""
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def _initialize(Base):
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from sqlalchemy.orm import relation, mapper, dynamic_loader
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from sqlalchemy import MetaData, Table, Column, ForeignKey, Sequence
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from sqlalchemy import String, Unicode, Integer, DateTime, Float
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# -- Standard BioSQL tables
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class Biodatabase(Base):
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"""Entry point to BioSQL databases.
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"""
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__tablename__ = 'biodatabase'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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biodatabase_id = Column(Integer, primary_key = True)
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entries = relation("Bioentry", backref = "biodb")
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class Bioentry(Base):
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"""The main bioentry object in BioSQL, containing a biological item.
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"""
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__tablename__ = 'bioentry'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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bioentry_id = Column(Integer, primary_key = True)
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biodatabase_id = Column(Integer,
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ForeignKey('biodatabase.biodatabase_id'))
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qualifiers = relation("BioentryQualifierValue", backref = "bioentry")
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parent_maps = relation("BioentryRelationship", primaryjoin =
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"Bioentry.bioentry_id == BioentryRelationship.object_bioentry_id",
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lazy="dynamic")
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child_maps = relation("BioentryRelationship", primaryjoin =
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"Bioentry.bioentry_id == BioentryRelationship.subject_bioentry_id",
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order_by = "BioentryRelationship.object_bioentry_id.asc()",
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lazy="dynamic")
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features = relation("SeqFeature", backref="bioentry")
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sequence = relation("Biosequence")
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class Biosequence(Base):
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"""Represent a sequence attached to a bioentry.
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"""
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__tablename__ = 'biosequence'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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bioentry_id = Column(Integer, ForeignKey('bioentry.bioentry_id'),
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primary_key = True)
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class Ontology(Base):
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"""Defined a high level dictionary of ontology key terms.
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"""
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__tablename__ = 'ontology'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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ontology_id = Column(Integer, primary_key = True)
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class Term(Base):
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"""Explicitly describe terminology used in key/value pair relationships
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"""
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__tablename__ = 'term'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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term_id = Column(Integer, primary_key = True)
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ontology_id = Column(Integer, ForeignKey('ontology.ontology_id'))
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ontology = relation("Ontology", backref = "terms")
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class BioentryQualifierValue(Base):
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"""A key/value annotation pair associated with a Bioentry.
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"""
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__tablename__ = 'bioentry_qualifier_value'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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bioentry_id = Column(Integer,
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ForeignKey('bioentry.bioentry_id'), primary_key = True)
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term_id = Column(Integer, ForeignKey('term.term_id'), primary_key = True)
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rank = Column(Integer, primary_key = True)
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term = relation("Term", lazy=True)
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class BioentryRelationship(Base):
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"""Define a relationship between two bioentry objects.
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"""
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__tablename__ = 'bioentry_relationship'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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object_bioentry_id = Column(Integer,
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ForeignKey('bioentry.bioentry_id'), primary_key = True)
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subject_bioentry_id = Column(Integer,
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ForeignKey('bioentry.bioentry_id'))
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term_id = Column(Integer, ForeignKey('term.term_id'),
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primary_key = True)
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rank = Column(Integer, primary_key = True)
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term = relation("Term")
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parent = relation("Bioentry", primaryjoin =
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"Bioentry.bioentry_id == BioentryRelationship.object_bioentry_id")
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child = relation("Bioentry", primaryjoin =
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"Bioentry.bioentry_id == BioentryRelationship.subject_bioentry_id")
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seqfeature_dbxref_table = Table('seqfeature_dbxref', Base.metadata,
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Column('seqfeature_id', Integer,
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ForeignKey('seqfeature.seqfeature_id')),
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Column('dbxref_id', Integer, ForeignKey('dbxref.dbxref_id')),
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Column('rank', Integer))
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class DBXref(Base):
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"""Database cross reference.
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"""
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__tablename__ = 'dbxref'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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dbxref_id = Column(Integer, primary_key = True)
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class SeqFeature(Base):
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"""Provide a feature connected to a bioentry.
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"""
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__tablename__ = 'seqfeature'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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seqfeature_id = Column(Integer, primary_key = True)
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bioentry_id = Column(Integer, ForeignKey('bioentry.bioentry_id'))
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type_term_id = Column(Integer, ForeignKey('term.term_id'))
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source_term_id = Column(Integer, ForeignKey('term.term_id'))
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type_term = relation("Term", primaryjoin =
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"SeqFeature.type_term_id == Term.term_id")
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source_term = relation("Term", primaryjoin =
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"SeqFeature.source_term_id == Term.term_id")
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qualifiers = relation("SeqFeatureQualifierValue")
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locations = relation("Location")
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dbxrefs = relation("DBXref", secondary=seqfeature_dbxref_table,
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order_by=seqfeature_dbxref_table.columns.rank)
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class SeqFeatureQualifierValue(Base):
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"""A key/value annotation pair associated with a SeqFeature.
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"""
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__tablename__ = 'seqfeature_qualifier_value'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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seqfeature_id = Column(Integer,
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ForeignKey('seqfeature.seqfeature_id'), primary_key = True)
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term_id = Column(Integer, ForeignKey('term.term_id'),
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primary_key = True)
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rank = Column(Integer, primary_key = True)
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term = relation("Term", lazy=True)
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class Location(Base):
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"""Describe a location on a biological sequence.
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"""
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__tablename__ = 'location'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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location_id = Column(Integer, primary_key = True)
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seqfeature_id = Column(Integer, ForeignKey('seqfeature.seqfeature_id'))
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dbxref_id = Column(Integer, ForeignKey('dbxref.dbxref_id'))
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qualifiers = relation("LocationQualifierValue")
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dbxref = relation("DBXref")
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class LocationQualifierValue(Base):
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"""A key/value annotation pair associated with a Location.
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"""
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__tablename__ = 'location_qualifier_value'
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__table_args__ = {'mysql_engine':'InnoDB', 'autoload' : True}
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location_id = Column(Integer,
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ForeignKey('location.location_id'), primary_key = True)
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term_id = Column(Integer, ForeignKey('term.term_id'),
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primary_key = True)
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rank = Column(Integer, primary_key = True)
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term = relation("Term", lazy=True)
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# ugly assignment of classes to the top level for use
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globals()['Biodatabase'] = Biodatabase
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globals()['Bioentry'] = Bioentry
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globals()['Biosequence'] = Biosequence
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globals()['BioentryQualifierValue'] = BioentryQualifierValue
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globals()['Ontology'] = Ontology
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globals()['Term'] = Term
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globals()['BioentryRelationship'] = BioentryRelationship
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globals()['SeqFeatureQualifierValue'] = SeqFeatureQualifierValue
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globals()['SeqFeature'] = SeqFeature
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globals()['DBXref'] = DBXref
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globals()['LocationQualifierValue'] = LocationQualifierValue
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globals()['Location'] = Location

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