feat: separated simulation and pre-processing

jonrkarr · jonrkarr · commit 7f78eeea86fb · 2021-09-03T01:16:11.000-04:00
diff --git a/Dockerfile b/Dockerfile
@@ -22,7 +22,7 @@
 
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.12"
+ARG VERSION="0.1.13"
 ARG SIMULATOR_VERSION=2.6.0
 
 # metadata
diff --git a/biosimulators_bionetgen/_version.py b/biosimulators_bionetgen/_version.py
@@ -1 +1 @@
-__version__ = '0.1.12'
+__version__ = '0.1.13'
diff --git a/biosimulators_bionetgen/core.py b/biosimulators_bionetgen/core.py
@@ -8,7 +8,7 @@
 """
 
 from .io import read_task
-from .utils import (exec_bionetgen_task, add_model_attribute_change_to_task, add_simulation_to_task,
+from .utils import (exec_bionetgen_task, preprocess_model_attribute_change, add_model_attribute_change_to_task, add_simulation_to_task,
                     get_variables_results_from_observable_results, add_variables_to_model)
 from .warnings import IgnoredBnglFileContentWarning
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
@@ -100,7 +100,7 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     Args:
         task (:obj:`Task`): SED 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
@@ -136,12 +136,56 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
         * :obj:`get_variables_results_from_observable_results`
     """
     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)
 
+    # read the model from the BNGL file
+    bionetgen_task = preprocessed_task['bionetgen_task']
+
+    # validate and apply the model attribute changes to the BioNetGen task
+    for change in task.model.changes:
+        add_model_attribute_change_to_task(bionetgen_task, change, preprocessed_task['model_changes'][change.target])
+
+    # apply the SED algorithm and its parameters to the BioNetGen task
+    alg_kisao_id = preprocessed_task['algorithm_kisao_id']
+
+    # execute the task
+    observable_results = exec_bionetgen_task(bionetgen_task)
+
+    # get predicted values of the variables
+    variable_results = get_variables_results_from_observable_results(observable_results, variables)
+    for key in variable_results.keys():
+        variable_results[key] = variable_results[key][-(task.simulation.number_of_points + 1):]
+
+    # log action
+    if config.LOG:
+        log.algorithm = alg_kisao_id
+        log.simulator_details = {
+            'actions': bionetgen_task.actions,
+        }
+
+    # return the values of the variables 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()
+
     if config.VALIDATE_SEDML:
         raise_errors_warnings(
             validation.validate_task(task),
@@ -174,47 +218,19 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
         bionetgen_task.actions = []
 
     # validate and apply the model attribute changes to the BioNetGen task
+    model_changes = {}
     for change in task.model.changes:
-        add_model_attribute_change_to_task(bionetgen_task, change)
+        model_changes[change.target] = preprocess_model_attribute_change(bionetgen_task, change)
 
     # add observables for the variables to the BioNetGen model
     add_variables_to_model(bionetgen_task.model, variables)
 
     # apply the SED algorithm and its parameters to the BioNetGen task
     alg_kisao_id = add_simulation_to_task(bionetgen_task, task.simulation)
 
-    # execute the task
-    observable_results = exec_bionetgen_task(bionetgen_task)
-
-    # get predicted values of the variables
-    variable_results = get_variables_results_from_observable_results(observable_results, variables)
-    for key in variable_results.keys():
-        variable_results[key] = variable_results[key][-(task.simulation.number_of_points + 1):]
-
-    # log action
-    if config.LOG:
-        log.algorithm = alg_kisao_id
-        log.simulator_details = {
-            'actions': bionetgen_task.actions,
-        }
-
     # return the values of the variables 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
-        preprocessed_task (:obj:`PreprocessedTask`, 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.
-        config (:obj:`Config`, optional): BioSimulators common configuration
-
-    Returns:
-        :obj:`object`: preprocessed information about the task
-    """
-    pass
+    return {
+        'bionetgen_task': bionetgen_task,
+        'model_changes': model_changes,
+        'algorithm_kisao_id': alg_kisao_id,
+    }
diff --git a/biosimulators_bionetgen/utils.py b/biosimulators_bionetgen/utils.py
@@ -26,6 +26,7 @@
 import tempfile
 
 __all__ = [
+    'preprocess_model_attribute_change',
     'add_model_attribute_change_to_task',
     'add_variables_to_model',
     'add_simulation_to_task',
@@ -34,8 +35,8 @@
 ]
 
 
-def add_model_attribute_change_to_task(task, change):
-    """ Encode SED model attribute changes into a BioNetGen task
+def preprocess_model_attribute_change(task, change):
+    """ Process a model change
 
     * Compartment sizes: targets should follow the pattern ``compartments.<compartment_id>.size``
     * Function expressions: targets should follow the pattern ``functions.<function_id>.expression``
@@ -46,11 +47,13 @@ def add_model_attribute_change_to_task(task, change):
         task (:obj:`Task`): BioNetGen task
         change (:obj:`ModelAttributeChange`): model attribute change
 
