| Oracle® Life Sciences Data Hub Installation Guide Release 2.4 E52194-03 |
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PDF · Mobi · ePub |
| Oracle® Life Sciences Data Hub Installation Guide Release 2.4 E52194-03 |
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PDF · Mobi · ePub |
This section contains the following topics:
Section 6.1, "Integrating Oracle Clinical with the Oracle Life Sciences Data Hub"
Section 6.2, "Integrating SAS with the Oracle Life Sciences Data Hub"
Section 6.3, "Integrating Informatica with the Oracle Life Sciences Data Hub"
Section 6.6, "Integrating Oracle Business Intelligence Publisher for Programs"
The Oracle Life Sciences Data Hub (Oracle LSH) supports integration with other systems as sources of data, as means of visualizing and reporting on Oracle LSH data, and as processing engines for transforming Oracle LSH data. Oracle LSH handles integration with such systems with adapters custom made for each external system. Adapters for the systems included in this chapter are included with Oracle LSH.
You must install the adapters and grant them security privileges. These tasks are covered in Section 5.8.3, "Load the Adapter Files" and Section 5.13, "Grant Security Rights to Seeded Adapters."
Each external system you choose to integrate with Oracle LSH requires installation and some additional setup, described here. The exception is Oracle Reports, which is installed as part of Oracle Applications and requires no further setup.
For information on supported versions of these products, see Section 2.3, "Integrated External Systems" or for the most current information, see My Oracle Support article 180430.1, Oracle Life Sciences Applications Supported Technology Stacks.
Oracle LSH 2.4 is compatible with Oracle Clinical 4.6, or Oracle Clinical 4.5.1 or 4.5.3 with patch 4.5.1.14 or its successor 4.5.1.75, applied. Both patches are compatible with 4.5.3 as well as 4.5.1.
Oracle LSH includes a set of adapters custom-designed for the purpose of loading data and metadata from Oracle Clinical into Oracle LSH.
To load data and metadata from Oracle Clinical into Oracle LSH you must do the following:
In the Oracle LSH user interface, define a remote location and connection to each Oracle Clinical location from which you want to load data. See "Registering Locations and Connections" in the Oracle Life Sciences Data Hub System Administrator's Guide for further information.
Define, check in, install, and run one or more Oracle Clinical Load Sets in Oracle LSH. See "Defining Load Sets" in the Oracle Life Sciences Data Hub Application Developer's Guide for further information.
You can also use APIs to create Load Sets. These packages are documented in the Oracle Life Sciences Data Hub Application Programming Interface Guide.
This section includes the following topics:
Oracle LSH is designed for close integration with SAS at several levels. You can load SAS data set files into Oracle LSH, use SAS as an integrated development environment to create Oracle LSH Programs with SAS source code, and use the SAS engine to run these Programs on Oracle LSH data.
Oracle LSH supports integration with SAS 9.1.3, SAS 9.2, or SAS 9.3.
Note:
Oracle Life Sciences Data Hub does not support a SAS Windows server.SAS with connectivity to Oracle LSH requires an Oracle 11g library. Oracle recommends that the Oracle 11g Release 2 Client reside on the same server computer as the SAS installation.
To install Oracle LSH and SAS as a processing engine on the same computer:
Create an 11g Oracle Home by installing the Oracle Client 11g Release 2.
Install SAS.
Set the UNIX environment variable LD_LIBRARY_PATH to the 11g $ORACLE_HOME/lib.
To enable running SAS jobs from Oracle LSH, you must integrate the SAS server with Oracle LSH and start the server in UTF8 mode.
Do each of the following:
Install SAS Access to Oracle on the SAS server.
Install the Oracle LSH Distributed Processing (DP) Server on the computer where the SAS server is installed. See Section 5.16, "Set Up the Distributed Processing Server."
Define a service location in Oracle LSH for the computer where the SAS server is installed. See "Defining Service Locations" in the Oracle Life Sciences Data Hub System Administrator's Guide for instructions.
