Installation Guide. Vitic Nexus 2013

Transcription

1 Installation Guide Vitic Nexus 2013

2 Information in this document is subject to change without notice and does not represent a commitment on the part of Lhasa Limited. The software described in the online help is furnished under a licence agreement or nondisclosure agreement and may be used or copied only in accordance with the terms of that agreement. It is against the law to copy the software except as specifically allowed in the licence or nondisclosure agreement. No part of the online help file may be copied without the express written permission of Lhasa Limited Lhasa Limited. All rights reserved. Trademarks Vitic is a registered trademark of Lhasa Limited. Microsoft is a registered trademark and Windows is a trademark of the Microsoft Corporation. Other product names mentioned in this document may be trademarks or registered trademarks of their respective companies and are hereby acknowledged. Limited Warranty Lhasa Limited makes no warranties, either expressed or implied, regarding the software described in this document or the online help, its merchantability, or its fitness for any particular purpose. In no event will Lhasa Limited be liable for any special, consequential, indirect or similar damages including any loss of profits or lost data arising out of the use of the software or data described in this document. Acknowledgements Lhasa Limited acknowledges all contributions to the development of Vitic, and to the ITIC SAR Database project, ChemAxon's MarvinSketch application and TELERIK's Premium Collection products. Statement of Intended Purpose Vitic Nexus is a chemical database with database management software, which can search on chemical properties, including sub-structure. It is intended for use within a structured decision support system as part of the users overall risk strategy. References JChem Cartridge for Oracle, Version 5.9, Admin Guide Guide, ChemAxon Ltd., CAS Registry Number is a Registered Trademark of the American Chemical Society. Contact Details Lhasa Limited Blenheim Terrace LEEDS LS2 9HD United Kingdom Reception +44 (0) Support +44 (0) Facsimile +44 (0) info@lhasalimited.org lhasasupport@lhasalimited.org Lhasa Limited is a not-for-profit organisation. Registered charity number Vitic Nexus 2013 Installation Guide Version 1.3 2/42

3 Table of Contents 1. Introduction System Requirements Database Server Web Server Client PC Vitic Nexus Database Server ChemAxon JChem Install JChem Install JChem Cartridge into Oracle Configuring JChem When it is not Installed on localhost Configure JChem Cartridge in Oracle Starting and Stopping the JChem Server Upgrading to JChem Vitic Nexus Database Admin Schema Vitic Nexus Web Server Prerequisite Checklist Installation Configuration Changing Permissions Enabling 64bit Mode Configuring Vitic Nexus Website Configuring Scheduled Queries Configuring Error Notification s Configuring Reports Populating the Vitic Nexus Database Oracle Passwords Requiring a Number Importing the Latest Vitic Nexus Data Testing the imported Vitic Nexus Database Upgrading Vitic Nexus Upgrading the Vitic Nexus Admin Schema Upgrading the Vitic Nexus Website Uninstalling Vitic Nexus Uninstalling the Vitic Nexus Website Uninstalling the Database Server Uninstalling JChem Appendix A Installing to Other Supported Environments A.1 ChemAxon JChem Vitic Nexus 2013 Installation Guide Version 1.3 3/42

4 A.1.1 Prerequisites A.1.2 Install JChem A.1.3 Install JChem Cartridge A.1.4 Configure JChem Cartridge A.1.5 Starting / Stopping the JChem Server A.2 Vitic Nexus Admin Schema A.3 Vitic Nexus Web Server A.3.1 Prerequisite Checklist A.3.2 Installation A.3.3 Configuration A.4 Upgrading Vitic Nexus A.4.1 Upgrading Vitic Nexus Admin Schema A.5 Uninstallation Appendix B Moving User Data B.1 Exporting from an Old Database Server B.2 Preparing the New Database Server B.3 Importing the User Data B.4 Instructions for API users (connection to Derek) Appendix C Expected Errors Appendix D Glossary Of Terms Appendix E Oracle Installation Options Appendix F VDB_ADMIN Required Permissions Appendix G Creating Hyperlinks with a Common Base URL Appendix H - Configuring Security Settings H.1 Setting the secure flag for all SSL cookies H.2 Enabling SSL and Redirection Appendix I Non-English Character Support in PDF Reports Vitic Nexus 2013 Installation Guide Version 1.3 4/42

5 1. Introduction Vitic Nexus is a client / server application that requires a database server and web server. The database and web server software can be installed onto a single server, or onto two separate servers. This guide details the installation process on a single-server in the following environment: Windows 2008 (database and web server) Oracle 10g and 11g (database server) Internet Information Services web server version 7 (web server) ODP.NET v (web server) Alternative installation instructions for other supported environments are included in Appendix A Installing to Other Supported Environments. The Vitic Nexus installation media is provided as a downloadable zip file with the following structure: Figure 1 Installation Media Structure Before installing Vitic Nexus you should download the in-house program files from the Download area of your personal Membership page on the Lhasa website (or from Products Vitic Nexus Member Only Content Downloads and IT Support Downloads). Once downloaded unzip the files to a hard drive. The location you choose will be referred to as the 'installation media' throughout the rest of the document. The following illustrates the architecture of a single server installation of Vitic Nexus. Figure 2 Server Configuration Vitic Nexus 2013 Installation Guide Version 1.3 5/42

6 2. System Requirements The following hardware and software are supported by Vitic Nexus. 2.1 Database Server 2 GB of RAM (4 GB required if also hosting the Web Server). 10 GB free disk space. Intel Xeon CPU 3.00GHz. Operating systems: o Windows Server 2008 Standard 32bit, 64bit (SP2). o Windows Server bit or 64bit. o Red Hat Enterprise Linux ES release 5.8 (64bit). Oracle 10g (v ) or 11g (v ). Please note that if you have upgraded your Oracle version from 10g to 11g you cannot upgrade Vitic Nexus: you must perform a clean installation (refer to Vitic Nexus Database Server on page 7). Java SE 6 Development Kit. ChemAxon JChem Cartridge (supplied by Lhasa). The TCP port 1521, for oracle-tns, version Oracle TNS Listener or (for 32-bit Windows), needs to be accessible by the internet. 2.2 Web Server 2 GB of RAM (4 GB required if also hosting the Database Server). 10 GB free disk space. Intel Xeon CPU 3.00GHz. Windows Server 2008 Standard 32bit, 64bit (SP2) or Windows Server bit or 64bit..Net Framework 3.5. Internet Information Services web server version 6 or 7 (IIS6 or IIS7). ODP.NET v (32bit, 64bit). Use the 32bit version on a server running a 32bit operating system and the 64bit version on a server running a 64bit operating system. Access to Microsoft Exchange 2003 (SP2) or an SMTP server/relay for sending s. The following TCP ports need to be accessible by the internet: o 80, for http, version Microsoft IIS webserver 7.0 o 443, for https, version Microsoft IIS webserver Client PC Window-based Operating system that supports the following browsers: Java Enabled Web Browser, such as: o Internet Explorer 8 to 10. o Firefox 19 to 20. Note Users should choose to "always allow pop ups from this site" when using Vitic Nexus, otherwise some windows will be blocked. JavaScript needs to be enabled. Microsoft Office 2007 or later. Java JRE 1.6 or 1.7 (excluding u45). A network connection to the web server. Vitic Nexus 2013 Installation Guide Version 1.3 6/42

