mid refactor for improved rebustness and readability

src/submissions/frontend/__init__.py

@@ -1,12 +1,11 @@
 import json
 import re
-from typing import Tuple
 from PyQt6.QtWidgets import (
     QMainWindow, QLabel, QToolBar, 
     QTabWidget, QWidget, QVBoxLayout,
     QPushButton, QFileDialog,
     QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
-    QSpinBox, QScrollArea
+    QScrollArea
 )
 from PyQt6.QtGui import QAction
 from PyQt6.QtCore import QSignalBlocker
@@ -27,15 +26,13 @@ from backend.db import (construct_submission_info, lookup_reagent,
     lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
     get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
     get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num,
-    create_org_from_yaml
+    create_org_from_yaml, store_reagent
 )
 from backend.db import lookup_kittype_by_name
 
 from .functions import check_kit_integrity
-from tools import check_not_nan
+from tools import check_not_nan, extract_form_info
 from backend.excel.reports import make_report_xlsx, make_report_html
-
-import numpy
 from frontend.custom_widgets.sub_details import SubmissionsSheet
 from frontend.custom_widgets.pop_ups import AlertPop, QuestionAsker
 from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
@@ -233,12 +230,18 @@ class App(QMainWindow):
                     # hold samples in 'self' until form submitted
                     logger.debug(f"{item}: {prsr.sub[item]}")
                     self.samples = prsr.sub[item]
+                    add_widget = None
                 case _:
                     # anything else gets added in as a line edit
                     self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     add_widget = QLineEdit()
                     add_widget.setText(str(prsr.sub[item]).replace("_", " "))
-            self.table_widget.formlayout.addWidget(add_widget)
+            try:
+                add_widget.setObjectName(item)
+                logger.debug(f"Widget name set to: {add_widget.objectName()}")
+                self.table_widget.formlayout.addWidget(add_widget)
+            except AttributeError as e:
+                logger.error(e)
         # compare self.reagents with expected reagents in kit
         if hasattr(self, 'ext_kit'):
             kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
@@ -261,9 +264,10 @@ class App(QMainWindow):
         Attempt to add sample to database when 'submit' button clicked
         """        
         # get info from form
-        labels, values = self.extract_form_info(self.table_widget.tab1)
-        info = {item[0]:item[1] for item in zip(labels, values) if not item[0].startswith("lot_")}
-        reagents = {item[0]:item[1] for item in zip(labels, values) if item[0].startswith("lot_")}
+        info = extract_form_info(self.table_widget.tab1)
+        reagents = {k:v for k,v in info.items() if k.startswith("lot_")}
+        info = {k:v for k,v in info.items() if not k.startswith("lot_")}
+        logger.debug(f"Info: {info}")
         logger.debug(f"Reagents: {reagents}")
         parsed_reagents = []
         # compare reagents in form to reagent database
@@ -308,7 +312,6 @@ class App(QMainWindow):
         # add reagents to submission object
         for reagent in parsed_reagents:
             base_submission.reagents.append(reagent)
-            # base_submission.reagents_id = reagent.id
         logger.debug("Checking kit integrity...")
         kit_integrity = check_kit_integrity(base_submission)
         if kit_integrity != None:
@@ -317,7 +320,7 @@ class App(QMainWindow):
             return
         logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
         result = store_submission(ctx=self.ctx, base_submission=base_submission)
-        # # check result of storing for issues
+        # check result of storing for issues
         if result != None:
             msg = AlertPop(result['message'])
             msg.exec()
@@ -345,48 +348,17 @@ class App(QMainWindow):
         dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry)
         if dlg.exec():
             # extract form info
-            labels, values = self.extract_form_info(dlg)
-            info = {item[0]:item[1] for item in zip(labels, values)}
+            info = extract_form_info(dlg)
+            logger.debug(f"dictionary from form: {info}")
+            # return None
             logger.debug(f"Reagent info: {info}")
             # create reagent object
             reagent = construct_reagent(ctx=self.ctx, info_dict=info)
             # send reagent to db
-            # store_reagent(ctx=self.ctx, reagent=reagent)
+            store_reagent(ctx=self.ctx, reagent=reagent)
             return reagent
             
