Development environment Setup - eSciDoc environment Setup 0.15 - DRAFT Authors: BKR, ......

Development environment

Setup

0.15 - DRAFT

Authors: BKR, TTE

Last Changed: 22.07.2008

Technical Specification Prototype

eSciDoc Project Distribution: eSciDoc project team

Changed by: TTE Last changed: TTE Page: 2 of 25 Filename: cpt_eSciDoc_DevelopmentEnvironment_Setup_v0.15.doc

Revision History

Version Date Author Comments 0.1 15.12.2005 BKR Initial document. 0.2 10.01.2006 BKR Fedora, Subversion 0.3 10.01.2006 BKR Project 0.4 11.01.2006 BKR Database, snv:ignore, Code format 0.5 12.01.2006 BKR Start the project 0.6 12.01.2006 BKR Checkstyle, CodeFormat 0.7 26.01.2006 BKR StarUML – Java/EJB Profile 0.8 18.07.2006 MSC Changes for new build environment 0.9 25.07.2006 ROW Changed installation process for Fedora – now runs with Postgres

Changed section 2.7 to now describe eSciDoc project and not Prototype project any more

0.10 27.11.2006 TTE Fixed name of fedora database 0.11 02.04.2007 MIH TPTP Profiler, Checkstyle and Jupiter Plugins included 0.12 05.11.2007 TTE Updated Eclipse plugins. Extracted FIZ Karlsruhe specific parts to

new document 0.13 08.11.2007 TTE Updated build process in eclipse, removed database configuration

section and properties section from Escidoc project chapter. Added eSciDoc properties section.

0.14 21.11.2007 TTE Added requirement JDK>= 1.5.0_11 0.15 22.07.2008 TTE Revised document,

updated to jboss 4.2.2.ga, updated to fedora 3.0 beta 1, referencing eSciDoc wiki in jboss installation section, Referencing eSciDoc wiki in configuration properties section,

Referenced and related documents: -




Table of Content

1 INTRODUCTION 4

2 DEVELOPMENT ENVIRONMENT 5 2.1 SETUP THE ENVIRONMENT 5

2.1.1 Pre-requisites 5 2.1.2 Folder Structure 5

2.2 JAVA 5 2.2.1 Download 6 2.2.2 Installation 6

2.3 JBOSS 6 2.3.1 Download 6 2.3.2 Installation 6 2.3.3 Configuration 6

2.4 DEVELOPMENT DATABASE 7 2.4.1 Download 7 2.4.2 Installation 7 2.4.3 Configuration 7

2.5 FEDORA REPOSITORY SYSTEM 8 2.5.1 Install 8 2.5.2 Configuration 8 2.5.3 Start the services 8 2.5.4 Stop the services 9

2.6 UML TOOL (STARUML) 10 2.6.1 Download 10 2.6.2 Install 10

2.7 ECLIPSE 10 2.7.1 Download: 10 2.7.2 Installation 11 2.7.3 Useful plug-ins 12 2.7.4 Configuration of the environment 15

2.8 ABSOLUTE PATHS 21 2.9 ESCIDOC PROJECT (SOURCES) 21

2.9.1 Install 21 2.9.2 Configuration 22 2.9.3 Build and Start the project 22

3 ANNEX 25 3.1 GLOSSARY 25 3.2 TABLE OF FIGURES AND TABLES 25




1 Introduction

This document should be considered as the initial setup step for the development environment infrastructure for the eSciDoc project. The document describes the components necessary for the development environment. There are several steps required to install and configure these components.

Steps to install/configure the development environment:

• Copy package from server to “C:\workarea” (Eclipse Ide, Eclipse plug-ins, Application server, Java, workspace folder, Fedora).

• Install Database

• Install / Configure Database Tool

• Initialization of the Fedora Repository System (Postgres database)

• Adapt configuration if necessary

• Install UML Tool

• Get project from Subversion

After executing all the steps above the development environment should be ready to use.




