Moments before disaster.

src/config.yml

@@ -4,3 +4,4 @@ database_schema: null
 database_user: null
 database_password: null
 database_name: null
+logging_enabled: false

src/submissions/backend/db/__init__.py

@@ -1,10 +1,8 @@
 """
 All database related operations.
 """
-import sqlalchemy.orm
 from sqlalchemy import event, inspect
 from sqlalchemy.engine import Engine
-
 from tools import ctx
 
 
@@ -48,7 +46,11 @@ def update_log(mapper, connection, target):
         hist = attr.load_history()
         if not hist.has_changes():
             continue
+        if attr.key == "custom":
+            continue
         added = [str(item) for item in hist.added]
+        if attr.key in ['submission_sample_associations', 'submission_reagent_associations']:
+            added = ['Numbers truncated for space purposes.']
         deleted = [str(item) for item in hist.deleted]
         change = dict(field=attr.key, added=added, deleted=deleted)
         # logger.debug(f"Adding: {pformat(change)}")
@@ -69,6 +71,6 @@ def update_log(mapper, connection, target):
     else:
         logger.info(f"No changes detected, not updating logs.")
 
-# if ctx.database_schema == "sqlite":
+# if ctx.logging_enabled:
 event.listen(LogMixin, 'after_update', update_log, propagate=True)
 event.listen(LogMixin, 'after_insert', update_log, propagate=True)

src/submissions/backend/db/models/kits.py

@@ -1414,25 +1414,6 @@ class Equipment(BaseClass):
             if extraction_kit and extraction_kit not in process.kit_types:
                 continue
             yield process
-        # processes = (process for process in self.processes if submission_type in process.submission_types)
-        # match extraction_kit:
-        #     case str():
-        #         # logger.debug(f"Filtering processes by extraction_kit str {extraction_kit}")
-        #         processes = (process for process in processes if
-        #                      extraction_kit in [kit.name for kit in process.kit_types])
-        #     case KitType():
-        #         # logger.debug(f"Filtering processes by extraction_kit KitType {extraction_kit}")
-        #         processes = (process for process in processes if extraction_kit in process.kit_types)
-        #     case _:
-        #         pass
-        # # NOTE: Convert to strings
-        # # processes = [process.name for process in processes]
-        # # assert all([isinstance(process, str) for process in processes])
-        # # if len(processes) == 0:
-        # #     processes = ['']
-        # # return processes
-        # for process in processes:
-        #     yield process.name
 
     @classmethod
     @setup_lookup
@@ -1650,25 +1631,6 @@ class EquipmentRole(BaseClass):
             if extraction_kit and extraction_kit not in process.kit_types:
                     continue
             yield process.name
-        # if submission_type is not None:
-        #     # logger.debug("Getting all processes for this EquipmentRole")
-        #     processes = [process for process in self.processes if submission_type in process.submission_types]
-        # else:
-        #     processes = self.processes
-        # match extraction_kit:
-        #     case str():
-        #         # logger.debug(f"Filtering processes by extraction_kit str {extraction_kit}")
-        #         processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_types]]
-        #     case KitType():
-        #         # logger.debug(f"Filtering processes by extraction_kit KitType {extraction_kit}")
-        #         processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_types]]
-        #     case _:
-        #         pass
-        # output = [item.name for item in processes]
-        # if len(output) == 0:
-        #     return ['']
-        # else:
-        #     return output
 
     def to_export_dict(self, submission_type: SubmissionType, kit_type: KitType):
         """
@@ -1730,9 +1692,8 @@ class SubmissionEquipmentAssociation(BaseClass):
 
     @classmethod
     @setup_lookup
-    def query(cls, equipment_id: int, submission_id: int, role: str | None = None, limit: int = 0, **kwargs) -> Any | \
-                                                                                                                List[
-                                                                                                                    Any]:
+    def query(cls, equipment_id: int, submission_id: int, role: str | None = None, limit: int = 0, **kwargs) \
+            -> Any | List[Any]:
         query: Query = cls.__database_session__.query(cls)
         query = query.filter(cls.equipment_id == equipment_id)
         query = query.filter(cls.submission_id == submission_id)
@@ -1777,44 +1738,22 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
             raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
         return value
 
-    def get_all_processes(self, extraction_kit: KitType | str | None = None) -> List[Process]:
-        """
-        Get all processes associated with this SubmissionTypeEquipmentRole
-
-        Args:
-            extraction_kit (KitType | str | None, optional): KitType of interest. Defaults to None.
-
-        Returns:
-            List[Process]: All associated processes
-        """
-        processes = [equipment.get_processes(self.submission_type) for equipment in self.equipment_role.instances]
-        # NOTE: flatten list
-        processes = [item for items in processes for item in items if item is not None]
-        match extraction_kit:
-            case str():
-                # logger.debug(f"Filtering Processes by extraction_kit str {extraction_kit}")
-                processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_type]]
-            case KitType():
-                # logger.debug(f"Filtering Processes by extraction_kit KitType {extraction_kit}")
-                processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_type]]
-            case _:
-                pass
-        return processes
-
     @check_authorization
     def save(self):
         super().save()
 
-    def to_export_dict(self, extraction_kit: KitType) -> dict:
+    def to_export_dict(self, extraction_kit: KitType | str) -> dict:
         """
         Creates dictionary for exporting to yml used in new SubmissionType Construction
 
         Args:
-            kit_type (KitType): KitType of interest.
+            extraction_kit (KitType | str): KitType of interest.
 
         Returns:
             dict: Dictionary containing relevant info for SubmissionType construction
         """
+        if isinstance(extraction_kit, str):
+            extraction_kit = KitType.query(name=extraction_kit)
         base_dict = {k: v for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type,
                                                                          kit_type=extraction_kit).items()}
         base_dict['static'] = self.static
@@ -2013,8 +1952,8 @@ class SubmissionTipsAssociation(BaseClass):
 
     @classmethod
     @setup_lookup
-    def query(cls, tip_id: int, role: str, submission_id: int | None = None, limit: int = 0, **kwargs) -> Any | List[
-        Any]:
+    def query(cls, tip_id: int, role: str, submission_id: int | None = None, limit: int = 0, **kwargs) \
+            -> Any | List[Any]:
         query: Query = cls.__database_session__.query(cls)
         query = query.filter(cls.tip_id == tip_id)
         if submission_id is not None:

src/submissions/backend/db/models/submissions.py

@@ -2,13 +2,10 @@
 Models for the main submission and sample types.
 """
 from __future__ import annotations
-# import sys
-# import types
-# import zipfile
 from copy import deepcopy
 from getpass import getuser
 import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
-from zipfile import ZipFile
+from zipfile import ZipFile, BadZipfile
 from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
 from pprint import pformat
@@ -20,7 +17,6 @@ from sqlalchemy.ext.associationproxy import association_proxy
 from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError, \
     ArgumentError
 from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
-# import pandas as pd
 from openpyxl import Workbook
 from openpyxl.drawing.image import Image as OpenpyxlImage
 from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
@@ -1276,7 +1272,7 @@ class BasicSubmission(BaseClass, LogMixin):
         if msg.exec():
             try:
                 self.backup(fname=fname, full_backup=True)
-            except zipfile.BadZipfile:
+            except BadZipfile:
                 logger.error("Couldn't open zipfile for writing.")
             self.__database_session__.delete(self)
             try:
@@ -2261,7 +2257,7 @@ class WastewaterArtic(BasicSubmission):
 
 # Sample Classes
 
-class BasicSample(BaseClass):
+class BasicSample(BaseClass, LogMixin):
     """
     Base of basic sample which polymorphs into BCSample and WWSample
     """

src/submissions/backend/excel/parser.py

@@ -1,8 +1,7 @@
 '''
 contains parser objects for pulling values from client generated submission sheets.
 '''
-import json
-import sys
+import logging
 from copy import copy
 from getpass import getuser
 from pprint import pformat
@@ -11,7 +10,6 @@ from openpyxl import load_workbook, Workbook
 from pathlib import Path
 from backend.db.models import *
 from backend.validators import PydSubmission, RSLNamer
-import logging, re
 from collections import OrderedDict
 from tools import check_not_nan, is_missing, check_key_or_attr
 
@@ -195,7 +193,7 @@ class InfoParser(object):
             ws = self.xl[sheet]
             relevant = []
             for k, v in self.map.items():
-                # NOTE: If the value is hardcoded put it in the dictionary directly.
+                # NOTE: If the value is hardcoded put it in the dictionary directly. Ex. Artic kit
                 if k == "custom":
                     continue
                 if isinstance(v, str):
@@ -230,7 +228,7 @@ class InfoParser(object):
                     case "submitted_date":
                         value, missing = is_missing(value)
                         logger.debug(f"Parsed submitted date: {value}")
-                    # NOTE: is field a JSON?
+                    # NOTE: is field a JSON? Includes: Extraction info, PCR info, comment, custom
                     case thing if thing in self.sub_object.jsons():
                         value, missing = is_missing(value)
                         if missing: continue
@@ -300,11 +298,11 @@ class ReagentParser(object):
             del reagent_map['info']
         except KeyError:
             pass
-        logger.debug(f"Reagent map: {pformat(reagent_map)}")
+        # logger.debug(f"Reagent map: {pformat(reagent_map)}")
         # NOTE: If reagent map is empty, maybe the wrong kit was given, check if there's only one kit for that submission type and use it if so.
         if not reagent_map:
             temp_kit_object = self.submission_type_obj.get_default_kit()
-            logger.debug(f"Temp kit: {temp_kit_object}")
+            # logger.debug(f"Temp kit: {temp_kit_object}")
             if temp_kit_object:
                 self.kit_object = temp_kit_object
                 # reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
@@ -333,7 +331,7 @@ class ReagentParser(object):
         for sheet in self.xl.sheetnames:
             ws = self.xl[sheet]
             relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
-            logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
+            # logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
             if relevant == {}:
                 continue
             for item in relevant:
@@ -499,8 +497,7 @@ class SampleParser(object):
                 yield new
         else:
             merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
-            # plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
-            # lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
+            logger.info(f"Merging sample info using {merge_on_id}")
             plate_map_samples = sorted(copy(self.plate_map_samples), key=itemgetter('id'))
             lookup_samples = sorted(copy(self.lookup_samples), key=itemgetter(merge_on_id))
             for ii, psample in enumerate(plate_map_samples):
@@ -517,20 +514,9 @@ class SampleParser(object):
                     logger.warning(f"Match for {psample['id']} not direct, running search.")
                     searchables = [(jj, sample) for jj, sample in enumerate(lookup_samples)
                                    if merge_on_id in sample.keys()]
-                    # for jj, lsample in enumerate(lookup_samples):
-                    #     try:
-                    #         check = lsample[merge_on_id] == psample['id']
-                    #     except KeyError:
-                    #         check = False
-                    #     if check:
-                    #         new = lsample | psample
-                    #         lookup_samples[jj] = {}
-                    #         break
-                    #     else:
-                    #         new = psample
                     jj, new = next(((jj, lsample | psample) for jj, lsample in searchables
                                     if lsample[merge_on_id] == psample['id']), (-1, psample))
-                    logger.debug(f"Assigning from index {jj} - {new}")
+                    # logger.debug(f"Assigning from index {jj} - {new}")
                     if jj >= 0:
                         lookup_samples[jj] = {}
                 if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
@@ -554,7 +540,7 @@ class EquipmentParser(object):
             xl (Workbook): Openpyxl workbook from submitted excel file.
             submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
         """
-        logger.debug("\n\nHello from EquipmentParser!\n\n")
+        logger.info("\n\nHello from EquipmentParser!\n\n")
         if isinstance(submission_type, str):
             submission_type = SubmissionType.query(name=submission_type)
         self.submission_type = submission_type
@@ -568,7 +554,6 @@ class EquipmentParser(object):
         Returns:
             List[dict]: List of locations
         """
-        # return {k: v for k, v in self.submission_type.construct_equipment_map()}
         return {k: v for k, v in self.submission_type.construct_field_map("equipment")}
 
     def get_asset_number(self, input: str) -> str:
@@ -638,7 +623,7 @@ class TipParser(object):
             xl (Workbook): Openpyxl workbook from submitted excel file.
             submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
         """
-        logger.debug("\n\nHello from TipParser!\n\n")
+        logger.info("\n\nHello from TipParser!\n\n")
         if isinstance(submission_type, str):
             submission_type = SubmissionType.query(name=submission_type)
         self.submission_type = submission_type
@@ -652,7 +637,6 @@ class TipParser(object):
         Returns:
             List[dict]: List of locations
         """
-        # return {k: v for k, v in self.submission_type.construct_tips_map()}
         return {k: v for k, v in self.submission_type.construct_field_map("tip")}
 
     def parse_tips(self) -> List[dict]:

src/submissions/backend/excel/reports.py

@@ -2,7 +2,6 @@
 Contains functions for generating summary reports
 '''
 from pprint import pformat
-
 from pandas import DataFrame, ExcelWriter
 import logging
 from pathlib import Path
@@ -72,7 +71,6 @@ class ReportMaker(object):
         for row in df.iterrows():
             # logger.debug(f"Row {ii}: {row}")
             lab = row[0][0]
-            # logger.debug(type(row))
             # logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
             # logger.debug(f"Name: {row[0][1]}")
             data = [item for item in row[1]]
@@ -151,7 +149,16 @@ class TurnaroundMaker(object):
         self.df = DataFrame.from_records(records)
 
     @classmethod
-    def build_record(cls, sub):
+    def build_record(cls, sub: BasicSubmission) -> dict:
+        """
+        Build a turnaround dictionary from a submission
+
+        Args:
+            sub (BasicSubmission): The submission to be processed.
+
+        Returns:
+
+        """
         days, tat_ok = sub.get_turnaround_time()
         return dict(name=str(sub.rsl_plate_num), days=days, submitted_date=sub.submitted_date,
                         completed_date=sub.completed_date, acceptable=tat_ok)

src/submissions/backend/excel/writer.py

@@ -41,21 +41,11 @@ class SheetWriter(object):
                         self.sub[k] = v['value']
                     else:
                         self.sub[k] = v
-        # logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n")
-        # if self.filepath.stem.startswith("tmp"):
-        #     template = self.submission_type.template_file
-        #     workbook = load_workbook(BytesIO(template))
-        # else:
-        #     try:
-        #         workbook = load_workbook(self.filepath)
-        #     except Exception as e:
-        #         logger.error(f"Couldn't open workbook due to {e}")
         template = self.submission_type.template_file
         if not template:
             logger.error(f"No template file found, falling back to Bacterial Culture")
             template = SubmissionType.retrieve_template_file()
         workbook = load_workbook(BytesIO(template))
-        # self.workbook = workbook
         self.xl = workbook
         self.write_info()
         self.write_reagents()
@@ -152,11 +142,9 @@ class InfoWriter(object):
             try:
                 dicto['locations'] = info_map[k]
             except KeyError:
-                # continue
                 pass
             dicto['value'] = v
             if len(dicto) > 0:
-                # output[k] = dicto
                 yield k, dicto
 
     def write_info(self) -> Workbook:
@@ -279,7 +267,6 @@ class SampleWriter(object):
         self.sample_map = submission_type.construct_sample_map()['lookup_table']
         # NOTE: exclude any samples without a submission rank.
         samples = [item for item in self.reconcile_map(sample_list) if item['submission_rank'] > 0]
-        # self.samples = sorted(samples, key=lambda k: k['submission_rank'])
         self.samples = sorted(samples, key=itemgetter('submission_rank'))
 
     def reconcile_map(self, sample_list: list) -> Generator[dict, None, None]:
@@ -368,7 +355,8 @@ class EquipmentWriter(object):
                 logger.error(f"No {equipment['role']} in {pformat(equipment_map)}")
             # logger.debug(f"{equipment['role']} map: {mp_info}")
             placeholder = copy(equipment)
-            if mp_info == {}:
+            # if mp_info == {}:
+            if not mp_info:
                 for jj, (k, v) in enumerate(equipment.items(), start=1):
                     dicto = dict(value=v, row=ii, column=jj)
                     placeholder[k] = dicto

src/submissions/backend/validators/pydant.py

@@ -2,8 +2,7 @@
 Contains pydantic models and accompanying validators
 '''
 from __future__ import annotations
-import sys
-import uuid, re, logging, csv
+import uuid, re, logging, csv, sys
 from pydantic import BaseModel, field_validator, Field, model_validator
 from datetime import date, datetime, timedelta
 from dateutil.parser import parse
@@ -165,13 +164,7 @@ class PydReagent(BaseModel):
             report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
         else:
             if submission is not None and reagent not in submission.reagents:
-                # assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
-                # assoc.comments = self.comment
                 submission.update_reagentassoc(reagent=reagent, role=self.role)
-            # else:
-            #     assoc = None
-                # add end-of-life extension from reagent type to expiry date
-                # NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
         return reagent, report
 
 
@@ -191,11 +184,7 @@ class PydSample(BaseModel, extra='allow'):
         for k, v in data.model_extra.items():
             if k in model.timestamps():
                 if isinstance(v, str):
-                    # try:
                     v = datetime.strptime(v, "%Y-%m-%d")
-                    # except ValueError:
-                    #     logger.warning(f"Attribute {k} value {v} for sample {data.submitter_id} could not be coerced into date. Setting to None.")
-                    #     v = None
                 data.__setattr__(k, v)
         # logger.debug(f"Data coming out of validation: {pformat(data)}")
         return data
@@ -379,7 +368,6 @@ class PydEquipment(BaseModel, extra='ignore'):
                                                              role=self.role, limit=1)
             except TypeError as e:
                 logger.error(f"Couldn't get association due to {e}, returning...")
-                # return equipment, None
                 assoc = None
             if assoc is None:
                 assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
@@ -830,11 +818,6 @@ class PydSubmission(BaseModel, extra='allow'):
                         logger.debug(f"Checking reagent {reagent.lot}")
                         reagent, _ = reagent.toSQL(submission=instance)
                         # logger.debug(f"Association: {assoc}")
-                        # if assoc is not None:  # and assoc not in instance.submission_reagent_associations:
-                        #     if assoc not in instance.submission_reagent_associations:
-                        #         instance.submission_reagent_associations.append(assoc)
-                        #     else:
-                        #         logger.warning(f"Reagent association {assoc} is already present in {instance.submission_reagent_associations}")
                 case "samples":
                     for sample in self.samples:
                         sample, associations, _ = sample.toSQL(submission=instance)
@@ -871,7 +854,6 @@ class PydSubmission(BaseModel, extra='allow'):
                                 logger.warning(f"Tips association {association} is already present in {instance}")
                 case item if item in instance.timestamps():
                     logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
-                    # value = value.replace(tzinfo=timezone)
                     if isinstance(value, date):
                         value = datetime.combine(value, datetime.min.time())
                         value = value.replace(tzinfo=timezone)
@@ -903,7 +885,6 @@ class PydSubmission(BaseModel, extra='allow'):
                     if check:
                         try:
                             instance.set_attribute(key=key, value=value)
-                            # instance.update({key:value})
                         except AttributeError as e:
                             logger.error(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
                             continue

