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Various bug fixes for new forms.

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This commit is contained in:
Landon Wark
2024-04-25 08:55:32 -05:00
parent 5466c78c3a
commit 8cc161ec56
18 changed files with 520 additions and 218 deletions
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4
src/submissions/backend/validators/__init__.py
View File

@@ -74,8 +74,8 @@ class RSLNamer(object):
check = True
if check:
# logger.debug("Final option, ask the user for submission type")
from frontend.widgets import SubmissionTypeSelector
dlg = SubmissionTypeSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.")
from frontend.widgets import ObjectSelector
dlg = ObjectSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.", obj_type=SubmissionType)
if dlg.exec():
submission_type = dlg.parse_form()
submission_type = submission_type.replace("_", " ")

117
src/submissions/backend/validators/pydant.py
View File

@@ -8,13 +8,13 @@ from pydantic import BaseModel, field_validator, Field
from datetime import date, datetime, timedelta
from dateutil.parser import parse
from dateutil.parser._parser import ParserError
from typing import List, Tuple
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 backend.db.models import *
from sqlalchemy.exc import StatementError, IntegrityError
from PyQt6.QtWidgets import QComboBox, QWidget
from PyQt6.QtWidgets import QWidget
from openpyxl import load_workbook, Workbook
from io import BytesIO
@@ -24,7 +24,7 @@ class PydReagent(BaseModel):
lot: str|None
type: str|None
expiry: date|None
expiry: date|Literal['NA']|None
name: str|None
missing: bool = Field(default=True)
comment: str|None = Field(default="", validate_default=True)
@@ -77,6 +77,8 @@ class PydReagent(BaseModel):
match value:
case int():
return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2).date()
case 'NA':
return value
case str():
return parse(value)
case date():
@@ -87,6 +89,13 @@ class PydReagent(BaseModel):
value = date.today()
return value
@field_validator("expiry")
@classmethod
def date_na(cls, value):
if isinstance(value, date) and value.year == 1970:
value = "NA"
return value
@field_validator("name", mode="before")
@classmethod
def enforce_name(cls, value, values):
@@ -125,6 +134,10 @@ class PydReagent(BaseModel):
reagent.type.append(reagent_type)
case "comment":
continue
case "expiry":
if isinstance(value, str):
value = date(year=1970, month=1, day=1)
reagent.expiry = value
case _:
try:
reagent.__setattr__(key, value)
@@ -271,6 +284,7 @@ class PydSubmission(BaseModel, extra='allow'):
reagents: List[dict]|List[PydReagent] = []
samples: List[PydSample]
equipment: List[PydEquipment]|None =[]
cost_centre: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
@field_validator('equipment', mode='before')
@classmethod
@@ -332,10 +346,28 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submitting_lab", mode="before")
@classmethod
def rescue_submitting_lab(cls, value):
if value == None:
if value is None:
return dict(value=None, missing=True)
return value
@field_validator("submitting_lab")
@classmethod
def lookup_submitting_lab(cls, value):
if isinstance(value['value'], str):
try:
value['value'] = Organization.query(name=value['value']).name
except AttributeError:
value['value'] = None
if value['value'] is None:
value['missing'] = True
from frontend.widgets.pop_ups import ObjectSelector
dlg = ObjectSelector(title="Missing Submitting Lab", message="We need a submitting lab. Please select from the list.", obj_type=Organization)
if dlg.exec():
value['value'] = dlg.getValues()
else:
value['value'] = None
return value
@field_validator("rsl_plate_num", mode='before')
@classmethod
def rescue_rsl_number(cls, value):
@@ -427,6 +459,30 @@ class PydSubmission(BaseModel, extra='allow'):
output.append(sample)
return output
@field_validator("cost_centre", mode="before")
@classmethod
def rescue_cost_centre(cls, value):
match value:
case dict():
return value
case _:
return dict(value=value, missing=True)
@field_validator("cost_centre")
@classmethod
def get_cost_centre(cls, value, values):
# logger.debug(f"Value coming in for cost_centre: {value}")
match value['value']:
case None:
from backend.db.models import Organization
org = Organization.query(name=values.data['submitting_lab']['value'])
try:
return dict(value=org.cost_centre, missing=True)
except AttributeError:
return dict(value="xxx", missing=True)
case _:
return value