2 Development environment

2.1 Setup the environment

2.1.1 Pre-requisites

2.1.2 Folder Structure

The project should be located under the root folder: “C:\workarea”. This path is used because absolute paths are part of the configuration (IDE and project) and should be used. If the folder “C:\workarea” is not possible, there are manual steps required, to change the configuration.

The subfolder structure:

- “\eclipse“ � Eclipse IDE

- “\projects“ � Eclipse project work area

- “\Java“ � Java SDK (JDK 1.5.0_11 or higher is required)

- “\jboss“ � Application server

- “\fedora“ � Fedora repository system

- “\installs“ � The software to install

The “eclipse“ folder contains the Eclipse development platform and consists of IDE and plugins. The Java projects (e.g. prototype, test projects…) should be stored in the “projects“ folder. This is the Eclipse workspace folder. The JSDKs e.g. JSDK 5.0 exist in the “Java” folder and JSDK 5.0 configured as the default JRE/JSDK for Eclipse IDE projects. The application server is part of the package (“jboss” folder) and the server access is pre-configured in the Eclipse jBossIDE plug-in. The “fedora” folder contains the Fedora repository system installation for the local developer PC.

The package should be available either as CD media or on a network drive. The developers can simply copy the folder to their system to make the basic development environment available.

2.2 Java

The eSciDoc infrastructure requires Java 1.5.x. For building the eSciDoc infrastructure from the sources, at least JDK 1.5.0_11 is required. Please note that Java 1.6.x will not work. This issue will be fixed in the near future, but we still wait for Fedora to support the latest Java version.




2.2.1 Download

http://java.sun.com/javase/downloads/index_jdk5.jsp

2.2.2 Installation

Please refer to the installation notes that come with Java 1.5.x.

2.3 Jboss

The eSciDoc infrastructure requires Jboss Application Server 4.2.2.GA. Newer versions might work, but have not been tested. As we currently have to customize the server, we strongly recommend to use this version.

2.3.1 Download

http://labs.jboss.com/jbossas/downloads/

2.3.2 Installation

Please refer to the installation notes that come with Jboss Application Server. You will need to configure and customize your Jboss Application Server after installation. We will refer to the installation directory as ${jboss.dir} in the following.

2.3.3 Configuration

Details about the customization and configuration can be found in the eSciDoc Wiki at

http://www.escidoc-project.de/JSPWiki/en/InstallJbossForRelease1.0.

The configuration can be done by applying the JBoss Patch (see 2.3.3.1).

2.3.3.1 Customization

Download JBoss Patch:

http://www.escidoc-project.de/software/jboss-patch-rel.zip (for the latest release), or

http://www.escidoc-project.de/software/jboss-patch.zip (for the latest developer build)

1. Extract the Jboss patch archive and copy the contents of the contained jboss directory to ${jboss.dir} .




2.4 Development Database

The eSciDoc infrastructure uses PostgreSQL in version 8.3 or higher. The contrib module XML-2 must be enabled.

2.4.1 Download

http://www.postgresql.org/ftp/binary/

2.4.2 Installation

Please refer to the installation notes that come with PostgreSQL DBMS. During the installation process of PostgreSQL, a screen with title 'Enable contrib modules' will appear. Please make sure to enable the contrib module XML-2.

If run on windows, the database should be installed with default options as windows service.

2.4.3 Configuration

Several Objects in the postgres databases have to be created:

• Database escidoc • Role fedoraAdmin • Database fedora22 • Database riTriples

SQL instructions to configure the databases: CREATE DATABASE "escidoc" WITH ENCODING='UTF8' OWNE R="postgres"; CREATE ROLE "fedoraAdmin" LOGIN PASSWORD 'fedoraAdm in' NOINHERIT CREATEDB VALID UNTIL 'infinity'; CREATE DATABASE "fedora22" WITH ENCODING='UTF8' OWN ER="fedoraAdmin"; CREATE DATABASE "riTriples" WITH ENCODING='SQL_ASCI I' OWNER="fedoraAdmin";




2.5 Fedora Repository System

The eSciDoc infrastructure requires Fedora 3.0 beta1 or higher.

