X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2d8508738cc5ae65818f5e6a0ca4e0af15fb6b0c..5bcba288077488791daa43a15d5fd5fb0c6e653c:/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 0c1b04758a..ada6d1fbab 100644 --- a/doc/user/tutorials/tutorial-keep.html.textile.liquid +++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid @@ -4,47 +4,53 @@ navsection: userguide 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.personalgenomes.org subject "hu599905.":https://my.personalgenomes.org/profile/hu599905 +This tutorial describes how to to upload new Arvados data collections using the command line tool @arv keep put@. notextile.
-# 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.) - -
~$ 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
-
- -# Now upload the file to Keep using @arv-put@: +{% include 'tutorial_expectations' %} + +h3. Upload + +To upload a file to Keep using @arv keep put@: -
~$ arv-put var-GS000016015-ASM.tsv.bz2
+
~$ arv keep put var-GS000016015-ASM.tsv.bz2
 216M / 216M 100.0%
-c1bad4b39ca5a924e481008009d94e32+210
+Collection saved as ...
+qr1hi-4zz18-xxxxxxxxxxxxxxx
 

 
 
-* The output value @c1bad4b39ca5a924e481008009d94e32+210@ is the Arvados collection locator that uniquely describes this file.
-
-Now go to the workbench collections page: https://{{ site.arvados_workbench_host }}/collections.  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 * 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   Add to project....  This will open a modal dialog allowing you to select a destination project for your collection.
-
-notextile.
+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: +It is also possible to upload an entire directory with @arv keep put@: 
~$ mkdir tmp
 ~$ echo "hello alice" > tmp/alice.txt
 ~$ echo "hello bob" > tmp/bob.txt
 ~$ echo "hello carol" > tmp/carol.txt
-~$ arv-put tmp
+~$ arv keep put tmp
 0M / 0M 100.0%
-887cd41e9c613463eab2f0d885c6dd96+83
+Collection saved as ...
+qr1hi-4zz18-yyyyyyyyyyyyyyy
+ +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* 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...* 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 Move button. + +!{{ site.baseurl }}/images/workbench-move-selected.png! + +Click on the * 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.