commit before refactor to use pyqt6 input field names

2023-03-14 13:13:10 -05:00
parent 285ccecd73
commit fc334155ff
11 changed files with 193 additions and 150 deletions
--- a/src/submissions/frontend/init.py
+++ b/src/submissions/frontend/init.py
@@ -1,5 +1,6 @@
 import json
 import re
+from typing import Tuple
 from PyQt6.QtWidgets import (
    QMainWindow, QLabel, QToolBar, 
    QTabWidget, QWidget, QVBoxLayout,
@@ -30,14 +31,14 @@ from backend.db import (construct_submission_info, lookup_reagent,
 )
 from backend.db import lookup_kittype_by_name

-from .functions import check_kit_integrity, insert_reagent_import
-from tools import check_not_nan, create_reagent_list
+from .functions import check_kit_integrity
+from tools import check_not_nan
 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
+from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
 import logging
 import difflib
 from getpass import getuser
@@ -172,7 +173,6 @@ class App(QMainWindow):
            (?P<samples>)^samples$ |
            (?P<reagent>^lot_.*$)
        """, re.VERBOSE)
-        # reagents = []
        for item in prsr.sub:
            logger.debug(f"Item: {item}")
            # attempt to match variable name to regex group
@@ -201,16 +201,16 @@ class App(QMainWindow):
                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                    # if extraction kit not available, all other values fail
                    if not check_not_nan(prsr.sub[item]):
-                        msg = AlertPop(message="Make sure to check your extraction kit!", status="warning")
+                        msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
                        msg.exec()
                    # create combobox to hold looked up kits
                    add_widget = QComboBox()
                    # lookup existing kits by 'submission_type' decided on by sheetparser
                    uses = [item.__str__() for item in lookup_kittype_by_use(ctx=self.ctx, used_by=prsr.sub['submission_type'])]
-                    if len(uses) > 0:
-                        add_widget.addItems(uses)
-                    else:
-                        add_widget.addItems(['bacterial_culture'])
+                    # if len(uses) > 0:
+                    add_widget.addItems(uses)
+                    # else:
+                        # add_widget.addItems(['bacterial_culture'])
                    self.ext_kit = prsr.sub[item]
                case 'submitted_date':
                    # create label
@@ -224,40 +224,10 @@ class App(QMainWindow):
                    except:
                        add_widget.setDate(date.today())
                case 'reagent':
-                    
                    # create label
                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
-                    # add_widget = QComboBox()
-                    # add_widget.setEditable(True)
-                    # # Ensure that all reagenttypes have a name that matches the items in the excel parser
-                    # query_var = item.replace("lot_", "")
-                    # logger.debug(f"Query for: {query_var}")
-                    # if isinstance(prsr.sub[item], numpy.float64):
-                    #     logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
-                    #     try:
-                    #         prsr.sub[item] = int(prsr.sub[item]['lot'])
-                    #     except ValueError:
-                    #         pass
-                    # # query for reagents using type name from sheet and kit from sheet
-                    # 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=self.ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
-                    # output_reg = []
-                    # for reagent in relevant_reagents:
-                    #     if isinstance(reagent, set):
-                    #         for thing in reagent:
-                    #             output_reg.append(thing)
-                    #     elif isinstance(reagent, str):
-                    #         output_reg.append(reagent)
-                    # relevant_reagents = output_reg
-                    # logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
-                    # # if reagent in sheet is not found insert it into items
-                    # if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
-                    #     if check_not_nan(prsr.sub[item]['lot']):
-                    #         relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
-                    # logger.debug(f"New relevant reagents: {relevant_reagents}")
-                    # add_widget.addItems(relevant_reagents)
-                    add_widget = insert_reagent_import(ctx=self.ctx, item=item, prsr=prsr)
+                    # create reagent choice widget
+                    add_widget = ImportReagent(ctx=self.ctx, item=item, prsr=prsr)
                    self.reagents[item] = prsr.sub[item]
                case 'samples':
                    # hold samples in 'self' until form submitted
@@ -278,7 +248,7 @@ class App(QMainWindow):
                msg.exec()
                for item in kit_integrity['missing']:
                    self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
-                    add_widget = insert_reagent_import(ctx=self.ctx, item=item)
+                    add_widget = ImportReagent(ctx=self.ctx, item=item)
                    self.table_widget.formlayout.addWidget(add_widget)
        # create submission button
        submit_btn = QPushButton("Submit")
@@ -302,7 +272,6 @@ class App(QMainWindow):
            logger.debug(f"Looked up reagent: {wanted_reagent}")
            # if reagent not found offer to add to database
            if wanted_reagent == None:
-                # dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
                r_lot = reagents[reagent]
                dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.replace('_', ' ').title().strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
                if dlg.exec():
@@ -310,10 +279,10 @@ class App(QMainWindow):
                    expiry_date = self.reagents[reagent]['exp']
                    wanted_reagent = self.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
                else:
+                    # In this case we will have an empty reagent and the submission will fail kit integrity check
                    logger.debug("Will not add reagent.")
            if wanted_reagent != None:
                parsed_reagents.append(wanted_reagent)
-                # logger.debug(info)
        # move samples into preliminary submission dict
        info['samples'] = self.samples
        info['uploaded_by'] = getuser()
@@ -322,14 +291,14 @@ class App(QMainWindow):
        base_submission, result = construct_submission_info(ctx=self.ctx, info_dict=info)
        # check output message for issues
        match result['code']:
+            # code 1: ask for overwrite
            case 1:
-        # if output['code'] > 0:
-            # dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
                if dlg.exec():
                    base_submission.reagents = []
                else:
                    return
+            # code 2: No RSL plate number given
            case 2:
                dlg = AlertPop(message=result['message'], status='critical')
                dlg.exec()
@@ -386,12 +355,12 @@ class App(QMainWindow):
            return reagent
            

