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derrickawahmedabu98
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ahmedabu98
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Normalize tf record io (apache#34411)
* create TFRecordReadSchemaTransform * create TFRecordWriteSchemaTransform * create TFRecordSchemaTransform Test * fix conflicts * add writeToTFRecord return * add translation file and getRowConfiguration method for said file * fix formatting * remove print * fix more lint issues * add support for bytes in yaml * update ReadTransform with error handling and use string compression * add error handling to writetransform and change compression to string * change compression to string * update compression type and no_spilling * update writeToTFRecord parameters * add tfrecord yaml test pipeline * remove old code * fix lint issue * update standard external transforms with tfrecord info * remove bad character and broken comment * fix lint issue * add no_spilling doc string * change tfrecord.yaml to write version * update parameter name * update read and write yaml for tfrecord * update pipeline to handle write and read * fix lint issues * fix lint * fix lint, precommit checker is broken for me, so hence many commits :) * minor fix * fix java comments * Update sdks/java/core/src/main/java/org/apache/beam/sdk/io/TFRecordWriteSchemaTransformProvider.java Co-authored-by: Ahmed Abualsaud <[email protected]> * Update sdks/java/core/src/main/java/org/apache/beam/sdk/io/TFRecordSchemaTransformTranslation.java Co-authored-by: Ahmed Abualsaud <[email protected]> * fix class name change * fix MakeItWork test case * fix spotless issues * Update sdks/java/core/src/main/java/org/apache/beam/sdk/io/TFRecordWriteSchemaTransformProvider.java Co-authored-by: Ahmed Abualsaud <[email protected]> * remove nullable for outputprefix per comments * remove no_spilling parameter and extra white space * update standard external transforms * remove one more no_spilling * fix nullable on no_spilling * rerun generate external transforms * fix order of python and java providers * revert java and python providers changes * update test and fix prior test failures --------- Co-authored-by: Ahmed Abualsaud <[email protected]>
1 parent 3af0398 commit c1650e9

12 files changed

Lines changed: 1575 additions & 2 deletions

‎sdks/java/core/src/main/java/org/apache/beam/sdk/io/TFRecordReadSchemaTransformConfiguration.java‎

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/*
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* Licensed to the Apache Software Foundation (ASF) under one
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* or more contributor license agreements. See the NOTICE file
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* distributed with this work for additional information
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* regarding copyright ownership. The ASF licenses this file
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* to you under the Apache License, Version 2.0 (the
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* "License"); you may not use this file except in compliance
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* with the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.apache.beam.sdk.io;
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import static org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.base.Preconditions.checkArgument;
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import static org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.base.Preconditions.checkState;
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import com.google.auto.value.AutoValue;
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import java.io.IOException;
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import java.io.Serializable;
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import javax.annotation.Nullable;
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import org.apache.beam.sdk.io.fs.MatchResult;
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import org.apache.beam.sdk.schemas.AutoValueSchema;
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import org.apache.beam.sdk.schemas.annotations.DefaultSchema;
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import org.apache.beam.sdk.schemas.annotations.SchemaFieldDescription;
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import org.apache.beam.sdk.schemas.transforms.providers.ErrorHandling;
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import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.base.Strings;
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/**
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* Configuration for reading from TFRecord.
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*
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* <p>This class is meant to be used with {@link TFRecordReadSchemaTransformProvider}.
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*
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* <p><b>Internal only:</b> This class is actively being worked on, and it will likely change. We
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* provide no backwards compatibility guarantees, and it should not be implemented outside the Beam
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* repository.
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*/
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@DefaultSchema(AutoValueSchema.class)
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@AutoValue
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public abstract class TFRecordReadSchemaTransformConfiguration implements Serializable {
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public void validate() {
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String invalidConfigMessage = "Invalid TFRecord Read configuration: ";
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if (getValidate()) {
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String filePattern = getFilePattern();
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try {
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MatchResult matches = FileSystems.match(filePattern);
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checkState(
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!matches.metadata().isEmpty(), "Unable to find any files matching %s", filePattern);
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} catch (IOException e) {
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throw new IllegalStateException(
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String.format(invalidConfigMessage + "Failed to validate %s", filePattern), e);
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}
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}
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ErrorHandling errorHandling = getErrorHandling();
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if (errorHandling != null) {
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checkArgument(
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!Strings.isNullOrEmpty(errorHandling.getOutput()),
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invalidConfigMessage + "Output must not be empty if error handling specified.");
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}
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}
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/** Instantiates a {@link TFRecordReadSchemaTransformConfiguration.Builder} instance. */
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public static TFRecordReadSchemaTransformConfiguration.Builder builder() {
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return new AutoValue_TFRecordReadSchemaTransformConfiguration.Builder();
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}
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@SchemaFieldDescription("Validate file pattern.")
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public abstract boolean getValidate();
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@SchemaFieldDescription("Decompression type to use when reading input files.")
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public abstract String getCompression();
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@SchemaFieldDescription("Filename or file pattern used to find input files.")
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public abstract String getFilePattern();
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@SchemaFieldDescription("This option specifies whether and where to output unwritable rows.")
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public abstract @Nullable ErrorHandling getErrorHandling();
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abstract Builder toBuilder();
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/** Builder for {@link TFRecordReadSchemaTransformConfiguration}. */
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@AutoValue.Builder
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public abstract static class Builder {
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public abstract Builder setValidate(boolean value);
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public abstract Builder setCompression(String value);
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public abstract Builder setFilePattern(String value);
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public abstract Builder setErrorHandling(@Nullable ErrorHandling errorHandling);
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/** Builds the {@link TFRecordReadSchemaTransformConfiguration} configuration. */
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public abstract TFRecordReadSchemaTransformConfiguration build();
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}
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}

