[GitHub] [gobblin] umustafi commented on a diff in pull request #3598: [GOBBLIN-1741] Create manifest based dataset finder

[GitBox <gi...@apache.org>]

umustafi commented on code in PR #3598:
URL: https://github.com/apache/gobblin/pull/3598#discussion_r1023405736


##########
gobblin-data-management/src/main/java/org/apache/gobblin/data/management/copy/ManifestBasedDataset.java:
##########
@@ -0,0 +1,145 @@
+/*
+ * 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.gobblin.data.management.copy;
+
+import com.google.common.base.Optional;
+import com.google.common.collect.Iterators;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.gson.Gson;
+import com.google.gson.JsonIOException;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonSyntaxException;
+import com.google.gson.stream.JsonReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Properties;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.gobblin.commit.CommitStep;
+import org.apache.gobblin.data.management.copy.entities.PrePublishStep;
+import org.apache.gobblin.data.management.partition.FileSet;
+import org.apache.gobblin.util.commit.DeleteFileCommitStep;
+import org.apache.hadoop.fs.FileStatus;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
+
+/**
+ * A dataset that based on Manifest. We expect the Manifest contains the list of all the files for this dataset.
+ * At first phase, we only support copy across different clusters to the same location. (We can add more feature to support rename in the future)
+ */
+@Slf4j
+public class ManifestBasedDataset implements IterableCopyableDataset {
+
+  public static final String CONFIG_PREFIX = CopyConfiguration.COPY_PREFIX + ".manifestBased";
+  private static final String DELETE_FILE_NOT_EXIST_ON_SOURCE = CONFIG_PREFIX + ".deleteFileNotExistOnSource";
+  /** If true, will delete newly empty directories up to the config set in DELETE_EMPTY_DIRECTORIES_UPTO. */
+  public static final String DELETE_EMPTY_DIRECTORIES_KEY = CONFIG_PREFIX + ".deleteEmptyDirectories";
+  public static final String DELETE_EMPTY_DIRECTORIES_UPTO = CONFIG_PREFIX + ".deleteEmptyDirectoriesUpTo";
+  private final FileSystem fs;
+  private final Path manifestPath;
+  private final Properties properties;
+  private final boolean deleteEmptyDirectories;
+  private Gson GSON = new Gson();
+
+  public ManifestBasedDataset(final FileSystem fs, Path manifestPath, Properties properties) {
+    this.fs = fs;
+    this.manifestPath = manifestPath;
+    this.properties = properties;
+    this.deleteEmptyDirectories = Boolean.parseBoolean(properties.getProperty(DELETE_EMPTY_DIRECTORIES_KEY, "false"))
+        && properties.containsKey(DELETE_EMPTY_DIRECTORIES_UPTO);
+  }
+
+  @Override
+  public String datasetURN() {
+    return this.manifestPath.toString();
+  }
+
+  @Override
+  public Iterator<FileSet<CopyEntity>> getFileSetIterator(FileSystem targetFs, CopyConfiguration configuration)
+      throws IOException {
+    if (!fs.exists(manifestPath)) {
+      log.warn(String.format("Manifest path %s does not exist on filesystem %s, will not copy data in this manifest"
+          + ", probably due to wrong configuration of %s", manifestPath.toString(), fs.getUri().toString(), ManifestBasedDatasetFinder.MANIFEST_LOCATION));
+      return Iterators.emptyIterator();
+    } else if (fs.getFileStatus(manifestPath).isDirectory()) {
+      log.warn(String.format("Manifest path %s on filesystem %s is a directory, which is not supported. Please set the manifest file locations in"
+          + "%s, you can specify multi locations split by '',", manifestPath.toString(), fs.getUri().toString(), ManifestBasedDatasetFinder.MANIFEST_LOCATION));
+      return Iterators.emptyIterator();
+    }
+    JsonReader reader = null;
+    List<CopyEntity> copyEntities = Lists.newArrayList();
+    List<FileStatus> toDelete = Lists.newArrayList();
+    //todo: put permission preserve logic here?
+    try {
+      reader = new JsonReader(new InputStreamReader(fs.open(manifestPath), "UTF-8"));
+      reader.beginArray();
+      while (reader.hasNext()) {
+        //todo: We can use fileSet to partition the data in case of some softbound issue
+        //todo: After partition, change this to directly return iterator so that we can save time if we meet resources limitation
+        JsonObject file = GSON.fromJson(reader, JsonObject.class);
+        Path fileToCopy = new Path(file.get("fileName").getAsString());
+        if (this.fs.exists(fileToCopy)) {
+          if (!targetFs.exists(fileToCopy) || needCopy(this.fs.getFileStatus(fileToCopy), targetFs.getFileStatus(fileToCopy))) {
+            CopyableFile copyableFile =
+                CopyableFile.fromOriginAndDestination(this.fs, this.fs.getFileStatus(fileToCopy), fileToCopy, configuration)
+                    .fileSet(datasetURN())
+                    .datasetOutputPath(fileToCopy.toString())
+                    .ancestorsOwnerAndPermission(CopyableFile
+                        .resolveReplicatedOwnerAndPermissionsRecursively(this.fs, fileToCopy.getParent(),
+                            new Path("/"), configuration))
+                    .build();
+            copyableFile.setFsDatasets(this.fs, targetFs);
+            copyEntities.add(copyableFile);
+          }
+        } else if (targetFs.exists(fileToCopy)){
+          toDelete.add(targetFs.getFileStatus(fileToCopy));
+        }
+      }
+      if (Boolean.parseBoolean(this.properties.getProperty(DELETE_FILE_NOT_EXIST_ON_SOURCE, "false"))) {
+        CommitStep step = new DeleteFileCommitStep(targetFs, toDelete, this.properties,
+            this.deleteEmptyDirectories ? Optional.of(new Path(this.properties.getProperty(DELETE_EMPTY_DIRECTORIES_UPTO))) : Optional.<Path>absent());
+        copyEntities.add(new PrePublishStep(datasetURN(), Maps.newHashMap(), step, 1));
+      }
+    } catch (JsonIOException| JsonSyntaxException e) {
+      //todo: update error message to point to a sample json file instead of schema which is hard to understand
+      log.warn(String.format("Failed to read Manifest path %s on filesystem %s, please make sure it's in correct json format with schema"
+          + " {type:array, items:{type: object, properties:{id:{type:String}, fileName:{type:String}, fileGroup:{type:String}, fileSizeInBytes: {type:Long}}}}",
+          manifestPath.toString(), fs.getUri().toString()), e);

