Post code-cleanup, moments before disaster.

2025-03-26 14:19:13 -05:00
parent 3ec79fdcfe
commit d844211e1b
21 changed files with 183 additions and 285 deletions
--- a/src/submissions/frontend/visualizations/irida_charts.py
+++ b/src/submissions/frontend/visualizations/irida_charts.py
@@ -19,10 +19,6 @@ class IridaFigure(CustomFigure):

        super().__init__(df=df, modes=modes, settings=settings)
        self.df = df
-        # try:
-        #     months = int(settings['months'])
-        # except KeyError:
-        #     months = 6
        self.construct_chart(df=df, modes=modes, start_date=settings['start_date'], end_date=settings['end_date'])


--- a/src/submissions/frontend/visualizations/pcr_charts.py
+++ b/src/submissions/frontend/visualizations/pcr_charts.py
@@ -3,10 +3,8 @@ Functions for constructing irida controls graphs using plotly.
 """
 from pprint import pformat
 from . import CustomFigure
-import plotly.express as px
-import pandas as pd
 from PyQt6.QtWidgets import QWidget
-import logging
+import logging, plotly.express as px, pandas as pd

 logger = logging.getLogger(f"submissions.{__name__}")

@@ -17,10 +15,6 @@ class PCRFigure(CustomFigure):
                 months: int = 6):
        super().__init__(df=df, modes=modes, settings=settings)
        self.df = df
-        # try:
-        #     months = int(settings['months'])
-        # except KeyError:
-        #     months = 6
        self.construct_chart(df=df)

    def construct_chart(self, df: pd.DataFrame):
--- a/src/submissions/frontend/visualizations/turnaround_chart.py
+++ b/src/submissions/frontend/visualizations/turnaround_chart.py
@@ -3,10 +3,8 @@ Construct turnaround time charts
 """
 from pprint import pformat
 from . import CustomFigure
-import plotly.express as px
-import pandas as pd
 from PyQt6.QtWidgets import QWidget
-import logging
+import logging, plotly.express as px, pandas as pd

 logger = logging.getLogger(f"submissions.{__name__}")

--- a/src/submissions/frontend/widgets/app.py
+++ b/src/submissions/frontend/widgets/app.py
@@ -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()


--- a/src/submissions/frontend/widgets/controls_chart.py
+++ b/src/submissions/frontend/widgets/controls_chart.py
@@ -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
--- a/src/submissions/frontend/widgets/omni_add_edit.py
+++ b/src/submissions/frontend/widgets/omni_add_edit.py
@@ -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}")
--- a/src/submissions/frontend/widgets/omni_manager.py
+++ b/src/submissions/frontend/widgets/omni_manager.py
@@ -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


--- a/src/submissions/frontend/widgets/omni_manager_pydant.py
+++ b/src/submissions/frontend/widgets/omni_manager_pydant.py
@@ -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()
--- a/src/submissions/frontend/widgets/omni_search.py
+++ b/src/submissions/frontend/widgets/omni_search.py
@@ -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
--- a/src/submissions/frontend/widgets/submission_widget.py
+++ b/src/submissions/frontend/widgets/submission_widget.py
@@ -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))