+    Returns:
+        :obj:`dict`: processed information about the model change
+
     Raises:
         :obj:`ValueError`: if a target of a change is not valid
     """
     target = change.target
-    new_value = change.new_value
 
     compartment_size_match = re.match(r'^compartments\.([^\.]+)(\.size)?$', target)
     if compartment_size_match:
@@ -62,25 +65,32 @@ def add_model_attribute_change_to_task(task, change):
         for i_line, line in enumerate(block):
             match = re.match(pattern, line)
             if match:
-                block[i_line] = '{} {} {} {}'.format(obj_id, match.group(1), new_value, (match.group(3) or '').strip()).strip()
                 comp_changed = True
+                return {
+                    'type': 'replace_line_in_block',
+                    'block': block,
+                    'i_line': i_line,
+                    'new_line': lambda new_value: '{} {} {} {}'.format(obj_id, match.group(1), new_value, (match.group(3) or '').strip()).strip(),
+                }
 
         if not comp_changed:
             raise ValueError(('The size of compartment `{}` cannot be changed '
                               'because the model does not have a compartment with this id.').format(obj_id))
 
-        return
-
     parameter_values_match = re.match(r'^parameters\.([^\.]+)(\.value)?$', target)
     if parameter_values_match:
-        task.actions.append('setParameter("{}", {})'.format(parameter_values_match.group(1), new_value))
-        return
+        return {
+            'type': 'append_action',
+            'action': lambda new_value: 'setParameter("{}", {})'.format(parameter_values_match.group(1), new_value),
+        }
 
     species_counts_match = re.match(r'^species\.([^\.]+)\((.*?)\)(\.initialCount)?$', target)
     if species_counts_match:
-        task.actions.append('setConcentration("{}({})", {})'.format(
-            species_counts_match.group(1), species_counts_match.group(2), new_value))
-        return
+        return {
+            'type': 'append_action',
+            'action': lambda new_value: 'setConcentration("{}({})", {})'.format(
+                species_counts_match.group(1), species_counts_match.group(2), new_value),
+        }
 
     functions_expression_match = re.match(r'^functions\.([^\.\(\)]+)(\.expression)?$', target)
     if functions_expression_match:
@@ -94,14 +104,17 @@ def add_model_attribute_change_to_task(task, change):
             match = re.match(pattern, line)
             if match:
                 func_changed = True
-                block[i_line] = '{}({}) = {}'.format(obj_id, match.group(1), new_value)
+                return {
+                    'type': 'replace_line_in_block',
+                    'block': block,
+                    'i_line': i_line,
+                    'new_line': lambda new_value: '{}({}) = {}'.format(obj_id, match.group(1), new_value),
+                }
 
         if not func_changed:
             raise ValueError(('The expression of function `{}` cannot be changed '
                               'because the model does not have a function with this id.').format(obj_id))
 
-        return
-
     function_args_expression_match = re.match(r'^functions\.([^\.]+)\((.*?)\)(\.expression)?$', target)
     if function_args_expression_match:
         obj_id = function_args_expression_match.group(1)
@@ -115,14 +128,17 @@ def add_model_attribute_change_to_task(task, change):
             match = re.match(pattern, line)
             if match:
                 func_changed = True
-                block[i_line] = '{}({}) = {}'.format(obj_id, obj_args, new_value)
+                return {
+                    'type': 'replace_line_in_block',
+                    'block': block,
+                    'i_line': i_line,
+                    'new_line': lambda new_value: '{}({}) = {}'.format(obj_id, obj_args, new_value),
+                }
 
         if not func_changed:
             raise ValueError(('The expression of function `{}` cannot be changed '
                               'because the model does not have a function with this id.').format(obj_id))
 
-        return
-
     target_patterns = {
         'compartment size': compartment_size_match,
         'parameter value': parameter_values_match,
@@ -135,6 +151,33 @@ def add_model_attribute_change_to_task(task, change):
     raise NotImplementedError(msg)
 
 
+def add_model_attribute_change_to_task(task, change, preprocessed_change=None):
+    """ Encode SED model attribute changes into a BioNetGen task
+
+    * Compartment sizes: targets should follow the pattern ``compartments.<compartment_id>.size``
+    * Function expressions: targets should follow the pattern ``functions.<function_id>.expression``
+    * Initial species counts: targets should follow the pattern ``species.<species_id>.count``
+    * Parameter values: targets should follow the pattern ``parameters.<parameter_id>.value``
+
+    Args:
+        task (:obj:`Task`): BioNetGen task
+        change (:obj:`ModelAttributeChange`): model attribute change
+        preprocessed_change (:obj:`dict`): preprocessed information about the change
+
+    Raises:
+        :obj:`ValueError`: if a target of a change is not valid
+    """
+    if preprocessed_change is None:
+        preprocessed_change = preprocess_model_attribute_change(task, change)
+
+    new_value = change.new_value
+
+    if preprocessed_change['type'] == 'replace_line_in_block':
+        preprocessed_change['block'][preprocessed_change['i_line']] = preprocessed_change['new_line'](new_value)
+    else:
+        task.actions.append(preprocessed_change['action'](new_value))
+
+
 def add_variables_to_model(model, variables):
     """ Encode SED variables into observables in a BioNetGen task
 

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__version__ = '0.1.12'`
	`1`	`+__version__ = '0.1.13'`