title: "Uploading data"
...
-This tutorial describes how to to upload new Arvados data collections using the command line tool @arv-put@. This example uses a freely available TSV file containing variant annotations from "Personal Genome Project (PGP)":http://www.pgp-hms.org participant "hu599905.":https://my.pgp-hms.org/profile/hu599905
+This tutorial describes how to to upload new Arvados data collections using the command line tool @arv keep put@.
notextile. <div class="spaced-out">
-# Begin by installing the "Arvados Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html on the system from which you will upload the data (such as your workstation, or a server containing data from your sequencer). This will install the Arvados file upload tool, @arv-put@. Alternately, you can log into an Arvados VM (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
-# On system from which you will upload data, configure the environment with the Arvados instance host name and authentication token as decribed in "Getting an API token.":{{site.baseurl}}/user/reference/api-tokens.html (If you are logged into an Arvados VM, you can skip this step.)
-# Download the following example file. (If you are uploading your own data, you can skip this step.)
-<notextile>
-<pre><code>~$ <span class="userinput">curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.pgp-hms.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>
-# Now upload the file to Keep using @arv-put@:
+{% include 'tutorial_expectations' %}
+
+h3. Upload
+
+To upload a file to Keep using @arv keep put@:
<notextile>
-<pre><code>~$ <span class="userinput">arv-put var-GS000016015-ASM.tsv.bz2</span>
+<pre><code>~$ <span class="userinput">arv keep put var-GS000016015-ASM.tsv.bz2</span>
216M / 216M 100.0%
-c1bad4b39ca5a924e481008009d94e32+210
+Collection saved as ...
+qr1hi-4zz18-xxxxxxxxxxxxxxx
</code></pre>
</notextile>
-* The output value @c1bad4b39ca5a924e481008009d94e32+210@ is the Arvados collection locator that uniquely describes this file.
-
-Now go to the workbench collections page: <a href="https://{{ site.arvados_workbench_host }}/collections" target="_blank">https://{{ site.arvados_workbench_host }}/collections</a>. Your newly uploaded collection should appear near the top, with the value in the *uuid* column matching the Arvados collection locator that was printed by @arv-put@. Click on the *<i class="fa fa-fw fa-archive"></i> Show* button to go to the workbench page for your collection. Alternately, you can paste the Arvados collection locator into the *Search* box of the collections page to find your collection.
-
-The show collection page allows you to view the contents of the collection, download files from the collection, and set sharing options. To put your collection into a project, click on <span class="btn btn-xs btn-primary" ><i class="fa fa-fw fa-folder"></i> Add to project...</span>. This will open a modal dialog allowing you to select a destination project for your collection.
-
-notextile. </div>
+The output value @qr1hi-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
-h2(#dir). Putting a directory
+The file used in this example is a freely available TSV file containing variant annotations from "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.
-If you give @arv-put@ a directory, it will recursively upload the entire directory:
+<notextile><a name="dir"></a></notextile>It is also possible to upload an entire directory with @arv keep put@:
<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-put tmp</span>
+~$ <span class="userinput">arv keep put tmp</span>
0M / 0M 100.0%
-887cd41e9c613463eab2f0d885c6dd96+83
+Collection saved as ...
+qr1hi-4zz18-yyyyyyyyyyyyyyy
</code></pre>
</notextile>
+
+In both examples, the @arv keep put@ command created a collection. The first collection contains the single uploaded file. The second collection contains the entire uploaded directory.
+
+@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.
+
+h3. Locate your collection in Workbench
+
+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 locator printed by @arv keep put@ will appear under the *name* column.
+
+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*. 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.
+
+!{{ site.baseurl }}/images/workbench-move-selected.png!
+
+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.
+
+notextile. </div>
projects / arvados.git / blobdiff