Refactored to increase ui robustness.

src/submissions/frontend/all_window_functions.py

@@ -1,7 +1,4 @@
-'''
-contains operations used by multiple widgets.
-'''
-from backend.db.models import *
+from pathlib import Path
 import logging
 from PyQt6.QtWidgets import (
     QMainWindow, QLabel, QToolBar, 
@@ -11,9 +8,18 @@ from PyQt6.QtWidgets import (
     QSpinBox, QScrollArea
 )
 
-
 logger = logging.getLogger(f"submissions.{__name__}")
 
+def select_open_file(obj:QMainWindow, extension:str) -> Path:
+    home_dir = str(Path(obj.ctx["directory_path"]))
+    fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = f"{extension}(*.{extension})")[0])
+    return fname
+
+def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
+    home_dir = Path(obj.ctx["directory_path"]).joinpath(default_name).resolve().__str__()
+    fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter = f"{extension}(*.{extension})")[0])
+    return fname
+
 def extract_form_info(object) -> dict:
     """
     retrieves object names and values from form
@@ -24,6 +30,7 @@ def extract_form_info(object) -> dict:
     Returns:
         dict: dictionary of objectName:text items
     """        
+    
     from frontend.custom_widgets import ReagentTypeForm
     dicto = {}
     reagents = {}
@@ -51,4 +58,4 @@ def extract_form_info(object) -> dict:
         # value for ad hoc check above
     if reagents != {}:
         return dicto, reagents
-    return dicto
+    return dicto

src/submissions/frontend/custom_widgets/misc.py

@@ -14,7 +14,7 @@ from PyQt6.QtCore import Qt, QDate, QSize
 # from submissions.backend.db.functions import lookup_kittype_by_use
 # from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
 from tools import check_not_nan
-from ..functions import extract_form_info
+from ..all_window_functions import extract_form_info
 from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name, lookup_kittype_by_use#, lookup_regent_by_type_name_and_kit_name
 from backend.excel.parser import SheetParser
 from jinja2 import Environment, FileSystemLoader

src/submissions/frontend/main_window_functions.py

@@ -0,0 +1,658 @@
+'''
+contains operations used by multiple widgets.
+'''
+from datetime import date
+import difflib
+from getpass import getuser
+import inspect
+from pathlib import Path
+import pprint
+import re
+import yaml
+import json
+from typing import Tuple
+from openpyxl.utils import get_column_letter
+from xhtml2pdf import pisa
+import pandas as pd
+from backend.db.models import *
+import logging
+from PyQt6.QtWidgets import (
+    QMainWindow, QLabel, QWidget, QPushButton, QFileDialog,
+    QLineEdit, QMessageBox, QComboBox, QDateEdit
+)
+from .all_window_functions import extract_form_info, select_open_file, select_save_file
+from PyQt6.QtCore import QSignalBlocker
+from backend.db.functions import (
+    lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name, 
+    construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range, 
+    create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
+    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample
+)
+from backend.excel.parser import SheetParser, PCRParser
+from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
+from tools import RSLNamer, check_not_nan, check_kit_integrity
+from .custom_widgets.pop_ups import AlertPop, QuestionAsker
+from .custom_widgets import ReportDatePicker, ReagentTypeForm
+from .custom_widgets.misc import ImportReagent
+from .visualizations.control_charts import create_charts, construct_html
+
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]:
+    result = None
+    # from .custom_widgets.misc import ImportReagent
+    # from .custom_widgets.pop_ups import AlertPop
+    logger.debug(obj.ctx)
+    # initialize samples
+    obj.samples = []
+    obj.reagents = {}
+    # set file dialog
+    # home_dir = str(Path(obj.ctx["directory_path"]))
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir)[0])
+    fname = select_open_file(obj, extension="xlsx")
+    logger.debug(f"Attempting to parse file: {fname}")
+    if not fname.exists():
+        result = dict(message=f"File {fname.__str__()} not found.", status="critical")
+        return obj, result
+    # create sheetparser using excel sheet and context from gui
+    try:
+        prsr = SheetParser(fname, **obj.ctx)
+    except PermissionError:
+        logger.error(f"Couldn't get permission to access file: {fname}")
+        return
+    if prsr.sub['rsl_plate_num'] == None:
+        prsr.sub['rsl_plate_num'] = RSLNamer(fname.__str__()).parsed_name
