Product Developer's Technical Guide by guy21

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									                                                 C3PR V2
                                   Installation Guide




                                                   Updated January 9, 2009

caBIG™ is an initiative of the National Cancer Institute, NIH, DHHS
Development Team(s)
                                      Installation
      Development                                      Program Management
                                    Documentation
Kruttik Aggarwal2            Priyatam Mudivarti2     Bob Annechiarico1

Manav Kher2                  Manav Kher2             Jamie Cuticchia1

Priyatam Mudivarti2                                  Patrick McConnell1
                2                                                    2
Ram Chilukuri                                        Ram Chilukuri
                      2
Ramakrishna Gundala


1
 Duke Comprehensive Cancer   2
                                 SemanticBits
Center




                                                                            ii
                                                                                                                                     About This Guide
                                   Table of Contents

Chapter 1             About This                      Guide                1
      Overview of the Guide ............................................................................................................................... 1
      Audience .................................................................................................................................................... 1
      Getting Help............................................................................................................................................... 1
      Organization of This Guide ....................................................................................................................... 1
      Relevant Documents .................................................................................................................................. 2
      Document Text Conventions ..................................................................................................................... 2

Chapter 2             Hardware and Software Requirements ................................................................................ 5
      Overview of C3PRv2 ................................................................................................................................. 5
      Support for C3PRv1................................................................................................................................... 5
      Hardware Requirements ............................................................................................................................ 5
      Software Requirements .............................................................................................................................. 6
        Required Software ................................................................................................................................. 6
        Optional Software ................................................................................................................................. 7

Chapter 3             Installing C3PRv2 using the Graphical Installer ............................................................... 11
      Installation Overview ............................................................................................................................... 11
      Installation Instructions............................................................................................................................ 11
      Common Problems during Installation .................................................................................................... 16

Chapter 4             Installing Manually............................................................................................................... 17
      Installation Overview ............................................................................................................................... 17
      Installation Instructions............................................................................................................................ 17
         Download the C3PRv2 codebase ........................................................................................................ 17
         C3PRv2 Configuration ........................................................................................................................ 18
         Setting up the Database....................................................................................................................... 20
         Building/Deploying the Code (Ant) ..................................................................................................... 20

Chapter 5             Securing Tomcat ................................................................................................................... 21
      Overview ................................................................................................................................................. 21
      Instructions for Securing Tomcat............................................................................................................. 21

Chapter 6             Running C3PRv2 .................................................................................................................. 23
      Overview ................................................................................................................................................. 23
      Running C3PRv2 ..................................................................................................................................... 23

Appendix A               Configuring Multiple Tomcat Servers ............................................................................. 25
      Setting Tomcat Home .............................................................................................................................. 25

Appendix B               Setting up CVS clients ....................................................................................................... 27
      Setup Tortoise CVS client ....................................................................................................................... 27
         Downloading and Installing TortoiseCVS........................................................................................... 27
         Specifying the connection parameters and checking out c3prv2_elaboration_iteration3................... 29
      Setup Eclipse CVS Perspective ............................................................................................................... 31


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                                         iv
                                                                              About This Guide


Chapter 1 About This Guide

Overview of the Guide
       This installation guide outlines the supported configurations, prerequisites, installation,
       setup, and configuration of the application and databases for C3PRv2. The steps and
       screenshots included in this guide are Windows/Linux specific. If you are using a
       different platform, then modify the information as appropriate for your system.
       Topics in this chapter include:
               Audience
               Getting Help
               Organization of This Guide
               Relevant Documents
               Document Text Conventions


Audience
       The primary audience of this guide is the programmer responsible for installing C3PRv2.
       For more information about C3PRv2, see the C3PRv2 User‟s Guide.


Getting Help
       E-mail c3prv2-support@gforge.nci.nih.gov for installation support and general C3PR
       technical support queries.


Organization of This Guide
       This guide includes is divided into different sections that describes the installation
       process. The following table briefly describes each chapter.

