controls working

src/submissions/__main__.py

@@ -1,5 +1,10 @@
 import sys
 from pathlib import Path
+import os
+if getattr(sys, 'frozen', False):
+    os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
+else :
+    pass
 from configure import get_config, create_database_session, setup_logger
 ctx = get_config(None)
 from PyQt6.QtWidgets import QApplication
@@ -10,7 +15,7 @@ logger = setup_logger(verbose=True)
 ctx["database_session"] = create_database_session(Path(ctx['database']))
 
 if __name__ == '__main__':
-    app = QApplication(sys.argv)
+    app = QApplication(['', '--no-sandbox'])
     ex = App(ctx=ctx)
     sys.exit(app.exec())
 

src/submissions/backend/db/__init__.py

@@ -3,10 +3,13 @@ import pandas as pd
 # from sqlite3 import IntegrityError
 from sqlalchemy.exc import IntegrityError
 import logging
-import datetime
+from datetime import date, datetime
 from sqlalchemy import and_
 import uuid
 import base64
+from sqlalchemy import JSON
+import json
+from dateutil.relativedelta import relativedelta
 
 logger = logging.getLogger(__name__)
 
@@ -226,4 +229,52 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
 def lookup_all_sample_types(ctx:dict) -> list[str]:
     uses = [item.used_for for item in ctx['database_session'].query(models.KitType).all()]
     uses = list(set([item for sublist in uses for item in sublist]))
-    return uses
+    return uses
+
+
+
+def get_all_available_modes(ctx:dict) -> list[str]:
+    rel = ctx['database_session'].query(models.Control).first()
+    cols = [item.name for item in list(rel.__table__.columns) if isinstance(item.type, JSON)]
+    return cols
+
+
+
+def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None, end_date:date|None=None) -> list:
+    """
+    Returns a list of control objects that are instances of the input controltype.
+
+    Args:
+        con_type (str): Name of the control type.
+        ctx (dict): Settings passed down from gui.
+
+    Returns:
+        list: Control instances.
+    """
+    
+    # print(f"Using dates: {start_date} to {end_date}")
+    query = ctx['database_session'].query(models.ControlType).filter_by(name=con_type)
+    try:
+        output = query.first().instances
+    except AttributeError:
+        output = None
+    # Hacky solution to my not being able to get the sql query to work.
+    if start_date != None and end_date != None:
+        output = [item for item in output if item.submitted_date.date() > start_date and item.submitted_date.date() < end_date]
+    # print(f"Type {con_type}: {query.first()}")
+    return output
+
+
+def get_control_subtypes(ctx:dict, type:str, mode:str):
+    try:
+        outs = get_all_controls_by_type(ctx=ctx, con_type=type)[0]
+    except TypeError:
+        return []
+    jsoner = json.loads(getattr(outs, mode))
+    print(f"JSON out: {jsoner}")
+    try:
+        genera = list(jsoner.keys())[0]
+    except IndexError:
+        return []
+    subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
+    return subtypes

src/submissions/backend/excel/__init__.py

@@ -0,0 +1,43 @@
+
+from pandas import DataFrame
+import re
+
+
+
+def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
+    """
+    _summary_
+
+    Args:
+        df (DataFrame): _description_
+        column_name (str): _description_
+
+    Returns:
+        list: _description_
+    """    
+    return sorted(df[column_name].unique())
+
+
+def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
+    """
+    Removes semi-duplicates from dataframe after finding sequencing repeats.
+
+    Args:
+        settings (dict): settings passed down from click
+        df (DataFrame): initial dataframe
+
+    Returns:
+        DataFrame: dataframe with originals removed in favour of repeats.
+    """    
+    sample_names = get_unique_values_in_df_column(df, column_name="name")
+    if 'rerun_regex' in ctx:
+        # logger.debug(f"Compiling regex from: {settings['rerun_regex']}")
+        rerun_regex = re.compile(fr"{ctx['rerun_regex']}")
+        for sample in sample_names:
+            # logger.debug(f'Running search on {sample}')
+            if rerun_regex.search(sample):
+                # logger.debug(f'Match on {sample}')
+                first_run = re.sub(rerun_regex, "", sample)
+                # logger.debug(f"First run: {first_run}")
+                df = df.drop(df[df.name == first_run].index)
+        return df

src/submissions/backend/excel/parser.py

@@ -54,7 +54,6 @@ class SheetParser(object):
 
