SampleManager LIMS

Installation Guide

Version 12.2
© 2019 Thermo Fisher Scientific Inc. All rights reserved.

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All trademarks recognized.

 C

Contents
Preface ...................................................................................................................... ix
Related Documentation ................................................................................. ix
Special Notices................................................................................................ x
Contacting Us................................................................................................. x

Chapter 1 Introduction ................................................................................................................ 1

Architecture .................................................................................................... 2
Deployment .................................................................................................... 5
Single-Tier Systems ..................................................................................... 6
Two-Tier Systems ....................................................................................... 7
Three-Tier Systems ..................................................................................... 8
System Requirements .................................................................................... 14
Operating System ..................................................................................... 14
Database ................................................................................................... 14
Overall Setup Procedure ............................................................................... 15
3-Tier Installation with an Oracle Database .............................................. 15
3-Tier Installation with a SQL Server Database ......................................... 16

Chapter 2 Installing SampleManager Server for an Oracle Database ............................ 19

Installation Procedure Summary ................................................................... 20
Pre-Installation Checks ............................................................................. 20
Installing Oracle........................................................................................ 21
Installing SampleManager Server .............................................................. 23
Installing the Thermo Licensing Server ..................................................... 25
Creating a SampleManager Instance ............................................................. 26
Creating a New Instance ........................................................................... 27
Creating a Cloned Instance ....................................................................... 37
Creating an Application Server Instance .................................................... 41
Creating a New Site Instance .................................................................... 47
Removing a SampleManager Instance ........................................................... 55

Chapter 3 Installing SampleManager Server for a SQL Server Database....................... 59

Installation Procedure Summary ................................................................... 60
Pre-Installation Checks ............................................................................. 60
Installing SQL Server ................................................................................ 62

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Installing SampleManager Server .............................................................. 62

Installing the Thermo Licensing Server ..................................................... 65
Creating a SampleManager Instance ............................................................. 66
Creating a New Instance ........................................................................... 67
Creating a Cloned Instance ....................................................................... 76
Creating an Application Server Instance .................................................... 81
Creating a New Site Instance .................................................................... 87
Removing a SampleManager Instance ........................................................... 93

Chapter 4 Post-Installation Tasks .......................................................................................... 97

SampleManager Licenses............................................................................... 98
Generating the Installation Details File ................................................... 100
Obtaining the License File ...................................................................... 101
Installing your New Licenses ................................................................... 101
Assigning Named Licenses to SampleManager Users ............................... 102
Running SampleManager Client for the First Time .................................... 104
Configuring the Application Server Firewall................................................ 105
Setting the Server Timezone ....................................................................... 105
Configuring the Server Warm Start Feature ................................................ 106
Smart Client Deployment ........................................................................... 107
Encrypting the Database Connection String in the Windows Registry ........ 108
Adding Dictionaries for the Spell Checking Feature .................................... 109
Configuring ADO Cursor Locations and Cache Size .................................. 110
Adding the ActiveRecord Task to the Watch Dog Timer ............................ 111
Add DLLs for Report Designer OLE Previews to Exe Folder ...................... 113

Chapter 5 Installing SampleManager Client ...................................................................... 115

Prerequisites ................................................................................................ 116
Installing SampleManager Client Software .................................................. 116
Suppressing the SampleManager Splash Screen ....................................... 117
Silent Installation of the SampleManager Client ..................................... 118
Enabling Tab Reports ............................................................................. 118
Connecting to a SampleManager Server Instance ........................................ 119
Proxy Login ............................................................................................ 121
Setting SampleManager Fonts ................................................................. 122
Managing Server Instance Connections ....................................................... 123
Manage Servers Window ......................................................................... 124
Deployment with Pre-Configured Servers ............................................... 126

Chapter 6 Upgrading SampleManager ................................................................................ 129

Prerequisites ................................................................................................ 130
Upgrading SampleManager Server .............................................................. 131
Overall Upgrade Procedure ..................................................................... 132
Overall Upgrade Procedure for an Application Server Cluster ................. 133
Running the Upgrade Server Instance Wizard ......................................... 138

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Thermo License Server Handshake Error ................................................ 142

Upgrading the SampleManager Web Interface ........................................ 144
Manual Upgrade Procedures ....................................................................... 144
Required Tools ....................................................................................... 144
Upgrading structure.txt ........................................................................... 145
Identifying Files That Require a Manual Upgrade ................................... 146
Upgrading Files Manually ....................................................................... 147
Upgrading SampleManager Clients ............................................................. 149
Upgrading the Password Encryption ........................................................... 150
New Menu Items ........................................................................................ 151
Fixing Form Upgrade Errors ....................................................................... 151
Entity-Specific Changes .............................................................................. 153
Rack Templates ...................................................................................... 153
Report Designer .......................................................................................... 154
Upgrading the SampleManager Web Application ....................................... 155

Chapter 7 Installing LIMS Reporter ...................................................................................... 157

Connections Between LIMS Reporter and the Database ............................. 158
LIMS Driver and Unicode Data.............................................................. 159
Installation Procedures for SampleManager on Oracle ................................ 160
Installation on a SampleManager Server PC ............................................ 160
Installation on a SampleManager Client PC ............................................ 160
Setting up an Oracle ODBC Data Source ............................................... 161
Setting Up a SampleManager ODBC Data Source ................................. 162
Installation Procedures for SampleManager on SQL Server ......................... 163
Installation on a SampleManager Server PC ............................................ 163
Installation on a SampleManager Client PC ............................................ 164
Setting Up a SQL Server ODBC Data Source......................................... 164
Setting up a SampleManager ODBC Data Source .................................. 165
Installing LIMS Reporter ............................................................................ 166
Setting up a Database Profile ...................................................................... 166
Connecting to the Database .................................................................... 168
Producing Reports in PDF Format ............................................................. 168
Installing Adobe Acrobat Reader ............................................................. 169
Installing GhostScript ............................................................................. 169
Add a Printer that Uses the GhostScript Printer Driver ........................... 172
Sending Reports to PDF ......................................................................... 172

Chapter 8 Installing Chromeleon Link Components .......................................................... 173

Prerequisites ................................................................................................ 174
Installing Chromeleon Link Web API ......................................................... 175
Configure the API User Account............................................................. 177
Installing SampleManager Chromeleon Interface ........................................ 178
Electronic Signature Settings in Chromeleon .......................................... 182
Chromeleon Link Add-In ........................................................................... 183

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Contents

Chapter 9 Installing Data Manager Components ............................................................... 185

Prerequisites ................................................................................................ 186
Install and Configure Data Manager Components Overview ...................... 187
Upgrade from Previous Versions of Data Manager .................................. 188
Run the Data Manager Install Utility .......................................................... 190
Install the Data Manager Data Provider Service .......................................... 190
Data Manager Components ........................................................................ 191
Install Data Manager Components ............................................................. 192
Install the Envision GAML Viewer ............................................................. 197
Install the GRAMSShellHandlers64 Component ........................................ 199
Install the GRAMS Converters ................................................................... 202
Install Bruker CompassExtract (Bruker MALDI and Bruker ESI Converters
only) ........................................................................................................... 205
Configure the Data Manager Messaging Service.......................................... 210
Configure the SampleManager Data Provider ............................................. 211
Configure the Data Manager Server ............................................................ 212
Configure the Data Manager Client ............................................................ 214
Enable the Packaging Agent Service ............................................................ 215
Configure the Packaging Agent ................................................................... 217
Configure System Tracing .......................................................................... 219
Licensing GRAMS Envision ....................................................................... 220
Instrument Data File Converters Help ........................................................ 221

Chapter 10 Oracle Setup .......................................................................................................... 223

Installing and Configuring Oracle for Use with SampleManager ................. 224
Setting the OPEN_CURSORS Parameter .............................................. 225
Setting the NLS_LENGTH_SEMANTICS Parameter ........................... 226
Creating a Tablespace ............................................................................. 226
Creating a User ....................................................................................... 227
Configuring a Connection from the Oracle NET Client to the Oracle
Server .......................................................................................................... 228
Configuring Naming Methods ................................................................ 228
Creating a Local Net Service Name ......................................................... 229
Installing the Oracle ODBC Driver ............................................................ 230
Example Installation and Configuration ...................................................... 231

Chapter 11 SQL Server Setup................................................................................................... 233

Installing and Configuring SQL Server for Use with SampleManager ......... 234
Unicode and the Sqlserver_use_nvarchar Attribute in Structure.txt ......... 235
Configuring SQL Server Security ................................................................ 237
Permissions Required to Create a New SampleManager Instance in the
Database ................................................................................................. 238
Permissions for Connecting through SampleManager Client .................. 238
Permissions for Connecting through SQL Server ODBC Data Source .... 239
Recommended Database Options ............................................................... 239

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Index ........................................................................................................................ 241

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 P

Preface
Thermo Scientific™ SampleManager LIMS™ software can plan, manage, and maintain an
accurate record of work performed in a laboratory environment. The SampleManager
LIMS software incorporates Laboratory Information Management (LIMS), Data
Management (SDMS), and Process Execution and Procedural Electronic Lab Notebook
(LES) capabilities in a single solution.

This manual describes how to install SampleManager.

Contents
• Related Documentation
• Special Notices
• Contacting Us

Related Documentation
SampleManager includes Help, manuals, and guides as PDF files.

 To view the SampleManager product manuals

Navigate to the Docs folder on the SampleManager installation media.

 To open the Help

With the SampleManager client running, you can access Help in the following ways:
• Press the F1 key.
• From the main menu bar at the top of the SampleManager window, choose Help
and then click Contents.
• Click a Help button.

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Preface

Special Notices
Make sure that you follow the precautionary statements presented in this guide. The
special notices appear in boxes.

Special notices include the following:

CAUTION Highlights information necessary to prevent damage to software, loss of

data, invalid test results, or information that is critical for optimal performance of the
system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.

 To contact Technical Support

Email [email protected]

Web https://support.thermoinformatics.com/contacts

 To suggest changes or provide feedback on the documentation

Send an email to the Informatics Documentation Manager:

[email protected].

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 1

Introduction
This manual describes how to install and configure SampleManager, including:
• Introduction (this chapter) – SampleManager architecture, deployment, and general
information.
• Installing SampleManager Server for an Oracle Database (page 19) – How to set up
the server software and create a SampleManager server instance that uses an Oracle
database.
• Installing SampleManager Server for a SQL Server Database (page 59) – How to set
up the server software and create a SampleManager server instance that uses a SQL
Server database.
• Post-Installation Tasks (page 97) – How to install licenses and perform the initial
configuration of your SampleManager system.
• Installing SampleManager Client (page 115) – How to install the client software, set
up a connection to the server instance, and add licenses.
• Upgrading SampleManager (page 129) – How to upgrade the server and client.
• Installing LIMS Reporter (page 157) – How to install the reporting software and
configure it for your database.
• Installing Chromeleon Link Components (page 173) – How to install the
components that connect your SampleManager LIMS system to a Thermo Scientific
Dionex Chromeleon Chromatography Data System.
• Installing Data Manager Components (page 185) – How to install the components
that let your SampleManager LIMS system store, retrieve and view data created by
external applications, such as instrument control software.
• Oracle Setup (page 223) – An outline of how to set up Oracle Server and Oracle Net
Client for SampleManager.
• SQL Server Setup (page 233) – An outline of how to set up SQL Server for
SampleManager.

Thermo Scientific SampleManager LIMS Installation Guide 1

1 Introduction
Architecture

Contents
• Architecture
• Deployment
• System Requirements
• Overall Setup Procedure

Architecture
SampleManager systems use a three-tier architecture. The tiers are:
• Client – SampleManager supports two clients:

– SampleManager LIMS desktop client is an application that is installed on client

workstations. For more information, see Installing SampleManager Client (page
115). The desktop client is required for some implementation and configuration
tasks, such as development of custom forms, report templates, and label
templates.

– SampleManager LIMS web client can be accessed from any supported web
browser. The web client connects to the SampleManager web server component.
For more information, see the SampleManager Web Client Installation and
Configuration Guide.
• Application server – The application server hosts the SampleManager Server
application and the SampleManager instance that connects to a specific database.
• Database server – The database server hosts the SampleManager database.

Messages that are transmitted between the SampleManager Client and SampleManager
Server are encrypted before they are sent, using unique encryption keys that are generated
for each session. The encryption algorithms and code constructs are FIPS-compliant.

The SampleManager Server communicates with the database through an ADO

connection. See the documentation for your database platform for information about
configuring the database connection to use SSL.

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 1 Introduction
Architecture

The following diagram shows the architecture of a SampleManager system with a SQL
Server database. Client workstations can connect using both the SampleManager desktop
client and the SampleManager web client. The SampleManager Web Server component
is only required for systems where some clients connect using the SampleManager web
client. The SQL Server Connectivity Components are required when the
SampleManager Server and the database are hosted on separate servers.
Figure 1-1. SampleManager architecture with a SQL Server database

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1 Introduction
Architecture

The following diagram shows the architecture of a SampleManager system with an

Oracle database. Client workstations can connect using both the SampleManager
desktop client and the SampleManager web client. The SampleManager Web Server
component is only required for systems where some clients connect using the
SampleManager web client. The 32-bit Oracle Net Client is required to handle
communication between the 32-bit SampleManager Server and the 64-bit Oracle
database.
Figure 1-2. SampleManager architecture with an Oracle database

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 1 Introduction
Deployment

The SampleManager Web Client can be opened in a web browser, such as Google
Chrome. Most of the features of the SampleManager Client are available in the
SampleManager Web Client. For more information, see the SampleManager Web Client
User Guide and SampleManager Web Client Installation and Configuration Guide.

The database server, application server, and SampleManager Web Server can be hosted
on virtual servers in the cloud. SampleManager 12.2 has been validated on virtual
machines hosted by Amazon Web Services (AWS).

A single PC can host multiple tiers. Small systems can use one machine as a database
server, application server, and client PC. Larger systems typically use separate database
and application servers, with many client PCs. For more information, see Deployment
(page 5).

Deployment
SampleManager is designed for deployment as a distributed system, with many possible
configurations of the database, server, and client tiers. This section provides a basic
overview of the following possible configurations:
• Single-tier systems (page 6) suitable for demonstrations or development.
• Two-tier systems (page 7) suitable for testing, training, or other lower-usage
implementations.
• Three-tier systems (page 8) suitable for production systems. Complex three-tier
systems use technology such as high-availability databases and SampleManager
application server clusters to enhance performance and reliability for large
production implementations.

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1 Introduction
Deployment

Single-Tier Systems
In a single-tier system, a single machine hosts the database, the SampleManager server,
and the SampleManager client. Single-tier systems are useful for purposes such as
demonstrations, or developing and testing of custom code.
Figure 1-3. Single-tier system

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 1 Introduction
Deployment

Two-Tier Systems
In a two-tier system, the database and application server are installed on one server, and
users connect to the system from client workstations.

The following example shows a two-tier system that is configured to support both the
SampleManager desktop client and the SampleManager web client.

A two-tier system is easy to set up, but installing the database and application server on
the same server is not optimal for performance. This configuration is best suited for
demonstration, development, or training systems.

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1 Introduction
Deployment

Three-Tier Systems
In a three-tier system, the database, SampleManager server, and SampleManager client
are hosted on separate machines. The optional SampleManager web server lets users
connect with the SampleManager web client in a browser, without installing the
SampleManager desktop client on the client workstation.
Figure 1-4. Three-tier system

Large SampleManager systems that require high availability and performance can use
SampleManager application server clusters (page 10) for load balancing and high
availability database configurations to maximize performance and reliability. Each
component of the system can be tuned individually.

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 1 Introduction
Deployment

SampleManager LIMS does not maintain a central record of the instances that belong to
an application server cluster. For maintenance and upgrade purposes, we recommend
that you keep a record of your application server cluster architecture.
Figure 1-5. Complex three-tier system

SampleManager clients can be installed on a Citrix server farm to permit a high number
of clients and load balancing. The database server and application server can be hosted in
the Cloud to reduce management overheads.

Configuration and management of complex SampleManager systems requires more

expertise and management effort.

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1 Introduction
Deployment

Lock Daemon Operation with SampleManager Application Server Clusters

To increase the resilience of a SampleManager system, the application server for a
SampleManager instance can be installed on multiple servers that connect to a single
database. When SampleManager operates in this configuration, the lock daemon on the
first application server that connects to the database becomes the cluster manager lock
daemon. The connection details for the current cluster manager lock daemon are stored
in the USER_SETTINGS table. The lock daemons on the other application servers for
the instance act as local lock daemons. Each lock daemon has a connection to the
SampleManager database, which it uses to obtain the connection details for the current
cluster manager lock daemon.

When a SampleManager client connects to a SampleManager application server, it

connects to the lock daemon on that application server. All the lock daemons keep track
of the transaction requests and responses that pass through them.
Figure 1-6. SampleManager with clustered application servers

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 1 Introduction
Deployment

If the lock daemon on the application server is the current cluster manager lock daemon,
the transaction requests and responses for each connected client are handled locally.
Figure 1-7. Handling a lock request from a client connected to the cluster manager
lock daemon

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1 Introduction
Deployment

If the lock daemon on the application server is not the cluster manager lock daemon, the
transaction requests and responses for each connected client are passed to the cluster
manager lock daemon.
Figure 1-8. Handling a lock request from a client connected to a local lock daemon

If an application server that is not hosting the cluster manager lock daemon goes down,
the cluster manager lock daemon detects the failure and removes all locks associated with
the local lock daemon on that application server.

If the application server that is hosting the cluster manager lock daemon goes down, the
lock daemons on the remaining application servers reconfigure to continue operations.
The first local lock daemon that detects the failure of the cluster manager lock daemon
writes its connection details to the USER_SETTINGS table, becoming the new cluster
manager. The new cluster manager lock daemon re-establishes the lock transactions it has
handled with the database. The new cluster manager then accepts connections from the
other operational lock daemons in the cluster. Each of the other lock daemons passes its
list of active locks to the new cluster manager, and operations continue as normal.

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 1 Introduction
Deployment

Configuring Lock Daemon Clustering

To use lock daemon clusters, the Windows registry key for the lock daemon must
contain a use_cluster entry with the value set to true.

If the use_cluster value is false, or use_cluster is not present in the Windows registry key,
the lock daemon cluster mechanism is not used.

Configuring Lock Daemon Log File Generation

To generate a log file for a lock daemon, the Windows registry key for the lock daemon
must contain a debug entry.

The debug entry does not require a value.

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1 Introduction
System Requirements

System Requirements
This section provides a summary of the system requirements for a SampleManager
installation. For detailed information, see the SampleManager LIMS 12.2 Release Notes in
the installation kit.

For information about web browsers and other software supported for this release, see the
SampleManager LIMS 12.2 Release Notes in the installation kit.

Operating System
SampleManager is supported on the following operating systems:

Operating System and Version

Server
Microsoft Windows Server 2016

Client
Microsoft Windows 7 x64 Professional SP1

Microsoft Windows 7 x32 Professional SP1

Microsoft Windows 10 x64 Professional

Microsoft Windows 10 x64 Enterprise

Microsoft Windows Server 2016

+ Citrix XenApp Server 7.15, connecting using Citrix

Receiver for Web

Notes Any combination of the server and client operating systems can be used. If the
database is installed on the same machine as the SampleManager server, the database
version must be compatible with the server operating system. For more information,
see the documentation for your chosen database.

Database
SampleManager supports the following database platforms:
• Oracle 12c
• SQL Server 2016 SP1
• SQL Server 2016 SP2
• SQL Server 2017

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 1 Introduction
Overall Setup Procedure

Overall Setup Procedure

This section contains summaries of the setup procedure for a three-tier SampleManager
system. The procedure varies slightly depending on whether Oracle or SQL Server is
used for the database.

This section describes the overall setup procedure for the following databases:
• Oracle Database (page 15)
• SQL Server Database (page 16)

3-Tier Installation with an Oracle Database

This section describes the overall setup procedure when the SampleManager server
connects to an Oracle database.

1. Install and configure the Oracle database.

a. Perform the pre-installation checks (page 20).
a. Install Oracle and create an Oracle database on the database server machine.
b. Install a 32-bit Oracle client on the application server machine, and configure it
to connect to the database.
This step is also required for systems where the database server and
SampleManager server are on the same machine.
Note If you are using a single PC as the database and application server, restart the
server between installing Oracle and installing SampleManager.
See the Installing Oracle chapter (page 223).

2. Install SampleManager server.

a. Install SampleManager on the application server PC, and create a
SampleManager server instance that uses the Oracle database.
b. Obtain and install the license for SampleManager.

See the Installing SampleManager Server for an Oracle Database chapter (page 19).

3. Install SampleManager client software.

Set up your client PCs by installing SampleManager client software and configuring
a connection to the SampleManager server instance.

See the Installing SampleManager Client chapter (page 115).

4. If you want users to connect with the SampleManager web client, install and
configure the SampleManager Web Server.

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1 Introduction
Overall Setup Procedure

See the SampleManager Web Client Installation and Configuration Guide.

5. If you want to connect your SampleManager LIMS to a Chromeleon CDS, install

the Chromeleon Link components on your Chromeleon CDS application server.

See the Installing Chromeleon Link Components chapter (page 173).

6. If you want to use the Data Manager functionality to store and manage data created
by external applications, install the Data Manager components.
See the Installing Data Manager Components chapter (page 185).

3-Tier Installation with a SQL Server Database

This section describes the overall setup procedure when the SampleManager server
connects to a SQL Server database.
1. Install and configure the SQL Server database.
a. Perform the pre-installation checks (page 60).
a. Install SQL Server and create a SQL Server database on the database server
machine.
b. If your database and SampleManager application server are on separate
machines, install SQL Server connectivity components on the application server
machine.

See the SQL Server Setup chapter (page 233).

2. Install SampleManager server.
a. Install SampleManager on the application server machine, and create a
SampleManager server instance that uses the SQL Server database.
b. Obtain and install the license for SampleManager.

See the Installing SampleManager Server for a SQL Server Database chapter (page
59).

3. Install SampleManager client software.

Set up your client PCs by installing SampleManager client software and configuring
a connection to the SampleManager server instance.

See the Installing SampleManager Client chapter (page 115).

4. If you want users to connect with the SampleManager web client, install and
configure the SampleManager Web Server.
See the SampleManager Web Client Installation and Configuration Guide.

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 1 Introduction
Overall Setup Procedure

5. If you want to connect your SampleManager LIMS to a Chromeleon CDS, install

the Chromeleon Link components on your Chromeleon CDS application server.

See the Installing Chromeleon Link Components chapter (page 173).

6. If you want to use the Data Manager functionality to store and manage data created
by external applications, install the Data Manager components.

See the Installing Data Manager Components chapter (page 185).

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 2

Installing SampleManager Server for an Oracle

Database
This chapter describes the installation procedure for SampleManager server on a 64-bit
application server for connection to an Oracle database.

SampleManager is a true 32-bit application.

Contents
• Installation Procedure Summary
• Creating a SampleManager Instance
• Removing a SampleManager Instance

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2 Installing SampleManager Server for an Oracle Database
Installation Procedure Summary

Installation Procedure Summary

 To install SampleManager Server for use with a 64-bit Oracle database

1. Perform the Pre-Installation Checks (page 20).

2. Install Oracle (page 224) and create an Oracle database.

3. Make sure that the Oracle Net Listener for your database can connect to the
database.

4. Install and configure the 32-bit Oracle Net Client on the SampleManager Server
machine. See Configuring a Connection from the Oracle NET Client to the Oracle
Server (page 228).

5. Make sure that the Local Net Service Name for the 32-bit Oracle Net Client can
connect to your database through the Oracle Net Listener.
6. Install SampleManager Server (page 23).

7. Create a SampleManager instance (page 26).

If your instance will use the legacy LIMS Reporter tool (page 157) to generate reports,
install an Oracle ODBC driver (page 230) that LIMS Reporter can use to connect to the
database. LIMS Reporter is only available for existing SampleManager systems that have
custom InfoMaker reports.

Pre-Installation Checks
Before installing SampleManager server, perform the following tasks:

1. Make sure that the correct operating system is installed (page 14).
2. Back up your system as appropriate.

3. Make sure that your network is functioning correctly and uses the TCP/IP protocol.

4. Make a note of the full name of the computer on which you are installing
SampleManager server.

5. Make sure that the Microsoft .NET Framework 4.6.2 is installed on the server where
you will install SampleManager Server.
The installer for the required version of the Microsoft .NET Framework is included
in the following folder of the SampleManager installation kit:
..\SampleManager 12.2\Server\Redistributables

6. Make sure that the Microsoft Visual C++ 2017 Redistributable is installed on the
server where you will install SampleManager Server.

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 2 Installing SampleManager Server for an Oracle Database
Installation Procedure Summary

The installer for the Microsoft Visual C++ 2017 Redistributable is included in the
following folder of the SampleManager installation kit:
..\SampleManager 12.2\Server\Redistributables

Pre-Installation Requirement for the SampleManager Web Application

Note This requirement applies if you want to install the website and SampleManager
Web Application supplied with SampleManager. The website and SampleManager
Web Application are optional features. For more information, see the SampleManager
LIMS Web Interface Configuration Guide.

If you want to use the standard SampleManager website, you must install the
SampleManager Web Application on a separate server that uses the Windows Server
2008 R2 SP1 operating system.

The SampleManager Web Application requires Microsoft .NET Framework version 1.1.
You can download all editions of the .NET Framework from:

http://www.microsoft.com

You must install the Microsoft .NET Framework version 1.1 before you install any later
version of the .NET Framework. It is not possible to install the .NET Framework
version 1.1 after a later version of the .NET Framework.

Windows Server operating systems later than Windows Server 2008 R2 SP1 do not
support Microsoft .NET Framework version 1.1.

For more information about installing and configuring the SampleManager Web
Application and website, see the SampleManager LIMS Web Interface Configuration
Guide.

Installing Oracle
Before installing SampleManager, install and configure Oracle on the database server and
application server machines:

1. On your database server machine, install Oracle Server.

2. Create a fresh Oracle database, ready for conversion to a SampleManager database.

3. Make sure that the Oracle Net Listener for your database can connect to the
database.

4. Create a tablespace (page 226) in your database for SampleManager server data.
If you supply the password for the Oracle SYS account when you create a
SampleManager instance, the SampleManager Add Server Instance Wizard can
create a tablespace for you.

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2 Installing SampleManager Server for an Oracle Database
Installation Procedure Summary

5. Create a user (page 227) that the SampleManager instance will use to connect to
your Oracle database.

If you supply the password for the Oracle SYS account when you create a
SampleManager instance, the SampleManager Add Server Instance Wizard can
create a user account for you.

6. On your application server machine, install the 32-bit Oracle Net Client and
configure it to connect to your Oracle database (page 228).
Note If you install the SampleManager Server on the same computer as the Oracle
database, you must configure the 32-bit Oracle client to connect to the database
through a Net Service Name, in the same way as for a remote database server.
SampleManager Server cannot connect to the database using a 64-bit Oracle Client.
7. On the application server machine, run the Oracle Net Manager and make a note of
the exact Net Service Name that connects to your Oracle database.

By default, the Net Service Name is the same as the database name.

8. If your instance will use the legacy LIMS Reporter tool (page 157) to generate
reports, on the application server machine, install the Oracle ODBC driver (page
230). LIMS Reporter is only available for existing SampleManager systems that have
custom InfoMaker reports.

For more information, see Oracle Setup (page 223).

CAUTION If you are installing SampleManager server immediately after installing

Oracle, restart the application server PC.

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 2 Installing SampleManager Server for an Oracle Database
Installation Procedure Summary

Installing SampleManager Server

After Oracle is set up correctly, you can install SampleManager Server on the application
server PC. Install the software using an account with administrator rights.

1. In Windows Explorer, open the folder that contains your SampleManager

installation kit.

2. Open the following folder:

..\SampleManager 12.2\Server\en-US

3. Double-click the SampleManagerInstaller.msi file. The installation is prepared and

the Welcome page of the SampleManager LIMS 12.2 Setup wizard appears.
Figure 2-1. SampleManager Setup Wizard

4. If the Microsoft .NET Framework version 4.6.2 is not installed on your server, the
installation fails. To correct this problem:
a. Close the SampleManager Setup wizard and install Microsoft .NET Framework
version 4.6.2.
The installer for the required version of the Microsoft .NET Framework is
included in the following folder of the SampleManager installation kit:

..\SampleManager 12.2\Server\Redistributables

b. After the Microsoft .NET Framework version 4.6.2 is installed, repeat steps 1–2
to restart the installation of SampleManager Server.

If the Microsoft .NET Framework version 4.6.2 is installed on your server, you can
proceed with the installation.

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2 Installing SampleManager Server for an Oracle Database
Installation Procedure Summary

5. If the Microsoft Visual C++ 2017 Redistributable is not installed on your server, the
installation fails. To correct this problem:
a. Close the SampleManager Setup wizard and install Microsoft Visual C++ 2017
Redistributable.
The installer for the Microsoft Visual C++ 2017 Redistributable is included in
the following folder of the SampleManager installation kit:

..\SampleManager 12.2\Server\Redistributables

b. After the Microsoft Visual C++ 2017 Redistributable is installed, repeat steps
1–2 to restart the installation of SampleManager Server.

