feat: separated task preprocessing from simulation

Dockerfile-brian2

@@ -1,7 +1,7 @@
 # Base OS
 FROM ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:latest
 
-ARG VERSION=0.0.9
+ARG VERSION=0.0.10
 ARG SIMULATOR_VERSION="2.4.2"
 
 # metadata

Dockerfile-netpyne

@@ -1,7 +1,7 @@
 # Base OS
 FROM ghcr.io/biosimulators/biosimulators_pyneuroml/neuron:latest
 
-ARG VERSION=0.0.9
+ARG VERSION=0.0.10
 ARG SIMULATOR_VERSION="1.0.0.2"
 
 # metadata

Dockerfile-neuron

@@ -1,7 +1,7 @@
 # Base OS
 FROM ghcr.io/biosimulators/biosimulators_pyneuroml/pyneuroml:latest
 
-ARG VERSION=0.0.9
+ARG VERSION=0.0.10
 ARG SIMULATOR_VERSION="8.0.0"
 
 # metadata

Dockerfile-pyneuroml

@@ -1,7 +1,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION=0.0.9
+ARG VERSION=0.0.10
 ARG SIMULATOR_VERSION="0.5.11"
 
 # metadata

biosimulators_pyneuroml/_version.py

@@ -1 +1 @@
-__version__ = '0.0.9'
+__version__ = '0.0.10'

biosimulators_pyneuroml/core.py

@@ -7,15 +7,18 @@
 """
 
 from .data_model import Simulator, KISAO_ALGORITHM_MAP, SEDML_TIME_OUTPUT_COLUMN_ID, SEDML_OUTPUT_FILE_ID
-from .utils import validate_task, read_xml_file, set_sim_in_lems_xml, run_lems_xml, get_simulator_run_lems_method
+from .utils import validate_task, read_xml_file, set_sim_in_lems_xml, run_lems_xml, get_simulator_run_lems_method, validate_lems_document
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
 from biosimulators_utils.config import get_config, Config  # noqa: F401
 from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog, StandardOutputErrorCapturerLevel  # noqa: F401
 from biosimulators_utils.viz.data_model import VizFormat  # noqa: F401
 from biosimulators_utils.report.data_model import ReportFormat, VariableResults, SedDocumentResults  # noqa: F401
-from biosimulators_utils.sedml.data_model import (Task, UniformTimeCourseSimulation,  # noqa: F401
+from biosimulators_utils.sedml import validation
+from biosimulators_utils.sedml.data_model import (Task, ModelAttributeChange, UniformTimeCourseSimulation,  # noqa: F401
                                                   Variable, Symbol)
 from biosimulators_utils.sedml.exec import exec_sed_doc as base_exec_sed_doc
+from biosimulators_utils.sedml.utils import apply_changes_to_xml_model
+from biosimulators_utils.utils.core import raise_errors_warnings
 import copy
 import functools
 import os
@@ -105,7 +108,7 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     Args:
         task (:obj:`Task`): task
         variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
-        preprocessed_task (:obj:`object`, optional): preprocessed information about the task, including possible
+        preprocessed_task (:obj:`dict`, optional): preprocessed information about the task, including possible
             model changes and variables. This can be used to avoid repeatedly executing the same initialization
             for repeated calls to this method.
         log (:obj:`TaskLog`, optional): log for the task
@@ -124,22 +127,38 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
         :obj:`NotImplementedError`: if the task is not of a supported type or involves an unsuported feature
     '''
     config = config or get_config()
+
     if config.LOG and not log:
         log = TaskLog()
 
     if preprocessed_task is None:
         preprocessed_task = preprocess_sed_task(task, variables, config=config, simulator=simulator)
 
+    lems_root = preprocessed_task['model']
+
+    if task.model.changes:
+        raise_errors_warnings(validation.validate_model_change_types(task.model.changes, (ModelAttributeChange,)),
+                              error_summary='Changes for model `{}` are not supported.'.format(task.model.id))
+
+        model = copy.deepcopy(task.model)
+        for change in model.changes:
+            change.new_value = str(change.new_value)
+
+        apply_changes_to_xml_model(model, lems_root, sed_doc=None, working_dir=None)
+
+    lems_simulation = preprocessed_task['simulation']
     sim = task.simulation
     sim.algorithm = copy.deepcopy(sim.algorithm)
-    sim.algorithm.kisao_id = validate_task(task, variables, simulator, config=config)
+    sim.algorithm.kisao_id = preprocessed_task['algorithm_kisao_id']
 
-    lems_root = read_xml_file(task.model.source)
-
-    set_sim_in_lems_xml(lems_root, task, variables)
-    lems_results = run_lems_xml(lems_root, working_dirname=os.path.dirname(
-        task.model.source), lems_filename=task.model.source,
-        verbose=config.VERBOSE, config=config)[SEDML_OUTPUT_FILE_ID]
+    set_sim_in_lems_xml(lems_simulation, task, variables)
+    lems_results = run_lems_xml(
+        lems_root,
+        working_dirname=os.path.dirname(task.model.source),
+        lems_filename=task.model.source,
+        verbose=config.VERBOSE,
+        config=config,
+    )[SEDML_OUTPUT_FILE_ID]
 
