Fix iso_date_regex_pattern config in file_batcher module and allow override (nv-morpheus#1580)

- Update `file_batcher`module to use documented module config key `iso_date_regex_pattern` instead of `batch_iso_date_regex_pattern`.
- Allow override of `iso_date_regex_pattern` with control message.
- Add tests for `file_batcher` module

Closes nv-morpheus#1576 
Closes nv-morpheus#1577

## By Submitting this PR I confirm:
- I am familiar with the [Contributing Guidelines](https://github.com/nv-morpheus/Morpheus/blob/main/docs/source/developer_guide/contributing.md).
- When the PR is ready for review, new or existing tests cover these changes.
- When the PR is ready for review, the documentation is up to date with these changes.

Authors:
  - Eli Fajardo (https://github.com/efajardo-nv)

Approvers:
  - Michael Demoret (https://github.com/mdemoret-nv)

URL: nv-morpheus#1580

Author: efajardo-nv

morpheus/modules/file_batcher.py

@@ -80,7 +80,7 @@ def file_batcher(builder: mrc.Builder):
     sampling = config.get("sampling", None)
     sampling_rate_s = config.get("sampling_rate_s", None)
 
-    iso_date_regex_pattern = config.get("batch_iso_date_regex_pattern", DEFAULT_ISO_DATE_REGEX_PATTERN)
+    iso_date_regex_pattern = config.get("iso_date_regex_pattern", DEFAULT_ISO_DATE_REGEX_PATTERN)
     iso_date_regex = re.compile(iso_date_regex_pattern)
 
     if (sampling_rate_s is not None and sampling_rate_s > 0):
@@ -99,6 +99,7 @@ def file_batcher(builder: mrc.Builder):
         "sampling": sampling,
         "start_time": config.get("start_time"),
         "end_time": config.get("end_time"),
+        "iso_date_regex_pattern": iso_date_regex_pattern
     }
 
     default_file_to_df_opts = {
@@ -123,11 +124,19 @@ def build_period_batches(files: typing.List[str],
                              params: typing.Dict[any, any]) -> typing.List[typing.Tuple[typing.List[str], int]]:
         file_objects: fsspec.core.OpenFiles = fsspec.open_files(files)
 
+        nonlocal iso_date_regex_pattern
+        nonlocal iso_date_regex
+
+        if params["iso_date_regex_pattern"] != iso_date_regex_pattern:
+            iso_date_regex_pattern = params["iso_date_regex_pattern"]
+            iso_date_regex = re.compile(iso_date_regex_pattern)
+
         try:
             start_time = params["start_time"]
             end_time = params["end_time"]
             period = params["period"]
             sampling_rate_s = params["sampling_rate_s"]
+            sampling = params["sampling"]
 
             if not isinstance(start_time, (str, type(None))) or (start_time is not None
                                                                  and not re.match(r"\d{4}-\d{2}-\d{2}", start_time)):
@@ -137,8 +146,15 @@ def build_period_batches(files: typing.List[str],
                                                                and not re.match(r"\d{4}-\d{2}-\d{2}", end_time)):
                 raise ValueError(f"Invalid 'end_time' value: {end_time}")
 
-            if not isinstance(sampling_rate_s, int) or sampling_rate_s < 0:
-                raise ValueError(f"Invalid 'sampling_rate_s' value: {sampling_rate_s}")
+            if (sampling_rate_s is not None and sampling_rate_s > 0):
+                assert sampling is None, "Cannot set both sampling and sampling_rate_s at the same time"
+
+                # Show the deprecation message
+                warnings.warn(("The `sampling_rate_s` argument has been deprecated. "
+                               "Please use `sampling={sampling_rate_s}S` instead"),
+                              DeprecationWarning)
+
+                sampling = f"{sampling_rate_s}S"
 
             if (start_time is not None):
                 start_time = datetime.datetime.strptime(start_time, '%Y-%m-%d').replace(tzinfo=datetime.timezone.utc)

