gnmatcher

README

gnmatcher

import "github.com/gnames/gnmatcher"

The GNmatcher is a utility for checking scientific name-strings against canonical names derived from a variety of biodiversity datasets. The matching can be exact, partial, or fuzzy. GNmatcher does not tell which datasets provided found canonical name. For this purpose use GNames project.

Introduction

The GNmatcher takes an array of strings and returns back zero or more canonical names for each string. If it is not important which biodiversity repositories provided matched canonical names, the project can be used as a stand-alone RESTful service. If such information is important, the project is used as a component of a scientific names verification service (GNames API).

The project aims to do canonical names matching as fast and accurate as possible. Quite often, humans or character-recognition software (OCR) introduce misspellings in the strings. For this reason, GNmatcher uses fuzzy-matching algorithms when no exact match exists. Also, for cases where full string does not have a match, gnmatcher tries to match it against parts of the string. For example, if a string did not get a match on a subspecies level, the algorithm will try to match it on species and genus levels.

Reconciliation is the normalization of lexical variants of the same name. Resolution is a determination of how a nomenclaturally registered name can be interpreted from the point of taxonomy. For example, a name can be an accepted name for species, a synonym, or a discarded one.

The gnmatcher app functions as an HTTP service. A client access it wia HTTP protocol. The API's methods and structures are described in by the OpenAPI specification.

Input and Output

A user calls HTTP resource /match sending an array of strings to the service and gets back matched canonical names, the match type, as well as other metadata described as a Match object in the OpenAPI specification.

The optimal size of the input is 5-10 thousand strings per array. Note that 10,000 is the maximal size, and larger arrays will be truncated.

Performance

For performance measurement we took 100,000 strings where only 30% of them were 'real' names. On a modern CPU with 12 hyper threads and GNM_JOBS_NUM environment variable set to 8, the service was able to process about 8,000 strings per second. For 'clean' data where most of the names are "real", you should see an even higher performance.

Prerequisites

• You will need PostgreSQL with a restored dump of gnames database.
• For PostgreSQL collation to work correctly set LC_COLLATE=C in /etc/default/locale
• Docker service

Usage

Usage with docker

• Install docker gnmatcher image: docker pull gnames/gnmatcher.

• Copy .env.example file on user's disk and change values of environment variables accordingly.

• Start the service:

  docker run -p 8080:8080 -d --env-file your-env-file \
  gnames/gnmatcher -- rest -p 8080`
  

  This command will set the service on port 8080 and will make it available through port 8080 on a local machine.

Usage from command line

• Download the [latest verion] of gnmatcher binary, untar and put somewhere in PATH.

• Run gnmatcher -V to generate configuration at ~/.config/gnmatcher.yaml

• Edit ~/.config/gnmatcher.yaml accordingly.

• Run gnmatcher rest -p 1234

The service will run on the given port.

Usage as a library

package main

import (
  "fmt"
  "github.com/gnames/gnmatcher"
  "github.com/gnames/gnmatcher/config"
  "github.com/gnames/gnmatcher/io/bloom"
  "github.com/gnames/gnmatcher/io/trie"
)

func Example() {
  // Note that it takes several minutes to initialize lookup data structures.
  // Requirement for initialization: Postgresql database with loaded
  // http://opendata.globalnames.org/dumps/gnames-latest.sql.gz
  //
  // If data are imported already, it still takes several seconds to
  // load lookup data into memory.
  cfg := config.New()
  em := bloom.NewExactMatcher(cfg)
  fm := trie.NewFuzzyMatcher(cfg)
  gnm := gnmatcher.New(em, fm, cfg)
  res := gnm.MatchNames([]string{"Pomatomus saltator", "Pardosa moesta"})
  for _, match := range res {
    fmt.Println(match.Name)
    fmt.Println(match.MatchType)
    for _, item := range match.MatchItems {
      fmt.Println(item.MatchStr)
      fmt.Println(item.EditDistance)
    }
  }
}

Configuration

You can use either cofiguration file, or environment variables. Configuration file is usually located at $HOME/.config/gnmatcher.yaml. When gnmatcher runs first time, it will create the configuration file. Logs provide the location of the configuration file with every run of gnmatcher. The meanings of configuration options are documented in the config file.

To make it easier to run gnmatcher in a container, or a Kubernetes pod, there are also environment variables that override configuration file values.

