- 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:
{% 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:
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!
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
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.
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
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
--- /dev/null
+---
+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*.
projects / arvados.git / commitdiff