feat: added option to supress BNGL2 output

biosimulators · Sep 30, 2021 · ed74af4 · ed74af4
1 parent 1cf6fec
commit ed74af4
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/biosimulators_bionetgen/_version.py b/biosimulators_bionetgen/_version.py
@@ -1 +1 @@
-__version__ = '0.1.17'
+__version__ = '0.1.18'
diff --git a/biosimulators_bionetgen/core.py b/biosimulators_bionetgen/core.py
@@ -160,7 +160,7 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     # execute the task
     bionetgen_task.actions.extend(preprocessed_task['simulation_actions'])
 
-    observable_results = exec_bionetgen_task(bionetgen_task)
+    observable_results = exec_bionetgen_task(bionetgen_task, verbose=config.VERBOSE)
 
     # get predicted values of the variables
     variable_results = get_variables_results_from_observable_results(observable_results, variables)

diff --git a/biosimulators_bionetgen/utils.py b/biosimulators_bionetgen/utils.py
@@ -332,11 +332,12 @@ def create_actions_for_simulation(simulation, config=None):
     return actions, exec_kisao_id
 
 
-def exec_bionetgen_task(task):
+def exec_bionetgen_task(task, verbose=True):
     """ Execute a task and return the predicted values of the observables
 
     Args:
         task (:obj:`Task`): task
+        verbose (:obj:`bool`, optional): whether to display diagnostic information
 
     Returns:
         :obj:`pandas.DataFrame`: predicted values of the observables
@@ -355,7 +356,8 @@ def exec_bionetgen_task(task):
     # execute the task
     bionetgen_path = SimulatorConfig().bionetgen_path
     try:
-        subprocess.check_call([bionetgen_path, task_filename, '--outdir', temp_dirname])
+        subprocess.check_call([bionetgen_path, task_filename, '--outdir', temp_dirname],
+                              stdout=None if verbose else subprocess.DEVNULL)
     except Exception:
         # cleanup temporary files
         shutil.rmtree(temp_dirname)