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Bug fixes

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This commit is contained in:
lwark
2025-04-02 13:08:32 -05:00
parent d3807dac57
commit 3a318fff38
4 changed files with 82 additions and 76 deletions
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56
src/submissions/backend/db/models/submissions.py
View File

@@ -1880,34 +1880,34 @@ class Wastewater(BasicSubmission):
new_control.save()
return report
def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
"""
Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
Args:
sample (BasicSample): Associated sample.
input_dict (dict): values to be updated
Returns:
SubmissionSampleAssociation: Updated association
"""
# logger.debug(f"Input dict: {pformat(input_dict)}")
#
assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
# targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
# assert 0 < len(targets) <= 2
# for k, v in targets.items():
# # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
# # update_key = f"ct_n{i}"
# current_value = getattr(assoc, k)
# logger.debug(f"Current value came back as: {current_value}")
# if current_value is None:
# setattr(assoc, k, v)
# else:
# logger.debug(f"Have a value already, {current_value}... skipping.")
if assoc.column == 3:
logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
return assoc
# def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
# """
# Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
#
# Args:
# sample (BasicSample): Associated sample.
# input_dict (dict): values to be updated
#
# Returns:
# SubmissionSampleAssociation: Updated association
# """
# # logger.debug(f"Input dict: {pformat(input_dict)}")
# #
# assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
# # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
# # assert 0 < len(targets) <= 2
# # for k, v in targets.items():
# # # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
# # # update_key = f"ct_n{i}"
# # current_value = getattr(assoc, k)
# # logger.debug(f"Current value came back as: {current_value}")
# # if current_value is None:
# # setattr(assoc, k, v)
# # else:
# # logger.debug(f"Have a value already, {current_value}... skipping.")
# if assoc.column == 3:
# logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
# return assoc
class WastewaterArtic(BasicSubmission):

10
src/submissions/backend/excel/reports.py
View File

@@ -2,6 +2,7 @@
Contains functions for generating summary reports
"""
import itertools
import re
import sys
from pprint import pformat
from pandas import DataFrame, ExcelWriter
@@ -211,8 +212,13 @@ class ConcentrationMaker(ReportArchetype):
@classmethod
def build_record(cls, control) -> dict:
positive = not control.submitter_id.lower().startswith("en")
regex = re.compile(r"^(ATCC)|(MCS)", flags=re.IGNORECASE)
if bool(regex.match(control.submitter_id)):
positive = "positive"
elif control.submitter_id.lower().startswith("en"):
positive = "negative"
else:
positive = "sample"
try:
concentration = float(control.concentration)
except (TypeError, ValueError):