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Pydantic switchover for omni is largely complete. Will need some debugging.

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lwark
2025-02-27 10:00:43 -06:00
parent f57aa3c3f0
commit abcdbac5b8
8 changed files with 431 additions and 33 deletions
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25
src/submissions/backend/db/models/submissions.py
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@@ -10,9 +10,7 @@ from zipfile import ZipFile, BadZipfile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
from sqlalchemy.ext.hybrid import hybrid_property
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin, SubmissionReagentAssociation
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func
from sqlalchemy.orm import relationship, validates, Query
@@ -24,7 +22,7 @@ from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as S
from openpyxl import Workbook
from openpyxl.drawing.image import Image as OpenpyxlImage
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
report_result, create_holidays_for_year
report_result, create_holidays_for_year, check_dictionary_inclusion_equality
from datetime import datetime, date, timedelta
from typing import List, Any, Tuple, Literal, Generator, Type
from dateutil.parser import parse
@@ -558,12 +556,14 @@ class BasicSubmission(BaseClass, LogMixin):
existing = value
case _:
existing = self.__getattribute__(key)
logger.debug(f"Existing value is {pformat(existing)}")
if value in ['', 'null', None]:
logger.error(f"No value given, not setting.")
return
if existing is None:
existing = []
if value in existing:
# if value in existing:
if check_dictionary_inclusion_equality(existing, value):
logger.warning("Value already exists. Preventing duplicate addition.")
return
else:
@@ -572,6 +572,7 @@ class BasicSubmission(BaseClass, LogMixin):
else:
if value:
existing.append(value)
self.__setattr__(key, existing)
# NOTE: Make sure this gets updated by telling SQLAlchemy it's been modified.
flag_modified(self, key)
@@ -1223,10 +1224,19 @@ class BasicSubmission(BaseClass, LogMixin):
if "submitted_date" not in kwargs.keys():
instance.submitted_date = date.today()
else:
from frontend.widgets.pop_ups import QuestionAsker
logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
code = 1
msg = "This submission already exists.\nWould you like to overwrite?"
report.add_result(Result(msg=msg, code=code))
# code = 1
# msg = "This submission already exists.\nWould you like to overwrite?"
# report.add_result(Result(msg=msg, code=code))
dlg = QuestionAsker(title="Overwrite?", message="This submission already exists.\nWould you like to overwrite?")
if dlg.exec():
pass
else:
code = 1
msg = "This submission already exists.\nWould you like to overwrite?"
report.add_result(Result(msg=msg, code=code))
return None, report
return instance, report
# NOTE: Custom context events for the ui
@@ -1528,6 +1538,7 @@ class Wastewater(BasicSubmission):
dummy_samples.append(thing)
output['origin_plate'] = self.__class__.make_plate_map(sample_list=dummy_samples, plate_rows=4,
plate_columns=6)
# logger.debug(f"PCR info: {output['pcr_info']}")
return output
@classmethod