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Oracle® Clinical Administrator's Guide
Release 5.0.1
E36994-02
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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
Part I Configuration Tasks
1
Setting Up User Accounts
Creating an Administrator User Account
Running the Add User Script
Granting Users Access to the ocpsub Account
About the Add User Script
Running the Add User Script
Required Parameters
Optional Parameters
Running the Migrate Users Script
Adding or Revoking OCPSUB Access
Maintaining Oracle User and Group User Accounts
Adding a User to a Group User Account
Granting Data Access to User and Group User Accounts
Granting Data Access to Programs and Projects
Granting Data Access to a Study
Superuser and Study Access Interaction
Revoking User Access
Granting Data Access to RDC Users
Granting Automatic Access in RDC to Studies Granted in Oracle Clinical
Configuring Study and Site Security Privileges
Changing the Default Access to DCIs
Granting Additional Database Roles to User Accounts
Additional Database Roles for RDC Users
Additional Database Roles for Oracle Clinical Users
Setting Up Data Extract Users
Setting Up PSUB Administrator Users
Setting Up Power Users
UNIX
Windows
Changing Passwords
Changing the Password for a User
Changing the Password for a Schema or Role Using the SET_PWD Utility
Synchronizing Passwords in the WebLogic Admin Server
Auditing Passwords
Changing the Password for the OCPSUB or RXC_DISC_REP Account
Setting Password Requirements for User Accounts
Default Behavior
Creating a Profile
Assigning a Profile to Users
Getting More Information
2
Oracle Clinical Menu-Based Security
Predefined Database Roles
Creating and Modifying Database Roles
Viewing Menu-Role Associations
Organization of the Menu Module Tree
Navigating the Menu Modules
Modifying Menu-Role Associations
Creating Custom Database Roles
Creating Custom Roles for Restricting DCI Access
Associating Roles with Menus
Adding a Custom Role to OPA_MENU_ROLES
Granting a Custom Role Access to a Custom Module
Adding Menu Items to Oracle Clinical
3
Configuring Discrepancy Management
Mapping Database Roles to User Roles
Specifying User Roles for the Oracle Clinical Discrepancy Database
Assigning Function Privileges and Layouts
Assigning and Removing Function Privileges
Assigning Custom Layouts
Customizing Layout Definitions
Customizing Profiles
Toggling Between View Modes in the Profile Administration Window
Specifying Default Profile Criteria
Locking Profile Criteria
Adding SQL Statements
Filtering Profile Views by Review Status
Updating Status Codes
Filtering Profile Views by Discrepancy Field
Adding Update Privileges by Review Status Code
Setting Update Privileges by Discrepancy Field
Setting Review Status Updating Privileges
Customizing Flexfields
DISC_FLEX1 and DISC_FLEX2
DISC_FLEX1_VALUES and DISC_FLEX2_VALUES
Example
Defining Reason Codes for Discrepancies
Reason Codes and Descriptions for Manual Discrepancies
Reason Codes and Descriptions for Univariate Discrepancies
Reason Codes and Descriptions for Multivariate Discrepancies
Defining the Possible Review Statuses for Discrepancies
Default Entries for the DISCREPANCY REV STATUS CODE Codelist
Rules for the DISCREPANCY REV STATUS CODE Codelist
Defining Resolution Reasons for Discrepancies