     # transform the results to an instance of :obj:`VariableResults`
     variable_results = VariableResults()
@@ -156,11 +175,11 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     if config.LOG:
         log.algorithm = sim.algorithm.kisao_id
         log.simulator_details = {
-            'method': 'pyneuroml.pynml.' + get_simulator_run_lems_method(simulator).__name__,
+            'method': preprocessed_task['simulation_method'],
             'lemsSimulation': {
                 'length': '{}s'.format(sim.output_end_time),
                 'step': '{}s'.format((sim.output_end_time - sim.output_start_time) / sim.number_of_steps),
-                'method': KISAO_ALGORITHM_MAP[sim.algorithm.kisao_id]['id'],
+                'method': preprocessed_task['algorithm_method'],
             },
         }
 
@@ -179,6 +198,22 @@ def preprocess_sed_task(task, variables, config=None, simulator=Simulator.pyneur
         simulator (:obj:`Simulator`, optional): simulator
 
     Returns:
-        :obj:`object`: preprocessed information about the task
+        :obj:`dict`: preprocessed information about the task
     """
-    pass
+    config = config or get_config()
+
+    algorithm_kisao_id = validate_task(task, variables, simulator, config=config)
+
+    lems_root = read_xml_file(task.model.source)
+    lems_simulation = lems_root.xpath('/Lems/Simulation')[0]
+
+    validate_lems_document(lems_root)
+
+    # return preprocessed information
+    return {
+        'model': lems_root,
+        'simulation': lems_simulation,
+        'algorithm_kisao_id': algorithm_kisao_id,
+        'simulation_method': 'pyneuroml.pynml.' + get_simulator_run_lems_method(simulator).__name__,
+        'algorithm_method': KISAO_ALGORITHM_MAP[algorithm_kisao_id]['id'],
+    }

biosimulators_pyneuroml/utils.py

@@ -9,7 +9,8 @@
 from .data_model import Simulator, KISAO_ALGORITHM_MAP, RunLemsOptions, SEDML_TIME_OUTPUT_COLUMN_ID, SEDML_OUTPUT_FILE_ID
 from biosimulators_utils.config import get_config
 from biosimulators_utils.log.utils import StandardOutputErrorCapturer
-from biosimulators_utils.sedml.data_model import ModelLanguage, UniformTimeCourseSimulation, Task, Variable, Symbol  # noqa: F401
+from biosimulators_utils.sedml.data_model import (ModelLanguage, ModelAttributeChange, UniformTimeCourseSimulation,   # noqa: F401
+                                                  Task, Variable, Symbol)
 from biosimulators_utils.sedml import validation
 from biosimulators_utils.simulator.utils import get_algorithm_substitution_policy
 from biosimulators_utils.utils.core import raise_errors_warnings
@@ -24,6 +25,7 @@
 
 __all__ = [
     'validate_task',
+    'validate_lems_document',
     'set_sim_in_lems_xml',
     'run_lems_xml',
     'get_simulator_run_lems_method',
@@ -59,7 +61,7 @@ def validate_task(task, variables, simulator, config=None):
                               error_summary='Task `{}` is invalid.'.format(task.id))
         raise_errors_warnings(validation.validate_model_language(task.model.language, ModelLanguage.LEMS),
                               error_summary='Language for model `{}` is not supported.'.format(model.id))
-        raise_errors_warnings(validation.validate_model_change_types(task.model.changes, ()),
+        raise_errors_warnings(validation.validate_model_change_types(task.model.changes, (ModelAttributeChange,)),
                               error_summary='Changes for model `{}` are not supported.'.format(model.id))
         raise_errors_warnings(*validation.validate_model_changes(task.model),
                               error_summary='Changes for model `{}` are invalid.'.format(model.id))
@@ -108,13 +110,11 @@ def validate_task(task, variables, simulator, config=None):
     return exec_kisao_id
 
 
-def set_sim_in_lems_xml(lems_xml_root, task, variables):
-    """ Set the simulation in a LEMS document
+def validate_lems_document(lems_xml_root):
+    """ Validate LEMS document
 
     Args:
         lems_xml_root (:obj:`lxml.etree._Element`): LEMS document
-        task (:obj:`Task`): task
-        variables (:obj:`list` of :obj:`Variable`): variables to record
     """
     lems_xml = lems_xml_root.xpath('/Lems')
     if len(lems_xml) != 1:
@@ -127,12 +127,20 @@ def set_sim_in_lems_xml(lems_xml_root, task, variables):
         raise ValueError('LEMS document must have a `Simulation` element.')
     elif len(simulation_xml) > 1:
         raise ValueError('LEMS document must have a single `Simulation` element, not {}.'.format(len(simulation_xml)))
-    simulation_xml = simulation_xml[0]
 
