def stem_statistics():
stem = Name.filter(Name.group == db.constants.GROUP_GENUS, ~(Name.stem >> None)).count()
gender = Name.filter(Name.group == db.constants.GROUP_GENUS, ~(Name.gender >> None)).count()
total = Name.filter(Name.group == db.constants.GROUP_GENUS).count()
print("Genus-group names:")
print("stem: %s/%s (%.02f%%)" % (stem, total, stem / total * 100))
print("gender: %s/%s (%.02f%%)" % (gender, total, gender / total * 100))
print("Family-group names:")
total = Name.filter(Name.group == db.constants.GROUP_FAMILY).count()
typ = Name.filter(Name.group == db.constants.GROUP_FAMILY, ~(Name.type >> None)).count()
print("type: %s/%s (%.02f%%)" % (typ, total, typ / total * 100))
def detect_types(max_count=None, verbose=False):
"""Converts verbatim_types into references to the actual names."""
count = 0
successful_count = 0
group = (db.constants.GROUP_FAMILY, db.constants.GROUP_GENUS)
for name in Name.filter(Name.verbatim_type != None, Name.type >> None, Name.group << group).limit(max_count):
count += 1
if name.detect_and_set_type(verbatim_type=name.verbatim_type, verbose=verbose):
successful_count += 1
print("Success: %d/%d" % (successful_count, count))
def detect_from_root_name(name, root_name):
candidates = Name.filter(
Name.group == db.constants.GROUP_GENUS, (Name.stem == root_name) | (Name.stem == root_name + "i")
)
candidates = list(filter(lambda c: c.taxon.is_child_of(name.taxon), candidates))
if len(candidates) == 1:
print("Detected type for name %s: %s" % (name, candidates[0]))
name.type = candidates[0]
name.save()
return True
else:
return False
def add_page_described():
for name in Name.filter(
Name.original_citation != None, Name.page_described >> None, Name.year != "in press"
).order_by(Name.original_citation):
message = "Name %s is missing page described, but has original citation {%s}" % (
name.description(),
name.original_citation,
)
name.page_described = getinput.get_line(
message, handlers={"o": lambda _: name.open_description()}, should_stop=lambda line: line == "s"
)
name.save()
def detect_stems():
for name in Name.filter(Name.group == db.constants.GROUP_GENUS, Name.stem >> None):
inferred = db.detection.detect_stem_and_gender(name.root_name)
if inferred is None:
continue
if not inferred.confident:
print("%s: stem %s, gender %s" % (name.description(), inferred.stem, inferred.gender))
if not getinput.yes_no("Is this correct? "):
continue
print("Inferred stem and gender for %s: %s, %s" % (name, inferred.stem, inferred.gender))
name.stem = inferred.stem
name.gender = inferred.gender
name.save()
def add_types():
for name in Name.filter(
Name.original_citation != None, Name.type >> None, Name.year > "1930", Name.group == db.constants.GROUP_GENUS
).order_by(Name.original_citation):
name.taxon.display(full=True, max_depth=1)
message = "Name %s is missing type, but has original citation {%s}" % (
name.description(),
name.original_citation,
)
verbatim_type = getinput.get_line(
message, handlers={"o": lambda _: name.open_description()}, should_stop=lambda line: line == "s"
)
if verbatim_type is not None:
name.detect_and_set_type(verbatim_type, verbose=True)
def root_name_mismatch():
for name in Name.filter(Name.group == db.constants.GROUP_FAMILY, ~(Name.type >> None)):
if name.is_unavailable():
continue
stem_name = name.type.stem
if stem_name is None:
continue
if name.root_name == stem_name:
continue
for stripped in db.helpers.name_with_suffixes_removed(name.root_name):
if stripped == stem_name or stripped + "i" == stem_name:
print("Autocorrecting root name: %s -> %s" % (name.root_name, stem_name))
name.root_name = stem_name
name.save()
break
if name.root_name != stem_name:
print("Stem mismatch for %s: %s vs. %s" % (name, name.root_name, stem_name))
yield name
def detect_types_from_root_names(max_count=None):
"""Detects types for family-group names on the basis of the root_name."""
def detect_from_root_name(name, root_name):
candidates = Name.filter(
Name.group == db.constants.GROUP_GENUS, (Name.stem == root_name) | (Name.stem == root_name + "i")
)
candidates = list(filter(lambda c: c.taxon.is_child_of(name.taxon), candidates))
if len(candidates) == 1:
print("Detected type for name %s: %s" % (name, candidates[0]))
name.type = candidates[0]
name.save()
return True
else:
return False
count = 0
successful_count = 0
for name in (
Name.filter(Name.group == db.constants.GROUP_FAMILY, Name.type >> None)
.order_by(Name.id.desc())
.limit(max_count)
):
if name.is_unavailable():
continue
count += 1
if detect_from_root_name(name, name.root_name):
successful_count += 1
else:
for stripped in db.helpers.name_with_suffixes_removed(name.root_name):
if detect_from_root_name(name, stripped):
successful_count += 1
break
else:
print("Could not detect type for name %s (root_name = %s)" % (name, name.root_name))
print("Success: %d/%d" % (successful_count, count))
def dup_genus():
names = collections.defaultdict(list)
for name in Name.filter(Name.group == db.constants.GROUP_GENUS):
full_name = "%s %s, %s" % (name.root_name, name.authority, name.year)
names[full_name].append(name)
return [names]
def endswith(end):
return list(Name.filter(Name.group == db.constants.GROUP_GENUS, Name.root_name % ("%%%s" % end)))
def n(name):
"""Finds names with the given root name or original name."""
return list(Name.filter((Name.root_name == name) | (Name.original_name == name)))
