Before creating info and reagent parser classes.
This commit is contained in:
Landon Wark
@@ -7,7 +7,7 @@ Base = declarative_base()
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metadata = Base.metadata
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from .controls import Control, ControlType
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from .kits import KitType, ReagentType, Reagent, Discount
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from .kits import KitType, ReagentType, Reagent, Discount, KitTypeReagentTypeAssociation
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from .organizations import Organization, Contact
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from .samples import WWSample, BCSample
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from .submissions import BasicSubmission, BacterialCulture, Wastewater, WastewaterArtic
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# from .samples import WWSample, BCSample, BasicSample
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from .submissions import BasicSubmission, BacterialCulture, Wastewater, WastewaterArtic, WastewaterSample, BacterialCultureSample, BasicSample, SubmissionSampleAssociation, WastewaterAssociation
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@@ -4,14 +4,23 @@ All kit and reagent related models
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from . import Base
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from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, CheckConstraint
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from sqlalchemy.orm import relationship, validates
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from sqlalchemy.ext.associationproxy import association_proxy
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from datetime import date
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import logging
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logger = logging.getLogger(f'submissions.{__name__}')
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# Table containing reagenttype-kittype relationships
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reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata, Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")), Column("kits_id", INTEGER, ForeignKey("_kits.id")))
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# # Table containing reagenttype-kittype relationships
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# reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata,
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# Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")),
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# Column("kits_id", INTEGER, ForeignKey("_kits.id")),
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# # The entry will look like ["Bacteria Culture":{"row":1, "column":4}]
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# Column("uses", JSON),
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# # is the reagent required for that kit?
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# Column("required", INTEGER)
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# )
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class KitType(Base):
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@@ -25,12 +34,24 @@ class KitType(Base):
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submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
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used_for = Column(JSON) #: list of names of sample types this kit can process
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cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit NOTE: depreciated, use the constant and mutable costs instead
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# TODO: Change below to 'mutable_cost_column' and 'mutable_cost_sample' before moving to production.
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mutable_cost_column = Column(FLOAT(2)) #: dollar amount per 96 well plate that can change with number of columns (reagents, tips, etc)
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mutable_cost_sample = Column(FLOAT(2)) #: dollar amount that can change with number of samples (reagents, tips, etc)
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constant_cost = Column(FLOAT(2)) #: dollar amount per plate that will remain constant (plates, man hours, etc)
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reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
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reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
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# reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
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# reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
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# kit_reagenttype_association =
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kit_reagenttype_associations = relationship(
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"KitTypeReagentTypeAssociation",
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back_populates="kit_type",
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cascade="all, delete-orphan",
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)
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# association proxy of "user_keyword_associations" collection
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# to "keyword" attribute
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reagent_types = association_proxy("kit_reagenttype_associations", "reagenttype")
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def __repr__(self) -> str:
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return f"KitType({self.name})"
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def __str__(self) -> str:
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"""
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@@ -41,6 +62,61 @@ class KitType(Base):
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"""
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return self.name
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def get_reagents(self, required:bool=False) -> list:
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if required:
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return [item.reagenttype for item in self.kit_reagenttype_associations if item.required == 1]
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else:
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return [item.reagenttype for item in self.kit_reagenttype_associations]
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def construct_xl_map_for_use(self, use:str) -> dict:
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# map = self.used_for[use]
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map = {}
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assocs = [item for item in self.kit_reagenttype_associations if use in item.uses]
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for assoc in assocs:
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try:
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map[assoc.reagenttype.name] = assoc.uses[use]
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except TypeError:
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continue
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return map
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class KitTypeReagentTypeAssociation(Base):
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"""
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table containing reagenttype/kittype associations
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DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
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"""
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__tablename__ = "_reagenttypes_kittypes"
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reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True)
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kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
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uses = Column(JSON)
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required = Column(INTEGER)
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# reagent_type_name = Column(INTEGER, ForeignKey("_reagent_types.name"))
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kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
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# reference to the "ReagentType" object
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reagenttype = relationship("ReagentType")
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def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
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self.kit = kit_type
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self.reagenttype = reagent_type
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self.uses = uses
