Simplify API for specifying observable patterns

gyorilab · Sep 20, 2024 · f26b909 · f26b909
1 parent d24064d
commit f26b909
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Showing 3 changed files with 21 additions and 29 deletions.
diff --git a/mira/metamodel/ops.py b/mira/metamodel/ops.py
@@ -20,7 +20,8 @@
     "aggregate_parameters",
     "get_term_roles",
     "counts_to_dimensionless",
-    "deactivate_templates"
+    "deactivate_templates",
+    "add_observable_pattern",
 ]
 
 
@@ -748,43 +749,34 @@ def deactivate_templates(
 
 def add_observable_pattern(
     template_model: TemplateModel,
-    concept_pattern: Concept,
     name: str,
-    refinement_func=None,
+    identifiers: Mapping = None,
+    context: Mapping = None,
 ):
     """Add an observable for a pattern of concepts.
 
     Parameters
     ----------
     template_model :
         A template model.
-    concept_pattern :
-        A concept pattern.
     name :
         The name of the observable.
-
-    Returns
-    -------
-    :
-        A template model with the observable added.
+    identifiers :
+        Identifiers serving as a pattern for concepts to observe.
+    context :
+        Context serving as a pattern for concepts to observe.
     """
     observable_concepts = []
-    identifiers = set(concept_pattern.identifiers.items())
-    contexts = set(concept_pattern.context.items())
-    name_only = (not identifiers) and (not contexts)
+    identifiers = set(identifiers.items() if identifiers else {})
+    contexts = set(context.items() if context else {})
     for key, concept in template_model.get_concepts_map().items():
-        if name_only:
-            if concept.name == concept_pattern.name:
+        if (not identifiers) or identifiers.issubset(
+                set(concept.identifiers.items())):
+            if (not contexts) or contexts.issubset(
+                    set(concept.context.items())):
                 observable_concepts.append(concept)
-        else:
-            if (not identifiers) or identifiers.issubset(
-                    set(concept.identifiers.items())):
-                if (not contexts) or contexts.issubset(
-                        set(concept.context.items())):
-                    observable_concepts.append(concept)
     obs = get_observable_for_concepts(observable_concepts, name)
     template_model.observables[name] = obs
-    return template_model
 
 
 def get_observable_for_concepts(concepts: List[Concept], name: str):

diff --git a/notebooks/viz_strat_petri.ipynb b/notebooks/viz_strat_petri.ipynb
@@ -329,7 +329,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

diff --git a/tests/test_ops.py b/tests/test_ops.py
@@ -607,12 +607,12 @@ def test_add_observable_pattern():
     tm = TemplateModel(templates=templates,
                        parameters={'alpha': Parameter(name='alpha', value=0.1)})
     tm = stratify(tm, key='age', strata=['young', 'old'], structure=[])
-    add_observable_pattern(tm, Concept(name='A', identifiers={'ido': '0000514'}), 'obs')
-    assert 'obs' in tm.observables
-    obs = tm.observables['obs']
+    add_observable_pattern(tm, name='A', identifiers={'ido': '0000514'})
+    assert 'A' in tm.observables
+    obs = tm.observables['A']
     assert obs.expression.args[0] == sympy.Symbol('A_old') + sympy.Symbol('A_young')
 
-    add_observable_pattern(tm, Concept(name='young', context={'age': 'young'}), 'obs2')
-    assert 'obs2' in tm.observables
-    obs = tm.observables['obs2']
+    add_observable_pattern(tm, 'young', context={'age': 'young'})
+    assert 'young' in tm.observables
+    obs = tm.observables['young']
     assert obs.expression.args[0] == sympy.Symbol('A_young') + sympy.Symbol('B_young')