7 3. Vitic Nexus Database Server The following instructions assume that the database has the following components installed, configured and running: Windows Server 2008 Standard 32bit, 64bit (SP2) Oracle 10g (v ) or 11g (v ).- Java SE 6 Development Kit Java JDK 6 Downloads These instructions will guide you through the installation and configuration of the following components: ChemAxon JChem v5.9 Vitic Nexus Admin Schema Before starting, copy the Vitic Nexus installation media to your database server. 3.1 ChemAxon JChem 5.9 Lhasa Limited is a value added reseller of JChem 5.9, and the software is included in the Vitic Nexus installation media. The Vitic Nexus Database Server will already meet the system requirements for JChem 5.9. Installation and configuration instructions for JChem on other supported environments are available from Appendix A Installing to Other Supported Environments on page 26. The JChem installation consists of three main tasks: Install JChem. Install the JChem cartridge into Oracle. Configure JChem cartridge in Oracle Install JChem 1. Double-click on the installation file within the Vitic Nexus Database\JChem folder (see Installation Media Structure on page 5): o jchem windows_with_jre.exe 2. When prompted, accept the licence. 3. Click Next on the following screens to accept the defaults: o Default destination (C:\Program Files\ChemAxon\JChem) o Start menu folder o Deselect the options to Create desktop icons and Insert JChem scripts into PATH. 4. After the install, uncheck the Run Marvin Beans Installer option. 5. Click Finish to complete the installation. ChemAxon's installation instructions for JChem are available from Install JChem Cartridge into Oracle 1. Create the following 2 folders in the cartridge folder, within the JChem installation folder (C:\Program Files\ChemAxon\JChem\cartridge): o licenses o logs 2. Copy the license.cxl file supplied by Lhasa Limited into the licenses folder. 3. Open the Control Panel System Properties Advanced tab. 4. Click Environment Variables then in the System Variables area set the following two variables (create new variables if they don't already exist): o ORACLE_HOME = Oracle installation folder (e.g. C:\oracle\product\10.2.0\db_1 or C:\oracle\product\11.2.0\dbhome_1) o JAVA_HOME = Java JDK installation folder (e.g. C:\Program Files\java\jdk1.6.0_18) 5. Start a new Command Prompt and change to the directory C:\Program Files\ChemAxon\JChem\cartridge. Note If you are using Windows Server 2008 with UAC enabled, the Command Prompt must be Run as Administrator. 6. Run the interactive installation by entering the following command and answer the questions appropriately. install.bat o To accept the default values given in [square brackets], press <Enter>. o Enter a question mark '?' for a more detailed description of the property. o When prompted; start the JChem Server (see Starting and Stopping the JChem Server on page 9). o Note you will be prompted to create a JChem password. Please make a note of this in order to complete installation later. 7. At the Proceed with the Install? prompt, press Y and then <Enter>. The install will then take place. Vitic Nexus 2013 Installation Guide Version 1.3 7/42

8 Screenshot 1 JChem Installer with sample parameters 8. If you are asked whether you want to install the JChem Server as an operating system service, press <y> Configuring JChem When it is not Installed on localhost If JChem has been installed on a separate server, then the correct permissions are not granted during the Vitic Nexus installation as Vitic presumes that JChem is on localhost. This manifests itself with the error "Failed to create Jchem index" when importing VXD files. To fix this you need to: 1. Log into SQL*Plus as the SYS user. 2. Run the following: begin dbms_java.grant_permission( 'PUBLIC', 'SYS:java.net.SocketPermission', **JChem server name**, 'resolve'); dbms_java.grant_permission( 'PUBLIC', 'SYS:java.net.SocketPermission', '****Put IP address here****', 'connect,resolve'); end; / ChemAxon's installation instructions for the JChem Cartridge are available from Configure JChem Cartridge in Oracle 1. Open the jcart.properties file in the C:\Program Files\ChemAxon\JChem\cartridge\conf directory, using a text editor such as Notepad. 2. Add the following section somewhere amongst the Oracle details (where jchem and pswd are the JChem username and password chosen previously): # Oracle connection details oracle.server.login=jchem oracle.server.password=pswd 3. Save the file. 4. Stop and re-start the JChem Server (see Starting and Stopping the JChem Server on page 9). 5. Run SQL*Plus as the JChem user, by opening a command prompt, running sqlplus and supplying the jchem credentials created earlier. sqlplus jchem 6. At the SQL> prompt enter the following commands (where the first 'jchem' in each command is the name of the jchem user created above): exec jchem.jchem_core_pkg.init(); select jchem.jchem_core_pkg.getenvironment() from dual; call privman_pkg.grants_on_jcobjs('jchem','public'); Vitic Nexus 2013 Installation Guide Version 1.3 8/42

9 Screenshot 2 SQL*Plus commands and output 7. Type exit to leave SQL*Plus and return to the command prompt. 8. Change to the C:\Program Files\ChemAxon\JChem\cartridge directory and enter the following command (where jchem/pswd is the user name and password chosen previously). loadjava -grant PUBLIC -user jchem/pswd jcart.jar 9. The JChem Cartridge is now installed and configured. Note The service must be started for the Vitic Nexus application to run Starting and Stopping the JChem Server Initially the server must be started from the command prompt, but the installation of the JChem cartridge should prompt to install the JChem Server as a windows service. At the end of the installation you should stop the command prompt started service, and use the Windows Services Console instructions below to start and stop the server Via Command Prompt 1. Open a command prompt as an administrator, and navigate to the JChem Cartridge folder (C:\Program Files\ChemAxon\JChem\cartridge). 2. Enter the command: server start Vitic Nexus 2013 Installation Guide Version 1.3 9/42

10 Screenshot 3 The JChem Server running in a command prompt 3. Wait until the server process has started (INFO: Server process start-ed). 4. Press Ctrl+c in this command prompt to display the Terminate the batch job? Prompt. Press <n> to return control to the command prompt window and leave the service running in the background messages will no longer be logged to this window. To stop the JChem Server: 1. Open a command prompt as an administrator and navigate to the JChem Cartridge folder (C:\Program Files\ChemAxon\JChem\cartridge). 2. Enter the command: server stop Via Windows Services Console 1. Either: o Open the Control Panel Administrative Tools Services Window. o Click Start then select Run. Type services.msc and press <Enter>. 2. Locate and select the JChem Cartridge Service and control it using the play/stop/restart buttons on the tool bar. Screenshot 4 Services Console with play/stop/restart buttons highlighted Upgrading to JChem 5.9 This section details instructions for upgrading from JChem 5.5 to JChem 5.9, which is required for the latest release of Vitic Nexus. Vitic Nexus 2013 Installation Guide Version /42