If the Microsoft Visual C++ 2017 Redistributable is installed on your server, you can
proceed with the installation.

6. Welcome to the SampleManager LIMS 12.2 Setup Wizard

Click Next to continue.

7. End-User License Agreement

a. Read the license agreement.
b. Select the check box to accept the license agreement. The installation cannot
proceed unless you accept the license agreement.

Click Next to continue.

8. Custom Setup
Choose the SampleManager components to install:
a. In the tree, click the Client + Server > Oracle item and choose Will be
installed on local hard drive.
b. The Thermo Licensing Server item is selected by default. If you want to use a
Thermo Licensing Server installed elsewhere on your network, click the Thermo
Licensing Server item and choose Entire feature will be unavailable.
c. If you want to use the Service Monitor, click the Service Monitor item and
choose Will be installed on local hard drive. The Service Monitor tool lets you
manage the services associated with SampleManager instances on your server.
d. If you want to change the location where SampleManager will be installed, click
Browse and select the location.
e. Click Next to continue.

9. Ready to Install SampleManager LIMS 12.2

Click Install to start installing the software.

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 2 Installing SampleManager Server for an Oracle Database
Installation Procedure Summary

10. Installing SampleManager LIMS 12.2

This page shows the progress of the installation.

11. Completed the Thermo SampleManager 12.2 Setup Wizard

If you chose to install the Thermo Licensing Server component, click Continue. The
Thermo Licensing Server – InstallShield Wizard appears.
12. If you did not choose to install the Thermo Licensing Server component, click
Finish to close the wizard.

The SampleManager Server software installation is complete.

Installing the Thermo Licensing Server

SampleManager uses FlexNet licensing, which is implemented through the Thermo
Licensing Server.

To use SampleManager, you must install the Thermo Licensing Server and then install
suitable licenses. If you want to host Thermo Licensing Server on your SampleManager
application server, you can include it in the SampleManager Server installation process.

If you want to host the Thermo Licensing Server on a remote machine, you can start the
installation wizard manually.

 To start the Thermo Licensing Server – InstallShield Wizard

1. Open the License folder of the SampleManager installation kit:

..\Server\en-US\PFiles\Thermo\SampleManager\12.2\License

Note When SampleManager Server is installed, the License folder is copied to the
root folder for the SampleManager Server installation. The default location for the
root folder is:
c:\Program Files (x86)\Thermo\SampleManager\12.2

2. Run ThermoLicensingServerSetup.exe. The Thermo Licensing Server –

InstallShield Wizard appears.

 To install the Thermo Licensing Server

1. Welcome to the InstallShield Wizard for Thermo Licensing Server

Click Next to continue.

2. Destination Folder
a. Either accept the default location for the installation, or browse for an
alternative.
b. Click Next to continue.

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2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

3. Network Share
SampleManager does not use the network share feature. Click Next to continue.

4. Ready to Install the Program

Click Install to begin the installation.

5. InstallShield Wizard Completed

Click Finish to close the wizard.

SampleManager allows the SYSTEM user to connect to the SampleManager server if

there is no other user connected at that time. This feature lets you install and test your
SampleManager client. For information about obtaining and installing your
SampleManager licenses, see Product Licenses (page 98).

Creating a SampleManager Instance

After the SampleManager Server software installation is complete, you can create a
SampleManager instance from your Oracle database.

This Setup Wizard can create different types of SampleManager instance. The following
sections describe the settings required to create each type:
• Creating a New Instance (page 27)
This procedure creates a new standalone SampleManager instance with a database
that is populated with default SampleManager data.
• Creating a Cloned Instance (page 37)

This procedure creates a copy of an existing SampleManager instance, which

connects to a copy of the database associated with the original instance.
• Creating an Application Server (page 41)

This procedure creates a SampleManager instance that shares a database and files
with another instance. Application server instances are useful for large
SampleManager implementations that require load-balancing and sharing to enhance
performance.
• Creating a New Site Instance (page 47)

This procedure creates a SampleManager instance that shares files with another
instance, but has its own database that is populated with default SampleManager
data.

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

Creating a New Instance

This section describes the creation of a new SampleManager instance with the following
features:
• Database – The instance connects to an Oracle database, which is populated with
default SampleManager data by the instance creation process. See Oracle Setup (page
223) for information about configuring Oracle and creating a suitable database.
• Folders and files – The wizard creates an instance folder that contains the files
associated with the instance. See the "Operating Environment" chapter in the
SampleManager LIMS System Administration Guide for a description of each
subfolder in the instance folder.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon. See the "Operating
Environment" chapter in the SampleManager LIMS System Administration Guide for
a description of each service.
• Windows Registry – The wizard creates Windows registry entries associated with
the instance.
Figure 2-2. New instance

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2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

 To create a new SampleManager instance

1. In Oracle (page 21), create an empty database ready for the SampleManager instance
data.

2. On the server that will host your instance, install SampleManager Server (page 23).

3. The instance will require a connection to a Thermo Licensing Server. Use one of the
following methods to provide the connection:
• Install the Thermo Licensing Server (page 25) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.

4. From the Start menu, click Thermo SampleManager 12.2 > Add Oracle Instance.

The Setup Wizard appears.

5. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.
Figure 2-3. Setup Wizard

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

6. Choose setup procedure

a. Click New Instance.
b. Click Next to continue.
Figure 2-4. Setup Wizard – Choose setup procedure

7. Choose Server Instance Details

a. Enter a name for the SampleManager server instance. The default instance name
is VGSM.
b. Specify the base port number that the services associated with the instance will
use. The default base port number is 56100.
c. Click Next to continue.
Figure 2-5. Setup Wizard – Choose Server Instance Details

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2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

8. Choose Location
a. Either accept the default location for the instance files, or browse for an
alternative.
b. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:
• port is the port number of the Thermo Licensing service on the remote
server
• hostname is the name of the remote server
c. Click Next to continue.
Figure 2-6. Setup Wizard – Choose Location

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

9. Choose Oracle Database

a. Choose the Oracle database that the instance will use.
The Database list contains all the Oracle Net Service Names that have been set
up on the SampleManager application server. If your database is a pluggable
database (PDB) in a multitenant container database (CDB), choose the Oracle
Net Service Name that connects to the pluggable database.
b. Enter the password for the SYS account of the selected database.
The wizard uses the SYS user and corresponding password for system
administration operations during the creation of the SampleManager server
instance. The SYS password will be used to connect to Oracle during the
instance creation process, but will not be stored or cached by SampleManager.
c. If you cannot supply the SYS password for your Oracle database, select I don't
know the SYS password. Please let me continue. Selecting this check box
restricts the options available in the remaining pages of the wizard.
d. Click Next to continue.
Figure 2-7. Setup Wizard – Choose Oracle Database

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Creating a SampleManager Instance

10. Choose Database Account

The SampleManager server instance will always use the account specified on this
page when creating tables and other database structures in Oracle.
a. Enter an Oracle username and password.
If you supplied the SYS account password on the Choose Oracle Database page,
the following options are available:
• Enter the name and password of an existing account that SampleManager
can use. The account must have the necessary permissions to create the
tables and other structures.

• Enter the name and password for an account that does not exist. The wizard
will create an account for SampleManager using the details you enter. The
default username and password are the same as the name of the instance.
If you did not supply the SYS account password, enter the username and
password of an existing account.
b. Click Next to continue.
The next page that appears depends on whether you supplied the SYS password
on the Choose Oracle Database page.
Figure 2-8. Setup Wizard – Choose Database Account

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

11. Choose Oracle Tablespace (SYS password supplied)

This step applies if you supplied the SYS password for your Oracle database on the
Choose Oracle Database page.
a. If you want to use an existing tablespace in your Oracle database for the
SampleManager data, select Use an existing tablespace and choose the
tablespace you want to use. The list contains all the tablespaces in the Oracle
database.
b. If you want the Add Instance Wizard to create a tablespace for your data, select
Create a new tablespace and enter the SQL command that you want the wizard
to use. For example:
CREATE TABLESPACE SMDB_DB DATAFILE
'D:\oracle\oradata\SMDB\SMDB_DB.DBF' SIZE 100M REUSE AUTOEXTEND
ON NEXT 50M MAXSIZE 500M
We recommend that you use '[instance name]_DB' as your tablespace name.
This option is only available if you supplied the SYS password for the Oracle
database.
c. If you have created a new version of structure.txt containing customized
tablespace information for any of the tables, clear Update oracle_location
details in Structure.txt. For more information, see the "Data Storage and
Handling in Oracle" chapter in the SampleManager LIMS System
Administration Guide.
If this check box is selected, the structure.txt file will be updated with details of
the specified tablespace before the instance is created.
d. Click Next to continue.
Figure 2-9. Setup Wizard – Choose Oracle Tablespace (SYS password supplied)

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Creating a SampleManager Instance

12. Choose Oracle Tablespace (SYS password not supplied)

This step applies if you selected I don't know the SYS password. Please let me
continue on the Choose Oracle Database page.
a. Enter the name of the tablespace that has been created for SampleManager in
your Oracle database.
b. Click Next to continue.
Figure 2-10. Setup Wizard – Choose Oracle Tablespace (SYS password not
supplied)

13. Connection String Configuration

The Connection String prompt contains the default ADO connection string that the
wizard has constructed from the information you supplied in the preceding pages.
If you specified the details of an existing Oracle user, test the ADO string:
a. Click Test. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. Click Next to continue.

If you have chosen to let the wizard create the Oracle user, click Next to continue. If
you test the connection, it will fail because the user account specified in the
connection string has not been created yet.

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Creating a SampleManager Instance

Figure 2-11. Setup Wizard – Connection String Configuration

14. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.
Figure 2-12. Setup Wizard – Confirm Details

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Creating a SampleManager Instance

15. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.
Figure 2-13. Setup Wizard – Instance Creation in Progress

16. Server Instance Created

To close the Setup Wizard, click Finish.
Figure 2-14. Setup Wizard – Server Instance Created

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

Creating a Cloned Instance

This section describes the creation of a SampleManager instance that uses a
pre-populated SampleManager database. This type of instance is useful if you want to
create an instance that duplicates the features and data of an existing SampleManager
system. This example creates an instance with the following features:
• Database – The instance connects to an existing SampleManager database that is
not associated with any other SampleManager instance. For example, a copy of an
existing SampleManager database from a production system.
• Folders and files – The wizard creates a new instance folder that contains the files
associated with the instance. The files are copied from the SampleManager instance
associated with the database that you copied.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon.
• Windows registry – The wizard creates Windows registry entries associated with the
instance.
Figure 2-15. Cloned instance

 To create a cloned SampleManager instance

1. Use Oracle tools to create a copy of the SampleManager database that the instance
you want to clone connects to. See your Oracle documentation for more
information.
2. On the SampleManager application server, use the 32-bit Oracle Client tools to
create a local net service name (page 229) that connects to the copy of the database
that you created in step 1.

3. On the server that will host your instance, install SampleManager Server (page 23).

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2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

4. The instance will require a connection to a Thermo Licensing Server. Use one of the
following methods to provide the connection:
• Install the Thermo Licensing Server (page 25) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.

5. From the Start menu, click Thermo SampleManager 12.2 > Add Oracle Instance.

The Setup Wizard appears.

6. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.

7. Choose Instance Type

a. Click Clone Instance.
b. Click Next to continue.
Figure 2-16. Setup Wizard – Choose setup procedure

8. Choose Server Instance Details

a. Enter a unique name for the SampleManager server instance.
b. Specify the base port number that the services associated with the instance will
use. Make sure that you choose a base port number that is not used by any other
service on the server.
c. Click Next to continue.

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Creating a SampleManager Instance

9. Choose Location
a. Either accept the default location for the cloned instance files, or browse for an
alternative.
b. Specify the location of the root folder for the SampleManager instance that you
want to clone. For example:
C:\Thermo\SampleManager\Server\VGSM
c. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:
• port is the port number of the Thermo Licensing service on the remote
server
• hostname is the name of the remote server
d. Click Next to continue.
Figure 2-17. Setup Wizard – Choose Location

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Creating a SampleManager Instance

10. Choose Oracle Database

a. Choose the Oracle database that the instance will use.
The Database list contains all the Oracle Net Service Names that have been set
up on the SampleManager application server. Choose the item that corresponds
to the Oracle Net Service Name you created in step 1 of this procedure.
b. Select I don't know the SYS password. Please let me continue.
As the application server will connect to an existing SampleManager database
with an existing Oracle user account, the SYS password is not required to create
this type of instance.
c. Click Next to continue.

11. Choose Database Account

The SampleManager server instance will always use the account specified on this
page when creating tables and other database structures in Oracle.
a. Enter the Oracle username and password that were created for SampleManager
in this database.
b. Click Next to continue.

12. Connection String Configuration

a. Click Test to check the ADO connection string for the instance. The string is
constructed using the information you entered on the preceding pages of the
wizard. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. When the ADO connection string test is successful, click Next to continue.

13. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.

14. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.

15. Server Instance Created

To close the Setup Wizard, click Finish.

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

Creating an Application Server Instance

This section describes the creation of a new SampleManager instance with the following
features:
• Database – The instance connects to an existing SampleManager database that it
shares with one or more other SampleManager instances.
• Instance Name – The instance has the same name as the other application server
instances that connect to the shared database.
• Folders and files – The wizard creates an instance folder that contains the executable
files associated with the instance.

All the other files required for SampleManager operations, such as report designs and
VGL libraries, are obtained from a shared folder that is specified during the instance
creation process. All the application instances that connect to the shared database
should use the same shared folder.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon. For a description of each
service, see the "Operating Environment" chapter in the SampleManager LIMS
System Administration Guide. The lock daemon for the application server operates as
one of the cluster of lock daemons associated with the applications servers that
connect to the shared database. For more information about lock daemon clustering,
see Lock Daemon Operation with SampleManager Application Server Clusters (page
10).
• Windows registry – The wizard creates Windows registry entries associated with the
instance.

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Creating a SampleManager Instance

Figure 2-18. Application server instance

Each application server instance in the cluster that connects to a single database must be
installed on a separate server.

SampleManager LIMS does not maintain a central record of the instances that belong to
an application server cluster. For maintenance and upgrade purposes, we recommend
that you keep a record of your application server cluster architecture.

To create the first instance in a planned cluster of application server instances, create a
new instance, as described in Creating a New Instance (page 27). When the new instance
is operating correctly, configure the Lock Daemon to operate as part of a cluster.

Note When you install an application server with the Setup Wizard, the installation
process configures the lock daemon to run in cluster mode. The lock daemon must be
configured manually for the first instance in an application server cluster.

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Creating a SampleManager Instance

 To configure the lock daemon to operate as part of a cluster

1. On the server that hosts your new SampleManager instance, open the Registry
Editor.

2. Navigate to the following registry key:

Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\
LabSystems\SampleManager Server\smplock<instance_name>
Where <instance_name> is the name of the instance.

3. Set the use_cluster value to true.

 To create an application server SampleManager instance

1. On the server that will host your instance, install SampleManager Server (page 23).

2. The instance will require a connection to a Thermo Licensing Server. Use one of the
following methods to provide the connection:
• Install the Thermo Licensing Server (page 25) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.
3. From the Start menu, click Thermo SampleManager 12.2 > Add Oracle Instance.
The Setup Wizard appears.

4. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.

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Creating a SampleManager Instance

5. Choose Instance Type

a. Click Application Server.
b. Click Next to continue.
Figure 2-19. Setup Wizard – Choose setup procedure

6. Choose Server Instance Details

a. Enter a name for the application server instance. The name must match the
name of the other application server instances that share the same
SampleManager database.
b. Specify the base port number that the services associated with the instance will
use. Make sure that you choose a base port number that is not used by any other
service on the server.
c. Click Next to continue.

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Creating a SampleManager Instance

7. Choose Location
a. Either accept the default location for the instance files, or browse for an
alternative.
b. Specify the location of the SampleManager instance root folder that contains the
files you want this instance to share. The folder must be shared and accessible to
the user accounts that will be associated with the Windows services for your new
instance.
Specify the shared folder location as a UNC path, not a mapped drive.
c. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:

• port is the port number of the Thermo Licensing service on the remote
server

• hostname is the name of the remote server

d. Click Next to continue.
Figure 2-20. Setup Wizard – Choose Location

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Creating a SampleManager Instance

8. Choose Oracle Database

a. Choose the Oracle database that the instance will use.
The Database list contains all the Oracle Net Service Names that have been set
up on the SampleManager application server. If your database is a pluggable
database (PDB) in a multitenant container database (CDB), choose the Oracle
Net Service Name that connects to the pluggable database.
b. Select I don't know the SYS password. Please let me continue.
As the application server will connect to an existing SampleManager database
with an existing Oracle user account, the SYS password is not required to create
this type of instance.
c. Click Next to continue.

9. Choose Database Account

The SampleManager server instance will always use the account specified on this
page when creating tables and other database structures in Oracle.
a. Enter the Oracle username and password used by the other SampleManager
instances that connect to this database.
b. Click Next to continue.

10. Connection String Configuration

a. Click Test to check the ADO connection string for the instance. The string is
constructed using the information you entered on the preceding pages of the
wizard. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. When the ADO connection string test is successful, click Next to continue.

11. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.

12. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.

13. Server Instance Created

To close the Setup Wizard, click Finish.

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

Creating a New Site Instance

This example demonstrates the creation of a new SampleManager instance with the
following features:
• Database – The instance connects to an Oracle database, which is populated with
default SampleManager data by the instance creation process. See Oracle Setup (page
223) for information about configuring Oracle and creating a suitable database.
• Folders and files – The wizard creates an instance folder that contains the executable
files associated with the instance. The instance shares data files such as report
templates and VGL reports with another instance. See the "Operating Environment"
chapter in the SampleManager LIMS System Administration Guide for a description of
each subfolder in the instance folder.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon. See the "Operating
Environment" chapter in the SampleManager LIMS System Administration Guide for
a description of each service.
• Windows Registry – The wizard creates Windows registry entries associated with
the instance.

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2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

Figure 2-21. Site instance

SampleManager LIMS does not maintain a central record of the site instances that share
files with another instance. For maintenance and upgrade purposes, we recommend that
you keep a record of your site instance architecture.

 To create a new site instance

1. In Oracle (page 21), create an empty database ready for the SampleManager instance
data.

2. On the server that will host your instance, install the 32-bit Oracle Net Client, and
configure it to connect to your Oracle database (page 228).

3. On the server that will host your instance, install SampleManager Server (page 23).

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Creating a SampleManager Instance

4. The instance will require a connection to a Thermo Licensing Server. Use one of the
following methods to provide the connection:
• Install the Thermo Licensing Server (page 25) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.

5. From the Start menu, click Thermo SampleManager 12.2 > Add Oracle Instance.

The Setup Wizard appears.

6. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.

7. Choose setup procedure

a. Click New Site Instance.
b. Click Next to continue.
Figure 2-22. Setup Wizard – Choose setup procedure

8. Choose Server Instance Details

a. Enter a unique name for the site instance.
b. Specify the base port number that the services associated with the instance will
use. Make sure that you choose a base port number that is not used by any other
service on the server.
c. Click Next to continue.

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Creating a SampleManager Instance

9. Choose Location
a. Either accept the default location for the cloned instance files, or browse for an
alternative.
b. Specify the location of the root folder for the SampleManager instance that you
want the site to share files with. For example:
C:\Thermo\SampleManager\Server\VGSM
c. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:
• port is the port number of the Thermo Licensing service on the remote
server
• hostname is the name of the remote server
d. Click Next to continue.
Figure 2-23. Setup Wizard – Choose Location

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 2 Installing SampleManager Server for an Oracle Database
Creating a SampleManager Instance

10. Choose Oracle Database

a. Choose the Oracle database that the instance will use.
The Database list contains all the Oracle Net Service Names that have been set
up on the SampleManager application server. If your database is a pluggable
database (PDB) in a multitenant container database (CDB), choose the Oracle
Net Service Name that connects to the pluggable database.
b. Enter the password for the SYS account of the selected database.
The wizard uses the SYS user and corresponding password for system
administration operations during the creation of the SampleManager server
instance. The SYS password will be used to connect to Oracle during the
instance creation process, but will not be stored or cached by SampleManager.
c. If you cannot supply the SYS password for your Oracle database, select I don't
know the SYS password. Please let me continue. Selecting this check box
restricts the options available in the remaining pages of the wizard.
d. Click Next to continue.

11. Choose Database Account

The SampleManager server instance will always use the account specified on this
page when creating tables and other database structures in Oracle.
a. Enter an Oracle username and password.
If you supplied the SYS account password on the Choose Oracle Database page,
the following options are available:

• Enter the name and password of an existing account that SampleManager

can use. The account must have the necessary permissions to create the
tables and other structures.
• Enter the name and password for an account that does not exist. The wizard
will create an account for SampleManager using the details you enter. The
default username and password are the same as the name of the instance.
If you did not supply the SYS account password, enter the username and
password of an existing account.
b. Click Next to continue.
c. The next page that appears depends on whether you supplied the SYS password
on the Choose Oracle Database page.

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12. Choose Oracle Tablespace (SYS password supplied)

This step applies if you supplied the SYS password for your Oracle database on the
Choose Oracle Database page.
a. If you want to use an existing tablespace in your Oracle database for the
SampleManager data, select Use an existing tablespace and choose the
tablespace you want to use. The list contains all the tablespaces in the Oracle
database.
b. If you want the Add Instance Wizard to create a tablespace for your data, select
Create a new tablespace and enter the SQL command that you want the wizard
to use. For example:
CREATE TABLESPACE SMDB_DB DATAFILE
'D:\oracle\oradata\SMDB\SMDB_DB.DBF' SIZE 100M REUSE AUTOEXTEND
ON NEXT 50M MAXSIZE 500M
We recommend that you use '[instance name]_DB' as your tablespace name.
This option is only available if you supplied the SYS password for the Oracle
database.
c. If you have created a new version of structure.txt containing customized
tablespace information for any of the tables, clear Update oracle_location
details in Structure.txt. For more information, see the "Data Storage and
Handling in Oracle" chapter in the SampleManager LIMS System
Administration Guide.
If this check box is selected, the structure.txt file will be updated with details of
the specified tablespace before the instance is created.
d. Click Next to continue.
Figure 2-24. Setup Wizard – Choose Oracle Tablespace (SYS password supplied)

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Creating a SampleManager Instance

13. Choose Oracle Tablespace (SYS password not supplied)

This step applies if you selected I don't know the SYS password. Please let me
continue on the Choose Oracle Database page.
a. Enter the name of the tablespace that has been created for SampleManager in
your Oracle database.
b. Click Next to continue.
Figure 2-25. Setup Wizard – Choose Oracle Tablespace (SYS password not
supplied)

14. Connection String Configuration

The Connection String prompt contains the default ADO connection string that the
wizard has constructed from the information you supplied in the preceding pages.
If you specified the details of an existing Oracle user, test the ADO string:
a. Click Test. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. Click Next to continue.

If you have chosen to let the wizard create the Oracle user, click Next to continue. If
you test the connection, it will fail because the user account specified in the
connection string has not been created yet.

15. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.

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Creating a SampleManager Instance

16. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.

17. Server Instance Created

To close the Setup Wizard, click Finish.

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

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Removing a SampleManager Instance

Removing a SampleManager Instance

Use the Delete Server Instance Wizard to remove a SampleManager server instance.

Note This wizard removes the SampleManager server instance and gives you the
option to remove the data associated with the instance. The underlying Oracle
database structure is left on your system. You can remove the database afterwards,
using standard Oracle tools.

1. From the Start menu, click Thermo SampleManager 12.2 > Remove Oracle
Instance.

The Setup Wizard appears.

2. Welcome to the Delete Server Instance Wizard

Click Next to continue.
Figure 2-26. Delete Server Instance wizard

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Removing a SampleManager Instance

3. Choose Instance
a. Select the instance that you want to delete
b. Click Next to continue.
Figure 2-27. Delete Server Instance wizard – Choose Instance

4. Enter Oracle Details

If you want the wizard to delete the data associated with the instance in the database:
a. Select the Delete the database account and table data check box.
b. Enter the password for the SYS account in the Oracle database.
If the check box is not selected, SampleManager user accounts and data will be
left in the Oracle database. Clear the check box if the underlying database
cannot be accessed, for example if it has been deleted manually.
c. Click Next to continue.
CAUTION Selecting the check box results in the permanent deletion of
SampleManager data from the database. You will not be able to restore the database
or recover its data.
If the instance is an application server that shares its database with other <product
instances, selecting the check box deletes the data from the shared database.

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Removing a SampleManager Instance

Figure 2-28. Delete Server Instance wizard – Enter Oracle Details

5. Confirm Details
Check the details shown and click Next to continue.
Figure 2-29. Delete Server Instance wizard – Confirm Details

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Removing a SampleManager Instance

6. Instance Deletion in Progress

The wizard deletes the instance. When the instance deletion is complete, the Save
Log and Next buttons are enabled.

Click Save Log to save a log file of the instance deletion. Click Next to continue.
Figure 2-30. Delete Server Instance Wizard – Instance Deletion in Progress

7. Server Instance Deleted

The final page of the wizard appears. Click Finish to close the Delete Server Instance
Wizard.
Figure 2-31. Delete Server Instance wizard – Server Instance Deleted

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 3

Installing SampleManager Server for a SQL

Server Database
This chapter describes the installation procedure for SampleManager server on a 64-bit
application server for connection to a SQL Server database.

SampleManager is a true 32-bit application.

Contents
• Installation Procedure Summary
• Creating a SampleManager Instance
• Removing a SampleManager Instance

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Installation Procedure Summary

Installation Procedure Summary

 To install SampleManager Server for use with a SQL Server database

1. Perform the pre-installation checks (page 60).

2. On the database server, install SQL Server (page 62) and create a SQL Server
database.
3. Restart the database server.

4. If you intend to install SampleManager Server and the SQL Server database on
separate machines, install and configure the SQL Server Client Tools Connectivity
feature on the SampleManager application server machine.

The Imprint reporting tool requires a SQL Server Native Client ODBC data source
to connect to the database.

5. If the database and SampleManager application server are on separate machines,

make sure that the SQL Server Client Tools on the application server can connect to
the database.

6. Install SampleManager Server (page 62).

7. Create a SampleManager instance (page 66).

Pre-Installation Checks
Before installing SampleManager server, perform the following tasks:

1. Make sure that the correct operating system is installed (page 14).
2. Back up your system as appropriate.

3. Make sure that your network is functioning correctly and uses the TCP/IP protocol.

4. Make a note of the full name of the computer on which you are installing
SampleManager server.

5. Make sure that the Microsoft .NET Framework 4.6.2 is installed on the server where
you will install SampleManager Server.

The installer for the required version of the Microsoft .NET Framework is included
in the following folder of the SampleManager installation kit:
..\SampleManager 12.2\Server\Redistributables

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6. Make sure that the Microsoft Visual C++ 2017 Redistributable is installed on the
server where you will install SampleManager Server.

The installer for the Microsoft Visual C++ 2017 Redistributable is included in the
following folder of the SampleManager installation kit:
..\SampleManager 12.2\Server\Redistributables

7. If SampleManager will connect to SQL Server using Windows Authentication,

create an appropriate Windows user account for the smdaemon service to use.

Pre-Installation Requirement for the SampleManager Web Application

Note This requirement applies if you want to install the website and SampleManager
Web Application supplied with SampleManager. The website and SampleManager
Web Application are optional features. For more information, see the SampleManager
LIMS Web Interface Configuration Guide.

If you want to use the standard SampleManager website, you must install the
SampleManager Web Application on a separate server that uses the Windows Server
2008 R2 SP1 operating system.

The SampleManager Web Application requires Microsoft .NET Framework version 1.1.
You can download all editions of the .NET Framework from:

http://www.microsoft.com

You must install the Microsoft .NET Framework version 1.1 before you install any later
version of the .NET Framework. It is not possible to install the .NET Framework
version 1.1 after a later version of the .NET Framework.

Windows Server operating systems later than Windows Server 2008 R2 SP1 do not
support Microsoft .NET Framework version 1.1.

For more information about installing and configuring the SampleManager Web
Application and website, see the SampleManager LIMS Web Interface Configuration
Guide.

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Installation Procedure Summary

Installing SQL Server

Before you install SampleManager, install and configure SQL Server on the database
server and application server PCs:

1. Install SQL Server on your database server PC.

2. Create a fresh SQL Server database, ready for conversion to a SampleManager

database.

3. Restart the database server.

4. Install the SQL Server Connectivity Components on your application server PC and
configure the connection to the database server. The Imprint reporting tool requires
a SQL Server Native Client ODBC data source to connect to the database.
Note The SQL Server installation includes the SQL Server Connectivity
Components. You can omit this step if the SQL Server and SampleManager server
will be installed on the same machine.
5. If SampleManager will connect to SQL Server using Windows authentication, grant
the Windows user account that SampleManager will use appropriate access to the
database that will contain your SampleManager data.
If SampleManager will connect to SQL Server using SQL Server authentication, set
up the login that SampleManager will use. Make sure that the login has been granted
the appropriate access to the database that will contain your SampleManager data.

