Biodiversity data validation actors and workflows derived from the FP-Akka package
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
packages/kurator_fp
src
.gitignore
.project
LICENSE
README.md
occurrence_demoset.tsv
pom.xml

README.md

kurator-fp-validation

Actors and workflows derived from FP-Akka package at http://sourceforge.net/p/filteredpush/svn/HEAD/tree/trunk/FP-Akka

Prerequisites

Clone and build the FP-CurationServices project

$ git clone https://github.com/FilteredPush/FP-KurationServices.git
$ cd FP-KurationServices
$ mvn clean install

Clone and build the kurator-akka dependencies

Build the kurator-akka project first and kurator-validation second.

$ git clone https://github.com/kurator-org/kurator-akka.git
$ git clone https://github.com/kurator-org/kurator-validation.git

$ cd kurator-akka
$ mvn clean install

$ cd ../kurator-validation
$ mvn clean install

Install Jython and set environment variables

Download the Jython 2.7.1.b3 installer jar. Run the installer from the command line in the kurator home directory.

$ java -jar jython-installer-2.7.1b3.jar

Select the standard installation when prompted (option 2) and when asked to provide the target directory enter "jython2.7.1b3". This will install jython to "/home/kurator/jython2.7.1b3".

Set the JYTHON_HOME environment variable to point the directory you installed to:

$ export JYTHON_HOME=/path/to/jython

Lastly, the JYTHON_PATH environment variable should point to the directory containing python packages for workflow actors. (for example the packages directory found in the root of this project)

$ export JYTHON_PATH=/path/to/packages

Pip install outcomeStats.py dependencies

Use the pip installer bundled with jython to install python dependencies for the Outcome Stats workflow:

$ ./pip install --upgrade pip

$ cd $JYHTON_HOME/bin
$ ./pip install unidecode
$ ./pip install unicodecsv
$ ./pip install chardet
$ ./pip install xlsxwriter
$ ./pip install ConfigParser

An additional change to the configparser is required, the backports package directory is missing an init.py file after installing. Manually adding this file fixes the issue:

$ cd $JYHTON_HOME/Lib/site-packages/backports
$ touch __init__.py

Build kurator-fp-validation and run workflows

Build this project via maven:

$ mvn clean package

This will produce a jar-with-dependencies in the target directory of this project. Run this jar from the command-line via the following:

$ java -jar target/kurator-fp-validation-1.0.0-jar-with-dependencies.jar -f packages/kurator_fp/workflows/outcome_stats.yaml -p configfile=packages/kurator_fp/config/stats.ini -p inputfile=packages/kurator_fp/data/occurrence_qc.json -p outputfile=outcomeStats.xlsx -l DEBUG