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self.required = required
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@validates('required')
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def validate_age(self, key, value):
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if not 0 <= value < 2:
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raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
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return value
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@validates('reagenttype')
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def validate_reagenttype(self, key, value):
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if not isinstance(value, ReagentType):
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raise ValueError(f'{value} is not a reagenttype')
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return value
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class ReagentType(Base):
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"""
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@@ -50,17 +126,17 @@ class ReagentType(Base):
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id = Column(INTEGER, primary_key=True) #: primary key
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name = Column(String(64)) #: name of reagent type
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kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
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kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
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# kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
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# kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
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instances = relationship("Reagent", back_populates="type") #: concrete instances of this reagent type
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eol_ext = Column(Interval()) #: extension of life interval
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required = Column(INTEGER, server_default="1") #: sqlite boolean to determine if reagent type is essential for the kit
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# required = Column(INTEGER, server_default="1") #: sqlite boolean to determine if reagent type is essential for the kit
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last_used = Column(String(32)) #: last used lot number of this type of reagent
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@validates('required')
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def validate_age(self, key, value):
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if not 0 <= value < 2:
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raise ValueError(f'Invalid required value {value}')
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raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
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return value
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def __str__(self) -> str:
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@@ -71,6 +147,9 @@ class ReagentType(Base):
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str: string representing this object's name
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"""
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return self.name
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def __repr__(self):
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return f"ReagentType({self.name})"
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class Reagent(Base):
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@@ -87,6 +166,13 @@ class Reagent(Base):
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expiry = Column(TIMESTAMP) #: expiry date - extended by eol_ext of parent programmatically
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submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True) #: submissions this reagent is used in
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def __repr__(self):
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if self.name != None:
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return f"Reagent({self.name}-{self.lot})"
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else:
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return f"Reagent({self.type.name}-{self.lot})"
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def __str__(self) -> str:
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"""
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string representing this object
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@@ -142,4 +228,6 @@ class Discount(Base):
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client = relationship("Organization") #: joined client lab
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client_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete='SET NULL', name="fk_org_id"))
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name = Column(String(128))
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amount = Column(FLOAT(2))
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amount = Column(FLOAT(2))
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@@ -21,7 +21,7 @@ class Organization(Base):
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submissions = relationship("BasicSubmission", back_populates="submitting_lab") #: submissions this organization has submitted
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cost_centre = Column(String()) #: cost centre used by org for payment
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contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts) #: contacts involved with this org
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contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id")) #: contact ids of this organization
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# contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id")) #: contact ids of this organization
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def __str__(self) -> str:
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"""
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@@ -44,5 +44,5 @@ class Contact(Base):
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email = Column(String(64)) #: contact email
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phone = Column(String(32)) #: contact phone number
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organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
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organization_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_contact_org_id")) #: joined organization ids
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# organization_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_contact_org_id")) #: joined organization ids
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@@ -1,158 +0,0 @@
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'''
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All models for individual samples.
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'''
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from . import Base
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from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BOOLEAN, JSON
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from sqlalchemy.orm import relationship
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import logging
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logger = logging.getLogger(f"submissions.{__name__}")
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class WWSample(Base):
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"""
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Base wastewater sample
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"""
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__tablename__ = "_ww_samples"
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id = Column(INTEGER, primary_key=True) #: primary key
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ww_processing_num = Column(String(64)) #: wastewater processing number
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ww_sample_full_id = Column(String(64), nullable=False, unique=True)
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rsl_number = Column(String(64)) #: rsl plate identification number
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rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
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rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
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collection_date = Column(TIMESTAMP) #: Date submission received
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well_number = Column(String(8)) #: location on 96 well plate
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# The following are fields from the sample tracking excel sheet Ruth put together.
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# I have no idea when they will be implemented or how.