11 Lhasa Limited is a value added reseller of JChem 5.9, and the software is included in the Vitic Nexus installation media. To upgrade to JChem 5.9: 1. Double-click on the installation file within the Vitic Nexus Database\JChem folder (see Installation Media Structure on page 5): o jchem windows_with_jre.exe 2. When prompted, accept the licence. 3. Click Next on the following screens to accept the defaults: o Default destination (C:\Program Files\ChemAxon\JChem) You may wish to create a new directory if the previous version of JChem exists in this location (e.g. C:\Program Files\ChemAxon\JChem5.9) o Deselect the options to Create desktop icons and Insert JChem scripts into PATH 4. After the install, uncheck the Run Marvin Beans Installer option. 5. Click Finish to complete the installation. 6. Stop the current JChem service (see section Starting and Stopping the JChem Server) Via Command Prompt 1. Open a command prompt as an administrator, and navigate to the JChem Cartridge folder you wish to upgrade (...\JChem5.9\cartridge). 2. Run the upgrade by entering the following command and answer the questions appropriately: upgrade.bat o Enter the path of the home directory of the old JChem version :e.g. C:\Program Files\ChemAxon\JChem o The license files will be moved from the old Jchem licenses directory to...\jchem \jchem\cartridge\licenses. o The directory...\jchem \jchem\cartridge\licenses will be created (y,n): press <y> o Choose a password for the staging schema e.g. jcc_upgr_stage Screenshot 5 Upgrading via a command prompt o When prompted, proceed with the upgrade. o When asked if you would like to upgrade JChemServer as an operating system service, enter <n> if you prefer to control the service via command line. 3. The upgrade will then take place and you will be informed of the successful upgrade. Screenshot 6 Upgrade success message 4. Start the upgraded JChem service (see section Starting and Stopping the JChem Server). 5. Configure the JChem Cartridge in Oracle following the instructions detailed in section 3.1.4Configure JChem Cartridge in Oracle. Vitic Nexus 2013 Installation Guide Version /42

12 3.2 Vitic Nexus Database Admin Schema The Vitic Nexus Database Admin Schema is the database code that supports Vitic Nexus. It is installed into the Oracle instance containing JChem. The following instructions detail the installation on a Standard Windows 2008 Server (see 2.1 Database Server on page 6). If you are upgrading an existing Vitic Nexus installation, please see 6.1 Upgrading the Vitic Nexus Admin Schema on page 23. Alternative installation instructions for other supported environments are available in Appendix A Installing to Other Supported Environments on page 26, although the process is generally the same. 1. Open a command prompt and run SQL*Plus as the SYS user, connecting as sysdba. 2. Create the following tablespaces to store the Vitic Nexus data, by executing the commands: Note The tablespace names must exactly match those below, though the rest of the settings are only recommendations. create tablespace VDBADMIN datafile 'C:\Oracle\product\[version: or ]\oradata\VITICDB\VDBADMIN.dbf' size 200m autoextend on; create tablespace VDBDATA datafile 'C:\Oracle\product\[version: or ]\oradata\VITICDB\VDBDATA.dbf' size 2g autoextend on; create temporary tablespace VDBTEMP tempfile 'C:\Oracle\product\[version: or ]\oradata\VITICDB\VDBTEMP.dbf' size 600m autoextend on; 3. Open a command prompt, navigate to the Vitic Nexus Database Admin Schema installation media directory, and run the install_vdb_admin.bat file with the /i flag to indicate a clean install. install_vdb_admin.bat /i 4. When prompted enter the following information: o Oracle hostname: [localhost] o Port number: [1521] o Service / Oracle Instance name: [viticdb] o Oracle SYS Password Note The password entered will be visible on the screen. If this is a security concern you may wish to use a password for the purposes of installation and change it later. o A password for the VDB_ADMIN user, which will be created. o A password for the VDB_ASPNET user, which will be created. Note These passwords must respect any Oracle password restrictions. o The directory for the import export files: [C:\vdb] This directory name cannot contain spaces. This is the folder on the server where Vitic Nexus will import and export database files from and to. It does not need to exist at this time, but it must be created before you attempt to use Vitic Nexus. Note The Oracle service account needs read and write permissions to this folder. o The JChem username in Oracle: [jchem] 5. When all the information has been provided the VDB_ADMIN install scripts will run. Progress will be reported on screen and a more detailed log file (called logfile.txt) is created in the current directory. Note Some 'errors' may be reported in the log file which can be safely ignored; these are detailed in Appendix C Expected Errors page The install process will complete and return to the command prompt. Vitic Nexus 2013 Installation Guide Version /42

13 Screenshot 7 Installing the VDB Admin Schema 7. Check that VDB_ADMIN is populated correctly and can communicate with JChem, by entering the following commands: sqlplus vdb_admin select vdb_utility.get_vdb_version from dual; select jchem.jchem_core_pkg.getenvironment() from dual; 8. The output should be as follows: Vitic Nexus 2013 Installation Guide Version /42

14 Screenshot 8 Checking the VDB_Admin Schema installation If you wish to move all Vitic users (including passwords and the relevant querying privileges to each database) to a new install of Vitic (if you have moved from Oracle 10g to 11g for example) follow the instructions provided in Appendix B Moving User Data on page 31. Vitic Nexus 2013 Installation Guide Version /42

15 4. Vitic Nexus Web Server In this section we detail the steps required to install the Vitic Nexus web site onto the following environment: Windows 2008 Internet Information Services web server version 7 (IIS7) ODP.NET v Alternative installation instructions for other supported environments are available in Appendix A Installing to Other Supported Environments on page 26. This is broken down into the following stages: Prerequisite Checklist Installation Configuration 4.1 Prerequisite Checklist These instructions assume the following software is already installed and configured on the web server this list includes details of how to check their status and / or install them: Windows Server 2008 Standard Edition (SP2).NET Runtime v3.5 Open My Computer and inspect the contents of C:\WINDOWS\Microsoft.NET\Framework each version of.net installed will have its own folder. If necessary, v3.5 can be installed via Windows Update or downloaded from: Internet Information Services 7 (IIS7) Open the Server Manager application to add the Web Server (IIS) role, with the following options enabled Common HTTP (all), Application Development (all), Heath & Diagnostics (HTTP Logging, Request Monitor), Security (Request Filtering), Performance (Static Content Compression), Management Tools (IIS Management Console, IIS6 Management Compatibility (all). Virtual Memory Limit It is recommended that the Virtual Memory limit is set to 0, which means no upper limit, as running out of virtual memory can cause problems within Vitic. In Administrative Tools IIS Manager Application Pools Classic.Net Application Pool (which Vitic should be installed onto) Advanced Settings set the Virtual Memory Limit to 0. Oracle ODP.NET data provider This is needed so Vitic Nexus can talk to the Oracle database. Open My Computer and inspect the contents of C:\WINDOWS\Assembly for the Oracle.DataAccess v dll. If necessary, download ODP.NET from either: o 32bit - then select ODAC Xcopy.zip. o 64bit - then select ODAC112021Xcopy_x64.zip. Extract all the files to a temporary folder and run the command: install.bat all C:\odac odac This installs the ODP.NET components to folder C:\odac. Lhasa recommends using C:\odac rather than C:\oracle as the readme.txt suggests, preventing a clash with the Oracle database server installation, which is also typically installed under C:\oracle. Scheduled Query Service Account Create a service account to run the scheduled query tasks. This account needs to have local administrator privileges (for access to the command processor: cmd.exe) on the Web Server and it's recommended that the account is set to password never expires and user cannot change password. For a local server service account: Right-click on My Computer and select Manage. Expand the Server Manager tree to Configuration/Local Users and Groups then right-click on the Users folder and select New User. For a domain level service account, consult your domain administrator. (See section Configuring Scheduled Queries on page 16 for further information). 4.2 Installation 1. Navigate to the Vitic Nexus Website folder in the installation media (see Installation Media Structure on page 5) and double-click Setup.exe. 2. Follow the wizard clicking Next to proceed to the next step. In the Application Pool screen select the Classic.NET AppPool and accept all other defaults. o Note: it is required that the application pool has a virtual memory of at least 1GB. 3. When prompted, complete the following fields to configure your and click OK: o From Address - The address shown on s sent from Vitic Nexus to your users (i.e. viticnexus@[yourcompany].com). o Server Host - the host name or IP address of your server (e.g. localhost). o Server Port - the port number of your server (e.g. 25) Vitic Nexus 2013 Installation Guide Version /42

