From de4006ba39f20899d3b7d565153221c3b7a697d5 Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Thu, 20 Jun 2024 12:07:46 +0200
Subject: [PATCH 1/2] Further distinction between initial value override based
 on parameter or value.

---
 .../roadrunner/petab_importer_roadrunner.py   | 42 +++++++++++++++----
 1 file changed, 34 insertions(+), 8 deletions(-)

diff --git a/pypesto/objective/roadrunner/petab_importer_roadrunner.py b/pypesto/objective/roadrunner/petab_importer_roadrunner.py
index 88feed223..202b758dd 100644
--- a/pypesto/objective/roadrunner/petab_importer_roadrunner.py
+++ b/pypesto/objective/roadrunner/petab_importer_roadrunner.py
@@ -211,15 +211,41 @@ def create_parameter_mapping(self):
                 preeq_id = condition.get(PREEQUILIBRATION_CONDITION_ID)
                 sim_id = condition.get(SIMULATION_CONDITION_ID)
                 if preeq_id:
-                    mapping_per_condition[0][
-                        override
-                    ] = self.petab_problem.condition_df.loc[preeq_id, override]
-                    mapping_per_condition[2][override] = "lin"
+                    parameter_id_or_value = (
+                        self.petab_problem.condition_df.loc[preeq_id, override]
+                    )
+                    mapping_per_condition[0][override] = parameter_id_or_value
+                    if isinstance(parameter_id_or_value, str):
+                        mapping_per_condition[2][
+                            override
+                        ] = self.petab_problem.parameter_df.loc[
+                            parameter_id_or_value, "parameterScale"
+                        ]
+                    elif isinstance(parameter_id_or_value, numbers.Number):
+                        mapping_per_condition[2][override] = "lin"
+                    else:
+                        raise ValueError(
+                            "The parameter value in the condition table "
+                            "is not a number or a parameter_id."
+                        )
                 if sim_id:
-                    mapping_per_condition[1][
-                        override
-                    ] = self.petab_problem.condition_df.loc[sim_id, override]
-                    mapping_per_condition[3][override] = "lin"
+                    parameter_id_or_value = (
+                        self.petab_problem.condition_df.loc[sim_id, override]
+                    )
+                    mapping_per_condition[1][override] = parameter_id_or_value
+                    if isinstance(parameter_id_or_value, str):
+                        mapping_per_condition[3][
+                            override
+                        ] = self.petab_problem.parameter_df.loc[
+                            parameter_id_or_value, "parameterScale"
+                        ]
+                    elif isinstance(parameter_id_or_value, numbers.Number):
+                        mapping_per_condition[3][override] = "lin"
+                    else:
+                        raise ValueError(
+                            "The parameter value in the condition table "
+                            "is not a number or a parameter_id."
+                        )
         return mapping
 
     def create_objective(

From 91cc859a0e745867e65af104e7792ff057da831c Mon Sep 17 00:00:00 2001
From: PaulJonasJost <jost.pauljonas@gmail.com>
Date: Tue, 25 Jun 2024 14:38:52 +0200
Subject: [PATCH 2/2] Suggestions from PR

---
 .../roadrunner/petab_importer_roadrunner.py        | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/pypesto/objective/roadrunner/petab_importer_roadrunner.py b/pypesto/objective/roadrunner/petab_importer_roadrunner.py
index 202b758dd..4d8b4d2ba 100644
--- a/pypesto/objective/roadrunner/petab_importer_roadrunner.py
+++ b/pypesto/objective/roadrunner/petab_importer_roadrunner.py
@@ -24,6 +24,8 @@
 from petab.models.sbml_model import SbmlModel
 from petab.parameter_mapping import ParMappingDictQuadruple
 
+import pypesto.C
+
 from ...petab.importer import PetabStartpoints
 from ...problem import Problem
 from ...startpoint import StartpointMethod
@@ -219,14 +221,14 @@ def create_parameter_mapping(self):
                         mapping_per_condition[2][
                             override
                         ] = self.petab_problem.parameter_df.loc[
-                            parameter_id_or_value, "parameterScale"
+                            parameter_id_or_value, petab.PARAMETER_SCALE
                         ]
                     elif isinstance(parameter_id_or_value, numbers.Number):
-                        mapping_per_condition[2][override] = "lin"
+                        mapping_per_condition[2][override] = pypesto.C.LIN
                     else:
                         raise ValueError(
                             "The parameter value in the condition table "
-                            "is not a number or a parameter_id."
+                            "is not a number or a parameter ID."
                         )
                 if sim_id:
                     parameter_id_or_value = (
@@ -237,14 +239,14 @@ def create_parameter_mapping(self):
                         mapping_per_condition[3][
                             override
                         ] = self.petab_problem.parameter_df.loc[
-                            parameter_id_or_value, "parameterScale"
+                            parameter_id_or_value, petab.PARAMETER_SCALE
                         ]
                     elif isinstance(parameter_id_or_value, numbers.Number):
-                        mapping_per_condition[3][override] = "lin"
+                        mapping_per_condition[3][override] = pypesto.C.LIN
                     else:
                         raise ValueError(
                             "The parameter value in the condition table "
-                            "is not a number or a parameter_id."
+                            "is not a number or a parameter ID."
                         )
         return mapping