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Post code-cleanup, moments before disaster.

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This commit is contained in:
lwark
2025-03-26 14:19:13 -05:00
parent 3ec79fdcfe
commit d844211e1b
21 changed files with 183 additions and 285 deletions
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6
src/submissions/frontend/widgets/app.py
View File

@@ -230,7 +230,9 @@ class App(QMainWindow):
def update_data(self):
self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
# TODO: Change this to the Pydantic version.
def manage_orgs(self):
from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
if dlg.exec():
new_org = dlg.parse_form()
@@ -245,13 +247,9 @@ class App(QMainWindow):
logger.debug("\n\nBeginning parsing\n\n")
output = dlg.parse_form()
logger.debug(f"Kit output: {pformat(output.__dict__)}")
# with open(f"{output.name}.obj", "wb") as f:
# pickle.dump(output, f)
logger.debug("\n\nBeginning transformation\n\n")
sql = output.to_sql()
assert isinstance(sql, KitType)
# with open(f"{output.name}.sql", "wb") as f:
# pickle.dump(sql, f)
sql.save()

4
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -113,10 +113,6 @@ class ControlsViewer(InfoPane):
if issubclass(self.fig.__class__, CustomFigure):
self.save_button.setEnabled(True)
# NOTE: construct html for webview
# try:
# html = self.fig.html
# except AttributeError:
# html = ""
self.webview.setHtml(self.fig.html)
self.webview.update()
return report

15
src/submissions/frontend/widgets/omni_add_edit.py
View File

@@ -28,12 +28,12 @@ class AddEdit(QDialog):
self.object_type = instance.__class__
# self.managers = deepcopy(managers)
self.managers = managers
if instance.level < 2:
try:
logger.debug(f"Parent instance: {self.parent().instance}")
self.managers.add(self.parent().instance)
except AttributeError:
pass
# if instance.level < 2:
# try:
# logger.debug(f"Parent instance: {self.parent().instance}")
# self.managers.add(self.parent().instance)
# except AttributeError:
# pass
logger.debug(f"Managers: {managers}")
self.layout = QGridLayout(self)
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
@@ -111,14 +111,13 @@ class EditProperty(QWidget):
case _:
logger.error(f"{column_type} not a supported type.")
return
# if not self.is_list:
self.layout.addWidget(self.label, 0, 0, 1, 1)
self.layout.addWidget(self.widget, 0, 1, 1, 3)
self.setLayout(self.layout)
def relationship_property_set(self, relationship, value=None):
self.widget = QComboBox()
logger.debug(self.parent().managers)
# logger.debug(self.parent().managers)
for manager in self.parent().managers:
if self.name in manager.aliases:
logger.debug(f"Name: {self.name} is in aliases: {manager.aliases}")

17
src/submissions/frontend/widgets/omni_manager.py
View File

@@ -47,7 +47,6 @@ class ManagerWindow(QDialog):
self.manager = None
else:
self.manager = manager
# logger.debug(f"Managers: {managers}")
self.extras = extras
self.context = kwargs
@@ -104,7 +103,6 @@ class ManagerWindow(QDialog):
self.options.setEditable(False)
self.options.setMinimumWidth(self.minimumWidth())
self.layout.addWidget(self.options, 1, 0, 1, 1)
# if len(options) > 0:
self.add_button = QPushButton("Add New")
self.layout.addWidget(self.add_button, 1, 1, 1, 1)
self.add_button.clicked.connect(self.add_new)
@@ -126,12 +124,6 @@ class ManagerWindow(QDialog):
for item in deletes:
item.setParent(None)
# logger.debug(f"Current options text lower: {self.options.currentText().lower()}")
# NOTE: Find the instance this manager will update
# try:
# check = "blank" not in self.options.currentText().lower() and self.options.currentText() != ""
# except AttributeError:
# check = False
# if check:
if self.add_edit == "edit" and initial:
# logger.debug(f"Querying with {self.options.currentText()}")
self.instance = self.class_object.query(name=self.options.currentText(), limit=1)
@@ -173,7 +165,6 @@ class ManagerWindow(QDialog):
Returns:
Any: The instance with updated fields.
"""
# TODO: Need Relationship property here too?
results = [item.parse_form() for item in self.findChildren(EditProperty)]
for result in results:
# logger.debug(f"Incoming result: {result}")
@@ -211,7 +202,6 @@ class ManagerWindow(QDialog):
else:
value = current_value + [data]
setattr(self.instance, name, value)
# self.instance.save()
def toggle_textedit(self, caller_child=None):
already_exists = self.findChildren(LargeTextEdit)
@@ -305,7 +295,6 @@ class EditRelationship(QWidget):
# logger.debug(f"self.relationship: {self.relationship}")
# logger.debug(f"Relationship uses list: {self.relationship.property.uselist}")
# NOTE: value is a database object in this case.
# logger.debug(f"Data for edit relationship: {self.data}")
self.widget = QTableView()
self.add_button = QPushButton("Add New")
@@ -319,7 +308,6 @@ class EditRelationship(QWidget):
else:
value = []
self.data = value
# self.update_buttons()
checked_manager, is_primary = check_object_in_manager(self.parent().manager, self.objectName())
if checked_manager:
logger.debug(f"Checked manager for {self.objectName()}: {checked_manager}")
@@ -369,7 +357,6 @@ class EditRelationship(QWidget):
new_instance = dlg.parse_form()
# NOTE: My custom __setattr__ should take care of any list problems.
self.parent().instance.__setattr__(self.objectName(), new_instance)
# self.parent().instance.save()
self.parent().update_data()
def add_existing(self):
@@ -381,7 +368,6 @@ class EditRelationship(QWidget):
instance = self.class_object.query(**row)
# NOTE: My custom __setattr__ should take care of any list problems.
self.parent().instance.__setattr__(self.objectName(), instance)
# self.parent().instance.save()
self.parent().update_data()
def set_data(self) -> None:
@@ -420,7 +406,6 @@ class EditRelationship(QWidget):
Args:
event (_type_): the item of interest
"""
# print(self.widget.isEnabled())
if not self.widget.isEnabled():
logger.warning(f"{self.objectName()} is disabled.")
return
@@ -471,7 +456,6 @@ class EditRelationship(QWidget):
except ValueError as e:
logger.error(f"Remove failed for {self.objectName().lower()} due to {e}.")
self.parent().instance.save()
# self.parent().update_data()
self.set_data()
def parse_form(self):
@@ -555,7 +539,6 @@ class JsonEditScreen(QDialog):
output.append(value)
else:
raise ValueError(f"Inappropriate data type: {type(self.json_field)}")
# output[key] = value
return output

9
src/submissions/frontend/widgets/omni_manager_pydant.py
View File

@@ -120,7 +120,6 @@ class ManagerWindow(QDialog):
# logger.debug(f"Querying with {self.options.currentText()}")
self.instance = self.class_object.query(name=self.options.currentText(), limit=1)
except AttributeError:
# self.instance = None
pass
# logger.debug(f"Instance: {self.instance}")
if not self.instance:
@@ -164,11 +163,6 @@ class ManagerWindow(QDialog):
# NOTE: RelationshipDeclareds will be given a list of existing related objects.
case "relationship":
# NOTE: field.comparator.class_object.class_ gives the relationship class
# try:
# logger.debug(
# f"Creating relationship widget with value: {[pformat(item.__dict__) for item in value]}")
# except AttributeError:
# logger.debug(f"Creating relationship widget with value: {value}")
widget = EditRelationship(self, key=key, class_object=info.title, value=value)
case _:
continue
@@ -294,7 +288,6 @@ class EditRelationship(QWidget):
value = []
self.data = value
# logger.debug(f"Set data: {self.data}")
# self.update_buttons()
# logger.debug(f"Parent manager: {self.parent().manager}")
checked_manager, is_primary = check_object_in_manager(self.parent().manager, self.objectName())
if checked_manager:
@@ -374,8 +367,6 @@ class EditRelationship(QWidget):
return
logger.debug(f"Updating \n{pformat(obj)} with \n{pformat(new_instance.__dict__)}")
obj.__dict__.update(new_instance.__dict__)
# # self.parent().omni_object.__setattr__(self.objectName(), obj)
# # instance.__dict__.update(new_instance.__dict__)
logger.debug(f"Final instance: {pformat(self.parent().omni_object.__dict__)}")
# NOTE: somewhere in the update_data I'm losing changes.
self.parent().update_data()

3
src/submissions/frontend/widgets/omni_search.py
View File

@@ -45,7 +45,6 @@ class SearchBox(QDialog):
self.setLayout(self.layout)
self.setWindowTitle(f"Search {self.object_type.__name__}")
self.update_widgets()
# self.update_data()
if returnable:
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
@@ -60,7 +59,6 @@ class SearchBox(QDialog):
Changes form inputs based on sample type
"""
search_fields = []
# search_fields = self.object_type.searchables
logger.debug(f"Search fields: {search_fields}")
deletes = [item for item in self.findChildren(FieldSearch)]
for item in deletes:
@@ -69,7 +67,6 @@ class SearchBox(QDialog):
if not self.sub_class:
logger.warning(f"No subclass selected.")
self.update_data()
# return
else:
if self.sub_class.currentText() == "Any":
self.object_type = self.original_type

6
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -315,8 +315,6 @@ class SubmissionFormWidget(QWidget):
query = self.findChildren(QWidget, name=object_name)
else:
query = self.findChildren(QWidget)
# if object_name is not None:
# query = [widget for widget in query if widget.objectName() == object_name]
return query
@report_result
@@ -338,7 +336,6 @@ class SubmissionFormWidget(QWidget):
if self.disabler.checkbox.isChecked():
_, result, _ = self.pyd.check_kit_integrity(exempt=exempt)
report.add_result(result)
# result = self.pyd.check_reagent_expiries(exempt=exempt)
if len(result.results) > 0:
return report
base_submission = self.pyd.to_sql()
@@ -372,7 +369,6 @@ class SubmissionFormWidget(QWidget):
pass
# NOTE: add reagents to submission object
if base_submission is None:
# self.app.table_widget.sub_wid.setData()
return
for reagent in base_submission.reagents:
reagent.update_last_used(kit=base_submission.extraction_kit)
@@ -752,11 +748,9 @@ class SubmissionFormWidget(QWidget):
looked_up_reg = None
if looked_up_reg:
try:
# relevant_reagents.remove(str(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}")
# relevant_reagents.insert(0, str(looked_up_reg.lot))
else:
if len(relevant_reagents) > 1:
idx = relevant_reagents.index(str(reagent.lot))