4 title: "Mounting Keep as a filesystem"
7 Copyright (C) The Arvados Authors. All rights reserved.
9 SPDX-License-Identifier: CC-BY-SA-3.0
12 This tutoral describes how to access Arvados collections using traditional filesystem tools by mounting Keep as a read-only file system using @arv-mount@.
14 {% include 'tutorial_expectations' %}
18 @arv-mount@ provides several features:
20 * You can browse, open and read Keep entries as if they are regular files.
21 * It is easy for existing tools to access files in Keep.
22 * Data is streamed on demand. It is not necessary to download an entire file or collection to start processing.
24 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.
27 <pre><code>~$ <span class="userinput">mkdir -p keep</span>
28 ~$ <span class="userinput">arv-mount keep</span>
29 ~$ <span class="userinput">cd keep/by_id/c1bad4b39ca5a924e481008009d94e32+210</span>
30 ~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">ls</span>
31 var-GS000016015-ASM.tsv.bz2
32 ~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">md5sum var-GS000016015-ASM.tsv.bz2</span>
33 44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
34 ~/keep/by_id/c1bad4b39ca5a924e481008009d94e32+210$ <span class="userinput">cd ../..</span>
35 ~$ <span class="userinput">fusermount -u keep</span>
39 The last line unmounts Keep. Subdirectories will no longer be accessible.
41 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@.
43 h3. Modifying files and directories in Keep
45 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:
47 * Create, update, rename and delete individual files within collections
48 * Create and delete subdirectories inside collections
49 * Move files and directories within and between collections
50 * Create and delete collections within a project (using @mkdir@ and @rmdir@ in a project directory)
54 * Symlinks, hard links
55 * Changing permissions
57 * Moving a subdirectory of a collection into a project, or moving a collection from a project into another collection
59 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~@.
61 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.