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vivarium-collective · Jul 19, 2023 · d03d24e · d03d24e
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diff --git a/template/experiments/glucose_phosphorylation.py b/template/experiments/glucose_phosphorylation.py
diff --git a/template/processes/glucose_phosphorylation.py b/template/processes/glucose_phosphorylation.py
diff --git a/template/__init__.py → vivarium_tellurium/__init__.py b/template/__init__.py → vivarium_tellurium/__init__.py
diff --git a/template/composites/__init__.py → vivarium_tellurium/composites/__init__.py b/template/composites/__init__.py → vivarium_tellurium/composites/__init__.py
diff --git a/...omposites/injected_glc_phosphorylation.py → ...omposites/injected_glc_phosphorylation.py b/...omposites/injected_glc_phosphorylation.py → ...omposites/injected_glc_phosphorylation.py
diff --git a/template/experiments/__init__.py → vivarium_tellurium/experiments/__init__.py b/template/experiments/__init__.py → vivarium_tellurium/experiments/__init__.py
diff --git a/template/library/__init__.py → vivarium_tellurium/library/__init__.py b/template/library/__init__.py → vivarium_tellurium/library/__init__.py
diff --git a/template/processes/__init__.py → vivarium_tellurium/processes/__init__.py b/template/processes/__init__.py → vivarium_tellurium/processes/__init__.py
diff --git a/template/processes/template_process.py → ..._tellurium/processes/tellurium_process.py b/template/processes/template_process.py → ..._tellurium/processes/tellurium_process.py
@@ -1,33 +1,15 @@
-'''
-Execute by running: ``python template/processes/template_process.py``
-
-TODO: Replace the template code to implement your own process.
-'''
-
-import os
-
 from vivarium.core.process import Process
-from vivarium.core.composition import (
-    simulate_process,
-    PROCESS_OUT_DIR,
-)
-from vivarium.plots.simulation_output import plot_simulation_output
-
+from vivarium.core.engine import Engine, pp
 
-# a global NAME is used for the output directory and for the process name
-NAME = 'template'
+# TODO import tellurium
 
 
-class Template(Process):
-    '''
-    This mock process provides a basic template that can be used for a new process
-    '''
-
-    # give the process a name, so that it can register in the process_repository
-    name = NAME
+class TelluriumProcess(Process):
+    ''' Vivarium Process for Tellurium '''
 
     # declare default parameters as class variables
     defaults = {
+        'model_path': '',
         'uptake_rate': 0.1,
     }
 
@@ -50,6 +32,7 @@ def ports_schema(self):
         * `_serializer`
         '''
 
+        # TODO this needs to be done automatically by reading the tellurium model. Maybe study vivarium-biosimulators
         return {
             'internal': {
                 'A': {
@@ -67,36 +50,35 @@ def ports_schema(self):
             },
         }
 
-    def next_update(self, timestep, states):
+    def next_update(self, interval, states):
 
-        # get the states
+        # get the states from the tellurium model
         internal_A = states['internal']['A']
         external_A = states['external']['A']
 
-        # calculate timestep-dependent updates
-        internal_update = self.parameters['uptake_rate'] * external_A * timestep
+        # run tellurium here
+        internal_update = self.parameters['uptake_rate'] * external_A * interval
         external_update = -1 * internal_update
 
-        # return an update that mirrors the ports structure
-        return {
+        # get the results from tellurium
+        update = {
             'internal': {
                 'A': internal_update},
             'external': {
                 'A': external_update}
         }
 
+        # return an update that mirrors the ports structure
+        return update
 
-# functions to configure and run the process
-def run_template_process():
-    '''Run a simulation of the process.
 
-    Returns:
-        The simulation output.
-    '''
 
-    # initialize the process by passing in parameters
-    parameters = {}
-    template_process = Template(parameters)
+def test_tellurium():
+    totaltime = 10.0
+
+    # initialize the process
+    config = {}
+    tellurium_process = TelluriumProcess(config)
 
     # declare the initial state, mirroring the ports structure
     initial_state = {
@@ -108,38 +90,26 @@ def run_template_process():
         },
     }
 
-    # run the simulation
-    sim_settings = {
-        'total_time': 10,
-        'initial_state': initial_state}
-    output = simulate_process(template_process, sim_settings)
-
-    return output
-
+    ports = tellurium_process.ports_schema()
+    print('PORTS')
+    print(ports)
 
-def test_template_process():
-    '''Test that the process runs correctly.
+    # make the simulation
+    sim = Engine(
+        processes={'tellurium_process': tellurium_process},
+        topology={'tellurium_process': {port_id: (port_id,) for port_id in ports.keys()}},
+        initial_state=initial_state
+    )
 
-    This will be executed by pytest.
-    '''
-    output = run_template_process()
-    # TODO: Add assert statements to ensure correct performance.
-
-
-def main():
-    '''Simulate the process and plot results.'''
-    # make an output directory to save plots
-    out_dir = os.path.join(PROCESS_OUT_DIR, NAME)
-    if not os.path.exists(out_dir):
-        os.makedirs(out_dir)
+    # run the simulation
+    sim.update(totaltime)
 
-    output = run_template_process()
+    # get the results
+    data = sim.emitter.get_data()
 
-    # plot the simulation output
-    plot_settings = {}
-    plot_simulation_output(output, plot_settings, out_dir)
+    print(pp(data))
 
 
 # run module with python template/processes/template_process.py
 if __name__ == '__main__':
-    main()
+    test_tellurium()