Addition of turnaround time tracking.

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202412.02
+
+- Addition of turnaround time tracking
+
 ## 202411.05
 
 - Can now calculate turnaround time including holidays. 

src/submissions/backend/db/__init__.py

@@ -69,6 +69,6 @@ def update_log(mapper, connection, target):
     else:
         logger.info(f"No changes detected, not updating logs.")
 
-if ctx.database_schema == "sqlite":
+# if ctx.database_schema == "sqlite":
-    event.listen(LogMixin, 'after_update', update_log, propagate=True)
+event.listen(LogMixin, 'after_update', update_log, propagate=True)
-    event.listen(LogMixin, 'after_insert', update_log, propagate=True)
+event.listen(LogMixin, 'after_insert', update_log, propagate=True)

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

@@ -279,7 +279,7 @@ class Control(BaseClass):
     @classmethod
     def make_parent_buttons(cls, parent: QWidget) -> None:
         """
-        Super that will make buttons in a CustomFigure. Made to be overrided.
+        Super that will make buttons in a CustomFigure. Made to be overridden.
         
         Args:
             parent (QWidget): chart holding widget to add buttons to.
@@ -299,6 +299,10 @@ class Control(BaseClass):
 
 
 class PCRControl(Control):
+    """
+    Class made to hold info from Design & Analysis software.
+    """
+
     id = Column(INTEGER, ForeignKey('_control.id'), primary_key=True)
     subtype = Column(String(16))  #: PC or NC
     target = Column(String(16))  #: N1, N2, etc.
@@ -348,7 +352,7 @@ class PCRControl(Control):
             df = df[df.ct > 0.0]
         except AttributeError:
             df = df
-        fig = PCRFigure(df=df, modes=[])
+        fig = PCRFigure(df=df, modes=[], settings=chart_settings)
         return report, fig
 
     def to_pydantic(self):
@@ -433,12 +437,12 @@ class IridaControl(Control):
     def convert_by_mode(self, control_sub_type: str, mode: Literal['kraken', 'matches', 'contains'],
                         consolidate: bool = False) -> Generator[dict, None, None]:
         """
-        split this instance into analysis types for controls graphs
+        split this instance into analysis types ('kraken', 'matches', 'contains') for controls graphs
 
         Args:
             consolidate (bool): whether to merge all off-target genera. Defaults to False
             control_sub_type (str): control subtype, 'MCS-NOS', etc.
-            mode (str): analysis type, 'contains', etc.
+            mode (Literal['kraken', 'matches', 'contains']): analysis type, 'contains', etc.
 
         Returns:
             List[dict]: list of records
@@ -562,7 +566,7 @@ class IridaControl(Control):
         df, modes = cls.prep_df(ctx=ctx, df=df)
         # logger.debug(f"prepped df: \n {df}")
         fig = IridaFigure(df=df, ytitle=title, modes=modes, parent=parent,
-                          months=chart_settings['months'])
+                          settings=chart_settings)
         return report, fig
 
     @classmethod
@@ -571,9 +575,8 @@ class IridaControl(Control):
         Convert list of control records to dataframe
 
         Args:
-            ctx (dict): settings passed from gui
             input_df (list[dict]): list of dictionaries containing records
-            sub_type (str | None, optional): sub_type of submission type. Defaults to None.
+            sub_mode (str | None, optional): sub_type of submission type. Defaults to None.
 
         Returns:
             DataFrame: dataframe of controls

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

@@ -168,7 +168,6 @@ class KitType(BaseClass):
         else:
             return (item.reagent_role for item in relevant_associations)
 
