def test_arffreader_performance(self):
attributes = "\n".join(
[f"@attribute {i} {{1,2}}" for i in range(1000)])
data_line = ",".join(["1"] * 1000)
data_lines = "\n".join([data_line] * 700)
arff = f"{attributes}\n@data\n{data_lines}".split('\n')
reader = ArffReader()
time = timeit.timeit(lambda: list(reader.filter(arff)), number=1)
#.045 was my final time
self.assertLess(time, 0.45)
def test_no_lazy_encoding_no_header_indexes_sparse(self):
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute b numeric",
"@attribute c {class_B, class_C, class_D}",
"@data",
"{0 1,1 2,2 class_B}",
"{0 2,1 3,2 class_C}",
]
expected = [{
0: 1,
1: 2,
2: (0, 1, 0, 0)
}, {
0: 2,
1: 3,
2: (0, 0, 1, 0)
}]
actual = list(
ArffReader(lazy_encoding=False,
header_indexing=False).filter(lines))
self.assertEqual(expected, actual)
self.assertIsInstance(actual[0], dict)
self.assertIsInstance(actual[1], dict)
def test_sparse_with_spaces_after_comma(self):
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute b numeric",
"@attribute c {class_B, class_C, class_D}",
"@data",
"{0 2, 1 3}",
"{0 1, 1 1,2 class_B}",
"{1 1}",
"{0 1, 2 class_D}",
]
expected = [{
0: 2,
1: 3,
2: (1, 0, 0, 0)
}, {
0: 1,
1: 1,
2: (0, 1, 0, 0)
}, {
1: 1,
2: (1, 0, 0, 0)
}, {
0: 1,
2: (0, 0, 0, 1)
}]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_dense_with_strings(self):
lines = [
"@relation news20", "@attribute a string", "@attribute b string",
"@attribute c {0, class_B, class_C, class_D}", "@data",
"1,2,class_B", "2,3,0"
]
expected = [['1', '2', (0, 1, 0, 0)], ['2', '3', (1, 0, 0, 0)]]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_dense_with_empty_lines(self):
lines = [
"@relation news20", "@attribute A numeric", "@attribute B numeric",
"@attribute C {0, class_B, class_C, class_D}", "@data", "", "",
"1,2,class_B", "2,3,0", ""
]
expected = [[1, 2, (0, 1, 0, 0)], [2, 3, (1, 0, 0, 0)]]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_dense_with_comments(self):
lines = [
"%This is a comment", "@relation news20", "@attribute a numeric",
"@attribute b numeric",
"@attribute c {0, class_B, class_C, class_D}", "@data",
"1,2,class_B", "2,3,0"
]
expected = [[1, 2, (0, 1, 0, 0)], [2, 3, (1, 0, 0, 0)]]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_leading_and_trailing_comments(self):
lines = [
"%", "%", "@relation news20", "@attribute a string",
"@attribute b string",
"@attribute c {0, class_B, class_C, class_D}", "@data",
"1,2,class_B", "2,3,0", "%"
]
expected = [['1', '2', (0, 1, 0, 0)], ['2', '3', (1, 0, 0, 0)]]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_sans_data(self):
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute B numeric",
"@attribute c {0, class_B, class_C, class_D}",
"@data",
]
expected = []
self.assertEqual(expected, list(ArffReader().filter(lines)))
def read(self) -> Iterable[Tuple[Any, Any]]:
"""Read and parse the openml source."""
try:
dataset_description = self._get_dataset_description(self._data_id)
if dataset_description['status'] == 'deactivated':
raise CobaException(
f"Openml {self._data_id} has been deactivated. This is often due to flags on the data."