+    logger.debug(f"prsr.sub = {prsr.sub}")
+    # destroy any widgets from previous imports
+    for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
+        item.setParent(None)
+    # regex to parser out different variable types for decision making
+    variable_parser = re.compile(r"""
+        # (?x)
+        (?P<extraction_kit>^extraction_kit$) |
+        (?P<submitted_date>^submitted_date$) |
+        (?P<submitting_lab>)^submitting_lab$ |
+        (?P<samples>)^samples$ |
+        (?P<reagent>^lot_.*$) |
+        (?P<csv>^csv$)
+    """, re.VERBOSE)
+    for item in prsr.sub:
+        logger.debug(f"Item: {item}")
+        # attempt to match variable name to regex group
+        try:
+            mo = variable_parser.fullmatch(item).lastgroup
+        except AttributeError:
+            mo = "other"
+        logger.debug(f"Mo: {mo}")
+        match mo:
+            case 'submitting_lab':
+                # create label
+                obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
+                logger.debug(f"{item}: {prsr.sub[item]}")
+                # create combobox to hold looked up submitting labs
+                add_widget = QComboBox()
+                labs = [item.__str__() for item in lookup_all_orgs(ctx=obj.ctx)]
+                # try to set closest match to top of list
+                try:
+                    labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
+                except (TypeError, ValueError):
+                    pass
+                # set combobox values to lookedup values
+                add_widget.addItems(labs)
+            case 'extraction_kit':
+                # create label
+                obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
+                # if extraction kit not available, all other values fail
+                if not check_not_nan(prsr.sub[item]):
+                    msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
+                    msg.exec()
+                # create combobox to hold looked up kits
+                add_widget = QComboBox()
+                # lookup existing kits by 'submission_type' decided on by sheetparser
+                uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=prsr.sub['submission_type'])]
+                add_widget.addItems(uses)
+                if check_not_nan(prsr.sub[item]):
+                    obj.ext_kit = prsr.sub[item]
+                else:
+                    obj.ext_kit = add_widget.currentText()
+            case 'submitted_date':
+                # create label
+                obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
+                # uses base calendar
+                add_widget = QDateEdit(calendarPopup=True)
+                # sets submitted date based on date found in excel sheet
+                try:
+                    add_widget.setDate(prsr.sub[item])
+                # if not found, use today
+                except:
+                    add_widget.setDate(date.today())
+            case 'reagent':
+                # create label
+                reg_label = QLabel(item.replace("_", " ").title())
+                reg_label.setObjectName(f"lot_{item}_label")
+                obj.table_widget.formlayout.addWidget(reg_label)
+                # create reagent choice widget
+                add_widget = ImportReagent(ctx=obj.ctx, item=item, prsr=prsr)
+                obj.reagents[item] = prsr.sub[item]
+            case 'samples':
+                # hold samples in 'obj' until form submitted
+                logger.debug(f"{item}: {prsr.sub[item]}")
+                obj.samples = prsr.sub[item]
+                add_widget = None
+            case 'csv':
+                obj.csv = prsr.sub[item]
+            case _:
+                # anything else gets added in as a line edit
+                obj.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
+                add_widget = QLineEdit()
+                logger.debug(f"Setting widget text to {str(prsr.sub[item]).replace('_', ' ')}")
+                add_widget.setText(str(prsr.sub[item]).replace("_", " "))
+        try:
+            add_widget.setObjectName(item)
+            logger.debug(f"Widget name set to: {add_widget.objectName()}")
+            obj.table_widget.formlayout.addWidget(add_widget)
+        except AttributeError as e:
+            logger.error(e)
+    # compare obj.reagents with expected reagents in kit
+    if hasattr(obj, 'ext_kit'):
+        obj.kit_integrity_completion()
+    logger.debug(f"Imported reagents: {obj.reagents}")
+    
+    return obj, result
+
