Reformat notebook, improve composition tests

mira/metamodel/composition.py

@@ -157,10 +157,11 @@ def compose_two_models(tm0, tm1):
  new_parameters,
  new_initials, new_observables)
 
+ # it's a refinement relation
  # get the more specific template
- # if it's a refinement, we check to see if the outer or
+ # we check to see if the outer or
  # inner template is the more refined version
- if result == REFINEMENT_OF:
+ else:
  if outer_template_is_more_refined:
  process_template(new_templates, outer_template,
  tm0,

notebooks/Model_Composition_Demo.ipynb

@@ -24,7 +24,7 @@
  "id": "5aca8c9e-abe6-47e4-bf9a-b0a51bbc0688",
  "metadata": {},
  "source": [
- "## Create concepts to use for synthetic template models"
+ "## Create concepts to use for template models"
  ]
  },
  {
@@ -34,9 +34,7 @@
  "metadata": {},
  "outputs": [],
  "source": [
- "susceptible = Concept(\n",
- " name=\"susceptible_population\", identifiers={\"ido\": \"0000514\"}\n",
- ")\n",
+ "susceptible = Concept(name=\"susceptible_population\", identifiers={\"ido\": \"0000514\"})\n",
  "hospitalized = Concept(name=\"hospitalized\", identifiers={\"ncit\": \"C25179\"})\n",
  "infected = Concept(name=\"infected_population\", identifiers={\"ido\": \"0000511\"})\n",
  "recovered = Concept(name=\"immune_population\", identifiers={\"ido\": \"0000592\"})\n",
@@ -75,15 +73,35 @@
  " controller=infected,\n",
  ")\n",
  "\n",
- "to_quarantine = NaturalConversion(subject=susceptible, outcome=quarantined)\n",
+ "to_quarantine = NaturalConversion(\n",
+ " subject=susceptible, \n",
+ " outcome=quarantined\n",
+ ")\n",
  "\n",
- "from_quarantine = NaturalConversion(subject=quarantined, outcome=susceptible)\n",
+ "from_quarantine = NaturalConversion(\n",
+ " subject=quarantined, \n",
+ " outcome=susceptible\n",
+ ")\n",
  "\n",
- "dying = NaturalConversion(subject=infected, outcome=dead)\n",
+ "dying = NaturalConversion(\n",
+ " subject=infected, \n",
+ " outcome=dead\n",
+ ")\n",
  "\n",
- "hospitalization = NaturalConversion(subject=infected, outcome= hospitalized)\n",
- "hospitalization_to_recovery = NaturalConversion(subject=hospitalized, outcome=recovered)\n",
- "hospitalization_to_death = NaturalConversion(subject=hospitalized, outcome=dead)"
+ "hospitalization = NaturalConversion(\n",
+ " subject=infected, \n",
+ " outcome=hospitalized\n",
+ ")\n",
+ "\n",
+ "hospitalization_to_recovery = NaturalConversion(\n",
+ " subject=hospitalized, \n",
+ " outcome=recovered\n",
+ ")\n",
+ "\n",
+ "hospitalization_to_death = NaturalConversion(\n",
+ " subject=hospitalized, \n",
+ " outcome=dead\n",
+ ")"
  ]
  },
  {
@@ -108,10 +126,21 @@
  " ]\n",
  ")\n",
  "\n",
- "sir_reinfection = TemplateModel(templates=[infection, recovery, reinfection])\n",
+ "sir_reinfection = TemplateModel(\n",
+ " templates=[\n",
+ " infection, \n",
+ " recovery, \n",
+ " reinfection\n",
+ " ]\n",
+ ")\n",
  "\n",
  "sir_quarantined = TemplateModel(\n",
- " templates=[infection, to_quarantine, from_quarantine, recovery]\n",
+ " templates=[\n",
+ " infection, \n",
+ " to_quarantine, \n",
+ " from_quarantine, \n",
+ " recovery\n",
+ " ]\n",
  ")\n",
  "\n",
  "sir_dying = TemplateModel(\n",
@@ -127,11 +156,17 @@
  " infection,\n",
  " hospitalization,\n",
  " hospitalization_to_recovery,\n",
- " hospitalization_to_death\n",
+ " hospitalization_to_death,\n",
  " ]\n",
  ")\n",
  "\n",
- "model_list = [sir_reinfection, sir_quarantined, sir_dying, sir_hospitalized, sir]"
+ "model_list = [\n",
+ " sir_reinfection,\n",
+ " sir_quarantined,\n",
+ " sir_dying,\n",
+ " sir_hospitalized,\n",
+ " sir,\n",
+ "]"
  ]
  },
  {

tests/test_model_composition.py

@@ -1,17 +1,59 @@
-from mira.metamodel.composition import *
-from mira.sources.amr import model_from_url
-from mira.examples.sir import sir, sir_2_city
+from mira.metamodel.composition import compose_two_models, compose
+from mira.metamodel.template_model import TemplateModel
+from mira.metamodel.templates import *
+from mira.examples.concepts import *
 
+infection = ControlledConversion(
+ subject=susceptible,
+ outcome=infected,
+ controller=infected,
+)
+recovery = NaturalConversion(
+ subject=infected,
+ outcome=recovered,
+)
 
-def test_model_compose():
- sir_petrinet_url = 'https://raw.githubusercontent.com/DARPA-ASKEM/' \
- 'Model-Representations/main/petrinet/examples/sir.json'
- lotka_regnet_url = ('https://raw.githubusercontent.com/DARPA-ASKEM'
- '/Model-Representations/main/regnet'
- '/examples/lotka_volterra.json')
+reinfection = ControlledConversion(
+ subject=recovered,
+ outcome=infected,
+ controller=infected,
+)
 
- tm0 = model_from_url(sir_petrinet_url)
- tm1 = model_from_url(lotka_regnet_url)
+dying = NaturalConversion(
+ subject=infected,
+ outcome=dead
+)
 
- new_tm = compose([tm0, tm1, sir, sir_2_city])
+sir = TemplateModel(
+ templates=[
+ infection,
+ recovery,
+ ]
+)
 
+sir_reinfection = TemplateModel(
+ templates=[
+ infection,
+ recovery,
+ reinfection
+ ]
+)
+
+sir_dying = TemplateModel(
+ templates=[
+ infection,
+ dying,
+ recovery,
+ ]
+)
+
+
+def test_compose_two_models():
+ composed_model = compose_two_models(sir_reinfection, sir)
+ assert len(composed_model.templates) == 3
+
+
+def test_compose_list():
+ model_list = [sir_reinfection, sir_dying, sir]
+ composed_model = compose(model_list)
+ assert len(composed_model.templates) == 4