See the SQL Server Setup chapter (page 233) for more details.

Installing SampleManager Server

After the SQL Server installation is complete, you can install SampleManager server on
the application server PC.

 To install SampleManager server

1. In Windows Explorer, open the folder that contains your SampleManager

installation kit.
2. Open the following folder:

..\SampleManager 12.2\Server\en-US

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3. Double-click the SampleManagerInstaller.msi file. The installation is prepared and

the Welcome page of the SampleManager LIMS 12.2 Setup wizard appears.
Figure 3-1. SampleManager Setup Wizard

4. If the Microsoft .NET Framework version 4.6.2 is not installed on your server, the
installation fails. To correct this problem:
a. Close the SampleManager Setup wizard and install Microsoft .NET Framework
version 4.6.2.
The installer for the required version of the Microsoft .NET Framework is
included in the following folder of the SampleManager installation kit:

..\SampleManager 12.2\Server\Redistributables

b. After the Microsoft .NET Framework version 4.6.2 is installed, repeat steps 1–2
to restart the installation of SampleManager Server.
If the Microsoft .NET Framework version 4.6.2 is installed on your server, you can
proceed with the installation.

5. If the Microsoft Visual C++ 2017 Redistributable is not installed on your server, the
installation fails. To correct this problem:
a. Close the SampleManager Setup wizard and install Microsoft Visual C++ 2017
Redistributable.
The installer for the Microsoft Visual C++ 2017 Redistributable is included in
the following folder of the SampleManager installation kit:

..\SampleManager 12.2\Server\Redistributables

b. After the Microsoft Visual C++ 2017 Redistributable is installed, repeat steps
1–2 to restart the installation of SampleManager Server.

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If the Microsoft Visual C++ 2017 Redistributable is installed on your server, you can
proceed with the installation.

6. Welcome to the SampleManager LIMS 12.2 Setup Wizard

Click Next to continue.

7. End-User License Agreement

a. Read the license agreement.
b. Select the check box to accept the license agreement. The installation cannot
proceed unless you accept the license agreement.
c. Click Next to continue.

8. Custom Setup
Choose the SampleManager components to install:
a. In the tree, click the Client + Server > SQL item and choose Will be installed
on local hard drive.
b. The Thermo Licensing Server item is selected by default. If you want to use a
Thermo Licensing Server installed elsewhere on your network, click the Thermo
Licensing Server item and choose Entire feature will be unavailable.
c. If you want to use the Service Monitor, click the Service Monitor item and
choose Will be installed on local hard drive. The Service Monitor tool lets you
manage the services associated with SampleManager instances on your server.
d. If you want to change the location where SampleManager will be installed, click
Browse and select the location.
e. Click Next to continue.

9. Ready to Install SampleManager LIMS 12.2

Click Install to start installing the software.

10. Installing SampleManager LIMS 12.2

This page shows the progress of the installation.

11. Completed the Thermo SampleManager 12.2 Setup Wizard

If you chose to install the Thermo Licensing Server component, click Continue. The
Thermo Licensing Server – InstallShield Wizard appears.

If you did not choose to install the Thermo Licensing Server component, click
Finish to close the wizard.

The SampleManager Server installation is complete.

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Installation Procedure Summary

Installing the Thermo Licensing Server

SampleManager uses FlexNet licensing, which is implemented through the Thermo
Licensing Server.

To use SampleManager, you must install the Thermo Licensing Server and then install
suitable licenses. If you want to host Thermo Licensing Server on your SampleManager
application server, you can include it in the SampleManager Server installation process.

If you want to host the Thermo Licensing Server on a remote machine, you can start the
installation wizard manually.

 To start the Thermo Licensing Server – InstallShield Wizard

1. Open the License folder of the SampleManager installation kit:

..\Server\en-US\PFiles\Thermo\SampleManager\12.2\License

Note When SampleManager Server is installed, the License folder is copied to the
root folder for the SampleManager Server installation. The default location for the
root folder is:
c:\Program Files (x86)\Thermo\SampleManager\12.2

2. Run ThermoLicensingServerSetup.exe. The Thermo Licensing Server –

InstallShield Wizard appears.

 To install the Thermo Licensing Server

1. Welcome to the InstallShield Wizard for Thermo Licensing Server

Click Next to continue.

2. Destination Folder
a. Either accept the default location for the installation, or browse for an
alternative.
b. Click Next to continue.

3. Network Share
SampleManager does not use the network share feature. Click Next to continue.

4. Ready to Install the Program

Click Install to begin the installation.

5. InstallShield Wizard Completed

Click Finish to close the wizard.

SampleManager allows the SYSTEM user to connect to the SampleManager server if

there is no other user connected at that time. This feature lets you install and test your

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Creating a SampleManager Instance

SampleManager client. For information about obtaining and installing your

SampleManager licenses, see Product Licenses (page 98).

Creating a SampleManager Instance

After the SampleManager Server software installation is complete, you can create a
SampleManager instance from your SQL Server database.

This Setup Wizard can create different types of SampleManager instance. The following
sections describe the settings required to create each type:
• Creating a New Instance (page 67)

This procedure creates a new standalone SampleManager instance with a database

that is populated with default SampleManager data.
• Creating a Cloned Instance (page 76)
This procedure creates a copy of an existing SampleManager instance, which
connects to a copy of the database associated with the original instance.
• Creating an Application Server (page 81)
This procedure creates a SampleManager instance that shares a database and files
with another instance. Application server instances are useful for large
SampleManager implementations that require load-balancing and sharing to enhance
performance.
• Creating a New Site Instance (page 87)

This procedure creates a SampleManager instance that shares files with another
instance, but has its own database that is populated with default SampleManager
data.

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Creating a New Instance

This section describes the creation of a new SampleManager instance with the following
features:
• Database – The instance connects to a SQL Server database, which is populated
with default SampleManager data by the instance creation process. See SQL Server
Setup (page 233) for information about configuring SQL Server and creating a
suitable database.
• Folders and files – The wizard creates an instance folder that contains the files
associated with the instance. See the "Operating Environment" chapter in the
SampleManager LIMS System Administration Guide for a description of each
subfolder in the instance folder.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon. See the "Operating
Environment" chapter in the SampleManager LIMS System Administration Guide for
a description of each service.
• Windows Registry – The wizard creates Windows registry entries associated with
the instance.
Figure 3-2. New instance

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Creating a SampleManager Instance

 To create a new SampleManager instance

1. In SQL Server (page 62), create an empty database ready for the SampleManager
instance data.

2. On the server that will host your instance, install SampleManager Server (page 62).

3. The instance will require a connection to a Thermo Licensing Server. Do one of the
following:
• Install the Thermo Licensing Server (page 65) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.

4. From the Start menu, click Thermo SampleManager 12.2 > Add SQL Instance.

The Setup Wizard appears.

5. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.
Figure 3-3. Setup Wizard

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 3 Installing SampleManager Server for a SQL Server Database
Creating a SampleManager Instance

6. Choose setup procedure

a. Click New Instance.
b. Click Next to continue.
Figure 3-4. Setup Wizard – Choose setup procedure

7. Choose Server Instance Details

a. Enter a name for the SampleManager server instance. The default instance name
is VGSM.
b. Specify the base port number that the services associated with the instance will
use. The default base port number is 56100.
c. Click Next to continue.
Figure 3-5. Setup Wizard – Choose Server Instance Details

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Creating a SampleManager Instance

8. Choose Location
a. Either accept the default location for the instance files, or browse for an
alternative.
b. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:
• port is the port number of the Thermo Licensing service on the remote
server
• hostname is the name of the remote server
c. Click Next to continue.
Figure 3-6. Setup Wizard – Choose Location

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Creating a SampleManager Instance

9. Choose SQL Server

a. Select the SQL Server that contains the database you want to use.
b. Click Next to continue.
Figure 3-7. Setup Wizard – Choose SQL Server

10. Configure Database Connection

a. Select the method that SampleManager will use to connect to SQL Server:

• Use Windows Integrated Security – SampleManager will connect using

the Windows account specified for the smdaemon service. You will specify
the account used by SampleManager services on a later page of the wizard.
• Use SQL Server Authentication – SampleManager will connect using the
details you supply in the Username and Password fields. The specified login
must already exist in SQL Server. Choose this option if your SQL Server
uses SQL Server Authentication. The connection details will be stored in a
Windows Registry value. For instructions about encrypting the contents of
this Registry value, see the "Data Storage and Handling in SQL Server"
chapter in the SampleManager LIMS System Administration Guide.
b. Click Next to continue.

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Creating a SampleManager Instance

Figure 3-8. Setup Wizard – Configure Database Connection

11. Choose SQL Server Database

a. Specify the database to use for the SampleManager data.
b. Click Next to continue.
Figure 3-9. Setup Wizard – Choose SQL Server Database

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Creating a SampleManager Instance

12. Choose Service Account

a. Specify the Windows user account that the SampleManager services will use.
The options are:

• Built-in LocalSystem account – The services will use the LocalSystem

account for the machine where the SampleManager Server is installed. This
option is less secure and is not compatible with the default security settings
of SQL Server.

• This account – Enter the name and password of the account that the
services will use. This is the recommended option.
The account must have appropriate permissions for your SQL Server database
and the server that hosts the database. See SQL Server Setup (page 233) for
more information.
b. Click Next to continue.
Figure 3-10. Setup Wizard – Choose Service Account

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13. Connection String Configuration

a. Click Test to check the ADO connection string for the instance. The string is
constructed using the information you entered on the preceding pages of the
wizard. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. When the ADO connection string test is successful, click Next to continue.
Figure 3-11. Setup Wizard – Connection String Configuration

14. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.
Figure 3-12. Setup Wizard – Confirm Details

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15. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.
Figure 3-13. Setup Wizard – Instance Creation in Progress

16. Server Instance Created

To close the Setup Wizard, click Finish.
Figure 3-14. Setup Wizard – Server Instance Created

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

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Creating a Cloned Instance

This section describes the creation of a SampleManager instance that uses a
pre-populated SampleManager database. This type of instance is useful if you want to
create an instance that duplicates the features and data of an existing SampleManager
system. This example creates an instance with the following features:
• Database – The instance connects to an existing SampleManager database that is
not associated with any other SampleManager instance. For example, a copy of an
existing SampleManager database from a production system.
• Folders and files – The wizard creates a new instance folder that contains the files
associated with the instance. The files are copied from the SampleManager instance
associated with the database that you copied.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon.
• Windows registry – The wizard creates Windows registry entries associated with the
instance.
Figure 3-15. Cloned instance

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Creating a SampleManager Instance

 To create a cloned SampleManager instance

1. Use SQL Server tools to create a copy of the database. See your SQL Server
documentation for more information.

2. On the server that will host your instance, install SampleManager Server (page 62).

3. The instance will require a connection to a Thermo Licensing Server. Do one of the
following:
• Install the Thermo Licensing Server (page 65) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.

4. From the Start menu, click Thermo SampleManager 12.2 > Add SQL Instance.

The Setup Wizard appears.

5. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.

6. Choose setup procedure

a. Click Clone Instance.
b. Click Next to continue.
Figure 3-16. Setup Wizard – Choose setup procedure

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Creating a SampleManager Instance

7. Choose Server Instance Details

a. Enter a unique name for the SampleManager server instance.
b. Specify the base port number that the services associated with the instance will
use. Make sure that you choose a base port number that is not used by any other
service on the server.
c. Click Next to continue.

8. Choose Location
a. Either accept the default location for the cloned instance files, or browse for an
alternative.
b. Specify the location of the root folder for the SampleManager instance that you
want to clone. For example:
C:\Thermo\SampleManager\Server\VGSM
c. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:
• port is the port number of the Thermo Licensing service on the remote
server

• hostname is the name of the remote server

d. Click Next to continue.
Figure 3-17. Setup Wizard – Choose Location

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Creating a SampleManager Instance

9. Choose SQL Server

a. Select the SQL Server that contains the database you want to use.
b. Click Next to continue.

10. Configure Database Connection

a. Select the method that SampleManager will use to connect to SQL Server:

• Use Windows Integrated Security – SampleManager will connect using

the Windows account specified for the smdaemon service. You will specify
the account used by SampleManager services on a later page of the wizard.

• Use SQL Server Authentication – SampleManager will connect using the

details you supply in the Username and Password fields. The specified login
must already exist in SQL Server. Choose this option if your SQL Server
uses SQL Server Authentication. The connection details will be stored in a
Windows Registry value. For instructions about encrypting the contents of
this Registry value, see the "Data Storage and Handling in SQL Server"
chapter in the SampleManager LIMS System Administration Guide.
b. Click Next to continue.

11. Choose SQL Server Database

a. Specify the database that contains the SampleManager data you want to use.
This database must not be used by another SampleManager instance.
b. Click Next to continue.

12. Choose Service Account

a. Specify the Windows user account that the SampleManager services will use.
The options are:

• Built-in LocalSystem account – The services will use the LocalSystem

account for the machine where the SampleManager Server is installed. This
option is less secure and is not compatible with the default security settings
of SQL Server.

• This account – Enter the name and password of the account that the
services will use. This is the recommended option.
The account must have appropriate permissions for your SQL Server database
and the server that hosts the database. See SQL Server Setup (page 233) for
more information.
b. Click Next to continue.

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13. Connection String Configuration

a. Click Test to check the ADO connection string for the instance. The string is
constructed using the information you entered on the preceding pages of the
wizard. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. When the ADO connection string test is successful, click Next to continue.

14. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.

15. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.

16. Server Instance Created

To close the Setup Wizard, click Finish.

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

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Creating a SampleManager Instance

Creating an Application Server Instance

This section describes the creation of a new SampleManager instance with the following
features:
• Database – The instance connects to an existing SampleManager database that it
shares with one or more other SampleManager instances.
• Instance Name – The instance has the same name as the other application server
instances that connect to the shared database.
• Folders and files – The wizard creates an instance folder that contains the executable
files associated with the instance.

All the other files required for SampleManager operations, such as report designs and
VGL libraries, are obtained from a shared folder that is specified during the instance
creation process. All the application instances that connect to the shared database
should use the same shared folder.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon. For a description of each
service, see the "Operating Environment" chapter in the SampleManager LIMS
System Administration Guide. The lock daemon for the application server operates as
one of the cluster of lock daemons associated with the applications servers that
connect to the shared database. For more information about lock daemon clustering,
see Lock Daemon Operation with SampleManager Application Server Clusters (page
10).
• Windows registry – The wizard creates Windows registry entries associated with the
instance.

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Creating a SampleManager Instance

Figure 3-18. Application server instance

Each application server instance in the cluster that connects to a single database must be
installed on a separate server.

SampleManager LIMS does not maintain a central record of the instances that belong to
an application server cluster. For maintenance and upgrade purposes, we recommend
that you keep a record of your application server cluster architecture.

To create the first instance in a planned cluster of application server instances, create a
new instance, as described in Creating a New Instance (page 67). When the new instance
is operating correctly, configure the Lock Daemon to operate as part of a cluster.

Note When you install an application server with the Setup Wizard, the installation
process configures the lock daemon to run in cluster mode. The lock daemon must be
configured manually for the first instance in an application server cluster.

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Creating a SampleManager Instance

 To configure the lock daemon to operate as part of a cluster

1. On the server that hosts your new SampleManager instance, open the Registry
Editor.

2. Navigate to the following registry key:

Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\
LabSystems\SampleManager Server\smplock<instance_name>
Where <instance_name> is the name of the instance.

3. Set the use_cluster value to true.

 To create an application server SampleManager instance

1. On the server that will host your instance, install SampleManager Server (page 62).

2. The instance will require a connection to a Thermo Licensing Server. Do one of the
following:
• Install the Thermo Licensing Server (page 65) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.
3. From the Start menu, click Thermo SampleManager 12.2 > Add SQL Instance.
The Setup Wizard appears.

4. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.

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Creating a SampleManager Instance

5. Choose setup procedure

a. Click Application Server.
b. Click Next to continue.
Figure 3-19. Setup Wizard – Choose setup procedure

6. Choose Server Instance Details

a. Enter a name for the application server instance. The name must match the
name of the other application server instances that share the same
SampleManager database.
b. Specify the base port number that the services associated with the instance will
use. Make sure that you choose a base port number that is not used by any other
service on the server.
c. Click Next to continue.

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Creating a SampleManager Instance

7. Choose Location
a. Either accept the default location for the instance files, or browse for an
alternative.
b. Specify the location of the SampleManager instance root folder that contains the
files you want this instance to share. The folder must be shared and accessible to
the user accounts that will be associated with the Windows services for your new
instance.
Specify the shared folder location as a UNC path, not a mapped drive.
c. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:

• port is the port number of the Thermo Licensing service on the remote
server

• hostname is the name of the remote server

d. Click Next to continue.
Figure 3-20. Setup Wizard – Choose Location

8. Choose SQL Server

a. Select the SQL Server that contains the database you want to use.
b. Click Next to continue.

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Creating a SampleManager Instance

9. Configure Database Connection

a. Select the method that SampleManager will use to connect to SQL Server:

• Use Windows Integrated Security – SampleManager will connect using

the Windows account specified for the smdaemon service. You will specify
the account used by SampleManager services on a later page of the wizard.
• Use SQL Server Authentication – SampleManager will connect using the
details you supply in the Username and Password fields. The specified login
must already exist in SQL Server. Choose this option if your SQL Server
uses SQL Server Authentication. The connection details will be stored in a
Windows Registry value. For instructions about encrypting the contents of
this Registry value, see the "Data Storage and Handling in SQL Server"
chapter in the SampleManager LIMS System Administration Guide.
b. Click Next to continue.

10. Choose SQL Server Database

a. Specify the database that you want the application server to share.
b. Click Next to continue.

11. Choose Service Account

a. Specify the Windows user account that the SampleManager services will use.
The options are:

• Built-in LocalSystem account – The services will use the LocalSystem

account for the machine where the SampleManager Server is installed. This
option is less secure and is not compatible with the default security settings
of SQL Server.

• This account – Enter the name and password of the account that the
services will use. This is the recommended option.
The account must have appropriate permissions for your SQL Server database
and the server that hosts the database. See SQL Server Setup (page 233) for
more information.
b. Click Next to continue.

12. Connection String Configuration

a. Click Test to check the ADO connection string for the instance. The string is
constructed using the information you entered on the preceding pages of the
wizard. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. When the ADO connection string test is successful, click Next to continue.

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Creating a SampleManager Instance

13. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.

14. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.

15. Server Instance Created

To close the Setup Wizard, click Finish.

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

Creating a New Site Instance

This example demonstrates the creation of a new SampleManager instance with the
following features:
• Database – The instance connects to a SQL Server database, which is populated
with default SampleManager data by the instance creation process. See SQL Server
Setup (page 233) for information about configuring SQL Server and creating a
suitable database.
• Folders and files – The wizard creates an instance folder that contains the executable
files associated with the instance. The instance shares data files such as report
templates and VGL reports with another instance. See the "Operating Environment"
chapter in the SampleManager LIMS System Administration Guide for a description of
each subfolder in the instance folder.
• Windows services – The wizard creates Windows services associated with the
instance, such as the increment daemon and lock daemon. See the "Operating
Environment" chapter in the SampleManager LIMS System Administration Guide for
a description of each service.
• Windows Registry – The wizard creates Windows registry entries associated with
the instance.

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Creating a SampleManager Instance

Figure 3-21. Site instance

SampleManager LIMS does not maintain a central record of the site instances that share
files with another instance. For maintenance and upgrade purposes, we recommend that
you keep a record of your site instance architecture.

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Creating a SampleManager Instance

 To create a new site instance

1. In SQL Server, create an empty database ready for the SampleManager instance data.
2. On the server that will host your instance, install SampleManager Server (page 62).

3. The instance will require a connection to a Thermo Licensing Server. Do one of the
following:
• Install the Thermo Licensing Server (page 65) on the server that will host your
new application server.
• Obtain the name of a remote server that hosts a Thermo Licensing Server and
the port number for the Thermo Licensing service on that server. Multiple
SampleManager instances can share a single Thermo Licensing Server.

4. From the Start menu, click Thermo SampleManager 12.2 > Add SQL Instance.

The Setup Wizard appears.

5. Welcome to the SampleManager 12.2 Add Server Instance Wizard

Click Next to continue.

6. Choose setup procedure

a. Click New Site Instance.
b. Click Next to continue.
Figure 3-22. Setup Wizard – Choose setup procedure

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Creating a SampleManager Instance

7. Choose Server Instance Details

a. Enter a unique name for the site instance.
b. Specify the base port number that the services associated with the instance will
use. Make sure that you choose a base port number that is not used by any other
service on the server.
c. Click Next to continue.

8. Choose Location
a. Either accept the default location for the cloned instance files, or browse for an
alternative.
b. Specify the location of the root folder for the SampleManager instance that you
want the site to share files with. For example:
C:\Thermo\SampleManager\Server\VGSM
c. If you want to use a remote Thermo Licensing Server, enter the connection
string for the machine that hosts the Thermo Licensing Server. The syntax for
the connection string is:
port@hostname
Where:
• port is the port number of the Thermo Licensing service on the remote
server

• hostname is the name of the remote server

d. Click Next to continue.
Figure 3-23. Setup Wizard – Choose Location

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Creating a SampleManager Instance

9. Choose SQL Server

a. Select the SQL Server that contains the database you want to use.
b. Click Next to continue.

10. Configure Database Connection

a. Select the method that SampleManager will use to connect to SQL Server:

• Use Windows Integrated Security – SampleManager will connect using

the Windows account specified for the smdaemon service. You will specify
the account used by SampleManager services on a later page of the wizard.

• Use SQL Server Authentication – SampleManager will connect using the

details you supply in the Username and Password fields. The specified login
must already exist in SQL Server. Choose this option if your SQL Server
uses SQL Server Authentication. The connection details will be stored in a
Windows Registry value. For instructions about encrypting the contents of
this Registry value, see the "Data Storage and Handling in SQL Server"
chapter in the SampleManager LIMS System Administration Guide.
b. Click Next to continue.

11. Choose SQL Server Database

a. Specify the database to use for the SampleManager data.
b. Click Next to continue.

12. Choose Service Account

a. Specify the Windows user account that the SampleManager services will use.
The options are:

• Built-in LocalSystem account – The services will use the LocalSystem

account for the machine where the SampleManager Server is installed. This
option is less secure and is not compatible with the default security settings
of SQL Server.

• This account – Enter the name and password of the account that the
services will use. This is the recommended option.
The account must have appropriate permissions for your SQL Server database
and the server that hosts the database. See SQL Server Setup (page 233) for
more information.
b. Click Next to continue.

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Creating a SampleManager Instance

13. Connection String Configuration

a. Click Test to check the ADO connection string for the instance. The string is
constructed using the information you entered on the preceding pages of the
wizard. A message appears, showing the result of the connection test.
b. If the test fails, edit the connection string and repeat the test.
c. When the ADO connection string test is successful, click Next to continue.

14. Confirm Details

a. Verify that the details shown match the instance you want to create.
b. Click Next to create the instance.

15. Instance Creation in Progress

The wizard creates the instance. When the instance creation process is complete, a
logfile of the installation is saved to the root folder of the instance.
a. To save a logfile of the installation to a custom location, click Save Log.
b. Click Next to continue.

16. Server Instance Created

To close the Setup Wizard, click Finish.

After you create the instance, you can set up your SampleManager licenses, and configure
your application server to allow client workstations to access the SampleManager
instance. For more information, see Post-Installation Tasks (page 97).

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Removing a SampleManager Instance

Removing a SampleManager Instance

Use the Delete Server Instance Wizard to remove a SampleManager server instance.

Note This wizard removes the SampleManager server instance and gives you the
option to remove the data associated with the instance. The underlying SQL Server
database structure is left on your system. You can remove the database afterwards,
using standard SQL Server tools.

 To remove a SampleManager Server instance

1. From the Start menu, click Thermo SampleManager 12.2 > Remove SQL
Instance.
The Delete Server Instance Wizard appears.

2. Welcome to the Delete Server Instance Wizard

Click Next to continue.
Figure 3-24. Delete Server Instance wizard

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Removing a SampleManager Instance

3. Choose Instance
a. Select the instance that you want to delete
b. Click Next to continue.
Figure 3-25. Delete Server Instance wizard – Choose Instance

4. Database Cleanup
a. If you want to delete the data associated with the instance in the database, select
the Delete the SampleManager data and tables check box.
If the check box is not selected, SampleManager data and tables will be left in
the SQL Server database. Use this option if the underlying database cannot be
accessed, for example if it has been, or will be, deleted manually.
b. Click Next to continue.
CAUTION Selecting the check box results in the permanent deletion of
SampleManager data from the database. You will not be able to restore the database
or recover its data.
If the instance is an application server that shares its database with other <product
instances, selecting the check box deletes the data from the shared database.

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Removing a SampleManager Instance

Figure 3-26. Delete Server Instance wizard – Database Cleanup

5. Confirm Details
a. Check the details shown.
b. Click Next to delete the instance.
Figure 3-27. Delete Server Instance wizard – Confirm Details

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6. Instance Deletion in Progress

The wizard deletes the instance. When the instance deletion is complete, the Save
Log and Next buttons are enabled. A log file of the instance deletion process is saved
in the instance folder.
a. If you want to save a copy of the log file to a different location, click Save Log.
b. Click Next to continue.
Figure 3-28. Delete Server Instance wizard – Instance Deletion in Progress

7. Server Instance Deleted

Click Finish to close the Delete Server Instance Wizard.
Figure 3-29. Delete Server Instance wizard – Server Instance Deleted

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 4

Post-Installation Tasks
This chapter describes the tasks you must perform after you have installed
SampleManager on your application server.

Contents
• SampleManager Licenses
• Running SampleManager Client for the First Time
• Configuring the Application Server Firewall
• Setting the Server Timezone
• Configuring the Server Warm Start Feature
• Smart Client Deployment
• Encrypting the Database Connection String in the
Windows Registry
• Adding Dictionaries for the Spell Checking Feature
• Configuring ADO Cursor Locations and Cache Size
• Adding the ActiveRecord Task to the Watch Dog
Timer
• Add DLLs for Report Designer OLE Previews to Exe
Folder

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SampleManager Licenses

SampleManager Licenses
SampleManager uses FlexNet licensing, which is implemented through the Thermo
Licensing Server. The Thermo Licensing Server is installed as part of the main
SampleManager installation process, in the following folder by default:
C:\Program Files (x86)\Thermo\Thermo Licensing Server

The SYSTEM user account can log in to SampleManager at any time without taking a
license from the Full license pool. SampleManager allows one license-free connection
with the SYSTEM account at any time. This feature lets you install and test your
SampleManager client before you obtain your licenses.

SampleManager supports the following types of license:

• Full – A floating license that grants full access to all SampleManager features. Full is
the default SampleManager license type. When a user connects using a Full license,
they are allocated one license from the available pool of Full licenses. When a session
that uses a Full license ends, the license for that session returns to the pool of
available Full licenses. At any time, the maximum number of users who can be
connected to SampleManager with a Full license is equal to the number of Full
licenses purchased. Any number of operators can have their License Type set to Full.
The LICENSE_READ_ON_EXCEED configuration item determines what
happens when a user with their license type set to Full attempts to log in when all
available Full licenses are allocated to current sessions:
– If LICENSE_READ_ON_EXCEED is Yes, the user is connected to
SampleManager using a Read-Only license. If a Read-Only license is not
available, the connection attempt fails because the number of available licenses
was already reached.
– If LICENSE_READ_ON_EXCEED is No, the connection attempt fails
because the number of available licenses was already reached.
• Full Named – A license that grants a specific user full access to all SampleManager
features. Each Full Named license is assigned to a specific operator and is only
available for use by that operator.
• Read-Only – A floating license that grants read-only access to all SampleManager
features. If an operator connects to SampleManager with a Read-Only license, they
can view data but not create or modify it. The only records that are created in a
Read-Only session are background system records such as access logs and recently
used items. When a user connects using a Read-Only license, they are allocated one
license from the available pool of Read-Only licenses. When a session that uses a
Read-Only license ends, the license for that session returns to the pool of available
Read-Only licenses. At any time, the maximum number of users who can be
connected to SampleManager with a Read-Only license is equal to the number of

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SampleManager Licenses

Read-Only licenses purchased. Any number of operators can have their License Type
set to Read-Only.
• Read-Only Named – A license that grants a specific user read-only access to all
SampleManager features. If an operator connects to SampleManager with a
Read-Only license, they can view data but not create or modify it. The only records
that are created in a Read-Only session are background system records such as access
logs and recently used items. Each Read-Only Named license is assigned to a specific
operator and is only available for use by that operator.

Each module you install also requires a license. You must add the license for a module
before you install the module. If a valid license is not present, the module installation
process can fail.

After you have finished installing your SampleManager server, you must obtain a license
file for the licenses you have purchased, by sending details of your installation to:
[email protected]

The license is associated with the server machine on which you have installed the
Thermo Licensing Server. If you move this software to a new server machine in the
future, contact Support to obtain a new license file.

