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production.py
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5462 lines (4168 loc) · 228 KB
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"""Chado Object Classes.
:synopsis: Chado Object Classes.
:moduleauthor: Christopher Tabone <ctabone@morgan.harvard.edu>, Ian Longden <ilongden@morgan.harvard.edu>
Produced originally from production_gen_init.py
NOTE: If you run this again do not overwrite, instead do a diff.
many __str__ methods have been added to this file and this will be removed if overwritten.
method primary_id(): has been added to most classes which returns the primary id of that class.
This will allow simple calls of xxx.id() and it does not matter what the promary key is.
method first_id(): first_id has been added to most classes which returns the first id.
first id here is roughly defined as the first primary field id in a join table.
i.e. for CellLineprop first id would be cell_line_id i.e the prop primary key
GrpRelationshipPub it would be grp_relationship_id
method second_id(): has been added to those that need it and return the second id.
second id here is roughly defined as the second primary field id in a join table.
i.e. for CellLineprop second id would be type_id i.e the prop primary key
GrpRelationshipPub it would be grp_relationship_id
So roughly speaking for join two tables )okay there may be a cvterm etc in there too but...)
we have (first)(second) i.e. (CellLine)(prop)
"""
from sqlalchemy import (
Boolean, CheckConstraint, Column, Date, DateTime, Float, ForeignKey, Index, Integer,
SmallInteger, String, Table, Text, UniqueConstraint, text
)
from sqlalchemy.orm import (
relationship, registry
)
from sqlalchemy.orm.decl_api import DeclarativeMeta
from sqlalchemy.orm import Mapped
mapper_registry = registry()
class Base(metaclass=DeclarativeMeta):
__abstract__ = True
# these are supplied by the sqlalchemy2-stubs, so may be omitted
# when they are installed
registry = mapper_registry
metadata = mapper_registry.metadata
def __repr__(self):
name = self.__class__.__name__
attrs = (
"%s=%r" % (attr, getattr(self, attr))
for attr in self._sa_class_manager.keys()
if not (attr[-2:] == "id" or isinstance(getattr(self, attr), list))
)
return name + "(%s)" % ", ".join(attrs)
# Base = declarative_base()
metadata = Base.metadata
t_af_type = Table(
'af_type', metadata,
Column('feature_id', Integer),
Column('name', String(255)),
Column('uniquename', Text),
Column('dbxref_id', Integer),
Column('type', String(1024)),
Column('residues', Text),
Column('seqlen', Integer),
Column('md5checksum', String(32)),
Column('type_id', Integer),
Column('organism_id', Integer),
Column('analysis_id', Integer),
Column('timeaccessioned', DateTime),
Column('timelastmodified', DateTime)
)
t_alignment_evidence = Table(
'alignment_evidence', metadata,
Column('alignment_evidence_id', Text),
Column('feature_id', Integer),
Column('evidence_id', Integer),
Column('analysis_id', Integer)
)
class Analysis(Base):
__tablename__ = 'analysis'
__table_args__ = (
UniqueConstraint('program', 'programversion', 'sourcename'),
)
analysis_id = Column(Integer, primary_key=True, server_default=text("nextval('analysis_analysis_id_seq'::regclass)"))
name = Column(String(255))
description = Column(Text)
program = Column(String(255), nullable=False)
programversion = Column(String(255), nullable=False)
algorithm = Column(String(255))
sourcename = Column(String(255), index=True)
sourceversion = Column(String(255))
sourceuri = Column(Text)
timeexecuted = Column(DateTime, nullable=False, server_default=text("('now'::text)::timestamp(6) with time zone"))
is_obsolete = Column(Boolean, nullable=False, default=False)
def __str__(self):
"""Over write the default output."""
return "Analysis id={}: program:'{}' sourcename:'{}'".format(self.analysis_id, self.program, self.sourcename)
def primary_id(self):
"""Fetch primary_id."""
