Pre-major refactor
This commit is contained in:
Landon Wark
@@ -1,19 +1,20 @@
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'''
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All kit and reagent related models
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'''
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from . import Base
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from __future__ import annotations
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from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT
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from sqlalchemy.orm import relationship, validates
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from sqlalchemy.orm import relationship, validates, Query
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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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from tools import Settings, check_authorization
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from tools import Settings, check_authorization, Base, setup_lookup, query_return
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from typing import List
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from . import Organization
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logger = logging.getLogger(f'submissions.{__name__}')
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reagenttypes_reagents = Table("_reagenttypes_reagents", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("reagenttype_id", INTEGER, ForeignKey("_reagent_types.id")))
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class KitType(Base):
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"""
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Base of kits used in submission processing
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@@ -102,9 +103,59 @@ class KitType(Base):
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return map
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@check_authorization
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def save(self, ctx:Settings):
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ctx.database_session.add(self)
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ctx.database_session.commit()
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def save(self):
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self.metadata.session.add(self)
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self.metadata.session.commit()
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@classmethod
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@setup_lookup
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def query(cls,
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name:str=None,
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used_for:str|SubmissionType|None=None,
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id:int|None=None,
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limit:int=0
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) -> KitType|List[KitType]:
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"""
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Lookup a list of or single KitType.
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Args:
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ctx (Settings): Settings object passed down from gui
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name (str, optional): Name of desired kit (returns single instance). Defaults to None.
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used_for (str | models.Submissiontype | None, optional): Submission type the kit is used for. Defaults to None.
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id (int | None, optional): Kit id in the database. Defaults to None.
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limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
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Returns:
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models.KitType|List[models.KitType]: KitType(s) of interest.
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"""
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query: Query = cls.metadata.session.query(cls)
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match used_for:
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case str():
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logger.debug(f"Looking up kit type by use: {used_for}")
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query = query.filter(cls.used_for.any(name=used_for))
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case SubmissionType():
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query = query.filter(cls.used_for.contains(used_for))
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case _:
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pass
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match name:
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case str():
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logger.debug(f"Looking up kit type by name: {name}")
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query = query.filter(cls.name==name)
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limit = 1
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case _:
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pass
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match id:
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case int():
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logger.debug(f"Looking up kit type by id: {id}")
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query = query.filter(cls.id==id)
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limit = 1
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case str():
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logger.debug(f"Looking up kit type by id: {id}")
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query = query.filter(cls.id==int(id))
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limit = 1
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case _:
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pass
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return query_return(query=query, limit=limit)
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class ReagentType(Base):
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"""
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@@ -140,6 +191,60 @@ class ReagentType(Base):
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def __repr__(self):
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return f"ReagentType({self.name})"
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@classmethod
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@setup_lookup
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def query(cls,
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name: str|None=None,
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kit_type: KitType|str|None=None,
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reagent: Reagent|str|None=None,
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limit:int=0,
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) -> ReagentType|List[ReagentType]:
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"""
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Lookup reagent types in the database.
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Args:
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ctx (Settings): Settings object passed down from gui.
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name (str | None, optional): Reagent type name. Defaults to None.
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limit (int, optional): maxmimum number of results to return (0 = all). Defaults to 0.
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Returns:
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models.ReagentType|List[models.ReagentType]: ReagentType or list of ReagentTypes matching filter.
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"""
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query: Query = cls.metadata.session.query(cls)
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if (kit_type != None and reagent == None) or (reagent != None and kit_type == None):
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raise ValueError("Cannot filter without both reagent and kit type.")
