feat: enabled changing bounds in exec_sed_task

Author: jonrkarr

Dockerfile

@@ -14,7 +14,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.16"
+ARG VERSION="0.1.17"
 ARG SIMULATOR_VERSION="0.22.1"
 
 # metadata

biosimulators_cobrapy/_version.py

@@ -1 +1 @@
-__version__ = '0.1.16'
+__version__ = '0.1.17'

biosimulators_cobrapy/core.py

@@ -19,7 +19,6 @@
 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
@@ -30,7 +29,6 @@
 import cobra.io
 import copy
 import os
-import tempfile
 
 __all__ = [
     'exec_sedml_docs_in_combine_archive',
@@ -139,40 +137,23 @@ 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)
 
+    # get model
+    cobra_model = preprocessed_task['model']['model']
+
     # 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)
+        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_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)
+        model_change_obj_attr_map = preprocessed_task['model']['model_change_obj_attr_map']
+        for change in task.model.changes:
+            model_obj, attr_name = model_change_obj_attr_map[change.target]
+            new_value = float(change.new_value)
+            setattr(model_obj, attr_name, new_value)
 
     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'])
@@ -241,6 +222,50 @@ def preprocess_sed_task(task, variables, config=None):
     model_etree = etree.parse(model.source)
     namespaces = get_namespaces_for_xml_doc(model_etree)
 
+    # Read the model
+    cobra_model = cobra.io.read_sbml_model(model.source)
+
+    # preprocess model changes
+    model_change_sbml_id_map = validation.validate_target_xpaths(
+        model.changes, model_etree, attr='id')
+    model_change_obj_attr_map = {}
+    sbml_id_model_obj_map = {'R_' + reaction.id: reaction for reaction in cobra_model.reactions}
+    namespaces_list = namespaces.values()
+    invalid_changes = []
+    for change in model.changes:
+        sbml_id = model_change_sbml_id_map[change.target]
+        model_obj = sbml_id_model_obj_map.get(sbml_id, None)
+
+        attr_name = None
+
+        if model_obj is not None:
+            _, sep, attr = change.target.partition('/@')
+            ns, _, attr = attr.partition(':')
+            if change.target_namespaces.get(ns, None) in namespaces_list:
+                if attr == 'lowerFluxBound':
+                    attr_name = 'lower_bound'
+                elif attr == 'upperFluxBound':
+                    attr_name = 'upper_bound'
+
+        if attr_name:
+            model_change_obj_attr_map[change.target] = (model_obj, attr_name)
+        else:
+            invalid_changes.append(change.target)
+
+    if invalid_changes:
+        valid_changes = []
+        for reaction in cobra_model.reactions:
+            valid_changes.append(
+                "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_{}']/@fbc:lowerFluxBound".format(reaction.id))
+            valid_changes.append(
+                "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_{}']/@fbc:upperFluxBound".format(reaction.id))
+
+        msg = 'The following changes are invalid:\n  {}\n\nThe following targets are valid:\n  {}'.format(
+            '\n  '.join(sorted(invalid_changes)),
+            '\n  '.join(sorted(valid_changes)),
+        )
+        raise ValueError(msg)
+
     # preprocess variables
     variable_xpath_sbml_id_map = validation.validate_target_xpaths(
         variables, model_etree, attr='id')
@@ -256,9 +281,6 @@ def preprocess_sed_task(task, variables, config=None):
         }
     )
 
-    # Read the model
-    cobra_model = cobra.io.read_sbml_model(model.source)
-
     # get the SBML-FBC id of the active objective
     active_objective_sbml_fbc_id = get_active_objective_sbml_fbc_id(model.source)
 
@@ -306,15 +328,15 @@ def preprocess_sed_task(task, variables, config=None):
     # Return processed information about the task
     return {
         'model': {
-            'etree': model_etree,
+            'model': cobra_model,
             'active_objective_sbml_fbc_id': active_objective_sbml_fbc_id,
+            'model_change_obj_attr_map': model_change_obj_attr_map,
             '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,
         }
     }

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging] >= 0.1.119
+biosimulators_utils[logging] >= 0.1.121
 cobra
 kisao
 lxml

tests/test_core_main.py

@@ -226,13 +226,24 @@ def test_exec_sed_task_with_changes(self):
                 task=task),
         ]
 
+        task.model.changes.append(sedml_data_model.ModelAttributeChange(
+            target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_EX_glc__D_e']/@fbc:lowerFluxBound",
+            target_namespaces=self.NAMESPACES,
+            new_value=-1,
+        ))
+        task.model.changes.append(sedml_data_model.ModelAttributeChange(
+            target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_EX_glc__D_e']/@fbc:upperFluxBound",
+            target_namespaces=self.NAMESPACES,
+            new_value=10,
+        ))
         preprocessed_task = core.preprocess_sed_task(task, variables)
 
+        task.model.changes = []
         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="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_EX_glc__D_e']/@fbc:lowerFluxBound",
             target_namespaces=self.NAMESPACES,
             new_value=-1,
         ))
@@ -244,6 +255,26 @@ def test_exec_sed_task_with_changes(self):
         self.assertLess(results3['active_objective'].tolist(), results['active_objective'].tolist())
         self.assertGreater(results3['active_objective'].tolist(), results2['active_objective'].tolist())
 
+        task.model.changes = [
+            sedml_data_model.ModelAttributeChange(
+                target="/sbml:sbml",
+                target_namespaces=self.NAMESPACES,
+                new_value=10,
+            ),
+            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=10,
+            ),
+            sedml_data_model.ModelAttributeChange(
+                target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_EX_glc__D_e']/@fbc:id",
+                target_namespaces=self.NAMESPACES,
+                new_value=10,
+            ),
+        ]
+        with self.assertRaises(ValueError):
+            core.preprocess_sed_task(task, variables)
+
         task.model.source = 'not a file'
         with self.assertRaises(FileNotFoundError):
             core.preprocess_sed_task(task, variables)