Improve speed of AddId module (#36)

* Add fast id method

Signed-off-by: Ryan Wolf <[email protected]>

* Add type conversion

Signed-off-by: Ryan Wolf <[email protected]>

* Fix off by one errors in tests

Signed-off-by: Ryan Wolf <[email protected]>

---------

Signed-off-by: Ryan Wolf <[email protected]>

nemo_curator/modules/add_id.py

@@ -12,22 +12,58 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from typing import Optional
+
 import dask.dataframe as dd
 import numpy as np
 from dask import delayed
 
 from nemo_curator.datasets import DocumentDataset
+from nemo_curator.utils.module_utils import count_digits
 
 
 class AddId:
-    def __init__(self, id_field, id_prefix="doc_id", start_index=0) -> None:
+    def __init__(
+        self, id_field, id_prefix: str = "doc_id", start_index: Optional[int] = None
+    ) -> None:
         self.id_field = id_field
         self.id_prefix = id_prefix
         self.start_index = start_index
 
     def __call__(self, dataset: DocumentDataset) -> DocumentDataset:
+        if self.start_index is None:
+            return self._add_id_fast(dataset)
+        else:
+            return self._add_id_ordered(dataset)
+
+    def _add_id_fast(self, dataset: DocumentDataset) -> DocumentDataset:
+        meta = dataset.df.dtypes.to_dict()
+        meta[self.id_field] = "string"
+
+        partition_zero_padding = count_digits(dataset.df.npartitions)
+        id_df = dataset.df.map_partitions(
+            self._add_id_fast_partition,
+            partition_zero_padding,
+            meta=meta,
+        )
+
+        return DocumentDataset(id_df)
+
+    def _add_id_fast_partition(self, partition, global_padding, partition_info=None):
+        local_padding = count_digits(len(partition))
+        global_id = partition_info["number"]
+
+        id_column = [
+            f"{self.id_prefix}-{local_id:0{local_padding}d}{global_id:0{global_padding}d}"
+            for local_id in range(len(partition))
+        ]
+        partition[self.id_field] = id_column
+
+        return partition
+
+    def _add_id_ordered(self, dataset: DocumentDataset) -> DocumentDataset:
         original_meta = dataset.df.dtypes.to_dict()
-        original_meta[self.id_field] = "object"
+        original_meta[self.id_field] = "string"
         delayed_dataset = dataset.df.to_delayed()
 
         parition_lengths = [0]
@@ -38,7 +74,7 @@ def __call__(self, dataset: DocumentDataset) -> DocumentDataset:
         delayed_id_dataset = []
         for i, partition in enumerate(delayed_dataset):
             delayed_id_dataset.append(
-                delayed(self._add_id_to_partition)(partition, lower_id_bounds[i])
+                delayed(self._add_id_ordered_partition)(partition, lower_id_bounds[i])
             )
 
         id_dataset = DocumentDataset(
@@ -47,11 +83,12 @@ def __call__(self, dataset: DocumentDataset) -> DocumentDataset:
 
         return id_dataset
 
-    def _add_id_to_partition(self, partition, partition_start_id):
+    def _add_id_ordered_partition(self, partition, partition_start_id):
         id_column = [
             f"{self.id_prefix}-{int(i + self.start_index):010d}"
             for i in range(partition_start_id, len(partition) + partition_start_id)
         ]
         partition[self.id_field] = id_column
+        partition[self.id_field] = partition[self.id_field].astype("string")
 
         return partition

nemo_curator/scripts/add_id.py

@@ -79,8 +79,10 @@ def attach_args(
     parser.add_argument(
         "--starting-index",
         type=int,
-        default=0,
-        help="Starting index from which to start indexing the documents",
+        default=None,
+        help="If supplied, determines the starting index from which to start "
+        "indexing the documents. By default, it is unspecified, and uses an id"
+        " scheme that is fast to calculate and is not guaranteed to be ordered.",
     )
     parser.add_argument(
         "--output-data-dir",

nemo_curator/utils/module_utils.py

@@ -11,7 +11,12 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import math
 
 
 def is_batched(function):
     return hasattr(function, "batched") and function.batched
+
+
+def count_digits(num):
+    return math.floor(math.log10(num)) + 1

tests/test_add_id.py

@@ -16,7 +16,7 @@
 import pandas as pd
 import pytest
 
-import nemo_curator
+import nemo_curator as nc
 from nemo_curator.datasets import DocumentDataset
 
