update to First Strand constructor

CHANGELOG.md

@@ -1,3 +1,8 @@
+## 202310.02
+
+- Improvements to First strand constructor.
+- Submission forms can now be dragged and dropped into the form widget.
+
 ## 202310.01
 
 - Controls linker is now depreciated.

README.md

@@ -1,5 +1,5 @@
 ## Startup:
-1. Open the app using the shortcut in the Submissions folder. For example: 'L:\Robotics Laboratory Support\Submissions\submissions_v122b.exe - Shortcut.lnk' (Version may have changed).
+1. Open the app using the shortcut in the Submissions folder. For example: L:\\Robotics Laboratory Support\\Submissions\\submissions_v122b.exe - Shortcut.lnk (Version may have changed).
 	a. Ignore the large black window of fast scrolling text, it is there for debugging purposes.
 	b. The 'Submissions' tab should be open by default.
 
@@ -60,10 +60,6 @@ This is meant to import .xslx files created from the Design & Analysis Software
 	c. Repeat 6b for the Lot and the Expiry row and columns.
 7. Click the "Submit" button at the top.
 
-## Linking Controls:
-
-1. Click "Monthly" -> "Link Controls". Entire process should be handled automatically.
-
 ## Linking Extraction Logs:
 
 1. Click "Monthly" -> "Link Extraction Logs".

TODO.md

@@ -1,6 +1,7 @@
+- [x] Drag and drop files into submission form area?
 - [ ] Get info for controls into their sample hitpicks.
 - [x] Move submission-type specific parser functions into class methods in their respective models.
-- [ ] Improve results reporting.
+- [ ] Improve function results reporting.
     - Maybe make it a list until it gets to the reporter?
 - [x] Increase robustness of form parsers by adding custom procedures for each.
 - [x] Rerun Kit integrity if extraction kit changed in the form.

alembic.ini

@@ -56,8 +56,8 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 # output_encoding = utf-8
 
 ; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
-; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-new.db
-sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions-test.db
+sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-new.db
+; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions-test.db
 
 
 [post_write_hooks]

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202310.1b"
+__version__ = "202310.2b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 

src/submissions/backend/db/functions/lookups.py

@@ -417,7 +417,8 @@ def lookup_reagenttype_kittype_association(ctx:Settings,
 def lookup_submission_sample_association(ctx:Settings,
                                          submission:models.BasicSubmission|str|None=None,
                                          sample:models.BasicSample|str|None=None,
-                                         limit:int=0
+                                         limit:int=0,
+                                         chronologic:bool=False
                                          ) -> models.SubmissionSampleAssociation|List[models.SubmissionSampleAssociation]:
     query = setup_lookup(ctx=ctx, locals=locals()).query(models.SubmissionSampleAssociation)
     match submission:
@@ -435,6 +436,8 @@ def lookup_submission_sample_association(ctx:Settings,
         case _:
             pass
     logger.debug(f"Query count: {query.count()}")
+    if chronologic:
+        query.join(models.BasicSubmission).order_by(models.BasicSubmission.submitted_date)
     if query.count() == 1:
         limit = 1
     return query_return(query=query, limit=limit)

src/submissions/backend/db/functions/misc.py

@@ -247,6 +247,8 @@ def get_polymorphic_subclass(base:object, polymorphic_identity:str|None=None):
     Returns:
         _type_: Subclass, or parent class on 
     """    
+    if isinstance(polymorphic_identity, dict):
+        polymorphic_identity = polymorphic_identity['value']
     if polymorphic_identity == None:
         return base
     else:

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

@@ -1,6 +1,7 @@
 '''
 Models for the main submission types.
 '''
+from getpass import getuser
 import math
 from . import Base
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT, case
@@ -15,7 +16,8 @@ from pandas import Timestamp
 from dateutil.parser import parse
 import re
 import pandas as pd
-from tools import row_map
+from openpyxl import Workbook
+from tools import check_not_nan, row_map
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -238,6 +240,20 @@ class BasicSubmission(Base):
                 continue
         return output_list
     
+    @classmethod
+    def custom_platemap(cls, xl:pd.ExcelFile, plate_map:pd.DataFrame) -> pd.DataFrame:
+        """
+        Stupid stopgap solution to there being an issue with the Bacterial Culture plate map
+
+        Args:
+            xl (pd.ExcelFile): original xl workbook
+            plate_map (pd.DataFrame): original plate map
+
+        Returns:
+            pd.DataFrame: updated plate map.
+        """        
+        return plate_map
+    
     @classmethod
     def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
         """
@@ -266,6 +282,19 @@ class BasicSubmission(Base):
         logger.debug(f"Called {cls.__name__} sample parser")
         return input_dict
     
