Updated documentation. Improved import completion.

src/submissions/CHANGELOG.md

@@ -1,3 +1,8 @@
+**202303.04**
+
+- Completed partial imports that will add in missing reagents found in the kit indicated by the user.
+- Added web documentation to the help menu.
+
 **202303.03**
 
 - Increased robustness by utilizing PyQT6 widget names to pull data from forms instead of previously used label/input zip.

src/submissions/README.md

@@ -1 +1,42 @@
-**This is the readme file**
+## Logging in New Run:
+*should fit 90% of usage cases*
+
+	1. Ensure a properly formatted Submission Excel form has been filled out. (It will save you a few headaches)
+	    a. All fields should be filled in to ensure proper lookups of reagents.
+	2. Open the app using the shortcut in the Submissions folder. For example: "L:\Robotics Laboratory Support\Submissions\submissions_v122b.exe - Shortcut.lnk" (Version may have changed).
+		a. Ignore the large black window of fast scrolling text, it is there for debugging purposes.
+		b. The 'Submissions' tab should be open by default.
+	3. Click on 'File' in the menu bar, followed by 'Import' and use the locate the form you definitely made sure was properly filled out in step 1.
+	4. Click "Ok".
+	5. Most of the fields in the form should be automatically filled in from the form area to the left of the screen.
+	6. You may need to maximize the app to ensure you can see all the info.
+	7. Any fields that are not automatically filled in can be filled in manually from the drop down menus.
+	8. Once you are certain all the information is correct, click 'Submit' at the bottom of the form.
+	9. Add in any reagents the app doesn't recognize.
+	10. Once the new run shows up at the bottom of the Submissions, everything is fine.
+	11. In case of any mistakes, the run can be overwritten by a reimport.
+
+## Check existing Run:
+
+	1. Details of existing runs can be checked by double clicking on the row of interest in the summary sheet on the right of the 'Submissions' tab.
+	2. All information available on the run should be available in the resulting text window. This information can be exported by clicking 'Export PDF' at the top.
+
+## Generating a report:
+
+	1. Click on 'Reports' -> 'Make Report' in the menu bar.
+	2. Select the start date and the end date you want for the report. Click 'ok'.
+	3. Use the file dialog to select a location to save the report.
+		a. Both an excel sheet and a pdf should be generated containing summary information for submissions made by each client lab.
+	
+## Checking Controls:
+
+	1. Controls for bacterial runs are now incorporated directly into the submissions database using webview. (Admittedly this performance is not as good as with a browser, so you will have to triage your data)
+	2. Click on the "Controls" tab.
+	3. Range of dates for controls can be selected from the date pickers at the top.
+		a. If start date is set after end date, the start date will default back to 3 months before end date.
+		b. Recommendation is to use less than 6 month date range keeping in mind that higher data density will affect performance (with kraken being the worst so far)
+	4. Analysis type and subtype can be set using the drop down menus. (Only kraken has a subtype so far).
+
+## Adding new Kit:
+
+	1. Instructions to come.

src/submissions/__main__.py

@@ -1,7 +1,7 @@
 import sys
 from pathlib import Path
 import os
-# must be set to enable qtwebengine in network path
+# environment variable must be set to enable qtwebengine in network path
 if getattr(sys, 'frozen', False):
     os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
 else :

src/submissions/backend/db/functions.py

@@ -641,6 +641,16 @@ def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str) -> models.BasicSubmissio
 
 
 def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[models.BasicSubmission]:
+    """
+    Retrieves each submission using a specified reagent.
+
+    Args:
+        ctx (dict): settings passed down from gui
+        reagent (models.Reagent): reagent object in question
+
+    Returns:
+        list[models.BasicSubmission]: list of all submissions using specified reagent.
+    """    
     return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()
 
 

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

@@ -35,7 +35,7 @@ class BasicSubmission(Base):
     reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
     reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
     extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
-    run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from kit costs at time of creation.
+    run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from constant and mutable kit costs at time of creation.
     uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
 
     # Allows for subclassing into ex. BacterialCulture, Wastewater, etc.

src/submissions/backend/excel/parser.py

@@ -27,6 +27,7 @@ class SheetParser(object):
         # set attributes based on kwargs from gui ctx
         for kwarg in kwargs:
             setattr(self, f"_{kwarg}", kwargs[kwarg])
+        # self.__dict__.update(kwargs)
         if filepath == None:
             logger.error(f"No filepath given.")
             self.xl = None
@@ -38,12 +39,12 @@ class SheetParser(object):
                 self.xl = None
         self.sub = OrderedDict()
         # make decision about type of sample we have
-        self.sub['submission_type'] = self._type_decider()
+        self.sub['submission_type'] = self.type_decider()
         # select proper parser based on sample type
-        parse_sub = getattr(self, f"_parse_{self.sub['submission_type'].lower()}")
+        parse_sub = getattr(self, f"parse_{self.sub['submission_type'].lower()}")
         parse_sub()
 
-    def _type_decider(self) -> str:
+    def type_decider(self) -> str:
         """
         makes decisions about submission type based on structure of excel file
 
@@ -60,7 +61,7 @@ class SheetParser(object):
             return "Unknown"
 
 
-    def _parse_unknown(self) -> None:
+    def parse_unknown(self) -> None:
         """
         Dummy function to handle unknown excel structures
         """    
@@ -68,7 +69,7 @@ class SheetParser(object):
         self.sub = None
     
 
-    def _parse_generic(self, sheet_name:str) -> pd.DataFrame:
+    def parse_generic(self, sheet_name:str) -> pd.DataFrame:
         """
         Pulls information common to all submission types and passes on dataframe
 
@@ -89,12 +90,12 @@ class SheetParser(object):
         return submission_info
 
 
-    def _parse_bacterial_culture(self) -> None:
+    def parse_bacterial_culture(self) -> None:
         """
         pulls info specific to bacterial culture sample type
         """
 
-        def _parse_reagents(df:pd.DataFrame) -> None:
+        def parse_reagents(df:pd.DataFrame) -> None:
             """
             Pulls reagents from the bacterial sub-dataframe
 
@@ -126,7 +127,7 @@ class SheetParser(object):
                     else:
                         expiry = date.today()
                     self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
-        submission_info = self._parse_generic("Sample List")
+        submission_info = self.parse_generic("Sample List")
         # iloc is [row][column] and the first row is set as header row so -2
         tech = str(submission_info.iloc[11][1])
         if tech == "nan":
@@ -139,7 +140,7 @@ class SheetParser(object):
         # must be prefixed with 'lot_' to be recognized by gui
         # Todo: find a more adaptable way to read reagents.
         reagent_range = submission_info.iloc[1:13, 4:8]
-        _parse_reagents(reagent_range)
+        parse_reagents(reagent_range)
         # get individual sample info
         sample_parser = SampleParser(submission_info.iloc[15:111])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
@@ -147,12 +148,12 @@ class SheetParser(object):
         self.sub['samples'] = sample_parse()
 
 
-    def _parse_wastewater(self) -> None:
+    def parse_wastewater(self) -> None:
         """
         pulls info specific to wastewater sample type
         """        
 
-        def _parse_reagents(df:pd.DataFrame) -> None:
+        def parse_reagents(df:pd.DataFrame) -> None:
             """
             Pulls reagents from the bacterial sub-dataframe
 
@@ -180,7 +181,7 @@ class SheetParser(object):
                         expiry = date.today()
                     self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}
         # parse submission sheet
-        submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
+        submission_info = self.parse_generic("WW Submissions (ENTER HERE)")
         # parse enrichment sheet
         enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
         # set enrichment reagent range
@@ -195,9 +196,9 @@ class SheetParser(object):
         pcr_reagent_range = qprc_info.iloc[0:5, 9:20]
         # compile technician info
         self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
-        _parse_reagents(enr_reagent_range)
+        parse_reagents(enr_reagent_range)
-        _parse_reagents(ext_reagent_range)
+        parse_reagents(ext_reagent_range)
-        _parse_reagents(pcr_reagent_range)
+        parse_reagents(pcr_reagent_range)
         # parse samples
         sample_parser = SampleParser(submission_info.iloc[16:40])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")

