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Oracle® Health Sciences WebSDM and Empirica Study Installation Instructions
Release 3.1.2.1 for Windows 2003/2008 Server
E40537-02
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1 Installing WebSDM 3.1.2.1

To install WebSDM, you need to:

  1. Set up the database.

  2. Install the WebSDM software.

  3. Install the supporting software.

  4. Configure the properties files.

  5. Start the application service.

  6. Perform post-installation procedures.

  7. Optional: Customize WebSDM.

  8. Verify the WebSDM installation.

1.1 Prerequisites

1.1.1 Required Servers, Software, and Media

Before you begin the installation, ensure that you have the following servers, software, and installation media:

  • A Windows 2003 or 2008 server to host the WebSDM application. Note whether the server is 32-bit or 64-bit.

  • Oracle 10g (10.2.0.3 or higher) or Oracle 11g (11.2.0.2 or higher) installed on a server. The Oracle installation can be on the same or a different Windows server than the WebSDM software. If on different Windows servers:

    • The Oracle installation must be Oracle Database Enterprise Edition if you plan to encrypt the communications channel between the servers. The Windows server must have been restarted at least once since the Oracle installation.

    • Oracle Net Service must be installed on the Windows server where the WebSDM software is installed.

    • Both servers must be set to the same time zone.

  • An Oracle database instance (Oracle SID or Service) to support WebSDM.

  • IIS installed on the Windows server.

  • SMTP mailer enabled on the Windows server.

  • An installation of R for Windows (32-bit, version 2.13.2 only). See Appendix A, " Notes on the Installation of R" for installation notes.

  • A file compression and extraction utility, such as WinZip.

  • Internet Explorer version 7 or 8.

  • MedDRA ZIP files obtained under a subscription from MSSO.

  • The WebSDM 3.1.2.1 installation media. This is the product ZIP file from My Oracle Support (https://support.oracle.com).

  • If you are enabling SSO, a server with the Oracle Access Manager (OAM) installed. See Appendix C, "Configure WebSDM for SSO".

  • If you expect to load study data from an Oracle Life Sciences Data Hub (LSH) database, identifying information about that server. See Appendix D, "Configure WebSDM to Access an Oracle Life Sciences Data Hub Instance".

  • If you expect to load study data from an Oracle Health Sciences InForm database, identifying information about that server. See Appendix E, "Configure WebSDM to Access an Oracle Health Sciences InForm Instance".

You must also have access to the Java jar and jarsigner utilities and to your company's jar signing process.

1.1.2 Required Information about Existing Accounts and Services

You need the following names and passwords for accounts and services, which must already exist when you start the installation. In these procedures, the values are shown in <text_in_angle_brackets>.

  • Windows administrator account

    <win_admin_acct> and <win_admin_pass>

    Windows account and password on the Windows 2003 or 2008 server where you will install WebSDM. The account must be assigned the Administrator role.

  • Optional: Administrator account and password for the Oracle server

    < winDB_admin_acct> and <winDB_admin_pass>

    If the Oracle database is not installed on the same Windows server as the WebSDM software, you also need a Windows account and password on the server where the Oracle database is installed. The account must have sufficient permissions to edit the Oracle sqlnet.ora file.

  • Optional: Oracle root installation directory

    <oracle_root>

    If WebSDM and the Oracle database are to be installed on different Windows servers, and you plan to encrypt the communications channel between them, you must know the root directory where Oracle is installed.

  • Oracle DBA account

    <ora_dba_acct> and <ora_dba_pass>

    This is the Oracle account and password for the Oracle instance that supports WebSDM. The account must be assigned the DBA role.

  • Oracle service name or SID

    <ora_service_name> or <ORA_SID>

    Oracle SID or Oracle service name for the Oracle instance that supports WebSDM.

  • Oracle host name

    <ora_host>

    The server host on which the Oracle SID or Oracle Service is installed. If the server host is the same one on which you are installing the WebSDM software, use the host name localhost. If the Oracle database is hosted on a different server, use that server name.

  • Oracle port

    <ora_port>

    The port on which the Oracle SID or Oracle Service name is executing. The default is 1521.

  • First or subsequent install

    <is_first_install>

    To determine the procedures to follow for this installation, ascertain whether other related Oracle products are already installed on the server.

    Use Windows Explorer to inspect all root directories on the file system for a <root>\Lincoln subdirectory. If this subdirectory does not exist, the value of <is_first_install> is true. The instructions indicate those steps that need to be completed only for the first install.

    If a <root>\Lincoln subdirectory already exists on the application server, then <is_first_install> is false. Contact Oracle before proceeding with this installation.

  • Installation root

    <root>

    File system root where the \Lincoln subdirectory was found. If it was not found, select the drive where you want to install WebSDM. The recommended location is c:\.

  • Submissions folder

    <submissions_folder>

    File system drive and directory to serve as the root where clinical data submissions (applications and study data) will be stored. The recommended location is d:\ClinicalData.

  • Optional: OAM Server

    <oam_server>

    If you are enabling SSO and want to set a logout redirect page, you must provide the fully qualified name for the OAM server.

