Add regression test for serialization of template model into differen…

…t frameworks

tests/test_amr_source.py

@@ -1,18 +1,51 @@
 import requests
+import json
+
 import sympy
+
 from mira.metamodel import *
 from mira.sources.amr import model_from_url
 from mira.sources.amr import petrinet
 from mira.sources.amr import regnet
 from mira.sources.amr import stockflow
 from mira.modeling.amr.regnet import template_model_to_regnet_json
+from mira.modeling.amr.petrinet import template_model_to_petrinet_json
+from mira.modeling.amr.stockflow import template_model_to_stockflow_json
 
 petrinet_example = 'https://raw.githubusercontent.com/DARPA-ASKEM/' \
-    'Model-Representations/main/petrinet/examples/sir.json'
+                   'Model-Representations/main/petrinet/examples/sir.json'
 regnet_example = 'https://raw.githubusercontent.com/DARPA-ASKEM/' \
-    'Model-Representations/main/regnet/examples/lotka_volterra.json'
+                 'Model-Representations/main/regnet/examples/lotka_volterra.json'
 stockflow_example = 'https://raw.githubusercontent.com/DARPA-ASKEM/' \
-    'Model-Representations/7f5e377225675259baa6486c64102f559edfd79f/stockflow/examples/sir.json'
+                    'Model-Representations/7f5e377225675259baa6486c64102f559edfd79f/stockflow/examples/sir.json'
+
+template_model = TemplateModel(
+    templates=[
+        ControlledReplication(
+            name='replication',
+            controller=Concept(name='A'),
+            subject=Concept(name='B'),
+            rate_law=SympyExprStr(sympy.sympify('k * A * B / (1 + B)'))
+        ),
+        NaturalDegradation(
+            name='degradation',
+            subject=Concept(name='B'),
+            rate_law=SympyExprStr(sympy.sympify('k * B'))
+        )
+    ],
+    observables={
+        'obs1': Observable(
+            name='obs1',
+            expression=SympyExprStr(sympy.sympify('A + B')),
+            display_name='obs1'
+        )
+    },
+    annotations=Annotations(
+        time_start="2020-03-01T00:00:00",
+        time_end="2020-08-01T00:00:00"
+    ),
+    time=Time(name='timexx'),
+)
 
 
 def stockflow_set_up_file():
@@ -76,21 +109,25 @@ def test_stockflow_flow_to_template():
 def test_stockflow_parameter_to_mira():
     sfamr = stockflow_set_up_file()
     tm = stockflow.model_from_url(stockflow_example)
-    for amr_param, tm_param in zip(sfamr['semantics']['ode']['parameters'], tm.parameters.values()):
+    for amr_param, tm_param in zip(sfamr['semantics']['ode']['parameters'],
+                                   tm.parameters.values()):
         assert amr_param['id'] == tm_param.name
         assert amr_param['name'] == tm_param.display_name
         assert amr_param['description'] == tm_param.description
         assert amr_param['value'] == tm_param.value
-        assert amr_param.get('units', {}) == (tm_param.units if tm_param.units else {})
+        assert amr_param.get('units', {}) == (
+            tm_param.units if tm_param.units else {})
 
 
 def test_stockflow_initial_to_mira():
     sfamr = stockflow_set_up_file()
     tm = stockflow.model_from_url(stockflow_example)
-    for amr_initial, tm_initial in zip(sfamr['semantics']['ode']['initials'], tm.initials.values()):
+    for amr_initial, tm_initial in zip(sfamr['semantics']['ode']['initials'],
+                                       tm.initials.values()):
         assert amr_initial['target'] == tm_initial.concept.name
         assert amr_initial['expression'] == str(tm_initial.expression)
-        assert amr_initial['expression_mathml'] == expression_to_mathml(tm_initial.expression)
+        assert amr_initial['expression_mathml'] == expression_to_mathml(
+            tm_initial.expression)
 
 
 def test_stockflow_stock_to_concept():
@@ -118,33 +155,22 @@ def test_regnet_rate_laws():
     # Make a simple template model with rate laws, then export
     # into AMR, ingest, then make sure we get proper rate laws back
     # out.
-    template_model = TemplateModel(
-        templates=[
-            ControlledReplication(
-                name='replication',
-                controller=Concept(name='A'),
-                subject=Concept(name='B'),
-                rate_law=SympyExprStr(sympy.sympify('k * A * B / (1 + B)'))
-            ),
-            NaturalDegradation(
-                name='degradation',
-                subject=Concept(name='B'),
-                rate_law=SympyExprStr(sympy.sympify('k * B'))
-            )
-        ],
-        observables={
-            'obs1': Observable(
-                name='obs1',
-                expression=SympyExprStr(sympy.sympify('A + B')),
-                display_name='obs1'
-            )
-        },
-        time=Time(name='timexx')
-    )
     amr_json = template_model_to_regnet_json(template_model)
     tm = regnet.template_model_from_amr_json(amr_json)
     assert isinstance(tm.templates[0].rate_law, SympyExprStr)
     assert isinstance(tm.templates[1].rate_law, SympyExprStr)
-    assert tm.templates[1].rate_law.args[0].equals(sympy.sympify('k * A * B / (1 + B)'))
+    assert tm.templates[1].rate_law.args[0].equals(
+        sympy.sympify('k * A * B / (1 + B)'))
     assert tm.time.name == 'timexx'
-    assert isinstance(tm.observables['obs1'].expression, SympyExprStr)
+    assert isinstance(tm.observables['obs1'].expression, SympyExprStr)
+
+
+def test_serialization():
+    """Test to see if we can serialize template models that contain
+    datetime in their annotations into different frameworks"""
+    amrs = [template_model_to_regnet_json(template_model),
+            template_model_to_petrinet_json(template_model),
+            template_model_to_stockflow_json(template_model)
+            ]
+    for amr in amrs:
+        json.dumps(amr)