Fix issue with mangled IDs.

MassPy seems to assume that metabolite IDs start with "M_" and that reaction IDs start with "R_"... but doesn't *require* them to.  But it'll strip those parts of the IDs if left unprompted.  But the wrapper was assuming that every ID originally had those characters, and was stripping them back off afterwards.  This change lets both be true.  (And adds a new omex test that doesn't have those characters in the IDs.)

biosimulators_masspy/core.py

@@ -198,14 +198,21 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
         else:
             sbml_id = variable_target_sbml_id_map[variable.target]
 
-            if sbml_id.startswith('M_'):
-                if sbml_id[2:] in met_concs:
-                    variable_results[variable.id] = met_concs[sbml_id[2:]][-(sim.number_of_points + 1):]
-                else:
-                    variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), met_ics[sbml_id[2:]])
-
-            else:
+            if sbml_id in met_concs:
+                variable_results[variable.id] = met_concs[sbml_id][-(sim.number_of_points + 1):]
+            elif sbml_id[2:] in met_concs:
+                variable_results[variable.id] = met_concs[sbml_id[2:]][-(sim.number_of_points + 1):]
+            elif sbml_id in met_ics:
+                variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), met_ics[sbml_id])
+            elif sbml_id[2:] in met_ics:
+                variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), met_ics[sbml_id[2:]])
+            elif sbml_id in rxn_fluxes:
+                variable_results[variable.id] = rxn_fluxes[sbml_id][-(sim.number_of_points + 1):]
+            elif sbml_id[2:] in rxn_fluxes:
                 variable_results[variable.id] = rxn_fluxes[sbml_id[2:]][-(sim.number_of_points + 1):]
+            else:
+                raise_errors_warnings(validation.validate_task(task),
+                                      error_summary='Unable to find variable `{}` in output.'.format(sbml_id))
 
     # log action
     if config.LOG:
@@ -272,8 +279,10 @@ def preprocess_sed_task(task, variables, config=None):
     doc.setLevelAndVersion(3, 1)
     sbml = libsbml.writeSBMLToString(doc)
     mass_model = mass.io.sbml.read_sbml_model(sbml)
-    met_ids = ['M_' + mass_met.id for mass_met in mass_model.metabolites]
-    rxn_ids = ['R_' + mass_rxn.id for mass_rxn in mass_model.reactions]
+    met_ids = [mass_met.id for mass_met in mass_model.metabolites]
+    met_ids = met_ids + ['M_' + mass_met.id for mass_met in mass_model.metabolites]
+    rxn_ids = [mass_rxn.id for mass_rxn in mass_model.reactions]
+    rxn_ids = rxn_ids + ['R_' + mass_rxn.id for mass_rxn in mass_model.reactions]
 
     # validate model changes
     model_change_target_mass_map = {}
@@ -352,11 +361,9 @@ def preprocess_sed_task(task, variables, config=None):
         raise NotImplementedError(msg)
 
     if invalid_targets:
-        valid_targets = []
-        for mass_met in mass_model.metabolites:
-            valid_targets.append("/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='M_{}']".format(mass_met.id))
-        for mass_rxn in mass_model.reactions:
-            valid_targets.append("/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R_{}']".format(mass_rxn.id))
+        valid_targets = met_ids
+        valid_targets += rxn_ids
+        valid_targets += list(custom_parameters.keys())
 
         msg = (
             'The following targets are not supported:\n  - {}'

tests/test_core_main.py

@@ -645,3 +645,15 @@ def test_exec_sedml_docs_in_combine_archive_with_docker_image(self):
             archive_filename, out_dir, docker_image, environment=env, pull_docker_image=False)
 
         self._assert_combine_archive_outputs(doc, out_dir)
+
+    def test_exec_sedml_docs_in_combine_archive(self):
+            # with reports
+            archive_filename = 'fixtures/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex'
+
+            dirname = os.path.join(self.dirname, 'reports')
+            _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, dirname)
+            if log.exception:
+                raise log.exception
+
+if __name__ == "__main__":
+    unittest.main()