Added report tab with HTML and excel export.

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 - Reverted details exports from docx back to pdf.
 - Large scale speedups for control chart construction.
+- Reports are now given their own tab and can be updated in real time. 
 
 ## 202409.05
 

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

@@ -593,7 +593,7 @@ class BasicSubmission(BaseClass):
                 return
             case item if item in self.jsons():
                 match key:
-                    case "custom":
+                    case "custom" | "source_plates":
                         existing = value
                     case _:
                         # logger.debug(f"Setting JSON attribute.")

src/submissions/backend/excel/reports.py

@@ -1,13 +1,11 @@
 '''
 Contains functions for generating summary reports
 '''
-from PyQt6.QtCore import QMarginsF
-from PyQt6.QtGui import QPageLayout, QPageSize
 from pandas import DataFrame, ExcelWriter
-import logging, re
+import logging
 from pathlib import Path
-from datetime import date, timedelta
-from typing import List, Tuple, Any
+from datetime import date
+from typing import Tuple
 from backend.db.models import BasicSubmission
 from tools import jinja_template_loading, get_first_blank_df_row, \
     row_map
@@ -21,10 +19,12 @@ env = jinja_template_loading()
 
 class ReportMaker(object):
 
-    def __init__(self, start_date: date, end_date: date):
+    def __init__(self, start_date: date, end_date: date, organizations:list|None=None):
         self.start_date = start_date
         self.end_date = end_date
         self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date)
+        if organizations is not None:
+            self.subs = [sub for sub in self.subs if sub.submitting_lab.name in organizations]
         self.detailed_df, self.summary_df = self.make_report_xlsx()
         self.html = self.make_report_html(df=self.summary_df)
 
@@ -35,6 +35,8 @@ class ReportMaker(object):
         Returns:
             DataFrame: output dataframe
         """
+        if not self.subs:
+            return DataFrame(), DataFrame()
         df = DataFrame.from_records([item.to_dict(report=True) for item in self.subs])
         # NOTE: put submissions with the same lab together
         df = df.sort_values("submitting_lab")
@@ -100,17 +102,6 @@ class ReportMaker(object):
         if isinstance(filename, str):
             filename = Path(filename)
         filename = filename.absolute()
-        # NOTE: html_to_pdf doesn't function without a PyQt6 app
-        # if isinstance(obj, QWidget):
-            # logger.info(f"We're in PyQt environment, writing PDF to: {filename}")
-            # page_layout = QPageLayout()
-            # page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
-            # page_layout.setOrientation(QPageLayout.Orientation.Portrait)
-            # page_layout.setMargins(QMarginsF(25, 25, 25, 25))
-            # self.webview.page().printToPdf(fname.with_suffix(".pdf").__str__(), page_layout)
-        # else:
-        #     logger.info("Not in PyQt. Skipping PDF writing.")
-        # logger.debug("Finished writing.")
         self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl')
         self.summary_df.to_excel(self.writer, sheet_name="Report")
         self.detailed_df.to_excel(self.writer, sheet_name="Details", index=False)

src/submissions/backend/validators/__init__.py

@@ -70,7 +70,6 @@ class RSLNamer(object):
             logger.debug(f"Using string method for {filename}.")
             logger.debug(f"Using regex: {regex}")
             m = regex.search(filename)
-            print(m)
             try:
                 submission_type = m.lastgroup
                 logger.debug(f"Got submission type: {submission_type}")
@@ -98,7 +97,6 @@ class RSLNamer(object):
                                  message="Please select submission type from list below.", obj_type=SubmissionType)
             if dlg.exec():
                 submission_type = dlg.parse_form()
-        print(submission_type)
         submission_type = submission_type.replace("_", " ")
         return submission_type
 

src/submissions/frontend/widgets/app.py

@@ -24,6 +24,7 @@ from .controls_chart import ControlsViewer
 from .kit_creator import KitAdder
 from .submission_type_creator import SubmissionTypeAdder, SubmissionType
 from .sample_search import SearchBox
+from .summary import Summary
 
