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Oracle® Life Sciences Data Hub Application Developer's Guide
Release 2.4
E54089-01
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Contents
List of Examples
List of Figures
List of Tables
Title and Copyright Information
Preface
Audience
Documentation Accessibility
Finding Information and Patches on My Oracle Support
Finding Oracle Documentation
Related Documents
Conventions
1
Applications User Interface
Selecting a Domain
Set a Default Domain in Preferences
Select a Domain on the Applications Screen
Navigating in the Applications Tab
Browsing the Main Applications Screen
Navigating Using Breadcrumbs
Using the Actions Drop-Down
Creating Domains, Application Areas, Work Areas, and Objects
Creating Domains
Creating a Top-Level Domain
Creating a Child Domain
Creating Application Areas
Creating Work Areas
Creating or Adding Children, including Object Instances
Creating Object Definitions
Modifying Domains, Application Areas, and Work Areas
Duplicating, Removing, Moving and Promoting Domains
Duplicating or Copying a Domain
Removing a Domain
Moving a Domain
Promoting a Domain
Managing Object Definitions
Copying Object Definitions
Moving Object Definitions
Creating Object Definitions
2
Introduction to Application Development in the Oracle Life Sciences Data Hub
About Application Development
Defining Objects
Predefined Object Types
Object Definitions and Instances, and their Containers
Organizational Objects
Object Definitions and Instances
Developing a Business Application
Working in a Work Area
Mapping Executables to Tables
Example of a Business Application
Developing Standard Definitions and Modular Applications
Ensuring Data Currency
3
Common Development Tasks
Creating and Reusing Objects
Finding an Appropriate Definition
Reusing Existing Definitions
Creating an Instance of an Existing Definition
Using the Search and Select Window
Creating a New Definition and Instance
Creating and Using Object Descriptions
Naming Objects
Special Characters and Reserved Words
Duplicate Names: System Appends _1
Automatic Name Truncation
Keep Container and Object Names Short for Integrated Development Environments
Naming Rules for Specific Object Types
Naming Domains
Naming Source Code Objects
Naming Parameters
Naming OBIEE Business Areas
Customizable Naming Validation Package
Viewing Object Instances and Definitions
Viewing Object Instances
Viewing Object Definitions
Viewing Object Definitions in Domains and Application Areas
Viewing Object Definitions from Instances in a Work Area
Understanding Object Versions and Checkin/Checkout
About Object Versions
Checking Out Objects
Checking Out an Object Definition through an Instance
Checking Out an Object Definition Directly
Checking Out an Old Version of an Object Definition
Checking In Objects
Undoing Object Checkout
Version Labels
Version History
Versions of Component Objects
Upgrading Object Instances to a New Definition Version
Upgrading One or More Instances from the Definition
Upgrading to a Different Definition Version from an Instance
Upgrading to the Latest Version
Copying, Cloning, and Moving Objects
Copying Objects
Copying One Object Instance, Domain, Application Area, or Work Area
Copying One or More Objects at the Same Time
Copying an Old Version of an Object Definition
Comparison of Copying and Cloning Individual Objects
Cloning Objects
Comparison of Cloning Individual Objects and Whole Work Areas
Cloning Objects from the Application Development Screen
Cloning Objects from the Work Area Screen
Moving Objects
Pasting Objects
Removing Objects
Rules for Removing Objects
Classifying Objects and Outputs
About Classification
Classifying Objects
Classifying Outputs
Classifying Outputs Before They Are Generated
Classifying Outputs After They Are Generated
Applying Security to Objects and Outputs
Viewing User Group Assignments
Assigning User Groups to an Object
Removing User Group Assignments
Reassigning a User Group as Inherited
Validating Objects and Outputs
About Object Validation
About Output Validation
Validation Statuses
Changing Objects' Validation Status
Changing Outputs' Validation Status