1.1.3 Removing and Setting the Read-only Attribute

If the installation instructions require you to edit a file, check the file properties to see if the read-only attribute has been set. If set, you must remove it before editing. To remove the read-only attribute:

  1. Open Windows Explorer and navigate to the file.

  2. Right-click the file name and select Properties.

  3. Clear the Read-only option.

  4. Click OK.

When you are done editing the file, reset the read-only attribute:

  1. Open Windows Explorer and navigate to the file.

  2. Right-click the file name and select Properties.

  3. Select the Read-only option.

  4. Click OK.

1.1.4 Saving Files

If the installation instructions require you to edit a file, be sure to save the file with the original name. Some editors by default add the TXT extension to the file name.

1.1.5 Required Information for New Accounts and Services

During installation, you provide names and passwords for accounts and services that are created. Ensure that all passwords comply with your company security policy. Database passwords must also comply with password requirements for the Oracle version that you are using.

  • WebSDM instance name

    <instance>

    Name you provide for the WebSDM instance. The installation uses this name for several components, including a Windows service, a virtual directory, and a folder. The default name is websdm. Using the default name reduces the number of files you must edit during the installation. If you are installing more than one WebSDM instance on the Windows server, the <instance> name must be unique for each server.

  • Oracle net service name

    <ora_net_service>

    Name for the Oracle net service for the WebSDM database.

  • Oracle tablespace name

    <ora_tablespace>

    Name for the Oracle tablespace for the WebSDM database. Oracle recommends that you use the same name you used for the WebSDM instance name.

  • Oracle master account and password for WebSDM

    <websdm_master_acct> and <websdm_master_pass>

    Name and password for the Oracle account that the installation creates to store data for the WebSDM instance. Oracle recommends that you use the same name you used for the WebSDM instance name.

  • WebSDM application admin account default password

    <app_admin_pass_default>

    Password for the WebSDM user account with the reserved name 'admin'. Email Oracle at safetysupport_ww@oracle.com for the initial default password for the admin account.

  • WebSDM application admin account final password

    <app_admin_pass>

    You must change the password of the WebSDM application admin account the first time you log into WebSDM.

  • MedDRA account passwords

    <meddraX_ora_pass>

    You must provide passwords for the Oracle accounts that are created for each version of MedDRA.

  • IIS default application

    <is_IIS_default_app>

    Determine whether to make WebSDM the default application for your IIS installation. If you do, then <is_IIS_default_app> is true. Otherwise, it is false. The instructions include the steps to make WebSDM the default application for your IIS installation. If WebSDM is not the default applications for IIS, you can skip these steps.

1.2 Set Up the Database

1.2.1 Setting Up the Oracle Net Service

Create an Oracle net service that points to the Oracle service or SID that WebSDM will use to store data.


Note:

If <is_first_install> is false, complete this section only if the WebSDM instance you are installing uses a different Oracle Service or SID.

  1. Start Oracle > Configuration and Migration Tools > Net Manager.

  2. Click Local to see the options, and select Service Naming.

  3. Create a new service name.

    1. From the Edit menu, select Create.

      or

    2. Click the Create (green plus sign) icon.

  4. For the Net Service Name, type the value of <ora_net_service>.

  5. Click Next.

  6. For Protocol, select TCP/IP (Internet Protocol).

  7. Click Next.

  8. For Hostname, if WebSDM and the Oracle database are installed on the same Windows server, enter localhost. If the Oracle database is installed on a different Windows server, enter the <host_name>.

  9. For Port, accept the default 1521, unless your DBA has supplied a different value for <ora_port>.

  10. Click Next.

  11. If you are using an Oracle 10g database, select the Oracle 8 or Previous radio button.

    1. For SID, type the value of <ORA_SID>.

    2. Click Next.

      or

      if you are using an Oracle 11g database, for Service Name, type the value of <ora _service_name>.

    3. For Connection Type, select Dedicated Server.

    4. Click Next.

  12. Optionally, to verify the settings, click Test.

    1. If the test completes successfully, click Close.

    2. If the test fails, edit the settings and try the test again.

  13. Click Finish.

    The settings for the Oracle net service appear.

  14. From the File menu, select Save Network Configuration.

  15. Exit Oracle Net Manager.

1.2.2 Encrypting the Database Connection

If WebSDM and the Oracle installations are on different servers, complete the following instructions to encrypt the communications channel between the servers.

If the WebSDM and Oracle installations are on the same Windows server, continue to Section 1.2.3, "Setting Up the Oracle Master Account and Tablespaces for WebSDM".

  1. Log onto the <winDB_admin_acct> account on the machine where the Oracle database is installed.

  2. Navigate to the <ora_root>\network\admin folder.

  3. Use a text editor, such as Notepad, to open the SQLNET.ORA file and add these lines at the end:

    SQLNET.ENCRYPTION_SERVER = accepted
    SQLNET.CRYPTO_CHECKSUM_SERVER = accepted
    SQLNET.ENCRYPTION_TYPES_SERVER = (RC4_256)
    SQLNET.CRYPTO_CHECKSUM_TYPES_SERVER = (MD5,SHA1)
    

    These settings enable both encrypted and unencrypted connections.

