def create_root(): Taxon.create(rank=ROOT, valid_name='root', is_page_root=True)
def read_file(filename):
with codecs.open(filename, mode='r') as file:
reader = csv.reader(file)
first_line = reader.next()
# name of parent of root taxon should be in cell A1
root_name = first_line[0]
if root_name:
root_parent = Taxon.filter(Taxon.valid_name == root_name)[0]
# maintain stack of taxa that are parents of the current taxon
stack = [root_parent]
else:
stack = []
# current valid taxon (for synonyms)
current_valid = None
# whether current taxon should be marked as root of a page
is_page_root = True
error_occurred = False
for row in reader:
try:
# ignore blank rows
if row[3] == '' and row[0] == '':
continue
data = parse_row(row)
if data['status'] == STATUS_VALID:
# get stuff off the stack
rank = data['rank']
# TODO: make this somehow unranked-clade-aware
while len(stack) > 0 and rank >= stack[-1].rank:
stack.pop()
# create new Taxon
current_valid = Taxon.create(valid_name=data['valid_name'], age=data['age'],
rank=data['rank'], is_page_root=is_page_root,
comments=data['comments_taxon'], data=data['data_taxon'])
if len(stack) > 0:
current_valid.parent = stack[-1]
if is_page_root:
is_page_root = False
stack.append(current_valid)
# create new Name
data['taxon'] = current_valid
assert current_valid.valid_name == data['valid_name'], \
"Valid name %s does not match expected %s" % (data['valid_name'], current_valid.valid_name)
data['data'] = helpers.fix_data(data['data'])
# Detect whether a name object is already present (Principle of Coordination)
nm = None
if data['root_name'][0:4] == 'see ':
seen = data['root_name'][4:]
nm = Taxon.get(Taxon.valid_name == seen).base_name
# create a new Name if none was found
if nm is None:
nm = Name.create(**data)
# set base_name field
if data['status'] == STATUS_VALID:
current_valid.base_name = nm
except Exception:
traceback.print_exc()
print('Error parsing row: %s' % row)
error_occurred = True
# ignore error and happily go on with the next
return not error_occurred
