MSCK REPAIR TABLE - Amazon Athena
Considerations and limitationsSynopsisExamplesTroubleshooting
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MSCK REPAIR TABLE

Use the MSCK REPAIR TABLE command to update the metadata in the catalog after you add Hive compatible partitions.

The MSCK REPAIR TABLE command scans a file system such as Amazon S3 for Hive compatible partitions that were added to the file system after the table was created. MSCK REPAIR TABLE compares the partitions in the table metadata and the partitions in S3. If new partitions are present in the S3 location that you specified when you created the table, it adds those partitions to the metadata and to the Athena table.

When you add physical partitions, the metadata in the catalog becomes inconsistent with the layout of the data in the file system, and information about the new partitions needs to be added to the catalog. To update the metadata, run MSCK REPAIR TABLE so that you can query the data in the new partitions from Athena.

Note

MSCK REPAIR TABLE only adds partitions to metadata; it does not remove them. To remove partitions from metadata after the partitions have been manually deleted in Amazon S3, run the command ALTER TABLE table-name DROP PARTITION. For more information see ALTER TABLE DROP PARTITION.

Considerations and limitations

When using MSCK REPAIR TABLE, keep in mind the following points:

  • It is possible it will take some time to add all partitions. If this operation times out, it will be in an incomplete state where only a few partitions are added to the catalog. You should run MSCK REPAIR TABLE on the same table until all partitions are added. For more information, see Partitioning data in Athena.

  • For partitions that are not compatible with Hive, use ALTER TABLE ADD PARTITION to load the partitions so that you can query their data.

  • Partition locations to be used with Athena must use the s3 protocol (for example, s3://bucket/folder/). In Athena, locations that use other protocols (for example, s3a://bucket/folder/) will result in query failures when MSCK REPAIR TABLE queries are run on the containing tables.

  • Because MSCK REPAIR TABLE scans both a folder and its subfolders to find a matching partition scheme, be sure to keep data for separate tables in separate folder hierarchies. For example, suppose you have data for table A in s3://table-a-data and data for table B in s3://table-a-data/table-b-data. If both tables are partitioned by string, MSCK REPAIR TABLE will add the partitions for table B to table A. To avoid this, use separate folder structures like s3://table-a-data and s3://table-b-data instead. Note that this behavior is consistent with Amazon EMR and Apache Hive.

  • Due to a known issue, MSCK REPAIR TABLE fails silently when partition values contain a colon (:) character (for example, when the partition value is a timestamp). As a workaround, use ALTER TABLE ADD PARTITION.

  • MSCK REPAIR TABLE does not add partition column names that begin with an underscore (_). To work around this limitation, use ALTER TABLE ADD PARTITION.

Synopsis

MSCK REPAIR TABLE table_name

Examples

MSCK REPAIR TABLE orders;

Troubleshooting

After you run MSCK REPAIR TABLE, if Athena does not add the partitions to the table in the Amazon Glue Data Catalog, check the following:

  • Amazon Glue access – Make sure that the Amazon Identity and Access Management (IAM) role has a policy that allows the glue:BatchCreatePartition action. For more information, see Allow glue:BatchCreatePartition in the IAM policy later in this document.

  • Amazon S3 access – Make sure that the role has a policy with sufficient permissions to access Amazon S3, including the s3:DescribeJob action. For an example of which Amazon S3 actions to allow, see the example bucket policy in Cross-account access in Athena to Amazon S3 buckets.

  • Amazon S3 object key casing – Make sure that the Amazon S3 path is in lower case instead of camel case (for example, userid instead of userId), or use ALTER TABLE ADD PARTITION to specify the object key names. For more information, see Change or redefine the Amazon S3 path later in this document.

  • Query timeouts – MSCK REPAIR TABLE is best used when creating a table for the first time or when there is uncertainty about parity between data and partition metadata. If you use MSCK REPAIR TABLE to add new partitions frequently (for example, on a daily basis) and are experiencing query timeouts, consider using ALTER TABLE ADD PARTITION.

  • Partitions missing from file system – If you delete a partition manually in Amazon S3 and then run MSCK REPAIR TABLE, you may receive the error message Partitions missing from filesystem. This occurs because MSCK REPAIR TABLE doesn't remove stale partitions from table metadata. To remove the deleted partitions from table metadata, run ALTER TABLE DROP PARTITION instead. Note that SHOW PARTITIONS similarly lists only the partitions in metadata, not the partitions in the file system.

  • "NullPointerException name is null" error

    If you use the Amazon Glue CreateTable API operation or the Amazon CloudFormation AWS::Glue::Table template to create a table for use in Athena without specifying the TableType property and then run a DDL query like SHOW CREATE TABLE or MSCK REPAIR TABLE, you can receive the error message FAILED: NullPointerException Name is null.

    To resolve the error, specify a value for the TableInput TableType attribute as part of the Amazon Glue CreateTable API call or Amazon CloudFormation template. Possible values for TableType include EXTERNAL_TABLE or VIRTUAL_VIEW.

    This requirement applies only when you create a table using the Amazon Glue CreateTable API operation or the AWS::Glue::Table template. If you create a table for Athena by using a DDL statement or an Amazon Glue crawler, the TableType property is defined for you automatically.

The following sections provide some additional detail.

Allow glue:BatchCreatePartition in the IAM policy

Review the IAM policies attached to the role that you're using to run MSCK REPAIR TABLE. When you use the Amazon Glue Data Catalog with Athena, the IAM policy must allow the glue:BatchCreatePartition action. For an example of an IAM policy that allows the glue:BatchCreatePartition action, see Amazon managed policy: AmazonAthenaFullAccess.

Change or redefine the Amazon S3 path

If one or more object keys in the Amazon S3 path are in camel case instead of lower case, MSCK REPAIR TABLE might not add the partitions to the Amazon Glue Data Catalog. For example, if your Amazon S3 path includes the object key name userId, the following partitions might not be added to the Amazon Glue Data Catalog:

s3://DOC-EXAMPLE-BUCKET/path/userId=1/

s3://DOC-EXAMPLE-BUCKET/path/userId=2/

s3://DOC-EXAMPLE-BUCKET/path/userId=3/

To resolve this issue, do one of the following:

  • Use lower case instead of camel case when you create your Amazon S3 object keys:

    s3://DOC-EXAMPLE-BUCKET/path/userid=1/

s3://DOC-EXAMPLE-BUCKET/path/userid=2/

s3://DOC-EXAMPLE-BUCKET/path/userid=3/

  • Use ALTER TABLE ADD PARTITION to redefine the location, as in the following example:

    ALTER TABLE table_name ADD [IF NOT EXISTS]
PARTITION (userId=1)
LOCATION 's3://DOC-EXAMPLE-BUCKET/path/userId=1/'
PARTITION (userId=2)
LOCATION 's3://DOC-EXAMPLE-BUCKET/path/userId=2/'
PARTITION (userId=3)
LOCATION 's3://DOC-EXAMPLE-BUCKET/path/userId=3/'

Note that although Amazon S3 object key names can use upper case, Amazon S3 bucket names themselves must always be in lower case. For more information, see Object key naming guidelines and Bucket naming rules in the Amazon S3 User Guide.