 
     def _parse_bacterial_culture(self):
-        # submission_info = self.xl.parse("Sample List")
         submission_info = self._parse_generic("Sample List")
         # iloc is [row][column] and the first row is set as header row so -2
         tech = str(submission_info.iloc[11][1])
@@ -86,13 +85,6 @@ class SheetParser(object):
         enrichment_info = self.xl.parse("Enrichment Worksheet")
         extraction_info = self.xl.parse("Extraction Worksheet")
         qprc_info = self.xl.parse("qPCR Worksheet")
-        # iloc is [row][column] and the first row is set as header row so -2
-        # self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
-        # self.sub['rsl_plate_num'] = str(submission_info.iloc[10][1])
-        # self.sub['submitted_date'] = submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
-        # self.sub['submitting_lab'] = submission_info.iloc[0][3]
-        # self.sub['sample_count'] = str(submission_info.iloc[2][3])
-        # self.sub['extraction_kit'] = submission_info.iloc[3][3]
         self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
         # reagents
         self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14]
@@ -112,24 +104,6 @@ class SheetParser(object):
         sample_parser = SampleParser(submission_info.iloc[16:40])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
         self.sub['samples'] = sample_parse()
-        # tech = str(submission_info.iloc[11][1])
-        # if tech == "nan":
-        #     tech = "Unknown"
-        # elif len(tech.split(",")) > 1:
-        #     tech_reg = re.compile(r"[A-Z]{2}")
-        #     tech = ", ".join(tech_reg.findall(tech))
-        
-        
-        # self.sub['lot_wash_1'] = submission_info.iloc[1][6]
-        # self.sub['lot_wash_2'] = submission_info.iloc[2][6]
-        # self.sub['lot_binding_buffer'] = submission_info.iloc[3][6]
-        # self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6]
-        # self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6]
-        # self.sub['lot_elution_buffer'] = submission_info.iloc[6][6]
-        # self.sub['lot_isopropanol'] = submission_info.iloc[9][6]
-        # self.sub['lot_ethanol'] = submission_info.iloc[10][6]
-        # self.sub['lot_positive_control'] = None #submission_info.iloc[103][1]
-        # self.sub['lot_plate'] = submission_info.iloc[12][6]
 
 
 class SampleParser(object):
@@ -147,9 +121,9 @@ class SampleParser(object):
             new.sample_id = sample['Unnamed: 1']
             new.organism = sample['Unnamed: 2']
             new.concentration = sample['Unnamed: 3']
-            print(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
+            # print(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
             try:
-                not_a_nan = not np.isnan(new.sample_id)
+                not_a_nan = not np.isnan(new.sample_id) and new.sample_id.lower() != 'blank'
             except TypeError:
                 not_a_nan = True
             if not_a_nan:

src/submissions/backend/excel/reports.py

@@ -1,5 +1,8 @@
+import pandas as pd
 from pandas import DataFrame
 import numpy as np
+from backend.db import models
+import json
 