Setting Values in the OCL_STATE Local Reference Codelist
Configuring Role-Specific Discrepancy Management for RDC
Configuring Discrepancy Display by User Role
How RDC Indicates Discrepancies in the User Interface
Rules for the DISCREPANCY STATUS
role
Codelists
Comparison of the Default Values for the DISCREPANCY STATUS
role
Codelists
DISCREPANCY STATUS CRA
DISCREPANCY STATUS DM
DISCREPANCY STATUS INV
DISCREPANCY STATUS SITE
Configuring the Actions Allowed on Discrepancies
Rules for the DISCREPANCY ACTIONS
role
Codelists
DISCREPANCY ACTIONS CRA
DISCREPANCY ACTIONS DM
DISCREPANCY ACTIONS INV
DISCREPANCY ACTIONS SITE
Preventing Update to OTHER Discrepancies
Adding Reference Codelists for Custom Roles
Configuring Study and Site Security for Discrepancy Management
Updating a Discrepancy
Navigating to Data Entry
Setting Up Data Clarification Forms (DCFs)
Defining DCF Statuses and their Behavior
Laying Out the DCF
Replacing the Placeholder DCF Logo Graphic
Customizing and Upgrading DCF Reports
Creating Reusable Standard Text for Discrepancies and DCFs
Creating New Standard Text
Inserting Replacement Parameters
Customizing Default Standard Text Entries
4
Configuring the Mass Changes Utility
Creating and Assigning Mass Changes Roles
Customizing Mass Changes Local Codelists
Customizing the Field Display on the Candidate Data Set Form
5
Configuring Data Entry and User Preferences
Customizing Data Entry Behavior
Define Data Entry Configuration Settings
Configure Database-Level Data Entry Settings
Configure Study-Level Data Entry Settings
Configure User-Level Data Entry Settings
Configuring Additional Data Entry User Preferences
Configuring Privileged Update
Set Privileged Update Using Configuration Settings
Set Privileged Update Using Study/Site Security
Customizing the Oracle Clinical Log-in Window Layout
Using the Log-in Layout Editor
Modifying the Received DCI Window
Modifying the Received DCM Window
Modifying the Smart Received DCM Window
Setting DCI Form Default Values for RDC Data Entry and Patient Data Reports
Setting and Enforcing Values
Settings
DCI Form Definition
DCI Form Runtime
General
Graphic Layout Editor/Updater
Graphic Layout Generator - General
Graphic Layout Generation - DCMS
DCI Form Generation Defaults
Default Settings for Showing DCM Header Fields
Default DCM Header Field Prompts
Version Migration
Patient Data Report
Validation
Options in Group Verify dialog
Options in Group Approve dialog
Customizing Flex Fields for DCI Forms
How Flex Fields Work
Flex Field Components
Shipped Functions
Customizing Online Help
Modifying Calls to Online Help Topic Files
Copying Xhelp Topic Files
Creating Custom Help Files
Viewing Xhelp Without Oracle Clinical
6
Configuring Data Extract
Adding the opapps User to the OCLSASCR User Group
Authenticating the SAS Connection
Using Oracle Wallet for SAS Authentication
Using SAS Encryption for SAS Authentication
Regenerating SAS Views Created in Pre-5.0 Oracle Clinical Releases
Creating SAS Output File Directories
Configuring Default Installation Data Extract Settings
Setting Values in Data Extract-Related Reference Codelists
Creating Tablespaces for Data Extract Tables and Indexes
Creating Tablespaces
Entering Tablespace Names in Reference Codelists
Creating Data Extract Access Accounts Using Local Tablespaces