 logger = logging.getLogger(f'submissions.{__name__}')
 logger.info("Hello, I am a logger")
@@ -69,7 +70,7 @@ class App(QMainWindow):
         fileMenu = menuBar.addMenu("&File")
         # NOTE: Creating menus using a title
         methodsMenu = menuBar.addMenu("&Methods")
-        reportMenu = menuBar.addMenu("&Reports")
+        # reportMenu = menuBar.addMenu("&Reports")
         maintenanceMenu = menuBar.addMenu("&Monthly")
         helpMenu = menuBar.addMenu("&Help")
         helpMenu.addAction(self.helpAction)
@@ -80,7 +81,7 @@ class App(QMainWindow):
         fileMenu.addAction(self.yamlImportAction)
         methodsMenu.addAction(self.searchLog)
         methodsMenu.addAction(self.searchSample)
-        reportMenu.addAction(self.generateReportAction)
+        # reportMenu.addAction(self.generateReportAction)
         maintenanceMenu.addAction(self.joinExtractionAction)
         maintenanceMenu.addAction(self.joinPCRAction)
         
@@ -102,7 +103,7 @@ class App(QMainWindow):
         # logger.debug(f"Creating actions...")
         self.importAction = QAction("&Import Submission", self)
         self.addReagentAction = QAction("Add Reagent", self)
-        self.generateReportAction = QAction("Make Report", self)
+        # self.generateReportAction = QAction("Make Report", self)
         self.addKitAction = QAction("Import Kit", self)
         self.addOrgAction = QAction("Import Org", self)
         self.joinExtractionAction = QAction("Link Extraction Logs")
@@ -122,7 +123,7 @@ class App(QMainWindow):
         # logger.debug(f"Connecting actions...")
         self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
         self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
-        self.generateReportAction.triggered.connect(self.table_widget.sub_wid.generate_report)
+        # self.generateReportAction.triggered.connect(self.table_widget.sub_wid.generate_report)
         self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
         self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
         self.helpAction.triggered.connect(self.showAbout)
@@ -254,8 +255,8 @@ class AddSubForm(QWidget):
         # NOTE: Add tabs
         self.tabs.addTab(self.tab1,"Submissions")
         self.tabs.addTab(self.tab2,"Controls")
-        self.tabs.addTab(self.tab3, "Add SubmissionType")
-        self.tabs.addTab(self.tab4, "Add Kit")
+        self.tabs.addTab(self.tab3, "Summary Report")
+        # self.tabs.addTab(self.tab4, "Add Kit")
         # NOTE: Create submission adder form
         self.formwidget = SubmissionFormContainer(self)
         self.formlayout = QVBoxLayout(self)
@@ -282,14 +283,15 @@ class AddSubForm(QWidget):
         self.tab2.layout.addWidget(self.controls_viewer)
         self.tab2.setLayout(self.tab2.layout)
         # NOTE: create custom widget to add new tabs
-        ST_adder = SubmissionTypeAdder(self)
+        # ST_adder = SubmissionTypeAdder(self)
+        summary_report = Summary(self)
         self.tab3.layout = QVBoxLayout(self)
-        self.tab3.layout.addWidget(ST_adder)
+        self.tab3.layout.addWidget(summary_report)
         self.tab3.setLayout(self.tab3.layout)
-        kit_adder = KitAdder(self)
-        self.tab4.layout = QVBoxLayout(self)
-        self.tab4.layout.addWidget(kit_adder)
-        self.tab4.setLayout(self.tab4.layout)
+        # kit_adder = KitAdder(self)
+        # self.tab4.layout = QVBoxLayout(self)
+        # self.tab4.layout.addWidget(kit_adder)
+        # self.tab4.setLayout(self.tab4.layout)
         # NOTE: add tabs to main widget
         self.layout.addWidget(self.tabs)
         self.setLayout(self.layout)