 
-    def extract_form_info(self, object) -> Tuple[list, list]:
-        """
-        retrieves arbitrary number of labels, values from form
-
-        Args:
-            object (_type_): the form widget
-
-        Returns:
-            _type_: _description_
-        """        
-        labels = []
-        values = []
-        # grab all widgets in form
-        prev_item = None
-        for item in object.layout.parentWidget().findChildren(QWidget):
-            match item:
-                case QLabel():
-                    labels.append(item.text().replace(" ", "_").lower())
-                case QLineEdit():
-                    # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
-                    if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox):
-                        logger.debug(f"Previous: {prev_item}")
-                        logger.debug(f"Item: {item}")
-                        values.append(item.text())
-                case QComboBox():
-                    values.append(item.currentText())
-                case QDateEdit():
-                    values.append(item.date().toPyDate())
-            # value for ad hoc check above
-            prev_item = item
-        return labels, values
-
     def generateReport(self):
         """
         Action to create a summary of sheet data per client
@@ -394,8 +366,10 @@ class App(QMainWindow):
         # Custom two date picker for start & end dates
         dlg = ReportDatePicker()
         if dlg.exec():
-            labels, values = self.extract_form_info(dlg)
-            info = {item[0]:item[1] for item in zip(labels, values)}
+            # labels, values = extract_form_info(dlg)
+            # info = {item[0]:item[1] for item in zip(labels, values)}
+            info = extract_form_info(dlg)
+            logger.debug(f"Report info: {info}")
             # find submissions based on date range
             subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
             # convert each object to dict
@@ -404,7 +378,7 @@ class App(QMainWindow):
             html = make_report_html(df=df, start_date=info['start_date'], end_date=info['end_date'])
             # make dataframe from record dictionaries
             # df = make_report_xlsx(records=records)
-            # # setup filedialog to handle save location of report
+            # setup filedialog to handle save location of report
             home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
             # fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
             fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])