+    @classmethod
+    def custom_autofill(cls, input_excel:Workbook) -> Workbook:
+        """
+        Adds custom autofill methods for submission
+
+        Args:
+            input_excel (Workbook): input workbook
+
+        Returns:
+            Workbook: updated workbook
+        """        
+        return input_excel
+
 # Below are the custom submission types
 
 class BacterialCulture(BasicSubmission):
@@ -287,6 +316,49 @@ class BacterialCulture(BasicSubmission):
             output['controls'] = [item.to_sub_dict() for item in self.controls]
         return output
     
+    @classmethod
+    def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame:
+        """
+        Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
+
+        Args:
+            xl (pd.ExcelFile): original xl workbook
+            plate_map (pd.DataFrame): original plate map
+
+        Returns:
+            pd.DataFrame: updated plate map.
+        """        
+        plate_map = super().custom_platemap(xl, plate_map)
+        num1 = xl.parse("Sample List").iloc[40,1]
+        num2 = xl.parse("Sample List").iloc[41,1]
+        logger.debug(f"Broken: {plate_map.iloc[5,0]}, {plate_map.iloc[6,0]}")
+        logger.debug(f"Replace: {num1}, {num2}")
+        if not check_not_nan(plate_map.iloc[5,0]):
+            plate_map.iloc[5,0] = num1
+        if not check_not_nan(plate_map.iloc[6,0]):
+            plate_map.iloc[6,0] = num2
+        return plate_map
+    
+    @classmethod
+    def custom_autofill(cls, input_excel: Workbook) -> Workbook:
+        """
+        Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
+
+        Args:
+            input_excel (Workbook): Input openpyxl workbook
+
+        Returns:
+            Workbook: Updated openpyxl workbook
+        """        
+        input_excel = super().custom_autofill(input_excel)
+        sheet = input_excel['Plate Map']
+        if sheet.cell(12,2).value == None:
+            sheet.cell(row=12, column=2, value="=IF(ISBLANK('Sample List'!$B42),\"\",'Sample List'!$B42)")
+        if sheet.cell(13,2).value == None:
+            sheet.cell(row=13, column=2, value="=IF(ISBLANK('Sample List'!$B43),\"\",'Sample List'!$B43)")
+        input_excel["Sample List"].cell(row=15, column=2, value=getuser()[0:2].upper())
+        return input_excel
+
 class Wastewater(BasicSubmission):
     """
     derivative submission type from BasicSubmission
@@ -327,7 +399,6 @@ class Wastewater(BasicSubmission):
             input_dict['csv'] = xl.parse("Copy to import file")
         return input_dict
   
-    
 class WastewaterArtic(BasicSubmission):
     """
     derivative submission type for artic wastewater
@@ -371,7 +442,6 @@ class WastewaterArtic(BasicSubmission):
         input_dict['submitter_id'] = re.sub(r"\s\(.+\)$", "", str(input_dict['submitter_id'])).strip()
         return input_dict
 
-    
 class BasicSample(Base):
     """
     Base of basic sample which polymorphs into BCSample and WWSample
@@ -457,7 +527,7 @@ class BasicSample(Base):
                             Sample name: {self.submitter_id}<br>
                             Well: {row_map[assoc.row]}{assoc.column}
                         """
-        return dict(name=self.submitter_id, positive=False, tooltip=tooltip_text)
+        return dict(name=self.submitter_id[:10], positive=False, tooltip=tooltip_text)
 
 class WastewaterSample(BasicSample):
     """
@@ -539,6 +609,16 @@ class WastewaterSample(BasicSample):
             logger.error(f"Couldn't set tooltip for {self.rsl_number}. Looks like there isn't PCR data.")
         return sample
     
