update to output data

compose_worker/output_data.py

@@ -172,89 +172,54 @@ def handle_sbml_exception() -> str:
     return error_message
 
 
-# def run_sbml_pysces(sbml_fp: str, start, dur, steps):
-#     import pysces
-#     import os
-#     import shutil
-#     # model compilation
-#     compilation_dir = '/Pysces/psc'
-#     # compilation_dir = mkdtemp()
-#     sbml_filename = sbml_fp.split('/')[-1]
-#     psc_filename = sbml_filename + '.psc'
-#     psc_fp = os.path.join(compilation_dir, psc_filename)
-#     try:
-#         # convert sbml to psc
-#         # pysces.model_dir = compilation_dir
-#         # pysces.interface.convertSBML2PSC(sbmlfile=sbml_fp, pscfile=psc_fp)  # sbmldir=os.path.dirname(sbml_fp)
-#         # instantiate model from compilation contents
-#         # with open(psc_fp, 'r', encoding='utf-8', errors='replace') as F:
-#         #    pscS = F.read()
-#         # model = pysces.model(psc_fp, loader='string', fString=pscS)
-#         model = pysces.loadSBML(sbmlfile=sbml_fp, pscfile=psc_fp)
-#         # run the simulation with specified time params
-#         model.sim_time = np.linspace(start, dur, steps + 1)
-#         model.Simulate(1)  # specify userinit=1 to directly use model.sim_time (t) rather than the default
-#         # get output with mapping of internal species ids to external (shared) species names
-#         sbml_species_mapping = get_sbml_species_mapping(sbml_fp)
-#         obs_names = list(sbml_species_mapping.keys())
-#         obs_ids = list(sbml_species_mapping.values())
-#         data = {
-#             name: model.data_sim.getSimData(obs_id)[:, 1].tolist()
-#             for name, obs_id in sbml_species_mapping.items()
-#         }
-#         # clean up model dir
-#         shutil.rmtree(compilation_dir)
-#         return data
-#     except:
-#         error_message = handle_sbml_exception()
-#         return {"error": error_message}
-
-
 def run_sbml_pysces(sbml_fp: str, start, dur, steps):
     if PYSCES_ENABLED:
         # model compilation
         sbml_filename = sbml_fp.split('/')[-1]
         psc_filename = sbml_filename + '.psc'
         psc_fp = os.path.join(pysces.model_dir, psc_filename)
-        model = pysces.loadSBML(sbmlfile=sbml_fp, pscfile=psc_fp)
-
-        # run the simulation with specified time params
-        model.sim_time = np.linspace(start, dur, steps + 1)
-        model.Simulate(1)  # specify userinit=1 to directly use model.sim_time (t) rather than the default
 
         # get output with mapping of internal species ids to external (shared) species names
         sbml_species_mapping = get_sbml_species_mapping(sbml_fp)
         obs_names = list(sbml_species_mapping.keys())
         obs_ids = list(sbml_species_mapping.values())
-        data = {
-            name: model.data_sim.getSimData(obs_id)[:, 1].tolist()
-            for name, obs_id in sbml_species_mapping.items()
-        }
 
-        return data
+        # run the simulation with specified time params and get the data
+        try:
+            model = pysces.loadSBML(sbmlfile=sbml_fp, pscfile=psc_fp)
+            model.sim_time = np.linspace(start, dur, steps + 1)
+            model.Simulate(1)  # specify userinit=1 to directly use model.sim_time (t) rather than the default
+            return {
+                name: model.data_sim.getSimData(obs_id)[:, 1].tolist()
+                for name, obs_id in sbml_species_mapping.items()
+            }
+        except:
+            error_message = handle_sbml_exception()
+            return {"error": error_message}
     else:
         return OSError('Pysces is not properly installed in your environment.')
 