Customizing Data Extract Views
Generating Data Extract Views
Running gen_views on UNIX Platforms
Running gen_views on Windows
Enabling the View Builder and Converting Views
Converting Views
Enabling the View Builder in a Study
Controlling Access to Data Extract Views
7
Reference Codelists
Overview of Reference Codelists
Working in the Maintain or Query Reference Codelists Windows
Access
Components
Usage
Adding a Value to a Reference Codelist
Modifying a Value in a Reference Codelist
Running the Reference Codelists Report
Local Reference Codelists
BATCH QUEUE NAME Local Codelist
DB_LINKS Local Codelist
DCF COMMENT TEXT Local Codelist
DCF DEFAULT FOOTERS Local Codelist
DCF DEFAULT HEADERS Local Codelist
DCF REPORT LABELS Local Codelist
DISC COLS Local Codelist
DISC_FLEX1 and DISC_FLEX2 Local Codelists
DISC_FLEX1_VALUES and DISC_FLEX2_VALUES Local Codelists
FLD RXCMCMCD RDCI DELETE Local Codelist
FLD RXCMCMCD RDCI KEY Local Codelist
FLD RXCMCMCD RDCM KEY Local Codelist
FLD RXCMCMCD RESPONSE Local Codelist
IND DISC COLS Local Codelist
MAN DISC COLS Local Codelist
MANHD DISC COLS Local Codelist
MC CDS SORT ORDER Local Codelist
MC COLUMNS Local Codelist
MULTI DISC COLS Local Codelist
NLS_CONFIG Local Codelist
OCL_DE_CONFIG Local Codelist
DVG List of Values STYLE
COMMCHGREAS_REQ
JUSTENTERP1TIME
JUSTENTERP2TIME
RSTRCT LCKD CRF
OCL_DE_PREFS Local Codelist
OCL_JOB_PREF Local Codelist
OCL MC PREFS Local Codelist
OCL_MENU_ACCESS Local Codelist
OCL_STATE Local Codelist
SAS_CONNECTION
SERVER_OS
LOCATION_CODE
SERVER_NAME
DB_BLOCK_SIZE
TEMP_TABLES
DM_PROMPT
PROC_LAB_ALIAS
DISC_DCM_PROMPT
BOOK_ASSIGN
TMS_FAIL_BV_ACT
UPD_FV_INCREM
PRINT QUEUE NAME Local Codelist
PUBLIC_DB_LINKS Local Codelist
RDC CONFIGURATION
Role
Local Codelists
REPORT_SERVER Local Codelist
SAS_QUEUE Local Codelist
SQL FUNCTIONS Local Codelist
TMS_DSI Local Codelist
TMS_OPTIONS Local Codelist
UNI DISC COLS Local Codelist
WEB_DOCUMENT_CONFIG Local Codelist
WEB_DOCUMENT_GROUPS Local Codelist
Installation Reference Codelists
APPLICATION AREA CODE Installation Codelist
APPLICATION SYSTEM NAME Installation Codelist
APPROVE VERIFY RETAIN CODE Installation Codelist
APPROVE VERIFY REVERSE CODE Installation Codelist
BLIND TYPE CODE Installation Codelist
CLINICAL PHASE Installation Codelist
COUNTRIES Installation Codelist
CRF PAGE NUMBERING SCHEME Installation Codelist
CRF PAGE STATUS CODES Installation Codelist
CRF PAGE STATUS QUERY Installation Codelist
DATA CHANGE REASON TYPE CODE Installation Codelist
DATA CHANGE REASON2 TYPE CODE Installation Codelist
DCF LOCK CONDITIONS Installation Codelist
DCF OPTIONAL STATUS CODES Installation Codelist
DCF STATUS CODES Installation Codelist
DCIF CHECKBOX SIZE Installation Codelist
DCIF FONT TYPESIZE Installation Codelist
DCIF PAGE DEFINITION Installation Codelist
DCM DCI QG TYPE CODE Installation Codelist
DISCREPANCY ACTIONS
ROLE
Installation Codelist
DISCREPANCY MESSAGES Installation Codelist
DISCREPANCY NO OTHER UPDATE Installation Codelist
DISCREPANCY RESOLU TYPE CODE Installation Codelist
DISCREPANCY REV STATUS CODE Installation Codelist
DISCREPANCY STATUS
ROLE
Installation Codelists
DISCRETE VAL GRP TYPE CODE Installation Codelist
DISC_STDST_VALUES Installation Codelist
DOSE FORM TYPE CODE Installation Codelist
DOSE FREQUENCY TYPE CODE Installation Codelist