-    # TODO: Move to BasicSubmission?
     def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[(str, str), None, None]:
         """
         Creates map of locations in Excel workbook for a SubmissionType
@@ -274,8 +273,7 @@ class KitType(BaseClass):
             for kk, vv in assoc.to_export_dict().items():
                 v[kk] = vv
             base_dict['reagent roles'].append(v)
-        # for k, v in submission_type.construct_equipment_map():
+        for k, v in submission_type.construct_field_map("equipment"):
-        for k, v in submission_type.contstruct_field_map("equipment"):
             try:
                 assoc = next(item for item in submission_type.submissiontype_equipmentrole_associations if
                              item.equipment_role.name == k)
@@ -428,7 +426,7 @@ class Reagent(BaseClass, LogMixin):
                                         submission=sub))  #: Association proxy to SubmissionSampleAssociation.samples
 
     def __repr__(self):
-        if self.name is not None:
+        if self.name:
             return f"<Reagent({self.name}-{self.lot})>"
         else:
             return f"<Reagent({self.role.name}-{self.lot})>"
@@ -447,11 +445,12 @@ class Reagent(BaseClass, LogMixin):
 
         if extraction_kit is not None:
             # NOTE: Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
-            try:
+            reagent_role = next((item for item in set(self.role).intersection(extraction_kit.reagent_roles)), self.role[0])
-                reagent_role = list(set(self.role).intersection(extraction_kit.reagent_roles))[0]
+            # try:
-            # NOTE: Most will be able to fall back to first ReagentType in itself because most will only have 1.
+            #     reagent_role = list(set(self.role).intersection(extraction_kit.reagent_roles))[0]
-            except:
+            # # NOTE: Most will be able to fall back to first ReagentType in itself because most will only have 1.
-                reagent_role = self.role[0]
+            # except:
+            #     reagent_role = self.role[0]
         else:
             try:
                 reagent_role = self.role[0]

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

@@ -24,7 +24,7 @@ from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as S
 from openpyxl import Workbook
 from openpyxl.drawing.image import Image as OpenpyxlImage
 from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
-    report_result, create_holidays_for_year
+    report_result, create_holidays_for_year, ctx
 from datetime import datetime, date, timedelta
 from typing import List, Any, Tuple, Literal, Generator
 from dateutil.parser import parse
@@ -127,7 +127,7 @@ class BasicSubmission(BaseClass, LogMixin):
 
     def __repr__(self) -> str:
         submission_type = self.submission_type or "Basic"
-        return f"<{submission_type}Submission({self.rsl_plate_num})>"
+        return f"<Submission({self.rsl_plate_num})>"
 
     @classmethod
     def jsons(cls) -> List[str]:
@@ -1380,17 +1380,22 @@ class BasicSubmission(BaseClass, LogMixin):
         writer = pyd.to_writer()
         writer.xl.save(filename=fname.with_suffix(".xlsx"))
 
-    def get_turnaround_time(self):
+    def get_turnaround_time(self) -> Tuple[int|None, bool|None]:
-        completed = self.completed_date or datetime.now()
+        try:
-        return self.calculate_turnaround(start_date=self.submitted_date.date(), end_date=completed.date())
+            completed = self.completed_date.date()
+        except AttributeError:
+            completed = None
+        return self.calculate_turnaround(start_date=self.submitted_date.date(), end_date=completed)
 
     @classmethod
-    def calculate_turnaround(cls, start_date:date|None=None, end_date:date|None=None) -> int|None:
+    def calculate_turnaround(cls, start_date:date|None=None, end_date:date|None=None) -> Tuple[int|None, bool|None]:
+        if not end_date:
+            return None, None
         try:
-            delta = np.busday_count(start_date, end_date, holidays=create_holidays_for_year(start_date.year))
+            delta = np.busday_count(start_date, end_date, holidays=create_holidays_for_year(start_date.year)) + 1
         except ValueError:
-            return None
+            return None, None
-        return delta + 1
+        return delta, delta <= ctx.TaT_threshold
 
