def print_percentages():
attributes = ["original_name", "original_citation", "page_described", "authority", "year"]
parent_of_taxon = {}
def _find_parent(taxon):
if taxon.is_page_root:
return taxon.id
elif taxon.id in parent_of_taxon:
return parent_of_taxon[taxon.id]
else:
return _find_parent(taxon.parent)
for taxon in Taxon.select():
parent_of_taxon[taxon.id] = _find_parent(taxon)
counts_of_parent = collections.defaultdict(lambda: collections.defaultdict(int))
for name in Name.select():
parent_id = parent_of_taxon[name.taxon.id]
counts_of_parent[parent_id]["total"] += 1
for attribute in attributes:
if getattr(name, attribute) is not None:
counts_of_parent[parent_id][attribute] += 1
for parent_id, data in counts_of_parent.items():
parent = Taxon.filter(Taxon.id == parent_id)[0]
print("FILE", parent)
total = data["total"]
del data["total"]
print("Total", total)
for attribute in attributes:
percentage = data[attribute] * 100.0 / total
print("%s: %s (%.2f%%)" % (attribute, data[attribute], percentage))
def dup_taxa():
taxa = collections.defaultdict(list)
for txn in Taxon.select():
if txn.rank == db.constants.SUBGENUS and len(taxa[txn.valid_name]) > 0:
continue
taxa[txn.valid_name].append(txn)
return [taxa]
def find_rank_mismatch():
for taxon in Taxon.select():
expected_group = db.helpers.group_of_rank(taxon.rank)
if expected_group != taxon.base_name.group:
rank = db.constants.string_of_rank(taxon.rank)
group = db.constants.string_of_group(taxon.base_name.group)
print("Group mismatch for %s: rank %s but group %s" % (taxon, rank, group))
yield taxon
def keys(self):
keys = set(super(_ShellNamespace, self).keys())
keys |= set(dir(__builtins__))
if not hasattr(self, "_names"):
self._names = set(
_encode_name(taxon.valid_name)
for taxon in Taxon.select(Taxon.valid_name)
if taxon.valid_name is not None
)
return keys | self._names
def name_mismatches(max_count=None, correct=False, correct_undoubted=True):
count = 0
for taxon in Taxon.select():
computed = taxon.compute_valid_name()
if computed is not None and taxon.valid_name != computed:
print("Mismatch for %s: %s (actual) vs. %s (computed)" % (taxon, taxon.valid_name, computed))
yield taxon
count += 1
# for species-group taxa with a known genus parent, the computed valid name is almost
# always right (the mismatch will usually happen after a change in genus classification)
# one area that isn't well-covered yet is autocorrecting gender endings
if (
correct_undoubted
and taxon.base_name.group == db.constants.GROUP_SPECIES
and taxon.has_parent_of_rank(db.constants.GENUS)
):
taxon.recompute_name()
elif correct:
taxon.recompute_name()
if max_count is not None and count == max_count:
return