-    # add simulation
+
+def set_sim_in_lems_xml(simulation_xml, task, variables):
+    """ Set the simulation in a LEMS document
+
+    Args:
+        simulation_xml (:obj:`lxml.etree._Element`): LEMS simulation
+        task (:obj:`Task`): task
+        variables (:obj:`list` of :obj:`Variable`): variables to record
+    """
     model = task.model
     simulation = task.simulation
 
+    # modify simulation
     simulation_xml.attrib['target'] = model.id
     simulation_xml.attrib['length'] = '{}s'.format(simulation.output_end_time)
     simulation_xml.attrib['step'] = '{}s'.format((simulation.output_end_time - simulation.output_start_time) / simulation.number_of_steps)

tests/test_core_main.py

@@ -48,27 +48,45 @@ def tearDown(self):
     def test_exec_sed_task(self):
         task, variables = self._get_simulation()
         log = TaskLog()
-        results, log = core.exec_sed_task(task, variables, log)
+        results, log = core.exec_sed_task(task, variables, log=log)
         self._assert_variable_results(task, variables, results)
 
+    def test_exec_sed_task_with_changes(self):
+        # TODO: add test for continuation of time course
+        # - Simulation 1: 0-10 ms
+        # - Simulation 2: 0-5 ms
+        # - Simulation 3: 5-10 ms starting from simulation #2
+
+        task, variables = self._get_simulation()
+        preprocessed_task = core.preprocess_sed_task(task, variables)
+
+        core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
+
+        task.model.changes.append(sedml_data_model.ModelAttributeChange(
+            target="/Lems/Include[@file='Cells.xml']/@file",
+            new_value='Undefined.xml',
+        ))
+        with self.assertRaises(RuntimeError):
+            core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
+
     def test_exec_sed_task_neuron(self):
         task, variables = self._get_simulation()
         log = TaskLog()
-        results, log = core.exec_sed_task(task, variables, log, simulator=Simulator.neuron)
+        results, log = core.exec_sed_task(task, variables, log=log, simulator=Simulator.neuron)
         self._assert_variable_results(task, variables, results)
 
     def test_exec_sed_task_netpyne(self):
         task, variables = self._get_simulation()
         log = TaskLog()
-        results, log = core.exec_sed_task(task, variables, log, simulator=Simulator.netpyne)
+        results, log = core.exec_sed_task(task, variables, log=log, simulator=Simulator.netpyne)
         self._assert_variable_results(task, variables, results)
 
     def test_exec_sed_task_non_zero_output_start_time(self):
         task, variables = self._get_simulation()
         task.simulation.output_start_time = 100e-3
         task.simulation.number_of_steps = int(200 / 0.01)
         log = TaskLog()
-        results, log = core.exec_sed_task(task, variables, log)
+        results, log = core.exec_sed_task(task, variables, log=log)
         self._assert_variable_results(task, variables, results)
 
     def test_exec_sedml_docs_in_combine_archive(self):

tests/test_utils.py

@@ -101,25 +101,25 @@ def test_set_sim_in_lems_xml(self):
             Variable(id='v', target='hhpop[0]/v'),
         ]
         lems_xml_root = utils.read_xml_file(filename)
-        utils.set_sim_in_lems_xml(lems_xml_root, task, variables)
         sim_xml = lems_xml_root.xpath('/Lems/Simulation')[0]
+        utils.set_sim_in_lems_xml(sim_xml, task, variables)
         self.assertEqual(sim_xml.attrib['length'], '10.0s')
         self.assertEqual(sim_xml.attrib['step'], '1.0s')
         self.assertEqual(sim_xml.attrib['method'], 'eulerTree')
 
         lems_xml_root = lxml.etree.Element('Undefined')
         with self.assertRaisesRegex(ValueError, 'must contain a single `Lems`'):
-            utils.set_sim_in_lems_xml(lems_xml_root, task, variables)
+            utils.validate_lems_document(lems_xml_root)
 
         lems_xml_root = lxml.etree.Element('Lems')
         with self.assertRaisesRegex(ValueError, 'must have a `Simulation`'):
-            utils.set_sim_in_lems_xml(lems_xml_root, task, variables)
+            utils.validate_lems_document(lems_xml_root)
 
         lems_xml_root = lxml.etree.Element('Lems')
         lems_xml_root.append(lxml.etree.Element('Simulation'))
         lems_xml_root.append(lxml.etree.Element('Simulation'))
         with self.assertRaisesRegex(ValueError, 'must have a single `Simulation`'):
-            utils.set_sim_in_lems_xml(lems_xml_root, task, variables)
+            utils.validate_lems_document(lems_xml_root)
 
     def test_get_available_processors(self):
         processors = utils.get_available_processors()