Env. Var.	Configuration
GNM_CACHE_DIR	CacheDir
GNM_JOBS_NUM	JobsNum
GNM_MAX_EDIT_DIST	MaxEditDist
GNM_PG_HOST	PgHost
GNM_PG_PORT	PgPort
GNM_PG_USER	PgUser
GNM_PG_PASS	PgPass
GNM_PG_DB	PgDB
GNM_NSQD_TCP_ADDRESS	NsqdTCPAddress
GNM_NSQD_CONTAINS_FILTER	NsqdContainsFilter
GNM_NSQD_REGEX_FILTER	NsqdRegexFilter
GNM_WITH_WEB_LOGS	WithWebLogs

Client

A user can find an example of a client for the service in this test file.

The API is formally described in the OpenAPI specification

Development

There is a docker-compose file that sets up HTTP service to run tests. To run it to the following:

1. Copy .env.example file to the .env file in the project's root directory, change the settings accordingly.

2. Build the gnmatcher binary and docker image using make dc command.

3. Run docker-compose command docker compose up

4. Run tests via go test ./... -v

Documentation

Overview

package gnmatcher provides the main use-case of the project, which is matching of possible name-strings to scientific names registered in a variety of biodiversity databases.

The goal of the project is to return matched canonical forms of scientific names by tens of thousands a second, making it possible to work with hundreds of millions/billions of name-string matching events.

The package is intended to be used by long-running services because it takes a few seconds/minutes to initialize its lookup data structures.

Example

package main

import (
	"fmt"

	"github.com/gnames/gnmatcher"
	"github.com/gnames/gnmatcher/config"
	"github.com/gnames/gnmatcher/io/bloom"
	"github.com/gnames/gnmatcher/io/trie"
	"github.com/gnames/gnmatcher/io/virusio"
)

func main() {
	// Note that it takes several minutes to initialize lookup data structures.
	// Requirement for initialization: Postgresql database with loaded
	// http://opendata.globalnames.org/dumps/gnames-latest.sql.gz
	//
	// If data are imported already, it still takes several seconds to
	// load lookup data into memory.
	cfg := config.New()
	em := bloom.New(cfg)
	fm := trie.New(cfg)
	vm := virusio.New(cfg)
	gnm := gnmatcher.New(em, fm, vm, cfg)
	res := gnm.MatchNames([]string{"Pomatomus saltator", "Pardosa moesta"})
	for _, match := range res {
		fmt.Println(match.Name)
		fmt.Println(match.MatchType)
		for _, item := range match.MatchItems {
			fmt.Println(item.MatchStr)
			fmt.Println(item.EditDistance)
		}
	}
}

Index

• Variables
• type GNmatcher
  • func New(em exact.ExactMatcher, fm fuzzy.FuzzyMatcher, vm virus.VirusMatcher, ...) GNmatcher

Examples

• Package

Variables

var (
	// Version of the gnmatcher. When make runs, it automatically
	// sets the variable using git tags and hashes.
	Version = "v0.9.8+"
	// Build timestamp. When make runs, it automatically sets the variable.
	Build = "n/a"
)

Types

type GNmatcher

type GNmatcher interface {
	// MatchNames takes a slice of scientific name-strings with options and
	// returns back matches to canonical forms of known scientific names. The
	// following matches are attempted:
	// - Exact string match for viruses
	// - Exact match of the name-string's canonical form
	// - Fuzzy match of the canonical form
	// - Partial match of the canonical form where the middle parts of the name
	//   or last elements of the name are removed.
	// - Partial fuzzy match of the canonical form.
	//
	// In case if a name is determined as a "virus" (a non-celular entity like
	// virus, prion, plasmid etc.), It is not matched, and returned back
	// to be found in a database.
	//
	// The resulting output does provide canonical forms, but not the sources
	// where they are registered.
	MatchNames(names []string, opts ...config.Option) []mlib.Output

	// GetConfig provides configuration object of GNmatcher.
	GetConfig() config.Config

	// GetVersion returns version number and build timestamp.
	GetVersion() gnvers.Version
}

GNmatcher is a public API to the project functionality.

func New

func New(
	em exact.ExactMatcher,
	fm fuzzy.FuzzyMatcher,
	vm virus.VirusMatcher,
	cfg config.Config,
) GNmatcher

New is a constructor for GNmatcher interface. It takes two interfaces ExactMatcher and FuzzyMatcher.