Misc fixes

Author: dweindl

petab/v2/core.py

@@ -411,17 +411,21 @@ class ExperimentPeriod(BaseModel):
 
     #: The start time of the period in time units as defined in the model.
     start: float = Field(alias=C.TIME)
+    # TODO: decide if optional
     #: The ID of the condition to be applied at the start time.
     condition_id: str = Field(alias=C.CONDITION_ID)
 
     #: :meta private:
     model_config = ConfigDict(populate_by_name=True)
 
-    @field_validator("condition_id")
+    @field_validator("condition_id", mode="before")
     @classmethod
     def _validate_id(cls, condition_id):
-        if not condition_id:
-            raise ValueError("ID must not be empty.")
+        # TODO to be decided if optional
+        if pd.isna(condition_id):
+            return ""
+        # if not condition_id:
+        #     raise ValueError("ID must not be empty.")
         if not is_valid_identifier(condition_id):
             raise ValueError(f"Invalid ID: {condition_id}")
         return condition_id

petab/v2/lint.py

@@ -545,6 +545,8 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         missing_conditions = set(required_conditions) - set(
             existing_conditions
         )
+        # TODO NA allowed?
+        missing_conditions = {x for x in missing_conditions if not pd.isna(x)}
         if missing_conditions:
             return ValidationError(
                 f"Experiment table contains conditions that are not present "
@@ -842,7 +844,8 @@ def append_overrides(overrides):
     CheckExperimentTable(),
     CheckValidPetabIdColumn("measurement", EXPERIMENT_ID, ignore_nan=True),
     CheckValidPetabIdColumn("experiment", EXPERIMENT_ID),
-    CheckValidPetabIdColumn("experiment", CONDITION_ID),
+    # TODO: NAN allowed?
+    CheckValidPetabIdColumn("experiment", CONDITION_ID, ignore_nan=True),
     CheckExperimentConditionsExist(),
     CheckObservableTable(),
     CheckObservablesDoNotShadowModelEntities(),

petab/v2/problem.py

@@ -798,10 +798,12 @@ def add_condition(
             {
                 CONDITION_ID: id_,
                 TARGET_ID: target_id,
-                OPERATION_TYPE: op_type,
-                TARGET_VALUE: target_value,
+                OPERATION_TYPE: "setCurrentValue",
+                TARGET_VALUE: target_value
+                if not isinstance(target_value, tuple)
+                else target_value[1],
             }
-            for target_id, (op_type, target_value) in kwargs.items()
+            for target_id, target_value in kwargs.items()
         ]
         # TODO: is the condition name supported in v2?
         if name is not None: