talipot-python: Rework exception management in talipot python plugins

When a talipot plugin written in Python is invoked from the classical Python
interpreter and not from the talipot GUI, prefer to let exception that might
be raised by its implementation continue its way instead of caughting it.

This behavior is much more pythonic than simply printing the error traceback
and clearing the python error indicator as client code calling the plugin can
catch the errors it might raise.

library/talipot-python/bindings/talipot-core/Algorithm.sip

@@ -50,7 +50,7 @@ public:
 
   virtual ~Algorithm();
 
-  virtual bool run() = 0;
+  virtual bool run() = 0 /VirtualErrorHandler=pass_through/;
 %Docstring
 tlp.Algorithm.run()
 

library/talipot-python/bindings/talipot-core/ExportModule.sip

@@ -87,7 +87,7 @@ saves to.
 
   virtual std::string category() const;
 
-  virtual bool exportGraph(std::ostream &os) = 0;
+  virtual bool exportGraph(std::ostream &os) = 0 /VirtualErrorHandler=pass_through/;
 %Docstring
 tlp.ExportModule.exportGraph(os)
 

library/talipot-python/bindings/talipot-core/Graph.sip

@@ -84,6 +84,9 @@ bool callGraphPropertyAlgorithm(tlp::Graph *graph, const std::string &algoName,
     msg += ".";
     PyErr_SetString(PyExc_Exception, msg.c_str());
   }
+  if (PyErr_Occurred()) {
+    sipIsErr = -1;
+  }
   return ret;
 }
 
@@ -357,6 +360,9 @@ if (pluginExists<tlp::Algorithm>(*a0)) {
   msg += ".";
   PyErr_SetString(PyExc_Exception, msg.c_str());
 }
+if (PyErr_Occurred()) {
+  sipIsErr = -1;
+}
 %End
 
 //===========================================================================================
@@ -5267,6 +5273,9 @@ if (pluginExists<tlp::ImportModule>(*a0)) {
   msg += ".";
   PyErr_SetString(PyExc_Exception, msg.c_str());
 }
+if (PyErr_Occurred()) {
+  sipIsErr = -1;
+}
 %End
 
 tlp::Graph *importGraph(const std::string &importPluginName, tlp::DataSet dataSet /GetWrapper/ ) /TransferBack/;
@@ -5318,6 +5327,9 @@ if (pluginExists<tlp::ImportModule>(*a0)) {
   msg += ".";
   PyErr_SetString(PyExc_Exception, msg.c_str());
 }
+if (PyErr_Occurred()) {
+  sipIsErr = -1;
+}
 %End
 
 //===========================================================================================
@@ -5373,6 +5385,9 @@ if (pluginExists<tlp::ImportModule>(*a0)) {
   msg += ".";
   PyErr_SetString(PyExc_Exception, msg.c_str());
 }
+if (PyErr_Occurred()) {
+  sipIsErr = -1;
+}
 %End
 
 //===========================================================================================
@@ -5441,6 +5456,9 @@ if (pluginExists<tlp::ExportModule>(*a0)) {
   msg += ".";
   PyErr_SetString(PyExc_Exception, msg.c_str());
 }
+if (PyErr_Occurred()) {
+  sipIsErr = -1;
+}
 %End
 
 //===========================================================================================

library/talipot-python/bindings/talipot-core/ImportModule.sip

@@ -87,7 +87,7 @@ This method returns all the extensions (normal and gzipped) of file formats this
    list of string
 %End
 
-  virtual bool importGraph() = 0;
+  virtual bool importGraph() = 0 /VirtualErrorHandler=pass_through/;
 %Docstring
 tlp.ImportModule.importGraph()
 

library/talipot-python/bindings/talipot-core/talipot.sip

@@ -32,6 +32,12 @@
   PyRun_SimpleString("import sys;globals()['talipot'] = sys.modules['talipot']");
 %End
 