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elif kit_type == None and reagent == None:
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pass
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else:
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match kit_type:
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case str():
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kit_type = KitType.query(name=kit_type)
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case _:
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pass
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match reagent:
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case str():
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reagent = Reagent.query(lot_number=reagent)
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case _:
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pass
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assert reagent.type != []
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logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
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logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
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# logger.debug(f"Reagent reagent types: {reagent._sa_instance_state}")
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result = list(set(kit_type.reagent_types).intersection(reagent.type))
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logger.debug(f"Result: {result}")
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try:
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return result[0]
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except IndexError:
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return None
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match name:
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case str():
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logger.debug(f"Looking up reagent type by name: {name}")
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query = query.filter(cls.name==name)
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limit = 1
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case _:
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pass
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return query_return(query=query, limit=limit)
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class KitTypeReagentTypeAssociation(Base):
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"""
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table containing reagenttype/kittype associations
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@@ -178,6 +283,49 @@ class KitTypeReagentTypeAssociation(Base):
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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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@classmethod
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@setup_lookup
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def query(cls,
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kit_type:KitType|str|None,
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reagent_type:ReagentType|str|None,
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limit:int=0
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) -> KitTypeReagentTypeAssociation|List[KitTypeReagentTypeAssociation]:
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"""
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Lookup junction of ReagentType and KitType
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Args:
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ctx (Settings): Settings object passed down from gui.
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kit_type (models.KitType | str | None): KitType of interest.
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reagent_type (models.ReagentType | str | None): ReagentType of interest.
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limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
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Returns:
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models.KitTypeReagentTypeAssociation|List[models.KitTypeReagentTypeAssociation]: Junction of interest.
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"""
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query: Query = cls.metadata.session.query(cls)
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match kit_type:
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case KitType():
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query = query.filter(cls.kit_type==kit_type)
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case str():
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query = query.join(KitType).filter(KitType.name==kit_type)
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case _:
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pass
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match reagent_type:
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case ReagentType():
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query = query.filter(cls.reagent_type==reagent_type)
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case str():
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query = query.join(ReagentType).filter(ReagentType.name==reagent_type)
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case _:
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pass
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if kit_type != None and reagent_type != None:
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limit = 1
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return query_return(query=query, limit=limit)
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def save(self):
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self.metadata.session.add(self)
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self.metadata.session.commit()
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return None
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class Reagent(Base):
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"""
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@@ -199,7 +347,6 @@ class Reagent(Base):
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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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@@ -209,7 +356,6 @@ class Reagent(Base):
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"""
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return str(self.lot)
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def to_sub_dict(self, extraction_kit:KitType=None) -> dict:
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"""
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dictionary containing values necessary for gui
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@@ -282,10 +428,47 @@ class Reagent(Base):
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"expiry": self.expiry.strftime("%Y-%m-%d")
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}
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def save(self, ctx:Settings):
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ctx.database_session.add(self)
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ctx.database_session.commit()
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def save(self):
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self.metadata.session.add(self)
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self.metadata.session.commit()
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@classmethod
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@setup_lookup
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def query(cls, reagent_type:str|ReagentType|None=None,
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lot_number:str|None=None,
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limit:int=0
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) -> Reagent|List[Reagent]:
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"""
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Lookup a list of reagents from the database.
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Args:
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ctx (Settings): Settings object passed down from gui
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reagent_type (str | models.ReagentType | None, optional): Reagent type. Defaults to None.
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lot_number (str | None, optional): Reagent lot number. Defaults to None.
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limit (int, optional): limit of results returned. Defaults to 0.
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Returns:
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models.Reagent | List[models.Reagent]: reagent or list of reagents matching filter.
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"""
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query: Query = cls.metadata.session.query(cls)
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match reagent_type:
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case str():
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logger.debug(f"Looking up reagents by reagent type: {reagent_type}")
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query = query.join(cls.type, aliased=True).filter(ReagentType.name==reagent_type)
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case ReagentType():
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logger.debug(f"Looking up reagents by reagent type: {reagent_type}")
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query = query.filter(cls.type.contains(reagent_type))
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case _:
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pass
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match lot_number:
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case str():
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logger.debug(f"Looking up reagent by lot number: {lot_number}")
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query = query.filter(cls.lot==lot_number)
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# In this case limit number returned.
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limit = 1
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case _:
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pass
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return query_return(query=query, limit=limit)
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class Discount(Base):
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"""
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@@ -303,6 +486,56 @@ class Discount(Base):
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def __repr__(self) -> str:
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return f"<Discount({self.name})>"
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@classmethod
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@setup_lookup
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def query(cls,
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organization:Organization|str|int|None=None,
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kit_type:KitType|str|int|None=None,
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) -> Discount|List[Discount]:
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"""
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Lookup discount objects (union of kit and organization)
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Args:
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ctx (Settings): Settings object passed down from the gui.
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organization (models.Organization | str | int): Organization receiving discount.
