def do_geography(filename):
# geography changed slightly with Bauble 1.0 so just copy the
# default file and hope the ids are the same
rootdir = os.path.split(bauble.__file__)[0]
default_file = os.path.join(rootdir, 'plugins', 'plants', 'default',
'geography.txt')
default_reader = UnicodeReader(open(default_file))
geography_reader = UnicodeReader(open(filename))
columns = [
'id', 'name', 'tdwg_code', 'iso_code', 'parent_id', '_created',
'_last_updated'
]
writer = create_writer(os.path.join(dst_path, filename), columns)
# build map of default tdwg codes to geography.id
default_tdwg_map = {}
for line in default_reader:
default_tdwg_map[line['tdwg_code']] = line['id']
# built a map of the default geography id's to 0.9 geography.id's
for line in geography_reader:
# TODO: this might miss some id's and might need to be
# corrected but it works for us at the moment
try:
default_id = default_tdwg_map[line['tdwg_code']]
except:
pass
# print line
# print line['tdwg_code'].partition('-')
# head, middle, tail = line['tdwg_code'].partition('-')
# default_id = default_tdwg_map[head]
geography_id_map[line['id']] = default_id
# manually add 'Cultivated'
geography_id_map[None] = default_tdwg_map[None]
# now that the map is built just copy over the default geography
shutil.copy(default_file, dst_path)
def do_genus(filename):
"""
Convert genus.txt
"""
reader = UnicodeReader(open(filename))
genus_filename = os.path.join(dst_path, 'genus.txt')
genus_writer = UnicodeWriter(open(genus_filename, "wb"))
genus_columns = [
'id', 'epithet', 'hybrid_marker', 'author', 'aggregate', 'family_id',
'_created', '_last_updated'
]
genus_writer.writerow(genus_columns)
for line in reader:
genus_writer.writerow([
line['id'], line['genus'], '', line['author'], line['qualifier'],
line['family_id'], line['_created'], line['_last_updated']
])
print 'done'
def do_species(filename):
"""
Convert species.txt
"""
reader = UnicodeReader(open(filename))
species_filename = os.path.join(dst_path, 'species.txt')
writer = UnicodeWriter(open(species_filename, "wb"))
columns = [
'id', 'epithet', 'hybrid_marker', 'author', 'aggregate', 'cv_group',
'trade_name', 'infrasp1', 'infrasp1_rank', 'infrasp1_author',
'infrasp2', 'infrasp2_rank', 'infrasp2_author', 'infrasp3',
'infrasp3_rank', 'infrasp3_author', 'infrasp4', 'infrasp4_rank',
'infrasp4_author', 'genus_id', 'label_distribution', 'bc_distribution',
'habit_id', 'flower_color_id', 'awards', '_created', '_last_updated'
]
writer.writerow(columns)
post_process_hyop = []
for line in reader:
line = dict(line)
if line['sp'] and (line['sp'].find(u'×') > 0):
line['hybrid_marker'] = 'H'
line['epithet'] = ''
post_process_hyop.append(dict(line))
else:
line['hybrid_marker'] = (line['hybrid'] == 'True') and u'×' or ''
line['epithet'] = line['sp']
line['author'] = line['sp_author']
line['aggregate'] = line['sp_qual']
writer.writerow([line[k] for k in columns])
hybrid_operand = os.path.join(dst_path, 'hybrid_operands.txt')
hyop_columns = ['child_id', 'parent_id', 'role']
hyop_writer = create_writer(hybrid_operand, hyop_columns)
if post_process_hyop:
print post_process_hyop
print 'done'