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SampleManager Licenses

Generating the Installation Details File

Thermo Fisher Scientific requires details of the server hosting your SampleManager
installation to generate your license file.

 To generate the required information

1. Open your Thermo Licensing Server folder.

2. Run lmtools.exe.

The LMTOOLS window appears.

3. Open the System Settings page.

Figure 4-1. LMTOOLS System Settings page

4. Click Save HostID Info to a File.

The Save As dialog box appears, prompting you for a file name and location for the
installation details file.

5. Enter a suitable name and location for the file and click Save to create it.

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SampleManager Licenses

Obtaining the License File

Send your installation details file to this address:

[email protected]

Include the following information in the email:

• The name of the product you have purchased, SampleManager in this case.
• The number of each type of SampleManager license (page 98) you have purchased.
• The name of each module you have purchased.
• Your System Registration ID. This ID is the 8-digit number defined for each unique
installation of our products.
• The name of your SampleManager instance.

Your license file will be generated and sent to you.

Installing your New Licenses

When you receive your license file, install your licenses on your license server.

 To install your new licenses

1. Copy the .lic file to your Thermo Licensing Server folder.

2. Open the Windows Service panel and start the Thermo Licensing Server service.
Note If this service has already been started, stop and then start it again. Do not
use the Restart option.
3. You should now be able to run the SampleManager client and connect to your
SampleManager instance, as described in Running SampleManager Client for the
First Time (page 104).
4. If you purchased Full Named or Read-Only Named licenses, assign the licenses to
the corresponding users (page 102).

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SampleManager Licenses

Assigning Named Licenses to SampleManager Users

Use the License Group Editor window in SampleManager to assign Full Named and
Read-Only Named licenses to the corresponding SampleManager users. You must create
the required personnel records in SampleManager before you can assign the named
licenses. For more information, see the "Security" chapter in the SampleManager LIMS
System Administration Guide.

To open the License Group Editor, use one of the following methods:
• From the main menu, select Setup > System > Users > Named User License Setup.
• In Explorer, right-click an operator and select Operator > Modify. On the Definition
page of the Personnel Property sheet, click the ellipsis button in the License
Type prompt.
Figure 4-2. License Group Editor

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SampleManager Licenses

The explorer grid shows the type of license assigned to each SampleManager operator.
The selection criteria for the list of operators that appear depends on the value of the
LOGIN_LDAP_NEEDSPASSWORD configuration item:
• Yes – The list contains records from the PERSONNEL table that are associated with
a record in the PASSWORD table and that have the remove_flag set to False.
• No – The list contains records from the PERSONNEL table that have the
remove_flag set to False.

The Pool Size prompts below the explorer grid show the number of each type of license
that is included in your SampleManager license file. The progress bar beside each license
type shows how many licenses of that type have been allocated to operators in the grid.
You can assign any number of operators to the Full and Read-Only license types, as these
types of license limit the number of concurrent sessions. The Full Named and
Read-Only Named license types show a validation error if the number of operators
assigned that type of license exceeds the Pool Size.

 To assign licenses to operators

1. In the License Group Editor, select one or more operators.

To select a continuous series of operators, select the first operator then hold down
the SHIFT key and select the last operator.
To select a series of operators that are not continuous, hold down the CTRL key and
select each operator.
2. Right-click and choose the type of license you want to apply to the selected
operators.

3. To save changes to the license type allocations, click OK. Your changes will take
effect after a 12-hour delay.

To implement the license type allocation changes immediately, stop and restart the
Thermo Licensing service. If you stop the Thermo Licensing service, all current
sessions are terminated.

Licenses for the SYSTEM User

The SYSTEM user account can log in to SampleManager at any time without taking a
license from the Full license pool. SampleManager allows one license-free connection
with the SYSTEM account at any time. If more simultaneous sessions are started with
the SYSTEM account, those sessions will connect using licenses allocated from the
license pool.

This feature prevents the SYSTEM user from being locked out of SampleManager.

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Running SampleManager Client for the First Time

Running SampleManager Client for the First Time

When a SampleManager server instance has been created, you can connect to it using the
SampleManager client. The SampleManager client is installed on the application server
as part of SampleManager server installation.

 To run SampleManager Client for the first time

1. Open the All Apps view of the Start screen.

2. Scroll to the Thermo SampleManager section and click the SampleManager app.

Because no SampleManager server connections have been set up, the Create a new
server item window appears.
Figure 4-3. Create a new server item window

3. Enter a suitable name in the Server Name prompt.

4. Select the Remote Server option and enter the following values:
• Instance Name – The name of the instance. If this field is set to Default,
SampleManager will connect to the current Default Instance recorded in the
Windows registry on the remote server machine.
• Server Name – The name of the server where the instance is installed.
• Port Number – The port number for the instance.

5. Click OK to save changes and close the window.

The SampleManager Login screen appears.

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Configuring the Application Server Firewall

6. Log in to SampleManager, using the username 'SYSTEM', with the Password field
left blank. If the ThermoLicensing Service has not started, you might see an error. In
this case, start the ThermoLicensing service using the Services tool in Windows
Administrative Tools.
You can now configure your SampleManager system using the SampleManager
client.

Note We recommend that you configure the security settings for the SYSTEM user
immediately. Change the default password to a new, secure value.

For more information, see the SampleManager LIMS System Administration Guide.

Configuring the Application Server Firewall

The firewall on the application server must be configured to allow SampleManager
Clients to connect to the SampleManager Server. Use the following information to
develop firewall settings suitable for your network:
• The port used by the SMDaemon for each SampleManager instance hosted on the
application server must be open. The default port for a SampleManager instance is
56100.
• The SampleManagerServerHost.exe application must be added to the Exceptions list
to enable SampleManager Clients to communicate with the SampleManager Server.
• Ports in the range 49152–65535 must be open to allow the SampleManager
Debugger to communicate with the SampleManager Server.

Note The SampleManager Debugger is used to debug VGL reports. You might not
need to use the Debugger on all your client machines.

Setting the Server Timezone

If you are setting up a new SampleManager system, we recommend that the
TIMEZONE_SERVER configuration item is set to (UTC) Coordinated Universal
Time, and that the TIMEZONE_SERVER_DLS configuration item is set to No. The
operating system of the machine hosting the SampleManager Server must also be set to
the (UTC) Coordinated Universal Time timezone.

For more information, see the "Security" chapter in the SampleManager LIMS System
Administration Guide.

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Configuring the Server Warm Start Feature

Configuring the Server Warm Start Feature

The Server Warm Start feature reduces the amount of time required to establish a
connection between a SampleManager client and a SampleManager instance. If the
Server Warm Start feature is enabled, the SMDaemon creates a new
SampleManagerServerHost process after each connection has been established, so that
there is a process waiting for the next client to connect to.

If the Server Warm Start feature is enabled, the SMDaemon service operates as follows:

1. The SMDaemon service starts a SampleManagerServerHost process.

2. A client requests a connection to SampleManager.

3. The SMDaemon service passes the details of the SampleManagerServerHost process

created in step 1 to the client.
4. When the connection between the SampleManagerServerHost process and client is
established, the SMDaemon service drops out of the conversation.
5. The SMDaemon service waits for the period specified in the WarmStartInterval
application setting in the SMDaemon.exe.config file.
6. The SMDaemon service repeats the process from step 1, creating a new
SampleManagerServerHost process ready for the next client.

If a client attempts to connect before the SMDaemon service has created a

SampleManagerServerHost process, a new SampleManagerServerHost process will be
started for that client.

To configure the Server Warm Start feature for an instance, set the following application
settings in the SMDaemon.exe.config file:
• WarmStartInstance
• WarmStartInterval

The SMDaemon config file is found in the following folder on the SampleManager
server:
<SampleManager root>\Server\<instance>\Exe

Where <SampleManager root> is the root folder of the SampleManager installation and
<instance> is the name of the SampleManager instance.

For more information about the SampleManager config files, see the "Operating
Environment" chapter in the SampleManager LIMS System Administration Guide.

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 4 Post-Installation Tasks
Smart Client Deployment

Note If the Server Warm Start feature is enabled and you add a new SampleManager
server to the Manage Servers window, the server will not appear in the Manage Servers
list the next time a SampleManager client connects to the SampleManager application
server. This effect occurs because the SampleManagerServerHost process for that client
session was started by the Server Warm Start feature before the new SampleManager
server was added. The new server will appear on the list in subsequent SampleManager
client sessions.

Smart Client Deployment

The SampleManager client can be deployed as a ClickOnce application. To install the
SampleManager client, a user clicks a link to a setup application on the server. After it is
installed, the client checks for updates each time it is run. If the server version has been
updated, the client installs the new version automatically, eliminating the need to update
clients manually.

 To deploy the SampleManager Smart Client

1. Open the SmartClient folder of the installation kit:

SampleManager 12.2\SmartClient

2. Extract the following .zip file to a location that will be accessible to your
SampleManager users:
SampleManager 12.2 SmartClient.zip
Note The Smart Client files can be placed in a shared folder or hosted on an IIS
server.
3. Send each user a link to the setup.exe file in the extracted folder.
4. When a user clicks the link for the first time, the SampleManager client is installed
using ClickOnce deployment. A SampleManager icon appears on the Windows
desktop. Whenever the user runs SampleManager by clicking the icon, the Smart
Client checks for updates and runs an installation if any changes are found.

Note The SampleManager Smart Client is installed on a workstation for the current
user only.

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4 Post-Installation Tasks
Encrypting the Database Connection String in the Windows Registry

Encrypting the Database Connection String in the Windows

Registry
If your SampleManager instance uses an Oracle database, or a SQL Server database with
SQL Server authentication, the connection information is stored in the Windows
registry.

To prevent someone from gaining unauthorized access to the connection string through
the registry, you can use SampleManager to encrypt the registry value.

 To encrypt the connection string stored in the registry

1. Start the SampleManager client and log in to the instance.

2. From the main menu, select Setup > System > Encrypt Connection String.

For more information, see the following chapters in the SampleManager LIMS System
Administration Guide:
• "Data Storage and Handling in Oracle"
• "Data Storage and Handling in SQL Server"

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Adding Dictionaries for the Spell Checking Feature

Adding Dictionaries for the Spell Checking Feature

The spell checker functionality is available in a control at runtime when all the following
conditions are met:
• The SpellCheck property of the control is True. The following controls have a
SpellCheck property:

– Prompt

– Text Edit
– Rich Text Edit
• The SPELLCHECKING_ENABLED configuration item is set to Yes.
• Dictionary files exist in the Resource folder for the SampleManager instance.

To run a spell check in a control, use one of the following methods:

• Press Shift + F7.
• Right-click and select Check Spelling.

The spell check feature compares text with entries in the SampleManager dictionary files
in the following order:
1. The custom dictionary maintained on the current workstation.

2. The company dictionary maintained on the server and synchronized when a client
workstation connects to the server.

3. The language-specific dictionary for the language associated with the current
operator. Language-specific dictionaries are maintained on the server and
synchronized when a client workstation connects to the server.

For detailed instructions about obtaining and installing dictionary files, see the "Spell
Checker" chapter in the SampleManager LIMS Form Designer Manual.

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Configuring ADO Cursor Locations and Cache Size

Configuring ADO Cursor Locations and Cache Size

You can configure the location and cache size of the ADO cursors for each
SampleManager instance to optimize the performance of your SampleManager
implementation.

The ADO cursor location can be set to client-side or server-side:

• Client-side – When the SampleManager Server application requests data from the
database, the database server sends the entire result set across the network to the
SampleManager application server. The SampleManager application server provides
and manages the temporary resources needed by the cursor and result set. The
SampleManager Server application browses through the entire result set to determine
which rows it requires.
• Server-side – When the SampleManager Server application requests data from the
database, the database manages the result set using resources provided by the
database server computer. The server-side cursor returns only the requested data over
the network. This type of cursor can sometimes provide better performance than the
client-side cursor. Server-side is the default configuration.

The ADO cursor location for an instance is obtained from the Windows registry on the
SampleManager application server machine when the instance first connects to the
database. The setting is stored in the smp$ado_cursor_location registry item in the
following registry key:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\LabSystems\
SampleManager Server\<Instance_name>

The possible values of smp$ado_cursor_location are:

• CLIENT
• SERVER

The ADO cursor location value can be changed at runtime to optimize an individual
database operation. To change the value at runtime, set the value of the
ADO_CURSOR_LOCATION global to CLIENT or SERVER. For information about
setting global values, see the VGL Programmer's Guide Help and the SampleManager
Form Designer Help.

The ADO cache size property controls how many records the provider keeps in its buffer
and how many records are retrieved at one time into local memory. The setting is stored
in the smp$ado_cache_size registry item in the following registry key:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\LabSystems\
SampleManager Server\<Instance_name>

The default value for smp$ado_cache_size is 800.

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 4 Post-Installation Tasks
Adding the ActiveRecord Task to the Watch Dog Timer

The ADO cache size value can be changed at runtime to optimize an individual database
operation. To change the value at runtime, set the value of the ADO_CACHE_SIZE
global to the required integer. For information about setting global values, see the VGL
Programmer's Guide Help and the SampleManager Form Designer Help.

Adding the ActiveRecord Task to the Watch Dog Timer

Some entity types that support version management, such as analysis, have an active_flag
field. If a version is active, that entity can be used by other SampleManager entities and
processes. The ActiveRecord background process must run at regular intervals to
determine the correct value of the active_flag for each entity with an active_flag field. For
more information about the version management functionality and the ActiveRecord
background task, see the "Version Management" chapter in the SampleManager LIMS
Configuration Guide.

 To add the ActiveRecord task to the watch dog timer

1. From the main menu, select Setup > Scheduling > Watch Dog Timer > List
Entries.

The Background Schedule Manager screen appears.

Figure 4-4. Background Schedule Manager

2. Click New Report.

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Adding the ActiveRecord Task to the Watch Dog Timer

The Background Schedule Entry screen appears.

Figure 4-5. Background Schedule Entry screen

3. Select the Task option.

4. Enter ActiveRecord as the Task Name.

5. To run the ActiveRecord task for a specific table, enter the name of the table,
enclosed in double quotes, in the Task Parameters prompt. If the Task Parameters
prompt is left empty, the ActiveRecord task will run for all tables that have an Active
flag.
6. Set the Recurrence Pattern for the task. The task should run at least once per day, to
make sure that the active status values are kept up-to-date. See the "Background
Operations" chapter in the SampleManager LIMS System Administration Guide for
more information about setting the frequency pattern.
7. Set the Range of Recurrence for the task. In a production system, the No End Date
option should be selected. See the "Background Operations" chapter in the
SampleManager LIMS System Administration Guide for more information.

8. Click OK to add the task to the watch dog timer queue.

The spmtqinstance service processes the entries in the watch dog timer queue. Make sure
that the spmtqinstance service for your instance is running before you start to create and
update entities that use the version management feature. For more information about the
Windows services associated with SampleManager, see the "Operating Environment"
chapter in the SampleManager LIMS System Administration Guide.

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 4 Post-Installation Tasks
Add DLLs for Report Designer OLE Previews to Exe Folder

Add DLLs for Report Designer OLE Previews to Exe Folder

The SampleManager Report Designer can generate reports that include embedded
content from attachments stored as PDF or Microsoft Office files.

To enable this feature, you must add the DLLs required for each attachment type to the
Exe folder of your SampleManager instance.

To support PDF attachments, obtain Gsdll32.dll from GhostScript:

http://www.ghostscript.com/

To support Microsoft Office attachments, obtain the following Office primary interop
assemblies from Microsoft:
• Microsoft.Office.Interop.Excel.dll
• Microsoft.Office.Interop.Powerpoint.dll
• Microsoft.Office.Interop.Word.dll
• Office.dll

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 5

Installing SampleManager Client

This chapter describes the installation procedure for the SampleManager Client.

Note The SampleManager client can also be deployed to client workstations using
the Smart Client functionality (page 107).

Contents
• Prerequisites
• Installing SampleManager Client Software
• Connecting to a SampleManager Server Instance
• Managing Server Instance Connections

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5 Installing SampleManager Client
Prerequisites

Prerequisites
Make sure that a printer has been set up on the workstation. The printer does not have
to be a physical printer, for example, Adobe PDF can be used.

Installing SampleManager Client Software

You must install the SampleManager client software using an account with administrator
rights.

In the SampleManager LIMS 12.2 installation kit, there are two folders that contain
installation files for the SampleManager client:
• Client – The client installer to use for new implementations.
• Client_Inc_Imprint – The client installer to use for upgraded systems that require
support for the InfoMaker reporting tool or combit List and Label label design tool.
These tools are not required for new instances.

 To install SampleManager client

1. In Windows Explorer, open the folder that contains your SampleManager

installation kit.

2. Open the folder that contains the SampleManager client installer required for your
instance.
3. Double-click the SampleManagerInstaller.msi file.

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 5 Installing SampleManager Client
Installing SampleManager Client Software

Suppressing the SampleManager Splash Screen

When you run the SampleManager client, a SampleManager splash screen appears before
the SampleManager login window.

To suppress the SampleManager splash screen when the client starts, add the following
parameter to the Target value in the SampleManager shortcut:
-NoSplash

Figure 5-1. SampleManager shortcut showing -NoSplash parameter in Target

prompt

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5 Installing SampleManager Client
Installing SampleManager Client Software

Silent Installation of the SampleManager Client

The SampleManager client can be installed silently on a target workstation using a
command-line script.

 To perform a silent installation of SampleManager Client

1. Copy the following file from the SampleManager installation kit onto the target
machine:

..\Client\SampleManagerInstaller.msi

2. Execute the following command-line script:

msiexec /i <path to SampleManagerInstaller.msi>

SAMPLEMANAGERVERSION="<path to root folder>" EXE="path to exe folder>
HELP_1="path to help folder" /quiet|/qn /norestart [/log <path to
logfile>] ADDLOCAL=Client,Redistributables

Where:
• <path to SampleManagerInstaller.msi> is the path and file name of the
SampleManagerInstaller.msi file on the target machine.
• <path to root folder> is the path of the root folder where the
SampleManager client will be installed.
• <path to exe folder> is the path of the exe folder of the SampleManager client
installation.
• <path to help folder> is the path of the help folder of the SampleManager
client installation.
• <path to logfile> is the path of a folder where you want to save a log file of
the installation.

Enabling Tab Reports

To enable a user to create cross-tab reports in the csv or html output formats, appropriate
security settings must be applied to the Exe folder of the SampleManager client on the
workstation.

On a 32-bit operating system, the default location of the Exe folder is:
C:\Program Files\Thermo\SampleManager\<version>\Exe

On a 64-bit operating system, the default location of the Exe folder is:
C:\Program Files (x86)\Thermo\SampleManager\<version>\Exe

Where <version> is the version number for your SampleManager software.

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 5 Installing SampleManager Client
Connecting to a SampleManager Server Instance

Each user who will create csv or html tab reports must have Read/Write permissions on
the folder.

Connecting to a SampleManager Server Instance

When you run the SampleManager client for the first time, it prompts you to set up a
connection to a SampleManager server instance.

 To create a connection to a server instance

1. From the Windows Start menu, run the SampleManager client application.

By default, this option is found under Start > All Programs > Thermo
SampleManager > SampleManager.

Because no SampleManager server connections have been set up, the Create a new
server item window appears.
Figure 5-2. Create a new server item window

2. Enter a suitable name in the Server Name prompt.

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5 Installing SampleManager Client
Connecting to a SampleManager Server Instance

3. Select the Remote Server option and enter the following values:
• Instance Name – The name of the instance. If this field is set to Default,
SampleManager will connect to the current Default Instance recorded in the
Windows registry on the remote server machine.
• Server Name – The name of the server where the instance is installed.
• Port Number – The port number for the instance.

4. If the server is configured for proxy login, select the Use proxy login check box.

See the Proxy Login (page 121) section for more information.
5. Click OK to save changes and close the window.

The SampleManager Login window appears.

Figure 5-3. SampleManager Login window

6. Enter a suitable username and password, and click Login.

Note If proxy login (page 121) is being used, a username and password are not
required.

The SampleManager client attempts to connect to the specified SampleManager

server instance:
• If successful, the SampleManager Explorer appears.
• If unsuccessful, an error message appears. Close the dialog box and click the
Configuration button . The Manage Servers window (page 124) appears.
Verify and edit your server settings, then close the Manage Servers window and
try to log in again.

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 5 Installing SampleManager Client
Connecting to a SampleManager Server Instance

Proxy Login
If your server is configured to use proxy login, the Use proxy login check box must be
selected in the server connection details on each client.

When a client is configured for proxy login, the SampleManager Login window does not
have Username and Password fields.
Figure 5-4. SampleManager Login window for proxy login

To log in to SampleManager, click Login. Your current Windows login details will be
authenticated by the server and, if successful, the SampleManager Explorer will appear.

If your SampleManager instance is configured to use proxy login, you can create a
desktop shortcut that bypasses the SampleManager login window.

 To bypass the login window when using proxy login

1. On the Windows desktop, right-click the SampleManager icon and select

Properties. The Shortcut Properties window appears.

2. Click the Shortcut tab.

3. In the Target box, add the name of the SampleManager server to the end of the
target path:

-server "Your Server Name"

Where Your Server Name is the name given to the SampleManager server instance
in the Create a new server item window (page 119).

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5 Installing SampleManager Client
Connecting to a SampleManager Server Instance

For example, if the current Target is:

C:\Program Files (x86)\Thermo\SampleManager\12.2\Exe\

SampleManager.exe

The Target value required to connect to a server instance called vgsm local is:

"C:\Program Files (x86)\Thermo\SampleManager\12.2\Exe\

SampleManager.exe" -server="vgsm local"

Setting SampleManager Fonts

SampleManager can be localized so that the text in the user interface appears in the
language associated with the user for the current session. For more information, see
"Localizing the SampleManager Interface" in the SampleManager LIMS Configuration
Guide.

If the current user interface font does not contain all the characters required for your
preferred language, SampleManager will not render text correctly.

 To change the font settings so that text renders correctly

1. From the main menu, select View > Select Fonts. The Font Select dialog box
appears.
2. Change the SampleManager Font settings to one or more fonts that contain the
characters for your language.

Note SampleManager stores font settings on each workstation for the combination
of your Windows user account and the SampleManager server that you are currently
connected to.

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 5 Installing SampleManager Client
Managing Server Instance Connections

Managing Server Instance Connections

Each connection to a SampleManager server instance is stored as a server item on the
local PC, as part of the settings for the current user.

 To manage server items

1. From the Windows Start menu, run the SampleManager client application.
The SampleManager Login window appears.
Figure 5-5. SampleManager Login window

2. Click the Configuration button .

The Manage Servers window (page 124) appears, showing a list of configured server
items. Each server item is a set of connection details for a SampleManager server
instance.

3. Create, edit, or delete server items as required.

4. Click the Close Server Setup button to save changes and return to the
SampleManager Login window.

Note It is also possible to deploy the client with a list of pre-configured servers (page
126).

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5 Installing SampleManager Client
Managing Server Instance Connections

Manage Servers Window

The Manage Servers window appears when you click the Configuration button in
the SampleManager Login window. The window contains a list of the SampleManager
instances that the client has been configured to connect to.
Figure 5-6. Manage Servers window with SECURE_SERVER_SETUP set to No

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 5 Installing SampleManager Client
Managing Server Instance Connections

 To create a new server item

1. Click New. The Create a new server item window appears.

Figure 5-7. Create a new server item window

2. Follow the instructions in Connecting to a SampleManager Server Instance (page

119) to set the details for your new server connection.
Note The Local server for development and testing option can only be used when
the SampleManager server instance is running on the same machine as the
SampleManager client. If Local server for development and testing is selected, the
SampleManager client attempts to connect to the default SampleManager server
instance on the current machine. The identity of the default instance is stored in the
following Windows Registry entry:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\LabSystems\
SampleManager Server\DefaultInstance

3. Click OK to save changes and close the window.

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Managing Server Instance Connections

Deployment with Pre-Configured Servers

Encrypted details of the SampleManager server connections that have been added to a
SampleManager client are stored in a file called servers.xml (page 127).

If a user changes the server settings for a SampleManager client, the servers.xml file is
stored in the following location:
C:\Users\<UserName>\AppData\Roaming\Thermo Fisher Scientific
Inc\SampleManager\<version>

Where <UserName> is the Windows user name of the current user, and <version> is the
SampleManager version number. This copy of servers.xml is specific to the current user
and client workstation.

You can create a copy of servers.xml that will be common to all users of the
SampleManager client on a workstation.

 To deploy a servers.xml file that will apply to all users on a client PC

1. Create a servers.xml file that contains the server information you want to use.

2. Place a copy of the servers.xml file in the following location on the client PC:
C:\ProgramData\Thermo Fisher Scientific
Inc\SampleManager\<version>

Where <version> is the version number for your SampleManager software.

This copy of the servers.xml file will override the servers.xml file for individual user
accounts. The first time a SampleManager client reads the file, the information will
be encrypted.

3. If you want to prevent users changing the server settings, make the servers.xml file
read-only.

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 5 Installing SampleManager Client
Managing Server Instance Connections

Creating a Servers.xml File

The information in the servers.xml file is used to populate the list of servers in the
SampleManager login screen. A servers.xml file contains the connection details for one or
more SampleManager instances. The first time a SampleManager client reads a
servers.xml file, it encrypts the file contents.

The following example shows a simple servers.xml file:

<?xml version="1.0" encoding="UTF-8"?>

<Servers>

<Server>

<Name>Production</Name>

<Type>Remote</Type>

<MachineName>ukalt-production</MachineName>

<Port>56100</Port>

<InstanceName>Default</InstanceName>

<UseProxy>False</UseProxy>

</Server>

</Servers>

The elements in the servers.xml file are:

• Servers – Contains a set of child Server elements.
• Server – Contains a series of child elements that define the connection details for a
SampleManager instance.
• Name – Defines the server name that appears in the SampleManager Login screen.
• Type – Defines the type of connection. The value of the Type element can be:

– Local – The client will connect to the default SampleManager Server instance
hosted on the current machine. The default instance information is stored in the
Windows registry.

– Remote – The connection details are defined in the MachineName, Port, and
InstanceName elements.
• MachineName – The name of the server where the instance is installed.
• Port – The port number for the instance.

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5 Installing SampleManager Client
Managing Server Instance Connections

• InstanceName – The name of the instance. If the value of InstanceName is Default,

SampleManager will connect to the current Default Instance recorded in the
Windows registry on the remote server machine.
• UseProxy – Defines whether the instance is configured to use Proxy Login. If
UseProxy is True, the client will attempt to connect using the Windows login details
for the current user. If UseProxy is False, the user must enter a SampleManager user
name and password to log in.

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 6

Upgrading SampleManager
This chapter describes the procedure for upgrading to SampleManager 12.2 from one of
the following versions:
• SampleManager LIMS 12.1
• SampleManager LIMS 12.1 SP1
• SampleManager LIMS 12.1 SP2

The instructions in this chapter assume that you understand the basic principles of the
Windows operating system and are familiar with the use of file editors.

The upgrade of SampleManager differs from site to site depending on the hardware
configuration and other usage of the machine on which it is being installed. The
procedures described in this chapter provide one method of upgrade only, and different
sites should proceed according to company standard practices.

CAUTION Before starting the upgrade procedure, make a full backup of your
SampleManager system. In particular, make sure that you have backup copies of any
files that need manual upgrading, for example user-modified versions of structure.txt
and message.txt.

Contents
• Prerequisites
• Upgrading SampleManager Server
• Manual Upgrade Procedures
• Upgrading SampleManager Clients
• Upgrading the Password Encryption
• New Menu Items
• Fixing Form Upgrade Errors
• Entity-Specific Changes
• Report Designer

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6 Upgrading SampleManager
Prerequisites

• Upgrading the SampleManager Web Application

Prerequisites
Before you upgrade SampleManager, make sure that your database and application server
are ready for the upgrade process:

1. Back up your SampleManager instances. See the appropriate chapter in the

SampleManager LIMS System Administration Guide for guidance:
• "Data Storage and Handling in Oracle"
• "Data Storage and Handling in SQL Server"
2. Make sure that the correct operating system is installed (page 14).

3. Make sure that you have installed all the updates for the Windows operating system
on your servers.
4. Make sure that the Microsoft .NET Framework 4.6.2 is installed on the server where
you will install SampleManager Server.

The installer for the required version of the Microsoft .NET Framework is included
in the following folder of the SampleManager installation kit:
..\SampleManager 12.2\Server\Redistributables

5. Make sure that the Microsoft Visual C++ 2017 Redistributable is installed on the
server where you will install SampleManager Server.
The installer for the Microsoft Visual C++ 2017 Redistributable is included in the
following folder of the SampleManager installation kit:
..\SampleManager 12.2\Server\Redistributables

6. Check that the database account SampleManager uses has all the security
permissions required for SampleManager LIMS 12.2. See the following chapters for
more information:
• Oracle Setup (page 223)
• SQL Server Setup (page 233)

From SampleManager LIMS 12.2 onwards, frequently used increments can be

managed as database sequences instead of as records in the INCREMENTS table.
The database account that SampleManager uses must have permission to create and
update sequences.

