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Oracle® Clinical Administrator's Guide
Release 4.6
Part Number A83791-06
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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
Setting Up Required Accounts and Directories
Setting Up a Report Server Log Directory
Creating an Operating System Account
Accounts on UNIX Systems
Accounts on Windows Systems
Creating a PSUB Log Directory
Making the PSUB Root Directory Accessible
Ensuring PSUB Execution Permission (UNIX Only)
Modifying the RXCPROD Account's Profile
Running the Add User Script
About the Add User Script
Running the Add User Script in UNIX
Running the Add User Script in Windows
Required Parameters
Optional Parameters
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
Creating an Operating System Account on the SAS Server
Adding User to the OCLSASCR User Group (UNIX only)
Creating a Queries Table for a Data Extract User
Setting Up Power Users
UNIX
Windows
Setting Up Passwords
Changing the Password for a Schema or Role
Changing the Password for a User
Enforcing Password Security
Auditing Passwords
Operating System Passwords
UNIX Passwords
Windows Passwords
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
Filtering Profile Views
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
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
DISCREPANCYSTATUS 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
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
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
Modify 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 the Patient Data Report
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
Customizing Flex Fields for DCI Forms
How Flex Fields Work
Flex Field Components
Shipped Functions
Customizing CRF Column Headers in the RDC Classic Surround
Default Behavior
Functions Used to Modify CRF Column Headers
Functions
Customizing Online Help
Modifying Calls to Online Help Topic Files
Copying Xhelp Topic Files
Creating Custom Help Files
6
Configuring Data Extract
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
Adding a Value to a Reference Codelist
Modifying a Value in a Reference Codelist
Running the Reference Codelists Report
Maintain/Query Reference Codelists Windows
Access
Components
Usage
Local Reference Codelists
BATCH QUEUE NAME
DB_LINKS
DCF COMMENT TEXT
DCF DEFAULT FOOTERS
DCF DEFAULT HEADERS
DCF REPORT LABELS
DISC COLS
DISC_FLEX1 and DISC_FLEX2
DISC_FLEX1_VALUES and DISC_FLEX2_VALUES
FLD RXCMCMCD RDCI DELETE
FLD RXCMCMCD RDCI KEY
FLD RXCMCMCD RDCM KEY
FLD RXCMCMCD RESPONSE
IND DISC COLS
MAN DISC COLS
MANHD DISC COLS
MC CDS SORT ORDER
MC COLUMNS
MULTI DISC COLS
NLS_CONFIG
OCL MC PREFS
OCL_DE_CONFIG
DVG List of Values STYLE
COMMCHGREAS_REQ
JUSTENTERP1TIME
JUSTENTERP2TIME
RSTRCT LCKD CRF
OCL_DE_PREFS
OCL_JOB_PREF
OCL MC PREFS
OCL_MENU_ACCESS
OCL_STATE
SERVER_NAME
LOCATION_CODE
DB_BLOCK_SIZE
TEMP_TABLES
DM_PROMPT
DISC_DCM_PROMPT
PROC_LAB_ALIAS
BOOK_ASSIGN
TMS_FAIL_BV_ACT
UPD_FV_INCREM
PRINT QUEUE NAME
PUBLIC_DB_LINKS
REPORT_SERVER
SAS_QUEUE
SQL FUNCTIONS
TMS_OPTIONS
UNI DISC COLS
Installation Reference Codelists
APPLICATION AREA CODE
APPLICATION SYSTEM NAME
APPROVE VERIFY RETAIN CODE
APPROVE VERIFY REVERSE CODE
BLIND TYPE CODE
CLINICAL PHASE
COUNTRIES
CRF PAGE NUMBERING SCHEME
CRF PAGE STATUS CODES
CRF PAGE STATUS QUERY
DATA CHANGE REASON TYPE CODE
DATA CHANGE REASON2 TYPE CODE
DCF LOCK CONDITIONS