src/submissions/backend/excel/reports.py

@@ -8,11 +8,13 @@ from datetime import date, timedelta
 import sys
 from pathlib import Path
 import re
+from tools import check_if_app
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 # set path of templates depending on pyinstaller/raw python
-if getattr(sys, 'frozen', False):
+# if getattr(sys, 'frozen', False):
+if check_if_app():
     loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
 else:
     loader_path = Path(__file__).parents[2].joinpath('templates').absolute().__str__()

src/submissions/configure/__init__.py

@@ -8,6 +8,7 @@ from logging import handlers
 from pathlib import Path
 from sqlalchemy.orm import Session
 from sqlalchemy import create_engine
+from tools import check_if_app
 
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -102,7 +103,8 @@ def get_config(settings_path: Path|str|None=None) -> dict:
             settings_path = Path.home().joinpath(".submissions", "config.yml")
         # finally look in the local config
         else:
-            if getattr(sys, 'frozen', False):
+            # if getattr(sys, 'frozen', False):
+            if check_if_app():
                 settings_path = Path(sys._MEIPASS).joinpath("files", "config.yml")
             else:
                 settings_path = package_dir.joinpath('config.yml')
@@ -173,7 +175,7 @@ def setup_logger(verbosity:int=3):
     Set logger levels using settings.
 
     Args:
-        verbose (bool, optional): _description_. Defaults to False.
+        verbosit (int, optional): Level of verbosity desired 3 is highest. Defaults to 3.
 
     Returns:
         logger: logger object

src/submissions/frontend/__init__.py

@@ -3,6 +3,7 @@ Operations for all user interactions.
 '''
 import json
 import re
+import sys
 from PyQt6.QtWidgets import (
     QMainWindow, QLabel, QToolBar, 
     QTabWidget, QWidget, QVBoxLayout,
@@ -32,7 +33,7 @@ from backend.db import (construct_submission_info, lookup_reagent,
 )
 from backend.db import lookup_kittype_by_name
 from .functions import extract_form_info
-from tools import check_not_nan, check_kit_integrity
+from tools import check_not_nan, check_kit_integrity, check_if_app
 # from backend.excel.reports import 
 from frontend.custom_widgets import SubmissionsSheet, AlertPop, QuestionAsker, AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
 import logging
@@ -40,6 +41,7 @@ import difflib
 from getpass import getuser
 from datetime import date
 from frontend.visualizations import create_charts
+import webbrowser
 
 logger = logging.getLogger(f'submissions.{__name__}')
 logger.info("Hello, I am a logger")
@@ -49,6 +51,7 @@ class App(QMainWindow):
     def __init__(self, ctx: dict = {}):
         super().__init__()
         self.ctx = ctx
+        # indicate version and database connected in title bar
         try:
             self.title = f"Submissions App (v{ctx['package'].__version__}) - {ctx['database']}"
         except AttributeError:
@@ -84,6 +87,7 @@ class App(QMainWindow):
         maintenanceMenu = menuBar.addMenu("&Monthly")
         helpMenu = menuBar.addMenu("&Help")
         helpMenu.addAction(self.helpAction)
+        helpMenu.addAction(self.docsAction)
         fileMenu.addAction(self.importAction)
         reportMenu.addAction(self.generateReportAction)
         maintenanceMenu.addAction(self.joinControlsAction)
@@ -111,6 +115,7 @@ class App(QMainWindow):
         self.joinControlsAction = QAction("Link Controls")
         self.joinExtractionAction = QAction("Link Ext Logs")
         self.helpAction = QAction("&About", self)
+        self.docsAction = QAction("&Docs", self)
 
 
     def _connectActions(self):
@@ -129,12 +134,20 @@ class App(QMainWindow):
         self.joinControlsAction.triggered.connect(self.linkControls)
         self.joinExtractionAction.triggered.connect(self.linkExtractions)
         self.helpAction.triggered.connect(self.showAbout)
+        self.docsAction.triggered.connect(self.openDocs)
 
     def showAbout(self):
         output = f"Version: {self.ctx['package'].__version__}\n\nAuthor: {self.ctx['package'].__author__['name']} - {self.ctx['package'].__author__['email']}\n\nCopyright: {self.ctx['package'].__copyright__}"
         about = AlertPop(message=output, status="information")
         about.exec()
 
