Advertisement
Advertisement
ADMINISTRATOR’S GUIDE
GeneMapper
®
ID-X
Software
Version 1.5
Publication Number
100031703
Revision
A
For Research, Forensic Paternity and Cell Line Authentication.
Not for use in diagnostic and therapeutic applications.
The information in this guide is subject to change without notice.
DISCLAIMER
LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT,
EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR
NON-INFRINGEMENT. TO THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) BE
LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL,
INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING
BUT NOT LIMITED TO THE USE THEREOF.
Limited Use Label License No. 540: Sequencing or Fragment Analysis Intellectual Property for Human Identity Testing Software
Notice to Purchaser: No right to resell this software product, any upgrades, modified versions, updates, additions, copies, or any of its components is conveyed expressly, by implication, or by estoppel. This software product may be used to perform internal research and development for the sole benefit of the purchaser; provided, however, that Life Technologies Corporation (“LTC”) does not convey any right or license, whether expressly, by implication, by estoppels, or otherwise, under any LTC patents that claim DNA sequencing or fragment analysis methods, to the purchaser by the purchase of this software product to use such DNA sequencing or fragment analysis methods.
This software product is not for use in commercial applications of any kind, including, without limitation, quality control and commercial services such as reporting the results of purchaser’s activities for a fee or other form of consideration, except as follows. A limited license to use the DNA sequencing or fragment analysis methods covered by such patents can be obtained for certain research and development activities (a) through the purchase of certain LTC reagents that convey rights for commercial use (e.g., LTC kits for performing human identity testing and LTC kits for performing in vitro diagnostics testing) when such reagents are used on an authorized LTC instrument, or (b) directly from LTC. In addition, LTC grants the purchaser a limited right to use this software product in conjunction with: (1) a second product purchased from LTC or that conveys rights for commercial use (e.g., LTC kits for performing human identity testing and LTC kits for performing in vitro diagnostics testing) and (2) an authorized LTC instrument that conveys rights for commercial use to perform services on a fee per test or contract basis. For information on obtaining additional rights, please contact [email protected] or Out
Licensing, Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008.
TRADEMARKS
All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.
This product includes software developed by the Apache Software Foundation.
This product includes software developed by the ExoLab Project.
JNIRegistry is copyrighted © by ICE Engineering, Inc.
Microsoft and Windows are registered trademarks of Microsoft Corporation.
Oracle is a registered trademark of Oracle Corporation.
GeneMapper ®
ID-X
Software v1.5 has undergone a verification process pursuant to Life Technologies Corporation and/or its affiliate(s) internal quality process. However, we recommend that customers installing or using GeneMapper ® ID-X Software v1.5 perform any internal validation testing they deem necessary according to relevant guidelines. Each laboratory is solely responsible to ensure that its GeneMapper ®
ID-X
Software v1.5 satisfies or will satisfy SWGDAM Guidelines or other applicable guidelines and is fit for each laboratory’s applications.
© 2015 Thermo Fisher Scientific Inc. All rights reserved.
Contents
Chapter 1
About This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Setting Up User Accounts and User Access. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
GeneMapper ® ID-X Software Electronic Data Chain-of-Custody
Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Overview of the Security System . . . . . . . . . . . . . . . . . . . . . . . . . 11
Default Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Default Security Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Default User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Default User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Starting the Security Manager . . . . . . . . . . . . . . . . . . . . . . . . 20
Setting Password Policies . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Setting Up User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Using Default User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . 24
Creating New User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . 26
Using Security Groups to Control Data Access . . . . . . . . . . . . . . 29
Customizing Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Creating Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Editing or Deleting Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Profile Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Customizing User and Security Groups . . . . . . . . . . . . . . . . . . . . 39
Creating User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Creating Security Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
3
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2
Chapter 3
Maintaining User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Editing User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Changing the Password for a User Account . . . . . . . . . . . . . 44
Deleting a User Account . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Activating, Deactivating, and Suspending User Accounts . . 46
Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Exporting and Importing the Security Settings . . . . . . . . . . . . . . 49
Managing the Audit Trail System . . . . . . . . . . . . . . . 51
Overview of the Audit Trail System . . . . . . . . . . . . . . . . . . . . . . . 52
Default Audit Map Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Using the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Starting the Audit Manager . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Configuring the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Printing an Audit Map Settings Report . . . . . . . . . . . . . . . . . 59
Audit Map Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Viewing Audit History Records . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Starting the Audit History Viewer . . . . . . . . . . . . . . . . . . . . . . 63
Creating Audit Record Queries . . . . . . . . . . . . . . . . . . . . . . . 64
Performing Audit Record Queries and
Viewing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Example Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Printing Audit Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Backing Up, Removing, and Restoring Audit Records . . . . . . . . 69
Managing the E-Signature System . . . . . . . . . . . . . . 71
Overview of the Electronic Signature (E-Signature) System . . . . 72
Default E-Signature Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Configuring the E-Signature System . . . . . . . . . . . . . . . . . . . . . . 73
Starting the E-Signature Manager . . . . . . . . . . . . . . . . . . . . . 74
Enabling the E-Signature Function . . . . . . . . . . . . . . . . . . . . 74
Configuring E-Signature Actions . . . . . . . . . . . . . . . . . . . . . . 76
E-Signature Action Maps . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
4
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4
Viewing E-Signature Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Specifying E-Signature Queries . . . . . . . . . . . . . . . . . . . . . . . 78
Performing E-Signature Queries and Viewing
E-Signature Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Printing E-Signature Records . . . . . . . . . . . . . . . . . . . . . . . . . 80
Backing Up, Removing, and Restoring E-Signature Records . . . 80
Maintaining the Software and Database Application . . . . . . . . . . . . . . . . . . . . . 81
Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Recommended Maintenance Schedule . . . . . . . . . . . . . . . . . 82
Using and Maintaining the Oracle ® Database . . . . . . . . . . . . . . . 83
Database Access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Maintaining the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Using the Database Dashboard Software . . . . . . . . . . . . . . . . . . 85
Dashboard Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Setting a Dashboard Password . . . . . . . . . . . . . . . . . . . . . . 86
Starting the Database Dashboard . . . . . . . . . . . . . . . . . . . . . 87
Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . . . . . . 88
Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Options for Creating More Disk Space . . . . . . . . . . . . . . . . . 90
Allocating Additional Disk Space . . . . . . . . . . . . . . . . . . . . . . 91
Viewing Project Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
When to Back Up the Oracle Database . . . . . . . . . . . . . . . . . 94
Backing Up (Exporting) the Database . . . . . . . . . . . . . . . . . . 94
Restoring (Importing) the Database . . . . . . . . . . . . . . . . . . . . 95
Generating a Database Report . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
GeneMapper ® ID-X Software Administrator’s Guide
5
Appendix A Operating the Software from a Command Line
Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Operating the Software from a Command Line Interface . . . . . 100
Creating a Batch File to Run the Command Line Interface . 101
Example Batch File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Running the Batch File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Example #1: Analyze Sample Files . . . . . . . . . . . . . . . . . . . 105
Example #2: Analyze Sample Files with Named Ladders . . 106
Example #3: Export Project Data . . . . . . . . . . . . . . . . . . . . . 107
Example #6: Export a Project . . . . . . . . . . . . . . . . . . . . . . . 110
Command Line Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Appendix B Documentation and support . . . . . . . . . . . . . . . . . 121
Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
How to obtain support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
6
GeneMapper ® ID-X Software Administrator’s Guide
About This Guide
Revision history
Revision
A
Date
March 2015
Description
New document for v1.5 software.
Replaces v1.0 Pub. no.
4376327.
GeneMapper ® ID-X Software Administrator’s Guide
7
About This Guide
8
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1
Setting Up User Accounts and User Access
Chapter 1
Chapter 2
■
■
■
■
■
■
■
■
This chapter covers:
■
GeneMapper® ID-X Software Electronic Data Chain-of-
Custody Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
■
■
Overview of the Security System . . . . . . . . . . . . . . . . . . . . . . 11
Default User Accounts, Profiles, User Groups, and Security
Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Setting Up User Accounts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Using Security Groups to Control Data Access . . . . . . . . . . . 29
Customizing Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Customizing User and Security Groups . . . . . . . . . . . . . . . . . 39
Maintaining User Accounts. . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Viewing the Security Report . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Exporting and Importing the Security Settings . . . . . . . . . . . . 49
Chapter 3
Chapter 4
Maintaining the Software and Database Application
GeneMapper ® ID-X Software Administrator’s Guide
9
Chapter 1 Setting Up User Accounts and User Access
GeneMapper
®
ID-X Software Electronic Data Chain-of-Custody Systems
GeneMapper
®
ID-X
Software Electronic Data
Chain-of-Custody Systems
The GeneMapper ® ID-X Software contains three systems that assist with chain-of-custody of electronic data. These systems can be custom-configured or turned off by the GeneMapper ® ID-X Software system administrator as needed:
• Security system – Controls user access to software functions and data, and allows custom configuration that meets the datasharing needs of your laboratory (described in this chapter)
• Audit Trail system – Tracks changes and provides audit history
reports (described in Chapter 2)
• E-Signature system – Requires user-authentication before
changes are saved (described in Chapter 3)
10
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Overview of the Security System
Overview of the Security System
The GeneMapper ® ID-X Software Security system allows you to control user behavior by specifying:
• What data a user can access , based on the user and security group(s) the user belongs to.
• What functions a user can perform, based on the user profile .
A user with an Admin profile sets up user accounts, profiles, user groups, and security groups using wizards in the Access Control
Administration window.
Security System
Components
The four components of the Security system are defined below.
Table 1 Components of the Security system
Component Description
User account All users log in to the software with a user account created by the GeneMapper ® ID-
X Software system administrator.
Profile A profile defines the set of software functions that a user is allowed to perform. For example, profiles can allow or deny a user the right to view, create, edit, delete analysis methods, or analyze data.
The system administrator configures profiles, or uses default profiles provided with the software. When the system administrator creates a user account, the administrator assigns a profile to the user.
Users can have only one profile.
User group
Security group
User groups are associated with security groups, which control the data a user can access. Users can access data assigned to a security group only if their user group is associated with the security group.
The system administrator defines user groups or uses default user groups provided with the software.
When a user account is created, the user must be assigned to at least one user group, but the user can be assigned to several groups.
Security groups determine the data that user groups can access. A user group must be associated with at least one security group, but can be associated with several.
A user can access only data (for example, analysis methods, panels, size standards, matrices, or projects) that have been saved with a security group that is associated with one of the user groups to which the user belongs.
GeneMapper ® ID-X Software Administrator’s Guide
11
12
Chapter 1 Setting Up User Accounts and User Access
Overview of the Security System
In summary:
• Each user has only one profile.
• Each user belongs to one or more user groups and each user group is associated with one or more security groups.
• Security groups associated with a user group and data determine the data a user can access.
Therefore:
• A user can access the data in a security group that is associated with any of the user groups to which the user belongs.
• A user can perform any of the software functions permitted by the user’s profile.
User
Profile
A user can perform actions allowed by the user’s profile
User group
Users
A
Security groups
B
Security group Security group
A
Data
C cannot access
Users in a user group can access the data of the security groups associated with the user group
Data Access
Control
Security groups control access to any of the following items:
• Projects
• Plot settings
• Table settings
• Panels and binsets
• Report settings
• Size standards
• Analysis methods
• Matrix files
Items are associated with a security group when a user creates or edits, then saves the item (described on the next page).
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Associating a
Security Group with an Item
Whenever users save an item, they must select a security group from a drop-down list in the Save or Save As dialog box. Users can select the GeneMapper ID-X security group (available to everyone) or any other security group that they are allowed to use (see below).
For example, the figure below shows the drop-down list that appears when a user with access only to the Casework and GeneMapper ID-X security groups saves a new project.
Bypassing
Security Group
Access Control
If you do not want to control access to data in your laboratory, instruct all users to specify the GeneMapper ID-X security group when creating projects and settings. All users have access to items associated with the GeneMapper ID-X security group.
Default User Accounts, Profiles, User Groups, and
Security Groups
We provide default user accounts, profiles, user groups, and security groups so that you can use the Security system with minimal setup.
You can use the defaults without changes or as a starting point to customize your own Security system.
Note: If your GeneMapper ® ID-X Software system administrator has modified the default user accounts, profiles, user groups, and/or security groups, the tables in this section may no longer be accurate.
GeneMapper ® ID-X Software Administrator’s Guide
13
Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
The discussion in this section covers the default profiles, user groups, and security groups provided by the GeneMapper ® ID-X
Software. With these defaults, a system administrator can quickly create a working Security system.
Duplicating
Defaults Before
Modifying
Before modifying a default component of the Security system, duplicate it and save it under a new name.
To duplicate any default component, open the Security Manager, select the default, then select Edit Duplicate .
You will need to duplicate the default user accounts multiple times to provide each user with an account that has a unique or laboratory-specific login name.
Relationship
Between User
Accounts,
Profiles, and User
Groups
A user’s account determines what the user can do (profile) and access (user groups). Profiles and user groups must exist before you can create any accounts.
The GeneMapper ® ID-X Software system administrator is responsible for maintaining profiles and user groups. The administrator can:
• Use default profiles and user groups provided by the
GeneMapper ® ID-X Software.
• Create custom profiles and user groups.
• Use a combination of defaults and custom profiles, user groups, and security settings.
14
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Default Profiles
The profile that is specified in a user account determines the software functions a user can perform. Four default profiles are provided.
Note: If your GeneMapper ® ID-X Software system administrator has modified or customized the default profiles, they may differ from the defaults described in Table 2.
