feat: refactored task preprocessing, added license management for Gurobi

.gitignore

@@ -7,7 +7,7 @@ build/
 
 # coverage files
 htmlcov/
-.coverage
+.coverage*
 coverage.xml
 
 # compiled documentation

Dockerfile

@@ -14,7 +14,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.15"
+ARG VERSION="0.1.16"
 ARG SIMULATOR_VERSION="0.22.1"
 
 # metadata
@@ -48,7 +48,7 @@ RUN apt-get update -y \
 
 # Copy code for command-line interface into image and install it
 COPY . /root/Biosimulators_COBRApy
-RUN pip install /root/Biosimulators_COBRApy \
+RUN pip install /root/Biosimulators_COBRApy/[gurobi] \
     && mkdir -p /.cache/cobrapy \
     && chmod ugo+rw /.cache/cobrapy \
     && rm -rf /root/Biosimulators_COBRApy

biosimulators_cobrapy/_version.py

@@ -1 +1 @@
-__version__ = '0.1.15'
+__version__ = '0.1.16'

biosimulators_cobrapy/core.py

@@ -11,13 +11,15 @@
                     apply_variables_to_simulation_method_args, validate_variables, get_results_of_variables)
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
 from biosimulators_utils.config import get_config, Config  # noqa: F401
+from biosimulators_utils.licensing.gurobi import GurobiLicenseManager
 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, ModelLanguage, SteadyStateSimulation,  # noqa: F401
-                                                  Variable)
 from biosimulators_utils.sedml import validation
+from biosimulators_utils.sedml.data_model import (Task, ModelLanguage, ModelAttributeChange, SteadyStateSimulation,  # noqa: F401
+                                                  Variable)
 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.simulator.utils import get_algorithm_substitution_policy
 from biosimulators_utils.utils.core import raise_errors_warnings
 from biosimulators_utils.warnings import warn, BioSimulatorsWarning
@@ -26,7 +28,9 @@
 from kisao.utils import get_preferred_substitute_algorithm_by_ids
 from lxml import etree
 import cobra.io
+import copy
 import os
+import tempfile
 
 __all__ = [
     'exec_sedml_docs_in_combine_archive',
@@ -110,7 +114,7 @@ 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
@@ -135,24 +139,112 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     if preprocessed_task is None:
         preprocessed_task = preprocess_sed_task(task, variables, config=config)
 
+    # modify model
+    raise_errors_warnings(validation.validate_model_change_types(task.model.changes, (ModelAttributeChange, )),
+                          error_summary='Changes for model `{}` are not supported.'.format(task.model.id))
+    if task.model.changes:
+        model_etree = preprocessed_task['model']['etree']
+
+        model = copy.deepcopy(task.model)
+        for change in model.changes:
+            change.new_value = str(change.new_value)
+
+        apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=None)
+
+        model_file, model_filename = tempfile.mkstemp(suffix='.xml')
+        os.close(model_file)
+
+        model_etree.write(model_filename,
+                          xml_declaration=True,
+                          encoding="utf-8",
+                          standalone=False,
+                          pretty_print=False)
+    else:
+        model_filename = task.model.source
+
+    # get the model
+    cobra_model = cobra.io.read_sbml_model(model_filename)
+    if task.model.changes:
+        os.remove(model_filename)
+
+    variable_xpath_sbml_id_map = preprocessed_task['model']['variable_xpath_sbml_id_map']
+    variable_xpath_sbml_fbc_id_map = preprocessed_task['model']['variable_xpath_sbml_fbc_id_map']
+
+    # set solver
+    cobra_model.solver = preprocessed_task['simulation']['solver']
+
+    # Load the simulation method specified by ``sim.algorithm``
+    method_props = preprocessed_task['simulation']['method_props']
+    method_kw_args = copy.copy(preprocessed_task['simulation']['method_kw_args'])
+
+    # encode variables into arguments of the simulation methods
+    apply_variables_to_simulation_method_args(variable_xpath_sbml_id_map, method_props, variables, method_kw_args)
+
+    # execute simulation
+    with GurobiLicenseManager():
+        solution = method_props['method'](cobra_model, **method_kw_args)
+
+        # check that solution was optimal
+        if method_props['check_status'] and solution.status != 'optimal':
+            raise cobra.exceptions.OptimizationError("A solution could not be found. The solver status was `{}`.".format(
+                solution.status))
+
+        if method_props['kisao_id'] in ['KISAO_0000527', 'KISAO_0000528']:
+            solution.objective_value = cobra_model.optimize().objective_value
+
+    # Get the results of each variable
+    variable_results = get_results_of_variables(variable_xpath_sbml_id_map, variable_xpath_sbml_fbc_id_map,
+                                                preprocessed_task['model']['active_objective_sbml_fbc_id'],
+                                                method_props, variables, solution)
+
+    # log action
+    if config.LOG:
+        log.algorithm = preprocessed_task['simulation']['algorithm_kisao_id'],
+        log.simulator_details = {
+            'method': method_props['method'].__module__ + '.' + method_props['method'].__name__,
+            'arguments': method_kw_args,
+        }
+
+    # Return the results of each variable and log
+    return variable_results, log
+
+
+def preprocess_sed_task(task, variables, config=None):
+    """ Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
+    repeatedly initializing tasks on repeated calls of :obj:`exec_sed_task`.
+
+    Args:
+        task (:obj:`Task`): task
+        variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
+        config (:obj:`Config`, optional): BioSimulators common configuration
+
+    Returns:
+        :obj:`dict`: preprocessed information about the task
+    """
+    config = config or get_config()
+
     model = task.model
     sim = task.simulation
 