Define one or more services for the service location. See "Defining Services" in the Oracle Life Sciences Data Hub System Administrator's Guide for instructions.
To help ensure that Oracle LSH stores and displays special characters in your data correctly, start SAS in UTF8 mode by editing the DP Server execution command file sasNormal.sh, which you copied and edited in Section 5.16.5.5, "Copy, Edit, and Grant Permissions to Execution Command Files for Processing Engines".
If you are using SAS 9.2 or 9.3, add lines to sasNormal.sh as in the following examples:
In UNIX:
sas -encoding UTF8
In Windows, specify the version of SAS you are using. For example, for SAS 9.2:
C:\Program Files\SAS\SASFoundation\9.2\sas.exe" -CONFIG C:\Program Files\SAS\SASFoundation\9.2\nls\u8\SASV9.CFG"
Note:
The example above should not contain any line breaks. It is not possible to display it on one line.If you are using SAS 9.1.3, install SAS with the DBCS option and add lines to sasNormal.sh as follows (in UNIX):
/user/local/SAS/SAS_9.1/bin/sas_dbcs -encoding UTF-8 $*
For further information, see SAS Paper 1036, Multilingual Computing with the 9.1 SAS Unicode Server at: http://support.sas.com/rnd/papers/sugi28/unicodeserver.pdf
Oracle LSH includes an adapter custom-designed for the purpose of loading data from SAS database into Oracle LSH.
To enable loading data from SAS into Oracle LSH you must do the following:
Complete all steps listed in Section 6.2.2, "Set Up SAS Job Execution" above.
Make sure that the LOB Loader Oracle LSH post-installation job has been run; this job creates the SAS adapter. This is a required step in the installation of Oracle LSH; see Section 5.8.3, "Load the Adapter Files."
Make sure that you have followed instructions in Section 5.13, "Grant Security Rights to Seeded Adapters."
Assign at least one user group to the SAS adapter. See "Setting Up Adapters to External Systems" in the Oracle Life Sciences Data Hub System Administrator's Guide.
To use SAS as an integrated development environment (IDE) each Definer must do the following on his or her local PC:
Install SAS in the location specified by the system administrator.
Install the Oracle LSH client plug-in by inserting the CD-ROM supplied by the system administrator (see Section 5.17.2.1, "Install the Client Plug-In").
InstallShield runs cdrclient.exe, which loads cdrconfig.xml and cdrclient.exe either to the default location or to a location the Definer specifies on his or her local computer; see Section 5.17, "Set Up Client Computers".
Ensure that cdrconfig.xml has the correct directory path for the SAS executable.
Set the user preference for the SAS connection mode (details below). Instructions are in the "SAS Connection Type" section of the Getting Started chapter of the Oracle Life Sciences Data Hub User's Guide.
Install any software required to support the preferred connection mode (details below).
Set the NLS_LANG environment variable or registry settings to support UTF8 character encoding; see Section 6.4.1, "Set the NLS_LANG Environment Variable to UTF8".
SAS Connection Modes SAS can work as an integrated development environment (IDE) in different ways. Each user must set a preference for the way he or she wants to work. Oracle LSH Release 2.4 supports the following connection modes:
Connected Mode. The Definer has the SAS client installed on his or her personal computer. When he or she launches SAS as an IDE from an Oracle LSH Program, Oracle LSH downloads views based on the source Table Descriptors defined in the Program. The Definer works locally on the SAS client, using the views to read current data in Oracle LSH. The Definer's SAS program can write to local SAS data sets. When the SAS program is ready, the Definer goes into the Oracle LSH Program and uploads the SAS source code as an Oracle LSH Source Code file.
The client must use the SAS Access to Oracle tool to connect to Oracle LSH.
SAS Connected Mode with Work Area Data. This mode is the same as Connected mode except that it connects to the Work Area schema in the database. From SAS, the user can browse views of current data in all Table instances in the Work Area, not just the Table instances linked to Table Descriptors of the Program.
The client must use the SAS Access to Oracle tool to connect to Oracle LSH.
Disconnected Mode. The Definer has the SAS client installed on his or her personal computer. When the Definer launches SAS as an IDE, Oracle LSH uses the Distributed Processing Server to download the current data in the Table instances mapped to source Table Descriptors in the Program into the Definer's local SAS environment, creating data sets with the same structure as the Oracle LSH Table Descriptors. The Definer's SAS program can read from and write to local SAS data sets. When the SAS program is ready, the Definer goes into the Oracle LSH Program and uploads the SAS source code as an Oracle LSH Source Code file.
No connection other than a network is required to the Oracle LSH Distributed Processing Server.
This section includes the following topics:
You can use Informatica PowerCenter as an integrated development environment (IDE) and processing engine for Oracle LSH Programs of type Informatica. Informatica is required if you are installing Oracle Clinical Development Analytics with Oracle LSH.
Informatica is licensed separately. You must buy it from Informatica and follow installation instructions from Informatica.
Requirements The following are requirements for using Informatica with Oracle LSH:
The LSH System Admin user must have administration rights on the Informatica integration services used for Oracle LSH during installation and setup.
The Informatica repository used for LSH must be used only for LSH or LSH/OCDA.
When you create the Informatica repository to be used for Oracle LSH, set the following two parameters to False: Versioning and Global Repository.
Point the following Informatica integration service properties to valid directories on which the operating system account that starts the Informatica integration service has read/write permissions:
$PMSessionLogDir $PMBadFileDir $PMCacheDir $PMTargetFileDir $PMSourceFileDir $PMExtProcDir $PMTempDir $PMWorkflowLogDir $PMLookupFileDir $PMStorageDir
Tip:
Find the Informatica environment file, infaenv.sh, which contains information on the locations of your Oracle Home, Informatica Home, and other information about this computer. When you set up the Oracle LSH Distributed Processing Server you will need this information.Note:
Oracle Life Sciences Data Hub does not support an Informatica Windows server.To install and patch Informatica PowerCenter.
Install Informatica PowerCenter using Informatica installation documentation.
Apply Informatica PowerCenter 8.6.1 HotFix 11 or Informatica PowerCenter 9.0.1 with HotFix 2.
Note:
Oracle LSH 2.4 has been tested ONLY with Informatica PowerCenter 8.6.1 with HotFix 11 and Informatica PowerCenter 9.0.1 with HotFix 2. If more recent releases become available, do NOT install them unless explicitly instructed to do so by an Oracle LSH-specific note or alert on My Oracle Support.If a particular HotFix version is superseded by a later version, you can log a Service Request with Informatica to obtain it.
Create an environment file infa.env under $INFA_HOME (Informatica Installation Directory) and set the following environment variables:
INFA_HOME=<Informatica Installation Directory>
LANG=C
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<Informatica Installation
Directory>/server/bin
On a Linux platform, add this extra line to the file:
unset LD_ASSUME_KERNEL
To enable running Informatica Programs from Oracle LSH, integrate Informatica PowerCenter with Oracle LSH:
Install the Oracle LSH Distributed Processing (DP) Server on the computer where the Informatica server is installed. See Section 5.16, "Set Up the Distributed Processing Server" for instructions.
Create a symbolic link to the file impcntl.dtd and place it in the DP Server's Informatica working directory (for instructions on setting up this directory see Section 5.16.2, "Install the Distributed Processing Server"). This file is typically located in the server/bin directory of the Informatica installation.
Define a service location in Oracle LSH for the computer where the Informatica server is installed. See "Defining Service Locations" in the Oracle Life Sciences Data Hub System Administrator's Guide for instructions.
Define one or more services for the Informatica service type in the service location. See "Defining Services" in the Oracle Life Sciences Data Hub System Administrator's Guide for instructions.
Set up an Informatica administrator account and accounts for each Oracle LSH Definer who needs to work in Informatica, following instructions in the Informatica chapter of the Oracle Life Sciences Data Hub System Administrator's Guide.
Note:
The administrator account name must be exactly
LSHAdmin, including upper- and lowercase as written. For more information on all the required accounts, see the Oracle Life Sciences Data Hub System Administrator's Guide.Define a Remote Location and Remote Connection for Informatica, following instructions in the Informatica chapter of the Oracle Life Sciences Data Hub System Administrator's Guide.
To use Informatica PowerCenter Designer as an IDE for creating mappings and workflows from within Oracle LSH, each Oracle LSH Definer must do the following on his or her local PC:
Install the Informatica client in the location specified by the system administrator.
Install the Oracle LSH client plug-in by inserting the CD-ROM supplied by the system administrator (see Section 5.17.2.1, "Install the Client Plug-In").
Ensure that cdrconfig.xml has the correct directory path for the Informatica executable.
Create a system environment variable in Windows with the name INFA_DOMAINS_FILE and set its value to the full path of the Informatica Home.
Set up a user Data Source Name (DSN) with the name LSHModel for the Definer's Oracle LSH database account. See Microsoft Windows online help or documentation on setting up ODBC Data Source Names.
Install Winzip Pro 11.2 SR-1, Winzip 8.1, or any other Winzip that includes the WZUNZIP.exe
To use Oracle SQL Developer or SQL*Plus as an IDE for Oracle LSH PL/SQL Programs, each Definer must do the following on his or her local PC:
Install Oracle SQL Developer or SQL*Plus in the location specified by the system administrator.
Install the Oracle LSH client plug-in by inserting the CD-ROM supplied by the system administrator (see Section 5.17.2.1, "Install the Client Plug-In").
Ensure that cdrconfig.xml has the correct directory path for the Oracle SQL Developer (or SQL*Plus) executable.
Note:
If the Definer has both Oracle SQL Developer and SQL*Plus installed on the local computer, he or she can switch between the two IDEs by changing the executable directory path in cdrconfig.xml.Start Oracle SQL Developer or SQL*Plus and create a connection to the Oracle LSH database. The username and password for this connection must be those of an Oracle LSH database user account.
Install Winzip Pro 11.2 SR-1, Winzip 8.1, or any other Winzip that includes the WZUNZIP.exe
To set an Oracle client application like SQL*Plus to use the right encoding, you must set the environment variables on the client machine to UTF8. The required settings vary, depending on the operating system.
Check and set your NLS_LANG environment variable:
Right-click the My Computer icon on your desktop, then click Properties.
Click the Advanced tab, then click Environment Variables.
In User Variables and System Variables, check if there is a variable named NLS_LANG.
If there is an NLS_LANG variable, highlight it and click Edit.
Set the variable value to UTF8; for example: AMERICAN_AMERICA.UTF8
If you do not have the NLS_LANG environment variable, change your registry settings:
Click Start, then Run.
In the Run window, enter regedit and click OK.
Locate one of the following registry key entries:
HKEY_LOCAL_MACHINE\SOFTWARE\ORACLE
HKEY_LOCAL_MACHINE\SOFTWARE\ORACLE\HOMEx
where x is the unique number identifying the Oracle home
Add a new key named NLS_LANG with a value including UTF8; for example:
NLS_LANG=AMERICAN_AMERICA.UTF8
Do one of the following:
You can create Oracle LSH Business Areas of type OBIEE to make data available to visualizations in OBIEE Answers. Definers can install the Administrator's Tool on their PC to develop more complex OBIEE Repository (.rpd) files to support more complex data visualizations. Users can then launch the Oracle Business Intelligence Dashboard either through Oracle LSH or through a URL to see data visualizations.
Note:
Additional configuration is required. See the chapter on Oracle Business Intelligence visualizations in the Oracle Life Sciences Data Hub System Administrator's Guide.Oracle LSH Release 2.4 supports using OBIEE 10.1.3.4.1 for both programs and visualizations and OBIEE 11.1.1.3.0, 11.1.1.5.0, 11.1.1.6.4, 11.1.1.7, or 11.1.1.7.131017 for visualizations only.
You can use both OBIEE 10g and OBIEE 11g for visualizations if you want. For example, if you are using Oracle Clinical Development Analytics you may want to dedicate one OBIEE installation to Oracle OCDA and have another for Oracle LSH OBIEE visualizations. You can install both on the same computer or different ones, but even if they are on the same computer Oracle recommends defining a different service location and services for each. You must install the DP Server on each machine where the Oracle BI Server is installed.
Install OBIEE 10.1.3.41, 11.1.1.3.0, 11.1.1.5.0 or 11.1.1.6.4 to support visualizations.
Install Oracle Business Intelligence Enterprise Edition 11.1.1.x using Oracle Fusion Middleware Installation Guide for Oracle Business Intelligence 11g Release 1 (11.1.1) (E10539-01).
Note:
As noted in Oracle Fusion Middleware Installation Guide for Oracle Business Intelligence 11g Release 1 (11.1.1), you need to install Oracle Fusion Middleware Repository Creation Utility 11g (11.1.1.3.3) before installing OBIEE 11g.You must install the Oracle LSH DP Server on the same machine; see "Set Up the Distributed Processing Server".
Install Oracle Business Intelligence Enterprise Edition 10.1.3.4.1 to support OBIEE visualizations.
Install Oracle Business Intelligence Enterprise Edition 10.1.3.4.1 using the Oracle® Business Intelligence Publisher Installation Guide Release 10.1.3.4.
If you have not already done so, apply patch 12613341 to enable OBIEE 10.1.3.4.1 compatibility with Oracle LSH 2.4; see Section 5.3, "Install Oracle LSH Release 2.4".
If you plan to use OBIEE 10.1.3.4.1 for visualizations, apply patch 7642637.
You must install the Oracle LSH DP Server on the same machine; see "Set Up the Distributed Processing Server".
This section includes the following topics:
Section 6.6.1, "Install Oracle Business Intelligence Publisher 10.1.3.4.1"
Section 6.6.2, "Set Up Oracle Business Intelligence Publisher Programs"
You can create Oracle LSH Programs of type Oracle Business Intelligence Publisher (BIP) to generate reports on Oracle LSH data. Install Oracle Business Intelligence Publisher 10.1.3.4.1 to support BIP Programs and/or OBIEE visualizations.
Install Oracle Business Intelligence Publisher 10g using Oracle® Business Intelligence Publisher Installation Guide Release 10.1.3.4.
The software and documentation are not included in the Oracle LSH Release 2.4 media pack, but you can download them from the Oracle LSH Release 2.1.4 media pack.
On the Oracle BIP Server, do the following after installing OBIEE:
To enable running Oracle Business Intelligence Publisher Programs from Oracle LSH, you must:
Install the Oracle LSH Distributed Processing (DP) Server on the computer where the Oracle Business Intelligence Server is installed. See the Section 5.16, "Set Up the Distributed Processing Server" for instructions.
Define a service location in Oracle LSH for Oracle BIP. See "Defining Service Locations" in the Oracle Life Sciences Data Hub System Administrator's Guide for instructions.
Define one or more BIP-type services for each service location. See "Defining Services" in the Oracle Life Sciences Data Hub System Administrator's Guide for instructions.
Define a remote location and remote connection in Oracle LSH for Oracle BIP. See "Setting Up Security for Oracle Business Intelligence Publisher" in the Oracle Life Sciences Data Hub System Administrator's Guide for instructions.
You must complete a number of security-related tasks, including creating an Oracle Applications responsibility for each person who will use BIP with Oracle LSH. See "Setting Up Security for Oracle Business Intelligence Publisher" in the Oracle Life Sciences Data Hub System Administrator's Guide.
Oracle BIP has two tools that Definers may need in order to work on BIP Programs. The integrated development environment (IDE) for report logic design is web-based. The Template Builder for Word is used for developing layout templates. Definers can download this tool the first time they launch Oracle BIP or later from the web-based integrated development environment (IDE).
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