[arvados] created: 2.6.0-353-ge99b6b02a
git repository hosting
git at public.arvados.org
Tue Jul 11 21:07:14 UTC 2023
at e99b6b02afef8ce23f8a78826bf911c57b7026ee (commit)
commit e99b6b02afef8ce23f8a78826bf911c57b7026ee
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Tue Jul 11 17:06:47 2023 -0400
20731: Make some text changes & reorganization based on workbench 2 updates
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/doc/_config.yml b/doc/_config.yml
index 2a6a581e8..b42a3c8b9 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -25,47 +25,45 @@ navbar:
- user/index.html.textile.liquid
- user/getting_started/community.html.textile.liquid
- Walkthough:
- - user/tutorials/wgs-tutorial.html.textile.liquid
- - Using Workbench:
- user/getting_started/workbench.html.textile.liquid
- - user/tutorials/tutorial-workflow-workbench.html.textile.liquid
- - user/topics/workbench-migration.html.textile.liquid
+ - user/tutorials/wgs-tutorial.html.textile.liquid
- Working at the Command Line:
- user/getting_started/setup-cli.html.textile.liquid
- user/reference/api-tokens.html.textile.liquid
- user/getting_started/check-environment.html.textile.liquid
- - Access an Arvados virtual machine:
- - user/getting_started/vm-login-with-webshell.html.textile.liquid
- - user/getting_started/ssh-access-unix.html.textile.liquid
- - user/getting_started/ssh-access-windows.html.textile.liquid
- Working with data sets:
+ - user/tutorials/tutorial-projects.html.textile.liquid
- user/tutorials/tutorial-keep.html.textile.liquid
- user/tutorials/tutorial-keep-get.html.textile.liquid
+ - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
+ - user/topics/arv-copy.html.textile.liquid
- user/tutorials/tutorial-keep-mount-gnu-linux.html.textile.liquid
- user/tutorials/tutorial-keep-mount-os-x.html.textile.liquid
- user/tutorials/tutorial-keep-mount-windows.html.textile.liquid
- - user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
- - user/topics/arv-copy.html.textile.liquid
- user/topics/collection-versioning.html.textile.liquid
- user/topics/storage-classes.html.textile.liquid
- Data Analysis with Workflows:
- - user/cwl/arvados-vscode-training.html.md.liquid
- - user/cwl/rnaseq-cwl-training.html.textile.liquid
+ - user/tutorials/tutorial-workflow-workbench.html.textile.liquid
- user/cwl/cwl-runner.html.textile.liquid
- user/cwl/cwl-run-options.html.textile.liquid
- - user/tutorials/writing-cwl-workflow.html.textile.liquid
+ - user/cwl/crunchstat-summary.html.textile.liquid
+ - user/debugging/container-shell-access.html.textile.liquid
+ - user/cwl/costanalyzer.html.textile.liquid
+ - user/cwl/federated-workflows.html.textile.liquid
+ - Common Workflow Language:
+ - user/cwl/rnaseq-cwl-training.html.textile.liquid
+ - user/cwl/arvados-vscode-training.html.md.liquid
- user/topics/arv-docker.html.textile.liquid
- user/cwl/cwl-style.html.textile.liquid
+ - user/tutorials/writing-cwl-workflow.html.textile.liquid
- user/cwl/cwl-extensions.html.textile.liquid
- - user/cwl/federated-workflows.html.textile.liquid
- user/cwl/cwl-versions.html.textile.liquid
- - user/cwl/crunchstat-summary.html.textile.liquid
- - user/cwl/costanalyzer.html.textile.liquid
- - user/debugging/container-shell-access.html.textile.liquid
- - Working with git repositories:
- - user/tutorials/add-new-repository.html.textile.liquid
- - user/tutorials/git-arvados-guide.html.textile.liquid
+ - Access an Arvados virtual machine:
+ - user/getting_started/vm-login-with-webshell.html.textile.liquid
+ - user/getting_started/ssh-access-unix.html.textile.liquid
+ - user/getting_started/ssh-access-windows.html.textile.liquid
- Reference:
+ - user/topics/workbench-migration.html.textile.liquid
- user/topics/link-accounts.html.textile.liquid
- user/reference/cookbook.html.textile.liquid
- Arvados License:
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index dec4f5343..d96280d30 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -10,7 +10,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
{% include 'notebox_begin' %}
-These guides used to cover the classic Arvados Workbench web application, sometimes referred to as "Workbench 1". They are now being updated to cover the new "Workbench 2". See "Workbench 2 migration":{{site.baseurl}}/user/topics/workbench-migration.html for more information.
+This guide covers modern Arvados Workbench web application, which may be referred to as "Workbench 2" to distinguish it from the previous Arvados Workbench web application ("Workbench 1"). Documentation for the classic Workbench can be found in "older versions of the user guide":https://doc.arvados.org/v2.6/user/getting_started/workbench.html . See also "Workbench 2 migration":{{site.baseurl}}/user/topics/workbench-migration.html for more information.
{% include 'notebox_end' %}
You can access the Arvados Workbench used in this guide using this link:
diff --git a/doc/user/topics/workbench-migration.html.textile.liquid b/doc/user/topics/workbench-migration.html.textile.liquid
index 9a36435ea..d6960f9d7 100644
--- a/doc/user/topics/workbench-migration.html.textile.liquid
+++ b/doc/user/topics/workbench-migration.html.textile.liquid
@@ -9,15 +9,17 @@ Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-Arvados is in the process of migrating from the classic web application, referred to as "Workbench 1", to a completely new web application, referred to as "Workbench 2".
+Beginning in version 2.7, Arvados now defaults to a new web application, referred to as "Workbench 2". This is a major step in the migration from the classic web application, referred to as "Workbench 1". Workbench 1 should be considered deprecated and suppport for the Workbench 1 application will be dropped in a future Arvados release.
!{width: 90%}{{ site.baseurl }}/images/wb2-example.png!
-Workbench 2 is the new Workbench web application that will, over time, replace Workbench 1. Workbench 2 is being built based on user feedback, and it is approaching feature parity with Workbench 1. Workbench 2 has a modern look and feel and offers several advanced features and performance enhancements. Arvados clusters typically have both Workbench applications installed and have a dropdown menu option in the user menu to switch between versions.
+Workbench 2 is the new Workbench web application that replaces Workbench 1. Workbench 2 is being built based on user feedback, and has feature parity with Workbench 1. Workbench 2 has a modern look and feel and offers many advanced features and performance enhancements over the previous Workbench application.
+
+To facilitate migration, Arvados may have both Workbench applications installed and have a dropdown menu option in the user menu to switch between versions.
!{{ site.baseurl }}/images/switch-to-wb2.png!
-Workbench 2 is stable and recommended for general use, but still lacks some features available in the classic Workbench 1 application. When necessary, you can easily switch back:
+Workbench 2 is stable and recommended for general use. However, if you find that you need something in Workbench 1, you can easily switch back:
!{{ site.baseurl }}/images/switch-to-wb1.png!
diff --git a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
index 3402eafa1..5fa31970c 100644
--- a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
@@ -12,7 +12,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
Arvados Data collections can be downloaded using either the arv commands or using Workbench.
# "*Download using Workbench*":#download-using-workbench
-# "*Sharing collections*":#download-shared-collection
+# "*Creating a special download URL for a collection*":#download-shared-collection
# "*Download using command line tools*":#download-using-arv
h2(#download-using-workbench). Download using Workbench
@@ -21,26 +21,11 @@ You can also download Arvados data collections using the Workbench.
