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post documentation and code clean-up.

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This commit is contained in:
lwark
2024-07-05 14:00:25 -05:00
parent c460e5eeca
commit e589420815
8 changed files with 106 additions and 46 deletions
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49
src/submissions/backend/db/models/kits.py
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@@ -8,7 +8,7 @@ from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result
from typing import List, Literal, Any
from typing import List, Literal
from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization
@@ -126,8 +126,9 @@ class KitType(BaseClass):
cascade="all, delete-orphan",
) #: Relation to SubmissionType
used_for = association_proxy("kit_submissiontype_associations",
"submission_type") #: Association proxy to SubmissionTypeKitTypeAssociation
used_for = association_proxy("kit_submissiontype_associations", "submission_type",
creator=lambda ST: SubmissionTypeKitTypeAssociation(
submission_type=ST)) #: Association proxy to SubmissionTypeKitTypeAssociation
def __repr__(self) -> str:
"""
@@ -375,8 +376,9 @@ class Reagent(BaseClass):
cascade="all, delete-orphan",
) #: Relation to SubmissionSampleAssociation
submissions = association_proxy("reagent_submission_associations",
"submission") #: Association proxy to SubmissionSampleAssociation.samples
submissions = association_proxy("reagent_submission_associations", "submission",
creator=lambda sub: SubmissionReagentAssociation(
submission=sub)) #: Association proxy to SubmissionSampleAssociation.samples
def __repr__(self):
if self.name is not None:
@@ -597,7 +599,9 @@ class SubmissionType(BaseClass):
cascade="all, delete-orphan",
) #: Association of kittypes
kit_types = association_proxy("submissiontype_kit_associations", "kit_type") #: Proxy of kittype association
kit_types = association_proxy("submissiontype_kit_associations", "kit_type",
creator=lambda kit: SubmissionTypeKitTypeAssociation(
kit_type=kit)) #: Proxy of kittype association
submissiontype_equipmentrole_associations = relationship(
"SubmissionTypeEquipmentRoleAssociation",
@@ -605,8 +609,8 @@ class SubmissionType(BaseClass):
cascade="all, delete-orphan"
) #: Association of equipmentroles
equipment = association_proxy("submissiontype_equipmentrole_associations",
"equipment_role") #: Proxy of equipmentrole associations
equipment = association_proxy("submissiontype_equipmentrole_associations", "equipment_role",
creator=lambda eq: SubmissionTypeEquipmentRoleAssociation(equipment_role=eq)) #: Proxy of equipmentrole associations
submissiontype_kit_rt_associations = relationship(
"KitTypeReagentRoleAssociation",
@@ -710,7 +714,7 @@ class SubmissionType(BaseClass):
Returns:
dict: Tip locations in the excel sheet.
"""
"""
output = {}
for item in self.submissiontype_tiprole_associations:
tmap = item.uses
@@ -827,12 +831,13 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
submission_type = relationship(SubmissionType,
back_populates="submissiontype_kit_associations") #: joined submission type
def __init__(self, kit_type=None, submission_type=None):
def __init__(self, kit_type=None, submission_type=None,
mutable_cost_column: int = 0.00, mutable_cost_sample: int = 0.00, constant_cost: int = 0.00):
self.kit_type = kit_type
self.submission_type = submission_type
self.mutable_cost_column = 0.00
self.mutable_cost_sample = 0.00
self.constant_cost = 0.00
self.mutable_cost_column = mutable_cost_column
self.mutable_cost_sample = mutable_cost_sample
self.constant_cost = constant_cost
def __repr__(self) -> str:
"""
@@ -1539,15 +1544,15 @@ class Process(BaseClass):
pass
return cls.execute_query(query=query, limit=limit)
@check_authorization
def save(self):
super().save()
class TipRole(BaseClass):
"""
An abstract role that a tip fills during a process
"""
"""
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: name of reagent type
instances = relationship("Tips", back_populates="role",
@@ -1564,7 +1569,7 @@ class TipRole(BaseClass):
def __repr__(self):
return f"<TipRole({self.name})>"
@check_authorization
def save(self):
super().save()
@@ -1573,7 +1578,7 @@ class TipRole(BaseClass):
class Tips(BaseClass):
"""
A concrete instance of tips.
"""
"""
id = Column(INTEGER, primary_key=True) #: primary key
role = relationship("TipRole", back_populates="instances",
secondary=tiproles_tips) #: joined parent reagent type
@@ -1606,7 +1611,7 @@ class Tips(BaseClass):
Returns:
Tips | List[Tips]: Tips matching criteria
"""
"""
query = cls.__database_session__.query(cls)
match name:
case str():
@@ -1622,7 +1627,7 @@ class Tips(BaseClass):
case _:
pass
return cls.execute_query(query=query, limit=limit)
@check_authorization
def save(self):
super().save()
@@ -1642,7 +1647,7 @@ class SubmissionTypeTipRoleAssociation(BaseClass):
back_populates="submissiontype_tiprole_associations") #: associated submission
tip_role = relationship(TipRole,
back_populates="tiprole_submissiontype_associations") #: associated equipment
@check_authorization
def save(self):
super().save()
@@ -1651,7 +1656,7 @@ class SubmissionTypeTipRoleAssociation(BaseClass):
class SubmissionTipsAssociation(BaseClass):
"""
Association between a concrete submission instance and concrete tips
"""
"""
tip_id = Column(INTEGER, ForeignKey("_tips.id"), primary_key=True) #: id of associated equipment
submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True) #: id of associated submission
submission = relationship("BasicSubmission",
@@ -1668,5 +1673,5 @@ class SubmissionTipsAssociation(BaseClass):
Returns:
dict: Values of this object
"""
"""
return dict(role=self.role_name, name=self.tips.name, lot=self.tips.lot)