import os
from treestore import Treestore
try: taxonomy = sys.argv[1]
except: taxonomy = None
t = Treestore()
tree_files = [x for x in os.listdir('trees') if x.endswith('.nex')]
base_uri = 'http://www.phylocommons.org/trees/%s'
tree_list = set(t.list_trees())
if taxonomy:
sys.stdout.write('Loading taxonomy...')
sys.stdout.flush()
taxonomy = t.get_trees('%s_taxonomy' % taxonomy)[0]
taxonomy.index_labels()
print 'done.'
errors = set()
for tree_file in tree_files:
tree_id = 'TB2_' + tree_file[:-len('.nex')]
if Treestore.uri_from_id(tree_id) in tree_list: continue
print '**', tree_id
tree_path = os.path.join('trees', tree_file)
with open(tree_path) as input_file:
r = input_file.read()
if '<!DOCTYPE html' in r: continue
try:
t.add_trees(tree_path, 'nexus', tree_uri=tree_id, rooted=False,
taxonomy=taxonomy, tax_root=None)