When you visit a project in Workbench (for instance, the <i class="fa fa-fw fa-folder"></i> *Home Projects* or any projects under it), the collections will show up on the project details page, with "_Data collection_" in the *Type* column.
-Clicking on a collection will bring you to its details page. There, the <span class="btn btn-sw btn-primary">FILES</span> panel acts like a file manager where you can navigate to or search for files, select them for actions, and download them.
+Clicking on a collection will bring you to its details page. There, the lower panel acts like a file manager where you can navigate to or search for files, select them for actions, and download them.
To download a file, simply click on the file, or bring up the context menu using right-click or the triple-dot button on its row, and then select the menu item *Download*.
-h2(#download-shared-collection). Sharing collections
-
-Collections or their parent projects can be shared with other users on the Arvados cluster. First, locate the collection or project using any available means (for instance, by manually navigating in the Workbench, or using the Search bar). Then right-click on its link in a listing, or click on the triple-dot button in the details page. You will find the menu item *Share*, which opens the dialog box *Sharing settings*.
-
-h3. Sharing with other Arvados users
-
-To share with other Arvados users, select the *WITH USERS/GROUPS* tab in the *Sharing settings* dialog box. Under *Add people and groups*, in the input field you can search for the user or group names. Select one you will be sharing with, choose the *Authorization* level (Read/Write/Manage) in the drop-down menu, and click on the plus sign (+) on the right. This can be repeated for other users or groups, each with their own *Authorization* level. The selected ones will appear under *People with access*. You can revisit the *Sharing settings* dialog box to modify the users or their access levels at a later time.
-
-The *General access* drop-down menu controls the default sharing setting, with the following choices:
-
-* *Private*: This is the initial state when no users or groups have been selected for sharing. At any time, by setting *General access* to private, the current sharing setting will be cleared, and any users or groups formerly with access will lose that access.
-* *Public*: This means the list of *People with access* will include _Anonymous users_, even if they are not users of the current cluster. You can further set their access level in the *Authorization* level.
-* *All users*: This means sharing with other users who are logged in on the current cluster.
-* *Shared*: When you choose to share with specific people or groups, *General access* will be set to *Shared*. From this state, you can further specify the default sharing settings for *Public* and *All users*.
-
-h3. Creating a special download URL for a collection
+h2(#download-shared-collection). Creating a special download URL for a collection
To share a collection with users that do not have an account on your Arvados cluster, locate the collection and then go to the *Sharing settings* dialog box as described above. There, select the *SHARING URLS* tab.
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 649820af1..1832a1530 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -12,7 +12,6 @@ SPDX-License-Identifier: CC-BY-SA-3.0
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
h2(#upload-using-workbench). Upload using Workbench
@@ -47,17 +46,6 @@ Once the file upload completes, you will be notified by a message, and the files
notextile. <div class="spaced-out">
-h2(#creating-projects). Creating projects
-
-Files are organized into Collections, and Collections are organized by Projects.
-
-When you have navigated to any existing project, clicking on <span class="btn btn-sm btn-primary">+ NEW</span> <span class="rarr">→</span> <i class="fa fa-fw fa-folder"></i> *New project* will prompt you to create a new subproject under the current project.
-
-If you're at the top-level <i class="fa fa-fw fa-folder"></i> *Home Projects*, a new top-level project will be created.
-
-Alternatively, you can right-click on the link to an existing project to bring up a context menu, and select *New project*.
-
-See "Sharing collections":tutorial-keep-get.html#download-shared-collection for information about sharing projects and collections with other users.
h2(#upload-using-command). Upload using command line tool
diff --git a/doc/user/tutorials/tutorial-projects.html.textile.liquid b/doc/user/tutorials/tutorial-projects.html.textile.liquid
new file mode 100644
index 000000000..b4dc9edea
--- /dev/null
+++ b/doc/user/tutorials/tutorial-projects.html.textile.liquid
@@ -0,0 +1,41 @@
+---
+layout: default
+navsection: userguide
+title: "Organizating data"
+...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+h2. Projects and Collections
+
+In Arvados, files are organized into "collections", and collections are organized by "project".
+
+Only collections can contain files. A collection is a distinct database record identified by a universal unique id (UUID). Arvados maintains a history of changes to the collection. Every collection version has an immutable identifier called a "portable data hash" which is computed from the file content of the collection. This can be used to refer to the immutable file content independently of the collection UUID. If two collections have the same portable data hash, they have the same file content.
+
+Projects contain collections, workflows and workflow runs, and other projects (subprojects). Both collections and projects can have user-provided metadata.
+
+Projects are the main unit of organization and sharing. See "Sharing collections":#sharing-projects for information about sharing projects and collections with other users.
+
+h2(#creating-projects). Creating a project
+
+When you have navigated to any existing project, clicking on <span class="btn btn-sm btn-primary">+ NEW</span> <span class="rarr">→</span> <i class="fa fa-fw fa-folder"></i> *New project* will prompt you to create a new subproject under the current project.
+
+If you're at the top-level <i class="fa fa-fw fa-folder"></i> *Home Projects*, a new top-level project will be created.
+
+Alternatively, you can right-click on the link to an existing project to bring up a context menu, and select *New project*.
+
+h2(#sharing-projects). Sharing projects
+
+Projects can be shared with other users on the Arvados cluster. First, locate the collection or project using any available means (for instance, by manually navigating in the Workbench, or using the Search bar). Then right-click on its link in a listing, or click on the triple-dot button in the details page. You will find the menu item *Share*, which opens the dialog box *Sharing settings*.
+
+To share with other Arvados users, select the *WITH USERS/GROUPS* tab in the *Sharing settings* dialog box. Under *Add people and groups*, in the input field you can search for the user or group names. Select one you will be sharing with, choose the *Authorization* level (Read/Write/Manage) in the drop-down menu, and click on the plus sign (+) on the right. This can be repeated for other users or groups, each with their own *Authorization* level. The selected ones will appear under *People with access*. You can revisit the *Sharing settings* dialog box to modify the users or their access levels at a later time.
+
+The *General access* drop-down menu controls the default sharing setting, with the following choices:
+
+* *Private*: This is the initial state when no users or groups have been selected for sharing. At any time, by setting *General access* to private, the current sharing setting will be cleared, and any users or groups formerly with access will lose that access.
+* *Public*: This means the list of *People with access* will include _Anonymous users_, even if they are not users of the current cluster. You can further set their access level in the *Authorization* level.
+* *All users*: This means sharing with other users who are logged in on the current cluster.
+* *Shared*: When you choose to share with specific people or groups, *General access* will be set to *Shared*. From this state, you can further specify the default sharing settings for *Public* and *All users*.
commit 490f53109586e68cea80cbd3b3ad2063f2a12b96
Author: Zoë Ma <zoe.ma at curii.com>
Date: Fri Jun 30 15:24:55 2023 +0800
Doc: Update the included note about Workbench 2 transition.
Reword the text to center the Workbench 2.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index d2c95c943..dec4f5343 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -10,7 +10,7 @@ SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
{% include 'notebox_begin' %}
-This guide covers the classic Arvados Workbench web application, sometimes referred to as "Workbench 1". There is also a new Workbench web application under development called "Workbench 2". This guide will be updated to cover "Workbench 2" in the future. See "Workbench 2 migration":{{site.baseurl}}/user/topics/workbench-migration.html for more information.