return self.analysis_id
class Analysisfeature(Base):
__tablename__ = 'analysisfeature'
__table_args__ = (
UniqueConstraint('feature_id', 'analysis_id'),
)
analysisfeature_id = Column(Integer, primary_key=True, server_default=text("nextval('analysisfeature_analysisfeature_id_seq'::regclass)"))
feature_id: int = Column(ForeignKey('feature.feature_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
analysis_id: int = Column(ForeignKey('analysis.analysis_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
rawscore: float = Column(Float(53))
normscore: float = Column(Float(53))
significance: float = Column(Float(53))
identity: float = Column(Float(53))
analysis: 'Analysis' = relationship("Analysis") # type Analysis
feature: 'Feature' = relationship('Feature')
def __str__(self):
"""Over write the default output."""
return "AnalysisFeat id={}:\n\tAnalysis:({})\n\tFeature:({})".format(self.analysisfeature_id, self.analysis, self.feature)
def primary_id(self):
"""Fetch primary_id."""
return self.analysisfeature_id
def first_id(self):
"""Fetch first id"""
return self.analysis_id
def second_id(self):
"""Fetch second id"""
return self.feature_id
class Analysisgrp(Base):
__tablename__ = 'analysisgrp'
__table_args__ = (
UniqueConstraint('analysis_id', 'grp_id'),
)
analysisgrp_id = Column(Integer, primary_key=True, server_default=text("nextval('analysisgrp_analysisgrp_id_seq'::regclass)"))
rawscore = Column(Float(53))
normscore = Column(Float(53))
significance = Column(Float(53))
identity = Column(Float(53))
analysis_id: int = Column(ForeignKey('analysis.analysis_id', ondelete='CASCADE', onupdate='CASCADE',
deferrable=True, initially='DEFERRED'), nullable=False, index=True)
grp_id: int = Column(ForeignKey('grp.grp_id', ondelete='CASCADE', onupdate='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
analysis: 'Analysis' = relationship('Analysis')
grp: 'Grp' = relationship('Grp')
def __str__(self):
"""Over write the default output."""
return "Analysisgrp id={}:\n\tAnalysis:({})\n\tGrp:({})".format(self.analysisgrp_id, self.analysis, self.grp)
def primary_id(self):
"""Fetch primary_id."""
return self.analysisgrp_id
def first_id(self):
"""Fetch first id"""
return self.analysis_id
def second_id(self):
"""Fetch second id"""
return self.grp_id
class Analysisgrpmember(Base):
__tablename__ = 'analysisgrpmember'
__table_args__ = (
UniqueConstraint('analysis_id', 'grpmember_id'),
)
analysisgrpmember_id = Column(Integer, primary_key=True, server_default=text("nextval('analysisgrpmember_analysisgrpmember_id_seq'::regclass)"))
rawscore = Column(Float(53))
normscore = Column(Float(53))
significance = Column(Float(53))
identity = Column(Float(53))
analysis_id: int = Column(ForeignKey('analysis.analysis_id', ondelete='CASCADE', onupdate='CASCADE',
deferrable=True, initially='DEFERRED'), nullable=False, index=True)
grpmember_id: int = Column(ForeignKey('grpmember.grpmember_id', ondelete='CASCADE', onupdate='CASCADE',
deferrable=True, initially='DEFERRED'), nullable=False, index=True)
analysis: 'Analysis' = relationship('Analysis')
grpmember: 'Grpmember' = relationship('Grpmember')
def primary_id(self):
"""Fetch primary_id."""
return self.analysisgrpmember_id
def first_id(self):
"""Fetch first id"""
return self.analysis_id
def second_id(self):
"""Fetch second id"""
return self.grpmember_id
class Analysisprop(Base):
__tablename__ = 'analysisprop'
__table_args__ = (
UniqueConstraint('analysis_id', 'type_id', 'value'),
)
analysisprop_id = Column(Integer, primary_key=True, server_default=text("nextval('analysisprop_analysisprop_id_seq'::regclass)"))
analysis_id: int = Column(ForeignKey('analysis.analysis_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
value: str = Column(Text)
analysis: 'Analysis' = relationship('Analysis')
type: 'Cvterm' = relationship('Cvterm')
def primary_id(self):
"""Fetch primary_id."""