Review Comment:
   missing a `%s` for the exception e



##########
gobblin-data-management/src/main/java/org/apache/gobblin/data/management/copy/ManifestBasedDatasetFinder.java:
##########
@@ -0,0 +1,60 @@
+/*
+ * 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.gobblin.data.management.copy;
+
+import com.google.common.base.Preconditions;
+import com.google.common.base.Splitter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Properties;
+import java.util.stream.Collectors;
+import org.apache.gobblin.dataset.IterableDatasetFinder;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
+
+public class ManifestBasedDatasetFinder implements IterableDatasetFinder<ManifestBasedDataset> {
+
+  public static final String MANIFEST_LOCATION = ManifestBasedDataset.CONFIG_PREFIX + ".manifest.location";
+  private final FileSystem fs;
+  private final List<Path> manifestLocations;
+  private final  Properties properties;
+  public ManifestBasedDatasetFinder(final FileSystem fs, Properties properties) {
+    Preconditions.checkArgument(properties.containsKey(MANIFEST_LOCATION), "Please config " + MANIFEST_LOCATION);

Review Comment:
   improve config "manifest location key required in config. Please set"...



##########
gobblin-data-management/src/main/java/org/apache/gobblin/data/management/copy/ManifestBasedDataset.java:
##########
@@ -0,0 +1,145 @@
+/*
+ * 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.gobblin.data.management.copy;
+
+import com.google.common.base.Optional;
+import com.google.common.collect.Iterators;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
+import com.google.gson.Gson;
+import com.google.gson.JsonIOException;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonSyntaxException;
+import com.google.gson.stream.JsonReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Properties;
+import lombok.extern.slf4j.Slf4j;
+import org.apache.gobblin.commit.CommitStep;
+import org.apache.gobblin.data.management.copy.entities.PrePublishStep;
+import org.apache.gobblin.data.management.partition.FileSet;
+import org.apache.gobblin.util.commit.DeleteFileCommitStep;
+import org.apache.hadoop.fs.FileStatus;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
+
+/**
+ * A dataset that based on Manifest. We expect the Manifest contains the list of all the files for this dataset.
+ * At first phase, we only support copy across different clusters to the same location. (We can add more feature to support rename in the future)
+ */
+@Slf4j
+public class ManifestBasedDataset implements IterableCopyableDataset {
+
+  public static final String CONFIG_PREFIX = CopyConfiguration.COPY_PREFIX + ".manifestBased";
+  private static final String DELETE_FILE_NOT_EXIST_ON_SOURCE = CONFIG_PREFIX + ".deleteFileNotExistOnSource";
+  /** If true, will delete newly empty directories up to the config set in DELETE_EMPTY_DIRECTORIES_UPTO. */
+  public static final String DELETE_EMPTY_DIRECTORIES_KEY = CONFIG_PREFIX + ".deleteEmptyDirectories";
+  public static final String DELETE_EMPTY_DIRECTORIES_UPTO = CONFIG_PREFIX + ".deleteEmptyDirectoriesUpTo";
+  private final FileSystem fs;
+  private final Path manifestPath;
+  private final Properties properties;
+  private final boolean deleteEmptyDirectories;
+  private Gson GSON = new Gson();
+
+  public ManifestBasedDataset(final FileSystem fs, Path manifestPath, Properties properties) {
+    this.fs = fs;
+    this.manifestPath = manifestPath;
+    this.properties = properties;
+    this.deleteEmptyDirectories = Boolean.parseBoolean(properties.getProperty(DELETE_EMPTY_DIRECTORIES_KEY, "false"))
+        && properties.containsKey(DELETE_EMPTY_DIRECTORIES_UPTO);
+  }
+
+  @Override
+  public String datasetURN() {
+    return this.manifestPath.toString();
+  }
+
+  @Override
+  public Iterator<FileSet<CopyEntity>> getFileSetIterator(FileSystem targetFs, CopyConfiguration configuration)
+      throws IOException {
+    if (!fs.exists(manifestPath)) {
+      log.warn(String.format("Manifest path %s does not exist on filesystem %s, will not copy data in this manifest"
+          + ", probably due to wrong configuration of %s", manifestPath.toString(), fs.getUri().toString(), ManifestBasedDatasetFinder.MANIFEST_LOCATION));
+      return Iterators.emptyIterator();
+    } else if (fs.getFileStatus(manifestPath).isDirectory()) {
+      log.warn(String.format("Manifest path %s on filesystem %s is a directory, which is not supported. Please set the manifest file locations in"
+          + "%s, you can specify multi locations split by '',", manifestPath.toString(), fs.getUri().toString(), ManifestBasedDatasetFinder.MANIFEST_LOCATION));
+      return Iterators.emptyIterator();
+    }
+    JsonReader reader = null;
+    List<CopyEntity> copyEntities = Lists.newArrayList();
+    List<FileStatus> toDelete = Lists.newArrayList();
+    //todo: put permission preserve logic here?
+    try {
+      reader = new JsonReader(new InputStreamReader(fs.open(manifestPath), "UTF-8"));
+      reader.beginArray();
+      while (reader.hasNext()) {
+        //todo: We can use fileSet to partition the data in case of some softbound issue
+        //todo: After partition, change this to directly return iterator so that we can save time if we meet resources limitation
+        JsonObject file = GSON.fromJson(reader, JsonObject.class);
+        Path fileToCopy = new Path(file.get("fileName").getAsString());
+        if (this.fs.exists(fileToCopy)) {
+          if (!targetFs.exists(fileToCopy) || needCopy(this.fs.getFileStatus(fileToCopy), targetFs.getFileStatus(fileToCopy))) {
+            CopyableFile copyableFile =
+                CopyableFile.fromOriginAndDestination(this.fs, this.fs.getFileStatus(fileToCopy), fileToCopy, configuration)
+                    .fileSet(datasetURN())
+                    .datasetOutputPath(fileToCopy.toString())
+                    .ancestorsOwnerAndPermission(CopyableFile
+                        .resolveReplicatedOwnerAndPermissionsRecursively(this.fs, fileToCopy.getParent(),
+                            new Path("/"), configuration))
+                    .build();
+            copyableFile.setFsDatasets(this.fs, targetFs);
+            copyEntities.add(copyableFile);
+          }
+        } else if (targetFs.exists(fileToCopy)){
+          toDelete.add(targetFs.getFileStatus(fileToCopy));
+        }
+      }
+      if (Boolean.parseBoolean(this.properties.getProperty(DELETE_FILE_NOT_EXIST_ON_SOURCE, "false"))) {
+        CommitStep step = new DeleteFileCommitStep(targetFs, toDelete, this.properties,
+            this.deleteEmptyDirectories ? Optional.of(new Path(this.properties.getProperty(DELETE_EMPTY_DIRECTORIES_UPTO))) : Optional.<Path>absent());

Review Comment:
   is this to delete directories that are emptied after we remove the files that do not exist on source?



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