+These guides used to cover the classic Arvados Workbench web application, sometimes referred to as "Workbench 1". They are now being updated to cover the new "Workbench 2". See "Workbench 2 migration":{{site.baseurl}}/user/topics/workbench-migration.html for more information.
{% include 'notebox_end' %}
You can access the Arvados Workbench used in this guide using this link:
commit cf807b1f626184d656fd1cce083ee0a4a7daf580
Author: Zoë Ma <zoe.ma at curii.com>
Date: Fri Jun 30 14:57:31 2023 +0800
Doc: Update "Working with an Arvados git repository"
- Updated inline elements for Workbench 2.
TODO: Should double-check the instructions of using Workbench when a git
repo is ready.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/user/tutorials/git-arvados-guide.html.textile.liquid b/doc/user/tutorials/git-arvados-guide.html.textile.liquid
index a552e4ee0..a4ac2a579 100644
--- a/doc/user/tutorials/git-arvados-guide.html.textile.liquid
+++ b/doc/user/tutorials/git-arvados-guide.html.textile.liquid
@@ -24,7 +24,7 @@ Before you start using Git, you should do some basic configuration (you only nee
~$ <span class="userinput">git config --global user.email $USER at example.com</span></code></pre>
</notextile>
-On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*. In the *Repositories* page, you should see the @$USER/tutorial@ repository listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like <notextile><code>https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</code></notextile>. Alternatively, you can use <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
+On the Arvados Workbench, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> in the upper right corner of the top navigation menu to access the Account Management menu, and click on the menu item *Repositories*. In the *Repositories* page, you should see the @$USER/tutorial@ repository listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like <notextile><code>https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</code></notextile>. Alternatively, you can use <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
Next, on the Arvados virtual machine, clone your Git repository:
commit efb8d912841ca4b505402715cd766e09dfb8c29f
Author: Zoë Ma <zoe.ma at curii.com>
Date: Fri Jun 30 14:54:07 2023 +0800
Doc: Update "Adding a new Arvados git repository"
- Updated inline elements and the first 2 figures for Workbench 2.
TODO: The last figure remains to be updated.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/images/add-new-repository.png b/doc/images/add-new-repository.png
index 61938447f..d62a9869a 100644
Binary files a/doc/images/add-new-repository.png and b/doc/images/add-new-repository.png differ
diff --git a/doc/images/repositories-panel.png b/doc/images/repositories-panel.png
index 3e12860fb..c8f00f487 100644
Binary files a/doc/images/repositories-panel.png and b/doc/images/repositories-panel.png differ
diff --git a/doc/user/tutorials/add-new-repository.html.textile.liquid b/doc/user/tutorials/add-new-repository.html.textile.liquid
index e28b96123..6046e7d14 100644
--- a/doc/user/tutorials/add-new-repository.html.textile.liquid
+++ b/doc/user/tutorials/add-new-repository.html.textile.liquid
@@ -24,19 +24,19 @@ Before you start using Git and arvados repositories, you should do some basic co
h2. Add "tutorial" repository
-On the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*.
+On the Arvados Workbench, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> (Account Management) in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*.
-In the *Repositories* page, you will see the *Add new repository* button.
+In the *Repositories* page, you will see the <span class="btn btn-sm btn-primary">+ NEW REPOSITORY</span> button.
-!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/repositories-panel.png!
+!{width: 100%;}{{ site.baseurl }}/images/repositories-panel.png!
-Click the *Add new Repository* button to open the popup to add a new arvados repository. You will see a text box where you can enter the name of the repository. Enter *tutorial* in this text box and click on *Create*.
+Click the <span class="btn btn-sm btn-primary">+ NEW REPOSITORY</span> button to open the popup to add a new Arvados repository. You will see a text box where you can enter the name of the repository. Enter *tutorial* in this text box and click on *Create*.
{% include 'notebox_begin' %}
The name you enter here must begin with a letter and can only contain alphanumeric characters.
{% include 'notebox_end' %}
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/add-new-repository.png!
+!{width: 100%;}{{ site.baseurl }}/images/add-new-repository.png!
This will create a new repository with the name @$USER/tutorial at . It can be accessed using the URL <notextile><code>https://git.{{ site.arvados_api_host }}/$USER/tutorial.git</code></notextile> or <notextile><code>git at git.{{ site.arvados_api_host }}:$USER/tutorial.git</code></notextile>
commit 6f898963ceccd2b4c947917ff9a1bc63657d9b6e
Author: Zoë Ma <zoe.ma at curii.com>
Date: Wed Jun 28 23:52:03 2023 +0800
Doc: Update "Starting a Workflow at the Command Line"
A minor fix for the mention of starting a workflow from Workbench.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index d3aed6ce5..dcb2c850d 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -131,7 +131,7 @@ See "arvados-cwl-runner options":{{site.baseurl}}/user/cwl/cwl-run-options.html
h2(#registering). Registering a workflow to use in Workbench
-Use @--create-workflow@ to register a CWL workflow with Arvados. Use @--project-uuid@ to upload the workflow to a specific project, along with its dependencies. You can share the workflow with other Arvados users by sharing that project. You can run the workflow by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard, and on the command line by UUID.
+Use @--create-workflow@ to register a CWL workflow with Arvados. Use @--project-uuid@ to upload the workflow to a specific project, along with its dependencies. You can share the workflow with other Arvados users by sharing that project. You can run the workflow by clicking the <span class="btn btn-sm btn-primary">+ NEW</span> → <i class="fa fa-fw fa-gear"></i> *Run a process* menu items on the Workbench, and on the command line by UUID.
<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --project-uuid zzzzz-j7d0g-p32bi47ogkjke11 --create-workflow bwa-mem.cwl</span>
commit 278de9df8dfdb6a3ff3a4c3169e512bbbadff177
Author: Zoë Ma <zoe.ma at curii.com>
Date: Wed Jun 28 23:39:51 2023 +0800
Doc: Update "Trashing and untrashing data"
Revised the part about untrashing using Workbench for Workbench 2,
including replacing the figure.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/images/trash-button-topnav.png b/doc/images/trash-button-topnav.png
deleted file mode 100644
index d2664377d..000000000
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diff --git a/doc/images/trash-buttons.png b/doc/images/trash-buttons.png
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diff --git a/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid b/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
index 9ddec04f5..a4b94d2b6 100644
--- a/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
@@ -38,9 +38,9 @@ A collection can be untrashed / recovered using workbench or the arv command lin
h3. Untrashing a collection using workbench
-To untrash a collection using workbench, go to trash page on workbench by clicking on the "Trash" icon in the top navigation in workbench and use the recycle icon or selection dropdown option.
+To untrash a collection using Workbench, go to the *Trash* page from the right-side panel, locate the trashed collection, and click on the "clock" or _Restore_ button at the end of the row. The *Restore* button is also available from the right-click context menu.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/trash-button-topnav.png!
+!{width: 80%}{{ site.baseurl }}/images/trash-buttons.png!
h3. Untrashing a collection using arv command line tool
commit 03ee58cf9b847bceed297501f21f5daeb591be17
Author: Zoë Ma <zoe.ma at curii.com>
Date: Mon Jun 26 10:32:00 2023 +0800
Doc: Add a figure caption in "Downloading data".
