BIOVIA Insight: Install Guidehelp.accelrysonline.com/insight/2.6/content/pdf_files/insight_install.pdf · BIOVIA Insight: Install Guide Author BIOVIA Subject BIOVIA Insight Created

INSTALL GUIDEBIOVIA INSIGHT

2.6

Copyright Notice

©2015 Dassault Systèmes. All rights reserved. 3DEXPERIENCE, the Compass icon and the 3DS logo,CATIA, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, EXALEAD, 3D VIA, BIOVIA and NETVIBES arecommercial trademarks or registered trademarks of Dassault Systèmes or its subsidiaries in the U.S.and/or other countries. All other trademarks are owned by their respective owners. Use of any DassaultSystèmes or its subsidiaries trademarks is subject to their express written approval.

Acknowledgments and References

To print photographs or files of computational results (figures and/or data) obtained using BIOVIAsoftware, acknowledge the source in an appropriate format. For example:

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ContentsChapter 1: Introduction 1Documentation 1Further Information 1Chapter 2: Installation 2General Requirements 2Installation Steps 2BIOVIA Pipeline Pilot and Insight ApplicationInstaller 2Oracle Database 4Configure Oracle Database to SupportInsight 4Configure Pipeline Pilot Permissions forInsight Installer 5

Install MongoDB 6MongoDB versions 6

Configure Data Sources (IDS) for Query Service 6Run the Insight Project Database InstallerWizard 6Initial Insight Configuration 9Set permissions for users and groups 9Define the default settings for each datasource 9

Final Validation 11Searching 11Plugin Development 12

Chapter 3: Upgrading to Insight 2.6 13Chapter 4: Configuring your databases forbackup and recovery 14Chapter 5: Internationalization 15Configuring Fonts 15

Chapter 1:IntroductionBIOVIA Insight allows scientists to query or browse their database, visualize the results and refine andshare them as needed, and makes data available to other applications.

This guide provides information on the installation of Insight.

DocumentationThe following documents are supplied with Insight:

Insight Installation GuideInsight System Requirements

Other useful guides that administrators can refer to are included with Pipeline Pilot:

BIOVIA Pipeline Pilot Server 9.5 Installation GuideBIOVIA Pipeline Pilot Client Installation GuideBIOVIA Pipeline Pilot Server Admin Portal online helpWeb Services Guide

Further InformationFor more information about Insight and other BIOVIA software products, visit BIOVIA Support on theWeb: https://community.accelrys.com/index.jspa

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Chapter 2:Installation

General RequirementsIt is recommended that you use several servers for Insight within local network proximity.

1. A BIOVIA Pipeline Pilot Server 9.5 server with the Insight 2.6 application package installed.2. An Oracle Database account. Insight 2.6 requires a dedicated schema.3. AMongoDB Server.4. (Optional) A BIOVIAmachine for developing protocols or widgets.

This should be configured to connect to the Pipeline Pilot server and could be on the samemachine.

Installation StepsTo install Insight you should:

1. Install Pipeline Pilot 9.5 and Insight2. Install and configure Oracle (not required for upgrades)3. Run the Insight Install Wizard4. Install MongoDB5. Configure Data Sources (IDS) for Query Service6. Perform a Final Validation7. Configure Insight

Note: If you are upgrading from a previous version of Insight, refer to the Upgrading to Insight 2.6section for more information.

WARNING!

It is recommended that you back up your saved documents, forms, and templates before upgradingto Insight 2.6 to protect your data in case problems are encountered.

This involves backing up both the project database stored in Oracle and the document data stored inMongoDB. See Configuring your databases for backup and recovery for more information on backingup your data.

BIOVIA Pipeline Pilot and Insight Application Installer

IMPORTANT! After you have installed Pipeline Pilot with Insight 2.6 users will not be able to access theweb client until the Installer Wizard has been run.

1. Install Pipeline Pilot 9.5 using the document Pipeline Pilot 9.5 Server Installation Guide.

At the BIOVIA Download Center, log in and locate version 9.5 under the Pipeline Pilot link.