+def kit_reload_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
+        # item.setParent(None)
+        if isinstance(item, QLabel):
+            if item.text().startswith("Lot"):
+                item.setParent(None)
+        else:
+            logger.debug(f"Type of {item.objectName()} is {type(item)}")
+            if item.objectName().startswith("lot_"):
+                item.setParent(None)
+    obj.kit_integrity_completion_function()
+    return obj, result
+
+def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # from .custom_widgets.misc import ImportReagent
+    # from .custom_widgets.pop_ups import AlertPop
+    logger.debug(inspect.currentframe().f_back.f_code.co_name)
+    kit_widget = obj.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
+    logger.debug(f"Kit selector: {kit_widget}")
+    obj.ext_kit = kit_widget.currentText()
+    logger.debug(f"Checking integrity of {obj.ext_kit}")
+    kit = lookup_kittype_by_name(ctx=obj.ctx, name=obj.ext_kit)
+    reagents_to_lookup = [item.replace("lot_", "") for item in obj.reagents]
+    logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
+    kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
+    if kit_integrity != None:
+        # msg = AlertPop(message=kit_integrity['message'], status="critical")
+        # msg.exec()
+        result = dict(message=kit_integrity['message'], status="Warning")
+        for item in kit_integrity['missing']:
+            obj.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
+            add_widget = ImportReagent(ctx=obj.ctx, item=item)
+            obj.table_widget.formlayout.addWidget(add_widget)
+    submit_btn = QPushButton("Submit")
+    submit_btn.setObjectName("lot_submit_btn")
+    obj.table_widget.formlayout.addWidget(submit_btn)
+    submit_btn.clicked.connect(obj.submit_new_sample)
+    return obj, result
+
+def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # from .custom_widgets.misc import ImportReagent
+    # from .custom_widgets.pop_ups import AlertPop, QuestionAsker
+    info = extract_form_info(obj.table_widget.tab1)
+    reagents = {k:v for k,v in info.items() if k.startswith("lot_")}
+    info = {k:v for k,v in info.items() if not k.startswith("lot_")}
+    logger.debug(f"Info: {info}")
+    logger.debug(f"Reagents: {reagents}")
+    parsed_reagents = []
+    # compare reagents in form to reagent database
+    for reagent in reagents:
+        wanted_reagent = lookup_reagent(ctx=obj.ctx, reagent_lot=reagents[reagent])
+        logger.debug(f"Looked up reagent: {wanted_reagent}")
+        # if reagent not found offer to add to database
+        if wanted_reagent == None:
+            r_lot = reagents[reagent]
+            dlg = QuestionAsker(title=f"Add {r_lot}?", message=f"Couldn't find reagent type {reagent.replace('_', ' ').title().strip('Lot')}: {r_lot} in the database.\n\nWould you like to add it?")
+            if dlg.exec():
+                logger.debug(f"checking reagent: {reagent} in obj.reagents. Result: {obj.reagents[reagent]}")
+                expiry_date = obj.reagents[reagent]['exp']
+                wanted_reagent = obj.add_reagent(reagent_lot=r_lot, reagent_type=reagent.replace("lot_", ""), expiry=expiry_date)
+            else:
+                # In this case we will have an empty reagent and the submission will fail kit integrity check
+                logger.debug("Will not add reagent.")
+        if wanted_reagent != None:
+            parsed_reagents.append(wanted_reagent)
+    # move samples into preliminary submission dict
+    info['samples'] = obj.samples
+    info['uploaded_by'] = getuser()
+    # construct submission object
+    logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
+    base_submission, result = construct_submission_info(ctx=obj.ctx, info_dict=info)
+    # check output message for issues
+    match result['code']:
+        # code 1: ask for overwrite
+        case 1:
+            dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result['message'])
+            if dlg.exec():
+                # Do not add duplicate reagents.
+                base_submission.reagents = []
+            else:
+                return obj, dict(message="Overwrite cancelled", status="Information")
+        # code 2: No RSL plate number given
+        case 2:
+            return obj, dict(message=result['message'], status='critical')
+        case _:
+            pass
+    # add reagents to submission object
+    for reagent in parsed_reagents:
+        base_submission.reagents.append(reagent)
+    logger.debug("Checking kit integrity...")
