From 4daa8bc01a70b550e11b6c28a109398518687e70 Mon Sep 17 00:00:00 2001
From: Ben Gyori <ben.gyori@gmail.com>
Date: Fri, 4 Oct 2024 10:15:23 -0400
Subject: [PATCH 1/3] Use species ID as name if needed

---
 mira/sources/sbml/processor.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/mira/sources/sbml/processor.py b/mira/sources/sbml/processor.py
index 34e5821b0..2572978a3 100644
--- a/mira/sources/sbml/processor.py
+++ b/mira/sources/sbml/processor.py
@@ -564,9 +564,10 @@ def variables_from_ast(ast_node):
 
 
 def _extract_concept(species, units=None, model_id=None):
+    # Generally, species have an ID and a name
     species_id = species.getId()
-    species_name = species.getName()
-    display_name = species_name if species_name else species_id
+    # If the name is missing, we revert to the ID as the name
+    species_name = species.getName() or species_id
     if "(" in species_name or not species_name:
         species_name = species_id
 
@@ -576,7 +577,7 @@ def _extract_concept(species, units=None, model_id=None):
         mapped_ids, mapped_context = grounding_map[(model_id, species_name)]
         concept = Concept(
             name=species_name,
-            display_name=display_name,
+            display_name=species_name,
             identifiers=copy.deepcopy(mapped_ids),
             context=copy.deepcopy(mapped_context),
             units=units,
@@ -597,7 +598,7 @@ def _extract_concept(species, units=None, model_id=None):
         logger.debug(f"[{model_id} species:{species_id}] had no annotations")
         concept = Concept(
             name=species_name,
-            display_name=display_name,
+            display_name=species_name,
             identifiers={},
             context={},
             units=units,
@@ -709,7 +710,7 @@ def _extract_concept(species, units=None, model_id=None):
         identifiers["biomodels.species"] = f"{model_id}:{species_id}"
     concept = Concept(
         name=species_name or species_id,
-        display_name=display_name,
+        display_name=species_name,
         identifiers=identifiers,
         # TODO how to handle multiple properties? can we extend context to allow lists?
         context=context,

From 70cb8adb06f2b7bd178a37f24abf29ca3e000ac6 Mon Sep 17 00:00:00 2001
From: Ben Gyori <ben.gyori@gmail.com>
Date: Fri, 4 Oct 2024 10:25:39 -0400
Subject: [PATCH 2/3] Generalize initial concentration/amount extraction

---
 mira/sources/sbml/processor.py | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/mira/sources/sbml/processor.py b/mira/sources/sbml/processor.py
index 2572978a3..2eb849cc1 100644
--- a/mira/sources/sbml/processor.py
+++ b/mira/sources/sbml/processor.py
@@ -339,12 +339,23 @@ def _lookup_concepts_filtered(species_ids) -> List[Concept]:
         # Gather species-level initial conditions
         initials = {}
         for species in self.sbml_model.species:
-            # initial concentration is of type float
-            initials[species.name] = Initial(
-                concept=concepts[species.getId()],
-                expression=SympyExprStr(
-                    sympy.Float(species.initial_concentration)
-                ),
+            # Handle the case when there is no name
+            key = species.getName() or species.getId()
+            # In some models, initial_amount is used, and somewhat confusingly
+            # initial_concentration is still a float value (even if not
+            # defined in the XML) with value 0.0. So we have to do a more complex
+            # check here.
+            init_amount_falsy = not species.initial_amount
+            init_conc_falsy = not species.initial_concentration
+            if init_conc_falsy and not init_amount_falsy:
+                init_value = species.initial_amount
+            elif not init_conc_falsy:
+                init_value = species.initial_concentration
+            else:
+                init_value = 0.0
+            initials[key] = Initial(
+                concept=concepts[key],
+                expression=SympyExprStr(sympy.Float(init_value)),
             )
 
         param_objs = {

From fe0002dbefd8873be20691fe570c7490641cccc1 Mon Sep 17 00:00:00 2001
From: Ben Gyori <ben.gyori@gmail.com>
Date: Fri, 4 Oct 2024 16:43:59 -0400
Subject: [PATCH 3/3] Handle nan usage in initials

---
 mira/sources/sbml/processor.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/mira/sources/sbml/processor.py b/mira/sources/sbml/processor.py
index 2eb849cc1..fe877d5fc 100644
--- a/mira/sources/sbml/processor.py
+++ b/mira/sources/sbml/processor.py
@@ -345,8 +345,10 @@ def _lookup_concepts_filtered(species_ids) -> List[Concept]:
             # initial_concentration is still a float value (even if not
             # defined in the XML) with value 0.0. So we have to do a more complex
             # check here.
-            init_amount_falsy = not species.initial_amount
-            init_conc_falsy = not species.initial_concentration
+            init_amount_falsy = (not species.initial_amount) \
+                or math.isnan(species.initial_amount)
+            init_conc_falsy = (not species.initial_concentration) \
+                or math.isnan(species.initial_concentration)
             if init_conc_falsy and not init_amount_falsy:
                 init_value = species.initial_amount
             elif not init_conc_falsy: