BulkDecompressor.java

/*
 * Copyright (C) 2018 Google Inc.
 *
 * 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.
 */

package com.google.cloud.teleport.templates;

import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ImmutableList;
import com.google.common.io.ByteStreams;
import com.google.common.io.Files;
import java.io.IOException;
import java.io.StringWriter;
import java.nio.channels.ReadableByteChannel;
import java.nio.channels.WritableByteChannel;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.beam.sdk.Pipeline;
import org.apache.beam.sdk.PipelineResult;
import org.apache.beam.sdk.io.Compression;
import org.apache.beam.sdk.io.FileIO;
import org.apache.beam.sdk.io.FileSystems;
import org.apache.beam.sdk.io.TextIO;
import org.apache.beam.sdk.io.fs.MatchResult;
import org.apache.beam.sdk.io.fs.MoveOptions;
import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
import org.apache.beam.sdk.io.fs.ResourceId;
import org.apache.beam.sdk.options.Description;
import org.apache.beam.sdk.options.PipelineOptions;
import org.apache.beam.sdk.options.PipelineOptionsFactory;
import org.apache.beam.sdk.options.Validation.Required;
import org.apache.beam.sdk.options.ValueProvider;
import org.apache.beam.sdk.transforms.DoFn;
import org.apache.beam.sdk.transforms.MapElements;
import org.apache.beam.sdk.transforms.ParDo;
import org.apache.beam.sdk.util.MimeTypes;
import org.apache.beam.sdk.values.KV;
import org.apache.beam.sdk.values.PCollectionTuple;
import org.apache.beam.sdk.values.TupleTag;
import org.apache.beam.sdk.values.TupleTagList;
import org.apache.beam.sdk.values.TypeDescriptors;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVPrinter;
import org.apache.commons.csv.QuoteMode;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * This pipeline decompresses file(s) from Google Cloud Storage and re-uploads them to a destination
 * location.
 *
 * <p><b>Parameters</b>
 *
 * <p>The {@code --inputFilePattern} parameter specifies a file glob to process. Files found can be
 * expressed in the following formats:
 *
 * <pre>
 * --inputFilePattern=gs://bucket-name/compressed-dir/*
 * --inputFilePattern=gs://bucket-name/compressed-dir/demo*.gz
 * </pre>
 *
 * <p>The {@code --outputDirectory} parameter can be expressed in the following formats:
 *
 * <pre>
 * --outputDirectory=gs://bucket-name
 * --outputDirectory=gs://bucket-name/decompressed-dir
 * </pre>
 *
 * <p>The {@code --outputFailureFile} parameter indicates the file to write the names of the files
 * which failed decompression and their associated error messages. This file can then be used for
 * subsequent processing by another process outside of Dataflow (e.g. send an email with the
 * failures, etc.). If there are no failures, the file will still be created but will be empty. The
 * failure file structure contains both the file that caused the error and the error message in CSV
 * format. The file will contain one header row and two columns (Filename, Error). The filename
 * output to the failureFile will be the full path of the file for ease of debugging.
 *
 * <pre>
 * --outputFailureFile=gs://bucket-name/decompressed-dir/failed.csv
 * </pre>
 *
 * <p>Example Output File:
 *
 * <pre>
 * Filename,Error
 * gs://docs-demo/compressedFile.gz, File is malformed or not compressed in BZIP2 format.
 * </pre>
 *
 * <p><b>Example Usage</b>
 *
 * <pre>
 * mvn compile exec:java \
 * -Dexec.mainClass=com.google.cloud.teleport.templates.BulkDecompressor \
 * -Dexec.cleanupDaemonThreads=false \
 * -Dexec.args=" \
 * --project=${PROJECT_ID} \
 * --stagingLocation=gs://${PROJECT_ID}/dataflow/pipelines/${PIPELINE_FOLDER}/staging \
 * --tempLocation=gs://${PROJECT_ID}/dataflow/pipelines/${PIPELINE_FOLDER}/temp \
 * --runner=DataflowRunner \
 * --inputFilePattern=gs://${PROJECT_ID}/compressed-dir/*.gz \
 * --outputDirectory=gs://${PROJECT_ID}/decompressed-dir \
 * --outputFailureFile=gs://${PROJECT_ID}/decompressed-dir/failed.csv"
 * </pre>
 */
public class BulkDecompressor {

  /** The logger to output status messages to. */
  private static final Logger LOG = LoggerFactory.getLogger(BulkDecompressor.class);