src/submissions/frontend/visualizations/irida_charts.py

@@ -40,7 +40,6 @@ class IridaFigure(CustomFigure):
         Returns:
             Figure: output stacked bar chart.
         """
-        # fig = Figure()
         for ii, mode in enumerate(modes):
             if "count" in mode:
                 df[mode] = pd.to_numeric(df[mode], errors='coerce')

src/submissions/frontend/visualizations/turnaround_chart.py

@@ -1,8 +1,10 @@
+"""
+Construct turnaround time charts
+"""
 from pprint import pformat
 from . import CustomFigure
 import plotly.express as px
 import pandas as pd
-import numpy as np
 from PyQt6.QtWidgets import QWidget
 import logging
 
@@ -25,7 +27,6 @@ class TurnaroundChart(CustomFigure):
         self.construct_chart()
         if threshold:
             self.add_hline(y=threshold)
-        # self.update_xaxes()
         self.update_layout(showlegend=False)
 
     def construct_chart(self, df: pd.DataFrame | None = None):

src/submissions/frontend/widgets/app.py

@@ -1,7 +1,6 @@
 """
 Constructs main application.
 """
-import os
 from pprint import pformat
 from PyQt6.QtCore import qInstallMessageHandler
 from PyQt6.QtWidgets import (
@@ -18,12 +17,11 @@ from tools import check_if_app, Settings, Report, jinja_template_loading, check_
 from .functions import select_save_file, select_open_file
 from datetime import date
 from .pop_ups import HTMLPop, AlertPop
-from .misc import LogParser, Pagifier
+from .misc import Pagifier
 import logging, webbrowser, sys, shutil
 from .submission_table import SubmissionsSheet
 from .submission_widget import SubmissionFormContainer
 from .controls_chart import ControlsViewer
-# from .sample_search import SampleSearchBox
 from .summary import Summary
 from .turnaround import TurnaroundTime
 from .omni_search import SearchBox
@@ -84,7 +82,7 @@ class App(QMainWindow):
         fileMenu.addAction(self.importAction)
         fileMenu.addAction(self.yamlExportAction)
         fileMenu.addAction(self.yamlImportAction)
-        methodsMenu.addAction(self.searchLog)
+        # methodsMenu.addAction(self.searchLog)
         methodsMenu.addAction(self.searchSample)
         maintenanceMenu.addAction(self.joinExtractionAction)
         maintenanceMenu.addAction(self.joinPCRAction)
@@ -98,8 +96,8 @@ class App(QMainWindow):
         toolbar = QToolBar("My main toolbar")
         self.addToolBar(toolbar)
         toolbar.addAction(self.addReagentAction)
-        toolbar.addAction(self.addKitAction)
-        toolbar.addAction(self.addOrgAction)
+        # toolbar.addAction(self.addKitAction)
+        # toolbar.addAction(self.addOrgAction)
 
     def _createActions(self):
         """
@@ -108,13 +106,13 @@ class App(QMainWindow):
         # logger.debug(f"Creating actions...")
         self.importAction = QAction("&Import Submission", self)
         self.addReagentAction = QAction("Add Reagent", self)
-        self.addKitAction = QAction("Import Kit", self)
-        self.addOrgAction = QAction("Import Org", self)
+        # self.addKitAction = QAction("Import Kit", self)
+        # self.addOrgAction = QAction("Import Org", self)
         self.joinExtractionAction = QAction("Link Extraction Logs")
         self.joinPCRAction = QAction("Link PCR Logs")
         self.helpAction = QAction("&About", self)
         self.docsAction = QAction("&Docs", self)
-        self.searchLog = QAction("Search Log", self)
+        # self.searchLog = QAction("Search Log", self)
         self.searchSample = QAction("Search Sample", self)
         self.githubAction = QAction("Github", self)
         self.yamlExportAction = QAction("Export Type Example", self)
@@ -132,14 +130,13 @@ class App(QMainWindow):
         self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
         self.helpAction.triggered.connect(self.showAbout)
         self.docsAction.triggered.connect(self.openDocs)
-        self.searchLog.triggered.connect(self.runSearch)
+        # self.searchLog.triggered.connect(self.runSearch)
         self.searchSample.triggered.connect(self.runSampleSearch)
         self.githubAction.triggered.connect(self.openGithub)
         self.yamlExportAction.triggered.connect(self.export_ST_yaml)
         self.yamlImportAction.triggered.connect(self.import_ST_yaml)
         self.table_widget.pager.current_page.textChanged.connect(self.update_data)
         self.editReagentAction.triggered.connect(self.edit_reagent)
-        self.destroyed.connect(self.final_commit)
 
     def showAbout(self):
         """
@@ -180,15 +177,14 @@ class App(QMainWindow):
         instr = HTMLPop(html=html, title="Instructions")
         instr.exec()
 
-    def runSearch(self):
-        dlg = LogParser(self)
-        dlg.exec()
+    # def runSearch(self):
+    #     dlg = LogParser(self)
+    #     dlg.exec()
 
     def runSampleSearch(self):
         """
         Create a search for samples.
         """
-        # dlg = SampleSearchBox(self)
         dlg = SearchBox(self, object_type=BasicSample, extras=[])
         dlg.exec()
 