Table 2 Default profiles – actions allowed and not allowed
Profile
Technician/
Read Only
Analyst
Actions Allowed Actions Not Allowed
• Open, view, and export projects, analysis methods, panels, matrices, and size standards associated with the security groups that the user is permitted to access
• Generate reports
• Create, edit, delete, export, and import table settings, plot settings, and report settings associated with the security groups that the user is permitted to access
• Use the CODIS Export Manager
• Create projects
• Add samples to projects
• Create, edit, or change settings in a project (analysis method, panel, size standard, matrix)
• Analyze data
• Override GQ, CGQ, or SQ
• Edit allele labels
• Perform Remote Shutdown
• Add profiles to the Profile Manager
• Access and manage the Security,
Audit Trail, and E-Signature systems
All actions allowed for the
Technician/Read Only profile, plus:
• Create, import, edit, or delete projects, panels, matrices, and size standards associated with the security groups that the user is permitted to access
• Edit sizing range and analysis range in analysis methods
• Save or Save As analysis methods
• Add samples to projects
• Change selections in a project
(analysis method, panel, size standard, matrix)
• Analyze data
• Edit alleles
• Override SQ, GQ, and CGQ
• Create a new analysis method
• Edit analysis method parameters other than sizing range and analysis range
• Add profiles to the Profile Manager
• Access and manage the Security,
Audit Trail, and E-Signature systems
GeneMapper ® ID-X Software Administrator’s Guide
15
Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Table 2 Default profiles – actions allowed and not allowed (continued)
Profile
Scientist
Admin
(Administrator)
Actions Allowed Actions Not Allowed
All actions allowed for the Analyst profile, plus:
Access and manage the Security, Audit
Trail, and E-Signature systems
• Create or modify/save analysis methods
• Add profiles to the Profile Manager
All possible actions, which include:
• Access and manage the Security,
Audit Trail, and E-Signature systems
• All GeneMapper ® ID-X Software functions
None
Default Security Groups
The security groups specified in a user account determine the:
• Specific data (for example, analysis methods, panels, size standards, matrices, and projects) that a user can access.
• The read (view or select) or update (create, edit, delete, analyze) privileges allowed for the data.
The read/update privileges associated with a security group can clash with the actions permitted in user profiles (profiles also define read/write privileges). For this reason, all of the default security groups have both read and update privileges.
IMPORTANT!
There are software functions (for example, changing table or plot settings) that are not covered in profiles. You can use security group update privileges to control use of these functions.
The software contains three default security groups:
• GeneMapper ID-X (read and update)
• Casework (read and update)
• Databasing (read and update)
When users create or edit and then save an item, they select a security group from a drop-down list in the Save dialog box. Users can select any of the three default security groups to which they have access.
16
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Security group definitions are just names. Their significance depends entirely on the user groups they are associated with. When a user saves an item and assigns it a security group, it means that:
• Any user in any user group that is associated with that security group can access the data.
• Users who are only in user groups that are not associated with the selected security group cannot access the data.
Default User Groups
Four default user groups are associated with the default security groups.
Note: If your GeneMapper ® ID-X Software system administrator has modified or customized the default user groups, they may differ from the defaults described in Table 3.
Table 3 Default user groups and associated security groups
Default User
Group Name
Security Group/Privileges ‡
Read = View or select
Update = Create, edit, delete, analyze
GeneMapper ID-X /read+update
Accessible Data
All Users
Casework
Users
Casework/read+update
GeneMapper ID-X /read+update
Data assigned to the GeneMapper ID-X security group
Private data assigned to the Casework security group
Data assigned to the GeneMapper ID-X security group
Databasing
Users
Databasing/read+update
GeneMapper ID-X /read+update
Private data assigned to the Databasing security group
Data assigned to the GeneMapper ID-X security group
All data Administrators Casework/read+update
Databasing/read+update
GeneMapper ID-X /read+update
Admin/read+update
‡ A Practice user group and a Practice security group are also provided for use with the Getting Started
Guide.
GeneMapper ® ID-X Software Administrator’s Guide
17
Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
Default User Accounts
IMPORTANT!
If you migrate to the GeneMapper
®
ID-X Software from GeneMapper ® ID Software v3.1 or v3.2, user accounts from v3.1 or v3.2 are deleted and not available in the GeneMapper ® ID-X
Software. You must create new user accounts in the GeneMapper ®
ID-X Software.
Nine default user accounts are provided with the software. Each of these accounts has a profile and one or more user groups assigned.
Table 4 describes the intended user for each of the nine accounts.
Note: If your GeneMapper ® ID-X Software system administrator has modified or customized the default user accounts, they may differ from the defaults described in Table 4.
Table 4 Default user accounts
Default User Account
Name ‡
Intended User
Casework Tech
Databasing Tech
Casework Analyst
Databasing Analyst
Casework Tech Lead
Databasing Tech Lead gmidx
User who requires read-only access to the software. This user account does not allow analysis or changes to the software but does allow viewing, reporting, printing, and exporting data.
User who requires access to analyze (with limited ability to change analysis settings), view, edit, report, and print data.
User who requires full access to all functions of the software: analyze, view, edit, report, and print data; and all administrative functions: Security
Manager, Audit Manager, and E-Signature Manager.
Default user account with full access to all functions of the software: analyze, view, edit, report, and print data; and all administrative functions:
Security Manager, Audit Manager, and E-Signature Manager.
Administrator For Technical Support use only.
‡ A Practice user account with Scientist profile is also provided for use with the Getting Started Guide.
To add a new account for a user that matches one of these
descriptions, see “Using Default User Accounts” on page 24.
18
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Default User Accounts, Profiles, User Groups, and Security Groups
For more detail about the profiles, user groups, and security groups for the default user accounts, see Table 5.
Note: If your GeneMapper ® ID-X Software system administrator has modified or customized the default user accounts, profiles, user groups, and/or security groups, user access may differ from the defaults described in Table 5.
Table 5 Default user accounts – data access allowed
User Account
Casework Tech
Casework
Analyst
Casework Tech
Lead
‡
Databasing Tech
Databasing
Analyst
Databasing Tech
Lead
Profile
Technician/
Read Only
Analyst
Admin
Technician/
Read Only
Analyst
Admin
Belongs to User Groups
All Users
Casework Users
All Users
Casework Users
All Users
Casework Users
All Users
Databasing Users
All Users
Databasing Users
All Users
Databasing Users
Security Group/Privileges
Read = View or select
Update = Create, edit, delete, analyze
GeneMapper ID-X /read+update
Casework/read+update
GeneMapper ID-X /read+update
Casework/read+update
GeneMapper ID-X /read+update
Casework/read+update
GeneMapper ID-X /read+update
Databasing/read+update
GeneMapper ID-X /read+update
Databasing/read+update
GeneMapper ID-X /read+update
Databasing/read+update gmidx
Administrator
Admin All Users
Casework Users
Databasing Users
Administrators
GeneMapper ID-X /read+update
Casework/read+update
Databasing/read+update
Admin
‡ A Practice user account with Scientist profile is also provided for use with the Getting Started Guide. It is associated with the Practice user group and Practice security group.
GeneMapper ® ID-X Software Administrator’s Guide
19
Chapter 1 Setting Up User Accounts and User Access
Getting Started
Getting Started
When you set up the Security system for the first time, open the
Security Manager and set password policies.
Starting the Security Manager
To access the Security Manager, you must log in with an account that belongs to the Administrators user group and has an Admin profile.
1.
Select Start All Programs Applied Biosystems
GeneMapper GeneMapper ID-X .
2.
In the Login to GeneMapper ID-X dialog box, log in with an account that belongs to the Administrators user group and has an Admin profile. For example, use the gmidx user account: a.
User name – Enter or select gmidx . User names are not case-sensitive.
b.
Password – Enter the temporary password password .
Passwords are case-sensitive.
Note: The gmidx account requires that you set a new password when you log in for the first time. If you follow this procedure after first log in, the password for the account may be different than password . c.
Click OK .
3.
If prompted, specify a new password. Keep a record of the new password.
We cannot retrieve passwords. Do not lose the new password for the gmidx account. This account can be used to reset passwords for other accounts. We cannot reset the password for the gmidx account if it is lost.
4.
In the main window, select Admin Security Manager.
20
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Getting Started
5.
In the AdminToolAcc dialog box, log in with the gmidx account
OK . The Access Control
Administration window opens (below):
The File New Application command and the
Applications folder in the navigation pane are for Technical Support use only. Using these functions interferes with proper software operation.
GeneMapper ® ID-X Software Administrator’s Guide
21
Chapter 1 Setting Up User Accounts and User Access
Getting Started
Setting Password Policies
Password policies apply to all user accounts.
1.
Start the Security Manager (see page 20).
2.
Select Settings Password Policies .
3.
In the Password Policies dialog box, specify the password
settings (see Table 6 on page 23), then click
Save Changes .
22
4.
Close and restart the software to apply the changed settings.
Note: Settings are not applied until you close and restart the
GeneMapper ® ID-X Software.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Getting Started
Table 6 Password policies settings
Setting Description
Max Login
Attempts
Send log message
Set User State
– Remain active
Set User State
– Suspend for
___ min(s)
Attempts
Enter the number of failed login attempts that the software allows before suspending the user account. Works in conjunction with the User State.
Records the failed login attempts to the security log.
The security information for the GeneMapper ® ID-X Software is written to the
<drive>:\AppliedBiosystems\GeneMapperID-X\GeneMapper_Log.txt file.
Disables the “Maximum Login Attempts” setting. A user is allowed unlimited attempts to log in.
Suspends the user account for the specified number of minutes after a user exceeds the maximum login attempts. The user must wait for the specified number of minutes to elapse before attempting another login.
Note: If a user exceeds the maximum number of login attempts, you can reactivate the user account before the specified time period elapses as explained
in “Activating, Deactivating, and Suspending User Accounts” on page 46.
Password
Lifetime
Password
Grace Logins
Password
Retires the password of each user account after the specified number of days elapses. If this parameter is not selected, passwords do not expire.
Note: After retiring a password, the software automatically prompts the user to create a new password at the next login.
Enter the number of times that a user can delay changing the password after the software prompts the user to change it. After a user exceeds the specified number of grace logins, the software requires the user to change the password.
Password Reusability
Password
Reuse Period
Passwords kept per user
Allows a user to reuse a former password after the specified number of days has elapsed since its last use.
Enter the number of former passwords per user that the Security Manager should store.
Minimum
Password width
Password Format
Enter the minimum number of characters required in the password (alphanumeric, case-sensitive).
GeneMapper ® ID-X Software Administrator’s Guide
23
Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
Setting Up User Accounts
After setting password policies, you can:
• Accept and use all the default settings by duplicating a default user account, renaming it, and using it without further modification, or
• Create an entirely new user account, using any combination of defaults and your own custom settings.
Using Default User Accounts
To set up your Security system using the defaults for user accounts, profiles, user groups, and security groups, follow these steps:
1.
Start the Security Manager (see page 20).
2.
Select the default user account type that fits the new user (see
Table 2, “Default profiles – actions allowed and not allowed,” on page 15). For example, select Casework Analyst .
3.
Select Edit Duplicate to open the User Properties dialog box
(shown on the next page).
4.
In the Name field, replace the name “Clone of Casework
Analyst(1)” with the login name for the new account. For example, enter User1 . The login name is not case-sensitive and must be
≤
30 characters.
Note: You cannot create a user account with the same name as a user account that has been previously deleted.
24
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
5.
Set other values:
• (Optional) In the Description field, enter a description of the user account (
≤
1023 characters).
• In the Full Name field, enter the user’s real name.
• (Optional) Select Show EULA to display the End User
License Agreement (EULA) when the user logs in.
• Leave Status set to Active .
• (Optional) Select Pre-Expire to ensure that a user logging in to an account for the first time is prompted to change the password.
6.
Click Set Password .
GeneMapper ® ID-X Software Administrator’s Guide
25
Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
7.
In the Change Password dialog box, enter a new password twice, then click OK .
8.
Without making any other changes in the Access Control
Administration window, select File Save .
Note: Settings are not applied until you close and restart the software.
The new user account has the same profile and group associations as the default Casework Analyst user account.
Creating New User Accounts
Using Custom
Settings
If you will use the default profiles, user groups, and security groups,
skip to “Creating a User Account” on page 26.
If you want to use custom profiles, user groups, and/or security groups, you must create them before creating new user accounts.
To create custom:
• Profiles, see “Customizing Profiles” on page 31.
• User groups and security groups, see “Customizing User and
• User group/security group associations, see “Creating a New
Creating a User
Account
After you create any custom profiles, user groups, and/or security groups that you want to use:
1.
Start the Security Manager (see page 20).
2.
Select File New User .
26
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
3.
In the Create User wizard, click Next to open the Name page.
4.
In the Name field, enter the login name for the new account. For example, enter User1 . The login name is not case-sensitive and must be
≤
30 characters.
Note: You cannot create a user account with the same name as a user account that has been previously deleted.
5.
Set other values:
• (Optional) In the Description field, enter a description of the user account (
≤
1023 characters).
• In the Full Name field, enter the user’s real name.
• (Optional) Select Show EULA to display the End User
License Agreement (EULA) when the user logs in.
• Leave Status set to Active .
• (Optional) Select Pre-Expire to ensure that a user logging in to an account for the first time is prompted to change the password.
6.
Click Set Password .
GeneMapper ® ID-X Software Administrator’s Guide
27
Chapter 1 Setting Up User Accounts and User Access
Setting Up User Accounts
7.
In the Change Password dialog box, enter a new password twice, then click OK .
8.
In the Control Properties section, select the profile for the user.
9.
Click Next to open the User Groups page.
28
10.
Select the user groups for the user. If you have previously
associated user groups and security groups (see “Using Custom
Settings” on page 26), this selection also designates the security
groups for this user.
11.
Click Next to see a summary of the account, then click Finish .
Note: Settings are not applied until you close and restart the software.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Using Security Groups to Control Data Access
Using Security Groups to Control Data Access
In the GeneMapper ® ID-X Software, a user associates security groups with data items (such as analysis methods, table settings, plot settings, matrices, size standards, or report settings) when the user saves a data item to which he or she has access. Only users in user groups associated with that security group can later access the data items.
Using Open
Access
If you want all users to have access to all data, instruct your users to select the GeneMapper ID-X security group when they save data.
The data associated with this security group are accessible to every user.
Using Access
Control
If you want to restrict user access to data, instruct users to select a security group associated with their user group. For example, you can instruct the users in the Casework Users group to select the
Casework security group when they save items.
Changing the
Security Group
Default
The security groups that a user can select to associate with a data item (when saving the data item) include the GeneMapper ID-X security group as the default. However, any user can change the security group that appears as the default choice when he or she saves a data item.
1.
In the main window, select File Project Options to open the
Options dialog box.
2.
Select the General tab.
3.
In the Data Access Control pane, select the new default from the drop-down list.
4.
Click OK .
The new security group default applies only to the user who reset the default, unless the default is reset by a user who is a member of only one user group (other than the All Users group). In this case, the default applies to all other users who have identical group membership.