return self.analysisprop_id
def first_id(self):
"""Fetch first id"""
return self.analysis_id
def second_id(self):
"""Fetch second id"""
return self.type_id
t_audit_chado = Table(
'audit_chado', metadata,
Column('audit_transaction', String(1), nullable=False),
Column('transaction_timestamp', DateTime, nullable=False),
Column('userid', String(255), nullable=False),
Column('audited_table', String(255), nullable=False),
Column('record_pkey', Integer, nullable=False),
Column('record_ukey_cols', String, nullable=False),
Column('record_ukey_vals', Text, nullable=False),
Column('audited_cols', Text, nullable=False),
Column('audited_vals', Text, nullable=False),
Index('audit_idx1', 'audited_table', 'record_pkey')
)
class CellLine(Base):
__tablename__ = 'cell_line'
__table_args__ = (
UniqueConstraint('uniquename', 'organism_id'),
)
cell_line_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_cell_line_id_seq'::regclass)"))
name = Column(String(255))
uniquename = Column(String(255), nullable=False)
organism_id: int = Column(ForeignKey('organism.organism_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
timeaccessioned = Column(DateTime, nullable=False, server_default=text("now()"))
timelastmodified = Column(DateTime, nullable=False, server_default=text("now()"))
organism: 'Organism' = relationship('Organism')
def __str__(self):
"""Over write the default output."""
return "CellLine id={}: uniquename:'{}' name:'{}' organism:({})".format(self.cell_line_id, self.uniquename, self.name, self.organism)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_id
class CellLineCvterm(Base):
__tablename__ = 'cell_line_cvterm'
__table_args__ = (
UniqueConstraint('cell_line_id', 'cvterm_id', 'pub_id', 'rank'),
)
cell_line_cvterm_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_cvterm_cell_line_cvterm_id_seq'::regclass)"))
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
cvterm_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
pub_id: int = Column(ForeignKey('pub.pub_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
rank = Column(Integer, nullable=False, server_default=text("0"))
cell_line: 'CellLine' = relationship('CellLine')
cvterm: 'Cvterm' = relationship('Cvterm')
pub: 'Pub' = relationship('Pub')
def __str__(self):
"""Over write the default output."""
return "CellLineCvterm id={}:\n\tcellline:({})\n\tcvterm:({})\n\tpub:({})".format(self.cell_line_cvterm_id, self.cell_line, self.cvterm, self.pub)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_cvterm_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.cvterm_id
class CellLineCvtermprop(Base):
__tablename__ = 'cell_line_cvtermprop'
__table_args__ = (
UniqueConstraint('cell_line_cvterm_id', 'type_id', 'rank'),
)
cell_line_cvtermprop_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_cvtermprop_cell_line_cvtermprop_id_seq'::regclass)"))
cell_line_cvterm_id: int = Column(ForeignKey('cell_line_cvterm.cell_line_cvterm_id', ondelete='CASCADE',
deferrable=True, initially='DEFERRED'), nullable=False)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
value = Column(Text)
rank = Column(Integer, nullable=False, server_default=text("0"))
cell_line_cvterm: Mapped[CellLineCvterm] = relationship('CellLineCvterm') # type ignore
type: 'Cvterm' = relationship('Cvterm')
def __str__(self):
"""Over write the default output."""
return "CellLineCvtermprop id={}: value:'{}' type:({}) clc:({})".\
format(self.cell_line_cvtermprop_id, self.value, self.type, self.cell_line_cvterm)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_cvtermprop_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_cvterm_id
def second_id(self):
"""Fetch second id"""
return self.type_id
class CellLineDbxref(Base):
__tablename__ = 'cell_line_dbxref'
__table_args__ = (
UniqueConstraint('cell_line_id', 'dbxref_id'),
)
cell_line_dbxref_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_dbxref_cell_line_dbxref_id_seq'::regclass)"))
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
dbxref_id: int = Column(ForeignKey('dbxref.dbxref_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
is_current = Column(Boolean, nullable=False, server_default=text("true"))
cell_line: 'CellLine' = relationship('CellLine')
dbxref: 'Dbxref' = relationship('Dbxref')
def __str__(self):
"""Over write the default output."""