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testing_type = Column(String(64))
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site_status = Column(String(64))
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notes = Column(String(2000))
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ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
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ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
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n1_status = Column(String(32))
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n2_status = Column(String(32))
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seq_submitted = Column(BOOLEAN())
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ww_seq_run_id = Column(String(64))
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sample_type = Column(String(8))
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pcr_results = Column(JSON)
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well_24 = Column(String(8)) #: location on 24 well plate
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artic_rsl_plate = relationship("WastewaterArtic", back_populates="samples")
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artic_well_number = Column(String(8))
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def to_string(self) -> str:
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"""
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string representing sample object
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Returns:
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str: string representing location and sample id
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"""
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return f"{self.well_number}: {self.ww_sample_full_id}"
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def to_sub_dict(self) -> dict:
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"""
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gui friendly dictionary
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Returns:
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dict: well location and id NOTE: keys must sync with BCSample to_sub_dict below
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"""
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if self.ct_n1 != None and self.ct_n2 != None:
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# logger.debug(f"Using well info in name.")
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name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
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else:
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# logger.debug(f"NOT using well info in name for: {self.ww_sample_full_id}")
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name = self.ww_sample_full_id
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return {
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"well": self.well_number,
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"name": name,
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}
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def to_hitpick(self) -> dict|None:
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"""
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Outputs a dictionary of locations if sample is positive
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Returns:
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dict: dictionary of sample id, row and column in elution plate
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"""
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# dictionary to translate row letters into numbers
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row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
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# if either n1 or n2 is positive, include this sample
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try:
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positive = any(["positive" in item for item in [self.n1_status, self.n2_status]])
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except TypeError as e:
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logger.error(f"Couldn't check positives for {self.rsl_number}. Looks like there isn't PCR data.")
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return None
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well_row = row_dict[self.well_number[0]]
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well_col = self.well_number[1:]
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# if positive:
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# try:
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# # The first character of the elution well is the row
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# well_row = row_dict[self.elution_well[0]]
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# # The remaining charagers are the columns
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# well_col = self.elution_well[1:]
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# except TypeError as e:
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# logger.error(f"This sample doesn't have elution plate info.")
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# return None
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return dict(name=self.ww_sample_full_id,
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row=well_row,
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col=well_col,
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positive=positive)
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# else:
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# return None
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class BCSample(Base):
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"""
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base of bacterial culture sample
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"""
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__tablename__ = "_bc_samples"
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id = Column(INTEGER, primary_key=True) #: primary key
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well_number = Column(String(8)) #: location on parent plate
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sample_id = Column(String(64), nullable=False, unique=True) #: identification from submitter
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organism = Column(String(64)) #: bacterial specimen
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concentration = Column(String(16)) #:
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rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id")) #: id of parent plate
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rsl_plate = relationship("BacterialCulture", back_populates="samples") #: relationship to parent plate
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def to_string(self) -> str:
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"""
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string representing object
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Returns:
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str: string representing well location, sample id and organism
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"""
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return f"{self.well_number}: {self.sample_id} - {self.organism}"
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def to_sub_dict(self) -> dict:
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"""
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gui friendly dictionary
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Returns:
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dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
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"""
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return {
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"well": self.well_number,
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"name": f"{self.sample_id} - ({self.organism})",
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}
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def to_hitpick(self) -> dict|None:
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"""
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Outputs a dictionary of locations
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Returns:
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dict: dictionary of sample id, row and column in elution plate
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"""
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# dictionary to translate row letters into numbers
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row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
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# if either n1 or n2 is positive, include this sample
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well_row = row_dict[self.well_number[0]]
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# The remaining charagers are the columns
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well_col = self.well_number[1:]
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return dict(name=self.sample_id,
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row=well_row,
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col=well_col,
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positive=False)
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@@ -3,12 +3,15 @@ Models for the main submission types.
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'''
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import math
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from . import Base
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from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
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from sqlalchemy.orm import relationship
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from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT, BOOLEAN
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from sqlalchemy.orm import relationship, validates
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import logging
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import json
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from json.decoder import JSONDecodeError
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from math import ceil
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from sqlalchemy.ext.associationproxy import association_proxy
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import uuid
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from . import Base
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logger = logging.getLogger(f"submissions.{__name__}")
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@@ -40,6 +43,15 @@ class BasicSubmission(Base):
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uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
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comment = Column(JSON)
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submission_sample_associations = relationship(
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"SubmissionSampleAssociation",
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back_populates="submission",
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cascade="all, delete-orphan",
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)
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# association proxy of "user_keyword_associations" collection
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# to "keyword" attribute
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samples = association_proxy("submission_sample_associations", "sample")
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# Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
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__mapper_args__ = {
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"polymorphic_identity": "basic_submission",
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@@ -47,6 +59,9 @@ class BasicSubmission(Base):
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"with_polymorphic": "*",
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}
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def __repr__(self):
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return f"{self.submission_type}Submission({self.rsl_plate_num})"
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def to_string(self) -> str:
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"""
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string presenting basic submission
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@@ -64,6 +79,7 @@ class BasicSubmission(Base):
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dict: dictionary used in submissions summary
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"""
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# get lab from nested organization object
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try:
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sub_lab = self.submitting_lab.name
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except AttributeError:
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@@ -90,10 +106,20 @@ class BasicSubmission(Base):
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except Exception as e:
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logger.error(f"We got an error retrieving reagents: {e}")
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reagents = None
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try:
|
||||
samples = [item.to_sub_dict() for item in self.samples]
|
||||
except:
|
||||
samples = None
|
||||
# try:
|
||||
# samples = [item.sample.to_sub_dict(item.__dict__()) for item in self.submission_sample_associations]
|
||||
# except Exception as e:
|
||||
# logger.error(f"Problem making list of samples: {e}")
|
||||
# samples = None
|
||||
samples = []
|
||||
for item in self.submission_sample_associations:
|
||||
sample = item.sample.to_sub_dict(submission_rsl=self.rsl_plate_num)
|
||||
# try:
|
||||
# sample['well'] = f"{row_map[item.row]}{item.column}"
|
||||
# except KeyError as e:
|
||||
# logger.error(f"Unable to find row {item.row} in row_map.")
|
||||
# sample['well'] = None
|
||||
samples.append(sample)
|
||||
try:
|
||||
comments = self.comment
|
||||
except:
|
||||
@@ -115,11 +141,8 @@ class BasicSubmission(Base):
|
||||
"ext_info": ext_info,
|
||||
"comments": comments
|
||||
}