 def make_report_xlsx(records:list[dict]) -> DataFrame:
     df = DataFrame.from_records(records)
@@ -10,4 +13,82 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
     print(df2.columns)
     # df2['Cost']['sum'] = df2['Cost']['sum'].apply('${:,.2f}'.format)
     df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')] = df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')].applymap('${:,.2f}'.format)
-    return df2
+    return df2
+
+
+# def split_controls_dictionary(ctx:dict, input_dict) -> list[dict]:
+#     # this will be the date in string form
+#     dict_name = list(input_dict.keys())[0]
+#     # the data associated with the date key
+#     sub_dict = input_dict[dict_name]
+#     # How many "count", "Percent", etc are in the dictionary
+#     data_size = get_dict_size(sub_dict)
+#     output = []
+#     for ii in range(data_size):
+#         new_dict = {}
+#         for genus in sub_dict:
+#             print(genus)
+#             sub_name = list(sub_dict[genus].keys())[ii]
+#             new_dict[genus] = sub_dict[genus][sub_name]
+#         output.append({"date":dict_name, "name": sub_name, "data": new_dict})
+#     return output
+        
+        
+# def get_dict_size(input:dict):
+#     return max(len(input[item]) for item in input)
+
+
+# def convert_all_controls(ctx:dict, data:list) -> dict:
+#     dfs = {}
+#     dict_list = [split_controls_dictionary(ctx, datum) for datum in data]
+#     dict_list = [item for sublist in dict_list for item in sublist]
+#     names = list(set([datum['name'] for datum in dict_list]))
+#     for name in names:
+        
+        
+#         # df = DataFrame()
+#         # entries = [{item['date']:item['data']} for item in dict_list if item['name']==name]
+#         # series_list = []
+#         # df = pd.json_normalize(entries)
+#         # for entry in entries:
+#         #     col_name = list(entry.keys())[0]
+#         #     col_dict = entry[col_name]
+#         #     series = pd.Series(data=col_dict.values(), index=col_dict.keys(), name=col_name)
+#         #     # df[col_name] = series.values
+#         #     # print(df.index)
+#         #     series_list.append(series)
+#         # df = DataFrame(series_list).T.fillna(0)
+#         # print(df)
+#         dfs['name'] = df
+#     return dfs
+
+def convert_control_by_mode(ctx:dict, control:models.Control, mode:str):
+    output = []
+    data = json.loads(getattr(control, mode))
+    for genus in data:
+        _dict = {}
+        _dict['name'] = control.name
+        _dict['submitted_date'] = control.submitted_date
+        _dict['genus'] = genus
+        _dict['target'] = 'Target' if genus.strip("*") in control.controltype.targets else "Off-target"
+        for key in data[genus]:
+            _dict[key] = data[genus][key]
+        output.append(_dict)
+    # print(output)
+    return output
+
+
+def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -> DataFrame:
+    df = DataFrame.from_records(input)
+    safe = ['name', 'submitted_date', 'genus', 'target']
+    print(df)
+    for column in df.columns:
+        if "percent" in column:
+            count_col = [item for item in df.columns if "count" in item][0]
+            # The actual percentage from kraken was off due to exclusion of NaN, recalculating.
+            df[column] = 100 * df[count_col] / df.groupby('submitted_date')[count_col].transform('sum')
+        if column not in safe:
+            if subtype != None and column != subtype:
+                del df[column]
+    # print(df)
+    return df

src/submissions/frontend/__init__.py

@@ -7,7 +7,7 @@ from PyQt6.QtWidgets import (
     QSpinBox
 )
 from PyQt6.QtGui import QAction, QIcon
-from PyQt6.QtCore import QDateTime, QDate
+from PyQt6.QtCore import QDateTime, QDate, QSignalBlocker
 from PyQt6.QtCore import pyqtSlot
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 
@@ -19,17 +19,21 @@ import plotly.express as px
 import yaml
 
 from backend.excel.parser import SheetParser
+from backend.excel.reports import convert_control_by_mode, convert_data_list_to_df
 from backend.db import (construct_submission_info, lookup_reagent, 
     construct_reagent, store_reagent, store_submission, lookup_kittype_by_use,
     lookup_regent_by_type_name_and_kit_name, lookup_all_orgs, lookup_submissions_by_date_range,
-    get_all_Control_Types_names, create_kit_from_yaml
+    get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
+    get_control_subtypes
 )
 from backend.excel.reports import make_report_xlsx
 import numpy
-from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder
+from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker
 import logging
 import difflib
 
+from frontend.visualizations.charts import create_charts
+
 logger = logging.getLogger(__name__)
 logger.info("Hello, I am a logger")
 
@@ -54,7 +58,8 @@ class App(QMainWindow):
         self._createMenuBar()
         self._createToolBar()
         self._connectActions()
-        self.renderPage()
+        # self.renderPage()
+        self.controls_getter()
         self.show()
 
     def _createMenuBar(self):
@@ -86,6 +91,10 @@ class App(QMainWindow):
         self.addReagentAction.triggered.connect(self.add_reagent)
         self.generateReportAction.triggered.connect(self.generateReport)
         self.addKitAction.triggered.connect(self.add_kit)
+        self.table_widget.control_typer.currentIndexChanged.connect(self.controls_getter)
+        self.table_widget.mode_typer.currentIndexChanged.connect(self.controls_getter)
+        self.table_widget.datepicker.start_date.dateChanged.connect(self.controls_getter)
+        self.table_widget.datepicker.end_date.dateChanged.connect(self.controls_getter)
 
