Add example of real time Anomaly Detection using RunInference

sdks/python/apache_beam/examples/inference/anomaly_detection/anomaly_detection_pipeline/__init__.py

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+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You 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.
+#

sdks/python/apache_beam/examples/inference/anomaly_detection/anomaly_detection_pipeline/config.py

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+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You 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.
+#
+
+"""The file defines global variables."""
+
+PROJECT_ID = ""
+REGION = "us-central1"
+# Subscription for PubSub Topic
+SUBSCRIPTION_ID = f"projects/{PROJECT_ID}/subscriptions/newsgroup-dataset-subscription"
+JOB_NAME = "anomaly-detection-hdbscan"
+NUM_WORKERS = 1
+EMAIL_ADDRESS = "xyz@gmail.com"
+
+TABLE_SCHEMA = {
+    "fields": [
+        {
+            "name": "text", "type": "STRING", "mode": "NULLABLE"
+        },
+        {
+            "name": "id", "type": "STRING", "mode": "NULLABLE"
+        },
+        {
+            "name": "cluster", "type": "INTEGER", "mode": "NULLABLE"
+        },
+    ]
+}
+
+TABLE_URI = f"{PROJECT_ID}:deliverables_ml6.anomaly-detection"
+MODEL_NAME = "sentence-transformers-stsb-distilbert-base"
+TOKENIZER_NAME = "sentence-transformers/stsb-distilbert-base"
+MODEL_STATE_DICT_PATH = f"gs://{PROJECT_ID}-ml-examples/{MODEL_NAME}/pytorch_model.bin"
+MODEL_CONFIG_PATH = TOKENIZER_NAME
+
+CLUSTERING_MODEL_PATH = (
+    f"gs://{PROJECT_ID}-ml-examples/anomaly-detection/clustering.joblib")

sdks/python/apache_beam/examples/inference/anomaly_detection/anomaly_detection_pipeline/main.py

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+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You 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.
+#
+
+"""This file contains the pipeline for doing anomaly detection."""
+import argparse
+import sys
+
+import apache_beam as beam
+import config as cfg
+from apache_beam.io.gcp.pubsub import ReadFromPubSub
+from apache_beam.ml.inference.base import KeyedModelHandler
+from apache_beam.ml.inference.base import RunInference
+from apache_beam.ml.inference.pytorch_inference import PytorchModelHandlerKeyedTensor
+from apache_beam.ml.inference.sklearn_inference import ModelFileType
+from pipeline.options import get_pipeline_options
+from pipeline.transformations import CustomSklearnModelHandlerNumpy
+from pipeline.transformations import DecodePrediction
+from pipeline.transformations import DecodePubSubMessage
+from pipeline.transformations import ModelWrapper
+from pipeline.transformations import NormalizeEmbedding
+from pipeline.transformations import TriggerEmailAlert
+from pipeline.transformations import tokenize_sentence
+from transformers import AutoConfig
+
+
+def parse_arguments(argv):
+  """
+    Parses the arguments passed to the command line and returns them as an object
+
+    Args:
+      argv: The arguments passed to the command line.
+
+    Returns:
+      The arguments that are being passed in.
+    """
+  parser = argparse.ArgumentParser(description="online-clustering")
+
+  parser.add_argument(
+      "-m",
+      "--mode",
+      help="Mode to run pipeline in.",
+      choices=["local", "cloud"],
+      default="local",
+  )
+  parser.add_argument(
+      "-p",
+      "--project",
+      help="GCP project to run pipeline on.",
+      default=cfg.PROJECT_ID,
+  )
+
+  args, _ = parser.parse_known_args(args=argv)
+  return args
+
+
+# [START PytorchNoBatchModelHandler]
+# Can be removed once: https://github.com/apache/beam/issues/21863 is fixed
+class PytorchNoBatchModelHandler(PytorchModelHandlerKeyedTensor):
+  """Wrapper to PytorchModelHandler to limit batch size to 1.
+    The tokenized strings generated from BertTokenizer may have different
+    lengths, which doesn't work with torch.stack() in current RunInference
+    implementation since stack() requires tensors to be the same size.
+    Restricting max_batch_size to 1 means there is only 1 example per `batch`
+    in the run_inference() call.
+    """
+  def batch_elements_kwargs(self):
+    return {"max_batch_size": 1}
+
+
+# [END PytorchNoBatchModelHandler]
+
+
+def run():
+  """
+    Runs the interjector pipeline which reads from PubSub, decodes the message,
+    tokenizes the text, gets the embedding, normalizes the embedding,
+    does anomaly dectection using HDBSCAN trained model, and then
+    writes to BQ, and sending an email alert if anomaly detected.
+    """
+  args = parse_arguments(sys.argv)
+  pipeline_options = get_pipeline_options(
+      job_name=cfg.JOB_NAME,
+      num_workers=cfg.NUM_WORKERS,
+      project=args.project,
+      mode=args.mode,
+  )
+
+  embedding_model_handler = PytorchNoBatchModelHandler(
+      state_dict_path=cfg.MODEL_STATE_DICT_PATH,
+      model_class=ModelWrapper,
+      model_params={
+          "config": AutoConfig.from_pretrained(cfg.MODEL_CONFIG_PATH)
+      },
+      device="cpu",
+  )
+  clustering_model_handler = KeyedModelHandler(
+      CustomSklearnModelHandlerNumpy(
+          model_uri=cfg.CLUSTERING_MODEL_PATH,
+          model_file_type=ModelFileType.JOBLIB))
+
+  with beam.Pipeline(options=pipeline_options) as pipeline:
+    docs = (
+        pipeline | "Read from PubSub" >> ReadFromPubSub(
+            subscription=cfg.SUBSCRIPTION_ID, with_attributes=True)
+        | "Decode PubSubMessage" >> beam.ParDo(DecodePubSubMessage()))
+    normalized_embedding = (
+        docs | "Tokenize Text" >> beam.Map(tokenize_sentence)
+        | "Get Embedding" >> RunInference(
+            KeyedModelHandler(embedding_model_handler))
+        | "Normalize Embedding" >> beam.ParDo(NormalizeEmbedding()))
+    predictions = (
+        normalized_embedding
+        | "Get Prediction from Model" >>
+        RunInference(model_handler=clustering_model_handler))
+
+    _ = (
+        predictions
+        | "Decode Prediction" >> beam.ParDo(DecodePrediction())
+        | "Write to BQ" >> beam.io.WriteToBigQuery(
+            table=cfg.TABLE_URI,
+            schema=cfg.TABLE_SCHEMA,
+            write_disposition=beam.io.BigQueryDisposition.WRITE_APPEND,
+            create_disposition=beam.io.BigQueryDisposition.CREATE_IF_NEEDED,
+        ))
+
+    _ = predictions | "Alert by Email" >> beam.ParDo(TriggerEmailAlert())
+
+
+if __name__ == "__main__":
+  run()