+    kit_integrity = check_kit_integrity(base_submission)
+    if kit_integrity != None:
+        return obj, dict(message=kit_integrity['message'], status="critical")
+    logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
+    result = store_submission(ctx=obj.ctx, base_submission=base_submission)
+    # check result of storing for issues
+    # update summary sheet
+    obj.table_widget.sub_wid.setData()
+    # reset form
+    for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
+        item.setParent(None)
+    if hasattr(obj, 'csv'):
+        dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
+        if dlg.exec():
+            # home_dir = Path(obj.ctx["directory_path"]).joinpath(f"{base_submission.rsl_plate_num}.csv").resolve().__str__()
+            # fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter=".csv")[0])
+            fname = select_save_file(obj, f"{base_submission.rsl_plate_num}.csv", extension="csv")
+            try:
+                obj.csv.to_csv(fname.__str__(), index=False)
+            except PermissionError:
+                logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
+    return obj, result
+
+def generate_report_function(obj:QMainWindow) -> QMainWindow:
+    # from .custom_widgets import ReportDatePicker
+    result = None
+    dlg = ReportDatePicker()
+    if dlg.exec():
+        info = extract_form_info(dlg)
+        logger.debug(f"Report info: {info}")
+        # find submissions based on date range
+        subs = lookup_submissions_by_date_range(ctx=obj.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'])
+        # setup filedialog to handle save location of report
+        home_dir = Path(obj.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
+        fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter=".pdf")[0])
+        # logger.debug(f"report output name: {fname}")
+        with open(fname, "w+b") as f:
+            pisa.CreatePDF(html, dest=f)
+        writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
+        df.to_excel(writer, sheet_name="Report") 
+        worksheet = writer.sheets['Report']
+        for idx, col in enumerate(df):  # loop through all columns
+            series = df[col]
+            max_len = max((
+                series.astype(str).map(len).max(),  # len of largest item
+                len(str(series.name))  # len of column name/header
+                )) + 20  # adding a little extra space
+            try:
+                worksheet.column_dimensions[get_column_letter(idx)].width = max_len 
+            except ValueError:
+                pass
+        for cell in worksheet['D']:
+            if cell.row > 1:
+                cell.style = 'Currency'
+        writer.close()
+    return obj, result
+
+def add_kit_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # setup file dialog to find yaml flie
+    # home_dir = str(Path(obj.ctx["directory_path"]))
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "yml(*.yml)")[0])
+    fname = select_open_file(obj, extension="yml")
+    assert fname.exists()
+    # read yaml file
+    try:
+        with open(fname.__str__(), "r") as stream:
+            try:
+                exp = yaml.load(stream, Loader=yaml.Loader)
+            except yaml.YAMLError as exc:
+                logger.error(f'Error reading yaml file {fname}: {exc}')
+                return {}
+    except PermissionError:
+        return
+    # send to kit creator function
+    result = create_kit_from_yaml(ctx=obj.ctx, exp=exp)
+    # match result['code']:
+    #     case 0:
+    #         msg = AlertPop(message=result['message'], status='info')
+    #     case 1:
+    #         msg = AlertPop(message=result['message'], status='critical')
+    # msg.exec()
+    return obj, result
+
+def add_org_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # setup file dialog to find yaml flie
+    # home_dir = str(Path(obj.ctx["directory_path"]))
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "yml(*.yml)")[0])
+    fname = select_open_file(obj, extension="yml")
+    assert fname.exists()
+    # read yaml file
+    try:
+        with open(fname.__str__(), "r") as stream:
+            try:
+                org = yaml.load(stream, Loader=yaml.Loader)
+            except yaml.YAMLError as exc:
+                logger.error(f'Error reading yaml file {fname}: {exc}')
+                return obj, dict(message=f"There was a problem reading yaml file {fname.__str__()}", status="critical")
+    except PermissionError:
+        return obj, result
+    # send to kit creator function
+    result = create_org_from_yaml(ctx=obj.ctx, org=org)
+    # match result['code']:
+    #     case 0:
+    #         msg = AlertPop(message=result['message'], status='information')
+    #     case 1:
+    #         msg = AlertPop(message=result['message'], status='critical')
+    # msg.exec()
+    return obj, result
+
+def controls_getter_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # subtype defaults to disabled  
+    try:
+        obj.table_widget.sub_typer.disconnect()
+    except TypeError:
+        pass
+    # correct start date being more recent than end date and rerun
+    if obj.table_widget.datepicker.start_date.date() > obj.table_widget.datepicker.end_date.date():
+        logger.warning("Start date after end date is not allowed!")
