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Before creating info and reagent parser classes.

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This commit is contained in:
Landon Wark
2023-08-21 13:50:38 -05:00
parent af810ae528
commit b6de159631
20 changed files with 1176 additions and 571 deletions
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108
src/submissions/backend/db/models/kits.py
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@@ -4,14 +4,23 @@ All kit and reagent related models
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, CheckConstraint
from sqlalchemy.orm import relationship, validates
from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging
logger = logging.getLogger(f'submissions.{__name__}')
# Table containing reagenttype-kittype relationships
reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata, Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")), Column("kits_id", INTEGER, ForeignKey("_kits.id")))
# # Table containing reagenttype-kittype relationships
# reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata,
# Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")),
# Column("kits_id", INTEGER, ForeignKey("_kits.id")),
# # The entry will look like ["Bacteria Culture":{"row":1, "column":4}]
# Column("uses", JSON),
# # is the reagent required for that kit?
# Column("required", INTEGER)
# )
class KitType(Base):
@@ -25,12 +34,24 @@ class KitType(Base):
submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
used_for = Column(JSON) #: list of names of sample types this kit can process
cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit NOTE: depreciated, use the constant and mutable costs instead
# TODO: Change below to 'mutable_cost_column' and 'mutable_cost_sample' before moving to production.
mutable_cost_column = Column(FLOAT(2)) #: dollar amount per 96 well plate that can change with number of columns (reagents, tips, etc)
mutable_cost_sample = Column(FLOAT(2)) #: dollar amount that can change with number of samples (reagents, tips, etc)
constant_cost = Column(FLOAT(2)) #: dollar amount per plate that will remain constant (plates, man hours, etc)
reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
# reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
# reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
# kit_reagenttype_association =
kit_reagenttype_associations = relationship(
"KitTypeReagentTypeAssociation",
back_populates="kit_type",
cascade="all, delete-orphan",
)
# association proxy of "user_keyword_associations" collection
# to "keyword" attribute
reagent_types = association_proxy("kit_reagenttype_associations", "reagenttype")
def __repr__(self) -> str:
return f"KitType({self.name})"
def __str__(self) -> str:
"""
@@ -41,6 +62,61 @@ class KitType(Base):
"""
return self.name
def get_reagents(self, required:bool=False) -> list:
if required:
return [item.reagenttype for item in self.kit_reagenttype_associations if item.required == 1]
else:
return [item.reagenttype for item in self.kit_reagenttype_associations]
def construct_xl_map_for_use(self, use:str) -> dict:
# map = self.used_for[use]
map = {}
assocs = [item for item in self.kit_reagenttype_associations if use in item.uses]
for assoc in assocs:
try:
map[assoc.reagenttype.name] = assoc.uses[use]
except TypeError:
continue
return map
class KitTypeReagentTypeAssociation(Base):
"""
table containing reagenttype/kittype associations
DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
"""
__tablename__ = "_reagenttypes_kittypes"
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True)
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
uses = Column(JSON)
required = Column(INTEGER)
# reagent_type_name = Column(INTEGER, ForeignKey("_reagent_types.name"))
kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
# reference to the "ReagentType" object
reagenttype = relationship("ReagentType")
def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
self.kit = kit_type
self.reagenttype = reagent_type
self.uses = uses
self.required = required
@validates('required')
def validate_age(self, key, value):
if not 0 <= value < 2:
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
return value
@validates('reagenttype')
def validate_reagenttype(self, key, value):
if not isinstance(value, ReagentType):
raise ValueError(f'{value} is not a reagenttype')
return value
class ReagentType(Base):
"""
@@ -50,17 +126,17 @@ class ReagentType(Base):
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: name of reagent type
kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
# kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
# kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
instances = relationship("Reagent", back_populates="type") #: concrete instances of this reagent type
eol_ext = Column(Interval()) #: extension of life interval
required = Column(INTEGER, server_default="1") #: sqlite boolean to determine if reagent type is essential for the kit
# required = Column(INTEGER, server_default="1") #: sqlite boolean to determine if reagent type is essential for the kit
last_used = Column(String(32)) #: last used lot number of this type of reagent
@validates('required')
def validate_age(self, key, value):
if not 0 <= value < 2:
raise ValueError(f'Invalid required value {value}')
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
return value
def __str__(self) -> str:
@@ -71,6 +147,9 @@ class ReagentType(Base):
str: string representing this object's name
"""
return self.name
def __repr__(self):
return f"ReagentType({self.name})"
class Reagent(Base):
@@ -87,6 +166,13 @@ class Reagent(Base):
expiry = Column(TIMESTAMP) #: expiry date - extended by eol_ext of parent programmatically
submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True) #: submissions this reagent is used in
def __repr__(self):
if self.name != None:
return f"Reagent({self.name}-{self.lot})"
else:
return f"Reagent({self.type.name}-{self.lot})"
def __str__(self) -> str:
"""
string representing this object
@@ -142,4 +228,6 @@ class Discount(Base):
client = relationship("Organization") #: joined client lab
client_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete='SET NULL', name="fk_org_id"))
name = Column(String(128))
amount = Column(FLOAT(2))
amount = Column(FLOAT(2))