Adding Supporting Information
Adding a Supporting Document
Adding a Supporting Output
Validation Rules
Reordering and Renumbering Objects
Defining and Mapping Table Descriptors
About Table Descriptors
Creating a Table Descriptor
Adding Source Table Descriptors
Adding Target Table Descriptors from a Remote Location
Adding Target Table Descriptors from a SAS File
Adding a Target Table Descriptor from an Existing Table Definition
Adding a Table Descriptor from a Metadata File
Adding a New Target Table Descriptor
Setting Table Descriptor Attributes
Adding or Uploading Columns
Mapping Table Descriptors to Table Instances
Automatic Mapping by Name
Mapping Table Descriptors Manually
Remapping
The Effects of Modifying the Table Descriptor or Table Instance on a Mapping
Mapping Columns
Mapping Columns Automatically
Mapping Columns Manually
Mapping Columns to Constants
Creating and Mapping Table Descriptors and Table Instances at the Same Time
Creating and Mapping Table Instances during Single Instance Installation
Creating Table Descriptors from Table Instances and Simultaneously Mapping Them
Creating Table Instances from Table Descriptors and Simultaneously Mapping Them
Unmapping Table Descriptors
Modifying Table Descriptors
Creating, Modifying, and Submitting Execution Setups
About Execution Setups and Templates
Creating an Execution Setup
Creating a New Execution Setup
Creating an Execution Setup from an Execution Template
Modifying an Execution Setup and Setting Parameters
Name and Description
Allow Use as Execution Template
System Parameters
Runtime Parameters
Report Set and Workflow Execution Setups
About Report Set and Workflow Execution Setups
Modifying a Report Set or Workflow Execution Setup
Removing an Execution Setup
Activating a Version of an Execution Setup
Submitting an Execution Setup
Viewing Data
Viewing Data within the Oracle Life Sciences Data Hub
About Data Browsing
Customizing Data Browsing
Viewing Data with Visualizations
Viewing Data with Program-Generated Reports
Viewing Data Through an IDE
Viewing Jobs
Viewing All Outputs of a Program or Report Set
Viewing All Outputs of an Instance in the Work Area Properties Screen
Viewing All Outputs from the My Home or Reports Tab
Viewing All Outputs of a Program or Report Set
Viewing All Program Outputs
Viewing All Report Set or Report Set Entry Outputs
Information Displayed
Using the Actions Drop-Down List
Defining Planned Outputs
4
Defining Tables
About Tables
Creating a Table
Creating a New Table Definition and Instance
Creating an Oracle LSH Table From a SAS Data Set
Creating a New Instance of an Existing Table Definition
Setting and Modifying Table Attributes
Using the Table Properties Screen
Instance Properties
Definition Properties
Buttons
Defining Table Columns
Create a New Column and Variable
Create a Column from an Existing Variable
Defining Table Constraints and Indexes
About Constraints
Check Constraint
Non-Unique Index
Primary Key
Unique Key
Modifying Tables
Modifying Table Instance Properties
Modifying Table Definition Properties
Modifying Columns
Modifying Constraints and Indexes
5
Defining Programs
About Programs
Creating a Program
Creating a New Program Definition and Instance
Creating an Instance of an Existing Program Definition
Using the Program Properties Screen
Instance Properties
Definition Properties
Buttons
Defining Table Descriptors
Defining Source Code
About Source Code
Creating Source Code
Creating a New Source Code Definition and Instance
Creating an Instance of an Existing Source Code Definition
Calling APIs from Source Code
Creating and Using Static Reference Source Code
About Static Reference Source Code
Creating a Source Code for Use as a Static Reference
Using Static Reference Source Code
Upgrading Source Code And Undoing Source Code Upgrades
Upgrading a Single Source Code Instance
Upgrading Multiple Source Code Instances
Undoing Source Code Instance Upgrades
Defining Parameters
Defining Planned Outputs
About Planned Outputs
Defining a Planned Output
Planned Output Classification
Defining PL/SQL Programs
Writing Primary Source Code in PL/SQL
Testing PL/SQL Source Code
Creating a PL/SQL Package Storage Program
