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Bugs squashed.

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This commit is contained in:
Landon Wark
2023-11-15 14:12:16 -06:00
parent da714c355d
commit 9312a66bb7
8 changed files with 66 additions and 42 deletions
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2
src/submissions/__init__.py
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@@ -4,7 +4,7 @@ from pathlib import Path
# Version of the realpython-reader package
__project__ = "submissions"
__version__ = "202311.2b"
__version__ = "202311.3b"
__author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
__copyright__ = "2022-2023, Government of Canada"

6
src/submissions/__main__.py
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@@ -1,9 +1,11 @@
import sys
import os
# environment variable must be set to enable qtwebengine in network path
if getattr(sys, 'frozen', False):
# if getattr(sys, 'frozen', False):
# os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
from tools import get_config, setup_logger, check_if_app
if check_if_app():
os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
from tools import get_config, setup_logger
# setup custom logger
logger = setup_logger(verbosity=3)
# create settings object

15
src/submissions/backend/db/models/kits.py
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@@ -471,6 +471,21 @@ class Reagent(Base):
pass
return query_return(query=query, limit=limit)
def update_last_used(self, kit:KitType):
report = Report()
logger.debug(f"Attempting update of reagent type at intersection of ({self}), ({kit})")
rt = ReagentType.query(kit_type=kit, reagent=self, limit=1)
if rt != None:
logger.debug(f"got reagenttype {rt}")
assoc = KitTypeReagentTypeAssociation.query(kit_type=kit, reagent_type=rt)
if assoc != None:
if assoc.last_used != self.lot:
logger.debug(f"Updating {assoc} last used to {self.lot}")
assoc.last_used = self.lot
result = assoc.save()
return(report.add_result(result))
return report.add_result(Result(msg=f"Updating last used {rt} was not performed.", status="Information"))
class Discount(Base):
"""
Relationship table for client labs for certain kits.

18
src/submissions/backend/db/models/submissions.py
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@@ -25,7 +25,6 @@ from dateutil.parser._parser import ParserError
import yaml
from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError
from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
import sys
logger = logging.getLogger(f"submissions.{__name__}")
@@ -572,6 +571,17 @@ class BasicSubmission(Base):
except AttributeError:
logger.error(f"Could not set {self} attribute {key} to {value}")
def update_subsampassoc(self, sample:BasicSample, input_dict:dict):
assoc = SubmissionSampleAssociation.query(submission=self, sample=sample, limit=1)
for k,v in input_dict.items():
try:
setattr(assoc, k, v)
except AttributeError:
logger.error(f"Can't set {k} to {v}")
# result = store_object(ctx=ctx, object=assoc)
result = assoc.save()
return result
# Below are the custom submission types
class BacterialCulture(BasicSubmission):
@@ -925,6 +935,8 @@ class WastewaterArtic(BasicSubmission):
input_dict['csv'] = df
return input_dict
# Sample Classes
class BasicSample(Base):
"""
Base of basic sample which polymorphs into BCSample and WWSample
@@ -1115,6 +1127,8 @@ class BasicSample(Base):
instance.sample_type = sample_type
return instance
#Below are the custom sample types
class WastewaterSample(BasicSample):
"""
Derivative wastewater sample
@@ -1199,6 +1213,8 @@ class BacterialCultureSample(BasicSample):
sample['name'] = f"{self.submitter_id} - ({self.organism})"
return sample
# Submission to Sample Associations
class SubmissionSampleAssociation(Base):
"""
table containing submission/sample associations

11
src/submissions/backend/validators/pydant.py
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@@ -13,7 +13,7 @@ import re
import logging
from tools import check_not_nan, convert_nans_to_nones, jinja_template_loading, Report, Result
from backend.db.models import *
from sqlalchemy.exc import StatementError
from sqlalchemy.exc import StatementError, IntegrityError
from PyQt6.QtWidgets import QComboBox, QWidget
from pprint import pformat
from openpyxl import load_workbook
@@ -172,7 +172,10 @@ class PydSample(BaseModel, extra='allow'):
submission=submission,
sample=instance,
row=row, column=column)
try:
instance.sample_submission_associations.append(association)
except IntegrityError:
instance.metadata.session.rollback()
return instance, result
class PydSubmission(BaseModel, extra='allow'):
@@ -408,9 +411,9 @@ class PydSubmission(BaseModel, extra='allow'):
extraction_kit = KitType.query(name=self.extraction_kit['value'])
logger.debug(f"We have the extraction kit: {extraction_kit.name}")
excel_map = extraction_kit.construct_xl_map_for_use(self.submission_type['value'])
logger.debug(f"Extraction kit map:\n\n{pformat(excel_map)}")
logger.debug(f"Missing reagents going into autofile: {pformat(reagents)}")
logger.debug(f"Missing info going into autofile: {pformat(info)}")
# logger.debug(f"Extraction kit map:\n\n{pformat(excel_map)}")
# logger.debug(f"Missing reagents going into autofile: {pformat(reagents)}")
# logger.debug(f"Missing info going into autofile: {pformat(info)}")
new_reagents = []
for reagent in reagents:
new_reagent = {}

11
src/submissions/frontend/widgets/submission_table.py
View File

@@ -145,7 +145,7 @@ class SubmissionsSheet(QTableView):
index = (self.selectionModel().currentIndex())
value = index.sibling(index.row(),1).data()
logger.debug(f"Selected value: {value}")
dlg = SubmissionComment(ctx=self.ctx, rsl=value)
dlg = SubmissionComment(rsl=value)
if dlg.exec():
dlg.add_comment()
@@ -455,6 +455,8 @@ class SubmissionDetails(QDialog):
super().__init__(parent)
# self.ctx = ctx
self.app = parent.parent().parent().parent().parent().parent().parent
print(f"App: {self.app}")
self.setWindowTitle("Submission Details")
# create scrollable interior
interior = QScrollArea()
@@ -603,10 +605,10 @@ class SubmissionComment(QDialog):
"""
a window for adding comment text to a submission
"""
def __init__(self, ctx:Settings, rsl:str) -> None:
def __init__(self, rsl:str) -> None:
super().__init__()
self.ctx = ctx
# self.ctx = ctx
self.rsl = rsl
self.setWindowTitle(f"{self.rsl} Submission Comment")
# create text field
@@ -640,7 +642,6 @@ class SubmissionComment(QDialog):
except AttributeError:
sub.comment = [full_comment]
logger.debug(sub.__dict__)
self.ctx.database_session.add(sub)
self.ctx.database_session.commit()
sub.save()

41
src/submissions/frontend/widgets/submission_widget.py
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@@ -11,7 +11,7 @@ from tools import Report, Result, check_not_nan
from backend.excel.parser import SheetParser, PCRParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
check_kit_integrity, update_last_used, KitType, Organization, SubmissionType, Reagent,
check_kit_integrity, KitType, Organization, SubmissionType, Reagent,
ReagentType, KitTypeReagentTypeAssociation, BasicSubmission, update_subsampassoc_with_pcr
)
from pprint import pformat
@@ -22,7 +22,7 @@ import difflib
from datetime import date
import inspect
import json
import sys
logger = logging.getLogger(f"submissions.{__name__}")
@@ -80,27 +80,6 @@ class SubmissionFormContainer(QWidget):
case _:
self.app.result_reporter()
# def kit_reload_function(self):
# """
# Reload the fields in the form
# Args:
# obj (QMainWindow): original app window
# Returns:
# Tuple[QMainWindow, dict]: Collection of new main app window and result dict
# """
# report = Report()
# # for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
# logger.debug(f"Attempting to clear {obj.form.find_widgets()}")
# for item in self.form.find_widgets():
# if isinstance(item, ReagentFormWidget):
# item.setParent(None)
# self.kit_integrity_completion_function()
# self.report.add_result(report)
def kit_integrity_completion(self):
"""
Performs check of imported reagents
@@ -296,6 +275,8 @@ class SubmissionFormContainer(QWidget):
self.report.add_result(report)
return
base_submission, result = self.pyd.toSQL()
# logger.debug(f"Base submission: {base_submission.to_dict()}")
# sys.exit()
# check output message for issues
match result.code:
# code 0: everything is fine.
@@ -303,7 +284,7 @@ class SubmissionFormContainer(QWidget):
self.report.add_result(None)
# code 1: ask for overwrite
case 1:
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
if dlg.exec():
# Do not add duplicate reagents.
# base_submission.reagents = []
@@ -320,7 +301,10 @@ class SubmissionFormContainer(QWidget):
pass
# add reagents to submission object
for reagent in base_submission.reagents:
update_last_used(reagent=reagent, kit=base_submission.extraction_kit)
# logger.debug(f"Updating: {reagent} with {reagent.lot}")
# update_last_used(reagent=reagent, kit=base_submission.extraction_kit)
reagent.update_last_used(kit=base_submission.extraction_kit)
# sys.exit()
logger.debug(f"Here is the final submission: {pformat(base_submission.__dict__)}")
logger.debug(f"Parsed reagents: {pformat(base_submission.reagents)}")
logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
@@ -329,7 +313,7 @@ class SubmissionFormContainer(QWidget):
self.app.table_widget.sub_wid.setData()
# reset form
self.form.setParent(None)
logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
wkb = self.pyd.autofill_excel()
if wkb != None:
fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="xlsx")
@@ -352,6 +336,7 @@ class SubmissionFormContainer(QWidget):
fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
try:
self.pyd.csv.to_csv(fname.__str__(), index=False)
del self.pyd.csv
except PermissionError:
logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
@@ -424,7 +409,8 @@ class SubmissionFormContainer(QWidget):
sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
except IndexError:
continue
update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
# update_subsampassoc_with_pcr(submission=sub, sample=sample, input_dict=sample_dict)
sub.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'))
# return obj, result
@@ -481,6 +467,7 @@ class SubmissionFormWidget(QWidget):
info[field] = value
logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents: {pformat(reagents)}")
# sys.exit()
# app = self.parent().parent().parent().parent().parent().parent().parent().parent
submission = PydSubmission(filepath=self.filepath, reagents=reagents, samples=self.samples, **info)
return submission

2
src/submissions/templates/submission_details.html
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@@ -35,7 +35,7 @@
</style>
<title>Submission Details for {{ sub['Plate Number'] }}</title>
</head>
{% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments', 'barcode', 'platemap'] %}
{% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments', 'barcode', 'platemap', 'export_map'] %}
<body>
<h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>&nbsp;&nbsp;&nbsp;{% if sub['barcode'] %}<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">{% endif %}
<p>{% for key, value in sub.items() if key not in excluded %}