+    # validate simulation
     if config.VALIDATE_SEDML:
         raise_errors_warnings(validation.validate_model_language(model.language, ModelLanguage.SBML),
                               error_summary='Language for model `{}` is not supported.'.format(model.id))
-        raise_errors_warnings(validation.validate_model_change_types(model.changes, ()),
+        raise_errors_warnings(validation.validate_model_change_types(model.changes, (ModelAttributeChange, )),
                               error_summary='Changes for model `{}` are not supported.'.format(model.id))
         raise_errors_warnings(validation.validate_simulation_type(sim, (SteadyStateSimulation, )),
                               error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
 
-    if not os.path.isfile(model.source):
+    # check model source exists
+    if model.source and not os.path.isfile(model.source):
         raise FileNotFoundError('Model source `{}` is not a file.'.format(model.source))
     model_etree = etree.parse(model.source)
-    target_x_paths_ids = validation.validate_target_xpaths(
-        variables, model_etree, attr='id')
     namespaces = get_namespaces_for_xml_doc(model_etree)
-    target_x_paths_fbc_ids = validation.validate_target_xpaths(
+
+    # preprocess variables
+    variable_xpath_sbml_id_map = validation.validate_target_xpaths(
+        variables, model_etree, attr='id')
+    variable_xpath_sbml_fbc_id_map = validation.validate_target_xpaths(
         variables,
         model_etree,
         attr={
@@ -168,10 +260,9 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     cobra_model = cobra.io.read_sbml_model(model.source)
 
     # get the SBML-FBC id of the active objective
-    active_objective_fbc_id = get_active_objective_sbml_fbc_id(model.source)
+    active_objective_sbml_fbc_id = get_active_objective_sbml_fbc_id(model.source)
 
     # Load the simulation method specified by ``sim.algorithm``
-    algorithm_kisao_id = sim.algorithm.kisao_id
     algorithm_substitution_policy = get_algorithm_substitution_policy(config=config)
     exec_kisao_id = get_preferred_substitute_algorithm_by_ids(
         sim.algorithm.kisao_id, KISAO_ALGORITHMS_PARAMETERS_MAP.keys(),
@@ -180,7 +271,7 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
 
     # set up method parameters specified by ``simulation.algorithm.changes``
     method_kw_args = {}
-    if exec_kisao_id == algorithm_kisao_id:
+    if exec_kisao_id == sim.algorithm.kisao_id:
         for method_arg_change in sim.algorithm.changes:
             try:
                 set_simulation_method_arg(method_props, method_arg_change, cobra_model, method_kw_args)
@@ -205,49 +296,25 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
                 else:
                     raise
 
+    solver_change = next((change for change in sim.algorithm.changes if change.kisao_id == 'KISAO_0000553'), None)
+    if solver_change is None and GurobiLicenseManager().is_package_available():
+        cobra_model.solver = 'gurobi'
+
     # validate variables
     validate_variables(method_props, variables)
 