+        threemonthsago = obj.table_widget.datepicker.end_date.date().addDays(-60)
+        # block signal that will rerun controls getter and set start date
+        with QSignalBlocker(obj.table_widget.datepicker.start_date) as blocker:
+            obj.table_widget.datepicker.start_date.setDate(threemonthsago)
+        obj._controls_getter()
+        return obj, result
+        # convert to python useable date object
+    obj.start_date = obj.table_widget.datepicker.start_date.date().toPyDate()
+    obj.end_date = obj.table_widget.datepicker.end_date.date().toPyDate()
+    obj.con_type = obj.table_widget.control_typer.currentText()
+    obj.mode = obj.table_widget.mode_typer.currentText()
+    obj.table_widget.sub_typer.clear()
+    # lookup subtypes
+    sub_types = get_control_subtypes(ctx=obj.ctx, type=obj.con_type, mode=obj.mode)
+    if sub_types != []:
+        # block signal that will rerun controls getter and update sub_typer
+        with QSignalBlocker(obj.table_widget.sub_typer) as blocker: 
+            obj.table_widget.sub_typer.addItems(sub_types)
+        obj.table_widget.sub_typer.setEnabled(True)
+        obj.table_widget.sub_typer.currentTextChanged.connect(obj._chart_maker)
+    else:
+        obj.table_widget.sub_typer.clear()
+        obj.table_widget.sub_typer.setEnabled(False)
+    obj._chart_maker()
+    return obj, result
+
+def chart_maker_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    logger.debug(f"Control getter context: \n\tControl type: {obj.con_type}\n\tMode: {obj.mode}\n\tStart Date: {obj.start_date}\n\tEnd Date: {obj.end_date}")
+    if obj.table_widget.sub_typer.currentText() == "":
+        obj.subtype = None
+    else:
+        obj.subtype = obj.table_widget.sub_typer.currentText()
+    logger.debug(f"Subtype: {obj.subtype}")
+    # query all controls using the type/start and end dates from the gui
+    controls = get_all_controls_by_type(ctx=obj.ctx, con_type=obj.con_type, start_date=obj.start_date, end_date=obj.end_date)
+    # if no data found from query set fig to none for reporting in webview
+    if controls == None:
+        fig = None
+    else:
+        # change each control to list of dicts
+        data = [control.convert_by_mode(mode=obj.mode) for control in controls]
+        # flatten data to one dimensional list
+        data = [item for sublist in data for item in sublist]
+        logger.debug(f"Control objects going into df conversion: {data}")
+        # send to dataframe creator
+        df = convert_data_list_to_df(ctx=obj.ctx, input=data, subtype=obj.subtype)
+        if obj.subtype == None:
+            title = obj.mode
+        else:
+            title = f"{obj.mode} - {obj.subtype}"
+        # send dataframe to chart maker
+        fig = create_charts(ctx=obj.ctx, df=df, ytitle=title)
+    logger.debug(f"Updating figure...")
+    # construct html for webview
+    html = construct_html(figure=fig)
+    logger.debug(f"The length of html code is: {len(html)}")
+    obj.table_widget.webengineview.setHtml(html)
+    obj.table_widget.webengineview.update()
+    logger.debug("Figure updated... I hope.")
+    return obj, result
+
+def link_controls_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    all_bcs = lookup_all_submissions_by_type(obj.ctx, "Bacterial Culture")
+    logger.debug(all_bcs)
+    all_controls = get_all_controls(obj.ctx)
+    ac_list = [control.name for control in all_controls]
+    count = 0
+    for bcs in all_bcs:
+        logger.debug(f"Running for {bcs.rsl_plate_num}")
+        logger.debug(f"Here is the current control: {[control.name for control in bcs.controls]}")
+        samples = [sample.sample_id for sample in bcs.samples]
+        logger.debug(bcs.controls)
+        for sample in samples:
+            # 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!!!")