 
     def importSubmission(self):
@@ -207,6 +216,28 @@ class App(QMainWindow):
         html += '</body></html>'
         self.table_widget.webengineview.setHtml(html)
         self.table_widget.webengineview.update()
+        # type = self.table_widget.control_typer.currentText()
+        # mode = self.table_widget.mode_typer.currentText()
+        # controls = get_all_controls_by_type(ctx=self.ctx, type=type)
+        # data = []
+        # for control in controls:
+        #     dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=mode)
+        #     data.append(dicts)
+        # data = [item for sublist in data for item in sublist]
+        # # print(data)
+        # df = convert_data_list_to_df(ctx=self.ctx, input=data)
+        # fig = create_charts(ctx=self.ctx, df=df)
+        
+        # print(fig)
+        # html = '<html><body>'
+        # html += plotly.offline.plot(fig, output_type='div', auto_open=True, image = 'png', image_filename='plot_image')
+        # html += '</body></html>'
+        # html = plotly.io.to_html(fig)
+        # # print(html)
+        # # with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
+        # #     f.write(html)
+        # self.table_widget.webengineview.setHtml(html)
+        # self.table_widget.webengineview.update()
 
 
     def submit_new_sample(self):
@@ -294,19 +325,101 @@ class App(QMainWindow):
 
     def add_kit(self):
         home_dir = str(Path(self.ctx["directory_path"]))
-        fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir)[0])
+        fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "yml(*.yml)")[0])
         assert fname.exists()
-        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 {}
+        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
         create_kit_from_yaml(ctx=self.ctx, exp=exp)
+
+
+    def controls_getter(self):
+        # self.table_widget.webengineview.setHtml("")
+        try:
+            self.table_widget.sub_typer.disconnect()
+        except TypeError:
+            pass
+        if self.table_widget.datepicker.start_date.date() > self.table_widget.datepicker.end_date.date():
+            print("that is not allowed!")
+            # self.table_widget.datepicker.start_date.setDate(e_date)
+            threemonthsago = self.table_widget.datepicker.end_date.date().addDays(-90)
+            with QSignalBlocker(self.table_widget.datepicker.start_date) as blocker:
+                self.table_widget.datepicker.start_date.setDate(threemonthsago)
+            self.controls_getter()
+            return
+        self.start_date = self.table_widget.datepicker.start_date.date().toPyDate()
+        self.end_date = self.table_widget.datepicker.end_date.date().toPyDate()
+        self.con_type = self.table_widget.control_typer.currentText()
+        self.mode = self.table_widget.mode_typer.currentText()
+        self.table_widget.sub_typer.clear()
+        sub_types = get_control_subtypes(ctx=self.ctx, type=self.con_type, mode=self.mode)
+        if sub_types != []:
+            with QSignalBlocker(self.table_widget.sub_typer) as blocker: 
+                self.table_widget.sub_typer.addItems(sub_types)
+            self.table_widget.sub_typer.setEnabled(True)
+            self.table_widget.sub_typer.currentTextChanged.connect(self.chart_maker)
+        else:
+           
+            self.table_widget.sub_typer.clear()
+            self.table_widget.sub_typer.setEnabled(False)
+        self.chart_maker()
         
         
+    def chart_maker(self):
+        print(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
+        if self.table_widget.sub_typer.currentText() == "":
+            self.subtype = None
+        else:
+            self.subtype = self.table_widget.sub_typer.currentText()
+        print(f"Subtype: {self.subtype}")
+        controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
+        if controls == None:
+            return
+        data = []
+        for control in controls:
+            dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
+            data.append(dicts)
+        data = [item for sublist in data for item in sublist]
+        # print(data)
+        df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
+        if self.subtype == None:
+            title = self.mode
+        else:
+            title = f"{self.mode} - {self.subtype}"
+        fig = create_charts(ctx=self.ctx, df=df, ytitle=title)
+        print(f"Updating figure...")
+        html = '<html><body>'
+        if fig != None:
+            html += plotly.offline.plot(fig, 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>'
+        # with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
+        #     f.write(html)
+        self.table_widget.webengineview.setHtml(html)
+        self.table_widget.webengineview.update()
+        print("Figure updated... I hope.")
+
+
+    # def datechange(self):
         