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
index e102fddac..3402eafa1 100644
--- a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
@@ -46,7 +46,7 @@ To share a collection with users that do not have an account on your Arvados clu
You can then generate a new sharing URL using the <span class="btn btn-sm btn-primary">CREATE SHARING URL</span> button, with the option to set an expiration time for the URL. You can then copy the URL to the clipboard for sharing with others. To revoke (that is, delete) a sharing URL, click on the cross icon beside it.
-!{width: 80%}{{ site.baseurl }}/images/sharing-collection-url.png!
+<figure>!{width: 80%}{{ site.baseurl }}/images/sharing-collection-url.png!<figcaption>_The_ *SHARING URLS* _tab in the_ *Sharing settings* _dialog box, showing the created URL with an expiration time_</figcaption></figure>
Any user with the sharing URL can download this collection by simply accessing this URL using browser. It will present a downloadable version of the collection as shown below.
commit 48cb54ad8ca0c0ad86d87da348d9d05a9d517f3a
Author: Zoë Ma <zoe.ma at curii.com>
Date: Sun Jun 25 17:38:52 2023 +0800
Doc: Update "Downloading data".
- Updated the inline content for Workbench 2.
- Added a new screenshot for the creation of sharing URL.
TODO: The view of the URL from the PoV of the recipient has not been
updated.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/images/shared-collection.png b/doc/images/shared-collection.png
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index 446bab53d..000000000
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diff --git a/doc/images/sharing-collection-url.png b/doc/images/sharing-collection-url.png
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diff --git a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
index 05924f847..e102fddac 100644
--- a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
@@ -19,30 +19,43 @@ h2(#download-using-workbench). Download using Workbench
You can also download Arvados data collections using the Workbench.
-Visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project. You will see the *Data collections* tab, which lists the collections in this project.
+When you visit a project in Workbench (for instance, the <i class="fa fa-fw fa-folder"></i> *Home Projects* or any projects under it), the collections will show up on the project details page, with "_Data collection_" in the *Type* column.
-You can access the contents of a collection by clicking on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection. This will take you to the collection's page. Using this page you can see the collection's contents, and download individual files.
+Clicking on a collection will bring you to its details page. There, the <span class="btn btn-sw btn-primary">FILES</span> panel acts like a file manager where you can navigate to or search for files, select them for actions, and download them.
-You can now download the collection files by clicking on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> button(s).
+To download a file, simply click on the file, or bring up the context menu using right-click or the triple-dot button on its row, and then select the menu item *Download*.
h2(#download-shared-collection). Sharing collections
+Collections or their parent projects can be shared with other users on the Arvados cluster. First, locate the collection or project using any available means (for instance, by manually navigating in the Workbench, or using the Search bar). Then right-click on its link in a listing, or click on the triple-dot button in the details page. You will find the menu item *Share*, which opens the dialog box *Sharing settings*.
+
h3. Sharing with other Arvados users
-Collections can be shared with other users on the Arvados cluster by sharing the parent project. Navigate to the parent project using the "breadcrumbs" bar, then click on the *Sharing* tab. From the sharing tab, you can choose which users or groups to share with, and their level of access.
+To share with other Arvados users, select the *WITH USERS/GROUPS* tab in the *Sharing settings* dialog box. Under *Add people and groups*, in the input field you can search for the user or group names. Select one you will be sharing with, choose the *Authorization* level (Read/Write/Manage) in the drop-down menu, and click on the plus sign (+) on the right. This can be repeated for other users or groups, each with their own *Authorization* level. The selected ones will appear under *People with access*. You can revisit the *Sharing settings* dialog box to modify the users or their access levels at a later time.
+
+The *General access* drop-down menu controls the default sharing setting, with the following choices:
+
+* *Private*: This is the initial state when no users or groups have been selected for sharing. At any time, by setting *General access* to private, the current sharing setting will be cleared, and any users or groups formerly with access will lose that access.
+* *Public*: This means the list of *People with access* will include _Anonymous users_, even if they are not users of the current cluster. You can further set their access level in the *Authorization* level.
+* *All users*: This means sharing with other users who are logged in on the current cluster.
+* *Shared*: When you choose to share with specific people or groups, *General access* will be set to *Shared*. From this state, you can further specify the default sharing settings for *Public* and *All users*.
-h3. Creating a special download URL
+h3. Creating a special download URL for a collection
-To share a collection with users that do not have an account on your Arvados cluster, visit the collection page using Workbench as described in the above section. Once on this page, click on the <span class="btn btn-sm btn-primary" >Create sharing link</span> button.
+To share a collection with users that do not have an account on your Arvados cluster, locate the collection and then go to the *Sharing settings* dialog box as described above. There, select the *SHARING URLS* tab.
-This will create a sharing link for the collection as shown below. You can copy the sharing link in this page and share it with other users.
+You can then generate a new sharing URL using the <span class="btn btn-sm btn-primary">CREATE SHARING URL</span> button, with the option to set an expiration time for the URL. You can then copy the URL to the clipboard for sharing with others. To revoke (that is, delete) a sharing URL, click on the cross icon beside it.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/shared-collection.png!
+!{width: 80%}{{ site.baseurl }}/images/sharing-collection-url.png!
-A user with this url can download this collection by simply accessing this url using browser. It will present a downloadable version of the collection as shown below.
+Any user with the sharing URL can download this collection by simply accessing this URL using browser. It will present a downloadable version of the collection as shown below.
!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/download-shared-collection.png!
+When a collection is being shared by URL, in the *WITH USERS/GROUS* tab of *Sharing settings*, the following message will appear if *General access* is Private: _Although there aren't specific permissions set, this is publicly accessible via Sharing URL(s)._
+
+* *Note:* Sharing by URL is specific to collections. Projects or individual files cannot be shared in this way.
+
h2(#download-using-arv). Download using command line tools
{% include 'tutorial_expectations' %}
commit d619c2e6c9194bec9ecca580cab43e53596dff7b
Author: Zoë Ma <zoe.ma at curii.com>
Date: Sat Jun 24 17:09:30 2023 +0800
Doc: Update "Uploading data"
- Updated the text for Workbench 2 and expanded the steps.
- Removed the old figures and replaced them with new ones from Workbench
2.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/images/add-new-collection-wb2.png b/doc/images/add-new-collection-wb2.png
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diff --git a/doc/images/upload-tab-in-new-collection.png b/doc/images/upload-tab-in-new-collection.png
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diff --git a/doc/images/upload-using-workbench.png b/doc/images/upload-using-workbench.png
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diff --git a/doc/images/workbench-move-selected.png b/doc/images/workbench-move-selected.png
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diff --git a/doc/images/workbench-move-wb2.png b/doc/images/workbench-move-wb2.png
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diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 21efc475c..649820af1 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -17,23 +17,33 @@ Arvados Data collections can be uploaded using either Workbench or the @arv-put@
h2(#upload-using-workbench). Upload using Workbench
-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.
+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.
-To upload files into a new collection, click on *Add data*<span class="caret"></span> dropdown menu and select *Upload files from my computer*.
+Having navigated to the project, click on the <span class="btn btn-sm btn-primary">+ NEW</span> button in the top-left corner. In the pop-up menu, select the item *New collection*.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-using-workbench.png!
