Spark: Add flag to handle missing files for `importSparkTable` by jshmchenxi · Pull Request #12212 · apache/iceberg

jshmchenxi · 2025-02-10T02:19:46Z

When importing a partitioned Spark table into Iceberg via SparkTableUtil, any partition whose directory is missing on the underlying filesystem will cause the migration to fail:

Caused by: java.lang.RuntimeException: Unable to list files in partition: s3://bucket/table/partition=foo
	at org.apache.iceberg.data.TableMigrationUtil.listPartition(TableMigrationUtil.java:206)
	at org.apache.iceberg.spark.SparkTableUtil.listPartition(SparkTableUtil.java:309)
	at org.apache.iceberg.spark.SparkTableUtil.lambda$importSparkPartitions$37333fc7$1(SparkTableUtil.java:767)
	at org.apache.spark.sql.Dataset.$anonfun$flatMap$2(Dataset.scala:3484)
	at scala.collection.Iterator$$anon$11.nextCur(Iterator.scala:486)
	at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:492)
	at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:460)
	at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
	at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
	at org.apache.spark.sql.execution.WholeStageCodegenEvaluatorFactory$WholeStageCodegenPartitionEvaluator$$anon$1.hasNext(WholeStageCodegenEvaluatorFactory.scala:43)
	at org.apache.spark.sql.execution.UnsafeExternalRowSorter.sort(UnsafeExternalRowSorter.java:225)
	at org.apache.spark.sql.execution.exchange.ShuffleExchangeExec$.$anonfun$prepareShuffleDependency$10(ShuffleExchangeExec.scala:375)
	at org.apache.spark.rdd.RDD.$anonfun$mapPartitionsInternal$2(RDD.scala:893)
	at org.apache.spark.rdd.RDD.$anonfun$mapPartitionsInternal$2$adapted(RDD.scala:893)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:367)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:331)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:367)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:331)
	at org.apache.spark.shuffle.ShuffleWriteProcessor.write(ShuffleWriteProcessor.scala:59)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:104)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:54)
	at org.apache.spark.TaskContext.runTaskWithListeners(TaskContext.scala:166)
	at org.apache.spark.scheduler.Task.run(Task.scala:141)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:620)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally(SparkErrorUtils.scala:64)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally$(SparkErrorUtils.scala:61)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:94)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:623)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:840)
Caused by: java.io.FileNotFoundException: No such file or directory: s3://bucket/table/partition=foo
	at org.apache.hadoop.fs.s3a.S3AFileSystem.s3GetFileStatus(S3AFileSystem.java:3799)
	at org.apache.hadoop.fs.s3a.S3AFileSystem.innerGetFileStatus(S3AFileSystem.java:3650)
	at org.apache.hadoop.fs.s3a.S3AFileSystem.innerListStatus(S3AFileSystem.java:3373)
	at org.apache.hadoop.fs.s3a.S3AFileSystem.lambda$null$22(S3AFileSystem.java:3344)
	at org.apache.hadoop.fs.s3a.Invoker.once(Invoker.java:122)
	at org.apache.hadoop.fs.s3a.S3AFileSystem.lambda$listStatus$23(S3AFileSystem.java:3343)
	at org.apache.hadoop.fs.statistics.impl.IOStatisticsBinding.invokeTrackingDuration(IOStatisticsBinding.java:547)
	at org.apache.hadoop.fs.statistics.impl.IOStatisticsBinding.lambda$trackDurationOfOperation$5(IOStatisticsBinding.java:528)
	at org.apache.hadoop.fs.statistics.impl.IOStatisticsBinding.trackDuration(IOStatisticsBinding.java:449)
	at org.apache.hadoop.fs.s3a.S3AFileSystem.trackDurationAndSpan(S3AFileSystem.java:2478)
	at org.apache.hadoop.fs.s3a.S3AFileSystem.trackDurationAndSpan(S3AFileSystem.java:2497)
	at org.apache.hadoop.fs.s3a.S3AFileSystem.listStatus(S3AFileSystem.java:3342)
	at org.apache.hadoop.fs.FileSystem.listStatus(FileSystem.java:2078)
	at org.apache.hadoop.fs.FileSystem.listStatus(FileSystem.java:2122)
	at org.apache.iceberg.data.TableMigrationUtil.listPartition(TableMigrationUtil.java:167)
	... 32 more

This typically happens when a partition directory has been deleted—either manually or by an automated cleanup—while its metadata still exists in the metastore.