16 o Server Account Name - Only needed if authentication is required. o Server Password - Only needed if authentication is required. Note These details are stored in the web.config file in C:\inetpub\wwwroot\vitic1-0\ and can be edited from this location for future maintenance. 4. Configure the scheduled query task account by entering the username and password of the user account that the task will run as (configured in the prerequisites). 5. Click Close when the installation is complete. 4.3 Configuration Changing Permissions After installation, the permissions need changing on the Vitic folder. o Navigate to inetpub/wwwroot/vitic1-0. o Modify the permissions of the IIS_IUSERS user to allow full control to the vitic1-0 folder Enabling 64bit Mode To run Vitic Nexus in full 64-bit mode: o In the Internet Information Services settings for the application pool which Vitic is installed onto, ensure that the Enable 32-bit applications in App Pool settings is set to false. Screenshot 9 Enabling 64bit mode Configuring Vitic Nexus Website 1. To set the database connection details, go to Note that you need to be browsing from the local machine (either at the console or by a Remote Desktop session) to access this link. 2. Enter the database connection details as follows: o Server - localhost if the web server and database server are the same machine. If the database is on a separate server then specify the server name or IP address here. o Port - The port number that the Oracle TNS Listener is 'listening' on. The Oracle default is o Service/SID - This value is set when installing Oracle, for example viticdb. o Username - VDB_ADMIN. o Password - [your password]. Note If you want to use TNS names rather than a direct connection to the Oracle database you must leave the Server and Port fields blank. 3. Click Test to test the connection. 4. Click Save to store the connection details in the configuration file. Note You will need to re-enter the password as it is not returned to the web browser for security reasons. 5. In the Database Configuration Test area click Test to verify that JChem and the communication between the website and the database are functioning correctly Configuring Scheduled Queries Vitic Nexus provides the option for users to be notified by , at specific intervals, when the results of their queries have been affected by database changes. During the Vitic Nexus Website installation, the Vitic Nexus Scheduler was installed to drive the updates; follow these steps to enable the functionality: 1. Open the HttpGetMonitor.bat file which is located in the Vitic Nexus Scheduler's installation directory (e.g. C:\Program Files\Lhasa Ltd\Vitic Nexus Scheduler) using a text editor, such as Notepad. 2. Replace the ' portion of the URL on the second line of the file with the corresponding path to your installation (e.g. so that the line appears like: o HttpGetMonitor.exe Vitic Nexus 2013 Installation Guide Version /42

17 3. Save changes and close Notepad. 4. Open the Task Scheduler management console from the Start Administrator Tools Task Scheduler. 5. Click on the Vitic Nexus Scheduled Queries task in the lower Active Tasks pane then select the Properties option to the right. 6. In the Properties Actions tab click Edit, then in the Edit Action dialog enter the path of the folder containing HttpGetMonitor.bat in the Start in (optional): textbox (i.e. C:\Program Files\Lhasa Ltd\Vitic Nexus Scheduler). Do not include any quotation marks or delimiters, even if the path contains spaces. Screenshot 10 (1 of 4) Setting the 'Start in' property of the Scheduled Query Task Screenshot 11 (2 of 4): Setting the 'Start in' property of the Scheduled Query Task Vitic Nexus 2013 Installation Guide Version /42

18 Screenshot 12 (3 of 4): Setting the 'Start in' property of the Scheduled Query Task Screenshot 13 (4 of 4): Setting the 'Start in' property of the Scheduled Query Task 7. Accept the changes by clicking OK on all the open dialog screens. Enter the scheduled query task account's credentials when prompted. Please refer to the Vitic Nexus online help for details of how users request these update s for their queries Configuring Error Notification s To configure the settings for error notification: 1. Open the loggingconfiguration.config file which is located in the root folder of the website (e.g. C:\Inetpub\wwwroot\vitic1-0) in a text editor such as Notepad. 2. Locate the Add 'Error Trace Listener' section within the loggingconfiguration / listeners section (circled in the screenshot below), and enter the details of the server and address of the person you want to receive notifications. Vitic Nexus 2013 Installation Guide Version /42

19 Screenshot 14 Error Trace Listener configuration section See for more information on the configuration setting options. To disable error reporting: 1. Locate the Add 'Error Trace Listener' section within the loggingconfiguration / categorysource / add 'Error' / listeners section (circled in the screenshot below), and delete or comment it out as illustrated: <!-- <add name="error Trace Listener" /> --> Screenshot 15 Error Trace Listener source section Vitic Nexus 2013 Installation Guide Version /42

20 4.3.6 Configuring Reports PDF Report Size PDF reports can only contain a maximum of 30 records (rows of data) by default. You can change this limitation by editing the value in the MaxReportItems setting in the appsettings.config file located in the web site root (C:\Inetpub\wwwroot\vitic1-0). Note The default value has been set to prevent PDF reports from becoming too large. You should consider the file size before increasing this value Report Archiving It is possible for a database administrator to change the length of time for which reports are saved. To alter this you need to: 1. Connect to SQL*Plus as VDB_ADMIN: sqlplus vdb_admin 2. Run the following SQL statement to update the setting, where 24 is the length of time to keep the reports in hours. UPDATE vdb_config SET config_value = '24' WHERE config_key = 'KEEP_REQUEST_DURATION'; Vitic Nexus 2013 Installation Guide Version /42

21 5. Populating the Vitic Nexus Database Following the instructions below will result in your Vitic Nexus system containing the latest Vitic database supplied by Lhasa (V VITIC_LHASA-C48389-GILMKKQ-1405_ ). Once populated and tested; Vitic Nexus is ready for your end-users to start probing the Vitic database. If you wish to add data to the Vitic database you can create a customisable database based on the Vitic database supplied with Vitic Nexus. Custom databases contain the schema used in the Lhasa Limited Vitic database and the structures and lists. The endpoint tables are empty, ready for you to start populating with your custom data. Lhasa Limited supply a customisable Vitic database called V VITIC_CUSTOM-C54248-ONHHLKP-1548_ Only users with Edit Data rights to these databases can add custom data. The import and test processes are the same for both the core and custom databases. Blank schemas, containing all substances at the time of release are available for all databases, including DEREK_DB, on request from Lhasa Limited. Please refer to the Vitic Nexus online help for details about the functionality available in the application. 5.1 Oracle Passwords Requiring a Number When a new database is imported, Vitic creates a new database user automatically. You do not need to know the login details of this user as VDB_ADMIN supersedes it. However, if your Oracle configuration stipulates that passwords require a number then you need to do the following prior to importing any databases: Add a new row to the VDB_CONFIG table in the VDB_ADMIN schema with the following: o Config key: ORACLE_NUM_PSWD o Config value: YES Note the changes will only be applied to databases imported after the config file has been modified, any pre-existing databases will not have their passwords modified. 5.2 Importing the Latest Vitic Nexus Data 1. On the Vitic Nexus Web Server, browse to where you will be prompted for your login details. 2. Log in to Vitic Nexus using the administrator account as detailed in your distribution from Lhasa. Note It is recommended that you change the default password as soon as the installation is successful. Refer to the online help for details about changing the password. 3. Your browser may prompt you to install a Java VM in order to display the JChem Marvin structure editor. If you are browsing from the same server on which JChem is installed or a JVM is already be present, you may only be prompted to 'Trust content from sun.com' in order to allow Marvin to run. 4. Select the Database Import/Export menu. 5. Copy the latest Vitic Nexus Data files from the installation media (see Installation Media Structure on page 5) to the Import / Export folder on the Vitic Nexus Database Server. This location is specified on the Import form and was configured during the installation of the Vitic Nexus Database Admin Schema (see 3.2 Vitic Nexus Database Admin Schema on page 12). 6. Click. 7. Complete the following fields in the Import form (* = mandatory field): o Enter the New database name * (for example, VITIC_LHASA, EXCIPIENTS_LHASA, INTERMEDIATES_LHASA). Note The core databases can only be imported using the names specified above, whereas any name up to 15 characters long can be used for a custom database. o Enter a Description for your database as you want it to appear in Vitic Nexus. Do not include commas in this field. o Enter a comment in the Import Comment/Note field. Do not include commas in this field. o Ensure that the Drop existing database first option is selected. o Ensure that the Ignore active users warning option is selected. 8. Select the database file that you want to import from the list. 9. Click OK to import the database. 10. Depending on hardware and the database size, the import may take an hour. You can check progress by clicking Refresh on the Import / Export page, and the status is displayed on the right-hand side, next to the details of the database. 11. When the database is imported, publish the database by selecting the Database Schema menu, then clicking the Publish link next to the imported database and OK when prompted. Check the log file which is created in the import/export directory to confirm there are no issues with the import. Note Some 'errors' may be reported during the import, which can be safely ignored; these are detailed in Appendix C Expected Errors on page 35. Refer to the Publishing Databases topic in the Vitic Nexus online help for further details. Vitic Nexus 2013 Installation Guide Version /42