            Chapter                                     Chapter Contents
Chapter 1                     Provides an overview of the guide
Chapter 2                     Describes the support for C3PRv1 and then discusses sthe hardware
                              and software requirements
Chapter 3                     Provides the installation instructions if you use the graphical interface;
                              includes troubleshooting help if you run into problems
Chapter 4                     Provides the installation instructions if you want to manually install and
                              set up the software
Chapter 5                     Describes how to Secure Tomcat
Chapter 6                     Provides information on running C3PRv2
Appendix A                    Provides information on setting up multiple Tomcat Servers
Appendix B                    Provides information on setting up a CVS client

1
Table 1-1 Chapter Outline of the Installation Guide


Relevant Documents
        This Installation Guide addresses C3PRv2 installation. Additional information about
        C3PRv2 architecture, design, user-orient overview and examples, ad tool-specific guides
        can be found in:

               Document                                         Location
C3PRv2 User‟s Guide
C3PRv2 Use Cases


Table 1-2 List of relevant documents


Document Text Conventions
        The following table shows various typefaces to differentiate between regular text and
        menu commands, keyboard keys, and text that you type. This illustrates how
        conventions are represented in this guide.

        Convention                              Description                  Example




                                                                                        2
                                                                             About This Guide
Bold & Capitalized Command       Indicates a Menu command              Admin > Refresh
Capitalized command >            Indicates Sequential Menu
Capitalized command              commands
TEXT IN SMALL CAPS               Keyboard key that you press           Press ENTER
TEXT IN SMALL CAPS     + TEXT    Keyboard keys that you press          Press SHIFT + CTRL and then
IN SMALL CAPS                    simultaneously                        release both.

Special typestyle                Used for filenames, directory         URL_definition ::=
                                 names, commands, file listings,       url_string
                                 source code examples and anything
                                 that would appear in a Java
                                 program, such as methods,
                                 variables, and classes.
Boldface type                    Options that you select in dialog     In the Open dialog box, select the
                                 boxes or drop-down menus.             file and click the Open button.
                                 Buttons or icons that you click.
Italics                          Used to reference other documents,    caCORE Software Development
                                 sections, figures, and tables.        Kit 1.0 Programmer’s Guide
Italic boldface type             Text that you type                    In the New Subset text box, enter
                                                                       Proprietary Proteins.
Note:                            Highlights a concept of particular    Note: This concept is used
                                 interest                              throughout the installation manual.
Warning!                         Highlights information of which you   Warning! Deleting an object will
                                 should be particularly aware.         permanently delete it from the
                                                                       database.
{}                               Curly brackets are used for           Replace {root directory} with its
                                 replaceable items.                    proper value such as c:\cabio
Table 1-3 Document Conventions




3
                                                Hardware and Software Requirements




Chapter 2 Hardware and Software
Requirements
    Topics in this chapter include:
          Overview of C3PRv2
          Support for C3PRv1
          Hardware Requirements
          Software Requirements


Overview of C3PRv2
    C3PR is a central participant registry and underlying database that will allow the
    management of patient clinical trials registration information and protocol information
    across studies, sites, systems and organizations.
    C3PR operates on its own data tables for Patient, Study, and Registration Data. The
    implementation of the system will preserve the fundamental independence of the storage
    of the patient and registration information from the scientific and research data. System
    identifiers will be used to relate patient demographics and identifying information to
    eligibility, medical or treatment data.


Support for C3PRv1
    Although C3PRv2 is based on the underlying functionality of C3PRv1, much of C3PRv2
    has been redesigned with more accepted open source technologies to meet the current
    standards for interoperability and web application development in alignment with caBig
    initiative. Hence we are not supporting C3PRv1 as a part of C3PRv2 development.
    However, critical functionality and use cases would be reused/refactored into C3PRv2,
    wherever possible.


Hardware Requirements
    The hardware requirements for C3PRv2 are minimal because C3PRv2 is a lightweight
    web application, not intended to have a very large code base. See the following table for
    the minimum hardware requirements.