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2. Install the Insight 2.6 application package.a. At the BIOVIA Download Center, log in and locate version 9.5 under the BIOVIA Insight link.b. Download and unzip the appropriate installer archive:

Windows: Insight2.6_Win64.rarLinux: Insight2.6_Linux64.tgz

c. Run scitegicsetup.exe in the bin folder of the unzipped directory.d. When the installation starts, ensure that the Insight application is checked, and specify the

location of your Pipeline Pilot 9.5 install when prompted.

The Insight installer will also install List Management.

e. Proceed through the installer, using the Pipeline Pilot 9.5 Server Installation Guide if required.

IMPORTANT! You may get a warning about Insight and related packages being uninstalledduring upgrades from previous versions of Pipeline Pilot. Click OK in this warning dialog andproceed with the upgrade, Insight 2.6 will be installed during the upgrade and your data willnot be affected.

3. If you connected the BIOVIA Hub to your Pipeline Pilot 9.5 Server before installing the Insightapplication, you will need to update your Hub connection after installing Insight.a. Go to your BIOVIA Pipeline Pilot Server Home Page.b. Under the Administrators section, go to the Administration Portal.c. In the Admin Pages menu, expand the Security folder, and then go to Hub Connection.d. On Registered Applications, click Update to update the list applications.


https://accelrysdlc.subscribenet.com/control/acls/login?nextURL=%2Fcontrol%2Facls%2Findex

Oracle DatabaseInsight requires an Oracle database (with at least the default options). Access to the Oracle database canbe configured for multiple users. Thus, there can be a choice among the various users when configuringa specific connection, including the user <insight> in the procedures that follow. Each user owns allschema elements for the Insight database. It is created during installation before installing any exampledata, and the following privileges must be granted:

Roles connect, resource

System privileges unlimited tablespace

The Insight databases will grow as new data is added. Because the size of data for individual entries mayvary, it is not possible to determine howmuch storage will be needed upfront. Each user must havesufficient quota on their tablespaces to support application use. It is recommended that unlimitedtablespace privilege is given until actual usage can be estimated for your data. If unlimited tablespace isnot an option, it is recommended to set the limit to 100MB and monitor usage.

In addition to the Insight database, a List Management database is required. This can either use thesame schema and tablespace as Insight, or a different tablespace, or a different Oracle instance. If youchoose not to share the Insight schema and tablespace with List Management you will need to either setup a separate tablespace in the same instance or configure an instance dedicated to List Management.

Configure Oracle Database to Support Insight

IMPORTANT! If you wish to use a different schema (or the same schema but a different tablespace) tostore your List Management database you should follow these steps again with the appropriateusername, password, and tablespace name details.

In the Oracle Database, create a new database or use an existing database instance for Insight persistentdatastore in the directory containing the SQL files from the Oracle installation:

1. Start SQL*PLUS as a DBA user:

sqlplus system/<password>@<database>

Modify <password> and <database> for your system.

2. If this is the first time that Insight is being installed into a database instance you must first create theinitial tablespace. This can be done from any DBA account. Run the following at the SQL*PLUScommand prompt:

SQL> CREATE TABLESPACE <tablespacename> DATAFILE'<location>/<datafile>.dbf' SIZE 20M REUSE AUTOEXTEND ON NEXT 10M EXTENTMANAGEMENT LOCAL ONLINE;

Modify the <tablespacename>, <location>, and <datafile> for your system requirements. (Althoughthe size of your tablespace can extend automatically, consider monitoring the size of your databaseperiodically to be certain that the automatic extension parameter on your tablespace is enough toaccommodate your needs.)

3. (Optional) You can choose to store indexes in a separate tablespace. In this case prepare atablespace for this purpose:

SQL> CREATE TABLESPACE <indextablespacename> DATAFILE'<location>/<indexdatafile>.dbf' SIZE 5M REUSE AUTOEXTEND ON NEXT 1MEXTENT MANAGEMENT LOCAL ONLINE;


Modify the <indextablespacename>, <location>, and <indexdatafile> for your systemrequirements.

