Merge pull request #236 from dianakolusheva/gromet_uid

Gromet uid
gyorilab · Jun 28, 2021 · 0b078a1 · 0b078a1
2 parents 4fba85e + ac59005
commit 0b078a1
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Showing 3 changed files with 32,833 additions and 11 deletions.
diff --git a/emmaa/model.py b/emmaa/model.py
@@ -1059,8 +1059,9 @@ def pysb_to_gromet(pysb_model, model_name, statements=None, fname=None):
         rate_params = [rate_term for rate_term in rxn['rate'].args
                        if isinstance(rate_term, Parameter)]
         assert len(rate_params) == 1
-        rate_node = rate_params[0].name
-        rate_counts[rate_node] += 1
+        rate = rate_params[0].name
+        rate_counts[rate] += 1
+        rate_node = f'{rate}:{rate_counts[rate]}'
         # Get metadata for rate node
         assert len(rxn['rule']) == 1
         assert len(rxn['reverse']) == 1
@@ -1076,10 +1077,10 @@ def pysb_to_gromet(pysb_model, model_name, statements=None, fname=None):
             indra_stmt_hash=stmt.get_hash(),
             reaction_rule=rule,
             is_reverse=reverse)
-        junctions.append(Junction(uid=UidJunction(f'J:{rate_node}:'
-                                                  f'{rate_counts[rate_node]}'),
+        wire_count = defaultdict(int)
+        junctions.append(Junction(uid=UidJunction(f'J:{rate_node}'),
                                   type=UidType('Rate'),
-                                  name=rate_node,
+                                  name=rate,
                                   value=Literal(uid=None,
                                                 type=UidType("Float"),
                                                 value=Val(rate_params[0].value),
@@ -1090,26 +1091,28 @@ def pysb_to_gromet(pysb_model, model_name, statements=None, fname=None):
         # Add wires from reactant to rate
         for reactant_ix in rxn['reactants']:
             reactant = species_nodes[reactant_ix]
-            wires.append(Wire(uid=UidWire(f'W:{reactant}_{rate_node}'),
+            wire = f'{reactant}_{rate_node}'
+            wire_count[wire] += 1
+            wires.append(Wire(uid=UidWire(f'W:{wire}:w{wire_count[wire]}'),
                               type=None,
                               value_type=None,
                               name=None,
                               value=None,
                               metadata=None,
                               src=UidJunction(f'J:{reactant}'),
-                              tgt=UidJunction(f'J:{rate_node}:'
-                                              f'{rate_counts[rate_node]}')))
+                              tgt=UidJunction(f'J:{rate_node}')))
         # Add wires from rate to product
         for prod_ix in rxn['products']:
             prod = species_nodes[prod_ix]
-            wires.append(Wire(uid=UidWire(f'W:{rate_node}_{prod}'),
+            wire = f'{rate_node}_{prod}'
+            wire_count[wire] += 1
+            wires.append(Wire(uid=UidWire(f'W:{wire}:w{wire_count[wire]}'),
                               type=None,
                               value_type=None,
                               name=None,
                               value=None,
                               metadata=None,
-                              src=UidJunction(f'J:{rate_node}:'
-                                              f'{rate_counts[rate_node]}'),
+                              src=UidJunction(f'J:{rate_node}'),
                               tgt=UidJunction(f'J:{prod}')))
     # Create relation
     pnc = Relation(uid=UidBox(model_name),

diff --git a/emmaa/tests/test_model.py b/emmaa/tests/test_model.py
@@ -155,3 +155,6 @@ def test_pysb_to_gromet():
     assert sum([len(r['reactants']) + len(r['products'])
                 for r in pysb_model.reactions]) == 8
     assert len(gromet.wires) == 8
+    # All junctions and wires have unique uids
+    assert len(set([j.uid for j in gromet.junctions])) == len(gromet.junctions)
+    assert len(set([w.uid for w in gromet.wires])) == len(gromet.wires)