|
||||
# logger.debug(f"{self.rsl_plate_num} extraction: {output['Extraction Status']}")
|
||||
# logger.debug(f"Output dict: {output}")
|
||||
return output
|
||||
|
||||
|
||||
def report_dict(self) -> dict:
|
||||
"""
|
||||
dictionary used in creating reports
|
||||
@@ -141,13 +164,6 @@ class BasicSubmission(Base):
|
||||
ext_kit = self.extraction_kit.name
|
||||
except AttributeError:
|
||||
ext_kit = None
|
||||
# get extraction kit cost from nested kittype object
|
||||
# depreciated as it will change kit cost overtime
|
||||
# try:
|
||||
# cost = self.extraction_kit.cost_per_run
|
||||
# except AttributeError:
|
||||
# cost = None
|
||||
|
||||
output = {
|
||||
"id": self.id,
|
||||
"Plate Number": self.rsl_plate_num,
|
||||
@@ -168,24 +184,47 @@ class BasicSubmission(Base):
|
||||
except Exception as e:
|
||||
logger.error(f"Column count error: {e}")
|
||||
# cols_count_24 = ceil(int(self.sample_count) / 3)
|
||||
try:
|
||||
self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
|
||||
except Exception as e:
|
||||
logger.error(f"Calculation error: {e}")
|
||||
if all(item == 0.0 for item in [self.extraction_kit.constant_cost, self.extraction_kit.mutable_cost_column, self.extraction_kit.mutable_cost_sample]):
|
||||
try:
|
||||
self.run_cost = self.extraction_kit.cost_per_run
|
||||
except Exception as e:
|
||||
logger.error(f"Calculation error: {e}")
|
||||
else:
|
||||
try:
|
||||
self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
|
||||
except Exception as e:
|
||||
logger.error(f"Calculation error: {e}")
|
||||
|
||||
def calculate_column_count(self):
|
||||
columns = [int(sample.well_number[-2:]) for sample in self.samples]
|
||||
logger.debug(f"Here are the columns for {self.rsl_plate_num}: {columns}")
|
||||
return max(columns)
|
||||
logger.debug(f"Here's the samples: {self.samples}")
|
||||
# columns = [int(sample.well_number[-2:]) for sample in self.samples]
|
||||
columns = [assoc.column for assoc in self.submission_sample_associations]
|
||||
logger.debug(f"Here are the columns for {self.rsl_plate_num}: {columns}")
|
||||
return max(columns)
|
||||
|
||||
def hitpick_plate(self, plate_number:int|None=None) -> list:
|
||||
output_list = []
|
||||
for assoc in self.submission_sample_associations:
|
||||
samp = assoc.sample.to_hitpick(submission_rsl=self.rsl_plate_num)
|
||||
if samp != None:
|
||||
if plate_number != None:
|
||||
samp['plate_number'] = plate_number
|
||||
samp['row'] = assoc.row
|
||||
samp['column'] = assoc.column
|
||||
samp['plate_name'] = self.rsl_plate_num
|
||||
output_list.append(samp)
|
||||
else:
|
||||
continue
|
||||
return output_list
|
||||
|
||||
# Below are the custom submission types
|
||||
|
||||
class BacterialCulture(BasicSubmission):
|
||||
class BacterialCulture(BasicSubmission):
|
||||
"""
|
||||
derivative submission type from BasicSubmission
|
||||
"""
|
||||
controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
|
||||
samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
|
||||
# samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
|
||||
__mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
|
||||
|
||||
def to_dict(self) -> dict:
|
||||
@@ -197,26 +236,13 @@ class BacterialCulture(BasicSubmission):
|
||||
"""
|
||||
output = super().to_dict()
|
||||
output['controls'] = [item.to_sub_dict() for item in self.controls]
|
||||
return output
|
||||
|
||||
|
||||
# def calculate_base_cost(self):
|
||||
# try:
|
||||
# cols_count_96 = ceil(int(self.sample_count) / 8)
|
||||
# except Exception as e:
|
||||
# logger.error(f"Column count error: {e}")
|
||||
# # cols_count_24 = ceil(int(self.sample_count) / 3)
|
||||
# try:
|
||||
# self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
|
||||
# except Exception as e:
|
||||
# logger.error(f"Calculation error: {e}")
|
||||
|
||||
return output
|
||||
|
||||
class Wastewater(BasicSubmission):
|
||||
"""
|
||||
derivative submission type from BasicSubmission
|
||||
"""
|
||||
samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
|
||||
# samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
|
||||
pcr_info = Column(JSON)
|
||||
# ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
|
||||
__mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
|
||||
@@ -235,23 +261,11 @@ class Wastewater(BasicSubmission):
|
||||
pass
|
||||
return output
|
||||
|
||||
# def calculate_base_cost(self):
|
||||
# try:
|
||||
# cols_count_96 = ceil(int(self.sample_count) / 8) + 1 #: Adding in one column to account for 24 samples + ext negatives
|
||||
# except Exception as e:
|
||||
# logger.error(f"Column count error: {e}")
|
||||
# # cols_count_24 = ceil(int(self.sample_count) / 3)
|
||||
# try:
|
||||
# self.run_cost = self.extraction_kit.constant_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
|
||||
# except Exception as e:
|
||||
# logger.error(f"Calculation error: {e}")
|
||||
|
||||
|
||||
class WastewaterArtic(BasicSubmission):
|
||||
"""
|
||||
derivative submission type for artic wastewater
|
||||
"""
|
||||
samples = relationship("WWSample", back_populates="artic_rsl_plate", uselist=True)