+<figure> !{width: 80%;}{{ site.baseurl }}/images/add-new-collection-wb2.png! <figcaption> _Creating a new collection in the project "WGS Processing Tutorial"_ </figcaption></figure>
-<br/>This will create a new empty collection in your chosen project and will take you to the *Upload* tab for that collection.
+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.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-tab-in-new-collection.png!
+<figure>!{width: 100%;}{{ site.baseurl }}/images/new-collection-modal-wb2.png!<figcaption>_Providing the new collection with a name (required). Optionally, you can upload files in this step._</figcaption></figure>
-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.
+You can then click on the <span class="btn btn-sm btn-primary">CREATE A COLLECTION</span> 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.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/files-uploaded.png!
+<figure>!{width: 100%;}{{ site.baseurl }}/images/newly-created-collection-empty-wb2.png!<figcaption>_The newly-created collection without any files yet._</figcaption></figure>
+
+In the <span class="btn btn-sm btn-primary">FILES</span> panel, there is a button labeled <span class="btn btn-sm btn-primary">UPLOAD DATA</span>. 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 <span class="btn btn-sm btn-primary">UPLOAD DATA</span> button to initiate the actual file transfer.
+
+<figure>!{width: 100%;}{{ site.baseurl }}/images/upload-data-prompt-with-files-wb2.png!<figcaption>_Selecting the files to upload_</figcaption></figure>
+
+Once the file upload completes, you will be notified by a message, and the files will appear under the <span class="btn btn-sm btn-primary">FILES</span> panel shortly.
+
+<figure>!{width: 100%;}{{ site.baseurl }}/images/upload-data-progress-wb2.png!<figcaption>_Upload status being displayed, with the files to appear shortly_</figcaption></figure>
*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.
+*Note:* You can also use the <span class="btn btn-sm btn-primary">UPLOAD DATA</span> button to add additional files to an existing collection.
notextile. <div class="spaced-out">
@@ -41,9 +51,11 @@ h2(#creating-projects). Creating projects
Files are organized into Collections, and Collections are organized by Projects.
-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.
+When you have navigated to any existing project, clicking on <span class="btn btn-sm btn-primary">+ NEW</span> <span class="rarr">→</span> <i class="fa fa-fw fa-folder"></i> *New project* will prompt you to create a new subproject under the current project.
+
+If you're at the top-level <i class="fa fa-fw fa-folder"></i> *Home Projects*, a new top-level project will be created.
-To create a subproject, navigate to the parent project, and click on <i class="fa fa-fw fa-plus"></i>*Add a subproject*.
+Alternatively, you can right-click on the link to an existing project to bring up a context menu, and select *New project*.
See "Sharing collections":tutorial-keep-get.html#download-shared-collection for information about sharing projects and collections with other users.
@@ -85,12 +97,12 @@ In both examples, the @arv-put@ command created a collection. The first collecti
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 name printed by @arv-put@ will appear under the *name* column.
+Visit the Workbench and go to your <i class="fa fa-fw fa-folder"></i> *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...*<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.
+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 *<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.
+<figure>!{width: 80%;}{{ site.baseurl }}/images/workbench-move-wb2.png!<figcaption> _Context menu with the_ *Move to* _item_ </figcaption></figure>
notextile. </div>
commit bc057d1dc07b19526f59ef9339dd3d28d91f7cf3
Author: Zoë Ma <zoe.ma at curii.com>
Date: Sat Jun 24 14:17:41 2023 +0800
Doc: Remove reference to "dashboard" in template about adding SSH key
- The "dashboard" is no longer a named component of the Workbench UI.
- The <h3> under the <h1> is superfluous.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/_includes/_ssh_addkey.liquid b/doc/_includes/_ssh_addkey.liquid
index 6ee2bd58d..f2c4fe55c 100644
--- a/doc/_includes/_ssh_addkey.liquid
+++ b/doc/_includes/_ssh_addkey.liquid
@@ -9,8 +9,6 @@ You may now proceed to "adding your key to the Arvados Workbench.":#workbench
h1(#workbench). Adding your key to Arvados Workbench
-h3. From the Workbench dashboard
-
In the Workbench top navigation menu, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> to access the Account Management menu. Then, click on the menu item *Ssh keys* to go to the *SSH keys* page. Click on the <span class="btn btn-primary">+ ADD NEW SSH KEY</span> button in the upper-right on that page. You will see a popup as shown in this screenshot:
!{width: 100%;}{{ site.baseurl }}/images/ssh-adding-public-key.png!
commit 75d2e3a89af09906b76315cf4fedc5e012841fcc
Author: Zoë Ma <zoe.ma at curii.com>
Date: Sat Jun 24 14:12:58 2023 +0800
Doc: Update "Accessing an Arvados VM with SSH - Unix Environments"
- Updated the included template about adding SSH keys, to reflect
changes in Workbench 2. A screenshot was updated.
- Added slightly more context to instructions about using ssh keypair
and agent for the benefit of new users.
- Minor textual fixes for clarity.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/_includes/_ssh_addkey.liquid b/doc/_includes/_ssh_addkey.liquid
index de0da6a76..6ee2bd58d 100644
--- a/doc/_includes/_ssh_addkey.liquid
+++ b/doc/_includes/_ssh_addkey.liquid
@@ -11,17 +11,20 @@ h1(#workbench). Adding your key to Arvados Workbench
h3. From the Workbench dashboard
-In the Workbench top navigation menu, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> to access the user settings menu and click on the menu item *SSH keys* to go to the *SSH keys* page. Click on the <span class="btn btn-primary">*+* Add new SSH key</span> button in this page. This will open a popup as shown in this screenshot:
+In the Workbench top navigation menu, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> to access the Account Management menu. Then, click on the menu item *Ssh keys* to go to the *SSH keys* page. Click on the <span class="btn btn-primary">+ ADD NEW SSH KEY</span> button in the upper-right on that page. You will see a popup as shown in this screenshot:
-!{{ site.baseurl }}/images/ssh-adding-public-key.png!
-Paste your public key into the text area labeled *Public Key*, and click on the <span class="btn btn-primary">Submit</span> button. You are now ready to "log into an Arvados VM":#login.
+!{width: 100%;}{{ site.baseurl }}/images/ssh-adding-public-key.png!
+
+Paste your _public_ key into the text area labeled *Public Key*, and click on the <span class="btn btn-sm btn-primary">ADD NEW SSH KEY</span> button in lower-right. You are now ready to "log into an Arvados VM":#login.
h1(#login). Using SSH to log into an Arvados VM
-To see a list of virtual machines that you have access to, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, then click on the menu item *Virtual machines* to go to the Virtual machines page.
+To see a list of virtual machines that you have access to, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> in the upper right corner of the top navigation menu to access the Account Management menu. Then, click on the menu item *Virtual Machines*.
+
+You will then see a page that lists the virtual machines you can access. The *Host name* column lists the name of each available VM. The *Login name* column lists your login name on that VM. The *Command line* column provides a sample @ssh@ command.
-This page lists the virtual machines you can access. The *Host name* column lists the name of each available VM. The *Login name* column lists your login name on that VM. The *Command line* column provides a sample @ssh@ command line.
+!{width: 100%;}{{ site.baseurl }}/images/vm-access-with-webshell.png!
At the bottom of the page there may be additional instructions for connecting your specific Arvados instance. If so, follow your site-specific instructions. If there are no site-specific instructions, you can probably connect directly with @ssh at .