GeneMapper ® ID-X Software Administrator’s Guide
29
30
Chapter 1 Setting Up User Accounts and User Access
Using Security Groups to Control Data Access
For example, if you use accounts like those listed on page 19, and a
Casework Tech sets Casework as the new security group default, that will also become the default for Casework Analysts and Casework
Tech Leads. All other users continue to have the GeneMapper ID-X security group as default.
Changing the
Security Group
Association for a
Data Item
A user can change the security group associated with one or more data items if the user’s profile allows changing the data items.
To change the security group associated with a data item:
1.
In the main window, select Tools GeneMapper ID-X
Manager to open the GeneMapper ID-X Manager.
2.
Select the appropriate tab, then select the item to change.
3.
Click Open .
4.
Change the Security Group setting (for items that contain multiple tabs, the Security Group setting is in the General tab).
5.
Click OK .
Changing the
Security Group
Association for a
Project
A user can change the security group associated with a project if the user’s profile allows the user to change the project. However, the user must save the project with a new name.
1.
In the main window, select Tools GeneMapper ID-X
Manager to open the GeneMapper ID-X Manager.
2.
Select the Projects tab.
3.
Select the project to change.
4.
Click Save As .
5.
Enter a new name for the project, select a new security group, then click OK .
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Customizing Profiles
Profiles determine the software functions that a user can perform.
We recommend that you use the default profiles described in
“Default Profiles” on page 15, even if you use custom user and/or
security groups.
However, if the default profiles do not suit your needs, you can create custom profiles.
This section describes:
• Editing or Deleting Profiles
Creating Profiles
To create a custom profile, you can:
• Duplicate an existing default profile, then edit it to meet your requirements.
• Create a new profile.
We recommend that you duplicate a default profile, rename it, and then customize it, rather than change the default profile.
Duplicating and
Editing a Default
Profile
To base a new profile on an existing default profile (see Table 2,
“Default profiles – actions allowed and not allowed,” on page 15):
1.
Start the Security Manager (see page 20).
2.
In the navigation pane of the Access Control Administration window, select the profile to duplicate.
3.
Right-click, then select Duplicate (or select Edit Duplicate ).
4.
Select the Clone of ....
profile in the navigation pane.
5.
In the Profile Properties section, change the profile’s name and modify the settings as needed.
6.
Select File Save .
GeneMapper ® ID-X Software Administrator’s Guide
31
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Creating a Profile
1.
Start the Security Manager (see page 20).
2.
Select File New Profile .
3.
In the Create Profile wizard, click Next .
4.
Enter a Name (
≤
30 characters) and Description (
≤
1023 characters) for the new profile.
5.
In the Installed Elements table (shown on the next page), assign permissions to the new profile for the GeneMapper ID-X module based on the actions allowed in profiles (see Table 7 on page 36 and Table 8 on page 37): a.
For the GeneMapper ID-X module, select OIR (Override
Inherited Rights) , then select Execute . All functions are automatically set to Execute. See page 33 for an explanation of OIR.
b.
For each function you want to disable , select OIR
(Override Inherited Rights) , then deselect Execute .
6.
When you finish, click Next , then click Finish to complete the profile setup.
7.
Select File Save .
Note: Settings are not applied until you close and restart the software.
When you create a profile, do not set the
FoundationDataCollection module. This module is for Technical
Support use only.
32
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Do not set
To enable a action, select OIR and Execute .
To disable an action, select OIR and deselect
Execute .
Override Inherited
Rights (OIR)
The permissions listed in the Installed Elements tables can be
“inherited” in one of two ways:
• All actions ( ) are children of either an action group ( ) or an application ( ).
• Action groups ( ) are children of applications ( ).
• Whenever a parent is enabled for the first time, all its children are automatically enabled through “inheritance” and displayed in the Installed Elements Table Execute column with a gray check mark (disabled).
• To individually set the state of a child element, select OIR to enable the Execute box.
GeneMapper ® ID-X Software Administrator’s Guide
33
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Editing or Deleting Profiles
IMPORTANT!
Do not modify the Admin profile.
1.
Start the Security Manager (see page 20).
2.
In the navigation pane of the Access Control Administration window, select the profile to edit or to delete.
34
3.
To edit the rights for the profile, in the Installed Elements table:
• For each function you want to enable, select OIR
(Override Inherited Rights) and Execute (see “Override
Inherited Rights (OIR)” on page 33).
• For each function you want to disable, select OIR
(Override Inherited Rights) and deselect Execute .
Note: Table 7 on page 36 and Table 8 on page 37 describe the functions displayed in the Installed Elements table.
4.
To delete the profile, select Edit Delete , then click Yes .
5.
When you finish, click Next , then click Finish to complete the profile setup.
6.
Select File Save .
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Note: Settings are not applied until you close and restart the software.
Profile Elements
All users with an Admin profile have all the permissions in Table 7.
These permissions include:
• Managing user accounts, user groups, security groups, and profiles
• Using the Audit Manager
• Using the E-Signature Manager
• All GeneMapper ® ID-X Software functions (described in
Table 8 on page 37)
GeneMapper ® ID-X Software Administrator’s Guide
35
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Table 7 Profile elements – actions allowed in Admin profiles
Installed Elements
( Application/ Action
Group/ Action)
Permissions
Default Rights
Determines the default value (all or none) for all elements.
Admin Tool Acc(ess)
Does not affect functions in the
GeneMapper ® ID-X Software.
All aspects of the Security Manager (Access Control
Administration tool).
General
May Run Application
Add User to User Group
Associate User Groups with
Security Groups
Associate User Groups with Users
Use the general functions of the Security Manager (Access
Control Administration tool).
Change Password Policies
Import Security Data
Export Security Data
User Groups
Profiles
Applications
Users
Security Groups
Audit GUI
Does not affect functions in the
GeneMapper ® ID-X Software.
Create, modify, or delete user groups (
Create, modify, or delete user profiles ( ).
).
IMPORTANT!
Do not change. For Technical Support use only.
Create, modify, or delete user accounts ( ).
Create or modify security groups ( ).
All aspects of the Audit Manager, including the Audit Map
Configuration tool and Audit History Viewer.
All aspects of the ESig Administration tool.
ESig GUI
Does not affect functions in the
GeneMapper ® ID-X Software.
36
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
All users have permissions to use some of the GeneMapper ® ID-X
Software functions. Table 8 lists the defaults for each profile.
Table 8 Profile elements – actions allowed in Technician/Read Only, Analyst, Scientist, and Admin profiles
Installed Elements
( Application/ Action
Group/ Action)
Permissions
GeneMapper
Administration
Remote Shutdown
Panel Manager
READ_PANEL
UPDATE_PANEL
— ✓ ✓ ✓ All aspects of the GeneMapper ®
Software.
ID-X
For information on the elements listed in this column, refer to the GeneMapper ® ID-X
Software Online Help.
— ✓ ✓ ✓ Use the Remote Shutdown function.
—
✓ ✓ ✓
— ✓ ✓ ✓ Use the functions of the Panel Manager, including:
✓ ✓ ✓ ✓
• Viewing panels, binsets, and bin
— ✓ ✓ ✓ definitions
• Creating/modifying panels, binsets, and bins
Size Standard —
✓ ✓ ✓
View and create or modify the size standard definitions stored by the GeneMapper ® ID-X
READ_SIZE_ STANDARD ✓ ✓ ✓ ✓
Software.
UPDATE_SIZE_
STANDARD
— ✓ ✓ ✓
GeneMapper ® ID-X Software Administrator’s Guide
37
Chapter 1 Setting Up User Accounts and User Access
Customizing Profiles
Table 8 Profile elements – actions allowed in Technician/Read Only, Analyst, Scientist, and Admin profiles (continued)
Installed Elements
( Application/ Action
Group/ Action)
Permissions
Analysis Method
READ_ANALYSIS_
METHOD
— ✓ ✓ ✓ View and create or modify the analysis
✓ ✓ ✓ ✓ methods stored by the GeneMapper
Software.
® ID-X
UPDATE_ANALYSIS_
METHOD
— — ✓ ✓
UPDATE_ANALYSIS_
RANGE
— ✓ ✓ ✓
UPDATE_SIZING_RANGE — ✓ ✓ ✓
SAVE_AS_ANALYSIS_
METHOD
— ✓ ✓ ✓
Project
READ_PROJECT
UPDATE_PROJECT
Profile Manager
READ_PROFILE
UPDATE_PROFILE
Matrix
READ_MATRIX
UPDATE_MATRIX
— ✓ ✓ ✓ View and create or modify the projects stored
✓ ✓ ✓ ✓ by the GeneMapper ® ID-X Software.
— ✓ ✓ ✓
— — —
✓
Create, edit, and delete custom reference and control profiles.
✓ ✓ ✓ ✓
— — ✓ ✓
— ✓ ✓ ✓ View and create or modify the matrices
✓ ✓ ✓ ✓ stored by the GeneMapper ® ID-X Software.
— ✓ ✓ ✓
38
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Customizing User and Security Groups
Customizing User and Security Groups
This section describes:
IMPORTANT!
Before using the security groups and user groups you create, test them by creating, modifying, deleting, and viewing data using the appropriate user accounts.
User groups, with their associated security groups, determine the
data a user can access (described on page 11). We recommend that
you use the default user groups and security groups described in
“Default User Groups” on page 17 and “Default Security Groups” on page 16.
If the default user or security groups do not suit your needs, you can create custom groups.
Creating User Groups
To create a custom user group, you can:
• Duplicate an existing default user group, then edit it to meet your requirements, or
• Create a new user group.
Note: We recommend that you duplicate a default user group, rename it, and then customize it, rather than change the default user group.
Duplicating and
Editing a Default
User Group
To base a new user group on an existing default user group
(see “Default User Groups” on page 17):
1.
Start the Security Manager (see page 20).
2.
In the navigation pane of the Access Control Administration window, select the user group to duplicate.
GeneMapper ® ID-X Software Administrator’s Guide
39
40
Chapter 1 Setting Up User Accounts and User Access
Customizing User and Security Groups
3.
Right-click, then select Duplicate (or select Edit Duplicate ).
4.
Select the Clone of .... user group in the navigation pane.
5.
In the User Group Properties section, modify the settings for the selected user group.
6.
Select File Save .
Note: Settings are not applied until you close and restart the software.
Creating a New
User Group
1.
In the Security Manager, select File New User Group .
2.
In the Create User Group wizard, click Next .
3.
Enter a Name (
≤
30 characters) and Description
(
≤
1023 characters) for the new user group.
4.
In the Default rights when associated with a Security Group section, select both Read and Update .
Note: This is a default setting applied to the security groups that you add to a user group. You can override the default setting in the Security Group tab. See step 7.
5.
Click Next .
6.
Select Associate for each user account that you want to associate with the new user group, then click Next .
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Customizing User and Security Groups
7.
Associate security groups for this user group:
Note: You can associate a security group with a user group at any time.
a.
Select Associate for each security group that you want to associate with the user group.
b.
For each associated security group, select:
• Read – Allows the user to view or select the data
(projects, plot settings, table settings, panels and binsets, report settings, size standards, analysis methods, and matrix files) associated with the security group associated with the user group.
• Update – Allows the user to create, modify, delete, and analyze the data associated with the security groups associated with the user group (consistent with the user’s profile).
IMPORTANT!
We recommend that you change read and update rights only in the profile, and always enable both read and update rights in the user/security group. c.
Click Next .
8.
Click Finish to complete the user group setup.
9.
Select File Save .
Note: Settings are not applied until you close and restart the software.
Deleting User
Groups
You can delete a user group by selecting Edit Delete .
GeneMapper ® ID-X Software Administrator’s Guide
41
Chapter 1 Setting Up User Accounts and User Access
Customizing User and Security Groups
Creating Security Groups
To create a custom security group, you can:
• Duplicate an existing default security group, then edit it to meet your requirements, or
• Create a new security group.
Note: We recommend that you duplicate a default security group, rename it, and then customize it, rather than change the default security group.
Duplicating and
Editing Default
Security Groups
To base a new security group on an existing default security group
(see “Default Security Groups” on page 16):
1.
Start the Security Manager (see page 20).
2.
In the navigation pane, select the security group to duplicate.
3.
Right-click, then select Duplicate (or select Edit Duplicate ).
4.
Select the Clone of ....
security group in the navigation pane.
5.
In the Security Group Properties section, modify the settings for the selected security group.
6.
Select File Save .
Note: Settings are not applied until you close and restart the software.
42
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Customizing User and Security Groups
Creating a New
Security Group
1.
Start the Security Manager (see page 20).
2.
In the Security Manager, select File New Security Group .
3.
In the Create Security Group wizard, click Next .
4.
Enter a Name (
≤
30 characters) and Description
(
≤
1023 characters) for the new security group.
5.
Click Next .
6.
Associate user groups for this security group:
Note: You can associate a security group with a user group at any time.
a.
Select Associate for each user group that you want to associate with the security group.
b.
For each associated user group, select Read and/or Update to grant rights for the relationship to the security group.
IMPORTANT!
We recommend that you control functional access only through the profile, and that you enable both read and update rights for all security groups. c.
Click Next .
7.
Click Finish to complete the setup.
8.
Select File Save .
Note: Settings are not applied until you close and restart the software.
Deleting Security
Groups
You cannot delete a security group.
GeneMapper ® ID-X Software Administrator’s Guide
43
Chapter 1 Setting Up User Accounts and User Access
Maintaining User Accounts
Maintaining User Accounts
We cannot retrieve passwords. Do not lose the new password for the gmidx account. This account can be used to reset passwords for other accounts. We cannot reset the password for the gmidx account if it is lost.
Editing User Accounts
Note: We recommend that you duplicate a default user account, rename it, and then customize it, rather than change the default user account.
1.
Start the Security Manager (see page 20).
2.
In the navigation pane, select the user account of interest.
3.
Modify the settings for the selected user account.
4.
If you are changing an account name, enter the new name in the
Name field.
5.
Select File Save .
Note: Settings are not applied until you close and restart the software.
Changing the Password for a User Account
1.
Start the Security Manager (see page 20).
2.
In the navigation pane, select the user account.
3.
In the User Properties section, click Set Password .
44
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Maintaining User Accounts
4.
In the Change Password dialog box, enter a password in the
Type and Retype fields. The password is case-sensitive and can contain up to 17 alphanumeric and special characters.
5.
Click OK .
6.
