landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Increasing generator usage.

Browse Source
This commit is contained in:
lwark
2024-10-08 14:55:54 -05:00
parent eaf6c156b3
commit ae5fb1b48f
9 changed files with 81 additions and 151 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
src/submissions/backend/db/models/kits.py
View File

@@ -142,8 +142,8 @@ class KitType(BaseClass):
"""
return f"<KitType({self.name})>"
def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> List[
ReagentRole]:
def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> Generator[
ReagentRole, None, None]:
"""
Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
@@ -168,9 +168,9 @@ class KitType(BaseClass):
relevant_associations = [item for item in self.kit_reagentrole_associations]
if required:
# logger.debug(f"Filtering by required.")
return [item.reagent_role for item in relevant_associations if item.required == 1]
return (item.reagent_role for item in relevant_associations if item.required == 1)
else:
return [item.reagent_role for item in relevant_associations]
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)]:
@@ -198,6 +198,7 @@ class KitType(BaseClass):
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
for assoc in assocs:
try:
logger.debug(f"Yielding: {assoc.reagent_role.name}, {assoc.uses}")
yield assoc.reagent_role.name, assoc.uses
except TypeError:
continue
@@ -764,14 +765,14 @@ class SubmissionType(BaseClass):
tmap = {}
yield item.tip_role.name, tmap
def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
def get_equipment(self, extraction_kit: str | KitType | None = None) -> Generator['PydEquipmentRole', None, None]:
"""
Returns PydEquipmentRole of all equipment associated with this SubmissionType
Returns:
List[PydEquipmentRole]: List of equipment roles
"""
return [item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment]
return (item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment)
def get_processes_for_role(self, equipment_role: str | EquipmentRole, kit: str | KitType | None = None) -> list:
"""

11
src/submissions/backend/db/models/submissions.py
View File

@@ -219,11 +219,11 @@ class BasicSubmission(BaseClass):
if len(args) == 1:
try:
return output[args[0]]
except KeyError:
except KeyError as e:
if "pytest" in sys.modules and args[0] == "abbreviation":
return "BS"
else:
raise KeyError("args[0]")
raise KeyError(f"{args[0]} not found in {output}")
return output
@classmethod
@@ -237,6 +237,13 @@ class BasicSubmission(BaseClass):
Returns:
SubmissionType: SubmissionType with name equal to this polymorphic identity
"""
logger.debug(f"Running search for {sub_type}")
if isinstance(sub_type, dict):
try:
sub_type = sub_type['value']
except KeyError as e:
logger.error(f"Couldn't extract value from {sub_type}")
raise e
match sub_type:
case str():
return SubmissionType.query(name=sub_type)

