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This guide explains how to use the administrative features of the National Biomedical Imaging Archive (NBIA).
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Administration Functions Overview
Security applies to all administration tools in NBIA. When you log into NBIA, only the administration tools for which you have been granted permissions are visible in the Admin menu. Their use is described on this page.
Creating a New NBIA User
Only an NBIA administrator can create new users for NBIA.
Before NBIA users can be created, an administrator with access to the User Authorization Tool must register the NCIA application and assign an admin administrative user to the NCIA application there. The administrator can then assign users to NBIA and roles to each user. The following table describes the role structure in NBIA.
Role | Functionality | Can Perform Operation |
|---|---|---|
NCIA.READ | Search capability | Everything else Note: This role is applied to guest users. |
NCIA.MANAGE_VISIBILITY_STATUSPrivilege to access | Access the QC Tool | |
NCIA.VIEW_SUBMISSION_REPORTPrivilege to access Verify Submission | Access and verify a submission | |
NCIA.MANAGE_COLLECTION_DESCRIPTION | Privilege to edit Edit a collection description | |
NCIA.SUPER_CURATOR | Create, edit, and delete workflow items Review and delete saved queries Approve Privilege to approve the deletion of image series Delete a shared list | |
NCIA.DELETE_ADMIN | Privilege to execute the deletion of Delete images approved for deletion | |
| NCIA.ADMIN | Use the User Authorization Tool | Use the User Authorization Tool Note: This role is also needed to access CSM UPT. |
The roles you assign allow a user to perform tasks in TCIANBIA. Additionally, an administrator can perform the following tasks:
- Assign a user right the privilege to use the QC tool for the purpose of reviewing submitted imaging data and managing visibility status for the data. See Using the Quality Control Tool.
- Verify submitted files. This includes the permission to view the image submission report which includes submission statistics and information regarding what has been received by the image repositories. See Viewing Submission Reports.
- Configure security for data submitted to TCIA. For more information, see 5 - Configuring Security for Submitted DataNBIA.
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Do not use special characters in user names. You can use special characters in passwords. |
For more information about creating new TCIA NBIA users/user groups and performing other tasks in the User Authorization Tool, see the User Authorization Tool documentation.
Using the QC Tool
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Deleting Image Series
As an administrator, you can assist in the two-tier process of deleting TCIA NBIA data. To do so, you must have been granted specific roles. For more information about the roles and the deletion processes, see 6 - NBIA Administrator's GuideApproving Image Deletions and Manually Deleting Image Series.
Approving Image Deletions
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Manually Deleting Image Series
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Viewing Submission Reports
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Accrual Report
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Image Submission Report
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Annotation Submission Report
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Editing a Collection Description
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Managing Workflow Items
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Managing Saved Queries
You can review and delete queries saved by users in TCIA.
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This administrative feature is available only to logged in users who have "manage visibility" privileges, as defined in UPT. For more information, see Registering a New TCIA User. |
Reviewing Saved Query Information
To review a saved query
- Select Admin > Manage Saved Queries.
The Manage Saved Queries page appears listing all the queries saved by TCIA users.
The following information is listed for each query.
Info icon false title Sorting the table By default the table is sorted by Query Name, but you can also sort by the Last Executed or Query Creator columns.
Column Name Description Query Name Click the name of the query to display the Criteria Selected by the user. The selected field name(s) and data are listed.
Last Executed Lists the date and time that the query was run. New Data Available 
indicates that new data is available.Query Creator User name of the person who saved the query.
Deleting a Saved Query
To delete a saved query
- Select Admin > Manage Saved Queries.
The Manage Saved Queries page appears. Check the box next to the Query Creator column of a query to be removed. You can delete multiple queries at once.
Info title Removing All Saved Queriese To remove all of the saved queries, check the box next to column name, Query Creator. All queries are selected.
- Click Remove Selected Items.
You are prompted to confirm the deletion and the selected queries are removed.
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Using the User Authorization Tool
NBIA role required to use this feature: NCIA.ADMIN
For more information about roles, see Creating a New NBIA User.
Administrators use the User Authorization tool to manage data access by users, user groups, protection groups, and roles.
Topics in this section include:
- 6 - NBIA Administrator's GuideAccessing the User Authorization Tool
- Managing Users
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- Managing Protection Groups
- Managing User Groups
- Adding Protection Groups and Assigning Roles
- Resolving Errors in the User Authorization Tool6 - NBIA Administrator's Guide
Accessing the User Authorization Tool
To access and use the User Authorization Tool, you must be a TCIA an NBIA administrator.
- Log in to TCIANBIA.
- Select Admin > User Authorization Tool.
The User Authorization Tool appears, open to the User tab.
Managing Users
Once a user submits data, an administrator adds the user to TCIA. The administrator must create the user in LDAP to manage data access privileges.