tests/modules/test_file_batcher.py

@@ -0,0 +1,300 @@
+#!/usr/bin/env python
+# SPDX-FileCopyrightText: Copyright (c) 2024, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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 pytest
+
+import cudf
+
+import morpheus.modules  # noqa: F401 # pylint: disable=unused-import
+from morpheus.config import Config
+from morpheus.messages import ControlMessage
+from morpheus.messages.message_meta import MessageMeta
+from morpheus.pipeline import LinearPipeline
+from morpheus.pipeline.stage_decorator import source
+from morpheus.stages.general.linear_modules_stage import LinearModulesStage
+from morpheus.stages.output.in_memory_sink_stage import InMemorySinkStage
+from morpheus.utils.module_ids import FILE_BATCHER
+from morpheus.utils.module_ids import MORPHEUS_MODULE_NAMESPACE
+
+# pylint: disable=redundant-keyword-arg
+
+
+@source
+def source_test_stage(filenames: list[str], cm_batching_options: dict) -> ControlMessage:
+
+    df = cudf.DataFrame(filenames, columns=['files'])
+
+    control_message = ControlMessage()
+
+    control_message.set_metadata("batching_options", cm_batching_options)
+    control_message.set_metadata("data_type", "payload")
+
+    control_message.payload(MessageMeta(df=df))
+
+    yield control_message
+
+
+@pytest.fixture(name="default_module_config")
+def default_module_config_fixture():
+    yield {
+        "module_id": FILE_BATCHER,
+        "module_name": "file_batcher",
+        "namespace": MORPHEUS_MODULE_NAMESPACE,
+        "sampling_rate_s": 0,
+        "start_time": "2022-08-01",
+        "end_time": "2022-08-31",
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+
+@pytest.fixture(name="default_file_list")
+def default_file_list_fixture():
+    yield [
+        "DUO_2022-08-01T00_05_06.806Z.json",
+        "DUO_2022-08-01T03_02_04.418Z.json",
+        "DUO_2022-08-01T06_05_05.064Z.json",
+        "DUO_2022-08-02T00_05_06.806Z.json",
+        "DUO_2022-08-02T03_02_04.418Z.json",
+        "DUO_2022-08-02T06_05_05.064Z.json"
+    ]
+
+
+def test_no_overrides(config: Config, default_module_config, default_file_list):
+    pipeline = LinearPipeline(config)
+
+    cm_batching_opts = {
+        "sampling_rate_s": 0,
+        "start_time": "2022-08-01",
+        "end_time": "2022-08-31",
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+    pipeline.set_source(source_test_stage(config, filenames=default_file_list, cm_batching_options=cm_batching_opts))
+
+    pipeline.add_stage(
+        LinearModulesStage(config, default_module_config, input_port_name="input", output_port_name="output"))
+
+    sink_stage = pipeline.add_stage(InMemorySinkStage(config))
+
+    pipeline.run()
+
+    sink_messages = sink_stage.get_messages()
+    assert len(sink_messages) == 2
+    assert len(sink_messages[0].get_tasks()["load"][0]["files"]) == 3
+    assert sink_messages[0].get_tasks()["load"][0]["n_groups"] == 2
+    assert len(sink_messages[1].get_tasks()["load"][0]["files"]) == 3
+    assert sink_messages[1].get_tasks()["load"][0]["n_groups"] == 2
+
+
+def test_no_date_matches(config: Config, default_module_config, default_file_list):
+    pipeline = LinearPipeline(config)
+
+    cm_batching_opts = {
+        "sampling_rate_s": 0,
+        "start_time": "2022-09-01",
+        "end_time": "2022-09-30",
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+    pipeline.set_source(source_test_stage(config, filenames=default_file_list, cm_batching_options=cm_batching_opts))
+
+    pipeline.add_stage(
+        LinearModulesStage(config, default_module_config, input_port_name="input", output_port_name="output"))
+
+    sink_stage = pipeline.add_stage(InMemorySinkStage(config))
+
+    pipeline.run()
+
+    sink_messages = sink_stage.get_messages()
+    assert len(sink_messages) == 0
+
+
+def test_partial_date_matches(config: Config, default_module_config, default_file_list):
+    pipeline = LinearPipeline(config)
+
+    cm_batching_opts = {
+        "sampling_rate_s": 0,
+        "start_time": "2022-07-30",
+        "end_time": "2022-08-02",
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+    pipeline.set_source(source_test_stage(config, filenames=default_file_list, cm_batching_options=cm_batching_opts))
+
+    pipeline.add_stage(
+        LinearModulesStage(config, default_module_config, input_port_name="input", output_port_name="output"))
+
+    sink_stage = pipeline.add_stage(InMemorySinkStage(config))
+
+    pipeline.run()
+
+    sink_messages = sink_stage.get_messages()
+    sink_messages = sink_stage.get_messages()
+    assert len(sink_messages) == 1
+    assert len(sink_messages[0].get_tasks()["load"][0]["files"]) == 3
