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Bug fixing for new AddEdit forms.

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This commit is contained in:
lwark
2025-01-08 13:54:14 -06:00
parent 8662bbdc2f
commit 95ae203cc2
11 changed files with 217 additions and 85 deletions
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5
src/submissions/backend/db/models/__init__.py
View File

@@ -243,7 +243,10 @@ class BaseClass(Base):
@classmethod
def get_pydantic_model(cls):
from backend.validators import pydant
model = getattr(pydant, f"Pyd{cls.__name__}")
try:
model = getattr(pydant, f"Pyd{cls.__name__}")
except AttributeError:
return None
return model

6
src/submissions/backend/db/models/controls.py
View File

@@ -286,6 +286,10 @@ class Control(BaseClass):
"""
return None
def delete(self):
self.__database_session__.delete(self)
self.__database_session__.commit()
class PCRControl(Control):
"""
@@ -296,7 +300,7 @@ class PCRControl(Control):
subtype = Column(String(16)) #: PC or NC
target = Column(String(16)) #: N1, N2, etc.
ct = Column(FLOAT) #: PCR result
reagent_lot = Column(String(64), ForeignKey("_reagent.name", ondelete="SET NULL",
reagent_lot = Column(String(64), ForeignKey("_reagent.lot", ondelete="SET NULL",
name="fk_reagent_lot"))
reagent = relationship("Reagent", foreign_keys=reagent_lot) #: reagent used for this control

18
src/submissions/backend/db/models/kits.py
View File

@@ -540,6 +540,24 @@ class Reagent(BaseClass, LogMixin):
report.add_result(Result(msg=f"Updating last used {rt} was not performed.", status="Information"))
return report
@classmethod
def query_or_create(cls, **kwargs) -> Reagent:
from backend.validators.pydant import PydReagent
new = False
instance = cls.query(**kwargs)
if not instance or isinstance(instance, list):
if "role" not in kwargs:
try:
kwargs['role'] = kwargs['name']
except KeyError:
pass
instance = PydReagent(**kwargs)
new = True
instance, _ = instance.toSQL()
logger.debug(f"Instance: {instance}")
return instance, new
@classmethod
@setup_lookup
def query(cls,

19
src/submissions/backend/db/models/submissions.py
View File

@@ -936,14 +936,20 @@ class BasicSubmission(BaseClass, LogMixin):
Generator[dict, None, None]: Dictionaries of row values.
"""
location_map = cls.get_submission_type().sample_map['pcr_controls']
# logger.debug(f"Location map: {location_map}")
submission = cls.query(rsl_plate_num=rsl_plate_num)
name_column = 1
for item in location_map:
logger.debug(f"Checking {item}")
worksheet = xl[item['sheet']]
for iii, row in enumerate(worksheet.iter_rows(max_row=len(worksheet['A']), max_col=name_column), start=1):
logger.debug(f"Checking row {row}, {iii}")
for cell in row:
logger.debug(f"Checking cell: {cell}, with value {cell.value} against {item['name']}")
if cell.value == item['name']:
subtype, target = item['name'].split("-")
subtype, _ = item['name'].split("-")
target = item['target']
logger.debug(f"Subtype: {subtype}, target: {target}")
ct = worksheet.cell(row=iii, column=item['ct_column']).value
# NOTE: Kind of a stop gap solution to find control reagents.
if subtype == "PC":
@@ -955,6 +961,9 @@ class BasicSubmission(BaseClass, LogMixin):
ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations
if any(["molecular grade water" in item.name.lower() for item in
assoc.reagent.role])), None)
else:
ctrl = None
logger.debug(f"Control reagent: {ctrl.__dict__}")
try:
ct = float(ct)
except ValueError:
@@ -963,13 +972,15 @@ class BasicSubmission(BaseClass, LogMixin):
ctrl = ctrl.lot
else:
ctrl = None
yield dict(
name=f"{rsl_plate_num}<{item['name']}>",
output = dict(
name=f"{rsl_plate_num}<{item['name']}-{target}>",
ct=ct,
subtype=subtype,
target=target,
reagent_lot=ctrl
)
logger.debug(f"Control output: {pformat(output)}")
yield output
@classmethod
def filename_template(cls) -> str:
@@ -1663,10 +1674,12 @@ class Wastewater(BasicSubmission):
submitted_date = datetime.strptime(" ".join(parser.pcr['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p")
for control in pcr_controls:
logger.debug(f"Control coming into save: {control}")
new_control = PCRControl(**control)
new_control.submitted_date = submitted_date
new_control.controltype = controltype
new_control.submission = self
logger.debug(f"Control coming into save: {new_control.__dict__}")
new_control.save()
return report