82
src/submissions/backend/excel/parser.py
View File

@@ -80,14 +80,6 @@ class SheetParser(object):
self.submission_type = RSLNamer.retrieve_submission_type(filename=self.filepath)
self.parse_info()
[self.sub.__setitem__(k, v) for k, v in info.items()]
# for k, v in info.items():
# match k:
# # NOTE: exclude samples.
# case "sample":
# logger.debug(f"Sample found: {k}: {v}")
# continue
# case _:
# self.sub[k] = v
def parse_reagents(self, extraction_kit: str | None = None):
"""
@@ -147,30 +139,8 @@ class SheetParser(object):
Returns:
PydSubmission: output pydantic model
"""
# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
# pyd_dict = copy(self.sub)
# self.sub['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
# logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
# self.sub['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
# logger.debug(f"Equipment: {self.sub['equipment']}")
# try:
# check = bool(self.sub['equipment'])
# except TypeError:
# check = False
# if check:
# self.sub['equipment'] = [PydEquipment(**equipment) for equipment in self.sub['equipment']]
# else:
# self.sub['equipment'] = None
# try:
# check = bool(self.sub['tips'])
# except TypeError:
# check = False
# if check:
# self.sub['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
# else:
# self.sub['tips'] = None
return PydSubmission(filepath=self.filepath, run_custom=True, **self.sub)
# return psm
class InfoParser(object):
@@ -298,6 +268,7 @@ class ReagentParser(object):
if isinstance(extraction_kit, dict):
extraction_kit = extraction_kit['value']
self.kit_object = KitType.query(name=extraction_kit)
# logger.debug(f"Got extraction kit object: {self.kit_object}")
self.map = self.fetch_kit_info_map(submission_type=submission_type)
# logger.debug(f"Reagent Parser map: {self.map}")
self.xl = xl
@@ -329,15 +300,14 @@ class ReagentParser(object):
Returns:
List[PydReagent]: List of parsed reagents.
"""
# listo = []
for sheet in self.xl.sheetnames:
ws = self.xl[sheet]
relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
# logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if relevant == {}:
continue
for item in relevant:
# logger.debug(f"Attempting to scrape: {item}")
logger.debug(f"Attempting to scrape: {item}")
try:
reagent = relevant[item]
name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value
@@ -350,16 +320,15 @@ class ReagentParser(object):
comment = ""
except (KeyError, IndexError):
yield dict(role=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True)
# continue
# NOTE: If the cell is blank tell the PydReagent
if check_not_nan(lot):
missing = False
else:
missing = True
# logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
lot = str(lot)
# logger.debug(
# f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
logger.debug(
f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
try:
check = name.lower() != "not applicable"
except AttributeError:
@@ -368,7 +337,6 @@ class ReagentParser(object):
if check:
yield dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
missing=missing)
# return listo
class SampleParser(object):
@@ -480,34 +448,6 @@ class SampleParser(object):
lookup_samples.append(self.samp_object.parse_sample(row_dict))
return lookup_samples
# def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
# """
# Parse merged platemap/lookup info into dicts/samples
#
# Returns:
# List[dict]|List[models.BasicSample]: List of samples
# """
# result = None
# new_samples = []
# # logger.debug(f"Starting samples: {pformat(self.samples)}")
# for sample in self.samples:
# translated_dict = {}
# for k, v in sample.items():
# match v:
# case dict():
# v = None
# case float():
# v = convert_nans_to_nones(v)
# case _:
# v = v
# translated_dict[k] = convert_nans_to_nones(v)
# translated_dict['sample_type'] = f"{self.submission_type} Sample"
# translated_dict = self.sub_object.parse_samples(translated_dict)
# translated_dict = self.samp_object.parse_sample(translated_dict)
# # logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
# new_samples.append(PydSample(**translated_dict))
# return result, new_samples
def parse_samples(self) -> Generator[dict, None, None]:
"""
Merges sample info from lookup table and plate map.
@@ -522,9 +462,8 @@ class SampleParser(object):
merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
# print(pformat(plate_map_samples))
# print(pformat(lookup_samples))
for ii, psample in enumerate(plate_map_samples):
# NOTE: See if we can do this the easy way and just use the same list index.
try:
check = psample['id'] == lookup_samples[ii][merge_on_id]
except (KeyError, IndexError):
@@ -534,7 +473,7 @@ class SampleParser(object):
new = lookup_samples[ii] | psample
lookup_samples[ii] = {}
else:
# logger.warning(f"Match for {psample['id']} not direct, running search.")
logger.warning(f"Match for {psample['id']} not direct, running search.")
for jj, lsample in enumerate(lookup_samples):
try:
check = lsample[merge_on_id] == psample['id']
@@ -551,9 +490,6 @@ class SampleParser(object):
new = self.sub_object.parse_samples(new)
del new['id']
yield new
# samples.append(new)
# samples = remove_key_from_list_of_dicts(samples, "id")
# return sorted(samples, key=lambda k: (k['row'], k['column']))
class EquipmentParser(object):

46
src/submissions/frontend/visualizations/control_charts.py
View File

@@ -2,6 +2,7 @@
Functions for constructing controls graphs using plotly.
"""
from copy import deepcopy
from datetime import date
from pprint import pformat
import plotly
@@ -18,10 +19,12 @@ logger = logging.getLogger(f"submissions.{__name__}")
class CustomFigure(Figure):
def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None):
def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
months: int = 6):
super().__init__()
self.construct_chart(df=df, modes=modes)
self.generic_figure_markers(modes=modes, ytitle=ytitle)
self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
def construct_chart(self, df: pd.DataFrame, modes: list):
"""
@@ -67,7 +70,7 @@ class CustomFigure(Figure):
self.add_traces(bar.data)
# return generic_figure_markers(modes=modes, ytitle=ytitle)
def generic_figure_markers(self, modes: list = [], ytitle: str | None = None):
def generic_figure_markers(self, modes: list = [], ytitle: str | None = None, months: int = 6):
"""
Adds standard layout to figure.
@@ -94,27 +97,41 @@ class CustomFigure(Figure):
x=0.7,
y=1.2,
showactive=True,
buttons=[button for button in self.make_buttons(modes=modes)],
buttons=[button for button in self.make_pyqt_buttons(modes=modes)],
)
]
)
self.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")
])
# 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=12, label="1y", step="month", stepmode="backward"),
# dict(step="all")
# ])
buttons=[button for button in self.make_plotly_buttons(months=months)]
)
)
assert isinstance(self, Figure)
# return fig
def make_buttons(self, modes: list) -> list:
def make_plotly_buttons(self, months:int=6):
rng = [1]
if months > 2:
rng += [iii for iii in range(3, months, 3)]
logger.debug(f"Making buttons for months: {rng}")
buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng]
if months > date.today().month:
buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")]
buttons += [dict(step="all")]
for button in buttons:
yield button
def make_pyqt_buttons(self, modes: list) -> list:
"""
Creates list of buttons with one for each mode to be used in showing/hiding mode traces.
@@ -144,7 +161,7 @@ class CustomFigure(Figure):
{"yaxis.title.text": mode},
])
def save_figure(self, group_name: str = "plotly_output", parent:QWidget|None=None):
def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
"""
Writes plotly figure to html file.
@@ -158,7 +175,6 @@ class CustomFigure(Figure):
output = select_save_file(obj=parent, default_name=group_name, extension="png")
self.write_image(output.absolute().__str__(), engine="kaleido")
def to_html(self) -> str:
"""
Creates final html code from plotly

