Oracle® Health Sciences Network

Installation Guide

Release 2.0.0.0

E65879-01

September 2015

Oracle Health Sciences Network Installation Guide, Release 2.0.0.0

E65879-01

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Contents

List of Figures

Preface

- Audience

- Documentation Accessibility

- Related Documents

- Conventions

1 Installation Overview

- 1.1 Prerequisites

2 Installing the Platform

- 2.1 Installing HSN Database

- 2.1.1 Creating HSN Tablespace

- 2.1.2 Creating HSN Database User

- 2.1.3 Installing HSN Database Objects

- 2.2 Installing HSN ManApp

- 2.2.1 Enabling JPA 2.0

- 2.2.2 Configuring Data Source

- 2.2.3 Setting Transaction Timeout

- 2.2.4 Deploying EAR

- 2.2.5 Configuring Logging

- 2.2.6 Configuring the Oracle Web Services Manager

- 2.3 Configuring HSN-SOA

- 2.3.1 Increasing PermGen Memory When Using Sun JDK

- 2.3.2 Installing SOA Security Patch

- 2.3.3 Configuring Logging

- 2.3.4 Configuring Oracle Web Services Manager

- 2.4 Configuring SOA MDS

- 2.5 Configuring HSN Tracking for SOA Composites

- 2.5.1 Configuring Data Source

- 2.5.2 Configuring the SOA Server

- 2.6 Setting Transaction Timeout for Service-Oriented Architecture

- 2.7 Deploying SOA Composite

3 Installing PVPR

- 3.1 Installing PVPR Database

- 3.1.1 Prerequisites

- 3.1.1.1 Installing CDM

- 3.1.1.2 Installing ODB

- 3.1.2 Creating PVPR Tablespace

- 3.1.3 Creating PVPR Database User

- 3.1.4 Granting Privileges and Creating Synonyms

- 3.1.5 Configuring Dimension Data Export and Import

- 3.1.6 Installing PVPR Database Objects

- 3.1.7 Loading Data to ODB and CDM

- 3.1.7.1 Loading Data to ODB

- 3.1.7.2 Loading Data to CDM

- 3.2 Installing the PVPR Middle-Tier

- 3.2.1 Creating Data Source in the Oracle WebLogic Server

- 3.2.2 Setting Transaction Timeout for the WebLogic Application Server

- 3.2.3 Enabling JPA 2.0 and Jackson

- 3.2.4 Referring Shared Jersey Library

- 3.2.5 Deploying EAR

- 3.3 Configuring Logging

- 3.4 Configuring Oracle Web Services Manager

- 3.4.1 Generating Keystore and Configuring Trusted Certificate

- 3.4.2 Configuring Keystore on HSnP and SOA Server

- 3.4.3 Keystore Configuration on PVPR Server

4 Configuring Registry

- 4.1 Creating Seed Data

- 4.2 Creating Company

- 4.3 Provisioning Service

- 4.4 Creating Relationship

- 4.5 Updating Company

- 4.6 Deleting Provision

List of Figures

- 2-1 Log Configuration

- 2-2 Root Logger

- 2-3 Log Levels

- 2-4 WebLogic Domain Drop-down List

- 2-5 Platform Policy Configuration

- 2-6 Add New Distinguished Name (DN) Window

- 2-7 Log Configuration

- 2-8 Root Logger

- 2-9 Log Levels

- 2-10 WebLogic Domain Drop-down List

- 2-11 Platform Policy Configuration

- 2-12 Add New Distinguished Name (DN) Window

- 2-13 SOA Infra Home Page

- 2-14 MDS Configuration

- 2-15 Import Operation Successful

- 2-16 Enterprise Manager - SOA Default Node

- 2-17 Undeploying Composites from a Partition

- 2-18 Undeploying Composites

- 2-19 Selecting an Archive

- 3-1 Install Application Assistant

- 3-2 Install Application Assistant - Choose Targeting Style

- 3-3 Install Application Assistant - Optional Settings

- 3-4 Log Configuration

- 3-5 Root Logger

- 3-6 Log Levels

- 3-7 WebLogic Domain Drop-down List

- 3-8 Platform Policy Configuration

- 3-9 Add New Distinguished Name (DN) Window

- 4-1 PVPR Company Admin Screen

- 4-2 Create Relationship

Preface

Oracle Health Sciences Network (HSN) is a new SaaS services offering for both healthcare providers and pharmaceutical customer organizations. It brings together multiple customer organizations under a single cloud-based and Oracle-hosted business network, thus allowing them to exchange information and/or business services using HSN applications such as Protocol Validator and Patient Recruiter (PVPR).

HSN consists of two components: Patient Validator and Patient Recruiter (PVPR), and Platform.

Audience

This document is intended for users (having knowledge of WebLogic server administration and database administration) who want to install HSN applications.

Documentation Accessibility

For information about Oracle's commitment to accessibility, visit the Oracle Accessibility Program website at http://www.oracle.com/pls/topic/lookup?ctx=acc&id=docacc.

Access to Oracle Support

Oracle customers that have purchased support have access to electronic support through My Oracle Support. For information, visit http://www.oracle.com/pls/topic/lookup?ctx=acc&id=info or visit http://www.oracle.com/pls/topic/lookup?ctx=acc&id=trs if you are hearing impaired.

Related Documents

For more information, see the following documents:

- Oracle Health Sciences Network Installation Guide [this document]

- Oracle Health Sciences Network User's Guide

- Oracle Health Sciences Network Release Notes

- Oracle Health Sciences Network Security Guide

- Oracle Health Sciences Network Administrator's Guide

Conventions

The following text conventions are used in this document:

Convention

Meaning

boldface

Boldface type indicates graphical user interface elements associated with an action, or terms defined in text or the glossary.

italic

Italic type indicates book titles, emphasis, or placeholder variables for which you supply particular values.

monospace

Monospace type indicates commands within a paragraph, URLs, code in examples, text that appears on the screen, or text that you enter.

1 Installation Overview

You can download the Health Sciences Network (HSN) media pack from the Automated Release Update (ARU) system. Files mentioned in the installation steps are available in corresponding folder hierarchy. The HSN media pack contains the following applications:

- HSnPManApp

- EAR - Deployable EAR file for HSnPManApp

- SQL - SQL scripts to create and configure the registry schema

- HSnP-SOA

- MDS - Metadata Services (MDS) artifacts used in Service-Oriented Architecture (SOA) composites

- SCA - SOA composites for HSnP services

- Sensor - HSN sensor implementation to track the usage of HSnP services

- CDM-ODB

- CDM installation scripts

- ODB installation scripts

- CDM ETL scripts

- ODB Data Loaders

- PVPR

- EAR - Deployable EAR file for PVPR

- SQL - SQL scripts to create the Patient Validator and Patient Recruiter (PVPR) schema

- wls

- WebLogic Scripting Tool (WLST) scripts used for Oracle Web Services Manager (OWSM) configuration of PVPR and HSnPManApp

1.1 Prerequisites

The following servers must have synchronized clock:

- HSNManApp - Database server and Application server

- SOA server

- PVPR - Database server and Application server

You should set up the following:

- Oracle WebLogic Server (10.3.6) with OWSM and Enterprise Manager for HSNManApp and PVPR installations

- Oracle SOA Suite (11.1.1.6.0) and OWSM on WebLogic installation for HSN-SOA

2 Installing the Platform

This chapter provides the instructions to install the Platform services of the Health Sciences Network (HSN).

This chapter contains the following sections:

- Section 2.1, "Installing HSN Database"

- Section 2.2, "Installing HSN ManApp"

- Section 2.3, "Configuring HSN-SOA"

- Section 2.4, "Configuring SOA MDS"

- Section 2.5, "Configuring HSN Tracking for SOA Composites"

- Section 2.6, "Setting Transaction Timeout for Service-Oriented Architecture"

- Section 2.7, "Deploying SOA Composite"

2.1 Installing HSN Database

This section contains the following topics:

- Section 2.1.1, "Creating HSN Tablespace"

- Section 2.1.2, "Creating HSN Database User"

- Section 2.1.3, "Installing HSN Database Objects"

2.1.1 Creating HSN Tablespace

To create tablespace for the HSN database, perform the following:

1. Edit hsnp_create_tablespace.sql.

2. Enter the following details:

- appropriate path for data file (line starting with data file)

- size and auto extend size (line starting with SIZE)

3. Log in to the database as a user with privilege to create tablespace and execute the script.

4. Enter the name of the tablespace you want to create when prompted.

See also Section 3.1.

2.1.2 Creating HSN Database User

To create HSN database user, perform the following:

1. Log in to the database as a user with privilege to create user using SQLPlus.

2. In the SQLPlus prompt, execute the @hsnp_create_user.sql script.

3. Enter the corresponding values as prompted.

Note:
Ensure that you specify the tablespace name created in Section 2.1.1 when prompted.

4. Exit SQLPlus.

2.1.3 Installing HSN Database Objects

This section describes how to create database objects for HSN and initialize the database with seed data.

To install the HSN database objects, perform the following:

1. Log in to the database as HSN user (created in Section 2.1.2) using SQLPlus.

2. In the SQLPlus prompt, execute the HSNP_ddl.sql script.
This creates the required database objects.

3. Update the SOA and ManApp service URL in the BPEL_PROCESS_MASTER and MANAGEMENT_CONFIGURATION tables as per the environment in HSNP_seed.sql.

4. Execute the HSNP_seed.sql script.
This inserts the seed data in the database objects created.

5. Exit SQLPlus.

Running Post-Installation Scripts

During schema creation, access rights are granted to the schema user which are required only for database configuration. Post database schema creation, the access rights need to be revoked. The access rights can be revoked using the post installation scripts.

1. Connect to the database as a user with sysdba privilege.

2. Execute the @hsnp_post_install.sql script.

2.2 Installing HSN ManApp

This section contains the following topics:

- Section 2.2.1, "Enabling JPA 2.0"

- Section 2.2.2, "Configuring Data Source"

- Section 2.2.3, "Setting Transaction Timeout"

- Section 2.2.4, "Deploying EAR"

- Section 2.2.5, "Configuring Logging"

- Section 2.2.6, "Configuring the Oracle Web Services Manager"

2.2.1 Enabling JPA 2.0

To enable JPA 2.0, perform the following:

1. Edit the <MIDDLEWARE_HOME>/wlserver_10.3/common/bin/commEnv.sh file to add the PRE_CLASSPATH variable at the end of the file.

2. Verify the JAR version number in the <MIDDLEWARE_HOME>/modules folder and update the following statement accordingly:
PRE_CLASSPATH=${MODULES_DIR}/javax.persistence_1.1.0.0_2-

0.jar:${MODULES_DIR}/com.oracle.jpa2support_1.0.0.0_2-

1.jar

export PRE_CLASSPATH

2.2.2 Configuring Data Source

To configure data source, perform the following:

1. Log in to the Oracle WebLogic server console for the HSnP domain.

2. Create data source using the schema created in database setup steps.

3. Enter the jndi name as jdbc/HAFDBDS and assign it to the HSnPManApp server as target.

4. Restart the server.

2.2.3 Setting Transaction Timeout

To set the transaction timeout for the WebLogic application server, perform the following:

1. Go to Services > JTA in the WebLogic console.

2. Update timeout seconds to 600 and save.

2.2.4 Deploying EAR

To deploy EAR, perform the following:

Note:
Ensure that the application name is set to HSnPMan-EAR during deployment.