|
||||
# samples = relationship("WWSample", back_populates="artic_rsl_plate", uselist=True)
|
||||
# Can it use the pcr_info from the wastewater? Cause I can't define pcr_info here due to conflicts with that
|
||||
# Not necessary because we don't get any results for this procedure.
|
||||
__mapper_args__ = {"polymorphic_identity": "wastewater_artic", "polymorphic_load": "inline"}
|
||||
@@ -273,3 +287,252 @@ class WastewaterArtic(BasicSubmission):
|
||||
self.run_cost = const_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
|
||||
except Exception as e:
|
||||
logger.error(f"Calculation error: {e}")
|
||||
|
||||
class BasicSample(Base):
|
||||
"""
|
||||
Base of basic sample which polymorphs into BCSample and WWSample
|
||||
"""
|
||||
|
||||
__tablename__ = "_samples"
|
||||
|
||||
id = Column(INTEGER, primary_key=True) #: primary key
|
||||
submitter_id = Column(String(64), nullable=False, unique=True) #: identification from submitter
|
||||
sample_type = Column(String(32))
|
||||
|
||||
sample_submission_associations = relationship(
|
||||
"SubmissionSampleAssociation",
|
||||
back_populates="sample",
|
||||
cascade="all, delete-orphan",
|
||||
)
|
||||
|
||||
__mapper_args__ = {
|
||||
"polymorphic_identity": "basic_sample",
|
||||
"polymorphic_on": sample_type,
|
||||
"with_polymorphic": "*",
|
||||
}
|
||||
|
||||
submissions = association_proxy("sample_submission_associations", "submission")
|
||||
|
||||
@validates('submitter_id')
|
||||
def create_id(self, key, value):
|
||||
logger.debug(f"validating sample_id of: {value}")
|
||||
if value == None:
|
||||
return uuid.uuid4().hex.upper()
|
||||
else:
|
||||
return value
|
||||
|
||||
def __repr__(self) -> str:
|
||||
return f"{self.sample_type}Sample({self.submitter_id})"
|
||||
|
||||
def to_sub_dict(self, submission_rsl:str) -> dict:
|
||||
row_map = {1:"A", 2:"B", 3:"C", 4:"D", 5:"E", 6:"F", 7:"G", 8:"H"}
|
||||
self.assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
|
||||
sample = {}
|
||||
try:
|
||||
sample['well'] = f"{row_map[self.assoc.row]}{self.assoc.column}"
|
||||
except KeyError as e:
|
||||
logger.error(f"Unable to find row {self.assoc.row} in row_map.")
|
||||
sample['well'] = None
|
||||
sample['name'] = self.submitter_id
|
||||
return sample
|
||||
|
||||
def to_hitpick(self, submission_rsl:str) -> dict|None:
|
||||
"""
|
||||
Outputs a dictionary of locations
|
||||
|
||||
Returns:
|
||||
dict: dictionary of sample id, row and column in elution plate
|
||||
"""
|
||||
self.assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
|
||||
# dictionary to translate row letters into numbers
|
||||
# row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
|
||||
# if either n1 or n2 is positive, include this sample
|
||||
# well_row = row_dict[self.well_number[0]]
|
||||
# The remaining charagers are the columns
|
||||
# well_col = self.well_number[1:]
|
||||
return dict(name=self.submitter_id,
|
||||
# row=well_row,
|
||||
# col=well_col,
|
||||
positive=False)
|
||||
|
||||
class WastewaterSample(BasicSample):
|
||||
"""
|
||||
Base wastewater sample
|
||||
"""