5
Processor                 Pentium PIII, above 1.5 GHz
                          Minimum 512MB. (testing)
RAM
                          2 GB recommended
                          Windows 2000,XP, Linux Mac
Operating System
                          OS X 10.4.x
Hard Disk Space           Minimum 500MB free space
Table 2-1 Hardware requirements


Software Requirements
Required Software
        C3PRv2 does not include all the necessary packages. Download and install the
        additional software needed, as listed in Table 2-2).

 Software Name            Version         Description                          URL
Java Software Devel-     JDK 5.0       The J2SE Software      http://java.sun.com/javase/downloads/ind
opment Kit (SDK)         Update 11     Development Kit        ex_jdk5.jsp
                         or higher     (SDK) supports
                                       creating J2SE
                                       applications
Oracle 9i/10g            9i/10g        Oracle is a            http://www.oracle.com/technology/softwa
Database **                            commercially-          re/products/database/oracle10g/index.ht
                                       available relational   ml
                                       database
                                       management
                                       system (RDBMS)
                                       that can be used on
                                       all major operating
                                       systems
PostGreSQL**             8.2           PostgreSQL is a        http://www.postgresql.org/ftp/source/v8.2
                                       powerful, open         /
                                       source relational
                                       database system. It
                                       runs on all major
                                       operating systems
Globus Toolkit***        4.0.3         Globus toolkit is an   http://www.globus.org/toolkit/downloads/
                                       open source WSRF-      4.0.0/#wscore_bin
                                       compliant web
                                       services java
                                       container. Only the
                                       Java ws-core source
                                       version is needed




                                                                                              6
                                                             Hardware and Software Requirements


    Software Name           Version          Description                             URL
Tomcat Web Server*         5.0.28          Open source servlet     http://archive.apache.org/dist/tomcat/tom
                                           container               cat-5/v5.0.28/bin/jakarta-tomcat-
                                                                   5.0.28.zip


Ant*                       1.6.5           Ant is used for         http://archive.apache.org/dist/ant/binarie
                                           Building the C3PR       s/
                                           application
* Included with the Graphical installer
**Either Oracle OR PostGreSQL (not both) is required as an RDBMS for the C3PRv2 application. Note
that C3PRv2 doesn‟t support SQL Server (which has been supported by C3PRv1)
*** Installation occurs in step 3 of the Graphical Installation and step 2 of Download the C3PRv2
codebase.
     Table 2-2 Required software and technology for C3PRv2

         Note: Drivers for Oracle 9i/10g and PostGreSQL are included with C3PRv2. If you are
         using a different version of Oracle, you must obtain the appropriate drivers. JDBC
         drivers can be downloaded from the Sun Developer Network at
         http://developers.sun.com/product/jdbc/drivers/index.html, or from the individual vendors‟
         sites (for example, the Oracle 9i driver classes12.zip can be downloaded from
         http://www.oracle.com/technology/software/tech/java/sqlj_jdbc/htdocs/ jdbc817.html).
         These drivers should be placed in the {project_home}/lib directory and the
         {CATALINA_HOME}/common/lib directory to enable connection to the appropriate
         database. In addition, some manual modification of the Hibernate configuration files
         may be necessary.

Optional Software
         C3PRv2 supports some optional software, which is not included with the SDK. Table 2-3
         lists this software.