@@ -244,7 +240,6 @@ class App(QMainWindow):
         st = SubmissionType.import_from_json(filepath=fname)
         if st:
             # NOTE: Do not delete the print statement below.
-            # print(pformat(st.to_export_dict()))
             choice = input("Save the above submission type? [y/N]: ")
             if choice.lower() == "y":
                 pass
@@ -254,9 +249,6 @@ class App(QMainWindow):
     def update_data(self):
         self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
 
-    def final_commit(self):
-        logger.debug("Running final commit")
-        self.ctx.database_session.commit()
 
 class AddSubForm(QWidget):
 

src/submissions/frontend/widgets/controls_chart.py

@@ -10,9 +10,10 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtCore import QSignalBlocker
 from backend.db import ControlType, IridaControl
 import logging
-from tools import Report, report_result
+from tools import Report, report_result, Result
 from frontend.visualizations import CustomFigure
 from .misc import StartEndDatePicker
+from .info_tab import InfoPane
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -37,11 +38,11 @@ class ControlsViewer(QWidget):
         # NOTE: fetch types of controls
         con_sub_types = [item for item in self.archetype.targets.keys()]
         self.control_sub_typer.addItems(con_sub_types)
-        # NOTE: create custom widget to get types of analysis
+        # NOTE: create custom widget to get types of analysis -- disabled by PCR control
         self.mode_typer = QComboBox()
         mode_types = IridaControl.get_modes()
         self.mode_typer.addItems(mode_types)
-        # NOTE: create custom widget to get subtypes of analysis
+        # NOTE: create custom widget to get subtypes of analysis -- disabled by PCR control
         self.mode_sub_typer = QComboBox()
         self.mode_sub_typer.setEnabled(False)
         # NOTE: add widgets to tab2 layout
@@ -83,15 +84,15 @@ class ControlsViewer(QWidget):
             pass
         # NOTE: correct start date being more recent than end date and rerun
         if self.datepicker.start_date.date() > self.datepicker.end_date.date():
-            logger.warning("Start date after end date is not allowed!")
             threemonthsago = self.datepicker.end_date.date().addDays(-60)
-            # NOTE: block signal that will rerun controls getter and set start date
-            # Without triggering this function again
+            msg = f"Start date after end date is not allowed! Setting to {threemonthsago.toString()}."
+            logger.warning(msg)
+            # NOTE: block signal that will rerun controls getter and set start date Without triggering this function again
             with QSignalBlocker(self.datepicker.start_date) as blocker:
                 self.datepicker.start_date.setDate(threemonthsago)
-            self.controls_getter()
-            self.report.add_result(report)
-            return
+            self.controls_getter_function()
+            report.add_result(Result(owner=self.__str__(), msg=msg, status="Warning"))
+            return report
         # NOTE: convert to python useable date objects
         self.start_date = self.datepicker.start_date.date().toPyDate()
         self.end_date = self.datepicker.end_date.date().toPyDate()
@@ -167,4 +168,3 @@ class ControlsViewer(QWidget):
         self.webengineview.update()
         # logger.debug("Figure updated... I hope.")
         return report
-

src/submissions/frontend/widgets/equipment_usage.py

@@ -1,7 +1,6 @@
 '''
 Creates forms that the user can enter equipment info into.
 '''
-import time
 from pprint import pformat
 from PyQt6.QtCore import Qt, QSignalBlocker
 from PyQt6.QtWidgets import (QDialog, QComboBox, QCheckBox,

src/submissions/frontend/widgets/gel_checker.py

@@ -66,7 +66,6 @@ class GelBox(QDialog):
         layout.addWidget(self.imv, 0, 1, 20, 20)
         # NOTE: setting this widget as central widget of the main window
         try:
-            # control_info = sorted(self.submission.gel_controls, key=lambda d: d['location'])
             control_info = sorted(self.submission.gel_controls, key=itemgetter('location'))
         except KeyError:
             control_info = None
@@ -79,7 +78,6 @@ class GelBox(QDialog):
         layout.addWidget(self.buttonBox, 23, 1, 1, 1)
         self.setLayout(layout)
 
-
     def parse_form(self) -> Tuple[str, str | Path, list]:
         """
         Get relevant values from self/form
@@ -124,7 +122,6 @@ class ControlsForm(QWidget):
             self.layout.addWidget(label, iii, 1, 1, 1)
         for iii in range(3):
             for jjj in range(3):
-                # widge = QLineEdit()
                 widge = QComboBox()
                 widge.addItems(['Neg', 'Pos'])
                 widge.setCurrentIndex(0)

src/submissions/frontend/widgets/info_tab.py

@@ -1,6 +1,11 @@
+"""
+A pane to show info e.g. cost reports and turnaround times.
+TODO: Can I merge this with the controls chart pane?
+"""
+from PyQt6.QtCore import QSignalBlocker
 from PyQt6.QtWebEngineWidgets import QWebEngineView
-from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton
-from tools import Report
+from PyQt6.QtWidgets import QWidget, QGridLayout
+from tools import Report, report_result, Result
 from .misc import StartEndDatePicker, save_pdf
 from .functions import select_save_file
 import logging
@@ -17,22 +22,29 @@ class InfoPane(QWidget):
         self.report = Report()
         self.datepicker = StartEndDatePicker(default_start=-31)
         self.webview = QWebEngineView()
-        self.datepicker.start_date.dateChanged.connect(self.date_changed)
-        self.datepicker.end_date.dateChanged.connect(self.date_changed)
+        self.datepicker.start_date.dateChanged.connect(self.update_data)
+        self.datepicker.end_date.dateChanged.connect(self.update_data)
         self.layout = QGridLayout(self)
         self.layout.addWidget(self.datepicker, 0, 0, 1, 2)
-        self.save_excel_button = QPushButton("Save Excel", parent=self)
-        self.save_excel_button.pressed.connect(self.save_excel)
-        self.save_pdf_button = QPushButton("Save PDF", parent=self)
-        self.save_pdf_button.pressed.connect(self.save_pdf)
-        self.layout.addWidget(self.save_excel_button, 0, 2, 1, 1)
-        self.layout.addWidget(self.save_pdf_button, 0, 3, 1, 1)
         self.layout.addWidget(self.webview, 2, 0, 1, 4)
         self.setLayout(self.layout)
 