DX_CONFIG Installation Codelist
DX_EXTENDED_ATTRIBUTES Installation Codelist
DX_INDEX_TABLESPACE Installation Codelist
DX_KEY_NAME Installation Codelist
DX_ROLES Installation Codelist
DX_VIEW_TABLESPACE Installation Codelist
EXP DESIGN TYPE CODE Installation Codelist
EXTERNAL_TRANS_TYPE Installation Codelist
LAB RANGE SUBSET CODE Installation Codelist
MANUAL SOURCE TYPE CODE Installation Codelist
MAPPING_TYPE Installation Codelist
MEDICAL EVAL TYPE CODE Installation Codelist
OBJECTIVE TYPE CODE Installation Codelist
OCL_DOMAINS Installation Codelist
OCL_INSTALLATION Installation Codelist
OCL_OPTIONS_TYPE_CODE Installation Codelist
OPA_MENU_ROLES Installation Codelist
PATIENT STATUS CODE Installation Codelist
PLAN STUDY INT TYPE CODE Installation Codelist
PROCEDURE TYPE CODE Installation Codelist
QUESTION CATEGORY TYPE CODE Installation Codelist
RDCI CHANGE REASON TYPE CODE Installation Codelist
RDCI CHANGE REASON2 TYPE CODE Installation Codelist
REGION TYPE CODE Installation Codelist
RETIREMENT REASON TYPE CODE Installation Codelist
ROUTE OF ADMIN TYPE CODE Installation Codelist
SAS_FORMATS Installation Codelist
SINGLE DCI TYPES Installation Codelist
SOURCE LOCATION CODE Installation Codelist
STANDARDS AFFIL TYPE CODE Installation Codelist
STUDY STATUS TYPE CODE Installation Codelist
TMS_CONFIGURATION Installation Codelist
TMS_LANGUAGES Installation Codelist
TMS_QUERY_TYPE Installation Codelist
TMS_SOURCE_MAT_VIEWS Installation Codelist
TMS_TAL_POOL_CONFIGURATION Installation Codelist
TMS_X_SEARCH Installation Codelist
TREAT CHG REASON TYPE CODE Installation Codelist
UNITS_OF_MEASURE_TYPE_CODE Installation Codelist
USER GROUP ROLES Installation Codelist
USER GROUPS Installation Codelist
VALIDATION FAILURE TYPE CODE Installation Codelist
Design Installation Reference Codelists
System Reference Codelists
Part II Oracle Clinical Administration Tasks
8
Managing Batch Jobs
Account Requirements for Batch Jobs
How PSUB Handles a Request
Asynchronous PSUB Requests
Blocking and Nonblocking Jobs
Checking a Nonblocking Batch Job
Securing PSUB
Using PSUB in a RAC Environment
Starting and Stopping PSUB
Starting and Stopping PSUB Manually in UNIX
Starting PSUB Manually in UNIX
Stopping PSUB Manually in UNIX
Starting and Stopping PSUB Automatically in UNIX
Starting PSUB Automatically in UNIX
Stopping PSUB Automatically in UNIX
Starting and Stopping PSUB Manually in Windows
Installing PSUB in Windows
Starting PSUB Manually in Windows
Stopping PSUB Manually in Windows
Starting PSUB Automatically in Windows
Creating a System Environment Variable
Creating a Batch File
Scheduling the Batch File and Testing the Setup
Adding a Shortcut
Managing the PSUB Process
Changing PSUB Job Number Sequencing
Viewing the Status of a Submitted Batch Job
Removing the PSUB Service
Viewing Log and Output Files on the Screen
Viewing Logs that Concern Execution of PSUB Processes
Viewing Logs for Individual PSUB Jobs
Printing Output or Log Files
Using Job Sets to Control Execution Order
Create a Job Set
Submit a Job Set
Tracking PSUB Processes
Required Reference Codelist Settings for Batch Jobs
9
Partitioning and Indexing
Introduction
Timing Considerations and Deferral of Index or Partition Upgrade
Enforcing Pre-Version 4.0 Optimization
About Partitioning
How Has the Responses Table Been Partitioned?
Why Partition?
