abhiy13 commented on a change in pull request #12645: URL: https://github.com/apache/beam/pull/12645#discussion_r492474704
########## File path: sdks/java/io/contextual-text-io/src/main/java/org/apache/beam/sdk/io/contextualtextio/ContextualTextIOSource.java ########## @@ -0,0 +1,364 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.contextualtextio; + +import java.io.IOException; +import java.nio.ByteBuffer; +import java.nio.channels.ReadableByteChannel; +import java.nio.channels.SeekableByteChannel; +import java.util.NoSuchElementException; +import org.apache.beam.sdk.coders.Coder; +import org.apache.beam.sdk.io.FileBasedSource; +import org.apache.beam.sdk.io.fs.EmptyMatchTreatment; +import org.apache.beam.sdk.io.fs.MatchResult; +import org.apache.beam.sdk.options.PipelineOptions; +import org.apache.beam.sdk.options.ValueProvider; +import org.apache.beam.sdk.schemas.NoSuchSchemaException; +import org.apache.beam.sdk.schemas.SchemaCoder; +import org.apache.beam.sdk.schemas.SchemaRegistry; +import org.apache.beam.vendor.grpc.v1p26p0.com.google.protobuf.ByteString; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.annotations.VisibleForTesting; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions; +import org.checkerframework.checker.nullness.qual.Nullable; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Implementation detail of {@link ContextualTextIO.Read}. + * + * <p>A {@link FileBasedSource} which can decode records delimited by newline characters. + * + * <p>This source splits the data into records using {@code UTF-8} {@code \n}, {@code \r}, or {@code + * \r\n} as the delimiter. This source is not strict and supports decoding the last record even if + * it is not delimited. Finally, no records are decoded if the stream is empty. + * + * <p>This source supports reading from any arbitrary byte position within the stream. If the + * starting position is not {@code 0}, then bytes are skipped until the first delimiter is found + * representing the beginning of the first record to be decoded. + */ +@VisibleForTesting +class ContextualTextIOSource extends FileBasedSource<RecordWithMetadata> { + byte[] delimiter; + + private static final Logger LOG = LoggerFactory.getLogger(ContextualTextIOSource.class); + + // Used to Override isSplittable + private boolean hasMultilineCSVRecords; + + @Override + protected boolean isSplittable() throws Exception { + if (hasMultilineCSVRecords) { + // When Having Multiline CSV Records, + // Splitting the file may cause a split to be within a record, + // Disabling split prevents this from happening + return false; + } + return super.isSplittable(); + } + + ContextualTextIOSource( + ValueProvider<String> fileSpec, + EmptyMatchTreatment emptyMatchTreatment, + byte[] delimiter, + boolean hasMultilineCSVRecords) { + super(fileSpec, emptyMatchTreatment, 1L); + this.delimiter = delimiter; + this.hasMultilineCSVRecords = hasMultilineCSVRecords; + } + + private ContextualTextIOSource( + MatchResult.Metadata metadata, + long start, + long end, + byte[] delimiter, + boolean hasMultilineCSVRecords) { + super(metadata, 1L, start, end); + this.delimiter = delimiter; + this.hasMultilineCSVRecords = hasMultilineCSVRecords; + } + + @Override + protected FileBasedSource<RecordWithMetadata> createForSubrangeOfFile( + MatchResult.Metadata metadata, long start, long end) { + return new ContextualTextIOSource(metadata, start, end, delimiter, hasMultilineCSVRecords); + } + + @Override + protected FileBasedReader<RecordWithMetadata> createSingleFileReader(PipelineOptions options) { + return new MultiLineTextBasedReader(this, delimiter, hasMultilineCSVRecords); + } + + @Override + public Coder<RecordWithMetadata> getOutputCoder() { + SchemaCoder<RecordWithMetadata> coder = null; + try { + coder = SchemaRegistry.createDefault().getSchemaCoder(RecordWithMetadata.class); + } catch (NoSuchSchemaException e) { + LOG.error("No Coder Found for RecordWithMetadata"); + } + return coder; + } + + /** + * A {@link FileBasedReader FileBasedReader} which can decode records delimited by delimiter + * characters. + * + * <p>See {@link ContextualTextIOSource } for further details. + */ + @VisibleForTesting + static class MultiLineTextBasedReader extends FileBasedReader<RecordWithMetadata> { + public static final int READ_BUFFER_SIZE = 8192; + private static final ByteString UTF8_BOM = + ByteString.copyFrom(new byte[] {(byte) 0xEF, (byte) 0xBB, (byte) 0xBF}); + private final ByteBuffer readBuffer = ByteBuffer.allocate(READ_BUFFER_SIZE); + private ByteString buffer; + private int startOfDelimiterInBuffer; + private int endOfDelimiterInBuffer; + private long startOfRecord; + private volatile long startOfNextRecord; + private volatile boolean eof; + private volatile boolean elementIsPresent; + private @Nullable RecordWithMetadata currentValue; + private @Nullable ReadableByteChannel inChannel; + private byte @Nullable [] delimiter; + + // Add to override the isSplittable + private boolean hasMultilineCSVRecords; + + private long startingOffset; + private long totalRecordCount; + + private MultiLineTextBasedReader( + ContextualTextIOSource source, byte[] delimiter, boolean hasMultilineCSVRecords) { + super(source); + buffer = ByteString.EMPTY; + this.delimiter = delimiter; + this.hasMultilineCSVRecords = hasMultilineCSVRecords; + startingOffset = getCurrentSource().getStartOffset(); // Start offset; + } + + @Override + protected long getCurrentOffset() throws NoSuchElementException { + if (!elementIsPresent) { + throw new NoSuchElementException(); + } + return startOfRecord; + } + + @Override + public long getSplitPointsRemaining() { + if (isStarted() && startOfNextRecord >= getCurrentSource().getEndOffset()) { + return isDone() ? 0 : 1; + } + return super.getSplitPointsRemaining(); + } + + @Override + public RecordWithMetadata getCurrent() throws NoSuchElementException { + if (!elementIsPresent) { + throw new NoSuchElementException(); + } + return currentValue; + } + + @Override + protected void startReading(ReadableByteChannel channel) throws IOException { + this.inChannel = channel; + // If the first offset is greater than zero, we need to skip bytes until we see our + // first delimiter. + long startOffset = getCurrentSource().getStartOffset(); + if (startOffset > 0) { + Preconditions.checkState( + channel instanceof SeekableByteChannel, + "%s only supports reading from a SeekableByteChannel when given a start offset" + + " greater than 0.", + ContextualTextIOSource.class.getSimpleName()); + long requiredPosition = startOffset - 1; + if (delimiter != null && startOffset >= delimiter.length) { + // we need to move back the offset of at worse delimiter.size to be sure to see + // all the bytes of the delimiter in the call to findDelimiterBounds() below + requiredPosition = startOffset - delimiter.length; + } + ((SeekableByteChannel) channel).position(requiredPosition); + findDelimiterBoundsWithMultiLineCheck(); + buffer = buffer.substring(endOfDelimiterInBuffer); + startOfNextRecord = requiredPosition + endOfDelimiterInBuffer; + endOfDelimiterInBuffer = 0; + startOfDelimiterInBuffer = 0; + } + } + + private void findDelimiterBoundsWithMultiLineCheck() throws IOException { + findDelimiterBounds(); + } + + /** + * Locates the start position and end position of the next delimiter. Will consume the channel + * till either EOF or the delimiter bounds are found. + * + * <p>If {@link ContextualTextIOSource#hasMultilineCSVRecords} is set then the behaviour will + * change from the standard read seen in {@link org.apache.beam.sdk.io.TextIO}. The assumption + * when {@link ContextualTextIOSource#hasMultilineCSVRecords} is set is that the file is being + * read with a single thread. + * + * <p>This fills the buffer and updates the positions as follows: + * + * <pre>{@code + * ------------------------------------------------------ + * | element bytes | delimiter bytes | unconsumed bytes | + * ------------------------------------------------------ + * 0 start of end of buffer + * delimiter delimiter size + * in buffer in buffer + * }</pre> + */ + private void findDelimiterBounds() throws IOException { + int bytePositionInBuffer = 0; + boolean doubleQuoteClosed = true; + + while (true) { + if (!tryToEnsureNumberOfBytesInBuffer(bytePositionInBuffer + 1)) { + startOfDelimiterInBuffer = endOfDelimiterInBuffer = bytePositionInBuffer; + break; + } + + byte currentByte = buffer.byteAt(bytePositionInBuffer); + if (hasMultilineCSVRecords) { + // Check if we are inside an open Quote + if (currentByte == '"') { + doubleQuoteClosed = !doubleQuoteClosed; + } + } else { + doubleQuoteClosed = true; + } + + if (delimiter == null) { + // default delimiter + if (currentByte == '\n') { + startOfDelimiterInBuffer = bytePositionInBuffer; + endOfDelimiterInBuffer = startOfDelimiterInBuffer + 1; + if (doubleQuoteClosed) { + break; + } + } else if (currentByte == '\r') { + startOfDelimiterInBuffer = bytePositionInBuffer; + endOfDelimiterInBuffer = startOfDelimiterInBuffer + 1; + if (tryToEnsureNumberOfBytesInBuffer(bytePositionInBuffer + 2)) { + currentByte = buffer.byteAt(bytePositionInBuffer + 1); + if (currentByte == '\n') { + endOfDelimiterInBuffer += 1; + } + } + if (doubleQuoteClosed) { + break; + } + } + } else { + // when the user defines a delimiter + int i = 0; + startOfDelimiterInBuffer = endOfDelimiterInBuffer = bytePositionInBuffer; + while ((i < delimiter.length) && (currentByte == delimiter[i])) { + // read next byte; + i++; + if (tryToEnsureNumberOfBytesInBuffer(bytePositionInBuffer + i + 1)) { + currentByte = buffer.byteAt(bytePositionInBuffer + i); + } else { + // corner case: delimiter truncate at the end of file + startOfDelimiterInBuffer = endOfDelimiterInBuffer = bytePositionInBuffer; + break; + } + } + if (i == delimiter.length) { + endOfDelimiterInBuffer = bytePositionInBuffer + i; + if (doubleQuoteClosed) { + break; + } + } + } + bytePositionInBuffer += 1; + } + } + + @Override + protected boolean readNextRecord() throws IOException { + startOfRecord = startOfNextRecord; + + findDelimiterBoundsWithMultiLineCheck(); + + // If we have reached EOF file and consumed all of the buffer then we know + // that there are no more records. + if (eof && buffer.isEmpty()) { + elementIsPresent = false; + return false; + } + + decodeCurrentElement(); + startOfNextRecord = startOfRecord + endOfDelimiterInBuffer; + return true; + } + + /** + * Decodes the current element updating the buffer to only contain the unconsumed bytes. + * + * <p>This invalidates the currently stored {@code startOfDelimiterInBuffer} and {@code + * endOfDelimiterInBuffer}. + */ + private void decodeCurrentElement() throws IOException { + ByteString dataToDecode = buffer.substring(0, startOfDelimiterInBuffer); + // If present, the UTF8 Byte Order Mark (BOM) will be removed. + if (startOfRecord == 0 && dataToDecode.startsWith(UTF8_BOM)) { + dataToDecode = dataToDecode.substring(UTF8_BOM.size()); + } + + // The line num is: + Long recordUniqueNum = totalRecordCount++; + // The Complete FileName (with uri if this is a web url eg: temp/abc.txt) is: + String fileName = getCurrentSource().getSingleFileMetadata().resourceId().toString(); Review comment: @rezarokni thanks ! I was facing this same issue that is why could not make it part of the previous commit. FileName does seem to be the best option for now. ########## File path: sdks/java/io/contextual-text-io/src/main/java/org/apache/beam/sdk/io/contextualtextio/RecordWithMetadata.java ########## @@ -0,0 +1,85 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.contextualtextio; + +import com.google.auto.value.AutoValue; +import org.apache.beam.sdk.annotations.Experimental; +import org.apache.beam.sdk.io.fs.ResourceId; +import org.apache.beam.sdk.schemas.AutoValueSchema; +import org.apache.beam.sdk.schemas.annotations.DefaultSchema; + +/** + * Helper Class based on {@link AutoValueSchema}, it provides Metadata associated with each Record + * when reading from file(s) using {@link ContextualTextIO}. + * + * <h3>Fields:</h3> + * + * <ul> + * <li>recordOffset: The offset of a record (the byte at which the record begins) in a file. This + * information can be useful if you wish to reconstruct the file. {@link + * RecordWithMetadata#getRecordOffset()} + * <li>recordNum: The ordinal number of the record in its file. {@link + * RecordWithMetadata#getRecordNum()} + * <li>recordValue: The value / contents of the record {@link RecordWithMetadata#getValue()} + * <li>rangeOffset: The starting offset of the range (split), which contained the record, when the + * record was read. {@link RecordWithMetadata#getRangeOffset()} + * <li>recordNumInOffset: The record number relative to the Range. (line number within the range) + * {@link RecordWithMetadata#getRecordNumInOffset()} + * <li>fileName: Name of the file to which the record belongs (this is the full filename, + * eg:path/to/file.txt) {@link RecordWithMetadata#getFileName()} + * </ul> + */ +@Experimental(Experimental.Kind.SCHEMAS) +@DefaultSchema(AutoValueSchema.class) +@AutoValue +public abstract class RecordWithMetadata { + public abstract long getRecordOffset(); + + public abstract long getRecordNum(); + + public abstract String getValue(); + + public abstract long getRangeOffset(); + + public abstract long getRecordNumInOffset(); + + public abstract Builder toBuilder(); + + public abstract String getFileName(); + + public static Builder newBuilder() { + return new AutoValue_RecordWithMetadata.Builder(); + } + + @AutoValue.Builder + public abstract static class Builder { + public abstract Builder setRecordNum(long lineNum); + + public abstract Builder setRecordOffset(long recordOffset); + + public abstract Builder setValue(String Value); Review comment: Done. ########## File path: sdks/java/io/contextual-text-io/src/main/java/org/apache/beam/sdk/io/contextualtextio/ContextualTextIO.java ########## @@ -0,0 +1,631 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.contextualtextio; + +import static org.apache.beam.sdk.io.FileIO.ReadMatches.DirectoryTreatment; +import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkArgument; +import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkNotNull; + +import com.google.auto.value.AutoValue; +import java.nio.ByteBuffer; +import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; +import java.util.Map; +import java.util.SortedMap; +import java.util.TreeMap; +import org.apache.beam.sdk.coders.StringUtf8Coder; +import org.apache.beam.sdk.io.CompressedSource; +import org.apache.beam.sdk.io.Compression; +import org.apache.beam.sdk.io.FileBasedSource; +import org.apache.beam.sdk.io.FileIO; +import org.apache.beam.sdk.io.FileIO.MatchConfiguration; +import org.apache.beam.sdk.io.ReadAllViaFileBasedSource; +import org.apache.beam.sdk.io.TextIO; +import org.apache.beam.sdk.io.fs.EmptyMatchTreatment; +import org.apache.beam.sdk.options.ValueProvider; +import org.apache.beam.sdk.options.ValueProvider.StaticValueProvider; +import org.apache.beam.sdk.schemas.NoSuchSchemaException; +import org.apache.beam.sdk.schemas.SchemaCoder; +import org.apache.beam.sdk.transforms.Count; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.transforms.SerializableFunction; +import org.apache.beam.sdk.transforms.View; +import org.apache.beam.sdk.transforms.Watch.Growth.TerminationCondition; +import org.apache.beam.sdk.transforms.display.DisplayData; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PBegin; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PCollectionView; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.annotations.VisibleForTesting; +import org.checkerframework.checker.nullness.qual.Nullable; +import org.joda.time.Duration; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * {@link PTransform}s that read text files and collect contextual information of the elements in + * the input. + * + * <p>Use {@link TextIO} when not reading file with Multiline Records or additional metadata is not + * required. + * + * <h2>Reading from text files</h2> + * + * <p>To read a {@link PCollection} from one or more text files, use {@code + * ContextualTextIO.read()}. To instantiate a transform use {@link + * ContextualTextIO.Read#from(String)} and specify the path of the file(s) to be read. + * Alternatively, if the filenames to be read are themselves in a {@link PCollection} you can use + * {@link FileIO} to match them and {@link ContextualTextIO#readFiles()} to read them. + * + * <p>{@link #read} returns a {@link PCollection} of {@link RecordWithMetadata RecordWithMetadata}, + * each corresponding to one line of an input UTF-8 text file (split into lines delimited by '\n', + * '\r', '\r\n', or specified delimiter see {@link ContextualTextIO.Read#withDelimiter}) + * + * <h3>Filepattern expansion and watching</h3> + * + * <p>By default, the filepatterns are expanded only once. The combination of {@link + * FileIO.Match#continuously(Duration, TerminationCondition)} and {@link #readFiles()} allow + * streaming of new files matching the filepattern(s). + * + * <p>By default, {@link #read} prohibits filepatterns that match no files, and {@link #readFiles()} + * allows them in case the filepattern contains a glob wildcard character. Use {@link + * ContextualTextIO.Read#withEmptyMatchTreatment} or {@link + * FileIO.Match#withEmptyMatchTreatment(EmptyMatchTreatment)} plus {@link #readFiles()} to configure + * this behavior. + * + * <p>Example 1: reading a file or filepattern. + * + * <pre>{@code + * Pipeline p = ...; + * + * // A simple Read of a file: + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read().from("/local/path/to/file.txt")); + * }</pre> + * + * <p>Example 2: reading a PCollection of filenames. + * + * <pre>{@code + * Pipeline p = ...; + * + * // E.g. the filenames might be computed from other data in the pipeline, or + * // read from a data source. + * PCollection<String> filenames = ...; + * + * // Read all files in the collection. + * PCollection<RecordWithMetadata> records = + * filenames + * .apply(FileIO.matchAll()) + * .apply(FileIO.readMatches()) + * .apply(ContextualTextIO.readFiles()); + * }</pre> + * + * <p>Example 3: streaming new files matching a filepattern. + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read() + * .from("/local/path/to/files/*") + * .watchForNewFiles( + * // Check for new files every minute + * Duration.standardMinutes(1), + * // Stop watching the filepattern if no new files appear within an hour + * afterTimeSinceNewOutput(Duration.standardHours(1)))); + * }</pre> + * + * <p>Example 4: reading a file or file pattern of RFC4180-compliant CSV files with fields that may + * contain line breaks. + * + * Example of such a file could be: + * + * "aaa","b CRLF + * bb","ccc" CRLF + * zzz,yyy,xxx + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read() + * .from("/local/path/to/files/*.csv") + * .withHasMultilineCSVRecords(true)); + * }</pre> + * + * <p>Example 5: reading while watching for new files + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(FileIO.match() + * .filepattern("filepattern") + * .continuously( + * Duration.millis(100), + * Watch.Growth.afterTimeSinceNewOutput(Duration.standardSeconds(3)))) + * .apply(FileIO.readMatches()) + * .apply(ContextualTextIO.readFiles()); + * }</pre> + * + * <p>Example 6: reading without recordNum metadata, or only fileName associated Metadata. (the + * Objects would still contain recordNums, but these recordNums would correspond to their positions + * in their respective offsets rather than their positions within the entire file). + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read() + * .from("/local/path/to/files/*.csv") + * .setWithoutRecordNumMetadata(true)); + * }</pre> + * + * <p>NOTE: When using {@link ContextualTextIO.Read#withHasMultilineCSVRecords(Boolean)} this + * option, a single reader will be used to process the file, rather than multiple readers which can + * read from different offsets. For a large file this can result in lower performance. + * + * <p>NOTE: Use {@link Read#withoutRecordNumMetadata()} when recordNum metadata is not required, for + * example, when when only filename metadata is required. Computing record positions currently + * introduces a shuffle step, which increases the resources used by the pipeline. <b> By default + * withoutRecordNumMetadata is set to false, so the shuffle step is performed.</b> + * + * <h3>Reading a very large number of files</h3> + * + * <p>If it is known that the filepattern will match a very large number of files (e.g. tens of + * thousands or more), use {@link ContextualTextIO.Read#withHintMatchesManyFiles} for better + * performance and scalability. Note that it may decrease performance if the filepattern matches + * only a small number of files. + */ +public class ContextualTextIO { + private static final long DEFAULT_BUNDLE_SIZE_BYTES = 64 * 1024 * 1024L; + private static final Logger LOG = LoggerFactory.getLogger(ContextualTextIO.class); + + /** + * A {@link PTransform} that reads from one or more text files and returns a bounded {@link + * PCollection} containing one {@link RecordWithMetadata}element for each line of the input files. + */ + public static Read read() { + return new AutoValue_ContextualTextIO_Read.Builder() + .setCompression(Compression.AUTO) + .setHintMatchesManyFiles(false) + .setWithoutRecordNumMetadata(false) + .setMatchConfiguration(MatchConfiguration.create(EmptyMatchTreatment.DISALLOW)) + .setHasMultilineCSVRecords(false) + .build(); + } + + /** + * Like {@link #read}, but reads each file in a {@link PCollection} of {@link + * FileIO.ReadableFile}, returned by {@link FileIO#readMatches}. + */ + public static ReadFiles readFiles() { + return new AutoValue_ContextualTextIO_ReadFiles.Builder() + // 64MB is a reasonable value that allows to amortize the cost of opening files, + // but is not so large as to exhaust a typical runner's maximum amount of output per + // ProcessElement call. + .setDesiredBundleSizeBytes(DEFAULT_BUNDLE_SIZE_BYTES) + .setHasMultilineCSVRecords(false) + .build(); + } + + /** Implementation of {@link #read}. */ + @AutoValue + public abstract static class Read extends PTransform<PBegin, PCollection<RecordWithMetadata>> { + abstract @Nullable ValueProvider<String> getFilepattern(); + + abstract MatchConfiguration getMatchConfiguration(); + + abstract boolean getHintMatchesManyFiles(); + + abstract boolean getWithoutRecordNumMetadata(); + + abstract Compression getCompression(); + + abstract @Nullable Boolean getHasMultilineCSVRecords(); + + @SuppressWarnings("mutable") // this returns an