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Global Names Recognition and Discovery (GNRD)

This repository is archived and inactive. For finding scientific names in texts use https://github.com/gnames/gnfinder.

Continuous Integration Status Coverage Status CodePolice Dependency Status

GNRD is a web-application. It finds scientific names in texts, PDF files, images, web-pages, MS Word and MS Excel documents. RESTful API allows to search for scientific names using scripts.

Install

There are quite a few moving parts in the system -- Tesseract for OCR, Libre Office to read various file formats, Postgresql for data, Redis for asyncronous execution of commands, gnfinder for name-finding etc. We recommend to install Docker and Docker Compose to dramatically simplify the installation process.

You can follow .travis.yml file to see necessary components for the system on a Debian-based GNU/Linux distribution. You can see docker-compose file to get an insight on how to make a complete Docker-based installation.

Prerequisites

  • Docker >= 1.10
  • Docker Compose >= 1.6
  • Git

Install in production environment on one machine

NOTE: This install is not safe, and is given to test installation by new users. You need to create real passwords and change settings in .env file accordingly, also you need to remove POSTGRES_HOST_AUTH_METHOD=trust environment variable from .env file.

Here we will assume installation is done by a user john with a group john

Add user john to docker group in /etc/group and relog. This will give the user privileges to operate docker.

Get source code and swich to production branch

git clone https://github.com/GlobalNamesArchitecture/gnrd.git
cd gnrd git checkout production ```

Create directory for the database

```bash
sudo mkdir -p /opt/gna/data/gnrd/postgresql/data
sudo chown john:john -R /opt/gna/data/gnrd/postgresql

Optionally pull gnames/gnrd from dockerhub to save time on the gnrd docker image building step

docker pull gnames/gnrd

Run docker compose from the project's root directory

docker-compose up
# or in daemon mode:
nohup docker-compose up -d

Initialize database:

docker-compose run app rake db:reset

Now you should have a working version of GNRD on http://0.0.0.0:9292 and the following command should work as expected

curl -L http://0.0.0.0:9292/name_finder.json?url=http://en.wikipedia.org/wiki/Araneae

The response should include a URL that will contain the found names.

You can change the placement of default directories, and ports by modifying docker-compose file

After you made it working login to PostgreSQL, set an account and password and change .env file accordingly. Remove the POSTGRES_HOST_AUTH_METHOD=trust environment variable from .env file.

Development and Testing

You need Docker >= 1.10 and Docker Compose >= 1.6

Build application's image (needs to be done only if a new gem or new Ubuntu package are added)

docker-compose build

Start Docker Compose (in the background)

docker-compose up -d

Create/update database

docker-compose run app rake db:reset

should be sufficient

Run all tests

docker-compose run app rake

Run a specific test

# with rake
docker-compose run app rake spec SPEC=spec/lib/some_spec.rb:44

# with rspec
docker-compose run app rspec -r factories spec/lib/some_spec.rb:44

Contributing to GNRD

  • 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: Dmitry Mozzherin, David Shorthouse

Copyright © 2012-2019 Marine Biological Laboratory. See LICENSE.txt for further details.