8 User Management

This section contains the following topics:

User Accounts

In the current release of OHTR, the user has permissions to make a few changes to basic accessibility options. However, the viewing screens cannot be customized.

If Oracle Access Manager (OAM) is configured, the user has the following functions:

  1. The user can log into the OHTR application by using the single sign-on interface, which can be shared among multiple applications.

    For example, with an Oracle Business Intelligence Enterprise Edition Plus (OBIEE) full license, the same credentials can be used for generating OBIEE reports.

  2. The user creates the password, which is not visible to an administrator.

  3. After a configurable number of unsuccessful login attempts, the user is locked out.

  4. After a configurable amount of inactive time, the login session times out.

  5. Roles are automatically setup as described in Roles and Permissions.

If OAM is not configured, the identified roles must be manually set up in a WebLogic instance. For more information, see Create Users and Add Users to Groups in the Oracle® Fusion Middleware Oracle WebLogic Server Administration Console Online Help available at

https://docs.oracle.com/middleware/1221/wls/WLACH/taskhelp/security/ManageUsersAndGroups.html

You may need to perform policy migration in OBIEE to see the roles. For details on policy migration, see the Oracle® Healthcare Translational Research Installation Guide.

Roles and Permissions

The OHTR user is assigned one or more of the following roles:

Role Permissions Accessible Screens
trc-bioinformatician-group
  • Download files that have a link stored in Oracle Healthcare Omics (OHO, formerly known as ODB) and can be located in the middle tier in an accessible location.
  • Cannot build new reports or modify the content of existing reports.

  • Cohort Query Tab
  • Cohort Query Tab: Genomic Data (tab in accordion)

  • Query Tab: Relative Time Events: gene variant (radio button)

  • Cohort Viewer (top tab)

  • Cohort Viewer: Cohort List

  • Cohort Viewer: Cohort Timeline

  • Cohort Reports

  • Cohort Viewer: Genomic Data Export

  • Single Patient Viewer: View Record

  • Single Patient Viewer: View Record: Genomic Data Collected

  • Circular Genomic Viewer (Visquick)

  • Genomic Query

  • Genomic Query: Columns after searching for gene/variant coming from CDM (Patient Count, Specimen Anatomical Site columns)

  • My Workspace: My Recent Queries

  • My Cohort Lists

  • Queries or Lists shared with me

  • Queries or Lists shared with All

  • My Queries

  • Gene Sets

  • Manage Gene Sets

  • Jobs

trc-cohort-group
  • Query any data from CDM but cannot query OHO directly.
  • Export the clinical data in a supported format and view the Dashboard.

  • Cannot build new reports or modify the content of existing reports.

  • Cohort Query Tab
  • Cohort Query Tab: Relative Time Events: gene variant (radio button)

  • Cohort Viewer (top tab)

  • Cohort Viewer: Cohort List

  • Cohort Viewer: Cohort Timeline

  • Single Patient Viewer: View Record

  • My Workspace: My Recent Queries

  • Short Cuts

  • My Cohort Lists

  • Queries or Lists shared with me

  • Queries or Lists shared with All

  • My Queries

trc-limited-user-group
  • View the patient count on the Query Patients page
  • Cannot build new reports or modify the content of existing reports.

  • Cohort Query Tab (Save Query button is not accessible)
  • My Workspace: My Recent Queries

trc-omics-group
  • Query and read data from OHO
  • Export omics data in file formats readable by genome viewers. For example, VCF, SEG, RES formats for IGV.

  • Cannot build new reports or modify the content of existing reports.

  • Genomic Query
  • My Workspace: My Recent Queries

  • Short Cuts

  • Gene Sets

  • Jobs

trc-comics-limited-user-group
  • Query data from CDM and OHO using Query Patients interface
  • Can only access Patient Genomic Data export within the Patient Viewer interface

  • Create Gene Sets

  • View queries and gene sets

  • Cohort Query Tab
  • Cohort Query Tab: Genomic Data (tab in accordion)

  • Query Tab: Relative Time Events: gene variant (radio button)

  • Cohort Viewer (top tab)

  • Cohort Viewer: Genomic Data Export

  • My Workspace: My Recent Queries

  • Gene Sets

  • Jobs

trc-pi-user-group
  • Specific privileges allowing access to identifiable information on patients or subjects
  • In Subject context, can view merged version of Patient and Subject clinical data all in one View Record page.

  • View personally identifiable (PI) information on the Cohort List page.
  • View PI data in Single Patient or Subject Viewer > View Record page.

  • Cohort Query Tab

  • Cohort Query Tab: Genomic Data (tab in accordion)

  • Query Tab: Relative Time Events: gene variant (radio button)

  • Cohort Viewer (top tab)

  • Cohort Viewer: Cohort List

  • Cohort List (PI attributes)

  • Cohort Viewer: Cohort Timeline

  • Cohort Reports

  • Cohort Viewer: Genomic Data Export

  • Single Patient Viewer: View Record

  • Single Patient Viewer: View Record (PI attributes)

  • Single Subject Viewer: View Record (PI attributes)

  • Single Subject Viewer: View Record (show patient data together)

  • Single Patient Viewer: View Record: Genomic Data Collected

  • Circular Genomic Viewer (Visquick)

  • Genomic Query

  • Genomic Query: Columns after searching for gene/variant coming from CDM (Patient Count, Specimen Anatomical Site columns)

  • My Workspace: My Recent Queries

  • Short Cuts

  • My Cohort Lists

  • Queries or Lists shared with me

  • Queries or Lists shared with All

  • My Queries

  • Gene Sets

  • Saved Queries

  • Jobs

trc-admin-group
  • Create new user groups and so on for sharing cohort queries or lists
  • Add or remove users from groups

  • Manage user roles

Manage User Group

Users belonging only to the following groups have limited functionality based on the assigned roles:

  • trc-comics-limited-user-group

  • trc-limited-user-group

  • trc-basic-user-group

Working with User Groups

To simplify sharing, create user groups and assign users to them. Instead of sharing queries or lists with each user individually, set up a list of users to share multiple items.

Note that only the user that is the owner of a given list can modify members of a given list. However, any user can elect to utilize a given list for sharing and see members of a list, even if he or she is not the owner.

Creating a User Group

To create a user group:

  1. Navigate to Manage User Groups > User groups.

  2. Click Create. The Create User Group box is displayed.

  3. Enter a name and description for the user group.

  4. Click Submit.

Assigning Users to a Group

To assign users to a group:

Immediately After you Create a Group

  1. Navigate to Manage User Groups > Group has members.

  2. Click Add. The Add Users box is displayed.

  3. Enter the user name you want to add. A drop-down list displays the matching choices.

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  4. Select the names you want to add.

  5. Click Add. The selected users are added to the group.

  6. Click Done.

Searching for a Group you Created Earlier

  1. Navigate to Manage User Groups > Search User Groups.

  2. Enter the details of the group you want to find.

  3. Click Search. The user group and its details are displayed.

  4. Navigate to Manage User Groups > Group has members.

  5. Click Add. The Add Users box is displayed.

  6. Enter the user name you want to add. A drop-down list displays the matching choices.

  7. Select the names you want to add.

  8. Click Add. The selected users are added to the group.

  9. Click Done.

Removing Users from a Group

To remove users from a group:

  1. Navigate to Manage User Groups > Search User Groups.

  2. Enter the details of the group you want to find.

  3. Click Search. The user group and its details are displayed.

  4. Navigate to Manage User Groups > Group has members.

  5. Select the user you want to remove.

  6. Click Remove.

Managing User Groups

You can edit, duplicate or delete a user group using the buttons at the top of the User Groups section.

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Editing a User Group

To edit the name and description of a user group:

  1. Navigate to Manage User Groups > Search User Groups.

  2. Enter the details of the group you want to find.

  3. Click Search. The user group and its details are displayed in the User Groups section.

  4. Select the user group you want to modify.

  5. Click Edit.

  6. The Edit User Group box is displayed. Modify the name and description of the gene set.

  7. Click Submit.

Duplicating a User Group

To edit the name and description of a user group:

  1. Navigate to Manage User Groups > Search User Groups.

  2. Enter the details of the group you want to find.

  3. Click Search. The user group and its details are displayed in the User Groups section.

  4. Select the user group you want to duplicate.

  5. Click Duplicate.

  6. The Duplicate User Group box is displayed. Modify the name and description of the user group.

  7. Click Submit.

Deleting a User Group

To delete a user group:

  1. Navigate to Manage User Groups > Search User Groups.

  2. Enter the details of the group you want to find.

  3. Click Search. The user group and its details are displayed in the User Groups section.

  4. Select the user group you want to delete.

  5. Click Delete. A confirmation box is displayed.

  6. Click Submit. The user group is deleted.