gnparser

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 Go to latest Published: Feb 7, 2019 License: MIT Imports: 9 Imported by: 3

README

Global Names Parser: gnparser written in Go

Try in online.

gnparser splits scientific names into their component elements with associated meta information. For example, "Homo sapiens Linnaeus" is parsed into human readable information as follows:

Element Meaning Position
Homo genus (0,4)
sapiens specificEpithet (5,12)
Linnaeus author (13,21)

This parser, written in Go, is the 3rd iteration of the project. The first, biodiversity had been written in Ruby, the second, also gnparser, had been written in Scala. This project learned from previous ones, and, when it matures, it is going to be the a substitution for other two, and will be the only one that is maintained further. All three projects were developed as a part of Global Names Architecture Project.

Try as a command tool under Windows, Mac or Linux by downloading the latest release, uncompressing it, and copying gnparser binary somewhere in your PATH.

wget https://www.dropbox.com/s/blvmejmp4378cao/gnparser-v0.5.1-linux.tar.gz
tar xvf gnparser-v0.5.1-linux.tar.gz
sudo cp gnparser /usr/local/bin
# for JSON output
gnparser -f pretty "Homo sapiens Linnaeus"
# for very simple text output
gnparser -f simple "Homo sapiens Linnaeus"
gnparser -h

Introduction

Global Names Parser or gnparser is a program written in Go for breaking up scientific names into their different elements. It uses peg -- a Parsing Expression Grammar (PEG) tool.

Many other parsing algorithms for scientific names use regular expressions. This approach works well for extracting canonical forms in simple cases. However, for complex scientific names and to parse scientific names into all semantic elements regular expressions often fail, unable to overcome the recursive nature of data embedded in names. By contrast, gnparser is able to deal with the most complex scientific name-strings.

gnparser takes a name-string like Drosophila (Sophophora) melanogaster Meigen, 1830 and returns parsed components in JSON format. This behavior is defined in its tests and the test file is a good source of information about parser's capabilities, its input and output.

Speed

Number of names parsed per hour on a i7-8750H CPU (6 cores, 12 threads, at 2.20 GHz), parser v0.5.1

Threads names/hr
1 48,000,000
2 63,000,000
4 128,000,000
8 202,000,000
16 248,000,000
100 293,000,000

For simplest output Go gnparser is roughly 2 times faster than Scala gnparser and about 100 times faster than Ruby biodiversity parser. For JSON formats the parser is approximately 8 times faster than Scala one, due to more efficient JSON conversion.

Features

  • Fastest parser ever.
  • Very easy to install, just placing executable somewhere in the PATH is sufficient.
  • Extracts all elements from a name, not only canonical forms.
  • Works with very complex scientific names, including hybrids.
  • Includes gRPC server that can be used as if a native method call from C++, C#, Java, Python, Ruby, PHP, JavaScript, Objective C, Dart.
  • Use as a native library from Go projects.
  • Can run as a command line application.
  • Can be scaled to many CPUs and computers (if 300 millions names an hour is not enough).
  • Calculates a stable UUID version 5 ID from the content of a string.

Use Cases

Getting the simplest possible canonical form

Canonical forms of a scientific name are the latinized components without annotations, authors or dates. They are great for matching names despite alternative spellings. Use the canonicalName -> simple or canonicalName -> full fields from parsing results for this use case. Full version of canonical form includes infra-specific ranks and hybrid character for named hybrids.

The canonicalName -> simple field is good for matching names from different sources, because sometimes dataset curators omit hybrid sign in named hybrids, or remove ranks for infraspecific epithets.

The canonicalName -> full is good for presentation, as it keeps more details.

If you only care about canonical form of a name you can use --format simple flag with command line tool or gRPC service.

Normalizing name-strings

There are many inconsistencies in how scientific names may be written. Use normalized field to bring them all to a common form (spelling, spacing, ranks).

Removing authorships in the middle of the name

Many data administrators store name-strings in two columns and split them into "name part" and "authorship part". This practice misses some information when dealing with names like "Prosthechea cochleata (L.) W.E.Higgins var. grandiflora (Mutel) Christenson". However, if this is the use case, a combination of canonicalName -> valueRanked with the authorship from the lowest taxon will do the job. You can also use --format simple flag for gnparse command line tool.

Figuring out if names are well-formed

If there are problems with parsing a name, parser generates qualityWarnings messages and lowers parsing quality of the name. Quality values mean the following:

  • "quality": 1 - No problems were detected
  • "quality": 2 - There were small problems, normalized result should still be good
  • "quality": 3 - There were serious problems with the name, and the final result is rather doubtful
  • "quality": 0 - A string could not be recognized as a scientific name and parsing fails
Creating stable GUIDs for name-strings

gnparser uses UUID version 5 to generate its id field. There is algorithmic 1:1 relationship between the name-string and the UUID. Moreover the same algorithm can be used in any popular language to generate the same UUID. Such IDs can be used to globally connect information about name-strings or information associated with name-strings.