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 6 Upgrading SampleManager
Upgrading SampleManager Server

7. Check whether the instance that you want to upgrade is part of an application server
cluster:
a. On the server that hosts your SampleManager instance, open the Registry
Editor.
b. Navigate to the following registry key:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\
LabSystems\SampleManager Server\smplock<instance_name>
Where <instance_name> is the name of the instance.
c. Examine the use_cluster value. If use_cluster is true, the instance is part of an
application server cluster.

Upgrading SampleManager Server

The main upgrade procedure consists of the Upgrade Server Instance Wizard, which
performs the following steps:
• The folder structure for the instance is updated.
• Executable files are updated, unless they contain user modifications.
• Other files are updated, unless they contain user modifications.
• The registry entries for the instance are upgraded.
• VGL reports are recompiled.
• Services are updated if necessary.
• Any differences applied to database structure files are made to the database.
• User message files are rebuilt.
• Data (.csv) files are loaded into the database.
• Forms are updated.

Files containing user modifications must be upgraded manually during the upgrade
process.

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6 Upgrading SampleManager
Upgrading SampleManager Server

Overall Upgrade Procedure

This procedure applies to instances that are not part of an application server cluster (page
8). See Overall Upgrade Procedure for an Application Server Cluster (page 133) for an
overview of the upgrade procedure for application server clusters.

 To upgrade your SampleManager instance

1. Create a full backup of your SampleManager instance, including the database and
the Thermo\SampleManager\Server\<instance_name> folder.
Keep a copy of the original structure.txt file in an accessible location, as you will
require it when you upgrade the database.
2. Disable the following services for the instance:
• smptq<instance_name>
• smpwcf<instance_name>
• All batch services for the instance. Batch service names use the following naming
convention:

smpbatch<instance_name>_<program_name>

3. Install the latest version of the SampleManager server software.

Follow the instructions in the appropriate Installing SampleManager Server chapter
of this guide.

The files for SampleManager Server 12.2 will be installed in the following folder by
default:
C:\Program Files (x86)\Thermo\SampleManager\12.2

Note If you choose to install the Thermo Licensing Server component, it will be
upgraded if necessary.
4. Run the Upgrade Server Instance Wizard.

See Running the Upgrade Server Instance Wizard (page 138).

5. Upgrade structure.txt manually if it differs from the default structure.txt file for the
original SampleManager version.

If the Upgrade Server Instance Wizard detects that the structure.txt file for the
instance is not the same as the default structure.txt file for the version that you are
upgrading from, the upgrade process will pause and prompt you to upgrade the file
manually.

See Upgrading structure.txt (page 145) for more information.

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6. Upgrade modified SampleManager files manually.

Some files, such as message.txt and VGL reports, might contain user modifications
specific to your installation.

If these files contain modifications, the Upgrade Server Instance Wizard will not
overwrite them. The wizard will inform you that they have been modified and
prompt you to upgrade them manually.

See Manual Upgrade Procedures (page 144).

7. Before any users attempt to log in, make sure that the password encryption
mechanism is correctly configured.
See Upgrading the Password Encryption (page 150).

8. Restart the timerqueue service and batch services that you suspended in step 2.

Overall Upgrade Procedure for an Application Server Cluster

This procedure applies to instances that are part of an application server cluster (page 8).
An application server cluster has two types of instance:
• A single primary instance that has all the files required for a SampleManager
instance.
• One or more secondary instances that have a full set of SampleManager instance
executable files. The secondary instances obtain all the other files required for
SampleManager operations, such as report designs and VGL libraries, from the
primary instance.

In the following diagram, Application Server 1 hosts the primary instance in the
application server cluster and Application Server 2 hosts a secondary instance. All the
instances in an application server cluster have the same instance name.

Note In SampleManager versions before SampleManager LIMS 12.2, multiple

instances in an application server cluster could be hosted on a single server. This
configuration is no longer supported. Each instance in an application server cluster
must be hosted on a separate server.

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Figure 6-1. Application server instance

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 To upgrade an application server cluster

1. Identify all the SampleManager instances in the application server cluster.

SampleManager LIMS does not maintain a central record of the instances that
belong to an application server cluster. For maintenance and upgrade purposes, we
recommend that you keep a record of your application server cluster architecture.

2. Locate the shared files for the application server cluster. If you do not have a record
of the shared folder locations, you can obtain this information from the Windows
registry of one of the servers that hosts an application server instance:
a. On the server that hosts your SampleManager instance, open the Registry
Editor.
b. Navigate to the following registry key:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\
LabSystems\SampleManager Server\smplock<instance_name>
Where <instance_name> is the name of the instance.
c. Examine the smp$archivefiles value. This value contains the location of the
shared Archive folder for the instance. All the shared folders are normally in the
same location.
3. Create a full backup of the database and all the shared folders.

Keep a copy of the original structure.txt file in an accessible location, as you will
require it when you upgrade the database.

4. On each server that hosts an instance in the application server cluster, disable all the
services for the instance:
• SMDaemon<instance_name>
• smplock<instance_name>
• smp<instance_name>
• smptq<instance_name>
• smpwcf<instance_name>
• All batch services for the instance. Batch service names use the following naming
convention:

smpbatch<instance_name>_<program_name>

5. On each server that hosts an instance in the application server cluster, install the
latest version of the SampleManager server software.

Follow the instructions in the appropriate Installing SampleManager Server chapter

of this guide.

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The files for SampleManager Server 12.2 will be installed in the following folder by
default:
C:\Program Files (x86)\Thermo\SampleManager\12.2

Note If you choose to install the Thermo Licensing Server component, it will be
upgraded if necessary.
6. Choose one instance to upgrade in the application server cluster.

7. On the server that hosts the instance you have chosen to upgrade, start the following
services:
• SMDaemon<instance_name>
• smplock<instance_name>
• smp<instance_name>
8. Run the Upgrade Server Instance Wizard.

See Running the Upgrade Server Instance Wizard (page 138).

9. Upgrade structure.txt manually if it differs from the default structure.txt file for the
original SampleManager version.
If the Upgrade Server Instance Wizard detects that the structure.txt file for the
instance is not the same as the default structure.txt file for the version that you are
upgrading from, the upgrade process will pause and prompt you to upgrade the file
manually.
See Upgrading structure.txt (page 145) for more information.
10. Upgrade modified SampleManager files manually.

Some files, such as message.txt and VGL reports, might contain user modifications
specific to your installation.

If these files contain modifications, the Upgrade Server Instance Wizard will not
overwrite them. The wizard will inform you that they have been modified and
prompt you to upgrade them manually.

See Manual Upgrade Procedures (page 144).

11. Before any users attempt to log in, make sure that the password encryption
mechanism is correctly configured.

See Upgrading the Password Encryption (page 150).

12. For the instance that you have upgraded, restart the other services that you
suspended in step 4.

13. Test the instance to make sure that it is operating correctly.

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14. Upgrade each of the remaining application server instances in the cluster one at a
time:
a. On the server that hosts the application server instance, install the latest version
of the SampleManager server software.
b. Use the Delete Server Instance Wizard to remove the old version of the instance:
• Oracle – Removing a SampleManager Instance (page 55)

• SQL Server – Removing a SampleManager Instance (page 93)

c. Add a new application server instance that has the same instance name as the
instance you removed and that connects to the upgraded shared folders:
• Oracle – Creating an Application Server Instance (page 41)
• SQL Server – Creating an Application Server Instance (page 81)
d. Before any users attempt to log in, make sure that the password encryption
mechanism is correctly configured.
See Upgrading the Password Encryption (page 150).
e. Test the instance to make sure that it is operating correctly before you upgrade
the next instance in the application server instance cluster.

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Running the Upgrade Server Instance Wizard

 To run the Upgrade Server Instance Wizard for an existing SampleManager
instance
1. From the Start menu, click Thermo SampleManager 12.2 > Upgrade <Database>
Instance.
Where <Database> is SQL or Oracle, depending on the database platform that your
SampleManager installation uses.
The Upgrade Server Instance Wizard appears.
Figure 6-2. Upgrade Server Instance wizard

2. Welcome to the SampleManager 12.2 Upgrade Server Instance

Click Next to continue.

3. Choose Server Instance

a. Select the instance to be upgraded
b. Check that the Original Version and Target Version shown are as expected.
c. Set the base port number for the instance. This value is used if the upgrade
process creates new services for the instance.
d. Click Next to continue.

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4. Set Oracle Connection

This page only appears if your instance connects to an Oracle database.

The Database prompt shows the Oracle Net Service Name of the database that your
instance connects to.
a. Enter the password for the SYS account of the selected database.
The wizard uses the SYS user and corresponding password for system
administration operations during the upgrade process. The SYS password will be
used to connect to Oracle during the upgrade process, but will not be stored or
cached by SampleManager.
b. If you cannot supply the SYS password for your Oracle database, select I don't
know the SYS password. Please let me continue. Make sure the Oracle
account that the instance uses to connect to the database has all the required
permissions (page 227) before you proceed.
c. Click Next to continue.

5. Confirm Details
a. Check that the details shown for the instance are correct.
b. Click Next to start the upgrade procedure.

6. Instance Upgrade in Progress

This page shows the progress of the first phase of the automatic upgrade procedure.
During this phase, new and original versions of files are compared to check for any
required modifications.
When the process is complete, a log file of the first phase is saved to the root folder
of your SampleManager instance.
a. Click Save Log to save a copy of the log file to a different location.
b. Click Next to continue.

7. Connection String Configuration

SampleManager 12.2 uses an ADO connection to the database.
a. Click Test to test the database connection string.
b. If the test fails, edit the connection string and repeat the test.
c. When the connection test is successful, click Next to continue.

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8. Confirm Schema Modifications

If your SampleManager server instance features modifications to structure.txt, the
Confirm Schema Modifications page appears.

The instance upgrade process pauses to let you perform a manual upgrade of the
structure.txt file.
a. If you want to stop the instance upgrade process until you have upgraded your
structure.txt file, click Cancel. You can start the Upgrade Server Instance
Wizard again later to resume the upgrade process. For more details, see
Upgrading structure.txt (page 145).
b. If you want to upgrade your structure.txt file immediately, follow the
instructions in Upgrading structure.txt (page 145) without closing the wizard.
c. When you have applied all the modifications to the structure.txt file for the
instance, select the check box at the bottom of the page.
d. Click Next to continue.

9. Data Files Upgraded

This page lists files that have been modified for the instance and that must be
upgraded manually. For more information, see Identifying Files That Require a
Manual Upgrade (page 146).
a. If you want to stop the instance upgrade process until you have upgraded your
files, click Cancel. You can start the Upgrade Server Instance Wizard again later
to resume the upgrade process. For more details, see Upgrading Files Manually
(page 147).
b. If you want to upgrade your files immediately, follow the instructions in
Upgrading Files Manually (page 147) without closing the wizard.
c. When you have applied all the modifications, select the check box at the bottom
of the page.
d. Click Next to continue.

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10. Instance Upgrade in Progress

This page shows the progress of the second phase of the automatic upgrade
procedure. At this stage, the following changes are made to your instance:
• The database structure is upgraded.
• The VGL reports are compiled.
• The services are upgraded.
• The records in the database are upgraded.
• The forms are upgraded
a. If the Upgrade Server Instance Wizard cannot update your database structure
because it finds errors in your copy of structure.txt, the upgrade process stops. A
message appears prompting you to choose one of three options:

• Abort – Stops the upgrade process. You can run the Upgrade Server
Instance Wizard again later.
• Retry – Resumes the upgrade process after you have modified your copy of
structure.txt. The updated copy of structure.txt is checked and if problems
are identified, the upgrade process will pause again.

• Ignore – Resumes the upgrade process without changing structure.txt or

checking for errors.
b. If the instance upgrade process cannot upgrade one or more forms, the process
reports an error:

Errors occurred performing second pass of the upgrade: Errors occurred in

rebuilding forms dll
Click OK to close the error window and continue the upgrade process. When
you reach the final page of the instance wizard, it will report that the upgrade
failed. To address the form upgrade errors, see Fixing Form Upgrade Errors
(page 151).
c. When the upgrade processes are complete, a log file is saved to the root folder of
your SampleManager instance. To save a copy of the log file to a different
location, click Save Log.
d. Click Next to continue.

11. Upgrade Complete

Click Finish to close the wizard.

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Fixing Character Set Rendering Issues for an Oracle Instance with a Database that Contains
Multiple Languages
This section applies if you are upgrading a SampleManager instance that matches all the
following criteria:
• The database is Oracle.
• The database contains SampleManager data in more than one language.
• Some or all characters in existing SampleManager data are not rendered correctly
when viewed in a SampleManager 12.2 client after your upgrade.

The character rendering issue occurs because SampleManager dynamically assigns a code
page that does not match the code page of the SampleManager application server that
created the data.

 To fix character set rendering issues

1. On the server that hosts your SampleManager instance, open the Registry Editor.

2. Navigate to the following registry key:

Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\LabSystems\Sam
pleManager Server\<instance name>

Where <instance name> is the name of your SampleManager instance.

3. Set the value of smp$ado_database_code_page to the identifier of the code page on
the SampleManager application server that created the data. For example, the
Western European code page identifier is 1252.

Note Set smp$ado_database_code_page to -1 to disable this feature.

Thermo License Server Handshake Error

If you upgrade the license server, a bad handshake error appears if the license server fails
to deploy the licenses correctly. To restore the license server, uninstall the license server,
delete additional files in the Thermo Licensing Server folder, and reinstall the license
server.

 To restore the license server using the Windows Uninstall or Change a Program
window
1. To uninstall the Thermo Licensing Server, use the Windows Uninstall or change a
program window.

2. In a Windows Explorer, open the Thermo Licensing Server folder and make a
backup copy of the .lic license file.

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3. In the Thermo Licensing Server folder, delete all files except the .lic license file.

4. To install the Thermo Licensing Server, in a Windows Explorer, open the

SampleManager LIMS 12.1.2 License folder and double-click the
ThermoLicensingServerSetup.exe file.

The Installation Wizard appears.

5. To install the Thermo Licensing Server, follow the installation instructions on the
installation wizard.
The license server should now deploy correctly.

If the problem is not resolved by restoring the license server using the Windows Uninstall
or Change a Program window, you must restore the license server using
ThermoLicensingServerSetup.exe.

 To restore the license server using ThermoLicensingServerSetup.exe

1. In a Windows Explorer, open the SampleManager LIMS 12.1.2 License folder,

double-click ThermoLicensingServerSetup.exe.

The Installation Wizard appears.

2. To uninstall the Thermo Licensing Server, follow the uninstallation instructions on
the installation wizard.
3. In a Windows Explorer, open the Thermo Licensing Server folder and make a
backup copy of the .lic license file.
4. In the Thermo Licensing Server folder, delete all files except the .lic license file.
5. To install the Thermo Licensing Server, in a Windows Explorer, open the
SampleManager LIMS 12.1.2 License folder and double-click the
ThermoLicensingServerSetup.exe file.
The Installation Wizard appears.

6. To install the Thermo Licensing Server, follow the installation instructions on the
installation wizard.

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Upgrading the SampleManager Web Interface

During an upgrade, you might have to upgrade the SampleManager Web interface. For
more information, see the SampleManager LIMS Web Interface Configuration Guide.

If a SampleManager WCF service for the instance does not exist, the upgrade procedure
creates one. If you are upgrading from a version of SampleManager 10.0 that did not use
a SampleManager WCF service, you must reconfigure any connections to the instance
that used the old LIMSML Web service and COM+ interface to connect through the
SampleManager WCF service. The WCF service implements the same
ILIMSWebService interface as the LIMSML Web service, so any external applications
developed to communicate with the LIMSML Web service will work in the same way
with the WCF service.

When the upgrade is complete, restart the SampleManager WCF service to make sure
that it recognizes the changes to the database structure.

Manual Upgrade Procedures

The automatic upgrade process cannot upgrade SampleManager files that contain user
modifications. You must upgrade modified files manually before you can complete the
Upgrade Server Instance Wizard. To upgrade a file, you must merge your existing
version of the file with its SampleManager 12.2 counterpart.

This section describes the processes by which you can upgrade these files manually.

Required Tools
We recommend that you use a file comparison tool to merge existing versions of
SampleManager files with the corresponding SampleManager 12.2 versions.

From SampleManager LIMS version 12.2, the SampleManager client software,

SampleManager server software, and all associated applications support UTF-8 Unicode
character encoding. Data stored with Unicode encoding in the database is passed to the
SampleManager client and shown as Unicode characters in the user interface. All text,
.csv, and .xml files created by SampleManager are encoded in UTF-8 with a byte order
marker (BOM).

Note All the SampleManager files that might need to be edited are text files, and can
be edited using any standard text editor, such as Windows Notepad.

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Upgrading structure.txt
The database schema file, structure.txt, is subject to the most common user
modifications, so it often needs upgrading manually. See Required Tools (page 144) for
information about tools that can be used for the manual upgrade.

You must create a version of structure.txt file for your instance that includes:
• The customizations contained in the original copy of structure.txt for your instance
• The changes made to the default structure.txt for SampleManager 12.2

The new structure.txt file will be used to build the database structure for your upgraded
SampleManager instance.

There are many significant differences between the default structure.txt files for older
versions of SampleManager and SampleManager 12.2. The simplest way to upgrade
structure.txt is usually to transfer the modifications in the current structure.txt for the
instance into a copy of the default structure.txt file for SampleManager 12.2.

Version-specific Upgrade Files

During the automatic upgrade process, the following folder will be created in the
Upgrade folder for your SampleManager instance:
<original_version> to 12.2

Where <original_version> is the SampleManager version you are upgrading from.

The following version-specific files will be created in the folder during the automatic
upgrade procedure:
• structure_<original_version>.txt
A copy of the default structure.txt for the version of the product that you are
upgrading from.
• structure_122.txt
A copy of the default structure.txt for SampleManager 12.2.

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Example Upgrade Procedure for Structure.txt

This procedure transfers modifications made to structure.txt in your SampleManager
12.1 instance to the default structure.txt file for SampleManager 12.2.

 To upgrade your structure.txt file

1. Use a file comparison tool to compare the version of structure.txt for your instance
with the standard version of structure.txt for SampleManager 12.1.
The standard version of structure.txt for SampleManager 12.1 can be found here:
<instance_root>\Upgrade\12.1 to 12.2\structure_121.txt

Where <instance_root> is the root folder for your instance.

2. Identify each difference between the two files, and copy all the differences to the
standard version of structure.txt for SampleManager 12.2.
The standard version of structure.txt for SampleManager 12.2 can be found here:
<instance_root>\Upgrade\12.0 to 12.2\structure_122.txt

3. Save the modified version of the SampleManager 12.2 structure.txt file to the
following file path:
<instance_root>\data\structure.txt

Identifying Files That Require a Manual Upgrade

The Upgrade Server Instance Wizard produces a log file called Upgrade Diffs.log in the
Upgrade folder of your SampleManager instance:
<instance_root>\Upgrade\<original_version> to 12.2

Where:
• <instance_root> is the root folder of your instance
• <original_version> is the version you are upgrading from

This file contains a list of all the files that could not be overwritten by the upgrade
process. A file cannot be overwritten when the existing version of the file is not the same
as the original file distributed with SampleManager.

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The following text is an example of the Upgrade Diffs.log file:

The following files are different in this version but have been modified in your instance

WARNING - Modified file detected : C:\Thermo\SampleManager\Server\VGSM\data\structure.txt

different to C:\Program Files (x86)\Thermo\SampleManager\12.2\Data\structure.txt
WARNING - Modified version of a new file : C:\Thermo\SampleManager\Server\VGSM\message\aql.txt
WARNING - Modified version of a new file :
C:\Thermo\SampleManager\Server\VGSM\report\$jobstat.rpf
WARNING - Modified version of a new file :
C:\Thermo\SampleManager\Server\VGSM\report\$reslstat.rpf
WARNING - Modified version of a new file :
C:\Thermo\SampleManager\Server\VGSM\report\$sampstat.rpf

Notes Files in the Imprint folder of the instance can be ignored. These files are
updated automatically by the upgrade process.

Upgrading Files Manually

The SampleManager installation contains all the files required to perform a manual
upgrade of user-modified files.
• The distribution versions of the SampleManager 12.2 files can be found by default
in:
C:\Program Files (x86)\Thermo\SampleManager\12.2

• The distribution versions of the files from the SampleManager version you are
upgrading from can be found by default in:
C:\Program Files
(x86)\Thermo\SampleManager\12.2\Upgrade\<original_version>

Where <original_version> is the version you are upgrading from.

Use a file comparison tool to compare each modified file with the corresponding
SampleManager 12.2 version. Merge the changes to create a version of the file that
contains:
• All user modifications made to the original version for the instance, compared to the
standard file distributed with the version of SampleManager you are upgrading from.
AND
• All modifications made between the standard file in the version of SampleManager
you are upgrading from and the SampleManager 12.2 version.

Note Rather than editing the original version of the file for the instance, it is often
easier to copy the SampleManager 12.2 distribution version to the instance folder and
reapply the user modifications. In this case, you must remove the read-only attribute
from the copied file.

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As an example of manually upgrading a user-modified file, the procedure for upgrading

result_entry_messages.txt is described in the next section.

Example Upgrade Procedure for result_entry_messages.txt

Perform the following comparisons to identify the changes that you must make to
upgrade the copy of result_entry_messages.txt for your instance.

To identify the user modifications to result_entry_messages.txt, compare the following

two files:
• The existing copy for your instance:
<instance_root>\Message\result_entry_messages.txt

Where <instance_root> is the root folder for your instance.

• The unmodified copy for the version of SampleManager you are upgrading from:
C:\Program Files
(x86)\Thermo\SampleManager\12.2\Upgrade\<original_version>\Mess
age\result_entry_messages.txt

Where <original_version> is the version you are upgrading from.

To identify the changes that you must make to your result_entry_messages.txt file to
bring it in line with SampleManager 12.2 requirements, compare the following files:
• The existing copy for your instance:
<instance_root>\Message\result_entry_messages.txt

• The unmodified SampleManager 12.2 version:

C:\Program Files
(x86)\Thermo\SampleManager\12.2\Message\result_entry_messages.t
xt

To identify the changes made to the default versions of the file between the version of
SampleManager you are upgrading from and SampleManager 12.2, compare the
following files:
• The unmodified SampleManager 12.2 version:
C:\Program Files
(x86)\Thermo\SampleManager\12.2\Message\result_entry_messages.t
xt
• The unmodified copy for the version of SampleManager you are upgrading from:
C:\Program Files
(x86)\Thermo\SampleManager\12.2\Upgrade\<original_version>\Mess
age\result_entry_messages.txt

Edit your version of the file, so that it includes changes from all three of these difference
checks.

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Upgrading SampleManager Clients

Upgrading SampleManager Clients

The standard SampleManager 12.2 client does not include the components required to
support the following deprecated functionality:
• InfoMaker reports
• Label templates designed with combit List & Label

If your instance uses these features, you can install a version of the SampleManager
desktop client that supports them.

 To upgrade your SampleManager clients

1. In the SampleManager LIMS 12.2 installation kit, open the Client_Inc_Imprint

folder.
This folder contains a version of the SampleManager 12.2 client that supports labels
designed in combit List & Label, and reports designed in InfoMaker.
2. Double-click SampleManagerInstaller.msi.
3. Follow the instructions in the Installing SampleManager Client chapter (page 115).

4. If necessary, uninstall the old version of the SampleManager client.

Use the Programs and Features tool in the Windows Control Panel to uninstall the
client.

Note Multiple versions of the SampleManager client can be installed on a single

workstation. If the SampleManager instances you want to connect to are different
SampleManager versions, you will need multiple versions of the client.

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Upgrading the Password Encryption

Upgrading the Password Encryption

SampleManager 12.2 has a new encryption mechanism for passwords. When you
upgrade an instance, SampleManager forces each user to change their password the first
time they log in. The new password records include the information required by the new
encryption mechanism.

 To upgrade the password encryption

1. In a text editor, open a backup copy of the structure.txt file that was created before
you upgraded the instance.
2. Find the section that defines the PASSWORD table:
table password;

field identity
links_to personnel.identity
used_for unique_key;
field cryptpass datatype identity;
field expires datatype date;
field frozen
datatype boolean
true_word 'Frozen'
false_word 'Active'
default 'Active' ;
field attempts
datatype integer
default 0 ;
field last_login datatype date;

3. If the cryptpass field definition matches the following example, the field length is 10,
which is the default length for an identity field:
field cryptpass datatype identity;

If the cryptpass field length is 10, the default registry settings match the values
required for your instance and no further changes are necessary.
4. If the cryptpass field length is not 10, make a note of the length value. For example,
the following definition specifies the field length as 20:
field cryptpass datatype identity (20);

5. If the cryptpass field length is not 10, you must update the registry settings for the
instance before users can connect:
a. On the SampleManager application server, open the Registry Editor.
b. Navigate to the registry key for your SampleManager instance:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\
LabSystems\SampleManager Server\<instance_name>
c. Set the LoginAllowLegacy value to True.

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New Menu Items

d. Set the LoginCryptLength value to the value that you noted in step 4.

SampleManager has new configuration items that let you define complexity rules for
passwords. If necessary, define the complexity rules before your users reset their
passwords. For more information, see the "Electronic Signatures" chapter in the
SampleManager LIMS System Administration Guide.

New Menu Items

Any new menu items are inserted into the current SYSTEM menu in a top-level menu
group called SM12.2. We recommend that you customize the menu in the
SampleManager desktop client to move these menu items to the appropriate top-level
menus.

When you view the SM12.2 menu in Customize mode, the SM12.2 > View menu
contains two Quick Launcher options. One of the Quick Launcher options is visible in
the desktop client and the other is visible in the web client.

For information about customizing the structure of the main menu, see the "Toolbars
and Menus" chapter in the SampleManager LIMS Configuration Guide.

Fixing Form Upgrade Errors

As part of the upgrade process, SampleManager updates all the form definitions to
include any new or modified controls included in the default form definition distributed
with SampleManager LIMS 12.2.

If a form definition in your instance includes custom controls with names that match
default controls in the new version of the form, the form compilation process reports
errors similar to the following example:
Personnel.cs(1202,25): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureBoxControlName'
Personnel.cs(1132,25): (Location of symbol related to previous error)
Personnel.cs(1208,25): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureBoxControlLabel'
Personnel.cs(1138,25): (Location of symbol related to previous error)
Personnel.cs(1213,21): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureBox'
Personnel.cs(1143,21): (Location of symbol related to previous error)
Personnel.cs(1265,25): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureButtonControlName'
Personnel.cs(1090,25): (Location of symbol related to previous error)

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Fixing Form Upgrade Errors

Personnel.cs(1271,25): error CS0102: The type

'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureButtonControlLabel'
Personnel.cs(1096,25): (Location of symbol related to previous error)
Personnel.cs(1276,21): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureButton'
Personnel.cs(1101,21): (Location of symbol related to previous error)
Personnel.cs(1307,25): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureLabelControlName'
Personnel.cs(1111,25): (Location of symbol related to previous error)
Personnel.cs(1313,25): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureLabelControlLabel'
Personnel.cs(1117,25): (Location of symbol related to previous error)
Personnel.cs(1318,16): error CS0102: The type
'Thermo.SampleManager.Library.FormDefinition.FormPersonnel' already
contains a definition for 'SignatureLabel'
Personnel.cs(1122,16): (Location of symbol related to previous error)
Form definition batch file completed
Error 'Failed to build form definition assembly. Check the output file
'C:\Thermo\SAMPLE~1\Server\VGSM\code\FORMDE~1\Output.log' for more
details.'
Errors occurred performing second pass of the upgrade: Errors occurred
in rebuilding forms dll

 To address the form upgrade errors

1. Complete the remaining tasks in the upgrade process.

2. Run the SampleManager desktop client and log in to your instance.

3. In the Explorer, open the System Folders/Forms folder.

4. Right-click and select Tools > Import Form(s). The Form Import window appears.
5. Navigate to the Form folder for the SampleManager LIMS server application. By
default this folder is found at the following location:

C:\Program Files (x86)\Thermo\SampleManager\12.2\Form

6. Select the .frm file for the form that caused the error.

7. Click Open. SampleManager imports the default definition of the form for
SampleManager LIMS 12.2.

8. If necessary, reimplement your original customizations in Form Designer and update

the C# tasks associated with the form to reflect the new controls.

For property sheet forms, we recommend that you use the Tools > Extend option to
add custom controls to separate overlay pages. This mechanism preserves your
customizations when the forms are upgraded.

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Entity-Specific Changes

Entity-Specific Changes
This section describes significant changes to SampleManager entities that occur after
upgrading to SampleManager12.2.

Rack Templates
The Rack Template property sheet has been updated to relocate the settings related to
the structure and appearance of rack templates. Therefore, the following Rack Template
property sheet pages are only available in rack templates created in SampleManager 12.1
or earlier:
• Rack Layout
• Status Icons
• Expression Icons
• Preview Layout

For more information about these pages, see "Sequences" in the SampleManager LIMS
12.1 Laboratory Execution Guide.

