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Context menu for runs working.

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This commit is contained in:
lwark
2025-05-22 10:00:25 -05:00
parent 75c665ea05
commit d850166e08
40 changed files with 2852 additions and 3329 deletions
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153
src/submissions/frontend/widgets/submission_widget.py
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@@ -1,5 +1,5 @@
"""
Contains all run related frontend functions
Contains all procedure related frontend functions
"""
from PyQt6.QtWidgets import (
QWidget, QPushButton, QVBoxLayout,
@@ -10,11 +10,11 @@ from .functions import select_open_file, select_save_file
import logging
from pathlib import Path
from tools import Report, Result, check_not_nan, main_form_style, report_result, get_application_from_parent
from backend.excel import SheetParser, InfoParser
from backend.validators import PydSubmission, PydReagent
from backend.excel import ClientSubmissionParser, SampleParser
from backend.validators import PydSubmission, PydReagent, PydClientSubmission, PydSample
from backend.db import (
Organization, SubmissionType, Reagent,
ReagentRole, KitTypeReagentRoleAssociation, BasicRun
ClientLab, SubmissionType, Reagent,
ReagentRole, KitTypeReagentRoleAssociation, Run
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
@@ -93,7 +93,7 @@ class SubmissionFormContainer(QWidget):
@report_result
def import_submission_function(self, fname: Path | None = None) -> Report:
"""
Import a new run to the app window
Import a new procedure to the app window
Args:
obj (QMainWindow): original app window
@@ -110,7 +110,7 @@ class SubmissionFormContainer(QWidget):
self.form.setParent(None)
except AttributeError:
pass
# NOTE: initialize samples
# NOTE: initialize sample
self.samples = []
self.missing_info = []
# NOTE: set file dialog
@@ -121,19 +121,28 @@ class SubmissionFormContainer(QWidget):
return report
# NOTE: create sheetparser using excel sheet and context from gui
try:
# self.prsr = SheetParser(filepath=fname)
self.parser = InfoParser(filepath=fname)
self.clientsubmissionparser = ClientSubmissionParser(filepath=fname)
except PermissionError:
logger.error(f"Couldn't get permission to access file: {fname}")
return
except AttributeError:
self.parser = InfoParser(filepath=fname)
self.pyd = self.parser.to_pydantic()
# logger.debug(f"Samples: {pformat(self.pyd.samples)}")
checker = SampleChecker(self, "Sample Checker", self.pyd)
self.clientsubmissionparser = ClientSubmissionParser(filepath=fname)
try:
# self.prsr = SheetParser(filepath=fname)
self.sampleparser = SampleParser(filepath=fname)
except PermissionError:
logger.error(f"Couldn't get permission to access file: {fname}")
return
except AttributeError:
self.sampleparser = SampleParser(filepath=fname)
self.pydclientsubmission = self.clientsubmissionparser.to_pydantic()
self.pydsamples = self.sampleparser.to_pydantic()
# logger.debug(f"Samples: {pformat(self.pydclientsubmission.sample)}")
checker = SampleChecker(self, "Sample Checker", self.pydsamples)
if checker.exec():
# logger.debug(pformat(self.pyd.samples))
self.form = self.pyd.to_form(parent=self)
# logger.debug(pformat(self.pydclientsubmission.sample))
self.form = self.pydclientsubmission.to_form(parent=self)
self.form.samples = self.pydsamples
self.layout().addWidget(self.form)
else:
message = "Submission cancelled."
@@ -150,7 +159,7 @@ class SubmissionFormContainer(QWidget):
instance (Reagent | None): Blank reagent instance to be edited and then added.
