Updated for renaming 'biosimulators_utils.exec_status' to 'biosimulat…

…ors_utils.log'

Set 'VERBOSE' environment variable in Dockerfile
Added log argument to 'exec_sed_task'
Added simulation method, argument info to log

.flake8

@@ -2,4 +2,4 @@
 max-line-length = 150
 exclude =
     tests/*
-    docs/*
+    docs-src/*

Dockerfile

@@ -1,7 +1,7 @@
 # Base OS
 FROM continuumio/miniconda3:4.9.2
 
-ARG VERSION=0.1.5
+ARG VERSION=0.1.6
 ARG SIMULATOR_VERSION="0.9.9"
 ARG PYTHON_VERSION=3.7
 
@@ -68,7 +68,8 @@ RUN pip install /root/Biosimulators_PySCeS \
     && rm -rf /root/Biosimulators_PySCeS
 
 # supported environment variables
-ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES
+ENV ALGORITHM_SUBSTITUTION_POLICY=SIMILAR_VARIABLES \
+    VERBOSE=0
 
 # Entrypoint
 ENTRYPOINT ["pysces"]

biosimulators_pysces/_version.py

@@ -1 +1 @@
-__version__ = '0.1.5'
+__version__ = '0.1.6'

biosimulators_pysces/core.py

@@ -8,6 +8,7 @@
 
 from .data_model import KISAO_ALGORITHM_MAP
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
+from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog  # noqa: F401
 from biosimulators_utils.plot.data_model import PlotFormat  # noqa: F401
 from biosimulators_utils.report.data_model import ReportFormat, DataGeneratorVariableResults  # noqa: F401
 from biosimulators_utils.sedml.data_model import (Task, ModelLanguage, UniformTimeCourseSimulation,  # noqa: F401
@@ -50,26 +51,35 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
         plot_formats (:obj:`list` of :obj:`PlotFormat`, optional): report format (e.g., pdf)
         bundle_outputs (:obj:`bool`, optional): if :obj:`True`, bundle outputs into archives for reports and plots
         keep_individual_outputs (:obj:`bool`, optional): if :obj:`True`, keep individual output files
+
+    Returns:
+        :obj:`CombineArchiveLog`: log
     """
     sed_doc_executer = functools.partial(exec_sed_doc, exec_sed_task)
-    exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir,
-                               apply_xml_model_changes=True,
-                               report_formats=report_formats,
-                               plot_formats=plot_formats,
-                               bundle_outputs=bundle_outputs,
-                               keep_individual_outputs=keep_individual_outputs)
+    return exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir,
+                                      apply_xml_model_changes=True,
+                                      report_formats=report_formats,
+                                      plot_formats=plot_formats,
+                                      bundle_outputs=bundle_outputs,
+                                      keep_individual_outputs=keep_individual_outputs)
 
 
-def exec_sed_task(task, variables):
+def exec_sed_task(task, variables, log=None):
     ''' Execute a task and save its results
 
     Args:
        task (:obj:`Task`): task
        variables (:obj:`list` of :obj:`DataGeneratorVariable`): variables that should be recorded
+       log (:obj:`TaskLog`, optional): log for the task
 
     Returns:
-        :obj:`DataGeneratorVariableResults`: results of variables
+        :obj:`tuple`:
+
+            :obj:`DataGeneratorVariableResults`: results of variables
+            :obj:`TaskLog`: log
     '''
+    log = log or TaskLog()
+
     validation.validate_task(task)
     validation.validate_model_language(task.model.language, ModelLanguage.SBML)
     validation.validate_model_change_types(task.model.changes, ())
@@ -208,5 +218,22 @@ def exec_sed_task(task, variables):
     # restore working directory
     os.chdir(cwd)
 
-    # return results
-    return variable_results
+    # log action
+    log.algorithm = 'KISAO_0000019' if model.mode_integrator == 'CVODE' else 'KISAO_0000088'
+
+    arguments = {}
+    for key, val in model.__settings__.items():
+        if model.mode_integrator == 'CVODE':
+            if key.startswith('cvode_'):
+                arguments[key] = val
+        else:
+            if key.startswith('lsoda_'):
+                arguments[key] = val
+
+    log.simulator_details = {
+        'method': model.Simulate.__module__ + '.' + model.Simulate.__name__,
+        'arguments': arguments,
+    }
+
+    # return results and log
+    return variable_results, log

requirements.txt

@@ -1,3 +1,3 @@
-biosimulators_utils >= 0.1.30
+biosimulators_utils >= 0.1.32
 numpy
 pysces

tests/test_core_main.py

@@ -9,6 +9,7 @@
 from biosimulators_pysces import __main__
 from biosimulators_pysces import core
 from biosimulators_utils.combine import data_model as combine_data_model
+from biosimulators_utils.combine.exceptions import CombineArchiveExecutionError
 from biosimulators_utils.combine.io import CombineArchiveWriter
 from biosimulators_utils.report import data_model as report_data_model
 from biosimulators_utils.report.io import ReportReader
@@ -71,7 +72,7 @@ def test_exec_sed_task_successfully(self):
             sedml_data_model.DataGeneratorVariable(id='IL', target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='IL']"),
         ]
 
-        variable_results = core.exec_sed_task(task, variables)
+        variable_results, _ = core.exec_sed_task(task, variables)
 
         self.assertTrue(sorted(variable_results.keys()), sorted([var.id for var in variables]))
         self.assertEqual(variable_results[variables[0].id].shape, (task.simulation.number_of_points + 1,))
@@ -343,7 +344,7 @@ def pysces_model(filename):
 
         with mock.patch.dict(os.environ, env):
             with mock.patch('pysces.model', side_effect=pysces_model):
-                with self.assertRaises(AlgorithmDoesNotSupportModelFeatureException):
+                with self.assertRaises(CombineArchiveExecutionError):
                     core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
                                                             report_formats=[
                                                                 report_data_model.ReportFormat.h5,
@@ -357,7 +358,7 @@ def pysces_model(filename):
         with mock.patch.dict(os.environ, env):
             with mock.patch('pysces.model', side_effect=pysces_model):
                 with mock.patch.object(pysces.PyscesModel.PysMod, 'Simulate', side_effect=Exception('Stop')):
-                    with self.assertRaisesRegex(Exception, '^Stop$'):
+                    with self.assertRaisesRegex(CombineArchiveExecutionError, 'Stop$'):
                         with self.assertWarns(AlgorithmSubstitutedWarning):
                             core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
                                                                     report_formats=[