The Preview Layout page has been directly replaced with the Plate Preview page, which
contains the same information. The new locations of the settings that were on the Rack
Layout, Status Icons, and Expressions Icons pages are listed in the table:

Rack template setting Setting location in Setting location in

SampleManager 12.1 and earlier SampleManager 12.1 and
(rack template property sheet) earlier

Structure of the rack Rack Layout page Plate Type and Plate
Appearance entities

Order in which the rack Rack Layout page Plate Fill Order entity
cells are populated

Icons used to represent Status Icons Batch Entry Type phrase

batch entries

Icons used as test Status Icons Test Stat phrase

overlays

Expressions used to Expression Icons Plate Appearance entity

define batch entry icons
and overlay icons

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Report Designer

You can specify the plate type, plate appearance, and plate fill order for a rack template
on the General page of the Rack template property sheet. For more information about
plate types, plate appearances, and plate fill orders, see "Plates" in the SampleManager
LIMS 12.2 Laboratory Execution Guide.

Modifying Rack Templates Created in SampleManager 12.1 or Earlier

If you modify a rack template created in SampleManager 12.1 or earlier, you cannot save
it without specifying the Plate Type, Appearance, and Fill Order on the General page. If
you do set these values and save the rack template, when you next modify the rack
template the Plate Preview page is available and the following pages are hidden:
• Rack Layout
• Status Icons
• Expression Icons
• Preview Layout

Report Designer
SampleManager Report Designer now supports the use of expressions for binding
controls to data and applying conditional formatting.

You can use expression binding to:

• Applying conditional formatting to controls
• Create summary results
• Create controls that contain more than one property value

Expression binding is the default mechanism that is used by all report designs created
from SampleManager 12.1 SP2 onwards.

You can convert report designs that use the data binding mechanism to use the new
expression binding mechanism. Before you convert your report designs, back up the
.repx report design files in the smp$textfiles folder of your SampleManager instance.
There is no mechanism to convert a report design from expression bindings to data
bindings.

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Upgrading the SampleManager Web Application

 To convert a report design to use the expression binding mechanism

1. Open the report design in the Report Designer. The following message appears:
The XtraReport contains bindings. Do you want to convert them to expressions?

2. Click Yes to convert the report design to use expressions, or No to retain the original
data bindings.

3. After you convert the report design, validate the report template. If the validation
fails, either restore the original version of the report design from the backup file, or
correct the issues in the current version.

Upgrading the SampleManager Web Application

Note This topic applies if you have installed the SampleManager Web Application
supplied with SampleManager and its accompanying website. For more information,
see the SampleManager LIMS Web Interface Configuration Guide.
This topic does not apply to the SampleManager Web Client.

From SampleManager LIMS version 12.2, SampleManager uses Unicode to handle text
within the application. To support Unicode, the web application server requires an
updated DLL for the encryption functionality.

 To update the encryption DLL

1. On the SampleManager web application server, in Windows Explorer, navigate to

the following folder in your SampleManager installation kit:

\Modules\SampleManager Web 12.2 update\Web\bin

2. Copy the Thermo.SM.LIMSML.Helper.dll file into the bin folder of your
SampleManager web application. The default path for the bin folder is:
C:\Program Files (x86)\Thermo\SampleManager\11.0\Web\bin

3. Restart the web application server.

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Installing LIMS Reporter

LIMS Reporter, which is a rebadged version of Sybase InfoMaker, lets you write and
produce reports for use with SampleManager.

From SampleManager LIMS 12.2, LIMS Reporter and Imprint are no longer shipped
with SampleManager. The explorer folders, configuration items, and menu options
related to Imprint and LIMS Reporter reports are only available in instances that were
upgraded from an earlier version of SampleManager. SampleManager Report Designer is
the standard mechanism for generating reports. This chapter applies when you are
moving an existing SampleManager instance that uses InfoMaker reports to a new server.
For more information, see the Reports chapters in the SampleManager LIMS System
Administration Guide.

Note The terms LIMS Reporter and InfoMaker are interchangeable.

Contents
• Connections Between LIMS Reporter and the
Database
• Installation Procedures for SampleManager on
Oracle
• Installation Procedures for SampleManager on SQL
Server
• Installing LIMS Reporter
• Setting up a Database Profile
• Producing Reports in PDF Format

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Connections Between LIMS Reporter and the Database

Connections Between LIMS Reporter and the Database

The following diagrams show the connection between LIMS Reporter and
SampleManager databases hosted on Oracle and SQL Server.
Figure 7-1. Connection between LIMS Reporter and a SampleManager Oracle
database

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Connections Between LIMS Reporter and the Database

Figure 7-2. Connection between LIMS Reporter and a SampleManager SQL Server
database

LIMS Driver and Unicode Data

If your SampleManager database stores data in Unicode, the LIMS Driver translates the
Unicode characters it receives from the database into the appropriate character set before
passing it to LIMS Reporter.

The required character set is obtained from the currently active code page on the
machine where the LIMS Driver is running. If the currently active code page does not
match the code page of the system used to enter the data, the characters might not be
rendered correctly.

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Installation Procedures for SampleManager on Oracle

Installation Procedures for SampleManager on Oracle

The exact steps required to install and configure LIMS Reporter depend on the
configuration of your system and the PC on which you are installing it. For example, the
installation procedure varies depending on whether Oracle and SampleManager are
already installed, and how you intend to produce reports.

The main platforms for installation are:

• SampleManager server PC

This configuration is used to generate LIMS Reporter reports from SampleManager

client and SampleManager background operations.
• SampleManager client PC

LIMS Reporter can be installed on a SampleManager client PC to let reports be

developed in LIMS Reporter. SampleManager does not support LIMS Reporter on a
PC without SampleManager or Oracle installed.

Installation on a SampleManager Server PC

The following steps are required to install and configure LIMS Reporter on a
SampleManager server PC:
1. Install LIMS Reporter software (page 166).
2. Set up a database profile (page 166).

Installation on a SampleManager Client PC

The following steps are required to install and configure LIMS Reporter on a
SampleManager client PC:
1. Install an Oracle Net Client, and create a Net Service Name that connects to your
database. See Oracle Setup (page 223) for more information.

2. Set up an Oracle ODBC data source (page 161).

You can either install an Oracle ODBC driver, or use an alternative driver, for
example, Microsoft ODBC for Oracle.

3. Set up a SampleManager ODBC data source (page 162).

4. Install LIMS Reporter (page 166).

5. Set up a database profile (page 166).

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Installation Procedures for SampleManager on Oracle

Setting up an Oracle ODBC Data Source

An Oracle ODBC data source lets external applications connect to an Oracle database,
using a Net Service Name.

Note When reporting on a SampleManager database, an Oracle ODBC data source

alone is not sufficient. You must connect to the Oracle ODBC data source through a
SampleManager ODBC data source. The SampleManager ODBC data source applies
SampleManager Group security to the data returned to the report.

 To set up an Oracle ODBC data source

1. If your PC has a 32-bit operating system, from the Windows Control Panel, open
Administrative Tools and then run the Data Sources (ODBC) application.

On 64-bit operating systems, there are separate ODBC Data Source Administrators
for 32-bit and 64-bit ODBC data sources. SampleManager uses 32-bit data sources.
To open the 32-bit ODBC Data Source Administrator, run the following
application:
c:\windows\SysWow64\odbcad32.exe

The ODBC Data Source Administrator window appears.

2. Click the System DSN tab.

3. Click Add.

The Create New Data Source window appears, showing a list of available drivers.

4. Select the Oracle ODBC Driver that corresponds to your Oracle installation, for
example, Oracle in OraClient11g_home1_32bit.
Note The Oracle ODBC Driver is not installed as part of the standard Oracle Net
Client installation. Use one of the following methods to install the Oracle ODBC
driver:
• Perform a custom installation of Oracle Net Client and include the Oracle
ODBC Driver in the list of components to install
• Download the Oracle ODBC Driver from the Oracle website
5. Click Finish. The Oracle ODBC Driver Configuration window appears.

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Installation Procedures for SampleManager on Oracle

6. In the Data Source Name field, enter a name for the data source. The name must be
of the form Ora<hostname><SID>, for example:
OraHostPCSMDB

Where:
• HostPC is the name of the host PC
• SMDB is the Oracle System ID of the database

7. In the Description field, enter a short description for the data source.

8. In the TNS Service Name list, choose the Net Service Name of the database
associated with your SampleManager instance.

If you are installing LIMS Reporter on the SampleManager application server or a

SampleManager client PC, the Net Service Name was created for your database
when the Oracle Net Client was set up. See Oracle Setup (page 223).
If you are installing LIMS Reporter on the database server PC, a Net Service Name
was created by Oracle when the database was created.
9. Click OK to save the data source and close the Oracle ODBC Driver Configuration
window.
The new data source appears in the ODBC Data Source Administrator.

Setting Up a SampleManager ODBC Data Source

A SampleManager ODBC data source connects to an Oracle ODBC data source for that
database. The SampleManager ODBC source appends extra SQL statements to each
query submitted to the database to apply SampleManager Group security to the data
returned to the report.

 To set up a SampleManager ODBC data source

1. If your PC has a 32-bit operating system, from the Windows Control Panel, open
Administrative Tools and then run the Data Sources (ODBC) application.

On 64-bit operating systems, there are separate ODBC Data Source Administrators
for 32-bit and 64-bit ODBC data sources. SampleManager uses 32-bit data sources.
To open the 32-bit ODBC Data Source Administrator, run the following
application:
c:\windows\SysWow64\odbcad32.exe

The ODBC Data Source Administrator window appears.

2. Click the System DSN tab.

3. Click Add.

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Installation Procedures for SampleManager on SQL Server

The Create New Data Source window appears, showing a list of available drivers.

4. Select LIMS Driver, and click Finish.

The LIMS Setup dialog box appears.

5. In the Data Source Name field, enter a name for the data source. The name must be
of the form Lims<hostname><SID>, for example:

LimsHostPCSMDB

Where:
• HostPC is the name of the host PC
• SMDB is the Oracle System ID of the database

6. In the Description field, enter a short description for the data source.
7. In the Oracle Source field, select your Oracle DBC data source (page 164).
8. Click OK to save the data source and close the LIMS Setup dialog box.

The new data source appears in the ODBC Data Source Administrator.

Installation Procedures for SampleManager on SQL Server

The exact steps required to install and configure LIMS Reporter depend on the
configuration of your system and the PC on which you are installing it.

The main platforms for installation are:

• SampleManager server PC (page 163)

This configuration is used to generate LIMS Reporter reports from SampleManager

client and SampleManager background operations.
• SampleManager client PC (page 164)

LIMS Reporter can be installed on a SampleManager client PC to let reports be

developed in LIMS Reporter. SampleManager does not support LIMS Reporter on a
PC without SampleManager or SQL Server installed.

Installation on a SampleManager Server PC

The following steps are required to install and configure LIMS Reporter on a
SampleManager server PC:
1. Install LIMS Reporter (page 166).

2. Set up a database profile (page 166).

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Installation Procedures for SampleManager on SQL Server

Installation on a SampleManager Client PC

The following steps are required to install and configure LIMS Reporter on a
SampleManager client PC:

1. Install the SQL Server connectivity components.

2. Set up a SQL Server ODBC Data Source (page 164) that connects to your
SampleManager database.

3. Set up a SampleManager ODBC data source (page 165) that connects to the SQL
Server ODBC data source created in step 2.
4. Install LIMS Reporter (page 166).

5. Set up a database profile (page 166).

Setting Up a SQL Server ODBC Data Source

A SQL Server ODBC data source lets external applications connect to a SQL Server
database. The following procedure describes the basic settings that are required to
configure the data source. For more detailed information, see the Help accessible from
the Create a New Data Source to SQL Server window.

 To create a SQL Server ODBC data source

1. If your PC has a 32-bit operating system, from the Windows Control Panel, open
Administrative Tools and then run the Data Sources (ODBC) application.

On 64-bit operating systems, there are separate ODBC Data Source Administrators
for 32-bit and 64-bit ODBC data sources. SampleManager uses 32-bit data sources.
To open the 32-bit ODBC Data Source Administrator, run the following
application:
c:\windows\SysWow64\odbcad32.exe

The ODBC Data Source Administrator window appears.

2. Click the System DSN tab.

3. Click Add. The Create New Data Source window appears, showing a list of available
drivers.
4. Select the SQL Native Client, and click Finish. The Create a New Data Source to
SQL Server window appears.

5. Enter a name and description for your data source.

6. In the Server field, select the SQL Server that contains the target SampleManager
database.

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Installation Procedures for SampleManager on SQL Server

7. Click Next.

8. Select the authentication method that SQL Server will use for the connection:
• With integrated Windows authentication – SQL Server will use the Windows
account of the currently logged-in user that is running the LIMS Reporter. If
you select this option, the Windows account for each user who will generate
reports must be granted appropriate access to the SQL Server database.
• With SQL Server authentication using a login ID and password entered by
the user – Enter a SQL Server login ID and password for the data source to use.
If you select this option, the SQL Server must have been configured to allow
SQL Server authentication.

9. Click Next.

10. Select the Change the default database to check box and select the database
associated with your target SampleManager instance.
11. Click Next.

12. Click Finish to complete the data source configuration process.

The new data source appears in the ODBC Data Source Administrator window.

Setting up a SampleManager ODBC Data Source

A SampleManager ODBC data source connects to a SQL Server ODBC data source for
that database. The SampleManager ODBC source appends extra SQL statements to each
query submitted to the database to apply SampleManager Group security to the data
returned to the report.

 To set up a SampleManager ODBC data source

1. If your PC has a 32-bit operating system, from the Windows Control Panel, open
Administrative Tools and then run the Data Sources (ODBC) application.

On 64-bit operating systems, there are separate ODBC Data Source Administrators
for 32-bit and 64-bit ODBC data sources. SampleManager uses 32-bit data sources.
To open the 32-bit ODBC Data Source Administrator, run the following
application:
c:\windows\SysWow64\odbcad32.exe

The ODBC Data Source Administrator window appears.

2. Click the System DSN tab.

3. Click Add.

The Create New Data Source window appears, showing a list of available drivers.

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Installing LIMS Reporter

4. Select LIMS Driver, and click Finish.

The LIMS Setup dialog box appears.

5. In the Data Source Name field, enter a name for the data source.
6. In the Description field, enter a short description for the data source.

7. In the Database Source field, select your SQL Server ODBC data source (page 164).

8. Click OK to save the data source and close the LIMS Setup dialog box.

The new data source appears in the ODBC Data Source Administrator.

Installing LIMS Reporter

 To install LIMS Reporter

1. In Windows Explorer, open the root folder for the LIMS Reporter kit.

2. Double-click Autorun.exe.

3. Follow the instructions in the installer to install LIMS Reporter.

The only required component is the InfoMaker product itself; SampleManager does
not require SQL Anywhere.

After LIMS Reporter is installed, you must set up a database profile to connect to your
SampleManager ODBC data source.

Setting up a Database Profile

After LIMS Reporter has been installed, a database profile must be set up to specify a
connection to the SampleManager ODBC data source.

 To create a LIMS Reporter database profile

1. From the Windows Start menu, run LIMS Reporter.

2. From the main menu, select Tools > Database Profile.

The Database Profiles window appears, showing a list of installed database interfaces.

3. Select the ODB ODBC interface, and click New to create a new profile.
The Database Profile Setup window appears.

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Setting up a Database Profile

4. Enter the following information:

• Profile Name – The name that you will use to refer to your profile.
• Data Source – Your SampleManager ODBC data source. If the SampleManager
ODBC data source was created automatically during SampleManager
installation, its name will begin with "Lims".
Note If LIMS Reporter is installed on a client PC for report development, we
recommend that you use the SQL Server or Oracle ODBC data source instead of the
SampleManager ODBC data source. This data source will provide a direct
connection to the database, but will not implement SampleManager Group security
when selecting data for reports.
5. Click OK to save details and close the window.
The Database Profiles window appears.

6. Select the new profile, and click Connect to test the connection.
7. If you selected the SampleManager ODBC data source in step 4, the
SampleManager Login Details dialog box appears, prompting for login details for use
with the SampleManager ODBC data source. Enter a SampleManager username and
password, and click OK.
8. If you are connecting to a SampleManager Oracle database, the Oracle ODBC
Driver Connect dialog box appears, prompting for login details for use with the
Oracle ODBC data source. Enter the Oracle username and password for your
SampleManager instance, and click OK.

You might need to contact your Oracle administrator for these details. Unless you
create a new SampleManager ODBC data source, you should not need to enter these
details again.
9. If you are connecting to a SampleManager SQL Server database, the SQL Server
ODBC Driver Connect dialog box appears, prompting for login details for use with
the SQL Server ODBC data source. Enter a suitable username and password for
your SQL Server database, and click OK.

You might need to contact your SQL Server administrator for these details. Unless
you create a new SampleManager ODBC data source, you should not need to enter
these details again.

10. LIMS Reporter connects to your SampleManager database. From the main menu,
select Tools > Database Painter to show the details of the database.
The Database window appears. See the documentation provided with LIMS
Reporter for more information.

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Connecting to the Database

When a database profile has been set up and tested, the initial connection between LIMS
Reporter and your SampleManager database is complete.

When you next run LIMS Reporter and select Tools > Database Painter from the main
menu, the connection defined by the database profile will be used. If your database
profile uses the SampleManager ODBC data source, you will be prompted for a
SampleManager username and password.

Note If you are connecting to a SampleManager database for a first time, you might
be prompted for Oracle or SQL Server database login details. After a database profile
has been set up and you have connected for the first time, you should not be
prompted for these details again.

Producing Reports in PDF Format

It is possible to output LIMS Reporter (InfoMaker) reports from SampleManager in
PDF format instead of the default PSR format.

 To produce LIMS Reporter reports in PDF format

1. Install Adobe Acrobat Reader (page 169).

2. Install GhostScript (page 169) and add an appropriate link to the Path environment
variable (page 169).

3. Install a suitable PostScript printer driver (page 172).

4. Configure your SampleManager server to output reports in PDF format. For more
information, see the "Printers and InfoMaker Reports" chapter in the
SampleManager LIMS System Administration Guide.

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Producing Reports in PDF Format

Installing Adobe Acrobat Reader

The Adobe Acrobat Reader lets you view PDF reports.

Adobe Acrobat reader can be downloaded and installed from:

http://www.adobe.com/products/reader/

Installing GhostScript
GhostScript enables InfoMaker to save reports in PDF format.

GhostScript can be downloaded from:

http://www.ghostscript.com/

If the SampleManager server has a 64-bit operating system, download and install both
the 32-bit and 64-bit versions of GhostScript.

Adding GhostScript to the Path Environment Variable

After installation, GhostScript must be added to the Path environment variable.

After you have updated the Path environment variable, the PC must be rebooted.

 To add GhostScript to the Path environment variable

1. Open the Environment Variables window:

a. In Windows Explorer, right-click This PC and select Properties.
The System window appears.
a. Click Advanced system settings. The System Properties window appears.
b. On the Advanced page, click Environment Variables.
The Environment Variables window appears.

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Producing Reports in PDF Format

Figure 7-3. Environment Variables window

2. Before you change the Path variable, we recommend that you make a copy:
a. In the System variables area of the Environment Variables window, select the
Path variable and click Edit.
The Edit System Variable dialog box appears.
b. In the Edit System Variable dialog box, select the contents of the Variable value
field.
c. Press CTRL+C to copy the details to the Windows clipboard.
d. Click Cancel to close the Edit System Variable dialog box.
e. In the System variables area of the Environment Variables window, click New.
The New System Variable dialog box appears.
f. In the Variable Name field, enter an appropriate name, for example, Path_copy.
g. In the Variable Value field, paste the copied details.
h. Click OK to accept the new entry.
3. In the System variables area of the Environment Variables window, select the Path
variable.

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Producing Reports in PDF Format

4. Click Edit.

The Edit System Variable dialog box appears.

Figure 7-4. Edit System Variable dialog box

5. Add the location of the gswin32.exe file to the list of locations in the Variable Value
field. Each value in the list is separated by a semicolon. The default location is:

C:\Program Files (x86)\gs\gs<version>\bin

Where <version> is the GhostScript version number.

6. Add the location of the gswin64.exe file to the list of locations in the Variable Value
field. Each value in the list is separated by a semi-colon. The default location is:

C:\Program Files\gs\gs<version>\bin

Where <version> is the GhostScript version number.

7. Click OK to close the Edit System Variable dialog box.

8. Click OK to close the Environment Variables window.

9. Click OK to save the change and close the System Properties window.

10. Close down all active programs and reboot the system.

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Producing Reports in PDF Format

Add a Printer that Uses the GhostScript Printer Driver

For server-side reporting, you must install a suitable PostScript printer driver.

Add a local printer with the following characteristics:

• Port – FILE: (Print to file)
• Model – Install the 64-bit GhostScript PDF printer driver. The printer driver can be
installed from the lib folder of your 64-bit GhostScript folder. The default location
is:
C:\Program Files\gs\gs9.10\lib

• Sharing – Do not share this printer

• Name – Sybase DataWindow PS

Note The name of the printer must be exactly as shown, with the same spaces and
capitalization.

When the installation is complete, there should be a Sybase DataWindow PS printer

visible in the Devices and Printers window.

If the PDF output appears in black and white, check that the Printer Preferences for the
Sybase DataWindow PS printer are configured to produce color output.

Sending Reports to PDF

To create reports in PDF format, set the OLEIMPRINT_SAVE_FILETYPE
configuration item in your SampleManager instance to PDF.

Note The PDF report generation process requires a Windows user account with
sufficient permissions to create and save the .pdf file. If errors are reported when
SampleManager attempts to save the .pdf file, set the Log On As properties of the
smdaemon service for the instance to use an account with administrator rights.

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 8

Installing Chromeleon Link Components

This chapter describes the installation procedures for the following Chromeleon Link
components:
• Chromeleon Link Web API (page 175)
• SampleManager Chromeleon Interface (page 178)

The Chromeleon Link functionality creates an integrated, bidirectional data transfer

connection between SampleManager LIMS and Chromeleon CDS.

Use the Chromeleon Link features to perform the following tasks:

• Create a sequence in SampleManager LIMS from samples, tests, or a batch and send
the sequence to Chromeleon CDS.
• Add injections based on SampleManager LIMS tests to sequences or eWorkflows in
Chromeleon CDS.
• Transfer results from Chromeleon CDS to SampleManager LIMS. Manual transfer
of results can be triggered in either Chromeleon CDS or SampleManager LIMS. A
SampleManager LIMS background process can transfer results automatically.
• Show Chromeleon results in SampleManager.
• Access real-time status information from Chromeleon CDS in SampleManager
LIMS.
• Check that the instrument used for a sequence in Chromeleon CDS is In Service and
Calibrated in SampleManager LIMS.
• Check that the user responsible for running a sequence is recorded as trained to use
the instrument and perform the analysis in SampleManager LIMS.

For more information, see the "Chromeleon Link" chapter in the SampleManager LIMS
Configuration Guide.

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Prerequisites

Contents
• Prerequisites
• Installing Chromeleon Link Web API
• Installing SampleManager Chromeleon Interface
• Chromeleon Link Add-In

Prerequisites
CAUTION To prevent potential loss of data, make a full backup of your system
before installing the Chromeleon link components.

Make sure all the following conditions are satisfied before you install the Chromeleon
Link components:
• SampleManager LIMS is installed and running correctly.
• Chromeleon CDS is installed and running correctly.

See the SampleManager LIMS 12.2 Release Notes for information about the version
of Chromeleon CDS required for the SampleManager LIMS Chromeleon Link
functionality.
• The Microsoft .NET Framework 4 is installed on the Chromeleon CDS application
server.
• The Microsoft .NET Framework 4.5.2 is installed on the Chromeleon CDS
application server.

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Installing Chromeleon Link Web API

Installing Chromeleon Link Web API

Install the SampleManager Chromeleon Link Web API component on the Chromeleon
CDS application server. See the SampleManager LIMS 12.2 Release Notes for
information about the version of Chromeleon CDS required for the Chromeleon Link
Web API.

Note The authentication and configuration settings for the Chromeleon Link Web
API are stored as an encrypted string and cannot be edited after installation. To
change the values after installation, repeat the installation process.

 To install SampleManager Chromeleon Link Web API

1. Make sure that all users are logged out of Chromeleon CDS.

2. Stop any Chromeleon CDS processes.

3. In Windows Explorer, open the following folder in your SampleManager LIMS
installation kit:

Modules\SampleManager ChromeleonLink 12.2\Chromeleon Link

4. Right-click the ChromeleonLinkWebAPISetup.msi file and select Install. The

Thermo SampleManager Chromeleon Link Web API Setup wizard appears.

5. Welcome to the SampleManager Chromeleon Link Web API Setup Wizard

Click Next.

6. End-User License Agreement

a. Read the license agreement.
b. Select the check box to accept the license agreement. The installation cannot
proceed unless you accept the license agreement.
c. Click Next.

7. Destination Folder
a. If you want to change the location where Thermo SampleManager Chromeleon
Link Web API will be installed, click Browse and select the location.
b. Click Next.

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Installing Chromeleon Link Web API

8. Authentication
a. If User Mode is enabled on your Chromeleon CDS, select Enable User Mode.
b. If User Mode is enabled on your Chromeleon CDS, enter the name and
password of the Chromeleon CDS user account you want the Chromeleon Link
to use.
If User Mode is enabled and you do not specify a Username and Password, the
Chromeleon CDS user name will be obtained from the PERSONNEL record
for the SampleManager user associated with each session. Users will be
prompted to enter their Chromeleon password when they perform a task that
uses the Chromeleon Link Web API.
c. Make a note of the information you have entered on this page. The
authentication information is stored as an encrypted string when the
Chromeleon Link Web API is installed.
d. Click Next.

9. Service Configuration
a. Enter a name for the Windows service that will be created for the Thermo
SampleManager Chromeleon Link Web API.
b. Specify the port that the service will use. The default value is 8082.
c. If you want the Chromeleon Link to use the https protocol, select Enable
HTTPS.
If Enable HTTPS is cleared, the Chromeleon link will use the HTTP protocol.
d. Make a note of the information you have entered on this page. The
configuration information is stored as an encrypted string when the Chromeleon
Link Web API is installed.
e. Click Next.

10. Ready to install SampleManager Chromeleon Link Web API

Click Install.

11. Completed the SampleManager Chromeleon Link Web API Setup Wizard
Click Finish.

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Installing Chromeleon Link Web API

Configure the API User Account

If you want to generate PDF reports, the Chromeleon Link Web API must run using a
specific account that has permission to listen on the port assigned to the API.

 To configure the API user account

1. On the Chromeleon CDS application server, open the Services window.

2. Right-click the Chromeleon Web API service and choose Properties. The
Chromeleon Web API Properties window appears.
3. Click the Log On tab.

4. Click This account.

5. Enter the login credentials of the account you want the service to use.
6. Click OK.

7. Restart the service.

If the account you specified in step 5 does not have administrator rights on the
server, the service fails to start and the following error appears in the event log:

Service cannot be started. System.Net.HttpListenerException

(0x80004005): Access is denied

8. To resolve the error, grant the user account permission to listen on the Chromeleon
Web API port:
a. Log in to the server as an administrator.
b. Open a command prompt.
c. Enter the following command:
netsh http add urlacl url=<proto>://*:<port>/ user=<User/Group>
listen=yes
Where:

• <proto> is either http or https, depending on the protocol that Chromeleon

Link uses.
• <port> is the port assigned to the Chromeleon Web API
• <User/Group> is the name of the user account, or a user group that the user
account belongs to.
For example:
netsh http add urlacl url=http://*:8082/ user=ChromeleonService
listen=yes

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Installing SampleManager Chromeleon Interface

If the command executes successfully, the following response appears:

URL reservation successfully added

9. Restart the service.

Installing SampleManager Chromeleon Interface

Install the SampleManager Chromeleon Interface component on the Chromeleon CDS
application server. See the SampleManager LIMS 12.2 Release Notes for information
about the version of Chromeleon CDS required for the SampleManager Chromeleon
Interface.

Note The configuration settings for the SampleManager Chromeleon Interface are
stored as an encrypted string and cannot be edited after installation. To change the
values after installation, repeat the installation process.

 To install SampleManager Chromeleon Link Interface

1. Make sure that all users are logged out of Chromeleon CDS.

2. Stop any Chromeleon CDS processes.

3. In Windows Explorer, open the following folder in your SampleManager LIMS

installation kit:

Modules\SampleManager ChromeleonLink 12.2\Chromeleon Link

4. Right-click the SampleManagerChromeleonInterface.msi file and select Install. The

SampleManager Chromeleon Interface Setup wizard appears.

5. Welcome to the SampleManager Chromeleon Interface Setup Wizard

Click Next.

6. End-User License Agreement

a. Read the license agreement.
b. Select the check box to accept the license agreement. The installation cannot
proceed unless you accept the license agreement.
c. Click Next.

7. Destination Folder
a. If you want to change the location where SampleManager Chromeleon Interface
will be installed, click Browse and select the location.
b. Click Next.