Select or deselect Pre-Expire . If Pre-Expire is selected, the software prompts the user to enter a new password at the next log in. If Pre-Expire is deselected, the user continues to use the password you entered in step 4.
7.
Select File Save .
Note: Settings are not applied until you close and restart the software.
Deleting a User Account
After you delete a user account, you cannot retrieve or restore the deleted account, and you cannot create another user account with the same name.
An alternative to deleting a user account is to deactivate or suspend the account, as explained in the next section.
To delete a user account:
1.
In the navigation pane of the Access Control Administration window, select the user account to delete.
2.
Select Edit Delete .
GeneMapper ® ID-X Software Administrator’s Guide
45
Chapter 1 Setting Up User Accounts and User Access
Maintaining User Accounts
Activating, Deactivating, and Suspending User Accounts
You can change the status of a user account if:
• You want to deactivate a user account without deleting it.
• A user exceeds the maximum number of failed login attempts, and you want to activate the user account manually.
1.
Start the Security Manager (see page 20).
2.
In the navigation pane, select the user account of interest.
3.
In the User Details section, select the appropriate user account status from the Status drop-down list.
46
Select a user account.
Select a status.
Table 9 Account statuses
Status
Active
Inactive
Suspended
Description
The user can log in to and use the software.
The user cannot log in. Set by a user with an
Admin profile.
The user cannot log in. Set by the software when a user exceeds the limit of unsuccessful login attempts.
4.
Select File Save .
Note: Settings are not applied until you close and restart the software.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Viewing the Security Report
Viewing the Security Report
About the
Security Report
The security report summarizes the current Security Manager settings.
You can print a summary of one or more components of the Security system (such as access rights for a particular user). See below.
Note: The Security Manager does not monitor login attempts or other user activity (such as creating projects). To monitor and record
user activity, configure the Audit Trail system (see Chapter 2,
Managing the Audit Trail System, on page 51).
Printing the
Security Report
1.
Start the Security Manager (see page 20).
2.
In the navigation pane, select a user account or profile.
3.
Select File Report .
4.
In the Print Access Control Identifiers dialog box, select options to specify the content of the report.
GeneMapper ® ID-X Software Administrator’s Guide
47
Chapter 1 Setting Up User Accounts and User Access
Viewing the Security Report
• Entire Access Control – Prints a summary of all user accounts, applications, and profiles.
• Selection only – Prints a report of the user account, application, or profile that is selected in the navigation pane of the Security
Manager.
• Print checked objects below – Prints a report for the elements that you select:
– Users – A report of all user accounts
– Applications – A report of all applications
– User Groups – A report of all user groups
– Security Groups – A report of all security groups
– Profiles – A report of all profiles
5.
Click Preview to view a preview of the report.
48
6.
Click Print . Otherwise, click Close , then repeat step 4 to modify the report settings as needed.
7.
Click Cancel to close the Print Access Control Identifiers dialog box.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1 Setting Up User Accounts and User Access
Exporting and Importing the Security Settings
Exporting and Importing the Security Settings
Transferring
Security Settings
Between
Computers
You can export a summary of all security settings to back up or transfer to another computer. The exported security file contains password policies, user accounts, profiles, user groups, and security groups.
IMPORTANT!
The GeneMapper ® ID-X Software does not automatically back up the security data when you back up the database. You must manually back up by exporting a file. We recommend that you back up security settings after you make any change to the system. For more information on backing up, see
Chapter 4, Maintaining the Software and Database Application, on page 81.
Exporting the
Security Settings
1.
Start the Security Manager (see page 20).
2.
Select File Export Database.
3.
In the Save dialog box, enter a file name for the exported file, select Access Control files (.acc) , then click Save .
4.
In the Export Users dialog box, click OK .
Importing the
Security Settings
IMPORTANT!
Importing security settings from an *.acc file automatically replaces all existing security settings.
1.
Start the Security Manager (see page 20).
2.
Select File Import Database .
3.
In the Save dialog box, navigate to the appropriate location, select the *.acc file of interest, then click Open .
4.
In the Import Users dialog box, click OK .
GeneMapper ® ID-X Software Administrator’s Guide
49
Chapter 1 Setting Up User Accounts and User Access
Exporting and Importing the Security Settings
50
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 1
Chapter 2
Managing the Audit
Trail System
■
■
■
■
■
Overview of the Audit Trail System . . . . . . . . . . . . . . . . . . . . 52
Default Audit Map Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Using the Audit Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Viewing Audit History Records . . . . . . . . . . . . . . . . . . . . . . . 63
Backing Up, Removing, and Restoring Audit Records. . . . . . 69
Chapter 2
Chapter 3
Chapter 4
Maintaining the Software and Database Application
GeneMapper ® ID-X Software Administrator’s Guide
51
Chapter 2 Managing the Audit Trail System
Overview of the Audit Trail System
Overview of the Audit Trail System
Use the GeneMapper ® ID-X Software Audit Trail system to specify the types of actions to audit (for example, allele edits) and the auditing mode ( Silent , On , or Off ).
The components of the Audit Trail system are defined in Table 10.
Table 10 Components of the Audit Trail system
Component
Audit Map
(To open, select Admin
Audit Manager Setting...
)
Auditing in the
GeneMapper ® ID-X
Software
Definition
Set of instructions specified by the GeneMapper ® ID-X Software system administrator that defines the types of data to audit, the actions to audit, and whether auditing is On (prompts the user for a
Reason for Change) or Silent (tracks the change, but does not prompt the user).
The cumulative record of changes to all audited objects. When a user creates or deletes an audited item, the change is tracked. If auditing is
On instead of Silent , the user must enter a reason for the change in the Reason(s) for Change dialog box. When a user changes an audited item (instead of creating or deleting), the dialog box also includes an Apply To All option that applies the reason for change to future changes of the same type, until the project is saved. (For example, when editing alleles, the same reason is used for all future edits of alleles until you save the project.)
IMPORTANT!
Audit records are saved only when a user saves the project, analysis method, size standard, or other object being changed. Audit records are not saved when a user clicks OK in the
Reasons for Change dialog box. If a user clicks Cancel without saving the change, the software discards all possible audit records.
Action
Name of the affected audit object attribute
Former (Old) and current
(New) values of the audit object (if applicable)
Reason for the change entered by user
52
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Overview of the Audit Trail System
Table 10 Components of the Audit Trail system (continued)
Component
Audit History Viewer
(open with
Admin Audit
Manager Report...
)
Audit Record Backup
(open from the Admin menu)
Definition
The tool that provides the GeneMapper ® ID-X Software system administrator with advanced query options for retrieving and reporting
audit records. Described in “Viewing Audit History Records” on page 63.
Allows the GeneMapper ® ID-X Software system administrator to back
up, remove, and restore audit records. Described in “Backing Up,
Removing, and Restoring Audit Records” on page 69.
Example
Configuration
The figure below displays the settings for the Allele audit object. In the example configuration, the Audit Trail:
• Does not track the change when a user creates an allele label
(Audit State for Created is set to Off ).
• Displays the Reason(s) for Change dialog box when a user deletes an allele label and saves the changes to the project
(Audit State for Deleted is set to On ).
• Silently creates a record when a user changes an allele label and saves the changes to the project (Audit State for Modified is set to Silent ).
When Audit
Records Are
Saved
Does not track change
Tracks change and prompts for reason
Tracks change
Audit records for actions related to a project (for example, editing alleles) are saved when the user saves the project.
Audit records for actions not related to a project (for example, creating analysis methods or panels) are saved when the user clicks
OK to save the item, then returns to the Project window.
GeneMapper ® ID-X Software Administrator’s Guide
53
Chapter 2 Managing the Audit Trail System
Default Audit Map Settings
IMPORTANT!
Audit records are saved only when a user saves the item being changed. Audit records are not saved when a user clicks
OK in the Reasons for Change dialog box. If a user clicks Cancel without saving the change, the software discards all possible audit records.
Default Audit Map Settings
By default:
• Allele Edit is set to On and the software prompts for a Reason for Change for allele edits. You can change the state to Silent
(tracks the change but does not prompt for a Reason for
Change) or Off (does not track the change).
• All other audited items (primitive, parent items) are set to Off , except for those that are children of other auditable items.
Auditable items are related hierarchically. For example, a Kit contains (is a parent of) Panels and Binsets, Panels contain Markers, and Markers contain Bins.
54
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Default Audit Map Settings
In the example above, the attributes named PANEL, BINSET,
MARKER, and BIN have their states set to On . This does not mean that they are set to be audited because they are not primitive types
(parent items); only primitive object attributes can be selected for auditing.
PANEL, BINSET, MARKER, and BIN have their attribute states set to On to allow one of their primitive types to be enabled for auditing.
For example, you can set the “modified” attribute of the Bin object to
On because this attribute is a primitive type.
Modified attribute is a primitive type and can be audited
If the BIN attribute states of all parent objects are not set to On , then the Bin auditing does not occur.
All the child Attributes are set to On by default. You do not need to set them to On to audit an object with parents.
In Table 11, “Elements of the audit map,” on page 60, none of the
Attributes that are On are primitive types, except for Allele. This means that the only object being audited by default is Allele.
GeneMapper ® ID-X Software Administrator’s Guide
55
Chapter 2 Managing the Audit Trail System
Using the Audit Map
Using the Audit Map
This section describes:
• Printing an Audit Map Settings Report
• Audit Map Elements (with their defaults)
Note: The Audit Trail does not track printing or exporting.
Starting the Audit Manager
1.
Start the GeneMapper ® ID-X Software
( Start All Programs Applied Biosystems
GeneMapper GeneMapper ID-X ) , then log in.
2.
In the main window, select Admin Audit Manager
Setting .
3.
In the AuditMapConfiguration dialog box, log in with an administrator user name and password (for example, gmidx ).
4.
Click OK to open the Audit Map Configuration window.
56
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Using the Audit Map
Note: The settings on the Auditing menu in this window apply to changes made in the Audit Map Configuration window. If you select
On and you make a change in the Audit Map Configuration window, you are prompted for a Reason for Change. If you select Silent , changes are tracked, but without a prompt. You cannot turn auditing of the Audit Map Configuration off.
5.
Close the Audit Map Configuration window to save your changes to the audit map.
Note: Settings are not applied until you close and restart the software
Configuring the Audit Map
IMPORTANT!
Each audited item generates an audit record that takes up space in the database. Instead of enabling auditing for an action such as modifying an analysis method, consider creating a set of analysis methods with expected settings to minimize the number of audit records that are generated.
IMPORTANT!
We recommend that you review the audit map configuration every 6 months and modify them as needed. For more
information on routine maintenance, see Chapter 4, Maintaining the
Software and Database Application.
1.
Start the Audit Manager (see page 56).
GeneMapper ® ID-X Software Administrator’s Guide
57
Chapter 2 Managing the Audit Trail System
Using the Audit Map
2.
In the Audit Map Objects pane of the Audit Map Configuration window, select the Enabled check box of each object audit.
(Enabled) – Audits all object attributes (created, modified, deleted, and so on) according to their individual attribute states.
58
Note: An object is not audited unless the Enabled check box is selected, even if the State in Attributes list is set to On .
3.
For each audit map object that you enable for auditing (only primitive objects can be audited), change its attribute states, as needed: a.
Select the audit map object.
b.
Click the cell in the State column for each attribute you want to modify. A drop-down list appears. c.
In the drop-down list, select the attribute state that determines the software behavior when a user performs the action associated with the attribute:
•
•
•
On – Creates an audit record and prompts the user for the reasons for change (see page 52).
Silent – Creates an audit record, but does not prompt the user for reasons.
Off – Does not create an audit record.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Using the Audit Map
Note: If you disable an audit map object, the attribute states for the object are shown in italic text and have no effect on the audit status of the object.
4.
Repeat step 3 for each audit map object that you enable.
5.
Close the Audit Map Configuration window to save your changes.
Note: Settings are not applied until you close and restart the software
Printing an Audit Map Settings Report
1.
Start the Audit Manager (see page 56).
2.
In the Audit Map Configuration window, select File Print .
3.
Select a column width, then click OK .
4.
Select a printer, then click OK to print the report.
Audit Map Elements
Table 11 lists all potential audit map objects, their attributes, the
default settings for each attribute, and the audit category to which they belong (items in the same audit category are related to each other).
Note: The Allele object is the only object enabled by default for auditing. All other audited objects are set to Off , except for those that are children of other auditable items (for example, RUN under the
Project object is set to On . Only primitive objects (objects listed in lowercase) can be audited.
GeneMapper ® ID-X Software Administrator’s Guide
59
Chapter 2 Managing the Audit Trail System
Using the Audit Map
Table 11 Elements of the audit map
Object
Project
Run
IMPORTANT!
To audit the Run object, you must enable the
Project object and set the Project RUN attribute to On or
Silent .
Sample
IMPORTANT!
To audit the Sample object, you must enable the Run object and set the
Run SAMPLE attribute to On or
Silent .
Attribute
analyzed
created
deleted
modified
RUN
created
deleted
SAMPLE
ALLELE
created
deleted
modified
OverrideGQ
OverrideCGQ
OverrideSQ
On
Off
Off
Off
Off
Off
Off
Default
State
Off
Off
Off
Off
On
Off
Off
On
Action Recorded When State Is
On or Silent
Creating, deleting, or changing a project in the Project window, or renaming a project in the Projects tab of the GeneMapper ID-X
Manager.
When RUN is activated, auditing for the
Run object (described below) is allowed.
You must also enable the Run object and set its attributes.
Audit category: ProjectT
Adding samples from a new run folder, or deleting all samples in a run folder from a project.
When SAMPLE is activated, auditing for the
Sample object (described below) is allowed. You must also enable the Sample object and set its attributes.
Audit category: ProjectT
Adding, deleting, or modifying samples
(change the sample name) in the Project window, or deleting samples from the
Samples plot.
When ALLELE is activated, auditing for the
Allele object (described below) is allowed.
You must also enable the Allele object and set its attributes.
When OverrideGQ or Override CGQ is activated, creates a record when a user overrides the GQ PQV or CGQ PQV in the
Samples or Genotypes plot.
When OverrideSQ is activated, creates a record when a user overrides the SQ PQV in the Size Match Editor.
Audit category: ProjectT
60
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Using the Audit Map
Table 11 Elements of the audit map (continued)
Object
Allele
IMPORTANT!
To audit the Allele object, you must enable the Sample object and set the
Sample ALLELE attribute to On or
Silent .