  4. In an environment where encryption is required for all connections, change the setting of the first added line as follows:

    SQLNET.ENCRYPTION_SERVER = required
    
  5. Save your changes to the SQLNET.ORA file.

  6. Log onto the <win_admin_acct> on the Windows server where you are installing WebSDM.

  7. Navigate to the <ora_root>\network\admin folder.

  8. Use a text editor, such as Notepad, to open the SQLNET.ORA file and add these lines at the end:

    # This line is optional
    SQLNET.CRYPTO_SEED = 'at least 10 chars'
    SQLNET.ENCRYPTION_CLIENT = requested
    SQLNET.CRYPTO_CHECKSUM_CLIENT = requested
    SQLNET.ENCRYPTION_TYPES_CLIENT = (RC4_256)
    SQLNET.CRYPTO_CHECKSUM_TYPES_CLIENT = (MD5, SHA1)
    

    These settings ensure that connections from the WebSDM server always request an encrypted channel, and also work if the database does not support encrypted connections.

  9. Save your changes to the SQLNET.ORA file.

1.2.3 Setting Up the Oracle Master Account and Tablespaces for WebSDM

Run scripts to create the Oracle master account and tablespaces for WebSDM.

  1. Locate the database-3_1_2_1_xxx.zip file (where xxx represents a specific build number) on the installation media, and extract the contents of this file to a temporary location, such as c:\install\database.

  2. Use a text editor, such as Notepad, to open the 1_create_tablespace.sql file and review the DEFINE statements.

  3. Verify that the ORADATA file path points to your preferred location for the tablespace data files.

  4. If the value of <ora _tablespace> is something other than websdm, change the value of TABLESPACE_NAME to that value.

  5. Verify that the referenced TABLESPACE_NAME and DATAFILE do not already exist. You can do so by executing each of these SQL queries in order:

    select tablespace_name from dba_tablespaces;8
    select file_name from dba_data_files;
    
  6. Review the default sizing parameter values. The default values are suited to an environment where study data is loaded into application-specific tablespaces. If, instead, you are loading all study data into a single tablespace and registering 100+ studies, it might be reasonable to double the size parameters.

  7. If changes are needed, edit, save, and close the file.

  8. Use a text editor to open the 2_create_oracle_user.sql file and review the DEFINE statements. This script creates the WebSDM master account and grants permissions to it.

  9. If the value of <websdm_master_account> is something other than websdm, change the value of USER_NAME to that value.

  10. If the value of <ora _tablespace> is something other than websdm, change the value of TABLESPACE to that value.


    Note:

    For WebSDM to be fully functional, this script must be executed with the SQL statements it currently contains. If certain permissions are not granted to the Oracle master account for WebSDM, the application runs with some functionality disabled. Specifically:
    • If the CREATE TABLESPACE permission is not granted, the Create a new tablespace for each Application radio button is disabled on the Site Options page. In addition, all application and study level accounts will use a common tablespace

    • If the DROP USER permission is not granted, the Action menus attached to Applications, Studies, and Study Pools on the Setup tab does not contain entries that allow properly authorized users to delete those objects.

    • If the DROP TABLESPACE permission is not granted, but CREATE TABLESPACE and DROP USER are granted, the dedicated tablespace contents are deleted when an application is deleted, but the tablespace itself is not deleted.


  11. If changes are needed, edit, save, and close the file.

  12. Open a command window and change the directory to the temporary directory.

  13. From the <ora_dba_acct> account, run the 1_create_tablespace SQL script. For example:

    1. Type this command on one line:

      C:> sqlplus <ora_dba_acct>@<ora_net_service>
      @c:\install\database\1_create_tablespace
      
    2. When prompted for the password, enter <ora_dba_pass>.

    3. Scroll up to review the results of running script 1_create_tablespace. There should be no errors.

  14. From the <ora_dba_acct> account, run the 2_create_oracle_user SQL script. For example:

    1. Type this command on one line:

      C:> sqlplus <ora_dba_acct>@<ora_net_service>
      @c:\install\database\2_create_oracle_user
      
    2. When prompted for the password, enter <ora_dba_pass>.

    3. When the script prompts you for the WebSDM master account password, type the value of <websdm_master_pass>.

    4. When prompted to confirm the password, again type the value of <websdm_master_pass>. If confirmation fails, the script exits and you can run it again.

    5. Scroll up to review the results of running script 2_create_oracle_user. There should be no errors.

  15. From the newly created WebSDM master account, run the 3_create_all SQL script. For example:

    1. Type this command on one line:

      C:> sqlplus <websdm_master_acct>@<ora_net_service> @c:\install\database\3_create_all
      
    2. When prompted for the password, enter <websdm_master_pass>.

    3. Review the contents of the C:\install\database\3_create_all.log file created by running this script. There should be no errors.

  16. Close the command window.

1.3 Install the WebSDM Software

1.3.1 Installing New Website Files

Complete these steps only if <is_first_install> is true.

  1. Use Windows Explorer to view the installation media. Locate the following file:

    32-bit server: Lincoln.zip

    64-bit server: Lincoln_x64.zip

  2. Extract the contents of this file to <root>, making sure the path names stored in the archive are used. For example, in the WinZip Extract dialog box, be sure to check the Use folder names checkbox.

1.3.2 Configuring Existing Website Files

Complete these steps only if <is_first_install> is false or if the value of <instance> is something other than websdm.