src/submissions/frontend/widgets/controls_chart.py

@@ -8,7 +8,7 @@ from typing import Tuple
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import (
     QWidget, QVBoxLayout, QComboBox, QHBoxLayout,
-    QDateEdit, QLabel, QSizePolicy, QPushButton
+    QDateEdit, QLabel, QSizePolicy, QPushButton, QGridLayout
 )
 from PyQt6.QtCore import QSignalBlocker
 from backend.db import ControlType, Control
@@ -17,7 +17,7 @@ import logging
 from pandas import DataFrame
 from tools import Report, Result, get_unique_values_in_df_column, Settings, report_result
 from frontend.visualizations.control_charts import CustomFigure
-
+from .misc import StartEndDatePicker
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
@@ -28,10 +28,10 @@ class ControlsViewer(QWidget):
         self.app = self.parent().parent()
         # logger.debug(f"\n\n{self.app}\n\n")
         self.report = Report()
-        self.datepicker = ControlsDatePicker()
+        self.datepicker = StartEndDatePicker(default_start=-180)
         self.webengineview = QWebEngineView()
         # NOTE: set tab2 layout
-        self.layout = QVBoxLayout(self)
+        self.layout = QGridLayout(self)
         self.control_typer = QComboBox()
         # NOTE: fetch types of controls
         con_types = [item.name for item in ControlType.query()]
@@ -44,18 +44,20 @@ class ControlsViewer(QWidget):
         self.sub_typer = QComboBox()
         self.sub_typer.setEnabled(False)
         # NOTE: add widgets to tab2 layout
-        self.layout.addWidget(self.datepicker)
-        self.layout.addWidget(self.control_typer)
-        self.layout.addWidget(self.mode_typer)
-        self.layout.addWidget(self.sub_typer)
-        self.layout.addWidget(self.webengineview)
+        self.layout.addWidget(self.datepicker, 0,0,1,2)
+        self.save_button = QPushButton("Save Chart", parent=self)
+        self.layout.addWidget(self.save_button, 0,2,1,1)
+        self.layout.addWidget(self.control_typer, 1,0,1,3)
+        self.layout.addWidget(self.mode_typer, 2,0,1,3)
+        self.layout.addWidget(self.sub_typer, 3,0,1,3)
+        self.layout.addWidget(self.webengineview, 4,0,1,3)
         self.setLayout(self.layout)
         self.controls_getter()
         self.control_typer.currentIndexChanged.connect(self.controls_getter)
         self.mode_typer.currentIndexChanged.connect(self.controls_getter)
         self.datepicker.start_date.dateChanged.connect(self.controls_getter)
         self.datepicker.end_date.dateChanged.connect(self.controls_getter)
-        self.datepicker.save_button.pressed.connect(self.save_chart_function)
+        self.save_button.pressed.connect(self.save_chart_function)
 
     def save_chart_function(self):
         self.fig.save_figure(parent=self)
@@ -141,7 +143,7 @@ class ControlsViewer(QWidget):
         # NOTE: if no data found from query set fig to none for reporting in webview
         if controls is None:
             fig = None
-            self.datepicker.save_button.setEnabled(False)
+            self.save_button.setEnabled(False)
         else:
             # NOTE: change each control to list of dictionaries
             data = [control.convert_by_mode(mode=self.mode) for control in controls]
@@ -160,7 +162,7 @@ class ControlsViewer(QWidget):
             # NOTE: send dataframe to chart maker
             df, modes = self.prep_df(ctx=self.app.ctx, df=df)
             fig = CustomFigure(df=df, ytitle=title, modes=modes, parent=self)
-            self.datepicker.save_button.setEnabled(True)
+            self.save_button.setEnabled(True)
         # logger.debug(f"Updating figure...")
         self.fig = fig
         # NOTE: construct html for webview
@@ -200,8 +202,6 @@ class ControlsViewer(QWidget):
                     continue
                 # NOTE: The actual percentage from kraken was off due to exclusion of NaN, recalculating.
                 df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum')
-        logger.debug(df)
-        logger.debug(safe)
         df = df[[c for c in df.columns if c in safe]]
         # NOTE: move date of sample submitted on same date as previous ahead one.
         df = self.displace_date(df=df)
@@ -340,28 +340,27 @@ class ControlsViewer(QWidget):
         return df
 
