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post documentation and code clean-up.

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This commit is contained in:
lwark
2024-07-03 15:13:55 -05:00
parent 12ca3157e5
commit c460e5eeca
21 changed files with 421 additions and 238 deletions
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3
src/submissions/backend/validators/__init__.py
View File

@@ -1,3 +1,6 @@
'''
Contains all validators
'''
import logging, re
import sys
from pathlib import Path

93
src/submissions/backend/validators/pydant.py
View File

@@ -3,21 +3,18 @@ Contains pydantic models and accompanying validators
'''
from __future__ import annotations
import sys
from operator import attrgetter
import uuid, re, logging
from pydantic import BaseModel, field_validator, Field, model_validator, PrivateAttr
import uuid, re, logging, csv
from pydantic import BaseModel, field_validator, Field, model_validator
from datetime import date, datetime, timedelta
from dateutil.parser import parse
from dateutil.parser import ParserError
from typing import List, Tuple, Literal
from . import RSLNamer
from pathlib import Path
from tools import check_not_nan, convert_nans_to_nones, Report, Result, row_map
from tools import check_not_nan, convert_nans_to_nones, Report, Result
from backend.db.models import *
from sqlalchemy.exc import StatementError, IntegrityError
from PyQt6.QtWidgets import QWidget
from openpyxl import load_workbook, Workbook
from io import BytesIO
logger = logging.getLogger(f"submissions.{__name__}")
@@ -106,20 +103,17 @@ class PydReagent(BaseModel):
return values.data['role']
def improved_dict(self) -> dict:
"""
Constructs a dictionary consisting of model.fields and model.extras
Returns:
dict: Information dictionary
"""
try:
extras = list(self.model_extra.keys())
except AttributeError:
extras = []
fields = list(self.model_fields.keys()) + extras
# output = {}
# for k in fields:
# value = getattr(self, k)
# match value:
# case date():
# value = value.strftime("%Y-%m-%d")
# case _:
# pass
# output[k] = value
return {k: getattr(self, k) for k in fields}
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Reagent, SubmissionReagentAssociation, Report]:
@@ -142,7 +136,7 @@ class PydReagent(BaseModel):
if isinstance(value, dict):
value = value['value']
# logger.debug(f"Reagent info item for {key}: {value}")
# set fields based on keys in dictionary
# NOTE: set fields based on keys in dictionary
match key:
case "lot":
reagent.lot = value.upper()
@@ -177,11 +171,9 @@ class PydReagent(BaseModel):
assoc = None
# add end-of-life extension from reagent type to expiry date
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
return reagent, assoc, report
class PydSample(BaseModel, extra='allow'):
submitter_id: str
sample_type: str
@@ -220,6 +212,12 @@ class PydSample(BaseModel, extra='allow'):
return str(value)
def improved_dict(self) -> dict:
"""
Constructs a dictionary consisting of model.fields and model.extras
Returns:
dict: Information dictionary
"""
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
return {k: getattr(self, k) for k in fields}
@@ -249,7 +247,6 @@ class PydSample(BaseModel, extra='allow'):
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission)
assoc_type = submission.submission_type_name
# assoc_type = self.sample_type.replace("Sample", "").strip()
for row, column, aid, submission_rank in zip(self.row, self.column, self.assoc_id, self.submission_rank):
# logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
# logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
@@ -268,6 +265,12 @@ class PydSample(BaseModel, extra='allow'):
return instance, out_associations, report
def improved_dict(self) -> dict:
"""
Constructs a dictionary consisting of model.fields and model.extras
Returns:
dict: Information dictionary
"""
try:
extras = list(self.model_extra.keys())
except AttributeError:
@@ -281,7 +284,16 @@ class PydTips(BaseModel):
lot: str|None = Field(default=None)
role: str
def to_sql(self, submission:BasicSubmission):
def to_sql(self, submission:BasicSubmission) -> SubmissionTipsAssociation:
"""
Con
Args:
submission (BasicSubmission): A submission object to associate tips represented here.
Returns:
SubmissionTipsAssociation: Association between queried tips and submission
"""
tips = Tips.query(name=self.name, lot=self.lot, limit=1)
assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
return assoc
@@ -348,6 +360,12 @@ class PydEquipment(BaseModel, extra='ignore'):
return equipment, assoc
def improved_dict(self) -> dict:
"""
Constructs a dictionary consisting of model.fields and model.extras
Returns:
dict: Information dictionary
"""
try:
extras = list(self.model_extra.keys())
except AttributeError:
@@ -619,7 +637,14 @@ class PydSubmission(BaseModel, extra='allow'):
self.submission_object = BasicSubmission.find_polymorphic_subclass(
polymorphic_identity=self.submission_type['value'])
def set_attribute(self, key, value):
def set_attribute(self, key:str, value):
"""
Better handling of attribute setting.
Args:
key (str): Name of field to set
value (_type_): Value to set field to.
"""
self.__setattr__(name=key, value=value)
def handle_duplicate_samples(self):
@@ -775,15 +800,14 @@ class PydSubmission(BaseModel, extra='allow'):
except AttributeError:
instance.run_cost = 0
# logger.debug(f"Calculated base run cost of: {instance.run_cost}")
# Apply any discounts that are applicable for client and kit.
# NOTE: Apply any discounts that are applicable for client and kit.
try:
# logger.debug("Checking and applying discounts...")
discounts = [item.amount for item in
Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
# logger.debug(f"We got discounts: {discounts}")
if len(discounts) > 0:
discounts = sum(discounts)
instance.run_cost = instance.run_cost - discounts
instance.run_cost = instance.run_cost - sum(discounts)
except Exception as e:
logger.error(f"An unknown exception occurred when calculating discounts: {e}")
# We need to make sure there's a proper rsl plate number
@@ -808,7 +832,13 @@ class PydSubmission(BaseModel, extra='allow'):
from frontend.widgets.submission_widget import SubmissionFormWidget
return SubmissionFormWidget(parent=parent, submission=self)
def to_writer(self):
def to_writer(self) -> "SheetWriter":
"""
Sends data here to the sheet writer.
Returns:
SheetWriter: Sheetwriter object that will perform writing.
"""
from backend.excel.writer import SheetWriter
return SheetWriter(self)
@@ -866,6 +896,19 @@ class PydSubmission(BaseModel, extra='allow'):
status="Warning")
report.add_result(result)
return output_reagents, report
def export_csv(self, filename:Path|str):
try:
worksheet = self.csv
except AttributeError:
logger.error("No csv found.")
return
if isinstance(filename, str):
filename = Path(filename)
with open(filename, 'w', newline="") as f:
c = csv.writer(f)
for r in worksheet.rows:
c.writerow([cell.value for cell in r])
class PydContact(BaseModel):