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Removed logger.debugs for proven functions.

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This commit is contained in:
lwark
2024-12-12 12:17:21 -06:00
parent b174eb1221
commit 67520cb784
32 changed files with 80 additions and 758 deletions
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77
src/submissions/frontend/widgets/submission_widget.py
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@@ -1,9 +1,9 @@
'''
"""
Contains all submission related frontend functions
'''
"""
from PyQt6.QtWidgets import (
QWidget, QPushButton, QVBoxLayout,
QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QBoxLayout, QHBoxLayout, QGridLayout
QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QHBoxLayout, QGridLayout
)
from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
from . import select_open_file, select_save_file
@@ -34,7 +34,6 @@ class MyQComboBox(QComboBox):
super(MyQComboBox, self).__init__(*args, **kwargs)
self.scrollWidget = scrollWidget
self.setFocusPolicy(Qt.FocusPolicy.StrongFocus)
logger.debug(f"Scrollwidget: {scrollWidget}")
def wheelEvent(self, *args, **kwargs):
if self.hasFocus():
@@ -61,14 +60,12 @@ class MyQDateEdit(QDateEdit):
class SubmissionFormContainer(QWidget):
# A signal carrying a path
# NOTE: A signal carrying a path
import_drag = pyqtSignal(Path)
def __init__(self, parent: QWidget) -> None:
# logger.debug(f"Setting form widget...")
super().__init__(parent)
self.app = self.parent().parent()
# logger.debug(f"App: {self.app}")
self.report = Report()
self.setStyleSheet('background-color: light grey;')
self.setAcceptDrops(True)
@@ -89,7 +86,6 @@ class SubmissionFormContainer(QWidget):
Sets filename when file dropped
"""
fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
# logger.debug(f"App: {self.app}")
self.app.last_dir = fname.parent
self.import_drag.emit(fname)
@@ -127,7 +123,6 @@ class SubmissionFormContainer(QWidget):
# NOTE: set file dialog
if isinstance(fname, bool) or fname is None:
fname = select_open_file(self, file_extension="xlsx")
# logger.debug(f"Attempting to parse file: {fname}")
if not fname:
report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
return report
@@ -139,14 +134,10 @@ class SubmissionFormContainer(QWidget):
return
except AttributeError:
self.prsr = SheetParser(filepath=fname)
# logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic()
# logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
self.form = self.pyd.to_form(parent=self)
self.layout().addWidget(self.form)
return report
# 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,
@@ -172,14 +163,12 @@ class SubmissionFormContainer(QWidget):
if dlg.exec():
# NOTE: extract form info
info = dlg.parse_form()
# logger.debug(f"Reagent info: {info}")
# NOTE: create reagent object
reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# NOTE: send reagent to db
sqlobj, result = reagent.toSQL()
sqlobj.save()
report.add_result(result)
# logger.debug(f"Reagent: {reagent}, Report: {report}")
return reagent, report
@@ -189,7 +178,6 @@ class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
super().__init__(parent)
# logger.debug(f"Disable: {disable}")
if disable is None:
disable = []
self.app = parent.app
@@ -200,17 +188,13 @@ class SubmissionFormWidget(QWidget):
defaults = st.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
self.recover = defaults['form_recover']
self.ignore = defaults['form_ignore']
# logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}")
self.layout = QVBoxLayout()
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
# logger.debug(f"Creating widget: {k}")
if k in self.ignore:
logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget")
continue
try:
# logger.debug(f"Key: {k}, Disable: {disable}")
check = k in disable
# logger.debug(f"Check: {check}")
except TypeError:
check = False
try:
@@ -225,7 +209,6 @@ class SubmissionFormWidget(QWidget):
sub_obj=st, disable=check)
if add_widget is not None:
self.layout.addWidget(add_widget)
# if k == "extraction_kit":
if k in self.__class__.update_reagent_fields:
add_widget.input.currentTextChanged.connect(self.scrape_reagents)
self.disabler = self.DisableReagents(self)
@@ -236,15 +219,10 @@ class SubmissionFormWidget(QWidget):
self.scrape_reagents(self.extraction_kit)
def disable_reagents(self):
"""
Disables all ReagentFormWidgets in this form/
"""
for reagent in self.findChildren(self.ReagentFormWidget):
# if self.disabler.checkbox.isChecked():
# # reagent.setVisible(True)
# # with QSignalBlocker(self.disabler.checkbox) as b:
# reagent.flip_check()
# else:
# # reagent.setVisible(False)
# # with QSignalBlocker(self.disabler.checkbox) as b:
# reagent.check.setChecked(False)
reagent.flip_check(self.disabler.checkbox.isChecked())
@@ -263,7 +241,6 @@ class SubmissionFormWidget(QWidget):
Returns:
self.InfoItem: Form widget to hold name:value
"""
# logger.debug(f"Key: {key}, Disable: {disable}")
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
if key not in self.ignore:
@@ -276,7 +253,6 @@ class SubmissionFormWidget(QWidget):
case _:
widget = self.InfoItem(parent=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.")
