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Various bug fixes.

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This commit is contained in:
lwark
2024-05-30 13:54:35 -05:00
parent ecfc71bcc5
commit 5c52c02f7e
18 changed files with 447 additions and 375 deletions
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194
src/submissions/frontend/widgets/submission_widget.py
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@@ -13,7 +13,7 @@ from tools import Report, Result, check_not_nan, workbook_2_csv
from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
KitType, Organization, SubmissionType, Reagent,
KitType, Organization, SubmissionType, Reagent,
ReagentType, KitTypeReagentTypeAssociation
)
from pprint import pformat
@@ -24,9 +24,9 @@ from datetime import date
logger = logging.getLogger(f"submissions.{__name__}")
class SubmissionFormContainer(QWidget):
# A signal carrying a path
class SubmissionFormContainer(QWidget):
# A signal carrying a path
import_drag = pyqtSignal(Path)
def __init__(self, parent: QWidget) -> None:
@@ -41,7 +41,7 @@ class SubmissionFormContainer(QWidget):
def dragEnterEvent(self, event):
"""
Allow drag if file.
"""
"""
if event.mimeData().hasUrls():
event.accept()
else:
@@ -50,16 +50,16 @@ class SubmissionFormContainer(QWidget):
def dropEvent(self, event):
"""
Sets filename when file dropped
"""
"""
fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
# logger.debug(f"App: {self.app}")
self.app.last_dir = fname.parent
self.import_drag.emit(fname)
def importSubmission(self, fname:Path|None=None):
def importSubmission(self, fname: Path | None = None):
"""
import submission from excel sheet into form
"""
"""
self.app.raise_()
self.app.activateWindow()
self.import_submission_function(fname)
@@ -68,7 +68,7 @@ class SubmissionFormContainer(QWidget):
self.report = Report()
self.app.result_reporter()
def import_submission_function(self, fname:Path|None=None):
def import_submission_function(self, fname: Path | None = None):
"""
Import a new submission to the app window
@@ -77,17 +77,17 @@ class SubmissionFormContainer(QWidget):
Returns:
Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
"""
"""
logger.info(f"\n\nStarting Import...\n\n")
report = Report()
try:
self.form.setParent(None)
except AttributeError:
pass
# initialize samples
# NOTE: initialize samples
self.samples = []
self.missing_info = []
# set file dialog
# NOTE: set file dialog
if isinstance(fname, bool) or fname == None:
fname = select_open_file(self, file_extension="xlsx")
# logger.debug(f"Attempting to parse file: {fname}")
@@ -95,7 +95,7 @@ class SubmissionFormContainer(QWidget):
report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
self.report.add_result(report)
return
# create sheetparser using excel sheet and context from gui
# NOTE: create sheetparser using excel sheet and context from gui
try:
self.prsr = SheetParser(filepath=fname)
except PermissionError:
@@ -108,13 +108,12 @@ class SubmissionFormContainer(QWidget):
# logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
self.form = self.pyd.to_form(parent=self)
self.layout().addWidget(self.form)
# if self.prsr.sample_result != None:
# report.add_result(msg=self.prsr.sample_result, status="Warning")
self.report.add_result(report)
# logger.debug(f"Outgoing report: {self.report.results}")
# logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
def add_reagent(self, reagent_lot: str | None = None, reagent_type: str | None = None, expiry: date | None = None,
name: str | None = None):
"""
Action to create new reagent in DB.