    Software         Version              Description                         URL
     Name




7
Eclipse IDE        3.2           An open platform for tool      http://www.eclipse.org/downlo
                                 integration which              ads/ index.php
                                 provides tool developers
                                 with flexibility and control
                                 over their software
                                 technology. We
                                 recommend the use of
                                 eclipse for general
                                 purpose development,
                                 build, test and
                                 synchronize with CVS
                                 repository
Tortoise CVS                     An alternate CVS client if     http://prdownloads.sourceforge
Client                           eclipse is not installed       .net/tortoisecvs/TortoiseCVS-
                                 (Eclipse has a much            1.8.30.exe
                                 simpler, rich CVS
                                 synchronization feauture)
   Table 2-3 Optional software to use with C3PRv2




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                                             Hardware and Software Requirements

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9
                                                Installing C3PRv2 using the Graphical Installer



Chapter 3 Installing C3PRv2 using the
Graphical Installer
       Topics in this chapter include:
              Installation Overview
              Installation
              Common Problems (FAQ)


Installation Overview
       C3PRv2 has been tested with the operating systems and hardware specified in Table
       2-1 of this guide. We cannot guarantee C3PRV2 will work If you are using variations of
       these operating systems and/or hardware.
       This chapter describes the installation using the graphical installer. If you want to install
       manually, see Chapter 4.


Installation Instructions
       C3PRV2 has a graphical installer to ease the installation process. Follow the instructions
       below to install C3PRv2. After completing these steps, continue to Chapter 5.

    Step                                             Action
           Download the latest version of the installer from Gforge.
1          Note: There are two versions of the GUI installer – Online and Offline.
           The Online version is very compact in size (<2MB) but requires that you be connected to
           the Internet during the installation. The online installer downloads required software during
           the install process. The online installer will also download the latest release of C3PRv2.
           The offline installer packages all the required software and is fairly large download, but can
           be used in situations where Internet connection is not available or is severely limited
           (firewall). The offline installer will have to be downloaded for each new release of C3PRv2.
           The online GUI installer is recommended.
2          Delete your existing C3PRv2 web application (if a previous version was installed). This will
           usually mean deleting $CATALINA_HOME/webapps/c3prv2 directory.
3          Start the Globus install by unzipping the downloaded archive into a local folder (henceforth
           referred to as {globus_root_folder}




11
    Step                                              Action
4          Verify that the following environment variables are set

                  JAVA_HOME (pointing to the root directory of the Globus installation)

                  GLOBUS_LOCATION (pointing to {globus_root_folder})
           Also, ensure that your PATH statement includes the locations of the Java binaries.
           Optionally, set CATALINA_HOME if you wish to use an existing tomcat installation.
           Otherwise, the installer will install one for you.


           To set environment variables in Windows:
           Select My Computer > Properties (from the shortcut menu) > Advanced tab.
           Click the Environment_Variables button.
           In the New System Variable dialog box, add the Variable and Variable Value.
           Examples:

                  Variable = JAVA_HOME

                  Value = C:\j2sdk1.5.0_11

                  Variable=GLOBUS_LOCATION;

                  Value=C:\ws-core-4.0.3; (add to the beginning of existing value)


           To do this in Unix/Mac:
           $ export JAVA_HOME=/usr/java..1.5
           $ export GLOBUS_LOCATION=/usr/local/ws-core-4.0.3
           $ export CATALINA_HOME =/usr/apache-tomcat-5.0.28
5          Launch the installer by double-clicking on the installer jar file (in windows and Mac) or by
           running the following command (applies to any OS)
           java –jar c3prv2-installer-1.0.jar
           Note: Do not launch the jar using Java Jar Launcher tool (double-clicking on the file). This
           does not use the environment variables you set in Step 4 (see Common Problems during
           Installation)


6          This will launch the graphical installation wizard. Follow the installation wizard to configure
           and install C3PRv2. Most screens during the installation process are self explanatory,
           some of the crucial steps are explained below.




                                                                                                  12
                                               Installing C3PRv2 using the Graphical Installer


    Step                                            Action
7




           You can let the installer deploy and configure Tomcat or chose an existing installation of
           tomcat on your system. If you choose to use an existing tomcat, see the Tomcat SSL How
           To section to configure the tomcat server for the HTTPS protocol (C3PRv2 uses SSL to
           secure client server interaction). You may also want to see Appendix A.




13
    Step                                             Action
8          The most crucial step is to configure a database to use for C3PRv2. You will need to
           create an empty database in Oracle/PostgreSQL and the installer will run the database to
           create/update scripts.