-    def extract_form_info(self, object):
+    def extract_form_info(self, object) -> Tuple[list, list]:
        """
        retrieves arbitrary number of labels, values from form

        Args:
-            object (_type_): _description_
+            object (_type_): the form widget

        Returns:
            _type_: _description_
@@ -399,6 +368,7 @@ class App(QMainWindow):
        labels = []
        values = []
        # grab all widgets in form
+        prev_item = None
        for item in object.layout.parentWidget().findChildren(QWidget):
            match item:
                case QLabel():
--- a/src/submissions/frontend/custom_widgets/init.py
+++ b/src/submissions/frontend/custom_widgets/init.py
@@ -9,12 +9,15 @@ from PyQt6.QtWidgets import (
 )
 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 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 backend.excel.parser import SheetParser
 from jinja2 import Environment, FileSystemLoader
 import sys
 from pathlib import Path
 import logging
+import numpy as np
+from .pop_ups import AlertPop

 logger = logging.getLogger(f"submissions.{__name__}")

@@ -45,15 +48,18 @@ class AddReagentForm(QDialog):
        self.buttonBox.rejected.connect(self.reject)
        # get lot info
        lot_input = QLineEdit()
+        lot_input.setObjectName("lot")
        lot_input.setText(reagent_lot)
        # get expiry info
        exp_input = QDateEdit(calendarPopup=True)
+        exp_input.setObjectName('expiry')
        if expiry == None:
            exp_input.setDate(QDate.currentDate())
        else:
            exp_input.setDate(expiry)
        # 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)])
        logger.debug(f"Trying to find index of {reagent_type}")
        # convert input to user friendly string?
@@ -175,17 +181,18 @@ class KitAdder(QWidget):
        # 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 = QMessageBox()
-        # msg.setIcon(QMessageBox.critical)
-        match result['code']:
-            case 0:
-                msg.setText("Kit added")
-                msg.setInformativeText(result['message'])
-                msg.setWindowTitle("Kit added")
-            case 1:
-                msg.setText("Permission Error")
-                msg.setInformativeText(result['message'])
-                msg.setWindowTitle("Permission Error")
+        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):
@@ -276,3 +283,41 @@ class ControlsDatePicker(QWidget):