-The following are generic instructions. In the examples the login will be *_you_* and the hostname will be *_shell.ClusterID.example.com_* and . Replace these with your login name and hostname as appropriate.
+The following are generic instructions. In these examples, the login name will be *_you_* and the host domain will be *_ClusterID.example.com_*. Replace these with your login name and hostname as appropriate.
diff --git a/doc/images/ssh-adding-public-key.png b/doc/images/ssh-adding-public-key.png
index 8aea82747..ab6101657 100644
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diff --git a/doc/user/getting_started/ssh-access-unix.html.textile.liquid b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
index 80cb39131..b131b5b36 100644
--- a/doc/user/getting_started/ssh-access-unix.html.textile.liquid
+++ b/doc/user/getting_started/ssh-access-unix.html.textile.liquid
@@ -37,9 +37,9 @@ Enter same passphrase again:
* @-t@ specifies the key type (must be "rsa")
* @-C@ specifies a comment (to remember which account the key is associated with)
-We strongly recommend that you protect your key with a passphrase. This means that when the key is used, you will be required to enter the passphrase. However, unlike logging into remote system using a password, the passphrase is never sent over the network, it is only used to decrypt your private key.
+We strongly recommend that you protect your key with a passphrase. This means that when the key is used, you will be required to enter the passphrase. However, unlike logging into remote system using a password, the passphrase is never sent over the network; it is only used to decrypt your private key locally.
-Display the contents of @~/.ssh/id_rsa.pub@ (this is your public key) using @cat@ and then copy it onto the clipboard:
+Display the contents of @~/.ssh/id_rsa.pub@ (this is your public key) using @cat@, and then copy it onto the clipboard. The content of the public key may look similar to the following example:
<notextile>
<pre><code>$ <span class="userinput">cat ~/.ssh/id_rsa.pub</span>
@@ -47,6 +47,8 @@ ssh-rsa AAAAB3NzaC1ycEDoNotUseExampleKeyDoNotUseExampleKeyDoNotUseExampleKeyDoNo
</code></pre>
</notextile>
+* The above is a specimen that cannot be used as a valid public key.
+
Now you can set up @ssh-agent@ (next) or proceed with "adding your key to the Arvados Workbench.":#workbench
h3. Set up ssh-agent (optional)
@@ -55,13 +57,13 @@ If you find you are entering your passphrase frequently, you can use @ssh-agent@
notextile. <pre><code>$ <span class="userinput">ssh-add -l</span></code></pre>
-If you get the error "Could not open a connection to your authentication agent" you will need to run @ssh-agent@ with the following command:
+If you get the error "_Could not open a connection to your authentication agent_", you will need to run @ssh-agent@ with the following command:
-notextile. <pre><code>$ <span class="userinput">eval $(ssh-agent -s)</span></code></pre>
+notextile. <pre><code>$ <span class="userinput">eval "$(ssh-agent -s)"</span></code></pre>
- at ssh-agent -s@ prints out values for environment variables SSH_AUTH_SOCK and SSH_AGENT_PID and then runs in the background. Using "eval" on the output as shown here causes those variables to be set in the current shell environment so that subsequent calls to SSH can discover how to access the agent process.
+ at ssh-agent -s@ runs an agent process in the background to hold your SSH credentials, and it prints out the values of environment variables @SSH_AUTH_SOCK@ and @SSH_AGENT_PID at . By applying the shell builtin @eval@ to this output, as we show here using the shell command-substitution syntax, we set those variables in the current shell environment. In this way, subsequent invocations of @ssh@ in this shell session will be able to access the agent process for the credentials without asking you each time.
-After running @ssh-agent@, or if @ssh-add -l@ prints "The agent has no identities", add your key using the following command. The passphrase to decrypt the key is the same used to protect the key when it was created with @ssh-keygen@:
+After running @ssh-agent@, or if @ssh-add -l@ prints "_The agent has no identities_", add your private key to the SSH agent using the following command. The passphrase to decrypt the key is the same one used to protect the key when it was created with @ssh-keygen@:
<notextile>
<pre><code>$ <span class="userinput">ssh-add</span>
@@ -70,7 +72,7 @@ Identity added: /home/example/.ssh/id_rsa (/home/example/.ssh/id_rsa)
</code></pre>
</notextile>
-When everything is set up, @ssh-add -l@ should yield output that looks something like this:
+When everything is set up, @ssh-add -l@ should yield output that looks like this:
<notextile>
<pre><code>$ <span class="userinput">ssh-add -l</span>
@@ -82,29 +84,29 @@ When everything is set up, @ssh-add -l@ should yield output that looks something
h3. Connecting directly
-If the VM is available on the public Internet (or you are on the same private network as the VM) you can connect directly with @ssh at . You can probably copy-and-paste the text from *Command line* column directly into a terminal.
+If the VM is available on the public Internet (or you are on the same private network as the VM), you can connect directly with @ssh at . You can copy-and-paste the text from the *Command line* column (see the screenshot above) directly into a shell session.
-Use the following example command to connect as _you_ to the _shell.ClusterID.example.com_ VM instance. Replace *<code>you at shell.ClusterID.example.com</code>* at the end of the following command with your *login* and *hostname* from Workbench.
+Use the following example command to connect, as the user "_you_" to the VM instance at the hostname "_shell.ClusterID.example.com_". Replace *<code>you at shell.ClusterID.example.com</code>* at the end of the following command with your actual *login* and *hostname* from Workbench.
notextile. <pre><code>$ <span class="userinput">ssh <b>you at shell.ClusterID.example.com</b></span></code></pre>
h3. Connecting through switchyard
-Some Arvados installations use "switchyard" to isolate shell VMs from the public Internet.
+Some Arvados installations use "switchyard" to isolate shell VMs from the public Internet. In such cases, you cannot log in directly to virtual machines over the public Internet. Instead, you log into a "switchyard" server and then tell the switchyard which virtual machine you want to connect to.
Use the following example command to connect to the _shell_ VM instance as _you_. Replace *<code>you at shell</code>* at the end of the following command with your *login* and *hostname* from Workbench:
notextile. <pre><code>$ <span class="userinput">ssh -o "ProxyCommand ssh -p2222 turnout at switchyard.ClusterID.example.com -x -a <b>shell</b>" -x <b>you at shell</b></span></code></pre>
-This command does several things at once. You usually cannot log in directly to virtual machines over the public Internet. Instead, you log into a "switchyard" server and then tell the switchyard which virtual machine you want to connect to.
+This command does several things at once.
* @-o "ProxyCommand ..."@ configures SSH to run the specified command to create a proxy and route your connection through it.
* @-p2222@ specifies that the switchyard is running on non-standard port 2222.
* <code>turnout at switchyard.{{ site.arvados_api_host }}</code> specifies the user (@turnout@) and hostname (@switchyard.{{ site.arvados_api_host }}@) of the switchyard server that will proxy our connection to the VM.
* @-x@ tells SSH not to forward your X session to the switchyard.
* @-a@ tells SSH not to forward your ssh-agent credentials to the switchyard.
-* *@shell@* is the name of the VM that we want to connect to. This is sent to the switchyard server as if it were an SSH command, and the switchyard server connects to the VM on our behalf.
-* After the ProxyCommand section, we repeat @-x@ to disable X session forwarding to the virtual machine.
+* *@shell@* is the host name of the VM that we want to connect to. In summary, the string inside the quotation marks is sent to the switchyard server, as if it were an SSH command, and the switchyard server connects to the VM on our behalf.
+* After the @ProxyCommand@ section, we repeat @-x@ to disable X session forwarding to the virtual machine.
* Finally, *<code>you at shell</code>* specifies your login name and repeats the hostname of the VM. The username can be found in the *logins* column in the VMs Workbench page, discussed in the previous section.
You should now be able to log into the Arvados VM and "check your environment.":check-environment.html
commit 137f21665305e7519209807c746354cabb0d8711
Author: Zoë Ma <zoe.ma at curii.com>
Date: Sat Jun 24 08:33:19 2023 +0800
Doc: Update "Accessing an Arvados VM with Webshell"
- Updated inline elements for Workbench 2.
- Replaced screenshot with higher-definition and updated one.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/images/vm-access-with-webshell.png b/doc/images/vm-access-with-webshell.png
index b980fdc27..91954543e 100644
Binary files a/doc/images/vm-access-with-webshell.png and b/doc/images/vm-access-with-webshell.png differ
diff --git a/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid b/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
index 0aeabab11..33168dda3 100644
--- a/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
+++ b/doc/user/getting_started/vm-login-with-webshell.html.textile.liquid
@@ -19,10 +19,10 @@ Webshell gives you access to an arvados virtual machine from your browser with n
Some Arvados clusters may not have webshell set up. If you do not see a "Log in" button or "web shell" column, you will have to follow the "Unix":ssh-access-unix.html or "Windows":ssh-access-windows.html @ssh@ instructions.
{% include 'notebox_end' %}
-In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Virtual machines* to see the list of virtual machines you can access. If you do not have access to any virtual machines, please click on <span class="btn btn-sm btn-primary">Send request for shell access</span> (if present) or contact your system administrator. For the Arvados Playground, this is "info at curii.com":mailto:info at curii.com .
+In the Arvados Workbench, click on the dropdown menu icon <i class="fa fa-lg fa-user"></i> in the upper right corner of the top navigation menu to access the _Account Management_ menu, and click on the menu item *Virtual machines* to see the list of virtual machines you can access. If you do not have access to any virtual machines, please click on <span class="btn btn-sm btn-primary">SEND REQUEST FOR SHELL ACCESS</span> (if present) or contact your system administrator. For the Arvados Playground, this is "info at curii.com":mailto:info at curii.com .
-Each row in the Virtual Machines panel lists the hostname of the VM, along with a <code>Log in as *you*</code> button under the column "Web shell". Clicking on this button will open up a webshell terminal for you in a new browser tab and log you in.
+Each row in the Virtual Machines panel lists the hostname of the VM, along with a <span class="btn btn-sm btn-default" style="background-color: #e0e0e0">Log in as [your name]</span> button under the column "*Web shell*". Clicking on this button will open up a webshell terminal for you in a new browser tab and log you in.
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/vm-access-with-webshell.png!
+!{width: 100%;}{{ site.baseurl }}/images/vm-access-with-webshell.png!
You are now ready to work in your Arvados VM.
commit 475f319c833e6223440cae2cc5c10351adf37f5c
Author: Zoë Ma <zoe.ma at curii.com>
Date: Fri Jun 23 21:23:47 2023 +0800
Doc: Update "Getting an API token".
- Updated the references to Workbench 2 UI elements.
- Expand and reword some instructions about creating file in shell
(because a novice user may accidentally wipe out the file), and how
appending to .bashrc does its job.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 6afc20bf4..4c35530e6 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -15,11 +15,11 @@ Access the Arvados Workbench using this link: "{{site.arvados_workbench_host}}/"
Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with "Webshell":{{site.baseurl}}/user/getting_started/vm-login-with-webshell.html or SSH (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).
-In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Current token*, which lists your current token and instructions to set up your environment.
+In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> in the upper right corner of the top navigation menu to access the _Account Management_ menu. Then, in the pop-up menu, click on the menu item *Get API token*. This will open a dialog box that lists your current token and the instructions for setting up your environment.
h2. Setting environment variables
-The *Current token* page, accessed using the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu, includes a command you may copy and paste directly into the shell. It will look something as the following.
+In the dialog box opened after clicking on the *Get API token* menu item, there is a sequence of commands you may copy and paste directly into the shell. It will look something as the following.
bc. HISTIGNORE=$HISTIGNORE:'export ARVADOS_API_TOKEN=*'
export ARVADOS_API_TOKEN=2jv9346o396exampledonotuseexampledonotuseexes7j1ld
@@ -38,9 +38,12 @@ $ <span class="userinput">echo "ARVADOS_API_TOKEN=$ARVADOS_API_TOKEN" >> ~/.conf
</code></pre>
</notextile>
+* The output-redirection operator @>@ in the first command will cause the target file @~/.config/arvados/settings.conf@ to be created anew, wiping out the content of any existing file at that path.
+* The @>>@ operator in the second command appends to the target file.
+
h2. .bashrc
-Alternately, you may add the declarations of @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ to the @~/.bashrc@ file on the system on which you intend to use the Arvados client. If you have already put the variables into the environment following the instructions above, you can use these commands to append the environment variables to your @~/.bashrc@:
+Alternately, you may add the definitions of @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ to the @~/.bashrc@ file on the system where you intend to use the Arvados client. If you have already put the variables into the environment following the instructions above, you can use the commands below to append to your @~/.bashrc@, which tells Bash to export them as environment variables in newly-started interactive shell sessions:
<notextile>
<pre><code>$ <span class="userinput">echo "export ARVADOS_API_HOST=$ARVADOS_API_HOST" >> ~/.bashrc</span>
commit 4cd1011cc23e59d6e5ef5c3cb93cff3ec4d16f28
Author: Zoë Ma <zoe.ma at curii.com>
Date: Fri Jun 23 17:48:55 2023 +0800
Doc: Update "Running a workflow using Workbench"
- Updated the procedures to match the operations in Workbench2.
- Updated the styles of inline elements to match their roles in
Workbench2.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
index 8a0822572..3259f0d24 100644
--- a/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
@@ -21,18 +21,19 @@ h3. Steps
notextile. <div class="spaced-out">
-# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
-# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button. This will open a dialog box titled *Choose a pipeline or workflow to run*.
-# In the search box, type in *bwa-mem.cwl*.
-# Select *<i class="fa fa-fw fa-gear"></i> bwa-mem.cwl* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are populated with default values and you can change them if you prefer.
-# For example, let's see how to set read pair *read_p1* and *read_p2* for this workflow. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath the *read_p1* header. This will open a dialog box titled *Choose a file*.
-# In the file dialog, click on *Home <span class="caret"></span>* menu and then select *All Projects*.
-# Enter *HWI-ST1027* into the search box. You will see one or more collections. Click on *<i class="fa fa-fw fa-archive"></i> HWI-ST1027_129_D0THKACXX for CWL tutorial*
-# The right hand panel will list two files. Click on the first one ending in "_1" and click the <span class="btn btn-sm btn-primary" >OK</span> button.
-# Repeat the steps 5-8 to set the *read_p2* except selecting the second file ending in "_2"
-# Scroll to the bottom of the "Inputs" panel and click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> button. The page updates to show you that the process has been submitted to run on the Arvados cluster.
-# Once the process starts running, you can track the progress by watching log messages from the component(s). This page refreshes automatically. You will see a <span class="label label-success">complete</span> label when the process completes successfully.
-# Click on the *Output* link to see the results of the process. This will load a new page listing the output files from this process. You'll see the output SAM file from the alignment tool under the *Files* tab.
-# Click on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
+# Click on the <span class="btn btn-sm btn-primary">+ NEW</span> button in the top-left.
+# In the pop-up menu, select *<i class="fa fa-fw fa-gear"></i> Run a workflow*. This will open the _Run Process_ panel in the Workbench.
+# In the search field under *Choose a workflow*, type in _bwa-mem.cwl_.
+# Select *bwa-mem.cwl* in the search results, and click the <span class="btn btn-sm btn-primary" >NEXT</span> button. This will create a new process in one of your Home Projects and will open it. To specify the project for the workflow run, click on the input line below "*Project where the workflow will run*", and in the pop-up dialog box, choose a project under your Home Projects.
+# You can now supply the inputs for the process. Please note that all required inputs are populated with default values and you can change them if you prefer.
+# For example, let's see how to set read pair *read_p1* and *read_p2* for this workflow. Click on the input line under the *read_p1* header. This will open a dialog box titled *Choose a file*.
+# Enter the search terms _user guide resources_ into the *Search for a Project* field on the left. You will see one or more collections in the search results appearing below and, among them, the one with the exact title *<i class="fa fa-fw fa-folder"></i> User guide resources*. Your goal is to locate the file _HWI-ST1027_129_D0THKACXX.1_1.fastq_.
+# You may either locate the file manually, by clicking on the triangles ▶ to the left of each item to expand them (projects and the collections under it) until you find the file, or by filtering the search results using the *Filter Collections list in Projects* field, for example, with a term like "_HWI-ST1027_".
+# Either way, you will find the file <i class="fa fa-fw fa-file"></i> *HWI-ST1027_129_D0THKACXX.1_1.fastq* in the search results. Click on it, and then the <span class="btn btn-sm btn-primary">OK</span> button in the bottom-right.
+# Repeat the steps 7--9 to set the value for *read_p2*, except selecting the file ending in "_2"
+# Scroll to the bottom of the "Inputs" panel and click on the <span class="btn btn-sm btn-primary" >RUN WORKFLOW</span> button. The page updates to show you that the process has been queued to run on the Arvados cluster.
+# Once the process starts running, you can track the progress by watching the log messages from the component(s) (scroll down to the *Logs* panel). This page refreshes automatically, and you can also click on the <span class="btn btn-sm btn-primary">REFRESH</span> button on the top of the page. You will see a <span class="label label-success">Completed</span> label when the process completes successfully.
+# The output of the workflow can be found by following the link "Output from bwa-mem.cwl" under the heading *Output collection* in the main or <span class="btn btn-sm btn-primary">DETAILS</span> panel, or in the <span class="btn btn-sm btn-primary">OUTPUTS</span> panel further down. Click on the *Output from bwa-mem.cwl* link to see the detailed results from the workflow run. This will lead you to a page that lists the metadata of the outputs, and you'll see the output SAM file there, in the <span class="btn btn-sm btn-primary">FILES</span> panel.
+# To download your results, simply click on the SAM file name.
notextile. </div>
commit cc810d29fd64e1005dd7829640ea0fb9f4b638cd
Author: Zoë Ma <zoe.ma at curii.com>
Date: Fri Jun 23 17:47:58 2023 +0800
Doc: Update "Accessing Arvados Workbench" for Workbench 2
- Remove references to the "Dashboard"
- Replace the screenshot with higher-definition, updated one.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/images/workbench-dashboard.png b/doc/images/workbench-dashboard.png
deleted file mode 100644
index 3cdf1e4a6..000000000
Binary files a/doc/images/workbench-dashboard.png and /dev/null differ
diff --git a/doc/images/workbench-first-page.png b/doc/images/workbench-first-page.png
new file mode 100644
index 000000000..531c86fb2
Binary files /dev/null and b/doc/images/workbench-first-page.png differ
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index 7091e31ea..d2c95c943 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -27,6 +27,6 @@ h2. Logging in
You will be asked to log in. Arvados uses only your name and email address for identification, and will never access any personal information. If you are accessing Arvados for the first time, the Workbench may indicate your account status is *New / inactive*. If this is the case, contact the administrator of the Arvados instance to request activation of your account.
-Once your account is active, logging in to the Workbench will present you with the Dashboard. This gives a summary of your projects and recent activity in the Arvados instance. You are now ready to "upload data":{{ site.baseurl }}/user/tutorials/tutorial-keep.html or "run your first workflow.":{{ site.baseurl }}/user/tutorials/tutorial-workflow-workbench.html
+Once your account is active, logging in to the Workbench will present you with an overview of your Home Projects. You are now ready to "upload data":{{ site.baseurl }}/user/tutorials/tutorial-keep.html or "run your first workflow.":{{ site.baseurl }}/user/tutorials/tutorial-workflow-workbench.html
-!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/workbench-dashboard.png!
+!{width: 100%;}{{ site.baseurl }}/images/workbench-first-page.png!
commit 0348964d9a696f4b9596a128abdc6e5fc9ed43e5
Author: Zoë Ma <zoe.ma at curii.com>
Date: Fri Jun 23 14:50:50 2023 +0800
Doc: Update Ruby dependencies and fix Rakefile
- Updated rubygems with "bundle update" for dependencies.
- Fixed Rakefile by replacing the obsoleted method aliases.
Arvados-DCO-1.1-Signed-off-by: Zoë Ma <zoe.ma at curii.com>
diff --git a/doc/Gemfile.lock b/doc/Gemfile.lock
index 5fcdbb644..420e13146 100644
--- a/doc/Gemfile.lock
+++ b/doc/Gemfile.lock
@@ -3,16 +3,16 @@ GEM
specs:
RedCloth (4.3.2)
coderay (1.1.3)
- colorize (0.8.1)
+ colorize (1.0.5)
commonjs (0.2.7)
kramdown (1.17.0)
less (2.6.0)
commonjs (~> 0.2.7)
- liquid (4.0.3)
+ liquid (4.0.4)
makerakeworkwell (1.0.4)
rake (>= 0.9.2, < 15)
- rake (13.0.1)
- zenweb (3.10.4)
+ rake (13.0.6)
+ zenweb (3.10.6)
coderay (~> 1.0)
kramdown (~> 1.4)
less (~> 2.0)
diff --git a/doc/Rakefile b/doc/Rakefile
index 676f2845c..89454940c 100644
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -51,7 +51,7 @@ file ["install/new_cluster_checklist_Azure.xlsx", "install/new_cluster_checklist
end
file "sdk/python/arvados/index.html" do |t|
- if ENV['NO_SDK'] || File.exists?("no-sdk")
+ if ENV['NO_SDK'] || File.exist?("no-sdk")
next
end
`which pdoc`
@@ -66,7 +66,7 @@ file "sdk/python/arvados/index.html" do |t|
end
file "sdk/R/arvados/index.html" do |t|
- if ENV['NO_SDK'] || File.exists?("no-sdk")
+ if ENV['NO_SDK'] || File.exist?("no-sdk")
next
end
`which R`
@@ -132,7 +132,7 @@ EOF
end
file "sdk/java-v2/javadoc/index.html" do |t|
- if ENV['NO_SDK'] || File.exists?("no-sdk")
+ if ENV['NO_SDK'] || File.exist?("no-sdk")
next
end
`which java`
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