Problem:

Migrating Spark tables to Iceberg crashes on partitions whose directories don’t exist.
Users must manually recreate directories or clean up metadata before retrying.

Solution:

Introduce a new boolean flag, ignoreMissingFiles, in the importSparkPartitions and importSparkTable methods.
When enabled, partitions whose locations cannot be listed will be skipped rather than causing a hard failure.

Next Steps:

Extend ignoreMissingFiles support to the Spark procedures snapshot and migrate in a follow-up PR.

manuzhang · 2025-02-10T03:34:19Z

@jshmchenxi Thanks for the fix. Can you add a test?

RussellSpitzer

Looks good although I agree we need a test to check that this is working as expected.

jshmchenxi · 2025-02-11T06:52:48Z

@manuzhang @RussellSpitzer Thanks for the suggestion! I've added test cases to cover this change.

manuzhang · 2025-02-11T07:18:46Z

@jshmchenxi Can we add an end-to-end test in TestSnapshotTableAction?

jshmchenxi · 2025-02-16T02:37:42Z

@jshmchenxi Can we add an end-to-end test in TestSnapshotTableAction?

@manuzhang I've added the end-to-end test. Please take a look.

jshmchenxi · 2025-02-18T01:03:14Z

Kindly ping @manuzhang @RussellSpitzer @stevenzwu

jshmchenxi · 2025-02-24T02:41:21Z

@RussellSpitzer Hi, does anything else need to be updated for this PR?

jshmchenxi · 2025-02-28T02:51:32Z

Hi @manuzhang @RussellSpitzer @ebyhr, just checking in on this PR. All feedback from the previous rounds has been addressed, and I believe it’s ready for the final review. I know you’re busy, but I’d really appreciate it if you could take a look when you have some time. Thanks so much!

github-actions · 2025-03-31T00:17:58Z

This pull request has been marked as stale due to 30 days of inactivity. It will be closed in 1 week if no further activity occurs. If you think that’s incorrect or this pull request requires a review, please simply write any comment. If closed, you can revive the PR at any time and @mention a reviewer or discuss it on the dev@iceberg.apache.org list. Thank you for your contributions.

jshmchenxi · 2025-04-09T05:39:29Z

@Fokko Hi! When you get a chance, could you help review this PR? It’s been open for a little while. Appreciate it!

manuzhang · 2025-04-09T06:33:40Z

Let's wait for more time, since folks are busy with Iceberg Summit now.

jshmchenxi · 2025-04-22T00:39:05Z

Kindly pinging @RussellSpitzer @huaxingao — when you have a moment, could you please help review this change? Looking forward to getting it merged. Thanks in advance!

RussellSpitzer · 2025-04-22T16:20:27Z

Tests are currently failing, Could we get those fixed please?

RussellSpitzer · 2025-04-22T16:22:08Z

-              .filter(FileStatus::isFile)
-              .collect(Collectors.toList());
+      List<FileStatus> fileStatus;
+      if (fs.exists(partitionDir)) {


I'm actually a little worried now that we are going to silently error out on a permissions issue here. Should we have this behavior behind a flag?

We added a flag "checkDuplicateFiles" to Spark Table util.

I'm afraid we don't have a clean way of adding more parameters to this method method but i'm still not confident we should go from failure to warning for everyone all at once.

I think it may be best to have a flag in the caller so it looks something like

try { listPartition(ex) } Catch (FileNotFound ...) { if (ignoreMissingFiles) log.warn else throw FNF } ```

That makes sense. Should we add the flag to the Spark migrate and snapshot procedures as well?

That makes sense to me, but you can do that in a followup if you don't want this PR to get too large

Thanks for the suggestion! I've added the new flag to callers in SparkTableUtil.

RussellSpitzer · 2025-04-22T16:23:45Z

+                .filter(FileStatus::isFile)
+                .collect(Collectors.toList());
+      } else {
+        LOG.info(


This should probably be a "warn" at least

…tionUtil`

RussellSpitzer · 2025-05-02T22:09:11Z


 import static org.apache.spark.sql.functions.col;

+import java.io.FileNotFoundException;


Not a big deal since this change set is small, but usually we only do a change in one Spark version at a time, review and then backport.

Got it, I’ll follow this approach in the next PRs.

RussellSpitzer · 2025-05-02T22:12:37Z

  }

+  @Test
+  public void testSparkTableWithMissingFilesFailure() throws IOException {


testImportSparkTableWith...

Just want to make sure we note what's going on

RussellSpitzer · 2025-05-02T22:13:54Z

+        Lists.newArrayList(new SimpleRecord(1, "a"), new SimpleRecord(2, "b"));
+
+    Dataset<Row> inputDF = spark.createDataFrame(records, SimpleRecord.class);
+    inputDF.select("data", "id").write().mode("overwrite").insertInto("parquet_table");


minor question here, do we need to "select"?

No, we don't. It was copied from other tests. I'll remove this and the name mapping part as well.

RussellSpitzer · 2025-05-02T22:14:44Z

+                    new org.apache.spark.sql.catalyst.TableIdentifier("parquet_table"),
+                    table,
+                    stagingLocation))
+        .hasMessageContaining("Unable to list files in partition")


we can also check that the missing string contains partitionLocaltionPath

That makes sense!

RussellSpitzer · 2025-05-02T22:15:45Z

+    Path partitionLocationPath = parquetTablePath.toPath().resolve("id=1234");
+    java.nio.file.Files.delete(partitionLocationPath);
+
+    NameMapping mapping = MappingUtil.create(table.schema());


I don't think you actually need the name mapping for this test

RussellSpitzer

I have a few nits here, but I think we are pretty close! Let's clean those up and we can get this merged

jshmchenxi · 2025-05-03T15:02:15Z

@RussellSpitzer Thanks for the review! I've pushed an update to address the comments.

RussellSpitzer · 2025-05-05T16:21:51Z

Thanks @jshmchenxi for the PR! Thank you to @manuzhang , @rohanag12 and @ebyhr for reviews!

…rkTable` (apache#12212) (apache#1591) Co-authored-by: Xi Chen <jshmchenxi@gmail.com>

…rkTable` (apache#12212)

github-actions Bot added the data label Feb 10, 2025

jshmchenxi changed the title ~~Handle case where partition location is missing from the file system in TableMigrationUtil~~ Data: Handle case where partition location is missing for TableMigrationUtil Feb 10, 2025

jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch 2 times, most recently from 5b7ff64 to 658010c Compare February 10, 2025 02:31

rohanag12 approved these changes Feb 10, 2025

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jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch 2 times, most recently from 36e2b7b to f3c2e11 Compare February 11, 2025 06:52

jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch 2 times, most recently from 60ef66a to 23a1b11 Compare February 11, 2025 06:56

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jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch from 23a1b11 to 6b96233 Compare February 11, 2025 07:04

jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch from 6b96233 to 2aacf49 Compare February 16, 2025 02:34

github-actions Bot added the spark label Feb 16, 2025

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Comment thread data/src/main/java/org/apache/iceberg/data/TableMigrationUtil.java Outdated

jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch 2 times, most recently from 5e58ba9 to e0c9f62 Compare February 21, 2025 01:31

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manuzhang requested a review from RussellSpitzer March 31, 2025 02:53

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jshmchenxi added 3 commits May 2, 2025 17:29

Data: Handle case where partition location is missing for `TableMigra…

eedecdd

…tionUtil`

Add end-to-end test to TestSnapshotTableAction

66abe94

Add log when skipping partition with missing location

ce991f6

jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch 3 times, most recently from 00a7c87 to 084bc85 Compare May 2, 2025 09:52

Handle FileNotFoundException from caller

909f0c2

jshmchenxi force-pushed the bugfix/spark-util-partition-location-nonexist branch from 084bc85 to 909f0c2 Compare May 2, 2025 11:55

jshmchenxi changed the title ~~Data: Handle case where partition location is missing for TableMigrationUtil~~ Spark: Add flag to handle missing files for importSparkTable May 2, 2025

RussellSpitzer reviewed May 2, 2025

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RussellSpitzer approved these changes May 2, 2025

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Address comments

c63beab

RussellSpitzer approved these changes May 5, 2025

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RussellSpitzer merged commit af32a07 into apache:main May 5, 2025

anuragmantri added a commit to anuragmantri/iceberg that referenced this pull request Jul 25, 2025

Data, Spark 3.4, 3.5: Add flag to handle missing files for `importSpa…

ca40754

…rkTable` (apache#12212) (apache#1591) Co-authored-by: Xi Chen <jshmchenxi@gmail.com>

devendra-nr pushed a commit to devendra-nr/iceberg that referenced this pull request Dec 8, 2025

Data, Spark 3.4, 3.5: Add flag to handle missing files for `importSpa…

cff1272

…rkTable` (apache#12212)


		import static org.apache.spark.sql.functions.col;

		import java.io.FileNotFoundException;

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