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Pre-removal of constructors module.

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This commit is contained in:
Landon Wark
2023-10-23 09:36:57 -05:00
parent 39b94405e5
commit 4b1f88f1d0
16 changed files with 751 additions and 457 deletions
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51
src/submissions/backend/db/models/__init__.py
View File

@@ -1,43 +1,42 @@
'''
Contains all models for sqlalchemy
'''
from typing import Any
from sqlalchemy.orm import declarative_base, DeclarativeMeta
import logging
from pprint import pformat
Base: DeclarativeMeta = declarative_base()
metadata = Base.metadata
logger = logging.getLogger(f"submissions.{__name__}")
def find_subclasses(parent:Any, attrs:dict|None=None, rsl_number:str|None=None) -> Any:
"""
Finds subclasses of a parent that does contain all
attributes if the parent does not.
# def find_subclasses(parent:Any, attrs:dict|None=None, rsl_number:str|None=None) -> Any:
# """
# Finds subclasses of a parent that does contain all
# attributes if the parent does not.
# NOTE: Depreciated, moved to classmethods in individual base models.
Args:
parent (_type_): Parent class.
attrs (dict): Key:Value dictionary of attributes
# Args:
# parent (_type_): Parent class.
# attrs (dict): Key:Value dictionary of attributes
Raises:
AttributeError: Raised if no subclass is found.
# Raises:
# AttributeError: Raised if no subclass is found.
Returns:
_type_: Parent or subclass.
"""
if len(attrs) == 0 or attrs == None:
return parent
if any([not hasattr(parent, attr) for attr in attrs]):
# looks for first model that has all included kwargs
try:
model = [subclass for subclass in parent.__subclasses__() if all([hasattr(subclass, attr) for attr in attrs])][0]
except IndexError as e:
raise AttributeError(f"Couldn't find existing class/subclass of {parent} with all attributes:\n{pformat(attrs)}")
else:
model = parent
logger.debug(f"Using model: {model}")
return model
# Returns:
# _type_: Parent or subclass.
# """
# if len(attrs) == 0 or attrs == None:
# return parent
# if any([not hasattr(parent, attr) for attr in attrs]):
# # looks for first model that has all included kwargs
# try:
# model = [subclass for subclass in parent.__subclasses__() if all([hasattr(subclass, attr) for attr in attrs])][0]
# except IndexError as e:
# raise AttributeError(f"Couldn't find existing class/subclass of {parent} with all attributes:\n{pformat(attrs)}")
# else:
# model = parent
# logger.debug(f"Using model: {model}")
# return model
from .controls import Control, ControlType
from .kits import KitType, ReagentType, Reagent, Discount, KitTypeReagentTypeAssociation, SubmissionType, SubmissionTypeKitTypeAssociation

11
src/submissions/backend/db/models/kits.py
View File

@@ -31,7 +31,8 @@ class KitType(Base):
# association proxy of "user_keyword_associations" collection
# to "keyword" attribute
reagent_types = association_proxy("kit_reagenttype_associations", "reagent_type")
# creator function: https://stackoverflow.com/questions/11091491/keyerror-when-adding-objects-to-sqlalchemy-association-object/11116291#11116291
reagent_types = association_proxy("kit_reagenttype_associations", "reagent_type", creator=lambda RT: KitTypeReagentTypeAssociation(reagent_type=RT))
kit_submissiontype_associations = relationship(
"SubmissionTypeKitTypeAssociation",
@@ -118,7 +119,8 @@ class ReagentType(Base):
# association proxy of "user_keyword_associations" collection
# to "keyword" attribute
kit_types = association_proxy("reagenttype_kit_associations", "kit_type")
# creator function: https://stackoverflow.com/questions/11091491/keyerror-when-adding-objects-to-sqlalchemy-association-object/11116291#11116291
kit_types = association_proxy("reagenttype_kit_associations", "kit_type", creator=lambda kit: KitTypeReagentTypeAssociation(kit_type=kit))
def __str__(self) -> str:
"""
@@ -150,6 +152,7 @@ class KitTypeReagentTypeAssociation(Base):
reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations")
def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
logger.debug(f"Parameters: Kit={kit_type}, RT={reagent_type}, Uses={uses}, Required={required}")
self.kit_type = kit_type
self.reagent_type = reagent_type
self.uses = uses
@@ -186,9 +189,9 @@ class Reagent(Base):
def __repr__(self):
if self.name != None:
return f"Reagent({self.name}-{self.lot})"
return f"<Reagent({self.name}-{self.lot})>"
else:
return f"Reagent({self.type.name}-{self.lot})"
return f"<Reagent({self.type.name}-{self.lot})>"
def __str__(self) -> str:

7
src/submissions/backend/db/models/organizations.py
View File

@@ -32,6 +32,13 @@ class Organization(Base):
def __repr__(self) -> str:
return f"<Organization({self.name})>"
def save(self, ctx):
ctx.database_session.add(self)
ctx.database_session.commit()
def set_attribute(self, name:str, value):
setattr(self, name, value)
class Contact(Base):

