Upgrade of WastewaterArtic parsers/writers for flexibility.

CHANGELOG.md

@@ -1,3 +1,8 @@
+## 202407.02
+
+- HTML template for 'About'.
+- More flexible custom parsers/writers due to custom info items.
+
 ## 202407.01
 
 - Better documentation. 

README.md

@@ -1,7 +1,7 @@
 ## Startup:
 1. 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.
+   1. Ignore the large black window of fast scrolling text, it is there for debugging purposes.
-	b. The 'Submissions' tab should be open by default.
+   2. The 'Submissions' tab should be open by default.
 
 ## Logging in New Run:
 *should fit 90% of usage cases*
@@ -32,6 +32,7 @@
 ## Importing PCR results (Wastewater only):
 
 This is meant to import .xslx files created from the Design & Analysis Software
+
 1. Click on 'File' -> 'Import PCR Results'.
 2. Use the file dialog to locate the .xlsx file you want to import.
 3. Click 'Okay'.

src/submissions/__init__.py

@@ -15,10 +15,12 @@ def get_week_of_month() -> int:
         if day in week:
             return ii + 1
 
+# Automatically completes project info for help menu and compiling.
 __project__ = "submissions"
 __version__ = f"{year}{str(month).zfill(2)}.{get_week_of_month()}b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = f"2022-{date.today().year}, Government of Canada"
+__github__ = "https://github.com/landowark/submissions"
 
 project_path = Path(__file__).parents[2].absolute()
 

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

@@ -672,8 +672,8 @@ class SubmissionType(BaseClass):
         Returns:
             dict: Map of locations
         """
-        info = self.info_map
+        info = {k:v for k,v in self.info_map.items() if k != "custom"}
-        # logger.debug(f"Info map: {info}")
+        logger.debug(f"Info map: {info}")
         output = {}
         match mode:
             case "read":
@@ -681,6 +681,7 @@ class SubmissionType(BaseClass):
             case "write":
                 output = {k: v[mode] + v['read'] for k, v in info.items() if v[mode] or v['read']}
                 output = {k: v for k, v in output.items() if all([isinstance(item, dict) for item in v])}
+        output['custom'] = self.info_map['custom']
         return output
 
     def construct_sample_map(self) -> dict:

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

@@ -685,7 +685,7 @@ class BasicSubmission(BaseClass):
 
     # Child class custom functions
     @classmethod
-    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
+    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
         """
         Update submission dictionary with type specific information
 
@@ -731,7 +731,7 @@ class BasicSubmission(BaseClass):
         return input_dict
 
     @classmethod
-    def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
+    def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> Workbook:
         """
         Adds custom autofill methods for submission
 
@@ -1307,6 +1307,7 @@ class BacterialCulture(BasicSubmission):
         row = idx.index.to_list()[0]
         return row + 1
 
+
 class Wastewater(BasicSubmission):
     """
     derivative submission type from BasicSubmission
@@ -1345,7 +1346,7 @@ class Wastewater(BasicSubmission):
         return output
 
     @classmethod
-    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
+    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
         """
         Update submission dictionary with type specific information. Extends parent
 
@@ -1550,7 +1551,6 @@ class Wastewater(BasicSubmission):
         return input_dict
 
 
-
 class WastewaterArtic(BasicSubmission):
     """
     derivative submission type for artic wastewater
@@ -1597,7 +1597,7 @@ class WastewaterArtic(BasicSubmission):
         return output
 
     @classmethod
-    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
+    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields:dict={}) -> dict:
         """
         Update submission dictionary with type specific information
 