           In the above example, an empty database c3pr_dev exists in the local PostgreSQL
           database.
           Tip: Default values should be acceptable for most steps during the installation.




                                                                                              14
                                                 Installing C3PRv2 using the Graphical Installer


    Step                                              Action
9          The following screen shows the configuration for setting an outgoing mail server. This is
           needed to send administration emails to users. C3PRv2 sends out automatic emails to
           users (like new account creation mails etc).




           This is optional. Not filling out the correct information will mean that administrative emails
           won‟t be sent.
9          If you used the installer to install a new Tomcat then set your CATALINA_HOME
           environment variable (See Step 3 for details). If not, continue to Step 12.
10         Open acommand prompt and change the directory to {CATALINA_HOME}\bin
11         Run the following command to start tomcat server
           startup.bat (windows)
           startup.sh (unix)




15
  Step                                                 Action
 12         After your web application server has completely finished starting, go to the following URL:
            http://localhost:9080/c3pr
            NOTE: The installer‟s version of Tomcat runs on port 9080. Your existing Tomcat might be
            on a different URL/Port


 13         At this point your installation should be complete.
            See Common Problems during Installation if you encounter problems during installation.
            You may also send email to c3prv2-support@gforge.nci.nih.gov for support.




Common Problems during Installation

Problem 1: My installation failed with the message “class sun.tools.javac.Main not on the
classpath. Perhaps JAVA_HOME does not point to the JDK. It‟s currently set to c:/Program
Files/Java/jre_1.5.0_11”


Answer: This can happen when installing in the Microsoft Windows Operating system. First
ensure that you are running the installer from the command prompt (as described in Step 4 of
the Installing C3PRv2 using the Graphical Installer section).
If the above solution does not work, then copy the tools.jar file from $JAVA_HOME/lib/ to
c:/Program Files/Java/jre_1.5.0_11/lib/ext directory. If the $JAVA_HOME/jre/lib/ext does not
exist then go ahead and create it. Re-run the installer after doing this.
Note: c:/Program Files/Java/jre_1.5.0_11 can be different on your system


Problem 2: My installation failed at the final step with the message
“edu.northwestern.bioinformatics.bering.Migration’


Answer: This means the database create/update scripts did not work. Please check the
database URL you entered in the installer. Also, make sure that an empty database is available
to the installer. The installer can created the tables etc. but not create a database.
Problem: My installation failed at the final step with the message
“FATAL ERROR: c3pr_dev datbase does no exist”


Answer: This implies that you do not have an empty database created as instructed in Step 6 of
the Installing C3PRv2 using the Graphical Installer Section.




                                                                                                16
                                                                            Installing Manually



Chapter 4 Installing Manually
       Topics in this chapter include:
              Installation Overview
              Installation Instructions
           o   Download C3PRv2 codebase
           o   C3PR Configuration
           o   Setup the Database
           o   Build/Deploy the code (ant)


Installation Overview
       C3PRv2 has been tested with the operating systems and hardware specified in Table
       2-1 of this guide. We cannot guarantee C3PRV2 will work If you are using variations of
       these operating systems and/or hardware.
       This chapter describes the manual installation. If you want to install using the graphical
       installer, see Chapter 3.
       After completing these steps, continue to Chapter 5.


Installation Instructions
       Follow the instructions below to install C3PRv2.

Download the C3PRv2 codebase
       Complete the following steps to download the codebase:

    Step                                             Action
           Using your CVS Command Line Tool (or tortoise), connect to CVS as „anonymous‟ (no
           need of a password) using the following settings:-
1
           Export CVS_RSH=ext

           cvs -d:ext:anonymous@cbiocvs2.nci.nih.gov:/cvsshare/content/gforge/c3prv2 "checkout" "-
           r" "{branch nam}}" "-P" "c3prv2/codebase"
           Note: Replace {branch name} with the current release‟s branch. For example,
           construction_iteration9
           Separate instructions to download and configure cvs clients for Tortoise and Eclipse are
           given in Appendix B.
2          Start the Globus install by unzipping the downloaded archive into a local folder (henceforth
           referred to as {globus_root_folder}




17
    Step                                           Action
3          Verify that the environment variables ANT_HOME and JAVA_HOME, CATALINA_HOME,
           GLOBUS_LOCATION are set and that your PATH statement includes the locations of the
           Ant and Java binaries. For example., PATH should include C:\apache-ant-1.6.2\bin;
           C:\j2sdk1.5.0_11\bin.