array that can be mutated by the caller + abstract byte @Nullable [] getDelimiter(); + + abstract Builder toBuilder(); + + @AutoValue.Builder + abstract static class Builder { + abstract Builder setFilepattern(ValueProvider<String> filepattern); + + abstract Builder setMatchConfiguration(MatchConfiguration matchConfiguration); + + abstract Builder setHintMatchesManyFiles(boolean hintManyFiles); + + abstract Builder setWithoutRecordNumMetadata(boolean withoutLineNumMetadata); + + abstract Builder setCompression(Compression compression); + + abstract Builder setDelimiter(byte @Nullable [] delimiter); + + abstract Builder setHasMultilineCSVRecords(Boolean hasMultilineCSVRecords); + + abstract Read build(); + } + + /** + * Reads text from the file(s) with the given filename or filename pattern. + * + * <p>This can be a local path (if running locally), or a Google Cloud Storage filename or + * filename pattern of the form {@code "gs://<bucket>/<filepath>"} (if running locally or using + * remote execution service). + * + * <p>Standard <a href="http://docs.oracle.com/javase/tutorial/essential/io/find.html"; >Java + * Filesystem glob patterns</a> ("*", "?", "[..]") are supported. + * + * <p>If it is known that the filepattern will match a very large number of files (at least tens + * of thousands), use {@link #withHintMatchesManyFiles} for better performance and scalability. + */ + public Read from(String filepattern) { + checkArgument(filepattern != null, "filepattern can not be null"); + return from(StaticValueProvider.of(filepattern)); + } + + /** Same as {@code from(filepattern)}, but accepting a {@link ValueProvider}. */ + public Read from(ValueProvider<String> filepattern) { + checkArgument(filepattern != null, "filepattern can not be null"); + return toBuilder().setFilepattern(filepattern).build(); + } + + /** Sets the {@link MatchConfiguration}. */ + public Read withMatchConfiguration(MatchConfiguration matchConfiguration) { + return toBuilder().setMatchConfiguration(matchConfiguration).build(); + } + + /** + * When reading RFC4180 CSV files that have values that span multiple lines, set this to true. + * Note: this reduces the read performance (see: {@link ContextualTextIO}). + */ + public Read withHasMultilineCSVRecords(Boolean hasMultilineCSVRecords) { + return toBuilder().setHasMultilineCSVRecords(hasMultilineCSVRecords).build(); + } + + /** + * Reads from input sources using the specified compression type. + * + * <p>If no compression type is specified, the default is {@link Compression#AUTO}. + */ + public Read withCompression(Compression compression) { + return toBuilder().setCompression(compression).build(); + } + + /** + * Hints that the filepattern specified in {@link #from(String)} matches a very large number of + * files. + * + * <p>This hint may cause a runner to execute the transform differently, in a way that improves + * performance for this case, but it may worsen performance if the filepattern matches only a + * small number of files (e.g., in a runner that supports dynamic work rebalancing, it will + * happen less efficiently within individual files). + */ + public Read withHintMatchesManyFiles() { + return toBuilder().setHintMatchesManyFiles(true).build(); + } + + /** + * Allows the user to opt out of getting recordNums associated with each record. + * + * <p>When set to true, it will introduce a shuffle step to assemble the recordNums for each + * record, which will increase the resources used by the pipeline. + * + * <p>Use this when metadata like fileNames are required and their position/order can be + * ignored. + */ + public Read withoutRecordNumMetadata() { + return toBuilder().setWithoutRecordNumMetadata(true).build(); + } + + /** See {@link MatchConfiguration#withEmptyMatchTreatment}. */ + public Read withEmptyMatchTreatment(EmptyMatchTreatment treatment) { + return withMatchConfiguration(getMatchConfiguration().withEmptyMatchTreatment(treatment)); + } + + /** Set the custom delimiter to be used in place of the default ones ('\r', '\n' or '\r\n'). */ + public Read withDelimiter(byte[] delimiter) { + checkArgument(delimiter != null, "delimiter can not be null"); + checkArgument(!isSelfOverlapping(delimiter), "delimiter must not self-overlap"); + return toBuilder().setDelimiter(delimiter).build(); + } + + static boolean isSelfOverlapping(byte[] s) { + // s self-overlaps if v exists such as s = vu = wv with u and w non empty + for (int i = 1; i < s.length - 1; ++i) { + if (ByteBuffer.wrap(s, 0, i).equals(ByteBuffer.wrap(s, s.length - i, i))) { + return true; + } + } + return false; + } + + @Override + public PCollection<RecordWithMetadata> expand(PBegin input) { + checkNotNull( + getFilepattern(), "need to set the filepattern of a ContextualTextIO.Read transform"); + PCollection<RecordWithMetadata> records = null; + if (getMatchConfiguration().getWatchInterval() == null && !getHintMatchesManyFiles()) { + records = input.apply("Read", org.apache.beam.sdk.io.Read.from(getSource())); + } else { + // All other cases go through FileIO + ReadFiles + records = + input + .apply( + "Create filepattern", Create.ofProvider(getFilepattern(), StringUtf8Coder.of())) + .apply("Match All", FileIO.matchAll().withConfiguration(getMatchConfiguration())) + .apply( + "Read Matches", + FileIO.readMatches() + .withCompression(getCompression()) + .withDirectoryTreatment(DirectoryTreatment.PROHIBIT)) + .apply("Via ReadFiles", readFiles().withDelimiter(getDelimiter())); + } + + // Check if the user decided to opt out of recordNums associated with records + if (getWithoutRecordNumMetadata()) { + return records; + } + + /* + * At this point the line number in RecordWithMetadata contains the relative line offset from the beginning of the read range. + * + * To compute the absolute position from the beginning of the input we group the lines within the same ranges, and evaluate the size of each range. + */ + + PCollection<KV<KV<String, Long>, RecordWithMetadata>> recordsGroupedByFileAndRange = + records.apply("AddFileNameAndRange", ParDo.of(new AddFileNameAndRange())); + + PCollectionView<Map<KV<String, Long>, Long>> rangeSizes = + recordsGroupedByFileAndRange + .apply("CountRecordsForEachFileRange", Count.perKey()) + .apply("SizesAsView", View.asMap()); + + // Get Pipeline to create a dummy PCollection with one element to help compute the lines + // before each Range + PCollection<Integer> singletonPcoll = + input.getPipeline().apply("CreateSingletonPcoll", Create.of(Arrays.asList(1))); + + /* + * For each (File, Offset) pair, calculate the number of lines occurring before the Range for each file + * + * After computing the number of lines before each range, we can find the line number in original file as numLiesBeforeOffset + lineNumInCurrentOffset + */ + + PCollectionView<Map<KV<String, Long>, Long>> numRecordsBeforeEachRange = + singletonPcoll + .apply( + "ComputeRecordsBeforeRange", + ParDo.of(new ComputeRecordsBeforeEachRange(rangeSizes)) + .withSideInputs(rangeSizes)) + .apply("NumRecordsBeforeEachRangeAsView", View.asMap()); + + return recordsGroupedByFileAndRange.apply( + "AssignLineNums", + ParDo.of(new AssignRecordNums(numRecordsBeforeEachRange)) + .withSideInputs(numRecordsBeforeEachRange)); + } + + @VisibleForTesting + static class AddFileNameAndRange + extends DoFn<RecordWithMetadata, KV<KV<String, Long>, RecordWithMetadata>> { + @ProcessElement + public void processElement( + @Element RecordWithMetadata record, + OutputReceiver<KV<KV<String, Long>, RecordWithMetadata>> out) { + out.output(KV.of(KV.of(record.getFileName().toString(), record.getRangeOffset()), record)); + } + } + + /** + * Helper class for computing number of record in the File preceding the beginning of the Range + * in this file. + */ + @VisibleForTesting + static class ComputeRecordsBeforeEachRange extends DoFn<Integer, KV<KV<String, Long>, Long>> { + private final PCollectionView<Map<KV<String, Long>, Long>> rangeSizes; + + public ComputeRecordsBeforeEachRange( + PCollectionView<Map<KV<String, Long>, Long>> rangeSizes) { + this.rangeSizes = rangeSizes; + } + + // Add custom comparator as KV<K, V> is not comparable by default + private static class FileRangeComparator<K extends Comparable<K>, V extends Comparable<V>> + implements Comparator<KV<K, V>> { + @Override + public int compare(KV<K, V> a, KV<K, V> b) { + if (a.getKey().compareTo(b.getKey()) == 0) { + return a.getValue().compareTo(b.getValue()); + } + return a.getKey().compareTo(b.getKey()); + } + } + + @ProcessElement + public void processElement(ProcessContext p) { + // Get the Map Containing the size from side-input + Map<KV<String, Long>, Long> rangeSizesMap = p.sideInput(rangeSizes); + + // The FileRange Pair must be sorted + SortedMap<KV<String, Long>, Long> sorted = new TreeMap<>(new FileRangeComparator<>()); + + // Initialize sorted map with values + for (Map.Entry<KV<String, Long>, Long> entry : rangeSizesMap.entrySet()) { + sorted.put(entry.getKey(), entry.getValue()); + } + + // HashMap that tracks number of records passed for each file + Map<String, Long> pastRecords = new HashMap<>(); + + // For each (File, Range) Pair, compute the number of records before it + for (Map.Entry entry : sorted.entrySet()) { Review comment: Done ########## File path: sdks/java/io/contextual-text-io/src/main/java/org/apache/beam/sdk/io/contextualtextio/ContextualTextIO.java ########## @@ -0,0 +1,631 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.contextualtextio; + +import static org.apache.beam.sdk.io.FileIO.ReadMatches.DirectoryTreatment; +import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkArgument; +import static org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkNotNull; + +import com.google.auto.value.AutoValue; +import java.nio.ByteBuffer; +import java.util.Arrays; +import java.util.Comparator; +import java.util.HashMap; +import java.util.Map; +import java.util.SortedMap; +import java.util.TreeMap; +import org.apache.beam.sdk.coders.StringUtf8Coder; +import org.apache.beam.sdk.io.CompressedSource; +import org.apache.beam.sdk.io.Compression; +import org.apache.beam.sdk.io.FileBasedSource; +import org.apache.beam.sdk.io.FileIO; +import org.apache.beam.sdk.io.FileIO.MatchConfiguration; +import org.apache.beam.sdk.io.ReadAllViaFileBasedSource; +import org.apache.beam.sdk.io.TextIO; +import org.apache.beam.sdk.io.fs.EmptyMatchTreatment; +import org.apache.beam.sdk.options.ValueProvider; +import org.apache.beam.sdk.options.ValueProvider.StaticValueProvider; +import org.apache.beam.sdk.schemas.NoSuchSchemaException; +import org.apache.beam.sdk.schemas.SchemaCoder; +import org.apache.beam.sdk.transforms.Count; +import org.apache.beam.sdk.transforms.Create; +import org.apache.beam.sdk.transforms.DoFn; +import org.apache.beam.sdk.transforms.PTransform; +import org.apache.beam.sdk.transforms.ParDo; +import org.apache.beam.sdk.transforms.SerializableFunction; +import org.apache.beam.sdk.transforms.View; +import org.apache.beam.sdk.transforms.Watch.Growth.TerminationCondition; +import org.apache.beam.sdk.transforms.display.DisplayData; +import org.apache.beam.sdk.values.KV; +import org.apache.beam.sdk.values.PBegin; +import org.apache.beam.sdk.values.PCollection; +import org.apache.beam.sdk.values.PCollectionView; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.annotations.VisibleForTesting; +import org.checkerframework.checker.nullness.qual.Nullable; +import org.joda.time.Duration; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * {@link PTransform}s that read text files and collect contextual information of the elements in + * the input. + * + * <p>Use {@link TextIO} when not reading file with Multiline Records or additional metadata is not + * required. + * + * <h2>Reading from text files</h2> + * + * <p>To read a {@link PCollection} from one or more text files, use {@code + * ContextualTextIO.read()}. To instantiate a transform use {@link + * ContextualTextIO.Read#from(String)} and specify the path of the file(s) to be read. + * Alternatively, if the filenames to be read are themselves in a {@link PCollection} you can use + * {@link FileIO} to match them and {@link ContextualTextIO#readFiles()} to read them. + * + * <p>{@link #read} returns a {@link PCollection} of {@link RecordWithMetadata RecordWithMetadata}, + * each corresponding to one line of an input UTF-8 text file (split into lines delimited by '\n', + * '\r', '\r\n', or specified delimiter see {@link ContextualTextIO.Read#withDelimiter}) + * + * <h3>Filepattern expansion and watching</h3> + * + * <p>By default, the filepatterns are expanded only once. The combination of {@link + * FileIO.Match#continuously(Duration, TerminationCondition)} and {@link #readFiles()} allow + * streaming of new files matching the filepattern(s). + * + * <p>By default, {@link #read} prohibits filepatterns that match no files, and {@link #readFiles()} + * allows them in case the filepattern contains a glob wildcard character. Use {@link + * ContextualTextIO.Read#withEmptyMatchTreatment} or {@link + * FileIO.Match#withEmptyMatchTreatment(EmptyMatchTreatment)} plus {@link #readFiles()} to configure + * this behavior. + * + * <p>Example 1: reading a file or filepattern. + * + * <pre>{@code + * Pipeline p = ...; + * + * // A simple Read of a file: + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read().from("/local/path/to/file.txt")); + * }</pre> + * + * <p>Example 2: reading a PCollection of filenames. + * + * <pre>{@code + * Pipeline p = ...; + * + * // E.g. the filenames might be computed from other data in the pipeline, or + * // read from a data source. + * PCollection<String> filenames = ...; + * + * // Read all files in the collection. + * PCollection<RecordWithMetadata> records = + * filenames + * .apply(FileIO.matchAll()) + * .apply(FileIO.readMatches()) + * .apply(ContextualTextIO.readFiles()); + * }</pre> + * + * <p>Example 3: streaming new files matching a filepattern. + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read() + * .from("/local/path/to/files/*") + * .watchForNewFiles( + * // Check for new files every minute + * Duration.standardMinutes(1), + * // Stop watching the filepattern if no new files appear within an hour + * afterTimeSinceNewOutput(Duration.standardHours(1)))); + * }</pre> + * + * <p>Example 4: reading a file or file pattern of RFC4180-compliant CSV files with fields that may + * contain line breaks. + * + * Example of such a file could be: + * + * "aaa","b CRLF + * bb","ccc" CRLF + * zzz,yyy,xxx + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read() + * .from("/local/path/to/files/*.csv") + * .withHasMultilineCSVRecords(true)); + * }</pre> + * + * <p>Example 5: reading while watching for new files + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(FileIO.match() + * .filepattern("filepattern") + * .continuously( + * Duration.millis(100), + * Watch.Growth.afterTimeSinceNewOutput(Duration.standardSeconds(3)))) + * .apply(FileIO.readMatches()) + * .apply(ContextualTextIO.readFiles()); + * }</pre> + * + * <p>Example 6: reading without recordNum metadata, or only fileName associated Metadata. (the + * Objects would still contain recordNums, but these recordNums would correspond to their positions + * in their respective offsets rather than their positions within the entire file). + * + * <pre>{@code + * Pipeline p = ...; + * + * PCollection<RecordWithMetadata> records = p.apply(ContextualTextIO.read() + * .from("/local/path/to/files/*.csv") + * .setWithoutRecordNumMetadata(true)); + * }</pre> + * + * <p>NOTE: When using {@link ContextualTextIO.Read#withHasMultilineCSVRecords(Boolean)} this + * option, a single reader will be used to process the file, rather than multiple readers which can + * read from different offsets. For a large file this can result in lower performance. + * + * <p>NOTE: Use {@link Read#withoutRecordNumMetadata()} when recordNum metadata is not required, for + * example, when when only filename metadata is required. Computing record positions currently + * introduces a shuffle step, which increases the resources used by the pipeline. <b> By default + * withoutRecordNumMetadata is set to false, so the shuffle step is performed.</b> + * + * <h3>Reading a very large number of files</h3> + * + * <p>If it is known that the filepattern will match a very large number of files (e.g. tens of + * thousands or more), use {@link ContextualTextIO.Read#withHintMatchesManyFiles} for better + * performance and scalability. Note that it may decrease performance if the filepattern matches + * only a small number of files. + */ +public class ContextualTextIO { + private static final long DEFAULT_BUNDLE_SIZE_BYTES = 64 * 1024 * 1024L; + private static final Logger LOG = LoggerFactory.getLogger(ContextualTextIO.class); + + /** + * A {@link PTransform} that reads from one or more text files and returns a bounded {@link + * PCollection} containing one {@link RecordWithMetadata}element for each line of the input files. + */ + public static Read read() { + return new AutoValue_ContextualTextIO_Read.Builder() + .setCompression(Compression.AUTO) + .setHintMatchesManyFiles(false) + .setWithoutRecordNumMetadata(false) + .setMatchConfiguration(MatchConfiguration.create(EmptyMatchTreatment.DISALLOW)) + .setHasMultilineCSVRecords(false) + .build(); + } + + /** + * Like {@link #read}, but reads each file in a {@link PCollection} of {@link + * FileIO.ReadableFile}, returned by {@link FileIO#readMatches}. + */ + public static ReadFiles readFiles() { + return new AutoValue_ContextualTextIO_ReadFiles.Builder() + // 64MB is a reasonable value that allows to amortize the cost of opening files, + // but is not so large as to exhaust a typical runner's maximum amount of output per + // ProcessElement call. + .setDesiredBundleSizeBytes(DEFAULT_BUNDLE_SIZE_BYTES) + .setHasMultilineCSVRecords(false) + .build(); + } + + /** Implementation of {@link #read}. */ + @AutoValue + public abstract static class Read extends PTransform<PBegin, PCollection<RecordWithMetadata>> { + abstract @Nullable ValueProvider<String> getFilepattern(); + + abstract MatchConfiguration getMatchConfiguration(); + + abstract boolean getHintMatchesManyFiles(); + + abstract boolean getWithoutRecordNumMetadata(); + + abstract Compression getCompression(); + + abstract @Nullable Boolean getHasMultilineCSVRecords(); + + @SuppressWarnings("mutable") // this returns an array that can be mutated by the caller + abstract byte @Nullable [] getDelimiter(); + + abstract Builder toBuilder(); + + @AutoValue.Builder + abstract static class Builder { + abstract Builder setFilepattern(ValueProvider<String> filepattern); + + abstract Builder setMatchConfiguration(MatchConfiguration matchConfiguration); + + abstract Builder setHintMatchesManyFiles(boolean hintManyFiles); + + abstract Builder setWithoutRecordNumMetadata(boolean withoutLineNumMetadata); + + abstract Builder setCompression(Compression compression); + + abstract Builder setDelimiter(byte @Nullable [] delimiter); + + abstract Builder setHasMultilineCSVRecords(Boolean hasMultilineCSVRecords); + + abstract Read build(); + } + + /** + * Reads text from the file(s) with the given filename or filename pattern. + * + * <p>This can be a local path (if running locally), or a Google Cloud Storage filename or + * filename pattern of the form {@code "gs://<bucket>/<filepath>"} (if running locally or using + * remote execution service). + * + * <p>Standard <a href="http://docs.oracle.com/javase/tutorial/essential/io/find.html"; >Java + * Filesystem glob patterns</a> ("*", "?", "[..]") are supported. + * + * <p>If it is known that the filepattern will match a very large number of files (at least tens + * of thousands), use {@link #withHintMatchesManyFiles} for better performance and scalability. + */ + public Read from(String filepattern) { + checkArgument(filepattern != null, "filepattern can not be null"); + return from(StaticValueProvider.of(filepattern)); + } + + /** Same as {@code from(filepattern)}, but accepting a {@link ValueProvider}. */ + public Read from(ValueProvider<String> filepattern) { + checkArgument(filepattern != null, "filepattern can not be null"); + return toBuilder().setFilepattern(filepattern).build(); + } + + /** Sets the {@link MatchConfiguration}. */ + public Read withMatchConfiguration(MatchConfiguration matchConfiguration) { + return toBuilder().setMatchConfiguration(matchConfiguration).build(); + } + + /** + * When reading RFC4180 CSV files that have values that span multiple lines, set this to true. + * Note: this reduces the read performance (see: {@link ContextualTextIO}). + */ + public Read withHasMultilineCSVRecords(Boolean hasMultilineCSVRecords) { + return toBuilder().setHasMultilineCSVRecords(hasMultilineCSVRecords).build(); + } + + /** + * Reads from input sources using the specified compression type. + * + * <p>If no compression type is specified, the default is {@link Compression#AUTO}. + */ + public Read withCompression(Compression compression) { + return toBuilder().setCompression(compression).build(); + } + + /** + * Hints that the filepattern specified in {@link #from(String)} matches a very large number of + * files. + * + * <p>This hint may cause a runner to execute the transform differently, in a way that improves + * performance for this case, but it may worsen performance if the filepattern matches only a + * small number of files (e.g., in a runner that supports dynamic work rebalancing, it will + * happen less efficiently within individual files). + */ + public Read withHintMatchesManyFiles() { + return toBuilder().setHintMatchesManyFiles(true).build(); + } + + /** + * Allows the user to opt out of getting recordNums associated with each record. + * + * <p>When set to true, it will introduce a shuffle step to assemble the recordNums for each + * record, which will increase the resources used by the pipeline. + * + * <p>Use this when metadata like fileNames are required and their position/order can be + * ignored. + */ + public Read withoutRecordNumMetadata() { + return toBuilder().setWithoutRecordNumMetadata(true).build(); + } + + /** See {@link MatchConfiguration#withEmptyMatchTreatment}. */ + public Read withEmptyMatchTreatment(EmptyMatchTreatment treatment) { + return withMatchConfiguration(getMatchConfiguration().withEmptyMatchTreatment(treatment)); + } + + /** Set the custom delimiter to be used in place of the default ones ('\r', '\n' or '\r\n'). */ + public Read withDelimiter(byte[] delimiter) { + checkArgument(delimiter != null, "delimiter can not be null"); + checkArgument(!isSelfOverlapping(delimiter), "delimiter must not self-overlap"); + return toBuilder().setDelimiter(delimiter).build(); + } + + static boolean isSelfOverlapping(byte[] s) { + // s self-overlaps if v exists such as s = vu = wv with u and w non empty + for (int i = 1; i < s.length - 1; ++i) { + if (ByteBuffer.wrap(s, 0, i).equals(ByteBuffer.wrap(s, s.length - i, i))) { + return true; + } + } + return false; + } + + @Override + public PCollection<RecordWithMetadata> expand(PBegin input) { + checkNotNull( + getFilepattern(), "need to set the filepattern of a ContextualTextIO.Read transform"); + PCollection<RecordWithMetadata> records = null; + if (getMatchConfiguration().getWatchInterval() == null && !getHintMatchesManyFiles()) { + records = input.apply("Read", org.apache.beam.sdk.io.Read.from(getSource())); + } else { + // All other cases go through FileIO + ReadFiles + records = + input + .apply( + "Create filepattern", Create.ofProvider(getFilepattern(), StringUtf8Coder.of())) + .apply("Match All", FileIO.matchAll().withConfiguration(getMatchConfiguration())) + .apply( + "Read Matches", + FileIO.readMatches() + .withCompression(getCompression()) + .withDirectoryTreatment(DirectoryTreatment.PROHIBIT)) + .apply("Via ReadFiles", readFiles().withDelimiter(getDelimiter())); + } + + // Check if the user decided to opt out of recordNums associated with records + if (getWithoutRecordNumMetadata()) { + return records; + } + + /* + * At this point the line number in RecordWithMetadata contains the relative line offset from the beginning of the read range. + * + * To compute the absolute position from the beginning of the input we group the lines within the same ranges, and evaluate the size of each range. + */ + + PCollection<KV<KV<String, Long>, RecordWithMetadata>> recordsGroupedByFileAndRange = + records.apply("AddFileNameAndRange", ParDo.of(new AddFileNameAndRange())); + + PCollectionView<Map<KV<String, Long>, Long>> rangeSizes = + recordsGroupedByFileAndRange + .apply("CountRecordsForEachFileRange", Count.perKey()) + .apply("SizesAsView", View.asMap()); + + // Get Pipeline to create a dummy PCollection with one element to help compute the lines + // before each Range + PCollection<Integer> singletonPcoll = + input.getPipeline().apply("CreateSingletonPcoll", Create.of(Arrays.asList(1))); + + /* + * For each (File, Offset) pair, calculate the number of lines occurring before the Range for each file + * + * After computing the number of lines before each range, we can find the line number in original file as numLiesBeforeOffset + lineNumInCurrentOffset + */ + + PCollectionView<Map<KV<String, Long>, Long>> numRecordsBeforeEachRange = + singletonPcoll + .apply( + "ComputeRecordsBeforeRange", + ParDo.of(new ComputeRecordsBeforeEachRange(rangeSizes)) + .withSideInputs(rangeSizes)) + .apply("NumRecordsBeforeEachRangeAsView", View.asMap()); + + return recordsGroupedByFileAndRange.apply( + "AssignLineNums", + ParDo.of(new AssignRecordNums(numRecordsBeforeEachRange)) + .withSideInputs(numRecordsBeforeEachRange)); + } + + @VisibleForTesting + static class AddFileNameAndRange + extends DoFn<RecordWithMetadata, KV<KV<String, Long>, RecordWithMetadata>> { + @ProcessElement + public void processElement( + @Element RecordWithMetadata record, + OutputReceiver<KV<KV<String, Long>, RecordWithMetadata>> out) { + out.output(KV.of(KV.of(record.getFileName().toString(), record.getRangeOffset()), record)); + } + } + + /** + * Helper class for computing number of record in the File preceding the beginning of the Range + * in this file. + */ + @VisibleForTesting + static class ComputeRecordsBeforeEachRange extends DoFn<Integer, KV<KV<String, Long>, Long>> { + private final PCollectionView<Map<KV<String, Long>, Long>> rangeSizes; + + public ComputeRecordsBeforeEachRange( + PCollectionView<Map<KV<String, Long>, Long>> rangeSizes) { + this.rangeSizes = rangeSizes; + } + + // Add custom comparator as KV<K, V> is not comparable by default + private static class FileRangeComparator<K extends Comparable<K>, V extends Comparable<V>> + implements Comparator<KV<K, V>> { + @Override + public int compare(KV<K, V> a, KV<K, V> b) { + if (a.getKey().compareTo(b.getKey()) == 0) { + return a.getValue().compareTo(b.getValue()); + } + return a.getKey().compareTo(b.getKey()); + } + } + + @ProcessElement + public void processElement(ProcessContext p) { + // Get the Map Containing the size from side-input + Map<KV<String, Long>, Long> rangeSizesMap = p.sideInput(rangeSizes); + + // The FileRange Pair must be sorted + SortedMap<KV<String, Long>, Long> sorted = new TreeMap<>(new FileRangeComparator<>()); + + // Initialize sorted map with values + for (Map.Entry<KV<String, Long>, Long> entry : rangeSizesMap.entrySet()) { + sorted.put(entry.getKey(), entry.getValue()); + } + + // HashMap that tracks number of records passed for each file + Map<String, Long> pastRecords = new HashMap<>(); + + // For each (File, Range) Pair, compute the number of records before it + for (Map.Entry entry : sorted.entrySet()) { + Long numRecords = (long) entry.getValue(); + KV<String, Long> fileRange = (KV<String, Long>) entry.getKey(); + String file = fileRange.getKey(); + Long numRecordsBefore = 0L; + if (pastRecords.containsKey(file)) { + numRecordsBefore = pastRecords.get(file); + } + p.output(KV.of(fileRange, numRecordsBefore)); + pastRecords.put(file, numRecordsBefore + numRecords); + } + } + } + + static class AssignRecordNums + extends DoFn<KV<KV<String, Long>, RecordWithMetadata>, RecordWithMetadata> { + PCollectionView<Map<KV<String, Long>, Long>> numRecordsBeforeEachRange; + + public AssignRecordNums( + PCollectionView<Map<KV<String, Long>, Long>> numRecordsBeforeEachRange) { + this.numRecordsBeforeEachRange = numRecordsBeforeEachRange; + } + + @ProcessElement + public void processElement(ProcessContext p) { + Long range = p.element().getKey().getValue(); + String file = p.element().getKey().getKey(); + RecordWithMetadata record = p.element().getValue(); + Long numRecordsLessThanThisRange = + p.sideInput(numRecordsBeforeEachRange).get(KV.of(file, range)); + RecordWithMetadata newLine = + RecordWithMetadata.newBuilder() Review comment: Thanks ! Done. ########## File path: sdks/java/io/contextual-text-io/src/main/java/org/apache/beam/sdk/io/contextualtextio/RecordWithMetadata.java ########## @@ -0,0 +1,84 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.contextualtextio; + +import com.google.auto.value.AutoValue; +import org.apache.beam.sdk.annotations.Experimental; +import org.apache.beam.sdk.schemas.AutoValueSchema; +import org.apache.beam.sdk.schemas.annotations.DefaultSchema; + +/** + * Helper Class based on {@link AutoValueSchema}, it provides Metadata associated with each Record + * when reading from file(s) using {@link ContextualTextIO}. + * + * <h3>Fields:</h3> + * + * <ul> + * <li>recordOffset: The offset of a record (the byte at which the record begins) in a file. This + * information can be useful if you wish to reconstruct the file. {@link + * RecordWithMetadata#getRecordOffset()} + * <li>recordNum: The ordinal number of the record in its file. {@link + * RecordWithMetadata#getRecordNum()} + * <li>recordValue: The value / contents of the record {@link RecordWithMetadata#getRecordValue()} + * <li>rangeOffset: The starting offset of the range (split), which contained the record, when the + * record was read. {@link RecordWithMetadata#getRangeOffset()} + * <li>recordNumInOffset: The record number relative to the Range. (line number within the range) + * {@link RecordWithMetadata#getRecordNumInOffset()} + * <li>fileName: Name of the file to which the record belongs (this is the full filename, + * eg:path/to/file.txt) {@link RecordWithMetadata#getFileName()} + * </ul> + */ +@Experimental(Experimental.Kind.SCHEMAS) +@DefaultSchema(AutoValueSchema.class) +@AutoValue +public abstract class RecordWithMetadata { + public abstract Long getRecordOffset(); Review comment: Done ########## File path: sdks/java/io/contextual-text-io/build.gradle ########## @@ -0,0 +1,41 @@ +/* + * 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. + */ + +plugins { id 'org.apache.beam.module' } +applyJavaNature( + automaticModuleName: 'org.apache.beam.sdk.io.contextual-text-io', + enableChecker: false, + ignoreRawtypeErrors: true) + +description = "Apache Beam :: SDKs :: Java :: Contextual-Text-IO" +ext.summary = "Context-aware Text IO." + +dependencies { + + compile library.java.vendored_guava_26_0_jre + compile library.java.protobuf_java + compile project(path: ":sdks:java:core", configuration: "shadow") + testCompile project(path: ":sdks:java:core", configuration: "shadowTest") + + testCompile library.java.guava_testlib + testCompile library.java.junit + testCompile library.java.hamcrest_core + testRuntimeOnly library.java.slf4j_jdk14 + testCompile project(path: ":runners:direct-java", configuration: "shadow") + +} Review comment: Done ########## File path: sdks/java/io/contextual-text-io/build.gradle ########## @@ -0,0 +1,41 @@ +/* + * 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. + */ + +plugins { id 'org.apache.beam.module' } +applyJavaNature( + automaticModuleName: 'org.apache.beam.sdk.io.contextual-text-io', + enableChecker: false, + ignoreRawtypeErrors: true) + +description = "Apache Beam :: SDKs :: Java :: Contextual-Text-IO" +ext.summary = "Context-aware Text IO." + +dependencies { + Review comment: Done ########## File path: sdks/java/io/contextual-text-io/src/main/java/org/apache/beam/sdk/io/contextualtextio/RecordWithMetadata.java ########## @@ -0,0 +1,85 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.contextualtextio; + +import com.google.auto.value.AutoValue; +import org.apache.beam.sdk.annotations.Experimental; +import org.apache.beam.sdk.io.fs.ResourceId; +import org.apache.beam.sdk.schemas.AutoValueSchema; +import org.apache.beam.sdk.schemas.annotations.DefaultSchema; + +/** + * Helper Class based on {@link AutoValueSchema}, it provides Metadata associated with each Record + * when reading from file(s) using {@link ContextualTextIO}. + * + * <h3>Fields:</h3> + * + * <ul> + * <li>recordOffset: The offset of a record (the byte at which the record begins) in a file. This + * information can be useful if you wish to reconstruct the file. {@link + * RecordWithMetadata#getRecordOffset()} + * <li>recordNum: The ordinal number of the record in its file. {@link + * RecordWithMetadata#getRecordNum()} + * <li>recordValue: The value / contents of the record {@link RecordWithMetadata#getValue()} + * <li>rangeOffset: The starting offset of the range (split), which contained the record, when the + * record was read. {@link RecordWithMetadata#getRangeOffset()} + * <li>recordNumInOffset: The record number relative to the Range. (line number within the range) + * {@link RecordWithMetadata#getRecordNumInOffset()} + * <li>fileName: Name of the file to which the record belongs (this is the full filename, + * eg:path/to/file.txt) {@link RecordWithMetadata#getFileName()} + * </ul> + */ +@Experimental(Experimental.Kind.SCHEMAS) +@DefaultSchema(AutoValueSchema.class) +@AutoValue +public abstract class RecordWithMetadata { + public abstract long getRecordOffset(); Review comment: Done ########## File path: sdks/java/io/contextual-text-io/src/main/java/org/apache/beam/sdk/io/contextualtextio/ContextualTextIOSource.java ########## @@ -0,0 +1,364 @@ +/* + * 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. + */ +package org.apache.beam.sdk.io.contextualtextio; + +import java.io.IOException; +import java.nio.ByteBuffer; +import java.nio.channels.ReadableByteChannel; +import java.nio.channels.SeekableByteChannel; +import java.util.NoSuchElementException; +import org.apache.beam.sdk.coders.Coder; +import org.apache.beam.sdk.io.FileBasedSource; +import org.apache.beam.sdk.io.fs.EmptyMatchTreatment; +import org.apache.beam.sdk.io.fs.MatchResult; +import org.apache.beam.sdk.options.PipelineOptions; +import org.apache.beam.sdk.options.ValueProvider; +import org.apache.beam.sdk.schemas.NoSuchSchemaException; +import org.apache.beam.sdk.schemas.SchemaCoder; +import org.apache.beam.sdk.schemas.SchemaRegistry; +import org.apache.beam.vendor.grpc.v1p26p0.com.google.protobuf.ByteString; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.annotations.VisibleForTesting; +import org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions; +import org.checkerframework.checker.nullness.qual.Nullable; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * Implementation detail of {@link ContextualTextIO.Read}. + * + * <p>A {@link FileBasedSource} which can decode records delimited by newline characters. + * + * <p>This source splits the data into records using {@code UTF-8} {@code \n}, {@code \r}, or {@code + * \r\n} as the delimiter. This source is not strict and supports decoding the last record even if + * it is not delimited. Finally, no records are decoded if the stream is empty. + * + * <p>This source supports reading from any arbitrary byte position within the stream. If the + * starting position is not {@code 0}, then bytes are skipped until the first delimiter is found + * representing the beginning of the first record to be decoded. + */ +@VisibleForTesting +class ContextualTextIOSource extends FileBasedSource<RecordWithMetadata> { + byte[] delimiter; + + private static final Logger LOG = LoggerFactory.getLogger(ContextualTextIOSource.class); + + // Used to Override isSplittable + private boolean hasMultilineCSVRecords; + + @Override + protected boolean isSplittable() throws Exception { + if (hasMultilineCSVRecords) { + // When Having Multiline CSV Records, + // Splitting the file may cause a split to be within a record, + // Disabling split prevents this from happening + return false; + } + return super.isSplittable(); + } + + ContextualTextIOSource( + ValueProvider<String> fileSpec, + EmptyMatchTreatment emptyMatchTreatment, + byte[] delimiter, + boolean hasMultilineCSVRecords) { + super(fileSpec, emptyMatchTreatment, 1L); + this.delimiter = delimiter; + this.hasMultilineCSVRecords = hasMultilineCSVRecords; + } + + private ContextualTextIOSource( + MatchResult.Metadata metadata, + long start, + long end, + byte[] delimiter, + boolean hasMultilineCSVRecords) { + super(metadata, 1L, start, end); + this.delimiter = delimiter; + this.hasMultilineCSVRecords = hasMultilineCSVRecords; + } + + @Override + protected FileBasedSource<RecordWithMetadata> createForSubrangeOfFile( + MatchResult.Metadata metadata, long start, long end) { + return new ContextualTextIOSource(metadata, start, end, delimiter, hasMultilineCSVRecords); + } + + @Override + protected FileBasedReader<RecordWithMetadata> createSingleFileReader(PipelineOptions options) { + return new MultiLineTextBasedReader(this, delimiter, hasMultilineCSVRecords); + } + + @Override + public Coder<RecordWithMetadata> getOutputCoder() { Review comment: Done ---------------------------------------------------------------- This is an automated message from the Apache Git Service. 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