src/submissions/frontend/custom_widgets/__init__.py

@@ -5,12 +5,11 @@ from PyQt6.QtWidgets import (
     QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
     QGridLayout, QPushButton, QSpinBox,
     QScrollBar, QHBoxLayout,
-    QMessageBox
 )
 from PyQt6.QtCore import Qt, QDate, QSize
-# from PyQt6.QtGui import QFontMetrics, QAction
-from tools import check_not_nan
-from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name
+# from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
+from tools import check_not_nan, extract_form_info
+from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name, lookup_regent_by_type_name_and_kit_name
 from backend.excel.parser import SheetParser
 from jinja2 import Environment, FileSystemLoader
 import sys
@@ -46,18 +45,19 @@ class AddReagentForm(QDialog):
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
-        # get lot info
+        # widget to get lot info
         lot_input = QLineEdit()
         lot_input.setObjectName("lot")
         lot_input.setText(reagent_lot)
-        # get expiry info
+        # widget to get expiry info
         exp_input = QDateEdit(calendarPopup=True)
         exp_input.setObjectName('expiry')
+        # if expiry is not passed in from gui, use today
         if expiry == None:
             exp_input.setDate(QDate.currentDate())
         else:
             exp_input.setDate(expiry)
-        # get reagent type info
+        # widget to get reagent type info
         type_input = QComboBox()
         type_input.setObjectName('type')
         type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
@@ -97,8 +97,10 @@ class ReportDatePicker(QDialog):
         self.buttonBox.rejected.connect(self.reject)
         # widgets to ask for dates 
         start_date = QDateEdit(calendarPopup=True)
+        start_date.setObjectName("start_date")
         start_date.setDate(QDate.currentDate())
         end_date = QDateEdit(calendarPopup=True)
+        end_date.setObjectName("end_date")
         end_date.setDate(QDate.currentDate())
         self.layout = QVBoxLayout()
         self.layout.addWidget(QLabel("Start Date"))
@@ -121,28 +123,34 @@ class KitAdder(QWidget):
         # insert submit button at top
         self.submit_btn = QPushButton("Submit")
         self.grid.addWidget(self.submit_btn,0,0,1,1)
-        # need to exclude ordinary users to mitigate garbage database entries
-        # self.grid.addWidget(QLabel("Password:"),1,0)
-        # self.grid.addWidget(QLineEdit(),1,1)
         self.grid.addWidget(QLabel("Kit Name:"),2,0)
-        self.grid.addWidget(QLineEdit(),2,1)
+        # widget to get kit name
+        kit_name = QLineEdit()
+        kit_name.setObjectName("kit_name")
+        self.grid.addWidget(kit_name,2,1)
         self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
+        # widget to get uses of kit
         used_for = QComboBox()
+        used_for.setObjectName("used_for")
         # Insert all existing sample types
         used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
         used_for.setEditable(True)
         self.grid.addWidget(used_for,3,1)
         # set cost per run
         self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
-        cost = QSpinBox()
-        cost.setMinimum(0)
-        cost.setMaximum(9999)
-        self.grid.addWidget(cost,4,1)
+        # widget to get constant cost
+        const_cost = QSpinBox()
+        const_cost.setObjectName("const_cost")
+        const_cost.setMinimum(0)
+        const_cost.setMaximum(9999)
+        self.grid.addWidget(const_cost,4,1)
         self.grid.addWidget(QLabel("Mutable cost per full plate (tips, reagents, etc.):"),5,0)
-        cost = QSpinBox()
-        cost.setMinimum(0)
-        cost.setMaximum(9999)
-        self.grid.addWidget(cost,5,1)
+        # widget to get mutable costs
+        mut_cost = QSpinBox()
+        mut_cost.setObjectName("mut_cost")
+        mut_cost.setMinimum(0)
+        mut_cost.setMaximum(9999)
+        self.grid.addWidget(mut_cost,5,1)
         # button to add additional reagent types
         self.add_RT_btn = QPushButton("Add Reagent Type")
         self.grid.addWidget(self.add_RT_btn)
@@ -153,8 +161,11 @@ class KitAdder(QWidget):
         """
         insert new reagent type row
         """        
+        # get bottommost row
         maxrow = self.grid.rowCount()
-        self.grid.addWidget(ReagentTypeForm(parent_ctx=self.ctx), maxrow + 1,0,1,2)
+        reg_form = ReagentTypeForm(parent_ctx=self.ctx)
+        reg_form.setObjectName(f"ReagentForm_{maxrow}")
+        self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
 
 
     def submit(self) -> None:
@@ -162,80 +173,65 @@ class KitAdder(QWidget):
         send kit to database
         """        
         # get form info
-        labels, values, reagents = self.extract_form_info(self)
-        info = {item[0]:item[1] for item in zip(labels, values)}
-        logger.debug(info)
+        info, reagents = extract_form_info(self)
+        logger.debug(f"kit info: {info}")
         yml_type = {}
         try:
             yml_type['password'] = info['password']
         except KeyError:
             pass
-        used = info['used_for_sample_type'].replace(" ", "_").lower()
+        used = info['used_for'].replace(" ", "_").lower()
         yml_type[used] = {}
         yml_type[used]['kits'] = {}
         yml_type[used]['kits'][info['kit_name']] = {}
-        yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["Constant cost per full plate (plates, work hours, etc.)"]
-        yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["Mutable cost per full plate (tips, reagents, etc.)"]
+        yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["const_cost"]
+        yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["mut_cost"]
         yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
         logger.debug(yml_type)
         # send to kit constructor
         result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
-        # result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
         msg = AlertPop(message=result['message'], status=result['status'])
-        # match result['code']:
-        #     case 0:
-        #         msg = AlertPop(message=result['message'], status="information")
-        #         # msg.setText()
-        #         # msg.setInformativeText(result['message'])
-        #         # msg.setWindowTitle("Kit added")
-        #     case 1:
-        #         msg = AlertPop(m)
-        #         msg.setText("Permission Error")
-        #         msg.setInformativeText(result['message'])
-        #         msg.setWindowTitle("Permission Error")
         msg.exec()
 
