feat: improved use of KiSAO terms

biosimulators · Sep 16, 2021 · a4086e9 · a4086e9
1 parent cb1e290
commit a4086e9
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Showing 5 changed files with 15 additions and 15 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -14,7 +14,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.20"
+ARG VERSION="0.1.21"
 ARG SIMULATOR_VERSION="2.2.0"
 
 # metadata

diff --git a/biosimulators.json b/biosimulators.json
@@ -361,7 +361,7 @@
         {
           "kisaoId": {
             "namespace": "KISAO",
-            "id": "KISAO_0000332"
+            "id": "KISAO_0000559"
           },
           "id": "initial_time_step",
           "name": "Initial time step",
@@ -933,7 +933,7 @@
       "name": "Newton-type method for solveing non-linear (NL) equations (EQ)",
       "kisaoId": {
         "namespace": "KISAO",
-        "id": "KISAO_0000408"
+        "id": "KISAO_0000569"
       },
       "modelingFrameworks": [{
         "namespace": "SBO",

diff --git a/biosimulators_tellurium/_version.py b/biosimulators_tellurium/_version.py
@@ -1 +1 @@
-__version__ = '0.1.20'
+__version__ = '0.1.21'
diff --git a/biosimulators_tellurium/data_model.py b/biosimulators_tellurium/data_model.py
@@ -88,8 +88,8 @@ class PlottingEngine(str, enum.Enum):
                 'type': ValueType.float,
                 'default': None,
             },
-            'KISAO_0000332': {
-                'kisao_id': 'KISAO_0000332',
+            'KISAO_0000559': {
+                'kisao_id': 'KISAO_0000559',
                 'id': 'initial_time_step',
                 'name': 'Initial time step',
                 'type': ValueType.float,
@@ -172,8 +172,8 @@ class PlottingEngine(str, enum.Enum):
             },
         }
     }),
-    ('KISAO_0000408', {
-        'kisao_id': 'KISAO_0000408',
+    ('KISAO_0000569', {
+        'kisao_id': 'KISAO_0000569',
         'id': 'nleq2',
         'name': "Newton-type method for solveing non-linear (NL) equations (EQ)",
         'parameters': {

diff --git a/tests/test_core_main.py b/tests/test_core_main.py
@@ -290,7 +290,7 @@ def test_exec_sed_task_steady_state_with_biosimulators(self):
             ),
             simulation=sedml_data_model.SteadyStateSimulation(
                 algorithm=sedml_data_model.Algorithm(
-                    kisao_id='KISAO_0000408',
+                    kisao_id='KISAO_0000569',
                 ),
             ),
         )
@@ -638,7 +638,7 @@ def _build_sed_doc(self, algorithm=None):
             source='model.xml',
             language=sedml_data_model.ModelLanguage.SBML.value,
         ))
-        if algorithm.kisao_id == 'KISAO_0000408':
+        if algorithm.kisao_id == 'KISAO_0000569':
             doc.simulations.append(sedml_data_model.SteadyStateSimulation(
                 id='sim_steady_state',
                 algorithm=algorithm,
@@ -659,7 +659,7 @@ def _build_sed_doc(self, algorithm=None):
             simulation=doc.simulations[0],
         ))
 
-        if algorithm.kisao_id != 'KISAO_0000408':
+        if algorithm.kisao_id != 'KISAO_0000569':
             doc.data_generators.append(sedml_data_model.DataGenerator(
                 id='data_gen_time',
                 variables=[
@@ -686,7 +686,7 @@ def _build_sed_doc(self, algorithm=None):
 
         report = sedml_data_model.Report(id='report')
         doc.outputs.append(report)
-        if algorithm.kisao_id != 'KISAO_0000408':
+        if algorithm.kisao_id != 'KISAO_0000569':
             report.data_sets.append(sedml_data_model.DataSet(id='data_set_time', label='Time', data_generator=doc.data_generators[0]))
         report.data_sets.append(sedml_data_model.DataSet(id='data_set_C', label='C', data_generator=doc.data_generators[-1]))
 
@@ -702,7 +702,7 @@ def _assert_combine_archive_outputs(self, doc, out_dir):
         self.assertEqual(sorted(report.keys()), sorted([d.id for d in doc.outputs[0].data_sets]))
 
         sim = doc.tasks[0].simulation
-        if doc.simulations[0].algorithm.kisao_id == 'KISAO_0000408':
+        if doc.simulations[0].algorithm.kisao_id == 'KISAO_0000569':
             self.assertIn(report[doc.outputs[0].data_sets[0].id].shape, [(), (1,)])
             self.assertIsInstance(report[doc.outputs[0].data_sets[0].id].tolist(), (float, list))
         else:
@@ -711,7 +711,7 @@ def _assert_combine_archive_outputs(self, doc, out_dir):
         for data_set_result in report.values():
             self.assertFalse(numpy.any(numpy.isnan(data_set_result)))
 
-        if doc.simulations[0].algorithm.kisao_id != 'KISAO_0000408':
+        if doc.simulations[0].algorithm.kisao_id != 'KISAO_0000569':
             self.assertIn('data_set_time', report)
             numpy.testing.assert_allclose(report[doc.outputs[0].data_sets[0].id],
                                           numpy.linspace(sim.output_start_time, sim.output_end_time, sim.number_of_points + 1))
@@ -772,7 +772,7 @@ def test_exec_sedml_docs_in_combine_archive_with_all_algorithms(self):
                                                                        simulator_config=simulator_config)
                 self.assertEqual(set(results.keys()), set(['sim.sedml']))
                 self.assertEqual(set(results['sim.sedml'].keys()), set(['report']))
-                if alg.kisao_id == 'KISAO_0000408':
+                if alg.kisao_id == 'KISAO_0000569':
                     self.assertEqual(set(results['sim.sedml']['report'].keys()), set(['data_set_C']))
                 else:
                     self.assertEqual(set(results['sim.sedml']['report'].keys()), set(['data_set_time', 'data_set_C']))