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models

python.ensembl.ncbi_taxonomy.models

NCBI Taxonomy database ORM.

Base = declarative_base() module-attribute

NCBITaxaName

Bases: Base

Source code in src/python/ensembl/ncbi_taxonomy/models.py 
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class NCBITaxaName(Base):
    __tablename__ = "ncbi_taxa_name"

    taxon_id = Column(INTEGER(10), ForeignKey("ncbi_taxa_node.taxon_id"), index=True, primary_key=True)
    name = Column(VARCHAR(500), index=True, primary_key=True)
    name_class = Column(VARCHAR(50), nullable=False, index=True)

name = Column(VARCHAR(500), index=True, primary_key=True) class-attribute instance-attribute

name_class = Column(VARCHAR(50), nullable=False, index=True) class-attribute instance-attribute

taxon_id = Column(INTEGER(10), ForeignKey('ncbi_taxa_node.taxon_id'), index=True, primary_key=True) class-attribute instance-attribute

NCBITaxaNode

Bases: Base

Source code in src/python/ensembl/ncbi_taxonomy/models.py 
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class NCBITaxaNode(Base):
    __tablename__ = "ncbi_taxa_node"

    taxon_id = Column(INTEGER(10), primary_key=True)
    parent_id = Column(INTEGER(10), ForeignKey("ncbi_taxa_node.taxon_id"), nullable=False, index=True)
    rank = Column(CHAR(32), nullable=False, index=True)
    genbank_hidden_flag = Column(TINYINT(1), nullable=False, default=0)
    left_index = Column(INTEGER(10), nullable=False, default=0, index=True)
    right_index = Column(INTEGER(10), nullable=False, default=0, index=True)
    root_id = Column(INTEGER(10), nullable=False, default=1)

    parent = relationship("NCBITaxaNode", remote_side=[taxon_id])
    children = relationship("NCBITaxaName")

children = relationship('NCBITaxaName') class-attribute instance-attribute

genbank_hidden_flag = Column(TINYINT(1), nullable=False, default=0) class-attribute instance-attribute

left_index = Column(INTEGER(10), nullable=False, default=0, index=True) class-attribute instance-attribute

parent = relationship('NCBITaxaNode', remote_side=[taxon_id]) class-attribute instance-attribute

parent_id = Column(INTEGER(10), ForeignKey('ncbi_taxa_node.taxon_id'), nullable=False, index=True) class-attribute instance-attribute

rank = Column(CHAR(32), nullable=False, index=True) class-attribute instance-attribute

right_index = Column(INTEGER(10), nullable=False, default=0, index=True) class-attribute instance-attribute

root_id = Column(INTEGER(10), nullable=False, default=1) class-attribute instance-attribute

taxon_id = Column(INTEGER(10), primary_key=True) class-attribute instance-attribute

NCBITaxonomy

Bases: Base

Source code in src/python/ensembl/ncbi_taxonomy/models.py 
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class NCBITaxonomy(Base):
    ncbi_taxa_name_table = NCBITaxaName.__table__
    ncbi_taxa_node_table = NCBITaxaNode.__table__

    name_node_join = join(ncbi_taxa_name_table, ncbi_taxa_node_table)

    __table__ = name_node_join

    taxon_id = column_property(ncbi_taxa_name_table.c.taxon_id, ncbi_taxa_node_table.c.taxon_id)

name_node_join = join(ncbi_taxa_name_table, ncbi_taxa_node_table) class-attribute instance-attribute

ncbi_taxa_name_table = NCBITaxaName.__table__ class-attribute instance-attribute

ncbi_taxa_node_table = NCBITaxaNode.__table__ class-attribute instance-attribute

taxon_id = column_property(ncbi_taxa_name_table.c.taxon_id, ncbi_taxa_node_table.c.taxon_id) class-attribute instance-attribute