-    def extract_form_info(self, object):
-        """
-        retrieves arbitrary number of labels, values from form
-
-        Args:
-            object (_type_): the object to extract info from
-
-        Returns:
-            _type_: _description_
-        """
-        labels = []
-        values = []
-        reagents = {}
-        for item in object.findChildren(QWidget):
-            logger.debug(item.parentWidget())
-            # if not isinstance(item.parentWidget(), ReagentTypeForm):
-            match item:
-                case QLabel():
-                    labels.append(item.text().replace(" ", "_").strip(":").lower())
-                case QLineEdit():
-                    # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
-                    if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
-                        logger.debug(f"Previous: {prev_item}")
-                        logger.debug(f"Item: {item}, {item.text()}")
-                        values.append(item.text().strip())
-                case QComboBox():
-                    values.append(item.currentText().strip())
-                case QDateEdit():
-                    values.append(item.date().toPyDate())
-                case QSpinBox():
-                    values.append(item.value())
-                case ReagentTypeForm():
-                    re_labels, re_values, _ = self.extract_form_info(item) 
-                    reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
-                    logger.debug(reagent)
-                    # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
-                    reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
-            prev_item = item
-        return labels, values, reagents
+    # def extract_form_info(self, object):
+    #     """
+    #     retrieves arbitrary number of labels, values from form
 
+    #     Args:
+    #         object (_type_): the object to extract info from
 
+    #     Returns:
+    #         _type_: _description_
+    #     """
+    #     labels = []
+    #     values = []
+    #     reagents = {}
+    #     for item in object.findChildren(QWidget):
+    #         logger.debug(item.parentWidget())
+    #         # if not isinstance(item.parentWidget(), ReagentTypeForm):
+    #         match item:
+    #             case QLabel():
+    #                 labels.append(item.text().replace(" ", "_").strip(":").lower())
+    #             case QLineEdit():
+    #                 # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
+    #                 if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
+    #                     logger.debug(f"Previous: {prev_item}")
+    #                     logger.debug(f"Item: {item}, {item.text()}")
+    #                     values.append(item.text().strip())
+    #             case QComboBox():
+    #                 values.append(item.currentText().strip())
+    #             case QDateEdit():
+    #                 values.append(item.date().toPyDate())
+    #             case QSpinBox():
+    #                 values.append(item.value())
+    #             case ReagentTypeForm():
+    #                 re_labels, re_values, _ = self.extract_form_info(item) 
+    #                 reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
+    #                 logger.debug(reagent)
+    #                 # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
+    #                 reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
+    #         prev_item = item
+    #     return labels, values, reagents
 
 class ReagentTypeForm(QWidget):
     """
@@ -246,14 +242,17 @@ class ReagentTypeForm(QWidget):
         grid = QGridLayout()
         self.setLayout(grid)
         grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
+        # Widget to get reagent info
         reagent_getter = QComboBox()
+        reagent_getter.setObjectName("name")
         # lookup all reagent type names from db
         reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))
         reagent_getter.setEditable(True)
         grid.addWidget(reagent_getter,0,1)
         grid.addWidget(QLabel("Extension of Life (months):"),0,2)
-        # get extension of life
+        # widget toget extension of life
         eol = QSpinBox()
+        eol.setObjectName('eol')
         eol.setMinimum(0)
         grid.addWidget(eol, 0,3)
 