           To do this in Windows:
           Select My Computer > Properties (from the shortcut menu) > Advanced tab.
           Click the Environment_Variables button.
           In the New User Variable dialog box, add the Variable and Variable Value.


           Examples:
           Variable = ANT_HOME; Variable Value = C:\apache-ant-1.6.2
           Variable = JAVA_HOME; Variable Value = C:\j2sdk1.5.0_11
           Variable = CATALINA_HOME; Variable Value = C:\apache-tomcat-5.0.28
           Variable = GLOBUS_HOME; Variable Value = C:\ws-core-4.0.3


           To do this in Unix/Mac:
           $ export ANT_HOME=/usr/ant-1.6.2
           $ export JAVA_HOME=/usr/java..1.5
           $ export GLOBUS_LOCATION=/usr/local/ws-core-4.0.3
           $ export CATALINA_HOME =/usr/apache-tomcat-5.5.20



C3PRv2 Configuration
       C3PRv2 consists of multiple sub projects, namely core, web, grid, etc. Each project is
       configured to have a property file to externalize properties needed for the sub project.
       These properties are injected to the application via Spring. C3PRv2 works by
       externalizing these properties from Spring application context to a property file which in
       turn is built via an ant file.
       While installing C3PRv2, the user just needs to set all the properties just one place, ie,
       the build.properties file. This file can be located at
       build.properties - codebase/antfiles/build.properties
       The C3PRv2 example is configured to work with either Oracle 9i/10g or PostGreSQL
       8.2. However, you must assign the appropriate values for the database properties in the
       corresponding section
       Sample contents of this file:




                                                                                         18
                                                                              Installing Manually


                                                                                        Default
         Entry                            Sample Values
                                                                                    Values/Ignore?
datasource.url           jdbc:oracle:thin:@localhost:1521:c3pr - Oracle
                         jdbc:postgresql://localhost:5432/c3pr - PosgreSql
datasource.username      Enter username
datasource.password      Enter password
datasource.schema        (optional), by default it connects to the schema         (optional)
                         same as username
datasource.dialect       org.hibernate.dialect.Oracle9Dialect - Oracle            org.hibernate.dialect.Pos
                                                                                  tgreSQLDialect
                         org.hibernate.dialect.PostgreSQLDialect -
                         PosgreSql
datasource.driver        oracle.jdbc.OracleDriver – Oracle                        org.postgresql.Driver
                         org.postgresql.Driver - PostGreSql
broadcastEnable          false                                                    false (recommended)
esb.brokerUrl            tcp://cbiovdev5032.nci.nih.gov:61618                     Ignore this value
hotlinks.psc             http://                                                  Ignore this value
                         74.93.192.33:8041/studycalendar/pages/schedule
hotlinks.caaers          http:// 74.93.192.33:8030/caaers/pages/ae/list           Ignore this value
hotlinks.c3d             https://octrials-train.nci.nih.gov/opa45/rdclaunch.htm   Ignore this value
grid.idpUrl              https://                                                 Ignore this value
                         74.93.192.33:8446/wsrf/services/cagrid/Authenticati
                         onService
grid.ifsUrl              https://localhost:8443/wsrf/services/cagrid/Dorian       Ignore this value
authorizationSwitch      true, false                                              true (recommended)
log4j.file               /usr/local/apache-tomcat-5.5.23/logs                     Change this value as per
                                                                                  your CATALINA_HOME
                                                                                  installation folder
ctmsi.commons.versio     0.5                                                      Ignore this value
n


         Note: Most of the values with the Urls are currently not needed because Security is not
         enable for this installation. Leave these values with the defaults provided for now. Make
         sure you do not have settings given for both Oracle and PostGreSQL and comment out
         the unwanted lines preceded by “#”.
         Also note that all the above values should not have any trailing spaces before and after.
         For example,
               datasource.dialect=org.hibernate.dialect.Oracle9Dialect

         If you viewed the line above in Word, you‟d notice an extra space after “Dialect”. This is
         a common error that may occur while using copy/paste and should be thoroughly
         checked.

19
Setting up the Database
Do the following to setup/update the C3PRv2 database.
Note: The ant script cannot create a new instance, so an instance of the database (as entered in
C3PRv2 Configuration) should already exist.
cd codebase\antfiles
ant createOrUpdateDatabase

Building/Deploying the Code (Ant)
       Perform the following steps to build your system.

    Step                                             Action
            Open a command prompt and change the directory to codebase\antfiles
1           (Note: You can also use your your IDE‟s built in Ant tool and skip the above test)
            Run the following ant task by executing the following command
2           ant build-web
            ant deploy-webapp
            This deploys the software to the webapp directory of the web application server
            installation specified in the CATALINA_HOME\webapps\c3pr director.




                                                                                                 20
                                                                               Securing Tomcat



Chapter 5 Securing Tomcat
       Topics in this chapter include:
           o   Overview
           o   Securing Tomcat


Overview
       C3PRv2 requires a secure Tomcat container and uses https by default. After the initial
       installation is complete, use the following instructions to secure your Tomcat installation.


Instructions for Securing Tomcat

    Step                                             Action
            Open a command prompt and change the directory to codebase\antfiles
1
            Run the following command:
2           ant tomcat.security
            NOTE: There will be instructions after you run this target on how to edit your
            tomcat.properties
            Next follow these directions on configure SSL for your tomcat (if not completely
            previously)
3
            http://tomcat.apache.org/tomcat-4.0-doc/ssl-howto.html




21
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                                         22
                                                                              Running C3PRv2



Chapter 6 Running C3PRv2
       Topics in this chapter include:
             Overview
             Running C3PRv2


Overview
       C3PRv2 is completely installed and configured and ready to be run. Instructions on
       running C3PRv2 follow.


Running C3PRv2
       Perform the following steps to run the system

    Step                                             Action
            Open a command prompt and change the directory to {CATALINA_HOME}\bin
1
            Run the following command to start tomcat server/bin
2           Startup.bat
            After your web application server has completely finished starting, launch the following
            URL:
3

            http://localhost:8080/c3pr


            The C3PRv2 home page should be displayed.
            Note: The port (8080) could have a different value on your system


       Note: Once the application is running, follow a series of workflows, such as
             Create a Default Study
             Register a Participant for Study (Create a new Participant)

       For a detailed set of instructions for these workflows, refer to the C3PRv2 Use Cases
       document or contact support.
       If the following figure displays in the browser window, you have successfully tested the
       system.




23
24
                                                                      Running C3PRv2




Appendix A Configuring Multiple Tomcat
Servers

     If a Tomcat instant is already running another application, it may be necessary to
     configure multiple Tomcat servers. This requires a few modifications to be made to
     Tomcat.
     It is recommended to install a separate Tomcat instance for C3PR. During installation,
     make a note of the installation directory.


Setting Tomcat Home
     By default, C3PR assumes a single instance of Tomcat installation and looks for a
     CATALINA_HOME environment variable. If another tomcat instance already exists, it is
     probably using this environment variable. To override this, you need to manually set your
     CATALINA_HOME environment variable (see Step 4 of Installation Instructions) to your
     desired Tomcat installation and then run the installation process (GUI or manual).
     Additionally, you can install a new Tomcat instance with the GUI install. This Tomcat will
     run on a non-default http/https port (9080 and 9443). Once your installation is complete,
     reset your CATALINA_HOME environment variable and start/stop the instance.




