Pre- pydsubmission toForm method.

TODO.md

@@ -1,3 +1,5 @@
+- [ ] Make the kit verifier make more sense.
+- [ ] Slim down the Import and Submit functions in main_window_functions.
 - [x] Create custom store methods for submission, reagent and sample.
 - [x] Make pydantic models for other things that use constructors.
 - [x] Move backend.db.functions.constructor functions into Pydantic models.

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

@@ -138,7 +138,7 @@ def lookup_reagent_types(ctx:Settings,
         assert reagent.type != []
         logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
         logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
-        logger.debug(f"Reagent reagent types: {reagent._sa_instance_state}")
+        # logger.debug(f"Reagent reagent types: {reagent._sa_instance_state}")
         result = list(set(kit_type.reagent_types).intersection(reagent.type))
         logger.debug(f"Result: {result}")
         return result[0]

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

@@ -7,6 +7,7 @@ from sqlalchemy.orm import relationship, validates
 from sqlalchemy.ext.associationproxy import association_proxy
 from datetime import date
 import logging
+from tools import Settings, check_authorization
 
 logger = logging.getLogger(f'submissions.{__name__}')
 
@@ -100,6 +101,11 @@ class KitType(Base):
             map['info'] = {}
         return map
 
+    @check_authorization
+    def save(self, ctx:Settings):
+        ctx.database_session.add(self)
+        ctx.database_session.commit()
+
 class ReagentType(Base):
     """
     Base of reagent type abstract
@@ -265,6 +271,10 @@ class Reagent(Base):
             rtype = reagent_role.name
         except AttributeError:
             rtype = "Unknown"
+        try:
+            expiry = self.expiry.strftime("%Y-%m-%d")
+        except:
+            expiry = date.today()
         return {
             "name":self.name,
             "type": rtype,
@@ -272,6 +282,11 @@ class Reagent(Base):
             "expiry": self.expiry.strftime("%Y-%m-%d")
         }
     
+    def save(self, ctx:Settings):
+        ctx.database_session.add(self)
+        ctx.database_session.commit()
+
+
 class Discount(Base):
     """
     Relationship table for client labs for certain kits.

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

@@ -853,7 +853,6 @@ class WastewaterSample(BasicSample):
             output_dict["submitter_id"] = output_dict['ww_full_sample_id']
         return output_dict
 
-
 class BacterialCultureSample(BasicSample):
     """
     base of bacterial culture sample

src/submissions/backend/excel/parser.py

@@ -112,7 +112,8 @@ class SheetParser(object):
         kit = lookup_kit_types(ctx=self.ctx, name=self.sub['extraction_kit']['value'])
         allowed_reagents = [item.name for item in kit.get_reagents()]
         logger.debug(f"List of reagents for comparison with allowed_reagents: {pprint.pformat(self.sub['reagents'])}")
-        self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent['value'].type in allowed_reagents]
+        # self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent['value'].type in allowed_reagents]
+        self.sub['reagents'] = [reagent for reagent in self.sub['reagents'] if reagent.type in allowed_reagents]
         
     def to_pydantic(self) -> PydSubmission:
         """
@@ -231,8 +232,9 @@ class ReagentParser(object):
                     lot = df.iat[relevant[item]['lot']['row']-1, relevant[item]['lot']['column']-1]
                     expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1]
                 except (KeyError, IndexError):
-                    listo.append(dict(value=PydReagent(ctx=self.ctx, type=item.strip(), lot=None, exp=None, name=None), parsed=False))
+                    listo.append(PydReagent(ctx=self.ctx, type=item.strip(), lot=None, exp=None, name=None, parsed=False))
                     continue
+                # If the cell is blank tell the PydReagent
                 if check_not_nan(lot):
                     parsed = True
                 else:
@@ -240,7 +242,7 @@ class ReagentParser(object):
                 # logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
                 lot = str(lot)
                 logger.debug(f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}")
-                listo.append(dict(value=PydReagent(ctx=self.ctx, type=item.strip(), lot=lot, exp=expiry, name=name), parsed=parsed))
+                listo.append(PydReagent(ctx=self.ctx, type=item.strip(), lot=lot, expiry=expiry, name=name, parsed=parsed))
         logger.debug(f"Returning listo: {listo}")
         return listo
 