DCF_OPTIONAL_STATUS_CODES
DCF STATUS CODES
DCIF CHECKBOX SIZE
DCIF FONT TYPESIZE
DCIF PAGE DEFINITION
DCM DCI QG TYPE CODE
DISCREPANCY ACTIONS
ROLE
Codelists
DISCREPANCY MESSAGES
DISCREPANCY RESOLU TYPE CODE
DISCREPANCY REV STATUS CODE
DISCREPANCY STATUS
ROLE
Codelists
DISCREPANCY NO OTHER UPDATE
DISCRETE VAL GRP TYPE CODE
DISC_STDST_VALUES
DOSE FORM TYPE CODE
DOSE FREQUENCY TYPE CODE
DX_CONFIG
DX_EXTENDED_ATTRIBUTES
DX_INDEX_TABLESPACE
DX_KEY_NAME
DX_ROLES
DX_VIEW_TABLESPACE
EXECUTION SCHED CODE
EXP DESIGN TYPE CODE
EXTERNAL_TRANS_TYPE
LAB RANGE SUBSET CODE
MANUAL SOURCE TYPE CODE
MAPPING_TYPE
MEDICAL EVAL TYPE CODE
OBJECTIVE TYPE CODE
OCL_DOMAINS
OCL_INSTALLATION
OCL_OPTIONS_TYPE_CODE
OPA_MENU_ROLES
PATIENT STATUS CODE
PLAN STUDY INT TYPE CODE
PROCEDURE TYPE CODE
QUESTION CATEGORY TYPE CODE
RDCI CHANGE REASON TYPE CODE
RDCI CHANGE REASON2 TYPE CODE
REGION TYPE CODE
RETIREMENT REASON TYPE CODE
ROUTE OF ADMIN TYPE CODE
SAS_FORMATS
SINGLE DCI TYPES
SOURCE LOCATION CODE
STANDARDS AFFIL TYPE CODE
STUDY STATUS TYPE CODE
TMS_CONFIGURATION
TMS_OMISSIONASSIGNMENT
TMS_OMISSION_STATUS
TMS_QUERY_TYPE
TMS_X_SEARCH
TREAT CHG REASON TYPE CODE
UNITS_OF_MEASURE_TYPE_CODE
USER GROUP ROLES
USER GROUPS
VALIDATION FAILURE TYPE CODE
Design Installation Reference Codelists
System Reference Codelists
Part II Oracle Clinical Administration Tasks
8
Managing Batch Jobs
User Account Requirements for Batch Jobs
How PSUB Handles a Request
Asynchronous PSUB Requests
Blocking and Nonblocking Jobs
Checking a Nonblocking Batch Job
Managing the PSUB Process
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
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
Batch Job Reference Codelists
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, Optionally, 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 Platforms
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 Viewing
File Viewing Setup Overview
Editing formsweb.cfg to Change File Viewing Protocol
Setting Directory Mappings
Setting Up Image Viewing for DCI and DCM Form Layouts HTML Preview Feature
12
Enabling Image Viewing
Setting Up a Central Image Repository
Setting Up a Network User to Run the Oracle Process Manager Service
Setting Up Image Viewing During Data Entry
Copying Image Files to All Installations
Part III Appendixes
A
Environment Variables and Registry Settings
Summary of the Oracle Clinical Setup
Editing opa_settings.bat
Setting Up UNIX Environments
Changing Configuration Settings on UNIX Database Servers
Defaulting, Adding, and Customizing Values
Constraints on the opa_settings File
Checking for Errors in the opa_settings File
Changing Environment Variables on Windows
Settings that Affect Back-End Job Execution
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_CONNECT
RXC_USER
SASORA
TEMP
USER_BV_JOB
Windows Registry Settings
OPA Front End
Online Help
Oracle Clinical Front End
RDC Front End
OCN Front End
Report 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
B
SAS_VIEW Directory Tree
C
Troubleshooting
Managing High Sequence Numbers
Assessing Sequence Sizes
Reseeding Sequences
Error Messages
Message: ORA-12223
Message: ORA-04020
Message: Unable to Change Mode
System Malfunction: GPF Occurs During Data Entry
Situation: $ulimit unlimited
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
Tracking Previous PSUB Process Connections
Database Trace
D
Oracle Clinical Tablespaces
E
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
Glossary
Index