Primate Life Histories Database Codebase
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doc The PLHDB codebase that is running the database and the website. Feb 2, 2010
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README.md

Primate Life Histories 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 in the 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.

    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

    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: Spring
  • Other Libraries:
    • c3p0 Database Connection Pooling
    • struts
    • dojo

Source Code

Source code is available on GitHub (http://github.com/NESCent/plhdb) under a GPL v3 license. The original repository on SourceForge (http://sf.net/projects/plhdb) is no longer maintained.

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: Xianhua Liu (NESCent), Hilmar Lapp (NESCent).

How to Cite

If you use this code or parts of it, please cite the following publication:

Strier, K. B., Altmann, J., Brockman, D. K., Bronikowski, A. M., Cords, M., Fedigan, L. M., Lapp, H., Liu, X., Morris, W. F., Pusey, A. E., Stoinski, T. S., and Alberts, S. C. "The Primate Life History Database: A Unique Shared Ecological Data Resource". Methods in Ecology and Evolution 1, no. 2 (2010): 199–211. http://dx.doi.org/10.1111/j.2041-210X.2010.00023.x

License

This software is released under the GPL v3 license (see included LICENSE).

Primate Life Histories Database Copyright (C) 2007-2015 Hilmar Lapp, Xianhua Liu

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.