Last Published: 2008-08-06
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Version: 8.08-alpha
SyMBA Information
SyMBA Project Home
General Information
Installation
Deviations from the FuGE Hibernate STK
Next:
Introduction
SyMBA User Manual - Table Of Content
Introduction
Downloading These Instructions for Offline Use
Download These Instructions
The FuGE-OM and SyMBA
What is the relationship between SyMBA and the Object Model?
What You'll Need
Recommendations
Recommendations
Installing SSH
Installing SSH
Installing Java 5
Installing Sun Java 5 or Java 6
Installing Maven
Download and Install Maven 2.0.7 or Later
Maven Setup
Environment Variables and Settings for Maven
Test Maven (Part One)
Test Maven (Part Two)
Installing AndroMDA
Introduction
AndroMDA Installation
Choosing a UML Tool
Choosing a UML Tool
Installing a Supported Database
Installing a Supported Database
How To Check-Out SyMBA from Subversion
Setting Up, Compiling, and Running the Hibernate STK
Setting Up the FuGE Hibernate STK database
Maven Profiles
Create a database to hold the metadata
Point Maven at the correct jdbc jar
Providing Variables to the Web Interface
Filling in SyMBA variables within the top-level pom.xml
Compiling the Hibernate STK
Compilation
Optional Modification of the UML
Integrating This Project with your IDE
Creating the Database Tables
Default (Local) Profile
Testing (Validation) Profile
Assigning Identifiers
Checking the Connection to Your LSID Assigner
Preparing Your List of Users
Pre-loading Users into the Metadata Database
Pre-loading People into the Login/Security Database
Pre-loading Protocol Templates into the Metadata Database
Further Reference
Known Problems
The "Access Right" Assocation between SecurityAccess and OntologyTerm
The Chicken and the Egg
The Many2Many Software to Equipment Association
Linking Table Between Software and Equipment is Not Getting Filled
Testing the STK
TestNG
Unit Tests with Maven
Tips and Tricks
Tips and Tricks: Maven 2
Using the Maven 2 exec:java Command
Tips and Tricks: Subversion
Configuring Subversion to Automatically Enable Keywords in New Files
Tips and Tricks: Tomcat
Using the Tomcat Manager
"PermGen Space" Error
Tips and Tricks: Windows
MySQL on Windows: java.sql.SQLException: Can't create/write to file 'C:\WINDOWS\TEMP\#sql_318_0.MYD' (Errcode: 13)
Windows: Escaping Characters
Tips and Tricks: Proxies
Getting SyMBA Built Behind a Proxy
Would You Like to Contribute?
Becoming a SyMBA Developer
Do you wish to contribute to SyMBA?
Guidelines for Developing the FuGE HIbernate STK
Introduction
What to include in new Java Classes
Subversion Best-Practices
Beyond Javadoc: Documenting Your Work
Re-Building the SyMBA Website
Modifications to the FuGE-OM
Changes to the FuGE-OM
Modifications to the FuGE-OM for the Hibernate and the EJB3 STK
Hibernate-only FuGE-OM Modifications
Example Java Code Provided With the original Hibernate STK
Mapping Between the XML and Database Code
DatabaseObjectHelper: Making Your Life Easier
Loading and Unloading FuGE-ML Into the Database
PeopleUnmarshaler (Example Main in UnmarshalPeople)
XMLUnmarshaler (Example Main in UnmarshalXML and XMLRoundtrip)
XMLMarshaler (Example Main in MarshalXML and XMLRoundtrip)
Speedy Creation of OntologyCollections
Further Reading
Credits
Contributors to Documentation
Resources used in the creation of this document
Useful Links
FuGE
Subversion
Maven 2
Next:
Introduction