@@ -126,28 +125,29 @@ class SubmissionFormContainer(QWidget):
Returns:
models.Reagent: the constructed reagent object to add to submission
"""
"""
report = Report()
if isinstance(reagent_lot, bool):
reagent_lot = ""
# create form
# NOTE: create form
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry, reagent_name=name)
if dlg.exec():
# extract form info
info = dlg.parse_form()
# logger.debug(f"Reagent info: {info}")
# create reagent object
# NOTE: create reagent object
reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# send reagent to db
# NOTE: send reagent to db
sqlobj, result = reagent.toSQL()
sqlobj.save()
report.add_result(result)
self.app.result_reporter()
return reagent
class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, submission:PydSubmission) -> None:
def __init__(self, parent: QWidget, submission: PydSubmission) -> None:
super().__init__(parent)
# self.report = Report()
self.app = parent.app
@@ -157,10 +157,8 @@ class SubmissionFormWidget(QWidget):
defaults = st.get_default_info("form_recover", "form_ignore")
self.recover = defaults['form_recover']
self.ignore = defaults['form_ignore']
# self.ignore += self.recover
# logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}")
self.layout = QVBoxLayout()
# for k, v in kwargs.items():
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
if k in self.ignore:
continue
@@ -176,7 +174,8 @@ class SubmissionFormWidget(QWidget):
add_widget.input.currentTextChanged.connect(self.scrape_reagents)
self.scrape_reagents(self.pyd.extraction_kit)
def create_widget(self, key:str, value:dict|PydReagent, submission_type:str|None=None, extraction_kit:str|None=None) -> "self.InfoItem":
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | None = None,
extraction_kit: str | None = None) -> "self.InfoItem":
"""
Make an InfoItem widget to hold a field
@@ -187,7 +186,7 @@ class SubmissionFormWidget(QWidget):
Returns:
self.InfoItem: Form widget to hold name:value
"""
"""
if key not in self.ignore:
match value:
case PydReagent():
@@ -199,8 +198,8 @@ class SubmissionFormWidget(QWidget):
widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type)
return widget
return None
def scrape_reagents(self, *args, **kwargs):#extraction_kit:str, caller:str|None=None):
def scrape_reagents(self, *args, **kwargs): #extraction_kit:str, caller:str|None=None):
"""
Extracted scrape reagents function that will run when
form 'extraction_kit' widget is updated.
@@ -211,16 +210,15 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[QMainWindow, dict]: Updated application and result
"""
"""
extraction_kit = args[0]
caller = inspect.stack()[1].function.__repr__().replace("'", "")
# self.reagents = []
# logger.debug(f"Self.reagents: {self.reagents}")
# logger.debug(f"\n\n{pformat(caller)}\n\n")
# logger.debug(f"SubmissionType: {self.submission_type}")
report = Report()
# logger.debug(f"Extraction kit: {extraction_kit}")
# Remove previous reagent widgets
# NOTE: Remove previous reagent widgets
try:
old_reagents = self.find_widgets()
except AttributeError:
@@ -230,19 +228,6 @@ class SubmissionFormWidget(QWidget):
for reagent in old_reagents:
if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
reagent.setParent(None)
# match caller:
# case "import_submission_function":
# self.reagents = self.prsr.sub['reagents']
# case _:
# already_have = [reagent for reagent in self.prsr.sub['reagents'] if not reagent.missing]
# already_have = [reagent for reagent in self.pyd.reagents if not reagent.missing]
# names = list(set([item.type for item in already_have]))
# # logger.debug(f"Already have: {already_have}")
# reagents = [item.to_pydantic() for item in KitType.query(name=extraction_kit).get_reagents(submission_type=self.pyd.submission_type) if item.name not in names]
# # logger.debug(f"Missing: {reagents}")
# self.pyd.reagents = already_have + reagents
# logger.debug(f"Reagents: {self.reagents}")
# self.kit_integrity_completion_function(extraction_kit=extraction_kit)
reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit)
# logger.debug(f"Missing reagents: {obj.missing_reagents}")
for reagent in reagents:
@@ -266,11 +251,11 @@ class SubmissionFormWidget(QWidget):
def clear_form(self):
"""
Removes all form widgets
"""
"""
for item in self.findChildren(QWidget):
item.setParent(None)
def find_widgets(self, object_name:str|None=None) -> List[QWidget]:
def find_widgets(self, object_name: str | None = None) -> List[QWidget]:
"""
Gets all widgets filtered by object name
@@ -279,12 +264,12 @@ class SubmissionFormWidget(QWidget):
Returns:
List[QWidget]: Widgets matching filter
"""
"""
query = self.findChildren(QWidget)
if object_name != None:
query = [widget for widget in query if widget.objectName()==object_name]
if object_name is not None:
query = [widget for widget in query if widget.objectName() == object_name]
return query
def submit_new_sample_function(self) -> QWidget:
"""
Parse forms and add sample to the database.
@@ -294,7 +279,7 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict
"""
"""
logger.info(f"\n\nBeginning Submission\n\n")
report = Report()
result = self.parse_form()
@@ -320,8 +305,7 @@ class SubmissionFormWidget(QWidget):
case 1:
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
if dlg.exec():
# Do not add duplicate reagents.
# base_submission.reagents = []
# NOTE: Do not add duplicate reagents.
result = None
else:
self.app.ctx.database_session.rollback()
@@ -347,13 +331,13 @@ class SubmissionFormWidget(QWidget):
self.app.report.add_result(report)
self.app.result_reporter()
def export_csv_function(self, fname:Path|None=None):
def export_csv_function(self, fname: Path | None = None):
"""
Save the submission's csv file.
Args:
fname (Path | None, optional): Input filename. Defaults to None.
"""
"""
if isinstance(fname, bool) or fname == None:
fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
try:
@@ -371,7 +355,7 @@ class SubmissionFormWidget(QWidget):
Returns:
Report: Report on status of parse.
"""
"""
report = Report()
logger.info(f"Hello from form parser!")
info = {}
@@ -397,28 +381,28 @@ class SubmissionFormWidget(QWidget):
value = getattr(self, item)
# logger.debug(f"Setting {item}")
info[item] = value
for k,v in info.items():
for k, v in info.items():
self.pyd.set_attribute(key=k, value=v)
# NOTE: return submission
report.add_result(report)
return report
class InfoItem(QWidget):
def __init__(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> None:
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None) -> None:
super().__init__(parent)
layout = QVBoxLayout()
self.label = self.ParsedQLabel(key=key, value=value)
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type)
self.setObjectName(key)
try:
self.missing:bool = value['missing']
self.missing: bool = value['missing']
except (TypeError, KeyError):
self.missing:bool = True
if self.input != None:
self.missing: bool = True
if self.input is not None:
layout.addWidget(self.label)
layout.addWidget(self.input)
layout.setContentsMargins(0,0,0,0)
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
match self.input:
case QComboBox():
@@ -427,7 +411,7 @@ class SubmissionFormWidget(QWidget):
self.input.dateChanged.connect(self.update_missing)
case QLineEdit():
self.input.textChanged.connect(self.update_missing)
def parse_form(self) -> Tuple[str, dict]:
"""
Pulls info from widget into dict
@@ -445,8 +429,8 @@ class SubmissionFormWidget(QWidget):
case _:
return None, None
return self.input.objectName(), dict(value=value, missing=self.missing)
def set_widget(self, parent: QWidget, key:str, value:dict, submission_type:str|None=None) -> QWidget:
def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None) -> QWidget:
"""
Creates form widget
@@ -458,7 +442,7 @@ class SubmissionFormWidget(QWidget):
Returns:
QWidget: Form object
"""
"""
try:
value = value['value']
except (TypeError, KeyError):
@@ -480,11 +464,12 @@ class SubmissionFormWidget(QWidget):
case 'extraction_kit':
# if extraction kit not available, all other values fail
if not check_not_nan(value):
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!",
status="warning")
msg.exec()
# create combobox to hold looked up kits
# NOTE: create combobox to hold looked up kits
add_widget = QComboBox()
# lookup existing kits by 'submission_type' decided on by sheetparser
# NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
# logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.name for item in KitType.query(used_for=submission_type)]
obj.uses = uses
@@ -497,14 +482,13 @@ class SubmissionFormWidget(QWidget):
logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
obj.ext_kit = uses[0]
add_widget.addItems(uses)
case 'submitted_date':
# uses base calendar
# NOTE: uses base calendar
add_widget = QDateEdit(calendarPopup=True)
# sets submitted date based on date found in excel sheet
# NOTE: sets submitted date based on date found in excel sheet
try:
add_widget.setDate(value)
# if not found, use today
# NOTE: if not found, use today
except:
add_widget.setDate(date.today())
case 'submission_category':
@@ -517,25 +501,25 @@ class SubmissionFormWidget(QWidget):
cats.insert(0, cats.pop(cats.index(submission_type)))
add_widget.addItems(cats)
case _:
# anything else gets added in as a line edit
# NOTE: anything else gets added in as a line edit
add_widget = QLineEdit()
# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " "))
if add_widget != None:
if add_widget is not None:
add_widget.setObjectName(key)
add_widget.setParent(parent)
return add_widget
def update_missing(self):
"""
Set widget status to updated
"""
"""
self.missing = True
self.label.updated(self.objectName())
class ParsedQLabel(QLabel):
def __init__(self, key:str, value:dict, title:bool=True, label_name:str|None=None):
def __init__(self, key: str, value: dict, title: bool = True, label_name: str | None = None):
super().__init__()
try:
check = not value['missing']
@@ -546,7 +530,7 @@ class SubmissionFormWidget(QWidget):
else:
self.setObjectName(f"{key}_label")
if title:
output = key.replace('_', ' ').title()
output = key.replace('_', ' ').title().replace("Rsl", "RSL").replace("Pcr", "PCR")
else:
output = key.replace('_', ' ')
if check:
@@ -554,43 +538,38 @@ class SubmissionFormWidget(QWidget):
else:
self.setText(f"MISSING {output}")
def updated(self, key:str, title:bool=True):
def updated(self, key: str, title: bool = True):
"""
Mark widget as updated
Args:
key (str): Name of the field
title (bool, optional): Use title case. Defaults to True.