  1. Use Windows Explorer to view the installation media. Locate the following file:

    32-bit server: Lincoln.zip

    64-bit server: Lincoln_x64.zip

  2. Extract the contents of this file to a temporary folder on the server, such as C:\temp, making sure that the path names stored in the archive are used. For example, in the WinZip Extract dialog box, be sure to select the Use folder names checkbox.

  3. If the value of <instance> is something other than websdm, change the name of the directory from:

    C:\temp\Lincoln\apps\websdm

    to:

    C:\temp\Lincoln\apps\<instance>

  4. Copy the <instance> folder (and all its files and subdirectories) from:

    C:\temp\Lincoln\apps

    to:

    <root>\Lincoln\apps\

  5. Navigate to the <root>\Lincoln\IIS\conf\ folder.

  6. Use a text editor to open the uriworkermap.properties file.

  7. Scroll to the last line of this file. Change websdm to the value of <instance>. For example, if the <instance> is websdmProd, change:

    /*/*.jsp=websdm

    to:

    /*/*.jsp=websdmProd

  8. Add the following lines to this file, substituting the value of <instance> for all six occurrences of websdm.

    /*/websdm /*.jsp=websdm 
    /*/websdm /servlet/*=websdm 
    /*/websdm /services/*=websdm 
    

    Note:

    The file should contain the three lines for each instance of WebSDM that is installed on the machine. If Empirica Signal is also installed, there will be three slightly different lines for each instance of the Empirica Signal application.

  9. Save your changes to the uriworkermap.properties file.

  10. Edit the <root>\Lincoln\IIS\conf\workers.properties file to add <instance> to the end of the comma-separated list of applications for the worker.list property. For example, if the <instance> is websdmProd, the edited line is:

    worker.list=websdm, websdmProd


    Note:

    The worker.list element should contain an entry for each instance of an Oracle product (WebSDM or Empirica Signal) that is installed on the machine.

  11. Add the following lines to this file, substituting the value of <instance> for all three occurrences of websdm:

    worker.websdm.port=8009
    worker.websdm.host=localhost
    worker.websdm.type=ajp13
    

    Note:

    The file should contain the three lines for each instance of an Oracle product (WebSDM or Empirica Signal) that is installed on the machine.

  12. Compare the value specified for the newly added port property to the other port numbers already specified in this file. If this value (8009) is already assigned to another application, you must supply a different port number for this instance of WebSDM to use. Select a port number that is two greater than the highest port number specified elsewhere in the file and change the value for the port property to that value. For example, if the highest port number is 8009, use the value 8011.

  13. Save your changes to the workers.properties file.

  14. Check for the existence of the folder <root>\Lincoln\apache-tomcat-6.0.41 (earlier releases of WebSDM used other versions of tomcat, so this folder might not exist). If this folder does not exist, copy the folder named apache-tomcat-6.0.41 (and all its files and subdirectories) from C:\temp\Lincoln to <root>\Lincoln\.

    For example, from:

    C:\temp\Lincoln\apache-tomcat-6.0.41

    to:

    <root>\Lincoln\apache-tomcat-6.0.41


    Note:

    The apache-tomcat-6.0.41 folder required for WebSDM can coexist with other Tomcat versions that have been installed for other products.

  15. Check for the existence of the folder <root>\Lincoln\jdk1.6 (earlier releases of WebSDM used jdk 5, so this folder might not exist).

    1. If the <root>\Lincoln\jdk1.6 folder does not exist, copy the folder named jdk1.6 (and all its files and subdirectories) from C:\temp\Lincoln to <root>\Lincoln\.

    2. If the <root>\Lincoln\jdk1.6 folder exists, determine the specific version of the jdk by opening a command window and executing the following command:

      <root>\Lincoln\jdk1.6\bin\java.exe -version

      If the response indicates a version earlier than 6.0_81, replace the jdk1.6 folder in <root>\Lincoln with the one in C:\temp\Lincoln.

1.3.3 Configuring the server.xml File

Complete these steps if the value of <instance> is something other than websdm, or if you edited the workers.properties file to change the port number to a value other than 8009.

  1. Navigate to the <root>\Lincoln\apps\<instance>\conf folder.

  2. Use a text editor to open the server.xml file.

  3. If the value of <instance> is websdm, skip to step 6.

  4. Locate the Host element and its appbase attribute. Change websdm to the value of <instance>.

    <Host name="localhost" appBase="C:/lincoln/apps/websdm/webapps">

  5. Locate the Context element and its path attribute. Change websdm to the value of <instance>.

    <Context path="/websdm">

  6. Locate the Connector element and its port attribute. If you changed the value of the port element in the workers.properties file, change the value of the Connector port element to the same value. For example, if the value was changed to 8019:

    <Connector port="8019">

  7. Locate the Server element and its port attribute. Change the value of the port element to one less than the value you specified for the Connector port element. For example, if you changed the Connector port element to 8019, change the Server port element to 8018.

    <Server port="8018">

  8. Save your changes to the server.xml file.

1.3.4 Setting Up Website Files

  1. Locate the websdm-3_1_2_1_xxx.zip file (where xxx represents a specific build number) on the installation media. Extract the contents of this file to the <root>\Lincoln\apps\<instance>\webapps\web_root\ folder (created automatically in the previous task).