8
src/submissions/backend/excel/parser.py
View File

@@ -257,9 +257,10 @@ class ReagentParser(object):
extraction_kit = extraction_kit['value']
self.kit_object = KitType.query(name=extraction_kit)
self.map = self.fetch_kit_info_map(submission_type=submission_type)
logger.debug(f"Setting map: {self.map}")
self.xl = xl
@report_result
# @report_result
def fetch_kit_info_map(self, submission_type: str | SubmissionType) -> Tuple[Report, dict]:
"""
Gets location of kit reagents from database
@@ -298,7 +299,8 @@ class ReagentParser(object):
msg=f"No kit map found for {self.kit_object.name}.\n\n"
f"Are you sure you put the right kit in:\n\n{location_string}?",
status="Critical"))
return report, reagent_map
logger.debug(f"Here is the map coming out: {reagent_map}")
return reagent_map
def parse_reagents(self) -> Generator[dict, None, None]:
"""
@@ -310,7 +312,7 @@ class ReagentParser(object):
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']}
if relevant == {}:
if not relevant:
continue
for item in relevant:
try:

40
src/submissions/backend/validators/pydant.py
View File

@@ -22,8 +22,8 @@ logger = logging.getLogger(f"submissions.{__name__}")
class PydReagent(BaseModel):
lot: str | None
role: str | None
expiry: date | Literal['NA'] | None
name: str | None
expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
name: str | None = Field(default=None, validate_default=True)
missing: bool = Field(default=True)
comment: str | None = Field(default="", validate_default=True)
@@ -79,6 +79,8 @@ class PydReagent(BaseModel):
case str():
return parse(value)
case date():
return datetime.combine(value, datetime.max.time())
case datetime():
return value
case _:
return convert_nans_to_nones(str(value))
@@ -939,6 +941,7 @@ class PydSubmission(BaseModel, extra='allow'):
ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
# NOTE: Exclude any reagenttype found in this pyd not expected in kit.
expected_check = [item.role for item in ext_kit_rtypes]
logger.debug(self.reagents)
output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
missing_check = [item.role for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check and rt.role not in exempt]
@@ -956,7 +959,7 @@ class PydSubmission(BaseModel, extra='allow'):
report.add_result(result)
return output_reagents, report, missing_reagents
def check_reagent_expiries(self, exempt: List[PydReagent]=[]):
def check_reagent_expiries(self, exempt: List[PydReagent] = []):
report = Report()
expired = []
for reagent in self.reagents:
@@ -971,14 +974,11 @@ class PydSubmission(BaseModel, extra='allow'):
if expired:
output = '\n'.join(expired)
result = Result(status="Warning",
msg = f"The following reagents are expired:\n\n{output}"
msg=f"The following reagents are expired:\n\n{output}"
)
report.add_result(result)
return report
def export_csv(self, filename: Path | str):
try:
worksheet = self.csv
@@ -1009,14 +1009,34 @@ class PydContact(BaseModel):
logger.debug(f"Output phone: {value}")
return value
def toSQL(self) -> Contact:
def toSQL(self) -> Tuple[Contact, Report]:
"""
Converts this instance into a backend.db.models.organization.Contact instance
Converts this instance into a backend.db.models.organization. Contact instance.
Does not query for existing contacts.
Returns:
Contact: Contact instance
"""
return Contact(name=self.name, phone=self.phone, email=self.email)
report = Report()
instance = Contact.query(name=self.name, phone=self.phone, email=self.email)
if not instance or isinstance(instance, list):
instance = Contact()
try:
all_fields = self.model_fields + self.model_extra
except TypeError:
all_fields = self.model_fields
for field in all_fields:
value = getattr(self, field)
match field:
case "organization":
value = [Organization.query(name=value)]
case _:
pass
try:
instance.__setattr__(field, value)
except AttributeError as e:
logger.error(f"Could not set {instance} {field} to {value} due to {e}")
return instance, report
class PydOrganization(BaseModel):

