Major refactor for improved documentation and readability

src/submissions/tools/__init__.py

@@ -1,18 +1,14 @@
 import numpy as np
 import logging
 import getpass
-from PyQt6.QtWidgets import (
-    QMainWindow, QLabel, QToolBar, 
-    QTabWidget, QWidget, QVBoxLayout,
-    QPushButton, QFileDialog,
-    QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
-    QSpinBox, QScrollArea
-)
-
+from backend.db.models import BasicSubmission, KitType
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 def check_not_nan(cell_contents) -> bool:
+    # check for nan as a string first
+    if cell_contents == 'nan':
+        cell_contents = np.nan
     try:
         return not np.isnan(cell_contents)
     except TypeError:
@@ -28,7 +24,7 @@ def check_is_power_user(ctx:dict) -> bool:
     except KeyError as e:
         check = False
     except Exception as e:
-        logger.debug(f"Check encounteded unknown error: {type(e).__name__} - {e}")
+        logger.debug(f"Check encountered unknown error: {type(e).__name__} - {e}")
         check = False
     return check
 
@@ -37,43 +33,39 @@ def create_reagent_list(in_dict:dict) -> list[str]:
     return [item.strip("lot_") for item in in_dict.keys()]
 
 
-def extract_form_info(object) -> dict:
+def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
     """
-    retrieves object names and values from form
+    Ensures all reagents expected in kit are listed in Submission
 
     Args:
-        object (_type_): the form widget
+        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: dictionary of objectName:text items
-    """        
-    from frontend.custom_widgets import ReagentTypeForm
-    dicto = {}
-    reagents = {}
-    logger.debug(f"Object type: {type(object)}")
-    # grab all widgets in form
-    try:
-        all_children = object.layout.parentWidget().findChildren(QWidget)
-    except AttributeError:
-        all_children = object.layout().parentWidget().findChildren(QWidget)
-    for item in all_children:
-        logger.debug(f"Looking at: {item.objectName()}")
-        match item:
-            case QLineEdit():
-                dicto[item.objectName()] = item.text()
-            case QComboBox():
-                dicto[item.objectName()] = item.currentText()
-            case QDateEdit():
-                dicto[item.objectName()] = item.date().toPyDate()
-            case QSpinBox():
-                dicto[item.objectName()] = item.value()
-            case ReagentTypeForm():
-                reagent = 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"].strip()] = {'eol_ext':int(reagent['eol'])}
-        # value for ad hoc check above
-    if reagents != {}:
-        return dicto, reagents
-    return dicto
+        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]
+            # 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]
+    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))
+    missing = list(set(ext_kit_rtypes).difference(reagenttypes))
+    logger.debug(f"Missing reagents types: {missing}")
+    # if lists are equal return no problem
+    if len(missing)==0:
+        result = None
+    else:
+        # 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