22 5.3 Testing the imported Vitic Nexus Database This section contains a quick test, to check that the latest Vitic Nexus Database has been successfully imported and is ready for use. 1. Browse to and enter your login details. If you are not directed to the Query Builder form select Query New Query from the menu bar. 2. Select the latest, recently imported, database, then specify your parameters, and run the query. Refer to the topics in the Searching folder in the online help Contents for details. Note If you cannot see any databases or database tables in the Query Builder, or Adding your Structure to the query doesn't work, you may need to reset IIS by running the following command on a command prompt: iisreset Also, if your search fails, or you don't see any results, ensure that the JChem service is running (see Starting and Stopping the JChem Server on page 9). 3. After the query completes and results are returned click Results Gallery. Note The initial search may take several minutes as caches are being populated. 4. In the Results Gallery de-select the structures whose details you do not want to view then click Results Grid. Here you can browse through the different endpoint tables using the tree in the Results Explorer 5. Log out of Vitic Nexus. Vitic Nexus 2013 Installation Guide Version /42

23 6. Upgrading Vitic Nexus Existing Vitic Nexus installations can be upgraded to the latest release, while maintaining existing data and settings. You cannot upgrade Vitic Nexus if you have moved your Oracle version from 10g to 11g. A clean installation of Vitic Nexus is required to support Oracle 11g. See section 3 Vitic Nexus Database Server and Appendix B Moving User Data for further information. To perform an upgrade, you must have the most recent previous release of Vitic Nexus installed (for example, to upgrade to v2.5, you need to start with a v2.0.2, or later, installation). You must also have the supported version of JChem installed for the latest release of Vitic Nexus (JChem 5.9.1). Instructions of how to perform an upgrade to this version of JChem can be found in section Upgrading to JChem 5.9. Note To safeguard your data; it is recommended that appropriate systems are in place to backup the database. In addition, your custom databases can be exported using the Database Import/Export functionality in Vitic Nexus. Please refer to the Vitic Nexus online help for further information. 6.1 Upgrading the Vitic Nexus Admin Schema 1. Open a command prompt, navigate to the Vitic Nexus Database Admin Schema installation media directory, and run the install_vdb_admin.bat file with the /u flag to indicate an upgrade. install_vdb_admin.bat /u 2. When prompted enter the following information: o Oracle hostname - [localhost] o Port number - [1521] o Service / Oracle Instance name - [viticdb] o Oracle SYS Password o The VDB_ADMIN user password o o The VDB_ASPNET user password Note The passwords entered will be visible on the screen. If this is a security concern you may wish to use a password for the purposes of installation and change it later. 3. When all the information has been provided the VDB_ADMIN install scripts will run. Progress will be reported on screen and a more detailed log file (called logfile.txt) created in the current directory. 4. The install process will complete and return to the command prompt. Screenshot 16 Installing the VDB Admin Schema Vitic Nexus 2013 Installation Guide Version /42

24 5. Check that VDB_ADMIN is populated correctly and can communicate with JChem, by entering the following commands: sqlplus vdb_admin select vdb_utility.get_vdb_version from dual; select jchem.jchem_core_pkg.getenvironment() from dual; The output should be as follows: Screenshot 17 VDB Admin output 6.2 Upgrading the Vitic Nexus Website To upgrade the Vitic Nexus Website, follow the normal installation and configuration instructions (see section 4 Vitic Nexus Web Server on page 15). The installer will automatically detect an upgrade situation and uninstall the previous version of Vitic Nexus, keeping any customised configuration settings, before installing the new version. Note Any saved queries will be retained, but their cached-results will not. Immediately after the upgrade this may result in the Results Grid, or Results Gallery appearing empty. If this happens, select the Edit Query link on your Saved Queries page then re-run the query to re-generate the results and re-populate the cache. The cache will naturally expire after 12 hours (by default); so this action will only be required if the saved query has a status of "Ready" when first accessed immediately following the upgrade. Vitic Nexus 2013 Installation Guide Version /42

25 7. Uninstalling Vitic Nexus All software and data components of Vitic Nexus can be uninstalled by following the instructions in this section. Note The uninstallation process requires access to the Installation Media. Ensure you have this to hand before starting. 7.1 Uninstalling the Vitic Nexus Website This will deregister the Vitic Nexus Website from IIS and remove its content from the server. 1. Open Control Panel Programs and Features. 2. Select Vitic Nexus and click Uninstall/Change. 3. When prompted, confirm you want to uninstall the program. 7.2 Uninstalling the Database Server The following instructions will remove all the Vitic Nexus data and the Vitic Admin Schema from the database server. 1. On the database server, open a command prompt and navigate to the SQL folder within the installation media directory (see Installation Media Structure on page 5). 2. Run the following command, where [viticdb] is the name of the Oracle instance containing the Vitic Admin Schema. [vdb_aspnet] is a user created automatically during the installation process. sqlplus *pswd is the password you specified for the vdb_aspnet user (see section 3.2 Vitic Nexus Database Admin Schema on page 12). 3. Several messages will scroll by as the relevant database entities are dropped, and when the command has finished executing you will be returned to the command prompt. 4. Connect to SQL*Plus as the SYS user, connecting as sysdba then: a. Drop the VDB_ADMIN and VDB_ASPNET users. sqlplus sys/pswd* as sysdba drop user vdb_admin cascade; drop user vdb_aspnet cascade; b. Remove the vitic_acl.xml XML object by running the following command: call dbms_xdb.deleteresource( /sys/acls/vitic_acl.xml ); *pswd is the password for the SYS user. Screenshot 18 Dropping the VDB users 7.3 Uninstalling JChem To uninstall JChem 5.9 from the database server: 1. Stop the JChem server (see Starting and Stopping the JChem Server on page 9). 2. Windows users: remove the Windows service for the JChem Cartridge server by executing in the jchem\cartridge directory: prunsrv.exe //DS//JChemCartridgeService 3. Then open Control Panel Programs and Features, select ChemAxon JChem then click Uninstall/Change. Click OK to confirm you wish to uninstall JChem, then click Next and Finish when prompted. 4. Connect to SQL*Plus as the SYS user, connecting as sysdba and drop the JChem user. drop user jchem cascade; Note JChem removal instructions are available from Vitic Nexus 2013 Installation Guide Version /42

