Merge pull request #364 from gyorilab/obs_pattern

Implement adding observables by pattern

mira/dkg/askemo/generate_site.py

@@ -78,7 +78,7 @@ def main():
         resource=ASKEMO,
         metaregistry_name="MIRA Epi Metaregistry",
         metaregistry_metaprefix="askemr",
-        metaregistry_base_url="http://34.230.33.149:8772/",
+        metaregistry_base_url="http://mira-metaregistry-lb-be8a34d7051f5236.elb.us-east-1.amazonaws.com/",
     )
 
 

mira/dkg/client.py

@@ -34,7 +34,7 @@
 WIKIDATA_API = "https://www.wikidata.org/w/api.php"
 
 #: Base URL for the metaregistry, used in creating links
-METAREGISTRY_BASE = "http://34.230.33.149:8772"
+METAREGISTRY_BASE = "http://mira-metaregistry-lb-be8a34d7051f5236.elb.us-east-1.amazonaws.com"
 
 Node: TypeAlias = Mapping[str, Any]
 

mira/metamodel/ops.py

@@ -8,8 +8,9 @@
 
 import sympy
 
-from .template_model import TemplateModel, Initial, Parameter
+from .template_model import TemplateModel, Initial, Parameter, Observable
 from .templates import *
+from .comparison import get_dkg_refinement_closure
 from .units import Unit
 from .utils import SympyExprStr
 
@@ -19,7 +20,8 @@
     "aggregate_parameters",
     "get_term_roles",
     "counts_to_dimensionless",
-    "deactivate_templates"
+    "deactivate_templates",
+    "add_observable_pattern",
 ]
 
 
@@ -743,3 +745,59 @@ def deactivate_templates(
     for template in template_model.templates:
         if condition(template):
             template.deactivate()
+
+
+def add_observable_pattern(
+    template_model: TemplateModel,
+    name: str,
+    identifiers: Mapping = None,
+    context: Mapping = None,
+):
+    """Add an observable for a pattern of concepts.
+
+    Parameters
+    ----------
+    template_model :
+        A template model.
+    name :
+        The name of the observable.
+    identifiers :
+        Identifiers serving as a pattern for concepts to observe.
+    context :
+        Context serving as a pattern for concepts to observe.
+    """
+    observable_concepts = []
+    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 (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
+
+
+def get_observable_for_concepts(concepts: List[Concept], name: str):
+    """Return an observable expressing a sum of a set of concepts.
+
+    Parameters
+    ----------
+    concepts :
+        A list of concepts.
+    name :
+        The name of the observable.
+
+    Returns
+    -------
+    :
+        An observable that sums the given concepts.
+    """
+    expr = None
+    for concept in concepts:
+        if expr is None:
+            expr = sympy.Symbol(concept.name)
+        else:
+            expr += sympy.Symbol(concept.name)
+    return Observable(name=name, expression=SympyExprStr(expr))

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,

tests/test_ops.py

@@ -8,7 +8,9 @@
 import sympy
 
 from mira.metamodel import *
-from mira.metamodel.ops import stratify, simplify_rate_law, counts_to_dimensionless
+from mira.metamodel.ops import stratify, simplify_rate_law, \
+    counts_to_dimensionless, add_observable_pattern, \
+    get_observable_for_concepts
 from mira.examples.sir import cities, sir, sir_2_city, sir_parameterized
 from mira.examples.concepts import infected, susceptible
 from mira.examples.chime import sviivr
@@ -582,3 +584,35 @@ def test_stratify_parameter_consistency():
     # be the case when parameters would be incrementally numbered for each
     # new template
     assert len(tm.parameters) == 2
+
+
+def test_get_observable_for_concepts():
+    concepts = [
+        Concept(name='A'),
+        Concept(name='B'),
+        Concept(name='C'),
+    ]
+    obs = get_observable_for_concepts(concepts, 'obs')
+    assert obs.name == 'obs'
+    assert obs.expression.args[0] == sum([sympy.Symbol(c.name) for c in concepts])
+
+
+def test_add_observable_pattern():
+    templates = [
+        NaturalDegradation(subject=Concept(name='A', identifiers={'ido': '0000514'}),
+                           rate_law=sympy.Symbol('alpha') * sympy.Symbol('A')),
+        NaturalDegradation(subject=Concept(name='B', identifiers={'ido': '0000515'}),
+                           rate_law=sympy.Symbol('alpha') * sympy.Symbol('B')),
+    ]
+    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, 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, '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')