  /**
   * A list of the {@link Compression} values excluding {@link Compression#AUTO} and {@link
   * Compression#UNCOMPRESSED}.
   */
  @VisibleForTesting
  static final Set<Compression> SUPPORTED_COMPRESSIONS =
      Stream.of(Compression.values())
          .filter(value -> value != Compression.AUTO && value != Compression.UNCOMPRESSED)
          .collect(Collectors.toSet());

  /** The error msg given when the pipeline matches a file but cannot determine the compression. */
  @VisibleForTesting
  static final String UNCOMPRESSED_ERROR_MSG =
      "Skipping file %s because it did not match any compression mode (%s)";

  @VisibleForTesting
  static final String MALFORMED_ERROR_MSG =
      "The file resource %s is malformed or not in %s compressed format.";

  /** The tag used to identify the main output of the {@link Decompress} DoFn. */
  @VisibleForTesting
  static final TupleTag<String> DECOMPRESS_MAIN_OUT_TAG = new TupleTag<String>() {};

  /** The tag used to identify the dead-letter sideOutput of the {@link Decompress} DoFn. */
  @VisibleForTesting
  static final TupleTag<KV<String, String>> DEADLETTER_TAG = new TupleTag<KV<String, String>>() {};

  /**
   * The {@link Options} class provides the custom execution options passed by the executor at the
   * command-line.
   */
  public interface Options extends PipelineOptions {
    @Description("The input file pattern to read from (e.g. gs://bucket-name/compressed/*.gz)")
    @Required
    ValueProvider<String> getInputFilePattern();

    void setInputFilePattern(ValueProvider<String> value);

    @Description("The output location to write to (e.g. gs://bucket-name/decompressed)")
    @Required
    ValueProvider<String> getOutputDirectory();

    void setOutputDirectory(ValueProvider<String> value);

    @Description(
        "The output file to write failures during the decompression process "
            + "(e.g. gs://bucket-name/decompressed/failed.txt). The contents will be one line for "
            + "each file which failed decompression. Note that this parameter will "
            + "allow the pipeline to continue processing in the event of a failure.")
    @Required
    ValueProvider<String> getOutputFailureFile();

    void setOutputFailureFile(ValueProvider<String> value);
  }

  /**
   * The main entry-point for pipeline execution. This method will start the pipeline but will not
   * wait for it's execution to finish. If blocking execution is required, use the {@link
   * BulkDecompressor#run(Options)} method to start the pipeline and invoke {@code
   * result.waitUntilFinish()} on the {@link PipelineResult}.
   *
   * @param args The command-line args passed by the executor.
   */
  public static void main(String[] args) {

    Options options = PipelineOptionsFactory.fromArgs(args).withValidation().as(Options.class);

    run(options);
  }

  /**
   * Runs the pipeline to completion with the specified options. This method does not wait until the
   * pipeline is finished before returning. Invoke {@code result.waitUntilFinish()} on the result
   * object to block until the pipeline is finished running if blocking programmatic execution is
   * required.
   *
   * @param options The execution options.
   * @return The pipeline result.
   */
  public static PipelineResult run(Options options) {

    /*
     * Steps:
     *   1) Find all files matching the input pattern
     *   2) Decompress the files found and output them to the output directory
     *   3) Write any errors to the failure output file
     */

    // Create the pipeline
    Pipeline pipeline = Pipeline.create(options);

    // Run the pipeline over the work items.
    PCollectionTuple decompressOut =
        pipeline
            .apply("MatchFile(s)", FileIO.match().filepattern(options.getInputFilePattern()))
            .apply(
                "DecompressFile(s)",
                ParDo.of(new Decompress(options.getOutputDirectory()))
                    .withOutputTags(DECOMPRESS_MAIN_OUT_TAG, TupleTagList.of(DEADLETTER_TAG)));

    decompressOut
        .get(DEADLETTER_TAG)
        .apply(
            "FormatErrors",
            MapElements.into(TypeDescriptors.strings())
                .via(
                    kv -> {
                      StringWriter stringWriter = new StringWriter();
                      try {
                        CSVPrinter printer =
                            new CSVPrinter(
                                stringWriter,
                                CSVFormat.DEFAULT
                                    .withEscape('\\')
                                    .withQuoteMode(QuoteMode.NONE)
                                    .withRecordSeparator('\n')
                            );
                        printer.printRecord(kv.getKey(), kv.getValue());
                      } catch (IOException e) {
                        throw new RuntimeException(e);
                      }

                      return stringWriter.toString();
                    }))