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Contact the Help Desk to request that a user be added to LDAP. |
Managing users involves:
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
Adding a User to TCIA
- Select Admin > User Authorization Tool.
Select the User tab.
- Click
.
The User Details dialog box appears.
- Add the user's Login Name. The login name is not case-sensitive.
- Add a valid Email address of the user.
To activate the user, select Active Status. To deactivate the user in TCIA, clear Active Status.
Click
to save the changes.
The user is added to TCIA and the table on the User tab.
Finding a User
To find a user on the User tab, narrow the list by adding one or more characters to one or more column header boxes.
In the following example, the displayed users have 5523 as part of their login name and nlsc in their email address.
Updating User Information
- Select Admin > User Authentication Tool.
- Select the User tab.
Find the user whose information you want to update.
Click
.
The User Details window appears.Update the Email address as needed. The Login Name cannot be updated.
For an active user, maintain Active Status. To deactivate the user in TCIA, clear Active Status.
Click Save to save the changes.
The user information is updated in the table.
Deactivating a User
A user cannot be deleted from TCIA, only deactivated.
- Select Admin > User Authentication Tool.
Select the User tab.
Find the user you want to deactivate.
Click
.
The User Details window appears.Clear the Active Status box and then click Save.
The user's Active Status value changes to False.
Managing Protection Groups
A TCIA administrator uses the Protection Group tab to add protection groups and assign protection elements to limit data access and visibility by image collection and site(s).
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| TCIA automatically creates protection elements when data is submitted based on the image collection and site(s). |
Managing protection groups involves:
- Adding a Protection Group
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
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Adding a Protection Group
From the Protection Group tab, click Add Protection Group.
The Add Protection Group window appears.
The following table lists and describes protection group information.
Name
Description
Protection Group Name Start the name with "NCIA” and enter your name of choice.
Info title No Special Characters Do not use special characters such as
#or\in group names.Protection Group Description
Add a description (optional).
Click
to save the changes.
The protection group is added to the table.
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Managing Protection Elements
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Once you create the necessary protection group(s), assigning the associated protection element(s) is the beginning of setting up security for a collection's visibility in TCIA. The protection element identifies the collection, as well as the site, associated with the data.
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| If the protection element is set to Public, a user can be assigned the Public role and have access. For limited access to the data, assign a user to a protection group and a role that allows the user data access. |
To associate a protection element with a protection group
- On the Protection Group tab, find the protection group.
- Click
in the Assign Protection Element column.
The Add Protection Element(s) to Protection Group window appears.
Click Available Protection Elements.
Select the elements to be associated with the protection group.
Info title Narrowing a List To narrow a list, type the name or part of the name next to the magnifying glass icon (
).Click
to save the changes.The Associated Protection Element(s) column lists the elements that you added.
In the following example protection element,
NCIA.SportInjury//ACL- NCIA.SportInjury is the collection.
ACL is the site.
Info title Multiple Sites If there are multiple sites for a collection, you might want to create a protection group for each site. This process would grant access to verify submissions per site.
Removing Protection Elements from a Protection Group
- On the Protection Group tab, find the protection group.
- Click
in the Remove Protection Element(s) column.
The Remove Protection Element(s) from Protection Group window appears.
The Protection Group Name cannot be changed. Click Included Protection Elements, and select the elements to remove.
Info title Narrowing a List To narrow a list, type the name or part of the name next to the magnifying glass icon (
).Click x to return without saving.
Click
to save the changes.
The protection element(s) is no longer listed in the Associated Protection Elements column.
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Managing Protection
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On the Protection Group tab, you can perform a global search or a column search both described in the following table.
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You can perform both searching techniques to further filter a list, but do not forget to clear the search boxes to expand the list. |
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You can search for a term or part of a term in all the protection group columns in the table. All protection groups with the characters you entered are returned.
In the following example, a Global Search of colonography finds protection groups with the word in the Protection Group name and the Associated Protection Elements.
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You can also find protection groups in the table by adding a term to a column header or more than one column header to further narrow the list.
In the following example, bbb in the Protection Group column and demo in the Description column, displays two results.
Groups
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Updating a Protection Group Description
- On the Protection Group tab, find the protection group you want to update.
Click
.
The Protection Group Details window appears.Update the group description.
Note that you cannot update the protection group name.Click
to save the changes.
Deleting a Protection Group
- On the Protection Group tab, find the protection group you want to delete.
Click
.
The Protection Group Details window appears.Click
.
The row is removed from the table.
Managing User Groups
TCIA administrators create user groups to limit data access and visibility by protection group and user role. Before or after creating user groups, you can assign users and roles to protection groups.
Managing user groups involves:
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide
Viewing Protection Groups and Roles Associated with a User Group
- Select Admin > User Authentication Tool.
Select the User Group tab.
- Click the arrow in the first column to see the protection group(s) and role(s) associated with the user group in that row.
The row expands to show the protection group(s) and role(s) associated with that user group.
Managing User Groups
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Adding Protection Groups and Assigning Roles
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- View the protection group(s) and role(s) for a selected user group.
- Click
.
The Modify Authorization for Selected User Group window appears.
- To change the roles associated with this protection group, open the Role list. Click or clear the checkboxes you want to add or remove, respectively. Click
. - To remove this protection group from this user group, click
.
Assigning a Protection Group and Role to a User Group
You can associate a user group with a protection group and one or more roles.
To assign a protection group and role to a user group
- Select Admin > User Authentication Tool.
Select the User Group tab.
In the row associated with the user group whose access you want to specify, click
.
The Add Protection Group to Selected User Group window appears.Open the Protection Group list and click one protection group to select it.
Info title Narrowing a List To narrow the list of protection groups, type the name or part of the name next to the magnifying glass icon (
). All protection groups with the characters you entered are returned.
The list closes and shows your selection in the window.Open the Role list and and click the box to the left of each role you want to assign to the selected protection group.
Info title Narrowing a List To narrow the list of roles, type the name or part of the name next to the magnifying glass icon (
). All protection groups with the characters you entered are returned.
The list closes and shows your selection(s) in the window.- Click .
The user group is now associated with the selected protection group and roles.
Deleting a User Group
Deleting a user group does not delete the users in it.
To delete a user group
- Select Admin > User Authentication Tool.
Select the User Group tab.
- In the row of the user group you want to delete, click
.
The Delete the Following Group? window appears. - Click .
The user group no longer appears in the list.
Adding Protection Groups and Assigning Roles
A TCIA administrator creates protection groups to limit data access and visibility by image collection and site(s). Administrators add users to protection groups and can then further manage their access by assigning them one or more roles. Users can only access the protection group data in the way that the role specifies.
For example, John Smith needs to be a curator within the Mouse Astrocytoma protection group, so user johnsmith is assigned to protection group TCIA Mouse Astrocytoma with the role of CURATOR.
Topics in this section include:
- 6 - NBIA Administrator's Guide
- 6 - NBIA Administrator's Guide with Roles
- 6 - NBIA Administrator's Guide
Adding a Protection Group
- Select Admin > User Authentication Tool.
- Select the Protection Group tab.
- Scroll down to the bottom of the page and click
.
The Protection Group Details window appears.
Enter a name for the new group and optionally, a description.
Info title No Special Characters Do not use special characters such as
#or\in group names.Click
.
The protection group appears on the Protection Group tab.
Assigning a User to a Protection Group with Roles
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If you are a Super Administrator for one protection group, your privileges extend to all of the protection groups. |
To assign a user to a protection group and assign roles
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Select the User Authorization tab.
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Select a user from the list.
A page listing the protection groups and access roles associated with the selected user opens.
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Click 
.
The Grant Access to Selected User window opens.
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From the Role list, select the access role that the user should have in that protection group.
The following table lists and describes the access roles available in TCIA.
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Access the User Authorization Tool to manage users
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Add or modify curation data
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Super Administrator role for deletions
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Manage collection descriptions
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Access the Quality Control (QC) Tool
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Public role for searching
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Super Administrator role for approving deletions
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Access the Submission Reports option to verify submissions.
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The row is added to the table.
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To adjust how the table is sorted, click the arrows in the column header. To narrow the list, type the name or part of the name in the column header. You can also enter information in multiple column headers to further narrow the list. |
Changing a User's Access Role Within a Protection Group
- Select Admin > User Authentication Tool.
Select the User Authorization tab.
Select a user from the list.
A page listing the protection groups and access roles associated with the selected user opens.- In the row of the protection group you want to change, click
.
The Grant Access to Selected User dialog box opens.
To change the user's access to roles in this protection group, click the down arrow to open the Role list. Select the boxes next to roles you want to assign to the selected user. Clear the boxes next to roles you do not want the user to have. Click
to save your changes.To delete a role, open the Role list, select a role, and click
.The User Authentication tab appears.
Resolving Errors in the User Authorization Tool
The following table lists and describes how to resolve error messages returned by the User Authorization Tool (UAT). Error messages appear in a red box.
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Messages in a blue box, such as Info: Request sent to server. or Info: Sent., indicate that a request was sent to the server to save, update, or delete an item. |
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You performed a search and there were no results. Enter different search criteria.
If a selected user has not been assigned to a protection group with a role, you will receive the following message:
Error: No data found from server.
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Error: Error occurred while retrieving data from server. Check the server connection please.
Error code: <a number>
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Resolving Errors in the User Authorization Tool
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