125
src/submissions/backend/db/models/submissions.py
View File

@@ -13,7 +13,6 @@ from json.decoder import JSONDecodeError
from math import ceil
from sqlalchemy.ext.associationproxy import association_proxy
import uuid
from pandas import Timestamp
from dateutil.parser import parse
import re
import pandas as pd
@@ -301,6 +300,7 @@ class BasicSubmission(Base):
@classmethod
def enforce_name(cls, ctx:Settings, instr:str) -> str:
logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
logger.debug(f"Attempting enforcement on {instr}")
return instr
@classmethod
@@ -344,6 +344,11 @@ class BasicSubmission(Base):
logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
return []
def save(self, ctx:Settings):
self.uploaded_by = getuser()
ctx.database_session.add(self)
ctx.database_session.commit()
# Below are the custom submission types
class BacterialCulture(BasicSubmission):
@@ -536,6 +541,8 @@ class Wastewater(BasicSubmission):
def construct():
today = datetime.now()
return f"RSL-WW-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}"
if outstr == None:
outstr = construct()
try:
outstr = re.sub(r"PCR(-|_)", "", outstr)
except AttributeError as e:
@@ -743,6 +750,11 @@ class BasicSample(Base):
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
return cls
@classmethod
def parse_sample(cls, input_dict:dict) -> dict:
logger.debug(f"Called {cls.__name__} sample parser")
return input_dict
class WastewaterSample(BasicSample):
"""
Derivative wastewater sample
@@ -757,51 +769,51 @@ class WastewaterSample(BasicSample):
__mapper_args__ = {"polymorphic_identity": "Wastewater Sample", "polymorphic_load": "inline"}
@validates("collected-date")
def convert_cdate_time(self, key, value):
logger.debug(f"Validating {key}: {value}")
if isinstance(value, Timestamp):
return value.date()
if isinstance(value, str):
return parse(value)
return value
# @validates("collected-date")
# def convert_cdate_time(self, key, value):
# logger.debug(f"Validating {key}: {value}")
# if isinstance(value, Timestamp):
# return value.date()
# if isinstance(value, str):
# return parse(value)
# return value
@validates("rsl_number")
def use_submitter_id(self, key, value):
logger.debug(f"Validating {key}: {value}")
return value or self.submitter_id
# @validates("rsl_number")
# def use_submitter_id(self, key, value):
# logger.debug(f"Validating {key}: {value}")
# return value or self.submitter_id
def set_attribute(self, name:str, value):
"""
Set an attribute of this object. Extends parent.
# def set_attribute(self, name:str, value):
# """
# Set an attribute of this object. Extends parent.
Args:
name (str): name of the attribute
value (_type_): value to be set
"""
# Due to the plate map being populated with RSL numbers, we have to do some shuffling.
match name:
case "submitter_id":
# If submitter_id already has a value, stop
if self.submitter_id != None:
return
# otherwise also set rsl_number to the same value
else:
super().set_attribute("rsl_number", value)
case "ww_full_sample_id":
# If value present, set ww_full_sample_id and make this the submitter_id
if value != None:
super().set_attribute(name, value)
name = "submitter_id"
case 'collection_date':
# If this is a string use dateutils to parse into date()
if isinstance(value, str):
logger.debug(f"collection_date {value} is a string. Attempting parse...")
value = parse(value)
case "rsl_number":
if value == None:
value = self.submitter_id
super().set_attribute(name, value)
# Args:
# name (str): name of the attribute
# value (_type_): value to be set
# """
# # Due to the plate map being populated with RSL numbers, we have to do some shuffling.
# match name:
# case "submitter_id":
# # If submitter_id already has a value, stop
# if self.submitter_id != None:
# return
# # otherwise also set rsl_number to the same value
# else:
# super().set_attribute("rsl_number", value)
# case "ww_full_sample_id":
# # If value present, set ww_full_sample_id and make this the submitter_id
# if value != None:
# super().set_attribute(name, value)
# name = "submitter_id"
# case 'collection_date':
# # If this is a string use dateutils to parse into date()
# if isinstance(value, str):
# logger.debug(f"collection_date {value} is a string. Attempting parse...")
# value = parse(value)
# case "rsl_number":
# if value == None:
# value = self.submitter_id
# super().set_attribute(name, value)
def to_hitpick(self, submission_rsl:str) -> dict|None:
"""
@@ -832,6 +844,16 @@ class WastewaterSample(BasicSample):
except IndexError:
return None
@classmethod
def parse_sample(cls, input_dict: dict) -> dict:
output_dict = super().parse_sample(input_dict)
if output_dict['rsl_number'] == None:
output_dict['rsl_number'] = output_dict['submitter_id']
if output_dict['ww_full_sample_id'] != None:
output_dict["submitter_id"] = output_dict['ww_full_sample_id']
return output_dict
class BacterialCultureSample(BasicSample):
"""
base of bacterial culture sample
@@ -873,7 +895,7 @@ class SubmissionSampleAssociation(Base):
# Refers to the type of parent.
# Hooooooo boy, polymorphic association type, now we're getting into the weeds!
__mapper_args__ = {
"polymorphic_identity": "basic_association",
"polymorphic_identity": "Basic Association",
"polymorphic_on": base_sub_type,
"with_polymorphic": "*",
}
@@ -886,6 +908,19 @@ class SubmissionSampleAssociation(Base):
def __repr__(self) -> str:
return f"<SubmissionSampleAssociation({self.submission.rsl_plate_num} & {self.sample.submitter_id})"
@classmethod
def find_polymorphic_subclass(cls, polymorphic_identity:str|None=None):
if isinstance(polymorphic_identity, dict):
polymorphic_identity = polymorphic_identity['value']
if polymorphic_identity == None:
return cls
else:
try:
return [item for item in cls.__subclasses__() if item.__mapper_args__['polymorphic_identity']==polymorphic_identity][0]
except Exception as e:
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
return cls
class WastewaterAssociation(SubmissionSampleAssociation):
"""
@@ -897,5 +932,5 @@ class WastewaterAssociation(SubmissionSampleAssociation):
n2_status = Column(String(32)) #: positive or negative for N2
pcr_results = Column(JSON) #: imported PCR status from QuantStudio
__mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
__mapper_args__ = {"polymorphic_identity": "Wastewater Association", "polymorphic_load": "inline"}