return "CellLineDbxref id={}: CellLine:({}) dbxef:({}) current:{}".\
format(self.cell_line_dbxref_id, self.cell_line, self.dbxref, self.is_current)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_dbxref_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.dbxref_id
class CellLineFeature(Base):
__tablename__ = 'cell_line_feature'
__table_args__ = (
UniqueConstraint('cell_line_id', 'feature_id', 'pub_id'),
)
cell_line_feature_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_feature_cell_line_feature_id_seq'::regclass)"))
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
feature_id: int = Column(ForeignKey('feature.feature_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
pub_id: int = Column(ForeignKey('pub.pub_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
cell_line: 'CellLine' = relationship('CellLine')
feature: 'Feature' = relationship('Feature')
pub: 'Pub' = relationship('Pub')
def __str__(self):
"""Over write the default output."""
return "CellLineFeature id={}:\n\tcell line:({})\n\tfeature:({})\n\tpub:({})".\
format(self.cell_line_feature_id, self.cell_line, self.feature, self.pub)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_feature_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.feature_id
class CellLineLibrary(Base):
__tablename__ = 'cell_line_library'
__table_args__ = (
UniqueConstraint('cell_line_id', 'library_id', 'pub_id'),
)
cell_line_library_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_library_cell_line_library_id_seq'::regclass)"))
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
library_id: int = Column(ForeignKey('library.library_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
pub_id: int = Column(ForeignKey('pub.pub_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
cell_line: 'CellLine' = relationship('CellLine')
library: 'Library' = relationship('Library')
pub: 'Pub' = relationship('Pub')
def __str__(self):
"""Over write the default output."""
return "CellLineLibrary id={}:\n\tcell line:({})\n\tlibrary:({})\n\tpub:({})".\
format(self.cell_line_library_id, self.cell_line, self.library, self.pub)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_library_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.library_id
class CellLineLibraryprop(Base):
__tablename__ = 'cell_line_libraryprop'
__table_args__ = (
UniqueConstraint('cell_line_library_id', 'type_id', 'rank'),
)
cell_line_libraryprop_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_libraryprop_cell_line_libraryprop_id_seq'::regclass)"))
cell_line_library_id: int = Column(ForeignKey('cell_line_library.cell_line_library_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'),
nullable=False, index=True)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
value = Column(Text)
rank = Column(Integer, nullable=False, server_default=text("0"))
cell_line_library: 'CellLineLibrary' = relationship('CellLineLibrary')
type: 'Cvterm' = relationship('Cvterm')
def __str__(self):
"""Over write the default output."""
return "CellLineLibraryprop id={}: value:{} rank:{}\n\tLibrary:({})\n\tType:({})".\
format(self.cell_line_libraryprop_id, self.value, self.rank, self.cell_line_library, self.type)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_libraryprop_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_library_id
def second_id(self):
"""Fetch second id"""
return self.type_id
class CellLinePub(Base):
__tablename__ = 'cell_line_pub'
__table_args__ = (
UniqueConstraint('cell_line_id', 'pub_id'),
)
cell_line_pub_id: int = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_pub_cell_line_pub_id_seq'::regclass)"))
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
pub_id: int = Column(ForeignKey('pub.pub_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
cell_line: 'CellLine' = relationship('CellLine')
pub: 'Pub' = relationship('Pub')
def __str__(self):
"""Over write the default output."""
return "CellLinePub id={}:\n\tcell line:({})\n\tpub:({})".\
format(self.cell_line_pub_id, self.cell_line, self.pub)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_pub_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.pub_id
class CellLineRelationship(Base):
__tablename__ = 'cell_line_relationship'
__table_args__ = (
UniqueConstraint('subject_id', 'object_id', 'type_id'),
)
cell_line_relationship_id = Column(Integer, primary_key=True,
server_default=text("nextval('cell_line_relationship_cell_line_relationship_id_seq'::regclass)"))
subject_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
object_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
object: 'CellLine' = relationship('CellLine', primaryjoin='CellLineRelationship.object_id == CellLine.cell_line_id')
subject: 'CellLine' = relationship('CellLine', primaryjoin='CellLineRelationship.subject_id == CellLine.cell_line_id')
type: 'Cvterm' = relationship('Cvterm')
def __str__(self):
"""Over write the default output."""
