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Org Management
On DNAnexus, several users can form an organization, which is an entity with a common pool of funds that all users can draw from. All projects billed to that organization (as well as all jobs that are run in those projects) will incur charges using the same pool of funds, regardless of user.
The All Orgs tab, which you can select from Org Admin option on the top left menu, shows you a list of all orgs to which you have admin access. On this page, you can quickly see all of your orgs, the number of projects per org, and the funds available to the org. You can also see additional settings for each org by enabling optional columns (icon on the right side of the column headers).
These operations are restricted to only org admins - that is, org members with "Admin" membership level.
If you are an admin of an org, you will be able to access the org admin tools from the main Platform menu. From here, you can quickly navigate to the list of orgs you administer (via "All Orgs"), or to a specific org (e.g. Demo Organization in this example).
In the "Basic Information" section of the org settings tab, you will be able to see an overview of the org.
- View and edit the organization name. This is how the org will be referred to in the UI and in email notifications
- View the organization ID, the unique ID used to reference a particular org on the CLI (e.g. org-demo_org)
- View the number of org members, org projects and org apps
- View the list of organization admins
You can use the
dx update org command to update your org policies.To update the membership list visibility policy so all org members can view the list of org members, use the following command, replacing
org-demo with your org ID.$ dx update org org-demo --member-list-visibility MEMBER
Updated org-demo
To update the restrict project transfer policy so that only org admins can change the billing account of an org project, use the following command, replacing
org-demo with your org ID.$ dx update org org-demo --project-transfer-ability ADMIN
Updated org-demo
You can also update org policies for your org in the "Policies and Administration" section of the org settings tab. Here, you can both change the membership list visibility and restrict project transfer policies for the org and contact DNAnexus support to enable PHI data policies for org projects.
Within an org page, the Members tab allows you to view all the members of the org, invite new members, remove existing members, and update existing members' permission levels.
To add existing DNAnexus user to your org, you can use the "+ Invite New Member" button from the org's Members tab. This will open a dialog where you can enter the user's username (e.g. smithj) or user-ID (e.g. user-smithj). Then you can configure the user's access level in the org.
- Organization Membership: Whether they are a member or admin of the org.
- Billable Activities Access: Whether the user should be able to create projects and apps billed to the org.
- Shared Project Access: The maximum permission the user will have to projects that were shared with the org. For example, if this is set to "Contributor" but someone shares a project with the org at an Administrator level, this user will still only have Contributor access, even if other members of this org receive the full Administrator permissions.
- Shared Apps Access: Whether the user should have access to apps shared with the org.
If you add a member to the org with billable activities access set to billing allowed, they will have the ability to create new projects billed to the org. However, adding the member will not change their default billing account. If the user wishes to use the org as their default billing account, they will have to set their own default billing account.
Additionally, if the member has any pre-existing projects that are not billed to the org, the user will need to transfer the project to the org if they wish to have the project billed to the org.
The user will receive an email notification informing them that they have been added to the organization.
The
dx add member command allows org admins to add existing DNAnexus users to a pre-existing org. The command will add a member to the org but will not set their default billing account; the member will have to set their own default billing account. Additionally, if the member has any pre-existing projects that are not billed to the org, the user will need to transfer the project to the org if they wish to have the project billed to the org.Below are some examples of adding users to an org.
To add an existing user to an org with:
- Membership level: MEMBER
- Billable activities access: Allowed
- Shared apps access: Allowed
- Shared projects access: CONTRIBUTE
Use the following command, replacing
org-demo with your org ID and xxxx in user-xxxx with the new member's username.$ dx add member org-demo user-xxxx --level MEMBER --allow-billable-activities --project-access CONTRIBUTE
Invited user-xxxx to org-demo
To add an existing user to an org with:
- Membership level: MEMBER
- Billable activities access: Not allowed
- Shared apps access: Not allowed
- Shared projects access: VIEW
Use the following command, replacing
org-demo with your org ID and xxxx in user-xxxx with the new member's username.$ dx add member org-demo user-xxxx --level MEMBER --project-access VIEW --no-app-access
Invited user-xxxx to org-demo
To add another org admin to the org, use the following command, replacing
org-demo with your org ID and xxxx in user-xxxx with the new member's username.$ dx add member org-demo user-xxxx --level ADMIN
Invited user-xxxx to org-demo
For more information about adding members to an org, use the
dx add members command with the -h flag.From the org Members tab, you can edit the permissions for one or multiple members of the org. The option to "Edit Access" appears when you have one or more org members selected on the Members tab.
If you select only one member, you can specify their new access via the dialog.
You can also edit multiple members at the same time by selecting multiple members from the members list and clicking "Edit Access".
When you're editing multiple members, you have the option of changing only one access while leaving the rest as is. In the example below, we are editing the member access for User Alice and Jennifer Smith. In this case, we updating their access so both have the ability to create new projects billed to the org, Billing Allowed. We will keep all the rest of their permissions the same.
The
dx update member command allows org admins to update a member's access within an org.To grant an existing org member billable activities access, use the following command, replacing
org-demo with your org ID and xxxx in user-xxxx with the member's username.$ dx update member org-demo user-xxxx --level MEMBER --allow-billable-activities true
Updated membership of user-xxxx in org-demo
To grant an existing org member shared projects access, use the following command, replacing
org-demo with your org ID and xxxx in user-xxxx with the member's username.$ dx update member org-demo user-xxxx --level MEMBER --app-access true
Updated membership of user-xxxx in org-demo
To update an existing org member's shared projects access, use the following command, replacing
org-demo with your org ID, xxxx in user-xxxx with the member's username, and ACCESS with one of ADMINISTER, CONTRIBUTE, UPLOAD, VIEW, or NONE.$ dx update member org-demo user-xxxx --level MEMBER --project-access ADMINISTER
Updated membership of user-xxxx in org-demo
To make an existing org member an org admin, use the following command, replacing
org-demo with your org ID and xxxx in username with the member's username.$ dx update member org-demo user-xxxx --level ADMIN
Updated membership of user-xxxx in org-demo
For more information about updating members' access and level in an org, use the
dx update members command with the -h flag.Org admins can remove a member from an org using the
dx remove member command. This command will remove the user from the org, revoking the user's access to projects and apps shared with the org. This command will also, by default and if applicable, remove the user's access to apps and projects billed to the org.From the org Members tab, you can remove one or more members from the org. The option to "Remove" appears when you have one or more org members selected on the Members tab.
This will open the following dialog where you can confirm the action to remove members from the org. This action will revoke the user's access to all projects and apps billed to or shared with the org.
To remove a member from an org, use the following command, replacing
org-demo with your org ID and xxxx user-xxxx with the member's username. You will be prompted to confirm the removal of the user from the org.$ dx remove member org-demo user-xxxx
WARNING: About to remove user-xxxx from org-demo; project
permissions will be removed and app permissions will be removed
Please confirm [y/n]: y
Removed user-xxxx from org-demo
Removed user-xxxx from the following projects:
None
Removed user-xxxx from the following apps:
None
For more information about removing members from an org, use the
dx remove members command with the -h flag.The org's Projects tab allows you to see the list of all projects billed to the org. This list will include all projects in which you have View and above permissions as well as projects that are billed to the org in which you do not have permissions (Not a Member).
You will be able to view all project metadata (e.g. the members list, data usage, creation date), as well as some other optional columns (e.g. project creator). To enable the optional columns, select the column from the dropdown menu to the right of the column names.
In addition to viewing the list of projects, org admins can give themselves access to any project billed to the org. If you select a project in which you are not a member, you will still be able to navigate into the project's settings page. From the project settings page, you will see a button allowing you to grant yourself Administer permissions to the project.
You will also be able to grant yourself Administer permissions if you are currently a member of a project billed to your org but you only have View, Contribute, or Upload permissions.
To list all org projects, including projects to which you do not have access, use the
dx find org projects command, replacing org-demo with your org ID.# List all org projects
$ dx find org projects org-demo
project-xxxx : my_new_project (ADMINISTER)
project-yyyy : example_project (CONTRIBUTE)
# Return only the project IDs for all projects billed to the
org
$ dx find org projects org-demo --brief
project-xxxx
project-yyyy
# Return JSON-formatted string of org projects and project metadata
$ dx find org projects org-demo --json
[
{
"level": "ADMINISTER",
"describe": {
"id": "project-xxxx",
...
You can also use JQ (a [command-line JSON parser](https://stedolan.github.io/jq/))
to format a command-delimited list of project-ID, project name, your access
level , project creator, and number of bytes stored in the project.
$ dx find org projects org-demo --json | jq -r '.[] .describe | .id + "," + .name + "," + .level + "," + .createdBy.user + "," + (.dataUsage | tostring)'
project-xxxx,my_new_project,ADMINISTER,user-xxxx,0.059
project-yyyy,example_project,CONTRIBUTE,user-yyyy,0.048
To access billing info for an org of which you’re a member:
- 1.Click on your user icon in the top right corner of your screen.
- 2.Select Billing from the dropdown menu.
To set up billing for an org, or change billing information for that org:
- 1.Open the Billing screen by following the instructions in “Access org billing information” above.
- 2.For the org you wish to change the billing details for, follow the instructions in the Billing Details section of the org to set up or update your billing information.
As an org admin, you can request a spending limit increase for the org by contacting DNAnexus Support at [email protected]. Please include your user ID and attach a PO.
As an org admin, if you have the spending and usage reporting feature enabled, you can monitor both for your org, via the UI. To do so:
- 1.Select All Orgs from the Org Admin entry in the main Platform menu. The Organizations list will open. Select the org for which you want to see usage and billing information.
- 2.Click the Billing tab, then select Account Spending from the left-side menu on the Billing screen.
- 3.On the Account Spending screen, you'll be able to see a wide range of information on spending connected with the account, and the specific charges incurred, for both the most recent month, and the past 12 months.
From the org Members tab, you can quickly see the names and access levels for all org members.
To list all the members of an org using the CLI, use the
dx find org members command, replacing org-demo with your org ID.# List all org members & admin
$ dx find org members org-demo
user-xxxx : Jane Doe (ADMIN)
user-yyyy : John Doe (MEMBER)
# List only org admin
$ dx find org members org-demo --level ADMIN
user-xxxx : Jane Doe (ADMIN)
# Return only user IDs of org members & admin
$ dx find org members org-demo --brief
user-xxxx
user-yyyy
To list all the apps billed to your app, use the
dx find org apps command, replacing org-demo with your org ID.# Return list of all org apps
$ dx find org apps org-demo
Example App (example_app), v0.0.1
Org admins can give themselves access to any project billed to the org by using the
dx invite command. To invite yourself to a project with ADMINISTER access, use the following command, replacing project-xxxx with the project ID of the org project you want access to and user-xxxx with your username. The --no-email flag will suppress the email that would normally be sent notifying you that you have been given access to a project.$ dx invite user-xxxx project-xxxx --no-email
Invited user-xxxx to project-xxxx (accepted)
For more information about inviting yourself to a project, use the
dx invite command with the -h flag.Org admins can grant themselves developer access to any app billed to the org. App developers can publish new app versions, deprecate old app versions, and manage the group of developers and authorized users of the app.
$ dx add developers app-xxxx user-xxxx
If you would like to set up an org for several DNAnexus users to join, please contact us at DNAnexus support.
A license is required to enable org admins to provision accounts for other users. Contact DNAnexus Sales for more information.
Admins of orgs with the proper license have the ability to provision new DNAnexus accounts on behalf of the org. The user will then receive an email with instructions to activate their account and set their password.
If this feature has already been turned on for an org you administer, you can create new accounts using the
dx new user command.To create a new user and add them to your org as a member with billable activities access and set their default billing account to the org, use the following command. You will need to provide the following information:
EMAIL: the user's email -- there cannot be multiple accounts associated with the same emailUSERNAME: the user's username -- must be a unique usernameFIRST: the user's first nameLAST: the user's last name
$ dx new user --username USERNAME --email EMAIL --first FIRST --last LAST --org org-demo --level MEMBER --set-bill-to
Created new user account (user-xxxx)
For more information about provisioning new user accounts, run the
dx new user command with the -h flag.Org admins have the ability to create new DNAnexus accounts on behalf of the org. The user will then receive an email with instructions to activate their account and set their password.
Limited Feature Note
If this feature has already been turned on for an org you administer, you will see an option to "Create New User" when you invite a new member.
The dialog will expand to allow you to specify a username (e.g.
alice or smithj), the new user's name, and email address. This dialog will automatically create a new user account for the given email address and add them as a member in the org.Please note that if you create a new user and set their Billable Activities Access to "Billing Allowed", we recommend that you set the org as the user's default billing account. This option is available as a checkbox under the Billable Activities Access dropdown.
A license and a signed Business Associate Agreement are required to enable and use PHI Data Protection. Contact DNAnexus Sales for more information.
Protected Health Information, or PHI, refers to identifiable health information that can be linked to a specific person. Once enabled for a project, DNAnexus PHI Data Protection safeguards the confidentiality of data stored in that project, in compliance with HIPAA.
If the Data Protection Notice feature is enabled for a project, all users accessing the project for the first time will be required to review and confirm their acceptance of a requirement not to egress data from the project. This feature can be enabled or disabled for a project by the project administrator. For orgs licensed to use this feature, it can be enabled or disabled for a project within the Access Policies section of the project's Settings screen.
The video tutorials provide walkthroughs of key org admin tasks:
Last modified 6mo ago