2.5.1 Install

Download: http://www.fedora-commons.org/

Please refer to the installation notes that come with Fedora or are available online at http://www.fedora-commons.org/documentation/3.0b2/userdocs/distribution/installation.html.

We will refer to the installation directory as ${fedora.dir} in the following.

2.5.2 Configuration

• Please make sure that Fedora uses PostgreSQL as database engine (instead of the default McKoi). It should access the database named fedora30.

• Please select MPTStore as triplestore. The triplestore database in PostgreSQL has to be riTriples.

• Add new values to the user environment variables (Start � Einstellungen � Systemsteuerung � System � Tab Erweitert � Button Umgebungsvariablen � Benutzervariablen):

FEDORA_HOME=${fedora.dir}

• Add new path to the existing PATH variable:

PATH=…;${fedora.dir} \server\bin;${fedora.dir} \client\bin Note: The windows PATH variable does not allow any whitespaces.

• Initialize the postgres database (see Development Database, Configuration, p. 7). A new database for Fedora has now been created. The necessary tables will be created automatically on the first run of Fedora.

2.5.3 Start the services

The Fedora repository system consists of two services, the database and the fedora service itself. The database must be running before the Fedora system is started. If PostgreSQL is not installed as a service, it has to be made sure that PostgreSQL is running when starting Fedora.

• Start Fedora Repository system

o Linux: startup.sh




o Windows: startup-bat

The Fedora server has been started successfully.

2.5.4 Stop the services

If the fedora system has not been shut down, properly, it may cause failures during subsequent restarts.

• Stop fedora service

o Linux: shutdown.sh

o Windows: shutdown.bat




2.6 UML Tool (StarUML)

During developing eSciDoc, the StarUML tool has been used. The current version is 5.0

2.6.1 Download

http://staruml.sourceforge.net/en/download.php

2.6.2 Install

Download the installer (currently StarUML-5.0-with-cm.exe), start it and install StarUML at an appropriate location.

2.7 Eclipse

The eSciDoc development environment is based on the eclipse ide.

2.7.1 Download:

http://www.eclipse.org/downloads/.




2.7.2 Installation

Please refer to the installation notes that come with eclipse.

2.7.2.1 Proxy settings

Depending on the network environment, it may be necessary to define the proxy that has to be used to connect to the update sites.

In eclipse 3.2, the proxy is defined in Window � Preferences � Install/Update

In eclipse 3.3, the proxy is specified in Window � Preferences � General � Network Connections.




2.7.3 Useful plug-ins

The plug-ins used in the eSciDoc development environment are described below. To install these plugins, the usage of the eclipse update manager (Help � Software Updates � Find and Install…) is recommended. The update sites of the plug-ins are shown below.

2.7.3.1 JBossIDE

The JBossIDE provides several interesting features for the J2EE projects. The JBoss Application Server can be controlled (Start, Stop, Deploy files…) from the Eclipse Server Navigator view. The plug-in offers templates and wizards for web, business and persistence layer. The code generation tool XDoclet is configurable using a GUI. In addition packaging is supported by another GUI. Both Code generation and Packaging can be started using a hotkey. Another feature is a slime but smart XML editor.

Eclipse update site:

Stable versions, currently 2.1.2.GA: http://download.jboss.org/jbosside/updates/stable

Development versions, currently 2.1.0.cr1:

http://download.jboss.org/jbosside/updates/development

2.7.3.2 Subclipse

The Subclipse plug-in establishes connections to the Subversion repository. The plug-in can be used to handle the sources (fetch, merge, commit). Additional tools like a Diff tool are provided by the plug-in.


http://subclipse.tigris.org/update_1.4.x

2.7.3.3 TPTP Profiler

TPTP is an Open Source Profiling Tool that enables to Profile Execution Time and Memory Usage. TPTP can profile local and remote Application. If remote Applications or Applications running on a Application Server shall get Profiled, a running AgentController is needed on the remote machine.

