Merge pull request #184 from indralab/formulas

Clean formulas when processing askenet

mira/sources/__init__.py

@@ -1 +1,6 @@
 """Sources of models."""
+
+
+def clean_formula(f):
+    """Return an expression that can be parsed using sympy."""
+    return f.replace('lambda', 'XXlambdaXX')

mira/sources/askenet/petrinet.py

@@ -15,6 +15,7 @@
 import requests
 
 from mira.metamodel import *
+from .. import clean_formula
 
 
 def model_from_url(url: str) -> TemplateModel:
@@ -256,7 +257,8 @@ def transition_to_templates(transition_rate, input_concepts, output_concepts,
                             controller_concepts, symbols):
     """Return a list of templates from a transition"""
     rate_law_expression = transition_rate.get('expression')
-    rate_law = sympy.parse_expr(rate_law_expression, local_dict=symbols) \
+    rate_law = sympy.parse_expr(clean_formula(rate_law_expression),
+                                local_dict=symbols) \
         if rate_law_expression else None
     if not controller_concepts:
         if not input_concepts:

mira/sources/sbml/processor.py

@@ -20,6 +20,7 @@
 
 from mira.metamodel import *
 from mira.resources import get_resource_file
+from .. import clean_formula
 
 
 class TqdmLoggingHandler(logging.Handler):
@@ -814,7 +815,3 @@ def parse_context_grounding(grounding_str):
 
 
 grounding_map = _get_grounding_map()
-
-
-def clean_formula(f):
-    return f.replace('lambda', 'XXlambdaXX')