''' Contains all submission related frontend functions ''' import sys from PyQt6.QtWidgets import ( QWidget, QPushButton, QVBoxLayout, QComboBox, QDateEdit, QLineEdit, QLabel ) from PyQt6.QtCore import pyqtSignal, Qt from pathlib import Path from . import select_open_file, select_save_file import logging, difflib, inspect from pathlib import Path from tools import Report, Result, check_not_nan, main_form_style, report_result from backend.excel.parser import SheetParser from backend.validators import PydSubmission, PydReagent from backend.db import ( KitType, Organization, SubmissionType, Reagent, ReagentRole, KitTypeReagentRoleAssociation, BasicSubmission ) from pprint import pformat from .pop_ups import QuestionAsker, AlertPop from .misc import AddReagentForm from typing import List, Tuple from datetime import date logger = logging.getLogger(f"submissions.{__name__}") class MyQComboBox(QComboBox): def __init__(self, scrollWidget=None, *args, **kwargs): super(MyQComboBox, self).__init__(*args, **kwargs) self.scrollWidget=scrollWidget self.setFocusPolicy(Qt.FocusPolicy.StrongFocus) logger.debug(f"Scrollwidget: {scrollWidget}") def wheelEvent(self, *args, **kwargs): if self.hasFocus(): return QComboBox.wheelEvent(self, *args, **kwargs) else: return self.scrollWidget.wheelEvent(*args, **kwargs) class MyQDateEdit(QDateEdit): def __init__(self, scrollWidget=None, *args, **kwargs): super(MyQDateEdit, self).__init__(*args, **kwargs) self.scrollWidget=scrollWidget self.setFocusPolicy(Qt.FocusPolicy.StrongFocus) def wheelEvent(self, *args, **kwargs): if self.hasFocus(): return QDateEdit.wheelEvent(self, *args, **kwargs) else: return self.scrollWidget.wheelEvent(*args, **kwargs) class SubmissionFormContainer(QWidget): # A signal carrying a path import_drag = pyqtSignal(Path) def __init__(self, parent: QWidget) -> None: # logger.debug(f"Setting form widget...") super().__init__(parent) self.app = self.parent().parent() # logger.debug(f"App: {self.app}") self.report = Report() self.setStyleSheet('background-color: light grey;') self.setAcceptDrops(True) # NOTE: if import_drag is emitted, importSubmission will fire self.import_drag.connect(self.importSubmission) def dragEnterEvent(self, event): """ Allow drag if file. """ if event.mimeData().hasUrls(): event.accept() else: event.ignore() 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) @report_result def importSubmission(self, fname: Path | None = None): """ import submission from excel sheet into form """ self.app.raise_() self.app.activateWindow() self.report = Report() self.import_submission_function(fname) return self.report def import_submission_function(self, fname: Path | None = None): """ Import a new submission to the app window Args: obj (QMainWindow): original app window 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 # NOTE: initialize samples self.samples = [] self.missing_info = [] # NOTE: set file dialog if isinstance(fname, bool) or fname is None: fname = select_open_file(self, file_extension="xlsx") # logger.debug(f"Attempting to parse file: {fname}") if not fname.exists(): report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical")) self.report.add_result(report) return # NOTE: create sheetparser using excel sheet and context from gui try: self.prsr = SheetParser(filepath=fname) except PermissionError: logger.error(f"Couldn't get permission to access file: {fname}") return except AttributeError: self.prsr = SheetParser(filepath=fname) # logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}") self.pyd = self.prsr.to_pydantic() # 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) 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__)}") @report_result def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None, name: str | None = None) -> Tuple[PydReagent, Report]: """ Action to create new reagent in DB. Args: reagent_lot (str | None, optional): Parsed reagent from import form. Defaults to None. reagent_role (str | None, optional): Parsed reagent type from import form. Defaults to None. expiry (date | None, optional): Parsed reagent expiry data. Defaults to None. name (str | None, optional): Parsed reagent name. Defaults to None. Returns: models.Reagent: the constructed reagent object to add to submission """ report = Report() if isinstance(reagent_lot, bool): reagent_lot = "" # NOTE: create form dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_role=reagent_role, expiry=expiry, reagent_name=name) if dlg.exec(): # extract form info info = dlg.parse_form() # logger.debug(f"Reagent info: {info}") # NOTE: create reagent object reagent = PydReagent(ctx=self.app.ctx, **info, missing=False) # NOTE: send reagent to db sqlobj, assoc, result = reagent.toSQL() sqlobj.save() report.add_result(result) # logger.debug(f"Reagent: {reagent}, Report: {report}") return reagent, report class SubmissionFormWidget(QWidget): def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None: super().