The AgentController for TPTP is deployed under C:/workarea/tools/AgentController. Before first running, execute C:/workarea/tools/AgentController/bin/SetConfig.bat to configure the paths for your Java-VM and your Application Server.

The AgentController has to be included in PATH-Variable (C:/workarea/tools/AgentController).




2.7.3.4 Jupiter

Jupiter is a code review plug-in tool for the Eclipse IDE that helps finding and sharing defects of any files (including Java files) with a team. It allows management of code annotations, storing XML based file, which can be shared with the team by CVS. Team review mode can list all reviews in all opened projects in Eclipse. The source-linked review allows developers to quickly jump to the point of the source code, which is reviewed by reviewers.


http://csdl.ics.hawaii.edu/Tools/Jupiter/Download

2.7.3.5 Checkstyle

The eclipse-cs Checkstyle plug-in integrates the well-known source code analyzer Checkstyle into Eclipse. Checkstyle is a development tool that helps you ensure that your Java code adheres to a set of coding standards. Checkstyle does this by inspecting your Java source code and pointing out items that deviate from a defined set of coding rules. These rules can be defined in an xml-file.


http://eclipse-cs.sourceforge.net/update

2.7.3.6 Mylyn

The Mylyn plug-in supports a task-oriented development process. It offers an Eclipse view to Bugzilla and eases the view on projects, by sorting and hiding the objects, based on information about the developer’s daily work.


Eclipse 3.2: http://download.eclipse.org/tools/mylyn/update/e3.2



2.7.3.7 Veloedit

The Veloedit plug-in provides an editor for velocity template files. The velocity template engine is used to render the XML output of the core services.





http://veloedit.sourceforge.net/updates/

2.7.3.8 Spring IDE

The Spring IDE supports the creation and wiring of Spring objects.


http://springide.org/updatesite




2.7.4 Configuration of the environment

2.7.4.1 Checkstyle configuration

The Eclipse plug-in Checkstyle is used to verify e.g. code formatting and is also adapted for the project definitions. The Checkstyle configuration file can be found in the folder etc in the Escidoc project root folder. It is named eSciDoc_checkstyle.xml.

Sometimes the project implementation cannot comply with the CheckStyle settings, e.g. when extending a 3rd party framework. This will list a problem in the “Problems” view. To avoid these problems, CheckStyle is configured to disable check between certain comments:

• “CHECKSTYLE:OFF” and “CHECKSTYLE:ON”

• “CHECKSTYLE:JAVADOC-OFF” and “CHECKSTYLE: JAVADOC-ON”

Examples of disabling CheckStyle:

Activate the Checkstyle configuration:

Window � Preferences � Checkstyle

Press New to create new Checkstyle configuration

Select ‘Konfiguration relativ zum Projekt’

Name: escidoc

Location: /Escidoc/etc/eSciDoc_checkstyle.xml




Press two times OK.

2.7.4.2 Code style configuration

The code formatting (style) is pre-defined and consistent with the coding standards of the project. The configuration file is available in the Escidoc project in the etc folder. It is named eSciDoc_codestyle.xml.

Import the code style :

Window � Preferences � Java � Code Style � Formatter

Press Import

Select the file …/Escidoc/etc/eSciDoc_codestyle.xml

Press Open

Press OK

2.7.4.3 Compiler configuration

The compiler can throw additional warnings according to the settings, by default there are warnings e.g. for Serializable classes without serialVersionID.

- Ignore Serializable class without serialVersionUID:

� Preferences � Java � Compiler � Errors/Warnings

� Potential programming problems

- Ignore Unchecked generic type operation

� Preferences � Java � Compiler � Errors/Warnings � J2SE 5.0 options







2.7.4.4 JRE setup and Compiler

The Java Runtime Environment can be edited under:

� Window � Preferences � Java � Installed JRE’s




The compiler can be edited and the compliance settings can be changed.