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

@@ -16,3 +16,5 @@ from .submission_table import *
from .submission_widget import *
from .summary import *
from .turnaround import *
from .omni_add_edit import *
from .omni_manager import *

123
src/submissions/frontend/widgets/omni_add_edit.py
View File

@@ -1,59 +1,78 @@
from datetime import date
from typing import Any
from pprint import pformat
from typing import Any, List, Tuple
from pydantic import BaseModel
from PyQt6.QtWidgets import (
QLabel, QDialog, QTableView, QWidget, QLineEdit, QGridLayout, QComboBox, QPushButton, QDialogButtonBox, QDateEdit
)
from sqlalchemy import String, TIMESTAMP
from sqlalchemy.orm import InstrumentedAttribute
from sqlalchemy.orm import InstrumentedAttribute, ColumnProperty
import logging
from sqlalchemy.orm.relationships import _RelationshipDeclared
from tools import Report, Result
logger = logging.getLogger(f"submissions.{__name__}")
class AddEdit(QDialog):
def __init__(self, parent, instance: Any|None=None):
def __init__(self, parent, instance: Any | None = None, manager: str = ""):
super().__init__(parent)
self.instance = instance
self.object_type = instance.__class__
self.layout = QGridLayout(self)
logger.debug(f"Manager: {manager}")
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# fields = {k: v for k, v in self.object_type.__dict__.items() if
# isinstance(v, InstrumentedAttribute) and k != "id"}
fields = {k: v for k, v in self.object_type.__dict__.items() if k != "id"}
fields = {key: dict(class_attr=getattr(self.object_type, key), instance_attr=getattr(self.instance, key))
for key in dir(self.object_type) if isinstance(getattr(self.object_type, key), InstrumentedAttribute)
and "id" not in key and key != manager}
# NOTE: Move 'name' to the front
try:
fields = {'name': fields.pop('name'), **fields}
except KeyError:
pass
logger.debug(pformat(fields, indent=4))
height_counter = 0
for key, field in fields.items():
logger.debug(f"")
try:
widget = EditProperty(self, key=key, column_type=field.property.expression.type,
value=getattr(self.instance, key))
value = getattr(self.instance, key)
except AttributeError:
value = None
try:
logger.debug(f"{key} property: {type(field['class_attr'].property)}")
# widget = EditProperty(self, key=key, column_type=field.property.expression.type,
# value=getattr(self.instance, key))
logger.debug(f"Column type: {field}, Value: {value}")
widget = EditProperty(self, key=key, column_type=field, value=value)
except AttributeError as e:
logger.error(f"Problem setting widget {key}: {e}")
continue
self.layout.addWidget(widget, self.layout.rowCount(), 0)
if widget:
self.layout.addWidget(widget, self.layout.rowCount(), 0)
height_counter += 1
self.layout.addWidget(self.buttonBox)
self.setWindowTitle(f"Add/Edit {self.object_type.__name__}")
self.setMinimumSize(600, 50 * len(fields))
self.setMinimumSize(600, 50 * height_counter)
self.setLayout(self.layout)
def parse_form(self):
results = {result[0]:result[1] for result in [item.parse_form() for item in self.findChildren(EditProperty)]}
# logger.debug(results)
def parse_form(self) -> Tuple[BaseModel, Report]:
report = Report()
parsed = {result[0].strip(":"): result[1] for result in [item.parse_form() for item in self.findChildren(EditProperty)] if result[0]}
logger.debug(parsed)
model = self.object_type.get_pydantic_model()
model = model(**results)
try:
extras = list(model.model_extra.keys())
except AttributeError:
extras = []
fields = list(model.model_fields.keys()) + extras
for field in fields:
# logger.debug(result)
self.instance.__setattr__(field, model.__getattribute__(field))
return self.instance
# NOTE: Hand-off to pydantic model for validation.
# NOTE: Also, why am I not just using the toSQL method here. I could write one for contacts.
model = model(**parsed)
# output, result = model.toSQL()
# report.add_result(result)
# if len(report.results) < 1:
# report.add_result(Result(msg="Added new regeant.", icon="Information", owner=__name__))
return model, report
class EditProperty(QWidget):
@@ -64,7 +83,36 @@ class EditProperty(QWidget):
self.layout = QGridLayout()
self.layout.addWidget(self.label, 0, 0, 1, 1)
self.setObjectName(key)
match column_type:
match column_type['class_attr'].property:
case ColumnProperty():
self.column_property_set(column_type, value=value)
case _RelationshipDeclared():
self.relationship_property_set(column_type, value=value)
case _:
logger.error(f"{column_type} not a supported type.")
return
self.layout.addWidget(self.widget, 0, 1, 1, 3)
self.setLayout(self.layout)
def relationship_property_set(self, relationship_property, value=None):
# print(relationship_property)
self.property_class = relationship_property['class_attr'].property.entity.class_
self.is_list = relationship_property['class_attr'].property.uselist
choices = [item.name for item in self.property_class.query()]
try:
instance_value = getattr(self.parent().instance, self.objectName().strip(":"))
except AttributeError:
logger.debug(f"Unable to get instance {self.parent().instance} attribute: {self.objectName()}")
instance_value = None
if isinstance(instance_value, list):
instance_value = next((item.name for item in instance_value), None)
if instance_value:
choices.insert(0, choices.pop(choices.index(instance_value)))
self.widget = QComboBox()
self.widget.addItems(choices)
def column_property_set(self, column_property, value=None):
match column_property['class_attr'].expression.type:
case String():
if not value:
value = ""
@@ -76,22 +124,25 @@ class EditProperty(QWidget):
value = date.today()
self.widget.setDate(value)
case _:
logger.error(f"{column_type} not a supported type.")
logger.error(f"{column_property} not a supported property.")
self.widget = None
return
self.layout.addWidget(self.widget, 0, 1, 1, 3)
self.setLayout(self.layout)
def parse_form(self):
try:
check = self.widget
except AttributeError:
return None, None
match self.widget:
case QLineEdit():
value = self.widget.text()
case QDateEdit():
value = self.widget.date()
value = self.widget.date().toPyDate()
case QComboBox():
value = self.widget.currentText()
# if self.is_list:
# value = [self.property_class.query(name=prelim)]
# else:
# value = self.property_class.query(name=prelim)
case _:
value = None
return self.objectName(), value