Using a Sharable PL/SQL Package
Compiling and Executing a PL/SQL Program
Manipulating Documents through a PL/SQL Program
Defining View Programs
Creating Source Code for a View Program
About View Table Instances
About Table Descriptors in View Programs
Defining SAS Programs
SAS Program Development Process
Open SAS as an IDE from Oracle LSH
Upload Existing SAS Programs to Oracle LSH
Enter Source Code Directly in the Oracle LSH Source Code Definition
Connecting to SAS
SAS Program and Source Code Types
Writing SAS Primary Source Code
Using a SAS Macro Catalog
Using a SAS Format Catalog
Creating a SAS Macro Catalog
Creating a SAS Macro Catalog
Nesting SAS Macros
About SAS Format Catalogs in the Oracle Life Sciences Data Hub
Creating a SAS Format Catalog
Calling an API to Capture Output Parameter Values
Defining Oracle Reports Programs
Defining Informatica Programs
Creating a New Informatica Program
Using Your Existing Informatica Mappings and Workflows
Creating and Synchronizing Source Code
Using PL/SQL Source Code in an Oracle LSH Informatica Program
Updating Table Descriptors
Setting Informatica Program Parameters
User-Defined Parameters
Predefined Parameters
Selective Index Management
Adding Planned Outputs
Informatica Integration
Informatica Folder Creation
Informatica Security Configuration
Defining Oracle Business Intelligence Publisher Programs
Integration with Oracle BI Publisher
Performing Oracle LSH Tasks
Performing Oracle BI Publisher Tasks
Running the Program
Editing an Existing Program
About Oracle BI Publisher Program Source Code
About Oracle BI Publisher Program Planned Outputs
Setting Oracle BI Publisher Program Parameters
Installing Program Instances
IDE Launch Settings
About Launch Settings
Setting the Blind Break Value
Setting the Shared Snapshot Label Value
Modifying Programs
Modifying Program Instance Properties
Modifying Program Definition Properties
Modifying Table Descriptors
Modifying Source Code
Modifying Parameters
Modifying Planned Outputs
Setting Up Integrated Development Environments (IDEs)
Setting Up Oracle SQL Developer or SQL*Plus as an IDE
Setting Up SAS as an IDE
Setting Up Informatica as an IDE
6
Defining Variables and Parameters
About Variables, Parameters, and Columns
Defining Variables
Creating Variables Automatically
Creating Variables through Load Sets
Creating Variables by Uploading SAS Data Sets and Variables during Table Definition
Creating Variables Manually
Modifying Variables
Using the Variable Properties Screen
Definition Properties
Buttons
Defining Columns
Defining Parameters
About Parameters
Using Parameters
Parameters and Execution Setups
Creating a Parameter
Create a New Parameter Definition and Instance
Create Parameters from an Existing Parameter Set
Defining Parameter Details
Setting a Method of Determining Value
Defining Allowed Values
Setting Validation Rules
Using the Parameter Properties Screen
About the Parameter Properties Screen
Instance Properties
Define Values
Validate Values
Definition Properties
Variable Properties
Buttons
Setting Up Parameter Value Propagation
About Parameter Value Propagation
Setting Up Value Propagation from the Source Parameter
Setting Up Value Propagation Manually
Setting Up Value Propagation Automatically
Setting Up Value Propagation from the Target Parameter
Defining and Using Parameter Sets
Explicitly Defining Parameter Sets
Defining Programatically Generated Lists of Values and Value Validation
Modifying Parameters
Modifying a Parameter Instance
Modifying a Parameter Definition
7
Defining Load Sets
About Load Sets
Creating a Load Set
Creating a New Load Set Definition and Instance
Setting Load Set Attributes
Creating an Instance of an Existing Load Set Definition
Using the Load Set Properties Screen
Instance Properties
Definition Properties
Load Set Attributes
Buttons
Defining Table Descriptors
Setting Load Set Parameters
About Load Set Planned Outputs
Defining Different Load Set Types
Oracle Tables and Views
About Oracle Tables and Views Load Sets
Oracle Load Set Attributes
Oracle Load Set Table Descriptors
Oracle Load Set Parameters
Oracle Load Set Planned Outputs
Oracle Load Set Execution Setups
SAS
About SAS Load Sets