"""
"""
if title:
output = key.replace('_', ' ').title()
output = key.replace('_', ' ').title().replace("Rsl", "RSL").replace("Pcr", "PCR")
else:
output = key.replace('_', ' ')
self.setText(f"UPDATED {output}")
class ReagentFormWidget(QWidget):
def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
def __init__(self, parent: QWidget, reagent: PydReagent, extraction_kit: str):
super().__init__(parent)
self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
self.reagent = reagent
self.extraction_kit = extraction_kit
layout = QVBoxLayout()
# layout = QGridLayout()
# self.check_box = QCheckBox(self)
# self.check_box.setChecked(True)
# self.check_box.stateChanged.connect(self.check_uncheck)
# layout.addWidget(self.check_box, 0,0)
self.label = self.ReagentParsedLabel(reagent=reagent)
layout.addWidget(self.label)
self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
layout.addWidget(self.lot)
# Remove spacing between reagents
layout.setContentsMargins(0,0,0,0)
# NOTE: Remove spacing between reagents
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
self.setObjectName(reagent.name)
self.missing = reagent.missing
# If changed set self.missing to True and update self.label
# NOTE: If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated)
def parse_form(self) -> Tuple[PydReagent, dict]:
@@ -599,40 +578,42 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[PydReagent, dict]: PydReagent and Report(?)
"""
# if not self.check_box.isChecked():
# return None, None
"""
lot = self.lot.currentText()
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
# NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
if wanted_reagent == None:
dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
dlg = QuestionAsker(title=f"Add {lot}?",
message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type,
expiry=self.reagent.expiry,
name=self.reagent.name)
return wanted_reagent, None
else:
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
# logger.debug("Will not add reagent.")
return None, Result(msg="Failed integrity check", status="Critical")
else:
# Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
# NOTE: Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
# from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
rt = ReagentType.query(name=self.reagent.type)
if rt == None:
rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, missing=False), None
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name,
expiry=wanted_reagent.expiry, missing=False), None
def updated(self):
"""
Set widget status to updated
"""
"""
self.missing = True
self.label.updated(self.reagent.type)
class ReagentParsedLabel(QLabel):
def __init__(self, reagent:PydReagent):
def __init__(self, reagent: PydReagent):
super().__init__()
try:
check = not reagent.missing
@@ -643,19 +624,19 @@ class SubmissionFormWidget(QWidget):
self.setText(f"Parsed {reagent.type}")
else:
self.setText(f"MISSING {reagent.type}")
def updated(self, reagent_type:str):
def updated(self, reagent_type: str):
"""
Marks widget as updated
Args:
reagent_type (str): _description_
"""
"""
self.setText(f"UPDATED {reagent_type}")
class ReagentLot(QComboBox):
def __init__(self, reagent, extraction_kit:str) -> None:
def __init__(self, reagent, extraction_kit: str) -> None:
super().__init__()
self.setEditable(True)
# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
@@ -664,7 +645,7 @@ class SubmissionFormWidget(QWidget):
relevant_reagents = [str(item.lot) for item in lookup]
output_reg = []
for rel_reagent in relevant_reagents:
# extract strings from any sets.
# NOTE: extract strings from any sets.
if isinstance(rel_reagent, set):
for thing in rel_reagent:
output_reg.append(thing)
@@ -677,7 +658,8 @@ class SubmissionFormWidget(QWidget):
if check_not_nan(reagent.lot):
relevant_reagents.insert(0, str(reagent.lot))
else:
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type, kit_type=extraction_kit)
looked_up_rt = KitTypeReagentTypeAssociation.query(reagent_type=reagent.type,
kit_type=extraction_kit)
try:
looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
except AttributeError: