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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 The original repository on SourceForge (http://sf.net/projects/plhdb) is no longer maintained.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

Note that the currently online version of the Primate Life Histories Database at the URL reported in this paper is no longer based off of this codebase. To learn about the code for the online site or how to access its data, please contact the corresponding author of the above paper.

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/.