rdsr commented on a change in pull request #843: [WIP] InputFormat support for Iceberg URL: https://github.com/apache/incubator-iceberg/pull/843#discussion_r395389858
########## File path: mr/src/main/java/org/apache/iceberg/mr/IcebergInputFormat.java ########## @@ -0,0 +1,494 @@ +/* + * 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.iceberg.mr; + +import com.google.common.collect.Iterators; +import com.google.common.collect.Lists; +import com.google.common.collect.Sets; +import java.io.Closeable; +import java.io.DataInput; +import java.io.DataOutput; +import java.io.IOException; +import java.util.Arrays; +import java.util.Iterator; +import java.util.List; +import java.util.Set; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.BlockLocation; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.Writable; +import org.apache.hadoop.mapreduce.InputFormat; +import org.apache.hadoop.mapreduce.InputSplit; +import org.apache.hadoop.mapreduce.Job; +import org.apache.hadoop.mapreduce.JobContext; +import org.apache.hadoop.mapreduce.RecordReader; +import org.apache.hadoop.mapreduce.TaskAttemptContext; +import org.apache.iceberg.CombinedScanTask; +import org.apache.iceberg.DataFile; +import org.apache.iceberg.FileScanTask; +import org.apache.iceberg.PartitionField; +import org.apache.iceberg.PartitionSpec; +import org.apache.iceberg.Schema; +import org.apache.iceberg.SchemaParser; +import org.apache.iceberg.StructLike; +import org.apache.iceberg.Table; +import org.apache.iceberg.TableProperties; +import org.apache.iceberg.TableScan; +import org.apache.iceberg.avro.Avro; +import org.apache.iceberg.catalog.Catalog; +import org.apache.iceberg.catalog.TableIdentifier; +import org.apache.iceberg.data.GenericRecord; +import org.apache.iceberg.data.Record; +import org.apache.iceberg.data.avro.DataReader; +import org.apache.iceberg.data.parquet.GenericParquetReaders; +import org.apache.iceberg.exceptions.RuntimeIOException; +import org.apache.iceberg.expressions.Expression; +import org.apache.iceberg.hadoop.HadoopInputFile; +import org.apache.iceberg.hadoop.HadoopTables; +import org.apache.iceberg.hive.HiveCatalogs; +import org.apache.iceberg.io.CloseableIterable; +import org.apache.iceberg.io.InputFile; +import org.apache.iceberg.orc.ORC; +import org.apache.iceberg.parquet.Parquet; +import org.apache.iceberg.types.TypeUtil; +import org.apache.iceberg.types.Types; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + + +public class IcebergInputFormat<T> extends InputFormat<Void, T> { + private static final Logger LOG = LoggerFactory.getLogger(IcebergInputFormat.class); + + static final String AS_OF_TIMESTAMP = "iceberg.mr.as.of.time"; + static final String CASE_SENSITIVE = "iceberg.mr.case.sensitive"; + static final String FILTER_EXPRESSION = "iceberg.mr.filter.expression"; + static final String IN_MEMORY_DATA_MODEL = "iceberg.mr.in.memory.data.model"; + static final String READ_SCHEMA = "iceberg.mr.read.schema"; + static final String REUSE_CONTAINERS = "iceberg.mr.case.sensitive"; + static final String SNAPSHOT_ID = "iceberg.mr.snapshot.id"; + static final String SPLIT_SIZE = "iceberg.mr.split.size"; + static final String TABLE_PATH = "iceberg.mr.table.path"; + static final String TABLE_SCHEMA = "iceberg.mr.table.schema"; + private static final String LOCALITY = "iceberg.mr.locality"; + + private transient List<InputSplit> splits; + + public enum InMemoryDataModel { + PIG, + HIVE, + DEFAULT // Default data model is of Iceberg Generics + } + + /** + * Configures the {@code Job} to use the {@code IcebergInputFormat} and + * returns a helper to add further configuration. + * + * @param job the {@code Job} to configure + */ + public static ConfigBuilder configure(Job job) { + job.setInputFormatClass(IcebergInputFormat.class); + return new ConfigBuilder(job.getConfiguration()); + } + + public static class ConfigBuilder { + private final Configuration conf; + + public ConfigBuilder(Configuration conf) { + this.conf = conf; + } + + public ConfigBuilder readFrom(String path) { + conf.set(TABLE_PATH, path); + Table table = getTable(conf); + conf.set(TABLE_SCHEMA, SchemaParser.toJson(table.schema())); + return this; + } + + public ConfigBuilder filter(Expression expression) { + conf.set(FILTER_EXPRESSION, SerializationUtil.serializeToBase64(expression)); + return this; + } + + public ConfigBuilder project(Schema schema) { + conf.set(READ_SCHEMA, SchemaParser.toJson(schema)); + return this; + } + + public ConfigBuilder reuseContainers(boolean reuse) { + conf.setBoolean(REUSE_CONTAINERS, reuse); + return this; + } + + public ConfigBuilder caseSensitive(boolean caseSensitive) { + conf.setBoolean(CASE_SENSITIVE, caseSensitive); + return this; + } + + public ConfigBuilder snapshotId(long snapshotId) { + conf.setLong(SNAPSHOT_ID, snapshotId); + return this; + } + + public ConfigBuilder asOfTime(long asOfTime) { + conf.setLong(AS_OF_TIMESTAMP, asOfTime); + return this; + } + + public ConfigBuilder splitSize(long splitSize) { + conf.setLong(SPLIT_SIZE, splitSize); + return this; + } + + public ConfigBuilder locality(boolean localityPreferred) { + conf.setBoolean(LOCALITY, localityPreferred); + return this; + } + + public ConfigBuilder inMemoryDataModel(InMemoryDataModel inMemoryDataModel) { + conf.set(IN_MEMORY_DATA_MODEL, inMemoryDataModel.name()); + return this; + } + } + + @Override + public List<InputSplit> getSplits(JobContext context) { + if (splits != null) { + LOG.info("Returning cached splits: {}", splits.size()); + return splits; + } + + Configuration conf = context.getConfiguration(); + Table table = getTable(conf); + TableScan scan = table.newScan() + .caseSensitive(conf.getBoolean(CASE_SENSITIVE, true)); + long snapshotId = conf.getLong(SNAPSHOT_ID, -1); + if (snapshotId != -1) { + scan = scan.useSnapshot(snapshotId); + } + long asOfTime = conf.getLong(AS_OF_TIMESTAMP, -1); + if (asOfTime != -1) { + scan = scan.asOfTime(asOfTime); + } + long splitSize = conf.getLong(SPLIT_SIZE, -1); + if (splitSize != -1) { + scan = scan.option(TableProperties.SPLIT_SIZE, String.valueOf(splitSize)); + } + String schemaStr = conf.get(READ_SCHEMA); + if (schemaStr != null) { + scan.project(SchemaParser.fromJson(schemaStr)); + } + + // TODO add a filter parser to get rid of Serialization + Expression filterExpression = SerializationUtil.deserializeFromBase64(conf.get(FILTER_EXPRESSION)); + if (filterExpression != null) { + scan = scan.filter(filterExpression); + } + + splits = Lists.newArrayList(); + try (CloseableIterable<CombinedScanTask> tasksIterable = scan.planTasks()) { + tasksIterable.forEach(task -> splits.add(new IcebergSplit(conf, task))); + } catch (IOException e) { + throw new RuntimeIOException(e, "Failed to close table scan: %s", scan); + } + + return splits; + } + + @Override + public RecordReader<Void, T> createRecordReader(InputSplit split, TaskAttemptContext context) { + return new IcebergRecordReader<>(); + } + + private static final class IcebergRecordReader<T> extends RecordReader<Void, T> { + private TaskAttemptContext context; + private Iterator<FileScanTask> tasks; + private Iterator<T> currentIterator; + private T currentRow; + private Schema expectedSchema; + private Schema tableSchema; + private InMemoryDataModel inMemoryDataModel; + private Closeable currentCloseable; + private boolean reuseContainers; + private boolean caseSensitive; + + @Override + public void initialize(InputSplit split, TaskAttemptContext newContext) { + Configuration conf = newContext.getConfiguration(); + CombinedScanTask task = ((IcebergSplit) split).task; + this.context = newContext; + this.tasks = task.files().iterator(); + this.tableSchema = SchemaParser.fromJson(conf.get(TABLE_SCHEMA)); + String readSchemaStr = conf.get(READ_SCHEMA); + if (readSchemaStr != null) { + this.expectedSchema = SchemaParser.fromJson(readSchemaStr); + } + this.reuseContainers = conf.getBoolean(REUSE_CONTAINERS, false); + this.caseSensitive = conf.getBoolean(CASE_SENSITIVE, true); + this.inMemoryDataModel = conf.getEnum(IN_MEMORY_DATA_MODEL, InMemoryDataModel.DEFAULT); + this.currentIterator = open(tasks.next()); + } + + @Override + public boolean nextKeyValue() throws IOException { + while (true) { + if (currentIterator.hasNext()) { + currentRow = currentIterator.next(); + return true; + } else if (tasks.hasNext()) { + currentCloseable.close(); + currentIterator = open(tasks.next()); + } else { + return false; + } + } + } + + @Override + public Void getCurrentKey() { + return null; + } + + @Override + public T getCurrentValue() { + return currentRow; + } + + @Override + public float getProgress() { + return context.getProgress(); + } + + @Override + public void close() throws IOException { + currentCloseable.close(); + } + + private Iterator<T> open(FileScanTask currentTask) { + DataFile file = currentTask.file(); + // schema of rows returned by readers + PartitionSpec spec = currentTask.spec(); + Set<Integer> idColumns = spec.identitySourceIds(); + Schema readSchema = expectedSchema != null ? expectedSchema : tableSchema; + boolean hasJoinedPartitionColumns = !idColumns.isEmpty(); + if (hasJoinedPartitionColumns) { + readSchema = TypeUtil.selectNot(tableSchema, idColumns); + Schema identityPartitionSchema = TypeUtil.select(tableSchema, idColumns); + return Iterators.transform( + open(currentTask, readSchema), + row -> withPartitionColumns(row, identityPartitionSchema, spec, file.partition())); + } else { + return open(currentTask, readSchema); + } + } + + private Iterator<T> open(FileScanTask currentTask, Schema readSchema) { + DataFile file = currentTask.file(); + // TODO should we somehow make use of FileIO to create inputFile? + InputFile inputFile = HadoopInputFile.fromLocation(file.path(), context.getConfiguration()); + CloseableIterable<T> iterable; + switch (file.format()) { + case AVRO: + iterable = newAvroIterable(inputFile, currentTask, readSchema); + break; + case ORC: + iterable = newOrcIterable(inputFile, currentTask, readSchema); + break; + case PARQUET: + iterable = newParquetIterable(inputFile, currentTask, readSchema); + break; + default: + throw new UnsupportedOperationException( + String.format("Cannot read %s file: %s", file.format().name(), file.path())); + } + currentCloseable = iterable; + return iterable.iterator(); + } + + @SuppressWarnings("unchecked") + private T withPartitionColumns(T row, Schema identityPartitionSchema, PartitionSpec spec, StructLike partition) { + switch (inMemoryDataModel) { + case PIG: + case HIVE: + // TODO implement adding partition columns to records for Pig and Hive + throw new UnsupportedOperationException(); + case DEFAULT: + return (T) icebergRecordWithPartitionsColumns((Record) row, identityPartitionSchema, spec, partition); + } + return row; + } + + private static Record icebergRecordWithPartitionsColumns( + Record record, Schema identityPartitionSchema, PartitionSpec spec, StructLike partition) { + List<Types.NestedField> fields = Lists.newArrayList(record.struct().fields()); + fields.addAll(identityPartitionSchema.asStruct().fields()); + GenericRecord row = GenericRecord.create(Types.StructType.of(fields)); + int size = record.struct().fields().size(); + for (int i = 0; i < size; i++) { + row.set(i, record.get(i)); + } + List<PartitionField> partitionFields = spec.fields(); + List<Types.NestedField> identityColumns = identityPartitionSchema.columns(); + for (int i = 0; i < identityColumns.size(); i++) { + Types.NestedField identityColumn = identityColumns.get(i); + + for (int j = 0; j < partitionFields.size(); j++) { + PartitionField partitionField = partitionFields.get(j); + if (identityColumn.fieldId() == partitionField.sourceId() && + "identity".equals(partitionField.transform().toString())) { + row.set(size + i, partition.get(j, spec.javaClasses()[i])); + } + } + } + return row; + } + + private CloseableIterable<T> newAvroIterable(InputFile inputFile, FileScanTask task, Schema readSchema) { + Avro.ReadBuilder avroReadBuilder = Avro.read(inputFile) + .project(readSchema) + .split(task.start(), task.length()); + + if (reuseContainers) { + avroReadBuilder.reuseContainers(); + } + + switch (inMemoryDataModel) { + case PIG: + case HIVE: + //TODO implement value readers for Pig and Hive + throw new UnsupportedOperationException(); + case DEFAULT: + avroReadBuilder.createReaderFunc(DataReader::create); + } + return avroReadBuilder.build(); + } + + private CloseableIterable<T> newParquetIterable(InputFile inputFile, FileScanTask task, Schema readSchema) { + Parquet.ReadBuilder parquetReadBuilder = Parquet.read(inputFile) + .project(readSchema) + .filter(task.residual()) + .caseSensitive(caseSensitive) + .split(task.start(), task.length()); + if (reuseContainers) { + parquetReadBuilder.reuseContainers(); + } + + switch (inMemoryDataModel) { + case PIG: + case HIVE: + //TODO implement value readers for Pig and Hive + throw new UnsupportedOperationException(); + case DEFAULT: + parquetReadBuilder.createReaderFunc( + fileSchema -> GenericParquetReaders.buildReader(readSchema, fileSchema)); + } + return parquetReadBuilder.build(); + } + + private CloseableIterable<T> newOrcIterable(InputFile inputFile, FileScanTask task, Schema readSchema) { + ORC.ReadBuilder orcReadBuilder = ORC.read(inputFile) + .schema(readSchema) + .caseSensitive(caseSensitive) + .split(task.start(), task.length()); + // ORC does not support reuse containers yet + switch (inMemoryDataModel) { + case PIG: + case HIVE: + //TODO implement value readers for Pig and Hive + throw new UnsupportedOperationException(); + case DEFAULT: + //TODO: We do not have support for Iceberg generics for ORC + throw new UnsupportedOperationException(); + } + + return orcReadBuilder.build(); + } + } + + private static Table getTable(Configuration conf) { Review comment: Hmm, don't all our Catalogs rely on `Configuration` during instantiation? ---------------------------------------------------------------- This is an automated message from the Apache Git Service. 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