set strict=False in Reader().run to avoid "The model cannot be loaded…

… because ... the attributes must be defined in this order" errors
KarrLab · Apr 26, 2018 · 5e5352f · 5e5352f
1 parent 936f512
commit 5e5352f
Show file tree

Hide file tree

Showing 7 changed files with 9 additions and 10 deletions.
diff --git a/tests/multialgorithm/submodels/test_ssa.py b/tests/multialgorithm/submodels/test_ssa.py
@@ -28,7 +28,7 @@ def setUp(self):
         SimulationEngine.reset()
         self.MODEL_FILENAME = os.path.join(os.path.dirname(__file__), 'fixtures', 'test_model.xlsx')
         # make a model
-        self.model = Reader().run(self.MODEL_FILENAME)
+        self.model = Reader().run(self.MODEL_FILENAME, strict=False)
         ExecutableModel.set_up_simulation(self.model)
 
     @unittest.skip("skip")

diff --git a/tests/multialgorithm/submodels/test_submodels.py b/tests/multialgorithm/submodels/test_submodels.py
@@ -52,7 +52,7 @@ def setUp(self):
 
         self.MODEL_FILENAME = os.path.join(os.path.dirname(__file__), 'fixtures',
             'test_submodel_no_shared_species.xlsx')
-        self.model = Reader().run(self.MODEL_FILENAME)
+        self.model = Reader().run(self.MODEL_FILENAME, strict=False)
         prepare_model(self.model)
         self.dynamic_submodels = {}
         self.misconfigured_dynamic_submodels = {}
@@ -150,7 +150,7 @@ def setUp(self):
         warnings.simplefilter("ignore")
         self.MODEL_FILENAME = os.path.join(os.path.dirname(__file__), 'fixtures',
             'test_submodel_no_shared_species.xlsx')
-        self.model = Reader().run(self.MODEL_FILENAME)
+        self.model = Reader().run(self.MODEL_FILENAME, strict=False)
         prepare_model(self.model)
 
     def make_sim_w_skeleton_submodel(self, lang_submodel, behavior):

diff --git a/tests/multialgorithm/test_dynamic_components.py b/tests/multialgorithm/test_dynamic_components.py
@@ -68,7 +68,7 @@ def setUp(self):
 
     def read_model(self, model_filename):
         # read and initialize a model
-        self.model = Reader().run(model_filename)
+        self.model = Reader().run(model_filename, strict=False)
         multialgorithm_simulation = MultialgorithmSimulation(self.model, None)
         dynamic_compartments = list(multialgorithm_simulation.dynamic_compartments.values())
 

diff --git a/tests/multialgorithm/test_model_utilities.py b/tests/multialgorithm/test_model_utilities.py
@@ -24,7 +24,7 @@ def get_submodel(self, id_val):
     def setUp(self):
         # read a model
         Submodel.objects.reset()
-        self.model = Reader().run(self.MODEL_FILENAME)
+        self.model = Reader().run(self.MODEL_FILENAME, strict=False)
 
     def test_find_private_species(self):
         # since set() operations are being used, this test does not ensure that the methods being

diff --git a/tests/multialgorithm/test_multialgorithm_simulation.py b/tests/multialgorithm/test_multialgorithm_simulation.py
@@ -37,7 +37,7 @@ def setUp(self):
         for base_model in [Submodel, Species, SpeciesType]:
             base_model.objects.reset()
         # read and initialize a model
-        self.model = Reader().run(self.MODEL_FILENAME)
+        self.model = Reader().run(self.MODEL_FILENAME, strict=False)
         args = Namespace(FBA_time_step=1)
         self.multialgorithm_simulation = MultialgorithmSimulation(self.model, args)
 
@@ -125,7 +125,6 @@ def get_model_type_params(model_type):
 
     def make_test_model(self, model_type):
         """ Create a test model
-
         """
         num_species, num_reactions, reversible, rate_law_type = self.get_model_type_params(model_type)
         if 2<num_species or 1<num_reactions:
@@ -256,7 +255,7 @@ def test_make_test_model(self):
             # print('\n', model_type, ':')
             self.make_test_model(model_type)
         # TODO(Arthur): NEXT, unittest one of the models made
-        # TODO(Arthur): NEXT, write the models to spreadsheets
+        # TODO(Arthur): NEXT, write the models to spreadsheets and review them
         # TODO(Arthur): NEXT, run SSA with '1 species, 1 reaction'
 
     def setUp(self):

diff --git a/tests/multialgorithm/test_simple_stochastic_simulation_algorithm.py b/tests/multialgorithm/test_simple_stochastic_simulation_algorithm.py
@@ -30,7 +30,7 @@ def setUp(self):
         SimulationEngine.reset()
         self.MODEL_FILENAME = os.path.join(os.path.dirname(__file__), 'fixtures', 'test_model.xlsx')
         # make a model
-        self.model = Reader().run(self.MODEL_FILENAME)
+        self.model = Reader().run(self.MODEL_FILENAME, strict=False)
         ExecutableModel.set_up_simulation(self.model)
 
     @unittest.skip("skip")

diff --git a/tests/multialgorithm/test_species_populations.py b/tests/multialgorithm/test_species_populations.py
@@ -64,7 +64,7 @@ def set_up_simulation(self, model_file):
         '''
 
         # make a model
-        self.model = Reader().run(model_file)
+        self.model = Reader().run(model_file, strict=False)
 
         # make SpeciesPopSimObjects
         self.private_species = ModelUtilities.find_private_species(self.model, return_ids=True)