)
feature_descriptions = self._get_feature_descriptions(
self._data_id)
task_descriptions = self._get_task_descriptions(self._data_id)
is_ignore = lambda r: (r['is_ignore'] == 'true' or r[
'is_row_identifier'] == 'true' or r['data_type'] not in
['numeric', 'nominal'])
ignore = [
self._name_cleaning(f['name']) for f in feature_descriptions
if is_ignore(f)
]
target = self._name_cleaning(
self._get_target_for_problem_type(task_descriptions))
if target in ignore: ignore.pop(ignore.index(target))
def row_has_missing_values(row):
row_values = row._values.values() if isinstance(
row, SparseWithMeta) else row._values
return "?" in row_values or "" in row_values
source = ListSource(
self._get_dataset_lines(dataset_description["file_id"], None))
reader = ArffReader(cat_as_str=self._cat_as_str)
drop = Drop(drop_cols=ignore, drop_row=row_has_missing_values)
structure = Structure([None, target])
return Pipes.join(source, reader, drop, structure).read()
except KeyboardInterrupt:
#we don't want to clear the cache in the case of a KeyboardInterrupt
raise
except CobaException:
#we don't want to clear the cache if it is an error we know about (the original raise should clear if needed)
raise
except Exception:
#if something unexpected went wrong clear the cache just in case it was corrupted somehow
self._clear_cache()
raise
def test_all_good_tipes_do_not_raise_exception(self):
lines = [
"@relation news20",
"@ATTRIBUTE a numeric",
"@ATTRIBUTE b integer",
"@ATTRIBUTE c real",
"@attribute d date",
"@attribute e {class_B, class_C, class_D}",
"@attribute f relational",
"@data",
]
list(ArffReader().filter(lines))
def test_dense_with_missing_value(self):
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute B numeric",
"@attribute c {class_B, class_C, class_D}",
"@data",
"1,2,class_B",
"2,3,?",
]
expected = [[1, 2, (1, 0, 0)], [2, 3, None]]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_str_as_cat(self):
lines = [
"@relation news20",
"@attribute A numeric",
"@attribute C {0, class_B, class_C, class_D}",
"@data",
"1,class_B",
"2,0",
]
expected = [[1, "class_B"], [2, "0"]]
self.assertEqual(expected,
list(ArffReader(cat_as_str=True).filter(lines)))
def test_headers_with_quotes_and_pct(self):
lines = [
"@relation news20",
"@attribute 'a%3' string",
"@attribute 'b%4' string",
"@attribute 'c%5' {class_B, class_C, class_D}",
"@data",
"1,2,class_B",
"2,3,class_C",
]
expected = [['1', '2', (1, 0, 0)], ['2', '3', (0, 1, 0)]]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_dense_with_spaces_after_commas(self):
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute B numeric",
"@attribute c {class_B, class_C, class_D}",
"@data",
"1, 2, class_B",
"2, 3, class_C",
]
expected = [[1, 2, (1, 0, 0)], [2, 3, (0, 1, 0)]]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_quotes_from_hell_dense_cat_as_str_true_bad_categories(self):
lines = [
"@relation news20",
"@attribute 'A a' numeric",
"@attribute '\"' {0, \"class'B\", '\"class_C\"', 'class\",D'}",
"@attribute '\'' {0, \"class'B\", '\"class_C\"', 'class\",D'}",
"@attribute ',' {0, \"class'B\", '\"class_C\"', 'class\",D'}",
"@data",
"1, 'class\'B', '\"class_C\"', 'class\",G'",
]
with self.assertRaises(CobaException):
list(
ArffReader(cat_as_str=True, lazy_encoding=False).filter(lines))
def test_skip_encoding(self):
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute B numeric",
"@attribute c {class_B, class_C, class_D}",
"@data",
"1, 2, class_B",
"2, 3, class_C",
]
expected = [['1', '2', 'class_B'], ['2', '3', 'class_C']]
self.assertEqual(expected,
list(ArffReader(skip_encoding=True).filter(lines)))
def test_tab_delimieted_attributes(self):
lines = [
"@relation news20",
"@attribute a string",
'@attribute b string',
"@attribute c {class_B, class_C, class_D}",
"@data",
"1,2,class_B",
]
expected = [
['1', '2', (1, 0, 0)],
]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_spaces_in_attribute_name(self):
lines = [
"@relation news20",
"@attribute 'a a' string",
'@attribute "b b" string',
"@attribute 'c c' {class_B, class_C, class_D}",
"@data",
"1,2,class_B",
]
expected = [
['1', '2', (1, 0, 0)],
]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_capitalized_attribute(self):
lines = [
"@relation news20",
"@ATTRIBUTE 'a\\'a' numeric",
"@attribute 'b b' string",
"@attribute 'c c' {class_B, class_C, class_D}",
"@data",
"1,2,class_B",
]
expected = [
[1, '2', (1, 0, 0)],
]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def test_bad_tipe_raises_exception(self):
lines = [
"@relation news20",
"@ATTRIBUTE 'a\\'a' numeric",
"@attribute 'b b' abcd",
"@attribute 'c c' {class_B, class_C, class_D}",
"@data",
"1,2,class_B",
]
with self.assertRaises(CobaException) as ex:
list(ArffReader().filter(lines))
self.assertEqual(
'An unrecognized encoding was found in the arff attributes: abcd.',
str(ex.exception))
def test_bad_class_labels_throws_exception(self):
lines = [
"@relation news20",
"@attribute 'a' string",
"@attribute 'b' string",
"@attribute 'c' {class_B, class_C, class_D}",
"@data",
"1,2,class_A",
]
with self.assertRaises(CobaException) as e:
list(list(ArffReader().filter(lines))[0])
self.assertIn(
"We were unable to find one of the categorical values in the arff data.",
str(e.exception))
def test_max_unknown_sparse_elements(self):
lines = [
"@relation news20",
"@attribute A numeric",
"@attribute C {0, class_B, class_C, class_D}",
"@data",
"{0 2,1 3,2 4}",
]
with self.assertRaises(CobaException) as e:
list(ArffReader().filter(lines))
self.assertEqual(
str(e.exception),
"We were unable to parse line 0 in a way that matched the expected attributes."
)
def test_quotes_with_csv(self):
lines = [
"@relation news20",
"@attribute 'value' numeric",
"@attribute 'class' {'0','1'}",
"@data",
"1,'0'",
]
expected = [[1, (1, 0)]]
items = list(ArffReader(cat_as_str=False).filter(lines))
self.assertEqual(expected, items)
self.assertEqual(1, items[0]['value'])
self.assertEqual((1, 0), items[0]['class'])
def __init__(self,
source: Union[str, Source[Iterable[str]]],
cat_as_str: bool = False,
skip_encoding: bool = False,
lazy_encoding: bool = True,
header_indexing: bool = True) -> None:
"""Instantiate an ArffSource.
Args:
source: The data source. Accepts either a string representing the source location or another Source.
cat_as_str: Indicates that categorical features should be encoded as a string rather than one hot encoded.
skip_encoding: Indicates that features should not be encoded (this means all features will be strings).
lazy_encoding: Indicates that features should be encoded lazily (this can save time if rows will be dropped).
header_indexing: Indicates that header data should be preserved so rows can be indexed by header name.
