Default Values from SBML (#89)

* Get values from sbml model in case of Parameters

* In max/min of parameter bounds, account for the value that is inserted

* Updating data refined

Author: PaulJonasJost

src/petab_gui/C.py

@@ -67,6 +67,7 @@
 MIN_COLUMN = "use column min"
 MAX_COLUMN = "use column max"
 MODE = "use most frequent"
+SBML_LOOK = "sbml value"
 STRATEGIES_DEFAULT = [COPY_FROM, USE_DEFAULT, NO_DEFAULT]
 STRATEGIES_DEFAULT_EXT = STRATEGIES_DEFAULT + [MODE]
 STRATEGIES_DEFAULT_ALL = STRATEGIES_DEFAULT_EXT + [MIN_COLUMN, MAX_COLUMN]
@@ -77,6 +78,7 @@
     MIN_COLUMN: "Use the minimum value of the column",
     MAX_COLUMN: "Use the maximum value of the column",
     MODE: "Use the most frequent value of the column",
+    SBML_LOOK: "Use the value from the SBML model",
 }
 SOURCE_COLUMN = "source_column"
 DEFAULT_VALUE = "default_value"
@@ -96,7 +98,7 @@
     "parameterScale": [USE_DEFAULT, NO_DEFAULT, MODE],
     "lowerBound": [MIN_COLUMN, MAX_COLUMN, USE_DEFAULT, NO_DEFAULT, MODE],
     "upperBound": [MAX_COLUMN, MAX_COLUMN, USE_DEFAULT, NO_DEFAULT, MODE],
-    "nominalValue": [USE_DEFAULT, NO_DEFAULT],
+    "nominalValue": [USE_DEFAULT, NO_DEFAULT, SBML_LOOK],
     "estimate": [USE_DEFAULT, NO_DEFAULT, MODE],
 }
 ALLOWED_STRATEGIES_COND = {
@@ -157,6 +159,9 @@
     "estimate": {
         "strategy": USE_DEFAULT, DEFAULT_VALUE: 1
     },
+    "nominalValue": {
+        "strategy": SBML_LOOK
+    },
 }
 DEFAULT_COND_CONFIG = {
     "conditionId": {

src/petab_gui/commands.py

@@ -99,7 +99,7 @@ def redo(self):
             position = df.shape[0] - 1  # insert *before* the auto-row
             self.model.beginInsertRows(QModelIndex(), position, position + len(self.row_indices) - 1)
             for i, idx in enumerate(self.row_indices):
-                df.loc[idx] = [""] * df.shape[1]
+                df.loc[idx] = [np.nan] * df.shape[1]
             self.model.endInsertRows()
         else:
             self.model.beginRemoveRows(QModelIndex(), min(self.row_indices), max(self.row_indices))

src/petab_gui/controllers/default_handler.py

@@ -5,11 +5,11 @@
 
 from collections import Counter
 from ..C import (COPY_FROM, USE_DEFAULT, NO_DEFAULT, MIN_COLUMN, MAX_COLUMN,
-                 MODE, DEFAULT_VALUE, SOURCE_COLUMN, STRATEGIES_DEFAULT)
+                 MODE, DEFAULT_VALUE, SOURCE_COLUMN, SBML_LOOK)
 
 
 class DefaultHandlerModel:
-    def __init__(self, model, config):
+    def __init__(self, model, config, sbml_model = None):
         """
         Initialize the handler for the model.
         :param model: The PandasTable Model containing the Data.
@@ -20,12 +20,21 @@ def __init__(self, model, config):
         self.model = model._data_frame
         self.config = config
         self.model_index = self.model.index.name
+        self._sbml_model = sbml_model
 
-    def get_default(self, column_name, row_index=None):
+    def get_default(
+        self,
+        column_name,
+        row_index=None,
+        par_scale=None,
+        changed: dict | None = None,
+    ):
         """
         Get the default value for a column based on its strategy.
         :param column_name: The name of the column to compute the default for.
         :param row_index: Optional index of the row (needed for some strategies).
+        :param par_scale: Optional parameter scale (needed for some strategies).
+        :param changed: Optional tuple containing the column name and index of the changed cell.
         :return: The computed default value.
         """
         source_column = column_name
@@ -40,40 +49,64 @@ def get_default(self, column_name, row_index=None):
         default_value = column_config.get(DEFAULT_VALUE, "")
 
         if strategy == USE_DEFAULT:
+            if self.model.dtypes[column_name] == float:
+                return float(default_value)
             return default_value
         elif strategy == NO_DEFAULT:
             return ""
         elif strategy == MIN_COLUMN:
-            return self._min_column(column_name)
+            return self._min_column(column_name, par_scale)
         elif strategy == MAX_COLUMN:
-            return self._max_column(column_name)
+            return self._max_column(column_name, par_scale)
         elif strategy == COPY_FROM:
-            return self._copy_column(column_name, column_config, row_index)
+            return self._copy_column(
+                column_name, column_config, row_index, changed
+            )
         elif strategy == MODE:
             column_config[SOURCE_COLUMN] = source_column
             return self._majority_vote(column_name, column_config)
+        elif strategy == SBML_LOOK:
+            return self._sbml_lookup(row_index)
         else:
             raise ValueError(f"Unknown strategy '{strategy}' for column '{column_name}'.")
 
-    def _min_column(self, column_name):
-        if column_name in self.model:
-            column_data = self.model[column_name].replace("", np.nan).dropna()
-            if not column_data.empty:
-                return column_data.min()
-        return ""
+    def _min_column(self, column_name, par_scale=None):
+        if column_name not in self.model:
+            return ""
+        column_data = self.model[column_name].replace("", np.nan).dropna()
+        if column_name in ["upperBound", "lowerBound"]:
+            column_data = column_data.loc[
+                self.model["parameterScale"] == par_scale
+            ]
+        if not column_data.empty:
+            return column_data.min()
 
-    def _max_column(self, column_name):
-        if column_name in self.model:
-            column_data = self.model[column_name].replace("", np.nan).dropna()
-            if not column_data.empty:
-                return column_data.max()
-        return ""
+    def _max_column(self, column_name, par_scale=None):
+        if column_name not in self.model:
+            return ""
+        column_data = self.model[column_name].replace("", np.nan).dropna()
+        if column_name in ["upperBound", "lowerBound"]:
+            column_data = column_data.loc[
+                self.model["parameterScale"] == par_scale
+            ]
+        if not column_data.empty:
+            return column_data.max()
 
-    def _copy_column(self, column_name, config, row_index):
+    def _copy_column(
+        self,
+        column_name,
+        config,
+        row_index,
+        changed: dict | None = None
+    ):
+        """Copy the value from another column in the same row."""
         source_column = config.get(SOURCE_COLUMN, column_name)
         source_column_valid = (
             source_column in self.model or source_column == self.model_index
         )
+        if changed:
+            if source_column in changed.keys():
+                return changed[source_column]
         if source_column and source_column_valid and row_index is not None:
             prefix = config.get("prefix", "")
             if row_index in self.model.index:
@@ -100,3 +133,20 @@ def _majority_vote(self, column_name, config):
             value_counts = Counter(valid_values)
             return value_counts.most_common(1)[0][0]
         return ""
+
+    def _sbml_lookup(self, row_key):
+        """Use the most frequent value in the column as the default.
+
+        Defaults to last used value in case of a tie.
+        """
+        if self._sbml_model is None:
+            return 1
+        if row_key is None:
+            return 1
+        curr_model = self._sbml_model.get_current_sbml_model()
+        if curr_model is None:
+            return 1
+        parameters = curr_model.get_valid_parameters_for_parameter_table()
+        if row_key not in list(parameters):
+            return 1
+        return curr_model.get_parameter_value(row_key)

src/petab_gui/controllers/logger_controller.py

@@ -32,7 +32,8 @@ def log_message(self, message, color="black", loglevel=1):
             return
         timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
         full_message = \
-            f"[{timestamp}]\t <span style='color: {color};'>{message}</span>"
+            (f"[{timestamp}]\t <span style='color: {color};'>"
+             f"{message}</span>")
         for view in self.views:
             view.logger.append(full_message)
 

src/petab_gui/controllers/mother_controller.py

@@ -186,6 +186,10 @@ def setup_connections(self):
         settings_manager.new_log_message.connect(
             self.logger.log_message
         )
+        # Update Parameter SBML Model
+        self.sbml_controller.overwritten_model.connect(
+            self.parameter_controller.update_handler_sbml
+        )
 
     def setup_actions(self):
         """Setup actions for the main controller."""

src/petab_gui/controllers/sbml_controller.py

@@ -34,6 +34,7 @@ def __init__(
             The main controller of the application. Needed for signal
             forwarding.
         """
+        super().__init__()
         self.view = view
         self.model = model
         self.logger = logger
@@ -119,7 +120,8 @@ def overwrite_sbml(self, file_path=None):
             self.view.antimony_text_edit.setPlainText(
                 self.model.antimony_text
             )
-            # self.overwritten_model.emit()  # Deactivated for now. Discuss!
+
+            self.overwritten_model.emit()
             self.logger.log_message(
                 "SBML model successfully opened and overwritten.",
                 color="green"

src/petab_gui/controllers/table_controllers.py

@@ -978,6 +978,9 @@ def update_handler_model(self):
         """Update the handler model."""
         self.model.default_handler.model = self.model._data_frame
 
+    def update_handler_sbml(self):
+        self.model.default_handler._sbml_model = self.mother_controller.model.sbml
+
     def setup_completers(self):
         """Set completers for the parameter table."""
         table_view = self.view.table_view

src/petab_gui/controllers/utils.py

@@ -6,6 +6,7 @@
 import functools
 import pandas as pd
 import re
+import html
 
 from ..settings_manager import settings_manager
 from ..C import COMMON_ERRORS
@@ -23,6 +24,7 @@ def wrapper(self, row_data: pd.DataFrame = None, row_name:
                 return True
             except Exception as e:
                 err_msg = filtered_error(e)
+                err_msg = html.escape(err_msg)
                 if additional_error_check:
                     if "Missing parameter(s)" in err_msg:
                         match = re.search(r"\{(.+?)\}", err_msg)