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Installing SampleManager Chromeleon Interface

8. Configuration
a. Enter the username and password of the SampleManager user that you want the
SampleManager Chromeleon Interface to use. The username setting is
mandatory.
b. In the Web API Address prompt, specify the address, including the port
number, of the REST interface of the SampleManager WCF service for the
SampleManager LIMS instance that you want to connect to. This setting is
mandatory.
For example:
http://localhost:56105
c. In the Chromeleon Server ID prompt, specify the identity of the Chromeleon
entity in SampleManager LIMS that you want to use as the default when the
interface searches for instruments and analyses in SampleManager. This value is
optional.
d. If you want to disable Ready Check warnings that occur when multiple
instruments or analyses match mapping criteria, select Allow Multiple
Mapping. The default setting is False.
e. Make a note of the information that you have entered on this page. The
configuration settings are stored as an encrypted string when the
SampleManager Chromeleon Interface is installed.
f. Click Next.

9. Ready to install SampleManager Chromeleon Interface

Click Install.

10. Completed the SampleManager Chromeleon Interface Setup Wizard

Click Finish.

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Installing SampleManager Chromeleon Interface

The Interface Components dialog box appears.

Figure 8-1. Interface Components dialog box

11. Clear any Add-In functions that you do not want to activate and click OK. By
default, all Add-In functions are selected. For more information about the Add-In
Functions, see the "Chromeleon Link" chapter in the SampleManager LIMS
Configuration Guide.

To select none of the Add-In functions, click Select None.

If you chose not to activate an Add-In function that you need later, you must
reinstall SampleManager Chromeleon Interface and select the desired Add-In
function.
12. Make sure that Chromeleon CDS has detected the SampleManager Chromeleon
Interface add-in:
a. Start Chromeleon CDS and log in.
b. Launch the eWorkflow Wizard. For detailed information about this wizard, see
the Chromeleon CDS documentation.
c. On the Sample Configuration page of the wizard, make sure that there is a
Select Batch button in the upper right pane.

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Installing SampleManager Chromeleon Interface

Figure 8-2. eWorkflow Wizard – Sample Configuration page

If the Select Batch button is visible, Chromeleon CDS has detected the
SampleManager Chromeleon Interface add-in. The installation process is
complete.
d. If the Select Batch button is not visible, close the eWorkflow Wizard.
e. Close Chromeleon CDS.
f. In Windows Explorer, delete the following folder and all its subfolders:
C:\ProgramData\Dionex\Chromeleon\Addins
Chromeleon will recreate the Addins folder next time it starts. This step makes
Chromeleon CDS detect the SampleManager Chromeleon Interface add-in.

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Installing SampleManager Chromeleon Interface

Electronic Signature Settings in Chromeleon

To transfer sequence results to SampleManager LIMS from Chromeleon CDS using the
SampleManager Chromeleon interface, in Chromeleon CDS you must specify when
sequences are ready for transfer. In Chromeleon CDS, you can use an electronic
signature to specify when sequences can be transferred.

 To configure, in Chromeleon CDS, when sequences are ready to send to

SampleManager LIMS:
1. Click the Windows Start button.

2. Open the list of applications and select Thermo Chromeleon 7 > Administration
Console.

3. Expand Organizational Units and Global. (only required if Organizational Units are
enabled)

4. Click User Database > Electronic Signature tab.

Figure 8-3. Chromeleon Administration Console showing the Electronic Signature settings

5. From the A sequence will be ready for LIMS transfer list, select the desired option.
Available options are:
• never
• when the sequence is submitted
• when the sequence is reviewed
• when the sequence is approved

When the electronic signature of a sequence has the status selected, the
SampleManager Chromeleon Interface sets the Send Approved flag of the sequence
in SampleManager LIMS to Yes. If the communication between Chromeleon CDS

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Chromeleon Link Add-In

and SampleManager LIMS is unsuccessful, you are notified in Chromeleon CDS.

You can determine what the problem is by inspecting the logs in the Windows Event
Log Viewer.

Chromeleon Link Add-In

The SampleManager Chromeleon Link Add-In included with SampleManager LIMS
releases before SampleManager LIMS 7.1 SP2 is no longer supplied. The
SampleManager Chromeleon Interface (page 178) lets you interact with SampleManager
LIMS from Chromeleon CDS.

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 9

Installing Data Manager Components

The Data Manager feature lets you store, retrieve, and view data created by external
applications, such as instrument control software. Although it is mainly used to store
data created by instruments, Data Manager can store any other type of file, and includes
specific features for handling other common file types such as Microsoft Office files and
PDF files.

When the Data Manager functionality stores data, it packages all the original files
associated with a data set into a single zip file that is stored in a specified location on the
Data Manager server. During the packaging process, Data Manager can convert the
original data into Generalized Analytical Markup Language (GAML), a neutral format
that offers long-term data preservation independent of the original instrument software.

You can configure Data Manager to extract information from the data during the
conversion process. The extracted information is stored as metadata linked to the data
package, which you can use to search archived data in future.

The SampleManager entity types that support the Data Manager functionality are
included in the core SampleManager Server installation. The Data Manager functionality
also requires a set of Windows services and supporting applications, such as file
converters, which must be installed separately on the appropriate machines in your
SampleManager system. This chapter describes the installation of the Data Manager
components. For information about configuring and using the Data Manager feature, see
the "Data Manager" chapters in the SampleManager LIMS Configuration Guide.

Contents
• Prerequisites
• Install and Configure Data Manager Components
Overview
• Run the Data Manager Install Utility
• Install the Data Manager Data Provider Service
• Data Manager Components
• Install Data Manager Components

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Prerequisites

• Install the Envision GAML Viewer

• Install the GRAMSShellHandlers64 Component
• Install the GRAMS Converters
• Install Bruker CompassExtract (Bruker MALDI and
Bruker ESI Converters only)
• Configure the Data Manager Messaging Service
• Configure the SampleManager Data Provider
• Configure the Data Manager Server
• Configure the Data Manager Client
• Enable the Packaging Agent Service
• Configure the Packaging Agent
• Configure System Tracing
• Licensing GRAMS Envision
• Instrument Data File Converters Help

Prerequisites
Before you install and configure the Data Manager components, make sure of the
following:
• SampleManager is successfully installed and working.
• All users have logged out of SampleManager.
• You have obtained and installed a license for the Data Manager capture sources that
you intend to use. If you do not have the correct license, the Data Manager feature
will not work correctly. For more information about licenses, see the
"Post-Installation Tasks" chapter in the SampleManager Installation Guide. For more
information about capture sources, see "Data Manager Packaging Configuration" in
the SampleManager LIMS Configuration Guide.

CAUTION To prevent potential loss of data, we recommend that you make a full
backup of your system before you install the Data Manager components.

Logging out and stopping processes makes certain that SampleManager updates correctly
when processes restart and users log in.

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Install and Configure Data Manager Components Overview

Install and Configure Data Manager Components Overview

This section contains an overview of the steps required to install and configure the Data
Manager components.

To assure a successful installation, perform these procedures and steps in the order they
appear.

1. In SampleManager, run the Data Manager Install Utility (page 190).

2. Install the Data Manager Data Provider service (page 190).

3. Install the Data Manager components.
a. Install the appropriate Data Manager components on each machine in your
SampleManager implementation. See Install Data Manager Components on
page 192 for details.
b. Install the Envision GAML Viewer. See Install the Envision GAML Viewer on
page 197 for details.
This step is only required for the Data Manager Client installation option.
c. Install the GRAMS converters. See Install the GRAMS Converters on page 202
for details.

Multiple SampleManager instances on your server can share a single set of Data
Manager components. Do not repeat this step for each SampleManager instance.

4. Configure the Data Manager components.

a. Configure the Data Manager Messaging Service. See Configure the Data
Manager Messaging Service on page 210 for more information.
b. Configure the SampleManager Data Provider for each SampleManager instance.
See Configure the SampleManager Data Provider on page 211 for more
information.
c. Configure the Data Manager server. See Configure the Data Manager Server on
page 212 for more information.
d. Configure any Data Manager clients. See Configure the Data Manager Client
on page 214 for more information.
e. Configure the Packaging Agent. See Configure the Packaging Agent on page
217 for more information.
f. Configure system tracing. See Configure System Tracing on page 219 for more
information.

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Install and Configure Data Manager Components Overview

Upgrade from Previous Versions of Data Manager

If you are upgrading from a previous version of SampleManager LIMS that had Data
Manager installed as a separate module, the Data Manager tables, menus, and other
supporting elements of the SampleManager Server application are now included as core
features in the SampleManager Server installation kit. To upgrade the Data Manager
tables in the database and the Data Manager features that are available in the
SampleManager user interface, follow the instructions in Upgrading SampleManager
(page 129). Take great care not to overwrite customizations that are applied to your
system.

To upgrade the Data Manager components, follow the steps for a new installation in this
chapter.

Note After installation of a new version of Data Manager is complete, the previous
versions will not work.

If you are upgrading from a previous version of Data Manager, run the following steps to
adjust the settings on a few menu items.

 For upgrades from a version older than Data Manager 5.1

1. From the SampleManager Navigator, select System Folders > Global Table
Defaults.
2. In the Explorer, right-click Data Package and select Table Defaults > Modify. The
Table Defaults window appears.

3. Click the Popup Menu tab.

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Install and Configure Data Manager Components Overview

Figure 9-1. Table Defaults window

4. On the Popup Menu page, select the General tab.

5. From the RMB list on the left, select Download Items, and select the check box for
Allow Multiple on the General subpage.
6. Repeat these steps for the Download Files and View Items RMB options.

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Run the Data Manager Install Utility

Run the Data Manager Install Utility

The Data Manager Install Utility prepares a SampleManager instance to use the Data
Manager functionality.

 To run the Data Manager Install Utility

1. Log in to the SampleManager instance that you want to use the Data Manager
functionality.

2. From the main menu, select File > Run. The Run window appears.
3. Enter GRL $DM_INSTALL and click OK. A message appears that asks if you want
to compile the Data Manager VGL Reports.
4. Click Yes.

Install the Data Manager Data Provider Service

 To install the Data Manager Data Provider service

1. In Windows Explorer, navigate to the Exe folder for the SampleManager instance.
The default path for this folder is:

C:\Thermo\SampleManager\Server\<instance>\Exe
Where <instance> is the name of your SampleManager instance.
2. Right-click InstallDataManagerDataProviderWindowsServiceNoStart.bat and
select Run as Administrator.
A Command prompt window opens and messages appear as the installation
progresses. When the process completes, the message "Press any key to continue"
appears.

3. Check the window for errors, and then press any key to close the window.

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Data Manager Components

Data Manager Components

This section describes the items that are created during a full installation of Data
Manager.
• Server computer – The server computer is responsible for the following operations:

– Convert files to a platform-neutral format.

– Reconvert existing data packages.

– Upload .zip files from the agent computer to the server computer.
– Download .zip files from the server computer to the agent computer.
– Create .zip file checksums.
– Remap existing data packages.

– Create and link database records for data packages.

• Agent computer – The agent computer is responsible for the following operations:

– Compress analytical data into .zip format.

– Delete analytical data.

– Determine whether to delete or to package analytical data.

• Packaging Agent: The Packaging Agent is installed as part of the Data Manager
agent computer installation. It is used for scheduled searches and the automatic
packaging of files.

The following items are also installed:

• Envision GAML Viewer – Used for opening and viewing GAML files.
• GRAMSShellExtensionHandlers64 – Enhances the Windows Explorer to provide
thumbnails and previews for GAML files.
• Converters – Used to control the conversion of files to a platform-neutral format.

For descriptions of the security and configuration items that are installed with the Data
Manager module, see "Data Manager Configuration Items" in the "Configuration"
chapter in the SampleManager LIMS Configuration Guide.

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Install Data Manager Components

Install Data Manager Components

This section describes the steps and actions required to install the Data Manager
components.

Note The instructions in this section describe how to install Data Manager
components on a 64-bit Windows system. If you are installing on a 32-bit system,
amend the installation path.

 To install the Data Manager components

1. In Windows Explorer, navigate to the following folder in your SampleManager

LIMS installation kit:
\Modules\Data Manager 5.2 for SampleManager 12.2\Data Manager 5.2

2. Double-click the DataManager52.exe file.

A WinZip Self-Extractor dialog box appears.

3. Click Setup.

A progress bar appears as the necessary files are unzipped for the installation process.
When the files are ready for installation, the Data Manager InstallShield Wizard runs
and the Preparing Setup page appears.
When the preparation has completed, the Welcome page appears.
Figure 9-2. InstallShield Wizard – Welcome page

4. Click Next to continue.

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Install Data Manager Components

The License Agreement page appears.

Figure 9-3. InstallShield Wizard – License Agreement page

5. When you have read the terms and conditions on the License Agreement page,
accept the terms of the license agreement, and click Next to continue.

The Choose Destination Location page appears.

Figure 9-4. InstallShield Wizard – Choose Destination Location page

6. Accept the default location for the software installation, or browse for an alternative
location. The default destination folder is:
C:\Program Files (x86)\Thermo\Data Manager

7. Click Next when you have selected a location.

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Install Data Manager Components

The Select Features page appears.

Figure 9-5. InstallShield Wizard – Select Features page

8. Select the features that you want to install:

• Data Manager Server – Installs the Data Manager Server software.
We recommend that you install the Data Manager Server onto the same system
as the SampleManager Application Server. In some environments, additional
Data Manager Servers might be installed at remote sites.
• Data Manager Packaging Agent – Installs the Packaging Agent software.
We recommend that you install the Data Manager Packaging Agents on the
systems that contain the data to be used in the system. Sometimes, the
Packaging Agent can be installed on a different system and the data pulled from
one or more shared folders.
• Data Manager Client – Installs the Data Manager Client software.
Install the Data Manager Client on every computer that will use the Data
Manager features in the SampleManager client.
9. Click Next to continue.

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The Ready to Install the Program page appears.

Figure 9-6. InstallShield Wizard – Ready to Install the Program page

10. Click Install to start the installation.

The Setup Status page appears, showing the progress of the installation.
Figure 9-7. InstallShield Wizard – Setup Status page

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When the installation is complete, the InstallShield Wizard Complete page appears.
Figure 9-8. InstallShield Wizard – Complete page

11. Click Finish to close the InstallShield Wizard. The InstallShield Wizard for the
Envision GAML Viewer opens. See Install the Envision GAML Viewer on page 197
for details.

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Install the Envision GAML Viewer

Install the Envision GAML Viewer

This section describes the steps and actions required to install the Envision GAML
Viewer. This procedure only occurs during the Data Manager Client installation.

Note The InstallShield Wizard for the Envision GAML Viewer opens automatically
at the end of a standard Data Manager Client installation.

 To install the Envision GAML Viewer

1. After successful completion of the Data Manager installation, the Welcome page of
the Envision GAML Viewer InstallShield Wizard appears. Click Next to continue.
Figure 9-9. InstallShield Wizard – Welcome page

The License Agreement page appears.

Figure 9-10. InstallShield Wizard – License Agreement page

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Install the Envision GAML Viewer

2. When you have read the terms and conditions of the License Agreement, accept the
terms in the license agreement, and then click Next to continue.

The Destination Folder page appears.

Figure 9-11. InstallShield Wizard – Destination Folder page

3. Accept the default location for the software installation, or browse for an alternative
location. The default destination folder is:
C:\Program Files (x86)\Thermo\Envision

4. Click Next when you have selected a location.

The Ready to Install the Program page appears.

Figure 9-12. InstallShield Wizard – Ready to Install the Program page

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Install the GRAMSShellHandlers64 Component

5. Click Install to start the installation.

The Installing GRAMS Envision Viewer page appears, showing the progress of the
installation.
Figure 9-13. InstallShield Wizard – Installing GRAMS Envision Viewer page

When the installation is complete, the InstallShield Wizard Complete page appears.
6. Click Finish to close the InstallShield Wizard. The InstallShield Wizard for the
GRAMSShellHandlers64 component opens. See Install the
GRAMSShellHandlers64 Component (page 199) for details.

Install the GRAMSShellHandlers64 Component

This section describes the steps and actions required to install the
GRAMSShellHandlers64 component. This procedure only occurs during the Data
Manager Client installation.

Notes The InstallShield Wizard for GRAMSShellHandlers64 opens automatically at

the end of the GAML Viewer installation.

If you install the GAML Viewer on a 32-bit Windows system, the 32-bit version of
the GRAMS Shell Extension Handlers component is installed instead of
GRAMSShellHandlers64. The InstallShield Wizard for GRAMS Shell Extension
Handlers contains the same pages as the InstallShield Wizard for
GRAMSShellHandlers64.

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Install the GRAMSShellHandlers64 Component

 To install GRAMSShellHandlers64

1. After successful completion of the GAML Viewer installation, the Welcome page of
the GRAMSShellHandlers64 InstallShield Wizard appears. Click Next to continue.
Figure 9-14. InstallSheld Wizard – Welcome page

The License Agreement page appears.

Figure 9-15. InstallShield Wizard – License Agreement page

2. When you have read the terms and conditions of the License Agreement, accept the
terms in the license agreement, and then click Next to continue.

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Install the GRAMSShellHandlers64 Component

The Ready to Install the Program page appears.

Figure 9-16. InstallShield Wizard – Ready to Install Program page

3. Click Install to start the installation.

The Installing GRAMSShellHandlers64 page appears, showing the progress of the

installation.
Figure 9-17. InstallShield Wizard – Installing GRAMSShellHandlers64 page

When the installation is complete, the InstallShield Wizard Complete page appears.
4. Click Finish to close the InstallShield Wizard. The InstallShield Wizard for the
GRAMS converters opens. See Install the GRAMS Converters on page 202 for
details.

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Install the GRAMS Converters

Install the GRAMS Converters

This section describes the steps and actions required to install the GRAMS converters.
For a full list of the GRAMS converters, see the Instrument Data File Converters Help.

Note The InstallShield Wizard for the GRAMS converters opens automatically at
the end of a standard Data Manager installation.

 To install the GRAMS converters

1. After successful completion of the Data Manager installation, the Welcome page of
the GRAMS Converters Package InstallShield Wizard appears. Click Next to
continue.
Figure 9-18. InstallShield Wizard – Welcome page

2. The License Agreement page appears.

a. Read the terms and conditions.
b. Click I accept the terms in the license agreement.
c. Click Next to continue.

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Figure 9-19. InstallShield Wizard – License Agreement page

3. The Ready to Install the Program page appears. Click Install to start the installation
process.
Figure 9-20. InstallShield Wizard – Ready to Install the Program page

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Install the GRAMS Converters

A progress bar indicates the progress of the installation.

Figure 9-21. InstallShield Wizard – progress bar

In some situations, the following type of message might appear during the
installation.
Figure 9-22. InstallShield Wizard – Files In Use message

If this message appears, select Automatically close and attempt to restart

applications, and then click OK. If you prefer not to close the applications, select
Do not close applications before clicking OK.

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Install Bruker CompassExtract (Bruker MALDI and Bruker ESI Converters only)

When the installation of the GRAMS converters is complete, the final page of the
InstallShield Wizard appears.
Figure 9-23. InstallShield Wizard Completed page

4. Click Finish to complete the installation of the GRAMS Converters.

Install Bruker CompassExtract (Bruker MALDI and Bruker ESI

Converters only)
Installing the Bruker CompassXtract software is an important step for users of Bruker
MALDI or Bruker ESI data. The Bruker MALDI and the Bruker ESI converters require
the installation of the Bruker CompassXtract software. Run this installation only if one
of the two formats will be converted.

Install the Bruker CompassXtract software on the Data Manager server.

 To install Bruker CompassXtract

1. Locate the Bruker CompassXtract installation file: CompassXtract_3.2.201.exe.

The file is usually located in this folder:

C:\Program Files (x86)\Common

Files\ThermoGalactic\Installers\CompassXTract

2. Right-click the file and select Run as administrator.

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Install Bruker CompassExtract (Bruker MALDI and Bruker ESI Converters only)

The Bruker CompassXtract Installation Wizard appears.

Figure 9-24. Bruker CompassXtract Installation Wizard

3. Select a destination folder and click Install.

4. On the Welcome page, click Next.

5. On the License Agreement page, accept the terms of the license agreement and click
Next.

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Install Bruker CompassExtract (Bruker MALDI and Bruker ESI Converters only)

6. On the Setup Type page, select a setup type and click Next.
Figure 9-25. Setup Type page

7. On the Ready to Install Program page, click Next.

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Install Bruker CompassExtract (Bruker MALDI and Bruker ESI Converters only)

The wizard installs the program.

Figure 9-26. Bruker CompassXtract installation progress bar

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Install Bruker CompassExtract (Bruker MALDI and Bruker ESI Converters only)

8. When the installation completes, the Completed page appears. Click Finish.
Figure 9-27. Bruker CompassXtract installation completed

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Configure the Data Manager Messaging Service

Configure the Data Manager Messaging Service

Use the Data Manager Configuration window to configure the port number for the Data
Manager Messaging service, and to enable or disable the service.

 To configure the Data Manager Messaging service

1. From the Windows Start menu, select Thermo Data Manager > Data Manager
Configuration.

The Data Manager Configuration window appears.

2. In the Configurations pane, select Data Manager Messaging.
Figure 9-28. Data Manager Configuration window – Data Manager Messaging

3. In the Messaging Service Port Number field, enter the port number for the
Messaging service.

The Service Status field shows the status of the service.

4. Click Save.

5. If necessary, use the buttons to the right of the Service Status field to start, restart, or
stop the Messaging service.

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Configure the SampleManager Data Provider

Configure the SampleManager Data Provider

Use the Data Manager Configuration window to configure the SampleManager Data
Provider and the connection to the Data Manager Messaging service.

If your application server has multiple SampleManager instances that use the Data
Manager functionality, each SampleManager instance requires its own Data Provider.

Note The Data Manager Configuration window only shows the configurations that
are installed on the system where the tool is run. If you run this tool on a client
system, you will not see the windows for the Messaging, Provider, Server, and Agent
items.

 To configure the SampleManager Data Provider

1. From the Windows Start menu, select Thermo Data Manager > Data Manager
Configuration.
The Data Manager Configuration window appears.

2. In the Configurations pane, select a SampleManager Data Provider. The

SampleManager Data Providers use the following naming convention:

SampleManager Data Provider (instance_name)

Figure 9-29. Data Manager Configuration window – SampleManager Data
Provider

3. In the Port Number field, enter the port number for communication with the Data
Manager server. Each SampleManager Data Provider must have a unique Port
Number.

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Configure the Data Manager Server

4. Make a note of the Port Number you have specified for the instance. You will need
this value when you configure the Data Manager Server.

5. In the Messaging Host Name field, enter the messaging host name.

6. In the Messaging Port Number field, enter the messaging port number.
The Service Status field shows the status of the Data Provider.

7. Click Save.

8. If necessary, use the buttons to the right of the Service Status field to start, restart, or
stop the Data Provider.

Configure the Data Manager Server

Use the Data Manager Configuration window to specify the endpoint (or endpoints) for
the Data Manager server, and to configure the interface from the Data Manager Server to
the Data Provider.

 To access the configuration settings for the Data Manager server

1. From the Windows Start menu, select Thermo Data Manager > Data Manager
Configuration.
The Data Manager Configuration window appears.

2. In the Configurations pane, select Data Manager Server.

Figure 9-30. Data Manager Configuration window – Data Manager Server

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Configure the Data Manager Server

3. In the Application Settings tab, set the following properties:

• Server Endpoints – Enter the configured endpoints for the server. Available
values are TCP and HTTP, TCP, or HTTP.
• TCP Port Number – If applicable, enter the TCP port number.
• HTTP Port Number – If applicable, enter the HTTP port number.
Note If necessary, you can disable either the TCP port number or the HTTP port
number, but not both.

4. In the Data Provider property, click the ellipsis button . The SMDataProvider
Collection Editor appears.
Figure 9-31. SMDataProvider Collection Editor

5. Enter the connection details for each data provider:

• Host Name – The host name for communication to the SampleManager Data
Provider.
• Port Number – The port number for communication to the SampleManager
Data Provider. This value must match the port number you specified for the
SampleManager Data Provider for this instance.
• SMInstance – The name of the SampleManager instance.

6. Click OK to close the SMDataProvider Collection Editor.

7. Click Save.

8. In the Data Manager Configuration window, the Service Status field shows the
status of the Data Manager server. If necessary, use the buttons to the right of the
Service Status field to start, restart, or stop the Data Manager server.

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Configure the Data Manager Client

Configure the Data Manager Client

Use the Data Manager Configuration window to configure the connection between a
Data Manager client and the Data Manager server.

 To configure the Data Manager client

1. From the Windows Start menu, select Thermo Data Manager > Data Manager
Configuration.

The Data Manager Configuration window appears.

2. In the Configurations pane, select Data Manager Client.
Figure 9-32. Data Manager Configuration window – Data Manager Client

3. In the Application Settings tab, select one of the following options from the Default
Endpoint list:
• TCP
• HTTP

This option defines the default endpoint to use if more than one endpoint is
available.

4. If applicable, in the Data Manager Server Host Name field, enter the host name of
the Data Manager server.

5. If applicable, in the Data Manager Server TCP Port Number field, enter the TCP
port number of the Data Manager server.

6. If applicable, in the Data Manager Server HTTP Port Number field, enter the
HTTP port number of the Data Manager server.

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 9 Installing Data Manager Components
Enable the Packaging Agent Service

Note The Data Manager TCP Port Number and Data Manager HTTP Port
Number fields are only used when the server is accessed through the Data Manager
API.

7. In the Data Manager Server Name format field, select Hostname Only (default
setting) or Fully Qualified Domain Name.
Note The fully qualified domain name is useful in environments where there are
multiple domains that contain computers with the same name.
8. Click Save.

Enable the Packaging Agent Service

The packaging agent is responsible for the automatic packaging of data. It runs as a
Windows service on an agent computer.

The packaging agent scans the folders specified in the packaging rules defined for the
agent computer, searching for key files to package. The packaging agent can also locate
and delete previously packaged files, based on the criteria set in the packaging schedule
specified in each packaging rule.

For more information, see the "Extracting Data" chapter of the Data Manager User
Guide.

 To enable the Packaging Agent service

1. From the Windows Control Panel, double-click Administrative Tools.

2. Run the Services application.

3. In the Services window, double-click the Data Manager Packaging Agent entry.

The Packaging Agent property sheet appears.

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Enable the Packaging Agent Service

4. Click the Log On tab.

Figure 9-33. Packaging Agent – Log On page

5. Select This account.

6. Enter a valid user account for the agent computer.

Specify a valid Windows user account with the following permissions:

• Administrative privileges on the agent computer.
• Access to all computers that are named in the data destinations specified for the
packaging rules that are assigned to the agent computer.
• Read & Execute access to your Oracle Home folder.
• Full Control access to each folder specified as a file search path in packaging
rules that are assigned to the agent computer.
• Full access to the following registry key and its subkeys:
HKEY_LOCAL_MACHINE\Software\Thermo\Data Manager

7. In the Password field, enter the password for the account.

8. In the Confirm Password field, reenter the password, and then click OK.

The Data Manager Packaging Agent parameter values (username, password, or database)
are configured using the Data Manager Packaging Agent Configuration window. See
Configure the Packaging Agent on page 217 for details.

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Configure the Packaging Agent

Configure the Packaging Agent

Use the Data Manager Configuration window to configure the Data Manager packaging
agent.

 To access the Data Manager Configuration window

1. From the Windows Start menu, select Thermo Data Manager > Data Manager
Configuration.

The Data Manager Configuration window appears.

2. In the Configurations pane, select Data Manager Packaging Agent.
Figure 9-34. Data Manager Configuration window – Data Manager Packaging
Agent

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Configure the Packaging Agent

3. In the Application Settings tab, enter the following connection information for the
Data Manager server:
• Default Endpoint – Enter the default endpoint to use if more than one endpoint
is available. Available values are: TCP or HTTP.
• Data Manager Server Host Name – Enter the host name of the Data Manager
server.
• Data Manager Server TCP Port Number – If applicable, enter the TCP port
number of the Data Manager server.
• Data Manager Server HTTP Port Number – If applicable, enter the HTTP port
number of the Data Manager server.
• Data Manager Server Name Format – Enter Hostname Only (this option is the
default setting). If necessary, you can change the Data Manager Server Name
format to "Fully Qualified Domain Name", to include the domain name as part
of the server name. Including the server name can be useful in environments
where there are multiple domains that contain computers with the same name.
4. Enter the connection details for the Data Manager Messaging service:
• Messaging Host Name – Enter the host name for connecting to the Data
Manager Messaging service.
• Messaging Port Number – Enter the port number for connecting to the Data
Manager Messaging service.

The Service Status field shows the status of the Packaging Agent.

5. Click Save.
6. If necessary, use the buttons to the right of the Service Status field to start, restart, or
stop the Packaging Agent.

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Configure System Tracing

Configure System Tracing

Use the Data Manager Configuration window to identify the location where the log files
created by the system will be stored. You can also use it to specify the tracing level for the
system, the GRAMS converters, and components.