@@ -1608,16 +1608,20 @@ class WastewaterArtic(BasicSubmission):
         Returns:
             dict: Updated sample dictionary
         """
+        # TODO: Clean up and move range start/stops to db somehow.
         input_dict = super().custom_info_parser(input_dict)
-        ws = xl['Egel results']
+        egel_section = custom_fields['egel_results']
-        data = [ws.cell(row=ii, column=jj) for jj in range(15, 27) for ii in range(10, 18)]
+        ws = xl[egel_section['sheet']]
+        data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']) for ii in range(egel_section['start_row'], egel_section['end_row'])]
         data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
         input_dict['gel_controls'] = [
             dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
             data]
-        ws = xl['First Strand List']
+        # NOTE: Get source plate information
-        data = [dict(plate=ws.cell(row=ii, column=3).value, starting_sample=ws.cell(row=ii, column=4).value) for ii in
+        source_plates_section = custom_fields['source_plates']
-                range(8, 11)]
+        ws = xl[source_plates_section['sheet']]
+        data = [dict(plate=ws.cell(row=ii, column=source_plates_section['plate_column']).value, starting_sample=ws.cell(row=ii, column=source_plates_section['starting_sample_column']).value) for ii in
+                range(source_plates_section['start_row'], source_plates_section['end_row'])]
         for datum in data:
             if datum['plate'] in ["None", None, ""]:
                 continue
@@ -1808,7 +1812,7 @@ class WastewaterArtic(BasicSubmission):
         return input_dict
 
     @classmethod
-    def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
+    def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False, custom_fields:dict={}) -> Workbook:
         """
         Adds custom autofill methods for submission. Extends Parent
 
@@ -1822,30 +1826,33 @@ class WastewaterArtic(BasicSubmission):
         """
         input_excel = super().custom_info_writer(input_excel, info, backup)
         # logger.debug(f"Info:\n{pformat(info)}")
+        # logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
         # NOTE: check for source plate information
+        source_plates_section = custom_fields['source_plates']
         if check_key_or_attr(key='source_plates', interest=info, check_none=True):
-            worksheet = input_excel['First Strand List']
+            worksheet = input_excel[source_plates_section['sheet']]
-            start_row = 8
+            start_row = source_plates_section['start_row']
             # NOTE: write source plates to First strand list
             for iii, plate in enumerate(info['source_plates']['value']):
                 # logger.debug(f"Plate: {plate}")
                 row = start_row + iii
                 try:
-                    worksheet.cell(row=row, column=3, value=plate['plate'])
+                    worksheet.cell(row=row, column=source_plates_section['plate_column'], value=plate['plate'])
                 except TypeError:
                     pass
                 try:
-                    worksheet.cell(row=row, column=4, value=plate['starting_sample'])
+                    worksheet.cell(row=row, column=source_plates_section['starting_sample_column'], value=plate['starting_sample'])
                 except TypeError:
                     pass
         # NOTE: check for gel information
+        egel_section = custom_fields['egel_results']
         if check_key_or_attr(key='gel_info', interest=info, check_none=True):
             # logger.debug(f"Gel info check passed.")
             # NOTE: print json field gel results to Egel results
-            worksheet = input_excel['Egel results']
+            worksheet = input_excel[egel_section['sheet']]
             # TODO: Move all this into a seperate function?
-            start_row = 21
+            start_row = egel_section['start_row']
-            start_column = 15
+            start_column = egel_section['start_column']
             for row, ki in enumerate(info['gel_info']['value'], start=1):
                 # logger.debug(f"ki: {ki}")
                 # logger.debug(f"vi: {vi}")
@@ -1862,14 +1869,14 @@ class WastewaterArtic(BasicSubmission):
                     except AttributeError:
                         logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
         if check_key_or_attr(key='gel_image_path', interest=info, check_none=True):
-            worksheet = input_excel['Egel results']
+            worksheet = input_excel[egel_section['sheet']]
             # logger.debug(f"We got an image: {info['gel_image']}")
             with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
                 z = zipped.extract(info['gel_image_path']['value'], Path(TemporaryDirectory().name))
                 img = OpenpyxlImage(z)
                 img.height = 400  # insert image height in pixels as float or int (e.g. 305.5)
                 img.width = 600
-                img.anchor = 'B9'
+                img.anchor = egel_section['img_anchor']
                 worksheet.add_image(img)
         return input_excel
 