UTF8 Encoding
SAS Load Set Attributes
SAS Load Set Table Descriptors
SAS Load Set Parameters
SAS Load Set Planned Outputs
SAS Load Set Execution Setups
Text
About Text Load Sets
UTF8 Encoding
Text Load Set Attributes
Text Load Set Table Descriptors
Text Load Set Parameters
Text Load Set Planned Outputs
Text Load Set Execution Setup
Oracle Clinical Stable Interface
About Oracle Clinical Stable Interface Load Sets
OC Stable Interface Tables Load Set Attributes
OC Stable Interface Tables Load Set Table Descriptors
OC Stable Interface Tables Load Set Parameter
OC Stable Interface Tables Load Set Planned Outputs
OC Stable Interface Tables Load Set Execution Setups
Oracle Clinical Data Extract SAS Views
About OC DX SAS Views
OC DX SAS Views Load Set Attributes
OC DX SAS Views Load Set Parameters
OC DX SAS Views Load Set Table Descriptors
OC DX SAS Views Load Set Planned Outputs
OC DX SAS Views Load Set Execution Setups
Oracle Clinical Data Extract Views
About OC Data Extract View Load Sets
OC Data Extract Views Load Set Attributes
OC Data Extract Views Load Set Table Descriptors
OC Data Extract Views Load Set Parameters
OC Data Extract Views Load Set Planned Outputs
OC Data Extract Views Load Set Execution Setups
Oracle Clinical Design and Definition
About OC Design and Definition Load Sets
OC Design and Definition Load Set Attributes
OC Design and Definition Load Set Table Descriptors
OC Design and Definition Load Set Parameters
OC Design and Definition Load Set Planned Outputs
OC Design and Definition Load Set Execution Setups
Oracle Clinical Global Metadata
About OC Global Metadata Load Sets
OC Global Metadata Load Set Attributes
OC Global Metadata Load Set Table Descriptors
OC Global Metadata Load Set Parameters
OC Global Metadata Load Set Planned Outputs
OC Global Metadata Load Set Execution Setups
Oracle Clinical Labs
About OC Labs Load Sets
OC Labs Load Set Attribute
OC Labs Load Set Table Descriptors
OC Labs Load Set Parameters
OC Labs Load Set Planned Outputs
OC Labs Load Set Execution Setups
Oracle Clinical Randomization
About OC Randomization Load Sets
OC Randomization Load Set Attributes
OC Randomization Load Set Table Descriptor
OC Randomization Load Set Parameters
OC Randomization Load Set Planned Outputs
OC Randomization Load Set Execution Setups
Oracle Clinical Study Data
About OC Study Data Load sets
OC Study Data Load Set Attributes
OC Study Data Load Set Table Descriptors
OC Study Data Load Set Parameters
OC Study Data Load Set Planned Outputs
OC Randomization Load Set Execution Setups
Installing Load Set Instances
Modifying Load Sets
Modifying Load Set Instance Properties
Modifying Load Set Definition Properties
Modifying Table Descriptors
Modifying Attributes and Parameters
Modifying Planned Outputs
8
Defining Data Marts
About Data Marts
Creating a Data Mart
Creating a New Data Mart Definition and Instance
Creating an Instance of an Existing Data Mart
Using the Data Mart Properties Screen
Instance Properties
Definition Properties
Data Mart Attributes
Setting Data Mart Attribute Values
Buttons
Defining Table Descriptors
Setting Data Mart Parameter Values
About Data Mart Planned Outputs
Defining Different Types of Data Marts
Defining Text Data Marts
About Text Data Marts
Text Data Mart Attributes
Text Data Mart Parameters
Text Data Mart Planned Outputs
Defining SAS Data Marts
About SAS Data Marts
SAS Data Mart Attribute
SAS Data Mart Parameters
SAS Data Mart Planned Outputs
Defining Oracle Export Data Marts
About Oracle Export Data Marts
Oracle Export Data Mart Attribute
Oracle Export Data Mart Parameters
Oracle Export Data Mart Planned Outputs
Installing Data Mart Instances
Modifying Data Marts
Modifying Data Mart Instance Properties
Modifying Data Mart Definition Properties
Modifying Table Descriptors
Modifying Attributes and Parameters
Modifying Planned Outputs
9
Defining Report Sets
About Report Sets
How to Work on a Report Set
Creating Overlay Templates
About Overlay Templates
Creating Template Files
Creating an Overlay Template Definition
Creating an Overlay Template File Definition
Creating a Report Set
Creating a New Report Set Definition and Instance
