Overview of the Audit System
Use the GeneMapper®ID-X Software audit system to specify the
types of actions you want to audit (for example, allele edits) and the auditing mode (silent, or requiring the user to enter a reason for change).
The components of the audit system are defined in Table 10.
Table 10 Components of the audit system
Component Definition
Audit Map
(open in GeneMapper ID-X
Software by selecting Admin
Audit ManagerSetting...)
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).
Auditing in the GeneMapper
ID-X Software
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 (see figure on next page). 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.
Name of the affected Action
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
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.
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.
Audit History Viewer (open with
AdminAudit ManagerReport...)
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 57.
Audit Record Backup
(open from Admin menu)
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 63.
Table 10 Components of the audit system (continued)
Component Definition
Tracks change and prompts for reason
Tracks change Does not track change
Chapter 2 Managing the Auditing System Default Audit Map Settings
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.
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.
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 54, 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.
modified attribute is a primitive type and can be audited
Chapter 2 Managing the Auditing System Using the Audit Map
Using the Audit Map
This section describes:
• Starting the Audit Manager • Configuring the Audit Map
• 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
(StartAll ProgramsApplied Biosystems
GeneMapperGeneMapper ID-X v1.0), then log in.
2. In the GeneMapper ID-X main window, select
AdminAudit ManagerSetting.
3. In the AuditMapConfiguration dialog box, log in with an administrative user name and password (for example, gmidx).
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.
Saving Changes
When you close the Audit Map Configuration window, your changes to the audit map are saved. Settings are not applied until you close and restart the GeneMapper ID-X 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! Applied Biosystems recommends 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.
Chapter 2 Managing the Auditing System Using the Audit Map
2. In the Audit Map Configuration window (in the Audit Map Objects pane) 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.
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
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.
Note: If you run autoanalysis, auditing for objects set to On is automatically performed in Silent mode (because no user is available to be prompted for Reason for Change).
4. Repeat step 3 for each audit map object that you enable.
5. Close the Audit Map Configuration window.
6. Restart the GeneMapper ID-X Software to apply the settings.
Printing an Audit Map Settings Report
1. Start the Audit Manager (see page 50).
2. In the Audit Map Configuration window, select FileReport. You are prompted for formatting information, then the report prints.
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). If the GeneMapper ID-X Software is installed on a computer that contains other Applied Biosystems products, the audit map may contain elements additional to those listed in Table 11.
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 lower case) can be audited.
Chapter 2 Managing the Auditing System Using the Audit Map
Table 11 Elements of the audit map
Object Attribute Default
State
Action Recorded When State Is On or Silent
Project analyzed Off Creating, deleting, or changing a project in the Project window, or renaming a project in the Projects tab of the GeneMapper IDX
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
created Off deleted Off modified Off RUN On Run IMPORTANT! To audit the Run object, you must enable the Project object and set the Project RUN attribute to On or Silent (described above).
created Off 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
deleted Off
SAMPLE On
Sample IMPORTANT! To audit the Sample object, you must enable the Run object and set the Run SAMPLE attribute to On or Silent (described above).
ALLELE On 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 OverrideGQor Override CGQ is activated, creates a record when a user overrides the GQ PQV or CGQ PQV in the Samples or Genotypes plot.
created Off deleted Off modified Off OverrideGQ Off OverrideCGQ Off OverrideSQ Off
Allele
IMPORTANT! To audit the Allele object, you must enable the Sample object and set the Sample ALLELE attribute to On or Silent (described above).
created On Modifying allele labels in the Samples or Genotypes plot.
Audit category: ProjectT
deleted On
modified On
Analysis Method created Off Creating, deleting, or modifying an analysis method.
Audit category: Analysis MethodT
deleted Off
modified Off
Kit BINSET On 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
created Off deleted Off modified Off PANEL On BinSet IMPORTANT! To audit the BinSet object, you must enable the Kit object and set the Kit BINSET attribute to On or Silent (described above).
created Off Creating or deleting bin sets using the Panel Manager.