src/submissions/backend/excel/parser.py

@@ -212,12 +212,14 @@ class InfoParser(object):
         """
         dicto = {}
         # NOTE: This loop parses generic info
-        # logger.debug(f"Map: {self.map}")
+        logger.debug(f"Map: {self.map}")
         for sheet in self.xl.sheetnames:
             ws = self.xl[sheet]
             relevant = []
             for k, v in self.map.items():
                 # NOTE: If the value is hardcoded put it in the dictionary directly.
+                if k == "custom":
+                    continue
                 if isinstance(v, str):
                     dicto[k] = dict(value=v, missing=False)
                     continue
@@ -265,7 +267,7 @@ class InfoParser(object):
                     except (KeyError, IndexError):
                         continue
         # Return after running the parser components held in submission object.
-        return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl)
+        return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl, custom_fields=self.map['custom'])
 
 
 class ReagentParser(object):

src/submissions/backend/excel/writer.py

@@ -8,8 +8,6 @@ from pathlib import Path
 # from pathlib import Path
 from pprint import pformat
 from typing import List
-from collections import OrderedDict
-from jinja2 import TemplateNotFound
 from openpyxl import load_workbook, Workbook
 from backend.db.models import SubmissionType, KitType, BasicSubmission
 from backend.validators.pydant import PydSubmission
@@ -135,8 +133,8 @@ class InfoWriter(object):
         self.submission_type = submission_type
         self.sub_object = sub_object
         self.xl = xl
-        info_map = submission_type.construct_info_map(mode='write')
+        self.info_map = submission_type.construct_info_map(mode='write')
-        self.info = self.reconcile_map(info_dict, info_map)
+        self.info = self.reconcile_map(info_dict, self.info_map)
         # logger.debug(pformat(self.info))
 
     def reconcile_map(self, info_dict: dict, info_map: dict) -> dict:
@@ -154,6 +152,8 @@ class InfoWriter(object):
         for k, v in info_dict.items():
             if v is None:
                 continue
+            if k == "custom":
+                continue
             dicto = {}
             try:
                 dicto['locations'] = info_map[k]
@@ -187,7 +187,7 @@ class InfoWriter(object):
                 logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
                 sheet = self.xl[loc['sheet']]
                 sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
-        return self.sub_object.custom_info_writer(self.xl, info=self.info)
+        return self.sub_object.custom_info_writer(self.xl, info=self.info, custom_fields=self.info_map['custom'])
 
 
 class ReagentWriter(object):

src/submissions/frontend/widgets/app.py

@@ -8,9 +8,12 @@ from PyQt6.QtWidgets import (
 )
 from PyQt6.QtGui import QAction
 from pathlib import Path
-from tools import check_if_app, Settings, Report
+
+from markdown import markdown
+
+from tools import check_if_app, Settings, Report, jinja_template_loading
 from datetime import date
-from .pop_ups import  AlertPop
+from .pop_ups import AlertPop, HTMLPop
 from .misc import LogParser
 import logging, webbrowser, sys, shutil
 from .submission_table import SubmissionsSheet
@@ -31,22 +34,22 @@ class App(QMainWindow):
         self.ctx = ctx
         self.last_dir = ctx.directory_path
         self.report = Report()
-        # indicate version and connected database in title bar
+        # NOTE: indicate version and connected database in title bar
         try:
             self.title = f"Submissions App (v{ctx.package.__version__}) - {ctx.database_path}"
         except (AttributeError, KeyError):
             self.title = f"Submissions App"
-        # set initial app position and size
+        # NOTE: set initial app position and size
         self.left = 0
         self.top = 0
         self.width = 1300
         self.height = 1000
         self.setWindowTitle(self.title)
         self.setGeometry(self.left, self.top, self.width, self.height)
-        # insert tabs into main app
+        # NOTE: insert tabs into main app
         self.table_widget = AddSubForm(self)
         self.setCentralWidget(self.table_widget)
-        # run initial setups
+        # NOTE: run initial setups
         self._createActions()
         self._createMenuBar()
         self._createToolBar()
@@ -126,8 +129,11 @@ class App(QMainWindow):
         """
         Show the 'about' message
         """        
-        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__}"
+        j_env = jinja_template_loading()
-        about = AlertPop(message=output, status="Information")
+        template = j_env.get_template("project.html")
+        html = template.render(info=self.ctx.package.__dict__)
+        # logger.debug(html)
+        about = HTMLPop(html=html, title="About")
         about.exec()
 
     def openDocs(self):
@@ -143,11 +149,21 @@ class App(QMainWindow):
 
     def openGithub(self):
         """
-        Opens the instructions html page
+        Opens the github page
         """
         url = "https://github.com/landowark/submissions"
         webbrowser.get('windows-default').open(url)
 
