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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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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
View File

@@ -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