Tip: When you run the Installer Wizard you should use this <indextablespacename> for the IndexTablespace.

4. Create a user under which the schema will be installed:

SQL> create user <insight> identified by <insightpassword> defaulttablespace <tablespacename> temporary tablespace temp;

The <insight> user will be created with access to the <tablespacename> and the TEMP temporarytablespace.

5. Grant the proper permissions. For example:

SQL> GRANT create table, create view, create type, create session, createprocedure, create sequence, alter session, create synonym, create triggerTO <insight>;

The <insight> user will be granted the appropriate privileges. (User name and password values arecase-sensitive when logging into Oracle databases.)

Note: If you are setting up a separate List Management database, the user does not need all ofthese permissions, instead you should run:

SQL> GRANT create table, create session, alter session TO <listmgmt>;

The <listmgmt> user will be granted the appropriate privileges. (User name and password valuesare case-sensitive when logging into Oracle databases.)

6. Grant unlimited quota to the <insight> user:

SQL> alter user <insight> quota unlimited on <tablespacename>;

Note: If you are setting up a separate List Management database, you also need to specify thattablespace quota:

SQL> alter user <listmgmt> quota unlimited on <tablespacename>;

7. (Optional) If you have created a separate tablespace for indexes, grant unlimited quota to the<insight> user for this:

SQL> alter user <insight> quota unlimited on <indextablespacename>;

Configure Pipeline Pilot Permissions for Insight InstallerOnly users who have sufficient privileges are permitted to run the Insight Installer:

1. Go to the Pipeline Pilot Server Admin Portal:

http://<servername>:<port>/admin

where <servername> is the name of your Pipeline Pilot Server and <port> is the port number ("9944"is the default).

2. Log in as an Pipeline Pilot administrator. If an administrator account was not previously configured,you can find the default administrator username and password in the "Administration PortalOverview" page of the Admin section of the Pipeline Pilot Help Center:

http://<servername>:<port>/help/docs/?role=Admin


3. Select the appropriate security permissions. The user who will be the Insight administrator shouldbe granted the following permissions, which can be set using the Security > Permissions page in theAdmin Portal:

Platform | Administration | LogonInsight | AdministerListMgmt | Administer

Tip: Alternatively, in the default configuration of Pipeline Pilot add the Insight administrator userto the Platform/Administrators group.

Install MongoDBTo install MongoDB and configure Pipeline Pilot to useMongoDB, follow the Pipeline Pilot Help Centerinstructions:

1. Go to http://<server>:<port>.2. Click Help Center (Administrators).3. Install MongoDB using the instructions at Server Maintenance > MongoDB > Installing and

Deploying MongoDB.4. Configure Pipeline Pilot to useMongoDB using the instructions at Server Maintenance > MongoDB

> Configuring a Pipeline Pilot Server to use a MongoDB Server.

MongoDB versionsIf you are performing a new installation of Pipeline Pilot and Insight the installed version ofMongoDBwill be 2.6.If you are performing an upgrade of Pipeline Pilot and Insight where your MongoDB is installed onthe same server as Pipeline Pilot the installed version ofMongoDB will be upgraded to 2.6.If you are performing an upgrade of Pipeline Pilot and Insight where your MongoDB is installed on adifferent server from Pipeline Pilot the installed version ofMongoDB will not be changed, it willremain version 2.2.

Configure Data Sources (IDS) for Query ServiceTo customize the Query Service IDS, see Configuring Query Service data sources in the Query ServiceAdministration Guide.

Run the Insight Project Database Installer WizardAfter installing Pipeline Pilot 9.5, the Insight 2.6 application package, and configuring the Pipeline Pilotpermissions, you can then start Insight to begin the Insight Project Database Installer Wizard:

1. Open a web browser and navigate to http://<servername>:<port>/insight.Use an Insight Administrator account <insight-admin>.