+    def openInstructions(self):
+        if check_if_app():
+            url = Path(sys._MEIPASS).joinpath("files", "README.md")
+        else:
+            url = Path("README.md")
+        with open(url, "r", encoding="utf-8") as f:
+            html = markdown(f.read())
+        instr = HTMLPop(html=html, title="Instructions")
+        instr.exec()
+
 
     def result_reporter(self):
         """
@@ -199,35 +215,35 @@ class AddSubForm(QWidget):
         # logger.debug(f"Initializating subform...")
         super(QWidget, self).__init__(parent)
         self.layout = QVBoxLayout(self)
-        # Initialize tab screen
+        # NOTE: Initialize tab screen
         self.tabs = QTabWidget()
         self.tab1 = QWidget()
         self.tab2 = QWidget()
         self.tab3 = QWidget()
         self.tab4 = QWidget()
         self.tabs.resize(300,200)
-        # Add tabs
+        # 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")
-        # Create submission adder form
+        # NOTE: Create submission adder form
         self.formwidget = SubmissionFormContainer(self)
         self.formlayout = QVBoxLayout(self)
         self.formwidget.setLayout(self.formlayout)
         self.formwidget.setFixedWidth(300)
-        # Make scrollable interior for form
+        # NOTE: Make scrollable interior for form
         self.interior = QScrollArea(self.tab1)
         self.interior.setWidgetResizable(True)
         self.interior.setFixedWidth(325)
         self.interior.setWidget(self.formwidget)
-        # Create sheet to hold existing submissions
+        # NOTE: Create sheet to hold existing submissions
         self.sheetwidget = QWidget(self)
         self.sheetlayout = QVBoxLayout(self)
         self.sheetwidget.setLayout(self.sheetlayout)
         self.sub_wid = SubmissionsSheet(parent=parent)
         self.sheetlayout.addWidget(self.sub_wid)
-        # Create layout of first tab to hold form and sheet
+        # NOTE: Create layout of first tab to hold form and sheet
         self.tab1.layout = QHBoxLayout(self)
         self.tab1.setLayout(self.tab1.layout)
         self.tab1.layout.addWidget(self.interior)
@@ -236,7 +252,7 @@ class AddSubForm(QWidget):
         self.controls_viewer = ControlsViewer(self)
         self.tab2.layout.addWidget(self.controls_viewer)
         self.tab2.setLayout(self.tab2.layout)
-        # create custom widget to add new tabs
+        # NOTE: create custom widget to add new tabs
         ST_adder = SubmissionTypeAdder(self)
         self.tab3.layout = QVBoxLayout(self)
         self.tab3.layout.addWidget(ST_adder)
@@ -245,6 +261,6 @@ class AddSubForm(QWidget):
         self.tab4.layout = QVBoxLayout(self)
         self.tab4.layout.addWidget(kit_adder)
         self.tab4.setLayout(self.tab4.layout)
-        # add tabs to main widget
+        # NOTE: add tabs to main widget
         self.layout.addWidget(self.tabs)
         self.setLayout(self.layout)