 
 # Below are the custom submission types

src/submissions/backend/excel/parser.py

@@ -293,20 +293,24 @@ class ReagentParser(object):
         report = Report()
         if isinstance(submission_type, dict):
             submission_type = submission_type['value']
+        if isinstance(submission_type, str):
+            submission_type = SubmissionType.query(name=submission_type)
         reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
         try:
             del reagent_map['info']
         except KeyError:
             pass
-        # logger.debug(f"Reagent map: {pformat(reagent_map)}")
+        logger.debug(f"Reagent map: {pformat(reagent_map)}")
         # NOTE: If reagent map is empty, maybe the wrong kit was given, check if there's only one kit for that submission type and use it if so.
-        if not reagent_map.keys():
+        if not reagent_map:
             temp_kit_object = self.submission_type_obj.get_default_kit()
+            logger.debug(f"Temp kit: {temp_kit_object}")
             if temp_kit_object:
                 self.kit_object = temp_kit_object
-                reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
+                # reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
-                logger.warning(f"Attempting to salvage {self.kit_object} with default kit map: {reagent_map}")
+                logger.warning(f"Attempting to salvage with default kit {self.kit_object} and submission_type: {self.submission_type_obj}")
-            if not reagent_map.keys():
+                return self.fetch_kit_info_map(submission_type=self.submission_type_obj)
+            else:
                 logger.error(f"Still no reagent map, displaying error.")
                 try:
                     ext_kit_loc = self.submission_type_obj.info_map['extraction_kit']['read'][0]

src/submissions/backend/excel/reports.py

@@ -1,6 +1,8 @@
 '''
 Contains functions for generating summary reports
 '''
+from pprint import pformat
+
 from pandas import DataFrame, ExcelWriter
 import logging
 from pathlib import Path
@@ -137,3 +139,35 @@ class ReportMaker(object):
         for cell in worksheet['D']:
             if cell.row > 1:
                 cell.style = 'Currency'
+
+class TurnaroundMaker(object):
+
+    def __init__(self, start_date: date, end_date: date):
+        self.start_date = start_date
+        self.end_date = end_date
+        # NOTE: Set page size to zero to override limiting query size.
+        self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date, page_size=0)
+        records = [self.build_record(sub) for sub in self.subs]
+        self.df = DataFrame.from_records(records)
+
+    @classmethod
+    def build_record(cls, sub):
+        days, tat_ok = sub.get_turnaround_time()
+        return dict(name=sub.rsl_plate_num, days=days, submitted_date=sub.submitted_date,
+                        completed_date=sub.completed_date, acceptable=tat_ok)
+
+    def write_report(self, filename: Path | str, obj: QWidget | None = None):
+        """
+        Writes info to files.
+
+        Args:
+            filename (Path | str): Basename of output file
+            obj (QWidget | None, optional): Parent object. Defaults to None.
+        """
+        if isinstance(filename, str):
+            filename = Path(filename)
+        filename = filename.absolute()
+        self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl')
+        self.df.to_excel(self.writer, sheet_name="Turnaround")
+        # logger.debug(f"Writing report to: {filename}")
+        self.writer.close()

src/submissions/frontend/visualizations/__init__.py

@@ -1,6 +1,8 @@
 '''
 Contains all operations for creating charts, graphs and visual effects.
 '''
+from datetime import timedelta
+
 from PyQt6.QtWidgets import QWidget
 import plotly, logging
 from plotly.graph_objects import Figure
@@ -14,10 +16,15 @@ class CustomFigure(Figure):
 
     df = None
 
-    def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
+    def __init__(self, df: pd.DataFrame, settings: dict, modes: list, ytitle: str | None = None, parent: QWidget | None = None):
-                 months: int = 6):
         super().__init__()
+        # self.settings = settings
+        try:
+            months = int(settings['months'])
+        except KeyError:
+            months = 6
         self.df = df
+        self.update_xaxes(range=[settings['start_date'] - timedelta(days=1), settings['end_date']])
 
     def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
         """

src/submissions/frontend/visualizations/irida_charts.py

@@ -16,19 +16,23 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 class IridaFigure(CustomFigure):
 
-    def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
+    def __init__(self, df: pd.DataFrame, modes: list, settings: dict, ytitle: str | None = None, parent: QWidget | None = None):
-                 months: int = 6):
 
