Renaming observable and condition hint (#52)

* only prompt the "do you want to rename" in case the to be changed observable also exists in the measurement table

* Same renaming/adding schema for condition ids

Author: PaulJonasJost

src/petab_gui/controllers/mother_controller.py

@@ -1,3 +1,5 @@
+from functools import partial
+
 from PySide6.QtWidgets import QMessageBox, QFileDialog, QLineEdit, QWidget, \
     QHBoxLayout, QToolButton, QTableView
 from PySide6.QtGui import QAction
@@ -115,11 +117,25 @@ def setup_connections(self):
         """
         # Rename Observable
         self.observable_controller.observable_2be_renamed.connect(
-            self.measurement_controller.rename_observable
+            partial(
+                self.measurement_controller.rename_value,
+                column_names = "observableId"
+            )
+        )
+        # Rename Condition
+        self.condition_controller.condition_2be_renamed.connect(
+            partial(
+                self.measurement_controller.rename_value,
+                column_names = ["simulationConditionId",
+                "preequilibrationConditionId"]
+            )
         )
-        # Add new observable
-        self.model.measurement.observable_id_changed.connect(
-            self.observable_controller.maybe_add_observable
+        # Add new condition or observable
+        self.model.measurement.relevant_id_changed.connect(
+            lambda x, y, z: self.observable_controller.maybe_add_observable(
+                x, y) if z == "observable" else
+            self.condition_controller.maybe_add_condition(
+                x, y) if z == "condition" else None
         )
         # Maybe Move to a Plot Model
         self.view.measurement_dock.table_view.selectionModel().selectionChanged.connect(

src/petab_gui/controllers/table_controllers.py

@@ -270,7 +270,7 @@ def check_petab_lint(self, row_data):
             observable_df=observable_df,
         )
 
-    def rename_observable(self, old_id: str, new_id: str):
+    def rename_value(self, old_id: str, new_id: str, column_names: str | list[str]):
         """Rename the observables in the measurement_df.
 
         Triggered by changes in the original observable_df id.
@@ -282,10 +282,13 @@ def rename_observable(self, old_id: str, new_id: str):
         new_id:
             The new observable_id.
         """
+        if not isinstance(column_names, list):
+            column_names = [column_names]
         rows = self.model.get_df().shape[0]
         for row in range(rows):
-            if self.model._data_frame.at[row, "observableId"] == old_id:
-                self.model._data_frame.at[row, "observableId"] = new_id
+            for column_name in column_names:
+                if self.model._data_frame.at[row, column_name] == old_id:
+                    self.model._data_frame.at[row, column_name] = new_id
         self.model.something_changed.emit(True)
         self.model.layoutChanged.emit()
 
@@ -480,6 +483,16 @@ def setup_completers(self):
 
 class ConditionController(TableController):
     """Controller of the Condition table."""
+    condition_2be_renamed = Signal(str, str)  # Signal to mother controller
+
+    def setup_connections_specific(self):
+        """Setup connections specific to the condition controller.
+
+        Only handles connections from within the table controllers.
+        """
+        self.model.relevant_id_changed.connect(
+            self.maybe_rename_condition
+        )
 
     def check_petab_lint(self, row_data):
         """Check a single row of the model with petablint."""
@@ -491,16 +504,43 @@ def check_petab_lint(self, row_data):
             model=sbml_model,
         )
 
-    def maybe_add_condition(self, condition_id):
+    def maybe_rename_condition(self, new_id, old_id):
+        """Potentially rename condition_ids in measurement_df.
+
+        Opens a dialog to ask the user if they want to rename the conditions.
+        If so, emits a signal to rename the conditions in the measurement_df.
+        """
+        if old_id not in self.mother_controller.measurement_controller.model.get_df()["simulationConditionId"].values:
+            return
+        reply = QMessageBox.question(
+            self.view, 'Rename Condition',
+            f'Do you want to rename condition "{old_id}" to "{new_id}" '
+            f'in all measurements?',
+            QMessageBox.Yes | QMessageBox.No,
+            QMessageBox.No
+        )
+        if reply == QMessageBox.Yes:
+            self.logger.log_message(
+                f"Renaming condition '{old_id}' to '{new_id}' in all "
+                f"measurements",
+                color="green"
+            )
+            self.condition_2be_renamed.emit(old_id, new_id)
+
+
+    def maybe_add_condition(self, condition_id, old_id=None):
         """Add a condition to the condition table if it does not exist yet."""
-        if condition_id in self.model.get_df()["conditionId"].values:
+        if condition_id in self.model.get_df().index:
             return
         # add a row
         self.model.insertRows(position=None, rows=1)
         self.model.fill_row(
             self.model.get_df().shape[0] - 1,
             data={"conditionId": condition_id}
         )
+        self.model.cell_needs_validation.emit(
+            self.model.get_df().shape[0] - 1, 0
+        )
         self.logger.log_message(
             f"Automatically added condition '{condition_id}' to the condition "
             f"table.",
@@ -589,7 +629,7 @@ def setup_connections_specific(self):
 