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

@@ -110,7 +110,7 @@ class ManagerWindow(QDialog):
return self.instance
def add_new(self):
dlg = AddEdit(parent=self, instance=self.object_type())
dlg = AddEdit(parent=self, instance=self.object_type(), manager=self.object_type.__name__.lower())
if dlg.exec():
new_instance = dlg.parse_form()
# logger.debug(new_instance.__dict__)
@@ -182,7 +182,7 @@ class EditRelationship(QWidget):
def add_new(self, instance: Any = None):
if not instance:
instance = self.entity()
dlg = AddEdit(self, instance=instance)
dlg = AddEdit(self, instance=instance, manager=self.parent().object_type.__name__.lower())
if dlg.exec():
new_instance = dlg.parse_form()
# logger.debug(new_instance.__dict__)
@@ -190,16 +190,15 @@ class EditRelationship(QWidget):
if isinstance(addition, InstrumentedList):
addition.append(new_instance)
self.parent().instance.save()
self.parent().update_data()
def add_existing(self):
dlg = SearchBox(self, object_type=self.entity, returnable=True, extras=[])
if dlg.exec():
rows = dlg.return_selected_rows()
# print(f"Rows selected: {[row for row in rows]}")
for row in rows:
instance = self.entity.query(**row)
# logger.debug(instance)
addition = getattr(self.parent().instance, self.objectName())
if isinstance(addition, InstrumentedList):
addition.append(instance)

