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navsection: userguide
title: "Accessing Keep from GNU/Linux"
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Copyright (C) The Arvados Authors. All rights reserved.

SPDX-License-Identifier: CC-BY-SA-3.0
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This tutoral describes how to access Arvados collections on GNU/Linux using traditional filesystem tools by mounting Keep as a file system using @arv-mount@.

{% include 'tutorial_expectations' %}

h2. Arv-mount

@arv-mount@ provides several features:

* You can browse, open and read Keep entries as if they are regular files.
* It is easy for existing tools to access files in Keep.
* Data is streamed on demand.  It is not necessary to download an entire file or collection to start processing.

The default mode permits browsing any collection in Arvados as a subdirectory under the mount directory.  To avoid having to fetch a potentially large list of all collections, collection directories only come into existence when explicitly accessed by UUID or portable data hash. For instance, a collection may be found by its content hash in the @keep/by_id@ directory.

<notextile>
<pre><code>~$ <span class="userinput">mkdir -p keep</span>
~$ <span class="userinput">arv-mount keep</span>
~$ <span class="userinput">cd keep/by_id/c1bad4b39ca5a924e481008009d94e32+210</span>
~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">ls</span>
var-GS000016015-ASM.tsv.bz2
~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">md5sum var-GS000016015-ASM.tsv.bz2</span>
44b8ae3fde7a8a88d2f7ebd237625b4f  var-GS000016015-ASM.tsv.bz2
~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">cd ../..</span>
~$ <span class="userinput">fusermount -u keep</span>
</code></pre>
</notextile>

The last line unmounts Keep.  Subdirectories will no longer be accessible.

In the top level directory of each collection, arv-mount provides a special file called @.arvados#collection@ that contains a JSON-formatted API record for the collection. This can be used to determine the collection's @portable_data_hash@, @uuid@, etc. This file does not show up in @ls@ or @ls -a@.

h3. Modifying files and directories in Keep

By default, all files in the Keep mount are read only.  However, @arv-mount --read-write@ enables you to perform the following operations using normal Unix command line tools (@touch@, @mv@, @rm@, @mkdir@, @rmdir@) and your own programs using standard POSIX file system APIs:

* Create, update, rename and delete individual files within collections
* Create and delete subdirectories inside collections
* Move files and directories within and between collections
* Create and delete collections within a project (using @mkdir@ and @rmdir@ in a project directory)

Not supported:

* Symlinks, hard links
* Changing permissions
* Extended attributes
* Moving a subdirectory of a collection into a project, or moving a collection from a project into another collection

If multiple clients (separate instances of arv-mount or other arvados applications) modify the same file in the same collection within a short time interval, this may result in a conflict.  In this case, the most recent commit wins, and the "loser" will be renamed to a conflict file in the form @name~YYYYMMDD-HHMMSS~conflict~@.

Please note this feature is in beta testing.  In particular, the conflict mechanism is itself currently subject to race conditions with potential for data loss when a collection is being modified simultaneously by multiple clients.  This issue will be resolved in future development.