copy / paste (#60)

* Enable copy pasting as it is behaviour in Numbers/Excel

* Check that rows are enough

* Copy Pasting now also correctly cast into dtpye, and does not create empty condition id

Author: PaulJonasJost

src/petab_gui/C.py

@@ -1,40 +1,42 @@
 """Constants for the PEtab edit GUI."""
+import numpy as np
+
 COLUMNS = {
     "measurement": {
-        "observableId": {"type": "STRING", "optional": False},
-        "preequilibrationConditionId": {"type": "STRING", "optional": True},
-        "simulationConditionId": {"type": "STRING", "optional": False},
-        "time": {"type": "NUMERIC", "optional": False},
-        "measurement": {"type": "NUMERIC", "optional": False},
-        "observableParameters": {"type": "STRING", "optional": True},
-        "noiseParameters": {"type": "STRING", "optional": True},
-        "datasetId": {"type": "STRING", "optional": True},
-        "replicateId": {"type": "STRING", "optional": True},
+        "observableId": {"type": np.object_, "optional": False},
+        "preequilibrationConditionId": {"type": np.object_, "optional": True},
+        "simulationConditionId": {"type": np.object_, "optional": False},
+        "time": {"type": np.float64, "optional": False},
+        "measurement": {"type": np.float64, "optional": False},
+        "observableParameters": {"type": np.object_, "optional": True},
+        "noiseParameters": {"type": np.object_, "optional": True},
+        "datasetId": {"type": np.object_, "optional": True},
+        "replicateId": {"type": np.object_, "optional": True},
     },
     "observable": {
-        "observableId": {"type": "STRING", "optional": False},
-        "observableName": {"type": "STRING", "optional": True},
-        "observableFormula": {"type": "STRING", "optional": False},
-        "observableTransformation": {"type": "STRING", "optional": True},
-        "noiseFormula": {"type": "STRING", "optional": False},
-        "noiseDistribution": {"type": "STRING", "optional": True},
+        "observableId": {"type": np.object_, "optional": False},
+        "observableName": {"type": np.object_, "optional": True},
+        "observableFormula": {"type": np.object_, "optional": False},
+        "observableTransformation": {"type": np.object_, "optional": True},
+        "noiseFormula": {"type": np.object_, "optional": False},
+        "noiseDistribution": {"type": np.object_, "optional": True},
     },
     "parameter": {
-        "parameterId": {"type": "STRING", "optional": False},
-        "parameterName": {"type": "STRING", "optional": True},
-        "parameterScale": {"type": "STRING", "optional": False},
-        "lowerBound": {"type": "NUMERIC", "optional": False},
-        "upperBound": {"type": "NUMERIC", "optional": False},
-        "nominalValue": {"type": "NUMERIC", "optional": False},
-        "estimate": {"type": "STRING", "optional": False},
-        "initializationPriorType": {"type": "STRING", "optional": True},
-        "initializationPriorParameters": {"type": "STRING", "optional": True},
-        "objectivePriorType": {"type": "STRING", "optional": True},
-        "objectivePriorParameters": {"type": "STRING", "optional": True},
+        "parameterId": {"type": np.object_, "optional": False},
+        "parameterName": {"type": np.object_, "optional": True},
+        "parameterScale": {"type": np.object_, "optional": False},
+        "lowerBound": {"type": np.float64, "optional": False},
+        "upperBound": {"type": np.float64, "optional": False},
+        "nominalValue": {"type": np.float64, "optional": False},
+        "estimate": {"type": np.object_, "optional": False},
+        "initializationPriorType": {"type": np.object_, "optional": True},
+        "initializationPriorParameters": {"type": np.object_, "optional": True},
+        "objectivePriorType": {"type": np.object_, "optional": True},
+        "objectivePriorParameters": {"type": np.object_, "optional": True},
     },
     "condition": {
-        "conditionId": {"type": "STRING", "optional": False},
-        "conditionName": {"type": "STRING", "optional": False},
+        "conditionId": {"type": np.object_, "optional": False},
+        "conditionName": {"type": np.object_, "optional": False},
     }
     }
 

src/petab_gui/controllers/mother_controller.py

@@ -121,7 +121,7 @@ def setup_connections(self):
         self.observable_controller.observable_2be_renamed.connect(
             partial(
                 self.measurement_controller.rename_value,
-                column_names = "observableId"
+                column_names="observableId"
             )
         )
         # Rename Condition
@@ -236,6 +236,19 @@ def setup_actions(self):
         actions["find+replace"].setShortcut("Ctrl+R")
         actions["find+replace"].triggered.connect(
             self.open_find_replace_dialog)
+        # Copy / Paste
+        actions["copy"] = QAction(
+            qta.icon("mdi6.content-copy"),
+            "Copy", self.view
+        )
+        actions["copy"].setShortcut("Ctrl+C")
+        actions["copy"].triggered.connect(self.copy_to_clipboard)
+        actions["paste"] = QAction(
+            qta.icon("mdi6.content-paste"),
+            "Paste", self.view
+        )
+        actions["paste"].setShortcut("Ctrl+V")
+        actions["paste"].triggered.connect(self.paste_from_clipboard)
         # add/delete row
         actions["add_row"] = QAction(
             qta.icon("mdi6.table-row-plus-after"),
@@ -687,3 +700,13 @@ def delete_column(self):
         controller = self.active_controller()
         if controller:
             controller.delete_column()
+
+    def copy_to_clipboard(self):
+        controller = self.active_controller()
+        if controller:
+            controller.copy_to_clipboard()
+
+    def paste_from_clipboard(self):
+        controller = self.active_controller()
+        if controller:
+            controller.paste_from_clipboard()

src/petab_gui/controllers/table_controllers.py

@@ -1,6 +1,7 @@
 """Classes for the controllers of the tables in the GUI."""
 from PySide6.QtWidgets import QInputDialog, QMessageBox, QFileDialog, \
     QCompleter
+import numpy as np
 import pandas as pd
 import petab.v1 as petab
 from PySide6.QtCore import Signal, QObject, QModelIndex, QPoint
@@ -45,6 +46,7 @@ def __init__(
         self.model.view = self.view.table_view
         self.proxy_model = PandasTableFilterProxy(model)
         self.logger = logger
+        self.check_petab_lint_mode = True
         self.mother_controller = mother_controller
         self.view.table_view.setModel(self.model)
         self.setup_connections()
@@ -85,6 +87,8 @@ def setup_connections(self):
 
     def validate_changed_cell(self, row, column):
         """Validate the changed cell and whether its linting is correct."""
+        if not self.check_petab_lint_mode:
+            return
         row_data = self.model.get_df().iloc[row]
         index_name = self.model.get_df().index.name
         row_data = row_data.to_frame().T
@@ -137,6 +141,12 @@ def open_table(self, file_path=None, separator=None, mode="overwrite"):
                 color="red"
             )
             return
+        dtypes = {
+            col: self.model._allowed_columns.get(
+                col, {"type": np.object_}
+            )["type"] for col in new_df.columns
+        }
+        new_df = new_df.astype(dtypes)
         if mode is None:
             mode = prompt_overwrite_or_append(self)
         # Overwrite or append the table with the new DataFrame
@@ -259,12 +269,36 @@ def set_index_on_new_row(self, index: QModelIndex):
         """Set the index of the model when a new row is added."""
         self.view.table_view.setCurrentIndex(index)
 
+    def copy_to_clipboard(self):
+        """Copy the currently selected cells to the clipboard."""
+        self.view.copy_to_clipboard()
+
+    def paste_from_clipboard(self):
+        """Paste the clipboard content to the currently selected cells."""
+        self.check_petab_lint_mode = False
+        self.view.paste_from_clipboard()
+        self.check_petab_lint_mode = True
+        try:
+            self.check_petab_lint()
+        except Exception as e:
+            self.logger.log_message(
+                f"PEtab linter failed after copying: {str(e)}",
+                color="red"
+            )
+    def check_petab_lint(self, row_data):
+        """Check a single row of the model with petablint."""
+        raise NotImplementedError(
+            "This method must be implemented in child classes."
+        )
+
 
 class MeasurementController(TableController):
     """Controller of the Measurement table."""
 