58
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -140,14 +140,22 @@ class SubmissionFormContainer(QWidget):
self.layout().addWidget(self.form)
return report
def new_add_reagent(self):
instance = Reagent()
@report_result
def new_add_reagent(self, instance: Reagent | None = None):
report = Report()
if not instance:
instance = Reagent()
dlg = AddEdit(parent=self, instance=instance)
if dlg.exec():
obj = dlg.parse_form()
print(obj)
reagent, result = dlg.parse_form()
reagent.missing = False
logger.debug(f"Reagent: {reagent}, result: {result}")
report.add_result(result)
# NOTE: send reagent to db
sqlobj, result = reagent.toSQL()
sqlobj.save()
report.add_result(result)
return reagent, report
@report_result
def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
@@ -183,7 +191,6 @@ class SubmissionFormContainer(QWidget):
class SubmissionFormWidget(QWidget):
update_reagent_fields = ['extraction_kit']
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
@@ -235,7 +242,6 @@ class SubmissionFormWidget(QWidget):
for reagent in self.findChildren(self.ReagentFormWidget):
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, sub_obj: BasicSubmission | None = None,
disable: bool = False) -> "self.InfoItem":
@@ -294,8 +300,10 @@ class SubmissionFormWidget(QWidget):
if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
reagent.setParent(None)
reagents, integrity_report, missing_reagents = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
logger.debug(f"Reagents: {reagents}")
expiry_report = self.pyd.check_reagent_expiries(exempt=missing_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)
@@ -432,7 +440,7 @@ class SubmissionFormWidget(QWidget):
for widget in self.findChildren(QWidget):
match widget:
case self.ReagentFormWidget():
reagent, _ = widget.parse_form()
reagent = widget.parse_form()
if reagent is not None:
reagents.append(reagent)
case self.InfoItem():
@@ -440,6 +448,7 @@ class SubmissionFormWidget(QWidget):
if field is not None:
info[field] = value
self.pyd.reagents = reagents
logger.debug(f"Reagents from form: {reagents}")
for item in self.recover:
if hasattr(self, item):
value = getattr(self, item)
@@ -661,7 +670,7 @@ class SubmissionFormWidget(QWidget):
# NOTE: If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated)
def flip_check(self, checked:bool):
def flip_check(self, checked: bool):
with QSignalBlocker(self.check) as b:
self.check.setChecked(checked)
self.lot.setEnabled(checked)
@@ -675,6 +684,7 @@ class SubmissionFormWidget(QWidget):
else:
self.parent().disabler.checkbox.setChecked(True)
@report_result
def parse_form(self) -> Tuple[PydReagent | None, Report]:
"""
Pulls form info into PydReagent
@@ -686,18 +696,23 @@ class SubmissionFormWidget(QWidget):
if not self.lot.isEnabled():
return None, report
lot = self.lot.currentText()
wanted_reagent = Reagent.query(lot=lot, role=self.reagent.role)
wanted_reagent, new = Reagent.query_or_create(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:
logger.debug(f"Wanted reagent: {wanted_reagent}, New: {new}")
# if wanted_reagent is None:
if new:
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,
kit=self.extraction_kit
)
# wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot,
# reagent_role=self.reagent.role,
# expiry=self.reagent.expiry,
# name=self.reagent.name,
# kit=self.extraction_kit
# )
wanted_reagent = self.parent().parent().new_add_reagent(instance=wanted_reagent)
return wanted_reagent, report
else:
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
@@ -707,10 +722,13 @@ class SubmissionFormWidget(QWidget):
# 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.
rt = ReagentRole.query(name=self.reagent.role)
logger.debug(f"Reagent role: {rt}")
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), report
final = PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, role=rt.name,
expiry=wanted_reagent.expiry.date(), missing=False)
logger.debug(f"Final Reagent: {final}")
return final, report
def updated(self):
"""

16
src/submissions/tools/__init__.py
View File

@@ -1032,18 +1032,19 @@ def report_result(func):
def wrapper(*args, **kwargs):
logger.info(f"Report result being called by {func.__name__}")
output = func(*args, **kwargs)
# logger.debug(f"Function output: {output}")
match output:
case Report():
report = output
case tuple():
try:
report = [item for item in output if isinstance(item, Report)][0]
except IndexError:
report = None
# try:
report = next((item for item in output if isinstance(item, Report)), None)
# except IndexError:
# report = None
case _:
report = None
return report
logger.info(f"Got report: {report}")
report = Report()
# return report
# logger.info(f"Got report: {report}")
try:
results = report.results
except AttributeError:
@@ -1058,6 +1059,7 @@ def report_result(func):
logger.error(result.msg)
if output:
true_output = tuple(item for item in output if not isinstance(item, Report))
# logger.debug(f"True output: {true_output}")
if len(true_output) == 1:
true_output = true_output[0]
else: