Using UPT: Set up Application & Create caArray Users Fan Lin, Ph. D. Molecular Analysis Tools Knowledge Center Columbia University and The Broad Institute of MIT and Harvard

Overview LSD applications use Common Security Module's (CSM) API in their applications to enforce the Authorization Policy. The Authorization policy is stored in the CSM Schema and provisioned by the CSM User Provisioning Tool (UPT). In this presentation, we will demonstrate how to use UPT to manage:  caArray application  Users for caArray application For more information on how to use UPT, please refer to the UPT user guide:

Two Operation Modes UPT includes two operation modes – Super Admin and Admin.  The Super Admin operations are typically performed first, as they register the application and application administrators. The Super Admin operations happen in UPT’ csmupt scheme  The primary mode of the Admin operation is to perform user provisioning for a particular application. The operations include the creation of new application user and the authorization of user provisioning. The Admin operations happen in the individual application scheme Let’s start with the Super Admin mode to register a new application

Login CSM Scheme as Super Admin  Login in as “superadmin” (default password is “changeme”)  Application name for Super Admin mode is “csmupt” (case sensitive)

The Process of Creating a New Application There are three steps involved in the application creation cycle:  Create a new application  Create an admin user  Assign the admin user to this new application There is no preference in the order of creating a user or an application. In this demo, we start the process by creating a new application.

Create a New Application To create a new application:  Select “Application” from Menu Tool Bar (arrow 1)  Select “Create a New Application” (arrow 2) 1 2

Setting Parameters for New Application To succeed in creating and subsequently using caArray, please pay special attention to the parameters entered below  Application Name : The name is case sensitive. It must be the same name as that used during caArray installation.  Application database URL: where your database is hosted (check caArray’s install.properties file for more details)  Application database user name /Password  Application database Dialect: org.hibernate.dialect.MySQLDiale  Application database driver: com.mysql.jdbc.Driver (check caArray’s install.properties file for more details)

Verifying the New Application The new application name will be created in the csm_application table in UPT’s csmupt scheme, which can be verified at the database level:  select application_name from csmupt.csm_application (Application name was inserted into UPT’s csm_application table from Super Admin Mode) The new application name should be the same as that in caarray’s csm_application table:  select application_name from caarray_db.csm_application (Application name was inserted into caAaray’s csm_application table during caArray Installation)

Updating Application The information on an existing application can be changed at any time.  Go back to Application Home (arrow 1)  click on “Select an Existing Application” (Arrow 2). 1 2

Updating Application  Start searching by clicking on “Search” (Application name is unnecessary) (arrow 1)  Select application interested (arrow 2)  Update information, and submit by clicking on “Update” (arrow 3) 1 3 2

Create a New Admin user Now, we are ready to create a new admin user for the application created previously. Use one of the options below to go to User page  Select “User” on tool menu to open user provisioning tool (Arrow 1)  Select “User” in Menu link to open User element (Arrow 2) 2 1

Create a New Admin user  On the User Home page select “Create a New User”

Create a New Admin user  Only the fields with asterisks are mandatory with the exception of “User Password”.  A password must be entered unless the user is to be validated via a LDAP that is configured to work with UPT (For more information on LDAP, please refer to the knowledge entry: kc.nci.nih.gov/Molecular/KC/index.php/Caarray021). kc.nci.nih.gov/Molecular/KC/index.php/Caarray021  Submit the new user information by clicking on “Add”.

Updating User Information The information on “User” can be updated any time by:  Go back to User Home page (Arrow 1)  Select the option of “Select an Existing User” (Arrow 2)  Unless a large number of users are registered, there is no need to enter the details in the user search criteria. Click on “Search” to begin the process

Updating User Information 1 2  Select the admin user (arrow 1)  Update the user details and click on “Update” (arrow 2)

The Work Flow of Association There are 3 steps to associate an application with its administrator:  Select an application  Select an admin user  Assign the association between the application and the admin user

Associate Application with an Admin user 1. Select Application Step 1: Go to Application Home to select an existing application Step 2: Search for the application name by clicking on “Search” (no need to provide search term) Step 3: Select the application for the association Step 4: Select ‘Associated Admins” to active admin user selection page

Associate Application with an Admin user 2. Select Admin User Step 1. Select “Assign Admin” to start the admin user selection process Step 2: Click on “Search” to search for the admin users available 1 2

Associate Application with an Admin user 3. Associate Admin User with Application Step 1. Select the Admin user (arrow 1) and select “Assign Admin” (arrow 2) Step 2: Highlight the admin user selected from step 1 (arrow 3); select “Update Association” (arrow 4) Step 3: After association is successful (arrow 5), log out from “superadmin” (arrow 6)

Login In CSM as Application Admin After the admin user is successfully associated with the application, we are ready to login as the admin user to perform the user provision for our caArray application.  Login as admin user, “caarray-admin”, as created previously.  Enter the new application name. Please note: 1.Application Name is case sensitive. 2.The Application Name here is the application just created.

Create a New Application User Upon login as the application admin user, the flow chart illustrates the workflow on how user is created and authorized To start the process, select “Users” to start creating a new user (see arrow)

The Elements of UPT Within the UPT, there are several common operations that are repeated for the most elements. These operations include:  Create New,  Search  Update,  Delete,  Assign/Associate These operations, however, should be limited ONLY to “User” section. The different UPT elements can be easily accessed by going to Home page or from the menu tool bar as shown in below. UPT Menu Tool Bar For Elements

Create a New Application User Step 1: After activate “User” homepage, start the process by selecting “Create a New User” (arrow 1) Step 2: Select “Add” to save the new element (in this case User) to the database (arrow 2) Please Note: A password must be entered unless the user is to be validated via a LDAP that is configured to work with UPT (see slide 13). 1 2

Assign Application User to a Group  Upon a successful save to New User Details, the system displays Add Successful just below the menu and before the text.  In addition, a new set of buttons appears below the details table in Admin mode for managing user groups or privileges (see picture below).  In order for caArray to recognize the user just created, all users must be assigned to a group.  To start the association between the user and a group, select “Associated Groups” as indicated by arrow.

Assign Application User to a Group  At the time this presentation is written, the only group with the different privileges from the others is “System Administrator”.  The example below demonstrates how to assign a special group to the user created previously:  Select “Principal Investigator” from “Available Groups” and click on “Assign”  Highlight “Principal Investigator” in “Assigned Groups”, and select “Updated Association”

Assign Application User to a Group Upon the successful association between the application and the user, the new user is ready to log in to the caArray application

Login caArray as New User  Open a new browser, and point to the URL of caArray application  Login as the user created in the example before  Upon the successful login, the username is shown at the upper right corner of caArray (see arrow)

Need More Information? NCI is developing an extensive knowledge base to support various NCI molecular analysis tools. Visit the Molecular Analysis Tool Knowledge center at  For more information on how to use caArray, visit the caArray wiki at  Have a caArray related question? Find the answers in the caArray FAQ at  New more help? Post in caArray Forum at :