Recovering data

Arvados has several features to prevent accidental loss or deletion of data, but accidents can happen. This page lays out the options to recover deleted or overwritten collections.

For more detail on the data lifecycle in Arvados, see the Data lifecycle page.

Check the trash

When a collection is deleted, it is moved to the trash. It will remain there for the duration of Collections.DefaultTrashLifetime, and it can be untrashed via workbench or with the cli tools, as described in Recovering trashed collections.

Check for other collections with the same PDH

Multiple collections may share a portable data hash, i.e. have the same contents. If another collection exists with the same portable data hash, recovering data is not necessary, everything is still stored in Keep. A new copy of the collection can be made to make the data available in the correct project and with the correct permissions.

Consider collection versioning

Arvados supports collection versioning. If it has not been disabled on your cluster, the deleted collection may be recoverable from an older version. See Using collection versioning for details.

Recovering collections

When all the above options fail, it may still be possible to recover a collection that has been deleted.

To recover a collection the manifest is required. Arvados has a built-in audit log, which consists of a row added to the “logs” table in the PostgreSQL database each time an Arvados object is created, modified, or deleted. Collection manifests are included, unless they are listed in the AuditLogs.UnloggedAttributes configuration parameter. The audit log is retained for up to AuditLogs.MaxAge.

In some cases, it is possible to recover files that have been lost by modifying or deleting a collection.

Possibility of recovery depends on many factors, including:

Whether the collection manifest is still available, e.g., in an audit log entry
Whether the data blocks are also referenced by other collections
Whether the data blocks have been unreferenced long enough to be marked for deletion/trash by keep-balance
Blob signature TTL, trash lifetime, trash check interval, and other config settings

To attempt recovery of a previous version of a deleted/modified collection, use the arvados-server recover-collection command. It should be run on one of your server nodes where the arvados-server package is installed and the /etc/arvados/config.yml file is up to date.

Specify the collection you want to recover by passing either the UUID of an audit log entry, or a file containing the manifest.

If recovery is successful, the recover-collection program saves the recovered data a new collection belonging to the system user, and prints the new collection’s UUID on stdout.

# arvados-server recover-collection 9tee4-57u5n-nb5awmk1pahac2t
INFO[2020-06-05T19:52:29.557761245Z] loaded log entry                              logged_event_time="2020-06-05 16:48:01.438791 +0000 UTC" logged_event_type=update old_collection_uuid=9tee4-4zz18-1ex26g95epmgw5w src=9tee4-57u5n-nb5awmk1pahac2t
INFO[2020-06-05T19:52:29.642145127Z] recovery succeeded                            UUID=9tee4-4zz18-5trfp4k4xxg97f1 src=9tee4-57u5n-nb5awmk1pahac2t
9tee4-4zz18-5trfp4k4xxg97f1
INFO[2020-06-05T19:52:29.644699436Z] exiting

In this example, the original data has been restored and saved in a new collection with UUID 9tee4-4zz18-5trfp4k4xxg97f1.

For more options, run arvados-server recover-collection -help.

Untrashing lost blocks

In some cases it is possible to recover data blocks that were trashed erroneously by keep-balance (e.g. due to an install/config error).

If you suspect blocks have been trashed erroneously, you should immediately:

On all keepstore servers: set BlobTrashCheckInterval to a long time like 2400h
On all keepstore servers: restart keepstore
Stop the keep-balance service

When you think you have corrected the underlying problem, you should:

Set Collections.BlobMissingReport to a suitable value (perhaps “/tmp/keep-balance-lost-blocks.txt”).
Start keep-balance
After keep-balance completes its first sweep, inspect /tmp/keep-balance-lost-blocks.txt. If it’s not empty, you can request all keepstores to untrash any blocks that are still recoverable with a script like this:


#!/bin/bash
set -e

# see Client.AuthToken in /etc/arvados/keep-balance/keep-balance.yml
token=xxxxxxx-your-system-auth-token-xxxxxxx

# all keep server hostnames
hosts=(keep0 keep1 keep2 keep3 keep4 keep5)

while read hash pdhs; do
  echo "${hash}"
  for h in ${hosts[@]}; do
    if curl -fgs -H "Authorization: Bearer $token" -X PUT "http://${h}:25107/untrash/$hash"; then
      echo "${hash} ok ${host}"
    fi
  done
done < /tmp/keep-balance-lost-blocks.txt

Any blocks which were successfully untrashed can be removed from the list of blocks and collections which need to be recovered.

Regenerating lost blocks

For blocks which were trashed long enough ago that they’ve been deleted, it may be possible to regenerate them by rerunning the workflows which generated them. To do this, the process is:

Delete the affected collections so that job reuse doesn’t attempt to reuse them (it’s likely that if one block is missing, they all are, so they’re unlikely to contain any useful data)
Resubmit any container requests for which you want the output collections regenerated

The Arvados repository contains a tool that can be used to generate a report to help with this task at arvados/tools/keep-xref/keep-xref.py

Previous: Configuring storage classes Next: Measuring deduplication