26 Appendix A Installing to Other Supported Environments The following instructions detail installing the various components of Vitic Nexus in environments that are supported but differ to those detailed in the main document. This section covers: Database Server: Red Hat Enterprise Linux ES release 5.8 Oracle 10g (v ) or 11g (v ). Web Server: Windows Server 2003 IIS6 SMTP mail server A.1 ChemAxon JChem Complete JChem installation and administration guides are available from and Irrespective of environment, the JChem installation will consist of three main tasks: Install JChem. Install the JChem cartridge into Oracle. Configure JChem cartridge in Oracle. All the instructions assume the following prerequisites are met: Oracle 10g (v ) or 11g (v ) installed and configured. Java SE 6 Development Kit. These instructions detail an installation onto a Unix-like environment and were prepared using a default RedHat Linux Enterprise ES R5.8 installation and the bash command shell. They assume average UNIX administration skills and user privileges. Note Some of the command examples (i.e. chmod) show a simple way of achieving the required result, though it may not be the best or desired way for you to complete them. If in doubt consult your system administrator. A.1.1 Prerequisites 1. Create a JChem user, with home directory and read/execute permissions to the Oracle installation directory tree (logged in as the Oracle user). useradd p pswd jchem chmod o+rx oracle/app/oracle/product/[version: or ]/db1 2. Set the following environment variables for the JChem user: o ORACLE_HOME Oracle installation folder export ORACLE_HOME=/u01/app/oracle/product/[version: or ]/db_1/ o JAVA_HOME Java JDK installation folder export JAVA_HOME=/usr/java/default/ o ORACLE_SID SID of JChem / Vitic Nexus database instance export ORACLE_SID=viticdb o PATH needs to include the Oracle bin directory export PATH=$PATH\:$HOME/bin\:$ORACLE_HOME/bin This can be temporarily achieved by running the commands above in a console, or permanently by editing the.bash_profile file in the JChem user's home directory using a text editor such as Vim. Screenshot 19 Editing.bash_profile using Vim Vitic Nexus 2013 Installation Guide Version /42

27 3. Extract the Vitic Nexus installation media into the JChem user's home directory. unzip Vitic_Nexus_[version number].zip A.1.2 Install JChem These instructions assume that you are performing a new installation of JChem. If you are upgrading JChem you will need to rename the old installation folder before completing step 3 below [/home/jchem/chemaxon/jchem]. 1. Login as the JChem user created above. 2. Navigate to the JChem installer within the Vitic Nexus Installation media (see Installation Media Structure on page 5) and execute../jchem-5_9_1-linux.sh -c o -c flag used to run in non-gui / console mode o You may need to add execute permissions on the installer to run chmod u+x jchem-5_9_1-linux.sh 3. When prompted: o Accept licence? Yes [y] o Select installation folder: [/home/jchem/chemaxon/jchem] o Run Marvin Beans Installer? No [n] 4. The installation will finish and return control to the console. A.1.3 Install JChem Cartridge 1. Create the following 2 folders in the cartridge folder, within the JChem installation folder (/home/jchem/chemaxon/jchem/cartridge) o licenses o logs 2. Copy the license.cxl file received from Lhasa Limited into the licenses folder. 3. In the JChem Cartridge folder (/home/jchem/chemaxon/jchem/cartridge), run the interactive installation by entering the following command and answer the questions appropriately. To accept the default values given in [square brackets], press <Enter>../install.sh 4. At the Proceed with the Install? prompt, press <y> and then <Enter>. The install will then take place. Screenshot 20 JChem Installer with sample parameters A.1.4 Configure JChem Cartridge 1. Open the jcart.properties file in the ~jchem/chemaxon/jchem/cartridge/conf directory, using a text editor such as Vim. 2. Add the following section somewhere amongst the Oracle details (where jchem and pswd are the JChem username and password created previously): # Oracle connection details oracle.server.login=jchem oracle.server.password=pswd 3. Save the file. Vitic Nexus 2013 Installation Guide Version /42

28 4. Stop and re-start the JChem Server (see A.1.5 Starting / Stopping the JChem Server on page 28). 5. Run SQL*Plus as the JChem user, by opening a command prompt and run sqlplus and supplying the jchem credentials created earlier. sqlplus jchem 6. At the SQL> prompt enter the following commands (where the first 'jchem' in each command is the name of the jchem user created above): exec jchem.jchem_core_pkg.init(); select jchem.jchem_core_pkg.getenvironment() from dual; call privman_pkg.grants_on_jcobjs('jchem','public'); 7. Type exit to leave SQL*Plus and return to the command prompt. 8. Change to the ~jchem/chemaxon/jchem/cartridge directory and enter the following command (where jchem/pswd is the user name and password chosen previously). loadjava -grant PUBLIC -user jchem/pswd jcart.jar 9. The JChem Cartridge is now installed and configured. Note The service must be started for the Vitic Nexus application to run. A.1.5 Starting / Stopping the JChem Server The JChem server can be started from a console, by entering the following command in the ~jchem/chemaxon/jchem/cartridge directory, while logged in as the jchem user../server.sh start & The server can be stopped from a console, by running the following command in the ~jchem/chemaxon/jchem/cartridge directory, while logged in as the jchem user../server.sh stop The server could be added as a system service, allowing it to be automatically started / stopped when the server boots, by following these instructions Vitic Nexus 2013 Installation Guide Version /42

29 A.2 Vitic Nexus Admin Schema The Vitic Nexus Admin Schema is the database code that supports Vitic Nexus. It is installed into the Oracle instance containing JChem. These instructions cover only the differences between the instructions detailed in the main document (sections 3 Vitic Nexus Database Server and 4 Vitic Nexus Web Server) and installations onto a Unix-like environment (i.e. RedHat Linux). If you are upgrading an existing Vitic Nexus installation; please see A.4.1 Upgrading Vitic Nexus Admin Schema. 1. Open a command prompt and run SQL*Plus as the SYS user, connecting as sysdba. 2. Create the following tablespaces to store the Vitic Nexus data, by executing the commands: Note The tablespace names must exactly match those below, though the rest of the settings are only recommendations. create tablespace VDBADMIN datafile '/u02/oradata/viticdb/vdbadmin.dbf' size 200m autoextend on; create tablespace VDBDATA datafile '/u02/oradata/viticdb/vdbdata.dbf' size 2g autoextend on; create temporary tablespace VDBTEMP tempfile '/u02/oradata/viticdb/vdbtemp.dbf' size 600m autoextend on; 3. Open a console and log in as the Oracle user, navigate to the Vitic Nexus Database Admin Schema installation media directory, and run the install_vdb_admin.sh file with the /i flag to specify a clean install e.g. type./install_vdb_admin.sh /i 4. Continue the installation as described in the main document (see section 3.2 Vitic Nexus Database Admin Schema on page 12). A.3 Vitic Nexus Web Server This section includes details for installing the Vitic Nexus Web Server onto an environment meeting the following specification: Windows Server IIS6. SMTP mail server. It only contains the differences in the process compared to the process detailed in the main document. A.3.1 Prerequisite Checklist The checklist in the main document should be consulted with the following exceptions: Windows Server 2003 Standard Edition Internet Information Services 6 (IIS6) Open Control Panel Add or Remove Programs Add/Remove Windows Components select the Application Server component, click Details and ensure ASP.NET and Internet Information Services are selected. On IIS, click Details and ensure Common Files, IIS Manager and World Wide Web Service are selected. Click OK and Next to complete the wizard. SMTP Vitic Nexus uses to send notifications, such as password reminders, and so on. If you intend to use the Windows SMTP server on this machine you need to add the SMTP Server feature. Follow the instructions for IIS6, but also ensure that the SMTP option is selected under the Internet Information Services component. A.3.2 Installation The installation in the main document should be consulted with the following additional step at the end of the installation: Open command prompt and navigate to C:\Windows\Microsoft.NET\Framework\v and run: aspnet_regiis -i A.3.3 Configuration The configuration instructions for this environment are identical to the instructions in the main document. Vitic Nexus 2013 Installation Guide Version /42