return "CellLineRelationship id={}:\n\tObject:({})\n\tSubject:({})\n\tType({})".\
format(self.cell_line_relationship_id, self.object, self.subject, self.type)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_relationship_id
class CellLineStrain(Base):
__tablename__ = 'cell_line_strain'
__table_args__ = (
UniqueConstraint('strain_id', 'cell_line_id', 'pub_id'),
)
cell_line_strain_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_strain_cell_line_strain_id_seq'::regclass)"))
strain_id: int = Column(ForeignKey('strain.strain_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
pub_id: int = Column(ForeignKey('pub.pub_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
cell_line: 'CellLine' = relationship('CellLine')
pub: 'Pub' = relationship('Pub')
strain: 'Strain' = relationship('Strain')
def __str__(self):
"""Over write the default output."""
return "CellLineStrain id={}:\n\tcell line:({})\n\tstrain:({})\n\tpub:({})".\
format(self.cell_line_strain_id, self.cell_line, self.strain, self.pub)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_strain_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.strain_id
class CellLineStrainprop(Base):
__tablename__ = 'cell_line_strainprop'
__table_args__ = (
UniqueConstraint('cell_line_strain_id', 'type_id', 'rank'),
)
cell_line_strainprop_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_strainprop_cell_line_strainprop_id_seq'::regclass)"))
cell_line_strain_id: int = Column(ForeignKey('cell_line_strain.cell_line_strain_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'),
nullable=False, index=True)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
value = Column(Text)
rank = Column(Integer, nullable=False, server_default=text("0"))
cell_line_strain: 'CellLineStrain' = relationship('CellLineStrain')
type: 'Cvterm' = relationship('Cvterm')
def __str__(self):
"""Over write the default output."""
return "CellLineStrainprop id={}: value:'{}' rank:'{}'\n\tcell line strain:({})\n\tType:({})".\
format(self.cell_line_strainprop_id, self.value, self.rank, self.cell_line_strain, self.type)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_strainprop_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_strain_id
def second_id(self):
"""Fetch second id"""
return self.type_id
class CellLineSynonym(Base):
__tablename__ = 'cell_line_synonym'
__table_args__ = (
UniqueConstraint('synonym_id', 'cell_line_id', 'pub_id'),
)
cell_line_synonym_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_line_synonym_cell_line_synonym_id_seq'::regclass)"))
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
synonym_id: int = Column(ForeignKey('synonym.synonym_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
pub_id: int = Column(ForeignKey('pub.pub_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
is_current = Column(Boolean, nullable=False, server_default=text("false"))
is_internal = Column(Boolean, nullable=False, server_default=text("false"))
cell_line: 'CellLine' = relationship('CellLine')
pub: 'Pub' = relationship('Pub')
synonym: 'Synonym' = relationship('Synonym')
def __str__(self):
"""Over write the default output."""
return "CellLineSynonym id={}: is_current:{} is_internal:{}\n\tcell line:({})\n\tsynonym:({})\n\tpub:({})".\
format(self.cell_line_synonym_id, self.is_current, self.is_internal, self.cell_line, self.synonym, self.pub)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_line_synonym_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.synonym_id
class CellLineprop(Base):
__tablename__ = 'cell_lineprop'
__table_args__ = (
UniqueConstraint('cell_line_id', 'type_id', 'rank'),
)
cell_lineprop_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_lineprop_cell_lineprop_id_seq'::regclass)"))
cell_line_id: int = Column(ForeignKey('cell_line.cell_line_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
value = Column(Text)
rank = Column(Integer, nullable=False, server_default=text("0"))
cell_line: 'CellLine' = relationship('CellLine')
type: 'Cvterm' = relationship('Cvterm')
def __str__(self):
"""Over write the default output."""
return "CellLineprop id={}: value:'{}' rank:'{}'\n\tcell line:({})\n\ttype::({})".\
format(self.cell_lineprop_id, self.value, self.rank, self.cell_line, self.type)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_lineprop_id
def first_id(self):
"""Fetch first id"""
return self.cell_line_id
def second_id(self):
"""Fetch second id"""
return self.type_id
class CellLinepropPub(Base):
__tablename__ = 'cell_lineprop_pub'
__table_args__ = (
UniqueConstraint('cell_lineprop_id', 'pub_id'),
)
cell_lineprop_pub_id = Column(Integer, primary_key=True, server_default=text("nextval('cell_lineprop_pub_cell_lineprop_pub_id_seq'::regclass)"))
cell_lineprop_id: int = Column(ForeignKey('cell_lineprop.cell_lineprop_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
pub_id: int = Column(ForeignKey('pub.pub_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
cell_lineprop: 'CellLineprop' = relationship('CellLineprop')
pub: 'Pub' = relationship('Pub')
def __str__(self):
"""Over write the default output."""
return "CellLineproppub id={}:\n\tcell line prop:({})\n\tpub:{})".\
format(self.cell_lineprop_pub_id, self.cell_lineprop, self.pub)
def primary_id(self):
"""Fetch primary_id."""
return self.cell_lineprop_pub_id
def first_id(self):
"""Fetch first id"""
return self.cell_lineprop_id
def second_id(self):
"""Fetch second id"""
return self.pub_id
class Contact(Base):
__tablename__ = 'contact'
contact_id = Column(Integer, primary_key=True, server_default=text("nextval('contact_contact_id_seq'::regclass)"))
description = Column(String(255))
name = Column(String(30), nullable=False, unique=True)
def primary_id(self):
"""Fetch primary_id."""
return self.contact_id
class Cv(Base):
__tablename__ = 'cv'
cv_id = Column(Integer, primary_key=True, server_default=text("nextval('cv_cv_id_seq'::regclass)"))
name = Column(String(255), nullable=False, unique=True)
definition = Column(Text)
def __str__(self):
"""Over write the default output."""
return "Cv id={}: name:'{}'".format(self.cv_id, self.name)
def primary_id(self):
"""Fetch primary_id."""
return self.cv_id
class Cvterm(Base):
__tablename__ = 'cvterm'
__table_args__ = (
UniqueConstraint('cv_id', 'name', 'is_obsolete'),
)
cvterm_id = Column(Integer, primary_key=True, server_default=text("nextval('cvterm_cvterm_id_seq'::regclass)"))
cv_id: int = Column(ForeignKey('cv.cv_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
definition = Column(Text)
dbxref_id: int = Column(ForeignKey('dbxref.dbxref_id', ondelete='SET NULL'), nullable=False, unique=True)
is_obsolete = Column(Integer, nullable=False, server_default=text("0"))
is_relationshiptype = Column(Integer, nullable=False, server_default=text("0"))
name = Column(String(1024), nullable=False, index=True)
cv: 'Cv' = relationship('Cv')
dbxref: 'Dbxref' = relationship('Dbxref', uselist=False)
def __str__(self):
"""Over write the default output."""
return "Cvterm id={}: name:'{}' cv:({})".format(self.cvterm_id, self.name, self.cv)
def primary_id(self):
"""Fetch primary_id."""
return self.cvterm_id
class CvtermDbxref(Base):
__tablename__ = 'cvterm_dbxref'
__table_args__ = (
UniqueConstraint('cvterm_id', 'dbxref_id'),
)
cvterm_dbxref_id = Column(Integer, primary_key=True, server_default=text("nextval('cvterm_dbxref_cvterm_dbxref_id_seq'::regclass)"))
cvterm_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
dbxref_id: int = Column(ForeignKey('dbxref.dbxref_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
is_for_definition = Column(Integer, nullable=False, server_default=text("0"))
cvterm: 'Cvterm' = relationship('Cvterm')
dbxref: 'Dbxref' = relationship('Dbxref')
def __str__(self):
"""Over write the default output."""
return "CvtermDbxref id={}: is_for_definition:{}\n\tcvterm:({})\n\tdbxref:({})".\
format(self.cvterm_dbxref_id, self.is_for_definition, self.cvterm, self.dbxref)
def primary_id(self):
"""Fetch primary_id."""
return self.cvterm_dbxref_id
def first_id(self):
"""Fetch first id"""
return self.cvterm_id
def second_id(self):
"""Fetch second id"""
return self.dbxref_id
class CvtermRelationship(Base):
__tablename__ = 'cvterm_relationship'
__table_args__ = (
UniqueConstraint('type_id', 'subject_id', 'object_id'),
)
cvterm_relationship_id = Column(Integer, primary_key=True, server_default=text("nextval('cvterm_relationship_cvterm_relationship_id_seq'::regclass)"))
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
subject_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
object_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
object: 'Cvterm' = relationship('Cvterm', primaryjoin='CvtermRelationship.object_id == Cvterm.cvterm_id')
subject: 'Cvterm' = relationship('Cvterm', primaryjoin='CvtermRelationship.subject_id == Cvterm.cvterm_id')
type: 'Cvterm' = relationship('Cvterm', primaryjoin='CvtermRelationship.type_id == Cvterm.cvterm_id')
def __str__(self):
"""Over write the default output."""
return "CvtermRelationship id={}:\n\tobject:({})\n\tsubject:({})\n\ttype:({})".\
format(self.cvterm_relationship_id, self.object, self.subject, self.type)
def primary_id(self):
"""Fetch primary_id."""
return self.cvterm_relationship_id
def second_id(self):
"""Fetch second id"""
return self.type_id
t_cvterm_type = Table(
'cvterm_type', metadata,
Column('cvterm_id', Integer),
Column('name', String(1024)),
Column('termtype', String(255))
)
class Cvtermpath(Base):
__tablename__ = 'cvtermpath'
__table_args__ = (
UniqueConstraint('subject_id', 'object_id'),
)
cvtermpath_id = Column(Integer, primary_key=True, server_default=text("nextval('cvtermpath_cvtermpath_id_seq'::regclass)"))
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='SET NULL'), index=True)
subject_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
object_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
cv_id = Column(Integer, nullable=False, index=True)
pathdistance = Column(Integer)
object: 'Cvterm' = relationship('Cvterm', primaryjoin='Cvtermpath.object_id == Cvterm.cvterm_id')
subject: 'Cvterm' = relationship('Cvterm', primaryjoin='Cvtermpath.subject_id == Cvterm.cvterm_id')
type: 'Cvterm' = relationship('Cvterm', primaryjoin='Cvtermpath.type_id == Cvterm.cvterm_id')
class Cvtermprop(Base):
__tablename__ = 'cvtermprop'
__table_args__ = (
UniqueConstraint('cvterm_id', 'type_id', 'value', 'rank'),
)
cvtermprop_id = Column(Integer, primary_key=True, server_default=text("nextval('cvtermprop_cvtermprop_id_seq'::regclass)"))
cvterm_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
value = Column(Text, nullable=False, server_default=text("''::text"))
rank = Column(Integer, nullable=False, server_default=text("0"))
cvterm: 'Cvterm' = relationship('Cvterm', primaryjoin='Cvtermprop.cvterm_id == Cvterm.cvterm_id')
type: 'Cvterm' = relationship('Cvterm', primaryjoin='Cvtermprop.type_id == Cvterm.cvterm_id')
def primary_id(self):
"""Fetch primary_id."""
