valueType/operationType

Author: dweindl

petab/v2/C.py

@@ -129,30 +129,23 @@
 CONDITION_NAME = "conditionName"
 #: Column in the condition table with the ID of an entity that is changed
 TARGET_ID = "targetId"
-#: Column in the condition table with the type of value that is changed
-VALUE_TYPE = "valueType"
+#: Column in the condition table with the operation type
+OPERATION_TYPE = "operationType"
 #: Column in the condition table with the new value of the target entity
 TARGET_VALUE = "targetValue"
-# value types:
-VT_CONSTANT = "constant"
-VT_INITIAL = "initial"
-VT_RATE = "rate"
-VT_ASSIGNMENT = "assignment"
-VT_RELATIVE_RATE = "relativeRate"
-VT_RELATIVE_ASSIGNMENT = "relativeAssignment"
-VALUE_TYPES = [
-    VT_CONSTANT,
-    VT_INITIAL,
-    VT_RATE,
-    VT_ASSIGNMENT,
-    VT_RELATIVE_RATE,
-    VT_RELATIVE_ASSIGNMENT,
+# opeartion types:
+OT_CUR_VAL = "setCurrentValue"
+OT_NO_CHANGE = "noChange"
+
+OPERATION_TYPES = [
+    OT_CUR_VAL,
+    OT_NO_CHANGE,
 ]
 
 CONDITION_DF_COLS = [
     CONDITION_ID,
     TARGET_ID,
-    VALUE_TYPE,
+    OPERATION_TYPE,
     TARGET_VALUE,
 ]
 

petab/v2/core.py

@@ -231,7 +231,7 @@ class Change(BaseModel):
     """
 
     target_id: str | None = Field(alias=C.TARGET_ID, default=None)
-    operation_type: OperationType = Field(alias=C.VALUE_TYPE)
+    operation_type: OperationType = Field(alias=C.OPERATION_TYPE)
     target_value: sp.Basic | None = Field(alias=C.TARGET_VALUE, default=None)
 
     class Config:
@@ -242,8 +242,8 @@ class Config:
     @model_validator(mode="before")
     @classmethod
     def validate_id(cls, data: dict):
-        if data.get("operation_type") != OperationType.NO_CHANGE:
-            target_id = data.get("target_id")
+        if data.get(C.OPERATION_TYPE) != C.OT_NO_CHANGE:
+            target_id = data.get(C.TARGET_ID)
 
             if not is_valid_identifier(target_id):
                 raise ValueError(f"Invalid ID: {target_id}")

petab/v2/petab1to2.py

@@ -300,7 +300,7 @@ def v1v2_condition_df(
             columns=[
                 v2.C.CONDITION_ID,
                 v2.C.TARGET_ID,
-                v2.C.VALUE_TYPE,
+                v2.C.OPERATION_TYPE,
                 v2.C.TARGET_VALUE,
             ]
         )
@@ -319,7 +319,5 @@ def v1v2_condition_df(
                 f"Unable to determine value type {target} in the condition "
                 "table."
             )
-    condition_df[v2.C.VALUE_TYPE] = condition_df[v2.C.TARGET_ID].apply(
-        lambda x: v2.C.VT_INITIAL if x in initial else v2.C.VT_CONSTANT
-    )
+    condition_df[v2.C.OPERATION_TYPE] = v2.C.OT_CUR_VAL
     return condition_df

petab/v2/problem.py

@@ -795,10 +795,10 @@ def add_condition(
             {
                 CONDITION_ID: id_,
                 TARGET_ID: target_id,
-                VALUE_TYPE: value_type,
+                OPERATION_TYPE: op_type,
                 TARGET_VALUE: target_value,
             }
-            for target_id, (value_type, target_value) in kwargs.items()
+            for target_id, (op_type, target_value) in kwargs.items()
         ]
         # TODO: is the condition name supported in v2?
         if name is not None:

tests/v2/test_problem.py

@@ -16,13 +16,13 @@
     NOMINAL_VALUE,
     OBSERVABLE_FORMULA,
     OBSERVABLE_ID,
+    OPERATION_TYPE,
+    OT_CUR_VAL,
     PARAMETER_ID,
     PETAB_ENTITY_ID,
     TARGET_ID,
     TARGET_VALUE,
     UPPER_BOUND,
-    VALUE_TYPE,
-    VT_CONSTANT,
 )
 
 
@@ -73,7 +73,7 @@ def test_problem_from_yaml_multiple_files():
 
         for i in (1, 2):
             problem = Problem()
-            problem.add_condition(f"condition{i}", parameter1=(VT_CONSTANT, i))
+            problem.add_condition(f"condition{i}", parameter1=(OT_CUR_VAL, i))
             petab.write_condition_df(
                 problem.condition_df, Path(tmpdir, f"conditions{i}.tsv")
             )
@@ -109,14 +109,14 @@ def test_problem_from_yaml_multiple_files():
 def test_modify_problem():
     """Test modifying a problem via the API."""
     problem = Problem()
-    problem.add_condition("condition1", parameter1=(VT_CONSTANT, 1))
-    problem.add_condition("condition2", parameter2=(VT_CONSTANT, 2))
+    problem.add_condition("condition1", parameter1=(OT_CUR_VAL, 1))
+    problem.add_condition("condition2", parameter2=(OT_CUR_VAL, 2))
 
     exp_condition_df = pd.DataFrame(
         data={
             CONDITION_ID: ["condition1", "condition2"],
             TARGET_ID: ["parameter1", "parameter2"],
-            VALUE_TYPE: [VT_CONSTANT, VT_CONSTANT],
+            OPERATION_TYPE: [OT_CUR_VAL, OT_CUR_VAL],
             TARGET_VALUE: [1.0, 2.0],
         }
     )