-    def check_petab_lint(self, row_data):
-        """Check a single row of the model with petablint."""
+    def check_petab_lint(self, row_data: pd.DataFrame = None):
+        """Check a number of rows of the model with petablint."""
+        if row_data is None:
+            row_data = self.model.get_df()
         # Can this be done more elegantly?
         observable_df = self.mother_controller.model.observable.get_df()
         return petab.check_measurement_df(
@@ -496,8 +530,10 @@ def setup_connections_specific(self):
             self.maybe_rename_condition
         )
 
-    def check_petab_lint(self, row_data):
-        """Check a single row of the model with petablint."""
+    def check_petab_lint(self, row_data: pd.DataFrame = None):
+        """Check a number of rows of the model with petablint."""
+        if row_data is None:
+            row_data = self.model.get_df()
         observable_df = self.mother_controller.model.observable.get_df()
         sbml_model = self.mother_controller.model.sbml.get_current_sbml_model()
         return petab.check_condition_df(
@@ -532,7 +568,7 @@ def maybe_rename_condition(self, new_id, old_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().index:
+        if condition_id in self.model.get_df().index or not condition_id:
             return
         # add a row
         self.model.insertRows(position=None, rows=1)
@@ -635,8 +671,10 @@ def setup_connections_specific(self):
             self.maybe_rename_observable
         )
 
-    def check_petab_lint(self, row_data):
-        """Check a single row of the model with petablint."""
+    def check_petab_lint(self, row_data: pd.DataFrame = None):
+        """Check a number of rows of the model with petablint."""
+        if row_data is None:
+            row_data = self.model.get_df()
         return petab.check_observable_df(row_data)
 
     def maybe_rename_observable(self, new_id, old_id):
@@ -668,7 +706,7 @@ def maybe_add_observable(self, observable_id, old_id=None):
 
         Currently, `old_id` is not used.
         """
-        if observable_id in self.model.get_df().index:
+        if observable_id in self.model.get_df().index or not observable_id:
             return
         # add a row
         self.model.insertRows(position=None, rows=1)
@@ -754,8 +792,10 @@ def setup_completers(self):
                 self.completers["parameterId"]
             )
 
-    def check_petab_lint(self, row_data):
-        """Check a single row of the model with petablint."""
+    def check_petab_lint(self, row_data: pd.DataFrame = None):
+        """Check a number of rows of the model with petablint."""
+        if row_data is None:
+            row_data = self.model.get_df()
         observable_df = self.mother_controller.model.observable.get_df()
         measurement_df = self.mother_controller.model.measurement.get_df()
         condition_df = self.mother_controller.model.condition.get_df()

src/petab_gui/models/pandas_table_model.py

@@ -1,5 +1,6 @@
 import pandas as pd
-from PySide6.QtCore import Qt, QAbstractTableModel, QModelIndex, Signal, QSortFilterProxyModel
+from PySide6.QtCore import (Qt, QAbstractTableModel, QModelIndex, Signal,
+                            QSortFilterProxyModel, QMimeData)
 from PySide6.QtGui import QColor
 
 from ..C import COLUMNS
@@ -130,6 +131,8 @@ def insertColumn(self, column_name: str):
     def setData(self, index, value, role=Qt.EditRole):
         if not (index.isValid() and role == Qt.EditRole):
             return False
+        if is_invalid(value) or value == "":
+            value = None
         # check whether multiple rows but only one column is selected
         multi_row_change, selected = self.check_selection()
         if not multi_row_change:
@@ -157,6 +160,16 @@ def _set_data_single(self, index, value):
         # Handling non-index (regular data) columns
         column_name = self._data_frame.columns[column - col_setoff]
         old_value = self._data_frame.iloc[row, column - col_setoff]
+        # cast to numeric if necessary
+        if not self._data_frame[column_name].dtype == "object":
+            try:
+                value = float(value)
+            except ValueError:
+                self.new_log_message.emit(
+                    f"Column '{column_name}' expects a numeric value",
+                    "red"
+                )
+                return False
         if value == old_value:
             return False
 