30 A.4 Upgrading Vitic Nexus This section includes details for upgrading a Vitic Nexus installation. A.4.1 Upgrading Vitic Nexus Admin Schema The upgrade process is the same on Unix-like servers, with the following difference:- 1. Open a console window, navigate to the Vitic Nexus Database Admin Schema installation media directory, and run the install_vdb_admin.sh file with the /u flag to indicate an upgrade../install_vdb_admin.sh /u Screenshot 21 Vitic Nexus Admin Schema Upgrade A.5 Uninstallation The standard process can be followed to uninstall the Vitic Nexus Admin Schema (see section 6 Upgrading Vitic Nexus) and JChem (see Uninstalling JChem on page 25) on Unix-like environments. Vitic Nexus 2013 Installation Guide Version /42

31 Appendix B Moving User Data This process details how to move all Vitic users (including passwords and the relevant querying privileges to each database) to a new install of Vitic. This should be done after the completion of a new Vitic install. B.1 Exporting from an Old Database Server On the old database server, open a command prompt and type exp to begin the export of the user data from Oracle: Username: VDB_ASPNET. Password: [your password]. The export will begin and you will need to enter the following options: Enter array fetch buffer size: 4096 > accept the default 4096 by pressing <Enter>. Export file: EXPDAT.DMP > accept EXPDAT.DMP by pressing <Enter>. <2>U(sers), or <3>T<ables>: <2>U > accept the 'users' default by pressing <Enter>. Export grants (yes/no): yes > accept the 'yes' default by pressing <Enter>. Export table data (yes/no): yes > accept the 'yes' default by pressing <Enter>. Compress extents (yes/no): yes > press <n>. Screenshot 22 Exporting user data from Oracle Vitic Nexus 2013 Installation Guide Version /42

32 This creates a file on the database server called EXPDAT.DMP which you will need to copy in order to import onto the new database server. B.2 Preparing the New Database Server On the new database server: 1. Drop all tables within the VDB_ASPNET schema. These tables are: Figure 3 VDB_ASPNET schema tables 2. Log into SQL*Plus as the VDB_ASPNET user and run the script (located in the Vitic Nexus Admin Schema directory within your installation media) to recreate the VDB_ASPNET tables. to run this script. B.3 Importing the User Data The empty tables in the VDB_ASPNET schema can now be populated with user data by the following process: 1. Copy the EXPDAT.DMP file to the database server. 2. Open a command prompt on the new database server in the location of this EXPDAT.DMP and type imp to begin the import. o Username is VDB_ASPNET. o Password is VDB_ASPNET (or the password for this user if chosen on installation (from v2.5.0 onwards)). 3. The import will begin and you will need to enter the following options: o Import data only (yes/no): no> accept the default no by pressing <Enter>. o Import file: accept EXPDATA.DMP by pressing <Enter>. o Enter insert buffer size minimum is 8192: 30720> accept the default by pressing <Enter>. o List contents of import file only: (yes/no): no> accept the default by pressing <Enter>. o Ignore create error due to object existence: (yes/no): no> enter <y>. o Import grants (yes/no): yes > accept the default by pressing <Enter>. o Import table data (yes/no) yes >: accept the default by pressing <Enter>. o Import entire export file (yes/no): no > enter <y>. Vitic Nexus 2013 Installation Guide Version /42

33 Screenshot 23 Options for populating tables Screenshot 24 Populating tables This will populate the VDB_ASPNET tables with all Vitic users; user passwords and all privileges for each user against the databases imported from the old Vitic installation. 4. Complete the following to run the script to sync the Vitic users: o On the new database server connect to SQL*Plus as the VDB_ADMIN user and run the sync_users.sql script by B.4 Instructions for API users (connection to Derek) If any of your Vitic users have the Can Access API enabled in the Admin > User Management section of Vitic (this is usually done for use of Vitic and Derek together) then the following instructions are to recover the original passwords for these users. 1. On the old database server connect to SQL*Plus as the SYS user and create a temporary table (which you may drop after completion of this section) using the following : create table api_users as (select username, password from dba_users a, vdb_admin.vdb_api_users b where a.username=b.user_name); Vitic Nexus 2013 Installation Guide Version /42

34 2. Export this table and its contents using the exp tool: o Open a command prompt on the old database server and type: exp tables=api_users file=table_api.dmp Username is SYS as sysdba Password is the SYS password for this database o This creates the table_api.dmp file which will be used to import onto the new server. 3. Import this table and its contents into the SYS schema on the new database server: o Copy the table_api.dmp file to the new database server o Open a command prompt and navigate to the directory of this export file o Type the following to transfer the api user information to the new server: imp file=table_api.dmp full=y ignore=y Username is SYS as sysdba Password is the SYS password for this database 4. Log into SQL*Plus as the SYS user and run the script apiusers.sql (located in the Vitic Nexus Admin Schema directory in your installation media). 5. This populates the Vitic tables with the API user passwords stored in the temporary table api_users. All Vitic API user passwords will now be stored on the new server. 6. You can now drop the temporary table api_users within the SYS schema. Vitic Nexus 2013 Installation Guide Version /42

35 Appendix C Expected Errors Vitic Nexus Database Admin Schema Errors Errors of the following formats may be encountered while installing the Vitic Nexus Database Admin Schema (see section 3.2 Vitic Nexus Database Admin Schema) and can be safely ignored. errors : class chemaxon/license/licensemanager ORA-29534: referenced object VDB_ADMIN.chemaxon/license/LicenseManagerGUI could not be resolved errors : class chemaxon/license/licensemanagergui ORA-29521: referenced name com/jgoodies/forms/layout/cellconstraints could not be found VDB_ERRORS The following errors may be reported in VDB_ERRORS while importing a VXD file into Vitic Nexus (see section 5.2 Importing the Latest Vitic Nexus Data). These errors are logged when the import attempts to remove a database object which doesn't exist. Following the error, the relevant object is created and the import will continue unaffected. ORA-20000: Oracle Text error: DRG-10700: preference does not exist: english_lexer begin CTX_DDL.DROP_PREFERENCE('english_lexer'); end; Errors Installing on Oracle 10g In order for Vitic Nexus to be compatible with Oracle 11g, an Access Control List is created on installation. Consequently, if Vitic Nexus is installed on Oracle 10g, the following errors will be logged in the logfile and can be ignored. Vitic Nexus 2013 Installation Guide Version /42