 
-class ControlsDatePicker(QWidget):
-    """
-    custom widget to pick start and end dates for controls graphs
-    """
-
-    def __init__(self) -> None:
-        super().__init__()
-        self.start_date = QDateEdit(calendarPopup=True)
-        # NOTE: start date is two months prior to end date by default
-        sixmonthsago = QDate.currentDate().addDays(-180)
-        self.start_date.setDate(sixmonthsago)
-        self.end_date = QDateEdit(calendarPopup=True)
-        self.end_date.setDate(QDate.currentDate())
-        self.layout = QHBoxLayout()
-        self.layout.addWidget(QLabel("Start Date"))
-        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)
-        self.save_button = QPushButton("Save Chart", parent=self)
-        self.layout.addWidget(self.save_button)
-
-    def sizeHint(self) -> QSize:
-        return QSize(80, 20)
+# class ControlsDatePicker(QWidget):
+#     """
+#     custom widget to pick start and end dates for controls graphs
+#     """
+#
+#     def __init__(self) -> None:
+#         super().__init__()
+#         self.start_date = QDateEdit(calendarPopup=True)
+#         # NOTE: start date is two months prior to end date by default
+#         sixmonthsago = QDate.currentDate().addDays(-180)
+#         self.start_date.setDate(sixmonthsago)
+#         self.end_date = QDateEdit(calendarPopup=True)
+#         self.end_date.setDate(QDate.currentDate())
+#         self.layout = QHBoxLayout()
+#         self.layout.addWidget(QLabel("Start Date"))
+#         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)
+#
+#
+#     def sizeHint(self) -> QSize:
+#         return QSize(80, 20)

src/submissions/frontend/widgets/misc.py

@@ -2,17 +2,20 @@
 Contains miscellaneous widgets for frontend functions
 '''
 from datetime import date
+
+from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QStandardItemModel
+from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout,
-    QLineEdit, QComboBox, QDialog, 
-    QDialogButtonBox, QDateEdit, QPushButton, QFormLayout
+    QLineEdit, QComboBox, QDialog,
+    QDialogButtonBox, QDateEdit, QPushButton, QFormLayout, QWidget, QHBoxLayout, QSizePolicy
 )
-from PyQt6.QtCore import Qt, QDate
+from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF, pyqtSlot, pyqtSignal, QEvent
 from tools import jinja_template_loading
 from backend.db.models import *
 import logging
 from .pop_ups import AlertPop
-from .functions import select_open_file
+from .functions import select_open_file, select_save_file
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -22,8 +25,10 @@ env = jinja_template_loading()
 class AddReagentForm(QDialog):
     """
     dialog to add gather info about new reagent
-    """    
-    def __init__(self, reagent_lot:str|None=None, reagent_role: str | None=None, expiry: date | None=None, reagent_name: str | None=None) -> None:
+    """
+
+    def __init__(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
+                 reagent_name: str | None = None) -> None:
         super().__init__()
         if reagent_lot is None:
             reagent_lot = reagent_role
@@ -71,7 +76,8 @@ class AddReagentForm(QDialog):
         self.layout.addWidget(self.name_input)
         self.layout.addWidget(QLabel("Lot:"))
         self.layout.addWidget(self.lot_input)
-        self.layout.addWidget(QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)"))
+        self.layout.addWidget(
+            QLabel("Expiry:\n(use exact date on reagent.\nEOL will be calculated from kit automatically)"))
         self.layout.addWidget(self.exp_input)
         self.layout.addWidget(QLabel("Type:"))
         self.layout.addWidget(self.type_input)
@@ -85,57 +91,57 @@ class AddReagentForm(QDialog):
 
         Returns:
             dict: Output info
-        """        
-        return dict(name=self.name_input.currentText().strip(), 
-                    lot=self.lot_input.text().strip(), 
+        """
+        return dict(name=self.name_input.currentText().strip(),
+                    lot=self.lot_input.text().strip(),
                     expiry=self.exp_input.date().toPyDate(),
                     role=self.type_input.currentText().strip())
 
     def update_names(self):
         """
         Updates reagent names form field with examples from reagent type
-        """        
+        """
         # logger.debug(self.type_input.currentText())
         self.name_input.clear()
         lookup = Reagent.query(reagent_role=self.type_input.currentText())
         self.name_input.addItems(list(set([item.name for item in lookup])))
 