-    def date_changed(self):
+    @report_result
+    def update_data(self, *args, **kwargs):
+        report = Report()
         self.start_date = self.datepicker.start_date.date().toPyDate()
         self.end_date = self.datepicker.end_date.date().toPyDate()
+        if self.datepicker.start_date.date() > self.datepicker.end_date.date():
+            lastmonth = self.datepicker.end_date.date().addDays(-31)
+            msg = f"Start date after end date is not allowed! Setting to {lastmonth.toString()}."
+            logger.warning(msg)
+            # NOTE: block signal that will rerun controls getter and set start date
+            # Without triggering this function again
+            with QSignalBlocker(self.datepicker.start_date) as blocker:
+                self.datepicker.start_date.setDate(lastmonth)
+            self.update_data()
+            report.add_result(Result(owner=self.__str__(), msg=msg, status="Warning"))
+            return report
 
     def save_excel(self):
         fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
@@ -43,3 +55,9 @@ class InfoPane(QWidget):
                                  default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
                                  extension="pdf")
         save_pdf(obj=self.webview, filename=fname)
+
+    def save_png(self):
+        fname = select_save_file(obj=self,
+                                 default_name=f"Plotly {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
+                                 extension="png")
+        self.fig.write_image(fname.absolute().__str__(), engine="kaleido")

src/submissions/frontend/widgets/misc.py

@@ -14,8 +14,6 @@ from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF
 from tools import jinja_template_loading
 from backend.db.models import *
 import logging
-from .pop_ups import AlertPop
-from .functions import select_open_file
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -114,55 +112,6 @@ class AddReagentForm(QDialog):
         self.name_input.addItems(list(set([item.name for item in lookup])))
 
 
-class LogParser(QDialog):
-
-    def __init__(self, parent):
-        super().__init__(parent)
-        self.app = self.parent()
-        self.filebutton = QPushButton(self)
-        self.filebutton.setText("Import File")
-        self.phrase_looker = QComboBox(self)
-        self.phrase_looker.setEditable(True)
-        self.btn = QPushButton(self)
-        self.btn.setText("Search")
-        self.layout = QFormLayout(self)
-        self.layout.addRow(self.tr("&File:"), self.filebutton)
-        self.layout.addRow(self.tr("&Search Term:"), self.phrase_looker)
-        self.layout.addRow(self.btn)
-        self.filebutton.clicked.connect(self.filelookup)
-        self.btn.clicked.connect(self.runsearch)
-        self.setMinimumWidth(400)
-
-    def filelookup(self):
-        """
-        Select file to search
-        """
-        self.fname = select_open_file(self, "tabular")
-
-    def runsearch(self):
-        """
-        Gets total/percent occurences of string in tabular file.
-        """
-        count: int = 0
-        total: int = 0
-        # logger.debug(f"Current search term: {self.phrase_looker.currentText()}")
-        try:
-            with open(self.fname, "r") as f:
-                for chunk in readInChunks(fileObj=f):
-                    total += len(chunk)
-                    for line in chunk:
-                        if self.phrase_looker.currentText().lower() in line.lower():
-                            count += 1
-            percent = (count / total) * 100
-            msg = f"I found {count} instances of the search phrase out of {total} = {percent:.2f}%."
-            status = "Information"
-        except AttributeError:
-            msg = f"No file was selected."
-            status = "Error"
-        dlg = AlertPop(message=msg, status=status)
-        dlg.exec()
-
-
 class StartEndDatePicker(QWidget):
     """
     custom widget to pick start and end dates for controls graphs

src/submissions/frontend/widgets/omni_search.py

@@ -16,6 +16,9 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 
 class SearchBox(QDialog):
+    """
+    The full search widget.
+    """
 
     def __init__(self, parent, object_type: Any, extras: List[str], **kwargs):
         super().__init__(parent)
@@ -36,7 +39,7 @@ class SearchBox(QDialog):
         else:
             self.sub_class = None
         self.results = SearchResults(parent=self, object_type=self.object_type, extras=self.extras, **kwargs)
-        logger.debug(f"results: {self.results}")
+        # logger.debug(f"results: {self.results}")
         self.layout.addWidget(self.results, 5, 0)
         self.setLayout(self.layout)
         self.setWindowTitle(f"Search {self.object_type.__name__}")
@@ -51,6 +54,7 @@ class SearchBox(QDialog):
         # logger.debug(deletes)
         for item in deletes:
             item.setParent(None)
+        # NOTE: Handle any subclasses
         if not self.sub_class:
             self.update_data()
         else:
@@ -89,6 +93,9 @@ class SearchBox(QDialog):
 
 
 class FieldSearch(QWidget):
+    """
+    Search bar.
+    """
 
     def __init__(self, parent, label, field_name):
         super().__init__(parent)
@@ -115,6 +122,9 @@ class FieldSearch(QWidget):
 
 
 class SearchResults(QTableView):
+    """
+    Results table.
+    """
 
     def __init__(self, parent: SearchBox, object_type: Any, extras: List[str], **kwargs):
         super().__init__()
@@ -146,7 +156,6 @@ class SearchResults(QTableView):
         context = {item['name']: x.sibling(x.row(), item['column']).data() for item in self.columns_of_interest}
         logger.debug(f"Context: {context}")
         try:
-            # object = self.object_type.query(**{self.object_type.searchables: context[self.object_type.searchables]})
             object = self.object_type.query(**context)
         except KeyError:
             object = None

src/submissions/frontend/widgets/submission_details.py

@@ -42,7 +42,7 @@ class SubmissionDetails(QDialog):
         # NOTE: button to export a pdf version
         self.btn = QPushButton("Export PDF")
         self.btn.setFixedWidth(775)
-        self.btn.clicked.connect(self.export)
+        self.btn.clicked.connect(self.save_pdf)
         self.back = QPushButton("Back")
         self.back.setFixedWidth(100)
         # self.back.clicked.connect(self.back_function)
@@ -181,7 +181,7 @@ class SubmissionDetails(QDialog):
         submission.save()
         self.submission_details(submission=self.rsl_plate_num)
 