+                sample = sample.replace(" ", "")
+            # if sample not in ac_list:
+            if not any([ac.startswith(sample) for ac in ac_list]):
+                continue
+            else:
+                for control in all_controls:
+                    diff = difflib.SequenceMatcher(a=sample, b=control.name).ratio()
+                    if control.name.startswith(sample):
+                        logger.debug(f"Checking {sample} against {control.name}... {diff}")
+                        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")
+                            continue
+                        else:
+                            logger.debug(f"Adding {control.name} to {bcs.rsl_plate_num} as control")
+                            bcs.controls.append(control)
+                            # bcs.control_id.append(control.id)
+                            control.submission = bcs
+                            control.submission_id = bcs.id
+                            obj.ctx["database_session"].add(control)
+                            count += 1
+        obj.ctx["database_session"].add(bcs)
+        logger.debug(f"Here is the new control: {[control.name for control in bcs.controls]}")
+    result = dict(message=f"We added {count} controls to bacterial cultures.", status="information")
+    logger.debug(result)
+    obj.ctx['database_session'].commit()
+    # msg = QMessageBox()
+    # msg.setText("Controls added")
+    # msg.setInformativeText(result)
+    # msg.setWindowTitle("Controls added")
+    # msg.exec()
+    return obj, result
+
+def link_extractions_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # home_dir = str(Path(obj.ctx["directory_path"]))
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "csv(*.csv)")[0])
+    fname = select_open_file(obj, extension="csv")
+    with open(fname.__str__(), 'r') as f:
+        runs = [col.strip().split(",") for col in f.readlines()]
+    count = 0
+    for run in runs:
+        new_run = dict(
+                start_time=run[0].strip(), 
+                rsl_plate_num=run[1].strip(), 
+                sample_count=run[2].strip(), 
+                status=run[3].strip(),
+                experiment_name=run[4].strip(),
+                end_time=run[5].strip()
+            )
+        for ii in range(6, len(run)):
+            new_run[f"column{str(ii-5)}_vol"] = run[ii]
+        sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
+        try:
+            logger.debug(f"Found submission: {sub.rsl_plate_num}")
+            count += 1
+        except AttributeError:
+            continue
+        if sub.extraction_info != None:
+            existing = json.loads(sub.extraction_info)
+        else:
+            existing = None
+        try:
+            if json.dumps(new_run) in sub.extraction_info:
+                logger.debug(f"Looks like we already have that info.")
+                continue
+        except TypeError:
+            pass
+        if existing != None:
+            try:
+                logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
+                existing.append(new_run)
+                logger.debug(f"Setting: {existing}")
+                sub.extraction_info = json.dumps(existing)
+            except TypeError:
+                logger.error(f"Error updating!")
+                sub.extraction_info = json.dumps([new_run])
+            logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
+        else:
+            sub.extraction_info = json.dumps([new_run])        
+        obj.ctx['database_session'].add(sub)
+        obj.ctx["database_session"].commit()
+    result = dict(message=f"We added {count} logs to the database.", status='information') 
+    return obj, result
+
+def link_pcr_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # home_dir = str(Path(obj.ctx["directory_path"]))
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "csv(*.csv)")[0])
+    fname = select_open_file(obj, extension="csv")
+    with open(fname.__str__(), 'r') as f:
+        runs = [col.strip().split(",") for col in f.readlines()]
+    count = 0
+    for run in runs:
+        new_run = dict(
+                start_time=run[0].strip(), 
+                rsl_plate_num=run[1].strip(), 
+                biomek_status=run[2].strip(), 
+                quant_status=run[3].strip(),
+                experiment_name=run[4].strip(),
+                end_time=run[5].strip()
+            )
+        # for ii in range(6, len(run)):
+        #     obj[f"column{str(ii-5)}_vol"] = run[ii]
+        sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
+        try:
+            logger.debug(f"Found submission: {sub.rsl_plate_num}")
+        except AttributeError:
+            continue
+        if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
+            existing = json.loads(sub.pcr_info)
+        else:
+            existing = None
+        try:
+            if json.dumps(new_run) in sub.pcr_info:
+                logger.debug(f"Looks like we already have that info.")