‎sdks/java/core/src/main/java/org/apache/beam/sdk/io/TFRecordReadSchemaTransformProvider.java‎

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/*
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* Licensed to the Apache Software Foundation (ASF) under one
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* or more contributor license agreements. See the NOTICE file
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* distributed with this work for additional information
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* regarding copyright ownership. The ASF licenses this file
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* to you under the Apache License, Version 2.0 (the
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* "License"); you may not use this file except in compliance
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* with the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.apache.beam.sdk.io;
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import static org.apache.beam.sdk.util.Preconditions.checkArgumentNotNull;
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import com.google.auto.service.AutoService;
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import java.util.Arrays;
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import java.util.List;
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import org.apache.beam.sdk.metrics.Counter;
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import org.apache.beam.sdk.metrics.Metrics;
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import org.apache.beam.sdk.schemas.NoSuchSchemaException;
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import org.apache.beam.sdk.schemas.Schema;
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import org.apache.beam.sdk.schemas.SchemaRegistry;
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import org.apache.beam.sdk.schemas.transforms.SchemaTransform;
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import org.apache.beam.sdk.schemas.transforms.SchemaTransformProvider;
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import org.apache.beam.sdk.schemas.transforms.TypedSchemaTransformProvider;
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import org.apache.beam.sdk.schemas.transforms.providers.ErrorHandling;
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import org.apache.beam.sdk.transforms.DoFn;
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import org.apache.beam.sdk.transforms.DoFn.ProcessElement;
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import org.apache.beam.sdk.transforms.ParDo;
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import org.apache.beam.sdk.transforms.SerializableFunction;
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import org.apache.beam.sdk.transforms.SimpleFunction;
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import org.apache.beam.sdk.values.PCollection;
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import org.apache.beam.sdk.values.PCollectionRowTuple;
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import org.apache.beam.sdk.values.PCollectionTuple;
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import org.apache.beam.sdk.values.Row;
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import org.apache.beam.sdk.values.TupleTag;
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import org.apache.beam.sdk.values.TupleTagList;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@AutoService(SchemaTransformProvider.class)
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public class TFRecordReadSchemaTransformProvider
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extends TypedSchemaTransformProvider<TFRecordReadSchemaTransformConfiguration> {
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private static final String IDENTIFIER = "beam:schematransform:org.apache.beam:tfrecord_read:v1";
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private static final String OUTPUT = "output";
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private static final String ERROR = "errors";
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public static final TupleTag<Row> OUTPUT_TAG = new TupleTag<Row>() {};
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public static final TupleTag<Row> ERROR_TAG = new TupleTag<Row>() {};
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private static final Logger LOG =
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LoggerFactory.getLogger(TFRecordReadSchemaTransformProvider.class);
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/** Returns the expected {@link SchemaTransform} of the configuration. */
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@Override
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protected SchemaTransform from(TFRecordReadSchemaTransformConfiguration configuration) {
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return new TFRecordReadSchemaTransform(configuration);
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}
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/** Implementation of the {@link TypedSchemaTransformProvider} identifier method. */
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@Override
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public String identifier() {
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return IDENTIFIER;
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}
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/** Implementation of the {@link TypedSchemaTransformProvider} outputCollectionNames method. */
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@Override
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public List<String> outputCollectionNames() {
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return Arrays.asList(OUTPUT, ERROR);
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}
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/**
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* An implementation of {@link SchemaTransform} for TFRecord read jobs configured using {@link
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* TFRecordReadSchemaTransformConfiguration}.
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*/
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static class TFRecordReadSchemaTransform extends SchemaTransform {
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private final TFRecordReadSchemaTransformConfiguration configuration;
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TFRecordReadSchemaTransform(TFRecordReadSchemaTransformConfiguration configuration) {
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this.configuration = configuration;
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}
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public Row getConfigurationRow() {
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try {
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// To stay consistent with our SchemaTransform configuration naming conventions,
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// we sort lexicographically
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return SchemaRegistry.createDefault()
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.getToRowFunction(TFRecordReadSchemaTransformConfiguration.class)
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.apply(configuration)
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.sorted()
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.toSnakeCase();
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} catch (NoSuchSchemaException e) {