@@ -288,11 +301,67 @@ def reset_invalid_cells(self):
         self._invalid_cells = set()
         self.layoutChanged.emit()
 
+    def mimeData(self, rectangle, start_index):
+        """Return the data to be copied to the clipboard.
+
+        Parameters
+        ----------
+        rectangle: np.ndarray
+            The rectangle of selected cells. Creates a minimum rectangle
+            around all selected cells and is True if the cell is selected.
+        start_index: (int, int)
+            The start index of the selection. Used to determine the location
+            of the copied data.
+        """
+        copied_data = ""
+        for row in range(rectangle.shape[0]):
+            for col in range(rectangle.shape[1]):
+                if rectangle[row, col]:
+                    copied_data += self.data(
+                        self.index(start_index[0] + row, start_index[1] + col),
+                        Qt.DisplayRole
+                    )
+                else:
+                    copied_data += "SKIP"
+                if col < rectangle.shape[1] - 1:
+                    copied_data += "\t"
+            copied_data += "\n"
+        mime_data = QMimeData()
+        mime_data.setText(copied_data.strip())
+        return mime_data
+
+    def setDataFromText(self, text, start_row, start_column):
+        """Set the data from text."""
+        # TODO: Does this need to be more flexible in the separator?
+        lines = text.split("\n")
+        self.maybe_add_rows(start_row, len(lines))
+        for row_offset, line in enumerate(lines):
+            values = line.split("\t")
+            for col_offset, value in enumerate(values):
+                if value == "SKIP":
+                    continue
+                self.setData(
+                    self.index(
+                        start_row + row_offset, start_column + col_offset
+                    ),
+                    value,
+                    Qt.EditRole
+                )
+
+    def maybe_add_rows(self, start_row, n_rows):
+        """Add rows if needed."""
+        if start_row + n_rows > self._data_frame.shape[0]:
+            self.insertRows(
+                self._data_frame.shape[0],
+                start_row + n_rows - self._data_frame.shape[0]
+            )
+            self.layoutChanged.emit()
 
 
 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,
@@ -341,6 +410,7 @@ class MeasurementModel(PandasTableModel):
     """Table model for the measurement data."""
     possibly_new_condition = Signal(str)  # Signal for new condition
     possibly_new_observable = Signal(str)  # Signal for new observable
+
     def __init__(self, data_frame, parent=None):
         super().__init__(
             data_frame=data_frame,

src/petab_gui/utils.py

@@ -525,9 +525,8 @@ def connect_forwarded(self, slot):
 def create_empty_dataframe(column_dict: dict, table_type: str):
     columns = [col for col, props in column_dict.items() if not props["optional"]]
     dtypes = {
-        col: 'float64' if props["type"] == "NUMERIC"
-        else 'object'
-        for col, props in column_dict.items() if not props["optional"]
+        col: props["type"] for col, props in column_dict.items() if not
+        props["optional"]
     }
     df = pd.DataFrame(columns=columns).astype(dtypes)
     # set potential index columns
@@ -586,6 +585,29 @@ def get_selected(table_view: QTableView, mode: str = ROW) -> list[int]:
     return None
 
 
+def get_selected_rectangles(table_view: QTableView) -> np.array:
+    """Returns the selected cells in a rectangular view.
+
+    The size of the rectangle is determined by Max_row - Min_row and
+    Max_column - Min_column. The returned array is a boolean array with
+    True values for selected cells.
+    """
+    selected = get_selected(table_view, mode=INDEX)
+    if not selected:
+        return None
+    rows = [index.row() for index in selected]
+    cols = [index.column() for index in selected]
+    min_row, max_row = min(rows), max(rows)
+    min_col, max_col = min(cols), max(cols)
+    rect_start = (min_row, min_col)
+    selected_rect = np.zeros(
+        (max_row - min_row + 1, max_col - min_col + 1), dtype=bool
+    )
+    for index in selected:
+        selected_rect[index.row() - min_row, index.column() - min_col] = True
+    return selected_rect, rect_start
+
+
 def process_file(filepath, logger):
     """
     Utility function to process a file based on its type and content.