+    def openDocs(self):
+        if check_if_app():
+            url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
+        else:
+            url = Path("docs\\build\\index.html").absolute()
+        logger.debug(f"Attempting to open {url}")
+        webbrowser.get('windows-default').open(f"file://{url.__str__()}")
 
 
     def importSubmission(self):
@@ -365,24 +378,19 @@ class App(QMainWindow):
         # Custom two date picker for start & end dates
         dlg = ReportDatePicker()
         if dlg.exec():
-            # 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
             records = [item.report_dict() for item in subs]
+            # make dataframe from record dictionaries
             df = make_report_xlsx(records=records)
             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
             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])
             # logger.debug(f"report output name: {fname}")
-            # df.to_excel(fname, engine='openpyxl')
             with open(fname, "w+b") as f:
                 pisa.CreatePDF(html, dest=f)
             writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
@@ -398,14 +406,7 @@ class App(QMainWindow):
                     worksheet.column_dimensions[get_column_letter(idx)].width = max_len 
                 except ValueError:
                     pass
-                # set_column(idx, idx, max_len)  # set column width
-            # colu = worksheet.column_dimensions["C"]
-            # style = NamedStyle(name="custom_currency", number_format='Currency')
             for cell in worksheet['D']:
-                # try:
-                #     check = int(cell.row)
-                # except TypeError:
-                #     continue
                 if cell.row > 1:
                     cell.style = 'Currency'
             writer.close()
@@ -431,19 +432,11 @@ class App(QMainWindow):
             return
         # send to kit creator function
         result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
-        # msg = QMessageBox()
-        # msg.setIcon(QMessageBox.critical)
         match result['code']:
             case 0:
                 msg = AlertPop(message=result['message'], status='info')
-                # msg.setText("Kit added")
-                # msg.setInformativeText(result['message'])
-                # msg.setWindowTitle("Kit added")
             case 1:
                 msg = AlertPop(message=result['message'], status='critical')
-                # msg.setText("Permission Error")
-                # msg.setInformativeText(result['message'])
-                # msg.setWindowTitle("Permission Error")
         msg.exec()
 
 
@@ -467,19 +460,11 @@ class App(QMainWindow):
             return
         # send to kit creator function
         result = create_org_from_yaml(ctx=self.ctx, org=org)
-        # msg = QMessageBox()
-        # msg.setIcon(QMessageBox.critical)
         match result['code']:
             case 0:
                 msg = AlertPop(message=result['message'], status='information')
-                # msg.setText("Organization added")
-                # msg.setInformativeText(result['message'])
-                # msg.setWindowTitle("Kit added")
             case 1:
                 msg = AlertPop(message=result['message'], status='critical')
-                # msg.setText("Permission Error")
-                # msg.setInformativeText(result['message'])
-                # msg.setWindowTitle("Permission Error")
         msg.exec()
 
 
@@ -537,20 +522,12 @@ class App(QMainWindow):
         controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
         # if no data found from query set fig to none for reporting in webview
         if controls == None:
-            # return
             fig = None
         else:
-            # data = []
-            # for control in controls:
-            #     # change each control to list of dicts
-            #     # dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
-            #     dicts = control.convert_by_mode(mode=self.mode)
-            #     data.append(dicts)
             # change each control to list of dicts
             data = [control.convert_by_mode(mode=self.mode) for control in controls]
             # flatten data to one dimensional list
             data = [item for sublist in data for item in sublist]
-            # logger.debug(data)
             # send to dataframe creator
             df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
             if self.subtype == None:
@@ -567,16 +544,12 @@ class App(QMainWindow):
         else:
             html += "<h1>No data was retrieved for the given parameters.</h1>"
         html += '</body></html>'
-        # with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
-        #     f.write(html)
-        # add html to webview and update.
         self.table_widget.webengineview.setHtml(html)
         self.table_widget.webengineview.update()
         logger.debug("Figure updated... I hope.")
 