  2. Locate the Oracle installation folder on the WebSDM server. For example, D:\oracle\product\11.2.0\db_1.


    Note:

    If the database is running on a machine other than the application server, the Oracle installation folder refers to the path where Oracle client components were installed.

    From within the \jdbc\lib subfolder, copy the following .jar file to the <root>\Lincoln\apps\<instance>\webapps\web_root\WEB-INF\lib folder, overwriting the existing file, if necessary. If you are using Oracle 10g, locate ojdbc14.jar. If you are using Oracle 11g, locate ojdbc6.jar.


  3. Using Windows Explorer, navigate to the <root>\Lincoln\IIS\conf\ folder. Review the file paths in the iis_redirect.reg file using a text editor. Edit the file paths, if necessary, to reflect any changes you made for your installation.

  4. Double-click the iis_redirect.reg file. Click Yes, and then click OK.


    Note:

    This updates the registry. Perform this step even if you did not make any changes to the iis_redirect.reg file.

  5. In the same folder, double-click the iis_cipher_configuration.reg file. Click Yes, and then click OK.


    Note:

    This disables weak IIS ciphers.

1.3.5 Installing an Encryption Key

  1. Navigate to the folder <root>\Lincoln\apps\<instance>\webapps\web_root\WEB-INF\classes.

  2. Check for existence of the file license.config. If it exists, rename it to another name, such as license.old.

  3. Navigate to the folder <root>\Lincoln\apps\<instance>\bin.

  4. Use a text editor to open the file generate_keys.bat and review the values of INSTALL_ROOT and APPLICATION_DIR. If changes are needed, edit and save the file.

    1. If the value of <instance> is other than websdm, change the value of the APPLICATION_DIR to the value of <instance>.

    2. If the value of <root> is other than the c drive, change the value of the INSTALL_ROOT to the value of <root>.

  5. (Windows 2008 server) Right-click the generate_keys.bat file, and then select Run as administrator.

    or

    (Windows 2003 server) Double-click the generate_keys.bat file.

  6. Examine the script output. Verify that the last two lines are:

    [INFO] Generating <root>\Lincoln\apps\<instance>\webapps\web_root\WEB-INF\classes\license.config

    [INFO] Done

  7. When prompted, press any key.

  8. If the last two lines of script output are not as indicated, correct the error condition and repeat this procedure.

1.3.6 Optional: Making WebSDM the Default Application

If <is_IIS_default_app> is true (WebSDM is to be the default IIS application), perform the following steps:

  1. Open the <root>\Lincoln\apps\<instance>\webapps\web_root\index.html file in a text editor, such as Notepad.

  2. Insert <instance> into the URL in this line. For example, if the value of <instance> is websdm, change:

    <META HTTP-EQUIV=REFRESH CONTENT="0; URL=./login.jsp">

    to:

    <META HTTP-EQUIV=REFRESH CONTENT="0; URL=/websdm/login.jsp">

  3. Save your changes.

  4. Copy the <root>\Lincoln\apps\<instance>\webapps\web_root\index.html file to the C:\inetpub\wwwroot directory.

1.3.7 Configuring IIS

1.3.7.1 Configuring IIS for Windows 2008

This section is for Windows 2008 Server only.

  1. Launch Server Manager and expand the Roles node.

  2. Add the Web Server (IIS) role if it does not already exist.

  3. Add Services to the role:

    1. Right-click Web Server (IIS), and select Add Role Services.

    2. Select the following additional role services under Application Development:

      ISAPI Extensions

      ISAPI Filters

    3. Click Next.

    4. Click Install.

    5. Click Close.

  4. Click Start > Administrative Tools > Internet Information Services Manager.

  5. Select the first node in the tree control.

  6. Under IIS, in the middle pane, double click Mime Types. In the list of registered file types, check for the presence of the .app file extension.

  7. If the .app extension is not already listed, click Add. For Extension, type .app. For MIME type, type text/plain. Click OK.

  8. In the list of registered file types, check for the presence of the .wsdl file extension.

  9. If the .wsdl extension is not already listed, click Add. For Extension, type .wsdl. For MIME type, type text/plain. Click OK.

  10. If <is_first_install> is false, skip to step 24. If <is_first_install> is true, select your server name in the Connections pane.

  11. Under IIS, double-click ISAPI and CGI Restrictions.

  12. On the Actions pane, click Add.

  13. On the ISAPI or CGI Restrictions pop-up, complete the following:

    ISAPI or CGI Path: <root>\Lincoln\IIS\bin\isapi_redirect.dll

    Description: jakarta

  14. Select Allow extension path to execute, and click OK.

  15. On the Connections pane under Sites, under your server name, select Default Web Site.

  16. In the IIS section of the middle pane, double-click ISAPI Filters.

  17. On the Actions pane, click Add.

  18. Add a filter with the following characteristics, and click OK.

    Filter name: jakarta

    Executable: <root>\Lincoln\IIS\bin\isapi_redirect.dll

  19. Right-click Default Web Site, and select Add Virtual Directory. Type the following, and then click OK.

    Alias: jakarta

    Physical Path: <root>\Lincoln\IIS\bin

  20. From the Connections pane, select jakarta and, in the IIS section of the middle pane, double-click Handler Mappings.

  21. In the Actions pane, select Edit Feature Permissions.

  22. Ensure that Read, Script, and Execute are selected. If they are not, select them and click OK.

  23. Right-click Default Web Site and select Add Virtual Directory. Type the following, and click OK.

    Alias: <instance>

    Physical Path: <root>\Lincoln\apps\<instance>\webapps\web_root

  24. From the Connections pane, select <instance> and, in the IIS section of the middle pane, double-click Handler Mappings.