+    def get_recent_ww_submission(self):
+        results = [sub for sub in self.submissions if isinstance(sub, Wastewater)]
+        if len(results) > 1:
+            results = results.sort(key=lambda sub: sub.submitted_date)
+        try:
+            return results[0]
+        except IndexError:
+            return None
+        
+        
 class BacterialCultureSample(BasicSample):
     """
     base of bacterial culture sample

src/submissions/backend/excel/parser.py

@@ -376,6 +376,8 @@ class SampleParser(object):
         df = df.iloc[plate_map_location['start_row']-1:plate_map_location['end_row'], plate_map_location['start_column']-1:plate_map_location['end_column']]
         df = pd.DataFrame(df.values[1:], columns=df.iloc[0])
         df = df.set_index(df.columns[0])
+        custom_mapper = get_polymorphic_subclass(models.BasicSubmission, self.submission_type)
+        df = custom_mapper.custom_platemap(self.xl, df)
         return df
     
     def construct_lookup_table(self, lookup_table_location:dict) -> pd.DataFrame:

src/submissions/frontend/__init__.py

@@ -8,17 +8,15 @@ from PyQt6.QtWidgets import (
     QMainWindow, QToolBar, 
     QTabWidget, QWidget, QVBoxLayout,
     QComboBox, QHBoxLayout,
-    QScrollArea, QLineEdit, QDateEdit,
-    QSpinBox
+    QScrollArea, QLineEdit, QDateEdit
 )
-from PyQt6.QtCore import Qt
+from PyQt6.QtCore import Qt, pyqtSignal
 from PyQt6.QtGui import QAction
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from pathlib import Path
 from backend.db import (
     construct_reagent, store_object, lookup_control_types, lookup_modes
 )
-# from .all_window_functions import extract_form_info
 from tools import check_if_app, Settings
 from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker, ImportReagent
 import logging
@@ -55,7 +53,6 @@ class App(QMainWindow):
         self._createToolBar()
         self._connectActions()
         self._controls_getter()
-        # self.status_bar = self.statusBar()
         self.show()
         self.statusBar().showMessage('Ready', 5000)
         
@@ -68,7 +65,6 @@ class App(QMainWindow):
         menuBar = self.menuBar()
         fileMenu = menuBar.addMenu("&File")
         # Creating menus using a title
-        # editMenu = menuBar.addMenu("&Edit")
         methodsMenu = menuBar.addMenu("&Methods")
         reportMenu = menuBar.addMenu("&Reports")
         maintenanceMenu = menuBar.addMenu("&Monthly")
@@ -79,7 +75,6 @@ class App(QMainWindow):
         fileMenu.addAction(self.importPCRAction)
         methodsMenu.addAction(self.constructFS)
         reportMenu.addAction(self.generateReportAction)
-        # maintenanceMenu.addAction(self.joinControlsAction)
         maintenanceMenu.addAction(self.joinExtractionAction)
         maintenanceMenu.addAction(self.joinPCRAction)
         
@@ -105,7 +100,6 @@ class App(QMainWindow):
         self.generateReportAction = QAction("Make Report", self)
         self.addKitAction = QAction("Import Kit", self)
         self.addOrgAction = QAction("Import Org", self)
-        # self.joinControlsAction = QAction("Link Controls")
         self.joinExtractionAction = QAction("Link Extraction Logs")
         self.joinPCRAction = QAction("Link PCR Logs")
         self.helpAction = QAction("&About", self)
@@ -128,12 +122,12 @@ class App(QMainWindow):
         self.table_widget.mode_typer.currentIndexChanged.connect(self._controls_getter)
         self.table_widget.datepicker.start_date.dateChanged.connect(self._controls_getter)
         self.table_widget.datepicker.end_date.dateChanged.connect(self._controls_getter)
-        # self.joinControlsAction.triggered.connect(self.linkControls)
         self.joinExtractionAction.triggered.connect(self.linkExtractions)
         self.joinPCRAction.triggered.connect(self.linkPCR)
         self.helpAction.triggered.connect(self.showAbout)
         self.docsAction.triggered.connect(self.openDocs)
         self.constructFS.triggered.connect(self.construct_first_strand)
+        self.table_widget.formwidget.import_drag.connect(self.importSubmission)
 
     def showAbout(self):
         """
@@ -168,12 +162,14 @@ class App(QMainWindow):
         else:
             self.statusBar().showMessage("Action completed sucessfully.", 5000)
 
-    def importSubmission(self):
+    def importSubmission(self, fname:Path|None=None):
         """
         import submission from excel sheet into form
         """        
         from .main_window_functions import import_submission_function
-        self, result = import_submission_function(self)
+        self.raise_()
+        self.activateWindow()
+        self, result = import_submission_function(self, fname)
         logger.debug(f"Import result: {result}")
         self.result_reporter(result)
 
