X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ba64505e002d2d3a00d14ea567e80889534f14bf..7079ddb46ce3e855a30a4bd5b8f1f3e626ce7b7a:/doc/user/tutorials/tutorial-keep.html.textile.liquid
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 16c113d950..5a5e8796cb 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -1,17 +1,13 @@
---
layout: default
navsection: userguide
-navmenu: Tutorials
-title: "Storing and Retrieving data using Arvados Keep"
-
+title: "Storing and Retrieving data using Keep"
...
-h1. 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*
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/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.
@@ -27,14 +23,13 @@ In the following tutorials, replace you with your user id.
First, log into the Arvados VM instance and set up the staging area:
-notextile. $ mkdir /scratch/you
+notextile. ~$ mkdir /scratch/you
Next, download the file:
-$ mkdir /scratch/you
-$ cd /scratch/you
-$ curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.personalgenomes.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2'
+~$ cd /scratch/you
+/scratch/you$ 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
@@ -45,98 +40,127 @@ $ curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse
If you have your own data, for example @MyData.vcf@, you can use @scp@ or @rsync@ to copy from your local workstation to the shell VM (run this on your local workstation):
-notextile. $ scp MyData.vcf you@shell.arvados:/scratch/you/MyData.vcf
+notextile. ~$ scp MyData.vcf you@shell.arvados:/scratch/you/MyData.vcf
{% include 'notebox_end' %}
-Now use @arv keep put@ to add your VCF data to Keep:
+Now use @arv keep put@ to add your VCF data to Keep, then delete the local copy of the file:
-$ cd /scratch/you
-$ arv keep put var-GS000016015-ASM.tsv.bz2
+/scratch/you$ arv keep put var-GS000016015-ASM.tsv.bz2
c1bad4b39ca5a924e481008009d94e32+210
+/scratch/you$ rm var-GS000016015-ASM.tsv.bz2
-The output value @c1bad4b39ca5a924e481008009d94e32+210@ is the Keep locator. This enables you to access the file you just uploaded, and is explained in the next section.
+The output value @c1bad4b39ca5a924e481008009d94e32+210@ from @arv keep put@ 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
+h2(#dir). 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
+/scratch/you$ mkdir tmp
+/scratch/you$ echo "hello alice" > tmp/alice.txt
+/scratch/you$ echo "hello bob" > tmp/bob.txt
+/scratch/you$ echo "hello carol" > tmp/carol.txt
+/scratch/you$ arv keep put tmp
0M / 0M 100.0%
887cd41e9c613463eab2f0d885c6dd96+83
+The locator @887cd41e9c613463eab2f0d885c6dd96+83@ represents a collection with multiple files.
+
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.
+h2. Using Workbench
-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.
+You may access collections through the "Collections section of Arvados Workbench":https://{{ site.arvados_workbench_host }}/collections located at "https://{{ site.arvados_workbench_host }}/collections":https://{{ site.arvados_workbench_host }}/collections . You can also access individual collections and individual files within a collection. Some examples:
-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@:
+* "https://{{ site.arvados_workbench_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210":https://{{ site.arvados_workbench_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210
+* "https://{{ site.arvados_workbench_host }}/collections/887cd41e9c613463eab2f0d885c6dd96+83/alice.txt":https://{{ site.arvados_workbench_host }}/collections/887cd41e9c613463eab2f0d885c6dd96+83/alice.txt
+
+h2(#arv-get). Using arv-get
+
+You can view the contents of a collection using @arv keep ls@:
-$ arv keep get c1bad4b39ca5a924e481008009d94e32+210
-. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+/scratch/you$ arv keep ls c1bad4b39ca5a924e481008009d94e32+210
+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.
+/scratch/you$ arv keep ls 887cd41e9c613463eab2f0d885c6dd96+83
+alice.txt
+bob.txt
+carol.txt
+
+
-Let's use @arv keep get@ to download the first datablock:
+Use @-s@ to print file sizes rounded up to the nearest kilobyte:
-notextile. $ arv keep get 204e43b8a1185621ca55a94839582e6f+67108864 > block1
+
+/scratch/you$ arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210
+221887 var-GS000016015-ASM.tsv.bz2
+
+
-Let's look at the size and compute the md5 hash of @block1@:
+Use @arv keep get@ to download the contents of a collection and place it in the directory specified in the second argument (in this example, @.@ for the current directory):
-$ ls -l block1
--rw-r--r-- 1 you group 67108864 Dec 9 20:14 block1
-$ md5sum block1
-204e43b8a1185621ca55a94839582e6f block1
+/scratch/you$ arv keep get c1bad4b39ca5a924e481008009d94e32+210/ .
-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:
+You can also download individual files:
-notextile. $ arv keep get c1bad4b39ca5a924e481008009d94e32+210/var-GS000016015-ASM.tsv.bz2 .
+
+/scratch/you$ arv keep get 887cd41e9c613463eab2f0d885c6dd96+83/alice.txt .
+
+
-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:
+With a local copy of the file, we can do some computation, for example computing the md5 hash of the complete file:
-$ md5sum var-GS000016015-ASM.tsv.bz2
+/scratch/you$ md5sum var-GS000016015-ASM.tsv.bz2
44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-h2. Accessing Collections
+h2. Using arv-mount
-There are a couple of other ways to access a collection. You may view the contents of a collection using @arv keep ls@:
+Use @arv-mount@ to take advantage of the "File System in User Space / FUSE":http://fuse.sourceforge.net/ feature of the Linux kernel to mount a Keep collection as if it were a regular directory tree.
-$ arv keep ls c1bad4b39ca5a924e481008009d94e32+210
+/scratch/you$ mkdir mnt
+/scratch/you$ arv-mount --collection c1bad4b39ca5a924e481008009d94e32+210 mnt &
+/scratch/you$ cd mnt
+/scratch/you/mnt$ ls
var-GS000016015-ASM.tsv.bz2
-$ arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210
-221887 var-GS000016015-ASM.tsv.bz2
+/scratch/you/mnt$ md5sum var-GS000016015-ASM.tsv.bz2
+44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+/scratch/you/mnt$ cd ..
+/scratch/you$ fusermount -u mnt
-* @-s@ prints file sizes in kilobytes
+You can also mount the entire Keep namespace in "magic directory" mode:
-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:
+
+/scratch/you$ mkdir mnt
+/scratch/you$ arv-mount mnt &
+/scratch/you$ cd mnt/c1bad4b39ca5a924e481008009d94e32+210
+/scratch/you/mnt/c1bad4b39ca5a924e481008009d94e32+210$ ls
+var-GS000016015-ASM.tsv.bz2
+/scratch/you/mnt/c1bad4b39ca5a924e481008009d94e32+210$ md5sum var-GS000016015-ASM.tsv.bz2
+44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
+/scratch/you/mnt/c1bad4b39ca5a924e481008009d94e32+210$ cd ../..
+/scratch/you$ fusermount -u mnt
+
+
-"https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210":https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210
+Using @arv-mount@ has several significant benefits:
-You are now ready to proceed to the next tutorial, "running a crunch job.":tutorial-job1.html
+* 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 downloaded on demand, it is not necessary to download an entire file or collection to start processing