class MolarYields(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
sample_id = db.Column(
db.Integer,
db.ForeignKey("sample.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
sample = db.relationship(
Sample,
backref=db.backref("molar_yields",
cascade="all, delete-orphan",
lazy="dynamic"),
)
product_name = db.Column(db.Text(), nullable=False)
product_identifier = db.Column(db.Text(), nullable=False)
product_namespace = db.Column(db.Text(), nullable=False)
substrate_name = db.Column(db.Text(), nullable=False)
substrate_identifier = db.Column(db.Text(), nullable=False)
substrate_namespace = db.Column(db.Text(), nullable=False)
# Both in mmol-product / mmol-substrate
measurement = db.Column(db.Float, nullable=False)
uncertainty = db.Column(db.Float, nullable=True)
class Condition(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
experiment_id = db.Column(
db.Integer,
db.ForeignKey("experiment.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
experiment = db.relationship(
Experiment,
backref=db.backref("conditions",
cascade="all, delete-orphan",
lazy="dynamic"),
)
strain_id = db.Column(
db.Integer,
db.ForeignKey("strain.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
strain = db.relationship(Strain)
medium_id = db.Column(
db.Integer,
db.ForeignKey("medium.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
medium = db.relationship(Medium, foreign_keys=[medium_id])
name = db.Column(db.String(256), nullable=False)
class Growth(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
sample_id = db.Column(
db.Integer,
db.ForeignKey("sample.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
sample = db.relationship(
Sample,
backref=db.backref("growth_rate",
uselist=False,
cascade="all, delete-orphan",
lazy="select"),
)
measurement = db.Column(db.Float, nullable=False) # unit: 1/h
# unit: 1/h; 0 if no uncertainty or unknown
uncertainty = db.Column(db.Float, nullable=False)
class Sample(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
condition_id = db.Column(
db.Integer,
db.ForeignKey("condition.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
condition = db.relationship(
Condition,
backref=db.backref("samples",
cascade="all, delete-orphan",
lazy="dynamic"),
)
name = db.Column(db.Text(), nullable=False)
# Datetime fields for when the sample was taken. `end_time` is optional, used for
# interval measurements like uptake rates or fluxomics.
start_time = db.Column(db.DateTime, nullable=False)
end_time = db.Column(db.DateTime, nullable=True)
class Proteomics(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
sample_id = db.Column(
db.Integer,
db.ForeignKey("sample.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
sample = db.relationship(
Sample,
backref=db.backref("proteomics",
cascade="all, delete-orphan",
lazy="dynamic"),
)
identifier = db.Column(db.Text(), nullable=False)
name = db.Column(db.Text(), nullable=False)
full_name = db.Column(db.Text(), nullable=False)
gene = db.Column(postgresql.JSON, nullable=False)
measurement = db.Column(db.Float, nullable=False) # unit: mmol/gDW
uncertainty = db.Column(db.Float, nullable=True) # unit: mmol/gDW
class UptakeSecretionRates(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
sample_id = db.Column(
db.Integer,
db.ForeignKey("sample.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
sample = db.relationship(
Sample,
backref=db.backref("uptake_secretion_rates",
cascade="all, delete-orphan",
lazy="dynamic"),
)
compound_name = db.Column(db.Text(), nullable=False)
compound_identifier = db.Column(db.Text(), nullable=False)
compound_namespace = db.Column(db.Text(), nullable=False)
measurement = db.Column(db.Float, nullable=False) # unit: mmol/gDW/h
uncertainty = db.Column(db.Float, nullable=True) # unit: mmol/gDW/h
class Strain(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
project_id = db.Column(db.Integer)
organism_id = db.Column(
db.Integer,
db.ForeignKey("organism.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
organism = db.relationship(Organism)
parent_id = db.Column(
db.Integer,
db.ForeignKey("strain.id", onupdate="CASCADE", ondelete="CASCADE"))
parent = db.relationship("Strain", uselist=False)
name = db.Column(db.String(256), nullable=False)
genotype = db.Column(db.Text())
class MediumCompound(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
medium_id = db.Column(
db.Integer,
db.ForeignKey("medium.id", onupdate="CASCADE", ondelete="CASCADE"),
nullable=False,
)
medium = db.relationship(
Medium,
backref=db.backref("compounds",
cascade="all, delete-orphan",
lazy="dynamic"),
)
compound_name = db.Column(db.Text())
compound_identifier = db.Column(db.Text())
compound_namespace = db.Column(db.Text())
mass_concentration = db.Column(db.Float()) # unit: mmol/l
class Medium(TimestampMixin, db.Model):
project_id = db.Column(db.Integer)
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(256), nullable=False)
class Experiment(TimestampMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
project_id = db.Column(db.Integer)
name = db.Column(db.String(256), nullable=False)
description = db.Column(db.Text(), nullable=False)
class TimestampMixin(object):
created = db.Column(db.DateTime, nullable=False, default=datetime.utcnow)
updated = db.Column(db.DateTime, onupdate=datetime.utcnow)