        // We don't expect error files to be large so we'll create a single
        // file for ease of reprocessing by processes outside of Dataflow.
        .apply(
            "WriteErrorFile",
            TextIO.write()
                .to(options.getOutputFailureFile())
                .withHeader("Filename,Error")
                .withoutSharding());

    return pipeline.run();
  }

  /**
   * Performs the decompression of an object on Google Cloud Storage and uploads the decompressed
   * object back to a specified destination location.
   */
  @SuppressWarnings("serial")
  public static class Decompress extends DoFn<MatchResult.Metadata, String> {

    private final ValueProvider<String> destinationLocation;

    Decompress(ValueProvider<String> destinationLocation) {
      this.destinationLocation = destinationLocation;
    }

    @ProcessElement
    public void processElement(ProcessContext context) {
      ResourceId inputFile = context.element().resourceId();

      // Output a record to the failure file if the file doesn't match a known compression.
      if (!Compression.AUTO.isCompressed(inputFile.toString())) {
        String errorMsg =
            String.format(UNCOMPRESSED_ERROR_MSG, inputFile.toString(), SUPPORTED_COMPRESSIONS);

        context.output(DEADLETTER_TAG, KV.of(inputFile.toString(), errorMsg));
      } else {
        try {
          ResourceId outputFile = decompress(inputFile);
          context.output(outputFile.toString());
        } catch (IOException e) {
          LOG.error(e.getMessage());
          context.output(DEADLETTER_TAG, KV.of(inputFile.toString(), e.getMessage()));
        }
      }
    }

    /**
     * Decompresses the inputFile using the specified compression and outputs to the main output of
     * the {@link Decompress} doFn. Files output to the destination will be first written as temp
     * files with a "temp-" prefix within the output directory. If a file fails decompression, the
     * filename and the associated error will be output to the dead-letter.
     *
     * @param inputFile The inputFile to decompress.
     * @return A {@link ResourceId} which points to the resulting file from the decompression.
     */
    private ResourceId decompress(ResourceId inputFile) throws IOException {
      // Remove the compressed extension from the file. Example: demo.txt.gz -> demo.txt
      String outputFilename = Files.getNameWithoutExtension(inputFile.toString());

      // Resolve the necessary resources to perform the transfer.
      ResourceId outputDir = FileSystems.matchNewResource(destinationLocation.get(), true);
      ResourceId outputFile =
          outputDir.resolve(outputFilename, StandardResolveOptions.RESOLVE_FILE);
      ResourceId tempFile =
          outputDir.resolve(Files.getFileExtension(inputFile.toString())
              + "-temp-" + outputFilename, StandardResolveOptions.RESOLVE_FILE);

      // Resolve the compression
      Compression compression = Compression.detect(inputFile.toString());

      // Perform the copy of the decompressed channel into the destination.
      try (ReadableByteChannel readerChannel =
          compression.readDecompressed(FileSystems.open(inputFile))) {
        try (WritableByteChannel writerChannel = FileSystems.create(tempFile, MimeTypes.TEXT)) {
          ByteStreams.copy(readerChannel, writerChannel);
        }

        // Rename the temp file to the output file.
        FileSystems.rename(
            ImmutableList.of(tempFile),
            ImmutableList.of(outputFile),
            MoveOptions.StandardMoveOptions.IGNORE_MISSING_FILES);
      } catch (IOException e) {
        String msg = e.getMessage();

        LOG.error("Error occurred during decompression of {}", inputFile.toString(), e);
        throw new IOException(sanitizeDecompressionErrorMsg(msg, inputFile, compression));
      }

      return outputFile;
    }

    /**
     * The error messages coming from the compression library are not consistent across compression
     * modes. Here we'll attempt to unify the messages to inform the user more clearly when we've
     * encountered a file which is not compressed or malformed. Note that GZIP and ZIP compression
     * modes will not throw an exception when a decompression is attempted on a file which is not
     * compressed.
     *
     * @param errorMsg The error message thrown during decompression.
     * @param inputFile The input file which failed decompression.
     * @param compression The compression mode used during decompression.
     * @return The sanitized error message. If the error was not from a malformed file, the same
     *     error message passed will be returned.
     */
    private String sanitizeDecompressionErrorMsg(
        String errorMsg, ResourceId inputFile, Compression compression) {
      if (errorMsg != null
          && (errorMsg.contains("not in the BZip2 format")
              || errorMsg.contains("incorrect header check"))) {
        errorMsg = String.format(MALFORMED_ERROR_MSG, inputFile.toString(), compression);
      }

      return errorMsg;
    }
  }
}