-    def export(self):
+    def save_pdf(self):
         """
         Renders submission to html, then creates and saves .pdf file to user selected file.
         """

src/submissions/frontend/widgets/submission_table.py

@@ -83,6 +83,7 @@ class SubmissionsSheet(QTableView):
         self.resizeRowsToContents()
         self.setSortingEnabled(True)
         self.doubleClicked.connect(lambda x: BasicSubmission.query(id=x.sibling(x.row(), 0).data()).show_details(self))
+        # NOTE: Have to run native query here because mine just returns results?
         self.total_count = BasicSubmission.__database_session__.query(BasicSubmission).count()
 
     def setData(self, page: int = 1, page_size: int = 250) -> None:

src/submissions/frontend/widgets/submission_widget.py

@@ -1,15 +1,13 @@
 '''
 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 . import select_open_file, select_save_file
-import logging, difflib
+import logging
 from pathlib import Path
 from tools import Report, Result, check_not_nan, main_form_style, report_result
 from backend.excel.parser import SheetParser
@@ -187,6 +185,8 @@ class SubmissionFormContainer(QWidget):
 
 class SubmissionFormWidget(QWidget):
 
+    update_reagent_fields = ['extraction_kit']
+
     def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
         super().__init__(parent)
         # logger.debug(f"Disable: {disable}")
@@ -203,7 +203,7 @@ class SubmissionFormWidget(QWidget):
         # 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()):
-            logger.debug(f"Creating widget: {k}")
+            # logger.debug(f"Creating widget: {k}")
             if k in self.ignore:
                 logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget")
                 continue
@@ -225,10 +225,10 @@ class SubmissionFormWidget(QWidget):
                                             sub_obj=st, disable=check)
             if add_widget is not None:
                 self.layout.addWidget(add_widget)
-            if k == "extraction_kit":
+            # if k == "extraction_kit":
+            if k in self.__class__.update_reagent_fields:
                 add_widget.input.currentTextChanged.connect(self.scrape_reagents)
         self.setStyleSheet(main_form_style)
-        # self.scrape_reagents(self.pyd.extraction_kit)
         self.scrape_reagents(self.extraction_kit)
 
     def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | SubmissionType | None = None,
@@ -293,9 +293,8 @@ class SubmissionFormWidget(QWidget):
             if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
                 reagent.setParent(None)
         reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
-        logger.debug(f"Got reagents: {pformat(reagents)}")
+        # logger.debug(f"Got reagents: {pformat(reagents)}")
         for reagent in reagents:
-            # add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
             add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit)
             self.layout.addWidget(add_widget)
         report.add_result(integrity_report)
@@ -334,10 +333,6 @@ class SubmissionFormWidget(QWidget):
             query = [widget for widget in query if widget.objectName() == object_name]
         return query
 
-    # def update_pyd(self):
-    #     results = self.parse_form()
-    #     logger.debug(pformat(results))
-
     @report_result
     def submit_new_sample_function(self, *args) -> Report:
         """
@@ -538,19 +533,14 @@ class SubmissionFormWidget(QWidget):
             except (TypeError, KeyError):
                 pass
             obj = parent.parent().parent()
-            logger.debug(f"Object: {obj}")
-            logger.debug(f"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)
                     # NOTE: lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
                     labs = [item.name for item in Organization.query()]
-                    # NOTE: try to set closest match to top of list
-                    # try:
-                    #     labs = difflib.get_close_matches(value, labs, len(labs), 0)
-                    # except (TypeError, ValueError):
-                    #     pass
                     if isinstance(value, dict):
                         value = value['value']
                     if isinstance(value, Organization):
@@ -559,7 +549,7 @@ class SubmissionFormWidget(QWidget):
                         looked_up_lab = Organization.query(name=value, limit=1)
                     except AttributeError:
                         looked_up_lab = None
-                    logger.debug(f"\n\nLooked up lab: {looked_up_lab}")
+                    # logger.debug(f"\n\nLooked up lab: {looked_up_lab}")
                     if looked_up_lab:
                         try:
                             labs.remove(str(looked_up_lab.name))
@@ -579,7 +569,6 @@ class SubmissionFormWidget(QWidget):
                     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)]
                     uses = [item.name for item in submission_type.kit_types]
                     obj.uses = uses
                     # logger.debug(f"Kits received for {submission_type}: {uses}")

src/submissions/frontend/widgets/summary.py

@@ -1,12 +1,11 @@
-from PyQt6.QtCore import QSignalBlocker
-from PyQt6.QtWebEngineWidgets import QWebEngineView
+"""
+Pane to hold information e.g. cost summary.
+"""
 from .info_tab import InfoPane
-from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QLabel
+from PyQt6.QtWidgets import QWidget, QLabel, QPushButton
 from backend.db import Organization
 from backend.excel import ReportMaker
-from tools import Report
-from .misc import StartEndDatePicker, save_pdf, CheckableComboBox
-from .functions import select_save_file
+from .misc import CheckableComboBox
 import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -16,32 +15,27 @@ class Summary(InfoPane):
 
     def __init__(self, parent: QWidget) -> None:
         super().__init__(parent)
+        self.save_excel_button = QPushButton("Save Excel", parent=self)
+        self.save_excel_button.pressed.connect(self.save_excel)
+        self.save_pdf_button = QPushButton("Save PDF", parent=self)
+        self.save_pdf_button.pressed.connect(self.save_pdf)
+        self.layout.addWidget(self.save_excel_button, 0, 2, 1, 1)
+        self.layout.addWidget(self.save_pdf_button, 0, 3, 1, 1)
         self.org_select = CheckableComboBox()
         self.org_select.setEditable(False)
         self.org_select.addItem("Select", header=True)
         for org in [org.name for org in Organization.query()]:
             self.org_select.addItem(org)
-        self.org_select.model().itemChanged.connect(self.date_changed)
+        self.org_select.model().itemChanged.connect(self.update_data)
         self.layout.addWidget(QLabel("Client"), 1, 0, 1, 1)
         self.layout.addWidget(self.org_select, 1, 1, 1, 3)
-        self.date_changed()
+        self.update_data()
 
