RussellSpitzer commented on a change in pull request #2608: URL: https://github.com/apache/iceberg/pull/2608#discussion_r655739073
########## File path: spark/src/main/java/org/apache/iceberg/spark/actions/BaseRepairManifestsSparkAction.java ########## @@ -0,0 +1,313 @@ +/* + * 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.spark.actions; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.UUID; +import java.util.function.Predicate; +import java.util.stream.Collectors; +import java.util.stream.StreamSupport; +import org.apache.hadoop.fs.Path; +import org.apache.iceberg.DataFile; +import org.apache.iceberg.FileFormat; +import org.apache.iceberg.HasTableOperations; +import org.apache.iceberg.ManifestFile; +import org.apache.iceberg.ManifestFiles; +import org.apache.iceberg.ManifestWriter; +import org.apache.iceberg.PartitionSpec; +import org.apache.iceberg.SerializableTable; +import org.apache.iceberg.Snapshot; +import org.apache.iceberg.Table; +import org.apache.iceberg.TableOperations; +import org.apache.iceberg.actions.BaseRepairManifestsActionResult; +import org.apache.iceberg.actions.RepairManifests; +import org.apache.iceberg.io.FileIO; +import org.apache.iceberg.io.OutputFile; +import org.apache.iceberg.relocated.com.google.common.base.Preconditions; +import org.apache.iceberg.relocated.com.google.common.collect.ImmutableMap; +import org.apache.iceberg.relocated.com.google.common.collect.Lists; +import org.apache.iceberg.relocated.com.google.common.collect.Streams; +import org.apache.iceberg.spark.JobGroupInfo; +import org.apache.iceberg.spark.SparkDataFile; +import org.apache.iceberg.types.Types; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.broadcast.Broadcast; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.types.StructType; +import org.apache.spark.util.SerializableConfiguration; +import scala.Tuple2; + +import static org.apache.iceberg.MetadataTableType.ENTRIES; + +/** + * An action that repairs manifests in a distributed manner, reading metadata of the data files to repair + * manifest entries in each manifest. + * <p> + * By default, this action repairs all manifests by checking the data file status and reading the data file headers. + * This can be changed by passing in repair options like {@link #repairMetrics(boolean)}, and manifest predicates + * via {@link #repairIf(Predicate)}. + * <p> + * In addition, there is a way to configure a custom location for new manifests via {@link #stagingLocation}. + */ +public class BaseRepairManifestsSparkAction extends BaseManifestSparkAction<RepairManifests, RepairManifests.Result> + implements RepairManifests { + + private final int formatVersion; + private final SerializableConfiguration hadoopConf; + + private Predicate<ManifestFile> predicate = manifest -> true; + private String stagingLocation; + private boolean repairMetrics = true; + + public BaseRepairManifestsSparkAction(SparkSession spark, Table table) { + super(spark, table); + + this.hadoopConf = new SerializableConfiguration(spark.sessionState().newHadoopConf()); + + // default the staging location to the metadata location + TableOperations ops = ((HasTableOperations) getTable()).operations(); + Path metadataFilePath = new Path(ops.metadataFileLocation("file")); + this.stagingLocation = metadataFilePath.getParent().toString(); + + // use the current table format version for repaired manifests + this.formatVersion = ops.current().formatVersion(); + } + + @Override + public RepairManifests repairIf(Predicate<ManifestFile> newPredicate) { + this.predicate = newPredicate; + return this; + } + + @Override + public RepairManifests stagingLocation(String newStagingLocation) { + this.stagingLocation = newStagingLocation; + return this; + } + + @Override + public RepairManifests repairMetrics(boolean repair) { + this.repairMetrics = repair; + return this; + } + + @Override + protected RepairManifests self() { + return this; + } + + @Override + public Result execute() { + String desc = String.format("Rewriting manifests (staging location=%s) of %s", stagingLocation, getTable().name()); Review comment: Repairing manifests ? ########## File path: spark/src/main/java/org/apache/iceberg/spark/actions/BaseRepairManifestsSparkAction.java ########## @@ -0,0 +1,313 @@ +/* + * 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.spark.actions; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.UUID; +import java.util.function.Predicate; +import java.util.stream.Collectors; +import java.util.stream.StreamSupport; +import org.apache.hadoop.fs.Path; +import org.apache.iceberg.DataFile; +import org.apache.iceberg.FileFormat; +import org.apache.iceberg.HasTableOperations; +import org.apache.iceberg.ManifestFile; +import org.apache.iceberg.ManifestFiles; +import org.apache.iceberg.ManifestWriter; +import org.apache.iceberg.PartitionSpec; +import org.apache.iceberg.SerializableTable; +import org.apache.iceberg.Snapshot; +import org.apache.iceberg.Table; +import org.apache.iceberg.TableOperations; +import org.apache.iceberg.actions.BaseRepairManifestsActionResult; +import org.apache.iceberg.actions.RepairManifests; +import org.apache.iceberg.io.FileIO; +import org.apache.iceberg.io.OutputFile; +import org.apache.iceberg.relocated.com.google.common.base.Preconditions; +import org.apache.iceberg.relocated.com.google.common.collect.ImmutableMap; +import org.apache.iceberg.relocated.com.google.common.collect.Lists; +import org.apache.iceberg.relocated.com.google.common.collect.Streams; +import org.apache.iceberg.spark.JobGroupInfo; +import org.apache.iceberg.spark.SparkDataFile; +import org.apache.iceberg.types.Types; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.broadcast.Broadcast; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.types.StructType; +import org.apache.spark.util.SerializableConfiguration; +import scala.Tuple2; + +import static org.apache.iceberg.MetadataTableType.ENTRIES; + +/** + * An action that repairs manifests in a distributed manner, reading metadata of the data files to repair + * manifest entries in each manifest. + * <p> + * By default, this action repairs all manifests by checking the data file status and reading the data file headers. + * This can be changed by passing in repair options like {@link #repairMetrics(boolean)}, and manifest predicates + * via {@link #repairIf(Predicate)}. + * <p> + * In addition, there is a way to configure a custom location for new manifests via {@link #stagingLocation}. + */ +public class BaseRepairManifestsSparkAction extends BaseManifestSparkAction<RepairManifests, RepairManifests.Result> + implements RepairManifests { + + private final int formatVersion; + private final SerializableConfiguration hadoopConf; + + private Predicate<ManifestFile> predicate = manifest -> true; + private String stagingLocation; + private boolean repairMetrics = true; + + public BaseRepairManifestsSparkAction(SparkSession spark, Table table) { + super(spark, table); + + this.hadoopConf = new SerializableConfiguration(spark.sessionState().newHadoopConf()); + + // default the staging location to the metadata location + TableOperations ops = ((HasTableOperations) getTable()).operations(); + Path metadataFilePath = new Path(ops.metadataFileLocation("file")); + this.stagingLocation = metadataFilePath.getParent().toString(); + + // use the current table format version for repaired manifests + this.formatVersion = ops.current().formatVersion(); + } + + @Override + public RepairManifests repairIf(Predicate<ManifestFile> newPredicate) { + this.predicate = newPredicate; + return this; + } + + @Override + public RepairManifests stagingLocation(String newStagingLocation) { + this.stagingLocation = newStagingLocation; + return this; + } + + @Override + public RepairManifests repairMetrics(boolean repair) { + this.repairMetrics = repair; + return this; + } + + @Override + protected RepairManifests self() { + return this; + } + + @Override + public Result execute() { + String desc = String.format("Rewriting manifests (staging location=%s) of %s", stagingLocation, getTable().name()); + JobGroupInfo info = newJobGroupInfo("REWRITE-MANIFESTS", desc); Review comment: REPAIR-MANIFESTS ########## File path: spark/src/main/java/org/apache/iceberg/spark/actions/BaseRepairManifestsSparkAction.java ########## @@ -0,0 +1,313 @@ +/* + * 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.spark.actions; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.UUID; +import java.util.function.Predicate; +import java.util.stream.Collectors; +import java.util.stream.StreamSupport; +import org.apache.hadoop.fs.Path; +import org.apache.iceberg.DataFile; +import org.apache.iceberg.FileFormat; +import org.apache.iceberg.HasTableOperations; +import org.apache.iceberg.ManifestFile; +import org.apache.iceberg.ManifestFiles; +import org.apache.iceberg.ManifestWriter; +import org.apache.iceberg.PartitionSpec; +import org.apache.iceberg.SerializableTable; +import org.apache.iceberg.Snapshot; +import org.apache.iceberg.Table; +import org.apache.iceberg.TableOperations; +import org.apache.iceberg.actions.BaseRepairManifestsActionResult; +import org.apache.iceberg.actions.RepairManifests; +import org.apache.iceberg.io.FileIO; +import org.apache.iceberg.io.OutputFile; +import org.apache.iceberg.relocated.com.google.common.base.Preconditions; +import org.apache.iceberg.relocated.com.google.common.collect.ImmutableMap; +import org.apache.iceberg.relocated.com.google.common.collect.Lists; +import org.apache.iceberg.relocated.com.google.common.collect.Streams; +import org.apache.iceberg.spark.JobGroupInfo; +import org.apache.iceberg.spark.SparkDataFile; +import org.apache.iceberg.types.Types; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.broadcast.Broadcast; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.types.StructType; +import org.apache.spark.util.SerializableConfiguration; +import scala.Tuple2; + +import static org.apache.iceberg.MetadataTableType.ENTRIES; + +/** + * An action that repairs manifests in a distributed manner, reading metadata of the data files to repair + * manifest entries in each manifest. + * <p> + * By default, this action repairs all manifests by checking the data file status and reading the data file headers. + * This can be changed by passing in repair options like {@link #repairMetrics(boolean)}, and manifest predicates + * via {@link #repairIf(Predicate)}. + * <p> + * In addition, there is a way to configure a custom location for new manifests via {@link #stagingLocation}. + */ +public class BaseRepairManifestsSparkAction extends BaseManifestSparkAction<RepairManifests, RepairManifests.Result> + implements RepairManifests { + + private final int formatVersion; + private final SerializableConfiguration hadoopConf; + + private Predicate<ManifestFile> predicate = manifest -> true; + private String stagingLocation; + private boolean repairMetrics = true; + + public BaseRepairManifestsSparkAction(SparkSession spark, Table table) { + super(spark, table); + + this.hadoopConf = new SerializableConfiguration(spark.sessionState().newHadoopConf()); + + // default the staging location to the metadata location + TableOperations ops = ((HasTableOperations) getTable()).operations(); + Path metadataFilePath = new Path(ops.metadataFileLocation("file")); + this.stagingLocation = metadataFilePath.getParent().toString(); + + // use the current table format version for repaired manifests + this.formatVersion = ops.current().formatVersion(); + } + + @Override + public RepairManifests repairIf(Predicate<ManifestFile> newPredicate) { + this.predicate = newPredicate; + return this; + } + + @Override + public RepairManifests stagingLocation(String newStagingLocation) { + this.stagingLocation = newStagingLocation; + return this; + } + + @Override + public RepairManifests repairMetrics(boolean repair) { + this.repairMetrics = repair; + return this; + } + + @Override + protected RepairManifests self() { + return this; + } + + @Override + public Result execute() { + String desc = String.format("Rewriting manifests (staging location=%s) of %s", stagingLocation, getTable().name()); + JobGroupInfo info = newJobGroupInfo("REWRITE-MANIFESTS", desc); + return withJobGroupInfo(info, this::doExecute); + } + + private RepairManifests.Result doExecute() { + // Find matching manifest entries + Map<String, ManifestFile> manifestFiles = findMatchingManifests(); + Dataset<Row> manifestEntryDf = buildManifestEntryDF(new ArrayList<>(manifestFiles.values())); + StructType sparkType = (StructType) manifestEntryDf.schema().apply("data_file").dataType(); + JavaRDD<Row> manifestEntryRdd = manifestEntryDf.toJavaRDD(); + JavaPairRDD<ManifestFileInfo, Iterable<Row>> entriesByManifest = manifestEntryRdd.groupBy( + r -> new ManifestFileInfo(r.getString(0), r.getInt(1))); + + // Calculate manifest entries for repair + RepairManifestHelper.RepairOptions options = new RepairManifestHelper.RepairOptions(repairMetrics); + Broadcast<Table> broadcastTable = sparkContext().broadcast(SerializableTable.copyOf(getTable())); + Broadcast<SerializableConfiguration> conf = sparkContext().broadcast(hadoopConf); + JavaRDD<Tuple2<ManifestFileInfo, Iterable<PatchedManifestEntry>>> toRepair = + entriesByManifest.map(calculateRepairs(broadcastTable, conf, sparkType, options)) + // Process only manifest files with repaired entries + .filter(m -> StreamSupport.stream(m._2.spliterator(), false) + .anyMatch(p -> p.repaired)); + + // Write out repaired manifests + Broadcast<FileIO> io = sparkContext().broadcast(getFileIO()); + JavaRDD<ManifestFile> repairedManifests = toRepair.map( + writeRepairs(io, broadcastTable, formatVersion, stagingLocation)); + + // Prepare results + List<ManifestFile> addedManifests = repairedManifests.collect(); + List<ManifestFile> deletedManifests = toRepair.collect().stream().map(t -> { + String path = t._1().getPath(); + ManifestFile mf = manifestFiles.get(path); + // Sanity check deleted file existed in original list + Preconditions.checkNotNull(mf, "Manifest file cannot be null for " + path); + return mf; + }).collect(Collectors.toList()); + + Iterable<ManifestFile> newManifests = replaceManifests(deletedManifests, addedManifests); + return new BaseRepairManifestsActionResult(deletedManifests, Lists.newArrayList(newManifests)); + } + + + private Map<String, ManifestFile> findMatchingManifests() { + Snapshot currentSnapshot = getTable().currentSnapshot(); + if (currentSnapshot == null) { + return ImmutableMap.of(); + } + return currentSnapshot.dataManifests().stream() + .filter(manifest -> predicate.test(manifest)) + .collect(Collectors.toMap(ManifestFile::path, mf -> mf)); + } + + private Dataset<Row> buildManifestEntryDF(List<ManifestFile> manifests) { + Dataset<Row> manifestDF = spark() + .createDataset(Lists.transform(manifests, m -> new ManifestFileInfo(m.path(), m.partitionSpecId())), + Encoders.bean(ManifestFileInfo.class)) + .toDF("partition_spec_id", "manifest_path"); + Dataset<Row> manifestEntryDF = loadMetadataTable(getTable(), ENTRIES) + .filter("status < 2") // select only live entries + .selectExpr("input_file_name() as manifest_path", "snapshot_id", "sequence_number", "data_file"); + + return manifestEntryDF.as("manifest_entry") Review comment: I still think we should fix this in the actual ManfiestEntry Row and have the spec generated at read time, it feels a little odd to me to be joining to reconnect it when we knew the right ID when we read it the first time. I'm fine with this for now but we really need to get SpecID into that metadata table. ########## File path: spark/src/main/java/org/apache/iceberg/spark/actions/BaseRepairManifestsSparkAction.java ########## @@ -0,0 +1,313 @@ +/* + * 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.spark.actions; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.Optional; +import java.util.UUID; +import java.util.function.Predicate; +import java.util.stream.Collectors; +import java.util.stream.StreamSupport; +import org.apache.hadoop.fs.Path; +import org.apache.iceberg.DataFile; +import org.apache.iceberg.FileFormat; +import org.apache.iceberg.HasTableOperations; +import org.apache.iceberg.ManifestFile; +import org.apache.iceberg.ManifestFiles; +import org.apache.iceberg.ManifestWriter; +import org.apache.iceberg.PartitionSpec; +import org.apache.iceberg.SerializableTable; +import org.apache.iceberg.Snapshot; +import org.apache.iceberg.Table; +import org.apache.iceberg.TableOperations; +import org.apache.iceberg.actions.BaseRepairManifestsActionResult; +import org.apache.iceberg.actions.RepairManifests; +import org.apache.iceberg.io.FileIO; +import org.apache.iceberg.io.OutputFile; +import org.apache.iceberg.relocated.com.google.common.base.Preconditions; +import org.apache.iceberg.relocated.com.google.common.collect.ImmutableMap; +import org.apache.iceberg.relocated.com.google.common.collect.Lists; +import org.apache.iceberg.relocated.com.google.common.collect.Streams; +import org.apache.iceberg.spark.JobGroupInfo; +import org.apache.iceberg.spark.SparkDataFile; +import org.apache.iceberg.types.Types; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.function.Function; +import org.apache.spark.broadcast.Broadcast; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.types.StructType; +import org.apache.spark.util.SerializableConfiguration; +import scala.Tuple2; + +import static org.apache.iceberg.MetadataTableType.ENTRIES; + +/** + * An action that repairs manifests in a distributed manner, reading metadata of the data files to repair + * manifest entries in each manifest. + * <p> + * By default, this action repairs all manifests by checking the data file status and reading the data file headers. + * This can be changed by passing in repair options like {@link #repairMetrics(boolean)}, and manifest predicates + * via {@link #repairIf(Predicate)}. + * <p> + * In addition, there is a way to configure a custom location for new manifests via {@link #stagingLocation}. + */ +public class BaseRepairManifestsSparkAction extends BaseManifestSparkAction<RepairManifests, RepairManifests.Result> + implements RepairManifests { + + private final int formatVersion; + private final SerializableConfiguration hadoopConf; + + private Predicate<ManifestFile> predicate = manifest -> true; + private String stagingLocation; + private boolean repairMetrics = true; + + public BaseRepairManifestsSparkAction(SparkSession spark, Table table) { + super(spark, table); + + this.hadoopConf = new SerializableConfiguration(spark.sessionState().newHadoopConf()); + + // default the staging location to the metadata location + TableOperations ops = ((HasTableOperations) getTable()).operations(); + Path metadataFilePath = new Path(ops.metadataFileLocation("file")); + this.stagingLocation = metadataFilePath.getParent().toString(); + + // use the current table format version for repaired manifests + this.formatVersion = ops.current().formatVersion(); + } + + @Override + public RepairManifests repairIf(Predicate<ManifestFile> newPredicate) { + this.predicate = newPredicate; + return this; + } + + @Override + public RepairManifests stagingLocation(String newStagingLocation) { + this.stagingLocation = newStagingLocation; + return this; + } + + @Override + public RepairManifests repairMetrics(boolean repair) { + this.repairMetrics = repair; + return this; + } + + @Override + protected RepairManifests self() { + return this; + } + + @Override + public Result execute() { + String desc = String.format("Rewriting manifests (staging location=%s) of %s", stagingLocation, getTable().name()); + JobGroupInfo info = newJobGroupInfo("REWRITE-MANIFESTS", desc); + return withJobGroupInfo(info, this::doExecute); + } + + private RepairManifests.Result doExecute() { + // Find matching manifest entries + Map<String, ManifestFile> manifestFiles = findMatchingManifests(); + Dataset<Row> manifestEntryDf = buildManifestEntryDF(new ArrayList<>(manifestFiles.values())); + StructType sparkType = (StructType) manifestEntryDf.schema().apply("data_file").dataType(); + JavaRDD<Row> manifestEntryRdd = manifestEntryDf.toJavaRDD(); + JavaPairRDD<ManifestFileInfo, Iterable<Row>> entriesByManifest = manifestEntryRdd.groupBy( + r -> new ManifestFileInfo(r.getString(0), r.getInt(1))); + + // Calculate manifest entries for repair + RepairManifestHelper.RepairOptions options = new RepairManifestHelper.RepairOptions(repairMetrics); + Broadcast<Table> broadcastTable = sparkContext().broadcast(SerializableTable.copyOf(getTable())); + Broadcast<SerializableConfiguration> conf = sparkContext().broadcast(hadoopConf); + JavaRDD<Tuple2<ManifestFileInfo, Iterable<PatchedManifestEntry>>> toRepair = + entriesByManifest.map(calculateRepairs(broadcastTable, conf, sparkType, options)) + // Process only manifest files with repaired entries + .filter(m -> StreamSupport.stream(m._2.spliterator(), false) + .anyMatch(p -> p.repaired)); + + // Write out repaired manifests + Broadcast<FileIO> io = sparkContext().broadcast(getFileIO()); + JavaRDD<ManifestFile> repairedManifests = toRepair.map( + writeRepairs(io, broadcastTable, formatVersion, stagingLocation)); + + // Prepare results + List<ManifestFile> addedManifests = repairedManifests.collect(); + List<ManifestFile> deletedManifests = toRepair.collect().stream().map(t -> { + String path = t._1().getPath(); + ManifestFile mf = manifestFiles.get(path); + // Sanity check deleted file existed in original list + Preconditions.checkNotNull(mf, "Manifest file cannot be null for " + path); + return mf; + }).collect(Collectors.toList()); + + Iterable<ManifestFile> newManifests = replaceManifests(deletedManifests, addedManifests); + return new BaseRepairManifestsActionResult(deletedManifests, Lists.newArrayList(newManifests)); + } + + + private Map<String, ManifestFile> findMatchingManifests() { + Snapshot currentSnapshot = getTable().currentSnapshot(); + if (currentSnapshot == null) { + return ImmutableMap.of(); + } + return currentSnapshot.dataManifests().stream() + .filter(manifest -> predicate.test(manifest)) + .collect(Collectors.toMap(ManifestFile::path, mf -> mf)); + } + + private Dataset<Row> buildManifestEntryDF(List<ManifestFile> manifests) { + Dataset<Row> manifestDF = spark() + .createDataset(Lists.transform(manifests, m -> new ManifestFileInfo(m.path(), m.partitionSpecId())), + Encoders.bean(ManifestFileInfo.class)) + .toDF("partition_spec_id", "manifest_path"); + Dataset<Row> manifestEntryDF = loadMetadataTable(getTable(), ENTRIES) + .filter("status < 2") // select only live entries + .selectExpr("input_file_name() as manifest_path", "snapshot_id", "sequence_number", "data_file"); + + return manifestEntryDF.as("manifest_entry") + .join(manifestDF.as("manifest"), "manifest_path") + .select("manifest_entry.manifest_path", "manifest.partition_spec_id", + "snapshot_id", "sequence_number", "data_file"); + } + + private static Function<Tuple2<ManifestFileInfo, Iterable<Row>>, + Tuple2<ManifestFileInfo, Iterable<PatchedManifestEntry>>> calculateRepairs( + Broadcast<Table> broadcastTable, Broadcast<SerializableConfiguration> conf, + StructType sparkType, RepairManifestHelper.RepairOptions options) { + return manifestFile -> { + Iterator<Row> rowIterator = manifestFile._2().iterator(); + ManifestFileInfo manifestInfo = manifestFile._1(); + int specId = manifestInfo.partSpecId; + + PartitionSpec spec = broadcastTable.value().specs().get(specId); + Types.StructType dataFileType = DataFile.getType(spec.partitionType()); + SparkDataFile wrapper = new SparkDataFile(dataFileType, sparkType).withSpecId(spec.specId()); + + Iterable<PatchedManifestEntry> entries = + Streams.stream(rowIterator).map(r -> { + long snapshotId = r.getLong(2); + long sequenceNumber = r.getLong(3); + Row file = r.getStruct(4); + SparkDataFile dataFile = wrapper.wrap(file); + Optional<DataFile> repairedDataFile = RepairManifestHelper.repairDataFile( + dataFile, broadcastTable.value(), spec, conf.value().value(), options); + return repairedDataFile.map( + value -> new PatchedManifestEntry(snapshotId, sequenceNumber, value, true)) + .orElseGet(() -> new PatchedManifestEntry(snapshotId, sequenceNumber, dataFile, false)); + }).collect(Collectors.toList()); + return new Tuple2<>(manifestFile._1(), entries); + }; + } + + private static Function<Tuple2<ManifestFileInfo, Iterable<PatchedManifestEntry>>, ManifestFile> writeRepairs( + Broadcast<FileIO> io, Broadcast<Table> broadcastTable, + int formatVersion, String location) { + return rows -> { + Iterator<PatchedManifestEntry> entryIterator = rows._2().iterator(); + ManifestFileInfo manifestInfo = rows._1(); + int specId = manifestInfo.partSpecId; + PartitionSpec spec = broadcastTable.value().specs().get(specId); + + String manifestName = "repaired-m-" + UUID.randomUUID(); + Path newManifestPath = new Path(location, manifestName); + OutputFile outputFile = io.value().newOutputFile(FileFormat.AVRO.addExtension(newManifestPath.toString())); Review comment: would it make sense to parallelize this as well? Using Tasks.foreach? ########## File path: spark/src/main/java/org/apache/iceberg/spark/actions/RepairManifestHelper.java ########## @@ -0,0 +1,219 @@ +/* + * 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.spark.actions; + +import java.io.IOException; +import java.io.Serializable; +import java.io.UncheckedIOException; +import java.util.HashSet; +import java.util.Objects; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Stream; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileStatus; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.iceberg.DataFile; +import org.apache.iceberg.DataFiles; +import org.apache.iceberg.FileFormat; +import org.apache.iceberg.ManifestFile; +import org.apache.iceberg.Metrics; +import org.apache.iceberg.MetricsConfig; +import org.apache.iceberg.PartitionSpec; +import org.apache.iceberg.Table; +import org.apache.iceberg.TableProperties; +import org.apache.iceberg.hadoop.HadoopInputFile; +import org.apache.iceberg.mapping.NameMapping; +import org.apache.iceberg.mapping.NameMappingParser; +import org.apache.iceberg.orc.OrcMetrics; +import org.apache.iceberg.parquet.ParquetUtil; +import org.apache.iceberg.relocated.com.google.common.base.Preconditions; +import org.apache.iceberg.spark.SparkDataFile; +import org.apache.iceberg.spark.SparkExceptionUtil; +import org.apache.parquet.hadoop.ParquetFileReader; +import org.apache.parquet.hadoop.metadata.ParquetMetadata; + +/** + * Helper methods to repair manifest files. + * TODO- repair split offsets + */ +public class RepairManifestHelper { + + private RepairManifestHelper() { + // Prevent Construction + } + + /** + * Given a DataFile information, return Metrics + * @param format file format + * @param status file status + * @param conf Hadoop configuration + * @param metricsSpec metrics configuration + * @param mapping name mapping + * @return metrics + */ + private static Metrics getMetrics(FileFormat format, FileStatus status, Configuration conf, + MetricsConfig metricsSpec, NameMapping mapping) { + switch (format) { + case AVRO: + return new Metrics(-1L, null, null, null); + case ORC: + return OrcMetrics.fromInputFile(HadoopInputFile.fromPath(status.getPath(), conf), + metricsSpec, mapping); + case PARQUET: + try { + ParquetMetadata metadata = ParquetFileReader.readFooter(conf, status); + return ParquetUtil.footerMetrics(metadata, Stream.empty(), metricsSpec, mapping); + } catch (IOException e) { + throw SparkExceptionUtil.toUncheckedException( + e, "Unable to read the footer of the parquet file: %s", status.getPath()); + } + default: + throw new UnsupportedOperationException("Unknown file format: " + format); + } + } + + /** + * Diffs two DataFile for potential for repair + * @return a set of fields in human-readable format that differ between these DataFiles Review comment: Although for one liners I believe we do Return ..... 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