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Added Postgres support.

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This commit is contained in:
lwark
2024-07-25 08:41:44 -05:00
parent 54e1e55804
commit 4bc5e08ac6
32 changed files with 579 additions and 1030 deletions
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120
src/submissions/frontend/widgets/submission_widget.py
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@@ -11,7 +11,7 @@ from pathlib import Path
from . import select_open_file, select_save_file
import logging, difflib, inspect
from pathlib import Path
from tools import Report, Result, check_not_nan, workbook_2_csv, main_form_style
from tools import Report, Result, check_not_nan, workbook_2_csv, main_form_style, report_result
from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
@@ -59,17 +59,16 @@ class SubmissionFormContainer(QWidget):
self.app.last_dir = fname.parent
self.import_drag.emit(fname)
@report_result
def importSubmission(self, fname: Path | None = None):
"""
import submission from excel sheet into form
"""
self.app.raise_()
self.app.activateWindow()
self.import_submission_function(fname)
# logger.debug(f"Result from result reporter: {self.report.results}")
self.app.report.add_result(self.report)
self.report = Report()
self.app.result_reporter()
self.import_submission_function(fname)
return self.report
def import_submission_function(self, fname: Path | None = None):
"""
@@ -115,8 +114,9 @@ class SubmissionFormContainer(QWidget):
# logger.debug(f"Outgoing report: {self.report.results}")
# logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
@report_result
def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
name: str | None = None):
name: str | None = None) -> Tuple[PydReagent, Report]:
"""
Action to create new reagent in DB.
@@ -144,16 +144,18 @@ class SubmissionFormContainer(QWidget):
sqlobj, assoc, result = reagent.toSQL()
sqlobj.save()
report.add_result(result)
self.app.report.add_result(report)
self.app.result_reporter()
return reagent
# logger.debug(f"Reagent: {reagent}, Report: {report}")
return reagent, report
class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, submission: PydSubmission) -> None:
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
super().__init__(parent)
# self.report = Report()
# logger.debug(f"Disable: {disable}")
if disable is None:
disable = []
self.app = parent.app
self.pyd = submission
self.missing_info = []
@@ -166,12 +168,19 @@ class SubmissionFormWidget(QWidget):
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
if k in self.ignore:
continue
try:
# logger.debug(f"Key: {k}, Disable: {disable}")
check = k in disable
# logger.debug(f"Check: {check}")
except TypeError:
check = False
try:
value = self.pyd.__getattribute__(k)
except AttributeError:
logger.error(f"Couldn't get attribute from pyd: {k}")
value = dict(value=None, missing=True)
add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'], sub_obj=st)
add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'],
sub_obj=st, disable=check)
if add_widget is not None:
self.layout.addWidget(add_widget)
if k == "extraction_kit":
@@ -180,11 +189,13 @@ class SubmissionFormWidget(QWidget):
self.scrape_reagents(self.pyd.extraction_kit)
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | None = None,
extraction_kit: str | None = None, sub_obj:BasicSubmission|None=None) -> "self.InfoItem":
extraction_kit: str | None = None, sub_obj: BasicSubmission | None = None,
disable: bool = False) -> "self.InfoItem":
"""
Make an InfoItem widget to hold a field
Args:
disable ():
key (str): Name of the field
value (dict): Value of field
submission_type (str | None, optional): Submissiontype as str. Defaults to None.
@@ -192,18 +203,25 @@ class SubmissionFormWidget(QWidget):
Returns:
self.InfoItem: Form widget to hold name:value
"""
# logger.debug(f"Key: {key}, Disable: {disable}")
if key not in self.ignore:
match value:
case PydReagent():
if value.name.lower() != "not applicable":
widget = self.ReagentFormWidget(self, reagent=value, extraction_kit=extraction_kit)
else:
widget = None
case _:
widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj)
# logger.debug(f"Setting widget enabled to: {not disable}")
if disable:
widget.input.setEnabled(False)
widget.input.setToolTip("Widget disabled to protect database integrity.")
return widget
return None
@report_result
def scrape_reagents(self, *args, **kwargs): #extraction_kit:str, caller:str|None=None):
"""
Extracted scrape reagents function that will run when
@@ -250,8 +268,7 @@ class SubmissionFormWidget(QWidget):
self.layout.addWidget(submit_btn)
submit_btn.clicked.connect(self.submit_new_sample_function)
self.setLayout(self.layout)
self.app.report.add_result(report)
self.app.result_reporter()
return report
def clear_form(self):
"""
@@ -275,7 +292,8 @@ class SubmissionFormWidget(QWidget):
query = [widget for widget in query if widget.objectName() == object_name]
return query
def submit_new_sample_function(self) -> QWidget:
@report_result
def submit_new_sample_function(self, *args) -> Report:
"""
Parse forms and add sample to the database.
@@ -294,37 +312,40 @@ class SubmissionFormWidget(QWidget):
_, result = self.pyd.check_kit_integrity()
report.add_result(result)
if len(result.results) > 0:
self.app.report.add_result(report)
self.app.result_reporter()
# self.app.report.add_result(report)
# self.app.report_result()
return
# logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
base_submission, result = self.pyd.to_sql()
# logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
# logger.debug(f"Base submission: {base_submission.to_dict()}")
# NOTE: check output message for issues
match result.code:
try:
code = report.results[-1].code
except IndexError:
code = 0
match code:
# NOTE: code 0: everything is fine.
case 0:
report.add_result(None)
pass
# NOTE: code 1: ask for overwrite
case 1:
dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
if dlg.exec():
