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Moved import PCR results to context menu.

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This commit is contained in:
Landon Wark
2024-04-11 09:33:16 -05:00
parent dc5549486f
commit f994f81d11
5 changed files with 59 additions and 89 deletions
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55
src/submissions/backend/db/models/submissions.py
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@@ -3,7 +3,7 @@ Models for the main submission types.
'''
from __future__ import annotations
from getpass import getuser
import json, logging, uuid, tempfile, re, yaml, base64
import logging, uuid, tempfile, re, yaml, base64
from zipfile import ZipFile
from tempfile import TemporaryDirectory
from reportlab.graphics.barcode import createBarcodeImageInMemory
@@ -14,7 +14,6 @@ from pprint import pformat
from . import Reagent, SubmissionType, KitType, Organization
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy.orm import relationship, validates, Query
from json.decoder import JSONDecodeError
from sqlalchemy.ext.associationproxy import association_proxy
import pandas as pd
from openpyxl import Workbook
@@ -252,7 +251,7 @@ class BasicSubmission(BaseClass):
sample_list = self.hitpick_plate()
# logger.debug("Setting background colours")
for sample in sample_list:
if sample['Positive']:
if sample['positive']:
sample['background_color'] = "#f10f07"
else:
if "colour" in sample.keys():
@@ -1268,6 +1267,54 @@ class Wastewater(BasicSubmission):
row = idx.index.to_list()[0]
return row + 1
def custom_context_events(self) -> dict:
events = super().custom_context_events()
events['Link PCR'] = self.link_pcr
return events
def link_pcr(self, obj):
from backend.excel import PCRParser
from frontend.widgets import select_open_file
fname = select_open_file(obj=obj, file_extension="xlsx")
parser = PCRParser(filepath=fname)
# Check if PCR info already exists
if hasattr(self, 'pcr_info') and self.pcr_info != None:
# existing = json.loads(sub.pcr_info)
existing = self.pcr_info
else:
existing = None
if existing != None:
# update pcr_info
try:
logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
# if json.dumps(parser.pcr) not in sub.pcr_info:
if parser.pcr not in self.pcr_info:
existing.append(parser.pcr)
logger.debug(f"Setting: {existing}")
# sub.pcr_info = json.dumps(existing)
self.pcr_info = existing
except TypeError:
logger.error(f"Error updating!")
# sub.pcr_info = json.dumps([parser.pcr])
self.pcr_info = [parser.pcr]
logger.debug(f"Final pcr info for {self.rsl_plate_num}: {self.pcr_info}")
else:
# sub.pcr_info = json.dumps([parser.pcr])
self.pcr_info = [parser.pcr]
logger.debug(f"Existing {type(self.pcr_info)}: {self.pcr_info}")
logger.debug(f"Inserting {type(parser.pcr)}: {parser.pcr}")
self.save(original=False)
logger.debug(f"Got {len(parser.samples)} samples to update!")
logger.debug(f"Parser samples: {parser.samples}")
for sample in self.samples:
logger.debug(f"Running update on: {sample}")
try:
sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
except IndexError:
continue
self.update_subsampassoc(sample=sample, input_dict=sample_dict)
# self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
class WastewaterArtic(BasicSubmission):
"""
derivative submission type for artic wastewater
@@ -2094,7 +2141,7 @@ class SubmissionSampleAssociation(BaseClass):
logger.error(f"Unable to find row {self.row} in row_map.")
sample['Well'] = None
sample['Plate Name'] = self.submission.rsl_plate_num
sample['Positive'] = False
sample['positive'] = False
sample['submitted_date'] = self.submission.submitted_date
return sample