-        super().__init__(df=df, modes=modes)
+        super().__init__(df=df, modes=modes, settings=settings)
-
+        try:
-        self.construct_chart(df=df, modes=modes)
+            months = int(settings['months'])
+        except KeyError:
+            months = 6
+        self.construct_chart(df=df, modes=modes, start_date=settings['start_date'], end_date=settings['end_date'])
         self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
 
-    def construct_chart(self, df: pd.DataFrame, modes: list):
+    def construct_chart(self, df: pd.DataFrame, modes: list, start_date: date, end_date:date):
         """
         Creates a plotly chart for controls from a pandas dataframe
 
         Args:
+            end_date ():
+            start_date ():
             df (pd.DataFrame): input dataframe of controls
             modes (list): analysis modes to construct charts for
             ytitle (str | None, optional): title on the y-axis. Defaults to None.

src/submissions/frontend/visualizations/pcr_charts.py

@@ -13,9 +13,13 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 class PCRFigure(CustomFigure):
 
-    def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
+    def __init__(self, df: pd.DataFrame, modes: list, settings: dict, ytitle: str | None = None, parent: QWidget | None = None,
                  months: int = 6):
-        super().__init__(df=df, modes=modes)
+        super().__init__(df=df, modes=modes, settings=settings)
+        try:
+            months = int(settings['months'])
+        except KeyError:
+            months = 6
         # logger.debug(f"DF: {self.df}")
         self.construct_chart(df=df)
 

src/submissions/frontend/widgets/__init__.py

@@ -11,4 +11,6 @@ from .controls_chart import *
 from .submission_details import *
 from .equipment_usage import *
 from .gel_checker import *
+from .summary import Summary
+from .turnaround import TurnaroundTime
 from .app import App

src/submissions/frontend/widgets/app.py

@@ -25,6 +25,7 @@ from .submission_widget import SubmissionFormContainer
 from .controls_chart import ControlsViewer
 # from .sample_search import SampleSearchBox
 from .summary import Summary
+from .turnaround import TurnaroundTime
 from .omni_search import SearchBox
 
 logger = logging.getLogger(f'submissions.{__name__}')
@@ -269,12 +270,14 @@ class AddSubForm(QWidget):
         self.tab2 = QWidget()
         self.tab3 = QWidget()
         self.tab4 = QWidget()
+        self.tab5 = QWidget()
         self.tabs.resize(300, 200)
         # NOTE: Add tabs
         self.tabs.addTab(self.tab1, "Submissions")
         self.tabs.addTab(self.tab2, "Irida Controls")
         self.tabs.addTab(self.tab3, "PCR Controls")
         self.tabs.addTab(self.tab4, "Cost Report")
+        self.tabs.addTab(self.tab5, "Turnaround Times")
         # NOTE: Create submission adder form
         self.formwidget = SubmissionFormContainer(self)
         self.formlayout = QVBoxLayout(self)
@@ -310,6 +313,10 @@ class AddSubForm(QWidget):
         self.tab4.layout = QVBoxLayout(self)
         self.tab4.layout.addWidget(summary_report)
         self.tab4.setLayout(self.tab4.layout)
+        turnaround = TurnaroundTime(self)
+        self.tab5.layout = QVBoxLayout(self)
+        self.tab5.layout.addWidget(turnaround)
+        self.tab5.setLayout(self.tab5.layout)
         # NOTE: add tabs to main widget
         self.layout.addWidget(self.tabs)
         self.setLayout(self.layout)

src/submissions/frontend/widgets/submission_details.py

@@ -172,11 +172,11 @@ class SubmissionDetails(QDialog):
 
     @pyqtSlot(str)
     def sign_off(self, submission: str | BasicSubmission):
-        # logger.debug(f"Signing off on {submission} - ({getuser()})")
+        logger.debug(f"Signing off on {submission} - ({getuser()})")
         if isinstance(submission, str):
             submission = BasicSubmission.query(rsl_plate_num=submission)
         submission.signed_by = getuser()
-        submission.completed = datetime.now().date()
+        submission.completed_date = datetime.now().date()
         submission.save()
         self.submission_details(submission=self.rsl_plate_num)
 

src/submissions/frontend/widgets/summary.py

@@ -1,5 +1,6 @@
 from PyQt6.QtCore import QSignalBlocker
 from PyQt6.QtWebEngineWidgets import QWebEngineView
+from .info_tab import InfoPane
 from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QLabel
 from backend.db import Organization
 from backend.excel import ReportMaker
@@ -11,38 +12,21 @@ import logging
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
-class Summary(QWidget):
+class Summary(InfoPane):
 
     def __init__(self, parent: QWidget) -> None:
         super().__init__(parent)
-        self.app = self.parent().parent()
-        # logger.debug(f"\n\n{self.app}\n\n")
-        self.report = Report()
-        self.datepicker = StartEndDatePicker(default_start=-31)
-        self.webview = QWebEngineView()
-        self.datepicker.start_date.dateChanged.connect(self.get_report)
-        self.datepicker.end_date.dateChanged.connect(self.get_report)
-        self.layout = QGridLayout(self)
-        self.layout.addWidget(self.datepicker, 0, 0, 1, 2)
-        self.save_excel_button = QPushButton("Save Excel", parent=self)
-        self.save_excel_button.pressed.connect(self.save_excel)
-        self.save_pdf_button = QPushButton("Save PDF", parent=self)
-        self.save_pdf_button.pressed.connect(self.save_pdf)
         self.org_select = CheckableComboBox()
         self.org_select.setEditable(False)
         self.org_select.addItem("Select", header=True)
         for org in [org.name for org in Organization.query()]:
             self.org_select.addItem(org)
-        self.org_select.model().itemChanged.connect(self.get_report)
+        self.org_select.model().itemChanged.connect(self.date_changed)
-        self.layout.addWidget(self.save_excel_button, 0, 2, 1, 1)
-        self.layout.addWidget(self.save_pdf_button, 0, 3, 1, 1)
-        self.layout.addWidget(self.webview, 2, 0, 1, 4)
         self.layout.addWidget(QLabel("Client"), 1, 0, 1, 1)
         self.layout.addWidget(self.org_select, 1, 1, 1, 3)
-        self.setLayout(self.layout)
+        self.date_changed()
-        self.get_report()
 
-    def get_report(self):
+    def date_changed(self):
         orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)]
         if self.datepicker.start_date.date() > self.datepicker.end_date.date():
             logger.warning("Start date after end date is not allowed!")
@@ -51,11 +35,12 @@ class Summary(QWidget):
             # Without triggering this function again
             with QSignalBlocker(self.datepicker.start_date) as blocker:
                 self.datepicker.start_date.setDate(lastmonth)
-            self.get_report()
+            self.date_changed()
             return
         # NOTE: convert to python useable date objects
-        self.start_date = self.datepicker.start_date.date().toPyDate()
+        # self.start_date = self.datepicker.start_date.date().toPyDate()
-        self.end_date = self.datepicker.end_date.date().toPyDate()
+        # self.end_date = self.datepicker.end_date.date().toPyDate()
+        super().date_changed()
         logger.debug(f"Getting report from {self.start_date} to {self.end_date} using {orgs}")
         self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs)
         self.webview.setHtml(self.report_obj.html)
@@ -66,12 +51,12 @@ class Summary(QWidget):
             self.save_pdf_button.setEnabled(False)
             self.save_excel_button.setEnabled(False)
 
-    def save_excel(self):
+    # def save_excel(self):
-        fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
+    #     fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
-        self.report_obj.write_report(fname, obj=self)
+    #     self.report_obj.write_report(fname, obj=self)
-
+    #
-    def save_pdf(self):
+    # def save_pdf(self):
-        fname = select_save_file(obj=self,
+    #     fname = select_save_file(obj=self,
-                                 default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
+    #                              default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
-                                 extension="pdf")
+    #                              extension="pdf")
-        save_pdf(obj=self.webview, filename=fname)
+    #     save_pdf(obj=self.webview, filename=fname)