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throw new RuntimeException(e);
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}
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}
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@Override
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public PCollectionRowTuple expand(PCollectionRowTuple input) {
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// Validate configuration parameters
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configuration.validate();
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TFRecordIO.Read readTransform =
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TFRecordIO.read().withCompression(Compression.valueOf(configuration.getCompression()));
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String filePattern = configuration.getFilePattern();
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if (filePattern != null) {
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readTransform = readTransform.from(filePattern);
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}
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if (!configuration.getValidate()) {
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readTransform = readTransform.withoutValidation();
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}
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// Read TFRecord files into a PCollection of byte arrays.
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PCollection<byte[]> tfRecordValues = input.getPipeline().apply(readTransform);
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// Define the schema for the row
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final Schema schema = Schema.of(Schema.Field.of("record", Schema.FieldType.BYTES));
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Schema errorSchema = ErrorHandling.errorSchemaBytes();
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boolean handleErrors = ErrorHandling.hasOutput(configuration.getErrorHandling());
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SerializableFunction<byte[], Row> bytesToRowFn = getBytesToRowFn(schema);
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// Apply bytes to row fn
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PCollectionTuple outputTuple =
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tfRecordValues.apply(
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ParDo.of(
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new ErrorFn(
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"TFRecord-read-error-counter", bytesToRowFn, errorSchema, handleErrors))
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.withOutputTags(OUTPUT_TAG, TupleTagList.of(ERROR_TAG)));
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PCollectionRowTuple outputRows =
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PCollectionRowTuple.of("output", outputTuple.get(OUTPUT_TAG).setRowSchema(schema));
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// Error handling
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PCollection<Row> errorOutput = outputTuple.get(ERROR_TAG).setRowSchema(errorSchema);
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if (handleErrors) {
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outputRows =
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outputRows.and(
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checkArgumentNotNull(configuration.getErrorHandling()).getOutput(), errorOutput);
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}
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return outputRows;
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}
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}
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public static SerializableFunction<byte[], Row> getBytesToRowFn(Schema schema) {
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return new SimpleFunction<byte[], Row>() {
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@Override
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public Row apply(byte[] input) {
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return Row.withSchema(schema).addValues(input).build();
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}
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};
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}
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public static class ErrorFn extends DoFn<byte[], Row> {
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private final SerializableFunction<byte[], Row> valueMapper;
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private final Counter errorCounter;
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private Long errorsInBundle = 0L;
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private final boolean handleErrors;
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private final Schema errorSchema;
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public ErrorFn(
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String name,
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SerializableFunction<byte[], Row> valueMapper,
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Schema errorSchema,
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boolean handleErrors) {
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this.errorCounter = Metrics.counter(TFRecordReadSchemaTransformProvider.class, name);
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this.valueMapper = valueMapper;
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this.handleErrors = handleErrors;
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this.errorSchema = errorSchema;
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}
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@ProcessElement
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public void process(@DoFn.Element byte[] msg, MultiOutputReceiver receiver) {
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Row mappedRow = null;
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try {
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mappedRow = valueMapper.apply(msg);
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} catch (Exception e) {
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if (!handleErrors) {
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throw new RuntimeException(e);
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}
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errorsInBundle += 1;
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LOG.warn("Error while parsing the element", e);
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receiver.get(ERROR_TAG).output(ErrorHandling.errorRecord(errorSchema, msg, e));
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}
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if (mappedRow != null) {
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receiver.get(OUTPUT_TAG).output(mappedRow);
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}
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}
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@FinishBundle
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public void finish(FinishBundleContext c) {
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errorCounter.inc(errorsInBundle);
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errorsInBundle = 0L;
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}
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}
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}