36 Appendix D Glossary Of Terms The following terms are used within this document. Vitic Nexus The latest version of the Vitic software application. Vitic Database The database supplied with Vitic Nexus. Existing Vitic Database The database associated with any existing installation of Vitic (i.e. Vitic 2.0.2). Vitic Nexus Database Server The Oracle server which will host the database components of Vitic Nexus. Vitic Nexus Web Server The server which will host the Vitic Nexus website. Vitic Nexus Admin Schema The database component of Vitic Nexus. Vitic Nexus Website The user interface for Vitic Nexus. Vitic Nexus Data File(s) The VXD file(s) containing the latest data from Lhasa. Lhasa Lhasa Limited the organisation. [Vitic Nexus] installation media The media (usually in the form of a.zip file) downloaded from the Lhasa website, containing the various Vitic Nexus installation components. Unix-like A Unix operating system or one which behaves in a similar manner (i.e. RedHat Linux). Core Database A Vitic, Excipients or Intermediates database supplied pre-populated by Lhasa Limited. Custom Database An empty Vitic, Excipients or Intermediates database supplied by Lhasa and populated and customised by members. Vitic Nexus 2013 Installation Guide Version /42

37 Appendix E Oracle Installation Options Oracle Standard or Enterprise Editions can be used for the JChem / Vitic Nexus installation, with the following common options enabled:- Oracle JVM Oracle Data Mining (as a prerequisite for Oracle Text) Oracle Text Oracle XML DB Enterprise Manager Repository Oracle should be installed using Unicode character-set: AL32UTF8 (see also Appendix I Non-English Character Support in PDF Reports) The following default installation parameters might need increasing in high usage scenarios. Job queues are used to process certain elements of queries and the number of cursors and processes provides a definite limit on the number of concurrent users and hence queries that can be run. Your DBA should review these settings. job_queue_processes 10 open_cursors 300 processes 150 Vitic Nexus 2013 Installation Guide Version /42

38 Appendix F VDB_ADMIN Required Permissions The following are the permissions required by the VDB_ADMIN account in Oracle. This account and these permissions are automatically created as part of the installation and are included here for reference. grant connect,resource,unlimited tablespace, drop user,alter user,create user, create any sequence,drop any sequence, create any procedure, drop any procedure, create database link, drop any index,create any index, alter any index, insert any table, delete any table, select any table, update any table, grant any privilege, grant any object privilege, grant any role, create public synonym, drop public synonym, create any view, drop any view, create any table, drop any table, alter any table, create any directory, create any trigger, drop any trigger, alter any trigger, analyze any, exp_full_database, imp_full_database, create table, create session to vdb_admin; grant execute on ctxsys.ctx_ddl to vdb_admin; grant create job to vdb_admin; grant jcc_basic_role to vdb_admin with admin option; Vitic Nexus 2013 Installation Guide Version /42

39 Appendix G Creating Hyperlinks with a Common Base URL You can now hyperlink to files using just the file name so that Vitic users can link to files without entering the full path. These links are able to cope with changes to the directory location without users having to edit all the links in Vitic. Hyperlinks using a common base URL are created using only their filename and the rest of the file path is stored elsewhere so that if the server location changes, only one instance of the file path needs to be modified. To create a common base URL: Add a new row to the VDB_CONFIG table in the VDB_ADMIN schema with the following: o o Config key: COM_BASE_URL Config value: file:/// (for local) or file:///// (for server) For example: file:///c:/documents or file://///pc100 Note do not add another / to the end of the path. Note the COM_BASE_URL value can contain spaces. To add a new hyperlink to Vitic using the common base URL type baseurl[/path][/document]. The value is then pulled from the config table. Notes 1. Due to security restrictions, some browsers may prevent hyperlinks from being opened directly by clicking and may require the link to be copied and pasted, via the right-click menu. This is particularly likely with files stored locally. 2. The link should always be the final or only element within the field as anything following the baseurl tag is considered to be part of the link. Vitic Nexus 2013 Installation Guide Version /42

40 Appendix H - Configuring Security Settings H.1 Setting the secure flag for all SSL cookies To allow HTTPS: 1. Import a Certificate into Server Certificates. a. Self-signed certificates will work fine in a controlled environment, such as an internal network. b. If this server is accessed outside of your network, you may need to use a certificate from a valid issuing authority. 2. Edit the site Bindings as follows: a. Add a binding: i. Type: https ii. IP Address: input an appropriate IP address assigned to this machine (or all assigned) iii. SSL Certificate: Choose the SSL Certificate imported in step 1 To force HTTPS (so that if someone accesses the site on the default http they will receive error 403, SSL is required ): 1. Perform the steps to allow HTTPS above. 2. Expand Default Web Site, in the Connections list, then select the Vitic site. 3. Double-click SSL Settings then select Require SSL. 4. In the sites Error Pages edit the error response for 403 as follows: a. Set the response to a 302 redirect. b. Set the absolute url as the page you wish to redirect people to (with the HTTPS prefix). To make cookies secure (for https connection): 1. Open the file C:\inetpub\wwwroot\vitic1-0\web.config. 2. In the <system.web> section change <httpcookies requiressl="true" httponlycookies="true" />. 3. Within the forms tag add <forms requiressl="true". The web server should now be accessible only by HTTPS. Vitic Nexus 2013 Installation Guide Version /42

41 H.2 Enabling SSL and Redirection Here we detail how to enable, force and redirect SSL traffic on IIS Web Servers. Figure 4 IIS Web Server Architecture Server the server holds the settings for the certificate. Site (root) - Each site binds to particular ports. It has settings for URL redirection, SSL and Error page redirection. Virtual Direction - The virtual directory ( inherits settings from the root, unless you disable them. This process will achieve the following: Figure 5 Redirection Process To force HTTPS and keep the usage inside the virtual directory: 1. At the SERVER level of IIS: a. Add a valid SSL cert to the Server Certificates section. 2. At the WEBSITE (Default Web Site) level: a. Edit the site Bindings to add https or port 443 and the correct SSL certificate. The website will now respond to https only if requested. b. Edit the SSL Settings: i. Select Require SSL ii. Ignore Client Certificates The server will now give an error to http requests. c. Edit the Error Pages: i. Edit status code 403 Respond with a 302 redirect Set the url to d. Edit HTTP redirect: i. Select Redirect request to this destination ii. Set the url to iii. Select Only redirect requests to content in this directory (not subdirectories) 3. At the VIRTUAL DIRECTORY (Vitic1-0) level: a. Edit the SSL Settings: i. Select Require SSL ii. Ignore Client Certificates b. Edit the Error Pages: i. Edit status code 403 Respond with a 302 redirect Set the url to c. Edit HTTP redirect i. Clear Redirect request to this destination Vitic Nexus 2013 Installation Guide Version /42

42 Appendix I Non-English Character Support in PDF Reports Vitic Nexus supports the use of non-english characters in generated PDF Reports by using the Arial Unicode font, which includes support for the Asian languages (Simplified Chinese, Traditional Chinese, Japanese and Korean) as well as for all the languages used in major commercial markets. Initially Vitic Nexus will attempt to use the Arial Unicode font, but if that is not present on the web-server, it will revert to use the standard Arial font, which may not display non-english characters correctly. The Arial Unicode font can be acquired from and can be installed on the web server before or after the installation of the Vitic Nexus Website. Note This only applies to PDF Reports; non-english characters should be displayed normally in Vitic Nexus. Vitic Nexus 2013 Installation Guide Version /42

43