---
layout: default
navsection: userguide
navmenu: Tutorials
title: "Storing and Retrieving data using Arvados Keep"
navorder: 11
---
h1. Tutorial: Storing and Retrieving data using Arvados Keep
This tutorial introduces you to the Arvados file storage system.
*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
The Arvados distributed file system is called *Keep*. Keep is a content-addressable file system. This means that files are managed using special unique identifiers derived from the _contents_ of the file, rather than human-assigned file names (specifically, the md5 hash). This has a number of advantages:
* Files can be stored and replicated across a cluster of servers without requiring a central name server.
* Systematic validation of data integrity by both server and client because the checksum is built into the identifier.
* Minimizes data duplication (two files with the same contents will result in the same identifier, and will not be stored twice.)
* Avoids data race conditions (an identifier always points to the same data.)
h1. Putting Data into Keep
We will start with downloading a freely available VCF exome from the "Personal Genome Project (PGP)":http://www.personalgenomes.org subject "hu599905":https://my.personalgenomes.org/profile/hu599905 and add it to Keep. From an Arvados VM instance:
$ curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.personalgenomes.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 216M 100 216M 0 0 10.0M 0 0:00:21 0:00:21 --:--:-- 9361k
Alternately, if you have your own data, for example @MyExome.vcf@, you can use @rsync@ on your local computer to copy it to the shell VM:
notextile. $ rsync MyExome.vcf shell.qr1hi:MyExome.vcf
Now use @arv keep put@ to add your VCF data to Keep:
$ arv keep put var-GS000016015-ASM.tsv.bz2
33a9f3842b01ea3fdf27cc582f5ea2af
The output value @33a9f3842b01ea3fdf27cc582f5ea2af@ is the Keep locator. This enables you to access the file you just uploaded, and is explained in the next section.
h2. Putting a directory
You can also use @arv keep put@ to add an entire directory:
$ mkdir tmp
$ echo "hello alice" > tmp/alice.txt
$ echo "hello bob" > tmp/bob.txt
$ echo "hello carol" > tmp/carol.txt
$ arv keep put tmp
0M / 0M 100.0%
887cd41e9c613463eab2f0d885c6dd96+83
h1. Getting Data from Keep
In Keep, information is stored in *data blocks*. Data blocks are normally between 1 byte and 64 megabytes in size. If a file exceeds the maximum size of a single data block, the file will be split across multiple data blocks until the entire file can be stored. These data blocks may be stored and replicated across multiple disks, servers, or clusters. Each data block has its own identifier for the contents of that specific data block.
In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@ which we added to keep in the previous section. First let us examine the contents of this collection using @arv keep get@:
$ arv keep get c1bad4b39ca5a924e481008009d94e32+210
. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
@arv keep get@ fetches the contents of the locator @c1bad4b39ca5a924e481008009d94e32+210@. This is a locator for a collection data block, so it fetches the contents of the collection. In this example, this collection consists of a single file @var-GS000016015-ASM.tsv.bz2@ which is 227212247 bytes long, and is stored using four sequential data blocks, 204e43b8a1185621ca55a94839582e6f+67108864, b9677abbac956bd3e86b1deb28dfac03+67108864, fc15aff2a762b13f521baf042140acec+67108864, 323d2a3ce20370c4ca1d3462a344f8fd+25885655.
Let's use @arv keep get@ to download the first datablock:
notextile. $ arv keep get 204e43b8a1185621ca55a94839582e6f+67108864 > block1
Let's look at the size and compute the md5 hash of @block1@:
$ ls -l block1
-rw-r--r-- 1 you group 67108864 Dec 9 20:14 block1
$ md5sum block1
204e43b8a1185621ca55a94839582e6f block1
Notice that the block identifer 204e43b8a1185621ca55a94839582e6f+67108864 of:
* the md5 hash @204e43b8a1185621ca55a94839582e6f@ which matches the md5 hash of @block1@
* a size hint @67108864@ which matches the size of @block1@
Next, let's use @arv keep get@ to download and reassemble @var-GS000016015-ASM.tsv.bz2@ using the following command:
notextile. $ arv keep get c1bad4b39ca5a924e481008009d94e32+210/var-GS000016015-ASM.tsv.bz2 .
This downloads the file @var-GS000016015-ASM.tsv.bz2@ described by collection @c1bad4b39ca5a924e481008009d94e32+210@ from Keep and places it into the local directory. Now that we have the file, we can compute the md5 hash of the complete file:
$ md5sum var-GS000016015-ASM.tsv.bz2
44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
h2. Accessing Collections
There are a couple of other ways to access a collection. You may view the contents of a collection using @arv keep ls@:
$ arv keep ls c1bad4b39ca5a924e481008009d94e32+210
var-GS000016015-ASM.tsv.bz2
$ arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210
221887 var-GS000016015-ASM.tsv.bz2
* @-s@ prints file sizes in kilobytes
You may also access through the Arvados Workbench using a URI similar to this, where the last part of the path is the Keep locator:
"https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210":https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210
You are now ready to proceed to the next tutorial, "running a crunch job.":tutorial-job1.html