 
-class ReportDatePicker(QDialog):
-    """
-    custom dialog to ask for report start/stop dates
-    """    
-    def __init__(self) -> None:
-        super().__init__()
-        self.setWindowTitle("Select Report Date Range")
-        # NOTE: make confirm/reject buttons
-        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-        self.buttonBox = QDialogButtonBox(QBtn)
-        self.buttonBox.accepted.connect(self.accept)
-        self.buttonBox.rejected.connect(self.reject)
-        # NOTE: widgets to ask for dates 
-        self.start_date = QDateEdit(calendarPopup=True)
-        self.start_date.setObjectName("start_date")
-        self.start_date.setDate(QDate.currentDate())
-        self.end_date = QDateEdit(calendarPopup=True)
-        self.end_date.setObjectName("end_date")
-        self.end_date.setDate(QDate.currentDate())
-        self.layout = QVBoxLayout()
-        self.layout.addWidget(QLabel("Start Date"))
-        self.layout.addWidget(self.start_date)
-        self.layout.addWidget(QLabel("End Date"))
-        self.layout.addWidget(self.end_date)
-        self.layout.addWidget(self.buttonBox)
-        self.setLayout(self.layout)
-
-    def parse_form(self) -> dict:
-        """
-        Converts information in this object to a dict
-
-        Returns:
-            dict: output dict.
-        """        
-        return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
+# class ReportDatePicker(QDialog):
+#     """
+#     custom dialog to ask for report start/stop dates
+#     """
+#     def __init__(self) -> None:
+#         super().__init__()
+#         self.setWindowTitle("Select Report Date Range")
+#         # NOTE: make confirm/reject buttons
+#         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+#         self.buttonBox = QDialogButtonBox(QBtn)
+#         self.buttonBox.accepted.connect(self.accept)
+#         self.buttonBox.rejected.connect(self.reject)
+#         # NOTE: widgets to ask for dates
+#         self.start_date = QDateEdit(calendarPopup=True)
+#         self.start_date.setObjectName("start_date")
+#         self.start_date.setDate(QDate.currentDate())
+#         self.end_date = QDateEdit(calendarPopup=True)
+#         self.end_date.setObjectName("end_date")
+#         self.end_date.setDate(QDate.currentDate())
+#         self.layout = QVBoxLayout()
+#         self.layout.addWidget(QLabel("Start Date"))
+#         self.layout.addWidget(self.start_date)
+#         self.layout.addWidget(QLabel("End Date"))
+#         self.layout.addWidget(self.end_date)
+#         self.layout.addWidget(self.buttonBox)
+#         self.setLayout(self.layout)
+#
+#     def parse_form(self) -> dict:
+#         """
+#         Converts information in this object to a dict
+#
+#         Returns:
+#             dict: output dict.
+#         """
+#         return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
 
 
 class LogParser(QDialog):
@@ -160,13 +166,13 @@ class LogParser(QDialog):
     def filelookup(self):
         """
         Select file to search
-        """        
+        """
         self.fname = select_open_file(self, "tabular")
 
     def runsearch(self):
         """
         Gets total/percent occurences of string in tabular file.
-        """        
+        """
         count: int = 0
         total: int = 0
         # logger.debug(f"Current search term: {self.phrase_looker.currentText()}")
@@ -177,7 +183,7 @@ class LogParser(QDialog):
                     for line in chunk:
                         if self.phrase_looker.currentText().lower() in line.lower():
                             count += 1
-            percent = (count/total)*100
+            percent = (count / total) * 100
             msg = f"I found {count} instances of the search phrase out of {total} = {percent:.2f}%."
             status = "Information"
         except AttributeError:
@@ -186,3 +192,56 @@ class LogParser(QDialog):
         dlg = AlertPop(message=msg, status=status)
         dlg.exec()
 