@@ -298,24 +274,20 @@ class SubmissionFormWidget(QWidget):
"""
self.extraction_kit = args[0]
report = Report()
logger.debug(f"Extraction kit: {self.extraction_kit}")
# NOTE: Remove previous reagent widgets
try:
old_reagents = self.find_widgets()
except AttributeError:
logger.error(f"Couldn't find old reagents.")
old_reagents = []
# logger.debug(f"\n\nAttempting to clear: {old_reagents}\n\n")
for reagent in old_reagents:
if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
reagent.setParent(None)
reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
# logger.debug(f"Got reagents: {pformat(reagents)}")
for reagent in reagents:
add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit)
self.layout.addWidget(add_widget)
report.add_result(integrity_report)
# logger.debug(f"Outgoing report: {report.results}")
if hasattr(self.pyd, "csv"):
export_csv_btn = QPushButton("Export CSV")
export_csv_btn.setObjectName("export_csv_btn")
@@ -326,6 +298,7 @@ class SubmissionFormWidget(QWidget):
self.layout.addWidget(submit_btn)
submit_btn.clicked.connect(self.submit_new_sample_function)
self.setLayout(self.layout)
self.disabler.checkbox.setChecked(True)
return report
def clear_form(self):
@@ -365,23 +338,16 @@ class SubmissionFormWidget(QWidget):
report = Report()
result = self.parse_form()
report.add_result(result)
# logger.debug(f"Submission: {pformat(self.pyd)}")
# logger.debug("Checking kit integrity...")
if self.disabler.checkbox.isChecked():
_, result = self.pyd.check_kit_integrity()
report.add_result(result)
if len(result.results) > 0:
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
# logger.debug(f"Result of to_sql: {result}")
try:
trigger = result.results[-1]
code = trigger.code
# logger.debug(f"Code from return: {code}")
except IndexError as e:
logger.error(result.results)
logger.error(f"Problem getting error code: {e}")
@@ -408,11 +374,8 @@ class SubmissionFormWidget(QWidget):
pass
# NOTE: add reagents to submission object
for reagent in base_submission.reagents:
# logger.debug(f"Updating: {reagent} with {reagent.lot}")
reagent.update_last_used(kit=base_submission.extraction_kit)
# logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
save_output = base_submission.save()
# logger.debug(f"Save output: {save_output}")
# NOTE: update summary sheet
self.app.table_widget.sub_wid.setData()
# NOTE: reset form
@@ -423,7 +386,6 @@ class SubmissionFormWidget(QWidget):
check = True
if check:
self.setParent(None)
# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
return report
def export_csv_function(self, fname: Path | None = None):
@@ -454,7 +416,6 @@ class SubmissionFormWidget(QWidget):
info = {}
reagents = []
for widget in self.findChildren(QWidget):
# logger.debug(f"Parsed widget of type {type(widget)}")
match widget:
case self.ReagentFormWidget():
reagent, _ = widget.parse_form()
@@ -464,16 +425,10 @@ class SubmissionFormWidget(QWidget):
field, value = widget.parse_form()
if field is not None:
info[field] = value
# logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
self.pyd.reagents = reagents
logger.debug(f"Reagents after insertion in pyd: {pformat(self.pyd.reagents)}")
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
for item in self.recover:
# logger.debug(f"Attempting to recover: {item}")
if hasattr(self, item):
value = getattr(self, item)
# logger.debug(f"Setting {item}")
info[item] = value
for k, v in info.items():
self.pyd.set_attribute(key=k, value=v)
@@ -551,9 +506,6 @@ class SubmissionFormWidget(QWidget):
except (TypeError, KeyError):
pass
obj = parent.parent().parent()
# logger.debug(f"Object: {obj}")
# logger.debug(f"Parent: {parent.parent()}")
# logger.debug(f"Creating widget for: {key}")
match key:
case 'submitting_lab':
add_widget = MyQComboBox(scrollWidget=parent)
@@ -567,7 +519,6 @@ class SubmissionFormWidget(QWidget):
looked_up_lab = Organization.query(name=value, limit=1)
except AttributeError:
looked_up_lab = None
# logger.debug(f"\n\nLooked up lab: {looked_up_lab}")
if looked_up_lab:
try:
labs.remove(str(looked_up_lab.name))
@@ -586,12 +537,9 @@ class SubmissionFormWidget(QWidget):
# NOTE: create combobox to hold looked up kits
add_widget = MyQComboBox(scrollWidget=parent)
# NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
# logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.name for item in submission_type.kit_types]
obj.uses = uses
# logger.debug(f"Kits received for {submission_type}: {uses}")
if check_not_nan(value):
# logger.debug(f"The extraction kit in parser was: {value}")
try:
uses.insert(0, uses.pop(uses.index(value)))
except ValueError:
@@ -626,7 +574,6 @@ class SubmissionFormWidget(QWidget):
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:
@@ -725,7 +672,6 @@ class SubmissionFormWidget(QWidget):
if not self.lot.isEnabled():
return None, report
lot = self.lot.currentText()
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot=lot, role=self.reagent.role)
# NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
if wanted_reagent is None:
@@ -741,7 +687,6 @@ class SubmissionFormWidget(QWidget):
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.")
report.add_result(Result(msg="Failed integrity check", status="Critical"))
return None, report
else:
@@ -791,7 +736,6 @@ class SubmissionFormWidget(QWidget):
looked_up_rt = KitTypeReagentRoleAssociation.query(reagent_role=reagent.role,
kit_type=extraction_kit)
relevant_reagents = [str(item.lot) for item in looked_up_rt.get_all_relevant_reagents()]
logger.debug(f"Relevant reagents for {reagent}: {relevant_reagents}")
# NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
if str(reagent.lot) not in relevant_reagents:
if check_not_nan(reagent.lot):
@@ -803,7 +747,6 @@ class SubmissionFormWidget(QWidget):
looked_up_reg = None
if isinstance(looked_up_reg, list):
looked_up_reg = None
# logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}")
if looked_up_reg:
try:
relevant_reagents.remove(str(looked_up_reg.lot))
@@ -812,15 +755,11 @@ class SubmissionFormWidget(QWidget):
relevant_reagents.insert(0, str(looked_up_reg.lot))
else:
if len(relevant_reagents) > 1:
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
idx = relevant_reagents.index(str(reagent.lot))
# logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}")
moved_reag = relevant_reagents.pop(idx)
relevant_reagents.insert(0, moved_reag)
else:
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
pass
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}")