__init__(parent) # self.report = Report() # logger.debug(f"Disable: {disable}") if disable is None: disable = [] self.app = parent.app self.pyd = submission self.missing_info = [] st = SubmissionType.query(name=self.pyd.submission_type['value']).get_submission_class() defaults = st.get_default_info("form_recover", "form_ignore") self.recover = defaults['form_recover'] self.ignore = defaults['form_ignore'] # logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}") self.layout = QVBoxLayout() for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()): if k in self.ignore: continue try: # logger.debug(f"Key: {k}, Disable: {disable}") check = k in disable # logger.debug(f"Check: {check}") except TypeError: check = False try: value = self.pyd.__getattribute__(k) except AttributeError: logger.error(f"Couldn't get attribute from pyd: {k}") value = dict(value=None, missing=True) add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'], sub_obj=st, disable=check) if add_widget is not None: self.layout.addWidget(add_widget) if k == "extraction_kit": add_widget.input.currentTextChanged.connect(self.scrape_reagents) self.setStyleSheet(main_form_style) 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, sub_obj: BasicSubmission | None = None, disable: bool = False) -> "self.InfoItem": """ Make an InfoItem widget to hold a field Args: disable (): key (str): Name of the field value (dict): Value of field submission_type (str | None, optional): Submissiontype as str. Defaults to None. Returns: self.InfoItem: Form widget to hold name:value """ # logger.debug(f"Key: {key}, Disable: {disable}") if key not in self.ignore: match value: case PydReagent(): if value.name.lower() != "not applicable": widget = self.ReagentFormWidget(parent=self, reagent=value, extraction_kit=extraction_kit) else: widget = None case _: widget = self.InfoItem(parent=self, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj) # logger.debug(f"Setting widget enabled to: {not disable}") if disable: widget.input.setEnabled(False) widget.input.setToolTip("Widget disabled to protect database integrity.") return widget return None @report_result 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. Args: obj (QMainWindow): updated main application extraction_kit (str): name of extraction kit (in 'extraction_kit' widget) Returns: Tuple[QMainWindow, dict]: Updated application and result """ extraction_kit = args[0] caller = inspect.stack()[1].function.__repr__().replace("'", "") # 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}") # NOTE: Remove previous reagent widgets try: old_reagents = self.find_widgets() except AttributeError: logger.error(f"Couldn't find old reagents.") old_reagents = [] # logger.debug(f"\n\nAttempting to clear: {old_reagents}\n\n") for reagent in old_reagents: if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton): reagent.setParent(None) reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit) # logger.debug(f"Missing reagents: {obj.missing_reagents}") for reagent in reagents: add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit) self.layout.addWidget(add_widget) report.add_result(integrity_report) # logger.debug(f"Outgoing report: {report.results}") if hasattr(self.pyd, "csv"): export_csv_btn = QPushButton("Export CSV") export_csv_btn.setObjectName("export_csv_btn") self.layout.addWidget(export_csv_btn) export_csv_btn.clicked.connect(self.export_csv_function) submit_btn = QPushButton("Submit") submit_btn.setObjectName("submit_btn") self.layout.addWidget(submit_btn) submit_btn.clicked.connect(self.submit_new_sample_function) self.setLayout(self.layout) return report 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]: """ Gets all widgets filtered by object name Args: object_name (str | None, optional): name to filter by. Defaults to None. Returns: List[QWidget]: Widgets matching filter """ query = self.findChildren(QWidget) if object_name is not None: query = [widget for widget in query if widget.objectName() == object_name] return query @report_result def submit_new_sample_function(self, *args) -> Report: """ Parse forms and add sample to the database. Args: obj (QMainWindow): original app window 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() report.add_result(result) # logger.debug(f"Submission: {pformat(self.pyd)}") # logger.debug("Checking kit integrity...") _, result = self.pyd.check_kit_integrity() report.add_result(result) if len(result.results) > 0: # self.app.report.add_result(report) # self.app.report_result() return # logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n") base_submission, result = self.pyd.to_sql() # logger.debug(f"SQL object: {pformat(base_submission.__dict__)}") # logger.debug(f"Base submission: {base_submission.to_dict()}") # NOTE: check output message for issues try: code = report.results[-1].code except IndexError: code = 0 match code: # NOTE: code 0: everything is fine. case 0: pass # NOTE: code 1: ask for overwrite case 1: dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg) if dlg.exec(): # NOTE: Do not add duplicate reagents. pass else: self.app.ctx.database_session.rollback() report.add_result(Result(msg="Overwrite cancelled", status="Information")) # self.app.report.add_result(report) # self.app.report_result() return report # NOTE: code 2: No RSL plate number given case 2: report.add_result(result) # self.app.report.add_result(report) # self.app.report_result() return report case _: pass # NOTE: add reagents to submission object for reagent in base_submission.reagents: # logger.debug(f"Updating: {reagent} with {reagent.lot}") reagent.update_last_used(kit=base_submission.extraction_kit) # logger.debug(f"Final reagents: {pformat(base_submission.reagents)}") base_submission.save() # NOTE: update summary sheet self.app.table_widget.sub_wid.setData() # NOTE: reset form self.setParent(None) # logger.debug(f"All attributes of obj: {pformat(self.