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Addition of turnaround time tracking.

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This commit is contained in:
lwark
2024-12-04 12:11:10 -06:00
parent 37c5c1d3eb
commit cc53b894b2
14 changed files with 136 additions and 78 deletions
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6
src/submissions/backend/db/__init__.py
View File

@@ -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":
event.listen(LogMixin, 'after_update', update_log, propagate=True)
event.listen(LogMixin, 'after_insert', update_log, propagate=True)
# if ctx.database_schema == "sqlite":
event.listen(LogMixin, 'after_update', update_log, propagate=True)
event.listen(LogMixin, 'after_insert', update_log, propagate=True)

17
src/submissions/backend/db/models/controls.py
View File

@@ -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

17
src/submissions/backend/db/models/kits.py
View File

@@ -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.contstruct_field_map("equipment"):
for k, v in submission_type.construct_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 = list(set(self.role).intersection(extraction_kit.reagent_roles))[0]
# NOTE: Most will be able to fall back to first ReagentType in itself because most will only have 1.
except:
reagent_role = self.role[0]
reagent_role = next((item for item in set(self.role).intersection(extraction_kit.reagent_roles)), self.role[0])
# try:
# reagent_role = list(set(self.role).intersection(extraction_kit.reagent_roles))[0]
# # NOTE: Most will be able to fall back to first ReagentType in itself because most will only have 1.
# except:
# reagent_role = self.role[0]
else:
try:
reagent_role = self.role[0]

23
src/submissions/backend/db/models/submissions.py
View File

@@ -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):
completed = self.completed_date or datetime.now()
return self.calculate_turnaround(start_date=self.submitted_date.date(), end_date=completed.date())
def get_turnaround_time(self) -> Tuple[int|None, bool|None]:
try:
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 delta + 1
return None, None
return delta, delta <= ctx.TaT_threshold
# Below are the custom submission types

14
src/submissions/backend/excel/parser.py
View File

@@ -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)}
logger.warning(f"Attempting to salvage {self.kit_object} with default kit map: {reagent_map}")
if not reagent_map.keys():
# reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
logger.warning(f"Attempting to salvage with default kit {self.kit_object} and submission_type: {self.submission_type_obj}")
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]

34
src/submissions/backend/excel/reports.py
View File

@@ -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()

11
src/submissions/frontend/visualizations/__init__.py
View File

@@ -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,
months: int = 6):
def __init__(self, df: pd.DataFrame, settings: dict, modes: list, ytitle: str | None = None, parent: QWidget | None = None):
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):
"""

16
src/submissions/frontend/visualizations/irida_charts.py
View File

@@ -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,
months: int = 6):
def __init__(self, df: pd.DataFrame, modes: list, settings: dict, ytitle: str | None = None, parent: QWidget | None = None):
super().__init__(df=df, modes=modes)
self.construct_chart(df=df, modes=modes)
super().__init__(df=df, modes=modes, settings=settings)
try:
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.

8
src/submissions/frontend/visualizations/pcr_charts.py
View File

@@ -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)

2
src/submissions/frontend/widgets/__init__.py
View File

@@ -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

7
src/submissions/frontend/widgets/app.py
View File

@@ -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)

4
src/submissions/frontend/widgets/submission_details.py
View File

@@ -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)

51
src/submissions/frontend/widgets/summary.py
View File

@@ -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.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.org_select.model().itemChanged.connect(self.date_changed)
self.layout.addWidget(QLabel("Client"), 1, 0, 1, 1)
self.layout.addWidget(self.org_select, 1, 1, 1, 3)
self.setLayout(self.layout)
self.get_report()
self.date_changed()
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.end_date = self.datepicker.end_date.date().toPyDate()
# self.start_date = self.datepicker.start_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):
fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
self.report_obj.write_report(fname, obj=self)
def save_pdf(self):
fname = select_save_file(obj=self,
default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
extension="pdf")
save_pdf(obj=self.webview, filename=fname)
# def save_excel(self):
# fname = select_save_file(self, default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}", extension="xlsx")
# self.report_obj.write_report(fname, obj=self)
#
# def save_pdf(self):
# fname = select_save_file(obj=self,
# default_name=f"Report {self.start_date.strftime('%Y%m%d')} - {self.end_date.strftime('%Y%m%d')}",
# extension="pdf")
# save_pdf(obj=self.webview, filename=fname)