The VIVO Harvester is a library of tools written in Java for exporting data from external systems and importing it into VIVO. The code is released in two ways, as a debian file and as tar file. Linux machines that use apt-get style repositories (debian, ubuntu) can install the debian file by downloading it and using dpkg -i filename.deb to install. The tarball can be unpacked on any OS where java is supported and run.
In addition to the wiki information, screencasts of example harvester runs using the 1.0 version of the harvester can be found
For an overview of the components used and how they work together in a harvest, see Typical harvest
There are two ways to run the VIVO Harvester either as command-line tools (useful in a bash script) or use it as a Java library. We'll cover both ways.
All the Harvester tools, when used via the command-line share some common parameters and parameter formats. General information about the Harvester tools on the command-line can be found at Harvester Tools.
DEPRECATED – the struckout text is only for harvester 1.1.1 and previous versions
The first thing you should do is open your Environment Config File and make sure everything is in order. This file is located in scripts/env. Next you should look at your vivo configuration file to make sure this points to your VIVO installation. This file is located in config/models/vivo.xml. You can check out our example scripts or our walk throughs for how to create a bash file using the environment file.
Starting with the Harvester 1.2, there are several example scripts that now ship in the example-scripts folder. Following is a walkthru for each of them:
Using the harvester as a library works well when you want to embed it's functionality into an already existing java application. Utilizing the tools are straightforward. See our Javadoc  documentation for specifics on each tool. A working example harvest is also shipped starting with the harvester 1.0 release. See the DemoPSMerge.java file included the demos folder.
These images are diagrams to show how the data flows in some example cases.
Vivo - Final model in RDF visible from the webapp. |
The harvester is a collection of tools. Each of the following pages has detailed information about how to use that tool, what parameters it takes, and what methods it exposes. Please refer to these pages for more information on how to use each of the tools for the VIVO Harvester.
Currently the VIVO Harvester does not have an upgrade path, as all previous versions were considered beta versions. With the 1.0 release you can expect all subsequent releases follow standard software upgrade guidelines.