Audit category: KitT
deleted Off
Table 11 Elements of the audit map (continued)
Object Attribute Default
State
Action Recorded When State Is On or Silent
Chapter 2 Managing the Auditing System Using the Audit Map
Panel
IMPORTANT! To audit the Panel object, you must enable the Kit object and set the Kit PANEL attribute to On or Silent (described above).
created 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
deleted Off
MARKER On
modified Off
Marker IMPORTANT! To audit the Marker object, you must enable the Panel object and set the Panel MARKER attribute to On or Silent (described above).
BIN On 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
created Off
deleted Off
modified Off
Bin
IMPORTANT! To audit the Bin object, you must enable the Marker object and set the Marker BIN attribute to On or Silent (described above).
created Off Creating, deleting, or modifying individual bins of the bin sets in the Panel Manager, the Samples plot, or the Genotypes plot. Audit category: KitT
deleted Off
modified Off
Matrix created Off Creating, deleting, or modifying matrices using the GeneMapper ID-X Manager. Table 11 Elements of the audit map (continued)
Object Attribute Default
State
Action Recorded When State Is On or Silent
Viewing Audit History Records
This section describes:
• Starting the Audit History Viewer • Creating Audit Record Queries
• Performing Audit Record Queries and Viewing Audit Records • Example Audit Records
• Printing Audit Records
Starting the Audit History Viewer
1. Select StartAll ProgramsApplied Biosystems
GeneMapperGeneMapper ID-X v1.0, then log in.
2. In the Login to GeneMapper ID-X dialog box, log in with your user name and password, then click OK.
3. In the GeneMapper ID-X main window, select
AdminAudit ManagerReport.
4. In the AuditHistoryViewer dialog box, log in with an
administrative user name and password (for example, gmidx or
Lab Manager).
Chapter 2 Managing the Auditing System Viewing Audit History Records
Creating Audit Record Queries
1. Open the Audit History Viewer window (see above).
2. Select FileNewQuery to display the New Query dialog box.
User-defined queries
Audit objects Audit records for selected object
Details for selected Audit record
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.
4. Click OK. The query is listed in the Queries pane of the Audit History Viewer.
Field Description Example
Query Name 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
Old Value 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 New value after the item is changed. new variant
[KitT.AmpFLSTR_Panels_v1.PANEL. Identifiler_v1.MARKER.D2S1338. BASEPAIR.336.33.SAMPLE.Sample 3.PEAK_ID.1911.ANALYSIS_ID.44]
Instance Name of the item. ID_Control
Type Audit category SizeStandardT
Full Name Full name of user who made the change
Audit Record Audit record entry. RUN.identifiler data
files.SAMPLE.ID_Control.fsa. ALLELE.new.created
Reason Reason for the change that is specified, if audit state was set to On.
Change allele label
Date From and To
Chapter 2 Managing the Auditing System Viewing Audit History Records
Performing Audit Record Queries and Viewing Audit
Records
1. Open the Audit History Viewer window (see page 57).
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.
Example Audit Records
Table 12 Example audit recordsAudit Category
Objects With audit
Records
Example Audit Records
ProjectT Project 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
Allele RUN.identifiler data files.SAMPLE.ID_Control.fsa.ALLELE.new.created
Analysis MethodT
Analysis Method
modified
KitT Kit deleted
Panel PANEL.Blue_V1.deleted
BinSet BINSET.YFilerBinSetTest.created
Marker PANEL.Yfiler_v2.MARKER.Y_DYS392.deleted
Bin PANEL.Identifiler_CODIS_v1.MARKER.CSF1PO.BIN.7.modified
MatrixT Matrix created
SizeStandardT Size Standard
Chapter 2 Managing the Auditing 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. In the Audit History Viewer window, select the object to print from the Audit Objects list.
2. Select FilePrint Preview. The Select Columns dialog box opens.
Backing Up, Removing, and Restoring Audit
Records
This section describes:
• When to Back Up and Remove Audit Records • Backing Up and Removing Audit Records • Storing Audit Records
• Restoring 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 81). 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 Disk Space” on page 82,
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 87). Use this function to selectively back up, then remove audit records to free up space in the database.
1. Select StartAll ProgramsApplied Biosystems
GeneMapperGeneMapper ID-X v1.0.
2. Log in with an administrative account (for example, gmidx).
3. In the GeneMapper ID-X Software main window, select
AdminAudit ManagerBackup Audit Records.
4. In the Backup Audit Records dialog box:
a. Navigate to the location to which you want to export the