More information about UUID version 5 can be found in the Global Names blog

Assembling canonical forms etc. from original spelling

gnparser tries to correct problems with spelling, but sometimes it is important to keep original spelling of the canonical forms or authorships. The positions field attaches semantic meaning to every word in the original name-string and allows users to create canonical forms or other combinations using the original verbatim spelling of the words. Each element in positions contains 3 parts:

  1. semantic meaning of a word
  2. start position of the word
  3. end position of the word

For example ["specificEpithet", 6, 11] means that a specific epithet starts at 6th character and ends before 11th character of the string.

Installation

Compiled programs in Go are self-sufficient and small (gnparser is only a few megabytes). As a result the binary file of gnparser is all you need to make it work. You can install it by downloading the latest version of the binary for your operating system, and placing it in your PATH.

Linux or OS X

Move gnparser executable somewhere in your PATH (for example /usr/local/bin)

sudo mv path_to/gnparser /usr/local/bin
Windows

One possible way would be to create a default folder for executables and place gnparser there.

Use Windows+R keys combination and type "cmd". In the appeared terminal window type:

mkdir C:\bin
copy path_to\gnparser.exe C:\bin

Add C:\bin directory to your PATH environment variable.

Install with Go

If you have Go installed on your computer use

go get -u gitlab.com/gogna/gnparser
cd $GOPATH/srs/gitlab.com/gogna/gnparser
make install

You do need your PATH to include $HOME/go/bin

Usage

Command Line

Relevant flags:

--help -h : help information about flags

--format -f : output format. Can be compact, pretty, simple, or debug. Default is compact.

--jobs -j : number of jobs running concurrently.

--cleanup -c : cleans up input from HTML entities and tags instead of parsing

To parse one name:

# default compact format
gnparser "Parus major Linnaeus, 1788"

# pretty format
gnparser -f pretty "Parus major Linnaeus, 1788"

# simple pipe-delimited flat format
gnparser -f simple "Parus major Linnaeus, 1788"

# to parse a name from standard input
echo "Parus major Linnaeus, 1788" | gnparser

To parse a file:

There is no flag for parsing a file. If parser finds file path on your computer it will parse the content of the file, assuming every line is a new scientific name. If the file path is not found, gnparser will try to parse the "path" as a scientific name.

Parsed results will stream to STDOUT, while progress of the parsing will be directed to STDERR.

gnparser -j 200 names.txt > names_parsed.txt

# to parse files using pipes
cat names.txt | gnparser -f simple -j 200 > names_parsed.txt

# to clean names from html tags and entities first (no parsing
# or other changes), then parse
cat names.txt | gnparser -c | sed "s/.*|//" | gnparser > names_parsed.txt

To parse a file returning results in the same order as they are given (slower):

gnparser -j 1 names.txt > names_parsed.txt

Potentially the input file might contain millions of names, therefore creating one properly formatted JSON output might be prohibitively expensive. Therefore the parser creates one JSON line per name (when compact format is used)

You can use up to 20 times more "threads" than the number of your CPU cores to reach maximum speed of parsing (--jobs 200 flag). It is practical because additional threads are very cheap in Go and they try to fill out every idle gap in the CPU usage.

To cleanup a name (no parsing here, it just removes HTML tags and entities, and makes no other modifications):

The output contains the original name-string, and "HTML-normalized" one separated by a pipe ("|") character.

gnparser -c "<i>Abacopteris glandulosa</i> (Bl.) F&eacute;e &amp; Chin"

To cleanup a file of names

gnparser -j 200 -c names.txt > no_html_names.txt

# using pipes
cat names.txt | gnparser -c -j 200 > no_html_names.txt

If you have data that has names with tags or HTML entities, the --cleanup -c flag will help to normalize such names for parsing or other purposes.

gRPC server

Relevant flags:

--help -h : help information about flags

--grpc -g : sets a port to run gRPC server, and starts gnparser in gRPC mode.

--jobs -j : number or workers allocated per gRPC request. Default corresponds to the number of CPU threads.

gnparser -g 8989 -j 20

For an example how to use gRPC server check gnparser Ruby gem as well as gRPC documentation.

Usage as a REST API Interface

Use web-server REST API as a slower, but more wide-spread alternative to gRPC server. Web-based user interface and API are invoked by --web-port or -w flag. To start web server on http://0.0.0.0:9000

    gnparser -w 9000

Opening a browser with this address will now show an interactive interface to parser. API calls would be accessibe on http://0.0.0.0:9000/api.

Make sure to CGI-escape name-strings for GET requests. An '&' character needs to be converted to '%26'

  • GET /api?q=Aus+bus|Aus+bus+D.+%26+M.,+1870
  • POST /api with request body of JSON array of strings
require 'json'
require 'net/http'

uri = URI('https://parser.globalnames.org/api')
http = Net::HTTP.new(uri.host, uri.port)
http.use_ssl = true
request = Net::HTTP::Post.new(uri, 'Content-Type' => 'application/json',
                                   'accept' => 'json')
request.body = ['Solanum mariae Särkinen & S.Knapp',
                'Ahmadiago Vánky 2004'].to_json
response = http.request(request)
Use as a Docker image

You need to have docker runtime installed on your computer for these examples to work.

# run as a gRPC server on port 7777
docker run -p 0.0.0.0:7777:7777 gnames/gognparser -g 7777
# run grpc on 'default' 8778 port
docker run -p 0.0.0.0:8778:8778 gnames/gognparser
# to run as a daemon with 50 workers
docker run -d gnames/gognparser -g 7777 -j 50

# run as a website and a RESTful service
docker run -p 0.0.0.0:80:8080 gnames/gognparser -w 8080

# just parse something
docker run gnames/gognparser "Amaurorhinus bewichianus (Wollaston,1860) (s.str.)"
Use as a library in Go
package main

import (
	"fmt"

	"gitlab.com/gogna/gnparser"
)

func main() {
	opts := []gnparser.Option{
		gnparser.Format("simple"),
		gnparser.WorkersNum(100),
	}
	gnp := gnparser.NewGNparser(opts...)
	res, err := gnp.ParseAndFormat("Bubo bubo")
	if err != nil {
		fmt.Println(err)
	}
	fmt.Println(res)
}

Authors

Contributors

If you want to submit a bug or add a feature read CONTRIBUTING file.

License

Released under MIT license

Documentation

Index

Constants

View Source 
const (
	// Compact is a JSON format without new lines and spaces.
	Compact format = iota
	// Pretty is a JSON nested easy to read format.
	Pretty
	// Simple is a flat format with only few most 'popular' fields.
	Simple
	// Debug is a format that shows complete and truncated AST for debugging.
	Debug
)

Variables

This section is empty.

Functions

func AvailableFormats 

func AvailableFormats() []string

AvailableFormats function returns a string representation of supported output formats.

Types

type GNparser 

type GNparser struct {
	// contains filtered or unexported fields
}

GNparser is responsible for parsing operations.

func NewGNparser 

func NewGNparser(opts ...Option) GNparser

NewGNparser constructor function takes options and returns configured GNparser.

func (*GNparser) Build 

func (gnp *GNparser) Build() string

Build returns date and time when gnparser was built

func (*GNparser) Debug 

func (gnp *GNparser) Debug(s string) []byte

Debug returns byte representation of complete and 'output' syntax trees.

func (*GNparser) OutputFormat 

func (gnp *GNparser) OutputFormat() string

OutputFormat returns string representation of the current output format for GNparser

func (*GNparser) Parse 

func (gnp *GNparser) Parse(s string)

Parse function parses input using GNparser's supplied options. The abstract syntax tree formed by the parser is stored in an `gnp.parser.SN` field.

func (*GNparser) ParseAndFormat 

func (gnp *GNparser) ParseAndFormat(s string) (string, error)

ParseAndFormat function parses input and formats results according to format setting of GNparser.

func (*GNparser) ParseStream 

func (gnp *GNparser) ParseStream(in <-chan string, out chan<- *ParseResult,
	opts ...Option)

ParseStream function takes input/output channels to do concurrent parsing jobs. Output is pushed as ParseResult objects.

func (*GNparser) ParsedName 

func (gnp *GNparser) ParsedName() string

ParsedName returns the string of parsed result without a tail.

func (GNparser) String 

func (of GNparser) String() string

func (*GNparser) ToJSON 

func (gnp *GNparser) ToJSON() ([]byte, error)

ToJSON function creates a 'compact' output out of parsed results.

func (*GNparser) ToPrettyJSON 

func (gnp *GNparser) ToPrettyJSON() ([]byte, error)

ToPrettyJSON function creates pretty JSON output out of parsed results.

func (*GNparser) ToSlice 

func (gnp *GNparser) ToSlice() []string

ToSlice function creates a flat simplified output of parsed results.

func (*GNparser) Version 

func (gnp *GNparser) Version() string

Version function returns version number of `gnparser`.

func (*GNparser) WorkersNum 

func (gnp *GNparser) WorkersNum() int

WorkersNum returns the number of workers for concurrent parsing.

type Option 

type Option func(*GNparser)

Option is a function that creates a new option for GNparser.

func Format 

func Format(f string) Option

Format Option sets the output format to return/display parsing results.

func IsTest 

func IsTest() Option

IsTest Option to substitute real version of the parser with 'test_version' string.

func WorkersNum 

func WorkersNum(wn int) Option

WorkersNum Option sets the quantity of workers to run parsing jobs.

type ParseResult 

type ParseResult struct {
	Output string
	Error  error
}

ParseResult structure contains parsing output and/or error generated by the parser.

Source Files

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Directories

Path Synopsis
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