+                continue
+            else:
+                count += 1
+        except TypeError:
+            logger.error(f"No json to dump")
+        if existing != None:
+            try:
+                logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
+                existing.append(new_run)
+                logger.debug(f"Setting: {existing}")
+                sub.pcr_info = json.dumps(existing)
+            except TypeError:
+                logger.error(f"Error updating!")
+                sub.pcr_info = json.dumps([new_run])
+            logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
+        else:
+            sub.pcr_info = json.dumps([new_run])        
+        obj.ctx['database_session'].add(sub)
+        obj.ctx["database_session"].commit()
+    result = dict(message=f"We added {count} logs to the database.", status='information')
+    return obj, result
+
+def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
+    result = None
+    # home_dir = str(Path(obj.ctx["directory_path"]))
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "xlsx(*.xlsx)")[0])
+    fname = select_open_file(obj, extension="xlsx")
+    parser = PCRParser(ctx=obj.ctx, filepath=fname)
+    logger.debug(f"Attempting lookup for {parser.plate_num}")
+    sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
+    try:
+        logger.debug(f"Found submission: {sub.rsl_plate_num}")
+    except AttributeError:
+        logger.error(f"Submission of number {parser.plate_num} not found. Attempting rescue of plate repeat.")
+        parser.plate_num = "-".join(parser.plate_num.split("-")[:-1])
+        sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=parser.plate_num)
+        try:
+            logger.debug(f"Found submission: {sub.rsl_plate_num}")
+        except AttributeError:
+            logger.error(f"Rescue of {parser.plate_num} failed.")
+            return obj, dict(message="Couldn't find a submission with that RSL number.", status="warning")
+    # jout = json.dumps(parser.pcr)
+    count = 0
+    if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
+        existing = json.loads(sub.pcr_info)
+    else:
+        # jout = None
+        existing = None
+    if existing != None:
+        try:
+            logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
+            if json.dumps(parser.pcr) not in sub.pcr_info:
+                existing.append(parser.pcr)
+            logger.debug(f"Setting: {existing}")
+            sub.pcr_info = json.dumps(existing)
+        except TypeError:
+            logger.error(f"Error updating!")
+            sub.pcr_info = json.dumps([parser.pcr])
+        logger.debug(f"Final pcr info for {sub.rsl_plate_num}: {sub.pcr_info}")
+    else:
+        sub.pcr_info = json.dumps([parser.pcr])
+    obj.ctx['database_session'].add(sub)
+    logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
+    logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
+    obj.ctx["database_session"].commit()
+    logger.debug(f"Got {len(parser.samples)} to update!")
+    for sample in parser.samples:
+        logger.debug(f"Running update on: {sample['sample']}")
+        sample['plate_rsl'] = sub.rsl_plate_num
+        update_ww_sample(ctx=obj.ctx, sample_obj=sample)
+    result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
+    return obj, result
+    # dlg.exec()    
+
+
+
+
+
+
+
+
+

src/submissions/frontend/visualizations/control_charts.py

@@ -1,6 +1,7 @@
 '''
 Functions for constructing controls graphs using plotly.
 '''
+import plotly
 import plotly.express as px
 import pandas as pd
 from pathlib import Path
@@ -276,3 +277,13 @@ def divide_chunks(input_list:list, chunk_count:int):
     """    
     k, m = divmod(len(input_list), chunk_count)
     return (input_list[i*k+min(i, m):(i+1)*k+min(i+1, m)] for i in range(chunk_count))
+
+
+def construct_html(figure:Figure) -> str:
+    html = '<html><body>'
+    if figure != None:
+        html += plotly.offline.plot(figure, output_type='div', include_plotlyjs='cdn')#, image = 'png', auto_open=True, image_filename='plot_image')
+    else:
+        html += "<h1>No data was retrieved for the given parameters.</h1>"
+    html += '</body></html>'
+    return html