-    def date_changed(self):
+
+    def update_data(self):
+        super().update_data()
         orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)]
-        if self.datepicker.start_date.date() > self.datepicker.end_date.date():
-            logger.warning("Start date after end date is not allowed!")
-            lastmonth = self.datepicker.end_date.date().addDays(-31)
-            # NOTE: block signal that will rerun controls getter and set start date
-            # Without triggering this function again
-            with QSignalBlocker(self.datepicker.start_date) as blocker:
-                self.datepicker.start_date.setDate(lastmonth)
-            self.date_changed()
-            return
-        # NOTE: convert to python useable date objects
-        # self.start_date = self.datepicker.start_date.date().toPyDate()
-        # self.end_date = self.datepicker.end_date.date().toPyDate()
-        super().date_changed()
-        logger.debug(f"Getting report from {self.start_date} to {self.end_date} using {orgs}")
+        # logger.debug(f"Getting report from {self.start_date} to {self.end_date} using {orgs}")
         self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs)
         self.webview.setHtml(self.report_obj.html)
         if self.report_obj.subs:
@@ -50,13 +44,3 @@ class Summary(InfoPane):
         else:
             self.save_pdf_button.setEnabled(False)
             self.save_excel_button.setEnabled(False)
-
-    # def save_excel(self):
-    #     fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
-    #     self.report_obj.write_report(fname, obj=self)
-    #
-    # def save_pdf(self):
-    #     fname = select_save_file(obj=self,
-    #                              default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
-    #                              extension="pdf")
-    #     save_pdf(obj=self.webview, filename=fname)

src/submissions/frontend/widgets/turnaround.py

@@ -15,28 +15,25 @@ class TurnaroundTime(InfoPane):
 
     def __init__(self, parent: QWidget):
         super().__init__(parent)
-        self.chart = None
+        self.save_button = QPushButton("Save Chart", parent=self)
+        self.save_button.pressed.connect(self.save_png)
+        self.layout.addWidget(self.save_button, 0, 2, 1, 1)
+        self.export_button = QPushButton("Save Data", parent=self)
+        self.export_button.pressed.connect(self.save_excel)
+        self.layout.addWidget(self.export_button, 0, 3, 1, 1)
+        self.fig = None
         self.report_object = None
         self.submission_typer = QComboBox(self)
-        subs = ["Any"] + [item.name for item in SubmissionType.query()]
+        subs = ["All"] + [item.name for item in SubmissionType.query()]
         self.submission_typer.addItems(subs)
         self.layout.addWidget(self.submission_typer, 1, 1, 1, 3)
-        self.submission_typer.currentTextChanged.connect(self.date_changed)
-        self.date_changed()
+        self.submission_typer.currentTextChanged.connect(self.update_data)
+        self.update_data()
 
-    def date_changed(self):
-        if self.datepicker.start_date.date() > self.datepicker.end_date.date():
-            logger.warning("Start date after end date is not allowed!")
-            lastmonth = self.datepicker.end_date.date().addDays(-31)
-            # NOTE: block signal that will rerun controls getter and set start date
-            # Without triggering this function again
-            with QSignalBlocker(self.datepicker.start_date) as blocker:
-                self.datepicker.start_date.setDate(lastmonth)
-            self.date_changed()
-            return
-        super().date_changed()
+    def update_data(self):
+        super().update_data()
         chart_settings = dict(start_date=self.start_date, end_date=self.end_date)
-        if self.submission_typer.currentText() == "Any":
+        if self.submission_typer.currentText() == "All":
             submission_type = None
             subtype_obj = None
         else:
@@ -47,5 +44,5 @@ class TurnaroundTime(InfoPane):
             threshold = subtype_obj.defaults['turnaround_time'] + 0.5
         else:
             threshold = None
-        self.chart = TurnaroundChart(df=self.report_obj.df, settings=chart_settings, modes=[], threshold=threshold)
-        self.webview.setHtml(self.chart.to_html())
+        self.fig = TurnaroundChart(df=self.report_obj.df, settings=chart_settings, modes=[], threshold=threshold)
+        self.webview.setHtml(self.fig.to_html())

src/submissions/tools/__init__.py

@@ -3,13 +3,11 @@ Contains miscellaenous functions used by both frontend and backend.
 '''
 from __future__ import annotations
 
-import json
-import pprint
 from datetime import date, datetime, timedelta
 from json import JSONDecodeError
+from pprint import pprint
 import numpy as np
-import logging, re, yaml, sys, os, stat, platform, getpass, inspect
-import pandas as pd
+import logging, re, yaml, sys, os, stat, platform, getpass, inspect, json, pandas as pd
 from dateutil.easter import easter
 from jinja2 import Environment, FileSystemLoader
 from logging import handlers
@@ -20,7 +18,6 @@ from sqlalchemy import create_engine, text, MetaData
 from pydantic import field_validator, BaseModel, Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing import Any, Tuple, Literal, List
-# print(inspect.stack()[1])
 from __init__ import project_path
 from configparser import ConfigParser
 from tkinter import Tk  # NOTE: This is for choosing database path before app is created.
@@ -261,6 +258,7 @@ class Settings(BaseSettings, extra="allow"):
     submission_types: dict | None = None
     database_session: Session | None = None
     package: Any | None = None
+    logging_enabled: bool = Field(default=False)
 
     model_config = SettingsConfigDict(env_file_encoding='utf-8')
 
@@ -422,6 +420,7 @@ class Settings(BaseSettings, extra="allow"):
 
         super().__init__(*args, **kwargs)
         self.set_from_db()
+        pprint(f"User settings:\n{self.__dict__}")
 
     def set_from_db(self):
         if 'pytest' in sys.modules:
@@ -819,7 +818,7 @@ class Result(BaseModel, arbitrary_types_allowed=True):
         self.owner = inspect.stack()[1].function
 
     def report(self):
-        from frontend.widgets.misc import AlertPop
+        from frontend.widgets.pop_ups import AlertPop
         return AlertPop(message=self.msg, status=self.status, owner=self.owner)