If you get Java warnings due to the Chemistry Sketcher applet, click Install / Run / AlwaysAllow.If the Insight Project Database has not been installed, a dialog will be displayed.

2. To begin installation, click Insight Installation Wizard.


http://help.accelrysonline.com/insight/2.5/content/pdf_files/queryservice_admin.pdf

http://help.accelrysonline.com/insight/2.5/content/pdf_files/queryservice_admin.pdf

3. If needed, click Change Login and login as an <insight-admin> user who has the appropriatepermissions assigned.

Without installation permissions, you are not given any further options and you cannot continue.

4. When the installer starts you will see these one of thesemessages:New Insight database installation. indicates that there is no data source on this Pipeline PilotServer named Insight.

Tip: If you believe that Insight is already configured on this Pipeline Pilot Server, check theSetup | Data Sources tab in the Pipeline Pilot Server Admin Portal and rename a data sourceto Insight if necessary, then click Refresh in the Installer Wizard.

An existing older version of the Insight database has been detected. indicates that yoursystem contains an existing Insight database configuration.

Note: If you are upgrading from a previous version of Insight, refer to the Upgrading to Insight2.6 section for more information.

5. Choose the installation type that you require:Create a new Insight DatabaseUpgrade existing Insight DatabaseConnect to another Insight Database

6. To configure the Insight connection information:a. Click Next, and then enter the following:

Database: The type of database, always set to Oracle.Username: The database username, <insight>Password: The database password, <insightpassword>Database Server: Enter the hostname of the Oracle database.SID: Enter the service identifier (SID) for the Oracle instance on the server.Service Name: The name of the database service.

Note: This is always required for Oracle 12c databases but for older versions of Oracle thisis only necessary when no SID is entered.

Port: 1521For new installations select an option for each of Tablespace and Index Tablespace.This is not required for upgrades or when connecting to a different database. The IndexTablespace can be the same as the data Tablespace or separate if you havemade theappropriate preparations.

IMPORTANT! For upgrades do not change the database connection details.

Tip: Click theHelp button to access installation instructions.

b. If you are creating a new Insight database, choose whether to Use these details for ListManagement database?

If you want to use the same schema but a different tablespace for the List Managementdatabase you should uncheck this option and specify the details in the next step.

c. Click Install or Upgrade depending on your installation process.

The progress of the installation will be reported.


7. If you have not used the same details for the List Management database or you are performing anupgrade from Insight 2.2 or earlier you should configure the List Management connectioninformation:a. Click Next to continue to the List Management installer.b. Choose the installation type that you require:

Create a new List Management DatabaseConnect to another List Management Database

c. Click Next, and then enter the following:Database: The type of database, always set to Oracle.Username: Oracle username, <listmgmt> (or <insight> if you wish to use the same schema)Password: Oracle password, <listmgmtpassword> (or <insightpassword> if you wish to usethe same schema)Database Server: Enter the hostname of the Oracle database.SID: Enter the service identifier (SID) for the Oracle instance on the server.Service Name: The name of the database service.

Note: This is always required for Oracle 12c databases but for older versions of Oracle thisis only necessary when no SID is entered.

Port: 1521Enter the name for each of Tablespace and Index Tablespace.The Index Tablespace can be the same as the data Tablespace or separate if you havemadethe appropriate preparations.

d. Click Install or Upgrade depending on your installation process.

The progress of the installation will be reported.

8. Click Finish.9. Verify that http://<servername>:<port>/insight is accessible.10. If you need to re-run the Installer, go to Admin Portal > Setup > Data Sources, select the Insight

data source and click Remove. Repeat this to remove the List Management data source.Return to http://<servername>:<port>/insight.


Initial Insight Configuration

Set permissions for users and groupsA platform administrator can set permissions for specific users and groups. On the Security| Permissions page of the Pipeline Pilot Administrator Portal, set the following security permissions:

Insight | Administer. Permission to administer Insight.Insight | AuthorPlugins. Permission to see additional debugging information in the client for Insightplug-in developers.Insight | Logon. Permission to log into Insight.Insight | ManageProjects. Insight Users with elevated privileges.

Define the default settings for each data sourceOnly an Insight administrator can define the default settings for each data source, as follows:

1. From the Searchworkspace, click the arrow at the right of the data source (such as DataSource:ACD_IDS), and choose Settings... from the dropdown list.For example:

2. In theDefault Settings for Data Source dialog, you can do any of the following:To set a Search form as the default, click Form in the Search Defaults panel at the left, and thenchoose the public form to use by default from the dropdown list.In the following example, the Search form is also named “Search Form”:

Tip: Only public forms can be used for the default search form.

When a user opens the data source, this Search form appears by default. The user can switch toa different Search form for this or another data source at any time.

To set the Ad Hoc search as the default, click Ad Hoc Search in the Search Defaults panel at theleft, and choose the root category for the data source.For example:


When a user opens the data source, the Ad Hoc Search appears by default. The user can switchto a Search form at any time.

To set a Browse form as the default for a particular root category of the data source, choose thecategory from the For root dropdown list.For example:

Then select a form in the Browse Defaults panel.For example:

After a search, this Browse form appears. The user can switch Browse forms for any of the rootcategories or get the Table View of the data at any time.

To set Table View as the default, choose your root category from the For root dropdown list.For example:

Then click Table:

The user can switch to a Browse form for that data source at any time.

3. Click OK.


Final Validation

SearchingIn order to validate the installation (or upgrade) of your Insight database you should run a search,transfer the results to Insight, and save the document.

IMPORTANT!

If you do not have any data sources configured you should either:

use the Query Service to configure the data sources you requireproceed to install a BIOVIA product that automatically configures Insight data sources (forexample, Biological Registration or Chemical Registration).

The you should return to this validation step.

1. Go to http://<servername>:<port>/insight, where "servername” is the name of your Pipeline PilotServer and “port” is the port number (“9944” is the default).

2. Click Search in the Create New section of the home page, select a data source such as ACD_IDS(which checks Query Service IDS).

3. Click the arrow at the right of the Search: Unsaved Form* link, and then select Ad Hoc Search:

The Search link name changes from Search: Unsaved Form* to Search: Ad Hoc Search (as shown inthe next step).

4. The Fields panel at the left of the workspace displays all the available properties that you can use inan Ad Hoc search for each selected root category of the data source that is defined.

In the Fields panel, click Substance Registry Number. A form item that is associated with that fieldproperty appears at the right:

5. In the form item at the right, enter the query Substance Registry Number < 500 and run the query.6. Click Search.

The results are returned and a table is displayed.

7. Click Visualize Data.8. In the Transfer Data to Insight dialog, leave Table Data selected and click OK.


9. Click Save > Save As..., enter a name for the document to save in the Save Document dialog, andclick Save (this checks the Project database).

10. Return to theHome page.11. In the All Documents and Projects section of the Load Existing area, click your saved document to

display it.

Plugin DevelopmentUsers in the Insight/PluginAuthors group can access the templates for plugin development from thePipeline Pilot Client.

Refer to theGetting Started with Plugins Guide for more information.


Chapter 3:Upgrading to Insight 2.6If you have an existing Insight 2.5, 2.2, or 2.1 installation you can upgrade this using the Installer Wizardto Insight 2.6.

The following changes will bemade automatically when the Insight 2.6 application package is installedand the Install Wizard runs the upgrade:

The Pipeline Pilot packages will be updated to 2.6.000.The database version will be updated to 2.6.All existing saved documents, forms, and templates will remain unchanged.TheMongoDB storing your data will remain unchanged.

WARNING!

It is recommended that you back up your saved documents, forms, and templates before upgradingto Insight 2.6 to protect your data in case problems are encountered.

This involves backing up both the project database stored in Oracle and the document data stored inMongoDB. See Configuring your databases for backup and recovery for more information on backingup your data.

IMPORTANT! After you have installed Pipeline Pilot with Insight 2.6 users will not be able to access theweb client until the Installer Wizard has been run.