Planning for Partitioning Upgrade
Pre-upgrade Steps
Decide Partitions Needed
Define Partition Structure
Implement Partition Structure
Generating Table and Index Creation SQL
Partitioning the Responses Table
Step 1. Back Up the Database
Step 2. Export the Responses Table
Step 3. Prepare the Database
Drop Responses Table
Reorganize Tablespaces and System File Space
Create Partitioned Responses Table
Step 4. Import Responses Data
Step 5. Compute Statistics on the Responses Table
Step 6. Create Indexes on Partitioned Responses Table
Step 7. Compile Invalid Objects and Restore Database Trigger
Step 8. Back Up the Database
Step 9. Regenerate Procedures and Data Extract Views
Step 10. Back Up the Database
Partition Maintenance
Prospective Allocation of clinical_study_ids for Partitioning
Strategy for Ongoing Partition Maintenance
Instructions for Partition Maintenance
Rebuild Indexes after Partition Maintenance
Using Read-Only Partitions to Minimize Backup
Upgrading Indexes
Index Upgrade Process
Resizing the Storage Clause for Indexes
Response Index Upgrade
Regenerate Procedures and Data Extract Views
ResponsesT (Test Database) Index Upgrade
RECEIVED_DCI and RECEIVED_DCM Index Upgrades
Query Tuning Guidelines
10
Utilities
Computing the Validation Status of All Responses
Running cnvstatus on UNIX
Running cnvstatus on Windows
Generating Validation Procedures
Running gen_procs on UNIX Systems
Running gen_procs on Windows Systems
Deleting Inactive Procedures
11
Setting Up File and Image Viewing
Setting Up Reports Viewing
Install the Oracle Clinical Reports Server
Setting Up Reports Directories
Making the Reports Root Directory Sharable
Assigning Directories to Users
Setting Up Batch Job File Viewing
Setting Up Directories for PSUB
Creating a Directory for Log and Output Files and Registering it in OCL_STATE
Creating Directories for Input and Output Files of Certain Job Types
Entering Reference Codelist Values
Enter the Root Directory Path in OCL_STATE Local Reference Codelist
Enter Y or N in the USERDIRS OCL_STATE Setting
Setting Up Image Viewing
Put Images in dcif_images Directory
Sharing the Images Directory
Automatic Setup During Installation
Changing the Images Directory Location
12
Conducting Studies in a Distributed Environment
Distributed Study Environments and Replication
Locations in a Distributed Study Environment Installation
Global Library-owning Location
Study-owning Location
Lab-owning Location
What Types of Oracle Clinical Objects Can You Replicate?
What Methods of Replication Does Oracle Clinical Support?
Standard Replication
Disconnected Replication
Symmetric Replication
Comparison of Standard and Disconnected Replication
Prerequisites to Setting Up Replication
Oracle Accounts for Replication
RXA_READ Account
RXC_REP Account
RXC_DISC_REP Account
Tables that Store Replication Information
Seed Numbers for Databases Involved in Replication
Setting Up Replication
Configuring the SOURCE LOCATION CODE Installation Codelist for Replication
Configuring the OCL_INSTALLATION Installation Reference Codelist for Replication
Configuring the OCL_STATE Local Reference Codelist for Replication
Creating and Setting Up the Database Links for Standard Replication
Configuring the DB_LINKS Codelist for Standard Replication
Configuring the PUBLIC_DB_LINKS Codelist for Standard Replication
Creating the Private Database Links for the RXC_REP and RXA_DES Accounts
Creating the Public Database Link for RXA_READ
Creating the Study Design Replication Packages
Using the rxasrall.sql Script
About Running the rxasrall.sql Script for Each Location
Running the rxasrall.sql Script
Creating the Views and Synonyms Required to Replicate Study Design
Creating the Package for Replicating Investigators and Sites
Setting Up Symmetric Replication
Setting Up Symmetric Replication
Installing Symmetric Replication
Running the Symmetric Replication Scripts Required for Oracle Clinical
Verifying Data Is Replicating
Enabling Symmetric Replication
Reconciling Data
Conflict Resolution
Non-study-specific Tables Replicated
Troubleshooting Symmetric Replication
Problems During Installation of Symmetric Replication
Problems During Routine Use of Symmetric Replication
Problems after a Failure when Using Symmetric Replication
13
Using Replication
Example of an Oracle Clinical Distributed Study
Operating from the Study-Owning Location
Changing Ownership and Replicating Patient Positions
Changing the Ownership of Patient Positions
Retrieving Patient Positions
Maintaining Investigators and Sites
Constraints at the Study-Owning Location
Exceptions for Patient Positions
Exceptions for Study Design Activities
Replicating Data at a Study-Owning Location
Operating from a Sharing Location
Study Design at a Sharing Location
Study Definition at a Sharing Location
Study Conduct at a Study-Sharing Location
Data Replication at a Study-Sharing Location
Replication of Labs and Lab Ranges at a Sharing Location
Error if Flexible Study Setting Mismatch Between Locations
Enabling a Study for Replication
Using Standard Replication
Review of Setting Up Standard Replication
Replicating a Global Library
Replicating Study Designs
Replicating the Design of a Clinical Study
Creating a Local Configuration for the Replicated Study
Replicating a Study Definition
Replicating Data
What Does Oracle Clinical Include in Data Replication?