@@ -395,12 +391,25 @@ class AddSubForm(QWidget):
 
 class SubmissionFormWidget(QWidget):
 
+    import_drag = pyqtSignal(Path)
+
     def __init__(self, parent: QWidget) -> None:
         logger.debug(f"Setting form widget...")
         super().__init__(parent)
         self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
                        "qt_scrollarea_vcontainer", "submit_btn"
                        ]
+        self.setAcceptDrops(True)
+
+    def dragEnterEvent(self, event):
+        if event.mimeData().hasUrls():
+            event.accept()
+        else:
+            event.ignore()
+
+    def dropEvent(self, event):
+        fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
+        self.import_drag.emit(fname)
 
     def parse_form(self) -> Tuple[dict, list]:
         logger.debug(f"Hello from parser!")

src/submissions/frontend/custom_widgets/misc.py

@@ -3,17 +3,19 @@ Contains miscellaneous widgets for frontend functions
 '''
 from datetime import date
 from pprint import pformat
+from PyQt6 import QtCore
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout,
     QLineEdit, QComboBox, QDialog, 
     QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
     QGridLayout, QPushButton, QSpinBox, QDoubleSpinBox,
-    QHBoxLayout, QScrollArea
+    QHBoxLayout, QScrollArea, QFormLayout
 )
 from PyQt6.QtCore import Qt, QDate, QSize
 from tools import check_not_nan, jinja_template_loading, Settings
 from backend.db.functions import construct_kit_from_yaml, \
-    lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association
+    lookup_reagent_types, lookup_reagents, lookup_submission_type, lookup_reagenttype_kittype_association, \
+    lookup_submissions
 from backend.db.models import SubmissionTypeKitTypeAssociation
 from sqlalchemy import FLOAT, INTEGER, String
 import logging
@@ -277,7 +279,6 @@ class KitAdder(QWidget):
                     info[widget.objectName()] = widget.date().toPyDate()
         return info, reagents
         
-
 class ReagentTypeForm(QWidget):
     """
     custom widget to add information about a new reagenttype
@@ -458,3 +459,67 @@ class ParsedQLabel(QLabel):
         else:
             self.setText(f"MISSING {output}")
 
+class FirstStrandSalvage(QDialog):
+
+    def __init__(self, ctx:Settings, submitter_id:str, rsl_plate_num:str|None=None) -> None:
+        super().__init__()
+        if rsl_plate_num == None:
+            rsl_plate_num = ""
+        self.setWindowTitle("Add Reagent")
+
+        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+        self.submitter_id_input = QLineEdit()
+        self.submitter_id_input.setText(submitter_id)
+        self.rsl_plate_num = QLineEdit()
+        self.rsl_plate_num.setText(rsl_plate_num)
+        self.row_letter = QComboBox()
+        self.row_letter.addItems(['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'])
+        self.row_letter.setEditable(False)
+        self.column_number = QComboBox()
+        self.column_number.addItems(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12'])
+        self.column_number.setEditable(False)
+        self.layout = QFormLayout()
+        self.layout.addRow(self.tr("&Sample Number:"), self.submitter_id_input)
+        self.layout.addRow(self.tr("&Plate Number:"), self.rsl_plate_num)
+        self.layout.addRow(self.tr("&Source Row:"), self.row_letter)
+        self.layout.addRow(self.tr("&Source Column:"), self.column_number)
+        self.layout.addWidget(self.buttonBox)
+        self.setLayout(self.layout)
+
+    def parse_form(self):
+        return dict(plate=self.rsl_plate_num.text(), submitter_id=self.submitter_id_input.text(), well=f"{self.row_letter.currentText()}{self.column_number.currentText()}")
+
+class FirstStrandPlateList(QDialog):
+
+    def __init__(self, ctx:Settings) -> None:
+        super().__init__()
+        self.setWindowTitle("First Strand Plates")
+
+        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+        ww = [item.rsl_plate_num for item in lookup_submissions(ctx=ctx, submission_type="Wastewater")]
+        self.plate1 = QComboBox()
+        self.plate2 = QComboBox()
+        self.plate3 = QComboBox()
+        self.layout = QFormLayout()
+        for ii, plate in enumerate([self.plate1, self.plate2, self.plate3]):
+            plate.addItems(ww)
+            self.layout.addRow(self.tr(f"&Plate {ii+1}:"), plate)
+        self.layout.addWidget(self.buttonBox)
+        self.setLayout(self.layout)
+
+    def parse_form(self):
+        output = []
+        for plate in [self.plate1, self.plate2, self.plate3]:
+            output.append(plate.currentText())
+        return output
+
+
+