# NOTE: Do not add duplicate reagents.
result = None
pass
else:
self.app.ctx.database_session.rollback()
report.add_result(Result(msg="Overwrite cancelled", status="Information"))
self.app.report.add_result(report)
self.app.result_reporter()
return
# self.app.report.add_result(report)
# self.app.report_result()
return report
# NOTE: code 2: No RSL plate number given
case 2:
report.add_result(result)
self.app.report.add_result(report)
self.app.result_reporter()
return
# self.app.report.add_result(report)
# self.app.report_result()
return report
case _:
pass
# NOTE: add reagents to submission object
@@ -338,8 +359,7 @@ class SubmissionFormWidget(QWidget):
# NOTE: reset form
self.setParent(None)
# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
self.app.report.add_result(report)
self.app.result_reporter()
return report
def export_csv_function(self, fname: Path | None = None):
"""
@@ -352,7 +372,6 @@ class SubmissionFormWidget(QWidget):
fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
try:
self.pyd.export_csv(fname)
# workbook_2_csv(worksheet=self.pyd.csv, filename=fname)
except PermissionError:
logger.warning(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
except AttributeError:
@@ -398,11 +417,13 @@ class SubmissionFormWidget(QWidget):
class InfoItem(QWidget):
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None, sub_obj:BasicSubmission|None=None) -> None:
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None,
sub_obj: BasicSubmission | None = None) -> None:
super().__init__(parent)
layout = QVBoxLayout()
self.label = self.ParsedQLabel(key=key, value=value)
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj)
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type,
sub_obj=sub_obj)
self.setObjectName(key)
try:
self.missing: bool = value['missing']
@@ -439,7 +460,8 @@ class SubmissionFormWidget(QWidget):
return None, None
return self.input.objectName(), dict(value=value, missing=self.missing)
def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None, sub_obj:BasicSubmission|None=None) -> QWidget:
def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None,
sub_obj: BasicSubmission | None = None) -> QWidget:
"""
Creates form widget
@@ -472,6 +494,7 @@ class SubmissionFormWidget(QWidget):
pass
# set combobox values to lookedup values
add_widget.addItems(labs)
add_widget.setToolTip("Select submitting lab.")
case 'extraction_kit':
# if extraction kit not available, all other values fail
if not check_not_nan(value):
@@ -493,15 +516,7 @@ class SubmissionFormWidget(QWidget):
logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
obj.ext_kit = uses[0]
add_widget.addItems(uses)
# case 'submitted_date':
# # NOTE: uses base calendar
# add_widget = QDateEdit(calendarPopup=True)
# # NOTE: sets submitted date based on date found in excel sheet
# try:
# add_widget.setDate(value)
# # NOTE: if not found, use today
# except:
# add_widget.setDate(date.today())
add_widget.setToolTip("Select extraction kit.")
case 'submission_category':
add_widget = QComboBox()
cats = ['Diagnostic', "Surveillance", "Research"]
@@ -511,6 +526,7 @@ class SubmissionFormWidget(QWidget):
except ValueError:
cats.insert(0, cats.pop(cats.index(submission_type)))
add_widget.addItems(cats)
add_widget.setToolTip("Enter submission category or select from list.")
case _:
if key in sub_obj.timestamps():
add_widget = QDateEdit(calendarPopup=True)
@@ -520,11 +536,13 @@ class SubmissionFormWidget(QWidget):
# NOTE: if not found, use today
except:
add_widget.setDate(date.today())
add_widget.setToolTip(f"Select date for {key}")
else:
# NOTE: anything else gets added in as a line edit
add_widget = QLineEdit()
# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " "))
add_widget.setToolTip(f"Enter value for {key}")
if add_widget is not None:
add_widget.setObjectName(key)
add_widget.setParent(parent)
@@ -594,13 +612,14 @@ class SubmissionFormWidget(QWidget):
# NOTE: If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated)
def parse_form(self) -> Tuple[PydReagent, dict]:
def parse_form(self) -> Tuple[PydReagent | None, Report]:
"""
Pulls form info into PydReagent
Returns:
Tuple[PydReagent, dict]: PydReagent and Report(?)
"""
report = Report()
lot = self.lot.currentText()
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot_number=lot, reagent_role=self.reagent.role)
@@ -609,14 +628,16 @@ class SubmissionFormWidget(QWidget):
dlg = QuestionAsker(title=f"Add {lot}?",
message=f"Couldn't find reagent type {self.reagent.role}: {lot} in the database.\n\nWould you like to add it?")
if dlg.exec():
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_role=self.reagent.role,
expiry=self.reagent.expiry,
name=self.reagent.name)
return wanted_reagent, None
wanted_reagent, _ = self.parent().parent().add_reagent(reagent_lot=lot,
reagent_role=self.reagent.role,
expiry=self.reagent.expiry,
name=self.reagent.name)
return wanted_reagent, report
else:
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
# logger.debug("Will not add reagent.")
return None, Result(msg="Failed integrity check", status="Critical")
report.add_result(Result(msg="Failed integrity check", status="Critical"))
return None, report
else:
# NOTE: Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
# from the db, it should no longer be necessary to query the db with reagent/kit, but with rt name directly.
@@ -624,7 +645,7 @@ class SubmissionFormWidget(QWidget):
if rt is None:
rt = ReagentRole.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, role=rt.name,
expiry=wanted_reagent.expiry, missing=False), None
expiry=wanted_reagent.expiry, missing=False), report
def updated(self):
"""
@@ -708,4 +729,5 @@ class SubmissionFormWidget(QWidget):
# logger.debug(f"New relevant reagents: {relevant_reagents}")
self.setObjectName(f"lot_{reagent.role}")
self.addItems(relevant_reagents)
self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}")
# self.setStyleSheet(main_form_style)