def set_attribute(self, key, value):
self.__setattr__(name=key, value=value)
@@ -599,6 +655,7 @@ class PydSubmission(BaseModel, extra='allow'):
else:
info = {k:v for k,v in self.improved_dict().items() if isinstance(v, dict)}
reagents = self.reagents
if len(reagents + list(info.keys())) == 0:
# logger.warning("No info to fill in, returning")
return None
@@ -616,14 +673,14 @@ class PydSubmission(BaseModel, extra='allow'):
new_reagent = {}
new_reagent['type'] = reagent.type
new_reagent['lot'] = excel_map[new_reagent['type']]['lot']
new_reagent['lot']['value'] = reagent.lot
new_reagent['lot']['value'] = reagent.lot or "NA"
new_reagent['expiry'] = excel_map[new_reagent['type']]['expiry']
new_reagent['expiry']['value'] = reagent.expiry
new_reagent['expiry']['value'] = reagent.expiry or "NA"
new_reagent['sheet'] = excel_map[new_reagent['type']]['sheet']
# name is only present for Bacterial Culture
try:
new_reagent['name'] = excel_map[new_reagent['type']]['name']
new_reagent['name']['value'] = reagent.name
new_reagent['name']['value'] = reagent.name or "Not Applicable"
except Exception as e:
logger.error(f"Couldn't get name due to {e}")
new_reagents.append(new_reagent)
@@ -657,6 +714,8 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Attempting to write lot {reagent['lot']['value']} in: row {reagent['lot']['row']}, column {reagent['lot']['column']}")
worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value'])
# logger.debug(f"Attempting to write expiry {reagent['expiry']['value']} in: row {reagent['expiry']['row']}, column {reagent['expiry']['column']}")
if reagent['expiry']['value'].year == 1970:
reagent['expiry']['value'] = "NA"
worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
try:
# logger.debug(f"Attempting to write name {reagent['name']['value']} in: row {reagent['name']['row']}, column {reagent['name']['column']}")
@@ -790,14 +849,13 @@ class PydSubmission(BaseModel, extra='allow'):
logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
if isinstance(extraction_kit, str):
extraction_kit = dict(value=extraction_kit)
if extraction_kit is not None:
if extraction_kit != self.extraction_kit['value']:
if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
self.extraction_kit['value'] = extraction_kit['value']
reagenttypes = []
else:
reagenttypes = [item.type for item in self.reagents]
else:
reagenttypes = [item.type for item in self.reagents]
# reagenttypes = []
# else:
# reagenttypes = [item.type for item in self.reagents]
# else:
# reagenttypes = [item.type for item in self.reagents]
logger.debug(f"Looking up {self.extraction_kit['value']}")
ext_kit = KitType.query(name=self.extraction_kit['value'])
ext_kit_rtypes = [item.to_pydantic() for item in ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
@@ -808,21 +866,26 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Checking if reagents match kit contents: {check}")
# # what reagent types are in both lists?
# missing = list(set(ext_kit_rtypes).difference(reagenttypes))
missing = []
output_reagents = self.reagents
# output_reagents = ext_kit_rtypes
logger.debug(f"Already have these reagent types: {reagenttypes}")
for rt in ext_kit_rtypes:
if rt.type not in reagenttypes:
missing.append(rt)
if rt.type not in [item.type for item in output_reagents]:
output_reagents.append(rt)
logger.debug(f"Missing reagents types: {missing}")
# missing = []
# Exclude any reagenttype found in this pyd not expected in kit.
expected_check = [item.type for item in ext_kit_rtypes]
output_reagents = [rt for rt in self.reagents if rt.type in expected_check]
logger.debug(f"Already have these reagent types: {output_reagents}")
missing_check = [item.type for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.type not in missing_check]
missing_reagents += [rt for rt in output_reagents if rt.missing]
# for rt in ext_kit_rtypes:
# if rt.type not in [item.type for item in output_reagents]:
# missing.append(rt)
# if rt.type not in [item.type for item in output_reagents]:
# output_reagents.append(rt)
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
logger.debug(f"Missing reagents types: {missing_reagents}")
# if lists are equal return no problem
if len(missing)==0:
if len(missing_reagents)==0:
result = None
else:
result = Result(msg=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
result = Result(msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
report.add_result(result)
return output_reagents, report