# Requires python.security.respectJavaAccessibility = false

# on java command line or in .jython

from org.opentreeoflife.taxa import Taxonomy

from org.opentreeoflife.smasher import UnionTaxonomy, HomonymReport

union = UnionTaxonomy()

skel = Taxonomy.getTaxonomy('tax/skel/', 'skel')

union.setSkeleton(skel)

def report(tax, tag):

union.markDivisionsFromSkeleton(tax, skel)

HomonymReport.homonymReport(tax, 'reports/' + tag + '-homonym-report.tsv')

if True:

ott = Taxonomy.getTaxonomy('tax/ott/', 'ott')

report(ott, 'ott')

else:

import taxonomies

report(taxonomies.loadSilva(), 'silva')

report(taxonomies.loadH2007(), 'h2007')

report(taxonomies.loadFung(), 'worms')

report(taxonomies.loadFung(), 'if')

report(taxonomies.loadNcbi(), 'ncbi')

report(taxonomies.loadGbif(), 'gbif')

report(taxonomies.loadIrmng(), 'irmng')