    1. In the Actions pane, select Edit Feature Permissions.

    2. Ensure that Read and Script are selected. If not, select them and click OK.

  25. From the Connections pane, select <instance> and then, in the IIS section of the middle pane, double-click Default Document.

    1. From the list of documents, select index.html document and use the Move Up function until index.html is at the top of the list.

    2. If prompted to confirm the changed list order, click Yes.

    3. If document index.html is not listed, create it using the Add button. Move this document to the top of the list.

    4. In the Actions pane, verify that Disable appears as an action. If Enable appears instead, click it and verify that Disable appears as an action.

  26. On the Connections pane in the Sites folder under your server name, select Default Web Site.

    1. In the IIS section of the middle pane, double-click Error Pages.

    2. On the Actions pane, click Edit Feature Settings.

    3. On the Edit Error Pages Settings dialog, select Detailed errors.

    4. Click OK.

  27. Select Start > Control Panel > System and Security > Administrative Tools / Services.

  28. Right-click the World Wide Web Publishing Service, and click Restart.

    Alternatively, run the following commands at a DOS prompt:

    C:\ net stop w3svc

    C:\ net start w3svc

1.3.7.2 Configuring IIS for Windows 2003

This section is for Windows 2003 Server only.

  1. Select Start > Settings > Control Panel > Administrative Tools > Internet Services Manager.

  2. If <is_first_install> is false, (<root>\Lincoln already exists), expand the tree and skip to step 12 of this procedure.

  3. Right-click the first node in the tree control. Select Properties. In the MIME types section, click MIME Types.

    1. In the list of registered file types, check for the .app file extension. If the .app extension is not already listed, click New, type .app for Extension, and text/plain for MIME type.

    2. In the list of registered file types, check for the .wsdl file extension. If the .wsdl extension is not already listed, click New, type .wsdl for Extension, and text/plain for MIME type.

  4. To save your changes, click OK.

  5. Expand the tree. Right-click Default Web Site, and select Properties.

  6. On the ISAPI Filters tab, click Add.

  7. Add a filter with the following characteristics:

    Filter Name: jakarta

    Executable: <root>\Lincoln\IIS\bin\isapi_redirect.dll

  8. If <is_IIS_default_app> is true (WebSDM is the IIS default application), complete the following. Otherwise, continue with step 9.

    1. Select the Documents tab.

    2. Select the Enable Default Document (or Enable Default Content Page) checkbox, and set index.html as the top-most document.

    3. When you exit the Properties dialog for Default Web Site, if you do not want to keep the default document settings for other virtual directories (for example, printers), click OK.

  9. Right-click Default Web Site and select New > Virtual Directory. Set up a virtual directory for jakarta, as follows:

    Alias: jakarta

    Directory: <root>\Lincoln\IIS\bin

    Access Permissions: Select the Read and Execute checkboxes only.

  10. Add a web service extension:

    1. Select the Web Services Extensions node.

    2. Click the Add a new Web service extension link.

    3. Set Extension name to jakarta.

    4. Add the <root>\Lincoln\IIS\bin\isapi_redirect.dll file to the required files list.

    5. Select the Set extension status to Allowed checkbox.

    6. Click OK.

  11. Right-click Default Web Site and select New/Virtual Directory. Use the wizard to set up a virtual directory for WebSDM, as follows:

    Alias: <instance>

    Directory: <root>\Lincoln\apps\<instance>\webapps\web_root

    Access Permissions: Select the Read checkbox only.

  12. Make index.html the default document for the <instance> virtual directory.

    1. Right-click the <instance> virtual directory and select Properties.

    2. Select the Documents tab, select the Enable default content page checkbox, and set index.html as the top-most default document. (If document index.html is not listed, create it using the Add button, and move the document to the top of the list.)

    3. Click OK.

  13. Select Start > Control Panel > Administrative Tools > System and Security > Services. Right-click the World Wide Web Publishing Service, and then click Restart.

    Alternatively, run the following commands at the DOS prompt:

    C:\ net stop w3svc
    C:\ net start w3svc
    

1.3.8 Optional: Setting the System Timeout Interval

By default, WebSDM user sessions automatically time out after 30 minutes of inactivity. You can change this timeout interval to another value.

  1. Use a text editor, such as Notepad, to open: <root>\Lincoln\apps\<instance>\webapps\web_root\WEB-INF\web.xml.

  2. Locate the <session-timeout> element.

  3. Set the session timeout to another value (in minutes). For example:

    <session-timeout>15</session-timeout>

  4. Save your changes to the web.xml file.


    Note:

    If you are using Single Signon (SSO), the WebSDM timeout must be set to be longer than the SSO timeout.