"""
source = UrlSource(source) if isinstance(source, str) else source
reader = ArffReader(cat_as_str, skip_encoding, lazy_encoding,
header_indexing)
self._source = Pipes.join(source, reader)
def test_quotes_from_hell_dense_cat_as_str_true_good_categories(self):
lines = [
"@relation news20",
"@attribute 'A a' numeric",
"@attribute '\"' {0, \"class'B\", '\"class_C\"', 'class\",D'}",
"@attribute '\'' {0, \"class'B\", '\"class_C\"', 'class\",D'}",
"@attribute ',' {0, \"class'B\", '\"class_C\"', 'class\",D'}",
"@data",
"1, 'class\'B', '\"class_C\"', 'class\",D'",
]
expected = [[1, "class'B", '"class_C"', 'class",D']]
items = list(ArffReader(cat_as_str=True).filter(lines))
self.assertEqual(expected, items)
self.assertEqual(1, items[0]['A a'])
self.assertEqual("class'B", items[0]['"'])
self.assertEqual('"class_C"', items[0]["'"])
self.assertEqual('class",D', items[0][","])
def test_no_lazy_encoding_no_header_indexes_dense(self):
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute b numeric",
"@attribute c {class_B, class_C, class_D}",
"@data",
"1,2,class_B",
"2,3,class_C",
]
expected = [[1, 2, (1, 0, 0)], [2, 3, (0, 1, 0)]]
actual = list(
ArffReader(lazy_encoding=False,
header_indexing=False).filter(lines))
self.assertEqual(expected, actual)
self.assertIsInstance(actual[0], list)
self.assertIsInstance(actual[1], list)
def test_quotes_from_hell_dense_cat_as_str_false(self):
lines = [
"@relation news20",
"@attribute 'A a' numeric",
"@attribute '\"' {0, \"class'B\", '\"class_C\"', 'class\",D', 'class\\',E', 'class\\' ,F'}",
"@attribute '\'' {0, \"class'B\", '\"class_C\"', 'class\",D', 'class\\',E', 'class\\' ,F'}",
"@attribute ',' {0, \"class'B\", '\"class_C\"', 'class\",D', 'class\\',E', 'class\\' ,F'}",
"@data",
"1, 'class\\'B', '\"class_C\"', 'class\",D'",
]
expected = [[
1, (0, 1, 0, 0, 0, 0), (0, 0, 1, 0, 0, 0), (0, 0, 0, 1, 0, 0)
]]
items = list(ArffReader(cat_as_str=False).filter(lines))
self.assertEqual(expected, items)
self.assertEqual(1, items[0]['A a'])
self.assertEqual((0, 1, 0, 0, 0, 0), items[0]['"'])
self.assertEqual((0, 0, 1, 0, 0, 0), items[0]["'"])
self.assertEqual((0, 0, 0, 1, 0, 0), items[0][","])
def test_sparse_categorical_0_value(self):
#this is a bug in ARFF, it is not uncommon for the first class value in an ARFF class list
#to be dropped from the actual data because it is encoded as 0. Therefore our ARFF reader
#automatically adds a 0 value to all categorical one-hot encoders to protect against this.
#Below is what a dataset with this bug would look like, there is no class_B, instead all
#class_B's are encoded as 0.
lines = [
"@relation news20",
"@attribute a numeric",
"@attribute b numeric",
"@attribute c {class_B, class_C, class_D}",
"@data",
"{0 2,1 3}",
"{0 1,1 1,2 class_C}",
"{1 1}",
"{0 1,2 class_D}",
]
expected = [{
0: 2,
1: 3,
2: (1, 0, 0, 0)
}, {
0: 1,
1: 1,
2: (0, 0, 1, 0)
}, {
1: 1,
2: (1, 0, 0, 0)
}, {
0: 1,
2: (0, 0, 0, 1)
}]
self.assertEqual(expected, list(ArffReader().filter(lines)))
def read(self) -> Tuple[Sequence[Sequence[Any]], Sequence[Any]]:
#placing some of these at the top would cause circular references
from coba.encodings import Encoder, NumericEncoder, OneHotEncoder, StringEncoder
from coba.pipes import ArffReader, CsvReader, Encode, Flatten, Transpose
d_key = None
t_key = None
o_key = None
try:
data_id = self._data_id
md5_checksum = self._md5_checksum
d_key = f'https://www.openml.org/api/v1/json/data/{data_id}'
t_key = f'https://www.openml.org/api/v1/json/data/features/{data_id}'
d_bytes = self._query(d_key, "descr")
d_object = json.loads(
d_bytes.decode('utf-8'))["data_set_description"]
if d_object['status'] == 'deactivated':
raise Exception(
f"Openml {data_id} has been deactivated. This is often due to flags on the data."