Returns:
models.Reagent: the constructed reagent object to add to run
models.Reagent: the constructed reagent object to add to procedure
"""
report = Report()
if not instance:
@@ -167,23 +176,23 @@ class SubmissionFormContainer(QWidget):
class SubmissionFormWidget(QWidget):
update_reagent_fields = ['extraction_kit']
update_reagent_fields = ['kittype']
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
def __init__(self, parent: QWidget, pyd: PydSubmission, disable: list | None = None) -> None:
super().__init__(parent)
if disable is None:
disable = []
self.app = get_application_from_parent(parent)
self.pyd = submission
self.pyd = pyd
self.missing_info = []
self.submission_type = SubmissionType.query(name=self.pyd.submission_type['value'])
basic_submission_class = self.submission_type.submission_class
logger.debug(f"Basic run class: {basic_submission_class}")
defaults = basic_submission_class.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
self.submissiontype = SubmissionType.query(name=self.pyd.submissiontype['value'])
# basic_submission_class = self.submission_type.submission_class
# logger.debug(f"Basic procedure class: {basic_submission_class}")
defaults = Run.get_default_info("form_recover", "form_ignore", submissiontype=self.pyd.submissiontype['value'])
self.recover = defaults['form_recover']
self.ignore = defaults['form_ignore']
self.layout = QVBoxLayout()
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
for k in list(self.pyd.model_fields.keys()):# + list(self.pyd.model_extra.keys()):
logger.debug(f"Pydantic field: {k}")
if k in self.ignore:
logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget")
@@ -201,8 +210,8 @@ class SubmissionFormWidget(QWidget):
except KeyError:
value = dict(value=None, missing=True)
logger.debug(f"Pydantic value: {value}")
add_widget = self.create_widget(key=k, value=value, submission_type=self.submission_type,
run_object=basic_submission_class, disable=check)
add_widget = self.create_widget(key=k, value=value, submission_type=self.submissiontype,
run_object=Run(), disable=check)
if add_widget is not None:
self.layout.addWidget(add_widget)
if k in self.__class__.update_reagent_fields:
@@ -212,7 +221,7 @@ class SubmissionFormWidget(QWidget):
self.layout.addWidget(self.disabler)
self.disabler.checkbox.checkStateChanged.connect(self.disable_reagents)
self.setStyleSheet(main_form_style)
# self.scrape_reagents(self.extraction_kit)
# self.scrape_reagents(self.kittype)
self.setLayout(self.layout)
def disable_reagents(self):
@@ -223,7 +232,7 @@ class SubmissionFormWidget(QWidget):
reagent.flip_check(self.disabler.checkbox.isChecked())
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | SubmissionType | None = None,
extraction_kit: str | None = None, run_object: BasicRun | None = None,
extraction_kit: str | None = None, run_object: Run | None = None,
disable: bool = False) -> "self.InfoItem":
"""
Make an InfoItem widget to hold a field
@@ -256,14 +265,14 @@ class SubmissionFormWidget(QWidget):
return None
@report_result
def scrape_reagents(self, *args, **kwargs): #extraction_kit:str, caller:str|None=None):
def scrape_reagents(self, *args, **kwargs): #kittype:str, caller:str|None=None):
"""
Extracted scrape reagents function that will run when
form 'extraction_kit' widget is updated.
Extracted scrape reagents function that will procedure when
form 'kittype' widget is updated.
Args:
obj (QMainWindow): updated main application
extraction_kit (str): name of extraction kit (in 'extraction_kit' widget)
extraction_kit (str): name of extraction kittype (in 'kittype' widget)
Returns:
Tuple[QMainWindow, dict]: Updated application and result
@@ -373,7 +382,7 @@ class SubmissionFormWidget(QWidget):
return report
case _:
pass
# NOTE: add reagents to run object
# NOTE: add reagents to procedure object
if base_submission is None:
return
for reagent in base_submission.reagents:
@@ -393,7 +402,7 @@ class SubmissionFormWidget(QWidget):
def export_csv_function(self, fname: Path | None = None):
"""
Save the run's csv file.
Save the procedure's csv file.
Args:
fname (Path | None, optional): Input filename. Defaults to None.
@@ -405,7 +414,7 @@ class SubmissionFormWidget(QWidget):
except PermissionError:
logger.warning(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
except AttributeError:
logger.error(f"No csv file found in the run at this point.")
logger.error(f"No csv file found in the procedure at this point.")
def parse_form(self) -> Report:
"""
@@ -442,11 +451,10 @@ class SubmissionFormWidget(QWidget):
report.add_result(report)
return report
class InfoItem(QWidget):
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | SubmissionType | None = None,
run_object: BasicRun | None = None) -> None:
run_object: Run | None = None) -> None:
super().__init__(parent)
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -492,7 +500,7 @@ class SubmissionFormWidget(QWidget):
def set_widget(self, parent: QWidget, key: str, value: dict,
submission_type: str | SubmissionType | None = None,
sub_obj: BasicRun | None = None) -> QWidget:
sub_obj: Run | None = None) -> QWidget:
"""
Creates form widget
@@ -515,16 +523,16 @@ class SubmissionFormWidget(QWidget):
pass
obj = parent.parent().parent()
match key:
case 'submitting_lab':
case 'clientlab':
add_widget = MyQComboBox(scrollWidget=parent)
# NOTE: lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
labs = [item.name for item in Organization.query()]
# NOTE: lookup organizations suitable for clientlab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
labs = [item.name for item in ClientLab.query()]
if isinstance(value, dict):
value = value['value']
if isinstance(value, Organization):
if isinstance(value, ClientLab):
value = value.name
try:
looked_up_lab = Organization.query(name=value, limit=1)
looked_up_lab = ClientLab.query(name=value, limit=1)
except AttributeError:
looked_up_lab = None
if looked_up_lab:
@@ -536,28 +544,28 @@ class SubmissionFormWidget(QWidget):
# NOTE: set combobox values to lookedup values
add_widget.addItems(labs)
add_widget.setToolTip("Select submitting lab.")
case 'extraction_kit':
# NOTE: if extraction kit not available, all other values fail
case 'kittype':
# NOTE: if extraction kittype not available, all other values fail
if not check_not_nan(value):
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!",
msg = AlertPop(message="Make sure to check your extraction kittype in the excel sheet!",
status="warning")
msg.exec()
# NOTE: create combobox to hold looked up kits
add_widget = MyQComboBox(scrollWidget=parent)
# NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
# NOTE: lookup existing kits by 'proceduretype' decided on by sheetparser
uses = [item.name for item in submission_type.kit_types]
obj.uses = uses
if check_not_nan(value):
try:
uses.insert(0, uses.pop(uses.index(value)))
except ValueError:
logger.warning(f"Couldn't find kit in list, skipping move to top of list.")
logger.warning(f"Couldn't find kittype in list, skipping move to top of list.")
obj.ext_kit = value
else:
logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
logger.error(f"Couldn't find {obj.prsr.sub['kittype']}")
obj.ext_kit = uses[0]
add_widget.addItems(uses)
add_widget.setToolTip("Select extraction kit.")
add_widget.setToolTip("Select extraction kittype.")
parent.extraction_kit = add_widget.currentText()
case 'submission_category':
add_widget = MyQComboBox(scrollWidget=parent)
@@ -568,7 +576,7 @@ class SubmissionFormWidget(QWidget):
except ValueError:
categories.insert(0, categories.pop(categories.index(submission_type)))
add_widget.addItems(categories)
add_widget.setToolTip("Enter run category or select from list.")
add_widget.setToolTip("Enter procedure category or select from list.")
case _:
if key in sub_obj.timestamps:
add_widget = MyQDateEdit(calendarPopup=True, scrollWidget=parent)
@@ -692,10 +700,10 @@ class SubmissionFormWidget(QWidget):
wanted_reagent = self.parent.parent().add_reagent(instance=wanted_reagent)
return wanted_reagent, report
else:
# NOTE: In this case we will have an empty reagent and the run will fail kit integrity check
# NOTE: In this case we will have an empty reagent and the procedure will fail kittype integrity check
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.