@@ -277,7 +276,6 @@ class ControlsDatePicker(QWidget):
         self.layout.addWidget(self.start_date)
         self.layout.addWidget(QLabel("End Date"))
         self.layout.addWidget(self.end_date)
-        
         self.setLayout(self.layout)
         self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
 
@@ -304,15 +302,17 @@ class ImportReagent(QComboBox):
         logger.debug(f"Attempting lookup of reagents by type: {query_var}")
         # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
         relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
+        # relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
         output_reg = []
         for reagent in relevant_reagents:
+            # extract strings from any sets.
             if isinstance(reagent, set):
                 for thing in reagent:
                     output_reg.append(thing)
             elif isinstance(reagent, str):
                 output_reg.append(reagent)
         relevant_reagents = output_reg
-        # if reagent in sheet is not found insert it into items
+        # if reagent in sheet is not found insert it into the front of relevant reagents so it shows 
         if prsr != None:
             logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
             if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':

src/submissions/frontend/custom_widgets/pop_ups.py

@@ -1,12 +1,7 @@
-# from datetime import date
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout, QDialog, 
     QDialogButtonBox, QMessageBox
 )
-# from PyQt6.QtCore import Qt, QDate, QSize
-# from PyQt6.QtGui import QFontMetrics, QAction
-
-# from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml
 from jinja2 import Environment, FileSystemLoader
 import sys
 from pathlib import Path
@@ -14,6 +9,7 @@ import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
+# determine if pyinstaller launcher is being used
 if getattr(sys, 'frozen', False):
     loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
 else:
@@ -22,50 +18,6 @@ loader = FileSystemLoader(loader_path)
 env = Environment(loader=loader)
 
 
-# class AddReagentQuestion(QDialog):
-#     """
-#     dialog to ask about adding a new reagne to db
-#     """    
-#     def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
-#         super().__init__()
-
-#         self.setWindowTitle(f"Add {reagent_lot}?")
-
-#         QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
-
-#         self.buttonBox = QDialogButtonBox(QBtn)
-#         self.buttonBox.accepted.connect(self.accept)
-#         self.buttonBox.rejected.connect(self.reject)
-
-#         self.layout = QVBoxLayout()
-#         message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\n\nWould you like to add it?")
-#         self.layout.addWidget(message)
-#         self.layout.addWidget(self.buttonBox)
-#         self.setLayout(self.layout)
-
-
-# class OverwriteSubQuestion(QDialog):
-#     """
-#     dialog to ask about overwriting existing submission
-#     """    
-#     def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
-#         super().__init__()
-
-#         self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
-
-#         QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
-
-#         self.buttonBox = QDialogButtonBox(QBtn)
-#         self.buttonBox.accepted.connect(self.accept)
-#         self.buttonBox.rejected.connect(self.reject)
-
-#         self.layout = QVBoxLayout()
-#         message = QLabel(message)
-#         self.layout.addWidget(message)
-#         self.layout.addWidget(self.buttonBox)
-#         self.setLayout(self.layout)
-
-
 class QuestionAsker(QDialog):
     """
     dialog to ask yes/no questions
@@ -73,23 +25,27 @@ class QuestionAsker(QDialog):
     def __init__(self, title:str, message:str) -> QDialog:
         super().__init__()
         self.setWindowTitle(title)
+        # set yes/no buttons
         QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
         self.layout = QVBoxLayout()
+        # Text for the yes/no question
         message = QLabel(message)
         self.layout.addWidget(message)
         self.layout.addWidget(self.buttonBox)
         self.setLayout(self.layout)
 
 class AlertPop(QMessageBox):
-
+    """
+    Dialog to show an alert.
+    """    
     def __init__(self, message:str, status:str) -> QMessageBox:
         super().__init__()
+        # select icon by string
         icon = getattr(QMessageBox.Icon, status.title())
         self.setIcon(icon)
-        # msg.setText("Error")
         self.setInformativeText(message)
         self.setWindowTitle(status.title())
 

