X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4151af1d89da4c3f3fff3fb6732c0249d93dcda9..260fad7638148cadd52b9a2411a6717485553aea:/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 243a4834b4..21efc475c5 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -1,129 +1,96 @@
---
layout: default
navsection: userguide
-navmenu: Tutorials
-title: "Storing and Retrieving data using Arvados Keep"
-
+title: "Uploading data"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
-h1. Storing and Retrieving data using Arvados Keep
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
-This tutorial introduces you to the Arvados file storage system.
+Arvados Data collections can be uploaded using either Workbench or the @arv-put@ command line tool.
+# "*Upload using Workbench*":#upload-using-workbench
+# "*Creating projects*":#creating-projects
+# "*Upload using command line tool*":#upload-using-command
-*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*
+h2(#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.)
+To upload using Workbench, visit the Workbench *Dashboard*. Click on *Projects* dropdown menu in the top navigation menu and select your *Home* project or any other project of your choosing. You will see the *Data collections* tab for this project, which lists the collections in this project.
-h1. Putting Data into Keep
+To upload files into a new collection, click on *Add data* dropdown menu and select *Upload files from my computer*.
-We will start with downloading a freely available VCF file from the "Personal Genome Project (PGP)":http://www.personalgenomes.org subject "hu599905":https://my.personalgenomes.org/profile/hu599905 to a staging directory on the VM, and then add it to Keep.
+!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-using-workbench.png!
-In the following tutorials, replace you
with your user id.
+
This will create a new empty collection in your chosen project and will take you to the *Upload* tab for that collection.
-First, log into the Arvados VM instance and set up the staging area:
+!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-tab-in-new-collection.png!
-notextile.
~$ mkdir /scratch/you
+Click on the *Browse...* button and select the files you would like to upload. Selected files will be added to a list of files to be uploaded. After you are done selecting files to upload, click on the * Start* button to start upload. This will start uploading files to Arvados and Workbench will show you the progress bar. When upload is completed, you will see an indication to that effect.
-Next, download the file:
+!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/files-uploaded.png!
-~$ 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
-
-~$ scp MyData.vcf you@shell.arvados:/scratch/you/MyData.vcf
+h2(#creating-projects). Creating projects
-{% include 'notebox_end' %}
+Files are organized into Collections, and Collections are organized by Projects.
-Now use @arv keep put@ to add your VCF data to Keep, then delete the local copy of the file:
+Click on *Projects* → *Add a new project* to add a top level project.
-/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
+~$ arv-put var-GS000016015-ASM.tsv.bz2
+216M / 216M 100.0%
+Collection saved as ...
+zzzzz-4zz18-xxxxxxxxxxxxxxx
/scratch/you$ arv keep get c1bad4b39ca5a924e481008009d94e32+210
-. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+~$ mkdir tmp
+~$ echo "hello alice" > tmp/alice.txt
+~$ echo "hello bob" > tmp/bob.txt
+~$ echo "hello carol" > tmp/carol.txt
+~$ arv-put tmp
+0M / 0M 100.0%
+Collection saved as ...
+zzzzz-4zz18-yyyyyyyyyyyyyyy
204e43b8a1185621ca55a94839582e6f+67108864
, b9677abbac956bd3e86b1deb28dfac03+67108864
, fc15aff2a762b13f521baf042140acec+67108864
, 323d2a3ce20370c4ca1d3462a344f8fd+25885655
.
-
-Notice that the block identifer 204e43b8a1185621ca55a94839582e6f+67108864
consists 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:
-
-/scratch/you$ 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:
-
-/scratch/you$ md5sum var-GS000016015-ASM.tsv.bz2
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-
-/scratch/you$ arv keep ls c1bad4b39ca5a924e481008009d94e32+210
-var-GS000016015-ASM.tsv.bz2
-/scratch/you$ arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210
-221887 var-GS000016015-ASM.tsv.bz2
-
-