# NOTE: Since this now gets passed in directly from the clientsubmissionparser -> pydclientsubmission -> form and the clientsubmissionparser gets the name from the db, it should no longer be necessary to query the db with reagent/kittype, but with rt name directly.
rt = ReagentRole.query(name=self.reagent.role)
if rt is None:
rt = ReagentRole.query(kittype=self.extraction_kit, reagent=wanted_reagent)
@@ -738,7 +746,7 @@ class SubmissionFormWidget(QWidget):
def __init__(self, scrollWidget, reagent, extraction_kit: str) -> None:
super().__init__(scrollWidget=scrollWidget)
self.setEditable(True)
looked_up_rt = KitTypeReagentRoleAssociation.query(reagentrole=reagent.role,
looked_up_rt = KitTypeReagentRoleAssociation.query(reagentrole=reagent.equipmentrole,
kittype=extraction_kit)
relevant_reagents = [str(item.lot) for item in looked_up_rt.get_all_relevant_reagents()]
# NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
@@ -754,7 +762,8 @@ class SubmissionFormWidget(QWidget):
looked_up_reg = None
if looked_up_reg:
try:
relevant_reagents.insert(0, relevant_reagents.pop(relevant_reagents.index(looked_up_reg.lot)))
relevant_reagents.insert(0, relevant_reagents.pop(
relevant_reagents.index(looked_up_reg.lot)))
except ValueError as e:
logger.error(f"Error reordering relevant reagents: {e}")
else:
@@ -764,9 +773,9 @@ class SubmissionFormWidget(QWidget):
relevant_reagents.insert(0, moved_reag)
else:
pass
self.setObjectName(f"lot_{reagent.role}")
self.setObjectName(f"lot_{reagent.equipmentrole}")
self.addItems(relevant_reagents)
self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}")
self.setToolTip(f"Enter lot number for the reagent used for {reagent.equipmentrole}")
class DisableReagents(QWidget):
@@ -783,16 +792,22 @@ class SubmissionFormWidget(QWidget):
class ClientSubmissionFormWidget(SubmissionFormWidget):
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
super().__init__(parent, submission=submission, disable=disable)
self.disabler.setHidden(True)
def __init__(self, parent: QWidget, clientsubmission: PydClientSubmission, samples: List = [],
disable: list | None = None) -> None:
super().__init__(parent, pyd=clientsubmission, disable=disable)
try:
self.disabler.setHidden(True)
except AttributeError:
pass
# save_btn = QPushButton("Save")
self.samples = samples
logger.debug(f"Samples: {self.samples}")
start_run_btn = QPushButton("Save")
# self.layout.addWidget(save_btn)
self.layout.addWidget(start_run_btn)
start_run_btn.clicked.connect(self.create_new_submission)
@report_result
def parse_form(self) -> Report:
"""
Transforms form info into PydSubmission
@@ -801,7 +816,7 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
Report: Report on status of parse.
"""
report = Report()
logger.info(f"Hello from client run form parser!")
logger.info(f"Hello from client procedure form parser!")
info = {}
reagents = []
for widget in self.findChildren(QWidget):
@@ -827,18 +842,20 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
report.add_result(report)
return report
@report_result
# @report_result
def to_pydantic(self, *args):
self.parse_form()
return self.pyd
@report_result
def create_new_submission(self, *args) -> Report:
self.parse_form()
sql = self.pyd.to_sql()
pyd = self.to_pydantic()
sql = pyd.to_sql()
for sample in self.samples:
if isinstance(sample, PydSample):
sample = sample.to_sql()
sql.add_sample(sample=sample)
logger.debug(sql.__dict__)
sql.save()
self.app.table_widget.sub_wid.set_data()
self.setParent(None)