+
+class StartEndDatePicker(QWidget):
+    """
+    custom widget to pick start and end dates for controls graphs
+    """
+
+    def __init__(self, default_start: int) -> None:
+        super().__init__()
+        self.start_date = QDateEdit(calendarPopup=True)
+        # NOTE: start date is two months prior to end date by default
+        default_start = QDate.currentDate().addDays(default_start)
+        self.start_date.setDate(default_start)
+        self.end_date = QDateEdit(calendarPopup=True)
+        self.end_date.setDate(QDate.currentDate())
+        self.layout = QHBoxLayout()
+        self.layout.addWidget(QLabel("Start Date"))
+        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)
+
+    def sizeHint(self) -> QSize:
+        return QSize(80, 20)
+
+
+def save_pdf(obj: QWebEngineView, filename: Path):
+    page_layout = QPageLayout()
+    page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
+    page_layout.setOrientation(QPageLayout.Orientation.Portrait)
+    page_layout.setMargins(QMarginsF(25, 25, 25, 25))
+    obj.page().printToPdf(filename.absolute().__str__(), page_layout)
+
+
+# subclass
+class CheckableComboBox(QComboBox):
+    # once there is a checkState set, it is rendered
+    # here we assume default Unchecked
+
+    def addItem(self, item, header: bool = False):
+        super(CheckableComboBox, self).addItem(item)
+        item: QStandardItem = self.model().item(self.count() - 1, 0)
+        if not header:
+            item.setFlags(Qt.ItemFlag.ItemIsUserCheckable | Qt.ItemFlag.ItemIsEnabled)
+            item.setCheckState(Qt.CheckState.Checked)
+
+    def itemChecked(self, index):
+        item = self.model().item(index, 0)
+        return item.checkState() == Qt.CheckState.Checked
+
+    def changed(self):
+        logger.debug("emitting updated")
+        self.updated.emit()

src/submissions/frontend/widgets/submission_details.py

@@ -10,8 +10,9 @@ from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtCore import Qt, pyqtSlot, QMarginsF
 from jinja2 import TemplateNotFound
 from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType
-from tools import is_power_user, html_to_pdf, jinja_template_loading
+from tools import is_power_user, jinja_template_loading
 from .functions import select_save_file
+from .misc import save_pdf
 from pathlib import Path
 import logging
 from getpass import getuser
@@ -177,11 +178,12 @@ class SubmissionDetails(QDialog):
         Renders submission to html, then creates and saves .pdf file to user selected file.
         """
         fname = select_save_file(obj=self, default_name=self.export_plate, extension="pdf")
-        page_layout = QPageLayout()
-        page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
-        page_layout.setOrientation(QPageLayout.Orientation.Portrait)
-        page_layout.setMargins(QMarginsF(25, 25, 25, 25))
-        self.webview.page().printToPdf(fname.with_suffix(".pdf").__str__(), page_layout)
+        # page_layout = QPageLayout()
+        # page_layout.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
+        # page_layout.setOrientation(QPageLayout.Orientation.Portrait)
+        # page_layout.setMargins(QMarginsF(25, 25, 25, 25))
+        # self.webview.page().printToPdf(fname.with_suffix(".pdf").__str__(), page_layout)
+        save_pdf(obj=self, filename=fname)
 
 class SubmissionComment(QDialog):
     """

src/submissions/frontend/widgets/submission_table.py

@@ -10,7 +10,7 @@ from backend.db.models import BasicSubmission
 from backend.excel import ReportMaker
 from tools import Report, Result, report_result
 from .functions import select_save_file, select_open_file
-from .misc import ReportDatePicker
+# from .misc import ReportDatePicker
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -226,32 +226,32 @@ class SubmissionsSheet(QTableView):
         report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
         return report
 
-    @report_result
-    def generate_report(self, *args):
-        """
-        Make a report
-        """
-        report = Report()
-        result = self.generate_report_function()
-        report.add_result(result)
-        return report
-
-    def generate_report_function(self):
-        """
-        Generate a summary of activities for a time period
-
-        Args:
-            obj (QMainWindow): original app window
-
-        Returns:
-            Tuple[QMainWindow, dict]: Collection of new main app window and result dict
-        """    
-        report = Report()
-        # NOTE: ask for date ranges
-        dlg = ReportDatePicker()
-        if dlg.exec():
-            info = dlg.parse_form()
-            fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.xlsx", extension="xlsx")
-            rp = ReportMaker(start_date=info['start_date'], end_date=info['end_date'])
-            rp.write_report(filename=fname, obj=self)
-        return report
+    # @report_result
+    # def generate_report(self, *args):
+    #     """
+    #     Make a report
+    #     """
+    #     report = Report()
+    #     result = self.generate_report_function()
+    #     report.add_result(result)
+    #     return report
+    #
+    # def generate_report_function(self):
+    #     """
+    #     Generate a summary of activities for a time period
+    #
+    #     Args:
+    #         obj (QMainWindow): original app window
+    #
+    #     Returns:
+    #         Tuple[QMainWindow, dict]: Collection of new main app window and result dict
+    #     """
+    #     report = Report()
+    #     # NOTE: ask for date ranges
+    #     dlg = ReportDatePicker()
+    #     if dlg.exec():
+    #         info = dlg.parse_form()
+    #         fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.xlsx", extension="xlsx")
+    #         rp = ReportMaker(start_date=info['start_date'], end_date=info['end_date'])
+    #         rp.write_report(filename=fname, obj=self)
+    #     return report

src/submissions/frontend/widgets/summary.py

@@ -0,0 +1,78 @@
+from PyQt6.QtCore import QSignalBlocker
+from PyQt6.QtWebEngineWidgets import QWebEngineView
+from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QComboBox, QLabel
+from backend.db import Organization
+from backend.excel import ReportMaker
+from tools import Report
+from .misc import StartEndDatePicker, save_pdf, CheckableComboBox
+from .functions import select_save_file
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+
+class Summary(QWidget):
+
+    def __init__(self, parent: QWidget) -> None:
+        super().__init__(parent)
+        self.app = self.parent().parent()
+        # logger.debug(f"\n\n{self.app}\n\n")
+        self.report = Report()
+        self.datepicker = StartEndDatePicker(default_start=-31)
+        self.webview = QWebEngineView()
+        self.datepicker.start_date.dateChanged.connect(self.get_report)
+        self.datepicker.end_date.dateChanged.connect(self.get_report)
+        self.layout = QGridLayout(self)
+        self.layout.addWidget(self.datepicker, 0, 0, 1, 2)
+        self.save_excel_button = QPushButton("Save Excel", parent=self)
+        self.save_excel_button.pressed.connect(self.save_excel)
+        self.save_pdf_button = QPushButton("Save PDF", parent=self)
+        self.save_pdf_button.pressed.connect(self.save_pdf)
+        self.org_select = CheckableComboBox()
+        self.org_select.setEditable(False)
+        self.org_select.addItem("Select", header=True)
+        for org in [org.name for org in Organization.query()]:
+            self.org_select.addItem(org)
+        self.org_select.model().itemChanged.connect(self.get_report)
+        # self.org_select.itemChecked.connect(self.get_report)
+        self.layout.addWidget(self.save_excel_button, 0, 2, 1, 1)
+        self.layout.addWidget(self.save_pdf_button, 0, 3, 1, 1)
+        self.layout.addWidget(self.webview, 2, 0, 1, 4)
+        self.layout.addWidget(QLabel("Client"), 1, 0, 1, 1)
+        self.layout.addWidget(self.org_select, 1, 1, 1, 3)
+        self.setLayout(self.layout)
+        self.get_report()
+
+
+    def get_report(self):
+        orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)]
+        if self.datepicker.start_date.date() > self.datepicker.end_date.date():
+            logger.warning("Start date after end date is not allowed!")
+            lastmonth = self.datepicker.end_date.date().addDays(-31)
+            # NOTE: block signal that will rerun controls getter and set start date
+            # Without triggering this function again
+            with QSignalBlocker(self.datepicker.start_date) as blocker:
+                self.datepicker.start_date.setDate(lastmonth)
+            self.get_report()
+            return
+        # NOTE: convert to python useable date objects
+        self.start_date = self.datepicker.start_date.date().toPyDate()
+        self.end_date = self.datepicker.end_date.date().toPyDate()
+        self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs)
+        self.webview.setHtml(self.report_obj.html)
+        if self.report_obj.subs:
+            self.save_pdf_button.setEnabled(True)
+            self.save_excel_button.setEnabled(True)
+        else:
+            self.save_pdf_button.setEnabled(False)
+            self.save_excel_button.setEnabled(False)
+
+    def save_excel(self):
+        fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
+        self.report_obj.write_report(fname, obj=self)
+
+    def save_pdf(self):
+        fname = select_save_file(obj=self,
+                                 default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
+                                 extension="pdf")
+        save_pdf(obj=self.webview, filename=fname)

