Maintaining the Software
and Database Application
This chapter covers:■ Maintenance Overview . . . 76
■ Using and Maintaining the Oracle® Database. . . 77 ■ Using the Database Dashboard Software . . . 79
■ Reviewing the Database Statistics . . . 81
■ Allocating Disk Space . . . 82
■ Viewing Project Statistics . . . 86
■ Backing Up the Database . . . 87
■ Generating a Database Report. . . 90 Setting Up User
Accounts and User Access
Managing the Auditing System
Managing the E-Signature System
Maintaining the Software and Database
Chapter 4 Maintaining the Software and Database Application Maintenance Overview
Maintenance Overview
The GeneMapper®ID-X Software requires regular maintenance to
provide:
• Optimal performance of the software and database application • Protection against data loss (due to hardware or software
failure)
Recommended Maintenance Schedule
The maintenance schedule in Table 15 contains general
recommendations for routine maintenance of the GeneMapper ID-X
Software.
Table 15 Database maintenance activities
Frequency Tasks
Weekly • Exit the GeneMapper ID-X Software and restart the computer.
• Review the statistics for the database (seepage 81), and, if necessary:
– Export unused projects and data (see GeneMapper ID-X Software v1.0 Online Help) and then delete them.
– Allocate additional disk space (seepage 84).
• (Optional) Back up the GeneMapper ID-X Software database (seepage 87). Monthly • Defragment the computer hard drive.
As Needed • Review password policies, and modify them as necessary (see page 14). • If using the auditing system, review the audit map configuration, and modify as
needed (see page 50).
• If using the electronic signature system, review the electronic signature settings, and modify as needed (seepage 67).
Using and Maintaining the Oracle® Database
This section describes: • Database Access
• Maintaining the Database • Oracle Documentation
Database Access
The Database Dashboard Software provides tools for maintaining and evaluating the performance of the GeneMapper®ID-X Software
database application. The software is installed with the full version (co-installation, remote autoanalysis, and stand-alone
configurations) of the GeneMapper ID-X Software.
Do not install any other database applications on the computer running the GeneMapper ID-X Software. If
co-installed with the GeneMapper ID-X Software, other database applications can produce unexpected results, including loss of data and corruption of the GeneMapper ID-X Software database application.
IMPORTANT! The Oracle Database included in the
GeneMapper®ID-X Software package should serve as a data
repository for this software product only and should not be used for other data storage purposes.
Applied Biosystems does not support access to the Oracle Database through any means other than the GeneMapper ID-X Software and associated tools (Database Dashboard, Security Manager, Audit Manager, and E-signature Manager).
SQL Support
Applied Biosystems does not support the use of SQL (using SQLMGR or SQL*Plus) to query or modify the tables of the GeneMapper ID-X Software database application.Chapter 4 Maintaining the Software and Database Application Using and Maintaining the Oracle® Database
API Support
The GeneMapper ID-X Software does not include an application programming interface (API) for linking the GeneMapper ID-XSoftware database application with a LIMS. However, the
GeneMapper ID-X Software can export data from the database in a variety of formats, many of which can be imported by major third-party data storage and analysis applications.
Note: The GeneMapper ID-X Software includes a command-line interface that can be useful when integrating the software into an existing LIMS. The interface allows you to automate most of the software operations using a scripting language or batch file so that most maintenance and data-entry tasks can be minimized or eliminated. For more information, see Appendix A, “Operating the Software from a Command Line,” on page 91.
Maintaining the Database
Use the Database Dashboard software (described on page 79) to perform routine maintenance. You do not need Oracle training to use the Database Dashboard software. However, Applied Biosystems recommends that the maintenance of the Oracle Database be performed by a certified Oracle Database Administrator.
Advanced Oracle
Database Tools
The Oracle Corporation provides tools to optimize the performance of the Oracle Database. Applied Biosystems recommends use of these tools only by a certified Oracle database administrator.
Oracle
Documentation
Additional documentation for the Oracle Database is available at
Using the Database Dashboard Software
The Database Dashboard Software installed with the full version of the GeneMapper ID-X Software (software and database) provides tools for maintaining the GeneMapper ID-X Software database that reside in the Oracle Database.