 
@@ -41,10 +41,10 @@ def two_partition_dataset():
     )
 
 
-class TestPrepareTaskData:
+class TestAddId:
     def test_basic_id(self, single_partition_dataset):
         id_field = "id"
-        add_id = nemo_curator.AddId(id_field)
+        add_id = nc.AddId(id_field, start_index=0)
         id_dataset = add_id(single_partition_dataset)
         actual_ids = id_dataset.df[id_field].compute()
         expected_ids = pd.Series(
@@ -63,7 +63,7 @@ def test_basic_id(self, single_partition_dataset):
 
     def test_two_partitions(self, two_partition_dataset):
         id_field = "id"
-        add_id = nemo_curator.AddId(id_field)
+        add_id = nc.AddId(id_field, start_index=0)
         id_dataset = add_id(two_partition_dataset)
         actual_ids = id_dataset.df[id_field].compute()
         expected_ids = pd.Series(
@@ -83,7 +83,7 @@ def test_two_partitions(self, two_partition_dataset):
     def test_id_prefix(self, two_partition_dataset):
         id_field = "id"
         id_prefix = "my_id"
-        add_id = nemo_curator.AddId(id_field, id_prefix=id_prefix)
+        add_id = nc.AddId(id_field, id_prefix=id_prefix, start_index=0)
         id_dataset = add_id(two_partition_dataset)
         actual_ids = id_dataset.df[id_field].compute()
         expected_ids = pd.Series(
@@ -103,7 +103,7 @@ def test_id_prefix(self, two_partition_dataset):
     def test_start_index(self, two_partition_dataset):
         id_field = "id"
         start_index = 13
-        add_id = nemo_curator.AddId(id_field, start_index=start_index)
+        add_id = nc.AddId(id_field, start_index=start_index)
         id_dataset = add_id(two_partition_dataset)
         actual_ids = id_dataset.df[id_field].compute()
         expected_ids = pd.Series(
@@ -119,3 +119,41 @@ def test_start_index(self, two_partition_dataset):
         assert all(
             expected_ids == actual_ids
         ), f"Expected: {expected_ids}, got: {actual_ids}"
+
+    def test_fast_id_single_partition(self, single_partition_dataset):
+        id_field = "id"
+        add_id = nc.AddId(id_field)
+        id_dataset = add_id(single_partition_dataset)
+        actual_ids = id_dataset.df[id_field].compute()
+        expected_ids = pd.Series(
+            [
+                "doc_id-00",
+                "doc_id-10",
+                "doc_id-20",
+                "doc_id-30",
+                "doc_id-40",
+            ]
+        )
+
+        assert all(
+            expected_ids == actual_ids
+        ), f"Expected: {expected_ids}, got: {actual_ids}"
+
+    def test_fast_id_two_partitions(self, two_partition_dataset):
+        id_field = "id"
+        add_id = nc.AddId(id_field)
+        id_dataset = add_id(two_partition_dataset)
+        actual_ids = id_dataset.df[id_field].compute()
+        expected_ids = pd.Series(
+            [
+                "doc_id-00",
+                "doc_id-10",
+                "doc_id-20",
+                "doc_id-01",
+                "doc_id-11",
+            ]
+        )
+
+        assert all(
+            expected_ids == actual_ids
+        ), f"Expected: {expected_ids}, got: {actual_ids}"