1.3.9 Installing the websdm Service

For Windows 2003 SP2 only, update the icacls.exe utility by following the instructions located at http://support.microsoft.com/kb/943043.

  1. If using a WebSDM instance name other than websdm, edit the file:

    <root>\Lincoln\apps\<instance>\bin\install_service.bat

    1. Change the value of SERVICE_NAME from websdm to the value of <instance>.

    2. Change the value of the APPLICATION_DIR from websdm to the value of <instance>.

  2. If using a WebSDM instance name other than websdm, edit the file:

    <root>\Lincoln\apps\<instance>\bin\uninstall_service.bat

    Change the value of SERVICE_NAME from websdm to the value of <instance>.

  3. (Windows 2008 server) Right-click the <root>\Lincoln\apps\<instance>\bin\install_service.bat file, and then select Run as administrator.

    (Windows 2003 server) Double-click the <root>\Lincoln\apps\<instance>\bin\install_service.bat file.

  4. After install_service.bat has completed, inspect the transcript. There should be no errors. When you have finished, press any key.

  5. (Windows 2008 server) Open the Start menu, select Administrative Tools, then Server Manager. Expand Configuration > Local Users and Groups > Users.

    or

    (Windows 2003 server) Right-click the server's desktop My Computer icon and select Manage. Expand System Tools > Local Users and Groups > Users.

  6. Right-click <instance>_app and select Set Password.

  7. In the Set Password for <instance>_app dialog box, click Proceed.

  8. Change the password to satisfy site password policy restrictions, and then click OK.

  9. (Windows 2008 server) Click Services.

    or

    (Windows 2003 server) Expand the Services and Applications directory, and then click Services.

  10. Right-click the service named <instance> and select Properties.

  11. On the Log On tab, select the This account radio button, and then clear the password fields and enter the password that you just changed.

  12. On the Recovery tab, for both First Failure and Second Failure, select Restart the Service.

  13. (Windows 2008 server) On the General tab, set Startup type to Automatic (Delayed Start).


    Note:

    This allows time for the database service to start before the WebSDM application service.

  14. Click OK.

1.4 Install Supporting Software

1.4.1 Installing a Disk Space Monitoring Utility

To support monitoring of disk space allocated to Oracle tablespaces used by WebSDM, you install the lt_DiskUtil.dll utility, a standalone windows executable.

This process is required if the Oracle database is running on a Windows server and no related products were previously installed. If the Oracle database is running on a UNIX host, or if any related products are already installed on the server, continue to Section 1.4.2, "Optional: Installing a SAS File Viewer".

  1. Use Windows Explorer to view the installation media and locate the appropriate file:

    • 32-bit server: lt_DiskUtil.dll

    • 64-bit server: lt_DiskUtil_x64.dll

  2. Copy this file to C:\WINDOWS\system32.

  3. 64-bit server: Rename the file from:

    lt_DiskUtil_x64.dll

    to:

    lt_DiskUtil.dll


    Note:

    If WebSDM and Oracle are not installed on the same server, the WebSDM and Oracle servers must map the same drive letter for the Oracle data files for the disk space monitoring utility to function correctly.

1.4.2 Optional: Installing a SAS File Viewer

The SAS System Viewer or SAS Universal Viewer application is useful for inspecting the content of the SAS transport files that constitutes the data sources for WebSDM studies. This file viewer software is distributed without charge by SAS.

  1. Use a Web browser, such as Internet Explorer, to navigate to http://support.sas.com/downloads/index.htm.

  2. Choose the SAS System Viewer or SAS Universal Viewer appropriate to your client operating system.

  3. Follow the installation instructions provided for the download.

1.5 Configure WebSDM Application Properties Files

The website.properties file stores database connection information and points to the location of the executables. You review and modify this information as needed for your installation.

  1. Navigate to <root>\Lincoln\apps\<instance>\webapps\web_root\WEB-INF\classes\.

  2. Use an editor, such as Notepad, to open the website.properties file.

  3. Review the settings for the following values in the file:

    user=websdm
    pass=<password>
    connect=jdbc:oracle:oci8:@websdm
    
  4. If the value of <websdm_master_acct> is something other than websdm, change the value of user to that value.

  5. Change the password to the value of <websdm_master_pass>.


    Note:

    Later, you will configure WebSDM to encrypt this password.

  6. If the value of <ora_net_service> is something other than websdm, change the connect string @websdm to that value.


    Note:

    With Oracle 10g and Oracle 11g, use oci8.

  7. Examine the drive and directory specified for logfile= and process_dir=. Modify these if needed, keeping in mind that the parent directory for \logs and \procs is created as the WORKING_DIR by running script set_permissions.bat (see Section 1.7, "Set File Permissions".) The parent directory name should be set to the value of <instance>.

  8. Review the location specified for the R executable:

    r_path=C:/Program Files/R/R-2.13.2/bin/R.exe

    If necessary, modify this to match the location you specified when you installed R. For example, on a 64-bit server, the 32-bit version of R might have been installed by default to C:/Program Files (x86)/R/R-2.13.2/bin/R.exe.

  9. Review the location specified for the Oracle sqlldr executable:

    sqlldr_path=D:/oracle/product/11.2.0/dbhome_1/BIN/sqlldr.exe

    If necessary, modify this to the correct location.

