pydantic str to ObjectId rather than ObjectId directly

alab_management/experiment_view/experiment.py

@@ -22,11 +22,11 @@ def if_provided_must_be_valid_objectid(cls, v):
             return  # management will autogenerate a valid objectid
 
         try:
-            return ObjectId(v)
+            return str(ObjectId(v))
         except Exception as exc:
             raise ValueError(
                 "An experiment received over the API contained a sample with an invalid sample_id. The sample_id was "
-                "set to {v}, which is not a valid ObjectId."
+                f"set to {v}, which is not a valid ObjectId."
             ) from exc
 
     @field_validator("metadata")
@@ -55,7 +55,7 @@ def if_provided_must_be_valid_objectid(cls, v):
             return  # management will autogenerate a valid objectid
 
         try:
-            return ObjectId(v)
+            return str(ObjectId(v))
         except Exception as exc:
             raise ValueError(
                 "An experiment received over the API contained a task with an invalid task_id. The task_id was set to "

alab_management/experiment_view/experiment_view.py

@@ -53,19 +53,25 @@ def create_experiment(self, experiment: InputExperiment) -> ObjectId:
 
         # confirm that no task/sample id's already exist in the database. This is possible when users manually set
         # these id's
-        for sample in experiment.samples:
-            if sample.sample_id is None:
+        experiment=experiment.model_dump(mode="python")
+
+        for sample in experiment["samples"]:
+            if sample["sample_id"] is None:
                 continue  # ALabOS will assign a sample id, this is always safe
-            if self.sample_view.exists(sample_id=sample.sample_id):
+            else:
+                sample["sample_id"] = ObjectId(sample["sample_id"])
+            if self.sample_view.exists(sample_id=sample["sample_id"]):
                 raise ValueError(
                     f"Sample id {sample.sample_id} already exists in the database! Please use another id. This "
                     f"experiment was not submitted."
                 )
 
-        for task in experiment.tasks:
-            if task.task_id is None:
+        for task in experiment["tasks"]:
+            if task["task_id"] is None:
                 continue
-            if self.task_view.exists(task_id=task.task_id):
+            else:
+                task["task_id"] = ObjectId(task["task_id"])
+            if self.task_view.exists(task_id=task["task_id"]):
                 raise ValueError(
                     f"Task id {task.task_id} already exists in the database! Please use another id. This experiment "
                     f"was not submitted."
@@ -74,7 +80,7 @@ def create_experiment(self, experiment: InputExperiment) -> ObjectId:
         # all good, lets submit the experiment into ALabOS!
         result = self._experiment_collection.insert_one(
             {
-                **experiment.dict(),
+                **experiment,
                 "submitted_at": datetime.now(),
                 "status": ExperimentStatus.PENDING.name,
             }

tests/test_experiment_view.py

@@ -58,7 +58,7 @@ def test_create_experiment(self):
         exp_id = self.experiment_view.create_experiment(exp_template)
         exp = self.experiment_view.get_experiment(exp_id)
 
-        exp_dict = exp_template.dict()
+        exp_dict = exp_template.model_dump(mode="python")
         exp_dict["_id"] = exp_id
         exp_dict["status"] = "PENDING"