)
t_bytes = self._query(t_key, "types")
t_object = json.loads(
t_bytes.decode('utf-8'))["data_features"]["feature"]
headers: List[str] = []
encoders: List[Encoder] = []
ignored: List[bool] = []
target: str = ""
for tipe in t_object:
headers.append(tipe['name'].lower())
ignored.append(tipe['is_ignore'] == 'true'
or tipe['is_row_identifier'] == 'true')
if tipe['is_target'] == 'true':
target = tipe['name'].lower()
if tipe['data_type'] == 'numeric':
encoders.append(NumericEncoder())
elif tipe['data_type'] == 'nominal':
encoders.append(OneHotEncoder(singular_if_binary=True))
else:
encoders.append(StringEncoder())
if target == "" or isinstance(encoders[headers.index(target)],
NumericEncoder):
target = self._get_classification_target(data_id)
ignored[headers.index(target)] = False
encoders[headers.index(target)] = StringEncoder()
csv_url = f"http://www.openml.org/data/v1/get_csv/{d_object['file_id']}"
arff_url = f"http://www.openml.org/data/v1/download/{d_object['file_id']}"
try:
if csv_url in CobaConfig.Cacher or arff_url not in CobaConfig.Cacher:
o_key = csv_url
o_bytes = self._query(o_key, "obser", md5_checksum)
file_rows = list(CsvReader().filter(
o_bytes.decode('utf-8').splitlines()))
else:
o_key = arff_url
o_bytes = self._query(o_key, "obser", md5_checksum)
file_rows = list(
ArffReader(skip_encoding=[target]).filter(
o_bytes.decode('utf-8').splitlines()))
except:
if o_key == csv_url:
o_key = arff_url
o_bytes = self._query(o_key, "obser", md5_checksum)
file_rows = list(
ArffReader(skip_encoding=[target]).filter(
o_bytes.decode('utf-8').splitlines()))
else:
o_key = csv_url
o_bytes = self._query(o_key, "obser", md5_checksum)
file_rows = list(CsvReader().filter(
o_bytes.decode('utf-8').splitlines()))
is_sparse_data = isinstance(file_rows[0], tuple) and len(
file_rows[0]) == 2
if is_sparse_data:
file_headers = [
header.lower() for header in file_rows.pop(0)[1]
]
else:
file_headers = [header.lower() for header in file_rows.pop(0)]
file_cols = list(Transpose().filter(file_rows))
for ignored_header in compress(headers, ignored):
if ignored_header in file_headers:
file_cols.pop(file_headers.index(ignored_header))
file_headers.remove(ignored_header)
file_encoders = [
encoders[headers.index(file_header)]
for file_header in file_headers
]
file_cols = list(Encode(file_encoders).filter(file_cols))
label_col = file_cols.pop(file_headers.index(target))
feature_rows = list(Transpose().filter(
Flatten().filter(file_cols)))
#we only cache after all the data has been successfully loaded
for key, bytes in [(d_key, d_bytes), (t_key, t_bytes),
(o_key, o_bytes)]:
if key not in CobaConfig.Cacher:
CobaConfig.Cacher.put(key, bytes)
if is_sparse_data:
dense_label_col = ['0'] * len(feature_rows)
for index, value in zip(label_col[0], label_col[1]):
dense_label_col[index] = value
else:
dense_label_col = list(label_col)
return feature_rows, dense_label_col
except KeyboardInterrupt:
#we don't want to clear the cache in the case of a KeyboardInterrupt
raise
except Exception:
#if something went wrong we want to clear the
#cache just in case it was corrupted somehow
for k in [d_key, t_key, o_key]:
if k is not None: CobaConfig.Cacher.rmv(k)
raise
def __init__(self, source: Union[str, Source[Iterable[str]]],
label_column: Union[str, int]) -> None:
super().__init__(ArffReader(skip_encoding=[label_column]), source,
label_column)