  10. Review the default path provided for tablespace_datafileSpec. If necessary, modify the path to match your Oracle environment.

1.6 Add Manifest Entries and Sign JAR Files

If you do not perform these steps, security-related dialog boxes appear for end users when they work with DataMontage graphs in applet mode, and DataMontage may even be completely blocked by a client machine's security settings. To perform these steps, you need access to the Java jar and jarsigner utilities in the Java jdk1.6\bin directory (jdk1.6\bin must be in the application server's PATH), and you must have access to your company's jar signing process.

  1. From the <root>:\Lincoln\apps\<instance>\webapps\web_root\AppJars\DataMontage23\ folder, copy files lti.jar and DataMontage.jar to a temporary folder such as C:\temp\UpdateJarManifest\.

  2. Update the manifest is both JAR files:

    1. In the temporary folder where you copied the JAR files, create a text file and save it. The example later in this procedure uses the name MANIFEST.MF.

    2. Insert two lines of text in the file, supplying the fully qualified domain name of the Windows application server (or its IP address) and the connection port on each line. For example:

      Codebase: <server_name>.example.com:80
      Caller-Allowable-Codebase: <server_name>.example.com:80
      

      Alternatively you can use an asterisk (*) as a wildcard for the most specific part of the domain name, but this will result in a less secure deployment.

    3. Be sure to insert a line break after the second line of text. Then save and close the file.

    4. Open a DOS Command window and navigate to the temporary folder containing the JAR files and the text file you created.

    5. At the DOS prompt, issue the following commands, replacing MANIFEST.MF with the name of the text file you created:

      jar -ufm DataMontage.jar MANIFEST.MF
      jar -ufm lti.jar MANIFEST.MF
      
  3. You must now sign the modified JAR files before they will work correctly within the WebSDM application. Use your company's jar signing process to perform this signing task, which probably includes using Java's jarsigner utility. (See http://docs.oracle.com/javase/7/docs/technotes/tools/windows/jarsigner.html for additional information about this utility.)

  4. Copy both signed JAR files to the <root>:\Lincoln\apps\<instance>\webapps\web_root\AppJars\DataMontage23\ folder, replacing the original files.

  5. Finally, copy the signed DataMontage.jar file to the <root>:\Lincoln\apps\<instance>\webapps\web_root\WEB-INF\lib\folder, replacing the original file. (You do not need a copy of lti.jar in this location.)

1.7 Set File Permissions

  1. Navigate to the folder <root>\Lincoln\apps\<instance>\bin.

  2. Use a text editor to open the file set_permissions.bat and review the values of SERVICE_NAME, INSTALL_ROOT, APPLICATION_DIR, and WORKING_DIR:

    1. If the value of <Instance> is other than websdm, change the values of SERVICE_NAME, APPLICATION_DIR, and WORKING_DIR to the value of <instance>.

    2. If the value of <root> is other than the C drive, change the value of the INSTALL_ROOT to the value of <root>.

    3. If the D drive is not an acceptable location for the working directory, change the drive for WORKING_DIR to an acceptable drive.

    4. Verify that CATALINA_HOME is defined correctly.

  3. Optionally, grant permissions to a Windows group of non-administrator users who might require access to the log files and \web_root folder.

    1. While editing the set_permissions.bat file, locate the following lines:

      REM -
      REM - Local Administrators group
      REM - 
      REM SET ADMIN_GROUP=Study Operators
      
    2. Remove REM from the REM SET ADMIN_GROUP line.

    3. Replace Study Operators with the appropriate Windows user group that requires access.

  4. If changes are needed, edit, save, and close the file.

  5. (Windows 2008 server) Right-click the set_permissions.bat file, and then select Run as administrator.

    (Windows 2003 server) Double-click the set_permissions.bat file.

  6. When prompted, press any key.

  7. Examine the log file <root>\Lincoln\apps\<instance>\logs\set_permissions.log for errors. If there are errors, contact Oracle.

1.8 Create the Submissions Folder

  1. Create a directory, <submissions_folder>, to serve as the root for clinical data submissions. This directory will later be specified on the Site Options page in WebSDM as the highest level directory within which users can browse for data.

    • If <submissions_folder> will be located on the same drive as the WORKING_DIR specified in the previous procedure, it should not be set at or below WORKING_DIR.

    • If <submissions_folder> will be located on the same drive as the WebSDM application software, it should not be set at or below <root>\Lincoln\apps\<instance>.

    • The recommended <submissions_folder> location is at or below D:\ClinicalData.

  2. The Windows <instance>_app user (created in section 1.3.9) needs Read and Write permissions on the new directory. To ensure that these permissions are in place, right-click the <submissions_folder> directory in Windows Explorer. Select Properties, the Security tab, and the <instance>_app user.

  3. Save any changes.

1.9 Start the websdm Service

  1. In the Services Control Panel, right-click the <instance> Windows service, then click Start or, if the service is already running, click Restart.

    Alternatively, execute the net start command in a Command window. For example, if the value of <instance> is the default websdm:

    C:\> net start websdm

  2. In the Services Control Panel, right-click the World Wide Publishing Service, then click Start or, if the service is already running, click Restart.