1. Extract the HSnPManApp EAR file from the media pack.

2. Deploy the EAR file to the Oracle WebLogic server, where HSnPManApp need to be installed.

2.2.5 Configuring Logging

To configure logging, perform the following:

1. Log in to the Enterprise Manager of WebLogic server.

2. In the pane on the left side of the window, click the HSnPManApp domain in the WebLogic Domain folder and select the target HSnPManApp server.
For example, provider1.

3. From the WebLogic Server drop-down list, select Logs and then select Log Configuration.

Figure 2-1 Log Configuration

4. Expand Root Logger.

Figure 2-2 Root Logger

5. For Oracle, change the log level and select Inherited from Parent.

6. Select Persist log level state across component restarts and click Apply Changes.

Figure 2-3 Log Levels

2.2.6 Configuring the Oracle Web Services Manager

To execute the following commands you need to set the JAVA_HOME environment variable to point to JDK referred in the HSnP domain:

- export JAVA_HOME=<Path to JDK referred with hsnp domain>

- export PATH=$JAVA_HOME/bin:$PATH

1. Generate private key to be used in the HSnP ManApp and SOA servers using keytool utility available in the JDK bin directory.

2. In the following command, replace the <KEY_LOCATION> as required.
keytool -genkey -alias hsnp-key -keyalg "RSA" -sigalg "SHA1withRSA" -dname "cn=HSNP, ou=HSGBU, o=ORACLE, c=US" -keystore <KEY_LOCATION>/hsnpkey.jks -validity 3650

1. Enter the keystore password and the key password when prompted.

3. Copy the generated keystore hsnpkey.jks to the <HSNP_DOMAIN_HOME>/config/fmwconfig folder.

4. Open the <HSNP_DOMAIN_HOME>/config/fmwconfig/jps-config.xml file.

5. Search for default-keystore.jks in the file.
It should be similar to <serviceinstance name="keystore" provider="keystore.provider" location="./default-keystore.jks">.

6. Replace ./default-keystore.jks with ./hsnpkey.jks and save the file.

7. Restart the WebLogic server instances for the HSnP domain.

8. Copy the HSnP_OWSM_Config.py and GrantIdentity_to_HSnP.py files from the media pack to a location to which the operating system user has read and execute permissions.

9. Execute the following commands on the command prompt:

- cd <MIDDLEWARE_HOME>/oracle_common/common/bin

- ./wlst.sh <ABSOLUTE FILE_PATH to HSnP_OWSM_Config.py>

1. Enter the corresponding values as prompted by the script.

- ./wlst.sh <ABSOLUTE FILE PATH to GrantIdentity_to_HSnP.py>

1. Enter the corresponding values as prompted.

The HSnP_OWSM_Config.py script adds credentials for the hsnpkey.jks file. The GrantIdentity_to_HSnPMan.py file grants identity permission to the HSnPMan-Ear application.

10. Login to the Enterprise Manager of the HSnP domain.

11. In the left pane, click the HSnP domain in the WebLogic domain folder.

12. From the WebLogic Domain drop-down list, select Web Services and then select Platform Policy Configuration.

Figure 2-4 WebLogic Domain Drop-down List

13. Click the Trusted SAML clients tab in the Platform Policy Configuration page.

14. Select www.oracle.com issuer in the Trusted Issuers pane.

Figure 2-5 Platform Policy Configuration

15. Click Add in the Trusted SAML clients: www.oracle.com pane.
The Add New Distinguished Name (DN) window is displayed.

Figure 2-6 Add New Distinguished Name (DN) Window

16. Add text cn=HSN-PVPR, ou=HSGBU, o=ORACLE, c=US and click OK.

17. Repeat steps 14 and 15 to add cn=HSNP, ou=HSGBU, o=ORACLE, c=US as trusted SAML client.

18. Click Apply.

19. Log out of the Enterprise Manager.

20. Create the WebLogic user hsn_system to be used for the HSnP domain.

21. Restart the WebLogic server instances for the HSnP domain.

2.3 Configuring HSN-SOA

This chapter contains the following topics:

- Section 2.3.1, "Increasing PermGen Memory When Using Sun JDK"

- Section 2.3.2, "Installing SOA Security Patch"

- Section 2.3.3, "Configuring Logging"

- Section 2.3.4, "Configuring Oracle Web Services Manager"

2.3.1 Increasing PermGen Memory When Using Sun JDK

To increase PermGen memory, perform the following:

1. Edit the <HSNP-SOA_DOMAIN_HOME>/bin/setSOADomainEnv.sh file to increase the permgen memory allocation.

2. Increase the following values:
if [ "${JAVA_VENDOR}" != "Oracle" ] ; then DEFAULT_MEM_ARGS="${DEFAULT_MEM_ARGS} -XX:PermSize=128m -XX:MaxPermSize=256m" PORT_MEM_ARGS="${PORT_MEM_ARGS} -XX:PermSize=256m -XX:MaxPermSize=512m"fi

to these values:

if [ "${JAVA_VENDOR}" != "Oracle" ] ; then DEFAULT_MEM_ARGS="${DEFAULT_MEM_ARGS} -XX:PermSize=512m -XX:MaxPermSize=1024m" PORT_MEM_ARGS="${PORT_MEM_ARGS} -XX:PermSize=1024m -XX:MaxPermSize=1024m"fi

2.3.2 Installing SOA Security Patch

To install SOA security patch, perform the following:

1. Install the SOA Security Patch 16622432 for SOA version 11.1.1.6.0.

2. Download the patch from the following link and follow the install procedure for the Oracle SOA Platform:
https://support.oracle.com/epmos/faces/PatchDetail?_afrLoop=446908509299957&patchId=16622432&_afrWindowMode=0&_adf.ctrl-state=1dv0u5xlba_4

2.3.3 Configuring Logging

To configure logging, perform the following:

1. Log in to the Enterprise Manager.

2. In the pane on the left side of the window, click the SOA domain in the WebLogic Domain folder and select the target SOA server.

3. From the WebLogic Server drop-down list, select Logs and then select Log Configuration.

Figure 2-7 Log Configuration

4. Expand Root Logger.

5. For Oracle, change the log level and select Inherited from Parent.

Figure 2-8 Root Logger

6. Select Persist log level state across component restarts and click Apply Changes.

Figure 2-9 Log Levels

2.3.4 Configuring Oracle Web Services Manager

To configure Oracle Web Services Manager, perform the following:

1. Copy the hsnpkey.jks keystore file generated as part of OWSM configuration in the HSnP domain to the <HSNP-SOA_DOMAIN_HOME>/config/fmwconfig folder.

2. Open the <HSNP-SOA_DOMAIN_HOME>/config/fmwconfig/jps-config.xml file.

3. Search for default-keystore.jks in the file.
It should be like <serviceinstance name="keystore" provider="keystore.provider"location="./default-keystore.jks">

4. Replace ./default-keystore.jks with ./hsnpkey.jks and save the file.

5. Restart the WebLogic server instances for the HSnP-SOA domain.

6. Copy the HSnP_OWSM_Config.py file from the media pack to a location to which the operating system user has read and execute permissions.

7. Execute the following commands on the command prompt:

- cd <MIDDLEWARE_HOME>/oracle_common/common/bin

- ./wlst.sh <ABSOLUTE FILE_PATH to HSnP_OWSM_Config.py>

1. Enter the corresponding values as prompted by the script.

8. Log in to the Enterprise Manager of the HSnP-SOA domain.

9. In the left pane, click the HSnP-SOA domain in the WebLogic Domain folder.

10. From the WebLogic Domain drop-down list, select Web Services and then select Platform Policy Configuration.

Figure 2-10 WebLogic Domain Drop-down List

11. Click the Trusted SAML clients tab in the Platform Policy Configuration page.

12. Select www.oracle.com issuer in the Trusted Issuers pane.

Figure 2-11 Platform Policy Configuration

13. Click Add in the Trusted SAML clients: www.oracle.com pane.
The Add New Distinguished Name (DN) window is displayed.

Figure 2-12 Add New Distinguished Name (DN) Window

14. Add text cn=HSN-PVPR, ou=HSGBU, o=ORACLE, c=US and click OK.

15. Repeat steps 12 and 13 to add cn=HSNP, ou=HSGBU, o=ORACLE, c=US as trusted SAML client.

16. Log out of the Enterprise Manager.

17. Create the WebLogic user hsn_system to be used for the HSnP-SOA domain.

18. Restart the WebLogic server instances for the HSnP-SOA domain.

2.4 Configuring SOA MDS

To configure HSN-SOA MDS, perform the following:

1. Extract the soa_mds_<<buildNumber>>.zip file and soa_mds_endpoint_<<buildNumber>>.zip file for MDS from the media pack.

2. Create a folder named apps on your local system and extract the JAR file from the soa_mds_<<buildNumber>>.zip file in the folder.

3. Zip the apps folder.

4. Log in to the Enterprise Manager of the SOA server.

5. Expand SOA under Farm_soa_domain and click soa-infra (soa_server1).
The SOA Infra Home Page screen is displayed.

Figure 2-13 SOA Infra Home Page

6. Click SOA Infrastructure.

7. Select Administration and then select MDS Configuration.
The MDS Configuration screen is displayed. This screen lets you import and export MDS archives.

Figure 2-14 MDS Configuration

8. Click Import and select the apps.zip folder.

Note:
You cannot cancel the import operation once it is initiated.

You have successfully imported the archives.

Figure 2-15 Import Operation Successful

9. Create a folder named apps on your local system and extract the JAR file from the soa_mds_endpoint_<<buildNumber>>.zip file in the folder.

10. Navigate to the apps\soa_mds\Reference\dvm path within the apps folder.

11. Edit the SOAServiceEndpoint.dvm file.
This file contains endpoint URL for the SOA and registry services.

- For SOA services, update the domain and port as per the SOA server details.

- For registry services, update the domain and port as per the target server where HSnPManApp is deployed.

12. Update the URLs of SOA services as per the target SOA server and registry services as per the ManApp deployment server.

13. Repeat steps 3 through 8 to import the new apps.zip file.

2.5 Configuring HSN Tracking for SOA Composites

This section contains the following topics:

- Section 2.5.1, "Configuring Data Source"

- Section 2.5.2, "Configuring the SOA Server"

2.5.1 Configuring Data Source

To configure data source, perform the following:

1. Log in to the WebLogic console of the SOA server.

2. Create a data source using the ManApp schema credentials.

3. Enter jdbc/HAFDBDS as jndi name and assign it to the SOA server as target server.

4. Restart the SOA server.

2.5.2 Configuring the SOA Server

To configure SOA server, perform the following:

1. Extract the HsnSensor JAR from the media pack.

2. Shut down the server.

3. Copy the HsnSensor-<<buildNumber>>.jar file to <MIDDLEWARE_HOME>/Oracle_SOA1/soa/modules/oracle.soa.ext_11.1.1 on target server.

4. Navigate to <MIDDLEWARE_HOME>/Oracle_SOA1/soa/modules/oracle.soa.ext_11.1.1.

5. Execute the following commands:

1. /bin/sh

2. source <MIDDLEWARE_HOME>/wlserver_10.3/server/bin/setWLSEnv.sh

3. ant

6. Wait for the build successful message.

7. Start the server.

2.6 Setting Transaction Timeout for Service-Oriented Architecture

To set transaction timeout for SOA, the administrator need to set the SyncMaxWaitTime property value in seconds using the following steps:

1. To set timeout for BPEL:

1. Log in to the Enterprise Manager.

2. On the left of the navigation menu, expand the SOA folder and select soa-infra (soa_server1).

3. On the right top of the Details screen, expand the SOA Infrastructure drop-down menu and select SOA Administration, BPEL Properties.
The BPEL Service Engine Properties screen is displayed.

