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Oracle® Health Sciences Translational Research Center Installation Guide
Release 3.1
E66212-06
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4 Installing and Configuring the Middle Tier

This section describes the installation and configuration steps for the middle tier. This chapter includes the following topics:

4.1 Installing the Middle Tier for a New Installation


Note:

Make sure middleware homes are separate for Cohort Explorer and BI. For example,

WebLogic 12c (12.1.3) - [CE mwhome]

-CE_DOMAIN

-CE_SERVER1

Weblogic 11g (10.3.6) - [BI mwhome]

-[BI domain]

-[BI server]

4.1.1 Configuring AppDB JDBC Data Source

Perform the following steps to configure the JDBC data source called AppDB in the WebLogic Server.


Note:

AppDB is the database connection of application schema created in Chapter 2, "Installing the Database Tier".

  1. Log into the WebLogic Server Administration Console.

  2. In the Domain Structure pane, expand the Services node.

  3. Click Data Source Node.

    The Data Sources table displays in the right pane showing all the data sources defined in the domain.

  4. Click New. If the New button above Data Source table is disabled, click Lock & Edit in the Change Center pane and then click New.

  5. Select Generic Data Source.

  6. In the Name and JNDI Name fields, enter AppDB and jdbc/AppDBDS respectively.

  7. Click Next.

  8. Select the appropriate database driver for your database and click Next.


    Note:

    The application is not compatible with data sources defined with the JDBC XA driver including Oracle's Driver (Thin XA).

    Ensure that you select one of Oracle's Driver (Thin) drivers.

  9. Select Transaction Options and click Next.

  10. Enter connection properties for your database where the application schema is installed.

  11. Click Next.

  12. Click Test Configuration to verify the JDBC connection.

  13. Click Next and Select Targets.


    Note:

    The target must be a server or a cluster where the TrcApp.ear application will be deployed.

  14. Click Finish.

    The Data Sources table displays the new data source AppDB.

  15. Click Activate Changes in the Change Center pane, if it is enabled.

  16. To prevent wrapping Data Type Objects, perform the following steps:

    1. In the Change Center of the Administration Console, click Lock & Edit.

    2. In the Domain Structure tree, select Services > Data Sources.

    3. On the Summary of Data Sources page, click AppDB.

    4. Select the Configuration: tab.

    5. Scroll down and click Advanced to show the advanced connection pool options.

    6. In Wrap Data Types, deselect the checkbox to disable wrapping.

    7. Click Save.

    8. To activate these changes, in the Change Center of the Administration Console, click Activate Changes.

  17. JAX-RS 2.0 should be manually deployed using the following steps. This only needs to be done once for a domain.

    1. Log into the WebLogic Server Administration Console.

      For example,

      http://host:port/console

    2. Select Deployments.

    3. Click Install to install the shared library.

    4. In the Path field, navigate to the directory MW_HOME\wlserver\common\deployable-libraries.

    5. Select the jax-rs-2.0.war file.

    6. Click Next.

    7. Select Install this deployment as a library.

    8. Click Next.

    9. Select the server where TRC ear is going to be deployed.

    10. Click Finish.

For more information, refer to the Configuring JDBC Data Sources section of Oracle® Fusion Middleware Configuring and Managing JDBC Data Sources for Oracle WebLogic Server.

4.1.1.1 Frequently Asked Questions

Increasing the Connection Pool Size

Perform the following steps to increase the connection pool size:

  1. Log into the WebLogic console.

  2. Navigate to Services > Data Sources.

  3. Click the data source for which you want to increase the connection pool size.

  4. Navigate to the Connection Pool tab.

  5. Specify the number of connections in the attribute Maximum Capacity. Oracle recommends that you set this to at least 100.

  6. For details on this configuration, click More Info… right across this attribute.

Application Running Out of Connections

  • This issue can be resolved by increasing the number of connections as mentioned above.

  • Better performance can be achieved by modifying the following attributes:

    • Initial Capacity

    • Maximum Capacity: Maximum number of connections depends on the number of users. For example, if there are10 users the suggested number of connections should always be multiplied by 10 (that is, 10 *10 = 100).

    • Capacity Increment: This value depends upon the multiplication factor being used to calculate maximum capacity (as per above scenario, it is 10).

For more information, see Tuning Data Source Connection Pools in Oracle® Fusion Middleware Configuring and Managing JDBC Data Sources for Oracle WebLogic Server.

To optimize performance, Oracle recommends that you update the heap memory and fetch size of the WebLogic server with the following values:

  • Exadata

    Heap Memory: 15GB, Fetch Size: 150

  • Non-Exadata

    Heap Memory: 8GB, Fetch Size: 100

4.1.2 Uploading and Configuring TRC.properties File

The TRC.properties file contains configurable values used in the user interface of the OHSCE application. Upload the TRC.properties file in the root directory of WebLogic Server (<FMW_HOME>/user_projects/domains/<YOUR_DOMAIN_NAME>, where FMW_HOME is the home directory of Oracle Fusion Middleware).

Following are descriptions of the file properties.

Table 4-1 Properties in TRC.properties File

Property User Interface Description

SF_HOME

View Record

This corresponds to the location of the file system where the result files are stored. This should correspond to TRC_ODB_PERM oracle directory object used when loading result files into the ODB schema.

This location must have the necessary permissions to ensure that the WebLogic user can access this path and read from this location.

MAX_FILE_SIZE

View Record

This corresponds to the maximum file size (in MB) that a user can download.

PT_LIST.MAX_PATIENT_ID

Cohort List

This corresponds to the maximum number of patients or subjects that can be saved in the Cohort List. The maximum value that can be provided is 1000.

GENOMIC.MAX_PATIENT_COUNT

Genomic Data Export

This corresponds to the maximum count of patients or subjects that can be selected for generating the genomic data. This is applicable for all the 3 options on selecting the patients (active query, library query and the ad-hoc patients). If the count of patients or subjects selected is more than this value, an error message is displayed when the Submit button is clicked.

GENOMIC.REPORTS_MAX_PATIENT_COUNT

Cohort Reports

This corresponds to the maximum number of patients whose data can be viewed in the reports. This applies to all options of selecting the Patients/Subjects. If the count of patients or subjects selected is more than this value, a warning message is displayed. You can either continue to plot with a large number of patients/subjects, which might impact performance or change the selected cohort for a smaller number of patients / subjects.

DEFAULT_ACTIVE_QUERY_LIMIT

Cohort Reports

This corresponds to the maximum number of patients /subjects whose data will be plotted when the patient selection mode is Active Query, but the patients/subjects have not been filtered using the Cohort Query screen. If this count is exceeded, then an error message is displayed.

MAX_SPEC_REPORT

Cohort Reports

This corresponds to the maximum number of specimens for which a sample matrix can be plotted. If the number of specimens exceeds this limit, then a warning message is shown and a summary report of genomic information is displayed.

GENOMIC.MAX_GENE_COUNT

Cohort Reports or Genomic Data Export

This corresponds to the maximum count of Gene names that can be selected for generating genomic data. This applies to the Ad-hoc list Gene selection in the screen. If the count of Genes selected is more than this value, an error message is displayed when the Submit button is clicked.

VARIANT_DISPLAY_LIMIT

View Record

This corresponds to the maximum number of records that can be retrieved from the database for displaying variant data.

DEMOGRAPHICS_DISABLED

Cohort Query

Setting this value to True will disable the Demographics criteria on the Cohort Query screen.

CONSENT_DISABLED

Cohort Query

Setting this value to True will disable the Consent criteria on the Cohort Query screen.

DIAGNOSIS_DISABLED

Cohort Query

Setting this value to True will disable the Diagnosis criteria on the Cohort Query screen.

CLINICAL_ENCOUNTER_DISABLED

Cohort Query

Setting this value to True will disable the Clinical Encounter criteria on the Cohort Query screen.

PROCEDURE_DISABLED

Cohort Query

Setting this value to True will disable the Procedure criteria on the Cohort Query screen.

MEDICATION_DISABLED

Cohort Query

Setting this value to True will disable the Medication criteria on the Cohort Query screen.

PATIENT_HISTORY_DISABLED

Cohort Query

Setting this value to True will disable the History criteria on the Cohort Query screen.

TEST_OBSERVATION_DISABLED

Cohort Query

Setting this value to True will disable the Test Or Observation criteria on the Cohort Query screen.

SPECIMEN_DISABLED

Cohort Query

Setting this value to True will disable the Specimen criteria on the Cohort Query screen.

STUDY_DISABLED

Cohort Query

Setting this value to True will disable the Study criteria on the Cohort Query screen.