         Only handles connections from within the table controllers.
         """
-        self.model.observable_id_changed.connect(
+        self.model.relevant_id_changed.connect(
             self.maybe_rename_observable
         )
 
@@ -603,6 +643,8 @@ def maybe_rename_observable(self, new_id, old_id):
         Opens a dialog to ask the user if they want to rename the observables.
         If so, emits a signal to rename the observables in the measurement_df.
         """
+        if old_id not in self.mother_controller.measurement_controller.model.get_df()["observableId"].values:
+            return
         reply = QMessageBox.question(
             self.view, 'Rename Observable',
             f'Do you want to rename observable "{old_id}" to "{new_id}" '

src/petab_gui/models/pandas_table_model.py

@@ -1,3 +1,4 @@
+import pandas as pd
 from PySide6.QtCore import Qt, QAbstractTableModel, QModelIndex, Signal, QSortFilterProxyModel
 from PySide6.QtGui import QColor
 
@@ -8,7 +9,7 @@
 class PandasTableModel(QAbstractTableModel):
     """Basic table model for a pandas DataFrame."""
     # Signals
-    observable_id_changed = Signal(str, str)  # new_id, old_id
+    relevant_id_changed = Signal(str, str, str)  # new_id, old_id, type
     new_log_message = Signal(str, str)  # message, color
     cell_needs_validation = Signal(int, int)  # row, column
     something_changed = Signal(bool)
@@ -148,11 +149,17 @@ def setData(self, index, value, role=Qt.EditRole):
         if column_name == "observableId":
             self._data_frame.iloc[row, column - col_setoff] = value
             self.dataChanged.emit(index, index, [Qt.DisplayRole])
-            self.observable_id_changed.emit(value, old_value)
+            self.relevant_id_changed.emit(value, old_value, "observable")
+            self.cell_needs_validation.emit(row, column)
+            self.something_changed.emit(True)
+            return True
+        if column_name in ["conditionId", "simulationConditionId", "preequilibrationConditionId"]:
+            self._data_frame.iloc[row, column - col_setoff] = value
+            self.dataChanged.emit(index, index, [Qt.DisplayRole])
+            self.relevant_id_changed.emit(value, old_value, "condition")
             self.cell_needs_validation.emit(row, column)
             self.something_changed.emit(True)
             return True
-        # Maybe TODO: same for conditionId?
 
         # Validate data based on expected type
         expected_type = self._allowed_columns.get(column_name)["type"]
@@ -165,7 +172,7 @@ def setData(self, index, value, role=Qt.EditRole):
                 self.new_log_message.emit(
                     f"Column '{column_name}' expects a value of "
                     f"type {expected_type}, but got '{tried_value}'",
-                    color="red"
+                    "red"
                 )
                 return False
         # Set the new value
@@ -256,6 +263,7 @@ def clear_table(self):
 
 class IndexedPandasTableModel(PandasTableModel):
     """Table model for tables with named index."""
+    condition_2be_renamed = Signal(str, str)  # Signal to mother controller
     def __init__(self, data_frame, allowed_columns, table_type, parent=None):
         super().__init__(
             data_frame=data_frame,
@@ -274,20 +282,20 @@ def handle_named_index(self, index, value):
         if value in self._data_frame.index:
             self.new_log_message.emit(
                 f"Duplicate index value '{value}'",
-                color="red"
+                "red"
             )
             return False
         try:
             self._data_frame.rename(index={old_value: value}, inplace=True)
             self.dataChanged.emit(index, index, [Qt.DisplayRole])
-            self.observable_id_changed.emit(value, old_value)
+            self.relevant_id_changed.emit(value, old_value, self.table_type)
             self.cell_needs_validation.emit(row, 0)
             self.something_changed.emit(True)
             return True
         except Exception as e:
             self.new_log_message.emit(
                 f"Error renaming index value '{old_value}' to '{value}': {e}",
-                color="red"
+                "red"
             )
             return False
 
@@ -397,10 +405,11 @@ def fill_row(self, row_position: int, data: dict):
         data_to_add.update(data)
         # Maybe add default values for missing columns?
         new_index = self._data_frame.index.tolist()
+        index_name = self._data_frame.index.name
         new_index[row_position] = data_to_add.pop(
             "observableId"
         )
-        self._data_frame.index = new_index
+        self._data_frame.index = pd.Index(new_index, name=index_name)
         self._data_frame.iloc[row_position] = data_to_add
 
 
@@ -440,7 +449,12 @@ def fill_row(self, row_position: int, data: dict):
             column_name: "" for column_name in self._data_frame.columns
         }
         data_to_add.update(data)
-        self._data_frame.index[row_position] = data_to_add.pop("conditionId")
+        new_index = self._data_frame.index.tolist()
+        index_name = self._data_frame.index.name
+        new_index[row_position] = data_to_add.pop(
+            "conditionId"
+        )
+        self._data_frame.index = pd.Index(new_index, name=index_name)
         self._data_frame.iloc[row_position] = data_to_add