@@ -387,7 +389,11 @@ class SampleParser(object):
             # Set row in lookup table to blank values to prevent multipe lookups.
             try:
                 self.lookup_table.loc[self.lookup_table['Sample #']==addition['Sample #']] = np.nan
-            except ValueError:
+            except (ValueError, KeyError):
+                pass
+            try:
+                self.lookup_table.loc[self.lookup_table['Well']==addition['Well']] = np.nan
+            except (ValueError, KeyError):
                 pass
             logger.debug(f"Output sample dict: {sample}")
         logger.debug(f"Final lookup_table: \n\n {self.lookup_table}")

src/submissions/backend/validators/pydant.py

@@ -2,6 +2,7 @@
 Contains pydantic models and accompanying validators
 '''
 import uuid
+from PyQt6 import QtCore
 from pydantic import BaseModel, field_validator, Field
 from datetime import date, datetime, timedelta
 from dateutil.parser import parse
@@ -18,6 +19,7 @@ from backend.db.functions import (lookup_submissions, lookup_reagent_types, look
 )
 from backend.db.models import *
 from sqlalchemy.exc import InvalidRequestError, StatementError
+from PyQt6.QtWidgets import QComboBox, QWidget, QLabel, QVBoxLayout
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -25,8 +27,9 @@ class PydReagent(BaseModel):
     ctx: Settings
     lot: str|None
     type: str|None
-    exp: date|None
+    expiry: date|None
     name: str|None
+    parsed: bool = Field(default=False)
 
     @field_validator("type", mode='before')
     @classmethod
@@ -61,7 +64,7 @@ class PydReagent(BaseModel):
             return value.upper()
         return value
             
-    @field_validator("exp", mode="before")
+    @field_validator("expiry", mode="before")
     @classmethod
     def enforce_date(cls, value):
         if value != None:
@@ -86,7 +89,7 @@ class PydReagent(BaseModel):
         else:
             return values.data['type']
 
-    def toSQL(self):# -> Tuple[Reagent, dict]:
+    def toSQL(self) -> Tuple[Reagent, dict]:
         result = None
         logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
         reagent = lookup_reagents(ctx=self.ctx, lot_number=self.lot)
@@ -113,6 +116,10 @@ class PydReagent(BaseModel):
             # NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
         return reagent, result
 
+    def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
+        from frontend.custom_widgets.misc import ReagentFormWidget
+        return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
+    
 class PydSample(BaseModel, extra='allow'):
 
     submitter_id: str
@@ -127,13 +134,6 @@ class PydSample(BaseModel, extra='allow'):
             return [value]
         return value
     
-    # @field_validator(column)
-    # @classmethod
-    # def column_int_to_list(cls, value):
-    #     if isinstance(value, int):
-    #         return [value]
-    #     return value
-
     def toSQL(self, ctx:Settings, submission):
         result = None
         self.__dict__.update(self.model_extra)
@@ -302,6 +302,22 @@ class PydSubmission(BaseModel, extra='allow'):
             value['value'] = values.data['submission_type']['value']
         return value
 
+    def handle_duplicate_samples(self):
+        submitter_ids = list(set([sample.submitter_id for sample in self.samples]))
+        output = []
+        for id in submitter_ids:
+            relevants = [item for item in self.samples if item.submitter_id==id]
+            if len(relevants) <= 1:
+                output += relevants
+            else:
+                rows = [item.row[0] for item in relevants]
+                columns = [item.column[0] for item in relevants]
+                dummy = relevants[0]
+                dummy.row = rows
+                dummy.column = columns
+                output.append(dummy)
+        self.samples = output
+
     def toSQL(self):
         code = 0
         msg = None
@@ -380,21 +396,7 @@ class PydSubmission(BaseModel, extra='allow'):
         logger.debug(f"Constructed submissions message: {msg}")
         return instance, {'code':code, 'message':msg}
     
-    def handle_duplicate_samples(self):
+    def toForm(self):
-        submitter_ids = list(set([sample.submitter_id for sample in self.samples]))
-        output = []
-        for id in submitter_ids:
-            relevants = [item for item in self.samples if item.submitter_id==id]
-            if len(relevants) <= 1:
-                output += relevants
-            else:
-                rows = [item.row[0] for item in relevants]
-                columns = [item.column[0] for item in relevants]
-                dummy = relevants[0]
-                dummy.row = rows
-                dummy.column = columns
-                output.append(dummy)
-        self.samples = output
 
 class PydContact(BaseModel):
 
@@ -447,19 +449,21 @@ class PydReagentType(BaseModel):
             assoc = None
         if assoc == None:
             assoc = KitTypeReagentTypeAssociation(kit_type=kit, reagent_type=instance, uses=self.uses, required=self.required)
-            kit.kit_reagenttype_associations.append(assoc)
+            # kit.kit_reagenttype_associations.append(assoc)
         return instance
     
 class PydKit(BaseModel):
 
     name: str
-    reagent_types: List[PydReagentType]|None
+    reagent_types: List[PydReagentType] = []
 
     def toSQL(self, ctx):
+        result = dict(message=None, status='Information')
         instance = lookup_kit_types(ctx=ctx, name=self.name)
         if instance == None:
             instance = KitType(name=self.name)
-            instance.reagent_types = [item.toSQL(ctx, instance) for item in self.reagent_types]
+            # instance.reagent_types = [item.toSQL(ctx, instance) for item in self.reagent_types]
-        return instance
+            [item.toSQL(ctx, instance) for item in self.reagent_types]
+        return instance, result
 
 

src/submissions/frontend/__init__.py

@@ -3,23 +3,22 @@ Constructs main application.
 '''
 from pprint import pformat
 import sys
-from typing import Tuple
 from PyQt6.QtWidgets import (
     QMainWindow, QToolBar, 
     QTabWidget, QWidget, QVBoxLayout,
     QComboBox, QHBoxLayout,
     QScrollArea, QLineEdit, QDateEdit
 )
-from PyQt6.QtCore import Qt, pyqtSignal
+from PyQt6.QtCore import pyqtSignal
 from PyQt6.QtGui import QAction
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from pathlib import Path
 from backend.db import (
-    store_object, lookup_control_types, lookup_modes, #construct_reagent
+    lookup_control_types, lookup_modes
 )
 from backend.validators import PydSubmission, PydReagent
 from tools import check_if_app, Settings
-from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker, ImportReagent
+from frontend.custom_widgets import SubmissionsSheet, AlertPop, AddReagentForm, KitAdder, ControlsDatePicker, ImportReagent, ReagentFormWidget
 import logging
 from datetime import date
 import webbrowser
@@ -225,7 +224,9 @@ class App(QMainWindow):
             reagent = PydReagent(ctx=self.ctx, **info)
             # send reagent to db
             # store_reagent(ctx=self.ctx, reagent=reagent)
-            result = store_object(ctx=self.ctx, object=reagent.toSQL()[0])
+            sqlobj, result = reagent.toSQL()
+            sqlobj.save(ctx=self.ctx)
+            # result = store_object(ctx=self.ctx, object=reagent.toSQL()[0])
             self.result_reporter(result=result)
             return reagent
 
@@ -320,7 +321,7 @@ class App(QMainWindow):
 
 class AddSubForm(QWidget):
     
-    def __init__(self, parent):
+    def __init__(self, parent:QWidget):
         logger.debug(f"Initializating subform...")
         super(QWidget, self).__init__(parent)
         self.layout = QVBoxLayout(self)
@@ -337,7 +338,7 @@ class AddSubForm(QWidget):
         self.tabs.addTab(self.tab2,"Controls")
         self.tabs.addTab(self.tab3, "Add Kit")
         # Create submission adder form
-        self.formwidget = SubmissionFormWidget(self)
+        self.formwidget = SubmissionFormContainer(self)
         self.formlayout = QVBoxLayout(self)
         self.formwidget.setLayout(self.formlayout)
         self.formwidget.setFixedWidth(300)
@@ -391,7 +392,7 @@ class AddSubForm(QWidget):
         self.layout.addWidget(self.tabs)
         self.setLayout(self.layout)
 
-class SubmissionFormWidget(QWidget):
+class SubmissionFormContainer(QWidget):
 
     import_drag = pyqtSignal(Path)
 
@@ -399,9 +400,7 @@ class SubmissionFormWidget(QWidget):
         logger.debug(f"Setting form widget...")
         super().__init__(parent)
         self.parent = 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):
@@ -414,6 +413,10 @@ class SubmissionFormWidget(QWidget):
         fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
         self.import_drag.emit(fname)
 
+    def clear_form(self):
+        for item in self.findChildren(QWidget):
+            item.setParent(None)
+
     def parse_form(self) -> PydSubmission:
         logger.debug(f"Hello from form parser!")
         info = {}
@@ -421,11 +424,15 @@ class SubmissionFormWidget(QWidget):
         samples = self.parent.parent.samples
         logger.debug(f"Using samples: {pformat(samples)}")
         widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
+        # widgets = [widget for widget in self.findChildren(QWidget)]
         for widget in widgets:
             logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)}")
             match widget:
+                case ReagentFormWidget():
+                    reagent, _ = widget.parse_form()
+                    reagents.append(reagent)
                 case ImportReagent():
-                    reagent = dict(name=widget.objectName().replace("lot_", ""), lot=widget.currentText(), type=None, exp=None)
+                    reagent = dict(name=widget.objectName().replace("lot_", ""), lot=widget.currentText(), type=None, expiry=None)
                     reagents.append(PydReagent(ctx=self.parent.parent.ctx, **reagent))
                 case QLineEdit():
                     info[widget.objectName()] = dict(value=widget.text())
@@ -435,5 +442,6 @@ class SubmissionFormWidget(QWidget):
                     info[widget.objectName()] = dict(value=widget.date().toPyDate())
         logger.debug(f"Info: {pformat(info)}")
         logger.debug(f"Reagents: {pformat(reagents)}")
+        # sys.exit("Hi Landon. Check the reagents! frontend.__init__ line 442")
         submission = PydSubmission(ctx=self.parent.parent.ctx, filepath=self.parent.parent.current_file, reagents=reagents, samples=samples, **info)
         return submission

src/submissions/frontend/custom_widgets/misc.py

@@ -20,9 +20,10 @@ from backend.db.models import SubmissionTypeKitTypeAssociation
 from sqlalchemy import FLOAT, INTEGER
 import logging
 import numpy as np
-from .pop_ups import AlertPop
+from .pop_ups import AlertPop, QuestionAsker
-from backend.validators import PydReagent
+from backend.validators import PydReagent, PydKit, PydReagentType, PydSubmission
 from typing import Tuple
+from pprint import pformat
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -92,7 +93,7 @@ class AddReagentForm(QDialog):
     def parse_form(self):
         return dict(name=self.name_input.currentText(), 
                     lot=self.lot_input.text(), 
-                    exp=self.exp_input.date().toPyDate(),
+                    expiry=self.exp_input.date().toPyDate(),
                     type=self.type_input.currentText())
 
     def update_names(self):
@@ -242,21 +243,22 @@ class KitAdder(QWidget):
         logger.debug(f"kit info: {pformat(info)}")
         logger.debug(f"kit reagents: {pformat(reagents)}")
         info['reagent_types'] = reagents
-        # for reagent in reagents:
-        #     new_dict = {}
-        #     for k,v in reagent.items():
-        #         if "_" in k:
-        #             key, sub_key = k.split("_")
-        #             if key not in new_dict.keys():
-        #                 new_dict[key] = {}
-        #             logger.debug(f"Adding key {key}, {sub_key} and value {v} to {new_dict}")
-        #             new_dict[key][sub_key] = v
-        #         else:
-        #             new_dict[k] = v
-        #     info['reagent_types'].append(new_dict)
         logger.debug(pformat(info))
         # send to kit constructor
-        result = construct_kit_from_yaml(ctx=self.ctx, kit_dict=info)
+        kit = PydKit(name=info['kit_name'])
+        for reagent in info['reagent_types']:
+            uses = {
+                info['used_for']:
+                    {'sheet':reagent['sheet'],
+                     'name':reagent['name'],
+                     'lot':reagent['lot'],
+                     'expiry':reagent['expiry']
+                    }}
+            kit.reagent_types.append(PydReagentType(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
+        logger.debug(f"Output pyd object: {kit.__dict__}")
+        # result = construct_kit_from_yaml(ctx=self.ctx, kit_dict=info)
+        sqlobj, result = kit.toSQL(self.ctx)
+        sqlobj.save(ctx=self.ctx)
         msg = AlertPop(message=result['message'], status=result['status'])
         msg.exec()
         self.__init__(self.ctx)
@@ -521,5 +523,149 @@ class FirstStrandPlateList(QDialog):
             output.append(plate.currentText())
         return output
 
+class ReagentFormWidget(QWidget):
+
+    def __init__(self, parent:QWidget, reagent:PydReagent, extraction_kit:str):
+        super().__init__()
+        self.setParent(parent)
+        logger.debug(f"Reagent form widget parent is: {self.parent()}")
+        logger.debug(f"It's great grandparent is {self.parent().parent.parent} which has a method [add_reagent]: {hasattr(self.parent().parent.parent, 'add_reagent')}")
+        self.reagent = reagent
+        self.extraction_kit = extraction_kit
+        self.ctx = reagent.ctx
+        layout = QVBoxLayout()
+        self.label = self.ReagentParsedLabel(reagent=reagent)
+        layout.addWidget(self.label)
+        self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
+        layout.addWidget(self.lot)
+        self.setLayout(layout)
+        self.setObjectName(reagent.name)
+        self.missing = not reagent.parsed
+
+    def parse_form(self) -> Tuple[PydReagent, dict]:
+        lot = self.lot.currentText()
+        # type = self.label.text().replace("_label")
+        wanted_reagent = lookup_reagents(ctx=self.ctx, lot_number=lot, reagent_type=self.reagent.type)
+        if wanted_reagent == None:
+            dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
+            if dlg.exec():
+                # logger.debug(f"Looking through {pformat(self.parent.reagents)} for reagent {reagent.name}")
+                # try:
+                #     picked_reagent = [item for item in obj.reagents if item.type == reagent.name][0]
+                # except IndexError:
+                #     logger.error(f"Couldn't find {reagent.name} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
+                #     picked_reagent = [item for item in obj.missing_reagents if item.type == reagent.name][0]
+                # logger.debug(f"checking reagent: {reagent.name} in obj.reagents. Result: {picked_reagent}")
+                # expiry_date = picked_reagent.expiry
+                wanted_reagent = self.parent().parent.parent.add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
+                return wanted_reagent, None
+            else:
+                # In this case we will have an empty reagent and the submission will fail kit integrity check
+                logger.debug("Will not add reagent.")
+                return None, dict(message="Failed integrity check", status="critical")
+        else:
+            rt = lookup_reagent_types(ctx=self.ctx, kit_type=self.extraction_kit, reagent=wanted_reagent)
+            return PydReagent(ctx=self.ctx, name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None
 
 
+    class ReagentParsedLabel(QLabel):
+        
+        def __init__(self, reagent:PydReagent):
+            super().__init__()
+            try:
+                check = reagent.parsed
+            except:
+                return
+            self.setObjectName(f"{reagent.type}_label")
+            if check:
+                self.setText(f"Parsed {reagent.type}")
+            else:
+                self.setText(f"MISSING {reagent.type}")
+
+    class ReagentLot(QComboBox):
+
+        def __init__(self, reagent, extraction_kit:str) -> None:
+            super().__init__()
+            self.ctx = reagent.ctx
+            self.setEditable(True)
+            if reagent.parsed:
+                pass
+            logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
+            # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
+            lookup = lookup_reagents(ctx=self.ctx, reagent_type=reagent.type)
+            relevant_reagents = [item.__str__() for item in lookup]
+            output_reg = []
+            for rel_reagent in relevant_reagents:
+            # 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
+            # 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:
+                    # TODO: look up the last used reagent of this type in the database
+                    looked_up_rt = lookup_reagenttype_kittype_association(ctx=self.ctx, reagent_type=reagent.type, kit_type=extraction_kit)
+                    looked_up_reg = lookup_reagents(ctx=self.ctx, lot_number=looked_up_rt.last_used)
+                    logger.debug(f"Because there was no reagent listed for {reagent}, we will insert the last lot used: {looked_up_reg}")
+                    if looked_up_reg != None:
+                        relevant_reagents.remove(str(looked_up_reg.lot))
+                        relevant_reagents.insert(0, str(looked_up_reg.lot))
+            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.")
+            logger.debug(f"New relevant reagents: {relevant_reagents}")
+            self.setObjectName(f"lot_{reagent.type}")
+            self.addItems(relevant_reagents)
+
+class SubmissionFormWidget(QWidget):
+
+    def __init__(self, parent: QWidget) -> None:
+        super().__init__(parent)
+        self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
+                       "qt_scrollarea_vcontainer", "submit_btn"
+                       ]
+        
+    def clear_form(self):
+        for item in self.findChildren(QWidget):
+            item.setParent(None)
+
+    def parse_form(self) -> PydSubmission:
+        logger.debug(f"Hello from form parser!")
+        info = {}
+        reagents = []
+        samples = self.parent.parent.samples
+        logger.debug(f"Using samples: {pformat(samples)}")
+        widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
+        # widgets = [widget for widget in self.findChildren(QWidget)]
+        for widget in widgets:
+            logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)}")
+            match widget:
+                case ReagentFormWidget():
+                    reagent, _ = widget.parse_form()
+                    reagents.append(reagent)
+                case ImportReagent():
+                    reagent = dict(name=widget.objectName().replace("lot_", ""), lot=widget.currentText(), type=None, expiry=None)
+                    reagents.append(PydReagent(ctx=self.parent.parent.ctx, **reagent))
+                case QLineEdit():
+                    info[widget.objectName()] = dict(value=widget.text())
+                case QComboBox():
+                    info[widget.objectName()] = dict(value=widget.currentText())
+                case QDateEdit():
+                    info[widget.objectName()] = dict(value=widget.date().toPyDate())
+        logger.debug(f"Info: {pformat(info)}")
+        logger.debug(f"Reagents: {pformat(reagents)}")
+        # sys.exit("Hi Landon. Check the reagents! frontend.__init__ line 442")
+        submission = PydSubmission(ctx=self.parent.parent.ctx, filepath=self.parent.parent.current_file, reagents=reagents, samples=samples, **info)
+        return submission

src/submissions/frontend/custom_widgets/sub_details.py

@@ -393,7 +393,6 @@ class BarcodeWindow(QDialog):
         painter.drawPixmap(120, -20, image)
         painter.end()
         
-
 class SubmissionComment(QDialog):
     """
     a window for adding comment text to a submission

src/submissions/frontend/main_window_functions.py

@@ -38,7 +38,7 @@ 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
+from frontend.custom_widgets.misc import FirstStrandSalvage, FirstStrandPlateList, ReagentFormWidget
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -78,8 +78,7 @@ def import_submission_function(obj:QMainWindow, fname:Path|None=None) -> Tuple[Q
     except Exception as e:
         return obj, dict(message= f"Problem creating pydantic model:\n\n{e}", status="critical")
     # destroy any widgets from previous imports
-    for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
+    obj.table_widget.formwidget.clear_form()
-        item.setParent(None)
     obj.current_submission_type = pyd.submission_type['value']
     obj.current_file = pyd.filepath
     # Get list of fields from pydantic model.
@@ -216,24 +215,26 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
     logger.debug(f"Kit selector: {kit_widget}")
     # get current kit being used
     obj.ext_kit = kit_widget.currentText()
-    for item in obj.reagents:
+    for reagent in obj.reagents:
-        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':True}, item.type, title=False, label_name=f"lot_{item.type}"))
+        # 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)
+        # reagent = dict(type=item.type, lot=item.lot, expiry=item.expiry, name=item.name)
-        add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
+        # add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
+        # obj.table_widget.formlayout.addWidget(add_widget)
+        add_widget = ReagentFormWidget(parent=obj.table_widget.formwidget, reagent=reagent, extraction_kit=obj.ext_kit)
         obj.table_widget.formlayout.addWidget(add_widget)
     logger.debug(f"Checking integrity of {obj.ext_kit}")
     # see if there are any missing reagents
     if len(obj.missing_reagents) > 0:
         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:
+    # for item in obj.missing_reagents:
-        # Add label that has parsed as False to show "MISSING" label.
+    #     # Add label that has parsed as False to show "MISSING" label.
-        obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False, label_name=f"missing_{item.type}"))
+    #     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.
+    #     # Set default parameters for the empty reagent.
-        reagent = dict(type=item.type, lot=None, exp=date.today(), name=None)
+    #     reagent = dict(type=item.type, lot=None, expiry=date.today(), name=None)
-        # create and add widget
+    #     # create and add widget
-        # add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)
+    #     # add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)
-        add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
+    #     add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent, extraction_kit=obj.ext_kit)
-        obj.table_widget.formlayout.addWidget(add_widget)
+    #     obj.table_widget.formlayout.addWidget(add_widget)
     # Add submit button to the form.
     submit_btn = QPushButton("Submit")
     submit_btn.setObjectName("submit_btn")
@@ -264,34 +265,34 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     # info, reagents = obj.table_widget.formwidget.parse_form()
     submission: PydSubmission = obj.table_widget.formwidget.parse_form()
     logger.debug(f"Submission: {pprint.pformat(submission)}")
-    parsed_reagents = []
+    # parsed_reagents = []
     # compare reagents in form to reagent database
-    for reagent in submission.reagents:
+    # for reagent in submission.reagents:
-        # Lookup any existing reagent of this type with this lot number
+    #     # Lookup any existing reagent of this type with this lot number
-        wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagent.lot, reagent_type=reagent.name)
+    #     wanted_reagent = lookup_reagents(ctx=obj.ctx, lot_number=reagent.lot, reagent_type=reagent.name)
-        logger.debug(f"Looked up reagent: {wanted_reagent}")
+    #     logger.debug(f"Looked up reagent: {wanted_reagent}")
-        # if reagent not found offer to add to database
+    #     # if reagent not found offer to add to database
-        if wanted_reagent == None:
+    #     if wanted_reagent == None:
-            # r_lot = reagent[reagent]
+    #         # r_lot = reagent[reagent]
-            dlg = QuestionAsker(title=f"Add {reagent.lot}?", message=f"Couldn't find reagent type {reagent.name.strip('Lot')}: {reagent.lot} in the database.\n\nWould you like to add it?")
+    #         dlg = QuestionAsker(title=f"Add {reagent.lot}?", message=f"Couldn't find reagent type {reagent.name.strip('Lot')}: {reagent.lot} in the database.\n\nWould you like to add it?")
-            if dlg.exec():
+    #         if dlg.exec():
-                logger.debug(f"Looking through {pprint.pformat(obj.reagents)} for reagent {reagent.name}")
+    #             logger.debug(f"Looking through {pprint.pformat(obj.reagents)} for reagent {reagent.name}")
-                try:
+    #             try:
-                    picked_reagent = [item for item in obj.reagents if item.type == reagent.name][0]
+    #                 picked_reagent = [item for item in obj.reagents if item.type == reagent.name][0]
-                except IndexError:
+    #             except IndexError:
-                    logger.error(f"Couldn't find {reagent.name} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
+    #                 logger.error(f"Couldn't find {reagent.name} in obj.reagents. Checking missing reagents {pprint.pformat(obj.missing_reagents)}")
-                    picked_reagent = [item for item in obj.missing_reagents if item.type == reagent.name][0]
+    #                 picked_reagent = [item for item in obj.missing_reagents if item.type == reagent.name][0]
-                logger.debug(f"checking reagent: {reagent.name} in obj.reagents. Result: {picked_reagent}")
+    #             logger.debug(f"checking reagent: {reagent.name} in obj.reagents. Result: {picked_reagent}")
-                expiry_date = picked_reagent.exp
+    #             expiry_date = picked_reagent.expiry
-                wanted_reagent = obj.add_reagent(reagent_lot=reagent.lot, reagent_type=reagent.name.replace("lot_", ""), expiry=expiry_date, name=picked_reagent.name)
+    #             wanted_reagent = obj.add_reagent(reagent_lot=reagent.lot, reagent_type=reagent.name.replace("lot_", ""), expiry=expiry_date, name=picked_reagent.name)
-            else:
+    #         else:
-                # In this case we will have an empty reagent and the submission will fail kit integrity check
+    #             # In this case we will have an empty reagent and the submission will fail kit integrity check
-                logger.debug("Will not add reagent.")
+    #             logger.debug("Will not add reagent.")
-                return obj, dict(message="Failed integrity check", status="critical")
+    #             return obj, dict(message="Failed integrity check", status="critical")
-        # Append the PydReagent object o be added to the submission
+    #     # Append the PydReagent object o be added to the submission
-        parsed_reagents.append(reagent)
+    #     parsed_reagents.append(reagent)
-    # move samples into preliminary submission dict
+    # # move samples into preliminary submission dict
-    submission.reagents = parsed_reagents
+    # submission.reagents = parsed_reagents
     # submission.uploaded_by = getuser()
     # construct submission object
     # logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
@@ -1020,16 +1021,17 @@ def scrape_reagents(obj:QMainWindow, extraction_kit:str) -> Tuple[QMainWindow, d
     obj.reagents = []
     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(QWidget) if item.objectName().startswith("lot_") or item.objectName().startswith("missing_")]
-    [item.setParent(None) for item in obj.table_widget.formlayout.parentWidget().findChildren(QPushButton)]
+    # [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']:
+    # for reagent in obj.prsr.sub['reagents']:
-        # create label
+    #     # create label
-        if reagent['parsed']:
+    #     if reagent.parsed:
-            obj.reagents.append(reagent['value'])
+    #         obj.reagents.append(reagent)
-        else:
+    #     else:
-            obj.missing_reagents.append(reagent['value'])
+    #         obj.missing_reagents.append(reagent)
+    obj.reagents = obj.prsr.sub['reagents']
     logger.debug(f"Imported reagents: {obj.reagents}")
     logger.debug(f"Missing reagents: {obj.missing_reagents}")
     return obj, None

src/submissions/tools/__init__.py

@@ -65,6 +65,8 @@ def check_not_nan(cell_contents) -> bool:
         cell_contents = np.nan
     if cell_contents == None:
         cell_contents = np.nan
+    if str(cell_contents).lower() == "none":
+        cell_contents = np.nan
     try:
         if pd.isnull(cell_contents):
             cell_contents = np.nan