---
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*<span class="caret"></span> 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*<span class="caret"></span> 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!
-First, log into the Arvados VM instance and set up the staging area:
+<br/>This will create a new empty collection in your chosen project and will take you to the *Upload* tab for that collection.
-notextile. <pre><code>$ <span class="userinput">mkdir /scratch/<b>you</b></span></code></pre>
+!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-tab-in-new-collection.png!
-Next, download the file:
+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 *<i class="fa fa-fw fa-play"></i> 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.
-<notextile>
-<pre><code>$ <span class="userinput">mkdir /scratch/<b>you</b></span>
-$ <span class="userinput">cd /scratch/<b>you</b></span>
-$ <span class="userinput">curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.personalgenomes.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2'</span>
- % 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
-</code></pre>
-</notextile>
+!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/files-uploaded.png!
-Alternately, 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):
+*Note:* If you leave the collection page during the upload, the upload process will be aborted and you will need to upload the files again.
-notextile. <pre><code>$ <span class="userinput">scp MyData.vcf <b>you@shell</b>.arvados:/scratch/<b>you</b>/MyData.vcf</span></code></pre>
+*Note:* You can also use the Upload tab to add additional files to an existing collection.
-Now use @arv keep put@ to add your VCF data to Keep:
+notextile. <div class="spaced-out">
-<notextile>
-<pre><code>$ <span class="userinput">cd /scratch/<b>you</b></span>
-$ <span class="userinput">arv keep put var-GS000016015-ASM.tsv.bz2</span>
-c1bad4b39ca5a924e481008009d94e32+210
-</code></pre>
-</notextile>
-
-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.
-
-h2. Putting a directory
+h2(#creating-projects). Creating projects
-You can also use @arv keep put@ to add an entire directory:
+Files are organized into Collections, and Collections are organized by Projects.
-<notextile>
-<pre><code>$ <span class="userinput">mkdir tmp</span>
-$ <span class="userinput">echo "hello alice" > tmp/alice.txt</span>
-$ <span class="userinput">echo "hello bob" > tmp/bob.txt</span>
-$ <span class="userinput">echo "hello carol" > tmp/carol.txt</span>
-$ <span class="userinput">arv keep put tmp</span>
-0M / 0M 100.0%
-887cd41e9c613463eab2f0d885c6dd96+83
-</code></pre>
-</notextile>
+Click on *Projects*<span class="caret"></span> <span class="rarr">→</span> <i class="fa fa-fw fa-plus"></i>*Add a new project* to add a top level project.
-h1. Getting Data from Keep
+To create a subproject, navigate to the parent project, and click on <i class="fa fa-fw fa-plus"></i>*Add a subproject*.
-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.
+See "Sharing collections":tutorial-keep-get.html#download-shared-collection for information about sharing projects and collections with other users.
-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.
+h2(#upload-using-command). Upload using command line tool
-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@:
+{% include 'tutorial_expectations' %}
+To upload a file to Keep using @arv-put@:
<notextile>
-<pre><code>$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210</span>
-. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
+<pre><code>~$ <span class="userinput">arv-put var-GS000016015-ASM.tsv.bz2</span>
+216M / 216M 100.0%
+Collection saved as ...
+zzzzz-4zz18-xxxxxxxxxxxxxxx
</code></pre>
</notextile>
-@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, <code>204e43b8a1185621ca55a94839582e6f+67108864</code>, <code>b9677abbac956bd3e86b1deb28dfac03+67108864</code>, <code>fc15aff2a762b13f521baf042140acec+67108864</code>, <code>323d2a3ce20370c4ca1d3462a344f8fd+25885655</code>.
-Let's use @arv keep get@ to download the first datablock:
+The output value @zzzzz-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
-notextile. <pre><code>$ <span class="userinput">arv keep get 204e43b8a1185621ca55a94839582e6f+67108864 > block1</span></code></pre>
+Note: The file used in this example is a freely available TSV file containing variant annotations from the "Personal Genome Project (PGP)":http://www.pgp-hms.org participant "hu599905":https://my.pgp-hms.org/profile/hu599905), downloadable "here":https://warehouse.pgp-hms.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2. Alternatively, you can replace @var-GS000016015-ASM.tsv.bz2@ with the name of any file you have locally, or you could get the TSV file by "downloading it from Keep.":{{site.baseurl}}/user/tutorials/tutorial-keep-get.html
-Let's look at the size and compute the md5 hash of @block1@:
+<notextile><a name="dir"></a></notextile>It is also possible to upload an entire directory with @arv-put@:
<notextile>
-<pre><code>$ <span class="userinput">ls -l block1</span>
--rw-r--r-- 1 you group 67108864 Dec 9 20:14 block1
-$ <span class="userinput">md5sum block1</span>
-204e43b8a1185621ca55a94839582e6f block1
+<pre><code>~$ <span class="userinput">mkdir tmp</span>
+~$ <span class="userinput">echo "hello alice" > tmp/alice.txt</span>
+~$ <span class="userinput">echo "hello bob" > tmp/bob.txt</span>
+~$ <span class="userinput">echo "hello carol" > tmp/carol.txt</span>
+~$ <span class="userinput">arv-put tmp</span>
+0M / 0M 100.0%
+Collection saved as ...
+zzzzz-4zz18-yyyyyyyyyyyyyyy
</code></pre>
</notextile>
-Notice that the block identifer <code>204e43b8a1185621ca55a94839582e6f+67108864</code> 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. <pre><code>$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210/var-GS000016015-ASM.tsv.bz2 .</span></code></pre>
+In both examples, the @arv-put@ command created a collection. The first collection contains the single uploaded file. The second collection contains the entire uploaded directory.
-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:
+@arv-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.
-<notextile>
-<pre><code>$ <span class="userinput">md5sum var-GS000016015-ASM.tsv.bz2</span>
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-</code></pre>
-</notextile>
+h3. Locate your collection in Workbench
-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@:
-
-<notextile>
-<pre><code>$ <span class="userinput">arv keep ls c1bad4b39ca5a924e481008009d94e32+210</span>
-var-GS000016015-ASM.tsv.bz2
-$ <span class="userinput">arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210</span>
-221887 var-GS000016015-ASM.tsv.bz2
-</code></pre>
-</notextile>
+Visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection name printed by @arv-put@ will appear under the *name* column.
-* @-s@ prints file sizes in kilobytes
+To move the collection to a different project, check the box at the left of the collection row. Pull down the *Selection...*<span class="caret"></span> menu near the top of the page tab, and select *Move selected...* button. This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
-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:
+!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/workbench-move-selected.png!
-"https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210":https://workbench.{{ site.arvados_api_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210
+Click on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection's listing on a project page to go to the Workbench page for your collection. On this page, you can see the collection's contents, download individual files, and set sharing options.
-You are now ready to proceed to the next tutorial, "running a crunch job.":tutorial-job1.html
+notextile. </div>
projects / arvados.git / blobdiff