name spotter

Finds scientific names in texts using taxon-finder or neti-neti projects

Ruby

name-spotter

Finds biodiversity scientific names in texts using TaxonFinder
(by Patrick Leary) or NetiNeti (by Lakshmi Manohar Akella) libraries.
This gem works with Ruby >= 2.0

Requirements

Docker

Installation

Install the gem

gem install name-spotter

Install and run TaxonFinder and NetiNeti docker containers

docker pull gnames/netineti
docker pull gnames/taxonfinder
docker run -d -p 0.0.0.0:1234:1234 --name tf gnames/taxonfinder
docker run -d -p 0.0.0.0:6384:6384 --name nn gnames/netineti

Usage

If you are using localhost and default ports for NetiNeti and TaxonFinder:

require "name-spotter"

neti_client       = NameSpotter::NetiNetiClient.new()
tf_client         = NameSpotter::TaxonFinderClient.new()
neti_name_spotter = NameSpotter.new(neti_client)
tf_name_spotter   = NameSpotter.new(tf_client)

neti_name_spotter.find(your_text)
tf_name_spotter.find(your_text)

If you have installed NetiNeti and TaxonFinder on a machine
with non-default port:

neti_client = NameSpotter::NetiNetiClient.new(host: "example.com",
                                              port: 5555)
#or
neti_client = NameSpotter::NetiNetiClient.new(host: "123.123.123.111",
                                              port: 5555)

If you want to get results in JSON or XML formats

neti_name_spotter.find(your_text, "json")
neti_name_spotter.find(your_text, "xml")

Development

To run tests start TaxonFinder and NetiNeti on your local machine with
default configurations and run

bundle exec rake

Contributing to name-spotter

Check out the latest master to make sure the feature hasn’t been implemented
or the bug hasn’t been fixed yet
Check out the issue tracker to make sure someone already hasn’t requested
it and/or contributed it
Fork the project
Start a feature/bugfix branch
Commit and push until you are happy with your contribution
Make sure to add tests for it. This is important so I don’t break it in a
future version unintentionally.
Please try not to mess with the Rakefile, version, or history. If you want
to have your own version, or is otherwise necessary, that is fine, but please
isolate to its own commit so I can cherry-pick around it.

Copyright

Authors: Chuck Ha, Anthony Goddard, Dmitry Mozzherin,
David Shorthouse