Note System Tracing is NOT one setting that is read by all the systems. System
Tracing must be configured for each system that contains one or more of the following
Data Manager components: Data Manager Server, Data Manager Agent, and Data
Manager Client.

 To configure the system tracing options for Data Manager

1. From the Windows Start menu, select Thermo Data Manager > Data Manager
Configuration.
The Data Manager Configuration window appears.
2. In the Configurations pane, select System Tracing.
Figure 9-35. Data Manager Configuration window – System Tracing

3. In the Application Settings tab, set the following values for the Data Manager
Tracing section:
a. Trace Level – Enter the trace level for log file production, the following values
are available: Error, Warn, Info, and Debug.
b. Trace File – Enter the path to the location where the log files will be stored.
Browse to locate the correct destination for the files.
c. Maximum File Size – Enter the maximum permitted file size (in Mb) for a
single log file.

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9 Installing Data Manager Components
Licensing GRAMS Envision

d. Maximum Rollbackups – Enter the maximum permitted number of tracing

backup files.

4. In the GRAMS Converter and Component Tracing section, set the following values:
a. Trace Level – Enter the trace level for log files produced by the GRAMS
converters, or any associated components. The following values are available: (0)
Errors, (1) Warnings, (2) Information, (3) Debug, and (4) Verbose.
b. Trace File – Enter the path to the location where the log files will be stored.
Browse to locate the correct destination for the files.

5. Click Save, and then click Exit.

Licensing GRAMS Envision

Most of the licensing tasks for Data Manager functionality are provided as part of the
SampleManager licensing. However, there are more steps that must be performed for the
GRAMS Envision viewer to locate the license server.

 For each Data Manager Client system, perform the following steps to license the
GRAMS Envision viewer
1. From the Windows Start menu, select Thermo GRAMS Suite > Envision.
The License Failure dialog box appears for the first installation of GRAMS Envision.
Figure 9-36. License Failure dialog box

2. Click Cancel to skip the licensing instructions.

When Envision has started, select Help > About GRAMS Envision.

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 9 Installing Data Manager Components
Instrument Data File Converters Help

The About GRAMS Envision dialog box appears.

Figure 9-37. About GRAMS Envision dialog box

3. Click Select New License.

The Select License dialog box appears.

Figure 9-38. Select License dialog box

4. Select Specify License Server, enter the name of the license server, and click OK.

5. Exit the application.

Instrument Data File Converters Help

The Instrument Data File Converters Help contains information about the instrument
converters supplied with the Data Manager components. This information is useful for
users who are configuring the Data Manager functionality to package instrument data.

The Instrument Data File Converters Help is located in the following folder of the
SampleManager LIMS installation kit:

\Modules\Data Manager 5.2 for SampleManager 12.2\Docs

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 10

Oracle Setup
This chapter outlines the installation and configuration of Oracle 12c on a 64-bit
Windows server before installing SampleManager.

For detailed information about installing and configuring Oracle, see the documentation
provided with Oracle. For more information about how SampleManager uses an Oracle
database, see the "Data Storage and Handling in Oracle" chapter in the SampleManager
LIMS System Administration Guide.

Contents
• Installing and Configuring Oracle for Use with
SampleManager
• Configuring a Connection from the Oracle NET
Client to the Oracle Server
• Installing the Oracle ODBC Driver
• Example Installation and Configuration

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Installing and Configuring Oracle for Use with SampleManager

Installing and Configuring Oracle for Use with SampleManager

The Oracle database used by a SampleManager instance can be installed on the same
machine as the SampleManager Server software or on a different server.

The basic procedure for installing and configuring Oracle for use with SampleManager
is:

1. Install Oracle on your database server.

For more information, see your Oracle documentation.

2. Create a new database that will be used to store the data for a SampleManager
instance.
We recommend that the database character set of your Oracle database is set to
Unicode (AL32UTF8). This character set enables you to store multiple languages in
your database.
For more information, see your Oracle documentation.

3. Set the following parameters for your database:

• OPEN_CURSORS (page 225)
• NLS_LENGTH_SEMANTICS (page 226)

4. Create a tablespace in the new database that will contain your SampleManager data.
If you can supply the sys account password to the SampleManager Add Server
Instance wizard, you can skip this step and let the Add Server Instance wizard create
the tablespace.
5. Create a user in the new database that SampleManager Server will use.

If you can supply the sys account password to the SampleManager Add Server
Instance wizard, you can skip this step and let the Add Server Instance wizard create
the user.

6. If an Oracle Net Listener was not created during the Oracle installation process,
create a Listener.

For more information, see your Oracle documentation.

7. Make a note of the port number used by the Listener on the Oracle database server.
8. Install the 32-bit Oracle Net Client on the machine that will host the
SampleManager server software. Make sure that the 32-bit Oracle ODBC driver is
included in the installed components, as it is required by LIMS Reporter.

You must install a 32-bit Oracle Net Client on the application server PC, even if the
application server PC is also hosting the Oracle database. Without a 32-bit Oracle

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Installing and Configuring Oracle for Use with SampleManager

Net Client, the SampleManager server instance will not be able to access its Oracle
database.

For more information, see your Oracle documentation.

9. Configure a connection between the 32-bit Oracle Net Client that you installed in
step 5, and the Oracle Net Listener for the Oracle database server.

See Configuring a Connection to the Oracle Server (page 228).

Note If the database that SampleManager will use is a pluggable database (PDB) in
a multitenant container database (CDB), the connection must target the PDB. For
more information about multitenant architecture in Oracle 12c, see your Oracle
documentation.

10. Install SampleManager Server on your application server.

See Installing SampleManager Server (page 23).

11. Create a SampleManager instance that uses the Oracle database created in step 2.
See Creating a SampleManager Instance (page 26).

12. Configure the security of your Oracle database to grant access to the account that
will be used by LIMS Reporter to generate reports from the database.
13. Install LIMS Reporter and create the ODBC data sources required to connect to
your database.

See Installing LIMS Reporter (page 157).

14. Create a database profile that connects LIMS Reporter to your SampleManager
database in Oracle.

See Setting up a Database Profile (page 166).

Setting the OPEN_CURSORS Parameter

The OPEN_CURSORS parameter of an Oracle database specifies the maximum
number of open cursors a session can have at one time. If this parameter value is too low,
SampleManager might cause Oracle errors during some operations. For example,
rebuilding the database structure during a SampleManager upgrade might require more
than the default number of open cursors.

We recommend that you set the OPEN_CURSORS parameter to 700. For more
information, see your Oracle documentation.

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Installing and Configuring Oracle for Use with SampleManager

Setting the NLS_LENGTH_SEMANTICS Parameter

The NLS_LENGTH_SEMANTICS parameter of an Oracle database specifies whether
CHAR and VARCHAR2 columns use byte or character length semantics.

If you want your database to support Unicode, set the NLS_LENGTH_SEMANTICS

parameter to CHAR.

For more information, see your Oracle documentation.

Creating a Tablespace
A SampleManager instance requires a tablespace for its data.

If you can supply the sys account password during the instance creation process, the
SampleManager Add Server Instance wizard can create the tablespace for you. Otherwise,
you must create the tablespace before you create the instance.

Use the Oracle tools to create a tablespace. The following SQL statement creates a
suitable tablespace:
create tablespace VGSM_DB
datafile 'filename'
SIZE 100M REUSE
AUTOEXTEND ON NEXT 50M
MAXSIZE 500M;

Where filename is the path and file name of the file associated with the tablespace.

The default tablespace for tables in the SampleManager instance is defined in the
table_defaults section of the structure.txt file for your instance. For example:
table_defaults
oracle_location 'VGSM_DB' ;

If your instance will use a single tablespace in the Oracle database for all SampleManager
data, the Add Server Instance wizard can update the table_defaults section of
structure.txt to match the tablespace name you supply to the wizard. If you create
multiple tablespaces for your SampleManager data, you must edit structure.txt manually
to specify the default tablespace and the tablespace for individual tables and indexes
before running the Add Server Instance wizard.

You can use the oracle_location attribute in a table definition in structure.txt to specify
the tablespace that the table will be created in. For example:
TABLE my_table;
ORACLE_LOCATION 'MYTBLS_DB';

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Installing and Configuring Oracle for Use with SampleManager

It is also possible to specify the default tablespace for indexes:

index_defaults
oracle_location 'VGSM_DB' ;

Or to define the tablespace in which a specific index will be stored:

index sample_job_name_index on job_name
oracle_location 'MYTBLS_DB';

The oracle_specific attribute can be used to add further parameters to a table or index
definition for use by the Oracle database, such as a storage clause.

For more information about customizing the database using structure.txt, see the
"Customizing the Database Structure" chapter in the SampleManager LIMS
Configuration Guide.

Creating a User
The SampleManager instance requires an Oracle user account to connect to the database.

If you can supply the sys account password during the instance creation process, the
SampleManager Add Server Instance wizard can create the user for you. Otherwise, you
must create the user before you create the instance.

Use the Oracle tools to create the user in the database that your SampleManager will use.
Grant the following privileges to the user:
• CREATE SEQUENCE
• CREATE SESSION
• CREATE TABLE
• CREATE VIEW
• SELECT_CATALOG_ROLE

Give the user an unlimited quota on the tablespaces that will contain the
SampleManager data.

The following example shows the SQL statements generated by the SampleManager
Setup Wizard when it creates an Oracle user:
GRANT CREATE SESSION TO VGSM IDENTIFIED BY VGSM;
CREATE PROFILE VGSM LIMIT FAILED_LOGIN_ATTEMPTS UNLIMITED
PASSWORD_LIFE_TIME UNLIMITED;
ALTER USER VGSM PROFILE VGSM;
ALTER USER VGSM QUOTA UNLIMITED ON VGSM_DB DEFAULT TABLESPACE VGSM_DB;
GRANT CREATE TABLE TO VGSM;
GRANT CREATE VIEW TO VGSM;
GRANT CREATE SEQUENCE TO VGSM;
GRANT SELECT_CATALOG_ROLE TO VGSM;

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Configuring a Connection from the Oracle NET Client to the Oracle Server

In the example, the user is called VGSM. The tablespace that stores the SampleManager
data is called VGSM_DB. This example creates a profile called VGSM that specifies an
unlimited number of failed login attempts and unlimited password lifetime. The VGSM
profile is assigned to the VGSM user.

Configuring a Connection from the Oracle NET Client to the Oracle

Server
SampleManager requires a 32-bit Oracle NET client to connect to the Oracle database.

After the Oracle Net Client is installed, you must configure its connection to your
Oracle Server database:
• Configuring Naming Methods (page 228)
• Creating a Local Net Service Name (page 229)
Note If the database that SampleManager will use is a pluggable database (PDB) in
a multitenant container database (CDB), the connection must target the PDB. For
more information about multitenant architecture in Oracle 12c, see your Oracle
documentation.

Configuring Naming Methods

Oracle can use various naming methods to resolve connect identifiers. For use with
SampleManager, Local Naming must be specified.

 To specify Local Naming

1. From the Windows Start menu, run the Oracle Net Configuration Assistant.

The default location for this option is Oracle - [home name] > Configuration and
Migration Tools > Net Configuration Assistant.

The Welcome page of the Oracle Net Configuration Assistant appears.

2. Select Naming Methods configuration and click Next.

The Select Naming Methods page appears.

3. Using the arrow buttons, make sure that Local Naming is at the top of the Selected
Naming Methods list, and click Next.

The Naming Methods Configuration Done page appears.

4. Click Next to continue.

The Welcome page of the Oracle Net Configuration Wizard appears again.

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 10 Oracle Setup
Configuring a Connection from the Oracle NET Client to the Oracle Server

5. Click Finish to close the Assistant.

Naming Methods have now been configured.

Creating a Local Net Service Name

Before you can use the Oracle Client with your Oracle Server database, you must create a
Local Net Service Name that connects to it.

 To create a Local Net Service Name, and then test its connection to the database

1. From the Windows Start menu, run the Oracle Net Configuration Assistant.

The default location for this option is Oracle - [home name] > Configuration and
Migration Tools > Net Configuration Assistant.

The Welcome page of the Oracle Net Configuration Assistant appears.

2. Select Local Net Service Name configuration and click Next.

The Net Service Name Configuration page appears.

3. Select Add and click Next.
The Net Service Name Configuration, Service Name page appears.

4. Enter the Service Name of your database and click Next to continue. If your
database is a pluggable database (PDB) in a multitenant container database (CDB),
enter the name of the service associated with the PDB. For more information about
multitenant architecture in Oracle 12c, see your Oracle documentation.
The Net Service Name Configuration, Select Protocols page appears.

5. Select TCP and click Next to continue.

The Net Service Name Configuration, TCP/IP Protocol page appears.

6. Enter the network name of your Oracle Server and the port number for the
associated Listener. The standard port number, 1521, is normally used. Click Next
to continue.

The Net Service Name Configuration, Test page appears.

7. Select the Yes, perform a test option and click Next.

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Installing the Oracle ODBC Driver

8. The Oracle Net Configuration Assistant tries to connect to the specified database
using the information you supplied, and displays the results on the next page.

If the test is unsuccessful:

a. Click Change Login.
b. Enter a suitable username and password in the dialog box. For example,
SYSTEM and the SYSTEM account password.
c. Click OK to repeat the test.
d. If you still cannot connect to your database, click Back. Check the details that
you entered previously and try again.
9. Click Next to continue.

The Net Service Name Configuration, Net Service Name page appears.

10. Enter a name for the Net Service Name, and click Next.
11. We recommend that the Net Service Name is the same as the service name of your
database. You set the database service name on the Service Name page of the wizard.
12. The next page asks whether you want to configure another net service name. If you
want to connect to more servers, select Yes and click Next to repeat the process.
Otherwise, select No and click Next to continue.
The Net Service Name Configuration Done page appears.
13. Click Next to continue.

The Welcome screen of the Oracle Net Configuration Assistant appears again.

14. Click Finish to close the Assistant.

The Net Service Name has now been set up.

Installing the Oracle ODBC Driver

The Imprint reporting tool requires an Oracle ODBC driver to connect to the database.

 To install the Oracle ODBC driver

1. On the application server machine, run the Oracle Client Installer.

2. On the Select Installation Type page, click the Custom option.

3. On the Specify Installation Location page, set the Software Location prompt to the
existing Oracle client folder.

4. On the Available Product Components page, select the Oracle ODBC Driver check
box.

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Example Installation and Configuration

5. Accept the default settings on the remaining pages of the wizard to install the Oracle
ODBC driver.

If more than one Oracle ODBC driver is installed on the application server,
SampleManager will automatically use the latest version.

Example Installation and Configuration

This section describes how to install and configure Oracle for SampleManager using the
following three tier example configuration:

PC Tier Operating System Software

A Database Server Windows Server 2012 R2 Oracle Server

B Application Server Windows Server 2012 R2 Oracle Net Client (32-bit)

and SampleManager
Server

C Client Windows 7 Professional SampleManager Client

 To create this configuration

1. Install Oracle Server on computer A.

2. Create an Oracle database on computer A.

Use one of the following methods to create the database:

• Starter database using Oracle install.
If selected, a default database can be created automatically as part of the Oracle
Server installation.
• Manual creation using Oracle tools.
Use the Oracle Database Configuration Assistant to create a new database with
an appropriate Oracle instance name.

3. Configure an Oracle Net Listener on computer A.

The listener lets an Oracle Net Client on computer B access the database on
computer A.

4. Install a 32-bit Oracle Net Client on computer B.

5. Configure Naming Methods on computer B.

6. Create a Local Net Service Name on computer B.

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Example Installation and Configuration

The Local Net Service Name defines the connection to the database on computer A.

7. You can now install SampleManager:

a. Install SampleManager Server on computer B.
b. Create a SampleManager Server instance on computer B, which uses the Oracle
database on computer A.
c. Install SampleManager Client on computer C, and configure it to connect to
your SampleManager Server instance, computer B.

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 11

SQL Server Setup

This chapter outlines the installation and configuration of SQL Server for use with
SampleManager.

For detailed information about installing and configuring SQL Server, see the
documentation provided with SQL Server. For more information about how
SampleManager uses a SQL Server database, see the "Data Storage and Handling in SQL
Server" chapter in the SampleManager LIMS System Administration Guide.

Contents
• Installing and Configuring SQL Server for Use with
SampleManager
• Configuring SQL Server Security
• Recommended Database Options

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11 SQL Server Setup
Installing and Configuring SQL Server for Use with SampleManager

Installing and Configuring SQL Server for Use with

SampleManager
The SQL Server used by a SampleManager instance can be installed on the same
machine as the SampleManager Server software, or on a different server. The database
can be configured to optimize performance using the available hardware, for example, by
using multiple filegroups to make efficient use of RAID arrays for storing heavily
modified tables.

The basic procedure for installing and configuring SQL Server for use with
SampleManager is:
1. Install SQL Server on your database server.

For more information, see your SQL Server documentation.

2. Create a new database that will be used to store the data for a SampleManager
instance.

For more information, see your SQL Server documentation.

3. Configure the security of the SQL Server database to grant access to the account that
will be used by the smdaemon service. This service can use either a Windows user
account, or a SQL Server login.
See Configuring SQL Server Security (page 237).
4. Restart the database server.

5. If the application server is a different machine than the database server, install the
SQL Server Client Tools Connectivity feature on your application server.

6. If the application server is a different machine than the database server, make sure
that the SQL Server Client Tools on the application server can connect to the SQL
Server database that SampleManager will use.
7. Install SampleManager Server on your application server.

See Installing SampleManager Server (page 62).

8. Create a SampleManager instance that uses the SQL Server database created in step
2.

See Creating a SampleManager Instance (page 66).

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 11 SQL Server Setup
Installing and Configuring SQL Server for Use with SampleManager

9. If you want to customize your database for optimum performance:

a. Create any filegroups, partition functions, and partition schemes you require to
optimize the performance of your SampleManager database.
b. Edit the structure.txt file of the SampleManager instance so that the database
tables use the required filegroups and partitions. For more information, see the
"Customizing the Database Structure" chapter in the SampleManager LIMS
Configuration Guide.

10. Use the create_structure and convert_table utilities to alter the SampleManager table
definitions in the SQL Server database so that they use the filegroups and partitions
specified in structure.txt.
Note Convert_table must be run from the command line using the rebuild or
newtable mode if you have changed any table properties that are read-only in SQL
Server, such as the filegroup used to store the table data.
For more information, see the "Customizing the Database Structure" chapter in the
SampleManager LIMS Configuration Guide.

Unicode and the Sqlserver_use_nvarchar Attribute in Structure.txt

From SampleManager 12.2, the default value of the sqlserver_use_nvarchar attribute in
the structure.txt database definition file is TRUE. When sqlserver_use_nvarchar is
TRUE, fields in the SampleManager database that store strings have the nvarchar
datatype. Strings are stored as Unicode characters. If you are installing a new
SampleManager system, we recommend that you use the default configuration so that
strings are stored as Unicode in nvarchar fields in the SQL Server database.

In SampleManager versions older than SampleManager 12.2, the default value of the
sqlserver_use_nvarchar attribute in the structure.txt database definition file was FALSE.
When sqlserver_use_nvarchar is FALSE, fields in the SampleManager database that store
strings have the text datatype. Strings are stored as non-Unicode characters. The Imprint
reporting tool for LIMS Reporter (page 157) is not compatible with
sqlserver_use_nvarchar being set to True. LIMS Reporter is not included in the
SampleManager installation kit and is only available in upgraded SampleManager
instances.

If you are creating a SQL Server database that will contain data created in a
SampleManager instance that did not store strings as Unicode, or if you require LIMS
Reporter, configure your database to store strings as non-Unicode characters.

Note The SampleManager WMM module requires LIMS Reporter.

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11 SQL Server Setup
Installing and Configuring SQL Server for Use with SampleManager

 To configure the SampleManager instance to support Unicode

1. Create your instance (page 66).

2. Change the value of the sqlserver_use_nvarchar attribute:
a. Open the structure.txt file of the product instance in a text editor.
b. Change the sqlserver_use_nvarchar setting in the Table Defaults section to
FALSE:
sqlserver_use_nvarchar FALSE ;
See the "Customizing the Database Structure" chapter in the SampleManager
LIMS Configuration Guide.

3. Use the create_structure and convert_table utilities to alter the SampleManager table
definitions in the SQL Server database so that they use the filegroups and partitions
specified in structure.txt.
Note Convert_table must be run from the command line using the rebuild or
newtable mode if you have changed any table properties that are read-only in SQL
Server, such as the filegroup used to store the table data.
For more information, see the "Customizing the Database Structure" chapter in the
SampleManager LIMS Configuration Guide.

4. If you require LIMS Reporter:

a. Install LIMS Reporter and create the ODBC data sources required to connect to
your database.
See Installing LIMS Reporter (page 157).
b. Create a database profile that connects LIMS Reporter to your SampleManager
database on SQL Server.
See Setting up a Database Profile (page 166).

236 SampleManager LIMS Installation Guide Thermo Scientific

 11 SQL Server Setup
Configuring SQL Server Security

Configuring SQL Server Security

The login details used to attempt to connect to the SQL Server database depend on
method used to connect:
• A user who logs in using a SampleManager client installed on a different machine
than the SampleManager application server connects to the database through the
account specified for the smdaemon service.
• A user who logs in using the SampleManager client installed on the SampleManager
application server connects to the database using the Windows login details for the
currently logged in user.
• A user connecting through LIMS Reporter (page 157) connects to the database using
the login details configured for the SQL Server ODBC Data Source.
Note LIMS Reporter is not included in the SampleManager installation kit and is
only available in upgraded SampleManager instances.

SampleManager security features, such as groups and roles, are managed by the
SampleManager server when connecting through the SampleManager client, and by the
SampleManager ODBC data source when connecting through LIMS Reporter. Logins
used to connect to the SQL Server database require the minimum permissions described
in the following sections:
• Permissions Required to Create a New SampleManager Instance in the Database
(page 238)
• Permissions for Connecting through SampleManager Client (page 238)
• Permissions for Connecting through SQL Server ODBC Data Source (page 239)

Details of any logins that allow connection to the SQL Server database must be kept
secure to prevent users from bypassing the SampleManager security settings and
changing records in the database directly.

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11 SQL Server Setup
Configuring SQL Server Security

Permissions Required to Create a New SampleManager Instance in the

Database
The account used by the Add Server Instance wizard (page 66) must be given the
following roles so that it can create the required structures in the database:
• db_datareader
• db_datawriter
• db_ddladmin
• public

These roles allow the SampleManager Add Server Instance wizard to create a new
SampleManager instance.

If you want to use the Windows LocalSystem account to create your SampleManager
instance database, add the roles to the NT AUTHORITY\SYSTEM login in SQL Server
Management Studio.

Permissions for Connecting through SampleManager Client

Logins used to connect through a SampleManager client require the following
permissions.

Database permissions:
• CREATE TABLE
• CREATE VIEW

Permissions on the dbo schema that contains the SampleManager objects:

• CONNECT
• SELECT
• DELETE
• INSERT
• UPDATE

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 11 SQL Server Setup
Recommended Database Options

Permissions for Connecting through SQL Server ODBC Data Source

Logins used to connect through a LIMS Reporter using the SQL Server ODBC Data
Source require the following permissions on the dbo schema:
• CONNECT
• SELECT
Note LIMS Reporter is not included in the SampleManager installation kit and is
only available in upgraded SampleManager instances.

Recommended Database Options

We recommend that you use the following database options for the database used by
SampleManager:

Database Option Value

ANSI_NULLS ON

ANSI_PADDING ON

ANSI_WARNINGS ON

ARITHABORT ON

QUOTED_IDENTIFIER ON

CONCAT_NULL_YIELDS_NULL ON

NUMERIC_ROUNDABORT OFF

ALLOW_SNAPSHOT_ISOLATION ON

READ_COMMITTED_SNAPSHOT ON

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 I

Index

A G
Add Server Instance Wizard GhostScript
Oracle, 26 adding to the Path, 169
SQL Server, 66 installing, 169
Adobe Acrobat Reader
installing, 169
Adobe PostScript printer driver
I
InfoMakersee LIMS Reporter, 157
installing, 172
architecture, 2 installation
overview, 15
instances
C connecting to, 119
Chromeleon Link, 173 creating, 26, 66
Chromeleon Link AddIn, 183 deleting, 55, 93
Chromeleon Link Web API, 175 managing connections, 123, 124
ClickOnce deployment, 107 proxy login, 121
client side reporting, 160, 164
cross tab reports, 118 L
licensing
D installation details file, 100, 101
database profile installing licenses, 101
connecting to the database, 168 installing Thermo Licensing Server, 25, 65, 98
setup, 166 LIMS Reporter
Delete Server Instance Wizard database profile, 166
Oracle, 55 installing, 157, 166
SQL Server, 93 installing on client, 160, 164
deployment, 5 installing on server, 160, 163
example Oracle 64-Bit configuration, 231 PDF reports, 168, 172
pre-configured servers, 123, 126 LMTOOLS, 100

F M
firewall settings, 105 manage servers window, 124
FLEXnet licensing, 25, 65, 98 manual upgrade, 144, 146
LMTOOLS, 100 identifying files, 146
message.txt, 148
required tools, 144

Thermo Scientific SampleManager LIMS Installation Guide 241

Index

structure.txt, 145 setting up a database profile

upgrading files, 147 setup, 166
message.txt SQL Server ODBC data source, 164
upgrading, 148
S
O SampleManager client
ODBC data source connecting to a server instance, 119
Oracle setup, 161 installing, 115
SampleManager setup, 162, 165 installing LIMS Reporter, 160, 164
SQL Server permissions, 239 managing instance connections, 123
SQL Server setup, 164 pre-configured server connections, 126
operating system requirements, 14 proxy login, 121
Oracle running for the first time, 104, 119
installing LIMS Reporter, 160 setup, 116
installing SampleManager client, 116 silent installation, 118
ODBC data source, 161 Smart Client, 107
Oracle 64-Bit, 223 SQL Server permissions, 238
configuring naming methods, 228 tab reports, 118
configuring server connections, 228 upgrading, 149
connecting, 229 SampleManager ODBC data source, 162, 165
creating local net service names, 229 SampleManager remote services
example configuration, 231 upgrading, 144
installing, 21 SampleManager server
installing for SampleManager, 224 creating an instance, 26, 66
installing SampleManager server, 20, 23 installing, 19, 59
NLS_LENGTH_SEMANTICS parameter, 226 installing for Oracle 64-Bit, 20, 23
OPEN_CURSORS parameter, 225 installing for SQL Server, 62
Oracle ODBC driver, 230 installing LIMS Reporter, 160, 163
setup overview, 15 managing instance connections, 123
Oracle ODBC driver, 230 pre-installation checks, 20, 60
removing an instance, 55, 93
upgrading, 129, 131
P server connections
PDF reports, 168, 172 encrypting connection string, 108
installing Adobe Acrobat Reader, 169 managing, 123, 124
installing Adobe PostScript printer driver, 172 pre-configured, 126
installing GhostScript, 169 proxy login, 121
pre-installation checks, 20, 60 servers.xml file, 127
proxy login, 121 setup, 104, 119
server side reporting, 157, 160, 163
Windows Server 2003, 172
R servers.xml file, 127
reporting
setup
client sideclient side reporting, 157
Adobe Acrobat Reader, 169
installing for Oracle, 160
Adobe PostScript printer driver, 172
installing for SQL Server, 163
GhostScript, 169
installing LIMS Reporter, 157
installing licenses, 101
Oracle ODBC data source, 161
LIMS Reporter, 157
PDF format, 168
Oracle 64-Bit, 15
SampleManager ODBC data source, 162, 165
Oracle 64-Bit installation, 21
server side, 157
Oracle ODBC data source, 161

242 SampleManager LIMS Installation Guide Thermo Fisher Scientific

 Index

overview, 15 Upgrade Server Instance Wizard, 138

pre-installation checks, 20, 60 user-modified files, 147
proxy login, 121 web interface, 144
reporting for Oracle, 160 user-modified files
reporting for SQL Server, 163 upgrading, 147
SampleManager client, 115, 116 version-specific files, 147
SampleManager ODBC data source, 162, 165
SampleManager server, 19, 23, 59, 62
server connections, 119 W
SQL Server, 233 web interface
SQL Server installation, 62 upgrading, 144
SQL Server ODBC data source, 164
tab reports, 118
Thermo Licensing Server, 25, 65, 98
upgrading SampleManager, 129
Smart Client, 107
SQL Server, 233
authentication, 237
installing, 62
installing for SampleManager, 234
installing LIMS Reporter, 163
installing SampleManager client, 116
installing SampleManager server, 62
ODBC data source, 164, 239
permissions, 238, 239
recommended database options, 239
security, 237
structure.txt
upgrading, 145
version-specific files, 145
system
architecture, 2
deployment, 5
requirements, 14

T
tab reports, 118
Thermo Licensing Server, 25, 98
timezone settings, 105

U
upgrade.log, 146
upgrading, 129
manual procedures, 144, 146
menu items, 151
message.txt, 148
SampleManager client, 149
SampleManager remote services, 144
SampleManager server, 129, 131
structure.txt, 145

Thermo Scientific SampleManager LIMS Installation Guide 243