 
     def linkControls(self):
-        # all_bcs = self.ctx['database_session'].query(models.BacterialCulture).all()
         all_bcs = lookup_all_submissions_by_type(self.ctx, "Bacterial Culture")
         logger.debug(all_bcs)
         all_controls = get_all_controls(self.ctx)
@@ -588,9 +561,6 @@ class App(QMainWindow):
             samples = [sample.sample_id for sample in bcs.samples]
             logger.debug(bcs.controls)
             for sample in samples:
-                # if "Jan" in sample and "EN" in sample:
-                #     sample = sample.replace("EN-", "EN1-")
-                #     logger.debug(f"Checking for {sample}")
                 # replace below is a stopgap method because some dingus decided to add spaces in some of the ATCC49... so it looks like "ATCC 49"...
                 if " " in sample:
                     logger.warning(f"There is not supposed to be a space in the sample name!!!")
@@ -601,10 +571,8 @@ class App(QMainWindow):
                 else:
                     for control in all_controls:
                         diff = difflib.SequenceMatcher(a=sample, b=control.name).ratio()
-                        # if diff > 0.955:
                         if control.name.startswith(sample):
                             logger.debug(f"Checking {sample} against {control.name}... {diff}")
-                        # if sample == control.name:
                             logger.debug(f"Found match:\n\tSample: {sample}\n\tControl: {control.name}\n\tDifference: {diff}")
                             if control in bcs.controls:
                                 logger.debug(f"{control.name} already in {bcs.rsl_plate_num}, skipping")
@@ -618,28 +586,22 @@ class App(QMainWindow):
                                 self.ctx["database_session"].add(control)
                                 count += 1
             self.ctx["database_session"].add(bcs)
-            # logger.debug(f"To be added: {ctx['database_session'].new}")
             logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
-            # p = ctx["database_session"].query(models.BacterialCulture).filter(models.BacterialCulture.rsl_plate_num==bcs.rsl_plate_num).first()
         result = f"We added {count} controls to bacterial cultures."
         logger.debug(result)
-        # logger.debug(ctx["database_session"].new)
         self.ctx['database_session'].commit()
         msg = QMessageBox()
-        # msg.setIcon(QMessageBox.critical)
         msg.setText("Controls added")
         msg.setInformativeText(result)
         msg.setWindowTitle("Controls added")
         msg.exec()
 
 
-
     def linkExtractions(self):
         home_dir = str(Path(self.ctx["directory_path"]))
         fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "csv(*.csv)")[0])
         with open(fname.__str__(), 'r') as f:
             runs = [col.strip().split(",") for col in f.readlines()]
-        # check = []
         count = 0
         for run in runs:
             obj = dict(
@@ -652,21 +614,14 @@ class App(QMainWindow):
                 )
             for ii in range(6, len(run)):
                 obj[f"column{str(ii-5)}_vol"] = run[ii]
-            # check.append(json.dumps(obj))
-            # sub = self.ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num.startswith(obj["rsl_plate_num"])).first()
             sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
             try:
                 logger.debug(f"Found submission: {sub.rsl_plate_num}")
                 count += 1
             except AttributeError:
                 continue
-            # output = json.dumps(obj)
             if sub.extraction_info != None:
-                # try:
-                # logger.debug(f"Attempting update on ext info: {sub.extraction_info} for {sub.rsl_plate_num}")
                 existing = json.loads(sub.extraction_info)
-                # except:
-                    # existing = None
             else:
                 existing = None
             try:
@@ -677,7 +632,6 @@ class App(QMainWindow):
                 pass
             if existing != None:
                 try:
-                    # sub.extraction_info += output
                     logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
                     existing.append(obj)
                     logger.debug(f"Setting: {existing}")
@@ -694,7 +648,6 @@ class App(QMainWindow):
         dlg.exec()
 