src/submissions/templates/summary_report.html

@@ -1,10 +1,10 @@
 <!doctype html>
 <html>
     <head>
-        <title>Submissions Report for {{ input['start_date'] }} - {{ input['end_date'] }}</title>
+        <title>Submissions Report for {{ input['start_date'] }} to {{ input['end_date'] }}</title>
     </head>
     <body>
-        <h2>Submissions Report {{ input['start_date'] }} - {{ input['end_date'] }}</h2>
+        <h2>Submissions Report {{ input['start_date'] }} to {{ input['end_date'] }}</h2>
         <br>
         {{ input['table'] }}
         <br>
@@ -12,10 +12,10 @@
         <h3><u>{{ lab['lab'] }}:</u></h3>
             {% for kit in lab['kits'] %}
             <p><b>{{ kit['name'] }}</b></p>
-                <p>     Runs: {{ kit['run_count'] }}, Samples: {{ kit['sample_count'] }}, Cost: {{ "${:,.2f}".format(kit['cost']) }}</p>
+                <p>&nbsp;&nbsp;&nbsp;&nbsp;Runs: {{ kit['run_count'] }}, Samples: {{ kit['sample_count'] }}, Cost: {{ "${:,.2f}".format(kit['cost']) }}</p>
             {% endfor %}
-            <p><b>Lab total:</b></p>
-                <p>     Runs: {{ lab['total_runs'] }}, Samples: {{ lab['total_samples'] }}, Cost: {{ "${:,.2f}".format(lab['total_cost']) }}</p>
+            <p><b><u>Lab total:</u></b></p>
+                <p>&nbsp;&nbsp;&nbsp;&nbsp;Runs: {{ lab['total_runs'] }}, Samples: {{ lab['total_samples'] }}, Cost: {{ "${:,.2f}".format(lab['total_cost']) }}</p>
         <br>
         {% endfor %}
     </body>

src/submissions/tools/__init__.py

@@ -7,7 +7,7 @@ import json
 import pprint
 from json import JSONDecodeError
 import numpy as np
-import logging, re, yaml, sys, os, stat, platform, getpass, inspect, csv
+import logging, re, yaml, sys, os, stat, platform, getpass, inspect
 import pandas as pd
 from jinja2 import Environment, FileSystemLoader
 from logging import handlers
@@ -17,22 +17,15 @@ from sqlalchemy import create_engine, text, MetaData
 from pydantic import field_validator, BaseModel, Field
 from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing import Any, Tuple, Literal, List
-from PyQt6.QtGui import QPageSize
-from PyQt6.QtWebEngineWidgets import QWebEngineView
-from openpyxl.worksheet.worksheet import Worksheet
-from PyQt6.QtPrintSupport import QPrinter
 from __init__ import project_path
 from configparser import ConfigParser
 from tkinter import Tk  # from tkinter import Tk for Python 3.x
 from tkinter.filedialog import askdirectory
-# from .error_messaging import parse_exception_to_message
-from sqlalchemy.exc import ArgumentError, IntegrityError as sqlalcIntegrityError
+from sqlalchemy.exc import IntegrityError as sqlalcIntegrityError
 
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
-# package_dir = Path(__file__).parents[2].resolve()
-# package_dir = project_path
 logger.debug(f"Package dir: {project_path}")
 
 if platform.system() == "Windows":
@@ -154,11 +147,11 @@ def check_not_nan(cell_contents) -> bool:
         bool: True if cell has value, else, false.
     """
     # NOTE: check for nan as a string first
-    exclude = ['unnamed:', 'blank', 'void']
+    exclude = ['unnamed:', 'blank', 'void', 'nat', 'nan', ""]
     try:
         if cell_contents.lower() in exclude:
             cell_contents = np.nan
-        cell_contents = cell_contents.lower()
+        # cell_contents = cell_contents.lower()
     except (TypeError, AttributeError):
         pass
     try:
@@ -166,14 +159,6 @@ def check_not_nan(cell_contents) -> bool:
             cell_contents = np.nan
     except TypeError as e:
         pass
-    if cell_contents == "nat":
-        cell_contents = np.nan
-    if cell_contents == 'nan':
-        cell_contents = np.nan
-    if cell_contents is 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
@@ -899,7 +884,6 @@ def yaml_regex_creator(loader, node):
     return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
 
 
-
 ctx = get_config(None)