SBML export

Author: PaulJonasJost

src/petab_gui/controllers/mother_controller.py

@@ -341,6 +341,10 @@ def setup_actions(self):
             qta.icon("mdi6.table-arrow-down"), "Save This Table", self.view
         )
         actions["save_single_table"].triggered.connect(self.save_single_table)
+        actions["save_sbml"] = QAction(
+            qta.icon("mdi6.file-code"), "Export SBML Model", self.view
+        )
+        actions["save_sbml"].triggered.connect(self.save_sbml_model)
         # Find + Replace
         actions["find"] = QAction(qta.icon("mdi6.magnify"), "Find", self.view)
         actions["find"].setShortcut(QKeySequence.Find)
@@ -574,6 +578,7 @@ def sync_visibility_with_actions(self):
 
         # Store action reference in view for context menus
         self.view.sbml_viewer.sbml_toggle_action = sbml_action
+        self.view.sbml_viewer.save_sbml_action = self.actions["save_sbml"]
 
         # Connect menu action to widget visibility
         sbml_action.toggled.connect(sbml_widget.setVisible)
@@ -655,6 +660,40 @@ def save_single_table(self):
         active_controller.save_table(file_name)
         return True
 
+    def save_sbml_model(self):
+        """Export the SBML model to an XML file."""
+        if not self.model.sbml or not self.model.sbml.sbml_text:
+            QMessageBox.warning(
+                self.view,
+                "Export SBML Model",
+                "No SBML model to export.",
+            )
+            return False
+
+        file_name, _ = QFileDialog.getSaveFileName(
+            self.view,
+            "Export SBML Model",
+            f"{self.model.sbml.model_id}.xml",
+            "SBML Files (*.xml *.sbml);;All Files (*)",
+        )
+        if not file_name:
+            return False
+
+        try:
+            with open(file_name, "w") as f:
+                f.write(self.model.sbml.sbml_text)
+                self.logger.log_message(
+                    "SBML model exported successfully to file.", color="green"
+                )
+            return True
+        except Exception as e:
+            QMessageBox.critical(
+                self.view,
+                "Export SBML Model",
+                f"Failed to export SBML model: {e}",
+            )
+            return False
+
     def handle_selection_changed(self):
         """Update the plot when selection in the measurement table changes."""
         self.update_plot()
@@ -736,12 +775,18 @@ def open_file(self, file_path=None, mode=None):
             return
         # handle file appropriately
         actionable, sep = process_file(file_path, self.logger)
-        if actionable in ["yaml", "sbml", "omex"] and mode == "append":
+        if actionable in ["yaml", "omex"] and mode == "append":
             self.logger.log_message(
                 f"Append mode is not supported for *.{actionable} files.",
                 color="red",
             )
             return
+        if actionable in ["sbml"] and mode == "append":
+            self.logger.log_message(
+                "Append mode is not supported for SBML models.",
+                color="orange",
+            )
+            return
         if not actionable:
             return
         if mode is None:

src/petab_gui/views/sbml_view.py

@@ -23,6 +23,7 @@ def __init__(self, parent=None, logger_view=None):
 
         # Reference to menu action (set by controller)
         self.sbml_toggle_action = None
+        self.save_sbml_action = None
 
         # Main layout for the SBML tab
         layout = QVBoxLayout(self)
@@ -98,6 +99,11 @@ def _show_sbml_context_menu(self, position):
         menu = self.sbml_text_edit.createStandardContextMenu()
         menu.addSeparator()
 
+        # Add export SBML option
+        if self.save_sbml_action:
+            menu.addAction(self.save_sbml_action)
+            menu.addSeparator()
+
         # Add hide SBML option
         hide_action = menu.addAction(
             qta.icon("mdi6.chevron-left"), "Hide SBML Editor"
@@ -116,6 +122,11 @@ def _show_antimony_context_menu(self, position):
         menu = self.antimony_text_edit.createStandardContextMenu()
         menu.addSeparator()
 
+        # Add export SBML option
+        if self.save_sbml_action:
+            menu.addAction(self.save_sbml_action)
+            menu.addSeparator()
+
         # Add show/hide SBML option
         if self.sbml_widget.isVisible():
             action = menu.addAction(