Analysis Method
Attribute
created
deleted
modified
Default
State
On
On
On
Action Recorded When State Is
On or Silent
Modifying allele labels in the Samples or
Genotypes plot.
Audit category: ProjectT
Creating, deleting, or modifying an analysis method.
Audit category: Analysis MethodT
Kit
created
deleted
modified
BINSET
created
deleted
modified
PANEL
created
deleted
Off
Off
Off
On
Off
Off
Off
On
Off
Off
Creating, deleting, or modifying a kit in the
Panel Manager.
When BINSET or PANEL is activated, auditing for the Binset or Panel object
(described below) is allowed. You must also enable the Binset or Panel object and set its attributes.
Audit category: KitT
Creating or deleting binsets using the Panel
Manager.
Audit category: KitT
BinSet
IMPORTANT!
To audit the Binset object, you must enable the Kit object and set the Kit
BINSET attribute to
On or Silent .
Panel
IMPORTANT!
To audit the Panel object, you must enable the Kit object and set the Kit
PANEL attribute to
On or Silent .
created
deleted
MARKER
modified
Off
Off
On
Off
Creating, deleting, or modifying panels in the Panel Manager, the Samples plot, or the
Genotypes plot.
When MARKER is activated, auditing for the Marker object (described below) is allowed. You must also enable the Marker object and set its attributes.
Audit category: KitT
GeneMapper ® ID-X Software Administrator’s Guide
61
Chapter 2 Managing the Audit Trail System
Using the Audit Map
Table 11 Elements of the audit map (continued)
Object
Marker
IMPORTANT!
To audit the Marker object, you must enable the Panel object and set the
Panel MARKER attribute to On or
Silent .
Bin
IMPORTANT!
To audit the Bin object, you must enable the
Marker object and set the Marker BIN attribute to On or
Silent .
Matrix
Size Standard
Attribute
BIN
created
deleted
modified
created
deleted
modified
created
deleted
modified
created
deleted
modified
Off
Off
Off
Off
Off
Off
Default
State
On
Off
Off
Off
Action Recorded When State Is
On or Silent
Creating, deleting, or modifying markers of a panel in the Panel Manager, the Samples plot, or the Genotypes plot.
When BIN is activated, auditing for the Bin object (described below) is allowed. You must also enable the Bin object and set its attributes.
Audit category: KitT
Off
Off
Off
Creating, deleting, or modifying individual bins of the binsets in the Panel Manager, the Samples plot, or the Genotypes plot.
Audit category: KitT
Creating, deleting, or modifying matrices using the GeneMapper ID-X Manager.
Audit category: MatrixT
Creating, deleting, or modifying size standard definitions using the GeneMapper
ID-X Manager.
Audit category: SizeStandardT
62
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Viewing Audit History Records
Viewing Audit History Records
This section describes:
• Starting the Audit History Viewer
• Creating Audit Record Queries
• Performing Audit Record Queries and Viewing Audit Records
Starting the Audit History Viewer
1.
Select Start All Programs Applied Biosystems
GeneMapper GeneMapper ID-X .
2.
Log in with your user name and password, then click OK .
3.
In the main window, select Admin Audit Manager Report .
4.
In the AuditHistoryViewer dialog box, log in with an administrator user name and password (for example, gmidx or
Lab Manager ).
5.
Click OK to open the Audit History Viewer window (page 64).
GeneMapper ® ID-X Software Administrator’s Guide
63
Chapter 2 Managing the Audit Trail System
Viewing Audit History Records
User-defined queries
Audit objects Audit records for selected object
Details for selected
Audit record
Creating Audit Record Queries
1.
Open the Audit History Viewer window (see page 63).
2.
Select File New Query to display the New Query dialog box.
64
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Viewing Audit History Records
3.
Complete the fields in the New Query dialog box, as needed.
You can:
• Leave a field blank to find all records for a field.
• Enter a partial string in any field. For example, if you enter modified or Allele in the Audit Record field, the query finds all modified records or all records that relate to
Allele edits.
• Enter a full string in any field to limit the query to specific records.
Field
Query Name
Old Value
New Value
Instance
Type
Full Name
Audit Record
Reason
Description Example
Name of the query
IMPORTANT!
To create a query that lists all audit records, enter a Query
Name and leave the remaining fields blank.
Full Audit History
Original value before the item is changed 22
[KitT.AmpFLSTR_Panels_v1.PANEL.
Identifiler_v1.MARKER.D2S1338.
BASEPAIR.336.33.SAMPLE.Sample
3.PEAK_ID.1911.ANALYSIS_ID.44]
New value after the item is changed
Name of the item
Audit category
Full name of the user who made the change
Audit record entry new variant
[KitT.AmpFLSTR_Panels_v1.PANEL.
Identifiler_v1.MARKER.D2S1338.
BASEPAIR.336.33.SAMPLE.Sample
3.PEAK_ID.1911.ANALYSIS_ID.44]
ID_Control
SizeStandardT
RUN.identifiler data files.SAMPLE.ID_Control.fsa.
ALLELE.new.created
Change allele label Reason for the change that is specified, if the audit state was set to On
Dates for the record 12/10/2006 Date From and
To
4.
Click OK . The query is listed in the Queries pane of the Audit
History Viewer.
GeneMapper ® ID-X Software Administrator’s Guide
65
Chapter 2 Managing the Audit Trail System
Viewing Audit History Records
Performing Audit Record Queries and Viewing Audit
Records
1.
Open the Audit History Viewer window (see page 63).
2.
Select a query in the Queries pane.
3.
Click in the toolbar.
4.
In the Audit Objects pane, select the audited item to view records for.
5.
To view details for an audit record: a.
Click (Audit Record Details icon) in the toolbar to display the Audit Records Details section.
b.
In the Audit Records section, select a record of interest.
c.
Examine the Old Value, New Value, and Reason for
Change in the Audit Records Details section.
6.
(Optional) To show or hide columns, right-click a column header, then specify the columns to show or hide.
7.
(Optional) To sort the audit history records in the Audit Records list, click one of the column headers. A triangle (
▲
) appears inside the column header to indicate the direction of the sort.
66
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Viewing Audit History Records
Example Audit Records
Table 12 Example audit records
Audit
Category
Objects
With audit
Records
Example Audit Records
ProjectT analyzed deleted
Run RUN.identifiler data files.created
RUN.identifiler data files.deleted
Sample RUN.identifiler data files.SAMPLE.ID_Sample3.fsa.OverrideSQ
RUN.identifiler data files.SAMPLE.ID_Sample3.fsa.OverrideGQ
RUN.identifiler data files.SAMPLE.ID_Neg_cntrl.fsa.deleted
Analysis
MethodT
KitT
Allele RUN.identifiler data files.SAMPLE.ID_Control.fsa.ALLELE.new.created
Analysis
Method modified
Kit
Panel
Binset
Marker deleted
PANEL.Blue_V1.deleted
BINSET.YFilerBinSetTest.created
PANEL.Yfiler_v2.MARKER.Y_DYS392.deleted
Bin
Matrix MatrixT
SizeStandardT Size
Standard
PANEL.Identifiler_CODIS_v1.MARKER.CSF1PO.BIN.7.modified
created created
GeneMapper ® ID-X Software Administrator’s Guide
67
Chapter 2 Managing the Audit Trail System
Viewing Audit History Records
Printing Audit Records
You can print audit record reports for each object.
IMPORTANT!
Review audit reports every month. For more
information on routine maintenance, see Chapter 4, Maintaining the
Software and Database Application.
1.
Open the Audit History Viewer window (see page 63).
2.
Select the object to print from the Audit Objects list.
3.
Select File Print Preview to open the Select Columns dialog box.
68
4.
Select the columns to display in the report, then click OK . The
Preview Audit History Records window opens.
5.
Click Print to print the report.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 2 Managing the Audit Trail System
Backing Up, Removing, and Restoring Audit Records
Backing Up, Removing, and Restoring Audit
Records
This section describes:
• When to Back Up and Remove Audit Records
• Backing Up and Removing Audit Records
When to Back Up and Remove
Audit Records
Routinely review the amount of database space occupied by audit
records using the Database Dashboard (see “Reviewing the Database
Statistics” on page 88). As the amount of occupied disk space
approaches the maximum limit defined in the software, you must:
• Increase the amount of disk space, as explained in “Allocating
or
• Back up and remove the audit records, as explained below.
Backing Up and
Removing
Audit Records
IMPORTANT!
The GeneMapper
®
ID-X Software automatically
backs up the audit data when you back up the database (see “Backing
Up the Database” on page 93). Use this function to selectively back
up, then remove audit records to free up space in the database.
1.
Select Start All Programs Applied Biosystems
GeneMapper GeneMapper ID-X .
2.
Log in with an administrator user account (for example, gmidx ).
3.
In the main window, select
Admin Audit Manager Backup Audit Records .
4.
In the Backup Audit Records dialog box: a.
Navigate to an export location for the audit data.
b.
Enter a name for the exported audit file (*.aud).
c.
Click Backup .
GeneMapper ® ID-X Software Administrator’s Guide
69
70
Chapter 2 Managing the Audit Trail System
Backing Up, Removing, and Restoring Audit Records
5.
In the main window, select Admin Audit Manager
Delete All Audit Records .
6.
In the Delete All Audit Records dialog box, click Yes .
Storing Audit
Records
After exporting the audit records file, move the GeneMapper ® ID-X
Software audit file (*.aud) to a storage medium for archiving. If you need to view the archived records, restore the records as explained
below, then view them using the Audit History Viewer (see “Viewing
Audit History Records” on page 63).
Restoring Audit
Records
1.
Select Start All Programs Applied Biosystems
GeneMapper GeneMapper ID-X .
2.
Log in with an administrator user account (for example, gmidx ).
3.
In the main window, select Admin Audit Manager
Restore Audit Records .
4.
In the Backup Audit Records dialog box, locate and select the audit file (*.aud) of interest.
5.
Click Restore .
Note: Restoring audit records does not erase any current records. It adds the restored records to the current records in the Audit Trail.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 3
Managing the
E-Signature System
Chapter 1
This chapter covers:
■
■
■
■
■
Overview of the Electronic Signature (E-Signature) System . 72
Default E-Signature Settings . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Configuring the E-Signature System . . . . . . . . . . . . . . . . . . . 73
Viewing E-Signature Records . . . . . . . . . . . . . . . . . . . . . . . . . 78
Backing Up, Removing, and Restoring E-Signature Records. 80
Chapter 2
Chapter 3
Chapter 4
Maintaining the Software and Database Application
GeneMapper ® ID-X Software Administrator’s Guide
71
Chapter 3 Managing the E-Signature System
Overview of the Electronic Signature (E-Signature) System
Overview of the Electronic Signature (E-Signature)
System
The GeneMapper ® ID-X Software Electronic Signature (E-
Signature) system ensures that only authorized users are allowed to make certain changes (create, modify, or delete) in the software. You can configure the types of actions that require user authentication
(for example, analyze projects). A user must provide his or her
GeneMapper ® ID-X Software user name and password before changes are saved.
The E-Signature system also keeps track of who made certain changes. By comparison, the Audit Manager keeps track of only what was done.
The components of the E-Signature system are defined in Table 13.
Table 13 Components of the E-Signature system
Component
Esig
Administrator
Electronic
Signature
Verification
Definition
Configured by the GeneMapper ® ID-X Software system administrator to identify the actions that require a signature.
When a user performs actions (for example, deleting analysis methods) that have been specified for electronic signature, the GeneMapper ® ID-X Software automatically displays the Electronic Signature Verification dialog box (shown on the next page).
A user authenticates or “signs” for an action by entering his or her GeneMapper ®
ID-X Software user name and password.
If a user enters the correct password, the software performs the requested action and records the electronic signature transaction.
72
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 3 Managing the E-Signature System
Default E-Signature Settings
Table 13 Components of the E-Signature system (continued)
Definition Component
Electronic
Signature
Verification
(continued)
A default warning that indicates the action that prompted signature verification
An additional custom message to the user
User enters user name
User enters password
Default E-Signature Settings
By default, all E-Signature actions are disabled.
Configuring the E-Signature System
Note: The E-Signature system does not track printing or exporting of object types.
This section describes:
• Starting the E-Signature Manager
• Enabling the E-Signature Function
• Configuring E-Signature Actions
GeneMapper ® ID-X Software Administrator’s Guide
73
Chapter 3 Managing the E-Signature System
Configuring the E-Signature System
Starting the E-Signature Manager
1.
Select Start All Programs Applied Biosystems
GeneMapper GeneMapper ID-X , then log in.
2.
In the main window, select Admin ESig Administrator .
3.
In the ESig Administration dialog box, log in with an administrator user name and password (for example, gmidx ).
4.
Click OK . The ESig Administration window (E-Signature
Manager) opens.
Enabling the E-Signature Function
The E-Signature Configuration settings apply to all users. A user with an Admin profile can change settings for all users at any time.
1.
Start the E-Signature Manager (see page 74).
74
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 3 Managing the E-Signature System
Configuring the E-Signature System
2.
In the ESig Administration window, select the Configuration tab.
3.
For Is Electronic Signature Required?, select Yes .
4.
For Method, select UsernamePassword from the drop-down list.
5.
(Optional) To require the user to enter a user name as part of the electronic signature, select the Require UserID?
check box.
Otherwise, the software fills the user name field with the name of the user who is currently logged in to the software.
6.
(Optional) In the Description field, enter comments for internal use (for example, Configured by Admin ).
7.
Select File Save to save the settings.
Configure each E-Signature action as described in the next section.
GeneMapper ® ID-X Software Administrator’s Guide
75
Chapter 3 Managing the E-Signature System
Configuring the E-Signature System
Configuring E-Signature Actions
By default, all E-Signature actions are disabled.
IMPORTANT!
We recommend that you review the E-Signature administration settings every 6 months, and modify them as needed.
For more information on routine maintenance, see Chapter 4,
Maintaining the Software and Database Application, on page 81.
1.
Start the E-Signature Manager (see page 74).
2.
In the ESig Administration window, select the Action
Administration tab.
Enable Esig (disabled)
Selected object type
Custom message displayed to users when signature requested
Actions for the selected actions group
Definition text displayed to users when signature requested
3.
In the ESig Action Maps pane, define actions that require electronic signature: a.
Select a GM_ object type. The actions you specify for electronic signature (creating, modifying, deleting) are grouped together, unlike the actions in the Audit Manager, where you can specify actions individually.
76
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 3 Managing the E-Signature System
Configuring the E-Signature System b.
To require electronic signatures for the actions displayed in the Action List, select the Enable Esig check box.
Note: You may need to resize the ESig Administration window to see the Enable Esig check box.
c.
(Optional) In the Electronic Signature Challenge Text box, enter a custom message to the user that displays (for this object type) every time an electronic signature is requested
(for example, By entering your user name and password, you are signing this action ).
4.
Repeat step 3 for each object type in the ESig Action Maps pane.
5.
Select File Save to save the settings.
Note: Settings are not applied until you close and restart the software.
E-Signature Action Maps
Table 14 lists the actions that can be tracked by E-Signature.
Table 14 E-Signature action maps
Object
Default
State
Default Action Group
GM_PROJECT
GM_CHEMISTRY_ KIT
NA
Disabled
Disabled
GM_ANALYSIS_ METHOD Disabled
GM_SIZE STANDARD Disabled
GM_MATRIX Disabled
Actions Requiring an E-Signature (When Enabled)
Not used in the GeneMapper ® ID-X Software.
A project is created, modified, or deleted.
A chemistry kit is created, modified, or deleted.
An analysis method is created, modified, or deleted.
A size standard is created, modified, or deleted.
A matrix is created, modified, or deleted.
GeneMapper ® ID-X Software Administrator’s Guide
77
Chapter 3 Managing the E-Signature System
Viewing E-Signature Records
Viewing E-Signature Records
This section describes:
• Specifying E-Signature Queries
• Performing E-Signature Queries and Viewing E-Signature
• Printing E-Signature Records
Specifying E-Signature Queries
1.
Start the E-Signature Manager (see page 74).
2.
In the ESig Administration window, select the History Viewer tab.
78
3.
To view all records, leave blank all fields in the Query
Electronic Signature Events section, then click Find .
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 3 Managing the E-Signature System
Viewing E-Signature Records
4.
To refine the query of electronic signature records, in the Query
Electronic Signature Events pane, enter parameter values:
Note: Enter parameter values only in those fields that are relevant to your search.
• Object Name – Enter the name of an object. For example, entering Analysis Method 123 in this field retrieves all events for the analysis method named “Analysis Method
123”.
• Object Type – Enter the object type. For example, entering analysis method in the Object Type field retrieves events for all analysis methods.
• User ID – Enter the name of a user account to query the electronic signature events created by a specific user.
• Full Name – Enter the full name of a user to query the electronic signature events created by a specific user.
• Action Group – Select an action group to view all events for the group. For example, selecting Action Group
GM_ANALYSIS_METHOD retrieves all events created when a user created, modified, or deleted an analysis method.
• Action – After selecting an action group, select an action to further refine the search by isolating it to a specific action of the group. For example, after selecting
Action Group GM_ANALYSIS_METHOD , selecting
Action DELETE_ANALYSIS_METHOD retrieves all events created in which a user deleted an analysis method.
• Event Date/Time – Enter a date or dates to display records created in a specific time period.
GeneMapper ® ID-X Software Administrator’s Guide
79
Chapter 3 Managing the E-Signature System
Backing Up, Removing, and Restoring E-Signature Records
Performing E-Signature Queries and Viewing E-Signature
Records
1.
After specifying E-Signature queries in the History Viewer tab
of the ESig Administration window (page 78), click
Find .
Note: The Server Time is the local time on the database computer at which the action occurred. The Client Time is the local time on the software computer at which the action occurred. (Typically, these times are similar. However, if you make a change on a client computer in one time zone and the database computer is in another time zone, the times may differ.)
Note: The Version field is not used in the GeneMapper
Software.
® ID-X
2.
(Optional) In the Events list, select an event to view the Event
Details.
3.
If you want to run another query, click Clear , then repeat
Sorting
The GeneMapper
®
ID-X Software does not support sorting of
E-signature records.
Printing E-Signature Records
The GeneMapper ® ID-X Software does not support printing
E-signature records.
Backing Up, Removing, and Restoring E-Signature
Records
The GeneMapper ® ID-X Software does not support backing up, removing, or restoring E-signature records.
80
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4
Maintaining the Software and Database Application
Chapter 1
Chapter 2
This chapter covers:
■
■
■
■
■
■
■
■
Maintenance Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Using and Maintaining the Oracle® Database . . . . . . . . . . . . 83
Using the Database Dashboard Software . . . . . . . . . . . . . . . . 85
Reviewing the Database Statistics . . . . . . . . . . . . . . . . . . . . . . 88
Allocating Disk Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Viewing Project Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Generating a Database Report. . . . . . . . . . . . . . . . . . . . . . . . . 98
Chapter 3
Chapter 4
Maintaining the Software and Database
GeneMapper ® ID-X Software Administrator’s Guide
81
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
Weekly
Monthly
As Needed
Tasks
• Exit the GeneMapper ® ID-X Software and restart the computer.
• Review the statistics for the database (see page 88); if needed:
– Export unused projects and data, then delete them. (For more information, refer to the GeneMapper ® ID-X Software Online Help.
)
– Allocate additional disk space (see page 91).
• (Optional) Back up the GeneMapper ® ID-X
Software database (see page 93).
• Defragment the computer hard drive.
• Review password policies, and modify them as necessary (see page 22).
• If using the Audit Trail system, review the audit map configuration, and modify as
• If using the E-Signature system, review the electronic signature settings, and
modify as needed (see page 73).
• Manage user accounts (see page 44).
• Manage security groups (see page 42).
• Manage user groups (see page 39).
• Manage profiles (see page 31).
• Back up security settings after making any change to the Security system (see
• Back up, remove, and restore audit records (see page 69).
82
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4 Maintaining the Software and Database Application
Using and Maintaining the Oracle
®
Database
Using and Maintaining the Oracle
®
Database
This section describes:
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 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.
We do 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
We do 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.
GeneMapper ® ID-X Software Administrator’s Guide
83
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-X
Software 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 Interface,” on page 99.
Maintaining the Database
Use the Database Dashboard Software (described on page 85) to
perform routine maintenance. You do not need Oracle training to use the Database Dashboard Software. However, we recommend 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. We recommend use of these tools only by a certified Oracle Database administrator .
Oracle
Documentation
Additional documentation for the Oracle Database is available at www.oracle.com.
84
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4 Maintaining the Software and Database Application
Using the Database Dashboard Software
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 resides in the Oracle Database.
Note: The Database Dashboard Software is not installed on client computers.
This section describes:
• Setting a Dashboard Password
• Starting the Database Dashboard
Dashboard Features
The Database Dashboard includes the:
• Dashboard tab – Provides information about database performance, space usage, 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. 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.
GeneMapper ® ID-X Software Administrator’s Guide
85
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.
Select Start All Programs Applied Biosystems
Database Dashboard Dashboard .
2.
Click Yes when asked if you want to set a password.
3.
Enter a new password twice, then click OK .
IMPORTANT!
Do not lose the password for the Database
Dashboard Software. We cannot retrieve passwords.
86
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4 Maintaining the Software and Database Application
Using the Database Dashboard Software
Starting the Database Dashboard
Note: You must log in to the GeneMapper ® ID-X Software at least once before starting the Database Dashboard for the first time.
1.
Select Start All Programs Applied
Biosystems Database Dashboard Dashboard .
2.
Enter a password:
If a password...
Has already been set by the GeneMapper ®
ID-X Software system administrator (see
“Setting a Dashboard Password” on page 86),
Has already been set and you want to change the password,
Has not been set and you want to have a password,
Has not been set and you do not want to have a password,
Enter the password specified by the system administrator.
Then...
1. Enter the current password.
2. Select Database Change Password , then follow the prompts to change the password.
1. Select Database Set Password , then follow the prompts to create a password.
2. Select Database Security Enabled .
The next time that you log in to the software, security will be enabled and you will be required to enter the
password that you created in step 1.
No steps are required. The Database Dashboard
Software starts without requiring a password.
IMPORTANT!
Do not lose the password for the Database
Dashboard Software. We cannot retrieve the password.
GeneMapper ® ID-X Software Administrator’s Guide
87
Chapter 4 Maintaining the Software and Database Application
Reviewing the Database Statistics
Reviewing the Database Statistics
Review database statistics weekly to determine if database maintenance is required.
1.
Start the Database Dashboard (see page 86).
2.
In the Database Dashboard window, select the GeneMapper
ID-X tab.
3.
Select the Database Statistics tab.
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.
88
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)
Projects, including samples and results data Project Data
Reference Data Supporting data (analysis methods, size standards, panels, binsets, matrices, and so on)
GeneMapper ® ID-X Software Administrator’s Guide
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:
Used(%)
Value
(Used/
Allocated)
>80%
Auto
Extend
Value
Yes
Required Action
<80%
No
N/A
Allocate more space for data as
explained in “Allocating Additional
• Used (MB) is approaching
Allocated (MB), or
• Free disk space on the current drive is low. Allocate space on another drive.
Allocate more space for data, as
explained in “Allocating Additional
No maintenance required.
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
Software.
GeneMapper ® ID-X Software Administrator’s Guide
89
Chapter 4 Maintaining the Software and Database Application
Allocating Disk Space
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
Table Name
Audit Data
Project Data
Reference Data
Exportable Data Objects
Audit records
Projects
• Analysis methods
• Binsets
• Matrices
• Kits, panels, and markers
• Plot settings
• Size-standard definitions
• Report settings
• Table settings
To export audit data, see “Backing Up, Removing, and Restoring
To export project data and reference data, refer to the
GeneMapper ® ID-X Software Online Help .
90
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4 Maintaining the Software and Database Application
Allocating Disk Space
Allocating Additional Disk Space
1.
Start the Database Dashboard (see page 86).
2.
In the Database Dashboard window, select the Dashboard tab.
3.
In the Connections pane, determine if any users (clients) are logged in to the GeneMapper ® ID-X Software.
4.
Before you continue, instruct all users to log out of the
GeneMapper
®
ID-X Software.
5.
Select the GeneMapper ID-X tab, then select the Database
Statistics tab.
6.
At the bottom of the Database Dashboard, select the Default
Allocation tab.
7.
In the Available Drives drop-down list, select a drive.
8.
In the Table Space drop-down list, select a database table.
GeneMapper ® ID-X Software Administrator’s Guide
91
Chapter 4 Maintaining the Software and Database Application
Allocating Disk Space
92
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 or down arrow to increase or 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.
10.
Click Allocate .
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 Database Refresh (or press Alt+R ) to refresh the screen and verify that the software has updated the
Database Statistics table.
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4 Maintaining the Software and Database Application
Viewing Project Statistics
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 86).
2.
In the Database Dashboard window, select the GeneMapper
ID-X 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
GeneMapper ® ID-X Software Administrator’s Guide
93
Chapter 4 Maintaining the Software and Database Application
Backing Up the Database
When to Back Up the Oracle Database
We recommend 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 49 for more information.
Backing Up (Exporting) the Database
Performing this procedure backs up (exports) the entire database. If you want to back up individual data objects (for example, a project), use one of the following:
• The export function in the GeneMapper ID-X Manager; refer to the GeneMapper ® ID-X Software Online Help.
• The export arguments in the Command Line Interface; see
IMPORTANT!
The disk space required for backup can be 60–70% of the size of the database. The database size is the Allocated Space displayed in the Dashboard tab.
To back up (export) the entire database:
1.
Start the Database Dashboard (see page 86).
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 60–70% of the Allocated Table
94
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4 Maintaining the Software and Database Application
Backing Up the Database
5.
In the Connections pane, determine if any users (clients) are logged in to the GeneMapper ® ID-X Software.
6.
Before you continue, request and ensure that all users are logged out of 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
Administration Export Database .
9.
In the Full Database Backup pane, click Browse , navigate to an export location, enter a name for the backup file, then click
Open .
Note: Ensure that you have available for backup at least
60–70% 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
Performing this procedure restores (imports) the entire database. If you want to restore individual data objects (for example, a project), use one of the following:
• The restore function in the GeneMapper ID-X Manager; refer to the GeneMapper
®
ID-X Software Online Help.
• The import arguments in the Command Line Interface; see
GeneMapper ® ID-X Software Administrator’s Guide
95
96
Chapter 4 Maintaining the Software and Database Application
Backing Up the Database
Important
Computer and
Database
Requirements
Before restoring the database, ensure that:
• The target computer that you restore the database to has a configuration identical to the computer from which the database was backed up. For example, if you back up a database with
250 MB allocations on the C, D, and G drives, you can restore the database only on a computer that contains at least 250 MB on its C, D, and G drives.
• The database that you restore has the same GeneMapper
®
ID-X
Software version as the database installed on your computer. For example, a GeneMapper ® ID-X Software v1.4 database cannot be restored to a computer that has v1.5 installed.
For more information, refer to the GeneMapper ® ID-X Software
Installation Guide .
Restoring 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 (page 94), you can import
the resulting *.dmp file to recreate the database.
Note: The restore procedure does not restore the database directly. It creates a batch file that you run to restore the database.
To restore (import) the entire database:
1.
Start the Database Dashboard (see page 86).
2.
In the Database Dashboard window, select the Administration tab.
3.
In the navigation column of the Administration tab, select
Administration Import Database .
4.
Click Browse , locate and select the correct *.dmp file, then click Open .
GeneMapper ® ID-X Software Administrator’s Guide
Chapter 4 Maintaining the Software and Database Application
Backing Up the Database
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, locate the batch file, then double-click the file to run it. The software runs SQL scripts to import the data into the database.
10.
Restart your computer.
GeneMapper ® ID-X Software Administrator’s Guide
97
Chapter 4 Maintaining the Software and Database Application
Generating a Database Report
Generating a Database Report
1.
Start the Database Dashboard (see page 86).
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, locate and select a destination directory.
c.
Enter a name for the exported file.
d.
Select the desired file format ( HTML or tab-delimited text ).
e.
Click Save .
98
GeneMapper ® ID-X Software Administrator’s Guide
Appendix A Operating the Software from a Command Line Interface
Operating the Software from a
Command Line Interface
This appendix covers:
■
■
■
Operating the Software from a Command Line Interface . . 100
Example Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Command Line Arguments. . . . . . . . . . . . . . . . . . . . . . . . . . 111
GeneMapper ® ID-X Software Administrator’s Guide
99
Appendix A Operating the Software from a Command Line Interface
Operating the Software from a Command Line Interface
Operating the Software from a Command Line
Interface
Overview
This appendix explains how to analyze, import, and export data from the Command Line Interface of the GeneMapper ® ID-X Software.
IMPORTANT!
We support the use of the Command Line Interface only as it is explained in this appendix.
Note: If you are unfamiliar with Microsoft ® DOS, we do 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.
• -commandline is the argument that places the software into command line mode.
• < arguments > is the series of arguments that specify the operations to be performed.
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.
100
GeneMapper ® ID-X Software Administrator’s Guide
Appendix A Operating the Software from a Command Line Interface
Operating the Software from a Command Line Interface
Creating a Batch File to Run the Command Line Interface
1.
In the desktop, select
Start All Programs Accessories Notepad .
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:
@echo off
“ GeneMapper.exe
” -commandline -option h -username “ user ” -password
“ password ” -project “ project ”
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.exe
is 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.
GeneMapper ® ID-X Software Administrator’s Guide
101
Appendix A Operating the Software from a Command Line Interface
Operating the Software from a Command Line Interface
• –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).
Note: User names are not case-sensitive. Passwords are case-sensitive; that is, “Password1” is not the same as
“password1” .
• –project instructs the software to create or analyze a project named “ project” (enclosed in double quotes).
For example:
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gmidx” -password “password” –project “myProject”
5.
After the -project argument, enter any additional arguments to instruct the software to perform the desired functions. See
“Command Line Arguments” on page 111 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).
6.
(Optional) After entering the last argument in the command, repeat steps 3 through 5 to enter additional commands.
Note: The operating system executes the commands in the order in which they appear in the batch file (from top to bottom).
102
7.
(Optional) After entering the last command: a.
Press Enter to create a new line.
GeneMapper ® ID-X Software Administrator’s Guide
Appendix A Operating the Software from a Command Line Interface
Operating the Software from a Command Line Interface 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 106 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 File Save .
b.
In the File name field, enter a name for the batch file with a
*.bat file extension.
For example: mybatchfile.bat or GMIDXanalysis.bat
c.
Click Save .
10.
Select File Exit to close the batch file.
Example Batch File
@ECHO off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline
-option h -username “gmidx” -password “password” –project
“myProject” -analysismethod “myMethod” -sizestandard “mySS” -panel
“myPanel” -folder “D:\casework\case01 -ladder “D:\casework\case01 ladder1.fsa” -exportall “D:\casework\case01\case01_export.txt”
ECHO Batch file operation complete.
GeneMapper ® ID-X Software Administrator’s Guide
103
Appendix A Operating the Software from a Command Line Interface
Operating the Software from a Command Line Interface
Running the Batch File
Close the GeneMapper ® ID-X Software before you run the batch file.
Run the batch file containing the command line arguments from an
MS DOS command prompt window. Wait for the computer to run the scripted command. When the operating system finishes processing the batch file, the command prompt window displays “Press any key to continue”.
IMPORTANT!
The “Batch File Complete” message is displayed, even if the command does not generate the expected output file (for example, if the project name specified does not exist). If you do not find the expected output files after running a command, review the
*.bat file to ensure that all commands are valid.
Do not close the command prompt window before it displays “Press any key to continue.” Doing so prematurely terminates the commands executed by the batch file and could result in loss of data.
Note: Depending on the speed of your computer and the number of commands included in your batch file, the operating system may take several minutes to a number of hours to process the batch file.
104
GeneMapper ® ID-X Software Administrator’s Guide
Appendix A Operating the Software from a Command Line Interface
Example Commands
Example Commands
This section covers:
Example #1: Analyze Sample Files
Example #2: Analyze Sample Files with Named Ladders
Example #3: Export Project Data
Example #4: Export Sample Plot to PDF with the -splitfile argument
Example #5: Export Sample Plot to PDF with the -splitfile and samplelist arguments
Example #1: Analyze Sample Files
This example analyzes sample files generated by the Data Collection
Software using the analysis method, size standard, panel, and ladder specified by the Data Collection Software.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” -commandline option h -username “gmidx” -password “password” –project
“Case01 Project” -folder “d:\Casework\Case01”
ECHO Batch file operation complete.
Description
The example batch file logs in to the GeneMapper
®
ID-X Software using the default user account gmidx , and analyzes the sample files in the d:\Casework\Case01 directory. After the analysis, the command instructs the software to save the project as Case01
Project .
Each executed step of the batch file is not displayed in the command prompt window (–option h). “Batch file operation complete” is displayed in the command prompt window.
GeneMapper ® ID-X Software Administrator’s Guide
105
Appendix A Operating the Software from a Command Line Interface
Example Commands
Example #2: Analyze Sample Files with Named Ladders
This example analyzes sample files generated by the Data Collection
Software and specifies the analysis method, size standard, panel, and ladder to use.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline
–username “gmidx” –password “password” –project “Casework02 Project”
-analysismethod “myMethod” -sizestandard “mySS” -panel “myPanel”
–folder “e:\Casework\Case02” –ladder “e:\Casework\Case02”
“ladder1.fsa” “ladder2.fsa”
ECHO Batch file operation complete.
Description
The example logs in to the GeneMapper ® ID-X Software using the default user account gmidx , and analyzes the sample files in the e:\Casework\Case02 directory. The command instructs the software to use the myMethod analysis method, mySS size standard, and myPanel panel for the analysis. The command also instructs the software to use the ladder1.fsa
and ladder2.fsa
sample files in the e:\Casework\Case02 directory as the allelic ladders for the analysis.
After the analysis, the command instructs the software to save the project as Casework02 Project .
Each executed step of the batch file is displayed in the command prompt window. “Batch file operation complete” is displayed in the command prompt window.
106
GeneMapper ® ID-X Software Administrator’s Guide
Appendix A Operating the Software from a Command Line Interface
Example Commands
Example #3: Export Project Data
This example exports the sizing data and analyzed electropherogram data for the sample files of an existing project.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline option h –username “gmidx” –password “password” –project “Case03”
–exportsizemap “g:\Case03\size map.txt” -exportanalyzedeps “g:\
Case03\analyzed eps.txt”
ECHO Batch file operation complete.
Description
The example logs in to the GeneMapper ® ID-X Software using the default user account gmidx , and exports the sizing data and analyzed electropherogram data of the Case03 project as the g:\Case03\size map.txt
and g:\Case03\analyzed eps.txt
files.
Each executed step of the batch file is not displayed in the command prompt window (–option h). “Batch file operation complete” is displayed in the command prompt window.
GeneMapper ® ID-X Software Administrator’s Guide
107
Appendix A Operating the Software from a Command Line Interface
Example Commands
Example #4: Export Sample Plot to PDF with the -splitfile argument
This example exports the sample plots for an existing project to multiple PDF files. The sample plots of all samples in the project are exported.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline
-option h –username “gmidx” –password “password” –project “Case04”
–exportsampleplot “g:\Case04\Case04SamplePlot.PDF” -splitfile
“true”
ECHO Batch file operation complete.
Description
The example logs in to the GeneMapper ® ID-X Software using the default user account gmidx , and exports the sample plots of all samples in the Case04 project to the g:\Case04 directory. Because the -splitfile argument is set to true :
• The sample plot of each sample in the project is exported to individual PDF files. For example, if the project contains ten samples, ten PDF files are generated.
• The file name specified in the command is ignored and each
PDF file name is auto-generated; the format for auto-generated file names is:
<ProjectName>_<RunName>_<SampleFileName>.pdf
.
Each executed step of the batch file is not displayed in the command prompt window (–option h). “Batch file operation complete” is displayed in the command prompt window.
Note: If the -splitfile argument was set to false (or not provided), the sample plot of each sample in the project would be exported to one
PDF file. For example, if the project contained ten samples, one PDF file containing ten sample plots would be generated. The file name specified in the command ( Case04SamplePlot.pdf
) would be used.
108
GeneMapper ® ID-X Software Administrator’s Guide
Appendix A Operating the Software from a Command Line Interface
Example Commands
Example #5: Export Sample Plot to PDF with the -splitfile and -samplelist arguments
This example exports two sample plots for an existing project to two
PDF files. Only the sample plots of the samples listed in the command are exported.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline
-option h –username “gmidx” –password “password” –project “Case04”
–exportsampleplot “g:\Case04\Case04SamplePlot.PDF” -splitfile
“true” -samplelist “161467.hid 173320.fsa”
ECHO Batch file operation complete.
Description
The example logs in to the GeneMapper ® ID-X Software using the default user account gmidx , and exports the sample plots of the two samples in the Case04 project that are listed in the command
( 161467.hid
and 173320.fsa
) to the g:\Case04 directory. Because the
-splitfile argument is set to true :
• The two sample plots are exported to individual PDF files. That is, one PDF file is generated for 161467.hid
and a second PDF file is generated for 173320.fsa
.
• The file name specified in the command is ignored and the two
PDF file names are auto-generated; the format for autogenerated file names is:
<ProjectName>_<RunName>_<SampleFileName>.pdf
.
Each executed step of the batch file is not displayed in the command prompt window (–option h). “Batch file operation complete” is displayed in the command prompt window.
Note: If the -splitfile argument was set to false (or not provided), the sample plots for 161467.hid
and 173320.fsa
would be exported to one PDF file. That is, one PDF file containing the two sample plots would be generated. The file name specified in the command
( Case04SamplePlot.pdf
) would be used.
GeneMapper ® ID-X Software Administrator’s Guide
109
Appendix A Operating the Software from a Command Line Interface
Example Commands
Example #6: Export a Project
This example exports one project to one *.ser file in the specified export folder. Only the project listed in the command is exported.
@echo off
“D:\AppliedBiosystems\GeneMapper\app\GeneMapper.exe” –commandline
-option h –username “gmidx” –password “password” –exportObjectType
“Projects” –exportObjectName “ Case04 ” –exportfolder “g:\Case04”
ECHO Batch file operation complete.
Description
The example logs in to the GeneMapper ® ID-X Software using the default user account gmidx , and exports the Case04 project. The project is exported to a *.ser file in the g:\Case04 export folder.
Each executed step of the batch file is not displayed in the command prompt window (–option h). “Batch file operation complete” is displayed in the command prompt window.
Note: If the -exportObjectName argument was not provided, all projects in the database would be exported to individual *.ser files.
For example, if the database contained ten projects, ten *.ser files would be generated. If the -exportfolder argument was not provided, the project would be exported to the default system folder.
110
GeneMapper ® ID-X Software Administrator’s Guide
Appendix A Operating the Software from a Command Line Interface
Command Line Arguments
Command Line Arguments
Conventions
This section uses the following text conventions:
• “ italic text ” – Italic text appearing between double quotation marks (“”) must be substituted with custom values when entered as part of a command.
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.
• bold text – Bold text must be typed exactly as it appears.
• Grayed text – Gray table cells indicate the required elements of all commands issued with the Command Line Interface.
Commands
Table 17 contains a summary of all arguments for the Command
Line Interface.
GeneMapper ® ID-X Software Administrator’s Guide
111
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface
Argument
-analysismethod
-commandline
-deleteproject
-exportall
-exportanalyzedeps
-exportbinoffsettable
Action/Definition Usage
Specifies the name of the analysis method to use in the analysis of the specified project.
-analysismethod “ where method method ” is the name of the analysis method.
Configures the software to operate in command line mode.
-commandline
Deletes the specified project(s).
-deleteproject “ project1 ” “ project2 ” … where project1 and project2 are the names of the projects to be deleted.
Exports the combined contents of the Samples and Genotypes tables of the specified project as a tabdelimited text file of the specified name.
You can use this argument with the
-samplelist argument (see page 119) to export data for only the samples that are listed in the command.
-exportall “ filename ” where filename is the long path (file name appended to the export directory path) of the exported file.
Exports the analyzed electropherogram data for the samples of the specified project as a tab-delimited text file of the specified name.
You can use this argument with the
-samplelist argument (see page 119) to export data for only the samples that are listed in the command.
-exportanalyzedeps “ filename ” where filename is the long path (file name appended to the export directory path) of the exported file.
Exports the bin offsets for the specified project as a tab-delimited text file of the specified name.
-exportbinoffsettable “ filename ” where filename is the long path (file name appended to the export directory path) of the exported file.
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
-exportfolder
Argument
-exportgenotypetable
-exportObjectName
Action/Definition Usage
Specifies the destination folder to which the -exportObjectType argument exports the specified object(s).
The -exportfolder argument works only with the -exportObjectType argument. If -exportObjectType is not provided, no objects are exported to the specified folder.
See the -exportObjectType argument (page 114).
Exports the Genotypes table for the specified project as a tab-delimited text file of the specified name.
-exportgenotypetable “ exported file.
filename ” where filename is the long path (file name appended to the export directory path) of the
See the -exportObjectType argument (page 114).
Specifies one or more object names to be exported.
The -exportObjectName argument works only with the
-exportObjectType argument. If
-exportObjectType is not provided, no objects are exported.
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
Argument
-exportObjectType
Action/Definition Usage
Specifies the object type to be exported. The software can export only the following object types:
• Size standards
• Projects
• Analysis methods
You can use this argument with one or both of the following arguments:
• -exportObjectName argument
If -exportObjectName is not provided, all objects that belong to the object type are exported.
• -exportfolder argument (see
is not provided, the specified object is exported to the default system folder.
Size standards and analysis methods are exported as *.xml files. If multiple size standards or multiple analysis methods are specified in the command, a single *.xml file is generated for all of the specified objects. For example, if ten size standards are specified, one *.xml file that contains all ten size standards is generated.
Projects are exported as *.ser files. If multiple projects are specified in the command, an individual *.ser file is generated for each project. For example, if ten projects are specified, ten *.ser files are generated.
-exportObjectType “ object type ”
-exportObjectName “ object name ”
-exportfolder “ folder ” where:
• object type is the type of object to be exported. You can specify only the following values for the -exportObjectType argument:
– Size Standards
– Projects
– Analysis Methods
You can export only one object type in a single command. However, if you do not specify an object name (below), all objects that belong to the specified object type are exported.
• object name is the name of the object to be exported. For example:
– Size Standards – CE_F_HID_GS500 (75-
400)
– Projects – Project 1
– Analysis Methods – Method 1
To export multiple objects of the same type, enter multiple objects names, separated by a comma. For example, Method 1,Method 2 .
• folder is the export directory path to which the object will be exported. For example, C:/Test .
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
Argument
-exportplotsampletable
-exportsampleplot
Action/Definition Usage
Exports the Sizing table of the
Samples plot for the specified project as a tab-delimited text file of the specified name.
You can use this argument with the
-samplelist argument (see page 119) to export data for only the samples that are listed in the command.
-exportplotsampletable “ filename ” where filename is the long path (file name appended to the export directory path) of the exported file.
Exports the sample plots for the specified project to a PDF file.
You can use this argument with the:
• -splitfile argument (see page 120)
to export the sample plots to individual PDF files (Boolean value is “true”) or to a single PDF file
(Boolean value is “false”). If the splitfile argument is not used, the sample plots are exported to a single PDF file.
• -samplelist argument (see page 119) to export data for only the samples that are listed in the command.
The -splitfile and -samplelist arguments can be used together.
-exportsampleplot “ filename ” where filename is the long path (file name appended to the export directory path) of the exported file.
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
Argument
-exportsampletable
-exportsizemap
-folder
-help
-importanalysismethod
Action/Definition Usage
Exports the Samples table for the specified project as a tab-delimited text file of the specified name.
You can use this argument with the
-samplelist argument (see page 119) to export data for only the samples that are listed in the command.
-exportsampletable “ filename ” where filename is the long path (file name appended to the export directory path) of the exported file.
Exports data point/base pair data for the specified project as a tabdelimited text file of the specified name.
-exportsizemap “ filename ” where filename is the long path (file name appended to the export directory path) of the exported file.
Specifies the names of the affected run folders in the project:
• If analyzing by run, the argument specifies the run folder of interest.
• If analyzing by project, the argument specifies the run folders of interest in the specified project.
-folder “ folder1 ” “ folder2 ” … where folder1 is always required. Additional folders are needed only if analyzing by project (not used when analyzing by run).
Prints a summary of the commands for the Command Line Interface.
-help
Imports the specified file as an analysis method.
-importanalysismethod “ filename ” where filename is the long path (file name appended to the import directory path) of the imported file.
IMPORTANT!
The specified file must be formatted as an XML file that uses GeneMapper ®
ID-X Software-specific syntax and contains the necessary analysis method data in the format identical to that of an exported analysis method.
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
Argument
-importproject
-importsizestandard
-ladder
-negcontrol
Action/Definition Usage
Imports the project or projects stored by the specified file.
-importproject “ filename ” where filename is the long path (file name appended to the import directory path) of the imported file.
IMPORTANT!
The specified file must be an exported project file (*.ser) created by the export function of the GeneMapper ID-X Manager.
Imports the specified file as a size standard.
-importsizestandard “ filename ” where filename is the long path (file name appended to the import directory path) of the imported file.
IMPORTANT!
The specified file must be formatted as an XML file that uses GeneMapper ®
ID-X Software-specific syntax and contains the necessary size standard data in the format identical to that of an exported size standard.
Instructs the software to use the specified samples as allelic ladders in the analysis of the specified project.
-ladder “ folder ” “ ladder1 ” “ ladder2 ” … where:
• folder is the name of the project folder that contains the ladder samples.
• ladder1 and ladder2 … are the names of the allelic ladder sample files separated by a space.
Instructs the software to use the specified samples as negative controls in the analysis of the specified project.
-negcontrol “ where: folder ” “ ctrl1 ” “ ctrl2 ” …
• folder is the name of the project folder that contains the negative-control samples.
• ctrl1 and ctrl2 … are the names of the negative-control sample files separated by a space.
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
Argument
-option
-panel
-password
-poscontrol
-project
Action/Definition Usage
Specifies the options for the exported data.
-option “ option ”; “ option ”; … ; “ option ” where option is any of the following option letters:
• b – Attaches bin names to the exported
Genotype table.
• h – Hides the user interface.
• p “ port ” – Specifies the monitoring TCP/IP port number (default is 8393).
Specifies the name of the panel to use in the analysis of the specified project.
-panel “ where panel panel
” is the name of the panel.
Specifies the password for the user account defined by the -username argument.
-password “ password ” where password is the password for the user account.
Note: Passwords are case-sensitive; that is,
“Password1” is not the same as “password1” .
Instructs the software to use the specified samples as positive controls in the analysis of the specified project.
Specifies the name of the project to create or analyze.
-poscontrol “ folder ” “ ctrl1 ” “ ctrl2 ” … where:
• folder is the name of the project folder that contains the positive-control samples.
• ctrl1 and ctrl2 … are the names of the positive-control sample files separated by a space.
-project “ project ” where project is the name of project.
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
Argument
-samplelist
-sizestandard
Action/Definition Usage
When used with the appropriate export argument, exports the following types of data for the samples listed in the command:
• Electropherograms; works only with the -exportanalyzedeps
• Sample plot sizing tables; works only with the
-exportplotsampletable argument
• Sample plots; works only with the
-exportsampleplot argument (see
page 115), where it can be used
with the -splitfile argument (see
• Samples tables; works only with the -exportsampletable argument
• Combined contents of the
Samples and Genotypes tables; works only with the -exportall
• To export electropherograms:
-exportanalyzedeps “ filename ”
-samplelist “ sample file ”
• To export sample plot sizing tables:
-exportplotsampletable “ filename ”
-samplelist “ sample file ”
• To export sample plots:
-exportsampleplot “ filename ”
-samplelist “ sample file ”
• To export Samples tables:
-exportsampletable “ filename ”
-samplelist “ sample file ”
• To export combined Samples and Genotypes tables:
-exportall “ filename ”
-samplelist “ sample file ” where:
• filename is the long path (file name appended to the export directory path) of the exported file.
• sample file is the sample name. You can export data for multiple samples by appending more sample names to the command line:
-samplelist “ sample file 1 ” “ sample file 2 ” “ sample file 3 ” and so on
Specifies the name of the size standard to use in the analysis of the specified project.
-sizestandard “ standard ” where standard is the name of the size standard.
Table 17 Summary of arguments for the GeneMapper ® ID-X Software Command Line Interface (continued)
Argument
-splitfile
-username
Action/Definition Usage
Specifies the Boolean value for the export content of the
-exportsampleplot argument (see
page 115). When the -splitfile
argument is:
• Set to “ true ” , the sample plots are exported to individual PDF files.
• Set to “ false ” , the sample plots are exported to a single PDF file.
The PDF files are exported to the location specified in the
-exportsampleplot argument.
The -splitfile argument works only with the -exportsampleplot argument.
If you enter the -exportsampleplot argument without the -splitfile argument, only one PDF file is generated and the file name is the name specified in the command.
The -splitfile argument can be used together with the -samplelist argument (see page 119).
-exportsampleplot “ filename ”
-splitfile “ true ” or “ false ” where:
• filename is the long path (file name appended to the export directory path) of the exported file.
The file naming convention is:
< ProjectName >_< RunName >_
< SampleFileName >
• true and false are the Boolean values:
– true – The sample plots are exported to individual PDF files. The file name specified in the command is ignored and the file names are auto-generated.
– false – The sample plots are exported to a single PDF file. The file name specified in the command is used.
Specifies the user account with which to perform the actions of the command.
-username “ user ” where user is the name of a user account. User names are not case-sensitive.
IMPORTANT!
The user account that you use must have privileges sufficient to perform the specified actions. For more information, see
Chapter 1, “Setting Up User Accounts and User
Documentation and support
Related documentation
The following related documents are shipped with the system:
Document
GeneMapper ® ID-X Software
Version 1.5 Administrator’s
Guide
Part number
100031703
GeneMapper ® ID-X Software
Version 1.5 Integration User
Bulletin
GeneMapper ® ID-X Software
Version 1.5 Getting Started
Guide — Basic Features
GeneMapper ® ID-X Software
Version 1.5 Quick Reference
Card — Basic Features
GeneMapper ® ID-X Software
Version 1.5 Getting Started
Guide — Mixture Analysis
Tool
GeneMapper ® ID-X Software
Version 1.5 Quick Reference
Card — Mixture Analysis Tool
GeneMapper ® ID-X Software
Version 1.5 Reference Guide
100031709
100031701
100031702
100031704
100031705
100031707
Description
Describes how to configure the administrative features of the software, maintain the
GeneMapper ® ID-X and Database Dashboard
Software, and use the Command Line
Interface.
Describes Command Line Interface commands that can be scripted and used to automate
GeneMapper ® ID-X Software operations.
Explains how to set up the software, set up a project, and analyze the example data provided with the GeneMapper ® ID-X Software.
Provides an easy-to-follow workflow for using basic system features.
Explains how to set up the software for mixture analysis and analyze the example data provided with the GeneMapper ® ID-X Software.
Provides an easy-to-follow workflow for using the mixture analysis tool.
Describes process quality values (PQVs) and algorithms.
121
GeneMapper ® ID-X Software Administrator’s Guide
Documentation and support
How to obtain support
How to obtain support
For HID support:
• In the United States and Canada – send an email to
[email protected], or call 888-821-4443 option 1.
• Outside the United States and Canada – contact your local support office.
For the latest services and support information for all locations, go to: www.lifetechnologies.com/support
At the web site, you can:
• Access worldwide telephone and fax numbers to contact
Technical Support and Sales facilities.
• Search through frequently asked questions (FAQs).
• Submit a question directly to Technical Support.
• Search for user documents, Material Safety Data Sheets
(MSDSs), vector maps and sequences, application notes, formulations, handbooks, certificates of analysis, citations, and other product support documents.
• Download .pdf documents.
• Obtain information about customer training.
Limited product warranty
Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and
Conditions of Sale found on Life Technologies' website at www.lifetechnologies.com/termsandconditions. If you have any questions, please contact Life Technologies at www.lifetechnologies.com/support.
122
GeneMapper ® ID-X Software Administrator’s Guide
Index
A
Admin user account 18 intended user 18
ALLELE audit map object attribute 60
allelic ladders, specifying in a command line
Analysis Method audit map object 61
analysis methods
specifying in a command line 112 analysismethod argument 112
Audit History records
audit map
audit map objects
audit records
archiving 69 backing up 69 removing 69
Audit Trail system
automating software operations 100
B backing up
batch file, creating for command line
BIN audit map object attribute 62
bin offsets, export via a command line 112
GeneMapper ® ID-X Software Administrator’s Guide
123
Index
BINSET audit map object attribute 61
C
Casework Analyst user account
profile and actions allowed 15
Casework Tech Lead user account
Casework Tech user account
profile and actions allowed 15
chain-of-custody of electronic data 10
command line arguments
analysismethod 112 deleteproject 112 exportall 112 exportanalyzedeps 112 exportbinoffsettable 112
exportgenotypetable 113 exportObjectName 113
exportsampletable 116 exportsizemap 116 folder 116 help 116 importanalysismethod 116
importsizestandard 117 ladder 117 negcontrol 117
option 118 panel 118 password 118 poscontrol 118 project 118
samplelist 119 sizestandard 119
Command Line Interface
124
specifying allelic ladders 117
specifying analysis methods 112
specifying negative controls 117
specifying panels 118 specifying port setting 118 specifying positive controls 118
configuring
configuring E-Signature actions 76
controlling access to the software 51
creating
Database Dashboard Software
user groups 39 customizing user and security groups 39
D
data export via a command line 112
database
backing up 93 exporting 93 importing 93
Database Dashboard Software
maintaining database 86 setting password 86
Databasing Analyst user account
GeneMapper ® ID-X Software Administrator’s Guide
Index
profile and actions allowed 15
Databasing Tech Lead user account
Databasing Tech user account
profile and actions allowed 15
deleting
E editing
electronic data tracking systems, overview 10
Electronic Signature Challenge Text 77
electropherogram data, export via a command
enable/disable audit object 58
enabling
E-Signature History Viewer
printing records 80 running queries 80
E-Signature records
archiving 80 backing up 80 removing 80
E-Signature system
exportall argument 112 exportanalyzedeps argument 112 exportbinoffsettable argument 112
exportgenotypetable argument 113
exporting
exportplotsampletable argument 115
exportsampletable argument 116 exportsizemap argument 116
F
G
GeneMapper ID-X
Genotypes table, export via a command
gmidx user account
profile and actions allowed 16
H
I
importanalysismethod argument 116
importing
analysis methods (command line) 116
size standard definition (command
GeneMapper ® ID-X Software Administrator’s Guide
125
Index
importsizestandard argument 117
K
L
LIMS, linking the software using the
M
maintaining software and database 82 maintenance schedule 82
MARKER audit map object attribute 61
N negative controls, specifying in a command
line analysis 117 negcontrol argument 117
New Application command, do not use 21
O
Oracle ® database
Override Inherited Rights (OIR), meaning
126
OverrideCGQ audit map object attribute 60
OverrideGQ audit map object attribute 60
OverrideSQ audit map object attribute 60
overview, Audit Trail system 52
P
PANEL audit map object attribute 61
panel, specifying in a command line
password
password policies
Database Dashboard Software 86
password policies
Set User State - Remain Active 23
positive controls, specifying in a command
Practice user group and security group 17
profile
Admin, default actions allowed 16
Analyst, default actions allowed 15
GeneMapper ® ID-X Software Administrator’s Guide
Index
Scientist, default actions allowed 16
Technician/Read-Only, default actions
projects
deletion via a command line 112
specifying in a command line analysis 118
R read/write privileges in user and security
removing
restoring
RUN audit map object attribute 60
run folder, specifying in a command line
S
SAMPLE audit map object attribute 60
Samples table, export via a command line 112
Scientist profile, actions allowed 16
scripting software operations 100
SDSs
security groups
associating with data 13 bypassing 13
changing assignment for a data item 30 changing association for a project 30
creating 42 creating based on defaults 42
security settings
Security system
setting
Size Standard audit map object 62
size standard definition, import via a command
size standard, specifying in a command line
analysis 119 sizestandard argument 119
Sizing table (Samples Plot), export via a
software password, creating for Database
GeneMapper ® ID-X Software Administrator’s Guide
127
Index
T technical support
Technician/Read-Only profile. see
profiles
U user accounts
user groups actions and data access allowed by
creating 39 creating based on defaults 39
user name, not case-sensitive 20
V viewing
128
GeneMapper ® ID-X Software Administrator’s Guide
For support visit
lifetechnologies.com/support or email [email protected]
lifetechnologies.com
16 February 2015
Advertisement