+%VirtualErrorHandler pass_through
+// pass through virtual error handler used to not clear Python error indicator
+// in some Python implementation of C++ virtual methods
+%End
+
+
 %ModuleHeaderCode
 #include <talipot/Graph.h>
 #include <talipot/PluginsManager.h>

library/talipot-python/modules/talipotplugins.py

@@ -84,15 +84,13 @@ def runPlugin(plugin):
     except Exception:
         if plugin.pluginProgress:
             plugin.pluginProgress.setError(traceback.format_exc())
-        # Case where the plugin execution has not been launched through the
-        # Talipot GUI, so print the stack trace to stderr
         from talipot import tlp
         if type(plugin.pluginProgress) == tlp.SimplePluginProgress:
-            sys.stdout.write(('There was an error when running Python plugin '
-                              'named "%s". See stack trace below.\n') %
-                             plugin.name())
-            traceback.print_exc()
-    return ret
+            # case where the plugin execution has not been launched through the
+            # Talipot GUI, raise exception again in that case
+            raise
+    finally:
+        return ret
 
 
 def importGraph(plugin):
@@ -102,15 +100,13 @@ def importGraph(plugin):
     except Exception:
         if plugin.pluginProgress:
             plugin.pluginProgress.setError(traceback.format_exc())
-        # Case where the plugin execution has not been launched through
-        # the Talipot GUI, so print the stack trace to stderr
         from talipot import tlp
         if type(plugin.pluginProgress) == tlp.SimplePluginProgress:
-            sys.stdout.write(('There was an error when running Python plugin '
-                              'named "%s". See stack trace below.\n') %
-                             plugin.name())
-            traceback.print_exc()
-    return ret
+            # case where the plugin execution has not been launched through the
+            # Talipot GUI, raise exception again in that case
+            raise
+    finally:
+        return ret
 
 
 def exportGraph(plugin, os):
@@ -120,15 +116,13 @@ def exportGraph(plugin, os):
     except Exception:
         if plugin.pluginProgress:
             plugin.pluginProgress.setError(traceback.format_exc())
-        # Case where the plugin execution has not been launched through
-        # the Talipot GUI, so print the stack trace to stderr
         from talipot import tlp
         if type(plugin.pluginProgress) == tlp.SimplePluginProgress:
-            sys.stdout.write(('There was an error when running Python plugin '
-                              'named "%s". See stack trace below.\n') %
-                             plugin.name())
-            traceback.print_exc()
-    return ret
+            # case where the plugin execution has not been launched through the
+            # Talipot GUI, raise exception again in that case
+            raise
+    finally:
+        return ret
 
 
 def createPlugin(context, pluginModule, pluginClassName, pluginName,

tests/python/test_tgf_import.py

@@ -109,8 +109,12 @@ def test_load_tgf_graph_invalid_edge(self):
                         """
                     )
                 )
-            graph = tlp.importGraph(self.tgfPluginName, {"filename": tgfFile})
-            self.assertTrue(graph is None)
+            with self.assertRaises(ValueError) as cm:
+                tlp.importGraph(self.tgfPluginName, {"filename": tgfFile})
+                self.assertEquals(
+                    cm.exception.args[0],
+                    "Invalid edge definition: 4"
+                )
 
     def test_load_tgf_graph_invalid_node_id(self):
         with tempfile.TemporaryDirectory() as tgfDir:
@@ -128,5 +132,9 @@ def test_load_tgf_graph_invalid_node_id(self):
                         """
                     )
                 )
-            graph = tlp.importGraph(self.tgfPluginName, {"filename": tgfFile})
-            self.assertTrue(graph is None)
+            with self.assertRaises(ValueError) as cm:
+                tlp.importGraph(self.tgfPluginName, {"filename": tgfFile})
+                self.assertEquals(
+                    cm.exception.args[0],
+                    "Invalid node identifier found when parsing edges: 4"
+                )