initial commit

src/submissions/backend/db/models/controls.py

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+from . import Base
+from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, UniqueConstraint
+from sqlalchemy.orm import relationship
+
+class ControlType(Base):
+    """
+    Base class of a control archetype.
+    """    
+    __tablename__ = '_control_types'
+    
+    id = Column(INTEGER, primary_key=True) #: primary key   
+    name = Column(String(255), unique=True) #: controltype name (e.g. MCS)
+    targets = Column(JSON) #: organisms checked for
+    # instances_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_ctype_instances_id"))
+    instances = relationship("Control", back_populates="controltype") #: control samples created of this type.
+    # UniqueConstraint('name', name='uq_controltype_name')
+
+
+class Control(Base):
+    """
+    Base class of a control sample.
+    """    
+
+    __tablename__ = '_control_samples'
+    
+    id = Column(INTEGER, primary_key=True) #: primary key
+    parent_id = Column(String, ForeignKey("_control_types.id", name="fk_control_parent_id")) #: primary key of control type
+    controltype = relationship("ControlType", back_populates="instances", foreign_keys=[parent_id]) #: reference to parent control type
+    name = Column(String(255), unique=True) #: Sample ID
+    submitted_date = Column(TIMESTAMP) #: Date submitted to Robotics
+    contains = Column(JSON) #: unstructured hashes in contains.tsv for each organism
+    matches = Column(JSON) #: unstructured hashes in matches.tsv for each organism
+    kraken = Column(JSON) #: unstructured output from kraken_report
+    # UniqueConstraint('name', name='uq_control_name')
+    submissions = relationship("BacterialCulture", back_populates="control")
+