__dict__)}") return report 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 is None: fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv") try: self.pyd.export_csv(fname) except PermissionError: logger.warning(f"Could not get permissions to {fname}. Possibly the request was cancelled.") except AttributeError: logger.error(f"No csv file found in the submission at this point.") def parse_form(self) -> Report: """ Transforms form info into PydSubmission Returns: Report: Report on status of parse. """ report = Report() logger.info(f"Hello from form parser!") info = {} reagents = [] for widget in self.findChildren(QWidget): # logger.debug(f"Parsed widget of type {type(widget)}") match widget: case self.ReagentFormWidget(): reagent, _ = widget.parse_form() if reagent is not None: reagents.append(reagent) case self.InfoItem(): field, value = widget.parse_form() if field is not None: info[field] = value # logger.debug(f"Info: {pformat(info)}") # logger.debug(f"Reagents going into pyd: {pformat(reagents)}") self.pyd.reagents = reagents # logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}") for item in self.recover: # logger.debug(f"Attempting to recover: {item}") if hasattr(self, item): value = getattr(self, item) # logger.debug(f"Setting {item}") info[item] = value 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, sub_obj: BasicSubmission | None = None) -> None: super().__init__(parent) layout = QVBoxLayout() self.label = self.ParsedQLabel(key=key, value=value) self.input: QWidget = self.set_widget(parent=parent, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj) self.setObjectName(key) try: self.missing: bool = value['missing'] except (TypeError, KeyError): self.missing: bool = True if self.input is not None: layout.addWidget(self.label) layout.addWidget(self.input) layout.setContentsMargins(0, 0, 0, 0) self.setLayout(layout) match self.input: case QComboBox(): self.input.currentTextChanged.connect(self.update_missing) case QDateEdit(): 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 Returns: Tuple[str, dict]: name of field, {value, missing} """ match self.input: case QLineEdit(): value = self.input.text() case QComboBox(): value = self.input.currentText() case QDateEdit(): value = self.input.date().toPyDate() 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, sub_obj: BasicSubmission | None = None) -> QWidget: """ Creates form widget Args: parent (QWidget): parent widget key (str): name of field value (dict): value, and is it missing from scrape submission_type (str | None, optional): SubmissionType as str. Defaults to None. Returns: QWidget: Form object """ if sub_obj is None: sub_obj = SubmissionType.query(name=submission_type).get_submission_class() try: value = value['value'] except (TypeError, KeyError): pass obj = parent.parent().parent() logger.debug(f"Object: {obj}") logger.debug(f"Parent: {parent.parent()}") # logger.debug(f"Creating widget for: {key}") match key: case 'submitting_lab': add_widget = MyQComboBox(scrollWidget=parent) # lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm ) labs = [item.name for item in Organization.query()] # try to set closest match to top of list try: labs = difflib.get_close_matches(value, labs, len(labs), 0) except (TypeError, ValueError): pass # set combobox values to lookedup values add_widget.addItems(labs) add_widget.setToolTip("Select submitting lab.") 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.exec() # NOTE: create combobox to hold looked up kits add_widget = MyQComboBox(scrollWidget=parent) # 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 # logger.debug(f"Kits received for {submission_type}: {uses}") if check_not_nan(value): # logger.debug(f"The extraction kit in parser was: {value}") uses.insert(0, uses.pop(uses.index(value))) obj.ext_kit = value else: logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}") obj.ext_kit = uses[0] add_widget.addItems(uses) add_widget.setToolTip("Select extraction kit.") case 'submission_category': add_widget = MyQComboBox(scrollWidget=parent) cats = ['Diagnostic', "Surveillance", "Research"] cats += [item.name for item in SubmissionType.query()] try: cats.insert(0, cats.pop(cats.index(value))) except ValueError: cats.insert(0, cats.pop(cats.index(submission_type))) add_widget.addItems(cats) add_widget.setToolTip("Enter submission category or select from list.") case _: if key in sub_obj.timestamps(): add_widget = MyQDateEdit(calendarPopup=True, scrollWidget=parent) # NOTE: sets submitted date based on date found in excel sheet try: add_widget.setDate(value) # NOTE: if not found, use today except: add_widget.setDate(date.today()) add_widget.setToolTip(f"Select date for {key}") else: # 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("_", " ")) add_widget.setToolTip(f"Enter value for {key}") if add_widget is not None: add_widget.setObjectName(key) add_widget.setParent(parent) # add_widget.setStyleSheet(main_form_style) 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): super().