‎sdks/java/core/src/main/java/org/apache/beam/sdk/io/TFRecordSchemaTransformTranslation.java‎

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/*
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* Licensed to the Apache Software Foundation (ASF) under one
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* or more contributor license agreements. See the NOTICE file
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* distributed with this work for additional information
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* regarding copyright ownership. The ASF licenses this file
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* to you under the Apache License, Version 2.0 (the
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* "License"); you may not use this file except in compliance
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* with the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package org.apache.beam.sdk.io;
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import static org.apache.beam.sdk.io.TFRecordReadSchemaTransformProvider.TFRecordReadSchemaTransform;
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import static org.apache.beam.sdk.io.TFRecordWriteSchemaTransformProvider.TFRecordWriteSchemaTransform;
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import com.google.auto.service.AutoService;
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import java.util.Map;
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import org.apache.beam.sdk.schemas.transforms.SchemaTransformProvider;
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import org.apache.beam.sdk.schemas.transforms.SchemaTransformTranslation;
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import org.apache.beam.sdk.transforms.PTransform;
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import org.apache.beam.sdk.util.construction.PTransformTranslation;
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import org.apache.beam.sdk.util.construction.TransformPayloadTranslatorRegistrar;
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import org.apache.beam.sdk.values.Row;
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import org.apache.beam.vendor.guava.v32_1_2_jre.com.google.common.collect.ImmutableMap;
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public class TFRecordSchemaTransformTranslation {
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public static class TFRecordReadSchemaTransformTranslator
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extends SchemaTransformTranslation.SchemaTransformPayloadTranslator<
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TFRecordReadSchemaTransform> {
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@Override
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public SchemaTransformProvider provider() {
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return new TFRecordReadSchemaTransformProvider();
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}
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@Override
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public Row toConfigRow(TFRecordReadSchemaTransform transform) {
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return transform.getConfigurationRow();
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}
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}
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public static class TFRecordWriteSchemaTransformTranslator
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extends SchemaTransformTranslation.SchemaTransformPayloadTranslator<
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TFRecordWriteSchemaTransform> {
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@Override
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public SchemaTransformProvider provider() {
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return new TFRecordWriteSchemaTransformProvider();
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}
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@Override
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public Row toConfigRow(TFRecordWriteSchemaTransform transform) {
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return transform.getConfigurationRow();
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}
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}
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@AutoService(TransformPayloadTranslatorRegistrar.class)
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public static class ReadWriteRegistrar implements TransformPayloadTranslatorRegistrar {
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@Override
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@SuppressWarnings({
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"rawtypes",
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})
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public Map<
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? extends Class<? extends PTransform>,
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? extends PTransformTranslation.TransformPayloadTranslator>
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getTransformPayloadTranslators() {
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return ImmutableMap
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.<Class<? extends PTransform>, PTransformTranslation.TransformPayloadTranslator>builder()
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.put(TFRecordReadSchemaTransform.class, new TFRecordReadSchemaTransformTranslator())
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.put(TFRecordWriteSchemaTransform.class, new TFRecordWriteSchemaTransformTranslator())
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.build();
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}
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}
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}

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