4. Click More BPEL Configuration Properties.
The Application Defined MBeans: BPELConfig:bpel screen is displayed.

5. Edit the SyncMaxWaitTime setting in the list to set timeout to 720 seconds.

2. To set timeout in the SOA EJBs:

1. Log in to the WebLogic console.

2. On the left of the navigation menu, click Deployments.

3. Click soa-infra in the list of deployments.
The Settings for soa-infra screen is displayed.

4. In the Modules and Components list, click each of the following EJBs to increase the transaction timeout value in the corresponding Configuration tab.
BPELEngineBean

BPELDeliveryBean

BPELActivityManagerBean

BPELServerManagerBean

BPELProcessManagerBean

BPELInstanceManagerBean

BPELFinderBean

5. Set the timeout to 960 seconds.

3. To set timeout for JTA:

1. On the left side of the navigation menu, select soa_domain and increase the JTA timeout.

2. Select JTA in the Configuration tab.

3. Set the timeout to 1200 seconds.

2.7 Deploying SOA Composite

You can deploy the following SOA services from their respective JAR files:

- GetNetworkCountService

- PlantedQuerySerrvice

- RecruitmentService

- GetPatientCountService

- GetCriteriaAnalysisCountService

To deploy SOA services, perform the following:

1. Extract the following files from the media pack:

- sca_NetworkCountService_rev<<buildNumber>>.jar

- sca_PlantedQueryService_rev<<buildNumber>>.jar

- sca_RecruitmentService_rev<<buildNumber>>.jar

- sca_GetPatientCountService_rev<<buildNumber>>.jar

- sca_CriteriaSetAnalysisService_rev<<buildNumber>>.jar

2. Log in to the Enterprise Manager of the SOA server.

3. Expand SOA and select default.
The Enterprise Manager - SOA Default Node screen is displayed.

Figure 2-16 Enterprise Manager - SOA Default Node

4. From SOA Partition, select Deployment and then select Undeploy All From This Partition.

Figure 2-17 Undeploying Composites from a Partition

All the available composites are undeployed from the server.

Figure 2-18 Undeploying Composites

Note:
You cannot stop the undeploying operation once it is initiated.

5. From SOA Partition, select Deployment and then select Deploy To This Partition.

6. Select the deployable composite JAR from your system and keep clicking Next.

Figure 2-19 Selecting an Archive

The selected JAR file is deployed on the SOA server.

7. Repeat step 6 to deploy all the required services.

3 Installing PVPR

This chapter contains the following sections:

- Section 3.1, "Installing PVPR Database"

- Section 3.2, "Installing the PVPR Middle-Tier"

- Section 3.3, "Configuring Logging"

- Section 3.4, "Configuring Oracle Web Services Manager"

3.1 Installing PVPR Database

This section describes how to create schema for PVPR.

This section contains the following topics:

- Section 3.1.1, "Prerequisites"

- Section 3.1.2, "Creating PVPR Tablespace"

- Section 3.1.3, "Creating PVPR Database User"

- Section 3.1.4, "Granting Privileges and Creating Synonyms"

- Section 3.1.6, "Installing PVPR Database Objects"

3.1.1 Prerequisites

- The CDM installation for PVPR is completed.

- The ODB (if required) installation for PVPR is completed.

- Registry is configured with a new company and required services are provisioned to it.

The CDM installation scripts are part of installable bundle and are to be used for CDM installation. For a summary of steps involved in installing CDM, see Section 3.1.1.1.

If Omics Lite features are supported or used by a company, then Omics Data Bank (ODB) installation is also completed. For sponsor environment, ODB is to be installed if it has to query or perform recruitment on any partner on an Omics criterion. For provider environment, ODB is to be installed if the company supports Omics.

The ODB installation scripts are part of the installable bundle and are to be used for ODB installation. For a summary of steps involved in installing ODB, see Section 3.1.1.2.

3.1.1.1 Installing CDM

To install CDM, perform the following:

1. Create CDM data tablespace.

2. Create CDM Index tablespace.

3. Create CDM user.

4. Provide maximum quota for the CDM user on the data tablespace.

5. Create the following Datamart roles:

- CohortDatamartUser;

- CohortDatamartAdmin;

6. Provide grants to the CDM user by executing the grant_schema_priv.sql file in the cdm-odb folder.

7. Execute the CDM installation script by running the install_cdm.sql script, giving the runtime parameters as specified in the TRC installation guidelines.

For more information on how to install CDM, see Oracle Health Sciences Translational Research Center Installation Guide (release 3.0.1).

3.1.1.2 Installing ODB

To install ODB, perform the following:

1. Create ODB data tablespace.

2. Create ODB Index tablespace.

3. Create ODB LOB tablespace.

4. Create ODB user.

5. Provide maximum quota for the ODB user on the Data tablespace.

6. Provide grants to the ODB user by executing the grant_schema_priv.sql file in the cdm-odb folder.

7. Execute the ODB installation script by running the install_ODB.sh script in the odb_install folder, giving the runtime parameters as specified in the ODB installation guidelines.

For more information on how to install ODB, see Oracle Health Sciences Omics Data Bank Installation Guide (release 3.0.1).

3.1.2 Creating PVPR Tablespace

To create tablespace for the PVRR database, perform the following:

1. Log in to the database as a user with privilege to create tablespace.

2. Execute the pvpr_create_tablespace.sql script.

3. Edit the pvpr_create_tablespace.sql script.

4. Enter the following details:

- Appropriate path for the datafile (line starting with datafile)

- Size and autoextend size (line starting with SIZE)

5. Log in to the database as system user and execute the script. When prompted, enter the name of the tablespace you want to create.

3.1.3 Creating PVPR Database User

To create PVPR database user, perform the following:

1. Log in to the database as a user with privilege to create user.

2. In the SQLPlus prompt, execute the @pvpr_create_user.sql script.

3. Enter the corresponding values as prompted.

Note:
Ensure that you specify the tablespace name created in Section 3.1.2 when prompted.

3.1.4 Granting Privileges and Creating Synonyms

PVPR need to access the tables and views of CDM and ODB, and so you must grant privileges and create synonyms.

To grant privileges and create synonyms, perform the following:

CDM Installation

If only CDM is installed, then:

1. Go to the PVPR/SQL folder and run the following scripts:

- grant_cdm_select.sql

- create_synonyms.sql

2. Enter the values when prompted.

CDM-ODB Installation

If both CDM and are installed, then:

1. Go to the CDM-ODB-Install folder and edit the install_final.sql script.

2. Run the install_final.sql script.

3. Enter the values when prompted.

3.1.5 Configuring Dimension Data Export and Import

The dimension data from the Provider side should be exported and then imported on to the Sponsor side. From the Provider side, the dimension data is exported as files to the Sponser side. The data from these files is loaded to the dimension tables at Sponser side.

To configure dimension data export and import, perform the following:

1. In the SQLPlus prompt, log in as sys user and execute the following:

- CREATE OR REPLACE DIRECTORY PVPR_EXT_TAB_DIR AS '&&pvpr_external_dir';

- GRANT read, write on directory PVPR_EXT_TAB_DIR to &&pvpr_user;

- GRANT read, write on directory PVPR_EXT_TAB_DIR to &&cdm_user;

Notes:

- Replace &&pvpr_external_dir with the actual directory path in the database machine where you want to save the files.

- Replace &&pvpr_user with the schema name of the PVPR user.

- Replace &&cdm_user with the schema name of the CDM user.

2. If the installation is done for a Sponsor, then from the SQLPlus promt, execute the @PV_install_dim_ddl.sql script in the PVPR/SQL folder and enter the values as prompted.

3.1.6 Installing PVPR Database Objects

This section describes how to create database objects such as tables and procedures for PVPR, and to initialize the database with seed data.

1. In the SQL prompt, execute @install_pvpr_env.sql by providing the values as prompted.

2. Connect to the database as PVPR user.

3. In the SQL prompt, execute @config_pvpr_env.sql. This script prompts for the following inputs:

- SOA Server URL: URL of the server where SOA services are deployed.

- SOA Server PORT: Port of the SOA server.

- HSn-ManApp Server URL: URL of the server where Hsn-ManApp is deployed.

- HSn-ManApp Server PORT: Port of the Hsn-ManApp server.

- PVPR Server URL: URL of the server where PVPR is deployed.

- PVPR Server PORT: Port of the PVPR server.

- My Company Id: You need to configure the company ID during registry configuration of Hsn-ManApp.

- My Company Name: You need to configure the company name during registry configuration of Hsn-ManApp.

- Is Omics Supported (Y/N): Enter Y if Omics features are supported or used. Otherwise, enter N.

This configures the company ID, company name, and service URLs of the platform services in the PVPR application.

Seed Data

The initial seed data required for PVPR is populated as part of the preceeding PVPR database installation. This includes the default roles and privileges, among other basic data.

The default dimension codes for Gender and Marital Status codes are also included as a part of the preceeding installation.

Running Post-Installation Scripts

During schema creation, access rights are granted to the schema user, which are required only for database configuration. Post database schema creation, the access rights need to be revoked. The access rights are revoked using post-installation scripts.

1. Connect to the database as a user with sysdba privilege.

2. Run the @pvpr_post_install.sql script.

3.1.7 Loading Data to ODB and CDM

After the database is installed, the data is loaded to ODB and CDM.

3.1.7.1 Loading Data to ODB

At the Sponsor side, only the ODB reference data is required. Since this release supports only the searches by gene and mutation, only the EMBL and GVF reference loaders are required. However, the Providers require both reference loaders and result loaders. For more information on how to load data to ODB, see Oracle Health Sciences Omics Data Bank Programmer's Guide (release 3.0.1).

3.1.7.2 Loading Data to CDM

At the Sponsor side, only the CDM reference data is required. However, the reference (dimension) data has to be loaded from each Provider.

At the Provider side, perform the following steps to export data:

1. In the SQLPlus prompt, execute the @PR_run_exp_data_dim.sql script in the PVPR/SQL/ref-data folder.

2. Enter the values as prompted.

The required dimension data is exported into files present in the configured external directory. For more details, see Section 3.1.5.

At the Sponsor side, perform the following steps to load the data from the data files into the actual Sponsor dimension tables.

1. In the SQLPlus prompt, execute the @PV_merge_dim.sql script in the PVPR/SQL/ref-data folder.

2. Enter the values as prompted.

3.2 Installing the PVPR Middle-Tier

This section explains how to install the PVPR Middle-Tier.

3.2.1 Creating Data Source in the Oracle WebLogic Server

To create data source in the Oracle WebLogic server, perform the following:

1. Log in to the Oracle WebLogic server console.

2. Create a new data source by providing the following details:

- Data Source Name: Specify a name that represents the underlying database schema and environment. For example, JDBC-DS-Provider1

- JNDI Name: jdbc/PVPR.

3. Specify the PVPR database user and password on the Connection Pool details screen.

4. Specify database connection details for the PVPR database.

5. Apply the data source to the server in the Targets section.

3.2.2 Setting Transaction Timeout for the WebLogic Application Server

To set transaction timeout for the WebLogic application server, perform the following:

1. Go to Services > JTA in the WebLogic console.

2. Update timeout seconds to 600 and save.

3.2.3 Enabling JPA 2.0 and Jackson

To enable JPA 2.0 and Jackson, perform the following:

1. Edit the <MIDDLEWARE_HOME>/wlserver_10.3/common/bin/commEnv.sh file to add the PRE_CLASSPATH variable at the end of the file.