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kit_type (models.KitType | str | int): Kit discount received on.
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Raises:
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ValueError: Invalid Organization
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ValueError: Invalid kit.
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Returns:
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models.Discount|List[models.Discount]: Discount(s) of interest.
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"""
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query: Query = cls.metadata.session.query(cls)
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match organization:
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case Organization():
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logger.debug(f"Looking up discount with organization: {organization}")
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query = query.filter(cls.client==Organization)
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case str():
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logger.debug(f"Looking up discount with organization: {organization}")
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query = query.join(Organization).filter(Organization.name==organization)
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case int():
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logger.debug(f"Looking up discount with organization id: {organization}")
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query = query.join(Organization).filter(Organization.id==organization)
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case _:
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# raise ValueError(f"Invalid value for organization: {organization}")
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pass
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match kit_type:
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case KitType():
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logger.debug(f"Looking up discount with kit type: {kit_type}")
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query = query.filter(cls.kit==kit_type)
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case str():
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logger.debug(f"Looking up discount with kit type: {kit_type}")
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query = query.join(KitType).filter(KitType.name==kit_type)
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case int():
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logger.debug(f"Looking up discount with kit type id: {organization}")
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query = query.join(KitType).filter(KitType.id==kit_type)
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case _:
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# raise ValueError(f"Invalid value for kit type: {kit_type}")
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pass
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return query.all()
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class SubmissionType(Base):
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"""
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@@ -326,8 +559,34 @@ class SubmissionType(Base):
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def __repr__(self) -> str:
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return f"<SubmissionType({self.name})>"
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@classmethod
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@setup_lookup
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def query(cls,
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name:str|None=None,
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limit:int=0
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) -> SubmissionType|List[SubmissionType]:
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"""
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Lookup submission type in the database by a number of parameters
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Args:
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ctx (Settings): Settings object passed down from gui
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name (str | None, optional): Name of submission type. Defaults to None.
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limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
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Returns:
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models.SubmissionType|List[models.SubmissionType]: SubmissionType(s) of interest.
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"""
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query: Query = cls.metadata.session.query(cls)
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match name:
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case str():
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logger.debug(f"Looking up submission type by name: {name}")
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query = query.filter(cls.name==name)
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limit = 1
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case _:
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pass
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return query_return(query=query, limit=limit)
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class SubmissionTypeKitTypeAssociation(Base):
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"""
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Abstract of relationship between kits and their submission type.
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@@ -352,7 +611,39 @@ class SubmissionTypeKitTypeAssociation(Base):
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self.constant_cost = 0.00
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def __repr__(self) -> str:
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return f"<SubmissionTypeKitTypeAssociation({self.submission_type.name})"
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return f"<SubmissionTypeKitTypeAssociation({self.submission_type.name})>"
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def set_attrib(self, name, value):
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self.__setattr__(name, value)
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self.__setattr__(name, value)
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@classmethod
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@setup_lookup
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def query(cls,
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submission_type:SubmissionType|str|int|None=None,
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kit_type:KitType|str|int|None=None,
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limit:int=0
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):
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query: Query = cls.metadata.session.query(cls)
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match submission_type:
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case SubmissionType():
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logger.debug(f"Looking up {cls.__name__} by SubmissionType {submission_type}")
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query = query.filter(cls.submission_type==submission_type)
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case str():
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logger.debug(f"Looking up {cls.__name__} by name {submission_type}")
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query = query.join(SubmissionType).filter(SubmissionType.name==submission_type)
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case int():
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logger.debug(f"Looking up {cls.__name__} by id {submission_type}")
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query = query.join(SubmissionType).filter(SubmissionType.id==submission_type)
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match kit_type:
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case KitType():
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logger.debug(f"Looking up {cls.__name__} by KitType {kit_type}")
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query = query.filter(cls.kit_type==kit_type)
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case str():
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logger.debug(f"Looking up {cls.__name__} by name {kit_type}")
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query = query.join(KitType).filter(KitType.name==kit_type)
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case int():
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logger.debug(f"Looking up {cls.__name__} by id {kit_type}")
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query = query.join(KitType).filter(KitType.id==kit_type)
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limit = query.count()
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return query_return(query=query, limit=limit)
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