-    
+    #     s_date = self.table_widget.datepicker.start_date.date()
+    #     e_date = self.table_widget.datepicker.end_date.date()
+    #     if s_date > e_date:
+    #         print("that is not allowed!")
+    #         # self.table_widget.datepicker.start_date.setDate(e_date)
+    #         threemonthsago = e_date.addDays(-90)
+    #         self.table_widget.datepicker.start_date.setDate(threemonthsago)
+    #     self.chart_maker()
+
+        
+   
 class AddSubForm(QWidget):
     
     def __init__(self, parent):
@@ -354,7 +467,7 @@ class AddSubForm(QWidget):
         # self.tab1.layout.addWidget(self.scroller)
         # self.tab1.setWidget(self.scroller)
         # self.tab1.setMinimumHeight(300)
-
+        self.datepicker = ControlsDatePicker()
         self.webengineview = QWebEngineView()
         # data = '''<html>Hello World</html>'''
         # self.webengineview.setHtml(data)
@@ -362,7 +475,15 @@ class AddSubForm(QWidget):
         self.control_typer = QComboBox()
         con_types = get_all_Control_Types_names(ctx=parent.ctx)
         self.control_typer.addItems(con_types)
+        self.mode_typer = QComboBox()
+        mode_types = get_all_available_modes(ctx=parent.ctx)
+        self.mode_typer.addItems(mode_types)
+        self.sub_typer = QComboBox()
+        self.sub_typer.setEnabled(False)
+        self.tab2.layout.addWidget(self.datepicker)
         self.tab2.layout.addWidget(self.control_typer)
+        self.tab2.layout.addWidget(self.mode_typer)
+        self.tab2.layout.addWidget(self.sub_typer)
         self.tab2.layout.addWidget(self.webengineview)
         self.tab2.setLayout(self.tab2.layout)
         # Add tabs to widget
@@ -372,113 +493,3 @@ class AddSubForm(QWidget):
         self.tab3.setLayout(self.tab3.layout)
         self.layout.addWidget(self.tabs)
         self.setLayout(self.layout)
-
-        
-        
-    # @pyqtSlot()
-    # def on_click(self):
-    #     print("\n")
-    #     for currentQTableWidgetItem in self.tableWidget.selectedItems():
-    #         print(currentQTableWidgetItem.row(), currentQTableWidgetItem.column(), currentQTableWidgetItem.text())
-
-
-
-# import sys
-# from pathlib import Path
-
-# from textual import events
-# from textual.app import App, ComposeResult
-# from textual.containers import Container, Vertical
-# from textual.reactive import var
-# from textual.widgets import DirectoryTree, Footer, Header, Input, Label
-# from textual.css.query import NoMatches
-# sys.path.append(Path(__file__).absolute().parents[1].__str__())
-# from backend.excel.parser import SheetParser
-
-
-# class FormField(Input):
-
-#     def on_mount(self):
-#         self.placeholder = "Value not set."
-
-#     def update(self, input:str):
-#         self.value = input
-
-
-# class DataBrowser(App):
-#     """
-#     File browser input
-#     """    
-
-#     CSS_PATH = "static/css/data_browser.css"
-#     BINDINGS = [
-#         ("ctrl+f", "toggle_files", "Toggle Files"),
-#         ("ctrl+q", "quit", "Quit"),
-#     ]
-
-#     show_tree = var(True)
-#     context = {}
-
-#     def watch_show_tree(self, show_tree: bool) -> None:
-#         """Called when show_tree is modified."""
-#         self.set_class(show_tree, "-show-tree")
-
-#     def compose(self) -> ComposeResult:
-#         """Compose our UI."""
-#         if 'directory_path' in self.context:
-#             path = self.context['directory_path']
-#         else:
-#             path = "."
-#         yield Header()
-#         yield Container(
-#             DirectoryTree(path, id="tree-view"),
-#             Vertical(
-#                 Label("[b]File Name[/b]", classes='box'), FormField(id="file-name", classes='box'),
-#                 # Label("[b]Sample Type[/b]", classes='box'), FormField(id="sample-type", classes='box'),
-#                 id="form-view"
-#             )
-#         )
-#         yield Footer()
-
-
-#     def on_mount(self, event: events.Mount) -> None:
-#         self.query_one(DirectoryTree).focus()
-
-
-#     def on_directory_tree_file_selected(self, event: DirectoryTree.FileSelected) -> None:
-#         """Called when the user click a file in the directory tree."""
-#         event.stop()
-#         sample = SheetParser(Path(event.path), **self.context)
-#         sample_view = self.query_one("#file-name", FormField)
-#         # sample_type = self.query_one("#sample-type", FormField)
-#         sample_view.update(event.path)
-#         # sample_type.update(sample.sub['sample_type'])
-#         form_view = self.query_one("#form-view", Vertical)
-#         if sample.sub != None:
-#             for var in sample.sub.keys():
-#                 # if var == "sample_type":
-#                 #     continue
-#                 try:
-#                     deleter = self.query_one(f"#{var}_label")
-#                     deleter.remove()
-#                 except NoMatches:
-#                     pass
-#                 try:    
-#                     deleter = self.query_one(f"#{var}")
-#                     deleter.remove()
-#                 except NoMatches:
-#                     pass
-#                 form_view.mount(Label(var.replace("_", " ").upper(), id=f"{var}_label", classes='box added'))
-#                 form_view.mount(FormField(id=var, classes='box added', value=sample.sub[var]))
-#         else:
-#             adds = self.query(".added")
-#             for add in adds:
-#                 add.remove()
-
-#     def action_toggle_files(self) -> None:
-#         """Called in response to key binding."""
-#         self.show_tree = not self.show_tree
-
-# if __name__ == "__main__":
-#     app = DataBrowser()
-#     app.run()

src/submissions/frontend/custom_widgets/__init__.py

@@ -4,9 +4,9 @@ from PyQt6.QtWidgets import (
     QDialogButtonBox, QDateEdit, QTableView,
     QTextEdit, QSizePolicy, QWidget,
     QGridLayout, QPushButton, QSpinBox,
-    QScrollBar, QScrollArea
+    QScrollBar, QScrollArea, QHBoxLayout
 )
-from PyQt6.QtCore import Qt, QDate, QAbstractTableModel
+from PyQt6.QtCore import Qt, QDate, QAbstractTableModel, QSize
 from PyQt6.QtGui import QFontMetrics
 
 from backend.db import get_all_reagenttype_names, submissions_to_df, lookup_submission_by_id, lookup_all_sample_types, create_kit_from_yaml
@@ -35,7 +35,7 @@ class AddReagentQuestion(QDialog):
         self.buttonBox.rejected.connect(self.reject)
 
         self.layout = QVBoxLayout()
-        message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title()}: {reagent_lot} in the database.\nWould you like to add it?")
+        message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\nWould you like to add it?")
         self.layout.addWidget(message)
         self.layout.addWidget(self.buttonBox)
         self.setLayout(self.layout)
@@ -151,6 +151,7 @@ class SubmissionDetails(QDialog):
         interior.setParent(self)
         data = lookup_submission_by_id(ctx=ctx, id=id)
         base_dict = data.to_dict()
+        del base_dict['id']
         base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
         base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
         template = env.get_template("submission_details.txt")
@@ -306,4 +307,26 @@ class ReagentTypeForm(QWidget):
         grid.addWidget(QLabel("Extension of Life (months):"),0,2)
         eol = QSpinBox()
         eol.setMinimum(0)
-        grid.addWidget(eol, 0,3)
+        grid.addWidget(eol, 0,3)
+
+
+class ControlsDatePicker(QWidget):
+    def __init__(self) -> None:
+        super().__init__()
+
+        self.start_date = QDateEdit(calendarPopup=True)
+        threemonthsago = QDate.currentDate().addDays(-90)
+        self.start_date.setDate(threemonthsago)
+        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):
+        return QSize(80,20)  