src/submissions/frontend/custom_widgets/sub_details.py

@@ -291,8 +291,6 @@ class SubmissionDetails(QDialog):
         btn.setParent(self)
         btn.setFixedWidth(900)
         btn.clicked.connect(self.export)
-        with open("test.html", "w") as f:
-            f.write(self.html)
         
     def export(self):
         """

src/submissions/frontend/main_window_functions.py

@@ -22,10 +22,12 @@ from PyQt6.QtWidgets import (
 )
 from .all_window_functions import select_open_file, select_save_file
 from PyQt6.QtCore import QSignalBlocker
+from backend.db.models import BasicSubmission
 from backend.db.functions import (
     construct_submission_info, lookup_reagents, construct_kit_from_yaml, construct_org_from_yaml, get_control_subtypes,
     update_subsampassoc_with_pcr, check_kit_integrity, update_last_used, lookup_organizations, lookup_kit_types, 
-    lookup_submissions, lookup_controls, lookup_samples, lookup_submission_sample_association, store_object, lookup_submission_type
+    lookup_submissions, lookup_controls, lookup_samples, lookup_submission_sample_association, store_object, lookup_submission_type,
+    get_polymorphic_subclass
 )
 from backend.excel.parser import SheetParser, PCRParser, SampleParser
 from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
@@ -34,10 +36,12 @@ from .custom_widgets.pop_ups import AlertPop, QuestionAsker
 from .custom_widgets import ReportDatePicker
 from .custom_widgets.misc import ImportReagent, ParsedQLabel
 from .visualizations.control_charts import create_charts, construct_html
+from pathlib import Path
+from frontend.custom_widgets.misc import FirstStrandSalvage, FirstStrandPlateList
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
-def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]:
+def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[QMainWindow, dict|None]:
     """
     Import a new submission to the app window
 
@@ -56,7 +60,8 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
     obj.missing_info = []
     
     # set file dialog
-    fname = select_open_file(obj, file_extension="xlsx")
+    if isinstance(fname, bool) or fname == None:
+        fname = select_open_file(obj, file_extension="xlsx")
     logger.debug(f"Attempting to parse file: {fname}")
     if not fname.exists():
         result = dict(message=f"File {fname.__str__()} not found.", status="critical")
@@ -113,7 +118,6 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                 add_widget = QComboBox()
                 # lookup existing kits by 'submission_type' decided on by sheetparser
                 logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
-                # uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
                 uses = [item.__str__() for item in lookup_kit_types(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
                 logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
                 if check_not_nan(value['value']):
@@ -125,7 +129,6 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                     obj.ext_kit = uses[0]
                 # Run reagent scraper whenever extraction kit is changed.
                 add_widget.currentTextChanged.connect(obj.scrape_reagents)
-                # add_widget.addItems(uses)
             case 'submitted_date':
                 # uses base calendar
                 add_widget = QDateEdit(calendarPopup=True)
@@ -221,7 +224,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
     # get current kit being used
     obj.ext_kit = kit_widget.currentText()
     for item in obj.reagents:
-        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':True}, item.type, title=False))
+        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':True}, item.type, title=False, label_name=f"lot_{item.type}"))
         reagent = dict(type=item.type, lot=item.lot, exp=item.exp, name=item.name)
         add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
         obj.table_widget.formlayout.addWidget(add_widget)
@@ -231,7 +234,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
         result = dict(message=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in obj.missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
     for item in obj.missing_reagents:
         # Add label that has parsed as False to show "MISSING" label.
-        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False))
+        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False, label_name=f"missing_{item.type}"))
         # Set default parameters for the empty reagent.
         reagent = dict(type=item.type, lot=None, exp=date.today(), name=None)
         # create and add widget
@@ -896,8 +899,8 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
             logger.debug(f"Attempting: {item['type']}")
             worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
         # Hacky way to pop in 'signed by'
-        if info['submission_type'] == "Bacterial Culture":
-            workbook["Sample List"].cell(row=14, column=2, value=getuser()[0:2].upper())
+    custom_parser = get_polymorphic_subclass(BasicSubmission, info['submission_type'])
+    workbook = custom_parser.custom_autofill(workbook)
     fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")
     workbook.save(filename=fname.__str__())
 
@@ -934,46 +937,63 @@ def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]
     logger.debug(f"Samples: {pformat(samples)}")
     logger.debug("Called first strand sample parser")  
     plates = sprsr.grab_plates()
+    # Fix no plates found in form.
+    if plates == []:
+        dlg = FirstStrandPlateList(ctx=obj.ctx)
+        if dlg.exec():
+            plates = dlg.parse_form()
+    plates = list(set(plates))
     logger.debug(f"Plates: {pformat(plates)}")
     output_samples = []
     logger.debug(f"Samples: {pformat(samples)}")
     old_plate_number = 1
+    old_plate = ''
     for item in samples:
         try:
             item['well'] = re.search(r"\s\((.*)\)$", item['submitter_id']).groups()[0]
         except AttributeError:
-            item['well'] = item
+            pass
         item['submitter_id'] = re.sub(r"\s\(.*\)$", "", str(item['submitter_id'])).strip()
         new_dict = {}
         new_dict['sample'] = item['submitter_id']
-        if item['submitter_id'] == "NTC1":
-            new_dict['destination_row'] = 8
-            new_dict['destination_column'] = 2
-            new_dict['plate_number'] = 'control'
-        elif item['submitter_id'] == "NTC2":
-            new_dict['destination_row'] = 8
-            new_dict['destination_column'] = 5
-            new_dict['plate_number'] = 'control'
-        else:
-            new_dict['destination_row'] = item['row']
-            new_dict['destination_column'] = item['column']
         plate_num, plate = get_plates(input_sample_number=new_dict['sample'], plates=plates)
         if plate_num == None:
             plate_num = str(old_plate_number) + "*"
         else:
             old_plate_number = plate_num
         logger.debug(f"Got plate number: {plate_num}, plate: {plate}")
+        if item['submitter_id'] == "NTC1":
+            new_dict['destination_row'] = 8
+            new_dict['destination_column'] = 2
+            new_dict['plate_number'] = 'control'
+            new_dict['plate'] = None
+            output_samples.append(new_dict)
+            continue
+        elif item['submitter_id'] == "NTC2":
+            new_dict['destination_row'] = 8
+            new_dict['destination_column'] = 5
+            new_dict['plate_number'] = 'control'
+            new_dict['plate'] = None
+            output_samples.append(new_dict)
+            continue
+        else:
+            new_dict['destination_row'] = item['row']
+            new_dict['destination_column'] = item['column']
+            new_dict['plate_number'] = plate_num
+        # Fix plate association not found
         if plate == None:
+            dlg = FirstStrandSalvage(ctx=obj.ctx, submitter_id=item['submitter_id'], rsl_plate_num=old_plate)
+            if dlg.exec():
+                item.update(dlg.parse_form())
             try:
                 new_dict['source_row'], new_dict['source_column'] = convert_well_to_row_column(item['well'])
-                new_dict['plate_number'] = plate_num
             except KeyError:
                 pass
         else:
-            new_dict['plate_number'] = plate_num
             new_dict['plate'] = plate.submission.rsl_plate_num
             new_dict['source_row'] = plate.row
             new_dict['source_column'] = plate.column
+            old_plate = plate.submission.rsl_plate_num
         output_samples.append(new_dict)
     df = pd.DataFrame.from_records(output_samples)
     df.sort_values(by=['destination_column', 'destination_row'], ascending=True, inplace=True)
@@ -1001,6 +1021,7 @@ def scrape_reagents(obj:QMainWindow, extraction_kit:str) -> Tuple[QMainWindow, d
     obj.missing_reagents = []
     # Remove previous reagent widgets
     [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget) if item.objectName().startswith("lot_") or item.objectName().startswith("missing_")]
+    [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QPushButton)]
     reagents = obj.prsr.parse_reagents(extraction_kit=extraction_kit)
     logger.debug(f"Got reagents: {reagents}")
     for reagent in obj.prsr.sub['reagents']:
@@ -1013,5 +1034,3 @@ def scrape_reagents(obj:QMainWindow, extraction_kit:str) -> Tuple[QMainWindow, d
     logger.debug(f"Missing reagents: {obj.missing_reagents}")
     return obj, None
     
-
-