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Big update, semi-functional

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This commit is contained in:
Landon Wark
2023-08-28 13:20:30 -05:00
parent b6de159631
commit bc7a3b8f5f
13 changed files with 824 additions and 466 deletions
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82
src/submissions/backend/db/models/submissions.py
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@@ -12,6 +12,9 @@ from math import ceil
from sqlalchemy.ext.associationproxy import association_proxy
import uuid
from . import Base
from pandas import Timestamp
from dateutil.parser import parse
import pprint
logger = logging.getLogger(f"submissions.{__name__}")
@@ -33,7 +36,8 @@ class BasicSubmission(Base):
sample_count = Column(INTEGER) #: Number of samples in the submission
extraction_kit = relationship("KitType", back_populates="submissions") #: The extraction kit used
extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", name="fk_BS_extkit_id"))
submission_type = Column(String(32)) #: submission type (should be string in D3 of excel sheet)
# submission_type = Column(String(32)) #: submission type (should be string in D3 of excel sheet)
submission_type_name = Column(String, ForeignKey("_submission_types.name", ondelete="SET NULL", name="fk_BS_subtype_name"))
technician = Column(String(64)) #: initials of processing tech(s)
# Move this into custom types?
reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
@@ -55,7 +59,7 @@ class BasicSubmission(Base):
# Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
__mapper_args__ = {
"polymorphic_identity": "basic_submission",
"polymorphic_on": submission_type,
"polymorphic_on": submission_type_name,
"with_polymorphic": "*",
}
@@ -128,7 +132,7 @@ class BasicSubmission(Base):
output = {
"id": self.id,
"Plate Number": self.rsl_plate_num,
"Submission Type": self.submission_type.replace("_", " ").title(),
"Submission Type": self.submission_type_name,
"Submitter Plate Number": self.submitter_plate_num,
"Submitted Date": self.submitted_date.strftime("%Y-%m-%d"),
"Submitting Lab": sub_lab,
@@ -184,14 +188,18 @@ class BasicSubmission(Base):
except Exception as e:
logger.error(f"Column count error: {e}")
# cols_count_24 = ceil(int(self.sample_count) / 3)
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]):
logger.debug(f"Pre-association check. {pprint.pformat(self.__dict__)}")
assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if item.submission_type == self.submission_type][0]
logger.debug(f"Came up with association: {assoc}")
# 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]):
if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.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))
self.run_cost = assoc.constant_cost + (assoc.mutable_cost_column * cols_count_96) + (assoc.mutable_cost_sample * int(self.sample_count))
except Exception as e:
logger.error(f"Calculation error: {e}")
@@ -225,7 +233,7 @@ class BacterialCulture(BasicSubmission):
"""
controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
# samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
__mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
__mapper_args__ = {"polymorphic_identity": "Bacterial Culture", "polymorphic_load": "inline"}
def to_dict(self) -> dict:
"""
@@ -245,7 +253,7 @@ class Wastewater(BasicSubmission):
# 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"}
__mapper_args__ = {"polymorphic_identity": "Wastewater", "polymorphic_load": "inline"}
def to_dict(self) -> dict:
"""
@@ -315,14 +323,14 @@ class BasicSample(Base):
@validates('submitter_id')
def create_id(self, key, value):
logger.debug(f"validating sample_id of: {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})"
return f"<{self.sample_type.replace('_', ' ').title(). replace(' ', '')}({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"}
@@ -363,30 +371,31 @@ class WastewaterSample(BasicSample):
# 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)
ww_sample_full_id = Column(String(64))
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
collection_date = Column(TIMESTAMP) #: Date sample collected
received_date = Column(TIMESTAMP) #: Date sample 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))
# 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))
# 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
sample_location = 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"}
__mapper_args__ = {"polymorphic_identity": "Wastewater Sample", "polymorphic_load": "inline"}
# def to_string(self) -> str:
# """
@@ -397,6 +406,42 @@ class WastewaterSample(BasicSample):
# """
# return f"{self.well_number}: {self.ww_sample_full_id}"
# @validates("received-date")
# def convert_rdate_time(self, key, value):
# if isinstance(value, Timestamp):
# return value.date()
# 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
# @collection_date.setter
# def collection_date(self, value):
# match value:
# case Timestamp():
# self.collection_date = value.date()
# case str():
# self.collection_date = parse(value)
# case _:
# self.collection_date = value
def __init__(self, **kwargs):
if 'collection_date' in kwargs.keys():
logger.debug(f"Got collection_date: {kwargs['collection_date']}. Attempting parse.")
if isinstance(kwargs['collection_date'], str):
logger.debug(f"collection_date is a string...")
kwargs['collection_date'] = parse(kwargs['collection_date'])
logger.debug(f"output is {kwargs['collection_date']}")
super().__init__(**kwargs)
def to_sub_dict(self, submission_rsl:str) -> dict:
"""
Gui friendly dictionary. Inherited from BasicSample
@@ -451,7 +496,6 @@ class WastewaterSample(BasicSample):
# return None
return sample
class BacterialCultureSample(BasicSample):
"""
base of bacterial culture sample
@@ -493,8 +537,6 @@ class BacterialCultureSample(BasicSample):
# }
return sample
class SubmissionSampleAssociation(Base):
"""
table containing submission/sample associations