RELATIVE_TIME_EVENTS_DISABLED

Cohort Query

Setting this value to True will disable the Relative Time Events criteria on the Cohort Query screen.

SEQUENCE_VARIANTS_DISABLED

Cohort Query

Setting this value to True will disable the Sequence Variants criteria on the Cohort Query screen.

COPY_NUMBER_VARIATION_DISABLED

Cohort Query

Setting this value to True will disable the Copy Number Variation criteria on the Cohort Query screen.

DALLIANCE.AUTHORITY_XX

Note: XX is a numerical value; for example 37

View Record

This is one of four property values set to configure a header for a Dalliance instance. The header provides details of the common reference tracks available for display in the instance. This property specifies the Authority suffix (of the genomic reference) for the numeric (XX) value in the property label. For example, NCBI for 36 or GRCh for 37.

Note: A new property should be present for each supported Assembly version.

DALLIANCE.UCSC_NAME_XX

Note: XX is a numerical value; for example 37

View Record

This is one of four property values for a Dalliance instance reference tracks header. It stores the UCSC assembly alias of the reference. For example hg19 for XX value 37.

Note: A new property should be present for each supported Assembly version.

DALLIANCE.SEQ_URL_XXXX

Note: XXXX is the UCSC name value in the second property instance for Dalliance.

View Record

This is one of four property values for a Dalliance instance reference tracks header. It provides the URL for a reference sequence track.

Note: A new property should be present for each supported Assembly version.

DALLIANCE.GENES_URL_XXXX

Note: XXXX is the UCSC name value in the second property instance for Dalliance.

View Record

This is one of four property values for a Dalliance instance reference tracks header. It provides the URL for a reference gene track to be displayed in Dalliance.

Note: A new property should be present for each supported Assembly version.

MICROARRAY_EXPRESSION_DISABLED

Cohort Query

Setting this value to True will disable the MicroArray Expression criteria on the Cohort Query screen.

RNA_SEQ_EXPRESSION_DISABLED

Cohort Query

Setting this value to True will disable the RNA Sequencing criteria on the Cohort Query screen.

4.1.3 Installing MDS Repository Using Repository Creation Utility

Perform the following steps to install the MDS repository using the repository creation utility:

  1. Launch the installer from the RCU shiphome.

  2. Select Create.

  3. Enter the user credentials with sysdba privileges.

  4. After running validations, click OK,. Then click Next.

    The Component Selection page appears.

  5. Select the Create a new prefix option and enter TRC for the prefix.

  6. Expand the AS Common Schemas node and select the Metadata Services option.

  7. Click Next.

  8. Select Specify different passwords for all schemas option.

  9. Enter the password for the Metadata Services component.

  10. Create the MDS repository using the default options for the remaining screens.

4.1.4 Setting Up the MDS Database Connection on WebLogic Instance

Perform the following steps to set up the MDS database connection on the WebLogic instance where the TrcApp will be deployed:

  1. Set up scripts to run WLST to configure MDS and OBIEE Connection and Credential information for the deployed TrcApp.

    1. Execute the following command:

      cd [middlewareHome]/oracle_common/common/bin

    2. Start WLST.

  2. Configure the database-based MDS connection (use connection information from the MDS schema).

    1. Execute the following command and connect to the WebLogic instance:

      connect('weblogic','<password>','t3://<localhost>:7001')

      The WebLogic Administrator Console port is 7001. It may differ depending on custom configuration.

    2. Run the following WLST commands to set up the connection in WLS (database host, port, dbName, user, and password as requried):

      registerMetadataDBRepository(name='trc_ mds',dbVendor='ORACLE',host='server1',port='1121',dbName='devdb',user='trc_ mds',password='<password>')

      createMetadataPartition(repository='mds-trc_mds',partition='TrcApp')

  3. Exit WLST.

4.1.5 Setting Up OBIEE

Setting up OBIEE involves the following steps:

  1. Role Set Up

  2. Installing rpd and webcat

  3. Creating a BIImpersonateUser User and Granting Privileges

4.1.5.1 Role Set Up

To create roles in the WebLogic instance where OBIEE is installed perform the following steps:

  1. Log into WebLogic Enterprise Manager where the rpd and webcat are deployed.

  2. Expand the Weblogic Domain node.

  3. Right-click bifoundation_domain and then navigate to Security > Application Roles.

  4. Select Select Application Stripe to search and then select obi.

  5. Click Search.

  6. Click Create.

  7. Enter the role name and click OK.

  8. The following roles have to be created:

    • trc-basic-user-group

    • trc-bioinformatician-group

    • trc-cohort-group

    • trc-limited-user-group

    • trc-comics-limited-user-group

    • trc-omics-group

    • trc-pi-user-group

    • trc-standard-report-group

    • trc-custom-report-group

    • trc-admin-group

    • TRC-Developer

    • TRC-Administrator

4.1.5.2 Installing rpd and webcat

Perform the following steps to install OHSCE reports on Windows and Unix:

  1. Place the OracleHealthSciencesCohortExplorer.rpd in the following folder:

    • Windows: <DRIVE>:\Oracle\MiddleWare\instances\instance1\bifoundation\OracleBIServerComponent\coreapplication_obis1\repository

    • UNIX: Oracle/MiddleWare/instances/instance1/bifoundation/OracleBIServerComponent/coreapplication_obis1/repository

  2. Unzip OracleHealthSciencesCohortExplorer.zip in the following folder:

    • Windows: <DRIVE>:\Oracle\MiddleWare\instances\instance1\bifoundation\OracleBIPresentationServicesComponent\coreapplication_obips1\catalog

    • UNIX: Oracle/MiddleWare/instances/instance1/bifoundation/OracleBIPresentationServicesComponent\coreapplication_obips1/catalog

  3. In the Oracle BI Administration Tool, open the newly installed Oracle BI repository (OracleHealthSciencesCohortExplorer.rpd) in offline mode to configure the static variables and connections.


    Note:

    The OBIEE BI Administration Tool is supported only on Windows. If OHSCE is installed on Unix, copy OracleHealthSciencesCohortExplorer.rpd to a Windows system to perform modifications described in the following sections. Once the modifications are complete, copy the OracleHealthSciencesCohortExplorer.rpd back to the Unix system.

  4. In the Oracle BI Administration Tool, from the File menu, select Open > Offline.

  5. Navigate to the OracleHealthSciencesCohortExplorer.rpd, and then click Open.

    The Open Offline dialog box appears.

  6. Enter the repository password to log into the OracleHealthSciencesCohortExplorer.rpd file.

    The default password is cohort.

    To change the password:

    1. From the File menu, select Change Password.

    2. Enter the old password and then the new password.

    3. Confirm the new password.

  7. Click OK.

  8. In the Oracle BI Administration Tool, select Manage, and then select Variables.

    The Variable Manager dialog box appears.

  9. Expand Repository and then Variable in the left pane.

  10. Click Static.

  11. Double-click and modify the following static variables:

    Table 4-2 Static Variables

    Variable Name Instruction

    OLAP_DSN

    Provide the value of the database name. ODBC connection to OHSCE database has to be defined prior to this step. The connection Data Set Name will be provided to OLAP_DSN

    OLAP_USER

    Provide the value of the CDM schema user.

    ConsentTypeCode

    Provide the value of the type code for Consent.

    ConsetStatusCode

    Provide the value of the type code for Consent Status.

  12. Click OK after each modification.

  13. Close Variable Manager.

  14. Modify the connection pools in the RPD as follows:

    1. In the physical layer, expand the OracleHealthScienceCohortExplorer node and double-click the connection pool.

    2. Change the password to the password of the schema user.

    3. Confirm the new password.

    4. Click OK.

  15. Save the rpd as follows:

    1. From the File menu, select Save.

      The Do you wish to check global consistency dialog box appears.

    2. Click No.

  16. Log into Fusion Middleware Control:

    https://<host name>:<port number>/em

    where <port number> is the port where OBIEE WebLogic Enterprise Manager is installed.

  17. Expand the Business Intelligence folder and select the coreapplication node.

  18. Click the Repository tab on the Deployment page.

  19. Click Lock and Edit Configuration.

  20. In the Upload BI Server Repository section, click Browse to select the OracleHealthSciencesCohortExplorer.rpd.

  21. Enter the new password that you have set up in Repository Password and Confirm Password fields.

  22. Enter the location of the OracleHealthSciencesCohortExplorer catalog in the BI Presentation Catalog section.

  23. Click Apply.

  24. Click Activate Changes.

  25. Click the Overview tab.

  26. Click Restart.

  27. Click Yes.

  28. Open your browser and log into OBIEE:

    http://<host name>:<port number>/analytics

  29. Enter the User ID and password.

  30. Edit the file %MiddleWare_Home%\instances\instance1\bifoundation\OracleBIApplication\coreapplication\setup\user.cmd to set TNS_ADMIN to your Oracle client tnsnames.ora home directory path (in case it exists) or to your OBIEE tnsadmin %OBIEE_Client_Home%\Oracle_BI1\network\admin