sdks/python/apache_beam/examples/inference/anomaly_detection/anomaly_detection_pipeline/pipeline/__init__.py

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+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You 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.
+#

sdks/python/apache_beam/examples/inference/anomaly_detection/anomaly_detection_pipeline/pipeline/options.py

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+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You 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.
+#
+
+"""This file contains the pipeline options to configure the Dataflow pipeline."""
+from datetime import datetime
+
+import config as cfg
+from apache_beam.options.pipeline_options import PipelineOptions
+
+
+def get_pipeline_options(
+    project: str,
+    job_name: str,
+    mode: str,
+    num_workers: int = cfg.NUM_WORKERS,
+    streaming: bool = True,
+) -> PipelineOptions:
+  """Function to retrieve the pipeline options.
+    Args:
+        project: GCP project to run on
+        mode: Indicator to run local, cloud or template
+        num_workers: Number of Workers for running the job parallely
+        max_num_workers: Maximum number of workers running the job parallely
+    Returns:
+        Dataflow pipeline options
+    """
+  job_name = f'{job_name}-{datetime.now().strftime("%Y%m%d%H%M%S")}'
+
+  staging_bucket = f"gs://{cfg.PROJECT_ID}-ml-examples"
+
+  # For a list of available options, check:
+  # https://cloud.google.com/dataflow/docs/guides/specifying-exec-params#setting-other-cloud-dataflow-pipeline-options
+  dataflow_options = {
+      "runner": "DirectRunner" if mode == "local" else "DataflowRunner",
+      "job_name": job_name,
+      "project": project,
+      "region": cfg.REGION,
+      "staging_location": f"{staging_bucket}/dflow-staging",
+      "temp_location": f"{staging_bucket}/dflow-temp",
+      "setup_file": "./setup.py",
+      "streaming": streaming,
+  }
+
+  # Optional parameters
+  if num_workers:
+    dataflow_options.update({"num_workers": num_workers})
+
+  return PipelineOptions(flags=[], **dataflow_options)