src/submissions/frontend/custom_widgets/sub_details.py

@@ -1,20 +1,17 @@
-from datetime import date
 from PyQt6.QtWidgets import (
     QVBoxLayout, QDialog, QTableView,
     QTextEdit, QPushButton, QScrollArea, 
     QMessageBox, QFileDialog, QMenu
 )
-from PyQt6.QtCore import Qt, QAbstractTableModel
+from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
 from PyQt6.QtGui import QFontMetrics, QAction, QCursor
-
 from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id
 from jinja2 import Environment, FileSystemLoader
 from xhtml2pdf import pisa
 import sys
 from pathlib import Path
 import logging
-from .pop_ups import AlertPop, QuestionAsker
-from tools import check_is_power_user
+from .pop_ups import QuestionAsker
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -45,7 +42,7 @@ class pandasModel(QAbstractTableModel):
         """
         return self._data.shape[0]
 
-    def columnCount(self, parnet=None) -> int:
+    def columnCount(self, parent=None) -> int:
         """
         does what it says
 
@@ -85,7 +82,7 @@ class SubmissionsSheet(QTableView):
         self.setData()
         self.resizeColumnsToContents()
         self.resizeRowsToContents()
-        # self.clicked.connect(self.test)
+        self.setSortingEnabled(True)
         self.doubleClicked.connect(self.show_details)
  
     def setData(self) -> None: 
@@ -93,6 +90,8 @@ class SubmissionsSheet(QTableView):
         sets data in model
         """        
         self.data = submissions_to_df(ctx=self.ctx)
+        self.data['id'] = self.data['id'].apply(str)
+        self.data['id'] = self.data['id'].str.zfill(3)
         try:
             del self.data['samples']
         except KeyError:
@@ -101,8 +100,11 @@ class SubmissionsSheet(QTableView):
             del self.data['reagents']
         except KeyError:
             pass
-        self.model = pandasModel(self.data)
-        self.setModel(self.model)
+        proxyModel = QSortFilterProxyModel()
+        proxyModel.setSourceModel(pandasModel(self.data))
+        # self.model = pandasModel(self.data)
+        # self.setModel(self.model)
+        self.setModel(proxyModel)
         # self.resize(800,600)
 
     def show_details(self) -> None:
@@ -110,22 +112,22 @@ class SubmissionsSheet(QTableView):
         creates detailed data to show in seperate window
         """        
         index = (self.selectionModel().currentIndex())
-        # logger.debug(index)
         value = index.sibling(index.row(),0).data()
         dlg = SubmissionDetails(ctx=self.ctx, id=value)
-        # dlg.show()
         if dlg.exec():
             pass
 
 
     def contextMenuEvent(self, event):
+        """
+        Creates actions for right click menu events.
+
+        Args:
+            event (_type_): the item of interest
+        """        
         self.menu = QMenu(self)
         renameAction = QAction('Delete', self)
         detailsAction = QAction('Details', self)
-        # Originally I intended to limit deletions to power users.
-        # renameAction.setEnabled(False)
-        # if check_is_power_user(ctx=self.ctx):
-        #     renameAction.setEnabled(True)
         renameAction.triggered.connect(lambda: self.delete_item(event))
         detailsAction.triggered.connect(lambda: self.show_details())
         self.menu.addAction(detailsAction)
@@ -164,12 +166,8 @@ class SubmissionDetails(QDialog):
         # get submision from db
         data = lookup_submission_by_id(ctx=ctx, id=id)
         self.base_dict = data.to_dict()
-        # logger.debug(f"Base dict: {self.base_dict}")
         # don't want id
         del self.base_dict['id']
-        # convert sub objects to dicts
-        # self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
-        # self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
         # retrieve jinja template
         template = env.get_template("submission_details.txt")
         # render using object dict
@@ -192,24 +190,18 @@ class SubmissionDetails(QDialog):
         interior.setWidget(txt_editor)
         self.layout = QVBoxLayout()
         self.setFixedSize(w, 900)
+        # button to export a pdf version
         btn = QPushButton("Export PDF")
         btn.setParent(self)
         btn.setFixedWidth(w)
         btn.clicked.connect(self.export)
         