+    assert sink_messages[0].get_tasks()["load"][0]["n_groups"] == 1
+
+
+def test_override_date_regex(config: Config, default_module_config):
+    pipeline = LinearPipeline(config)
+
+    filenames = [
+        "DUO_2022-08-01_00_05_06.806Z.json",
+        "DUO_2022-08-01_03_02_04.418Z.json",
+        "DUO_2022-08-01_06_05_05.064Z.json",
+        "DUO_2022-08-02_00_05_06.806Z.json",
+        "DUO_2022-08-02_03_02_04.418Z.json",
+        "DUO_2022-08-02_06_05_05.064Z.json"
+    ]
+
+    cm_date_regex_pattern = (
+        r"(?P<year>\d{4})-(?P<month>\d{1,2})-(?P<day>\d{1,2})"
+        r"_(?P<hour>\d{1,2})(:|_)(?P<minute>\d{1,2})(:|_)(?P<second>\d{1,2})(?P<microsecond>\.\d{1,6})?Z")
+
+    cm_batching_opts = {
+        "sampling_rate_s": 0,
+        "start_time": "2022-08-01",
+        "end_time": "2022-08-31",
+        "iso_date_regex_pattern": cm_date_regex_pattern,
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+    pipeline.set_source(source_test_stage(config, filenames=filenames, cm_batching_options=cm_batching_opts))
+
+    pipeline.add_stage(
+        LinearModulesStage(config, default_module_config, input_port_name="input", output_port_name="output"))
+
+    sink_stage = pipeline.add_stage(InMemorySinkStage(config))
+
+    pipeline.run()
+
+    sink_messages = sink_stage.get_messages()
+    assert len(sink_messages) == 2
+    assert len(sink_messages[0].get_tasks()["load"][0]["files"]) == 3
+    assert sink_messages[0].get_tasks()["load"][0]["n_groups"] == 2
+    assert len(sink_messages[1].get_tasks()["load"][0]["files"]) == 3
+    assert sink_messages[1].get_tasks()["load"][0]["n_groups"] == 2
+
+
+def test_sampling_freq(config: Config, default_module_config):
+    pipeline = LinearPipeline(config)
+
+    filenames = [
+        "DUO_2022-08-01T00_05_06.806Z.json",
+        "DUO_2022-08-01T00_05_08.418Z.json",
+        "DUO_2022-08-01T00_05_12.064Z.json",
+        "DUO_2022-08-02T03_02_06.806Z.json",
+        "DUO_2022-08-02T03_02_14.418Z.json",
+        "DUO_2022-08-02T03_02_17.064Z.json"
+    ]
+
+    cm_batching_opts = {
+        "sampling_rate_s": None,
+        "sampling": "30S",
+        "start_time": "2022-08-01",
+        "end_time": "2022-08-31",
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+    pipeline.set_source(source_test_stage(config, filenames=filenames, cm_batching_options=cm_batching_opts))
+
+    pipeline.add_stage(
+        LinearModulesStage(config, default_module_config, input_port_name="input", output_port_name="output"))
+
+    sink_stage = pipeline.add_stage(InMemorySinkStage(config))
+
+    pipeline.run()
+
+    sink_messages = sink_stage.get_messages()
+    assert len(sink_messages) == 2
+    assert len(sink_messages[0].get_tasks()["load"][0]["files"]) == 1
+    assert sink_messages[0].get_tasks()["load"][0]["n_groups"] == 2
+    assert len(sink_messages[1].get_tasks()["load"][0]["files"]) == 1
+    assert sink_messages[1].get_tasks()["load"][0]["n_groups"] == 2
+
+
+def test_sampling_pct(config: Config, default_module_config, default_file_list):
+    pipeline = LinearPipeline(config)
+
+    cm_batching_opts = {
+        "sampling_rate_s": None,
+        "sampling": 0.5,
+        "start_time": "2022-08-01",
+        "end_time": "2022-08-31",
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+    pipeline.set_source(source_test_stage(config, filenames=default_file_list, cm_batching_options=cm_batching_opts))
+
+    pipeline.add_stage(
+        LinearModulesStage(config, default_module_config, input_port_name="input", output_port_name="output"))
+
+    sink_stage = pipeline.add_stage(InMemorySinkStage(config))
+
+    pipeline.run()
+
+    sink_messages = sink_stage.get_messages()
+    msg_counts = [len(m.get_tasks()["load"][0]["files"]) for m in sink_messages]
+    assert sum(msg_counts) == 3
+
+
+def test_sampling_fixed(config: Config, default_module_config, default_file_list):
+    pipeline = LinearPipeline(config)
+
+    cm_batching_opts = {
+        "sampling_rate_s": None,
+        "sampling": 5,
+        "start_time": "2022-08-01",
+        "end_time": "2022-08-31",
+        "parser_kwargs": None,
+        "schema": {
+            "schema_str": None, "encoding": None
+        }
+    }
+
+    pipeline.set_source(source_test_stage(config, filenames=default_file_list, cm_batching_options=cm_batching_opts))
+
+    pipeline.add_stage(
+        LinearModulesStage(config, default_module_config, input_port_name="input", output_port_name="output"))
+
+    sink_stage = pipeline.add_stage(InMemorySinkStage(config))
+
+    pipeline.run()
+
+    sink_messages = sink_stage.get_messages()
+    msg_counts = [len(m.get_tasks()["load"][0]["files"]) for m in sink_messages]
+    assert sum(msg_counts) == 5