IMPORTANT!

An issue in Insight 2.2means that Insight projects migrated from Insight 2.1 to 2.2 (or created using2.2) are not editable by members of the Insight/Administrators group using the Project Explorer.

If you are upgrading from Insight 2.2, and you require this functionality, a protocol is provided tocorrect this issue.

1. Ensure that the Insight upgrade wizard has been run2. Open the Pipeline Pilot Client as a user in the Insight/Administrators group.3. Open theUtilities\Accelrys\Insight\Update Insight 2.2 Project Permissions protocol.4. Run the protocol.

All of your projects from Insight 2.2 will be available to members of the Insight/Administrators groupusing the Project Explorer.


Chapter 4:Configuring your databases for backup andrecoveryThe backup and restoration documentation listed here gives you a full and consistent copy of the datathat you can use to bring up a new or replacement database instance. Keep in mind that logicalbackups, such as exporting database objects such as tables or tablespaces, are a useful supplement tophysical backups, but cannot protect your whole database. An effective backup strategy must be basedon physical backups.

Oracle: See 9 Performing Backup and Recovery, which describes backup and recovery methods withOracle EnterpriseManager Database Control. You will learn how to implement a disk-based backupstrategy and perform simple repairs to database files.

MongoDB: See Backup and Restoration Strategies. You will learn how to back up your MongoDB projectdata in two different ways:

1. Use system-level tools, such as disk image snapshots.2. Use various features in the mongodump tool.

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http://docs.oracle.com/cd/E11882_01/server.112/e10897/backrest.htm#i1004902

http://docs.mongodb.org/manual/administration/backup/

Chapter 5:Internationalization

Configuring Fonts

Note: The following information is only relevant for installations where the use of non-Latincharacters is common.

Insight property names and data may not be rendered properly in PDF or Excel documents or whengenerating charts unless a Unicode font containing all of the characters used in the data is available onthe Pipeline Pilot Server. When such a font is missing, non-Latin characters may not be rendered.

The simplest way to ensure that an appropriate font is available is to install Microsoft Office on thePipeline Pilot Server. This includes the Arial Unicode font, which has representations of characters inmost commonly used languages.

If you cannot install Microsoft Office you must define a default Unicode font in order for these types ofdocuments to be generated properly - this is configured in a server file, Fonts.xml.

IMPORTANT! <pps_install> is the root of the Pipeline Pilot Server installation.On Windows this is typically:C:\Program Files\BIOVIA\PPSOn Linux this depends on the location of your Pipeline Pilot Server installation, but may be:[Home]/BIOVIA/PPS

To define the default Unicode font:

1. Navigate to the <pps_install>/apps/scitegic/core/xml/Objects/ directory on yourPipeline Pilot Server and open the Fonts.xml file.

If this file does not exist:

Copy FontsTemplate.xml and rename it Fonts.xml.2. Open Fonts.xml in a text editor and add your font information. Find the block of code that

contains the default Unicode font entries. (often around line 20).

The default Unicode font definition is composed of five values; the flag that this is the default andfour font style locations in this order:

!DEFAULT_UNICODE_FONT!plainitalicboldbold-italic

3. For each font style, edit the value to use the location of the appropriate Unicode font file availableon this Pipeline Pilot Server, for example:

<sci:mpropval name="Arial Unicode MS" type="StringType"><sci:value>!DEFAULT_UNICODE_FONT!</sci:value><sci:value>C:\WINDOWS\Fonts\ARIALUNI.TTF</sci:value><sci:value>C:\WINDOWS\Fonts\ARIALUNI.TTF</sci:value><sci:value>C:\WINDOWS\Fonts\ARIALUNI.TTF</sci:value>


<sci:value>C:\WINDOWS\Fonts\ARIALUNI.TTF</sci:value></sci:mpropval>

4. Save Fonts.xml.

Tip: You can also add custom font definitions in Fonts.xml, refer to the Report Design EssentialsGuide for further information (available through the Pipeline Pilot Help Center on your Pipeline PilotServer).

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