src/submissions/frontend/widgets/gel_checker.py

@@ -3,7 +3,7 @@ Gel box for artic quality control
 """
 from PyQt6.QtWidgets import (QWidget, QDialog, QGridLayout,
                              QLabel, QLineEdit, QDialogButtonBox,
-                             QTextEdit
+                             QTextEdit, QComboBox
                              )
 import pyqtgraph as pg
 from PyQt6.QtGui import QIcon
@@ -119,8 +119,11 @@ class ControlsForm(QWidget):
             self.layout.addWidget(label, iii, 1, 1, 1)
         for iii in range(3):
             for jjj in range(3):
-                widge = QLineEdit()
+                # widge = QLineEdit()
-                widge.setText("Neg")
+                widge = QComboBox()
+                widge.addItems(['Neg', 'Pos'])
+                widge.setCurrentIndex(0)
+                widge.setEditable(True)
                 widge.setObjectName(f"{rows[iii]} : {columns[jjj]}")
                 self.layout.addWidget(widge, iii+1, jjj+2, 1, 1)
         self.layout.addWidget(QLabel("Comments:"), 0,5,1,1)
@@ -137,13 +140,13 @@ class ControlsForm(QWidget):
             List[dict]: output of values
         """        
         output = []
-        for le in self.findChildren(QLineEdit):
+        for le in self.findChildren(QComboBox):
             label = [item.strip() for item in le.objectName().split(" : ")]
             try:
                 dicto = [item for item in output if item['name']==label[0]][0]
             except IndexError:
                 dicto = dict(name=label[0], values=[])
-            dicto['values'].append(dict(name=label[1], value=le.text()))
+            dicto['values'].append(dict(name=label[1], value=le.currentText()))
             if label[0] not in [item['name'] for item in output]:
                 output.append(dicto)
         # logger.debug(pformat(output))

src/submissions/frontend/widgets/pop_ups.py

@@ -5,6 +5,8 @@ from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout, QDialog, 
     QDialogButtonBox, QMessageBox, QComboBox
 )
+from PyQt6.QtWebEngineWidgets import QWebEngineView
+from PyQt6.QtCore import Qt
 from tools import jinja_template_loading
 import logging
 from backend.db import models
@@ -19,7 +21,7 @@ class QuestionAsker(QDialog):
     """
     dialog to ask yes/no questions
     """    
-    def __init__(self, title:str, message:str) -> QDialog:
+    def __init__(self, title:str, message:str):
         super().__init__()
         self.setWindowTitle(title)
         # NOTE: set yes/no buttons
@@ -39,7 +41,7 @@ class AlertPop(QMessageBox):
     """
     Dialog to show an alert.
     """    
-    def __init__(self, message:str, status:Literal['Information', 'Question', 'Warning', 'Critical'], owner:str|None=None) -> QMessageBox:
+    def __init__(self, message:str, status:Literal['Information', 'Question', 'Warning', 'Critical'], owner:str|None=None):
         super().__init__()
         # NOTE: select icon by string
         icon = getattr(QMessageBox.Icon, status)
@@ -47,12 +49,25 @@ class AlertPop(QMessageBox):
         self.setInformativeText(message)
         self.setWindowTitle(f"{owner} - {status.title()}")
 
+class HTMLPop(QDialog):
+
+    def __init__(self, html:str, owner:str|None=None, title:str="python"):
+        super().__init__()
+
+        self.webview = QWebEngineView(parent=self)
+        self.layout = QVBoxLayout()
+        self.setWindowTitle(title)
+        self.webview.setHtml(html)
+        self.webview.setMinimumSize(600, 500)
+        self.webview.setMaximumSize(600, 500)
+        self.layout.addWidget(self.webview)
+
 
 class ObjectSelector(QDialog):
     """
     dialog to input BaseClass type manually
     """    
-    def __init__(self, title:str, message:str, obj_type:str|models.BaseClass) -> QDialog:
+    def __init__(self, title:str, message:str, obj_type:str|models.BaseClass):
         super().__init__()
         self.setWindowTitle(title)
         self.widget = QComboBox()

src/submissions/templates/project.html

@@ -0,0 +1,14 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <script src="qrc:///qtwebchannel/qwebchannel.js"></script>
+    <title>{{ title }}</title>
+</head>
+<body>
+    <p>Version: {{ info['__version__'] }}</p>
+    <p>Author: {{ info['__author__']['name'] }} - <a href="mailto:{{ info['__author__']['email' ] }}">{{ info['__author__']['email'] }}</a></p>
+    <p>Copyright: {{ info['__copyright__'] }}</p>
+    <p>Github: <a id="link" href="{{ info['__github__'] }}">{{ info['__github__'] }}</a></p>
+</body>
+</html>