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                                                                          Running C3PRv2




Appendix B Setting up CVS clients

Setup Tortoise CVS client
        There are 2 steps to this procedure, downloading and installing TortoiseCVS and then
        specifying the connection parameters and checking out c3prv2_elaboration_iteration3.

Downloading and Installing TortoiseCVS
        TortoiseCVS is only available for Windows 95, 98, ME, NT, 2000, XP, and 2003.
1. Go to http://tortoisecvs.org/download.shtml and select the appropriate version of
     TortoiseCVS for your Operating System.
2. This will take you to a SourceForge.net page to complete the download.

        NOTE: If you have a popup-blocker turned on, you may not see the download popup
        window. If this happens either right-click on the yellow bar at the top of the window (as
        shown in the image) and select download file. Or, you can temporarily disable the the
        pop-blocker.




3. Click on Save, select the destination folder if prompted, and save the file.



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4. Navigate to the folder where you saved the installer and double-click on it to start the
   installation.
5. Select English and then click the Next button.




6. Select the destination folder to install TortoiseCVS (click the Browse button and
   navigate to a different folder if you don‟t like the default one) and click the Next
   button.
7. Select Full installation and click the Next button. The setup wizard will copy some
   files and prompt for you to restart the computer to complete the installation.
8. Select restart computer now or restart later and then click on the Finish button.

       NOTE: Save and close all other applications before restarting your computer.




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                                                                        Running C3PRv2


Specifying the connection parameters and checking out

c3prv2_elaboration_iteration3
1. Once you restarted the computer, navigate to the folder, where you want to
     download the c3prv2 codebase, for example, c:\c3prv2.
2. Right-click on the folder and select CVS Checkout.

3. Fill out the Module tab using the information provided in the table below. You can
     see the CVSROOT being automatically built as you enter each field. Make sure there
     are no empty spaces or any other characters in any of the fields.

                             Field                           Value
                 Protocol                    Secure shell(ext)
                 Server                       cbiocvs2.nci.nih.gov
                 Repository folder            /share/content/gforge/c3prv2
                 User name                   anonymous
                 Module                      c3prv2




4. Click on the Revision tab and then select the radio button that corresponds to
     Choose branch or tag.
5. Select c3prv2_elaboration_iteration3 from the drop-down menu and then click OK.

6. If prompted for the password, type anonymous. The TortoiseCVS wizard will start


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   checking out the project from the module you selected (c3prv2). Wait for it to finish
   checking out. It may take a few minutes.




7. If you have successfully checked out c3prv2_elaboration_iteration3 , the tortoise will
   give a message that the download is complete. Click on OK to close the
   TortoiseCVS project checkout window. If for some reason the check out doesn‟t
   start, or stops in the middle, check the connection parameters, network connection
   and go back to step 1.




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                                                                        Running C3PRv2


Setup Eclipse CVS Perspective
        The following steps assume you are familiar with eclipse IDE as your development
        environment and you would like to use its cvs perspective to download files from the cvs
        repository. If you don‟t have eclipse IDE installed, we recommend you use the Tortoise
        CVS client since it is simple to download, setup, and use.


1. Access the Eclipse CVS Perspective by selecting Window>Open Perspective>
     CVS Perspective




2. Create a new repository by right-clicking in the navigation pane and selecting
     New>Repository Location.




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3. Enter the details for the Repository location as provided in the table following table
   and then click on the Apply button followed by the OK button.

                           Field                              Value




                Connection Type
                User
                Password                      anonymous
                Host


                Port
                Save password




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                                                                      Running C3PRv2

4. Refresh the Branches Section by right-clicking on a branch and selecting Refresh
     Branches.




5. Once you click the Finish button, you will get a dialog box. Click on deep search
     and wait for the process to complete.




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6. Right-click on the desired branch, and select Check Out.




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