X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/cf7e30873ef4b92cc8ec099b2bb344391a070e93..0f644e242ef37c911ad3dc25aca8135c339de349:/doc/user/tutorials/tutorial-keep.html.textile.liquid?ds=sidebyside diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid index 6a797c001a..53cdfe4a08 100644 --- a/doc/user/tutorials/tutorial-keep.html.textile.liquid +++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid @@ -1,166 +1,85 @@ --- layout: default navsection: userguide -title: "Storing and Retrieving data using Keep" +title: "Uploading data" ... +{% comment %} +Copyright (C) The Arvados Authors. All rights reserved. -This tutorial introduces you to the Arvados file storage system. +SPDX-License-Identifier: CC-BY-SA-3.0 +{% endcomment %} +Arvados Data collections can be uploaded using either the @arv keep put@ command line tool or using Workbench. -*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* +# "*Upload using command line tool*":#upload-using-command +# "*Upload using Workbench*":#upload-using-workbench -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.) +notextile.
you
with your user id.
-
-First, log into the Arvados VM instance and set up the staging area:
-
-notextile. ~$ mkdir /scratch/you
-
-Next, download the file:
+{% include 'tutorial_expectations' %}
+To upload a file to Keep using @arv keep put@:
~$ 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
+~$ arv keep put var-GS000016015-ASM.tsv.bz2
+216M / 216M 100.0%
+Collection saved as ...
+qr1hi-4zz18-xxxxxxxxxxxxxxx
~$ 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, then delete the local copy of the file:
-
-/scratch/you$ arv keep put var-GS000016015-ASM.tsv.bz2
-c1bad4b39ca5a924e481008009d94e32+210
-/scratch/you$ rm var-GS000016015-ASM.tsv.bz2
-
-/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
+~$ 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%
+Collection saved as ...
+qr1hi-4zz18-yyyyyyyyyyyyyyy
/scratch/you$ arv keep ls c1bad4b39ca5a924e481008009d94e32+210
-var-GS000016015-ASM.tsv.bz2
-
+@arv keep put@ accepts quite a few optional command line arguments, which are described on the "arv subcommands":{{site.baseurl}}/sdk/cli/subcommands.html#arv-keep-put page.
-/scratch/you$ arv keep ls 887cd41e9c613463eab2f0d885c6dd96+83
-alice.txt
-bob.txt
-carol.txt
-
-/scratch/you$ arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210
-221887 var-GS000016015-ASM.tsv.bz2
-
-/scratch/you$ arv keep get c1bad4b39ca5a924e481008009d94e32+210/ .
-
-/scratch/you$ arv keep get 887cd41e9c613463eab2f0d885c6dd96+83/alice.txt .
-
-/scratch/you$ md5sum var-GS000016015-ASM.tsv.bz2
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-
-/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
-/scratch/you/mnt$ md5sum var-GS000016015-ASM.tsv.bz2
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-/scratch/you/mnt$ cd ..
-/scratch/you$ fusermount -u mnt
-
-/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
-
-