__init__() try: check = not value['missing'] except: check = True if label_name is not None: self.setObjectName(label_name) else: self.setObjectName(f"{key}_label") if title: output = key.replace('_', ' ').title().replace("Rsl", "RSL").replace("Pcr", "PCR") else: output = key.replace('_', ' ') if check: self.setText(f"Parsed {output}") else: self.setText(f"MISSING {output}") 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().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): super().__init__(parent) self.app = self.parent().parent().parent().parent().parent().parent().parent().parent() self.reagent = reagent self.extraction_kit = extraction_kit layout = QVBoxLayout() self.label = self.ReagentParsedLabel(reagent=reagent) layout.addWidget(self.label) self.lot = self.ReagentLot(scrollWidget=parent, reagent=reagent, extraction_kit=extraction_kit) # self.lot.setStyleSheet(main_form_style) layout.addWidget(self.lot) # NOTE: Remove spacing between reagents layout.setContentsMargins(0, 0, 0, 0) self.setLayout(layout) self.setObjectName(reagent.name) self.missing = reagent.missing # NOTE: If changed set self.missing to True and update self.label self.lot.currentTextChanged.connect(self.updated) def parse_form(self) -> Tuple[PydReagent | None, Report]: """ Pulls form info into PydReagent Returns: Tuple[PydReagent, dict]: PydReagent and Report(?) """ report = Report() lot = self.lot.currentText() # logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}") wanted_reagent = Reagent.query(lot_number=lot, reagent_role=self.reagent.role) # NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent) if wanted_reagent is None: dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.role}: {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_role=self.reagent.role, expiry=self.reagent.expiry, name=self.reagent.name) return wanted_reagent, report 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.") report.add_result(Result(msg="Failed integrity check", status="Critical")) return None, report else: # 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 = ReagentRole.query(name=self.reagent.role) if rt is None: rt = ReagentRole.query(kit_type=self.extraction_kit, reagent=wanted_reagent) return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, role=rt.name, expiry=wanted_reagent.expiry, missing=False), report def updated(self): """ Set widget status to updated """ self.missing = True self.label.updated(self.reagent.role) class ReagentParsedLabel(QLabel): def __init__(self, reagent: PydReagent): super().__init__() try: check = not reagent.missing except: check = False self.setObjectName(f"{reagent.role}_label") if check: self.setText(f"Parsed {reagent.role}") else: self.setText(f"MISSING {reagent.role}") def updated(self, reagent_role: str): """ Marks widget as updated Args: reagent_role (str): _description_ """ self.setText(f"UPDATED {reagent_role}") class ReagentLot(MyQComboBox): def __init__(self, scrollWidget, reagent, extraction_kit: str) -> None: super().__init__(scrollWidget=scrollWidget) self.setEditable(True) # logger.debug(f"Attempting lookup of reagents by type: {reagent.type}") # NOTE: below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work. lookup = Reagent.query(reagent_role=reagent.role) relevant_reagents = [str(item.lot) for item in lookup] output_reg = [] for rel_reagent in relevant_reagents: # NOTE: extract strings from any sets. if isinstance(rel_reagent, set): for thing in rel_reagent: output_reg.append(thing) elif isinstance(rel_reagent, str): output_reg.append(rel_reagent) relevant_reagents = output_reg # NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows # logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}") if str(reagent.lot) not in relevant_reagents: if check_not_nan(reagent.lot): relevant_reagents.insert(0, str(reagent.lot)) else: looked_up_rt = KitTypeReagentRoleAssociation.query(reagent_role=reagent.role, kit_type=extraction_kit) try: looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used) except AttributeError: looked_up_reg = None if isinstance(looked_up_reg, list): looked_up_reg = None # logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}") if looked_up_reg is not None: try: relevant_reagents.remove(str(looked_up_reg.lot)) relevant_reagents.insert(0, str(looked_up_reg.lot)) except ValueError as e: logger.error(f"Error reordering relevant reagents: {e}") else: if len(relevant_reagents) > 1: # logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.") idx = relevant_reagents.index(str(reagent.lot)) # logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}") moved_reag = relevant_reagents.pop(idx) relevant_reagents.insert(0, moved_reag) else: # logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.") pass # logger.debug(f"New relevant reagents: {relevant_reagents}") self.setObjectName(f"lot_{reagent.role}") self.addItems(relevant_reagents) self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}") # self.setStyleSheet(main_form_style)