 
-    # def _create_actions(self):
-    #     self.exportAction = QAction("Export", self)
-        
-
     def export(self):
         template = env.get_template("submission_details.html")
         html = template.render(sub=self.base_dict)
-        # logger.debug(f"Submission details: {self.base_dict}")
         home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
         fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
-        # logger.debug(f"report output name: {fname}")
-        # df.to_excel(fname, engine='openpyxl')
         if fname.__str__() == ".":
             logger.debug("Saving pdf was cancelled.")
             return
@@ -223,4 +215,3 @@ class SubmissionDetails(QDialog):
             msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
             msg.setWindowTitle("Permission Error")
             msg.exec()
-        

src/submissions/frontend/functions.py

@@ -2,7 +2,6 @@
 from backend.db.models import *
 import logging
 
-
 logger = logging.getLogger(f"submissions.{__name__}")
 
 def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
@@ -21,6 +20,7 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
     match sub:
         case BasicSubmission():
             ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
+            # Overwrite function parameter reagenttypes
             reagenttypes = [reagent.type.name for reagent in sub.reagents]
         case KitType():
             ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
@@ -30,13 +30,14 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
     check = set(ext_kit_rtypes) == set(reagenttypes)
     logger.debug(f"Checking if reagents match kit contents: {check}")
     # what reagent types are in both lists?
-    common = list(set(ext_kit_rtypes).intersection(reagenttypes))
-    logger.debug(f"common reagents types: {common}")
+    # common = list(set(ext_kit_rtypes).intersection(reagenttypes))
+    missing = list(set(ext_kit_rtypes).difference(reagenttypes))
+    logger.debug(f"Missing reagents types: {missing}")
     # if lists are equal return no problem
-    if check:
+    if len(missing)==0:
         result = None
     else:
-        missing = [x for x in ext_kit_rtypes if x not in common]
+        # missing = [x for x in ext_kit_rtypes if x not in common]
         result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.", 'missing': missing}
     return result
 

src/submissions/frontend/visualizations/charts.py

@@ -25,7 +25,6 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
     genera = []
     if df.empty:
         return None
-
     for item in df['genus'].to_list():
         try:
             if item[-1] == "*":
@@ -95,7 +94,6 @@ def generic_figure_markers(fig:Figure, modes:list=[], ytitle:str|None=None) -> F
             ])
         )
     )
-    # logger.debug(f"Returning figure {fig}")
     assert type(fig) == Figure
     return fig
 
@@ -148,8 +146,7 @@ def output_figures(settings:dict, figs:list, group_name:str):
             except AttributeError:
                 logger.error(f"The following figure was a string: {fig}")
 
-# Below are the individual construction functions. They must be named "construct_{mode}_chart" and 
-# take only json_in and mode to hook into the main processor.
+
 
 def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None) -> Figure:
     fig = Figure()
@@ -186,14 +183,15 @@ def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None)
     # sys.exit(f"number of traces={len(fig.data)}")
     return generic_figure_markers(fig=fig, modes=modes, ytitle=ytitle)
 
-
+# Below are the individual construction functions. They must be named "construct_{mode}_chart" and 
+# take only json_in and mode to hook into the main processor.
 
 def construct_refseq_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:str) -> Figure:
     """
     Constructs intial refseq chart for both contains and matches (depreciated).
 
     Args:
-        settings (dict): settings passed down from click.
+        settings (dict): settings passed down from gui.
         df (pd.DataFrame): dataframe containing all sample data for the group.
         group_name (str): name of the group being processed.
         mode (str): contains or matches, overwritten by hardcoding, so don't think about it too hard.