fix: fixed logging of algorithms

biosimulators · Nov 8, 2021 · cc6978d · cc6978d
1 parent 554fbff
commit cc6978d
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Showing 4 changed files with 7 additions and 3 deletions.
diff --git a/biosimulators/Dockerfile b/biosimulators/Dockerfile
@@ -1,7 +1,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION=0.0.4
+ARG VERSION=0.0.5
 ARG SIMULATOR_VERSION=1.4.0
 ARG LIBSBML_VERSION=5.19.0
 

diff --git a/biosimulators/biosimulators_libsbmlsim/_version.py b/biosimulators/biosimulators_libsbmlsim/_version.py
@@ -1 +1 @@
-__version__ = '0.0.4'
+__version__ = '0.0.5'
diff --git a/biosimulators/biosimulators_libsbmlsim/core.py b/biosimulators/biosimulators_libsbmlsim/core.py
@@ -296,7 +296,7 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
 
     # log action
     if config.LOG:
-        log.algorithm = preprocessed_task['simulation']['algorithm_kisao_id'],
+        log.algorithm = preprocessed_task['simulation']['algorithm_kisao_id']
         log.simulator_details = {
             'method': "simulateSBMLFromFile",
             'arguments': {

diff --git a/biosimulators/tests/test_core_main.py b/biosimulators/tests/test_core_main.py
@@ -27,6 +27,7 @@
 import copy
 import datetime
 import dateutil.tz
+import json
 import os
 import numpy.testing
 import shutil
@@ -309,6 +310,9 @@ def test_exec_sedml_docs_in_combine_archive(self):
         if log.exception:
             raise log.exception
 
+        # check that log can be serialized to JSON
+        json.dumps(log.to_json())
+
         results = ReportReader().run(report, out_dir, 'sim.sedml/report', format=report_data_model.ReportFormat.h5)
 
         numpy.testing.assert_allclose(results['data_set_time'], numpy.linspace(0., 10., 11))