 
-
 class AddSubForm(QWidget):
     
     def __init__(self, parent):

src/submissions/frontend/custom_widgets/misc.py

@@ -294,7 +294,10 @@ class ImportReagent(QComboBox):
         self.setEditable(True)
         # Ensure that all reagenttypes have a name that matches the items in the excel parser
         query_var = item.replace("lot_", "")
+        if prsr != None:
             logger.debug(f"Import Reagent is looking at: {prsr.sub[item]} for {item}")
+        else:
+            logger.debug(f"Import Reagent is going to retrieve all reagents for {item}")
         logger.debug(f"Query for: {query_var}")
         if prsr != None:
             if isinstance(prsr.sub[item], np.float64):

src/submissions/frontend/custom_widgets/sub_details.py

@@ -50,7 +50,7 @@ class pandasModel(QAbstractTableModel):
         does what it says
 
         Args:
-            parnet (_type_, optional): _description_. Defaults to None.
+            parent (_type_, optional): _description_. Defaults to None.
 
         Returns:
             int: number of columns in data
@@ -140,6 +140,12 @@ class SubmissionsSheet(QTableView):
 
 
     def delete_item(self, event):
+        """
+        Confirms user deletion and sends id to backend for deletion.
+
+        Args:
+            event (_type_): _description_
+        """        
         index = (self.selectionModel().currentIndex())
         value = index.sibling(index.row(),0).data()
         logger.debug(index)
@@ -201,6 +207,9 @@ class SubmissionDetails(QDialog):
         
 
     def export(self):
+        """
+        Renders submission to html, then creates and saves .pdf file to user selected file.
+        """        
         template = env.get_template("submission_details.html")
         html = template.render(sub=self.base_dict)
         home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()

src/submissions/frontend/functions.py

@@ -1,3 +1,6 @@
+'''
+contains operations used by multiple widgets.
+'''
 from backend.db.models import *
 import logging
 from PyQt6.QtWidgets import (
@@ -43,9 +46,7 @@ def extract_form_info(object) -> dict:
                 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(f"Reagent found: {reagent}")
-                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 != {}:

src/submissions/tools/__init__.py

@@ -1,3 +1,7 @@
+'''
+Contains miscellaenous functions used by both frontend and backend.
+'''
+import sys
 import numpy as np
 import logging
 import getpass
@@ -6,6 +10,15 @@ from backend.db.models import BasicSubmission, KitType
 logger = logging.getLogger(f"submissions.{__name__}")
 
 def check_not_nan(cell_contents) -> bool:
+    """
+    Check to ensure excel sheet cell contents are not blank.
+
+    Args:
+        cell_contents (_type_): The contents of the cell in question.
+
+    Returns:
+        bool: True if cell has value, else, false.
+    """    
     # check for nan as a string first
     if cell_contents == 'nan':
         cell_contents = np.nan
@@ -19,6 +32,15 @@ def check_not_nan(cell_contents) -> bool:
 
 
 def check_is_power_user(ctx:dict) -> bool:
+    """
+    Check to ensure current user is in power users list.
+
+    Args:
+        ctx (dict): settings passed down from gui.
+
+    Returns:
+        bool: True if user is in power users, else false.
+    """    
     try:
         check = getpass.getuser() in ctx['power_users']
     except KeyError as e:
@@ -30,6 +52,15 @@ def check_is_power_user(ctx:dict) -> bool:
 
 
 def create_reagent_list(in_dict:dict) -> list[str]:
+    """
+    Makes list of reagent types without "lot\_" prefix for each key in a dictionary
+
+    Args:
+        in_dict (dict): input dictionary of reagents
+
+    Returns:
+        list[str]: list of reagent types with "lot\_" prefix removed.
+    """    
     return [item.strip("lot_") for item in in_dict.keys()]
 
 
@@ -67,5 +98,21 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
         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}
+        result = {'message' : f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\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!", 'missing': missing}
     return result
+
+
+def check_if_app(ctx:dict=None) -> bool:
+    """
+    Checks if the program is running from pyinstaller compiled
+
+    Args:
+        ctx (dict, optional): Settings passed down from gui. Defaults to None.
+
+    Returns:
+        bool: True if running from pyinstaller. Else False.
+    """    
+    if getattr(sys, 'frozen', False):
+        return True
+    else:
+        return False