2.7.4.5 Application Server

Add the application server:

• Window � Show view � Others � Server � Servers

• Click right mouse buttom � New � Server

• Select Jboss, a division of Red Hat � JBoss AS 4.0

• Select runtime environment

• Press Next

• Enter a name, e.g. eSciDoc, and press Finish.

Some VM arguments have to be set before starting the application server:

-Xmx1200m

-Dhttp.proxyHost="<proxy>" (If a proxy is needed to connect to the internet)

-Dhttp.proxyPort="<port>" (If a proxy is needed to connect to the internet)

-Dhttp.nonProxyHosts="localhost|127.0.0.1" etc. (If a proxy is needed to connect to the internet)

To specify these values before starting the server:

• Double click the eSciDoc server in the Servers view

• Click Open launch configuration in the opened editor

• Select the tab Arguments , enter the values in VM Arguments

• Press OK

To start the application server:

• Select the server in the Servers view.

• Press right mouse button � Start




To start the application server in debug mode:

• Select the server in the Servers view.

• Press right mouse button � Debug

2.7.4.6 Install / Update

In order to update the Eclipse IDE and Plug-ins, the proxy must be enabled. See section 2.7.2.1, p. 11.

2.8 Absolute paths

There is only one absolute path used in the Eclipse platform configuration file and this is the path to the workspaces.

C:\workarea\eclipse\configuration\.settings\org.eclipse.ui.ide.prefs:

� RECENT_WORKSPACES=C\:\\some_dir

2.9 eSciDoc Project (Sources)

2.9.1 Install

The sources of the eSciDoc project are available at

http://www.escidoc-project.de/JSPWiki/Wiki.jsp?page=Download.

Download the source ZIP archive, e.g. escidoc-src.0.9.build.123.zip.

Import the sources as new eclipse project:

File � Import � General � Existing Projects into Workspace � Select archive file

Select Escidoc project

Click Finish

Note: The project is looking for the generated files and errors will be displayed in the Problems view. This is okay, because the generated files should not be part of the sources in the repository. After building the project and refreshing, the errors should disappear.




2.9.2 Configuration

2.9.2.1 eSciDoc Properties

The properties to configure the eSciDoc core services are defined within the properties file placed in the JBoss application server’s install folder ${jboss}/server/default/conf/escidoc.properties

Default values exist for all properties. Therefore, only the values that shall be changed have to be defined in the file escidoc.properties . The default values are defined in the Escidoc project in the file Escidoc/common/src/escidoc.properties.default .

The eSciDoc wiki contains a list of all properties at http://www.escidoc-project.de/JSPWiki/en/InfrastructureConfigurationProperties.

2.9.3 Build and Start the project

• Start PostgreSQL (should already run as service). The database is needed during the build.

• Start Fedora repository system (“fedora-start postgres”)

• Start Eclipse

• Start the application server, see section 2.7.4.5, p. 20.

• Build the eSciDoc core services and deploy them on the application server: Open the eclipse ant view and drag the build file build.xml from the package-explorer to the ant view. A new entry named Main appears. Now select the new entry and press the right mouse button. From the context menu choose Run as � Ant build…. Select the tab JRE and insert the VM arguments -Xmx1024m -Xms512m -XX:MaxPermSize=256m . This must be done for all created ant tasks in the project.




Build and deploy the project by pressing Run.

The main steps of this build process can be executed, separately:

o Run XDoclet (Ant-View, file build/xdoclet-build.xml, Target XDoclet Generator � xdoclet_generation_all)

o Refresh




o Run AOP compile (Ant-View, file build/helper-build.xml, Target Helper Scripts � aop-compile)

o Deploy created ear to jBoss Application Server (Ant-View, file build.xml, Target Main � re-deploy-ear)

• Check axis in Browser (http://localhost:8080/axis/servlet/AxisServlet)

• Project is ready to use




3 Annex

3.1 Glossary

Acronym Description

3.2 Table of Figures and Tables

None.

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