2. Verify JAR version number in the <MIDDLEWARE_HOME>/modules folder and update the following statement accordingly:
PRE_CLASSPATH=${MODULES_DIR}/javax.persistence_1.1.0.0_2-

0.jar:${MODULES_DIR}/com.oracle.jpa2support_1.0.0.0_2-

1.jar:${MODULES_DIR}/org.codehaus.jackson.mapper.asl_1.0.0.0_1-8-

3.jar:${MODULES_DIR}/org.codehaus.jackson.core.asl_1.0.0.0_1-8-3.jar

export PRE_CLASSPATH

3.2.4 Referring Shared Jersey Library

To refer shared jersey libraries from PVPR, perform the following:

1. From the Administration Console, click Summary of Deployment.

2. Click Install.
The Install Application Assistant screen is displayed.

3. Navigate to the required path and select the required JAR file as shown in the figures 3-1, 3-2, and 3-3:

Figure 3-1 Install Application Assistant

Figure 3-2 Install Application Assistant - Choose Targeting Style

Figure 3-3 Install Application Assistant - Optional Settings

3.2.5 Deploying EAR

To deploy EAR, perform the following:

1. Extract the PVPR EAR file from the media pack.

2. Deploy the EAR file to the server, where PVPR need to be installed.

3.3 Configuring Logging

To configure logging, perform the following:

1. Log in to the Enterprise Manager.

2. In the pane on the left side of the window, click pvpr domain in the WebLogic Domain folder and select the target pvpr server.

3. From the WebLogic Server drop-down list, select Logs and then select Log Configuration.

Figure 3-4 Log Configuration

4. Expand Root Logger.

5. For Oracle, change the log level and select Inherited from Parent.

Figure 3-5 Root Logger

6. Select Persist log level state across component restarts and click Apply Changes.

Figure 3-6 Log Levels

3.4 Configuring Oracle Web Services Manager

This section contains the following topics:

- Section 3.4.1, "Generating Keystore and Configuring Trusted Certificate"

- Section 3.4.2, "Configuring Keystore on HSnP and SOA Server"

- Section 3.4.3, "Keystore Configuration on PVPR Server"

3.4.1 Generating Keystore and Configuring Trusted Certificate

Note:
: You need to perfrom the following steps only once. Share the generated and updated keystore file for all the PVPR instances.

To execute the following commands, you need to set the JAVA_HOME environment variable to point to JDK (version 1.6 and later) referred in the PVPR domain.

- export JAVA_HOME=<Path to JDK referred with pvpr domain>

- export PATH=$JAVA_HOME/bin:$PATH

1. Generate the private key to be used in the PVPR servers using the keytool utility available in JDK.

2. In the following command, replace <KEY_LOCATION> as required:
keytool -genkey -alias hsn-pvpr-key -keyalg "RSA" -sigalg "SHA1withRSA" -dname "cn=HSN-PVPR,ou=HSGBU,o=ORACLE,c=US" -keystore <KEY_LOCATION>/pvprkey.jks -validity 3650

1. Enter the keystore password and the key password when prompted.

3. Export the certificate of pvprkey using the following command:

Note:
Replace <PVPR_KEY_LOCATION>, <PVPR_CERTIFICATE_LOCATION>, <HSNP_KEY_LOCATION>, and <HSNP_CERTIFICATE_LOCATION as required in the following steps.

keytool -export -alias hsn-pvpr-key -keystore <PVPR_KEY_LOCATION >/pvprkey.jks -file <PVPR_CERTIFICATE_LOCATION>/hsn-pvpr.cer

1. Enter the keystore password when prompted.

4. Copy hsnpkey.jks from the HSNP ManApp server.
For more information on <HSNP_KEY_LOCATION>/hsnpkey.jks, see Section 2.2.6.

5. Export the certificate of hsnp-key using the following command:
keytool -exportcert -alias hsnp-key -keystore <HSNP_KEY_LOCATION>/hsnpkey.jks -file <HSNP_CERTIFICATE_LOCATION>/hsnp.cer

1. Enter the keystore password when prompted.

6. Use the following commands to import the keys in other keystore files for the trust:

- Command to import hsnp-key certificate to pvprkey:
keytool -import -alias hsnp-key -file <HSNP_CERTIFICATE_LOCATION>/hsnp.cer -keystore <PVPR_KEY_LOCATION>/pvprkey.jks

- Commands to import hsn-pvpr-key and orakey certificates to hsnpkey:

Note:
Enter the keystore password when prompted.

keytool -import -alias hsn-pvpr-key -file <PVPR_CERTIFICATE_LOCATION>/hsn-pvpr.cer -keystore <HSNP_KEY_LOCATION>/hsnpkey.jks

keytool -import -alias orakey -file <PVPR_CERTIFICATE_LOCATION>/hsn-pvpr.cer -keystore <HSNP_KEY_LOCATION>/hsnpkey.jks

3.4.2 Configuring Keystore on HSnP and SOA Server

Note:
You need to perform the following steps only once.

1. Copy the updated keystore hsnpkey.jks to the <HSNP_DOMAIN_HOME>/config/fmwconfig folder. You must perform this step on the HSnP SOA server also.

2. Restart the WebLogic server instances for HSnP and the SOA domain.

3.4.3 Keystore Configuration on PVPR Server

To configure keystore on the PVPR server, perform the following:

1. Copy the generated keystore pvprkey.jks to the <PVPR_DOMAIN_HOME>/config/fmwconfig folder.

2. Open the <PVPR_DOMAIN_HOME>/config/fmwconfig/jps-config.xml file.

3. Search for default-keystore.jks in the file.
It should be similar to the following:

<serviceinstance name="keystore" provider="keystore.provider" location="./default-keystore.jks">

4. Replace ./default-keystore.jks with ./pvprkey.jks and save the file.

5. Restart the WebLogic server instances for the PVPR domain.

6. Copy the PVPR_OWSM_Config.py file from the media pack to a location to which the operating system user has read and execute permissions.

7. Execute the following commands on the command prompt:

- cd <MIDDLEWARE_HOME>/oracle_common/common/bin

- ./wlst.sh <ABSOLUTE FILE_PATH to PVPR_OWSM_Config.py>

1. Enter corresponding values as prompted by the script.

The PVPR_OWSM_Config.py file adds credentials for the pvprkey.jks file.

8. Login to the Enterprise Manager of the PVPR domain.

9. In the left pane, click pvpr domain in the WebLogic domain folder.

10. From the WebLogic Domain drop-down list, select Web Services and then select Platform Policy Configuration.

Figure 3-7 WebLogic Domain Drop-down List

11. Click the Trusted SAML clients tab in the Platform Policy Configuration page.

12. Select www.oracle.com issuer in the Trusted Issuers pane.

Figure 3-8 Platform Policy Configuration

13. Click Add in the Trusted SAML clients: www.oracle.com pane.
The Add New Distinguished Name (DN) window is displayed.

Figure 3-9 Add New Distinguished Name (DN) Window

14. Add text cn=HSNP, ou=HSGBU, o=ORACLE, c=US and click OK.

15. Click Apply.

16. Log out of the Enterprise Manager.

17. Create the WebLogic user hsn_system, to be used for the PVPR domain.

18. Restart the WebLogic server instances for the PVPR domain.

4 Configuring Registry

Through the registry configuration feature, you can perform the following:

- Create companies (hospitals, pharmaceutical companies, research institutes, and so on) that participate on the HSN network.

- Provision service to companies in offer or consumer mode.

- Create relationship between companies for a service.

- Define restriction for a relationship.

SQL scripts are used to configure registry.

You can define the following restrictions for a relationship:

- Data restriction

- Protocol limit

Note:
Restrictions are set of policies through which a provider company (Provider) can restrict a consumer company (Sponsor) on a provisioned service usage. For example, a provider company can restrict number of protocols a consumer company can use.

This chapter contains the following topics:

- Section 4.1, "Creating Seed Data"

- Section 4.2, "Creating Company"

- Section 4.3, "Provisioning Service"

- Section 4.4, "Creating Relationship"

- Section 4.5, "Updating Company"

- Section 4.6, "Deleting Provision"

Note:
Log in to the database as a HSN user before executing the scripts provided in the following sections.

4.1 Creating Seed Data

To create static seed data required for registry configuration, execute the App_Service_Capability.sql seed script.

Note:
You need to execute this script under the user created in Section 2.1.2.

This script first deletes the existing entries and creates preconfigured entries in the following tables:

- APP: Creates single entry for application as PVPR_APP and Application ID (appId) as 1.

- Service: The application offers the following services:

- QUERYCOUNT (Validation service)

- RECRUITMENT (Recruitment service)

- CRITERIAANALYSIS (Criteria Analysis service)

- OMICS (Omics service)

- APP_CAPABILITY: This table contains mode for each that the application supports.

4.2 Creating Company

To create a company and provision an existing application to the company, execute the Company_AppProvision.sql script. Enter the following details:

- Name of the company.
For example, Company1.

- URL of the PVPR application instance.
For example, if the PVPR application for the company is deployed at http://<server name>:<port number>, the URL should be http://<server name>:<port number>.

Note:
If you specify wrong URL, the HSNP.SERVICE.001 is displayed.

The Company_AppProvision.sql script creates entries in the following tables:

- Company

- APP_PROVISIONED

You can update the company name or URL using the Update_Company_AppProvision.sql script.

4.3 Provisioning Service

To provision a service to a company in consume or offer mode, execute the Provision_Service.sql script. By default, t his script creates the activation policy for the company.

Enter the following details:

- Company Name: Name of the company to which you want to provision a service.

- Service Name: Name of the service that you want to provision.

- Consume Mode: Set to Y for service to be provisioned in the consume mode, else set to N.

- Offer Mode: Set to Y for service to be provisioned in offer mode, else set to N.

Is relationship required for consuming the service, if offered (Y/N) -

- Y - Service is accessible only if there is a relationship created between sponsor and provider.

- N - Service is accessible by all sponsors participating in the network without any restrictions.

Currently, service that can be provisioned for offer or consume mode can be any one of the services mentioned in the Creating Seed Data section.

The Provision_Service.sql script creates entries in the following tables:

- USE_POLICY

- POLICY

4.4 Creating Relationship

You can create a relationship between two companies to share protocols or for querying patient counts for a protocol.

Companies can offer or consume a service. Services offered to a company can be managed from the company admin screen. A user with the pr_admin role can restrict access to number of protocols and diagnosis codes.

The PVPR Company Admin screen displays the details of services offered to a company along with the status of the service and policies applied on the service.

Figure 4-1 PVPR Company Admin Screen

The admin can use the Create Relationship option to:

- Configure the available services to sponsors.

- Apply restrictions on a relationship with sponsor for the selected service.

- Update the existing restrictions defined for the relationship for the services to a sponsor.

Figure 4-2 Create Relationship

- Data Restriction: to restrict the sponsor to query only for the selected diagnostic codes.

- Protocol Limit: to restrict the sponsor to consume the service for the specified number of protocols.

4.5 Updating Company

You can update a company name, or URL, or both. To update, execute the Update_Company_AppProvision.sql script.

Note:
The URL would be the PVPR application instance URL for the company.
You have to enter the existing company name while updating the company name or URL.

4.6 Deleting Provision

To delete a de-provision service to a company, execute the Delete_Provision_Service.sql script. Enter the following details:

- Company Name: Name of the company from which you want to delete the service.

- Service Name: Name of the service that you want to delete.

- Consume Mode: Set to Y for service to be removed for consume mode, else set to N.

- Offer Mode: Set to Y for service to be removed for offer mode, else set to N.

The script deletes entries in the following tables:

- USE_POLICY

- POLICY

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