 
 def run_sbml_tellurium(sbml_fp: str, start, dur, steps):
-    simulator = te.loadSBMLModel(sbml_fp)
-    mapping = get_sbml_species_mapping(sbml_fp)
-
+    # in the case that the start time is set to a point after the simulation begins
+    result = None
     try:
-        # in the case that the start time is set to a point after the simulation begins
+        simulator = te.loadSBMLModel(sbml_fp)
         if start > 0:
             simulator.simulate(0, start)
-
-        # run for the specified time
         result = simulator.simulate(start, dur, steps + 1)
-        outputs = {}
-        for colname in result.colnames:
-            if 'time' not in colname:
-                for spec_name, spec_id in mapping.items():
-                    if colname.replace("[", "").replace("]", "") == spec_id:
-                        data = result[colname]
-                        outputs[spec_name] = data.tolist()
-        return outputs
+        species_mapping = get_sbml_species_mapping(sbml_fp)
+        if result is not None:
+            outputs = {}
+            for colname in result.colnames:
+                if 'time' not in colname:
+                    for spec_name, spec_id in species_mapping.items():
+                        if colname.replace("[", "").replace("]", "") == spec_id:
+                            data = result[colname]
+                            outputs[spec_name] = data.tolist()
+            return outputs
+        else:
+            raise Exception('Tellurium: Could not generate results.')
     except:
         error_message = handle_sbml_exception()
         return {"error": error_message}
@@ -414,32 +379,7 @@ def generate_biosimulator_utc_outputs(omex_fp: str, output_root_dir: str, simula
 
 
 def generate_sbml_utc_outputs(sbml_fp: str, start: int, dur: int, steps: int, simulators: list[str] = None, truth: str = None) -> dict:
-    # output = {}
-    # # TODO: add VCELL and pysces here
-    # sbml_species_ids = list(get_sbml_species_mapping(sbml_fp).values())
-    # simulators = simulators or ['amici', 'copasi', 'tellurium']
-    # all_output_ids = []
-    # for simulator in simulators:
-    #     simulator = simulator.lower()
-    #     results = {}
-    #     simulation_executor = SBML_EXECUTORS[simulator]
-    #     sim_result = simulation_executor(sbml_fp, start, dur, steps)
-    #     all_output_ids.append(list(sim_result.keys()))
-    #     for species_id in sbml_species_ids:
-    #         if species_id in sim_result.keys():
-    #             output_vals = sim_result[species_id]
-    #             if isinstance(output_vals, np.ndarray):
-    #                 output_vals = output_vals.tolist()
-    #             results[species_id] = output_vals
-    #     output[simulator] = results
-    # # get the commonly shared output ids
-    # shared_output_ids = min(all_output_ids)
-    # for simulator_name in output.keys():
-    #     sim_data = {}
-    #     for spec_id in output[simulator_name].keys():
-    #         if spec_id in shared_output_ids:
-    #             sim_data[spec_id] = output[simulator_name][spec_id]
-    #     output[simulator_name] = sim_data
+    # TODO: add VCELL and pysces here
     output = {}
     sbml_species_ids = list(get_sbml_species_mapping(sbml_fp).keys())
     simulators = simulators or ['amici', 'copasi', 'tellurium', 'pysces']
@@ -449,15 +389,6 @@ def generate_sbml_utc_outputs(sbml_fp: str, start: int, dur: int, steps: int, si
         simulator = simulator.lower()
         simulation_executor = SBML_EXECUTORS[simulator]
         sim_result = simulation_executor(sbml_fp=sbml_fp, start=start, dur=dur, steps=steps)
-        # sim_result = None
-        # if simulator == 'amici':
-        #     sim_result = run_sbml_amici(sbml_fp=sbml_fp, start=start, dur=dur, steps=steps)
-        # elif simulator == 'copasi':
-        #     sim_result = run_sbml_copasi(sbml_fp=sbml_fp, start=start, dur=dur, steps=steps)
-        # elif simulator == 'pysces':
-        #     sim_result = run_sbml_pysces(sbml_fp=sbml_fp, start=start, dur=dur, steps=steps)
-        # elif simulator == 'tellurium':
-        #     sim_result = run_sbml_tellurium(sbml_fp=sbml_fp, start=start, dur=dur, steps=steps)
 
         # case: simulation execution was successful
         if "error" not in sim_result.keys():