Note: The Database Dashboard software is not installed on client computers.
This section describes: • Dashboard Features
• Setting a Dashboard Password
Dashboard Features
The Database Dashboard includes the:
• Dashboard tab– Provides information about database performance, space utilization, and operating systems usage. The traffic light displays the current state of the database.
• Report tab– Provides a comprehensive view for
troubleshooting the Oracle Database database. The top of the report provides a list of potential problems that the Database Dashboard software identifies.
• Administration tab– Provides a limited set of database administration functions.
• GeneMapper ID-X tab– Provides statistical summaries and tools for the GeneMapper ID-X Software database.
Chapter 4 Maintaining the Software and Database Application Using the Database Dashboard Software
Setting a Dashboard Password
On all multi-user database computers, log in to the Database Dashboard and set a password to ensure that only authorized users can access the Database Dashboard software.
Note: The Database Dashboard software is not installed on client computers.
1. SelectStartAll ProgramsApplied Biosystems
Database DashboardDashboard.
2. Click Yes when asked if you want to set a password.
3. Enter the password: password.
4. Click OK.
IMPORTANT! Do not lose the password for the Database Dashboard software. Applied Biosystems cannot retrieve passwords.
Starting the Database Dashboard
Note: You must log in to GeneMapper ID-X Software at least once before starting the Database Dashboard for the first time.
1. SelectStartAll Programs
Applied BiosystemsDatabase DashboardDashboard.
Reviewing the Database Statistics
Review database statistics weekly to determine if database maintenance is required.
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the GeneMapper ID-X tab.
3. Select the Database Statistics tab (see below).
The Database Statistics table displays statistics for the GeneMapper ID-X Software database. The statistics are
approximate values that are calculated based on the space that is allocated for the database, including tables and indexes.
The columns of the Database Statistics table provide storage space information on the three tables (Audit Data, Project Data, and Reference Data) used by the GeneMapper ID-X Software database to store data.
Table Name Stored Content
Audit Data Audit records generated from changes made to the software (if auditing is turned on).
Project Data Projects, including samples and results data.
Reference Data Supporting data (analysis methods, size standards, panels, bin sets, matrices, and so on).
Chapter 4 Maintaining the Software and Database Application Allocating Disk Space
4. Review the content of the Database Statistics table for each category of data and determine whether or not database maintenance is required, based on the instructions in the following table:
Allocating Disk Space
This section describes:
• Options for Creating More Disk Space • Allocating Additional Disk Space
The Database Dashboard allows you to allocate additional space on the hard drive of a a computer that does not contain Data Collection
Used(%) Value (Used/ Allocated) Auto Extend Value Required Action
>80% Yes Allocate more space for data as explained in “Allocating Additional Disk Space” on page 84, if: • Used (MB) is approaching
Allocated (MB), or
• Free disk space on the current drive is low. Allocate space on another drive.
No Allocate more space for data, as explained in “Allocating Additional Disk Space” on page 84.
Options for Creating More Disk Space
When the Used (%) value of any database table approaches 80%: • Allocate additional hard disk space for the GeneMapper ID-X
Software database,
or
• Export and delete existing data objects to provide more room for new projects and settings.
Note: If available space on the computer’s hard disk is insufficient for allocation, you must export and remove data.
Table 16 indicates the data objects that you can export to increase the free space of the corresponding GeneMapper ID-X Software
database tables.
Table 16 Exportable data objects
To export audit data, see “Backing Up, Removing, and Restoring Audit Records” on page 63.
To export project data and reference data, see the
GeneMapper® ID-X Software Help.
Table Name Exportable Data Objects
Audit Data Audit records
Project Data Projects
Reference Data • Analysis methods • Binsets
• Matrices
• Kits, panels, and markers • Plot settings
• Size-standard definitions • Report settings
Chapter 4 Maintaining the Software and Database Application Allocating Disk Space
Allocating Additional Disk Space
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Dashboard tab.
3. In the Connections pane, determine if any users (clients) are logged on to the GeneMapper ID-X Software.
4. Before you continue, instruct all users to log off the GeneMapper ID-X Software.
5. Select the GeneMapper tab, then select the Database Statistics tab.
6. At the bottom of the Database Dashboard, select the Default Allocation tab.
Note: The Allocation feature is not available if the GeneMapper®ID-X Software is co-installed with the Data Collection Software.
8. In the Table Space drop-down list, select a database table.
Note: The Project Data table has three subdivisions that can be allocated separately in the Custom Allocation tab to optimize allocation. For information on refining the allocation of the Project Data tables, see the Database Dashboard Help.
9. In the Add Disk Space (MB) scroll box, click the up (down) arrow to increase (decrease) the disk space for the selected table space. You can also enter a number.
IMPORTANT! After disk space has been allocated by clicking
Allocate, the disk space cannot be reduced. You can use the allocation feature at a later date to increase the allocated space further, but you cannot undo a previous disk space allocation.
Chapter 4 Maintaining the Software and Database Application Viewing Project Statistics
11. In the Alert dialog box, click Yes.
IMPORTANT! Allocating disk space cannot be undone.
12. Wait until the progress bar indicates that the allocation is complete, then select DatabaseRefresh (or press Alt+R) to refresh the screen and verify that the software has updated the Database Statistics table.
Viewing Project Statistics
Use the Database Dashboard Software to view summary statistics for the projects that are stored by the GeneMapper®ID-X Software
database.
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the GeneMapper
tab.
3. Select the Project Statistics tab to display the project types and number of samples for each project type.
Backing Up the Database
This section describes:
• When to Back Up the Oracle Database • Backing Up (Exporting) the Database • Restoring (Importing) the Database
When to Back Up the Oracle Database
Applied Biosystems recommends that you back up the Oracle Database onto an external storage medium (for example, 4-mm tape) frequently, depending on software use.
Note: The Security Manager settings are not backed up when you back up the database. Back up Security Manager settings separately as an exported file. See “Exporting and Importing the Security Settings” on page 44 for more information.
Backing Up (Exporting) the Database
IMPORTANT! The disk space required for backup can be 60 to 70% of the size of the database. The database size is the Allocated Space displayed in the Dashboard tab.
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Dashboard tab.
3. In the Tablespace pane (lower left of the tab), note the Allocated Table Space.
4. Review your backup medium to ensure that you have space available to back up at least 60 to 70 percent of the Allocated Table Space noted in step 3.
5. In the Connections pane, determine if any users (clients) are logged on to the GeneMapper ID-X Software.
Chapter 4 Maintaining the Software and Database Application Backing Up the Database
6. Before you continue, request and ensure that all users are logged off the GeneMapper ID-X Software.
7. In the Database Dashboard window, select the Administration
tab.
8. In the navigation column of the Administration tab, select
AdministrationExport Database.
9. In the Full Database Backup pane, click Browse, navigate to the desired location, enter a name for the backup file, then click
Open.
Note: Ensure that you have available for backup at least 60 to 70% of the Allocated Table Space indicated in the Dashboard tab.
10. Click Export, then wait for the software to complete the operation. The software displays the progress of the export operation in the Log View field.
Restoring (Importing) the Database
IMPORTANT! When you restore the database, you erase the current data and recreate the database. You lose all existing data when you import the data from the exported *.dmp file.
After backing up (exporting) the database, you can import the resulting *.dmp file to recreate the database.
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Administration
tab.
3. In the navigation column of the Administration tab, select
AdministrationImport Database.
4. Click Browse, navigate to the desired location, select the correct .dmp file, then click Open.
5. In the Full Database Restore settings, click Check. The Database Dashboard Software runs a check to ensure that the .dmp file you are importing matches your system configuration. If the software displays an error message, the drive partitions of your computer do not match the original configuration, or they cannot support the amount of data you are attempting to restore. The software displays the required structure in the import log (the field below the Import controls). Click OK, correct the problem, then import again.
6. Click Import.
The software displays a message indicating the location of the batch file it creates to perform the import.
7. Make a note of the location of the batch file, then click OK.
8. Exit the Database Dashboard Software.
9. In Windows Explorer, navigate to the batch file, then
double-click the file to run it. The software runs SQL scripts to import the data into the database.
Chapter 4 Maintaining the Software and Database Application Generating a Database Report
Generating a Database Report
1. Start the Database Dashboard (see page 80).
2. In the Database Dashboard window, select the Report tab.
3. To print the report, click Print.
4. To e-mail the report, click E-mail, enter the e-mail address, then click OK.
5. To save the report as an HTML or tab-delimited text file:
a. Click Save.
b. In the Save dialog box, navigate to the desired destination directory.
c. Enter a name for the exported file.
d. Select the desired file format (HTML or tab-delimited text).
Operating the Software
from a Command Line
This appendix covers:■ Operating the Software from a Command Line . . . 92
■ Example Commands . . . 97
Appendix A Operating the Software from a Command Line Operating the Software from a Command Line
Operating the Software from a Command Line
Overview
This appendix explains how to analyze, import, and export data from the command-line interface of the GeneMapper®ID-X Software.IMPORTANT! Applied Biosystems supports the use of the command-line interface only as it is explained in this appendix.
Note: If you are unfamiliar with Microsoft DOS,
Applied Biosystems does not recommend using the command-line interface. Use the command-line interface only if you are an advanced user (systems administrator, bioinformatician, network administrator).
About the
Command-Line
Interface
The GeneMapper ID-X Software command-line interface can automate most software operations without using the graphic user interface. Commands can automate data-entry tasks associated with project analysis (for example, creating a project adding samples, and specifying analysis parameters).
Command Syntax
Commands are issued to the GeneMapper ID-X Software command-line interface in the MS DOS shell of the Windows operating system. The basic formula for all commands is:<GeneMapper.exe> -commandline <arguments>
where:
• <GeneMapper.exe> is the path and filename of the executable file for the GeneMapper ID-X Software.
Creating a Batch File to Run the Command-Line Interface
1. In the desktop, select
StartAll ProgramsAccessoriesNotepad.
2. In the Notepad window, enter @ECHO OFF to instruct the operating system to hide the batch file commands as they are executed.
Note: If you want the operating system to display each command in the MS DOS prompt as it is executed, replace @ECHO OFF with @ECHO ON. The @ECHO ON command can be useful when troubleshooting batch file errors. If the software encounters an error when executing the commands in the batch file, you can review the contents of the batch file to identify the offending command.
3. Press Enter to create a new line.
4. In the Notepad window, enter the following:
IMPORTANT! Always enclose italic text in double quotes (“This is an example”). The quotations allow the software to accommodate spaces in the user-defined text.
where:
• GeneMapper.exeis the directory path for the GeneMapper ID-X Software executable (enclosed in double quotes).
• –commandline signals the exe to run the command line. • –option h instructs the command line to execute without
displaying the GeneMapper®ID-X Software user interface. @echo off
“GeneMapper.exe” -commandline -option h -username “user” -password “password” -project “project”
Appendix A Operating the Software from a Command Line Operating the Software from a Command Line
• –username and –password instruct the command line to log in with user and password, a user account with privileges sufficient to perform the desired functions (enclosed in double quotes).
IMPORTANT! User names and passwords are case- sensitive. That is, “User1” is considered different from “user1.”
• –project instructs the software to create or analyze a project named project (enclosed in double quotes). For example:
5. After the -project argument, enter any additional arguments to instruct the GeneMapper ID-X Software to perform the desired functions. See “Command-Line Arguments” on page 100 for a complete list of all arguments.
When you enter arguments:
• Add them to the command in any order.
• Enter all arguments on the same line of text (the command cannot contain hard or soft returns).
• Enclose the user-defined component of arguments in double quotes (for example: -project “my project”).
• Separate all arguments using a space (ASCII character 32).
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline - option h -username “gmidx” -password “password” –project “myProject”
7. (Optional) After entering the last command:
a. Press Enter to create a new line.
b. Enter ECHO Batch file operation complete.
c. Press Enter to create a new line.
Note: See “Example #2: Analyze Sample Files with Named Ladders” on page 98 for an explanation of the example batch file.
8. Carefully review the text of the batch file for any errors or typos.
9. When satisfied with the content of the file, save the text as a batch file:
a. Select FileSave.
b. In the File name field, enter a name for the batch file with a