fixed the streaming bug

src/cehrbert/data_generators/hf_data_generator/hf_dataset.py

@@ -38,12 +38,7 @@ def create_cehrbert_pretraining_dataset(
     required_columns = TRANSFORMER_COLUMNS + CEHRBERT_COLUMNS
 
     # Remove patients without any records
-    dataset = dataset.filter(
-        lambda batch: [num_of_concepts > 0 for num_of_concepts in batch["num_of_concepts"]],
-        num_proc=data_args.preprocessing_num_workers if not data_args.streaming else None,
-        batched=True,
-        batch_size=data_args.preprocessing_batch_size,
-    )
+    dataset = filter_dataset(dataset, data_args)
 
     # If the data is already in meds, we don't need to sort the sequence anymore
     if data_args.is_data_in_meds:
@@ -82,12 +77,7 @@ def create_cehrbert_finetuning_dataset(
     required_columns = TRANSFORMER_COLUMNS + CEHRBERT_COLUMNS + FINETUNING_COLUMNS
 
     # Remove patients without any records
-    dataset = dataset.filter(
-        lambda batch: [num_of_concepts > 0 for num_of_concepts in batch["num_of_concepts"]],
-        num_proc=data_args.preprocessing_num_workers if not data_args.streaming else None,
-        batched=True,
-        batch_size=data_args.preprocessing_batch_size,
-    )
+    dataset = filter_dataset(dataset, data_args)
 
     if data_args.is_data_in_meds:
         mapping_functions = [
@@ -120,6 +110,26 @@ def create_cehrbert_finetuning_dataset(
     return dataset
 
 
+def filter_dataset(dataset: Union[Dataset, DatasetDict], data_args: DataTrainingArguments):
+    # Remove patients without any records
+    # check if DatatsetDict or IterableDatasetDict, if so, filter each dataset
+    if isinstance(dataset, DatasetDict) and data_args.streaming:
+        for key in dataset.keys():
+            dataset[key] = dataset[key].filter(
+                lambda batch: [num_of_concepts > 0 for num_of_concepts in batch["num_of_concepts"]],
+                batched=True,
+                batch_size=data_args.preprocessing_batch_size,
+            )
+    else:
+        dataset = dataset.filter(
+            lambda batch: [num_of_concepts > 0 for num_of_concepts in batch["num_of_concepts"]],
+            num_proc=data_args.preprocessing_num_workers if not data_args.streaming else None,
+            batched=True,
+            batch_size=data_args.preprocessing_batch_size,
+        )
+    return dataset
+
+
 def apply_cehrbert_dataset_mapping(
     dataset: Union[DatasetDict, Dataset, IterableDataset, IterableDatasetDict],
     mapping_function: DatasetMapping,

src/cehrbert/runners/hf_cehrbert_pretrain_runner.py

@@ -206,6 +206,7 @@ def main():
                     test_size=data_args.validation_split_percentage,
                     seed=training_args.seed,
                 )
+                dataset = DatasetDict({"train": dataset["train"], "validation": dataset["test"]})
             else:
                 raise RuntimeError(
                     f"Can not split the data. If streaming is enabled, validation_split_num needs  "
@@ -261,20 +262,11 @@ def filter_func(examples):
     if not data_args.streaming:
         processed_dataset.set_format("pt")
 
-    eval_dataset = None
-    if isinstance(processed_dataset, DatasetDict) or isinstance(processed_dataset, IterableDatasetDict):
-        train_dataset = processed_dataset["train"]
-        if "validation" in processed_dataset:
-            eval_dataset = processed_dataset["validation"]
-    else:
-        train_dataset = processed_dataset
-
     trainer = Trainer(
         model=model,
         data_collator=collator,
-        train_dataset=train_dataset,
-        eval_dataset=eval_dataset,
-        # compute_metrics=compute_metrics,
+        train_dataset=processed_dataset["train"],
+        eval_dataset=processed_dataset["validation"],
         args=training_args,
     )
 

tests/integration_tests/runners/hf_cehrbert_pretrain_runner_streaming_test.py

@@ -0,0 +1,55 @@
+import os
+import shutil
+import sys
+import tempfile
+import unittest
+from pathlib import Path
+
+from datasets import disable_caching
+
+from cehrbert.runners.hf_cehrbert_pretrain_runner import main
+
+disable_caching()
+os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
+os.environ["WANDB_MODE"] = "disabled"
+os.environ["TRANSFORMERS_VERBOSITY"] = "info"
+
+
+class HfCehrBertRunnerIntegrationTest(unittest.TestCase):
+    def setUp(self):
+        # Get the root folder of the project
+        root_folder = Path(os.path.abspath(__file__)).parent.parent.parent.parent
+        data_folder = os.path.join(root_folder, "sample_data", "pretrain")
+        # Create a temporary directory to store model and tokenizer
+        self.temp_dir = tempfile.mkdtemp()
+        self.model_folder_path = os.path.join(self.temp_dir, "model")
+        Path(self.model_folder_path).mkdir(parents=True, exist_ok=True)
+        self.dataset_prepared_path = os.path.join(self.temp_dir, "dataset_prepared_path")
+        Path(self.dataset_prepared_path).mkdir(parents=True, exist_ok=True)
+        sys.argv = [
+            "hf_cehrbert_pretraining_runner.py",
+            "--model_name_or_path",
+            self.model_folder_path,
+            "--tokenizer_name_or_path",
+            self.model_folder_path,
+            "--output_dir",
+            self.model_folder_path,
+            "--data_folder",
+            data_folder,
+            "--dataset_prepared_path",
+            self.dataset_prepared_path,
+            "--max_steps",
+            "10",
+            "--streaming",
+        ]
+
+    def tearDown(self):
+        # Remove the temporary directory
+        shutil.rmtree(self.temp_dir)
+
+    def test_train_model(self):
+        main()
+
+
+if __name__ == "__main__":
+    unittest.main()