    DESCRIPTION=(ADDRESS=(PROTOCOL=TCP)(HOST=<hostname>)(PORT=<port name>))(@ CONNECT_DATA=(SERVER=DEDICATED)(SERVICE_NAME/SID=<service name/SID>)))

  31. Select Cohort Explorer from the Dashboards drop-down list.

  32. Click Edit Dashboard on the right-hand corner in the Summary tab.

  33. Select Edit Analysis for report biospecimen_samples_r.

  34. Click the Criteria tab.

  35. Click Show/Hide Selection Steps Pane.

  36. Under the Specimen - Anatomical Site section, edit the first step Start with... to include the Anatomical Sites you want to see in report.

  37. Save the report.

  38. Click Apply on the Cohort Explorer Summary tab.

  39. Oracle recommends that you enable logging of queries in OBIEE. To enable logging, perform the following steps:

    1. Open the rpd.

    2. Click Tools.

    3. Select Options.

    4. Click the repository tab.

    5. Select system logging level information to 3.

    6. Save the rpd.

    7. The logged in user name, time of login as well as the query issued to the BI server is logged in the nqquery.log.

4.1.5.3 Creating a BIImpersonateUser User and Granting Privileges

To create a BIImpersonateUser user and grant privileges:

  1. Log into OBIEE Console.

    https://<host name>:<port number>/console

    where <port number> is the port where OBIEE WebLogic Enterprise Manager is installed.

  2. Click Security Realm in the Domain Structure panel.

  3. Click myrealm.

  4. Click the Users and Groups tab.

  5. Click New.

  6. Enter BIImpersonateUser in the Name field and the corresponding password in the Password.

  7. Click OK.

  8. Open Oracle Enterprise Manager for the Oracle BI EE instance.

  9. Select the Business Intelligence folder and then select the coreapplication node.

  10. Click the Security tab.

  11. Click the Single Sign On tab.

  12. Click Configure and Manage Application Policies.

  13. Select OBI for the Application Strip.

  14. Click Create.

  15. In the Permissions pane, click Add.

    The Add Permission dialog appears.

  16. Select the Permissions option.

  17. In the Permission Class field, select oracle.security.jps.ResourcePermission.

  18. In the Resource Name field, enter oracle.bi.server.impersonateUser and click the arrow icon button to search.

  19. Select oracle.bi.server.impersonateUser in the Search Results table and click Continue.

  20. Click Select.

  21. In the Grantees pane, click Add.

    The Add Principal dialog appears.

  22. Select User for the Type.

  23. In the Principal Name field, enter BIImpersonateUser and click the arrow icon button to search.

  24. Select BIImpersonateUser in the Searched Principals table and click OK.

  25. Click OK.

4.1.6 Setting Up OBIEE-ADF Integration

To alter the .ear file, execute the archive commands.

  1. Upload TrcApp.ear to <FMW_HOME>/user_projects/domains/<DOMAIN_NAME>/servers/<SERVER_NAME>/upload, where FMW_HOME is the home directory of Oracle Fusion Middleware that has the WebLogic server.

    Create the upload directory, if it does not exist.

  2. Execute the following command:

    cd [middlewareHome]/oracle_common/common/bin

  3. Start WLST.

  4. Execute the following archive commands:

    1. archive = getMDSArchiveConfig(fromLocation='/<FMW_HOME>/user_projects/domains/<DOMAIN_NAME>/servers/<SERVER_NAME>/upload/ TrcApp.ear')

      fromLocation - Use the location where your ear file is placed

    2. archive.setAppMetadataRepository(repository='trc_mds', partition='TrcApp', type='DB', jndi= 'jdbc/mds/trc_mds')

      Table 4-3 Variables and Descriptions

      Field Description

      repository

      The name of the application's repository.

      partition

      The name of the partition for the application's metadata.

      type

      The type of connection, file or database to the repository.Valid values are 'File' or 'DB' (case insensitive).

      jndi

      The JNDI location for the database connection. This argument is required if the type is set to DB.

    3. archive.save()

4.1.7 Deploying TrcApp.ear

Perform the following steps to deploy TrcApp.ear:

  1. Log into the WebLogic Server Administration Console.

  2. Select the Deployments node in the Domain Structure pane.

  3. If the Install button above the Deployments table in the right pane is disabled, click Lock & Edit in the Change Center pane.

  4. Click Install.

  5. Enter the directory where you uploaded TrcApp.ear in Setting Up OBIEE-ADF Integration (<FMW_HOME>/user_projects/domains/<DOMAIN_NAME>/servers/<SERVER_NAME>/upload) in the Path field.

  6. Press ENTER.

  7. Select TrcApp.ear in the Current Location and click Next.

  8. Select Install this deployment as an application and click Next.

  9. Select deployment target and click Next.


    Note:

    The target must be a server or a cluster where the TrcApp.ear application will be deployed. The target is not displayed if only admin server exists.

  10. Click Finish.

  11. Click Activate Changes in the Change Center pane, if it is enabled.

  12. Click the Deployments node in Domain Structure pane.

  13. If TrcApp is not in Active State in the Deployments pane, select TrcApp, click Start, and then select Servicing all requests.

  14. Click Yes.

  15. Click the Deployments node in Domain Structure pane to refresh the Deployments table.

    Ensure that the state of TrcApp is Active.

  16. Enter the URL of the application (http://HOST_NAME:PORT_NUMBER/trc/faces/shell or https://HOST_NAME:SSL_PORT_NUMBER/trc/faces/shell if SSL is enabled) in a browser to verify the deployment.

4.1.8 Setting OBIEE Connection and Credential Information for TrcApp

Perform the following steps to set the OBIEE connection and credential information for TrcApp:

  1. Before setting the connection information, ensure that WLS is running and TrcApp is deployed after executing the archive commands.

  2. The URL of the deployed OBIEE application must be of the form http://<host name>:<port number>/analytics.

  3. Copy the packaged setup_bi_connection.sh and set_bi_credentials.py script to WebLogic Home where TrcApp.ear was deployed.

  4. Execute the following command:

    cd to [middlewareHome]/oracle_common/common/bin

  5. If the deployment is on a clustered environment or a Managed Server, edit the script. Change the value set for Location to the name of the server where the .ear file is deployed.

    You must execute this script on every node of the clustered environment.

  6. Execute setup_bi_connection.sh, which prompts for the following inputs:


    Note:

    This step is for OBIEE running on Linux environment. For OBIEE running on Windows, see step 7.

    • Weblogic Admin User Id: name of admin user of WLS, for example, weblogic.

    • Weblogic Admin Password: password of admin user of WLS.

    • Weblogic AdminServer Connection: connection to AdminServer in Weblogic. For example, t3://localhost:7001.

    • Name of target server in WebLogic where TRC application is deployed: for example, AdminServer.

    • Name of deployed application: Name of deployed application (.ear). For example, TrcApp.

    • Host of OBIEE server: for example, devobiee.us.oracle.com

    • Password of BIImpersonateUser

  7. If the WebLogic server is installed on Windows OS, then set_bi_credentials.py has to be run from wlst.

    .\wlst.cmd set_bi_credentials.py -wluid <wlUser> -wlpwd <wlPassword> -wlcon <wlConnection> -wlserver <wlSer> -app <wlApp> -conn SummaryCE -host <wlOBIEEHost> -port 9704 -uid BIImpersonateUser -pwd <wlOBIEEPass> -protocol http -context analytics

4.1.9 Setting Up Oracle Health Sciences Cohort Explorer Roles in WebLogic

Perform the following steps to set up OHSCE roles in WebLogic:

  1. Log into the WebLogic console where the CE application is deployed.

  2. Click Security realm on the Domain Structure panel.

  3. Click myrealm.

  4. Click the Users and Groups tab.

  5. Click the Groups tab.

  6. Click New.

  7. Enter the name of the group.

  8. Click OK.

    The following groups should be created. For more details on these groups, see the section on Roles and Permissions in the Oracle Health Sciences Translational Research Center User's Guide.

    • trc-basic-user-group

    • trc-bioinformatician-group

    • trc-cohort-group

    • trc-limited-user-group

    • trc-comics-limited-user-group

    • trc-omics-group

    • trc-pi-user-group

    • trc-standard-report-group

    • trc-custom-report-group

    • trc-admin-group

4.1.10 Setting Up Logging for Oracle Health Sciences Translational Research Center in WebLogic

Perform the following steps to set the logging level of TRC modules for tracking users and activities within the application accessing data:


Note:

Access to server logs should be strictly restricted since it will contain information such as Specimen Number and Date of Birth.

  1. Execute wlst.sh (or wlst.cmd) in MW_HOME/oracle_common/common/bin, where MW_HOME is the Oracle Middleware home directory where TRC WebLogic server is installed.

  2. Connect to the WebLogic server.

    connect('username','password','t3://hostname:port_number')

  3. Run in domainRuntime tree, which is required for WLST logging commands.

    domainRuntime()

  4. Set the logging level of oracle.hsgbu.trc with the following command: setLogLevel(target='SERVER_NAME', logger='oracle.hsgbu.trc', level='NOTIFICATION:1', addLogger=1)

    where SERVER_NAME is the name of target server where TrcApp is deployed.

  5. Run the following command to verify the logging level:

    getLogLevel(target='SERVER_NAME', logger='oracle.hsgbu.trc')

    The following should be displayed:

    NOTIFICATION:1

For more information on WLST logging commands and logging levels, refer to Oracle® Fusion Middleware Administrator's Guide 11g Release 1.

4.2 Updating the Middle Tier for an Existing TRC Installation

This section describes the procedure to update the middle tier while upgrading an existing TRC installation.

4.2.1 Installing Cohort Explorer

Perform the following steps to install Cohort Explorer.

  1. Install Weblogic 12c (12.1.3) and create new domain as CE_DOMAIN with Application Development Runtime (ADR) 12.1.3.0. For details, see the Oracle® Fusion Middleware Installation Guide for Application Developer 12c (12.1.3).

  2. After creating the domain, perform the steps in Section 4.1, "Installing the Middle Tier for a New Installation" (except section 4.1.5).

4.2.2 Upgrading OBIEE

  1. Upgrade OBIEE 11.1.1.6 to OBIEE 11.1.1.7. For this upgrade, perform the steps in the Oracle Fusion Middleware documentation at

    http://docs.oracle.com/cd/E28280_01/upgrade.1111/e16452.pdf


    Important:

    Apply 11.1.1.7.151020 bundle patch on top of OBIEE 11.1.1.7.0. See the document OBIEE 11g: Required and Recommended Bundle Patches and Patch Sets (Doc ID 1488475.1) on MOS to apply the OBIEE bundle patch 11.1.1.7.151020. Currently, TRC 3.1 is certified only with this patch version.

  2. Ensure that the roles in:

4.2.2.1 Setting Up OBIEE-ADF Integration

To replace the new TrcApp.ear file, execute the archive commands.

  1. Upload the new TrcApp.ear to <CE_MW_HOME>/user_projects/domains/<DOMAIN_NAME>/servers/<SERVER_NAME>/upload, where CE_MW_HOME is the home directory of Oracle Fusion Middleware of WLS 12.1.3.

  2. Create the upload directory if it does not exist.

  3. Execute the following command:

    cd [middlewareHome]/oracle_common/common/bin

  4. Start WSLT.

  5. Execute the following archive commands:

    1. archive = getMDSArchiveConfig(fromLocation='/<CE_MW_HOME>/user_projects/domains/<DOMAIN_NAME>/servers/<SERVER_NAME>/upload/ TrcApp.ear'

      fromLocation - Use the location where your .ear file is placed.

    2. archive.setAppMetadataRepository(repository='trc_mds', partition='TrcApp', type='DB', jndi= 'jdbc/mds/trc_mds')

      repository - The name of the application's repository.

      partition - The name of the partition for the application's metadata.

      type - The type of connection, file or database to the repository. Valid values are File or DB (not case sensitive).

      jndi - The JNDI location for the database connection. This argument is required if the type is set to DB.

    3. archive.save()

4.2.2.2 Replacing rpd and webcat

Perform the following steps to install OHSCE reports on Windows and Unix:

  1. Place the OracleHealthSciencesCohortExplorer.rpd in the following folder:

    • Windows: <DRIVE>:\Oracle\MiddleWare\instances\instance1\bifoundation\OracleBIServerComponent\coreapplication_obis1\repository

    • UNIX: Oracle/MiddleWare/instances/instance1/bifoundation/OracleBIServerComponent/coreapplication_obis1/repository

  2. Unzip OracleHealthSciencesCohortExplorer.zip in the following folder:

    • Windows: <DRIVE>:\Oracle\MiddleWare\instances\instance1\bifoundation\OracleBIPresentationServicesComponent\coreapplication_obips1\catalog

    • UNIX: Oracle/MiddleWare/instances/instance1/bifoundation/OracleBIPresentationServicesComponent\coreapplication_obips1/catalog

  3. In the Oracle BI Administration Tool, open the newly installed Oracle BI repository (OracleHealthSciencesCohortExplorer.rpd) in offline mode to configure the static variables and connections.


    Note:

    The OBIEE BI Administration Tool is supported only on Windows. If OHSCE is installed on Unix, copy OracleHealthSciencesCohortExplorer.rpd to a Windows system to perform modifications described in the following sections. Once the modifications are complete, copy the OracleHealthSciencesCohortExplorer.rpd back to the Unix system.

  4. In the Oracle BI Administration Tool, from the File menu, select Open > Offline.

  5. Navigate to the OracleHealthSciencesCohortExplorer.rpd, and then click Open.

    The Open Offline dialog box appears.

  6. Enter the repository password to log into the OracleHealthSciencesCohortExplorer.rpd file.

    The default password is cohort.

    To change the password:

    1. From the File menu, select Change Password.

    2. Enter the old password and then the new password.

    3. Confirm the new password.

  7. Click OK.

  8. In the Oracle BI Administration Tool, select Manage, and then select Variables.

    The Variable Manager dialog box appears.

  9. Expand Repository and then Variable in the left pane.

  10. Click Static.

  11. Double-click and modify the following static variables:

    Table 4-4 Static Variables

    Variable Name Instruction

    OLAP_DSN

    Provide the value of the database name. ODBC connection to OHSCE database has to be defined prior to this step. The connection Data Set Name will be provided to OLAP_DSN

    OLAP_USER

    Provide the value of the CDM schema user.

    ConsentTypeCode

    Provide the value of the type code for Consent.

    ConsetStatusCode

    Provide the value of the type code for Consent Status.

  12. Click OK after each modification.

  13. Close Variable Manager.

  14. Modify the connection pools in the RPD as follows:

    1. In the physical layer, expand the OracleHealthScienceCohortExplorer node and double-click the connection pool.

    2. Change the password to the password of the schema user.

    3. Confirm the new password.

    4. Click OK.

  15. Save the rpd as follows:

    1. From the File menu, select Save.

      The Do you wish to check global consistency dialog box appears.

    2. Click No.

  16. Log into Fusion Middleware Control:

    https://<host name>:7001/em

  17. Expand the Business Intelligence folder and select the coreapplication node.

  18. Click the Repository tab on the Deployment page.

  19. Click Lock and Edit Configuration.

  20. In the Upload BI Server Repository section, click Browse to select the OracleHealthSciencesCohortExplorer.rpd.

  21. Enter the new password that you have set up in Repository Password and Confirm Password fields.

  22. Enter the location of the OracleHealthSciencesCohortExplorer catalog in the BI Presentation Catalog section.

  23. Click Apply.

  24. Click Activate Changes.

  25. Click the Overview tab.

  26. Click Restart.

  27. Click Yes.

4.3 Enabling iframe Support for OBIEE Reports

This is common for new installations as well as upgrades. Perform the following steps to enable iframe support for OBIEE reports in CE.

Ensure that the following configurations are enabled from OBIEE to render OBIEE reports in OHSCE:

  1. Open instanceconfig.xml located at <OBIEE_HOME>\instances\instance1\config\OracleBIPresentationServicesComponent\coreapplication_obips1\.

  2. Update the <security> tag as follows:

    <Security>
<InIFrameRenderingMode>allow</InIFrameRenderingMode>
<ClientSessionExpireMinutes>210</ClientSessionExpireMinutes>
</Security>

  3. Edit the web.xml file located at <OBIEE_HOME>\Oracle_BI1\bifoundation\web\appv2\WEB-INF.

  4. Add the following entry between the <servlet-mapping> and <login-config> tags.

    <context-param>
<param-name>oracle.adf.view.rich.security.FRAME_BUSTING</param-name>
<param-value>never</param-value>
</context-param>

  5. Restart all OBIEE 11g services either from the Enterprise Manager console as shown below or using opmnctl (Stop opmnctl and Start opmnctl).

    Description of iframe.gif follows
    Description of the illustration iframe.gif

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