src/submissions/frontend/visualizations/charts.py

@@ -0,0 +1,278 @@
+import plotly.express as px
+import pandas as pd
+from pathlib import Path
+from plotly.graph_objects import Figure
+import logging
+from backend.excel import get_unique_values_in_df_column
+
+logger = logging.getLogger("controls.tools.vis_functions")
+
+
+def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
+    """
+    Constructs figures based on parsed pandas dataframe.
+
+    Args:
+        settings (dict): settings passed down from click
+        df (pd.DataFrame): input dataframe
+        group_name (str): controltype
+
+    Returns:
+        Figure: _description_
+    """    
+    from backend.excel import drop_reruns_from_df
+    genera = []
+    if df.empty:
+        return None
+    for item in df['genus'].to_list():
+        try:
+            if item[-1] == "*":
+                genera.append(item[-1])    
+            else:
+                genera.append("")
+        except IndexError:
+            genera.append("")
+    df['genus'] = df['genus'].replace({'\*':''}, regex=True)
+    df['genera'] = genera
+    df = df.dropna()
+    df = drop_reruns_from_df(ctx=ctx, df=df)
+    sorts = ['submitted_date', "target", "genus"]
+    exclude = ['name', 'genera']
+    modes = [item for item in df.columns if item not in sorts and item not in exclude and "_hashes" not in item]
+    # Set descending for any columns that have "{mode}" in the header.
+    ascending = [False if item == "target" else True for item in sorts]
+    df = df.sort_values(by=sorts, ascending=ascending)
+    fig = construct_chart(ctx=ctx, df=df, modes=modes, ytitle=ytitle)
+    
+    return fig
+    
+
+
+def generic_figure_markers(fig:Figure, modes:list=[], ytitle:str|None=None) -> Figure:
+    """
+    Adds standard layout to figure.
+
+    Args:
+        fig (Figure): Input figure.
+        modes (list, optional): List of modes included in figure. Defaults to [].
+
+    Returns:
+        Figure: Output figure with updated titles, rangeslider, buttons.
+    """
+    if modes != []:
+        ytitle = modes[0]
+    # Creating visibles list for each mode.
+    fig.update_layout(
+        xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
+        yaxis_title=ytitle,
+        showlegend=True,
+        barmode='stack',
+        updatemenus=[
+            dict(
+                type="buttons",
+                direction="right",
+                x=0.7,
+                y=1.2,
+                showactive=True,
+                buttons=make_buttons(modes=modes, fig_len=len(fig.data)),
+            )
+        ]
+    )
+    fig.update_xaxes(
+        rangeslider_visible=True,
+        rangeselector=dict(
+            buttons=list([
+                dict(count=1, label="1m", step="month", stepmode="backward"),
+                dict(count=3, label="3m", step="month", stepmode="backward"),
+                dict(count=6, label="6m", step="month", stepmode="backward"),
+                dict(count=1, label="YTD", step="year", stepmode="todate"),
+                dict(count=1, label="1y", step="year", stepmode="backward"),
+                dict(step="all")
+            ])
+        )
+    )
+    logger.debug(f"Returning figure {fig}")
+    assert type(fig) == Figure
+    return fig
+
+
+def make_buttons(modes:list, fig_len:int) -> list:
+    """
+    Creates list of buttons with one for each mode to be used in showing/hiding mode traces.
+
+    Args:
+        modes (list): list of modes used by main parser.
+        fig_len (int): number of traces in the figure
+
+    Returns:
+        list: list of buttons.
+    """
+    buttons = []
+    if len(modes) > 1:
+        for ii, mode in enumerate(modes):
+            # What I need to do is create a list of bools with the same length as the fig.data
+            mode_vis = [True] * fig_len
+            # And break it into {len(modes)} chunks
+            mode_vis = list(divide_chunks(mode_vis, len(modes)))
+            # Then, for each chunk, if the chunk index isn't equal to the index of the current mode, set to false
+            for jj, sublist in enumerate(mode_vis):
+                if jj != ii:
+                    mode_vis[jj] = [not elem for elem in mode_vis[jj]]
+            # Finally, flatten list.
+            mode_vis = [item for sublist in mode_vis for item in sublist]
+            # Now, make button to add to list
+            buttons.append(dict(label=mode, method="update", args=[
+                                {"visible": mode_vis},
+                                {"yaxis.title.text": mode},
+                            ]
+                        ))
+    return buttons
+
+def output_figures(settings:dict, figs:list, group_name:str):
+    """
+    Writes plotly figure to html file.
+
+    Args:
+        settings (dict): settings passed down from click
+        fig (Figure): input figure object
+        group_name (str): controltype
+    """
+    with open(Path(settings['folder']['output']).joinpath(f'{group_name}.html'), "w") as f:
+        for fig in figs:
+            try:
+                f.write(fig.to_html(full_html=False, include_plotlyjs='cdn'))