return self.cvtermprop_id
def first_id(self):
"""Fetch first id"""
return self.cvterm_id
def second_id(self):
"""Fetch second id"""
return self.type_id
class Cvtermsynonym(Base):
__tablename__ = 'cvtermsynonym'
__table_args__ = (
UniqueConstraint('cvterm_id', 'name'),
)
cvtermsynonym_id = Column(Integer, primary_key=True, server_default=text("nextval('cvtermsynonym_cvtermsynonym_id_seq'::regclass)"))
cvterm_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False)
name = Column(String(1024), nullable=False)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'))
cvterm: 'Cvterm' = relationship('Cvterm', primaryjoin='Cvtermsynonym.cvterm_id == Cvterm.cvterm_id')
type: 'Cvterm' = relationship('Cvterm', primaryjoin='Cvtermsynonym.type_id == Cvterm.cvterm_id')
def primary_id(self):
"""Fetch primary_id."""
return self.cvtermsynonym_id
def first_id(self):
"""Fetch first id"""
return self.cvterm_id
def second_id(self):
"""Fetch second id"""
return self.synonym_id
class Db(Base):
__tablename__ = 'db'
db_id = Column(Integer, primary_key=True, server_default=text("nextval('db_db_id_seq'::regclass)"))
name = Column(String(255), nullable=False, unique=True)
contact_id: int = Column(ForeignKey('contact.contact_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'))
description = Column(String(255))
urlprefix = Column(String(255))
url = Column(String(255))
contact: 'Contact' = relationship('Contact')
def __str__(self):
"""Over write the default output."""
return "Db id={}: name:'{}'".format(self.db_id, self.name)
def primary_id(self):
"""Fetch primary_id."""
return self.db_id
class Dbxref(Base):
__tablename__ = 'dbxref'
__table_args__ = (
UniqueConstraint('db_id', 'accession', 'version'),
)
dbxref_id = Column(Integer, primary_key=True, server_default=text("nextval('dbxref_dbxref_id_seq'::regclass)"))
db_id: int = Column(ForeignKey('db.db_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
accession = Column(String(255), nullable=False, index=True)
version = Column(String(255), nullable=False, index=True, server_default=text("''::character varying"))
description = Column(Text)
url = Column(String(255))
db: 'Db' = relationship('Db')
def __str__(self):
"""Over write the default output."""
return "Dbxref id={}: acc:'{}' Db:({})".format(self.dbxref_id, self.accession, self.db)
def primary_id(self):
"""Fetch primary_id."""
return self.dbxref_id
class Dbxrefprop(Base):
__tablename__ = 'dbxrefprop'
__table_args__ = (
UniqueConstraint('dbxref_id', 'type_id', 'rank'),
)
dbxrefprop_id = Column(Integer, primary_key=True, server_default=text("nextval('dbxrefprop_dbxrefprop_id_seq'::regclass)"))
dbxref_id: int = Column(ForeignKey('dbxref.dbxref_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
type_id: int = Column(ForeignKey('cvterm.cvterm_id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'), nullable=False, index=True)
value = Column(Text, nullable=False, server_default=text("''::text"))
rank = Column(Integer, nullable=False, server_default=text("0"))
dbxref: 'Dbxref' = relationship('Dbxref')
type: 'Cvterm' = relationship('Cvterm')
def __str__(self):
"""Over write the default output."""
return "Dbxrefprop id={}: value:'{}' rank:'{}'\n\tdbxref:({})\n\ttype:({})".\
format(self.dbxrefprop_id, self.value, self.rank, self.dbxref, self.type)
def primary_id(self):
"""Fetch primary_id."""
return self.dbxrefprop_id
def first_id(self):
"""Fetch first id"""
return self.dbxref_id
def second_id(self):
"""Fetch second id"""
return self.type_id
class Eimage(Base):
__tablename__ = 'eimage'
eimage_id = Column(Integer, primary_key=True, server_default=text("nextval('eimage_eimage_id_seq'::regclass)"))
eimage_data = Column(Text)
eimage_type = Column(String(255), nullable=False)
image_uri = Column(String(255))
class Environment(Base):
__tablename__ = 'environment'
environment_id = Column(Integer, primary_key=True, server_default=text("nextval('environment_environment_id_seq'::regclass)"))
uniquename = Column(Text, nullable=False, unique=True)
description = Column(Text)
def __str__(self):
"""Over write the default output."""
return "environment_id id={}: uniquename:'{}' desc:'{}'".\
format(self.environment_id, self.uniquename, self.description)