    def sizeHint(self) -> QSize:
        return QSize(80,20)  
+
+
+class ImportReagent(QComboBox):
+
+    def __init__(self, ctx:dict, item:str, prsr:SheetParser|None=None):
+        super().__init__()
+        self.setEditable(True)
+        # Ensure that all reagenttypes have a name that matches the items in the excel parser
+        query_var = item.replace("lot_", "")
+        logger.debug(f"Query for: {query_var}")
+        if prsr != None:
+            if isinstance(prsr.sub[item], np.float64):
+                logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
+                try:
+                    prsr.sub[item] = int(prsr.sub[item]['lot'])
+                except ValueError:
+                    pass
+        # query for reagents using type name from sheet and kit from sheet
+        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'])]
+        output_reg = []
+        for reagent in relevant_reagents:
+            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 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':
+                if check_not_nan(prsr.sub[item]['lot']):
+                    relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
+        logger.debug(f"New relevant reagents: {relevant_reagents}")
+        self.addItems(relevant_reagents)
+        
--- a/src/submissions/frontend/custom_widgets/sub_details.py
+++ b/src/submissions/frontend/custom_widgets/sub_details.py
@@ -164,7 +164,7 @@ 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}")
+        # logger.debug(f"Base dict: {self.base_dict}")
        # don't want id
        del self.base_dict['id']
        # convert sub objects to dicts
--- a/src/submissions/frontend/functions.py
+++ b/src/submissions/frontend/functions.py
@@ -1,24 +1,23 @@
 # from ..models import *
 from backend.db.models import *
-from backend.db import lookup_regent_by_type_name
-from tools import check_not_nan
-# from backend.db import lookup_kittype_by_name
 import logging
-import numpy as np
-from backend.excel.parser import SheetParser
-from PyQt6.QtWidgets import (
-    QMainWindow, QLabel, QToolBar, 
-    QTabWidget, QWidget, QVBoxLayout,
-    QPushButton, QFileDialog,
-    QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
-    QSpinBox, QScrollArea
-)


 logger = logging.getLogger(f"submissions.{__name__}")

 def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
+    """
+    Ensures all reagents expected in kit are listed in Submission
+
+    Args:
+        sub (BasicSubmission | KitType): Object containing complete list of reagent types.
+        reagenttypes (list | None, optional): List to check against complete list. Defaults to None.
+
+    Returns:
+        dict|None: Result object containing a message and any missing components.
+    """    
    logger.debug(type(sub))
+    # What type is sub?
    match sub:
        case BasicSubmission():
            ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
@@ -27,10 +26,13 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
            ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
    logger.debug(f"Kit reagents: {ext_kit_rtypes}")
    logger.debug(f"Submission reagents: {reagenttypes}")
+    # check if lists are equal
    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}")
+    # if lists are equal return no problem
    if check:
        result = None
    else:
@@ -39,38 +41,39 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
    return result


-def insert_reagent_import(ctx:dict, item:str, prsr:SheetParser|None=None) -> QComboBox:
-    add_widget = QComboBox()
-    add_widget.setEditable(True)
-    # Ensure that all reagenttypes have a name that matches the items in the excel parser
-    query_var = item.replace("lot_", "")
-    logger.debug(f"Query for: {query_var}")
-    if prsr != None:
-        if isinstance(prsr.sub[item], np.float64):
-            logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
-            try:
-                prsr.sub[item] = int(prsr.sub[item]['lot'])
-            except ValueError:
-                pass
-    # query for reagents using type name from sheet and kit from sheet
-    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'])]
-    output_reg = []
-    for reagent in relevant_reagents:
-        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 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':
-            if check_not_nan(prsr.sub[item]['lot']):
-                relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
-    logger.debug(f"New relevant reagents: {relevant_reagents}")
-    add_widget.addItems(relevant_reagents)
-    return add_widget
+# Below is depreciated:
+# def insert_reagent_import(ctx:dict, item:str, prsr:SheetParser|None=None) -> QComboBox:
+#     add_widget = QComboBox()
+#     add_widget.setEditable(True)
+#     # Ensure that all reagenttypes have a name that matches the items in the excel parser
+#     query_var = item.replace("lot_", "")
+#     logger.debug(f"Query for: {query_var}")
+#     if prsr != None:
+#         if isinstance(prsr.sub[item], np.float64):
+#             logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
+#             try:
+#                 prsr.sub[item] = int(prsr.sub[item]['lot'])
+#             except ValueError:
+#                 pass
+#     # query for reagents using type name from sheet and kit from sheet
+#     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'])]
+#     output_reg = []
+#     for reagent in relevant_reagents:
+#         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 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':
+#             if check_not_nan(prsr.sub[item]['lot']):
+#                 relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
+#     logger.debug(f"New relevant reagents: {relevant_reagents}")
+#     add_widget.addItems(relevant_reagents)
+#     return add_widget