From 81e807e037f5606ece6aa869dae8e6949e3f6a63 Mon Sep 17 00:00:00 2001
From: "Frank T. Bergmann" <fbergman@caltech.edu>
Date: Tue, 26 Jul 2022 11:18:45 +0200
Subject: [PATCH] #25: use callback for model loading / simulation

---
 basico/model_io.py        | 11 ++++++-----
 basico/task_timecourse.py |  5 ++++-
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/basico/model_io.py b/basico/model_io.py
index adb0f21..84dedae 100644
--- a/basico/model_io.py
+++ b/basico/model_io.py
@@ -12,6 +12,7 @@
 import zipfile
 
 import basico.model_info
+from basico.callbacks import get_default_handler
 
 try:
     import urllib2
@@ -215,10 +216,10 @@ def load_model_from_string(content):
     if '<COPASI ' in content and model.loadModelFromString(content, os.getcwd()):
         return set_current_model(model)
 
-    if '<sbml ' in content and model.importSBMLFromString(content):
+    if '<sbml ' in content and model.importSBMLFromString(content, pImportHandler=get_default_handler()):
         return set_current_model(model)
 
-    if '<sedML '  in content and model.importSEDMLFromString(content):
+    if '<sedML '  in content and model.importSEDMLFromString(content, pImportHandler=get_default_handler()):
         return set_current_model(model)
 
     return remove_datamodel(model)
@@ -254,13 +255,13 @@ def load_model(location):
     if os.path.isfile(location):
         location = os.path.abspath(location)
         if zipfile.is_zipfile(location):
-            if model.openCombineArchive(location):
+            if model.openCombineArchive(location, pProgressReport=get_default_handler()):
                 return set_current_model(model)
-        if model.importSBML(location):
+        if model.importSBML(location, pImportHandler=get_default_handler()):
             return set_current_model(model)
         if model.loadModel(location):
             return set_current_model(model)
-        if model.importSEDML(location):
+        if model.importSEDML(location, pImportHandler=get_default_handler()):
             return set_current_model(model)
 
     remove_datamodel(model)
diff --git a/basico/task_timecourse.py b/basico/task_timecourse.py
index 955464a..a4ec9eb 100644
--- a/basico/task_timecourse.py
+++ b/basico/task_timecourse.py
@@ -28,6 +28,8 @@
 import basico
 from . import model_io
 from . import model_info
+from .callbacks import get_default_handler
+
 import pandas
 import numpy
 import logging
@@ -152,6 +154,7 @@ def run_time_course_with_output(output_selection, *args, **kwargs):
 
     model.addInterface(dh)
     result = task.initializeRaw(COPASI.CCopasiTask.OUTPUT_UI)
+    task.setCallBack(get_default_handler())
     if not result:
         logging.error("Error while initializing the simulation: " +
         COPASI.CCopasiMessage.getLastMessage().getText())
@@ -160,7 +163,7 @@ def run_time_course_with_output(output_selection, *args, **kwargs):
         if not result:
             logging.error("Error while running the simulation: " +
             COPASI.CCopasiMessage.getLastMessage().getText())
-
+    task.setCallBack(None)
     df = get_data_from_data_handler(dh, columns)
     model.removeInterface(dh)