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Primate Life Histories Database Codebase

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README
Primate Life Histories Online Database

Introduction

Primate Life Histories is an online database project with database and web interface to archive, manage, search and download individual-based life history data that have been collected from wild primate populations.

Installation:
1. check out source code to a desired location
2. Install required jar files (see Technology)
3. Create a postgresql database by running the sql scripts under the src/db.sql folder by folliwng order
   1) create tables, including:
      * plhdb.ddl.sql: create major tables to hold scientific data
      * plhdb.audit.sql: create table to store audit information 
      * plhdb.auth.sql: create auth schema with tables to store user and authentication and authorization information
   2) create views: plhdb.views.sql
   3) install the SQL procedural language if it is not already avalable: CREATE LANGUAGE plpgsql;
   4) create table: plhdb.bulkimp.sql: tables for bulk data import
   5) create functions:plhdb.funcs.sql
   6) create rules: plhdb.rules.sql
   7) initialize data: import cvterm data in the file src/db/data/event_types.txt with term relationship defined in src/db/data/cvterms.ttl
   
4. Create a user with access to the database
5. Compile java classes and generate web application war file
	The web-application is built using Apache Ant. You must have ant installed in
	order to build it. On MacOSX, installing the Developer package (which includes
	the C compiler) will also install ant in /Developer/Java/Ant/bin/ant.

	Properties need to be specified with the '-D' option:
	* project.version: the application version
	* hibernate.database: the hibernate database URL 
	* hibernate.username: the hibernate database user name  
	* hibernate.password: the hibernate database password 

	please use the database user account you created in step 4.    
6. Copy the war file generated in step 5 to Tomcat or Jboss deploy folder
7. Start Tomcat (restart is not necessary for Jboss)
8. The web application should be visible now at http://your.domain.name:8080/plhdb


Technology

    * Database: PostgreSQL 8.3
    * Database ORM : Hibernate
    * Programming Language: java
    * Web Framework: Sping
    * Other Libraries
          o c3p0 Database Connection Pooling
          o struts
          o dojo

Source Code

Source code is available on GitHub (http://github.com/plhdb/plhdb) and SourceForge (http://sf.net/projects/plhdb) under a GPL v3 license (http://www.gnu.org/copyleft/gpl.html). Git repositories are available 
on both Source Forge and Github:
    * SourceForge: git://plhdb.git.sourceforge.net/gitroot/plhdb/plhdb
    * GitHub: git://github.com/plhdb/plhdb.git

Credits
    * Concept, content, and scientific requirements: the Evolutionary Ecology of Primate Life Histories Working Group, Susan C Alberts (Duke University, PI), Karen B Strier (University of Wisconsin-Madison, PI)
    * Database and application programming: Hilmar Lapp (NESCent), Xianhua Liu (NESCent) 

Publications

Contact

    * The website is maintained by the National Evolutionary Synthesis Center (NESCent).
      2024 W. Main Street, Suite A200
      Durham, NC 27705-4667
      Tel: (919) 668-4551
      Fax: (919) 668-9198
    * Send email to
      leading scientists of the working group (plhdb-admin@nescent.org)
      report bugs or request technical help (plhdb-bug@nescent.org)


Released under the GPL v3 license (included)
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