-    # encode variables into arguments of the simulation metods
-    apply_variables_to_simulation_method_args(target_x_paths_ids, method_props, variables, method_kw_args)
-
-    # execute simulation
-    solution = method_props['method'](cobra_model, **method_kw_args)
-
-    # check that solution was optimal
-    if method_props['check_status'] and solution.status != 'optimal':
-        raise cobra.exceptions.OptimizationError("A solution could not be found. The solver status was `{}`.".format(
-            solution.status))
-
-    if method_props['kisao_id'] in ['KISAO_0000527', 'KISAO_0000528']:
-        solution.objective_value = cobra_model.optimize().objective_value
-
-    # Get the results of each variable
-    variable_results = get_results_of_variables(target_x_paths_ids, target_x_paths_fbc_ids,
-                                                active_objective_fbc_id, method_props, variables, solution)
-
-    # log action
-    if config.LOG:
-        log.algorithm = exec_kisao_id
-        log.simulator_details = {
-            'method': method_props['method'].__module__ + '.' + method_props['method'].__name__,
-            'arguments': method_kw_args,
+    # Return processed information about the task
+    return {
+        'model': {
+            'etree': model_etree,
+            'active_objective_sbml_fbc_id': active_objective_sbml_fbc_id,
+            'variable_xpath_sbml_id_map': variable_xpath_sbml_id_map,
+            'variable_xpath_sbml_fbc_id_map': variable_xpath_sbml_fbc_id_map,
+        },
+        'simulation': {
+            'algorithm_kisao_id': exec_kisao_id,
+            'method_props': method_props,
+            'method_kw_args': method_kw_args,
+            'solver': cobra_model.solver,
         }
-
-    # Return the results of each variable and log
-    return variable_results, log
-
-
-def preprocess_sed_task(task, variables, config=None):
-    """ Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
-    repeatedly initializing tasks on repeated calls of :obj:`exec_sed_task`.
-
-    Args:
-        task (:obj:`Task`): task
-        variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
-        config (:obj:`Config`, optional): BioSimulators common configuration
-
-    Returns:
-        :obj:`object`: preprocessed information about the task
-    """
-    pass
+    }

requirements.optional.txt

@@ -0,0 +1,2 @@
+[gurobi]
+gurobipy

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging] >= 0.1.116
+biosimulators_utils[logging] >= 0.1.119
 cobra
 kisao
 lxml

tests/test_core_main.py

@@ -205,6 +205,49 @@ def test_exec_sed_task_successfully(self):
         for var_id, result in variable_results.items():
             numpy.testing.assert_allclose(result, numpy.array(expected_results[var_id]), rtol=1e-4, atol=1e-8)
 
+    def test_exec_sed_task_with_changes(self):
+        task = sedml_data_model.Task(
+            model=sedml_data_model.Model(
+                source=os.path.join(os.path.dirname(__file__), 'fixtures', 'textbook.xml'),
+                language=sedml_data_model.ModelLanguage.SBML.value,
+            ),
+            simulation=sedml_data_model.SteadyStateSimulation(
+                algorithm=sedml_data_model.Algorithm(
+                    kisao_id='KISAO_0000437',
+                ),
+            ),
+        )
+
+        variables = [
+            sedml_data_model.Variable(
+                id='active_objective',
+                target="/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='obj']/@value",
+                target_namespaces=self.NAMESPACES,
+                task=task),
+        ]
+
+        preprocessed_task = core.preprocess_sed_task(task, variables)
+
+        results, _ = core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
+        numpy.testing.assert_allclose(results['active_objective'].tolist(), 0.8739215069684301, rtol=1e-4, atol=1e-8)
+
+        task.model.changes.append(sedml_data_model.ModelAttributeChange(
+            target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='R_EX_glc__D_e_lower_bound']/@value",
+            target_namespaces=self.NAMESPACES,
+            new_value=-1,
+        ))
+        results2, _ = core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
+        self.assertLess(results2['active_objective'].tolist(), results['active_objective'].tolist())
+
+        task.model.changes[-1].new_value = '-2'
+        results3, _ = core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
+        self.assertLess(results3['active_objective'].tolist(), results['active_objective'].tolist())
+        self.assertGreater(results3['active_objective'].tolist(), results2['active_objective'].tolist())
+
+        task.model.source = 'not a file'
+        with self.assertRaises(FileNotFoundError):
+            core.preprocess_sed_task(task, variables)
+
     def test_exec_sed_task_error_handling(self):
         # unsupported algorithm
         with self.assertRaisesRegex(ValueError, 'invalid KiSAO id'):