|
||||
# __tablename__ = "_ww_samples"
|
||||
|
||||
# id = Column(INTEGER, primary_key=True) #: primary key
|
||||
ww_processing_num = Column(String(64)) #: wastewater processing number
|
||||
# ww_sample_full_id = Column(String(64), nullable=False, unique=True)
|
||||
rsl_number = Column(String(64)) #: rsl plate identification number
|
||||
# rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
|
||||
# rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
|
||||
collection_date = Column(TIMESTAMP) #: Date submission received
|
||||
# well_number = Column(String(8)) #: location on 96 well plate
|
||||
# The following are fields from the sample tracking excel sheet Ruth put together.
|
||||
# I have no idea when they will be implemented or how.
|
||||
testing_type = Column(String(64))
|
||||
site_status = Column(String(64))
|
||||
notes = Column(String(2000))
|
||||
# ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
|
||||
# ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
|
||||
# n1_status = Column(String(32))
|
||||
# n2_status = Column(String(32))
|
||||
seq_submitted = Column(BOOLEAN())
|
||||
ww_seq_run_id = Column(String(64))
|
||||
# sample_type = Column(String(16))
|
||||
# pcr_results = Column(JSON)
|
||||
well_24 = Column(String(8)) #: location on 24 well plate
|
||||
# artic_rsl_plate = relationship("WastewaterArtic", back_populates="samples")
|
||||
# artic_well_number = Column(String(8))
|
||||
|
||||
__mapper_args__ = {"polymorphic_identity": "wastewater_sample", "polymorphic_load": "inline"}
|
||||
|
||||
# def to_string(self) -> str:
|
||||
# """
|
||||
# string representing sample object
|
||||
|
||||
# Returns:
|
||||
# str: string representing location and sample id
|
||||
# """
|
||||
# return f"{self.well_number}: {self.ww_sample_full_id}"
|
||||
|
||||
def to_sub_dict(self, submission_rsl:str) -> dict:
|
||||
"""
|
||||
Gui friendly dictionary. Inherited from BasicSample
|
||||
This version will include PCR status.
|
||||
|
||||
Args:
|
||||
submission_rsl (str): RSL plate number (passed down from the submission.to_dict() functino)
|
||||
|
||||
Returns:
|
||||
dict: Alphanumeric well id and sample name
|
||||
"""
|
||||
# Get the relevant submission association for this sample
|
||||
sample = super().to_sub_dict(submission_rsl=submission_rsl)
|
||||
try:
|
||||
check = self.assoc.ct_n1 != None and self.assoc.ct_n2 != None
|
||||
except AttributeError as e:
|
||||
check = False
|
||||
if check:
|
||||
logger.debug(f"Using well info in name.")
|
||||
sample['name'] = f"{self.submitter_id}\n\t- ct N1: {'{:.2f}'.format(self.assoc.ct_n1)} ({self.assoc.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.assoc.ct_n2)} ({self.assoc.n2_status})"
|
||||
else:
|
||||
logger.error(f"Couldn't get the pcr info")
|
||||
return sample
|
||||
|
||||
def to_hitpick(self, submission_rsl:str) -> dict|None:
|
||||
"""
|
||||
Outputs a dictionary of locations if sample is positive
|
||||
|
||||
Returns:
|
||||
dict: dictionary of sample id, row and column in elution plate
|
||||
"""
|
||||
sample = super().to_hitpick(submission_rsl=submission_rsl)
|
||||
# dictionary to translate row letters into numbers
|
||||
# row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
|
||||
# if either n1 or n2 is positive, include this sample
|
||||
try:
|
||||
sample['positive'] = any(["positive" in item for item in [self.assoc.n1_status, self.assoc.n2_status]])
|
||||
except (TypeError, AttributeError) as e:
|
||||
logger.error(f"Couldn't check positives for {self.rsl_number}. Looks like there isn't PCR data.")