Creating an Instance of an Existing Report Set Definition
Using the Report Set Properties Screen
Instance Properties
Definition Properties
Buttons
Using the Report Set Structure View
Navigating to the Report Set Structure View
Building and Modifying the Report Set
Modifying the Report Set
Report Set Entry Information Displayed
Creating and Setting Report Set Parameters
Setting Overlay Template Parameter Values
Overlay Template Parameters
Setting Overlay Template Parameters
OTD Parameter Value Sharing
Setting Post-Processing Parameter Values
Post-Processing Parameters at the Report Set Level Only
Post-Processing Parameters at the Report Set and Report Set Entry Levels
Setting Program Parameter Values
Creating Parameters for Sharing Values within the Report Set
Defining Report Set Entries
Creating Multiple Report Set Entries
Setting Report Set Entry Properties
Setting Overall Properties
Setting Title Properties
Setting Assigned Program Properties
Adding Narratives
Setting Numbering Properties
Setting Volume Break Properties
Adding Narratives
Defining Programs to Generate Reports
About Programs in Report Sets
Assigning a Planned Output to a Report Set Entry
Options from the Report Set Program View Screen
Viewing Planned Output Assignments
Passing Report Set Entry Values to and from Programs
Report Set Entry Properties Available for Passing
Passing Values from a Report Set Entry to a Program Instance
Passing Values from a Program Instance to the Report Set for Post-Processing
Installing Report Sets
Installing the Report Set as a Whole with All Programs Checked In
Installing the Report Set as a Whole with Some Programs Checked Out
Installing a Single Program Instance in the Report Set
Validating Report Set Definitions and Outputs
Output Reuse
Program Output Validation Flag
Report Set Validation Status
Summary Output Validation Status
Output-Oriented Validation
Definition-Oriented Validation
Changing Validation Status
Changing the Validation Status of an Output
Changing the Validation Status of a Report Set Entry
Changing the Validation Status of a Program Instance in a Report Set
About Report Set Planned Outputs
Modifying Report Sets
Modifying Report Set Instance Properties
Modifying Report Set Definition Properties
Modifying the Report Set Structure
Modifying Report Set Entries
Modifying Programs
10
Defining Workflows
About Workflows
Creating a Workflow
Creating a New Workflow Definition and Instance
Creating an Instance of an Existing Workflow
Using the Workflow Properties Screen
Instance Properties
Definition Properties
Buttons
Adding Executables
About Executables as Workflow Activities
Adding an Executable to a Workflow
Mapping Table Descriptors within a Workflow
Adding Workflow Structures
About Workflow Structures
Types of Workflow Structures
Adding Structures
Defining Notifications
About Notifications
Using Approvals
Creating a Notification
Creating a New Notification Definition and Instance
Creating an Instance of an Existing Notification
Specifying Notification Recipients
Defining a Link to a Planned Output
Writing Notification Messages
Defining Notification Parameters
Modifying Notifications
Defining Transitions
About Transitions
Creating Transitions
Defining Workflow Parameters
Workflow Planned Outputs
Installing Workflow Instances
Modifying Workflows
Modifying Workflow Instance Properties
Modifying Workflow Definition Properties
Modifying Activities and Transitions
Modifying Parameters
Modifying Table Descriptor Mappings
11
Defining Business Areas for Visualizations
About Visualizations
Creating a Business Area
Creating a New Business Area Definition and Instance
Creating an Instance of an Existing Business Area Definition
Using the Business Area Properties Screen
Instance Properties
Definition Properties
Business Area Attributes
Buttons
Defining Table Descriptors
Defining Joins
Defining a Join at the Table Level
Defining a Join at the Column Level
Defining Business Area Hierarchies
Understanding Business Area Source Code
Setting Business Area Attributes and Parameters
Defining Oracle Business Intelligence Business Areas
About OBIEE Business Areas
Defining an OBIEE Business Area
Manually Deploying the Master RPD File
Starting the WebLogic Server
Visualizing Business Area Data using OBIEE Answers
OBIEE Security
End User Security
Developer Security
Installing and Setting Up Oracle Business Intelligence Administration Tool
Set Up Database Connectivity
Defining Generic Visualization Business Areas
Generic Visualization Business Area Instance Properties
Assigning Security Privileges to Business Area Data
Launching Visualizations
Creating a Visualization
Setting Data Currency and Blinding Values
Setting the Blind Break Value
Setting the Shared Snapshot Value
Installing Business Area Instances
Modifying Business Areas
Modifying Business Area Instance Properties
Modifying Business Area Definition Properties
Modifying Table Descriptors
Modifying Joins
Modifying Business Area Hierarchies
Modifying Business Area Source Code
12
Using, Installing, and Cloning Work Areas
Using the Work Area Properties Screen
Work Area Properties
Viewing a Work Area's Installation History
Viewing a Work Area's Version History
Version Details
Changing a Work Area's Usage Intent
Object Instance Information
Object Instance Actions
Using the Icons in the Object's Row
Using the Drop-Down List
Adding Object Instances to a Work Area
Managing Table Instance Snapshot Labels in a Work Area
Querying for Snapshots
Table Instance Information Displayed
Adding, Removing, or Moving a Snapshot Label
Personalizing Your Work Area Properties Screen
Installing a Work Area and Its Objects
About Work Area Installation
Running a Work Area Installation
Installing Individual Objects
Viewing Installation Results
Failed Installations
Successful Installations
What Happens During a Work Area Installation
Schemas
Object Name Resolution
Work Area Objects Converted to Oracle LSH Schema and OWB Objects
Work Area Installation Phases and Statuses
Work Area Status
Cloning Work Areas for Testing and Production
Application Life Cycle
Cloning a Work Area
13
Execution and Data Handling
About Execution
Submitting Jobs for Execution
Data Processing Types
Processing Types Summary
Transactional Processing
Reload Processing
Staging Processing
Transactional High Throughput Processing
Using Tables as Pass-Through Views
Data Auditing, Snapshots and Refresh Groups
Data Auditing
Auditing in Transactional and Reload Processing
Auditing in Staging Processing
Data Snapshots
Refresh Groups
Processing Data Subsets
Forward Chaining
Backchaining
How Backchaining Works
Backchaining Rules
Backchaining Tips
Submit the Execution Setup
Recover from a Canceled Job
Supply Default Parameter Values
Do Not Include Workflows with Approval Requests
Expect Slower Performance
Managing Blinded Data
Loading Real and Dummy Data
Managing Blinding Along the Data Flow
Unblinding Table Instances
Using Message-Triggered Submission from External Systems
About Message-Triggered Submission
Setup Required
XML Message Requirements
Executable Specification
System Parameter Values
User ID
Request ID
Required XML Schema
14
System Reports
Running and Saving System Reports
Alphabetical Listing of Reports
Security Reports
Blinding Rights Report
Operations for a Role Report
User Group Assignments Report
Users in Group Report
Data Blinding Reports
Blind Breaks Report
Blinded Table Instances Audit Report
Blinded Table Instances Report
Unblinded Outputs Report
Container Reports
Application Area Library Report
Domain Library Report
Work Area - All Instances Report
Work Area Cloning Report
Work Area Installation History Report
Work Area Version History Report
Object Metadata Reports
Common Header Information
Header Information for Object Definitions
Header Information for Object Instances
All Instances of a Definition Report
Data Mart Report
Data Mart Instance Report
Load Set Report
Load Set Instance Report
Object Validation Report
Object Version History Report
Program Report
Program Instance Report
Report Set Report
Report Set Instance Report
Table Report
Table Instance Report
Workflow Report
Workflow Instance Report
A
Installation Requirements for Each Object Type
Installable Instances and their Definitions
Component Object Types
Organizational Objects
B
Object Ownership
Domains
Application Areas
Work Areas
Glossary
Index