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

@@ -240,7 +240,7 @@ class App(QMainWindow):
logger.warning("Save of submission type cancelled.")
def update_data(self):
self.table_widget.sub_wid.setData(page=int(self.table_widget.pager.current_page.text()), page_size=page_size)
self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
class AddSubForm(QWidget):

11
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -3,7 +3,7 @@ Handles display of control charts
"""
import re
import sys
from datetime import timedelta
from datetime import timedelta, date
from typing import Tuple
from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import (
@@ -113,6 +113,9 @@ class ControlsViewer(QWidget):
self.chart_maker()
return report
def diff_month(self, d1:date, d2:date):
return abs((d1.year - d2.year) * 12 + d1.month - d2.month)
def chart_maker(self):
"""
Creates plotly charts for webview
@@ -132,7 +135,8 @@ class ControlsViewer(QWidget):
"""
report = Report()
# logger.debug(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}") NOTE: set the subtype for kraken
# Date: {self.start_date}\n\tEnd Date: {self.end_date}")
# NOTE: set the subtype for kraken
if self.sub_typer.currentText() == "":
self.subtype = None
else:
@@ -161,7 +165,8 @@ class ControlsViewer(QWidget):
title = f"{self.mode} - {self.subtype}"
# NOTE: send dataframe to chart maker
df, modes = self.prep_df(ctx=self.app.ctx, df=df)
fig = CustomFigure(df=df, ytitle=title, modes=modes, parent=self)
months = self.diff_month(self.start_date, self.end_date)
fig = CustomFigure(df=df, ytitle=title, modes=modes, parent=self, months=months)
self.save_button.setEnabled(True)
# logger.debug(f"Updating figure...")
self.fig = fig

60
src/submissions/frontend/widgets/misc.py
View File

@@ -108,43 +108,6 @@ class AddReagentForm(QDialog):
self.name_input.addItems(list(set([item.name for item in lookup])))
# class ReportDatePicker(QDialog):
# """
# custom dialog to ask for report start/stop dates
# """
# def __init__(self) -> None:
# super().__init__()
# self.setWindowTitle("Select Report Date Range")
# # NOTE: make confirm/reject buttons
# QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# # NOTE: widgets to ask for dates
# self.start_date = QDateEdit(calendarPopup=True)
# self.start_date.setObjectName("start_date")
# self.start_date.setDate(QDate.currentDate())
# self.end_date = QDateEdit(calendarPopup=True)
# self.end_date.setObjectName("end_date")
# self.end_date.setDate(QDate.currentDate())
# self.layout = QVBoxLayout()
# 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.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
#
# def parse_form(self) -> dict:
# """
# Converts information in this object to a dict
#
# Returns:
# dict: output dict.
# """
# return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
class LogParser(QDialog):
def __init__(self, parent):
@@ -253,35 +216,32 @@ class Pagifier(QWidget):
def __init__(self, page_max:int):
super().__init__()
self.page_max = math.ceil(page_max)
self.page_anchor = 1
next = QPushButton(parent=self, icon = QIcon.fromTheme(QIcon.ThemeIcon.GoNext))
next.pressed.connect(self.increment_page)
previous = QPushButton(parent=self, icon=QIcon.fromTheme(QIcon.ThemeIcon.GoPrevious))
previous.pressed.connect(self.decrement_page)
label = QLabel(f"/ {self.page_max}")
label.setMinimumWidth(200)
label.setAlignment(Qt.AlignmentFlag.AlignCenter)
self.current_page = QLineEdit(self)
self.current_page.setEnabled(False)
# onlyInt = QIntValidator()
# onlyInt.setRange(1, 4)
# self.current_page.setValidator(onlyInt)
self.current_page.setText("1")
self.update_current_page()
self.current_page.setAlignment(Qt.AlignmentFlag.AlignCenter)
self.layout = QHBoxLayout()
self.layout.addWidget(previous)
self.layout.addWidget(self.current_page)
self.layout.addWidget(label)
self.layout.addWidget(next)
self.setLayout(self.layout)
def increment_page(self):
new = int(self.current_page.text())+1
new = self.page_anchor + 1
if new <= self.page_max:
self.current_page.setText(str(new))
self.page_anchor = new
self.update_current_page()
def decrement_page(self):
new = int(self.current_page.text())-1
new = self.page_anchor - 1
if new >= 1:
self.current_page.setText(str(new))
self.page_anchor = new
self.update_current_page()
def update_current_page(self):
self.current_page.setText(f"{self.page_anchor} of {self.page_max}")

2
src/submissions/tools/__init__.py
View File

@@ -19,7 +19,7 @@ from pydantic_settings import BaseSettings, SettingsConfigDict
from typing import Any, Tuple, Literal, List
from __init__ import project_path
from configparser import ConfigParser
from tkinter import Tk # from tkinter import Tk for Python 3.x
from tkinter import Tk # NOTE: This is for choosing database path before app is created.
from tkinter.filedialog import askdirectory
from sqlalchemy.exc import IntegrityError as sqlalcIntegrityError