bhlindex

README

Biodiversity Heritage Library Scientific Names Index

Creates an index of scientific names occurring in the collection of literature in Biodiversity Heritage Library

Usage

Linux

• Download bhlindex release for Linux
• Untar the file, go to script directory and read instructions.
• Use bhl testdata for testing.

Database Migrations

Install migrate

go get -u -d github.com/golang-migrate/migrate/cli github.com/lib/pq
go build -tags 'postgres' -o $GOPATH/bin/migrate github.com/golang-migrate/migrate/cli

Create migration

migrate create -ext pgsql -D db NAME

Run commands

migrate -database postgres://localhost:5432/database up 2

Commands

create [-ext E] [-dir D] NAME : Create a set of timestamped up/down migrations titled NAME, in directory D with extension E

version : current migration version

up [N] : up N migrations

down [N] : down N migrations

drop : nuke database

Testing

docker-compose build
docker-compose up

To update all dependencies change LAST_FULL_REBUILD line in Docker file and return docker-compose build

Documentation

Index

• func Check(err error)
• func DbInit() (*sql.DB, error)
• func UUID4() string
• type Env
  • func EnvVars() Env

Functions

func Check

func Check(err error)

Check handles error checking, and panicks if error is not nil.

func DbInit

func DbInit() (*sql.DB, error)

DbInit returns a connection to bhlindex database.

func UUID4

func UUID4() string

UUID4 returns random (version 4) UUID as a string.

Types

type Env

type Env struct {
	DbHost      string
	DbUser      string
	Db          string
	BHLDir      string
	PrefSources []int
}

Env is a collection of environment variables.

func EnvVars

func EnvVars() Env

EnvVars imports all environment variables relevant for the data conversion.