|
||||
# return None
|
||||
# positive = False
|
||||
# well_row = row_dict[self.well_number[0]]
|
||||
# well_col = self.well_number[1:]
|
||||
# if positive:
|
||||
# try:
|
||||
# # The first character of the elution well is the row
|
||||
# well_row = row_dict[self.elution_well[0]]
|
||||
# # The remaining charagers are the columns
|
||||
# well_col = self.elution_well[1:]
|
||||
# except TypeError as e:
|
||||
# logger.error(f"This sample doesn't have elution plate info.")
|
||||
# return None
|
||||
return sample
|
||||
|
||||
|
||||
class BacterialCultureSample(BasicSample):
|
||||
"""
|
||||
base of bacterial culture sample
|
||||
"""
|
||||
# __tablename__ = "_bc_samples"
|
||||
|
||||
# id = Column(INTEGER, primary_key=True) #: primary key
|
||||
# well_number = Column(String(8)) #: location on parent plate
|
||||
# sample_id = Column(String(64), nullable=False, unique=True) #: identification from submitter
|
||||
organism = Column(String(64)) #: bacterial specimen
|
||||
concentration = Column(String(16)) #:
|
||||
# sample_type = Column(String(16))
|
||||
# rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id")) #: id of parent plate
|
||||
# rsl_plate = relationship("BacterialCulture", back_populates="samples") #: relationship to parent plate
|
||||
|
||||
__mapper_args__ = {"polymorphic_identity": "bacterial_culture_sample", "polymorphic_load": "inline"}
|
||||
|
||||
# def to_string(self) -> str:
|
||||
# """
|
||||
# string representing object
|
||||
|
||||
# Returns:
|
||||
# str: string representing well location, sample id and organism
|
||||
# """
|
||||
# return f"{self.well_number}: {self.sample_id} - {self.organism}"
|
||||
|
||||
def to_sub_dict(self, submission_rsl:str) -> dict:
|
||||
"""
|
||||
gui friendly dictionary
|
||||
|
||||
Returns:
|
||||
dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
|
||||
"""
|
||||
sample = super().to_sub_dict(submission_rsl=submission_rsl)
|
||||
sample['name'] = f"{self.submitter_id} - ({self.organism})"
|
||||
# return {
|
||||
# # "well": self.well_number,
|
||||
# "name": f"{self.submitter_id} - ({self.organism})",
|
||||
# }
|
||||
return sample
|
||||
|
||||
|
||||
|
||||
class SubmissionSampleAssociation(Base):
|
||||
"""
|
||||
table containing submission/sample associations
|
||||
DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
|
||||
"""
|
||||
__tablename__ = "_submission_sample"
|
||||
sample_id = Column(INTEGER, ForeignKey("_samples.id"), primary_key=True)
|
||||
submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True)
|
||||
row = Column(INTEGER)
|
||||
column = Column(INTEGER)
|
||||
|
||||
submission = relationship(BasicSubmission, back_populates="submission_sample_associations")
|
||||
|
||||
# reference to the "ReagentType" object
|
||||
# sample = relationship("BasicSample")
|
||||
sample = relationship(BasicSample, back_populates="sample_submission_associations")
|
||||
|
||||
base_sub_type = Column(String)
|
||||
# """Refers to the type of parent."""
|
||||
|
||||
__mapper_args__ = {
|
||||
"polymorphic_identity": "basic_association",
|
||||
"polymorphic_on": base_sub_type,
|
||||
"with_polymorphic": "*",
|
||||
}
|
||||
|
||||
def __init__(self, submission:BasicSubmission=None, sample:BasicSample=None, row:int=1, column:int=1):
|
||||
self.submission = submission
|
||||
self.sample = sample
|
||||
self.row = row
|
||||
self.column = column
|
||||
|
||||
class WastewaterAssociation(SubmissionSampleAssociation):
|
||||
|
||||
ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
|
||||
ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
|
||||
n1_status = Column(String(32))
|
||||
n2_status = Column(String(32))
|
||||
pcr_results = Column(JSON)
|
||||
|
||||
__mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
|
||||
Reference in New Issue
Block a user