+            except AttributeError:
+                logger.error(f"The following figure was a string: {fig}")
+
+# Below are the individual construction functions. They must be named "construct_{mode}_chart" and 
+# take only json_in and mode to hook into the main processor.
+
+def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None) -> Figure:
+    fig = Figure()
+
+    for ii, mode in enumerate(modes):
+        if "count" in mode:
+            df[mode] = pd.to_numeric(df[mode],errors='coerce')
+            color = "genus"
+            color_discrete_sequence=None
+        elif 'percent' in mode:
+            color = "genus"
+            color_discrete_sequence=None
+        else:
+            color = "target"
+            print(get_unique_values_in_df_column(df, 'target'))
+            match get_unique_values_in_df_column(df, 'target'):
+                case ['Target']:
+                    color_discrete_sequence=["blue"]
+                case ['Off-target']:
+                    color_discrete_sequence=['red']
+                case _:
+                    color_discrete_sequence=['blue', 'red']
+        bar = px.bar(df, x="submitted_date", 
+            y=mode, 
+            color=color, 
+            title=mode,
+            barmode='stack', 
+            hover_data=["genus", "name", "target", mode], 
+            text="genera",
+            color_discrete_sequence=color_discrete_sequence
+        )
+        bar.update_traces(visible = ii == 0)
+        fig.add_traces(bar.data)
+    # sys.exit(f"number of traces={len(fig.data)}")
+    return generic_figure_markers(fig=fig, modes=modes, ytitle=ytitle)
+
+
+
+def construct_refseq_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:str) -> Figure:
+    """
+    Constructs intial refseq chart for both contains and matches.
+
+    Args:
+        settings (dict): settings passed down from click.
+        df (pd.DataFrame): dataframe containing all sample data for the group.
+        group_name (str): name of the group being processed.
+        mode (str): contains or matches, overwritten by hardcoding, so don't think about it too hard.
+
+    Returns:
+        Figure: initial figure with contains and matches traces.
+    """    
+    # This overwrites the mode from the signature, might get confusing.
+    fig = Figure()
+    modes = ['contains', 'matches']
+    for ii, mode in enumerate(modes): 
+        bar = px.bar(df, x="submitted_date", 
+            y=f"{mode}_ratio", 
+            color="target", 
+            title=f"{group_name}_{mode}", 
+            barmode='stack', 
+            hover_data=["genus", "name", f"{mode}_hashes"], 
+            text="genera"
+        )
+        bar.update_traces(visible = ii == 0)
+        # Plotly express returns a full figure, so we have to use the data from that figure only.
+        fig.add_traces(bar.data)
+    # sys.exit(f"number of traces={len(fig.data)}")
+    return generic_figure_markers(fig=fig, modes=modes)
+
+
+def construct_kraken_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:str) -> Figure:
+    """
+    Constructs intial refseq chart for each mode in the kraken config settings.
+
+    Args:
+        settings (dict): settings passed down from click.
+        df (pd.DataFrame): dataframe containing all sample data for the group.
+        group_name (str): name of the group being processed.
+        mode (str): kraken modes retrieved from config file by setup.
+
+    Returns:
+        Figure: initial figure with traces for modes
+    """    
+    df[f'{mode}_count'] = pd.to_numeric(df[f'{mode}_count'],errors='coerce')
+    # The actual percentage from kraken was off due to exclusion of NaN, recalculating.
+    df[f'{mode}_percent'] = 100 * df[f'{mode}_count'] / df.groupby('submitted_date')[f'{mode}_count'].transform('sum')
+    modes = settings['modes'][mode]
+    # This overwrites the mode from the signature, might get confusing.
+    fig = Figure()
+    for ii, entry in enumerate(modes):         
+        bar = px.bar(df, x="submitted_date", 
+            y=entry,
+            color="genus",
+            title=f"{group_name}_{entry}", 
+            barmode="stack", 
+            hover_data=["genus", "name", "target"],
+            text="genera",
+        )
+        bar.update_traces(visible = ii == 0)
+        fig.add_traces(bar.data)
+    return generic_figure_markers(fig=fig, modes=modes)
+
+
+def divide_chunks(input_list:list, chunk_count:int):
+    """
+    Divides a list into {chunk_count} equal parts
+
+    Args:
+        input_list (list): Initials list
+        chunk_count (int): size of each chunk
+
+    Returns:
+        tuple: tuple containing sublists.
+    """    
+    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))
+
+########This must be at bottom of module###########
+
+function_map = {}
+for item in dict(locals().items()):
+    try:
+        if dict(locals().items())[item].__module__ == __name__:
+            try:
+                function_map[item] = dict(locals().items())[item]
+            except KeyError:
+                pass
+    except AttributeError:
+        pass
+###################################################