Tracking the Execution of Data Replication
Invoking Study Data Replication
Managing Data at Multiple Locations
Data Replication for NLS-Enabled Studies
Replicating Lab Information
Replicating the Global Lab Information
Replicating Labs and Lab Ranges
Replication and Frequency
Using Disconnected Replication
Overview of Disconnected Replication
Users Who Can Run Disconnected Replication
Disconnected Replication Uses Full Replication Only
Advantages of Disconnected Replication
Security Concerns with Disconnected Replication
Example of How Disconnected Replication Is Used in Distributed Studies
Review of Setting Up Disconnected Replication
Extracting Source Data to an Export File
Defining the Extract Data Parameters
Target Location
Include GLIB
Include GLIB Labs
Include Labs
Study Code
Extract Level
Include Randomization
Export File
Loading Data from the Export File into a Target Location
How Disconnected Replication Commits Data
Changing Study Ownership
Replicated Tables
Part III Appendixes
A
Environment Variables and Registry Settings
Oracle Clinical Setup Files
Database Tier Settings
OPA Settings
NLS_DATE_FORMAT
NLS_LANG
RXC_BATCH_QUEUE
RXC_BDL_DIR
RXC_DEBUG_BUFFER_SIZE
RXC_IMMED_QUEUE
RXC_LOG
RXC_MAA_TAB_SPACE
RXC_NOW_STRING
RXC_PRINTER
RXC_SAS_BATCH_QUEUE
RXC_SAS_ROOT
RXC_SAS_VIEW
RXC_USER
SASORA
TEMP
USER_BV_JOB
Changing opa_settings on UNIX
Setting Up UNIX Environments
Changing Configuration Settings on UNIX Database Servers
Setting TNS_ADMIN on UNIX
Changing opa_settings.bat on Windows
Application Tier Settings
OPA Front End
Oracle Clinical Front End
RDC Front End
OCN Front End
Reports Server
Registry Keys
FORMS_PATH
OPA_JARS
OPA_XMLTEMP_UNC
OPA_XMLTEMP_HTTP
RDC_DCIF_IMAGES
OC_DE_FIELDFONT
OC_DE_TEXTFONT
RDC_PDF_PRINT_TOOL
Online Help
B
SAS_VIEW Directory Tree
C
Troubleshooting
Restart Application Server After Redeploying RDC Onsite
Managing High Sequence Numbers
Assessing Sequence Sizes
Assess the Sequence Numbers of RDCMs, RDCIs, and Discrepancies
Assess the Sequence Number of Responses
Reseeding Sequences
Error Messages
Message: Not Using Named Package
Message: ORA-12223
Message: ORA-04020
Message: Unable to Change Mode
Message: ConnectOCL - 970100
System Malfunction: GPF Occurs During Data Entry
PSUB Jobs
Check the Failure Text in the Submitted Batch Jobs Window
Check the PSUB Log Files
If Batch Jobs Hang and the Batch Queue Is Full
Stopping Batch Jobs on UNIX Systems
Stopping Batch Jobs on Windows
Determining if PSUB Is Running for a Database
What PSUB Processes Are Running on a Given UNIX Server?
Is PSUB Running on a Given Windows Server?
Troubleshooting PSUB Based on the Batch Job's Execution Status
ENTERED
SUBMITTED
SUBMIT_FAILED
STARTED
FAILED
Other Items to Check
Handling PSUB Failures that Return "Fatal two-task communication protocol" Error
Handling PSUB Failure that Returns "Illegal use of PSLAUNCH…" Error
Verify PSUB Account Uses C Shell
Modify launch.ps
Tracking Previous PSUB Process Connections
If PSUB Fails to Start
Troubleshooting PSUB on a Windows Database
Database Trace
Problems in Reports
Truncated Field Display
Preview for Form Layout Editor or DCI Form Generation Fails on Standalone Reports Servers
Unable to Stop a Reports Job
PDR Fails with "Generating Cover Page" Error
D
Routine Server Administration
Recreating Symbolic Links — UNIX Only
Relinking Server Code — UNIX Only
Relocating Oracle Clinical
Updating Oracle Clinical Seed Data
Collecting Statistics for Optimization
E
Oracle Clinical Tablespaces
Glossary
Index