X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/900b548097c68649ae2874ded5849f1d8164384c..HEAD:/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 5f212573bc..1832a1530e 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -3,78 +3,94 @@ layout: default
navsection: userguide
title: "Uploading data"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
-Arvados Data collections can be uploaded using either the @arv keep put@ command line tool or using Workbench.
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Arvados Data collections can be uploaded using either Workbench or the @arv-put@ command line tool.
-# "*Upload using command line tool*":#upload-using-command
# "*Upload using Workbench*":#upload-using-workbench
+# "*Upload using command line tool*":#upload-using-command
+
+h2(#upload-using-workbench). Upload using Workbench
+
+To upload using Workbench, first identify the project to upload the files into. This is done by browsing your projects in the navigation menu on the left, or to search for the project using the search field on the top.
+
+Having navigated to the project, click on the + NEW button in the top-left corner. In the pop-up menu, select the item *New collection*.
+
+ !{width: 80%;}{{ site.baseurl }}/images/add-new-collection-wb2.png! _Creating a new collection in the project "WGS Processing Tutorial"_
+
+In the dialog box that follows, you will be prompted to create a new collection in your chosen project. Here, the *Collection Name* field is required. After entering the name for this new collection (and optionally other fields), you have the choice to create it with new file updates -- by drag-and-drop into the *Files* area or with the traditional file-upload dialog opened by your browser.
+
+!{width: 100%;}{{ site.baseurl }}/images/new-collection-modal-wb2.png!_Providing the new collection with a name (required). Optionally, you can upload files in this step._
+
+You can then click on the CREATE A COLLECTION button and proceed to the newly-created collection's page. If you don't upload any data when creating the collection, the new collection will be empty, and you can upload files into it later.
+
+!{width: 100%;}{{ site.baseurl }}/images/newly-created-collection-empty-wb2.png!_The newly-created collection without any files yet._
+
+In the FILES panel, there is a button labeled UPLOAD DATA. Click on it, and you will be prompted to upload files by drag-and-drop or the file-selection dialog opened by your browser.
+
+The files you choose to upload will then be displayed, and you can review them before clicking on the UPLOAD DATA button to initiate the actual file transfer.
+
+!{width: 100%;}{{ site.baseurl }}/images/upload-data-prompt-with-files-wb2.png!_Selecting the files to upload_
+
+Once the file upload completes, you will be notified by a message, and the files will appear under the FILES panel shortly.
+
+!{width: 100%;}{{ site.baseurl }}/images/upload-data-progress-wb2.png!_Upload status being displayed, with the files to appear shortly_
+
+*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.
+
+*Note:* You can also use the UPLOAD DATA button to add additional files to an existing collection.
notextile.
+
h2(#upload-using-command). Upload using command line tool
{% include 'tutorial_expectations' %}
-To upload a file to Keep using @arv keep put@:
+To upload a file to Keep using @arv-put@:
-
-The output value @qr1hi-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
+The output value @zzzzz-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
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
-It is also possible to upload an entire directory with @arv keep put@:
+It is also possible to upload an entire directory with @arv-put@:
-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.
+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.
-@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.
+@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.
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 name printed by @arv keep put@ will appear under the *name* column.
+Visit the Workbench and go to your *Home Projects*. Your newly uploaded collection should appear in the main panel. The collection name printed by @arv-put@ will appear under the *Name* column, and its *Type* will be "_Data collection_".
-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...* button. This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the Move button.
+Click on the collection's name will lead you to its Workbench page, where you can see the collection's contents and download individual files.
-!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/workbench-move-selected.png!
+To move the collection to a different project, locate the collection and right-click on it. This will bring up a context menu with *Move to*. Click on this item, and you will see a dialog box where you can select the target project to move this collection to, by search or navigation. This context menu is also available from the triple-dot button in the project/collection listing or the collection details page.
-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.
+!{width: 80%;}{{ site.baseurl }}/images/workbench-move-wb2.png! _Context menu with the_ *Move to* _item_
notextile.
-
-h2(#upload-using-workbench). Upload using Workbench
-
-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.
-
-To upload files into a new collection, click on *Add data* dropdown menu and select *Upload files from my computer*.
-
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-using-workbench.png!
-
- This will create a new empty collection in your chosen project and will take you to the *Upload* tab for that collection.
-
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-tab-in-new-collection.png!
-
-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.
-
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/files-uploaded.png!
-
-*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.
-
-*Note:* You can also use the Upload tab to add additional files to an existing collection.