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Planteome / samara

extracts plant trait data from open data sources like apsnet and ars-grin
MIT License
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samara*

A commandline tool to extract plant trait data from open data sources.

Build Status DOI

Plants trait data from recent automated scrapes are available at APSNet or ARS-GRIN.

For more information about APSNet scraping process, including name matching, please go here.

*A samara is a winged achene, a type of fruit in which a flattened wing of fibrous, papery tissue develops from the ovary wall. (from https://en.wikipedia.org/wiki/Samara_(fruit) accessed at 2016-06-10).

prerequisites

sbt 0.13.8+/java jdk 8+/git/maven 3.3+

build/test

  1. clone this repo
  2. build jar by sbt assembly: a stand-alone jar samara-assembly-[version].jar will be available in target/scala-2.11/
  3. run tests by sbt test

download

Don't like building your own jar? Go to releases, pick a release and download the jar from there.

usage

  1. list available sources by java -jar samara-assembly-[version].jar list
  2. scrape a source called apsnet and put results into apsnet.tsv by java -jar samara-assembly-[version].jar scrape apsnet > apsnet.tsv